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

Learning to read aloud: A neural network approach using sparse distributed memory

NASA Technical Reports Server (NTRS)

Joglekar, Umesh Dwarkanath

1989-01-01

An attempt to solve a problem of text-to-phoneme mapping is described which does not appear amenable to solution by use of standard algorithmic procedures. Experiments based on a model of distributed processing are also described. This model (sparse distributed memory (SDM)) can be used in an iterative supervised learning mode to solve the problem. Additional improvements aimed at obtaining better performance are suggested.

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 successfully applied shiver to whole-genome samples of Hepatitis C Virus and Respiratory Syncytial Virus. shiver is publicly available from https://github.com/ChrisHIV/shiver. PMID:29876136

Acquired Dyslexia in a Turkish-English Speaker

ERIC Educational Resources Information Center

Raman, Ilhan; Weekes, Brendan S.

2005-01-01

The Turkish script is characterised by completely transparent bidirectional mappings between orthography and phonology. To date, there has been no reported evidence of acquired dyslexia in Turkish speakers leading to the naive view that reading and writing problems in Turkish are probably rare. We examined the extent to which phonological…

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.

Sequencing the Connectome

PubMed Central

Zador, Anthony M.; Dubnau, Joshua; Oyibo, Hassana K.; Zhan, Huiqing; Cao, Gang; Peikon, Ian D.

2012-01-01

Connectivity determines the function of neural circuits. Historically, circuit mapping has usually been viewed as a problem of microscopy, but no current method can achieve high-throughput mapping of entire circuits with single neuron precision. Here we describe a novel approach to determining connectivity. We propose BOINC (“barcoding of individual neuronal connections”), a method for converting the problem of connectivity into a form that can be read out by high-throughput DNA sequencing. The appeal of using sequencing is that its scale—sequencing billions of nucleotides per day is now routine—is a natural match to the complexity of neural circuits. An inexpensive high-throughput technique for establishing circuit connectivity at single neuron resolution could transform neuroscience research. PMID:23109909

Dynamics of Effective Study. Bulletin 1825.

ERIC Educational Resources Information Center

Louisiana State Dept. of Education, Baton Rouge.

This study skills curriculum addresses the problem of a lack of study skills demonstrated by students in grades 7-10. It focuses on 11 essential knowledge acquisition skills: (1) motivation and ice-breakers; (2) outlining and mapping; (3) time management; (4) PQ5R (Preview, Question, Read, Record, Recite, Review, and Reflect); (5) notetaking; (6)…

Flood inundation extent mapping based on block compressed tracing

NASA Astrophysics Data System (ADS)

Shen, Dingtao; Rui, Yikang; Wang, Jiechen; Zhang, Yu; Cheng, Liang

2015-07-01

Flood inundation extent, depth, and duration are important factors affecting flood hazard evaluation. At present, flood inundation analysis is based mainly on a seeded region-growing algorithm, which is an inefficient process because it requires excessive recursive computations and it is incapable of processing massive datasets. To address this problem, we propose a block compressed tracing algorithm for mapping the flood inundation extent, which reads the DEM data in blocks before transferring them to raster compression storage. This allows a smaller computer memory to process a larger amount of data, which solves the problem of the regular seeded region-growing algorithm. In addition, the use of a raster boundary tracing technique allows the algorithm to avoid the time-consuming computations required by the seeded region-growing. Finally, we conduct a comparative evaluation in the Chin-sha River basin, results show that the proposed method solves the problem of flood inundation extent mapping based on massive DEM datasets with higher computational efficiency than the original method, which makes it suitable for practical applications.

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

CLIP-seq analysis of multi-mapped reads discovers novel functional RNA regulatory sites in the human transcriptome.

PubMed

Zhang, Zijun; Xing, Yi

2017-09-19

Crosslinking or RNA immunoprecipitation followed by sequencing (CLIP-seq or RIP-seq) allows transcriptome-wide discovery of RNA regulatory sites. As CLIP-seq/RIP-seq reads are short, existing computational tools focus on uniquely mapped reads, while reads mapped to multiple loci are discarded. We present CLAM (CLIP-seq Analysis of Multi-mapped reads). CLAM uses an expectation-maximization algorithm to assign multi-mapped reads and calls peaks combining uniquely and multi-mapped reads. To demonstrate the utility of CLAM, we applied it to a wide range of public CLIP-seq/RIP-seq datasets involving numerous splicing factors, microRNAs and m6A RNA methylation. CLAM recovered a large number of novel RNA regulatory sites inaccessible by uniquely mapped reads. The functional significance of these sites was demonstrated by consensus motif patterns and association with alternative splicing (splicing factors), transcript abundance (AGO2) and mRNA half-life (m6A). CLAM provides a useful tool to discover novel protein-RNA interactions and RNA modification sites from CLIP-seq and RIP-seq data, and reveals the significant contribution of repetitive elements to the RNA regulatory landscape of the human transcriptome. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

A tesselated probabilistic representation for spatial robot perception and navigation

NASA Technical Reports Server (NTRS)

Elfes, Alberto

1989-01-01

The ability to recover robust spatial descriptions from sensory information and to efficiently utilize these descriptions in appropriate planning and problem-solving activities are crucial requirements for the development of more powerful robotic systems. Traditional approaches to sensor interpretation, with their emphasis on geometric models, are of limited use for autonomous mobile robots operating in and exploring unknown and unstructured environments. Here, researchers present a new approach to robot perception that addresses such scenarios using a probabilistic tesselated representation of spatial information called the Occupancy Grid. The Occupancy Grid is a multi-dimensional random field that maintains stochastic estimates of the occupancy state of each cell in the grid. The cell estimates are obtained by interpreting incoming range readings using probabilistic models that capture the uncertainty in the spatial information provided by the sensor. A Bayesian estimation procedure allows the incremental updating of the map using readings taken from several sensors over multiple points of view. An overview of the Occupancy Grid framework is given, and its application to a number of problems in mobile robot mapping and navigation are illustrated. It is argued that a number of robotic problem-solving activities can be performed directly on the Occupancy Grid representation. Some parallels are drawn between operations on Occupancy Grids and related image processing operations.

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

Review of USGS Open-file Report 95-525 ("Cartographic and digital standard for geologic map information") and plans for development of Federal draft standards for geologic map information

USGS Publications Warehouse

Soller, David R.

1996-01-01

This report summarizes a technical review of USGS Open-File Report 95-525, 'Cartographic and Digital Standard for Geologic Map Information' and OFR 95-526 (diskettes containing digital representations of the standard symbols). If you are considering the purchase or use of those documents, you should read this report first. For some purposes, OFR 95-525 (the printed document) will prove to be an excellent resource. However, technical review identified significant problems with the two documents that will be addressed by various Federal and State committees composed of geologists and cartographers, as noted below. Therefore, the 2-year review period noted in OFR 95-525 is no longer applicable. Until those problems are resolved and formal standards are issued, you may consult the following World-Wide Web (WWW) site which contains information about development of geologic map standards: URL: http://ncgmp.usgs.gov/ngmdbproject/home.html

ZOOM Lite: next-generation sequencing data mapping and visualization software

PubMed Central

Zhang, Zefeng; Lin, Hao; Ma, Bin

2010-01-01

High-throughput next-generation sequencing technologies pose increasing demands on the efficiency, accuracy and usability of data analysis software. In this article, we present ZOOM Lite, a software for efficient reads mapping and result visualization. With a kernel capable of mapping tens of millions of Illumina or AB SOLiD sequencing reads efficiently and accurately, and an intuitive graphical user interface, ZOOM Lite integrates reads mapping and result visualization into a easy to use pipeline on desktop PC. The software handles both single-end and paired-end reads, and can output both the unique mapping result or the top N mapping results for each read. Additionally, the software takes a variety of input file formats and outputs to several commonly used result formats. The software is freely available at http://bioinfor.com/zoom/lite/. PMID:20530531

Areas activated during naturalistic reading comprehension overlap topological visual, auditory, and somatotomotor maps

PubMed Central

2016-01-01

Abstract Cortical mapping techniques using fMRI have been instrumental in identifying the boundaries of topological (neighbor‐preserving) maps in early sensory areas. The presence of topological maps beyond early sensory areas raises the possibility that they might play a significant role in other cognitive systems, and that topological mapping might help to delineate areas involved in higher cognitive processes. In this study, we combine surface‐based visual, auditory, and somatomotor mapping methods with a naturalistic reading comprehension task in the same group of subjects to provide a qualitative and quantitative assessment of the cortical overlap between sensory‐motor maps in all major sensory modalities, and reading processing regions. Our results suggest that cortical activation during naturalistic reading comprehension overlaps more extensively with topological sensory‐motor maps than has been heretofore appreciated. Reading activation in regions adjacent to occipital lobe and inferior parietal lobe almost completely overlaps visual maps, whereas a significant portion of frontal activation for reading in dorsolateral and ventral prefrontal cortex overlaps both visual and auditory maps. Even classical language regions in superior temporal cortex are partially overlapped by topological visual and auditory maps. By contrast, the main overlap with somatomotor maps is restricted to a small region on the anterior bank of the central sulcus near the border between the face and hand representations of M‐I. Hum Brain Mapp 37:2784–2810, 2016. © 2016 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc. PMID:27061771

Story Map Instruction: A Road Map for Reading Comprehension.

ERIC Educational Resources Information Center

Davis, Zephaniah, T.; McPherson, Michael D.

1989-01-01

Introduces teachers to the development and use of story maps as a tool for promoting reading comprehension. Presents a definition and review of story map research. Explains how to construct story maps, and offers suggestions for starting story map instruction. Provides variations on the use of story maps. (MG)

Comparing the Effect of Thinking Maps Training Package Developed by the Thinking Maps Method on the Reading Performance of Dyslexic Students.

PubMed

Faramarzi, Salar; Moradi, Mohammadreza; Abedi, Ahmad

2018-06-01

The present study aimed to develop the thinking maps training package and compare its training effect with the thinking maps method on the reading performance of second and fifth grade of elementary school male dyslexic students. For this mixed method exploratory study, from among the above mentioned grades' students in Isfahan, 90 students who met the inclusion criteria were selected by multistage sampling and randomly assigned into six experimental and control groups. The data were collected by reading and dyslexia test and Wechsler Intelligence Scale for Children-fourth edition. The results of covariance analysis indicated a significant difference between the reading performance of the experimental (thinking maps training package and thinking maps method groups) and control groups ([Formula: see text]). Moreover, there were significant differences between the thinking maps training package group and thinking maps method group in some of the subtests ([Formula: see text]). It can be concluded that thinking maps training package and the thinking maps method exert a positive influence on the reading performance of dyslexic students; therefore, thinking maps can be used as an effective training and treatment method.

The Impact of the Measures of Academic Progress (MAP) Program on Student Reading Achievement. Final Report. NCEE 2013-4000

ERIC Educational Resources Information Center

Cordray, David; Pion, Georgine; Brandt, Chris; Molefe, Ayrin; Toby, Megan

2012-01-01

During the past decade, the use of standardized benchmark measures to differentiate and individualize instruction for students received renewed attention from educators. Although teachers may use their own assessments (tests, quizzes, homework, problem sets) for monitoring learning, it is challenging for them to equate performance on classroom…

Areas activated during naturalistic reading comprehension overlap topological visual, auditory, and somatotomotor maps.

PubMed

Sood, Mariam R; Sereno, Martin I

2016-08-01

Cortical mapping techniques using fMRI have been instrumental in identifying the boundaries of topological (neighbor-preserving) maps in early sensory areas. The presence of topological maps beyond early sensory areas raises the possibility that they might play a significant role in other cognitive systems, and that topological mapping might help to delineate areas involved in higher cognitive processes. In this study, we combine surface-based visual, auditory, and somatomotor mapping methods with a naturalistic reading comprehension task in the same group of subjects to provide a qualitative and quantitative assessment of the cortical overlap between sensory-motor maps in all major sensory modalities, and reading processing regions. Our results suggest that cortical activation during naturalistic reading comprehension overlaps more extensively with topological sensory-motor maps than has been heretofore appreciated. Reading activation in regions adjacent to occipital lobe and inferior parietal lobe almost completely overlaps visual maps, whereas a significant portion of frontal activation for reading in dorsolateral and ventral prefrontal cortex overlaps both visual and auditory maps. Even classical language regions in superior temporal cortex are partially overlapped by topological visual and auditory maps. By contrast, the main overlap with somatomotor maps is restricted to a small region on the anterior bank of the central sulcus near the border between the face and hand representations of M-I. Hum Brain Mapp 37:2784-2810, 2016. © 2016 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc. © 2016 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.

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.

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.

The Evaluation of Argument Mapping as a Learning Tool: Comparing the Effects of Map Reading versus Text Reading on Comprehension and Recall of Arguments

ERIC Educational Resources Information Center

Dwyer, Christopher P.; Hogan, Michael J.; Stewart, Ian

2010-01-01

The current study compared the effects on comprehension and memory of learning via text versus learning via argument map. Argument mapping is a method of diagrammatic representation of arguments designed to simplify the reading of an argument structure and allow for easy assimilation of core propositions and relations. In the current study, 400…

JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes

PubMed Central

2009-01-01

Background ESTs or variable sequence reads can be available in prokaryotic studies well before a complete genome is known. Use cases include (i) transcriptome studies or (ii) single cell sequencing of bacteria. Without suitable software their further analysis and mapping would have to await finalization of the corresponding genome. Results The tool JANE rapidly maps ESTs or variable sequence reads in prokaryotic sequencing and transcriptome efforts to related template genomes. It provides an easy-to-use graphics interface for information retrieval and a toolkit for EST or nucleotide sequence function prediction. Furthermore, we developed for rapid mapping an enhanced sequence alignment algorithm which reassembles and evaluates high scoring pairs provided from the BLAST algorithm. Rapid assembly on and replacement of the template genome by sequence reads or mapped ESTs is achieved. This is illustrated (i) by data from Staphylococci as well as from a Blattabacteria sequencing effort, (ii) mapping single cell sequencing reads is shown for poribacteria to sister phylum representative Rhodopirellula Baltica SH1. The algorithm has been implemented in a web-server accessible at http://jane.bioapps.biozentrum.uni-wuerzburg.de. Conclusion Rapid prokaryotic EST mapping or mapping of sequence reads is achieved applying JANE even without knowing the cognate genome sequence. PMID:19943962

Analogical processes in children's understanding of spatial representations.

PubMed

Yuan, Lei; Uttal, David; Gentner, Dedre

2017-06-01

We propose that map reading can be construed as a form of analogical mapping. We tested 2 predictions that follow from this claim: First, young children's patterns of performance in map reading tasks should parallel those found in analogical mapping tasks; and, second, children will benefit from guided alignment instructions that help them see the relational correspondences between the map and the space. In 4 experiments, 3-year-olds completed a map reading task in which they were asked to find hidden objects in a miniature room, using a corresponding map. We manipulated the availability of guided alignment (showing children the analogical mapping between maps and spaces; Experiments 1, 2, and 3a), the format of guided alignment (gesture or relational language; Experiment 2), and the iconicity of maps (Experiments 3a and 3b). We found that (a) young children's difficulties in map reading follow from known patterns of analogical development-for example, focusing on object similarity over relational similarity; and (b) guided alignment based on analogical reasoning led to substantially better performance. Results also indicated that children's map reading performance was affected by the format of guided alignment, the iconicity of the maps, and the order of tasks. The results bear on the developmental mechanisms underlying young children's learning of spatial representations and also suggest ways to support this learning. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

The Effect of College Students' Self-Generated Computerized Mind Mapping on Their Reading Achievement

ERIC Educational Resources Information Center

Sabbah, Sabah Salman

2015-01-01

This study explored the potential effect of college students' self-generated computerized mind maps on their reading comprehension. It also investigated the subjects' attitudes toward generating computerized mind maps for reading comprehension. The study was conducted in response to the inability of the foundation-level students, who were learning…

Three Reading Comprehension Strategies: TELLS, Story Mapping, and QARs.

ERIC Educational Resources Information Center

Sorrell, Adrian L.

1990-01-01

Three reading comprehension strategies are presented to assist learning-disabled students: an advance organizer technique called "TELLS Fact or Fiction" used before reading a passage, a schema-based technique called "Story Mapping" used while reading, and a postreading method of categorizing questions called…

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.

Quincy Market. [A Product of] the Regional Math Network: A Teacher Invigoration and Curriculum Development Project.

ERIC Educational Resources Information Center

Harvard Univ., Cambridge, MA. Graduate School of Education.

In this middle school mathematics unit two imaginary characters, Horatio and Portia, decide to make their fortune in Quincy Market (Boston, Massachusetts) running a Bull Market cart. In order to solve the problems that they encounter, they need to learn ratio and proportion, map reading, estimation, area and perimeter, population sampling, problem…

Mapping From an Instrumented Glove to a Robot Hand

NASA Technical Reports Server (NTRS)

Goza, Michael

2005-01-01

An algorithm has been developed to solve the problem of mapping from (1) a glove instrumented with joint-angle sensors to (2) an anthropomorphic robot hand. Such a mapping is needed to generate control signals to make the robot hand mimic the configuration of the hand of a human attempting to control the robot. The mapping problem is complicated by uncertainties in sensor locations caused by variations in sizes and shapes of hands and variations in the fit of the glove. The present mapping algorithm is robust in the face of these uncertainties, largely because it includes a calibration sub-algorithm that inherently adapts the mapping to the specific hand and glove, without need for measuring the hand and without regard for goodness of fit. The algorithm utilizes a forward-kinematics model of the glove derived from documentation provided by the manufacturer of the glove. In this case, forward-kinematics model signifies a mathematical model of the glove fingertip positions as functions of the sensor readings. More specifically, given the sensor readings, the forward-kinematics model calculates the glove fingertip positions in a Cartesian reference frame nominally attached to the palm. The algorithm also utilizes an inverse-kinematics model of the robot hand. In this case, inverse-kinematics model signifies a mathematical model of the robot finger-joint angles as functions of the robot fingertip positions. Again, more specifically, the inverse-kinematics model calculates the finger-joint commands needed to place the fingertips at specified positions in a Cartesian reference frame that is attached to the palm of the robot hand and that nominally corresponds to the Cartesian reference frame attached to the palm of the glove. Initially, because of the aforementioned uncertainties, the glove fingertip positions calculated by the forwardkinematics model in the glove Cartesian reference frame cannot be expected to match the robot fingertip positions in the robot-hand Cartesian reference frame. A calibration must be performed to make the glove and robot-hand fingertip positions correspond more precisely. The calibration procedure involves a few simple hand poses designed to provide well-defined fingertip positions. One of the poses is a fist. In each of the other poses, a finger touches the thumb. The calibration subalgorithm uses the sensor readings from these poses to modify the kinematical models to make the two sets of fingertip positions agree more closely.

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.

ABMapper: a suffix array-based tool for multi-location searching and splice-junction mapping.

PubMed

Lou, Shao-Ke; Ni, Bing; Lo, Leung-Yau; Tsui, Stephen Kwok-Wing; Chan, Ting-Fung; Leung, Kwong-Sak

2011-02-01

Sequencing reads generated by RNA-sequencing (RNA-seq) must first be mapped back to the genome through alignment before they can be further analyzed. Current fast and memory-saving short-read mappers could give us a quick view of the transcriptome. However, they are neither designed for reads that span across splice junctions nor for repetitive reads, which can be mapped to multiple locations in the genome (multi-reads). Here, we describe a new software package: ABMapper, which is specifically designed for exploring all putative locations of reads that are mapped to splice junctions or repetitive in nature. The software is freely available at: http://abmapper.sourceforge.net/. The software is written in C++ and PERL. It runs on all major platforms and operating systems including Windows, Mac OS X and LINUX.

The Emergence of Route Map Reading Skills in Young Children.

ERIC Educational Resources Information Center

Frank, Rita E.

There is little agreement about how the ability to read route maps initially emerges and about how it should be stimulated by early childhood educators. This study assessed the route map reading behavior of young children and the basic skills that might contribute to that behavior. In individual videotaped sessions, 120 four, five, and six year…

Effects of a Computer-Assisted Concept Mapping Learning Strategy on EFL College Students' English Reading Comprehension

ERIC Educational Resources Information Center

Liu, Pei-Lin; Chen, Chiu-Jung; Chang, Yu-Ju

2010-01-01

The purpose of this research was to investigate the effects of a computer-assisted concept mapping learning strategy on EFL college learners' English reading comprehension. The research questions were: (1) what was the influence of the computer-assisted concept mapping learning strategy on different learners' English reading comprehension? (2) did…

BM-Map: Bayesian Mapping of Multireads for Next-Generation Sequencing Data

PubMed Central

Ji, Yuan; Xu, Yanxun; Zhang, Qiong; Tsui, Kam-Wah; Yuan, Yuan; Norris, Clift; Liang, Shoudan; Liang, Han

2011-01-01

Summary Next-generation sequencing (NGS) technology generates millions of short reads, which provide valuable information for various aspects of cellular activities and biological functions. A key step in NGS applications (e.g., RNA-Seq) is to map short reads to correct genomic locations within the source genome. While most reads are mapped to a unique location, a significant proportion of reads align to multiple genomic locations with equal or similar numbers of mismatches; these are called multireads. The ambiguity in mapping the multireads may lead to bias in downstream analyses. Currently, most practitioners discard the multireads in their analysis, resulting in a loss of valuable information, especially for the genes with similar sequences. To refine the read mapping, we develop a Bayesian model that computes the posterior probability of mapping a multiread to each competing location. The probabilities are used for downstream analyses, such as the quantification of gene expression. We show through simulation studies and RNA-Seq analysis of real life data that the Bayesian method yields better mapping than the current leading methods. We provide a C++ program for downloading that is being packaged into a user-friendly software. PMID:21517792

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

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.

The Effectiveness of Using Group Story-Mapping Strategy to Improve Reading Comprehension of Students with Learning Disabilities

ERIC Educational Resources Information Center

Alturki, Nada

2017-01-01

The purpose of this study was to examine the effectiveness of using group story-mapping on ESL students with a learning disability in reading comprehension. The researcher focused on a specific graphic organizer in this study, called Group Story-Mapping. This strategy required students with learning disabilities involving reading comprehension to…

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 at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Tracking change over time: River flooding

USGS Publications Warehouse

,

2014-01-01

The objective of the Tracking Change Over Time lesson plan is to get students excited about studying the changing Earth. Intended for students in grades 5-8, the lesson plan is flexible and may be used as a student self-guided tutorial or as a teacher-led class lesson. Enhance students' learning of geography, map reading, earth science, and problem solving by seeing landscape changes from space.

How do Japanese escape from TSUNAMI? - Disaster Prevention Education through using Hazard Maps

NASA Astrophysics Data System (ADS)

Sakaue, Hiroaki

2013-04-01

After the disaster of the earthquake and tsunami in Tohoku, Japan in 2011, it is necessary to teach more "Disaster Prevention" in school. The government guideline for education of high school geography students emphasizes improving students' awareness of disaster prevention through acquiring geographical skills, for example reading hazard and thematic maps. The working group of the Ministry of Education, Culture, Sports, Science and Technology (MEXT) says that the purpose of Disaster Prevention Education is to develop the following competencies: 1. To acquire knowledge about disasters in the local area and the science of disaster prevention. 2. To teach individuals to protect themselves from natural hazards. 3. To safely support other people in the local area. 4. To build a safe society during rebuilding from the disasters. "Disaster Prevention Education" is part of the "Education for Sustainable Development" (ESD) curriculum. That is, teaching disaster prevention can contribute to developing abilities for sustainable development and building a sustainable society. I have tried to develop a high school geography class about "tsunami". The aim of this class is to develop the students' competencies to acquire the knowledge about tsunami and protect themselves from it through reading a hazard map. I especially think that in geography class, students can protect themselves from disasters through learning the risks of disasters and how to escape when disasters occur. In the first part of class, I have taught the mechanism of tsunami formation and where tsunamis occur in Japan. In the second part of class, I have shown students pictures that I had taken in Tohoku, for instance Ishinomaki-City, Minamisanriku-Town, Kesen'numa-City, and taught how to read hazard maps that show where safe and dangerous places are when natural hazards occur. I think that students can understand the features of the local area and how to escape from disasters that may occur in local area by learning a hazard map. I have used a comment paper to evaluate the following competencies: 1. Students can understand the mechanism of tsunami formation and its potential for damage. 2. Students can read the hazard map. 3. Students can explain or describe a detailed plan for disaster prevention. In conclusion, many students could read hazard maps and describe a detailed plan for disaster prevention. In other words, through developing mapping skills, geography students can contribute to developing abilities for Disaster Prevention Education and building a sustainable society. Disaster Prevention Education has many requirements. For example, the MEXT working group says that Disaster Prevention Education teaching should not only deliver knowledge but also develop students' problem solving competency, and that it is important to incorporate this education within each subject area in the school.

Cognitive Processes in Orienteering: A Review.

ERIC Educational Resources Information Center

Seiler, Roland

1996-01-01

Reviews recent research on information processing and decision making in orienteering. The main cognitive demands investigated were selection of relevant map information for route choice, comparison between map and terrain in map reading and in relocation, and quick awareness of mistakes. Presents a model of map reading based on results. Contains…

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

PubMed Central

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

2009-01-01

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

High-confidence coding and noncoding transcriptome maps

PubMed Central

2017-01-01

The advent of high-throughput RNA sequencing (RNA-seq) has led to the discovery of unprecedentedly immense transcriptomes encoded by eukaryotic genomes. However, the transcriptome maps are still incomplete partly because they were mostly reconstructed based on RNA-seq reads that lack their orientations (known as unstranded reads) and certain boundary information. Methods to expand the usability of unstranded RNA-seq data by predetermining the orientation of the reads and precisely determining the boundaries of assembled transcripts could significantly benefit the quality of the resulting transcriptome maps. Here, we present a high-performing transcriptome assembly pipeline, called CAFE, that significantly improves the original assemblies, respectively assembled with stranded and/or unstranded RNA-seq data, by orienting unstranded reads using the maximum likelihood estimation and by integrating information about transcription start sites and cleavage and polyadenylation sites. Applying large-scale transcriptomic data comprising 230 billion RNA-seq reads from the ENCODE, Human BodyMap 2.0, The Cancer Genome Atlas, and GTEx projects, CAFE enabled us to predict the directions of about 220 billion unstranded reads, which led to the construction of more accurate transcriptome maps, comparable to the manually curated map, and a comprehensive lncRNA catalog that includes thousands of novel lncRNAs. Our pipeline should not only help to build comprehensive, precise transcriptome maps from complex genomes but also to expand the universe of noncoding genomes. PMID:28396519

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

Unbiased Taxonomic Annotation of Metagenomic Samples

PubMed Central

Fosso, Bruno; Pesole, Graziano; Rosselló, Francesc

2018-01-01

Abstract The classification of reads from a metagenomic sample using a reference taxonomy is usually based on first mapping the reads to the reference sequences and then classifying each read at a node under the lowest common ancestor of the candidate sequences in the reference taxonomy with the least classification error. However, this taxonomic annotation can be biased by an imbalanced taxonomy and also by the presence of multiple nodes in the taxonomy with the least classification error for a given read. In this article, we show that the Rand index is a better indicator of classification error than the often used area under the receiver operating characteristic (ROC) curve and F-measure for both balanced and imbalanced reference taxonomies, and we also address the second source of bias by reducing the taxonomic annotation problem for a whole metagenomic sample to a set cover problem, for which a logarithmic approximation can be obtained in linear time and an exact solution can be obtained by integer linear programming. Experimental results with a proof-of-concept implementation of the set cover approach to taxonomic annotation in a next release of the TANGO software show that the set cover approach further reduces ambiguity in the taxonomic annotation obtained with TANGO without distorting the relative abundance profile of the metagenomic sample. PMID:29028181

Reading Angles in Maps

ERIC Educational Resources Information Center

Izard, Véronique; O'Donnell, Evan; Spelke, Elizabeth S.

2014-01-01

Preschool children can navigate by simple geometric maps of the environment, but the nature of the geometric relations they use in map reading remains unclear. Here, children were tested specifically on their sensitivity to angle. Forty-eight children (age 47:15-53:30 months) were presented with fragments of geometric maps, in which angle sections…

Analogical Processes in Children's Understanding of Spatial Representations

ERIC Educational Resources Information Center

Yuan, Lei; Uttal, David; Gentner, Dedre

2017-01-01

We propose that map reading can be construed as a form of analogical mapping. We tested 2 predictions that follow from this claim: First, young children's patterns of performance in map reading tasks should parallel those found in analogical mapping tasks; and, second, children will benefit from guided alignment instructions that help them see the…

Revealing the Relationship between Reading Interest and Critical Thinking Skills through Remap GI and Remap Jigsaw

ERIC Educational Resources Information Center

Zubaidah, Siti; Corebima, Aloysius Duran; Mahanal, Susriyati; Mistianah

2018-01-01

The aim of this research was to reveal the relationship between student's reading interest and critical thinking skills through Reading Concept Map Group Investigation (Remap GI) and Reading Concept Map Jigsaw (Remap Jigsaw) learning models. To do so, two science classes from first grade of two Senior High Schools in Malang, Indonesia were…

mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications.

PubMed

Hach, Faraz; Sarrafi, Iman; Hormozdiari, Farhad; Alkan, Can; Eichler, Evan E; Sahinalp, S Cenk

2014-07-01

High throughput sequencing (HTS) platforms generate unprecedented amounts of data that introduce challenges for processing and downstream analysis. While tools that report the 'best' mapping location of each read provide a fast way to process HTS data, they are not suitable for many types of downstream analysis such as structural variation detection, where it is important to report multiple mapping loci for each read. For this purpose we introduce mrsFAST-Ultra, a fast, cache oblivious, SNP-aware aligner that can handle the multi-mapping of HTS reads very efficiently. mrsFAST-Ultra improves mrsFAST, our first cache oblivious read aligner capable of handling multi-mapping reads, through new and compact index structures that reduce not only the overall memory usage but also the number of CPU operations per alignment. In fact the size of the index generated by mrsFAST-Ultra is 10 times smaller than that of mrsFAST. As importantly, mrsFAST-Ultra introduces new features such as being able to (i) obtain the best mapping loci for each read, and (ii) return all reads that have at most n mapping loci (within an error threshold), together with these loci, for any user specified n. Furthermore, mrsFAST-Ultra is SNP-aware, i.e. it can map reads to reference genome while discounting the mismatches that occur at common SNP locations provided by db-SNP; this significantly increases the number of reads that can be mapped to the reference genome. Notice that all of the above features are implemented within the index structure and are not simple post-processing steps and thus are performed highly efficiently. Finally, mrsFAST-Ultra utilizes multiple available cores and processors and can be tuned for various memory settings. Our results show that mrsFAST-Ultra is roughly five times faster than its predecessor mrsFAST. In comparison to newly enhanced popular tools such as Bowtie2, it is more sensitive (it can report 10 times or more mappings per read) and much faster (six times or more) in the multi-mapping mode. Furthermore, mrsFAST-Ultra has an index size of 2GB for the entire human reference genome, which is roughly half of that of Bowtie2. mrsFAST-Ultra is open source and it can be accessed at http://mrsfast.sourceforge.net. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Toward a Graded Psycholexical Space Mapping Model: Sublexical and Lexical Representations in Chinese Character Reading Development.

PubMed

Tong, Xiuli; McBride, Catherine

2017-07-01

Following a review of contemporary models of word-level processing for reading and their limitations, we propose a new hypothetical model of Chinese character reading, namely, the graded lexical space mapping model that characterizes how sublexical radicals and lexical information are involved in Chinese character reading development. The underlying assumption of this model is that Chinese character recognition is a process of competitive mappings of phonology, semantics, and orthography in both lexical and sublexical systems, operating as functions of statistical properties of print input based on the individual's specific level of reading. This model leads to several testable predictions concerning how the quasiregularity and continuity of Chinese-specific radicals are organized in memory for both child and adult readers at different developmental stages of reading.

High-Accuracy HLA Type Inference from Whole-Genome Sequencing Data Using Population Reference Graphs.

PubMed

Dilthey, Alexander T; Gourraud, Pierre-Antoine; Mentzer, Alexander J; Cereb, Nezih; Iqbal, Zamin; McVean, Gil

2016-10-01

Genetic variation at the Human Leucocyte Antigen (HLA) genes is associated with many autoimmune and infectious disease phenotypes, is an important element of the immunological distinction between self and non-self, and shapes immune epitope repertoires. Determining the allelic state of the HLA genes (HLA typing) as a by-product of standard whole-genome sequencing data would therefore be highly desirable and enable the immunogenetic characterization of samples in currently ongoing population sequencing projects. Extensive hyperpolymorphism and sequence similarity between the HLA genes, however, pose problems for accurate read mapping and make HLA type inference from whole-genome sequencing data a challenging problem. We describe how to address these challenges in a Population Reference Graph (PRG) framework. First, we construct a PRG for 46 (mostly HLA) genes and pseudogenes, their genomic context and their characterized sequence variants, integrating a database of over 10,000 known allele sequences. Second, we present a sequence-to-PRG paired-end read mapping algorithm that enables accurate read mapping for the HLA genes. Third, we infer the most likely pair of underlying alleles at G group resolution from the IMGT/HLA database at each locus, employing a simple likelihood framework. We show that HLA*PRG, our algorithm, outperforms existing methods by a wide margin. We evaluate HLA*PRG on six classical class I and class II HLA genes (HLA-A, -B, -C, -DQA1, -DQB1, -DRB1) and on a set of 14 samples (3 samples with 2 x 100bp, 11 samples with 2 x 250bp Illumina HiSeq data). Of 158 alleles tested, we correctly infer 157 alleles (99.4%). We also identify and re-type two erroneous alleles in the original validation data. We conclude that HLA*PRG for the first time achieves accuracies comparable to gold-standard reference methods from standard whole-genome sequencing data, though high computational demands (currently ~30-250 CPU hours per sample) remain a significant challenge to practical application.

High-Accuracy HLA Type Inference from Whole-Genome Sequencing Data Using Population Reference Graphs

PubMed Central

Dilthey, Alexander T.; Gourraud, Pierre-Antoine; McVean, Gil

2016-01-01

Genetic variation at the Human Leucocyte Antigen (HLA) genes is associated with many autoimmune and infectious disease phenotypes, is an important element of the immunological distinction between self and non-self, and shapes immune epitope repertoires. Determining the allelic state of the HLA genes (HLA typing) as a by-product of standard whole-genome sequencing data would therefore be highly desirable and enable the immunogenetic characterization of samples in currently ongoing population sequencing projects. Extensive hyperpolymorphism and sequence similarity between the HLA genes, however, pose problems for accurate read mapping and make HLA type inference from whole-genome sequencing data a challenging problem. We describe how to address these challenges in a Population Reference Graph (PRG) framework. First, we construct a PRG for 46 (mostly HLA) genes and pseudogenes, their genomic context and their characterized sequence variants, integrating a database of over 10,000 known allele sequences. Second, we present a sequence-to-PRG paired-end read mapping algorithm that enables accurate read mapping for the HLA genes. Third, we infer the most likely pair of underlying alleles at G group resolution from the IMGT/HLA database at each locus, employing a simple likelihood framework. We show that HLA*PRG, our algorithm, outperforms existing methods by a wide margin. We evaluate HLA*PRG on six classical class I and class II HLA genes (HLA-A, -B, -C, -DQA1, -DQB1, -DRB1) and on a set of 14 samples (3 samples with 2 x 100bp, 11 samples with 2 x 250bp Illumina HiSeq data). Of 158 alleles tested, we correctly infer 157 alleles (99.4%). We also identify and re-type two erroneous alleles in the original validation data. We conclude that HLA*PRG for the first time achieves accuracies comparable to gold-standard reference methods from standard whole-genome sequencing data, though high computational demands (currently ~30–250 CPU hours per sample) remain a significant challenge to practical application. PMID:27792722

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.

Idea-Mapping: The Technique and Its Use in the Classroom or Simulating the "Ups" and "Downs" of Reading Comprehension. Reading Education Report No. 36.

ERIC Educational Resources Information Center

Armbruster, Bonnie B.; Anderson, Thomas H.

Idea-mapping (i-mapping), a way of representing ideas from a text in the form of a diagram, is defined and illustrated in this document as a way to help students "see" how the ideas they read are linked to each other. The first portion of the document discusses the fundamental relationships found in texts (A is a characteristic of B, A…

Detection of microRNAs in color space.

PubMed

Marco, Antonio; Griffiths-Jones, Sam

2012-02-01

Deep sequencing provides inexpensive opportunities to characterize the transcriptional diversity of known genomes. The AB SOLiD technology generates millions of short sequencing reads in color-space; that is, the raw data is a sequence of colors, where each color represents 2 nt and each nucleotide is represented by two consecutive colors. This strategy is purported to have several advantages, including increased ability to distinguish sequencing errors from polymorphisms. Several programs have been developed to map short reads to genomes in color space. However, a number of previously unexplored technical issues arise when using SOLiD technology to characterize microRNAs. Here we explore these technical difficulties. First, since the sequenced reads are longer than the biological sequences, every read is expected to contain linker fragments. The color-calling error rate increases toward the 3(') end of the read such that recognizing the linker sequence for removal becomes problematic. Second, mapping in color space may lead to the loss of the first nucleotide of each read. We propose a sequential trimming and mapping approach to map small RNAs. Using our strategy, we reanalyze three published insect small RNA deep sequencing datasets and characterize 22 new microRNAs. A bash shell script to perform the sequential trimming and mapping procedure, called SeqTrimMap, is available at: http://www.mirbase.org/tools/seqtrimmap/ antonio.marco@manchester.ac.uk Supplementary data are available at Bioinformatics online.

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

A teaching-learning sequence about weather map reading

NASA Astrophysics Data System (ADS)

Mandrikas, Achilleas; Stavrou, Dimitrios; Skordoulis, Constantine

2017-07-01

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

Unified View of Backward Backtracking in Short Read Mapping

NASA Astrophysics Data System (ADS)

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

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

Reading Social wMaps.w

ERIC Educational Resources Information Center

Clements, Millard

1982-01-01

What should social studies teachers be trying to teach students how to do? Every culture provides its members with social "maps" that explain how things are--e.g., school materials, advertisements. Teaching students how to read these social "maps" should be the central task for social studies education. (RM)

Core Knowledge and the Emergence of Symbols: The Case of Maps

ERIC Educational Resources Information Center

Huang, Yi; Spelke, Elizabeth S.

2015-01-01

Map reading is unique to humans but is present in people of diverse cultures, at ages as young as 4 years old. Here, we explore the nature and sources of this ability and ask both what geometric information young children use in maps and what nonsymbolic systems are associated with their map-reading performance. Four-year-old children were given…

BACCardI--a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison.

PubMed

Bartels, Daniela; Kespohl, Sebastian; Albaum, Stefan; Drüke, Tanja; Goesmann, Alexander; Herold, Julia; Kaiser, Olaf; Pühler, Alfred; Pfeiffer, Friedhelm; Raddatz, Günter; Stoye, Jens; Meyer, Folker; Schuster, Stephan C

2005-04-01

We provide the graphical tool BACCardI for the construction of virtual clone maps from standard assembler output files or BLAST based sequence comparisons. This new tool has been applied to numerous genome projects to solve various problems including (a) validation of whole genome shotgun assemblies, (b) support for contig ordering in the finishing phase of a genome project, and (c) intergenome comparison between related strains when only one of the strains has been sequenced and a large insert library is available for the other. The BACCardI software can seamlessly interact with various sequence assembly packages. Genomic assemblies generated from sequence information need to be validated by independent methods such as physical maps. The time-consuming task of building physical maps can be circumvented by virtual clone maps derived from read pair information of large insert libraries.

Concept Maps and Informational Read-Alouds: Strengthening Both Science and Reading for Elementary Students

ERIC Educational Resources Information Center

Berry, Jaime; Potter, Jalene; Hollas, Victoria

2013-01-01

This quasi-experimental study compared the effects of concept mapping and teacher generated questioning on students' organization and retention of science knowledge when used along with interactive informational read-alouds. Fifty-eight third grade students completed an eight-day unit regarding "soil formation." Students who participated…

78 FR 7441 - Proposed Flood Hazard Determinations

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-01

... Online at:'' Link is corrected to read as follows: http://riskmap6.com/Community.aspx?cid=208&sid=4 3. On... ``Maps Available for Inspection Online at:'' Link is corrected to read as follows: http://riskmap6.com... Areas,'' the entry for the ``Maps Available for Inspection Online at:'' Link is corrected to read as...

Effects of Feedforward and Feedback Consistency on Reading and Spelling in Dyslexia

ERIC Educational Resources Information Center

Davies, Robert A. I.; Weekes, Brendan S.

2005-01-01

We investigated the effects of rime consistency on reading and spelling among dyslexic children and a group of matched reading age skilled readers by manipulating consistency of orthography-to-phonology (OP) mappings and consistency of mappings from phonology-to-orthography (PO). For both dyslexic and control children we found feedforward…

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.

Benchmarking short sequence mapping tools

PubMed Central

2013-01-01

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

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.

Prediction and stability of reading problems in middle childhood.

PubMed

Ritchey, Kristen D; Silverman, Rebecca D; Schatschneider, Christopher; Speece, Deborah L

2015-01-01

The longitudinal prediction of reading problems from fourth grade to sixth grade was investigated with a sample of 173 students. Reading problems at the end of sixth grade were defined by significantly below average performance (≤ 15th percentile) on reading factors defining word reading, fluency, and reading comprehension. Sixth grade poor reader status was predicted by fall of fourth grade passage reading fluency, spelling fluency, and the number of reading problems identified by teachers. Reading fluency and spelling fluency were significant predictors in logistic regression equation that combined to yield a screening battery with an area under the curve of .91. These results suggest that brief assessments of reading and spelling fluency in fourth grade may be able to identify students in middle childhood who have a reading problem or who are at risk for experiencing reading problems in sixth grade. © Hammill Institute on Disabilities 2013.

A Teaching-Learning Sequence about Weather Map Reading

ERIC Educational Resources Information Center

Mandrikas, Achilleas; Stavrou, Dimitrios; Skordoulis, Constantine

2017-01-01

In this paper a teaching-learning sequence (TLS) introducing pre-service elementary teachers (PET) to weather map reading, with emphasis on wind assignment, is presented. The TLS includes activities about recognition of wind symbols, assignment of wind direction and wind speed on a weather map and identification of wind characteristics in a…

An Examination of the Effects of Argument Mapping on Students' Memory and Comprehension Performance

ERIC Educational Resources Information Center

Dwyer, Christopher P.; Hogan, Michael J.; Stewart, Ian

2013-01-01

Argument mapping (AM) is a method of visually diagramming arguments to allow for easy comprehension of core statements and relations. A series of three experiments compared argument map reading and construction with hierarchical outlining, text summarisation, and text reading as learning methods by examining subsequent memory and comprehension…

Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data

PubMed Central

2014-01-01

Background The rapid evolution in high-throughput sequencing (HTS) technologies has opened up new perspectives in several research fields and led to the production of large volumes of sequence data. A fundamental step in HTS data analysis is the mapping of reads onto reference sequences. Choosing a suitable mapper for a given technology and a given application is a subtle task because of the difficulty of evaluating mapping algorithms. Results In this paper, we present a benchmark procedure to compare mapping algorithms used in HTS using both real and simulated datasets and considering four evaluation criteria: computational resource and time requirements, robustness of mapping, ability to report positions for reads in repetitive regions, and ability to retrieve true genetic variation positions. To measure robustness, we introduced a new definition for a correctly mapped read taking into account not only the expected start position of the read but also the end position and the number of indels and substitutions. We developed CuReSim, a new read simulator, that is able to generate customized benchmark data for any kind of HTS technology by adjusting parameters to the error types. CuReSim and CuReSimEval, a tool to evaluate the mapping quality of the CuReSim simulated reads, are freely available. We applied our benchmark procedure to evaluate 14 mappers in the context of whole genome sequencing of small genomes with Ion Torrent data for which such a comparison has not yet been established. Conclusions A benchmark procedure to compare HTS data mappers is introduced with a new definition for the mapping correctness as well as tools to generate simulated reads and evaluate mapping quality. The application of this procedure to Ion Torrent data from the whole genome sequencing of small genomes has allowed us to validate our benchmark procedure and demonstrate that it is helpful for selecting a mapper based on the intended application, questions to be addressed, and the technology used. This benchmark procedure can be used to evaluate existing or in-development mappers as well as to optimize parameters of a chosen mapper for any application and any sequencing platform. PMID:24708189

Comparing the Effect of Thinking Maps Training Package Developed by the Thinking Maps Method on the Reading Performance of Dyslexic Students

ERIC Educational Resources Information Center

Faramarzi, Salar; Moradi, Mohammadreza; Abedi, Ahmad

2018-01-01

The present study aimed to develop the thinking maps training package and compare its training effect with the thinking maps method on the reading performance of second and fifth grade of elementary school male dyslexic students. For this mixed method exploratory study, from among the above mentioned grades' students in Isfahan, 90 students who…

Electronic Spin Storage in an Electrically Readable Nuclear Spin Memory with a Lifetime >100 Seconds

NASA Astrophysics Data System (ADS)

McCamey, D. R.; Van Tol, J.; Morley, G. W.; Boehme, C.

2010-12-01

Electron spins are strong candidates with which to implement spintronics because they are both mobile and able to be manipulated. The relatively short lifetimes of electron spins, however, present a problem for the long-term storage of spin information. We demonstrated an ensemble nuclear spin memory in phosphorous-doped silicon, which can be read out electrically and has a lifetime exceeding 100 seconds. The electronic spin information can be mapped onto and stored in the nuclear spin of the phosphorus donors, and the nuclear spins can then be repetitively read out electrically for time periods that exceed the electron spin lifetime. We discuss how this memory can be used in conjunction with other silicon spintronic devices.

The workshop. [use and application of remotely sensed data

NASA Technical Reports Server (NTRS)

Wake, W. H.

1981-01-01

The plan is presented for a two day workshop held to provide educational and training experience in the reading, interpretation, and application of LANDSAT and correlated larger scale imagery, digital printout maps, and other collateral material for a large number of participants with widely diverse levels of expertise, backgrounds, and occupations in government, industry, and education. The need for using surface truth field studies with correlated aerial imagery in solving real world problems was demonstrated.

Effective Reading Comprehension in EFL Contexts: Individual and Collaborative Concept Mapping Strategies

ERIC Educational Resources Information Center

Riahi, Zahra; Pourdana, Natasha

2017-01-01

The present study attempted to investigate the possible impacts of Individual Concept Mapping (ICM) and Collaborative Concept Mapping (CCM) strategies on Iranian EFL learners' reading comprehension. For this purpose, 90 pre-intermediate female language learners ranged between 12 to 17 years of age were selected to randomly assign into ICM, CCM and…

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

PubMed

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

2014-08-08

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

A Model Critical Reading Lesson for Secondary High-Risk Students.

ERIC Educational Resources Information Center

Haney, Gail; Thistlethwaite, Linda

1991-01-01

This article defines critical reading, discusses associated frameworks, and lists considerations for choosing topics and reading materials. A sample critical reading lesson using a "mapping" approach with a reading on euthanasia demonstrates guiding secondary learning-disabled students in critical reading. (DB)

Edwin James' and John Hinton's revisions of Maclure's geologic map of the United States

NASA Astrophysics Data System (ADS)

Aalto, K. R.

2012-03-01

William Maclure's pioneering geologic map of the eastern United States, published first in 1809 with Observations on the Geology of the United States, provided a foundation for many later maps - a template from which geologists could extend their mapping westward from the Appalachians. Edwin James, botanist, geologist and surgeon for the 1819/1820 United States Army western exploring expedition under Major Stephen H. Long, published a full account of this expedition with map and geologic sections in 1822-1823. In this he extended Maclure's geology across the Mississippi Valley to the Colorado Rockies. John Howard Hinton (1791-1873) published his widely read text: The History and Topography of the United States in 1832, which included a compilations of Maclure's and James' work in a colored geologic map and vertical sections. All three men were to some degree confounded in their attempts to employ Wernerian rock classification in their mapping and interpretations of geologic history, a common problem in the early 19th Century prior to the demise of Neptunist theory and advent of biostratigraphic techniques of correlation. However, they provided a foundation for the later, more refined mapping and geologic interpretation of the eastern United States.

Home Economics Reading Skills: Problems and Selected References.

ERIC Educational Resources Information Center

Cranney, A. Garr; And Others

Home economics presents at least eight problems to secondary school reading teachers. These problems include poor readers, difficult reading material, lack of reading materials, teachers' lack of training in reading instruction, scarce information about home economics for reading teachers, diversity of the home economics field (requiring a wide…

Concept Mapping as a Reading Strategy: Does It Scaffold Comprehension and Recall?

ERIC Educational Resources Information Center

Tajeddin, Zia; Tabatabaei, Soudabeh

2016-01-01

Concept maps reflect the linkage of concepts or facts within a text. This study was set out to investigate whether concept mapping as a learning strategy would have any scaffolding effect on the reading comprehension and recall of propositions by L2 learners. Out of 60 high school students, 30 in the experimental group were exposed to concept…

The Effectiveness of Using Group Story-Mapping Strategy to Improve Reading Comprehension of Students with Learning Disabilities

ERIC Educational Resources Information Center

Alturki, Nada

2017-01-01

The purpose of this study was to examine the effectiveness of using group story-mapping of English as a second language (ESL) on students with learning disability while reading comprehension. The researcher focused on a specific graphic organizer in this study, called group story-mapping. This strategy required students with learning disabilities…

The Impact of Electronic Mind Maps on Students' Reading Comprehension

ERIC Educational Resources Information Center

Mohaidat, Mohammad Mahmoud Talal

2018-01-01

This study aimed to investigate the impact of the electronic mind map (IMindMap) on the development of reading comprehension among the ninth grade students in Jordan. The sample of the study consisted of two ninth grade sections from two public schools in Irbid First Directorate during the academic 2016-2017. Each section consisted of (30)…

Map reading tools for map libraries.

USGS Publications Warehouse

Greenberg, G.L.

1982-01-01

Engineers, navigators and military strategists employ a broad array of mechanical devices to facilitate map use. A larger number of map users such as educators, students, tourists, journalists, historians, politicians, economists and librarians are unaware of the available variety of tools which can be used with maps to increase the speed and efficiency of their application and interpretation. This paper identifies map reading tools such as coordinate readers, protractors, dividers, planimeters, and symbol-templets according to a functional classification. Particularly, arrays of tools are suggested for use in determining position, direction, distance, area and form (perimeter-shape-pattern-relief). -from Author

Soil pH Mapping with an On-The-Go Sensor

PubMed Central

Schirrmann, Michael; Gebbers, Robin; Kramer, Eckart; Seidel, Jan

2011-01-01

Soil pH is a key parameter for crop productivity, therefore, its spatial variation should be adequately addressed to improve precision management decisions. Recently, the Veris pH Manager™, a sensor for high-resolution mapping of soil pH at the field scale, has been made commercially available in the US. While driving over the field, soil pH is measured on-the-go directly within the soil by ion selective antimony electrodes. The aim of this study was to evaluate the Veris pH Manager™ under farming conditions in Germany. Sensor readings were compared with data obtained by standard protocols of soil pH assessment. Experiments took place under different scenarios: (a) controlled tests in the lab, (b) semicontrolled test on transects in a stop-and-go mode, and (c) tests under practical conditions in the field with the sensor working in its typical on-the-go mode. Accuracy issues, problems, options, and potential benefits of the Veris pH Manager™ were addressed. The tests demonstrated a high degree of linearity between standard laboratory values and sensor readings. Under practical conditions in the field (scenario c), the measure of fit (r2) for the regression between the on-the-go measurements and the reference data was 0.71, 0.63, and 0.84, respectively. Field-specific calibration was necessary to reduce systematic errors. Accuracy of the on-the-go maps was considerably higher compared with the pH maps obtained by following the standard protocols, and the error in calculating lime requirements was reduced by about one half. However, the system showed some weaknesses due to blockage by residual straw and weed roots. If these problems were solved, the on-the-go sensor investigated here could be an efficient alternative to standard sampling protocols as a basis for liming in Germany. PMID:22346591

Soil pH mapping with an on-the-go sensor.

PubMed

Schirrmann, Michael; Gebbers, Robin; Kramer, Eckart; Seidel, Jan

2011-01-01

Soil pH is a key parameter for crop productivity, therefore, its spatial variation should be adequately addressed to improve precision management decisions. Recently, the Veris pH Manager™, a sensor for high-resolution mapping of soil pH at the field scale, has been made commercially available in the US. While driving over the field, soil pH is measured on-the-go directly within the soil by ion selective antimony electrodes. The aim of this study was to evaluate the Veris pH Manager™ under farming conditions in Germany. Sensor readings were compared with data obtained by standard protocols of soil pH assessment. Experiments took place under different scenarios: (a) controlled tests in the lab, (b) semicontrolled test on transects in a stop-and-go mode, and (c) tests under practical conditions in the field with the sensor working in its typical on-the-go mode. Accuracy issues, problems, options, and potential benefits of the Veris pH Manager™ were addressed. The tests demonstrated a high degree of linearity between standard laboratory values and sensor readings. Under practical conditions in the field (scenario c), the measure of fit (r(2)) for the regression between the on-the-go measurements and the reference data was 0.71, 0.63, and 0.84, respectively. Field-specific calibration was necessary to reduce systematic errors. Accuracy of the on-the-go maps was considerably higher compared with the pH maps obtained by following the standard protocols, and the error in calculating lime requirements was reduced by about one half. However, the system showed some weaknesses due to blockage by residual straw and weed roots. If these problems were solved, the on-the-go sensor investigated here could be an efficient alternative to standard sampling protocols as a basis for liming in Germany.

Reading angles in maps.

PubMed

Izard, Véronique; O'Donnell, Evan; Spelke, Elizabeth S

2014-01-01

Preschool children can navigate by simple geometric maps of the environment, but the nature of the geometric relations they use in map reading remains unclear. Here, children were tested specifically on their sensitivity to angle. Forty-eight children (age 47:15-53:30 months) were presented with fragments of geometric maps, in which angle sections appeared without any relevant length or distance information. Children were able to read these map fragments and compare two-dimensional to three-dimensional angles. However, this ability appeared both variable and fragile among the youngest children of the sample. These findings suggest that 4-year-old children begin to form an abstract concept of angle that applies both to two-dimensional and three-dimensional displays and that serves to interpret novel spatial symbols. © 2013 The Authors. Child Development © 2013 Society for Research in Child Development, Inc.

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 pairwise short-read alignments. We show that libgapmis is better-suited and more efficient than existing algorithms for this task. The importance of our contribution is underlined by the fact that the provided functions may be seamlessly integrated into any short-read alignment pipeline. The open-source code of libgapmis is available at http://www.exelixis-lab.org/gapmis. PMID:24564250

Prediction and Stability of Reading Problems in Middle Childhood

ERIC Educational Resources Information Center

Ritchey, Kristen D.; Silverman, Rebecca D.; Schatschneider, Christopher; Speece, Deborah L.

2015-01-01

The longitudinal prediction of reading problems from fourth grade to sixth grade was investigated with a sample of 173 students. Reading problems at the end of sixth grade were defined by significantly below average performance (= 15th percentile) on reading factors defining word reading, fluency, and reading comprehension. Sixth grade poor reader…

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. All rights reserved. For Permissions, please email: journals.permissions@oup.com

An investigation of causes of false positive single nucleotide polymorphisms using simulated reads from a small eukaryote genome.

PubMed

Ribeiro, Antonio; Golicz, Agnieszka; Hackett, Christine Anne; Milne, Iain; Stephen, Gordon; Marshall, David; Flavell, Andrew J; Bayer, Micha

2015-11-11

Single Nucleotide Polymorphisms (SNPs) are widely used molecular markers, and their use has increased massively since the inception of Next Generation Sequencing (NGS) technologies, which allow detection of large numbers of SNPs at low cost. However, both NGS data and their analysis are error-prone, which can lead to the generation of false positive (FP) SNPs. We explored the relationship between FP SNPs and seven factors involved in mapping-based variant calling - quality of the reference sequence, read length, choice of mapper and variant caller, mapping stringency and filtering of SNPs by read mapping quality and read depth. This resulted in 576 possible factor level combinations. We used error- and variant-free simulated reads to ensure that every SNP found was indeed a false positive. The variation in the number of FP SNPs generated ranged from 0 to 36,621 for the 120 million base pairs (Mbp) genome. All of the experimental factors tested had statistically significant effects on the number of FP SNPs generated and there was a considerable amount of interaction between the different factors. Using a fragmented reference sequence led to a dramatic increase in the number of FP SNPs generated, as did relaxed read mapping and a lack of SNP filtering. The choice of reference assembler, mapper and variant caller also significantly affected the outcome. The effect of read length was more complex and suggests a possible interaction between mapping specificity and the potential for contributing more false positives as read length increases. The choice of tools and parameters involved in variant calling can have a dramatic effect on the number of FP SNPs produced, with particularly poor combinations of software and/or parameter settings yielding tens of thousands in this experiment. Between-factor interactions make simple recommendations difficult for a SNP discovery pipeline but the quality of the reference sequence is clearly of paramount importance. Our findings are also a stark reminder that it can be unwise to use the relaxed mismatch settings provided as defaults by some read mappers when reads are being mapped to a relatively unfinished reference sequence from e.g. a non-model organism in its early stages of genomic exploration.

Special Focus

PubMed Central

Nawrocki, Eric P.; Burge, Sarah W.

2013-01-01

The development of RNA bioinformatic tools began more than 30 y ago with the description of the Nussinov and Zuker dynamic programming algorithms for single sequence RNA secondary structure prediction. Since then, many tools have been developed for various RNA sequence analysis problems such as homology search, multiple sequence alignment, de novo RNA discovery, read-mapping, and many more. In this issue, we have collected a sampling of reviews and original research that demonstrate some of the many ways bioinformatics is integrated with current RNA biology research. PMID:23948768

Toward A Literate Society; The Report of the Committee on Reading.

ERIC Educational Resources Information Center

Carroll, John B., Ed.; Cahall, Jeanne S., Ed.

The problems and possibilities involved in developing a national Right-to-Read program are discussed in this book, and it is argued that there is no one reading problem but rather a series of reading problems calling for a wide variety of responses. The report begins with a definition and a diagnosis of the national reading problems, a national…

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

PubMed

Lee, Hayan; Schatz, Michael C

2012-08-15

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

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

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

Aspergillus flavus infection triggered immune responses and host-pathogen cross-talks in groundnut during in-vitro seed colonization.

PubMed

Nayak, Spurthi N; Agarwal, Gaurav; Pandey, Manish K; Sudini, Hari K; Jayale, Ashwin S; Purohit, Shilp; Desai, Aarthi; Wan, Liyun; Guo, Baozhu; Liao, Boshou; Varshney, Rajeev K

2017-08-29

Aflatoxin contamination, caused by fungal pathogen Aspergillus flavus, is a major quality and health problem delimiting the trade and consumption of groundnut (Arachis hypogaea L.) worldwide. RNA-seq approach was deployed to understand the host-pathogen interaction by identifying differentially expressed genes (DEGs) for resistance to in-vitro seed colonization (IVSC) at four critical stages after inoculation in J 11 (resistant) and JL 24 (susceptible) genotypes of groundnut. About 1,344.04 million sequencing reads have been generated from sixteen libraries representing four stages in control and infected conditions. About 64% and 67% of quality filtered reads (1,148.09 million) were mapped onto A (A. duranensis) and B (A. ipaёnsis) subgenomes of groundnut respectively. About 101 million unaligned reads each from J 11 and JL 24 were used to map onto A. flavus genome. As a result, 4,445 DEGs including defense-related genes like senescence-associated proteins, resveratrol synthase, 9s-lipoxygenase, pathogenesis-related proteins were identified. In A. flavus, about 578 DEGs coding for growth and development of fungus, aflatoxin biosynthesis, binding, transport, and signaling were identified in compatible interaction. Besides identifying candidate genes for IVSC resistance in groundnut, the study identified the genes involved in host-pathogen cross-talks and markers that can be used in breeding resistant varieties.

Efficient algorithms for polyploid haplotype phasing.

PubMed

He, Dan; Saha, Subrata; Finkers, Richard; Parida, Laxmi

2018-05-09

Inference of haplotypes, or the sequence of alleles along the same chromosomes, is a fundamental problem in genetics and is a key component for many analyses including admixture mapping, identifying regions of identity by descent and imputation. Haplotype phasing based on sequencing reads has attracted lots of attentions. Diploid haplotype phasing where the two haplotypes are complimentary have been studied extensively. In this work, we focused on Polyploid haplotype phasing where we aim to phase more than two haplotypes at the same time from sequencing data. The problem is much more complicated as the search space becomes much larger and the haplotypes do not need to be complimentary any more. We proposed two algorithms, (1) Poly-Harsh, a Gibbs Sampling based algorithm which alternatively samples haplotypes and the read assignments to minimize the mismatches between the reads and the phased haplotypes, (2) An efficient algorithm to concatenate haplotype blocks into contiguous haplotypes. Our experiments showed that our method is able to improve the quality of the phased haplotypes over the state-of-the-art methods. To our knowledge, our algorithm for haplotype blocks concatenation is the first algorithm that leverages the shared information across multiple individuals to construct contiguous haplotypes. Our experiments showed that it is both efficient and effective.

SciReader enables reading of medical content with instantaneous definitions.

PubMed

Gradie, Patrick R; Litster, Megan; Thomas, Rinu; Vyas, Jay; Schiller, Martin R

2011-01-25

A major problem patients encounter when reading about health related issues is document interpretation, which limits reading comprehension and therefore negatively impacts health care. Currently, searching for medical definitions from an external source is time consuming, distracting, and negatively impacts reading comprehension and memory of the material. SciReader was built as a Java application with a Flex-based front-end client. The dictionary used by SciReader was built by consolidating data from several sources and generating new definitions with a standardized syntax. The application was evaluated by measuring the percentage of words defined in different documents. A survey was used to test the perceived effect of SciReader on reading time and comprehension. We present SciReader, a web-application that simplifies document interpretation by allowing users to instantaneously view medical, English, and scientific definitions as they read any document. This tool reveals the definitions of any selected word in a small frame at the top of the application. SciReader relies on a dictionary of ~750,000 unique Biomedical and English word definitions. Evaluation of the application shows that it maps ~98% of words in several different types of documents and that most users tested in a survey indicate that the application decreases reading time and increases comprehension. SciReader is a web application useful for reading medical and scientific documents. The program makes jargon-laden content more accessible to patients, educators, health care professionals, and the general public.

One Size Doesn't Fit All - RefEditor: Building Personalized Diploid Reference Genome to Improve Read Mapping and Genotype Calling in Next Generation Sequencing Studies

PubMed Central

Yuan, Shuai; Johnston, H. Richard; Zhang, Guosheng; Li, Yun; Hu, Yi-Juan; Qin, Zhaohui S.

2015-01-01

With rapid decline of the sequencing cost, researchers today rush to embrace whole genome sequencing (WGS), or whole exome sequencing (WES) approach as the next powerful tool for relating genetic variants to human diseases and phenotypes. A fundamental step in analyzing WGS and WES data is mapping short sequencing reads back to the reference genome. This is an important issue because incorrectly mapped reads affect the downstream variant discovery, genotype calling and association analysis. Although many read mapping algorithms have been developed, the majority of them uses the universal reference genome and do not take sequence variants into consideration. Given that genetic variants are ubiquitous, it is highly desirable if they can be factored into the read mapping procedure. In this work, we developed a novel strategy that utilizes genotypes obtained a priori to customize the universal haploid reference genome into a personalized diploid reference genome. The new strategy is implemented in a program named RefEditor. When applying RefEditor to real data, we achieved encouraging improvements in read mapping, variant discovery and genotype calling. Compared to standard approaches, RefEditor can significantly increase genotype calling consistency (from 43% to 61% at 4X coverage; from 82% to 92% at 20X coverage) and reduce Mendelian inconsistency across various sequencing depths. Because many WGS and WES studies are conducted on cohorts that have been genotyped using array-based genotyping platforms previously or concurrently, we believe the proposed strategy will be of high value in practice, which can also be applied to the scenario where multiple NGS experiments are conducted on the same cohort. The RefEditor sources are available at https://github.com/superyuan/refeditor. PMID:26267278

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 applied to any read mapper. We hope that our results provide inspiration for new works to design other bioinformatics algorithms that take advantage of emerging technologies and new processing paradigms, such as processing-in-memory using 3D-stacked memory devices.

Differing effects of two synthetic phonics programmes on early reading development.

PubMed

Shapiro, Laura R; Solity, Jonathan

2016-06-01

Synthetic phonics is the widely accepted approach for teaching reading in English: Children are taught to sound out the letters in a word then blend these sounds together. We compared the impact of two synthetic phonics programmes on early reading. Children received Letters and Sounds (L&S; 7 schools) which teaches multiple letter-sound mappings or Early Reading Research (ERR; 10 schools) which teaches only the most consistent mappings plus frequent words by sight. We measured phonological awareness (PA) and reading from school entry to the end of the second (all schools) or third school year (4 ERR, 3 L&S schools). Phonological awareness was significantly related to all reading measures for the whole sample. However, there was a closer relationship between PA and exception word reading for children receiving the L&S programme. The programmes were equally effective overall, but their impact on reading significantly interacted with school-entry PA: Children with poor PA at school entry achieved higher reading attainments under ERR (significant group difference on exception word reading at the end of the first year), whereas children with good PA performed equally well under either programme. The more intensive phonics programme (L&S) heightened the association between PA and exception word reading. Although the programmes were equally effective for most children, results indicate potential benefits of ERR for children with poor PA. We suggest that phonics programmes could be simplified to teach only the most consistent mappings plus frequent words by sight. © 2015 The British Psychological Society.

Lexical processing and distributional knowledge in sound-spelling mapping in a consistent orthography: A longitudinal study of reading and spelling in dyslexic and typically developing children.

PubMed

Marinelli, Chiara Valeria; Cellini, Pamela; Zoccolotti, Pierluigi; Angelelli, Paola

This study examined the ability to master lexical processing and use knowledge of the relative frequency of sound-spelling mappings in both reading and spelling. Twenty-four dyslexic and dysgraphic children and 86 typically developing readers were followed longitudinally in 3rd and 5th grades. Effects of word regularity, word frequency, and probability of sound-spelling mappings were examined in two experimental tasks: (a) spelling to dictation; and (b) orthographic judgment. Dyslexic children showed larger regularity and frequency effects than controls in both tasks. Sensitivity to distributional information of sound-spelling mappings was already detected by third grade, indicating early acquisition even in children with dyslexia. Although with notable differences, knowledge of the relative frequencies of sound-spelling mapping influenced both reading and spelling. Results are discussed in terms of their theoretical and empirical implications.

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

PubMed

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

2014-02-01

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

Certainty grids for mobile robots

NASA Technical Reports Server (NTRS)

Moravec, H. P.

1987-01-01

A numerical representation of uncertain and incomplete sensor knowledge called Certainty Grids has been used successfully in several mobile robot control programs, and has proven itself to be a powerful and efficient unifying solution for sensor fusion, motion planning, landmark identification, and many other central problems. Researchers propose to build a software framework running on processors onboard the new Uranus mobile robot that will maintain a probabilistic, geometric map of the robot's surroundings as it moves. The certainty grid representation will allow this map to be incrementally updated in a uniform way from various sources including sonar, stereo vision, proximity and contact sensors. The approach can correctly model the fuzziness of each reading, while at the same time combining multiple measurements to produce sharper map features, and it can deal correctly with uncertainties in the robot's motion. The map will be used by planning programs to choose clear paths, identify locations (by correlating maps), identify well-known and insufficiently sensed terrain, and perhaps identify objects by shape. The certainty grid representation can be extended in the same dimension and used to detect and track moving objects.

Explorers of the Universe: Metacognitive Tools for Learning Science Concepts

NASA Technical Reports Server (NTRS)

Alvarez, Marino C.

1998-01-01

Much of school learning consists of rote memorization of facts with little emphasis on meaningful interpretations. Knowledge construction is reduced to factual knowledge production with little regard for critical thinking, problem solving, or clarifying misconceptions. An important role of a middle and secondary teacher when teaching science is to aid students' ability to reflect upon what they know about a given topic and make available strategies that will enhance their understanding of text and science experiments. Developing metacognition, the ability to monitor one's own knowledge about a topic of study and to activate appropriate strategies, enhances students' learning when faced with reading, writing and problem solving situations. Two instructional strategies that can involve students in developing metacognitive awareness are hierarchical concept mapping, and Vee diagrams. Concept maps enable students to organize their ideas and reveal visually these ideas to others. A Vee diagram is a structured visual means of relating the methodological aspects of an activity to its underlying conceptual aspect in ways that aid learners in meaningful understanding of scientific investigations.

Uniform, optimal signal processing of mapped deep-sequencing data.

PubMed

Kumar, Vibhor; Muratani, Masafumi; Rayan, Nirmala Arul; Kraus, Petra; Lufkin, Thomas; Ng, Huck Hui; Prabhakar, Shyam

2013-07-01

Despite their apparent diversity, many problems in the analysis of high-throughput sequencing data are merely special cases of two general problems, signal detection and signal estimation. Here we adapt formally optimal solutions from signal processing theory to analyze signals of DNA sequence reads mapped to a genome. We describe DFilter, a detection algorithm that identifies regulatory features in ChIP-seq, DNase-seq and FAIRE-seq data more accurately than assay-specific algorithms. We also describe EFilter, an estimation algorithm that accurately predicts mRNA levels from as few as 1-2 histone profiles (R ∼0.9). Notably, the presence of regulatory motifs in promoters correlates more with histone modifications than with mRNA levels, suggesting that histone profiles are more predictive of cis-regulatory mechanisms. We show by applying DFilter and EFilter to embryonic forebrain ChIP-seq data that regulatory protein identification and functional annotation are feasible despite tissue heterogeneity. The mathematical formalism underlying our tools facilitates integrative analysis of data from virtually any sequencing-based functional profile.

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.

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

The Effect of Learner Constructed, Fill in the Map Concept Map Technique, and Summarizing Strategy on Iranian Pre-University Students' Reading Comprehension

ERIC Educational Resources Information Center

Soleimani, Hassan; Nabizadeh, Fatemeh

2012-01-01

Concept maps (CM) are powerful tools which have different uses in educational contexts; however, this study limited its extension and explored its impact on the reading comprehension skill of Iranian EFL students. To this purpose, a proficiency test was employed and 90 intermediate pre-university students were chosen and divided into three groups:…

STORMSeq: an open-source, user-friendly pipeline for processing personal genomics data in the cloud.

PubMed

Karczewski, Konrad J; Fernald, Guy Haskin; Martin, Alicia R; Snyder, Michael; Tatonetti, Nicholas P; Dudley, Joel T

2014-01-01

The increasing public availability of personal complete genome sequencing data has ushered in an era of democratized genomics. However, read mapping and variant calling software is constantly improving and individuals with personal genomic data may prefer to customize and update their variant calls. Here, we describe STORMSeq (Scalable Tools for Open-Source Read Mapping), a graphical interface cloud computing solution that does not require a parallel computing environment or extensive technical experience. This customizable and modular system performs read mapping, read cleaning, and variant calling and annotation. At present, STORMSeq costs approximately $2 and 5-10 hours to process a full exome sequence and $30 and 3-8 days to process a whole genome sequence. We provide this open-access and open-source resource as a user-friendly interface in Amazon EC2.

Using pseudoalignment and base quality to accurately quantify microbial community composition

PubMed Central

Novembre, John

2018-01-01

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

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.

A MAP read-routine for IBM 7094 Fortran II binary tapes

Treesearch

Robert S. Helfman

1966-01-01

Two MAP (Macro Assembly Program) language routines are descrived. They permit Fortran IV programs to read binary tapes generated by Fortran II programs, on the IBM 7090 and 7094 computers. One routine is for use with 7040/44-IBSYS, the other for 7090/94-IBSYS.

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.

Why Reading Fluency Should Be Hot

ERIC Educational Resources Information Center

Rasinski, Timothy V.

2012-01-01

This article explores problems that have surfaced in the teaching of reading fluency and how teachers and reading coaches can resolve those problems. Specific issues addressed include reading fluency being defined as reading fast and instruction that is focused on having students read fast, reading fluency viewed as solely and oral reading…

Simultaneous isoform discovery and quantification from RNA-seq.

PubMed

Hiller, David; Wong, Wing Hung

2013-05-01

RNA sequencing is a recent technology which has seen an explosion of methods addressing all levels of analysis, from read mapping to transcript assembly to differential expression modeling. In particular the discovery of isoforms at the transcript assembly stage is a complex problem and current approaches suffer from various limitations. For instance, many approaches use graphs to construct a minimal set of isoforms which covers the observed reads, then perform a separate algorithm to quantify the isoforms, which can result in a loss of power. Current methods also use ad-hoc solutions to deal with the vast number of possible isoforms which can be constructed from a given set of reads. Finally, while the need of taking into account features such as read pairing and sampling rate of reads has been acknowledged, most existing methods do not seamlessly integrate these features as part of the model. We present Montebello, an integrated statistical approach which performs simultaneous isoform discovery and quantification by using a Monte Carlo simulation to find the most likely isoform composition leading to a set of observed reads. We compare Montebello to Cufflinks, a popular isoform discovery approach, on a simulated data set and on 46.3 million brain reads from an Illumina tissue panel. On this data set Montebello appears to offer a modest improvement over Cufflinks when considering discovery and parsimony metrics. In addition Montebello mitigates specific difficulties inherent in the Cufflinks approach. Finally, Montebello can be fine-tuned depending on the type of solution desired.

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

PubMed Central

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

2007-01-01

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

Reading problems and major mental disorders - co-occurrences and familial overlaps in a Swedish nationwide cohort.

PubMed

Cederlöf, Martin; Maughan, Barbara; Larsson, Henrik; D'Onofrio, Brian M; Plomin, Robert

2017-08-01

Reading problems often co-occur with ADHD and conduct disorder. However, the patterns of co-occurrence and familial overlap between reading problems and other psychiatric disorders have not been systematically explored. We conducted a register-based cohort study including 8719 individuals with reading problems and their siblings, along with matched comparison individuals. Conditional logistic regressions estimated risks for ADHD, autism, obsessive-compulsive disorder, anorexia nervosa, schizophrenia, bipolar disorder, depression, substance use disorder, and violent/non-violent criminality in individuals with reading problems and their siblings. Diagnoses of psychiatric disorders were physician-assigned and ascertained from the Swedish National Patient Register, and crime convictions from the Swedish National Crime Register. We found that individuals with reading problems had excess risks for all psychiatric disorders (except anorexia nervosa) and criminality, with risk ratios between 1.34 and 4.91. Siblings of individuals with reading problems showed excess risks for ADHD, autism, schizophrenia, bipolar disorder, depression, substance use disorder, and non-violent criminality, with risk ratios between 1.14 and 1.70. In summary, individuals with reading problems had increased risks of virtually all psychiatric disorders, and criminality. The origin of most of these overlaps was familial, in that siblings of individuals with reading problems also had elevated risks of ADHD, autism, schizophrenia, bipolar disorder, depression, substance use disorder, and non-violent criminality. These findings have implications for gene-searching efforts, and suggest that health care practitioners should be alert for signs of psychiatric disorders in families where reading problems exist. Copyright © 2017 Elsevier Ltd. All rights reserved.

A Case Study: The Implementation of a Problem-Solving Model with a Student with Reading Difficulties in Turkey

ERIC Educational Resources Information Center

Ozmen, E. Ruya; Doganay-Bilgi, Arzu

2016-01-01

The purpose of this case study was to improve the reading accuracy and reading comprehension of a 10-year-old fourth-grade female student with reading difficulties. For that purpose, the problem- solving model was implemented in four stages. These stages included problem identification, problem analysis, intervention, and evaluation. During the…

The Effect of Reading Comprehension and Problem Solving Strategies on Classifying Elementary 4th Grade Students with High and Low Problem Solving Success

ERIC Educational Resources Information Center

Ulu, Mustafa

2017-01-01

In this study, the effect of fluent reading (speed, reading accuracy percentage, prosodic reading), comprehension (literal comprehension, inferential comprehension) and problem solving strategies on classifying students with high and low problem solving success was researched. The sampling of the research is composed of 279 students at elementary…

Heuristic approach to image registration

NASA Astrophysics Data System (ADS)

Gertner, Izidor; Maslov, Igor V.

2000-08-01

Image registration, i.e. correct mapping of images obtained from different sensor readings onto common reference frame, is a critical part of multi-sensor ATR/AOR systems based on readings from different types of sensors. In order to fuse two different sensor readings of the same object, the readings have to be put into a common coordinate system. This task can be formulated as optimization problem in a space of all possible affine transformations of an image. In this paper, a combination of heuristic methods is explored to register gray- scale images. The modification of Genetic Algorithm is used as the first step in global search for optimal transformation. It covers the entire search space with (randomly or heuristically) scattered probe points and helps significantly reduce the search space to a subspace of potentially most successful transformations. Due to its discrete character, however, Genetic Algorithm in general can not converge while coming close to the optimum. Its termination point can be specified either as some predefined number of generations or as achievement of a certain acceptable convergence level. To refine the search, potential optimal subspaces are searched using more delicate and efficient for local search Taboo and Simulated Annealing methods.

Reading-Enhanced Word Problem Solving: A Theoretical Model

ERIC Educational Resources Information Center

Capraro, Robert M.; Capraro, Mary Margaret; Rupley, William H.

2012-01-01

There is a reciprocal relationship between mathematics and reading cognition. Metacognitive training within reading-enhanced problem solving should facilitate students developing an awareness of what good readers do when reading for meaning in solving mathematical problems enabling them to apply these strategies. The constructs for each cognitive…

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.

Weapons Storage Area Survey of 400 Series Buildings at Medina Annex, San Antonio, Texas

DTIC Science & Technology

2013-06-03

due to build u p of radon daughters Initial Ins trument Readin~ Results Inst. 1 lnst. lnst. Field Lab Sample Gross alpha Gross beta Gross Map...readings are due to build up of radon daughters ReadiJlg Results lust. lust. Field Lab San1ple Gross alpha Map Area Room # Location Inst. 1 Sample...outside) NOTE : High alph readings are due to build up of radon daughters Initial Instrument Reading Results Area on Room # Inst . 1 Inst. 2 Field

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).

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

Guide star catalogue data retrieval software 2

NASA Technical Reports Server (NTRS)

Smirnov, O. M.; Malkov, O. YU.

1992-01-01

The Guide Star Catalog (GSC), being the largest astronomical catalog to date, is widely used by the astronomical community for all sorts of applications, such as statistical studies of certain sky regions, searches for counterparts to observational phenomena, and generation of finder charts. It's format (2 CD-ROM's) requires minimum hardware and is ideally suited for all sorts of conditions, especially observations. Unfortunately, the actual GSC data is not easily accessible. It takes the form of FITS tables, and the coordinates of the objects are given in one coordinate system (equinox 2000). The included reading software is rudimentary at best. Thus, even generation of a simple finder chart is not a trivial undertaking. To solve this problem, at least for PC users, GUIDARES was created. GUIDARES is a user-friendly program that lets you look directly at the data in the GSC, either as a graphical sky map or as a text table. GUIDARES can read a sampling of GSC data from a given sky region, store this sampling in a text file, and display a graphical map of the sampled region in projected celestial coordinates (perfect for finder charts). GUIDARES supports rectangular and circular regions defined by coordinates in the equatorial, ecliptic (any equinox) or galactic systems.

STORMSeq: An Open-Source, User-Friendly Pipeline for Processing Personal Genomics Data in the Cloud

PubMed Central

Karczewski, Konrad J.; Fernald, Guy Haskin; Martin, Alicia R.; Snyder, Michael; Tatonetti, Nicholas P.; Dudley, Joel T.

2014-01-01

The increasing public availability of personal complete genome sequencing data has ushered in an era of democratized genomics. However, read mapping and variant calling software is constantly improving and individuals with personal genomic data may prefer to customize and update their variant calls. Here, we describe STORMSeq (Scalable Tools for Open-Source Read Mapping), a graphical interface cloud computing solution that does not require a parallel computing environment or extensive technical experience. This customizable and modular system performs read mapping, read cleaning, and variant calling and annotation. At present, STORMSeq costs approximately $2 and 5–10 hours to process a full exome sequence and $30 and 3–8 days to process a whole genome sequence. We provide this open-access and open-source resource as a user-friendly interface in Amazon EC2. PMID:24454756

Using Concept Mapping and Paraphrasing for Reading Comprehension

ERIC Educational Resources Information Center

Marashi, Hamid; Bagheri, Nazanin

2015-01-01

This study investigated the comparative impact of two types of teaching techniques, namely concept mapping and paraphrasing, on the reading comprehension of EFL learners. For this purpose, 60 learners of a total number of 90 intermediate learners studying at a language school in Karaj, Iran, were chosen through taking a piloted PET for…

Using Geospatial Analysis to Align Little Free Library Locations with Community Literacy Needs

ERIC Educational Resources Information Center

Rebori, Marlene K.; Burge, Peter

2017-01-01

We used geospatial analysis tools to develop community maps depicting fourth-grade reading proficiency test scores and locations of facilities offering public access to reading materials (i.e., public libraries, elementary schools, and Little Free Libraries). The maps visually highlighted areas with struggling readers and areas without adequate…

The Impact of Tutoring on Early Reading Achievement for Children With and Without Attention Problems

PubMed Central

Rabiner, David L.; Malone, Patrick S.

2009-01-01

This study examined whether the benefits of reading tutoring in first grade were moderated by children’s level of attention problems. Participants were 581 children from the intervention and control samples of Fast Track, a longitudinal multisite investigation of the development and prevention of conduct problems. Standardized reading achievement measures were administered after kindergarten and 1st grade, and teacher ratings of attention problems were obtained during 1st grade. During 1st grade, intervention participants received three 30-min tutoring sessions per week to promote the development of initial reading skills. Results replicated prior findings that attention problems predict reduced 1st grade reading achievement, even after controlling for IQ and earlier reading ability. Intervention was associated with modest reading achievement benefits for inattentive children without early reading difficulties, and substantial benefits for children with early reading difficulties who were not inattentive. It had no discernible impact, however, for children who were both inattentive and poor early readers. Results underscore the need to develop effective academic interventions for inattentive children, particularly for those with co-occurring reading difficulties. PMID:15228176

Specific Reading Comprehension Disability: Major Problem, Myth, or Misnomer?

PubMed Central

Spencer, Mercedes; Quinn, Jamie M.; Wagner, Richard K.

2013-01-01

The goal of the present study was to test three competing hypotheses about the nature of comprehension problems of students who are poor in reading comprehension. Participants in the study were first, second, and third graders, totaling 9 cohorts and over 425,000 participants in all. The pattern of results was consistent across all cohorts: Less than one percent of first- through third-grade students who scored as poor in reading comprehension were adequate in both decoding and vocabulary. Although poor reading comprehension certainly qualifies as a major problem rather than a myth, the term specific reading comprehension disability is a misnomer: Individuals with problems in reading comprehension that are not attributable to poor word recognition have comprehension problems that are general to language comprehension rather than specific to reading. Implications for assessment and intervention are discussed. PMID:25143666

Specific Reading Comprehension Disability: Major Problem, Myth, or Misnomer?

PubMed

Spencer, Mercedes; Quinn, Jamie M; Wagner, Richard K

2014-02-01

The goal of the present study was to test three competing hypotheses about the nature of comprehension problems of students who are poor in reading comprehension. Participants in the study were first, second, and third graders, totaling 9 cohorts and over 425,000 participants in all. The pattern of results was consistent across all cohorts: Less than one percent of first- through third-grade students who scored as poor in reading comprehension were adequate in both decoding and vocabulary. Although poor reading comprehension certainly qualifies as a major problem rather than a myth, the term specific reading comprehension disability is a misnomer: Individuals with problems in reading comprehension that are not attributable to poor word recognition have comprehension problems that are general to language comprehension rather than specific to reading. Implications for assessment and intervention are discussed.

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

PubMed Central

Rebolledo-Mendez, Jovan; Hestand, Matthew S.; Coleman, Stephen J.; Zeng, Zheng; Orlando, Ludovic; MacLeod, James N.; Kalbfleisch, Ted

2015-01-01

The reference assembly for the domestic horse, EquCab2, published in 2009, was built using approximately 30 million Sanger reads from a Thoroughbred mare named Twilight. Contiguity in the assembly was facilitated using nearly 315 thousand BAC end sequences from Twilight’s half brother Bravo. Since then, it has served as the foundation for many genome-wide analyses that include not only the modern horse, but ancient horses and other equid species as well. As data mapped to this reference has accumulated, consistent variation between mapped datasets and the reference, in terms of regions with no read coverage, single nucleotide variants, and small insertions/deletions have become apparent. In many cases, it is not clear whether these differences are the result of true sequence variation between the research subjects’ and Twilight’s genome or due to errors in the reference. EquCab2 is regarded as “The Twilight Assembly.” The objective of this study was to identify inconsistencies between the EquCab2 assembly and the source Twilight Sanger data used to build it. To that end, the original Sanger and BAC end reads have been mapped back to this equine reference and assessed with the addition of approximately 40X coverage of new Illumina Paired-End sequence data. The resulting mapped datasets identify those regions with low Sanger read coverage, as well as variation in genomic content that is not consistent with either the original Twilight Sanger data or the new genomic sequence data generated from Twilight on the Illumina platform. As the haploid EquCab2 reference assembly was created using Sanger reads derived largely from a single individual, the vast majority of variation detected in a mapped dataset comprised of those same Sanger reads should be heterozygous. In contrast, homozygous variations would represent either errors in the reference or contributions from Bravo's BAC end sequences. Our analysis identifies 720,843 homozygous discrepancies between new, high throughput genomic sequence data generated for Twilight and the EquCab2 reference assembly. Most of these represent errors in the assembly, while approximately 10,000 are demonstrated to be contributions from another horse. Other results are presented that include the binary alignment map file of the mapped Sanger reads, a list of variants identified as discrepancies between the source data and resulting reference, and a BED annotation file that lists the regions of the genome whose consensus was likely derived from low coverage alignments. PMID:26107638

The Effects of an Integrated Reading Comprehension Strategy: A Culturally Responsive Teaching Approach for Fifth-Grade Students' Reading Comprehension

ERIC Educational Resources Information Center

Bui, Yvonne N.; Fagan, Yvette M.

2013-01-01

The study evaluated the effects of the Integrated Reading Comprehension Strategy on two levels. The Integrated Reading Comprehension Strategy integrated story grammar instruction and story maps, prior knowledge and prediction method, and word webs through a culturally responsive teaching framework; the Integrated Reading Comprehension Strategy…

EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering.

PubMed

Lee, Soohyun; Seo, Chae Hwa; Alver, Burak Han; Lee, Sanghyuk; Park, Peter J

2015-09-03

RNA-seq has been widely used for genome-wide expression profiling. RNA-seq data typically consists of tens of millions of short sequenced reads from different transcripts. However, due to sequence similarity among genes and among isoforms, the source of a given read is often ambiguous. Existing approaches for estimating expression levels from RNA-seq reads tend to compromise between accuracy and computational cost. We introduce a new approach for quantifying transcript abundance from RNA-seq data. EMSAR (Estimation by Mappability-based Segmentation And Reclustering) groups reads according to the set of transcripts to which they are mapped and finds maximum likelihood estimates using a joint Poisson model for each optimal set of segments of transcripts. The method uses nearly all mapped reads, including those mapped to multiple genes. With an efficient transcriptome indexing based on modified suffix arrays, EMSAR minimizes the use of CPU time and memory while achieving accuracy comparable to the best existing methods. EMSAR is a method for quantifying transcripts from RNA-seq data with high accuracy and low computational cost. EMSAR is available at https://github.com/parklab/emsar.

Software development without languages

NASA Technical Reports Server (NTRS)

Osborne, Haywood S.

1988-01-01

Automatic programming generally involves the construction of a formal specification; i.e., one which allows unambiguous interpretation by tools for the subsequent production of the corresponding software. Previous practical efforts in this direction have focused on the serious problems of: (1) designing the optimum specification language; and (2) mapping (translating or compiling) from this specification language to the program itself. The approach proposed bypasses the above problems. It postulates that the specification proper should be an intermediate form, with the sole function of containing information sufficient to facilitate construction of programs and also of matching documentation. Thus, the means of forming the intermediary becomes a human factors task rather than a linguistic one; human users will read documents generated from the specification, rather than the specification itself.

Physical and Genetic Mechanisms Guiding the Evolution and Development of Dendritic, Flapping Insect-Wings

DTIC Science & Technology

2010-04-12

computer graphics, to music . Map L systems [2, 6, 7] extend the parallel rewriting in L systems to planar graphs with cycles, called maps [8]. The maps...carbon. For easy of reading , in the results below the mass is represented by the percentage carbon laminate coverage. As explained previously, the...previously, that value can be read in the left vertical axis. There are nine designs in the Pareto front. Depending on design goals any of these individuals

Designs of Concept Maps and Their Impacts on Readers' Performance in Memory and Reasoning while Reading

ERIC Educational Resources Information Center

Tzeng, Jeng-Yi

2010-01-01

From the perspective of the Fuzzy Trace Theory, this study investigated the impacts of concept maps with two strategic orientations (comprehensive and thematic representations) on readers' performance of cognitive operations (such as perception, verbatim memory, gist reasoning and syntheses) while the readers were reading two history articles that…

Mapping the Chapter: One Way to Tackle the CTE Textbook

ERIC Educational Resources Information Center

Laverick DeFelice, Catherine

2010-01-01

This reading specialist has come up with a strategy to help other CTE instructors map the CTE textbook, so that students can better comprehend the information in them and discover a joy of reading. CTE textbooks present a particular challenge because they are packed with information and can be quite different in structure than texts student have…

Effects of Story Mapping on Third-Grade Students with Attention Deficit Hyperactivity Disorder

ERIC Educational Resources Information Center

Chavez, Jaime N.; Martinez, James; Pienta, Rachel S.

2015-01-01

The purpose of this study was to examine the effects of story mapping on the reading comprehension scores, on-task behaviors, and attitudes of third- -grade students (N = 6) with ADHD. Students' reading grade equivalencies were assessed before and after the study. The teacher-researcher compared two other achievement measures before and during…

Linking Reading and Writing: Concept Mapping as an Organizing Tactic.

ERIC Educational Resources Information Center

Osman-Jouchoux, Rionda

Writers often must summarize others' texts as part of their own work. To succeed at this, they must first read and understand new information and then transform that information to fulfill a specific purpose. Concept mapping, used as a visual organizing technique, can be an effective link between the two processes. In a preliminary study, students…

Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA.

PubMed

Holt, Kathryn E; Teo, Yik Y; Li, Heng; Nair, Satheesh; Dougan, Gordon; Wain, John; Parkhill, Julian

2009-08-15

Here, we present a method for estimating the frequencies of SNP alleles present within pooled samples of DNA using high-throughput short-read sequencing. The method was tested on real data from six strains of the highly monomorphic pathogen Salmonella Paratyphi A, sequenced individually and in a pool. A variety of read mapping and quality-weighting procedures were tested to determine the optimal parameters, which afforded > or =80% sensitivity of SNP detection and strong correlation with true SNP frequency at poolwide read depth of 40x, declining only slightly at read depths 20-40x. The method was implemented in Perl and relies on the opensource software Maq for read mapping and SNP calling. The Perl script is freely available from ftp://ftp.sanger.ac.uk/pub/pathogens/pools/.

Problem Solving with Guided Repeated Oral Reading Instruction

ERIC Educational Resources Information Center

Conderman, Greg; Strobel, Debra

2006-01-01

Many students with disabilities require specialized instructional interventions and frequent progress monitoring in reading. The guided repeated oral reading technique promotes oral reading fluency while providing a reliable data-based monitoring system. This article emphasizes the importance of problem-solving when using this reading approach.

Preliminary Assessment of the Impact of Culture on Understanding Cartographic Representations

NASA Astrophysics Data System (ADS)

Reolon Schmidt, Marcio Augusto; de Alencar Mendonça, André Luiz; Wieczorek, Małgorzata

2018-05-01

When users read a topographic map, they have to decode the represented information. This decoding passes through various processes in order to perceive, interpret, and understand the reported information. This set of processes is intrinsically a question that is influenced by culture. In particular, when one thinks of maps distributed across the internet or representations of audiences from different origins, the chance of efficient communication is reduced or at least influenced. Therefore, there should be some degree of common visual communication, which the symbology of maps can be applied in order to assure the adequate communication of phenomenon being represented on it. In this context, the present work aims at testing which evaluation factors influence the reading of maps, the understanding of space and reasoning of the map user, in particular national topographic maps. The assessment was through internet considering official map representation from Brazil and Poland and questionnaires. The results shown that conventional topographic maps on the same scale are not capable of producing the correct interpretation of the user from another culture. This means that formal training has a direct influence on the quality of the interpretation and spatial reasoning. Those results indicate that high levels of formal training positively influence the reading and interpretation results of the map and that there is no evidence that the specialists with the symbology of their own country have significantly positive results, when compared to those used maps with systematic mapping from another country.

Relationship of nutrition and physical activity behaviors and fitness measures to academic performance for sixth graders in a midwest city school district.

PubMed

Edwards, Jane U; Mauch, Lois; Winkelman, Mark R

2011-02-01

To support curriculum and policy, a midwest city school district assessed the association of selected categories of nutrition and physical activity (NUTR/PA) behaviors, fitness measures, and body mass index (BMI) with academic performance (AP) for 800 sixth graders. Students completed an adapted Youth Risk Behavior Surveillance Survey (NUTR/PA behaviors), fitness assessments (mile run, curl-ups, push-ups, height, and weight) with results matched to standardized scores (Measures of Academic Progress [MAP]), meal price status, and gender. Differences in mean MAP scores (math and reading) were compared by selected categories of each variable utilizing 1-way analysis of variance. Associations were determined by stepwise multiple regression utilizing mean MAP scores (for math and for reading) as the dependent variable and NUTR/PA behaviors, fitness, and BMI categories as independent variables. Significance was set at α = 0.05. Higher MAP math scores were associated with NUTR (more milk and breakfast; less 100% fruit juice and sweetened beverages [SB]) and PA (increased vigorous PA and sports teams; reduced television), and fitness (higher mile run performance). Higher MAP reading scores were associated with NUTR (fewer SB) and PA (increased vigorous PA, reduced television). Regression analysis indicated about 11.1% of the variation in the mean MAP math scores and 6.7% of the mean MAP reading scores could be accounted for by selected NUTR/PA behaviors, fitness, meal price status, and gender. Many positive NUTR/PA behaviors and fitness measures were associated with higher MAP scores supporting the school district focus on healthy lifestyles. Additional factors, including meal price status and gender, contribute to AP. © 2011, Fargo Public School.

ORMAN: optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms.

PubMed

Dao, Phuong; Numanagić, Ibrahim; Lin, Yen-Yi; Hach, Faraz; Karakoc, Emre; Donmez, Nilgun; Collins, Colin; Eichler, Evan E; Sahinalp, S Cenk

2014-03-01

RNA-Seq technology is promising to uncover many novel alternative splicing events, gene fusions and other variations in RNA transcripts. For an accurate detection and quantification of transcripts, it is important to resolve the mapping ambiguity for those RNA-Seq reads that can be mapped to multiple loci: >17% of the reads from mouse RNA-Seq data and 50% of the reads from some plant RNA-Seq data have multiple mapping loci. In this study, we show how to resolve the mapping ambiguity in the presence of novel transcriptomic events such as exon skipping and novel indels towards accurate downstream analysis. We introduce ORMAN ( O ptimal R esolution of M ultimapping A mbiguity of R N A-Seq Reads), which aims to compute the minimum number of potential transcript products for each gene and to assign each multimapping read to one of these transcripts based on the estimated distribution of the region covering the read. ORMAN achieves this objective through a combinatorial optimization formulation, which is solved through well-known approximation algorithms, integer linear programs and heuristics. On a simulated RNA-Seq dataset including a random subset of transcripts from the UCSC database, the performance of several state-of-the-art methods for identifying and quantifying novel transcripts, such as Cufflinks, IsoLasso and CLIIQ, is significantly improved through the use of ORMAN. Furthermore, in an experiment using real RNA-Seq reads, we show that ORMAN is able to resolve multimapping to produce coverage values that are similar to the original distribution, even in genes with highly non-uniform coverage. ORMAN is available at http://orman.sf.net

Parietotemporal Stimulation Affects Acquisition of Novel Grapheme-Phoneme Mappings in Adult Readers

PubMed Central

Younger, Jessica W.; Booth, James R.

2018-01-01

Neuroimaging work from developmental and reading intervention research has suggested a cause of reading failure may be lack of engagement of parietotemporal cortex during initial acquisition of grapheme-phoneme (letter-sound) mappings. Parietotemporal activation increases following grapheme-phoneme learning and successful reading intervention. Further, stimulation of parietotemporal cortex improves reading skill in lower ability adults. However, it is unclear whether these improvements following stimulation are due to enhanced grapheme-phoneme mapping abilities. To test this hypothesis, we used transcranial direct current stimulation (tDCS) to manipulate parietotemporal function in adult readers as they learned a novel artificial orthography with new grapheme-phoneme mappings. Participants received real or sham stimulation to the left inferior parietal lobe (L IPL) for 20 min before training. They received explicit training over the course of 3 days on 10 novel words each day. Learning of the artificial orthography was assessed at a pre-training baseline session, the end of each of the three training sessions, an immediate post-training session and a delayed post-training session about 4 weeks after training. Stimulation interacted with baseline reading skill to affect learning of trained words and transfer to untrained words. Lower skill readers showed better acquisition, whereas higher skill readers showed worse acquisition, when training was paired with real stimulation, as compared to readers who received sham stimulation. However, readers of all skill levels showed better maintenance of trained material following parietotemporal stimulation, indicating a differential effect of stimulation on initial learning and consolidation. Overall, these results indicate that parietotemporal stimulation can enhance learning of new grapheme-phoneme relationships in readers with lower reading skill. Yet, while parietotemporal function is critical to new learning, its role in continued reading improvement likely changes as readers progress in skill. PMID:29628882

Measuring Reading Performance.

ERIC Educational Resources Information Center

Blanton, William E., Ed.; And Others

Designed to provide solutions to some of the problems related to measuring reading behavior, this publication explores some of the problems of test selection and usage which confront educators. Contents include "Reading Testing for Reading Evaluation" by Walter R. Hill, "Reading Tests and the Disadvantaged" by Thomas J. Fitzgibbon, "What Is…

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.

Optimizing the Usability of Brain-Computer Interfaces.

PubMed

Zhang, Yin; Chase, Steve M

2018-05-01

Brain-computer interfaces are in the process of moving from the laboratory to the clinic. These devices act by reading neural activity and using it to directly control a device, such as a cursor on a computer screen. An open question in the field is how to map neural activity to device movement in order to achieve the most proficient control. This question is complicated by the fact that learning, especially the long-term skill learning that accompanies weeks of practice, can allow subjects to improve performance over time. Typical approaches to this problem attempt to maximize the biomimetic properties of the device in order to limit the need for extensive training. However, it is unclear if this approach would ultimately be superior to performance that might be achieved with a nonbiomimetic device once the subject has engaged in extended practice and learned how to use it. Here we approach this problem using ideas from optimal control theory. Under the assumption that the brain acts as an optimal controller, we present a formal definition of the usability of a device and show that the optimal postlearning mapping can be written as the solution of a constrained optimization problem. We then derive the optimal mappings for particular cases common to most brain-computer interfaces. Our results suggest that the common approach of creating biomimetic interfaces may not be optimal when learning is taken into account. More broadly, our method provides a blueprint for optimal device design in general control-theoretic contexts.

Modeling the Effects of Reading Lessons on Text Processing.

ERIC Educational Resources Information Center

Omanson, Richard C.; And Others

A study evaluated the effectiveness of various models constructed to account for how children read and comprehended a story presented in a directed reading lesson. A commercial directed reading lesson was revised to introduce information related to the story and to help the children form a "map" of the central story content. Data were…

How Fifth-Grade Students Use Story Mapping to Aid Their Reading Comprehension

ERIC Educational Resources Information Center

Weih, Timothy G.

2000-01-01

This thesis examined the reading comprehension process of three fifth-grade students who demonstrated the ability to read and write fluently but had difficulties remembering and understanding important information about what they read. The aim of this research was to develop and implement an effective teaching strategy for low-achieving students…

Reading on Paper and Screen among Senior Adults: Cognitive Map and Technophobia

PubMed Central

Hou, Jinghui; Wu, Yijie; Harrell, Erin

2017-01-01

While the senior population has been increasingly engaged with reading on mobile technologies, research that specifically documents the impact of technologies on reading for this age group has still been lacking. The present study investigated how different reading media (screen versus paper) might result in different reading outcomes among older adults due to both cognitive and psychological factors. Using a laboratory experiment with 81participants aged 57 to 85, our results supported past research and showed the influence of cognitive map formation on readers’ feelings of fatigue. We contributed empirical evidence to the contention that reading on a screen could match that of reading from paper if the presentation of the text on screen resemble that of the print. Our findings also suggested that individual levels of technophobia was an important barrier to older adults’ effective use of mobile technologies for reading. In the post hoc analyses, we further showed that technophobia was correlated with technology experience, certain personality traits, and age. The present study highlights the importance of providing tailored support that helps older adults overcome psychological obstacles in using technologies. PMID:29312073

S-MART, a software toolbox to aid RNA-Seq data analysis.

PubMed

Zytnicki, Matthias; Quesneville, Hadi

2011-01-01

High-throughput sequencing is now routinely performed in many experiments. But the analysis of the millions of sequences generated, is often beyond the expertise of the wet labs who have no personnel specializing in bioinformatics. Whereas several tools are now available to map high-throughput sequencing data on a genome, few of these can extract biological knowledge from the mapped reads. We have developed a toolbox called S-MART, which handles mapped RNA-Seq data. S-MART is an intuitive and lightweight tool which performs many of the tasks usually required for the analysis of mapped RNA-Seq reads. S-MART does not require any computer science background and thus can be used by all of the biologist community through a graphical interface. S-MART can run on any personal computer, yielding results within an hour even for Gb of data for most queries. S-MART may perform the entire analysis of the mapped reads, without any need for other ad hoc scripts. With this tool, biologists can easily perform most of the analyses on their computer for their RNA-Seq data, from the mapped data to the discovery of important loci.

S-MART, A Software Toolbox to Aid RNA-seq Data Analysis

PubMed Central

Zytnicki, Matthias; Quesneville, Hadi

2011-01-01

High-throughput sequencing is now routinely performed in many experiments. But the analysis of the millions of sequences generated, is often beyond the expertise of the wet labs who have no personnel specializing in bioinformatics. Whereas several tools are now available to map high-throughput sequencing data on a genome, few of these can extract biological knowledge from the mapped reads. We have developed a toolbox called S-MART, which handles mapped RNA-Seq data. S-MART is an intuitive and lightweight tool which performs many of the tasks usually required for the analysis of mapped RNA-Seq reads. S-MART does not require any computer science background and thus can be used by all of the biologist community through a graphical interface. S-MART can run on any personal computer, yielding results within an hour even for Gb of data for most queries. S-MART may perform the entire analysis of the mapped reads, without any need for other ad hoc scripts. With this tool, biologists can easily perform most of the analyses on their computer for their RNA-Seq data, from the mapped data to the discovery of important loci. PMID:21998740

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…

Indel-tolerant read mapping with trinucleotide frequencies using cache-oblivious kd-trees.

PubMed

Mahmud, Md Pavel; Wiedenhoeft, John; Schliep, Alexander

2012-09-15

Mapping billions of reads from next generation sequencing experiments to reference genomes is a crucial task, which can require hundreds of hours of running time on a single CPU even for the fastest known implementations. Traditional approaches have difficulties dealing with matches of large edit distance, particularly in the presence of frequent or large insertions and deletions (indels). This is a serious obstacle both in determining the spectrum and abundance of genetic variations and in personal genomics. For the first time, we adopt the approximate string matching paradigm of geometric embedding to read mapping, thus rephrasing it to nearest neighbor queries in a q-gram frequency vector space. Using the L(1) distance between frequency vectors has the benefit of providing lower bounds for an edit distance with affine gap costs. Using a cache-oblivious kd-tree, we realize running times, which match the state-of-the-art. Additionally, running time and memory requirements are about constant for read lengths between 100 and 1000 bp. We provide a first proof-of-concept that geometric embedding is a promising paradigm for read mapping and that L(1) distance might serve to detect structural variations. TreQ, our initial implementation of that concept, performs more accurate than many popular read mappers over a wide range of structural variants. TreQ will be released under the GNU Public License (GPL), and precomputed genome indices will be provided for download at http://treq.sf.net. pavelm@cs.rutgers.edu Supplementary data are available at Bioinformatics online.

Indel-tolerant read mapping with trinucleotide frequencies using cache-oblivious kd-trees

PubMed Central

Mahmud, Md Pavel; Wiedenhoeft, John; Schliep, Alexander

2012-01-01

Motivation: Mapping billions of reads from next generation sequencing experiments to reference genomes is a crucial task, which can require hundreds of hours of running time on a single CPU even for the fastest known implementations. Traditional approaches have difficulties dealing with matches of large edit distance, particularly in the presence of frequent or large insertions and deletions (indels). This is a serious obstacle both in determining the spectrum and abundance of genetic variations and in personal genomics. Results: For the first time, we adopt the approximate string matching paradigm of geometric embedding to read mapping, thus rephrasing it to nearest neighbor queries in a q-gram frequency vector space. Using the L1 distance between frequency vectors has the benefit of providing lower bounds for an edit distance with affine gap costs. Using a cache-oblivious kd-tree, we realize running times, which match the state-of-the-art. Additionally, running time and memory requirements are about constant for read lengths between 100 and 1000 bp. We provide a first proof-of-concept that geometric embedding is a promising paradigm for read mapping and that L1 distance might serve to detect structural variations. TreQ, our initial implementation of that concept, performs more accurate than many popular read mappers over a wide range of structural variants. Availability and implementation: TreQ will be released under the GNU Public License (GPL), and precomputed genome indices will be provided for download at http://treq.sf.net. Contact: pavelm@cs.rutgers.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22962448

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.

G-CNV: A GPU-Based Tool for Preparing Data to Detect CNVs with Read-Depth Methods.

PubMed

Manconi, Andrea; Manca, Emanuele; Moscatelli, Marco; Gnocchi, Matteo; Orro, Alessandro; Armano, Giuliano; Milanesi, Luciano

2015-01-01

Copy number variations (CNVs) are the most prevalent types of structural variations (SVs) in the human genome and are involved in a wide range of common human diseases. Different computational methods have been devised to detect this type of SVs and to study how they are implicated in human diseases. Recently, computational methods based on high-throughput sequencing (HTS) are increasingly used. The majority of these methods focus on mapping short-read sequences generated from a donor against a reference genome to detect signatures distinctive of CNVs. In particular, read-depth based methods detect CNVs by analyzing genomic regions with significantly different read-depth from the other ones. The pipeline analysis of these methods consists of four main stages: (i) data preparation, (ii) data normalization, (iii) CNV regions identification, and (iv) copy number estimation. However, available tools do not support most of the operations required at the first two stages of this pipeline. Typically, they start the analysis by building the read-depth signal from pre-processed alignments. Therefore, third-party tools must be used to perform most of the preliminary operations required to build the read-depth signal. These data-intensive operations can be efficiently parallelized on graphics processing units (GPUs). In this article, we present G-CNV, a GPU-based tool devised to perform the common operations required at the first two stages of the analysis pipeline. G-CNV is able to filter low-quality read sequences, to mask low-quality nucleotides, to remove adapter sequences, to remove duplicated read sequences, to map the short-reads, to resolve multiple mapping ambiguities, to build the read-depth signal, and to normalize it. G-CNV can be efficiently used as a third-party tool able to prepare data for the subsequent read-depth signal generation and analysis. Moreover, it can also be integrated in CNV detection tools to generate read-depth signals.

Shared-Reading versus Oral Storytelling: Associations with Preschoolers' Prosocial Skills and Problem Behaviours

ERIC Educational Resources Information Center

Curenton, Stephanie M.; Craig, Michelle Jones

2011-01-01

Dyadic shared-reading and oral storytelling practices and their association to American preschoolers' (N = 33) prosocial and problem behaviour was examined. The frequency (how often dyads read) and history (the child's age at first reading) were examined within shared-reading; emotion state talk and evaluative judgments were examined in both…

Experimental Adiabatic Quantum Factorization under Ambient Conditions Based on a Solid-State Single Spin System.

PubMed

Xu, Kebiao; Xie, Tianyu; Li, Zhaokai; Xu, Xiangkun; Wang, Mengqi; Ye, Xiangyu; Kong, Fei; Geng, Jianpei; Duan, Changkui; Shi, Fazhan; Du, Jiangfeng

2017-03-31

The adiabatic quantum computation is a universal and robust method of quantum computing. In this architecture, the problem can be solved by adiabatically evolving the quantum processor from the ground state of a simple initial Hamiltonian to that of a final one, which encodes the solution of the problem. Adiabatic quantum computation has been proved to be a compatible candidate for scalable quantum computation. In this Letter, we report on the experimental realization of an adiabatic quantum algorithm on a single solid spin system under ambient conditions. All elements of adiabatic quantum computation, including initial state preparation, adiabatic evolution (simulated by optimal control), and final state read-out, are realized experimentally. As an example, we found the ground state of the problem Hamiltonian S_{z}I_{z} on our adiabatic quantum processor, which can be mapped to the factorization of 35 into its prime factors 5 and 7.

Experimental Adiabatic Quantum Factorization under Ambient Conditions Based on a Solid-State Single Spin System

NASA Astrophysics Data System (ADS)

Xu, Kebiao; Xie, Tianyu; Li, Zhaokai; Xu, Xiangkun; Wang, Mengqi; Ye, Xiangyu; Kong, Fei; Geng, Jianpei; Duan, Changkui; Shi, Fazhan; Du, Jiangfeng

2017-03-01

The adiabatic quantum computation is a universal and robust method of quantum computing. In this architecture, the problem can be solved by adiabatically evolving the quantum processor from the ground state of a simple initial Hamiltonian to that of a final one, which encodes the solution of the problem. Adiabatic quantum computation has been proved to be a compatible candidate for scalable quantum computation. In this Letter, we report on the experimental realization of an adiabatic quantum algorithm on a single solid spin system under ambient conditions. All elements of adiabatic quantum computation, including initial state preparation, adiabatic evolution (simulated by optimal control), and final state read-out, are realized experimentally. As an example, we found the ground state of the problem Hamiltonian SzIz on our adiabatic quantum processor, which can be mapped to the factorization of 35 into its prime factors 5 and 7.

Learning to Read Against All Odds: Using Precision Reading to Enhance Literacy in Students with Cognitive Impairments, Extreme Academic Deficits, and Severe Social, Emotional, and Psychiatric Problems

ERIC Educational Resources Information Center

Freeze, Rick; Cook, Paula

2005-01-01

The purpose of this study was to assess the efficacy and practicality of precision reading, a constructive reading intervention, with students with cognitive impairments, extreme academic deficits in reading, and severe social, emotional, and psychiatric problems. As precision reading had shown promise with students with low achievement, learning…

How Do Concept-Maps Function for Reading Comprehension Improvement of Iranian Advanced EFL Learners of Both Genders?

ERIC Educational Resources Information Center

Khaghaninejad, Mohammad Saber; Arefinejad, Mansour

2015-01-01

This study was an attempt to examine the effect of concept mapping on reading comprehension of Iranian EFL learners. Pretest-posttest design was employed to scrutinize the possible improvement of the study's participants who were male and female learners whose ages ranged from 19 to 40 and had taken general English courses at Islamic Azad…

Investigation of the Effectiveness of the Story-Map Method on Reading Comprehension Skills among Students with Mental Retardation

ERIC Educational Resources Information Center

Isikdogan, Necla; Kargin, Tevhide

2010-01-01

The purpose of this study was to investigate the effectiveness of the story-map technique on reading comprehension skills among students with mild mental retardation. The research group consisted of 14 students with mild mental retardation. The students in the research group were chosen from students who attended to an elementary school and a…

The Dilemmas of Teaching Reading. Eighth Yearbook of The American Reading Forum, 1988.

ERIC Educational Resources Information Center

Lumpkin, Donavon, Ed.; And Others

Articles in this eighth yearbook of the American Reading Forum address the dilemmas of teaching reading. Articles, listed with their authors, are as follows: (1) "Deepening a Dilemma: Stylus vs. Computer Writing at an Early Primary Level" (J. Heep); (2) "Concept Maps and Vee Diagrams: Strategies To Deal with the Dilemma of the Restricted…

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

PubMed Central

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

2011-01-01

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

Case study of rotating sonar sensor application in unmanned automated guided vehicle

NASA Astrophysics Data System (ADS)

Chandak, Pravin; Cao, Ming; Hall, Ernest L.

2001-10-01

A single rotating sonar element is used with a restricted angle of sweep to obtain readings to develop a range map for the unobstructed path of an autonomous guided vehicle (AGV). A Polaroid ultrasound transducer element is mounted on a micromotor with an encoder feedback. The motion of this motor is controlled using a Galil DMC 1000 motion control board. The encoder is interfaced with the DMC 1000 board using an intermediate IMC 1100 break-out board. By adjusting the parameters of the Polaroid element, it is possible to obtain range readings at known angles with respect to the center of the robot. The readings are mapped to obtain a range map of the unobstructed path in front of the robot. The idea can be extended to a 360 degree mapping by changing the assembly level programming on the Galil Motion control board. Such a system would be compact and reliable over a range of environments and AGV applications.

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.

Developmental reading disorder

MedlinePlus

... important. Many students with learning disabilities have poor self-esteem. Psychological counseling may be helpful. ... Problems in school, including behavior problems Loss of self-esteem Reading problems that continue Problems with job performance

How To Tutor Students with Reading Comprehension Problems.

ERIC Educational Resources Information Center

Parker, Richard; Hasbrouck, Jan E.; Denton, Carolyn

2002-01-01

Suggestions for tutoring students with reading comprehension problems include careful selection of books with readable text segments, use of comprehension strategies such as paraphrasing brief sections, and reading to find specific information. Several reading comprehension strategies for students are summarized. (Contains 7 references.) (DB)

ILP-based maximum likelihood genome scaffolding

PubMed Central

2014-01-01

Background Interest in de novo genome assembly has been renewed in the past decade due to rapid advances in high-throughput sequencing (HTS) technologies which generate relatively short reads resulting in highly fragmented assemblies consisting of contigs. Additional long-range linkage information is typically used to orient, order, and link contigs into larger structures referred to as scaffolds. Due to library preparation artifacts and erroneous mapping of reads originating from repeats, scaffolding remains a challenging problem. In this paper, we provide a scalable scaffolding algorithm (SILP2) employing a maximum likelihood model capturing read mapping uncertainty and/or non-uniformity of contig coverage which is solved using integer linear programming. A Non-Serial Dynamic Programming (NSDP) paradigm is applied to render our algorithm useful in the processing of larger mammalian genomes. To compare scaffolding tools, we employ novel quantitative metrics in addition to the extant metrics in the field. We have also expanded the set of experiments to include scaffolding of low-complexity metagenomic samples. Results SILP2 achieves better scalability throughg a more efficient NSDP algorithm than previous release of SILP. The results show that SILP2 compares favorably to previous methods OPERA and MIP in both scalability and accuracy for scaffolding single genomes of up to human size, and significantly outperforms them on scaffolding low-complexity metagenomic samples. Conclusions Equipped with NSDP, SILP2 is able to scaffold large mammalian genomes, resulting in the longest and most accurate scaffolds. The ILP formulation for the maximum likelihood model is shown to be flexible enough to handle metagenomic samples. PMID:25253180

Mapping and phasing of structural variation in patient genomes using nanopore sequencing.

PubMed

Cretu Stancu, Mircea; van Roosmalen, Markus J; Renkens, Ivo; Nieboer, Marleen M; Middelkamp, Sjors; de Ligt, Joep; Pregno, Giulia; Giachino, Daniela; Mandrile, Giorgia; Espejo Valle-Inclan, Jose; Korzelius, Jerome; de Bruijn, Ewart; Cuppen, Edwin; Talkowski, Michael E; Marschall, Tobias; de Ridder, Jeroen; Kloosterman, Wigard P

2017-11-06

Despite improvements in genomics technology, the detection of structural variants (SVs) from short-read sequencing still poses challenges, particularly for complex variation. Here we analyse the genomes of two patients with congenital abnormalities using the MinION nanopore sequencer and a novel computational pipeline-NanoSV. We demonstrate that nanopore long reads are superior to short reads with regard to detection of de novo chromothripsis rearrangements. The long reads also enable efficient phasing of genetic variations, which we leveraged to determine the parental origin of all de novo chromothripsis breakpoints and to resolve the structure of these complex rearrangements. Additionally, genome-wide surveillance of inherited SVs reveals novel variants, missed in short-read data sets, a large proportion of which are retrotransposon insertions. We provide a first exploration of patient genome sequencing with a nanopore sequencer and demonstrate the value of long-read sequencing in mapping and phasing of SVs for both clinical and research applications.

The Association between Mathematical Word Problems and Reading Comprehension

ERIC Educational Resources Information Center

Vilenius-Tuohimaa, Piia Maria; Aunola, Kaisa; Nurmi, Jari-Erik

2008-01-01

This study aimed to investigate the interplay between mathematical word problem skills and reading comprehension. The participants were 225 children aged 9-10 (Grade 4). The children's text comprehension and mathematical word problem-solving performance was tested. Technical reading skills were investigated in order to categorise participants as…

Topographic Maps and Coal Mining.

ERIC Educational Resources Information Center

Raitz, Karl B.

1984-01-01

Geography teachers can illustrate the patterns associated with mineral fuel production, especially coal, by using United States Geological Survey topographic maps, which are illustrated by symbols that indicate mine-related features, such as shafts and tailings. Map reading exercises are presented; an interpretative map key that can facilitate…

Adventures with Maps.

ERIC Educational Resources Information Center

Hofferber, Michael

1989-01-01

Orienteering--the game of following a map to find predetermined locations--can spark interest and develop skills in map making and map reading. This article gives background on orienteering; describes indoor and outdoor orienteering activities; offers suggestions for incorporating orienteering into science, math, and language arts; and provides a…

A Practical Framework for Cartographic Design

NASA Astrophysics Data System (ADS)

Denil, Mark

2018-05-01

Creation of a map artifact that can be recognized, accepted, read, and absorbed is the cartographer's chief responsibility. This involves bringing coherence and order out of chaos and randomness through the construction of map artifacts that mediate processes of social communication. Maps are artifacts, first and foremost: they are artifacts with particular formal attributes. It is the formal aspects of the map artifact that allows it to invoke and sustain a reading as a map. This paper examines Cartographic Design as the sole means at the cartographer's disposal for constructing the meaning bearing artifacts we know as maps, by placing it in a center of a practical analytic framework. The framework draws together the Theoretic and Craft aspects of map making, and examines how Style and Taste operate through the rubric of a schema of Mapicity to produce high quality maps. The role of the Cartographic Canon, and the role of Critique, are also explored, and a few design resources are identified.

Preventative Reading Interventions Teaching Direct Mapping of Graphemes in Texts and Set-for-Variability Aid At-Risk Learners

ERIC Educational Resources Information Center

Savage, Robert; Georgiou, George; Parrila, Rauno; Maiorino, Kristina

2018-01-01

We evaluated two experimenter-delivered, small-group word reading programs among at-risk poor readers in Grade 1 classes of regular elementary schools using a two-arm, dual-site-matched control trial intervention. At-risk poor word readers (n = 201) were allocated to either (a) Direct Mapping and Set-for-Variability (DMSfV) or (b) Current or…

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…

Second Language Reading Research: Problems and Possibilities.

ERIC Educational Resources Information Center

Koda, Keiko

1994-01-01

First-language (L1) reading theories are examined from second- language (L2) perspectives to identify significant research voids related to L2 problems. Unique aspects of L2 reading are considered and three distinct areas are discussed: consequences of prior reading experience, effects of cross-linguistic processing, and compensatory devices for…

The Reading Skills of Home Economics: Problems and Selected References.

ERIC Educational Resources Information Center

Cranney, A. Garr; And Others

Since most secondary school reading textbooks give home economics only minimal attention, this paper identifies selected information sources in home economics reading skills and in home economics for high school reading specialists. The first portion of the paper discusses eight principle problems that home economics poses for secondary school…

Text Mapping Plus: Improving Comprehension through Supported Retellings

ERIC Educational Resources Information Center

Lapp, Diane; Fisher, Douglas; Johnson, Kelly

2010-01-01

Modeled in this column is the teaching of a text mapping routine that supports students reading and remembering the salient features of the text. The authors renamed the story mapping technique "text mapping plus" because they found that as students added relational words and graphics to their maps their retells of both fiction and nonnarrative…

Executive Functions Contribute Uniquely to Reading Competence in Minority Youth.

PubMed

Jacobson, Lisa A; Koriakin, Taylor; Lipkin, Paul; Boada, Richard; Frijters, Jan C; Lovett, Maureen W; Hill, Dina; Willcutt, Erik; Gottwald, Stephanie; Wolf, Maryanne; Bosson-Heenan, Joan; Gruen, Jeffrey R; Mahone, E Mark

Competent reading requires various skills beyond those for basic word reading (i.e., core language skills, rapid naming, phonological processing). Contributing "higher-level" or domain-general processes include information processing speed and executive functions (working memory, strategic problem solving, attentional switching). Research in this area has relied on largely Caucasian samples, with limited representation of children from racial or ethnic minority groups. This study examined contributions of executive skills to reading competence in 761 children of minority backgrounds. Hierarchical linear regressions examined unique contributions of executive functions (EF) to word reading, fluency, and comprehension. EF contributed uniquely to reading performance, over and above reading-related language skills; working memory contributed uniquely to all components of reading; while attentional switching, but not problem solving, contributed to isolated and contextual word reading and reading fluency. Problem solving uniquely predicted comprehension, suggesting that this skill may be especially important for reading comprehension in minority youth. Attentional switching may play a unique role in development of reading fluency in minority youth, perhaps as a result of the increased demand for switching between spoken versus written dialects. Findings have implications for educational and clinical practice with regard to reading instruction, remedial reading intervention, and assessment of individuals with reading difficulty.

The Impact of Tutoring on Early Reading Achievement for Children with and without Attention Problems

ERIC Educational Resources Information Center

Rabiner, David L.; Malone, Patrick S.

2004-01-01

This study examined whether the benefits of reading tutoring in first grade were moderated by children's level of attention problems. Participants were 581 children from the intervention and control samples of Fast Track, a longitudinal multisite investigation of the development and prevention of conduct problems. Standardized reading achievement…

A Modified Direct-Reading Azimuth Protractor

ERIC Educational Resources Information Center

Larson, William C.; Pugliese, Joseph M.

1977-01-01

Describes the construction of a direct-reading azimuth protractor (DRAP) used for mapping fracture and joint-surface orientations in underground mines where magnetic disturbances affect typical geologic pocket transit. (SL)

Map Reading beyond Information Given: The Expert Orienteers' Internal Knowledge about Terrain.

ERIC Educational Resources Information Center

Murakoshi, Shin

1990-01-01

Compares novice and expert orienteers' map interpretation skills. Subjects asked to judge terrain from maps, including conditions inferable without corresponding map symbols. Experts' interpretation of identical symbols implies use of experiential knowledge. Internal knowledge characteristics discussed in terms of episodic-semantic memory…

The Problem of Reading and Reading Culture Improvement of Students-Bachelors of Elementary Education in Modern High Institution

ERIC Educational Resources Information Center

Kamalova, Lera A.; Koletvinova, Natal'ya D.

2016-01-01

This article is aimed to study the problems of reading and improve reading culture of students-bachelors of elementary education in modern high institutions and development of the most effective methods and techniques for improving of reading culture of students in the study of Humanities disciplines. The leading method to the study of this…

Assessing the prevalence of mycoplasma contamination in cell culture via a survey of NCBI's RNA-seq archive

PubMed Central

Olarerin-George, Anthony O.; Hogenesch, John B.

2015-01-01

Mycoplasmas are notorious contaminants of cell culture and can have profound effects on host cell biology by depriving cells of nutrients and inducing global changes in gene expression. Over the last two decades, sentinel testing has revealed wide-ranging contamination rates in mammalian culture. To obtain an unbiased assessment from hundreds of labs, we analyzed sequence data from 9395 rodent and primate samples from 884 series in the NCBI Sequence Read Archive. We found 11% of these series were contaminated (defined as ≥100 reads/million mapping to mycoplasma in one or more samples). Ninety percent of mycoplasma-mapped reads aligned to ribosomal RNA. This was unexpected given 37% of contaminated series used poly(A)-selection for mRNA enrichment. Lastly, we examined the relationship between mycoplasma contamination and host gene expression in a single cell RNA-seq dataset and found 61 host genes (P < 0.001) were significantly associated with mycoplasma-mapped read counts. In all, this study suggests mycoplasma contamination is still prevalent today and poses substantial risk to research quality. PMID:25712092

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...

HDF4 Maps: For Now and For the Future

NASA Astrophysics Data System (ADS)

Plutchak, J.; Aydt, R.; Folk, M. J.

2013-12-01

Data formats and access tools necessarily change as technology improves to address emerging requirements with new capabilities. This on-going process inevitably leaves behind significant data collections in legacy formats that are difficult to support and sustain. NASA ESDIS and The HDF Group currently face this problem with large and growing archives of data in HDF4, an older version of the HDF format. Indefinitely guaranteeing the ability to read these data with multi-platform libraries in many languages is very difficult. As an alternative, HDF and NASA worked together to create maps of the files that contain metadata and information about data types, locations, and sizes of data objects in the files. These maps are written in XML and have successfully been used to access and understand data in HDF4 files without the HDF libraries. While originally developed to support sustainable access to these data, these maps can also be used to provide access to HDF4 metadata, facilitate user understanding of files prior to download, and validate the files for compliance with particular conventions. These capabilities are now available as a service for HDF4 archives and users.

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

How Does My Child's Vision Affect His Reading?

ERIC Educational Resources Information Center

Eberly, Donald W.

Various eye problems and the effects they can have on children's reading abilities are explored in this pamphlet, which is one of a series designed to answer parents' questions about their children's reading development. Topics discussed are the demands on vision made by reading, problems that affect visual acuity (nearsightedness, farsightedness,…

Black Dialect, Reading Interference and Classroom Interaction.

ERIC Educational Resources Information Center

Simons, Herbert D.

A major problem that continues to plague United States education is the fact that large numbers of disadvantaged black students are not learning to read well enough to function in society. This paper discusses three reasons for the problem of teaching reading to these students. First, there exist no comprehensive developmental reading theories, no…

Towards on-chip time-resolved thermal mapping with micro-/nanosensor arrays

PubMed Central

2012-01-01

In recent years, thin-film thermocouple (TFTC) array emerged as a versatile candidate in micro-/nanoscale local temperature sensing for its high resolution, passive working mode, and easy fabrication. However, some key issues need to be taken into consideration before real instrumentation and industrial applications of TFTC array. In this work, we will demonstrate that TFTC array can be highly scalable from micrometers to nanometers and that there are potential applications of TFTC array in integrated circuits, including time-resolvable two-dimensional thermal mapping and tracing the heat source of a device. Some potential problems and relevant solutions from a view of industrial applications will be discussed in terms of material selection, multiplexer reading, pattern designing, and cold-junction compensation. We show that the TFTC array is a powerful tool for research fields such as chip thermal management, lab-on-a-chip, and other novel electrical, optical, or thermal devices. PMID:22931306

Wyoming Geology and Geography, Unit I.

ERIC Educational Resources Information Center

Robinson, Terry

This unit on the geology and geography of Wyoming for elementary school students provides activities for map and globe skills. Goals include reading and interpreting maps and globes, interpreting map symbols, comparing maps and drawing inferences, and understanding time and chronology. Outlines and charts are provided for Wyoming geology and…

Common Types of Reading Problems and How to Help Children Who Have Them

ERIC Educational Resources Information Center

Spear-Swerling, Louise

2016-01-01

Patterns of reading difficulty provide an educationally useful way to think about different kinds of reading problems, whether those problems are mainly experiential in nature (e.g., those common among English learners) or associated with disabilities (e.g., those typical of children with dyslexia). This article reviews research on three common…

Visualizing First and Second Language Interactions in Science Reading: A Knowledge Structure Network Approach

ERIC Educational Resources Information Center

Kim, Kyung

2017-01-01

The present study considers the potential influence of first language (L1) in reading second language (L2) science text. University mixed proficiency Korean English language learners (n = 136) were asked to complete pre- and post-reading "sorting maps" in L1 or L2 (e.g., sort Korean, read text, sort English). All of the participants'…

Mapping the Heart

ERIC Educational Resources Information Center

Hulse, Grace

2012-01-01

In this article, the author describes how her fourth graders made ceramic heart maps. The impetus for this project came from reading "My Map Book" by Sara Fanelli. This book is a collection of quirky, hand-drawn and collaged maps that diagram a child's world. There are maps of her stomach, her day, her family, and her heart, among others. The…

The World in Spatial Terms: Mapmaking and Map Reading

ERIC Educational Resources Information Center

Ekiss, Gale Olp; Trapido-Lurie, Barbara; Phillips, Judy; Hinde, Elizabeth

2007-01-01

Maps and mapping activities are essential in the primary grades. Maps are truly ubiquitous today, as evidenced by the popularity of websites such as Google Earth and Mapquest, and by devices such as Global Positioning System (GPS) units in cars, planes, and boats. Maps can give visual settings to travel stories and historical narratives and can…

CMOS Active Pixel Sensors as energy-range detectors for proton Computed Tomography.

PubMed

Esposito, M; Anaxagoras, T; Evans, P M; Green, S; Manolopoulos, S; Nieto-Camero, J; Parker, D J; Poludniowski, G; Price, T; Waltham, C; Allinson, N M

2015-06-03

Since the first proof of concept in the early 70s, a number of technologies has been proposed to perform proton CT (pCT), as a means of mapping tissue stopping power for accurate treatment planning in proton therapy. Previous prototypes of energy-range detectors for pCT have been mainly based on the use of scintillator-based calorimeters, to measure proton residual energy after passing through the patient. However, such an approach is limited by the need for only a single proton passing through the energy-range detector in a read-out cycle. A novel approach to this problem could be the use of pixelated detectors, where the independent read-out of each pixel allows to measure simultaneously the residual energy of a number of protons in the same read-out cycle, facilitating a faster and more efficient pCT scan. This paper investigates the suitability of CMOS Active Pixel Sensors (APSs) to track individual protons as they go through a number of CMOS layers, forming an energy-range telescope. Measurements performed at the iThemba Laboratories will be presented and analysed in terms of correlation, to confirm capability of proton tracking for CMOS APSs.

Word Problem Solving in Contemporary Math Education: A Plea for Reading Comprehension Skills Training

PubMed Central

Boonen, Anton J. H.; de Koning, Björn B.; Jolles, Jelle; van der Schoot, Menno

2016-01-01

Successfully solving mathematical word problems requires both mental representation skills and reading comprehension skills. In Realistic Math Education (RME), however, students primarily learn to apply the first of these skills (i.e., representational skills) in the context of word problem solving. Given this, it seems legitimate to assume that students from a RME curriculum experience difficulties when asked to solve semantically complex word problems. We investigated this assumption under 80 sixth grade students who were classified as successful and less successful word problem solvers based on a standardized mathematics test. To this end, students completed word problems that ask for both mental representation skills and reading comprehension skills. The results showed that even successful word problem solvers had a low performance on semantically complex word problems, despite adequate performance on semantically less complex word problems. Based on this study, we concluded that reading comprehension skills should be given a (more) prominent role during word problem solving instruction in RME. PMID:26925012

Word Problem Solving in Contemporary Math Education: A Plea for Reading Comprehension Skills Training.

PubMed

Boonen, Anton J H; de Koning, Björn B; Jolles, Jelle; van der Schoot, Menno

2016-01-01

Successfully solving mathematical word problems requires both mental representation skills and reading comprehension skills. In Realistic Math Education (RME), however, students primarily learn to apply the first of these skills (i.e., representational skills) in the context of word problem solving. Given this, it seems legitimate to assume that students from a RME curriculum experience difficulties when asked to solve semantically complex word problems. We investigated this assumption under 80 sixth grade students who were classified as successful and less successful word problem solvers based on a standardized mathematics test. To this end, students completed word problems that ask for both mental representation skills and reading comprehension skills. The results showed that even successful word problem solvers had a low performance on semantically complex word problems, despite adequate performance on semantically less complex word problems. Based on this study, we concluded that reading comprehension skills should be given a (more) prominent role during word problem solving instruction in RME.

Executive Functions Contribute Uniquely to Reading Competence in Minority Youth

PubMed Central

Jacobson, Lisa A.; Koriakin, Taylor; Lipkin, Paul; Boada, Richard; Frijters, Jan; Lovett, Maureen; Hill, Dina; Willcutt, Erik; Gottwald, Stephanie; Wolf, Maryanne; Bosson-Heenan, Joan; Gruen, Jeffrey R.; Mahone, E. Mark

2018-01-01

Competent reading requires various skills beyond those for basic word reading (i.e., core language skills, rapid naming, phonological processing). Contributing “higher-level” or domain-general processes include information processing speed and executive functions (working memory, strategic problem solving, attentional switching). Research in this area has relied on largely Caucasian samples, with limited representation of children from racial or ethnic minority groups. This study examined contributions of executive skills to reading competence in 761 children of minority backgrounds. Hierarchical linear regressions examined unique contributions of executive functions (EF) to word reading, fluency, and comprehension. EF contributed uniquely to reading performance, over and above reading-related language skills; working memory contributed uniquely to all components of reading; while attentional switching, but not problem solving, contributed to isolated and contextual word reading and reading fluency. Problem solving uniquely predicted comprehension, suggesting that this skill may be especially important for reading comprehension in minority youth. Attentional switching may play a unique role in development of reading fluency in minority youth, perhaps as a result of the increased demand for switching between spoken versus written dialects. Findings have implications for educational and clinical practice with regard to reading instruction, remedial reading intervention, and assessment of individuals with reading difficulty. PMID:26755569

"Seeing It on the Screen Isn't Really Seeing It": Reading Problems of Writers Using Word Processing.

ERIC Educational Resources Information Center

Haas, Christina

An observational study examined computer writers' use of hard copy for reading. The study begins with a description, based on interviews, of four kinds of reading problems encountered by writers using word processing; formatting, proofreading, reorganizing, and critical reading ("getting a sense of the text"). Subjects, six freshmen…

The Comprehension Problems of Children with Poor Reading Comprehension Despite Adequate Decoding: A Meta-Analysis

ERIC Educational Resources Information Center

Spencer, Mercedes; Wagner, Richard K.

2018-01-01

The purpose of this meta-analysis was to examine the comprehension problems of children who have a specific reading comprehension deficit (SCD), which is characterized by poor reading comprehension despite adequate decoding. The meta-analysis included 86 studies of children with SCD who were assessed in reading comprehension and oral language…

Reading Crisis: The Problem and Suggested Solutions. An EDUCATION U.S.A. Special Report.

ERIC Educational Resources Information Center

National School Public Relations Association, Washington, DC.

This report was written to provide the nation's education community with up-to-date information on the most significant recent studies on reading problems in concise, understandable language. Administrators, teachers, and school boards are anxious to improve their reading programs as part of the new national goal to end reading failures in America…

Disturbing Reading: J.M. Coetzee's "The Problem of Evil"

ERIC Educational Resources Information Center

Tarc, Aparna Mishra

2011-01-01

A literary representation can give us grief. J.M. Coetzee's "The Problem of Evil" follows the crisis of reading of his main character Elizabeth Costello as she struggles to comprehend discursive images of evil. Costello's trouble with reading is not attributed to a cognitive deficiency in her ability to read the text but to a psychical…

Comparison of next generation sequencing technologies for transcriptome characterization

PubMed Central

2009-01-01

Background We have developed a simulation approach to help determine the optimal mixture of sequencing methods for most complete and cost effective transcriptome sequencing. We compared simulation results for traditional capillary sequencing with "Next Generation" (NG) ultra high-throughput technologies. The simulation model was parameterized using mappings of 130,000 cDNA sequence reads to the Arabidopsis genome (NCBI Accession SRA008180.19). We also generated 454-GS20 sequences and de novo assemblies for the basal eudicot California poppy (Eschscholzia californica) and the magnoliid avocado (Persea americana) using a variety of methods for cDNA synthesis. Results The Arabidopsis reads tagged more than 15,000 genes, including new splice variants and extended UTR regions. Of the total 134,791 reads (13.8 MB), 119,518 (88.7%) mapped exactly to known exons, while 1,117 (0.8%) mapped to introns, 11,524 (8.6%) spanned annotated intron/exon boundaries, and 3,066 (2.3%) extended beyond the end of annotated UTRs. Sequence-based inference of relative gene expression levels correlated significantly with microarray data. As expected, NG sequencing of normalized libraries tagged more genes than non-normalized libraries, although non-normalized libraries yielded more full-length cDNA sequences. The Arabidopsis data were used to simulate additional rounds of NG and traditional EST sequencing, and various combinations of each. Our simulations suggest a combination of FLX and Solexa sequencing for optimal transcriptome coverage at modest cost. We have also developed ESTcalc http://fgp.huck.psu.edu/NG_Sims/ngsim.pl, an online webtool, which allows users to explore the results of this study by specifying individualized costs and sequencing characteristics. Conclusion NG sequencing technologies are a highly flexible set of platforms that can be scaled to suit different project goals. In terms of sequence coverage alone, the NG sequencing is a dramatic advance over capillary-based sequencing, but NG sequencing also presents significant challenges in assembly and sequence accuracy due to short read lengths, method-specific sequencing errors, and the absence of physical clones. These problems may be overcome by hybrid sequencing strategies using a mixture of sequencing methodologies, by new assemblers, and by sequencing more deeply. Sequencing and microarray outcomes from multiple experiments suggest that our simulator will be useful for guiding NG transcriptome sequencing projects in a wide range of organisms. PMID:19646272

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 datasets. Furthermore, the novel distance estimator in ARKS utilizes barcoding information from linked reads to estimate gap sizes. It accomplishes this by modeling the relationship between known distances of a region within contigs and calculating associated Jaccard indices. ARKS has the potential to provide correct, chromosome-scale genome assemblies, promptly. We expect ARKS to have broad utility in helping refine draft genomes.

RC-MAPS: Bridging the Comprehension Gap in EAP Reading

ERIC Educational Resources Information Center

Sterzik, Angela Meyer; Fraser, Carol

2012-01-01

In academic environments, reading is assigned not simply to transmit information; students are required to take the information, and based on the task set by the instructor, assess, analyze, and critique it on the basis of personal experiences, prior knowledge, and other readings (Grabe, 2009). Thus text-based comprehension (Kintsch, 1998) alone…

Strategies Training in the Teaching of Reading Comprehension for EFL Learners in Indonesia

ERIC Educational Resources Information Center

Mistar, Junaidi; Zuhairi, Alfan; Yanti, Nofita

2016-01-01

This study investigated the effect of reading strategies training on the students' literal and inferential reading comprehension. The training involved three concrete strategies: predicting, text mapping, and summarizing. To achieve the purpose of this study, a quasi experimental design was selected with the experimental group being given reading…

Everyday Reading and Writing: English. 5112.24.

ERIC Educational Resources Information Center

Knowles, Marlene; Wardell, Arlene

A curriculum guide to help students improve their everyday English skills has been designed for the Dade County Public Schools. The course, for grades 8 through 12, is to help students learn to read, write, and interpret letters, business forms, instructions, signs, maps, and magazines. The practical subject matter emphasizes basic reading and…

Characteristic Reading Problems of Adult Illiterates. Report Number 3. Summary Reports of Paths to Literacy and Illiteracy in Newfoundland and Labrador.

ERIC Educational Resources Information Center

Beebe, Mona

A study examined the reading problems of adults in Newfoundland (Canada) with low reading ability. It explored the genesis of these problems through a retrospective analysis of their lives as school children; and determined the relationship between literacy development and personal background factors, school factors, physiological factors, and…

Simultaneously uncovering the patterns of brain regions involved in different story reading subprocesses.

PubMed

Wehbe, Leila; Murphy, Brian; Talukdar, Partha; Fyshe, Alona; Ramdas, Aaditya; Mitchell, Tom

2014-01-01

Story understanding involves many perceptual and cognitive subprocesses, from perceiving individual words, to parsing sentences, to understanding the relationships among the story characters. We present an integrated computational model of reading that incorporates these and additional subprocesses, simultaneously discovering their fMRI signatures. Our model predicts the fMRI activity associated with reading arbitrary text passages, well enough to distinguish which of two story segments is being read with 74% accuracy. This approach is the first to simultaneously track diverse reading subprocesses during complex story processing and predict the detailed neural representation of diverse story features, ranging from visual word properties to the mention of different story characters and different actions they perform. We construct brain representation maps that replicate many results from a wide range of classical studies that focus each on one aspect of language processing and offer new insights on which type of information is processed by different areas involved in language processing. Additionally, this approach is promising for studying individual differences: it can be used to create single subject maps that may potentially be used to measure reading comprehension and diagnose reading disorders.

zUMIs - A fast and flexible pipeline to process RNA sequencing data with UMIs.

PubMed

Parekh, Swati; Ziegenhain, Christoph; Vieth, Beate; Enard, Wolfgang; Hellmann, Ines

2018-06-01

Single-cell RNA-sequencing (scRNA-seq) experiments typically analyze hundreds or thousands of cells after amplification of the cDNA. The high throughput is made possible by the early introduction of sample-specific bar codes (BCs), and the amplification bias is alleviated by unique molecular identifiers (UMIs). Thus, the ideal analysis pipeline for scRNA-seq data needs to efficiently tabulate reads according to both BC and UMI. zUMIs is a pipeline that can handle both known and random BCs and also efficiently collapse UMIs, either just for exon mapping reads or for both exon and intron mapping reads. If BC annotation is missing, zUMIs can accurately detect intact cells from the distribution of sequencing reads. Another unique feature of zUMIs is the adaptive downsampling function that facilitates dealing with hugely varying library sizes but also allows the user to evaluate whether the library has been sequenced to saturation. To illustrate the utility of zUMIs, we analyzed a single-nucleus RNA-seq dataset and show that more than 35% of all reads map to introns. Also, we show that these intronic reads are informative about expression levels, significantly increasing the number of detected genes and improving the cluster resolution. zUMIs flexibility makes if possible to accommodate data generated with any of the major scRNA-seq protocols that use BCs and UMIs and is the most feature-rich, fast, and user-friendly pipeline to process such scRNA-seq data.

The role of the left anterior temporal lobe in exception word reading: reconciling patient and neuroimaging findings.

PubMed

Wilson, Maximiliano A; Joubert, Sven; Ferré, Perrine; Belleville, Sylvie; Ansaldo, Ana Inés; Joanette, Yves; Rouleau, Isabelle; Brambati, Simona Maria

2012-05-01

Semantic dementia (SD) is a neurodegenerative disease that occurs following the atrophy of the anterior temporal lobes (ATLs). It is characterised by the degradation of semantic knowledge and difficulties in reading exception words (surface dyslexia). This disease has highlighted the role of the ATLs in the process of exception word reading. However, imaging studies in healthy subjects have failed to detect activation of the ATLs during exception word reading. The aim of the present study was to test whether the functional brain regions that mediate exception word reading in normal readers overlap those brain regions atrophied in SD. In Study One, we map the brain regions of grey matter atrophy in AF, a patient with mild SD and surface dyslexia profile. In Study Two, we map the activation pattern associated with exception word compared to pseudoword reading in young, healthy participants using fMRI. The results revealed areas of significant activation in healthy subjects engaged in the exception word reading task in the left anterior middle temporal gyrus, in a region observed to be atrophic in the patient AF. These results reconcile neuropsychological and functional imaging data, revealing the critical role of the left ATL in exception word reading. Copyright © 2012 Elsevier Inc. All rights reserved.

Learning from a Bike Trip

ERIC Educational Resources Information Center

Koren, Mike

2009-01-01

In this article, the author describes a bike trip which marks the culmination of a unit reviewing map-reading capabilities. In seventh grade, students develop various map skills, including cardinal and intermediate directions, how to measure distance on a map using a scale of miles, how to interpret the legend of a map, and how to locate places…

Normal and compound poisson approximations for pattern occurrences in NGS reads.

PubMed

Zhai, Zhiyuan; Reinert, Gesine; Song, Kai; Waterman, Michael S; Luan, Yihui; Sun, Fengzhu

2012-06-01

Next generation sequencing (NGS) technologies are now widely used in many biological studies. In NGS, sequence reads are randomly sampled from the genome sequence of interest. Most computational approaches for NGS data first map the reads to the genome and then analyze the data based on the mapped reads. Since many organisms have unknown genome sequences and many reads cannot be uniquely mapped to the genomes even if the genome sequences are known, alternative analytical methods are needed for the study of NGS data. Here we suggest using word patterns to analyze NGS data. Word pattern counting (the study of the probabilistic distribution of the number of occurrences of word patterns in one or multiple long sequences) has played an important role in molecular sequence analysis. However, no studies are available on the distribution of the number of occurrences of word patterns in NGS reads. In this article, we build probabilistic models for the background sequence and the sampling process of the sequence reads from the genome. Based on the models, we provide normal and compound Poisson approximations for the number of occurrences of word patterns from the sequence reads, with bounds on the approximation error. The main challenge is to consider the randomness in generating the long background sequence, as well as in the sampling of the reads using NGS. We show the accuracy of these approximations under a variety of conditions for different patterns with various characteristics. Under realistic assumptions, the compound Poisson approximation seems to outperform the normal approximation in most situations. These approximate distributions can be used to evaluate the statistical significance of the occurrence of patterns from NGS data. The theory and the computational algorithm for calculating the approximate distributions are then used to analyze ChIP-Seq data using transcription factor GABP. Software is available online (www-rcf.usc.edu/∼fsun/Programs/NGS_motif_power/NGS_motif_power.html). In addition, Supplementary Material can be found online (www.liebertonline.com/cmb).

Reading disorders and dyslexia.

PubMed

Hulme, Charles; Snowling, Margaret J

2016-12-01

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

Libraries, the MAP, and Student Achievement.

ERIC Educational Resources Information Center

Jones, Cherri; Singer, Marietta; Miller, David W.; Makemson, Carroll; Elliott, Kara; Litsch, Diana; Irwin, Barbara; Hoemann, Cheryl; Elmore, Jennifer; Roe, Patty; Gregg, Diane; Needham, Joyce; Stanley, Jerri; Reinert, John; Holtz, Judy; Jenkins, Sandra; Giles, Paula

2002-01-01

Includes 17 articles that discuss the Missouri Assessment Program (MAP) and the role of school library media centers. Highlights include improving student achievement; improving student scores on the MAP; graphic organizers; programs for volunteer student library workers; research process; research skills; reading initiatives; collaborative…

Supplemental Summer Literacy Instruction: Implications for Preventing Summer Reading Loss

ERIC Educational Resources Information Center

McDaniel, Sara C.; McLeod, Ragan; Carter, Coddy L.; Robinson, Cecil

2017-01-01

Summer reading loss is a prevalent problem that occurs primarily for students who are not exposed to or encouraged to read at home or in summer programs when school is out. This problem prevails among early readers from low-income backgrounds. This study provided 31 six and seven-year-old children with a structured guided reading program through…

The Effects of Repetitive Reading and PQRS Strategy in the Development of Reading Skill

ERIC Educational Resources Information Center

Ulu, Hacer; Akyol, Hayati

2016-01-01

Problem Statements: It is a fact that there are individual differences in education and it would be wrong to expect every individual to learn at the same speed. Certain individuals have difficulty in some subjects such as reading, writing and mathematics, yet the most common such problem is difficulty in reading. Particularly, the students who…

Emergent Literacy Skills, Behavior Problems and Familial Antecedents of Reading Difficulties: A Follow-Up Study of Reading Achievement from Kindergarten to Fifth Grade

ERIC Educational Resources Information Center

Costa, Hugo Camara; Perdry, Herve; Soria, Carmen; Pulgar, Salome; Cusin, Francoise; Dellatolas, Georges

2013-01-01

This study examined the relation between emergent literacy skills, teachers' reports of behavioral problems, and word reading achievement in a community sample of French students. Family background was investigated and included familial antecedents of reading difficulties (Fa/Rd) and parents' educational level. The analyses explored the pattern of…

Copy Number Variations Detection: Unravelling the Problem in Tangible Aspects.

PubMed

do Nascimento, Francisco; Guimaraes, Katia S

2017-01-01

In the midst of the important genomic variants associated to the susceptibility and resistance to complex diseases, Copy Number Variations (CNV) has emerged as a prevalent class of structural variation. Following the flood of next-generation sequencing data, numerous tools publicly available have been developed to provide computational strategies to identify CNV at improved accuracy. This review goes beyond scrutinizing the main approaches widely used for structural variants detection in general, including Split-Read, Paired-End Mapping, Read-Depth, and Assembly-based. In this paper, (1) we characterize the relevant technical details around the detection of CNV, which can affect the estimation of breakpoints and number of copies, (2) we pinpoint the most important insights related to GC-content and mappability biases, and (3) we discuss the paramount caveats in the tools evaluation process. The points brought out in this study emphasize common assumptions, a variety of possible limitations, valuable insights, and directions for desirable contributions to the state-of-the-art in CNV detection tools.

Geological Mapping Uses Landsat 4-5TM Satellite Data in Manlai Soum of Omnogovi Aimag

NASA Astrophysics Data System (ADS)

Norovsuren, B.

2014-12-01

Author: Bayanmonkh N1, Undram.G1, Tsolmon.R2, Ariunzul.Ya1, Bayartungalag B31 Environmental Research Information and Study Center 2NUM-ITC-UNESCO Space Science and Remote Sensing International Laboratory, National University of Mongolia 3Geology and Hydrology School, Korea University KEY WORDS: geology, mineral resources, fracture, structure, lithologyABSTRACTGeologic map is the most important map for mining when it does exploration job. In Mongolia geological map completed by Russian geologists which is done by earlier technology. Those maps doesn't satisfy for present requirements. Thus we want to study improve geological map which includes fracture, structural map and lithology use Landsat TM4-5 satellite data. If we can produce a geological map from satellite data with more specification then geologist can explain or read mineralogy very easily. We searched all methodology and researches of every single element of geological mapping. Then we used 3 different remote sensing methodologies to produce structural and lithology and fracture map based on geographic information system's softwares. There can be found a visible lithology border improvement and understandable structural map and we found fracture of the Russian geological map has a lot of distortion. The result of research geologist can read mineralogy elements very easy and discovered 3 unfound important elements from satellite image.

Phonological Coding Abilities: Identification of Impairments Related to Phonologically Based Reading Problems.

ERIC Educational Resources Information Center

Swank, Linda K.

1994-01-01

Relationships between phonological coding abilities and reading outcomes have implications for differential diagnosis of language-based reading problems. The theoretical construct of specific phonological coding ability is explained, including phonological encoding, phonological awareness and metaphonology, lexical access, working memory, and…

Reading in Two Writing Systems: Accommodation and Assimilation of the Brain's Reading Network

ERIC Educational Resources Information Center

Perfetti, Charles A.; Liu, Ying; Fiez, Julie; Nelson, Jessica; Bolger, Donald J.; Tan, Li-Hai

2007-01-01

Bilingual reading can require more than knowing two languages. Learners must acquire also the writing conventions of their second language, which can differ in its deep mapping principles (writing system) and its visual configurations (script). We review ERP (event-related potential) and fMRI studies of both Chinese-English bilingualism and…

Brief exposure to a self-paced computer-based reading programme and how it impacts reading ability and behaviour problems.

PubMed

Hughes, J Antony; Phillips, Gordon; Reed, Phil

2013-01-01

Basic literacy skills underlie much future adult functioning, and are targeted in children through a variety of means. Children with reading problems were exposed either to a self-paced computer programme that focused on improving phonetic ability, or underwent a classroom-based reading intervention. Exposure was limited to 3 40-min sessions a week, for six weeks. The children were assessed in terms of their reading, spelling, and mathematics abilities, as well as for their externalising and internalising behaviour problems, before the programme commenced, and immediately after the programme terminated. Relative to the control group, the computer-programme improved reading by about seven months in boys (but not in girls), but had no impact on either spelling or mathematics. Children on the programme also demonstrated fewer externalising and internalising behaviour problems than the control group. The results suggest that brief exposure to a self-paced phonetic computer-teaching programme had some benefits for the sample.

Exploring Differential Effects across Two Decoding Treatments on Item-Level Transfer in Children with Significant Word Reading Difficulties: A New Approach for Testing Intervention Elements

ERIC Educational Resources Information Center

Steacy, Laura M.; Elleman, Amy M.; Lovett, Maureen W.; Compton, Donald L.

2016-01-01

In English, gains in decoding skill do not map directly onto increases in word reading. However, beyond the Self-Teaching Hypothesis, little is known about the transfer of decoding skills to word reading. In this study, we offer a new approach to testing specific decoding elements on transfer to word reading. To illustrate, we modeled word-reading…

TopHat: discovering splice junctions with RNA-Seq

PubMed Central

Trapnell, Cole; Pachter, Lior; Salzberg, Steven L.

2009-01-01

Motivation: A new protocol for sequencing the messenger RNA in a cell, known as RNA-Seq, generates millions of short sequence fragments in a single run. These fragments, or ‘reads’, can be used to measure levels of gene expression and to identify novel splice variants of genes. However, current software for aligning RNA-Seq data to a genome relies on known splice junctions and cannot identify novel ones. TopHat is an efficient read-mapping algorithm designed to align reads from an RNA-Seq experiment to a reference genome without relying on known splice sites. Results: We mapped the RNA-Seq reads from a recent mammalian RNA-Seq experiment and recovered more than 72% of the splice junctions reported by the annotation-based software from that study, along with nearly 20 000 previously unreported junctions. The TopHat pipeline is much faster than previous systems, mapping nearly 2.2 million reads per CPU hour, which is sufficient to process an entire RNA-Seq experiment in less than a day on a standard desktop computer. We describe several challenges unique to ab initio splice site discovery from RNA-Seq reads that will require further algorithm development. Availability: TopHat is free, open-source software available from http://tophat.cbcb.umd.edu Contact: cole@cs.umd.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19289445

Description and measurement of concentration problems in depressed patients.

PubMed

Watts, F N; Sharrock, R

1985-05-01

Depressed patients commonly complain of concentration problems, yet these have seldom been the focus of systematic investigation. A structured interview about concentration problems was administered to a group of relatively severely depressed patients. Problems in reading and watching television were the most common, and were highly correlated with each other. Direct report of the number of concentration lapses on a reading task was the most generally satisfactory task-performance correlate of complaints of reading/TV concentration problems. Evidence both from this task and from the interview suggests that depressive concentration problems may often be due to 'mind-wandering'. The correlations with concentration problems with the severity and endogeneity of depression and with state anxiety were generally similar.

Concept Maps: Practice Applications in Adult Education and Human Resource Development

ERIC Educational Resources Information Center

Daley, Barbara J.

2010-01-01

Concept maps can be used as both a cognitive and constructivist learning strategy in teaching and learning in adult education and human resource development. The maps can be used to understand course readings, analyze case studies, develop reflective thinking and enhance research skills. The creation of concept maps can also be supported by the…

Surface Chemistry Maps

NASA Image and Video Library

2015-03-13

Maps of magnesium/silicon (left) and thermal neutron absorption (right) across Mercury's surface (red indicates high values, blue low) are shown. These maps, together with maps of other elemental abundances, reveal the presence of distinct geochemical terranes. Volcanic smooth plains deposits are outlined in white. Read the mission news story to learn more! http://photojournal.jpl.nasa.gov/catalog/PIA19242

Gender Moderates Association Between Emotional-Behavioral Problems and Text Comprehension in Children with Both Reading Difficulties and Adhd.

PubMed

Mano, Quintino R; Jastrowski Mano, Kristen E; Denton, Carolyn A; Epstein, Jeffery N; Tamm, Leanne

2017-05-01

Evidence suggests that higher order linguistic functioning such as text comprehension is particularly vulnerable to emotional modulation. Gender has been identified as an important moderating variable in emotional expression such that girls tend toward internalizing emotions (e.g., sadness, anxiety) whereas boys tend toward externalizing emotions (e.g., anger, combativeness), which may influence the relationship between emotion and text comprehension. The present study examined whether gender moderates the relationship between emotional-behavioral problems and text comprehension among children ( n = 187; boys= 115, girls = 72) with both word reading difficulties (RD) and attention-deficit/hyperactivity disorder (ADHD), a sample widely acknowledged to be at increased risk for developing emotional-behavioral problems such as anxiety, poor academic self-concept, and delinquency. A moderated regression analysis tested for the significance of two separate interaction terms (i.e., gender × externalizing problems, gender × internalizing problems) after controlling for gender, IQ, basic reading skills, cognitive-linguistic processes closely related to reading, attentional problems, internalizing problems, and externalizing problems. Results indicated that gender significantly and uniquely moderates the relationship between emotional-behavioral problems and text comprehension. Specifically, text comprehension was relatively lower among girls with relatively higher externalizing problems, whereas no such association was observed among boys. These results contribute to our understanding of cognition-emotion interactions within reading development and raise important implications.

Gender Moderates Association Between Emotional-Behavioral Problems and Text Comprehension in Children with Both Reading Difficulties and Adhd

PubMed Central

Mano, Quintino R.; Jastrowski Mano, Kristen E.; Denton, Carolyn A.; Epstein, Jeffery N.; Tamm, Leanne

2017-01-01

Evidence suggests that higher order linguistic functioning such as text comprehension is particularly vulnerable to emotional modulation. Gender has been identified as an important moderating variable in emotional expression such that girls tend toward internalizing emotions (e.g., sadness, anxiety) whereas boys tend toward externalizing emotions (e.g., anger, combativeness), which may influence the relationship between emotion and text comprehension. The present study examined whether gender moderates the relationship between emotional-behavioral problems and text comprehension among children (n = 187; boys= 115, girls = 72) with both word reading difficulties (RD) and attention-deficit/hyperactivity disorder (ADHD), a sample widely acknowledged to be at increased risk for developing emotional-behavioral problems such as anxiety, poor academic self-concept, and delinquency. A moderated regression analysis tested for the significance of two separate interaction terms (i.e., gender × externalizing problems, gender × internalizing problems) after controlling for gender, IQ, basic reading skills, cognitive-linguistic processes closely related to reading, attentional problems, internalizing problems, and externalizing problems. Results indicated that gender significantly and uniquely moderates the relationship between emotional-behavioral problems and text comprehension. Specifically, text comprehension was relatively lower among girls with relatively higher externalizing problems, whereas no such association was observed among boys. These results contribute to our understanding of cognition-emotion interactions within reading development and raise important implications. PMID:28751795

Problem-Solving during Shared Reading at Kindergarten

ERIC Educational Resources Information Center

Gosen, Myrte N.; Berenst, Jan; de Glopper, Kees

2015-01-01

This paper reports on a conversation analytic study of problem-solving interactions during shared reading at three kindergartens in the Netherlands. It illustrates how teachers and pupils discuss book characters' problems that arise in the events in the picture books. A close analysis of the data demonstrates that problem-solving interactions do…

Middle School Children's Problem-Solving Behavior: A Cognitive Analysis from a Reading Comprehension Perspective

ERIC Educational Resources Information Center

Pape, Stephen J.

2004-01-01

Many children read mathematics word problems and directly translate them to arithmetic operations. More sophisticated problem solvers transform word problems into object-based or mental models. Subsequent solutions are often qualitatively different because these models differentially support cognitive processing. Based on a conception of problem…

Individual differences in working memory and reasoning-remembering relationships in solving class-inclusion problems.

PubMed

Howe, M L; Rabinowitz, F M; Powell, T L

1998-09-01

In the present experiment, we evaluated the effects of individual differences in reading span and variation in memory demands on class-inclusion performance. One hundred twenty college students whose reading spans ranged from low to medium to high (as indexed by a computerized version of the Daneman and Carpenter [1980] reading-span task) solved 48 class-inclusion problems. Half of the subjects had the solution information available when the problems were presented; the other half performed a detection task between solution information and problem presentation. The results from both standard statistical analyses and from a mathematical model indicated that differences in reading span and memory load had predictable, similar effects. Specifically, the sophistication of reasoning strategies declined when memory demands increased or when reading spans decreased. Surprisingly, these effects were primarily additive. The results were interpreted in terms of global resource models and findings from the developmental literature.

Word Problem Wizardry.

ERIC Educational Resources Information Center

Cassidy, Jack

1991-01-01

Presents suggestions for teaching math word problems to elementary students. The strategies take into consideration differences between reading in math and reading in other areas. A problem-prediction game and four self-checking activities are included along with a magic password challenge. (SM)

Relationships among Learner Characteristics and Adolescents' Perceptions about Reading Strategy Use

ERIC Educational Resources Information Center

Cantrell, Susan Chambers; Carter, Janis C.

2009-01-01

This study investigates relationships among adolescent students' perceived use of academic reading strategies and reading achievement, age, and gender. Good readers reported using global and problem-solving strategies to a greater extent than poor readers. Surface-level problem-solving strategies were more strongly related to higher reading…

Measuring Children's Reading Development Using Leveled Texts.

ERIC Educational Resources Information Center

Paris, Scott G.

2002-01-01

Notes that the main problem with using Informal Reading Inventories (IRIs) for measuring reading growth is that running records and miscue analyses are gathered on variable levels of text that are appropriate for each child. Presents several possible solutions to the measurement problem beyond the simple profile descriptions usually reported from…

Phase II evaluation of clinical coding schemes: completeness, taxonomy, mapping, definitions, and clarity. CPRI Work Group on Codes and Structures.

PubMed

Campbell, J R; Carpenter, P; Sneiderman, C; Cohn, S; Chute, C G; Warren, J

1997-01-01

To compare three potential sources of controlled clinical terminology (READ codes version 3.1, SNOMED International, and Unified Medical Language System (UMLS) version 1.6) relative to attributes of completeness, clinical taxonomy, administrative mapping, term definitions and clarity (duplicate coding rate). The authors assembled 1929 source concept records from a variety of clinical information taken from four medical centers across the United States. The source data included medical as well as ample nursing terminology. The source records were coded in each scheme by an investigator and checked by the coding scheme owner. The codings were then scored by an independent panel of clinicians for acceptability. Codes were checked for definitions provided with the scheme. Codes for a random sample of source records were analyzed by an investigator for "parent" and "child" codes within the scheme. Parent and child pairs were scored by an independent panel of medical informatics specialists for clinical acceptability. Administrative and billing code mapping from the published scheme were reviewed for all coded records and analyzed by independent reviewers for accuracy. The investigator for each scheme exhaustively searched a sample of coded records for duplications. SNOMED was judged to be significantly more complete in coding the source material than the other schemes (SNOMED* 70%; READ 57%; UMLS 50%; *p < .00001). SNOMED also had a richer clinical taxonomy judged by the number of acceptable first-degree relatives per coded concept (SNOMED* 4.56, UMLS 3.17; READ 2.14, *p < .005). Only the UMLS provided any definitions; these were found for 49% of records which had a coding assignment. READ and UMLS had better administrative mappings (composite score: READ* 40.6%; UMLS* 36.1%; SNOMED 20.7%, *p < .00001), and SNOMED had substantially more duplications of coding assignments (duplication rate: READ 0%; UMLS 4.2%; SNOMED* 13.9%, *p < .004) associated with a loss of clarity. No major terminology source can lay claim to being the ideal resource for a computer-based patient record. However, based upon this analysis of releases for April 1995, SNOMED International is considerably more complete, has a compositional nature and a richer taxonomy. Is suffers from less clarity, resulting from a lack of syntax and evolutionary changes in its coding scheme. READ has greater clarity and better mapping to administrative schemes (ICD-10 and OPCS-4), is rapidly changing and is less complete. UMLS is a rich lexical resource, with mappings to many source vocabularies. It provides definitions for many of its terms. However, due to the varying granularities and purposes of its source schemes, it has limitations for representation of clinical concepts within a computer-based patient record.

Reading for Progress; A Conference on Perspectives of and Recommendations for Countering Reading Problems in Hawaii County (Waiakea Village Resort, March 8, 1975).

ERIC Educational Resources Information Center

Hawaii State Dept. of Education, Hilo.

The proceedings of the Reading for Progress Conference, held on Hilo (Hawaii) on 8 March 1975, are contained in this report. The purpose of this conference was a "refocus" on the reading problems of Hawaii's youth, as viewed by educators, the business and labor community, social agencies, and other government officials. This document…

Orthographic influences on division of labor in learning to read Chinese and English: Insights from computational modeling

PubMed Central

Yang, Jianfeng; Shu, Hua; McCandliss, Bruce D.; Zevin, Jason D.

2013-01-01

Learning to read any language requires learning to map among print, sound and meaning. Writing systems differ in a number of factors that influence both the ease and rate with which reading skill can be acquired, as well as the eventual division of labor between phonological and semantic processes. Further, developmental reading disability manifests differently across writing systems, and may be related to different deficits in constitutive processes. Here we simulate some aspects of reading acquisition in Chinese and English using the same model architecture for both writing systems. The contribution of semantic and phonological processing to literacy acquisition in the two languages is simulated, including specific effects of phonological and semantic deficits. Further, we demonstrate that similar patterns of performance are observed when the same model is trained on both Chinese and English as an "early bilingual." The results are consistent with the view that reading skill is acquired by the application of statistical learning rules to mappings among print, sound and meaning, and that differences in the typical and disordered acquisition of reading skill between writing systems are driven by differences in the statistical patterns of the writing systems themselves, rather than differences in cognitive architecture of the learner. PMID:24587693

Do fatty acids help in overcoming reading difficulties? A double-blind, placebo-controlled study of the effects of eicosapentaenoic acid and carnosine supplementation on children with dyslexia.

PubMed

Kairaluoma, L; Närhi, V; Ahonen, T; Westerholm, J; Aro, M

2009-01-01

There are claims that dietary supplementation of unsaturated fatty acids could help children with dyslexia to overcome their reading problems. However, these claims have not yet been empirically tested. This study was designed to test whether dietary supplementation was superior to placebo in treating reading, spelling or other reading-related skills of children with dyslexia. The experimental group (eicosapentaenoic acid, EPA, n = 30) ate dietary supplements and the control group (placebo, n = 31) placebos during the 90-day treatment period. The supplements contained omega-3 fatty acid (ethyl-EPA, 500 mg/day) and carnosine (400 mg/day). The groups were matched for reading skills, grade, gender, attention problems, intelligence and amount of special education. The literacy-related skills of the two groups were assessed before and after the treatment period. No group differences were observed between EPA and placebo in measures of reading accuracy or speed, spelling, decoding fluency, arithmetical skills, reading-related language skills, attention or behavioural problems. The present findings do not support the hypothesis that omega-3 fatty acid (ethyl-EPA) or carnosine has a role in the treatment of reading and spelling problems in children with dyslexia.

Genotyping in the cloud with Crossbow.

PubMed

Gurtowski, James; Schatz, Michael C; Langmead, Ben

2012-09-01

Crossbow is a scalable, portable, and automatic cloud computing tool for identifying SNPs from high-coverage, short-read resequencing data. It is built on Apache Hadoop, an implementation of the MapReduce software framework. Hadoop allows Crossbow to distribute read alignment and SNP calling subtasks over a cluster of commodity computers. Two robust tools, Bowtie and SOAPsnp, implement the fundamental alignment and variant calling operations respectively, and have demonstrated capabilities within Crossbow of analyzing approximately one billion short reads per hour on a commodity Hadoop cluster with 320 cores. Through protocol examples, this unit will demonstrate the use of Crossbow for identifying variations in three different operating modes: on a Hadoop cluster, on a single computer, and on the Amazon Elastic MapReduce cloud computing service.

Reading Guided by Automated Graphical Representations: How Model-Based Text Visualizations Facilitate Learning in Reading Comprehension Tasks

ERIC Educational Resources Information Center

Pirnay-Dummer, Pablo; Ifenthaler, Dirk

2011-01-01

Our study integrates automated natural language-oriented assessment and analysis methodologies into feasible reading comprehension tasks. With the newly developed T-MITOCAR toolset, prose text can be automatically converted into an association net which has similarities to a concept map. The "text to graph" feature of the software is based on…

Diffraction gratings used as identifying markers

DOEpatents

Deason, Vance A.; Ward, Michael B.

1991-01-01

A finely detailed defraction grating is applied to an object as an identifier or tag which is unambiguous, difficult to duplicate, or remove and transfer to another item, and can be read and compared with prior readings with relative ease. The exact pattern of the defraction grating is mapped by diffraction moire techniques and recorded for comparison with future readings of the same grating.

Academic Responding During Instruction and Reading Outcomes for Kindergarten Students At-risk for Reading Difficulties

PubMed Central

Wanzek, Jeanne; Roberts, Greg; Al Otaiba, Stephanie

2013-01-01

The purpose of this study was to investigate the academic responding of students at-risk for reading difficulties in beginning reading instruction. Opportunities for kindergarten students at-risk for reading difficulties to respond academically during teacher-facilitated reading instruction in the general education classroom were examined in relation to student reading achievement as well as social behaviors. Student academic responding during teacher-facilitated instruction significantly predicted end of year reading achievement. Teacher perceptions of students’ social skills (positive correlation) and problem behaviors (negative correlation) were significantly correlated with academic responding. When academic responding and teacher perceptions of social behaviors were examined together, only teacher perceptions of academic competence and problem behaviors predicted spring outcomes. PMID:24665162

Aphasia in Persian: Implications for cognitive models of lexical processing.

PubMed

Bakhtiar, Mehdi; Jafary, Reyhane; Weekes, Brendan S

2017-09-01

Current models of oral reading assume that different routes (sublexical, lexical, and semantic) mediate oral reading performance and reliance on different routes during oral reading depends on the characteristics of print to sound mappings. Studies of single cases of acquired dyslexia in aphasia have contributed to the development of such models by revealing patterns of double dissociation in object naming and oral reading skill that follow brain damage in Indo-European and Sino-Tibetan languages. Print to sound mapping in Persian varies in transparency because orthography to phonology translation depends uniquely on the presence or absence of vowel letters in print. Here a hypothesis is tested that oral reading in Persian requires a semantic reading pathway that is independent of a direct non-semantic reading pathway, by investigating whether Persian speakers with aphasia show selective impairments to object naming and reading aloud. A sample of 21 Persian speakers with aphasia ranging in age from 18 to 77 (mean = 53, SD = 16.9) was asked to name a same set of 200 objects and to read aloud the printed names of these objects in different sessions. As an additional measure of sublexical reading, patients were asked to read aloud 30 non-word stimuli. Results showed that oral reading is significantly more preserved than object naming in Persian speakers with aphasia. However, more preserved object naming than oral reading was also observed in some cases. There was a moderate positive correlation between picture naming and oral reading success (p < .05). Mixed-effects logistic regression revealed that word frequency, age of acquisition and imageability predict success across both tasks and there is an interaction between these variables and orthographic transparency in oral reading. Furthermore, opaque words were read less accurately than transparent words. The results reveal different patterns of acquired dyslexia in some cases that closely resemble phonological, deep, and surface dyslexia in other scripts - reported here in Persian for the first time. © 2016 The British Psychological Society.

State Highway Maps: A Route to a Learning Adventure

ERIC Educational Resources Information Center

McDuffie, Thomas E.; Cifelli, Joseph

2006-01-01

Science within the folds of highway maps is explored through a series of hands-on experiences designed to reinforce and extend map-reading skills in grades 6-8. The increasingly sophisticated, standards-related activities include measuring distances between population centers, finding communities named after trees, animals, and geologic features,…

The Impact of the Measures of Academic Progress (MAP) Program on Student Reading Achievement

ERIC Educational Resources Information Center

Cordray, David S.; Pion, Georgine M.; Brandt, Chris; Molefe, Ayrin

2013-01-01

One of the most widely used commercially available systems incorporating benchmark assessment and training in differentiated instruction is the Northwest Evaluation Association's (NWEA) Measures of Academic Progress (MAP) program. The MAP program involves two components: (1) computer-adaptive assessments administered to students three to four…

Changes in running pattern due to fatigue and cognitive load in orienteering.

PubMed

Millet, Guillaume Y; Divert, Caroline; Banizette, Marion; Morin, Jean-Benoit

2010-01-01

The aim of this study was to examine the influence of fatigue on running biomechanics in normal running, in normal running with a cognitive task, and in running while map reading. Nineteen international and less experienced orienteers performed a fatiguing running exercise of duration and intensity similar to a classic distance orienteering race on an instrumented treadmill while performing mental arithmetic, an orienteering simulation, and control running at regular intervals. Two-way repeated-measures analysis of variance did not reveal any significant difference between mental arithmetic and control running for any of the kinematic and kinetic parameters analysed eight times over the fatiguing protocol. However, these parameters were systematically different between the orienteering simulation and the other two conditions (mental arithmetic and control running). The adaptations in orienteering simulation running were significantly more pronounced in the elite group when step frequency, peak vertical ground reaction force, vertical stiffness, and maximal downward displacement of the centre of mass during contact were considered. The effects of fatigue on running biomechanics depended on whether the orienteers read their map or ran normally. It is concluded that adding a cognitive load does not modify running patterns. Therefore, all changes in running pattern observed during the orienteering simulation, particularly in elite orienteers, are the result of adaptations to enable efficient map reading and/or potentially prevent injuries. Finally, running patterns are not affected to the same extent by fatigue when a map reading task is added.

Looking through an adolescent literacy lens at the narrow view of reading.

PubMed

Ehren, Barbara J

2009-04-01

This commentary is a personal reaction to A. G. Kamhi's (2007) article on the "narrow view" of reading and his suggestion that this view be adopted as a way to address the reading problems of children and adolescents. In this article, I consider the narrow view of reading from an adolescent literacy perspective and discuss the practical implications of adopting this view in the schools. Discussion revolves around the complexities of reading comprehension, comprehension as a teachable set of complex processes, and the speech-language pathologist's role in reading comprehension. Although I acknowledge that the narrow view of reading may have merit, I opine that it may create more problems than it solves.

Dyslexia: Neuroanatomical/Neurolinguistic Perspectives.

ERIC Educational Resources Information Center

Hynd, George W.; Hynd, Cynthia R.

1984-01-01

Reviews attempts to adequately define dyslexia with a focus on recent efforts at developing a nosology of dyslexia and discusses the neurological basis of reading and severe reading failure with an emphasis on validating evidence provided through brain-mapping procedures and postmortem studies. (HOD)

The Effects of Leveled Literacy Intervention for Students in the RtI Process

ERIC Educational Resources Information Center

Taylor, Lisa

2017-01-01

Low reading skills constitute a serious achievement problem. Although there are remedial support in schools, between 2% and 6% of the student population continues to show persistent reading difficulties despite intensive intervention. The research problem in this study addressed the lack of effective reading interventions for students who were in…

How Consistent Is the Clinical Diagnosis of Reading Specialists?

ERIC Educational Resources Information Center

Weisberg, Renee K.

A series of research studies on the consistency of reading specialists' diagnoses of students with reading problems have indicated that clinical agreement has been astonishingly low. To investigate which factors seem to lead to consistency in clinical diagnosis, a study was conducted based on a theory of clinical problem solving called inquiry…

Desperately Seeking Everett: Some thoughts on Hermeneutic Reading

ERIC Educational Resources Information Center

Solway, David

2010-01-01

One of the major problems from which students suffer has to do with reading: reading with diligence, understanding, and, ideally, with the pleasure that attends discovery. Many students have long been hermeneutical-readers-of-a-sort. The problem has deep roots in a widely diffused media and technocyber environment that thins down and disperses the…

An Examination of the Relationship between Computation, Problem Solving, and Reading

ERIC Educational Resources Information Center

Cormier, Damien C.; Yeo, Seungsoo; Christ, Theodore J.; Offrey, Laura D.; Pratt, Katherine

2016-01-01

The purpose of this study is to evaluate the relationship of mathematics calculation rate (curriculum-based measurement of mathematics; CBM-M), reading rate (curriculum-based measurement of reading; CBM-R), and mathematics application and problem solving skills (mathematics screener) among students at four levels of proficiency on a statewide…

Comparing and validating methods of reading instruction using behavioural and neural findings in an artificial orthography.

PubMed

Taylor, J S H; Davis, Matthew H; Rastle, Kathleen

2017-06-01

There is strong scientific consensus that emphasizing print-to-sound relationships is critical when learning to read alphabetic languages. Nevertheless, reading instruction varies across English-speaking countries, from intensive phonic training to multicuing environments that teach sound- and meaning-based strategies. We sought to understand the behavioral and neural consequences of these differences in relative emphasis. We taught 24 English-speaking adults to read 2 sets of 24 novel words (e.g., /buv/, /sig/), written in 2 different unfamiliar orthographies. Following pretraining on oral vocabulary, participants learned to read the novel words over 8 days. Training in 1 language was biased toward print-to-sound mappings while training in the other language was biased toward print-to-meaning mappings. Results showed striking benefits of print-sound training on reading aloud, generalization, and comprehension of single words. Univariate analyses of fMRI data collected at the end of training showed that print-meaning relative to print-sound relative training increased neural effort in dorsal pathway regions involved in reading aloud. Conversely, activity in ventral pathway brain regions involved in reading comprehension was no different following print-meaning versus print-sound training. Multivariate analyses validated our artificial language approach, showing high similarity between the spatial distribution of fMRI activity during artificial and English word reading. Our results suggest that early literacy education should focus on the systematicities present in print-to-sound relationships in alphabetic languages, rather than teaching meaning-based strategies, in order to enhance both reading aloud and comprehension of written words. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Comparing and Validating Methods of Reading Instruction Using Behavioural and Neural Findings in an Artificial Orthography

PubMed Central

2017-01-01

There is strong scientific consensus that emphasizing print-to-sound relationships is critical when learning to read alphabetic languages. Nevertheless, reading instruction varies across English-speaking countries, from intensive phonic training to multicuing environments that teach sound- and meaning-based strategies. We sought to understand the behavioral and neural consequences of these differences in relative emphasis. We taught 24 English-speaking adults to read 2 sets of 24 novel words (e.g., /buv/, /sig/), written in 2 different unfamiliar orthographies. Following pretraining on oral vocabulary, participants learned to read the novel words over 8 days. Training in 1 language was biased toward print-to-sound mappings while training in the other language was biased toward print-to-meaning mappings. Results showed striking benefits of print–sound training on reading aloud, generalization, and comprehension of single words. Univariate analyses of fMRI data collected at the end of training showed that print–meaning relative to print–sound relative training increased neural effort in dorsal pathway regions involved in reading aloud. Conversely, activity in ventral pathway brain regions involved in reading comprehension was no different following print–meaning versus print–sound training. Multivariate analyses validated our artificial language approach, showing high similarity between the spatial distribution of fMRI activity during artificial and English word reading. Our results suggest that early literacy education should focus on the systematicities present in print-to-sound relationships in alphabetic languages, rather than teaching meaning-based strategies, in order to enhance both reading aloud and comprehension of written words. PMID:28425742

Validation of a standardized mapping system of the hip joint for radial MRA sequencing.

PubMed

Klenke, Frank M; Hoffmann, Daniel B; Cross, Brian J; Siebenrock, Klaus A

2015-03-01

Intraarticular gadolinium-enhanced magnetic resonance arthrography (MRA) is commonly applied to characterize morphological disorders of the hip. However, the reproducibility of retrieving anatomic landmarks on MRA scans and their correlation with intraarticular pathologies is unknown. A precise mapping system for the exact localization of hip pathomorphologies with radial MRA sequences is lacking. Therefore, the purpose of the study was the establishment and validation of a reproducible mapping system for radial sequences of hip MRA. Sixty-nine consecutive intraarticular gadolinium-enhanced hip MRAs were evaluated. Radial sequencing consisted of 14 cuts orientated along the axis of the femoral neck. Three orthopedic surgeons read the radial sequences independently. Each MRI was read twice with a minimum interval of 7 days from the first reading. The intra- and inter-observer reliability of the mapping procedure was determined. A clockwise system for hip MRA was established. The teardrop figure served to determine the 6 o'clock position of the acetabulum; the center of the greater trochanter served to determine the 12 o'clock position of the femoral head-neck junction. The intra- and inter-observer ICCs to retrieve the correct 6/12 o'clock positions were 0.906-0.996 and 0.978-0.988, respectively. The established mapping system for radial sequences of hip joint MRA is reproducible and easy to perform.

An Exploration of Factors Related to Reading Comprehension: A Study of Third Grade English Language Learners (ELLs)

ERIC Educational Resources Information Center

Torres Soto, Nayda E.

2013-01-01

Learning to read consists of processes that allow the reader to recognize print, understand words and comprehend text. Thus, vocabulary is one of the most fundamental elements for reading comprehension. Learners can acquire new words from text upon the first encounter with a new word on the basis of fast mapping. Teachers also contribute to…

Diffraction gratings used as identifying markers

DOEpatents

Deason, V.A.; Ward, M.B.

1991-03-26

A finely detailed diffraction grating is applied to an object as an identifier or tag which is unambiguous, difficult to duplicate, or remove and transfer to another item, and can be read and compared with prior readings with relative ease. The exact pattern of the diffraction grating is mapped by diffraction moire techniques and recorded for comparison with future readings of the same grating. 7 figures.

Into the Curriculum. Dramatics/Reading/Language Arts: Jellyfish Jiggle and More; Reading/Language Arts: Birthstone Folklore; Science: Jellyfish FAQ; Science: Minerals in Caves; Social Studies: Mapping the Oceans.

ERIC Educational Resources Information Center

School Library Media Activities Monthly, 2003

2003-01-01

Provides five fully developed library media activities that are designed for use with specific curriculum units in dramatics, reading, language arts, science, and social studies. Library media skills, curriculum objectives, grade levels, resources, instructional roles, activities and procedures, evaluation, and follow-up are describes for each…

Learning Disabilities

MedlinePlus

... a student to read, write, spell, or solve math problems. The way our brains process information is ... has difficulty speaking, reading, writing, figuring out a math problem, communicating with a parent, or paying attention ...

Shapes and sounds as self-objects in learning geography.

PubMed

Baum, E A

1978-01-01

The pleasure which some children find in maps and map reading is manifold in origin. Children cathect patterns of configuration and color and derive joy from the visual mastery of these. This gratification is enhanced by the child's knowledge that the map represents something bigger than and external to itself. Likewise, some children take pleasure in the pronunciation of names themselves. The phonetic transcription of multisyllabic names is often a plearurable challenge. The vocalized name has its origin in the self, becomes barely external to self, and is self-monitored. Thus, in children both the configurations and the vocalizations associated with map reading have the properties of "self=objects" (Kohut, 1971). From the author's observation the delight which some children take in sounding out geographic names on a map may, in some instances, indicate pre-existing gratifying sound associations. Childish amusement in punning on cognomens may be an even greater stimulant for learning than visual configurations or artificial cognitive devices.

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

Do Working Memory Deficits Underlie Reading Problems in Attention-Deficit/Hyperactivity Disorder (ADHD)?

PubMed

Kofler, Michael J; Spiegel, Jamie A; Soto, Elia F; Irwin, Lauren N; Wells, Erica L; Austin, Kristin E

2018-06-19

Reading problems are common in children with ADHD and show strong covariation with these children's underdeveloped working memory abilities. In contrast, working memory training does not appear to improve reading performance for children with ADHD or neurotypical children. The current study bridges the gap between these conflicting findings, and combines dual-task methodology with Bayesian modeling to examine the role of working memory for explaining ADHD-related reading problems. Children ages 8-13 (M = 10.50, SD = 1.59) with and without ADHD (N = 78; 29 girls; 63% Caucasian/Non-Hispanic) completed a counterbalanced series of reading tasks that systematically manipulated concurrent working memory demands. Adding working memory demands produced disproportionate decrements in reading comprehension for children with ADHD (d = -0.67) relative to Non-ADHD children (d = -0.18); comprehension was significantly reduced in both groups when working memory demands were increased. These effects were robust to controls for foundational reading skills (decoding, sight word vocabulary) and comorbid reading disability. Concurrent working memory demands did not slow reading speed for either group. The ADHD group showed lower comprehension (d = 1.02) and speed (d = 0.69) even before adding working memory demands beyond those inherently required for reading. Exploratory conditional effects analyses indicated that underdeveloped working memory overlapped with 41% (comprehension) and 85% (speed) of these between-group differences. Reading problems in ADHD appear attributable, at least in part, to their underdeveloped working memory abilities. Combined with prior cross-sectional and longitudinal findings, the current experimental evidence positions working memory as a potential causal mechanism that is necessary but not sufficient for effectively understanding written language.

Fast Mapping by Bilingual Children: Storybooks and Cartoons

ERIC Educational Resources Information Center

Van Horn, Danielle; Kan, Pui Fong

2016-01-01

The purpose of this study was to examine the fast mapping skills in Spanish-English bilingual preschool children in two learning contexts: storybook reading and cartoon viewing. Eighteen typically developing Spanish-English bilingual preschool children completed a fast mapping task in Spanish (L1) and in English (L2). In 4 different sessions, each…

Teaching Topographic Map Skills and Geomorphology Concepts with Google Earth in a One-Computer Classroom

ERIC Educational Resources Information Center

Hsu, Hsiao-Ping; Tsai, Bor-Wen; Chen, Che-Ming

2018-01-01

Teaching high-school geomorphological concepts and topographic map reading entails many challenges. This research reports the applicability and effectiveness of Google Earth in teaching topographic map skills and geomorphological concepts, by a single teacher, in a one-computer classroom. Compared to learning via a conventional instructional…

An Exploratory Study of Civil Servants Spatial Thinking, Awareness and Use of Maps in Africa-Nigeria

NASA Astrophysics Data System (ADS)

Asiyanbola, R. A.

2018-04-01

The paper is an exploratory study of spatial thinking, awareness and use of maps among civil servants in Nigeria with a view towards enhancing capacity building in the development and use of global mapping and geospatial information technologies products and services. The data used in the paper was from administration of 152 questionnaires to civil servants in Ibadan, Oyo State, Nigeria between February and August, 2017. Descriptive statistics were used to analyse the data. The study shows among others that majority of the civil servants had situations in their daily lives or specialty that require spatial thinking; the three top situations in their daily lives or specialty that require spatial thinking were identification of places, wayfinding and walking; majority of them asked from people information about location, direction, distances and other needed information about places they do not know; majority of them were aware of maps; majority of them could read maps; majority of them had interest to learn more how to read maps and were willing to pay for the training.

Taiwanese EFL Learners' Perceived Use of Online Reading Strategies

ERIC Educational Resources Information Center

Chen, Lisa Wen Chun

2015-01-01

Reading strategies are beneficial to learners' reading comprehension. The strategies can be divided into different categories, such as global reading strategies, problem solving strategies and support strategies. Most previous studies investigated the importance of reading strategies in the paper-based reading. However, relatively few studies…

Impacts of the Problem-Based Learning Pedagogy on English Learners' Reading Comprehension, Strategy Use, and Active Learning Attitudes

ERIC Educational Resources Information Center

Lin, Lu-Fang

2017-01-01

This study investigated whether an English reading course integrated with the problem-based learning approach could foster foreign language learners' reading comprehension ability, strategy use, and their active learning attitudes. The pedagogy was featured with the small group scaffolding. Two intact English classes in a Taiwanese university were…

Integrating the Problem-Based Learning Approach into a Web-Based English Reading Course

ERIC Educational Resources Information Center

Lin, Lu-Fang

2018-01-01

This study incorporated the problem-based learning (PBL) approach into a web-based English reading course. The purpose of the study was to examine the impact of PBL on the participants' English reading comprehension (RC) and to explore the participants' perceptions of PBL. The present study conducted a comparison of two teaching methods. Two…

Eye vs. Text Movement: Which Technique Leads to Faster Reading Comprehension?

ERIC Educational Resources Information Center

Abdellah, Antar Solhy

2009-01-01

Eye fixation is a frequent problem that faces foreign language learners and hinders the flow of their reading comprehension. Although students are usually advised to read fast/skim to overcome this problem, eye fixation persists. The present study investigates the effect of using a paper-based program as compared to a computer-based software in…

An Oral Language Based Reading Remedial Program for Special Education Children.

ERIC Educational Resources Information Center

Langdon, Tom

A problem was addressed within the context of the action based research practicum model. The problem was junior high school special education students who read at or below the 10th percentile when compared to age appropriate peers on standardized achievement instruments; and who have had all manner of reading interventions and yet continue to fall…

Instructional Design Implications about Comprehension of Listening to Music before and during Reading

ERIC Educational Resources Information Center

Hinrichs, Amy F.

2013-01-01

Low reading levels and lack of comprehension are current problems in high school classrooms confirmed by low standardized test scores and employer feedback as comprehension problems move into the workplace with students who do not have the necessary reading skills on the job. Midwestern high school science club students served as participants in…

GeoNotebook: Browser based Interactive analysis and visualization workflow for very large climate and geospatial datasets

NASA Astrophysics Data System (ADS)

Ozturk, D.; Chaudhary, A.; Votava, P.; Kotfila, C.

2016-12-01

Jointly developed by Kitware and NASA Ames, GeoNotebook is an open source tool designed to give the maximum amount of flexibility to analysts, while dramatically simplifying the process of exploring geospatially indexed datasets. Packages like Fiona (backed by GDAL), Shapely, Descartes, Geopandas, and PySAL provide a stack of technologies for reading, transforming, and analyzing geospatial data. Combined with the Jupyter notebook and libraries like matplotlib/Basemap it is possible to generate detailed geospatial visualizations. Unfortunately, visualizations generated is either static or does not perform well for very large datasets. Also, this setup requires a great deal of boilerplate code to create and maintain. Other extensions exist to remedy these problems, but they provide a separate map for each input cell and do not support map interactions that feed back into the python environment. To support interactive data exploration and visualization on large datasets we have developed an extension to the Jupyter notebook that provides a single dynamic map that can be managed from the Python environment, and that can communicate back with a server which can perform operations like data subsetting on a cloud-based cluster.

Eye Tracking to Explore the Impacts of Photorealistic 3d Representations in Pedstrian Navigation Performance

NASA Astrophysics Data System (ADS)

Dong, Weihua; Liao, Hua

2016-06-01

Despite the now-ubiquitous two-dimensional (2D) maps, photorealistic three-dimensional (3D) representations of cities (e.g., Google Earth) have gained much attention by scientists and public users as another option. However, there is no consistent evidence on the influences of 3D photorealism on pedestrian navigation. Whether 3D photorealism can communicate cartographic information for navigation with higher effectiveness and efficiency and lower cognitive workload compared to the traditional symbolic 2D maps remains unknown. This study aims to explore whether the photorealistic 3D representation can facilitate processes of map reading and navigation in digital environments using a lab-based eye tracking approach. Here we show the differences of symbolic 2D maps versus photorealistic 3D representations depending on users' eye-movement and navigation behaviour data. We found that the participants using the 3D representation were less effective, less efficient and were required higher cognitive workload than using the 2D map for map reading. However, participants using the 3D representation performed more efficiently in self-localization and orientation at the complex decision points. The empirical results can be helpful to improve the usability of pedestrian navigation maps in future designs.

Writing System Modulates the Association between Sensitivity to Acoustic Cues in Music and Reading Ability: Evidence from Chinese-English Bilingual Children.

PubMed

Zhang, Juan; Meng, Yaxuan; Wu, Chenggang; Zhou, Danny Q

2017-01-01

Music and language share many attributes and a large body of evidence shows that sensitivity to acoustic cues in music is positively related to language development and even subsequent reading acquisition. However, such association was mainly found in alphabetic languages. What remains unclear is whether sensitivity to acoustic cues in music is associated with reading in Chinese, a morphosyllabic language. The present study aimed to answer this question by measuring music (i.e., musical metric perception and pitch discrimination), language (i.e., phonological awareness, lexical tone sensitivity), and reading abilities (i.e., word recognition) among 54 third-grade Chinese-English bilingual children. After controlling for age and non-verbal intelligence, we found that both musical metric perception and pitch discrimination accounted for unique variance of Chinese phonological awareness while pitch discrimination rather than musical metric perception predicted Chinese lexical tone sensitivity. More importantly, neither musical metric perception nor pitch discrimination was associated with Chinese reading. As for English, musical metric perception and pitch discrimination were correlated with both English phonological awareness and English reading. Furthermore, sensitivity to acoustic cues in music was associated with English reading through the mediation of English phonological awareness. The current findings indicate that the association between sensitivity to acoustic cues in music and reading may be modulated by writing systems. In Chinese, the mapping between orthography and phonology is not as transparent as in alphabetic languages such as English. Thus, this opaque mapping may alter the auditory perceptual sensitivity in music to Chinese reading.

Writing System Modulates the Association between Sensitivity to Acoustic Cues in Music and Reading Ability: Evidence from Chinese–English Bilingual Children

PubMed Central

Zhang, Juan; Meng, Yaxuan; Wu, Chenggang; Zhou, Danny Q.

2017-01-01

Music and language share many attributes and a large body of evidence shows that sensitivity to acoustic cues in music is positively related to language development and even subsequent reading acquisition. However, such association was mainly found in alphabetic languages. What remains unclear is whether sensitivity to acoustic cues in music is associated with reading in Chinese, a morphosyllabic language. The present study aimed to answer this question by measuring music (i.e., musical metric perception and pitch discrimination), language (i.e., phonological awareness, lexical tone sensitivity), and reading abilities (i.e., word recognition) among 54 third-grade Chinese–English bilingual children. After controlling for age and non-verbal intelligence, we found that both musical metric perception and pitch discrimination accounted for unique variance of Chinese phonological awareness while pitch discrimination rather than musical metric perception predicted Chinese lexical tone sensitivity. More importantly, neither musical metric perception nor pitch discrimination was associated with Chinese reading. As for English, musical metric perception and pitch discrimination were correlated with both English phonological awareness and English reading. Furthermore, sensitivity to acoustic cues in music was associated with English reading through the mediation of English phonological awareness. The current findings indicate that the association between sensitivity to acoustic cues in music and reading may be modulated by writing systems. In Chinese, the mapping between orthography and phonology is not as transparent as in alphabetic languages such as English. Thus, this opaque mapping may alter the auditory perceptual sensitivity in music to Chinese reading. PMID:29170647

Cognitive Functioning in Children with Learning Problems

ERIC Educational Resources Information Center

Schwenck, Christina; Dummert, Friederike; Endlich, Darius; Schneider, Wolfgang

2015-01-01

Several cognitive deficits associated with reading and mathematics problems have been identified. However, only few studies assessed the impact of these variables in children with combined problems in reading and arithmetics, and none of these studies included children with low IQ. This longitudinal study was designed to assess the impact of…

The importance of correctly characterising the English spelling system when devising and evaluating methods of reading instruction: Comment on Taylor, Davis, and Rastle (2017).

PubMed

Bowers, Jeffrey S; Bowers, Peter N

2018-05-01

Taylor, Davis, and Rastle employed an artificial language learning paradigm to compare phonics and meaning-based approaches to reading instruction. Adults were taught consonant, vowel, and consonant (CVC) words composed of novel letters when the mappings between letters and sounds were completely systematic and the mappings between letters and meaning were completely arbitrary. At test, performance on naming tasks was better following training that emphasised the phonological rather than the semantic mappings, whereas performance on semantic tasks was similar in the two conditions. The authors concluded that these findings support phonics for early reading instruction in English. However, in our view, these conclusions are not justified given that the artificial language mischaracterised both the phonological and semantic mappings in English. Furthermore, the way participants studied the arbitrary letter-meaning correspondences bears little relation to meaning-based strategies used in schools. To compare phonics with meaning-based instruction it must be determined whether phonics is better than alternative forms of instruction that fully exploit the regularities within the semantic route. This is rarely assessed because of a widespread and mistaken assumption that underpins so much basic and applied research, namely, that the main function of spellings is to represent sounds.

Computer Game Play as an Imaginary Stage for Reading: Implicit Spatial Effects of Computer Games Embedded in Hard Copy Books

ERIC Educational Resources Information Center

Smith, Glenn Gordon

2012-01-01

This study compared books with embedded computer games (via pentop computers with microdot paper and audio feedback) with regular books with maps, in terms of fifth graders' comprehension and retention of spatial details from stories. One group read a story in hard copy with embedded computer games, the other group read it in regular book format…

Does testing with feedback improve adult spelling skills relative to copying and reading?

PubMed

Pan, Steven C; Rubin, Benjamin R; Rickard, Timothy C

2015-12-01

We examined testing's ability to enhance adult spelling acquisition, relative to copying and reading. Across 3 experiments in which testing with feedback was compared with copying, the spelling improvement after testing matched that following the same amount of time spent copying. A potent testing advantage, however, was observed for spelling words free-recalled. In the fourth experiment, a large testing advantage for both word free recall and spelling was observed, versus reading. Subjects also generally preferred testing and rated it as more effective than copying or reading. The equivalent performance of testing and copying for spelling contrasts with prior work involving children and suggests that retrieval practice may not be the only effective mechanism for spelling skill acquisition. Rather, we suggest that the critical learning event for spelling is focused study on phoneme-to-grapheme mappings for previously unlearned letter sequences. For adults with extensive spelling expertise, focused study is more automatic during both copying and testing with feedback than for individuals with beginning spelling skills. Reading, however, would not be expected to produce efficient focused study of phoneme-to-grapheme mappings, regardless of expertise level. Overall, adult spelling skill acquisition benefits both from testing and copying, and substantially less from reading. (c) 2015 APA, all rights reserved).

Consequences of Childhood Reading Difficulties and Behaviour Problems for Educational Achievement and Employment in Early Adulthood

ERIC Educational Resources Information Center

Smart, Diana; Youssef, George J.; Sanson, Ann; Prior, Margot; Toumbourou, John W.; Olsson, Craig A.

2017-01-01

Background: Reading difficulties (RDs) and behaviour problems (BPs) are two common childhood problems that have a high degree of stability and often negatively affect well-being in both the short and longer terms. Aims: The study aimed to shed light on the unique and joint consequences of these two childhood problems for educational and…

The impact of early behavior disturbances on academic achievement in high school.

PubMed

Breslau, Joshua; Miller, Elizabeth; Breslau, Naomi; Bohnert, Kipling; Lucia, Victoria; Schweitzer, Julie

2009-06-01

Previous research has indicated that childhood behavioral disturbances predict lower scores on academic tests and curtail educational attainment. It is unknown which types of childhood behavioral problems are most likely to predict these outcomes. An ethnically diverse cohort was assessed at 6 years of age for behavioral problems and IQ and at 17 years of age for academic achievement in math and reading. Of the original cohort of 823 children, 693 (84%) had complete data. Multiple regressions were used to estimate associations of attention and internalizing and externalizing problems at age 6 and with math and reading achievement at age 17, adjusting for IQ and indicators of family socioeconomic status. Adjusting for IQ, inner-city community, and maternal education and marital status, teacher ratings of attention, internalizing behavior, and externalizing problems at age 6 significantly predict math and reading achievement at age 17. When types of problems are examined simultaneously, attention problems predict math and reading achievement with little attenuation, whereas the influence of externalizing and internalizing problems is materially reduced and not significant. Interventions that target attention problems at school entry should be tested as a potential avenue for improving educational achievement.

The long-term significance of teacher-rated hyperactivity and reading ability in childhood: findings from two longitudinal studies.

PubMed

McGee, Rob; Prior, Margot; Willams, Sheila; Smart, Diana; Sanson, Anne

2002-11-01

The aims of this study were twofold: first, to examine behavioural and academic outcomes of children with hyperactivity, using data from two longitudinal studies; and second, to examine comparable psychosocial outcomes for children with early reading difficulties. Measures of teacher-rated persistent hyperactivity, and reading ability obtained during early primary school were available for children from the Australian Temperament Project and the Dunedin Multidisciplinary Health and Development Study. Both samples were followed up to assess behavioural and academic outcomes during the adolescent and early adult years. Family background, antisocial behaviour and literacy were controlled in the first set of analyses to examine the influence of early hyperactivity. There were strong linear relationships between early hyperactivity and later adverse outcomes. Adjustment for other childhood variables suggested that early hyperactivity was associated with continuing school difficulties, problems with attention and poor reading in adolescence. Early reading difficulties, after controlling for early hyperactivity, predicted continuing reading problems in high school and leaving school with no qualifications. The findings suggest that there are dual pathways from early inattentive behaviours to later inattention and reading problems, and from early reading difficulties to substantial impairments in later academic outcomes.

Assessment of the precision of smart phones and tablets for measurement of planar orientations: A case study

NASA Astrophysics Data System (ADS)

Novakova, Lucie; Pavlis, Terry L.

2017-04-01

Although paper and pencil approaches to geological mapping continue, digital mapping tools are being increasing implemented in field geology. Of particular note is the use of an electronic compass/inclinometer built into tablets and smartphones for obtaining orientation data where an important question is the reliability of these digital devices relative to conventional, analogue compass/inclinometers. This paper deals with this question through detailed tests of two android devices: an Honor 3C smartphone and a Lenovo B8080-F tablet. In order to evaluate potential electronic noise effects the devices were tested in two modes, standard and airplane. Over 14,000 readings from the sensors were collected to evaluate the stability of the sensor's readings and showed that the magnetic sensor in the tablet was unacceptably unstable. Seven geological compass applications were installed on the Honor 3C smartphone and tested against the analogue Freiberg geological compass in a field experiment. During the experiment 25 fractures varying in azimuth and dip were measured using both devices. A high level of disagreement was observed with discrepancies as high as 80° with azimuthal errors dominant. Analysis of the time series in the data suggest the source of the problem was instability in the magnetic sensor for the smartphone, despite the fact the device passed the initial stability test. Although only two devices were studied these data indicate care must be taken to evaluate compass accuracy on these devices.

The Efficacy of Phonological Awareness Training with First-Grade Students Who Have Behavior Problems and Reading Difficulties.

ERIC Educational Resources Information Center

Lane, Kathleen L.; O'Shaughnessy, Tam E.; Lambros, Katina M.; Gresham, Frank M.; Beebe-Frankenberger, Margaret E.

2001-01-01

This study examined the effectiveness of a phonological awareness reading intervention with seven first-graders at risk for conduct and attention problems. Findings support the efficacy of the program but suggest the intervention may not have been of sufficient intensity and duration to produce lasting changes and produce beginning reading skill…

Reading and the Emotionally Handicapped Child. Highlights of a Special Study Institute (Poughkeepsie, New York, October 5-7, 1970).

ERIC Educational Resources Information Center

Duchess County Board of Cooperative Educational Services, NY.

The conference proceedings include seven papers dealing with reading problems of emotionally disturbed children. Emotional resistance to reading is discussed by Jules Abrams, a psychiatrist. The purposes of testing and the problem of labeling are touched upon by Clifford Kolson. Some practical suggestions of classroom techniques for combining a…

Study of Thai Language Oral Reading Problems for Students with Down Syndrome: Grade Range 1

ERIC Educational Resources Information Center

Kaewchote, Nantawan; Chongchaikit, Maturos

2011-01-01

The purpose of the study was to explore the Thai Language Oral Reading Problems of students with Down syndrome, Grade Range1 at Watnonsaparam School, Saraburi Thailand in favor of Web Quest Lessons Development Enhancing Oral Reading Skills of Down syndrome Students. The research instruments were the 2 observation forms on Thai Language Reading…

The Administrative Problems Involved in Executing Clinical Recommendations for the Treatment of Severe Reading Disorders Within an Ongoing Educational System.

ERIC Educational Resources Information Center

Schiffman, Gilbert B.

Developing a program of treatment for dyslexic readers involves four major problems: (1) definition of the reading isability, (2) administrative and educational inertia, (3) organization of the treatment program, and (4) the need for evaluatio and research. There is great disagreement over definitions of reading disabilities, yet an effective…

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.

Enhanced expression of codon optimized Mycobacterium avium subsp. paratuberculosis antigens in Lactobacillus salivarius.

PubMed

Johnston, Christopher D; Bannantine, John P; Govender, Rodney; Endersen, Lorraine; Pletzer, Daniel; Weingart, Helge; Coffey, Aidan; O'Mahony, Jim; Sleator, Roy D

2014-01-01

It is well documented that open reading frames containing high GC content show poor expression in A+T rich hosts. Specifically, G+C-rich codon usage is a limiting factor in heterologous expression of Mycobacterium avium subsp. paratuberculosis (MAP) proteins using Lactobacillus salivarius. However, re-engineering opening reading frames through synonymous substitutions can offset codon bias and greatly enhance MAP protein production in this host. In this report, we demonstrate that codon-usage manipulation of MAP2121c can enhance the heterologous expression of the major membrane protein (MMP), analogous to the form in which it is produced natively by MAP bacilli. When heterologously over-expressed, antigenic determinants were preserved in synthetic MMP proteins as shown by monoclonal antibody mediated ELISA. Moreover, MMP is a membrane protein in MAP, which is also targeted to the cellular surface of recombinant L. salivarius at levels comparable to MAP. Additionally, we previously engineered MAP3733c (encoding MptD) and show herein that MptD displays the tendency to associate with the cytoplasmic membrane boundary under confocal microscopy and the intracellularly accumulated protein selectively adheres to the MptD-specific bacteriophage fMptD. This work demonstrates there is potential for L. salivarius as a viable antigen delivery vehicle for MAP, which may provide an effective mucosal vaccine against Johne's disease.

A Review of Story Mapping Instruction for Secondary Students with LD

ERIC Educational Resources Information Center

Boon, Richard T.; Paal, Michael; Hintz, Anna-Maria; Cornelius-Freyre, Melissa

2015-01-01

The purpose of this article is to provide a review on the effectiveness of story mapping to improve the reading comprehension skills of middle and high school (Grades 6-12) students with learning disabilities (LD). An extensive review of the special education research-base revealed twelve (N = 12) story mapping intervention studies that met our…

Automatic Scaffolding and Measurement of Concept Mapping for EFL Students to Write Summaries

ERIC Educational Resources Information Center

Yang, Yu-Fen

2015-01-01

An incorrect concept map may obstruct a student's comprehension when writing summaries if they are unable to grasp key concepts when reading texts. The purpose of this study was to investigate the effects of automatic scaffolding and measurement of three-layer concept maps on improving university students' writing summaries. The automatic…

Concept Maps: An Alternative Methodology to Assess Young Children

ERIC Educational Resources Information Center

Atiles, Julia T.; Dominique-Maikell, Nikole; McKean, Kathleen

2014-01-01

The authors investigated the utility and efficacy of using concepts maps as a research tool to assess young children. Pre- and post- concept maps have been used as an assessment and evaluation tool with teachers and with older students, typically children who can read and write; this article summarizes an investigation into the utility of using…

Growth trajectories of early aggression, overactivity, and inattention: Relations to second-grade reading.

PubMed

Gray, Sarah A O; Carter, Alice S; Briggs-Gowan, Margaret J; Jones, Stephanie M; Wagmiller, Robert L

2014-09-01

The link between behavior problems and low academic achievement is well established, but few studies have examined longitudinal relations between early externalizing behaviors before school entry and low academic achievement following transition to formal schooling. Early inattention has been particularly overlooked, despite strong associations between inattention and reading difficulties later in development. Trajectories of infant and toddler aggression, overactivity, and inattention, developed from parent reports about 1- to 3-year-old children, were examined as predictors of direct assessments of 2nd-grade reading in an at-risk epidemiological study subsample (N = 359). Reports of inattentive and overactive behaviors at ages 1-3 years and changes in inattention through toddlerhood predicted reading achievement in 2nd grade. A parallel process model suggested that the effects of early inattention on reading appear to be most robust. Findings underscore the contribution of social-emotional development to school readiness and the importance of early identification of children with externalizing problems, as early interventions designed to reduce externalizing problems may improve later reading skills.

Growth Trajectories of Early Aggression, Overactivity, and Inattention: Relations to Second Grade Reading

PubMed Central

Gray, Sarah A. O.; Carter, Alice S.; Briggs-Gowan, Margaret J.; Jones, Stephanie M.; Wagmiller, Robert L.

2015-01-01

The link between behavior problems and low academic achievement is well established, but few studies have examined longitudinal relations between early externalizing behaviors before school entry and low academic achievement following transition to formal schooling. Early inattention has been particularly overlooked, despite strong associations between inattention and reading difficulties later in development. Trajectories of infant/toddler aggression, overactivity, and inattention, developed from parent reports about 1- to 3-year-old children, were examined as predictors of direct assessments of second grade reading in an at-risk epidemiological study subsample (N = 359). Reports of inattentive and overactive behaviors at age 1-to-3 years and changes in inattention through toddlerhood predicted reading achievement in second grade. A parallel process model suggested that the effects of early inattention on reading appear to be most robust. Findings underscore the contribution of social-emotional development to school readiness and the importance of early identification of children with externalizing problems, as early interventions designed to reduce externalizing problems may improve later reading skills. PMID:25046126

Amphetamine primes motivation to gamble and gambling-related semantic networks in problem gamblers.

PubMed

Zack, Martin; Poulos, Constantine X

2004-01-01

Previous research suggests that gambling can induce effects that closely resemble a psychostimulant drug effect. Modest doses of addictive drugs can prime motivation for drugs with similar properties. Together, these findings imply that a dose of a psychostimulant drug could prime motivation to gamble in problem gamblers. This study assessed priming effects of oral D-amphetamine (AMPH) (30 mg) in a within-subject, counter-balanced, placebo-controlled design in problem gamblers (n=10), comorbid gamblerdrinkers (n=6), problem drinkers (n=8), and healthy controls (n=12). Modified visual analog scales assessed addictive motivation and subjective effects. A modified rapid reading task assessed pharmacological activation of words from motivationally relevant and irrelevant semantic domains (Gambling, Alcohol, Positive Affect, Negative Affect, Neutral). AMPH increased self-reported motivation for gambling in problem gamblers. Severity of problem gambling predicted positive subjective effects of AMPH and motivation to gamble under the drug. There was little evidence that AMPH directly primed motivation for alcohol in problem drinkers. On the reading task, AMPH produced undifferentiated improvement in reading speed to all word classes in Nongamblers. By contrast, in the two problem gambler groups, AMPH improved reading speed to Gambling words while profoundly slowing reading speed to motivationally irrelevant Neutral words. The latter finding was interpreted as directly congruent with models, which contend that priming of addictive motivation involves a linked suppression of motivationally irrelevant stimuli. This study provides experimental evidence that psychostimulant-like neurochemical activation is an important component of gambling addiction.

Early Identification of Reading Comprehension Difficulties

ERIC Educational Resources Information Center

Catts, Hugh W.; Nielsen, Diane Corcoran; Bridges, Mindy Sittner; Liu, Yi-Syuan

2016-01-01

Most research on early identification of reading disabilities has focused on word reading problems and little attention has been given to reading comprehension difficulties. In this study, we investigated whether measures of language ability and/or response to language intervention in kindergarten uniquely predicted reading comprehension…

Theme: Parents and Reading.

ERIC Educational Resources Information Center

Jund, Suzanne, Ed.

1977-01-01

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

Influence of Reading Attitude on Reading Achievement: A Test of the Temporal-Interaction Model

ERIC Educational Resources Information Center

Martinez, Rebecca S.; Aricak, O. Tolga; Jewell, Jeremy

2008-01-01

Despite widespread efforts to prevent reading problems and an abundance of research about best practices in remediating reading skills deficits, reading continues to be exceptionally difficult for many students. Researchers have become interested in investigating the degree to which affective factors such as reading attitude relates to reading…

Military Reading Assessment: What Theory Tells Us.

ERIC Educational Resources Information Center

Oxford-Carpenter, Rebecca L.; Schultz-Shiner, Linda J.

This paper addresses practical Army problems in reading assessment from a theory base reflecting the most recent research on reading comprehension. Military and occupational research shows that reading proficiency is related to job performance. Reading assessment is a key issue in the Army due to changes in the reading ability levels of the Army…

"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…

Specific problems in visual cognition of dyslexic readers: Face discrimination deficits predict dyslexia over and above discrimination of scrambled faces and novel objects.

PubMed

Sigurdardottir, Heida Maria; Fridriksdottir, Liv Elisabet; Gudjonsdottir, Sigridur; Kristjánsson, Árni

2018-06-01

Evidence of interdependencies of face and word processing mechanisms suggest possible links between reading problems and abnormal face processing. In two experiments we assessed such high-level visual deficits in people with a history of reading problems. Experiment 1 showed that people who were worse at face matching had greater reading problems. In experiment 2, matched dyslexic and typical readers were tested, and difficulties with face matching were consistently found to predict dyslexia over and above both novel-object matching as well as matching noise patterns that shared low-level visual properties with faces. Furthermore, ADHD measures could not account for face matching problems. We speculate that reading difficulties in dyslexia are partially caused by specific deficits in high-level visual processing, in particular for visual object categories such as faces and words with which people have extensive experience. Copyright © 2018 Elsevier B.V. All rights reserved.

RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries.

PubMed

Habegger, Lukas; Sboner, Andrea; Gianoulis, Tara A; Rozowsky, Joel; Agarwal, Ashish; Snyder, Michael; Gerstein, Mark

2011-01-15

The advent of next-generation sequencing for functional genomics has given rise to quantities of sequence information that are often so large that they are difficult to handle. Moreover, sequence reads from a specific individual can contain sufficient information to potentially identify and genetically characterize that person, raising privacy concerns. In order to address these issues, we have developed the Mapped Read Format (MRF), a compact data summary format for both short and long read alignments that enables the anonymization of confidential sequence information, while allowing one to still carry out many functional genomics studies. We have developed a suite of tools (RSEQtools) that use this format for the analysis of RNA-Seq experiments. These tools consist of a set of modules that perform common tasks such as calculating gene expression values, generating signal tracks of mapped reads and segmenting that signal into actively transcribed regions. Moreover, the tools can readily be used to build customizable RNA-Seq workflows. In addition to the anonymization afforded by MRF, this format also facilitates the decoupling of the alignment of reads from downstream analyses. RSEQtools is implemented in C and the source code is available at http://rseqtools.gersteinlab.org/.

Investigation of Antarctic Marine Metazoan Biodiversity Through Metagenomic Analysis of Environmental DNA

NASA Astrophysics Data System (ADS)

Cowart, D. A.; Cheng, C. C.; Murphy, K.

2016-02-01

Environmental DNA (eDNA), or DNA extracted from environmental collections, is frequently used to gauge biodiversity and identify the presence of rare or invasive species within a habitat. Previous studies have demonstrated that compared to traditional surveying methods, high-throughput sequencing of eDNA can provide increased detection sensitivity of aquatic taxa, holding promise for various conservation applications. To determine the potential of eDNA for assessing biodiversity of Antarctic marine metazoan communities, we have extracted eDNA from seawater sampled from four regions near Palmer Station in West Antarctic Peninsula. Metagenomic sequencing of the eDNA was performed on Illumina HiSeq2500, and produced 325 million quality-processed reads. Preliminary read mapping for two regions, Gerlache Strait and Bismarck Strait, identified approximately 4% of reads mapping to eukaryotes for each region, with >50% of the those reads mapping to metazoan animals. Key groups investigated include the nototheniidae family of Antarctic fishes, to which 0.2 and 0.8 % of the metazoan reads were assigned for each region respectively. The presence of the recently invading lithodidae king crabs was also detected at both regions. Additionally, to estimate the persistence of eDNA in polar seawater, a rate of eDNA decay will be quantified from seawater samples collected over 20 days from Antarctic fish holding tanks and held at ambient Antarctic water temperatures. The ability to detect animal signatures from eDNA, as well as the quantification of eDNA decay over time, could provide another method for reliable monitoring of polar habitats at various spatial and temporal scales.

Identifying high-functioning dyslexics: is self-report of early reading problems enough?

PubMed

Deacon, S Hélène; Cook, Kathryn; Parrila, Rauno

2012-07-01

We used a questionnaire to identify university students with self-reported difficulties in reading acquisition during elementary school (self-report; n=31). The performance of the self-report group on standardized measures of word and non-word reading and fluency, passage comprehension and reading rate, and phonological awareness was compared to that of two other groups of university students: one with a recent diagnosis (diagnosed; n=20) and one with no self-reported reading acquisition problems (comparison group; n=33). The comparison group outperformed both groups with a history of reading difficulties (self-report and diagnosed) on almost all measures. The self-report and diagnosed groups performed similarly on most tasks, with the exception of untimed reading comprehension (better performance for diagnosed) and reading rate (better performance for self-report). The two recruitment methods likely sample from the same underlying population but identify individuals with different adaptive strategies.

Is Poor Frequency Modulation Detection Linked to Literacy Problems? A Comparison of Specific Reading Disability and Mild to Moderate Sensorineural Hearing Loss

ERIC Educational Resources Information Center

Halliday, L. F.; Bishop, D. V. M.

2006-01-01

Specific reading disability (SRD) is now widely recognised as often being caused by phonological processing problems, affecting analysis of spoken as well as written language. According to one theoretical account, these phonological problems are due to low-level problems in auditory perception of dynamic acoustic cues. Evidence for this has come…

Red Cloud Reading Test: American Indian Form of the Test of Individual Needs in Reading, a Competency Based Test of Reading Skills [and] Instructor's Manual.

ERIC Educational Resources Information Center

Gilliland, Hap

The oral Red Cloud Reading Test provides a complete analysis of reading level and skills for American Indian students in grades 1-7 or for high school and adult students reading at or below high school levels. The test determines the basic and recreational reading levels, identifies reading problems, determines reading speeds, and analyzes the…

Evaluation of a Reading Comprehension Strategy Package to Improve Reading Comprehension of Adult College Students with Acquired Brain Injuries

ERIC Educational Resources Information Center

Griffiths, Gina G.

2013-01-01

Adults with mild to moderate acquired brain injury (ABI) often pursue post-secondary or professional education after their injuries in order to enter or re-enter the job market. An increasing number of these adults report problems with reading-to-learn. The problem is particularly concerning given the growing population of adult survivors of ABI.…

Developing a Problem-Based Course Based on Needs Analysis to Enhance English Reading Ability of Thai Undergraduate Students

ERIC Educational Resources Information Center

Bosuwon, Takwa; Woodrow, Lindy

2009-01-01

This paper reports on a needs analysis underlying a proposed business English reading course using a problem-based learning approach designed to enhance English reading abilities of Thai undergraduate students. As part of a work in progress, the needs analysis survey was done prior to the course design with the major stakeholders in business and…

Dynamics of Strategies-Based Language Instruction: A Study of Reading Comprehension and Problem Solving Abilities via Structural Equation Modeling

ERIC Educational Resources Information Center

Ghahari, Shima; Basanjideh, Mahin

2015-01-01

The study aimed at exploring the psychological as well as educational outcomes of strategies awareness and use. We set out to examine the effect of reading strategic investment on language achievement and problem solving ability (PSA). The participating EFL learners were heterogeneous in terms of reading instruction; two of the intact groups had…

Are families of children with reading difficulties at risk for immune disorders and nonrighthandedness?

PubMed

Crawford, S G; Kaplan, B J; Kinsbourne, M

1994-06-01

This study used questionnaire data to examine immune disorders and nonrighthandedness in the families of children enrolled in a learning disabilities school and children attending regular classrooms in public schools. Groups were organized according to their performance on a standardized test of reading comprehension to avoid overlap. In total, 468 questionnaires were returned, from which we were able to derive a final sample of carefully matched subjects: 55 subjects undergoing remediation for reading problems and 55 age- and sex-matched control subjects. The results indicated that children with reading problems and their families more frequently suffered from some immune and autoimmune disorders, particularly those involving the gastrointestinal tract and the thyroid gland. In addition, symptoms of attention deficit hyperactivity disorder were associated with Crohn's disease and migraine headache in the families. There was no evidence of an elevated prevalence of nonrighthandedness in the children with reading problems and their families.

Word Reading Aloud Skills: Their Positive Redefinition through Ageing

ERIC Educational Resources Information Center

Chapleau, Marianne; Wilson, Maximiliano A.; Potvin, Karel; Harvey-Langton, Alexandra; Montembeault, Maxime; Brambati, Simona M.

2017-01-01

Background: Successful reading can be achieved by means of two different procedures: sub-word processes for the pronunciation of words without semantics or pseudowords (PW) and whole-word processes that recruit word-specific information regarding the pronunciation of words with atypical orthography-to-phonology mappings (exception words, EW).…

Mapping a Rhizomatic Ecology of Reading

ERIC Educational Resources Information Center

Cole, Leslie

2009-01-01

Readers, texts, and readings can take unpredictable and seemingly tangential detours that educators might find undesirable and difficult to control. Readers can stray far from the text to seek out desired meanings. In the same way, media outlets can reappropriate favorite literary fictions in ways that can perturb educators and readers alike.…

Phase II Evaluation of Clinical Coding Schemes

PubMed Central

Campbell, James R.; Carpenter, Paul; Sneiderman, Charles; Cohn, Simon; Chute, Christopher G.; Warren, Judith

1997-01-01

Abstract Objective: To compare three potential sources of controlled clinical terminology (READ codes version 3.1, SNOMED International, and Unified Medical Language System (UMLS) version 1.6) relative to attributes of completeness, clinical taxonomy, administrative mapping, term definitions and clarity (duplicate coding rate). Methods: The authors assembled 1929 source concept records from a variety of clinical information taken from four medical centers across the United States. The source data included medical as well as ample nursing terminology. The source records were coded in each scheme by an investigator and checked by the coding scheme owner. The codings were then scored by an independent panel of clinicians for acceptability. Codes were checked for definitions provided with the scheme. Codes for a random sample of source records were analyzed by an investigator for “parent” and “child” codes within the scheme. Parent and child pairs were scored by an independent panel of medical informatics specialists for clinical acceptability. Administrative and billing code mapping from the published scheme were reviewed for all coded records and analyzed by independent reviewers for accuracy. The investigator for each scheme exhaustively searched a sample of coded records for duplications. Results: SNOMED was judged to be significantly more complete in coding the source material than the other schemes (SNOMED* 70%; READ 57%; UMLS 50%; *p <.00001). SNOMED also had a richer clinical taxonomy judged by the number of acceptable first-degree relatives per coded concept (SNOMED* 4.56; UMLS 3.17; READ 2.14, *p <.005). Only the UMLS provided any definitions; these were found for 49% of records which had a coding assignment. READ and UMLS had better administrative mappings (composite score: READ* 40.6%; UMLS* 36.1%; SNOMED 20.7%, *p <. 00001), and SNOMED had substantially more duplications of coding assignments (duplication rate: READ 0%; UMLS 4.2%; SNOMED* 13.9%, *p <. 004) associated with a loss of clarity. Conclusion: No major terminology source can lay claim to being the ideal resource for a computer-based patient record. However, based upon this analysis of releases for April 1995, SNOMED International is considerably more complete, has a compositional nature and a richer taxonomy. It suffers from less clarity, resulting from a lack of syntax and evolutionary changes in its coding scheme. READ has greater clarity and better mapping to administrative schemes (ICD-10 and OPCS-4), is rapidly changing and is less complete. UMLS is a rich lexical resource, with mappings to many source vocabularies. It provides definitions for many of its terms. However, due to the varying granularities and purposes of its source schemes, it has limitations for representation of clinical concepts within a computer-based patient record. PMID:9147343

Reading as Seduction: The Censorship Problem and the Educational Value of Literature.

ERIC Educational Resources Information Center

Bogdan, Deanne

1992-01-01

Uses examples from mass culture to show the relationship of the continuum theory and the gap theory to the connection between the censorship problem and the educational value of literary reading. (SR)

Repetitive DNA and Plant Domestication: Variation in Copy Number and Proximity to Genes of LTR-Retrotransposons among Wild and Cultivated Sunflower (Helianthus annuus) Genotypes

PubMed Central

Mascagni, Flavia; Barghini, Elena; Giordani, Tommaso; Rieseberg, Loren H.; Cavallini, Andrea; Natali, Lucia

2015-01-01

The sunflower (Helianthus annuus) genome contains a very large proportion of transposable elements, especially long terminal repeat retrotransposons. However, knowledge on the retrotransposon-related variability within this species is still limited. We used next-generation sequencing (NGS) technologies to perform a quantitative and qualitative survey of intraspecific variation of the retrotransposon fraction of the genome across 15 genotypes—7 wild accessions and 8 cultivars—of H. annuus. By mapping the Illumina reads of the 15 genotypes onto a library of sunflower long terminal repeat retrotransposons, we observed considerable variability in redundancy among genotypes, at both superfamily and family levels. In another analysis, we mapped Illumina paired reads to two sets of sequences, that is, long terminal repeat retrotransposons and protein-encoding sequences, and evaluated the extent of retrotransposon proximity to genes in the sunflower genome by counting the number of paired reads in which one read mapped to a retrotransposon and the other to a gene. Large variability among genotypes was also ascertained for retrotransposon proximity to genes. Both long terminal repeat retrotransposon redundancy and proximity to genes varied among retrotransposon families and also between cultivated and wild genotypes. Such differences are discussed in relation to the possible role of long terminal repeat retrotransposons in the domestication of sunflower. PMID:26608057

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.

Beyond the visual word form area: the orthography-semantics interface in spelling and reading.

PubMed

Purcell, Jeremy J; Shea, Jennifer; Rapp, Brenda

2014-01-01

Lexical orthographic information provides the basis for recovering the meanings of words in reading and for generating correct word spellings in writing. Research has provided evidence that an area of the left ventral temporal cortex, a subregion of what is often referred to as the visual word form area (VWFA), plays a significant role specifically in lexical orthographic processing. The current investigation goes beyond this previous work by examining the neurotopography of the interface of lexical orthography with semantics. We apply a novel lesion mapping approach with three individuals with acquired dysgraphia and dyslexia who suffered lesions to left ventral temporal cortex. To map cognitive processes to their neural substrates, this lesion mapping approach applies similar logical constraints to those used in cognitive neuropsychological research. Using this approach, this investigation: (a) identifies a region anterior to the VWFA that is important in the interface of orthographic information with semantics for reading and spelling; (b) determines that, within this orthography-semantics interface region (OSIR), access to orthography from semantics (spelling) is topographically distinct from access to semantics from orthography (reading); (c) provides evidence that, within this region, there is modality-specific access to and from lexical semantics for both spoken and written modalities, in both word production and comprehension. Overall, this study contributes to our understanding of the neural architecture at the lexical orthography-semantic-phonological interface within left ventral temporal cortex.

Beyond the VWFA: The orthography-semantics interface in spelling and reading

PubMed Central

Purcell, Jeremy J.; Shea, Jennifer; Rapp, Brenda

2014-01-01

Lexical orthographic information provides the basis for recovering the meanings of words in reading and for generating correct word spellings in writing. Research has provided evidence that an area of the left ventral temporal cortex, a sub-region of what is often referred to as the Visual Word Form Area (VWFA), plays a significant role specifically in lexical orthographic processing. The current investigation goes beyond this previous work by examining the neurotopography of the interface of lexical orthography with semantics. We apply a novel lesion mapping approach with three individuals with acquired dysgraphia and dyslexia who suffered lesions to left ventral temporal cortex. To map cognitive processes to their neural substrates, this lesion mapping approach applies similar logical constraints as used in cognitive neuropsychological research. Using this approach, this investigation: (1) Identifies a region anterior to the VWFA that is important in the interface of orthographic information with semantics for reading and spelling; (2) Determines that, within this Orthography-Semantics Interface Region (OSIR), access to orthography from semantics (spelling) is topographically distinct from access to semantics from orthography (reading); (3) Provides evidence that, within this region, there is modality-specific access to and from lexical semantics for both spoken and written modalities, in both word production and comprehension. Overall, this study contributes to our understanding of the neural architecture at the lexical orthography-semantic-phonological interface within left ventral temporal cortex. PMID:24833190

An Analysis of the Critical Reading Levels of Pre-Service Turkish and Literature Teachers

ERIC Educational Resources Information Center

Maltepe, Sadet

2016-01-01

Problem Statement: Critical reading refers to individuals' thinking about what they read, assessing what they have read, and using their own judgment about what they have read. In order to teach critical reading skills to students, a teacher is expected to have knowledge about text selection, use of appropriate methods, preparation of functional…

Child-Centered Reading Intervention: See, Talk, Dictate, Read, Write!

ERIC Educational Resources Information Center

Bastug, Muhammet; Demirtas, Gonca

2016-01-01

Poor reading achievement of children in elementary schools has been one of the major concerns in education. The aim of this study is to examine the effectiveness of a child-centered reading intervention in eliminating the reading problems of a student with poor reading achievement. The research was conducted with a student having difficulty in…

Investigating Metacognitive Awareness and Reading Strategy Use of EFL Korean University Students

ERIC Educational Resources Information Center

Hong-Nam, Kay; Page, Larkin

2014-01-01

The metacognitive awareness and reading strategy use by Korean university students in Korea was investigated. The relationships between reading strategy use, self-rated English proficiency, and self-rated reading proficiency were examined. Differences in reading strategy use were also explored by gender and academic classification. Problem-solving…

Silent Reading Fluency Using Underlining: Evidence for an Alternative Method of Assessment

ERIC Educational Resources Information Center

Price, Katherine W.; Meisinger, Elizabeth B.; Louwerse, Max M.; D'Mello, Sidney K.

2012-01-01

Assessing silent reading fluency in classroom environments is challenging. This article reports on a method of assessing silent reading using underlining, an approach that solves many problems other silent reading fluency assessment measures face. This method computationally monitors readers' silent reading fluency by the speed they underline…

Training Aids for Basic Combat Skills: Developing Map-Reading Skills

DTIC Science & Technology

2011-03-01

types of training aids were developed for determining grid coordinates. Each training aid consisted of a set of self-study flashcards . One set of... flashcards contained scaled sections of topological maps and asked the Soldiers to find map features based on grid coordinates or to provide the grid...coordinates for a given map feature. The reverse of each flashcard provided feedback (i.e., correct answers and rationale to help the Soldier

Comprehension by learning-disabled and nondisabled adolescents of personal/social problems presented in text.

PubMed

Williams, J P

1991-01-01

Four groups of 14-year-olds, differing in reading level, learning disability status, and socioeconomic status, read and retold short problem narratives and answered questions. The pattern of reporting components of the problem schema (goal/obstacles/choices) differed for problems presented with or without a statement of the character's priority for action, suggesting that including priorities adds another level of information to the problem text and changes its macrostructure. Even the poorest readers showed this sensitivity to text structure. Three of the four measures of problem representation (idea units recalled, problem-schema components reported, and error rate) reflected overall reading ability. However, the degree to which extraneous information was incorporated into problem representations did not. Learning-disabled students made more importations, and more implausible importations, than did non-disabled students. Moreover, this pattern was associated with poor problem solving. Only proficient readers showed awareness of the source of the information (text or extratext) on which their predictions were based.

Arsenic-Safe Aquifers in Coastal Bangladesh: AN Investigation with Ordinary Kriging Estimation

NASA Astrophysics Data System (ADS)

Hassan, M. M.; Ahamed, R.

2017-10-01

Spatial point pattern is one of the most suitable methods for analysing groundwater arsenic concentrations. Groundwater arsenic poisoning in Bangladesh has been one of the biggest environmental health disasters in recent times. About 85 million people are exposed to arsenic more than 50 μg/L in drinking water. The paper seeks to identify the existing suitable aquifers for arsenic-safe drinking water along with "spatial arsenic discontinuity" using GIS-based spatial geostatistical analysis in a small study site (12.69 km2) in the coastal belt of southwest Bangladesh (Dhopakhali union of Bagerhat district). The relevant spatial data were collected with Geographical Positioning Systems (GPS), arsenic data with field testing kits, tubewell attributes with observation and questionnaire survey. Geostatistics with kriging methods can design water quality monitoring in different aquifers with hydrochemical evaluation by spatial mapping. The paper presents the interpolation of the regional estimates of arsenic data for spatial discontinuity mapping with Ordinary Kriging (OK) method that overcomes the areal bias problem for administrative boundary. This paper also demonstrates the suitability of isopleth maps that is easier to read than choropleth maps. The OK method investigated that around 80 percent of the study site are contaminated following the Bangladesh Drinking Water Standards (BDWS) of 50 μg/L. The study identified a very few scattered "pockets" of arsenic-safe zone at the shallow aquifer.

Coming Full Circle in Standard Setting: A Commentary on Wyse

ERIC Educational Resources Information Center

Skaggs, Gary

2013-01-01

The construct map is a particularly good way to approach instrument development, and this author states that he was delighted to read Adam Wyse's thoughts about how to use construct maps for standard setting. For a number of popular standard-setting methods, Wyse shows how typical feedback to panelists fits within a construct map framework.…

Revisiting Age-of-Acquisition Effects in Spanish Visual Word Recognition: The Role of Item Imageability

ERIC Educational Resources Information Center

Wilson, Maximiliano A.; Cuetos, Fernando; Davies, Rob; Burani, Cristina

2013-01-01

Word age-of-acquisition (AoA) affects reading. The mapping hypothesis predicts AoA effects when input--output mappings are arbitrary. In Spanish, the orthography-to-phonology mappings required for word naming are consistent; therefore, no AoA effects are expected. Nevertheless, AoA effects have been found, motivating the present investigation of…

The Effects of Concept Mapping and Academic Self-Efficacy on Mastery Goals and Reading Comprehension Achievement

ERIC Educational Resources Information Center

Wilson, Andrew; Kim, Wonsun

2016-01-01

The purpose of the study is to investigate the effects of concept mapping on mastery goal orientation and academic self-efficacy in a collaborative learning environment. The current study employed a randomized controlled pretest-posttest group design to examine if learning strategies such as concept mapping can help students with both reading…

Image display device in digital TV

DOEpatents

Choi, Seung Jong [Seoul, KR

2006-07-18

Disclosed is an image display device in a digital TV that is capable of carrying out the conversion into various kinds of resolution by using single bit map data in the digital TV. The image display device includes: a data processing part for executing bit map conversion, compression, restoration and format-conversion for text data; a memory for storing the bit map data obtained according to the bit map conversion and compression in the data processing part and image data inputted from an arbitrary receiving part, the receiving part receiving one of digital image data and analog image data; an image outputting part for reading the image data from the memory; and a display processing part for mixing the image data read from the image outputting part and the bit map data converted in format from the a data processing part. Therefore, the image display device according to the present invention can convert text data in such a manner as to correspond with various resolution, carry out the compression for bit map data, thereby reducing the memory space, and support text data of an HTML format, thereby providing the image with the text data of various shapes.

Altered neural circuits accompany lower performance during narrative comprehension in children with reading difficulties: an fMRI study.

PubMed

Horowitz-Kraus, Tzipi; Buck, Catherine; Dorrmann, Dana

2016-10-01

Narrative comprehension is a linguistic ability that is foundational for future reading ability. The aim of the current study was to examine the neural circuitry of children with reading difficulties (RD) compared to typical readers during a narrative-comprehension task. We hypothesized that due to deficient executive functions, which support narrative comprehension abilities, children with RD would display altered activation and functional connectivity, as well as lower performance on a narrative-comprehension task. Children with RD and typical readers were scanned during a narrative-comprehension task and administered reading behavioral tests. Children with RD scored significantly lower on the narrative-comprehension task than did typical readers. Composite activation maps showed more diffused activation during narrative comprehension in the RD group. Maps comparing the two reading groups showed more activation in the frontal lobes (regions responsible for executive functions), and functional connectivity showed higher global efficiency in children with RD than in typical readers. Global efficiency was negatively correlated with phonological awareness and reading and executive function scores in the entire study group. Children with RD may suffer from narrative-comprehension difficulties due to diffused activation of language areas, as was observed during a narrative-comprehension task. Greater effort in this task may be reflected by the engagement of brain regions related to executive functions and higher functional connectivity or attributed to difficulties in phonological processing and reading and executive functions. Therefore, the accommodation given to children with RD of reading aloud may need to be revised due to the observed difficulty in this domain.

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

Off-site smartphone reading of CT images for patients with inconclusive diagnoses of appendicitis from on-call radiologists.

PubMed

Seong, Nak Jong; Kim, Bohyoung; Lee, Sungmin; Park, Hee Sun; Kim, Hyuk Jung; Woo, Hyunsik; Kang, Heung-Sik; Lee, Kyoung Ho

2014-07-01

The purpose of this study was to simulate a mobile consultation in patients with inconclusive diagnosis of appendicitis made by on-call radiologists, as well as to measure the diagnostic confidence and performance of the mobile consultation. Two off-site abdominal radiologists interpreted the CT images from 68 patients (including 29 patients with confirmed appendicitis) on a smart-phone for whom the preliminary CT reports by 25 in-house on-call radiologists were inconclusive. The smartphone readings were compared with the preliminary reports by on-call radiologists and with the original final reports by in-house abdominal radiologists. Heat maps, kappa statistics, Wilcoxon signed-rank tests, and ROC curves were used for data analysis. The heat maps and kappa statistics showed that the smartphone readings were more similar to the final reports than to the preliminary reports. In diagnosing or ruling out appendicitis, the smartphone readings were more confident than the preliminary reports (p ≤ 0.01) and did not significantly differ in diagnostic confidence from the final reports (p ≥ 0.19). The AUCs of the smartphone readings (0.91 and 0.92) did not differ significantly from those of the preliminary (0.85) or final (0.97) reports (p ≥ 0.09). With the given study sample, the diagnostic performance of the off-site smartphone readings did not differ significantly from that of the in-house preliminary reports. However, the smartphone readings provided higher diagnostic confidence than the preliminary reports.

MetaMap: An atlas of metatranscriptomic reads in human disease-related RNA-seq data.

PubMed

Simon, L M; Karg, S; Westermann, A J; Engel, M; Elbehery, A H A; Hense, B; Heinig, M; Deng, L; Theis, F J

2018-06-12

With the advent of the age of big data in bioinformatics, large volumes of data and high performance computing power enable researchers to perform re-analyses of publicly available datasets at an unprecedented scale. Ever more studies imply the microbiome in both normal human physiology and a wide range of diseases. RNA sequencing technology (RNA-seq) is commonly used to infer global eukaryotic gene expression patterns under defined conditions, including human disease-related contexts, but its generic nature also enables the detection of microbial and viral transcripts. We developed a bioinformatic pipeline to screen existing human RNA-seq datasets for the presence of microbial and viral reads by re-inspecting the non-human-mapping read fraction. We validated this approach by recapitulating outcomes from 6 independent controlled infection experiments of cell line models and comparison with an alternative metatranscriptomic mapping strategy. We then applied the pipeline to close to 150 terabytes of publicly available raw RNA-seq data from >17,000 samples from >400 studies relevant to human disease using state-of-the-art high performance computing systems. The resulting data of this large-scale re-analysis are made available in the presented MetaMap resource. Our results demonstrate that common human RNA-seq data, including those archived in public repositories, might contain valuable information to correlate microbial and viral detection patterns with diverse diseases. The presented MetaMap database thus provides a rich resource for hypothesis generation towards the role of the microbiome in human disease. Additionally, codes to process new datasets and perform statistical analyses are made available at https://github.com/theislab/MetaMap.

Development and testing of a tool for assessing and resolving medication-related problems in older adults in an ambulatory care setting: the individualized medication assessment and planning (iMAP) tool.

PubMed

Crisp, Ginny D; Burkhart, Jena Ivey; Esserman, Denise A; Weinberger, Morris; Roth, Mary T

2011-12-01

Medication is one of the most important interventions for improving the health of older adults, yet it has great potential for causing harm. Clinical pharmacists are well positioned to engage in medication assessment and planning. The Individualized Medication Assessment and Planning (iMAP) tool was developed to aid clinical pharmacists in documenting medication-related problems (MRPs) and associated recommendations. The purpose of our study was to assess the reliability and usability of the iMAP tool in classifying MRPs and associated recommendations in older adults in the ambulatory care setting. Three cases, representative of older adults seen in an outpatient setting, were developed. Pilot testing was conducted and a "gold standard" key developed. Eight eligible pharmacists consented to participate in the study. They were instructed to read each case, make an assessment of MRPs, formulate a plan, and document the information using the iMAP tool. Inter-rater reliability was assessed for each case, comparing the pharmacists' identified MRPs and recommendations to the gold standard. Consistency of categorization across reviewers was assessed using the κ statistic or percent agreement. The mean κ across the 8 pharmacists in classifying MRPs compared with the gold standard was 0.74 (range, 0.54-1.00) for case 1 and 0.68 (range, 0.36-1.00) for case 2, indicating substantial agreement. For case 3, percent agreement was 63% (range, 40%-100%). The mean κ across the 8 pharmacists when classifying recommendations compared with the gold standard was 0.87 (range, 0.58-1.00) for case 1 and 0.88 (range, 0.75-1.00) for case 2, indicating almost perfect agreement. For case 3, percent agreement was 68% (range, 40%-100%). Clinical pharmacists found the iMAP tool easy to use. The iMAP tool provides a reliable and standardized approach for clinical pharmacists to use in the ambulatory care setting to classify MRPs and associated recommendations. Future studies will explore the predictive validity of the tool on clinical outcomes such as health care utilization. Copyright © 2011 Elsevier HS Journals, Inc. All rights reserved.

Factors Influencing Filipino Children's Solutions to Addition and Subtraction Word Problems

ERIC Educational Resources Information Center

Bautista, Debbie; Mitchelmore, Michael; Mulligan, Joanne

2009-01-01

Young Filipino children are expected to solve mathematical word problems in English, which is not their mother tongue. Because of this, it is often assumed that Filipino children have difficulties in solving problems because they cannot read or comprehend what they have read. This study tested this assumption by determining whether presenting word…

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.

Match the Style of Instruction to the Style of Reading

ERIC Educational Resources Information Center

Carbo, Marie

2009-01-01

Many reading problems are caused by using the wrong teaching methods. This article advocates using a reading style inventory and matching the teaching method to the student's reading style. The author holds copyright to this article. (Contains 3 figures.)

a Study on Mental Representations for Realistic Visualization the Particular Case of Ski Trail Mapping

NASA Astrophysics Data System (ADS)

Balzarini, R.; Dalmasso, A.; Murat, M.

2015-08-01

This article presents preliminary results from a research project in progress that brings together geographers, cognitive scientists, historians and computer scientists. The project investigates the evolution of a particular territorial model: ski trails maps. Ski resorts, tourist and sporting innovations for mountain economies since the 1930s, have needed cartographic representations corresponding to new practices of the space.Painter artists have been involved in producing ski maps with painting techniques and panoramic views, which are by far the most common type of map, because they allow the resorts to look impressive to potential visitors. These techniques have evolved throughout the mutations of the ski resorts. Paper ski maps no longer meet the needs of a large part of the customers; the question now arises of their adaptation to digital media. In a computerized process perspective, the early stage of the project aims to identify the artist-representations, based on conceptual and technical rules, which are handled by users-skiers to perform a task (location, wayfinding, decision-making) and can be transferred to a computer system. This article presents the experimental phase that analyzes artist and user mental representations that are at stake during the making and the reading of a paper ski map. It particularly focuses on how the invention of the artist influences map reading.

Reading, Mathematics, and Behavioral Difficulties Interrelate: Evidence from a Cross-lagged Panel Design and Population-based Sample

PubMed Central

Lin, Yu-Chu; Morgan, Paul L.; Farkas, George; Hillemeier, Marianne; Cook, Michael

2015-01-01

We examined three questions. First, do reading difficulties increase children’s risk of behavior difficulties? Second, do behavioral difficulties increase children’s risk of reading difficulties? Third, do mathematics difficulties increase children’s risk of reading or behavioral difficulties? We investigated these questions using a sample of 9,324 children followed from third to fifth grade as they participated in a nationally representative dataset, conducting multilevel logistic regression modeling and including statistical control for many potential confounds. Results indicated that poor readers in third grade were significantly more likely to display poor task management, poor self-control, poor interpersonal skills, internalizing behavior problems, and externalizing behavior problems in fifth grade (odds ratio [OR] range = 1.30 – 1.57). Statistically controlling for a prior history of reading difficulties, children with poor mathematics skills in third grade were also significantly more likely to display poor task management, poor interpersonal skills, internalizing behavior problems, and reading difficulties in fifth grade (OR range = 1.38 – 5.14). In contrast, only those children exhibiting poor task management, but not other types of problem behaviors, in third grade were more likely to be poor readers in fifth grade (OR = 1.49). PMID:26097274

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

PubMed

Ishiwa, Koto; Sanjosé, Vicente; Otero, José

2013-09-01

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

E-Reading Comprehension versus Conventional Reading Comprehension of Junior High Students

ERIC Educational Resources Information Center

Stevens, Brian

2014-01-01

Technology is an increasing part in the lives of junior high students, but little is known about how this technology affects their reading. Reading comprehension from e-books is compared to reading comprehension from conventional print books with junior high students. The problem is that students may be reading from a medium that is less than the…

Integrating Reading and the English-Language Arts in the Geography Curriculum.

ERIC Educational Resources Information Center

Rushdoony, Haig A.

Suggested activities for integrating language concepts and comprehension skills into elementary school geography instruction are presented. The activities focus on concept formation through semantic mapping and making analogies, and on comprehension through recalling, generalizing, interpreting, and making inferences. Semantic maps indicate spoke…

Topographic Map Reading

DTIC Science & Technology

1991-05-12

MinnesotaREOTMBII Institute of Child Development tR * 51 East River Road JS I Minneapolis, MN 55455-0345 9. SPONSOInwG/MONTORING AGENCY NAME(S) AMD...Cognitive maps in children and men. [Clark, 1983] J. Clark. Integration of imagery and car- Child Development, 45:707-716, 1974. tographic data

Working memory deficits in children with reading difficulties: memory span and dual task coordination.

PubMed

Wang, Shinmin; Gathercole, Susan E

2013-05-01

The current study investigated the cause of the reported problems in working memory in children with reading difficulties. Verbal and visuospatial simple and complex span tasks, and digit span and reaction times tasks performed singly and in combination, were administered to 46 children with single word reading difficulties and 45 typically developing children matched for age and nonverbal ability. Children with reading difficulties had pervasive deficits in the simple and complex span tasks and had poorer abilities to coordinate two cognitive demanding tasks. These findings indicate that working memory problems in children with reading difficulties may reflect a core deficit in the central executive. Copyright © 2012 Elsevier Inc. All rights reserved.

Solving the Problem of Learning to Read: Children's Linguistic Awareness and Reading Progress.

ERIC Educational Resources Information Center

Abramson, Shareen

A study investigated suggested interrelationships of linguistic awareness, cognitive ability, and reading achievement. The extent to which differences in reading achievement were related to differences in the other areas was also explored. The Linguistic Awareness in Reading Test (LARR), the Coloured Progressive Matrices (CPM), and the Stanford…

Speaking My Mind: Stop Reading Shakespeare!

ERIC Educational Resources Information Center

Spangler, Susan

2009-01-01

Reading skills are vital to student success, and those skills could be practiced with Shakespeare "if students are taught reading skills in the classroom." The problem is that many teachers of English do not consider themselves reading specialists and do not teach reading skills to their students. Fred L. Hamel notes that teachers in a recent…

SPEED READING--IS THE PRESENT EMPHASIS DESIRABLE.

ERIC Educational Resources Information Center

BERGER, ALLEN

THE RESEARCH RESULTS FOR SEVEN AREAS OF THE SPEED READING CONTROVERSY ARE REPORTED. TERMINOLOGY FOR THE PROGRAM IS A PROBLEM AREA. MANY PEOPLE CONTEND THAT SPEED READING IS NOT READING IN THE TRADITIONAL SENSE. MEASUREMENT IS OFTEN LIMITED OR EMPHASIZES READING RATE ONLY. FIRMS, ESPECIALLY THOSE NOT CLOSELY CONNECTED WITH SCHOOLS, SOMETIMES MAKE…

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

ERIC Educational Resources Information Center

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

2017-01-01

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

Reading and Listening Comprehension and Their Relation to Inattention and Hyperactivity

ERIC Educational Resources Information Center

Cain, Kate; Bignell, Simon

2014-01-01

Background: Children with diagnoses of attention-deficit/hyperactivity disorder (ADHD) frequently have reading problems. To date, it is not clear whether poor reading is associated with both inattention and hyperactivity and also whether poor reading comprehension is the result of poor word reading skills or more general language comprehension…

Reading Researchers, Policymakers, and Practitioners. Yearbook of the American Reading Forum, Volume IX, 1989.

ERIC Educational Resources Information Center

Hayes, Bernard L., Ed.; Camperell, Kay, Ed.

Articles in this yearbook address the problems associated with how reading research informs practice. Articles, listed with their authors, are as follows: (1) "Reading Research into Policy and Practice: Practitioner's Viewpoint" (Deborah L. Thompson); (2) "Michigan's Reading Program: A Decade of Change" (Elaine M. Weber); (3)…

The Effect of Repeated Reading with Pairs of Students in a Large-Group Setting on Fluency and Comprehension for Students at Risk for Reading Failure

ERIC Educational Resources Information Center

Frame, John N.

2011-01-01

Problem: Some students are failing to develop acceptable reading skills; however, instructional time allocated to reading fluency can increase reading comprehension. The purpose of this study was to compare students who received repeated reading with pairs of students in a large-group setting with those who did not in terms of reading fluency,…

Audio Support Guidelines for Accessible Assessments: Insights from Cognitive Lab

ERIC Educational Resources Information Center

Christensen, Laurene L.; Shyyan, Vitaliy; Rogers, Christopher; Kincaid, Aleksis

2014-01-01

Some students, including students with print disabilities, students with low vision, and English language learners, may benefit from having test content read aloud. However, there have been challenges in standardizing the presentation of test content, including whether or not to read answer choices or to describe maps and cartoons, among many…

Statistical and Cooperative Learning in Reading: An Artificial Orthography Learning Study

ERIC Educational Resources Information Center

Zhao, Jingjing; Li, Tong; Elliott, Mark A.; Rueckl, Jay G.

2018-01-01

This article reports two experiments in which the artificial orthography paradigm was used to investigate the mechanisms underlying learning to read. In each experiment, participants were taught the meanings and pronunications of words written in an unfamiliar orthography, and the statistical structure of the mapping between written and spoken…

The Interaction between Semantic and the Nonsemantic Systems in Reading: Evidence from Chinese

ERIC Educational Resources Information Center

Bi, Yanchao; Han, Zaizhu; Weekes, Brendan; Shu, Hua

2007-01-01

We report a Chinese-speaking patient WJX with left temporal lobe ischemic damage resulting in dementia. Similar to English speaking patients with this pathology, WJX showed impaired semantic system functioning together with a well preserved ability to read aloud Chinese characters including characters with unpredictable mappings between…

Brain Networks Associated with Sublexical Properties of Chinese Characters

ERIC Educational Resources Information Center

Yang, Jianfeng; Wang, Xiaojuan; Shu, Hua; Zevin, Jason D.

2011-01-01

Cognitive models of reading all assume some division of labor among processing pathways in mapping among print, sound and meaning. Many studies of the neural basis of reading have used task manipulations such as rhyme or synonym judgment to tap these processes independently. Here we take advantage of specific properties of the Chinese writing…

Addressing the English Language Arts Technology Standard in a Secondary Reading Methodology Course.

ERIC Educational Resources Information Center

Merkley, Donna J.; Schmidt, Denise A.; Allen, Gayle

2001-01-01

Describes efforts to integrate technology into a reading methodology course for secondary English majors. Discusses the use of e-mail, multimedia, distance education for videoconferences, online discussion technology, subject-specific software, desktop publishing, a database management system, a concept mapping program, and the use of the World…

Gender Differences in Reading Performance on Documents across Countries.

ERIC Educational Resources Information Center

Rosen, Monica

2001-01-01

Notes how females are known to excel over males in most reading tasks, but not consistently so in tasks that require processing information from maps, tables, charts and diagrams, so called "Documents." Describes and analyzes gender differences on Document tasks, and investigates if and how the pattern of differences varies over countries. (SG)

Brain Routes for Reading in Adults with and without Autism: EMEG Evidence

ERIC Educational Resources Information Center

Moseley, Rachel L.; Pulvermüller, Friedemann; Mohr, Bettina; Lombardo, Michael V.; Baron-Cohen, Simon; Shtyrov, Yury

2014-01-01

Reading utilises at least two neural pathways. The temporal lexical route visually maps whole words to their lexical entries, whilst the nonlexical route decodes words phonologically via parietal cortex. Readers typically employ the lexical route for familiar words, but poor comprehension plus precocity at mechanically "sounding out"…

CDP++.Italian: Modelling Sublexical and Supralexical Inconsistency in a Shallow Orthography

PubMed Central

Perry, Conrad; Ziegler, Johannes C.; Zorzi, Marco

2014-01-01

Most models of reading aloud have been constructed to explain data in relatively complex orthographies like English and French. Here, we created an Italian version of the Connectionist Dual Process Model of Reading Aloud (CDP++) to examine the extent to which the model could predict data in a language which has relatively simple orthography-phonology relationships but is relatively complex at a suprasegmental (word stress) level. We show that the model exhibits good quantitative performance and accounts for key phenomena observed in naming studies, including some apparently contradictory findings. These effects include stress regularity and stress consistency, both of which have been especially important in studies of word recognition and reading aloud in Italian. Overall, the results of the model compare favourably to an alternative connectionist model that can learn non-linear spelling-to-sound mappings. This suggests that CDP++ is currently the leading computational model of reading aloud in Italian, and that its simple linear learning mechanism adequately captures the statistical regularities of the spelling-to-sound mapping both at the segmental and supra-segmental levels. PMID:24740261

A constraint optimization based virtual network mapping method

NASA Astrophysics Data System (ADS)

Li, Xiaoling; Guo, Changguo; Wang, Huaimin; Li, Zhendong; Yang, Zhiwen

2013-03-01

Virtual network mapping problem, maps different virtual networks onto the substrate network is an extremely challenging work. This paper proposes a constraint optimization based mapping method for solving virtual network mapping problem. This method divides the problem into two phases, node mapping phase and link mapping phase, which are all NP-hard problems. Node mapping algorithm and link mapping algorithm are proposed for solving node mapping phase and link mapping phase, respectively. Node mapping algorithm adopts the thinking of greedy algorithm, mainly considers two factors, available resources which are supplied by the nodes and distance between the nodes. Link mapping algorithm is based on the result of node mapping phase, adopts the thinking of distributed constraint optimization method, which can guarantee to obtain the optimal mapping with the minimum network cost. Finally, simulation experiments are used to validate the method, and results show that the method performs very well.

Stroop interference associated with efficient reading fluency and prelexical orthographic processing.

PubMed

Mano, Quintino R; Williamson, Brady J; Pae, Hye K; Osmon, David C

2016-01-01

The Stroop Color-Word Test involves a dynamic interplay between reading and executive functioning that elicits intuitions of word reading automaticity. One such intuition is that strong reading skills (i.e., more automatized word reading) play a disruptive role within the test, contributing to Stroop interference. However, evidence has accumulated that challenges this intuition. The present study examined associations among Stroop interference, reading skills (i.e., isolated word identification, grapheme-to-phoneme mapping, phonemic awareness, reading fluency) measured on standardized tests, and orthographic skills measured on experimental computerized tasks. Among university students (N = 152), correlational analyses showed greater Stroop interference to be associated with (a) relatively low scores on all standardized reading tests, and (b) longer response latencies on orthographic tasks. Hierarchical regression demonstrated that reading fluency and prelexical orthographic processing predicted unique and significant variance in Stroop interference beyond baseline rapid naming. Results suggest that strong reading skills, including orthographic processing, play a supportive role in resolving Stroop interference.

Exploring Differential Effects Across Two Decoding Treatments on Item-Level Transfer in Children with Significant Word Reading Difficulties: A New Approach for Testing Intervention Elements.

PubMed

Steacy, Laura M; Elleman, Amy M; Lovett, Maureen W; Compton, Donald L

2016-01-01

In English, gains in decoding skill do not map directly onto increases in word reading. However, beyond the Self-Teaching Hypothesis (Share, 1995), little is known about the transfer of decoding skills to word reading. In this study, we offer a new approach to testing specific decoding elements on transfer to word reading. To illustrate, we modeled word-reading gains among children with reading disability (RD) enrolled in Phonological and Strategy Training (PHAST) or Phonics for Reading (PFR). Conditions differed in sublexical training with PHAST stressing multi-level connections and PFR emphasizing simple grapheme-phoneme correspondences. Thirty-seven children with RD, 3 rd - 6 th grade, were randomly assigned 60 lessons of PHAST or PFR. Crossed random-effects models allowed us to identify specific intervention elements that differentially impacted word-reading performance at posttest, with children in PHAST better able to read words with variant vowel pronunciations. Results suggest that sublexical emphasis influences transfer gains to word reading.

Effects of Preventative Tutoring on the Mathematical Problem Solving of Third-Grade Students With Math and Reading Difficulties.

PubMed

Fuchs, Lynn S; Seethaler, Pamela M; Powell, Sarah R; Fuchs, Douglas; Hamlett, Carol L; Fletcher, Jack M

2008-01-01

This study assessed the effects of preventative tutoring on the math problem solving of third-grade students with math and reading difficulties. Students (n = 35) were assigned randomly to continue in their general education math program or to receive secondary preventative tutoring 3 times per week, 30 min per session, for 12 weeks. Schema-broadening tutoring taught students to (a) focus on the mathematical structure of 3 problem types; (b) recognize problems as belonging to those 3 problem-type schemas; (c) solve the 3 word-problem types; and (d) transfer solution methods to problems that include irrelevant information, 2-digit operands, missing information in the first or second positions in the algebraic equation, or relevant information in charts, graphs, and pictures. Also, students were taught to perform the calculation and algebraic skills foundational for problem solving. Analyses of variance revealed statistically significant effects on a wide range of word problems, with large effect sizes. Findings support the efficacy of the tutoring protocol for preventing word-problem deficits among third-grade students with math and reading deficits.

Effects of Preventative Tutoring on the Mathematical Problem Solving of Third-Grade Students With Math and Reading Difficulties

PubMed Central

Fuchs, Lynn S.; Seethaler, Pamela M.; Powell, Sarah R.; Fuchs, Douglas; Hamlett, Carol L.; Fletcher, Jack M.

2009-01-01

This study assessed the effects of preventative tutoring on the math problem solving of third-grade students with math and reading difficulties. Students (n = 35) were assigned randomly to continue in their general education math program or to receive secondary preventative tutoring 3 times per week, 30 min per session, for 12 weeks. Schema-broadening tutoring taught students to (a) focus on the mathematical structure of 3 problem types; (b) recognize problems as belonging to those 3 problem-type schemas; (c) solve the 3 word-problem types; and (d) transfer solution methods to problems that include irrelevant information, 2-digit operands, missing information in the first or second positions in the algebraic equation, or relevant information in charts, graphs, and pictures. Also, students were taught to perform the calculation and algebraic skills foundational for problem solving. Analyses of variance revealed statistically significant effects on a wide range of word problems, with large effect sizes. Findings support the efficacy of the tutoring protocol for preventing word-problem deficits among third-grade students with math and reading deficits. PMID:20209074

Are Balance Problems Connected to Reading Speed or the Familial Risk of Dyslexia?

ERIC Educational Resources Information Center

Viholainen, Helena; Aro, Mikko; Ahonen, Timo; Crawford, Susan; Cantell, Marja; Kooistra, Libbe

2011-01-01

Aim: The aim of this study was to examine the connection between balance problems and reading speed in children with and without a familial risk of dyslexia by controlling for the effects of attention, hyperactivity, and cognitive and motor functioning. Method: The prevalence of balance problems was studied in 94 children (48 females, 46 males)…

The Relation between Students' Math and Reading Ability and Their Mathematics, Physics, and Chemistry Examination Grades in Secondary Education

ERIC Educational Resources Information Center

Korpershoek, Hanke; Kuyper, Hans; van der Werf, Greetje

2015-01-01

Word problems are math- or science-related problems presented in the context of a story or real-life scenario. Literature suggests that, to solve these problems, advanced reading skills are required, in addition to content-related skills in, for example, mathematics. In the present study, we investigated the relation between students' reading…

Persian Native Speakers Reading Persian and English Texts: Their Strategic Behavior to Overcome Syntactic and Semantic Problems

ERIC Educational Resources Information Center

Alimorad, Zahra

2015-01-01

This study aimed to discover semantic and syntactic problems Persian native speakers might have while reading English and Persian texts and different strategies they use to overcome those problems. To this end, a convenient sample of 40 intermediate students studying English Literature at Shiraz University was selected. Twenty of them were asked…

An Investigation of Two Instructional Settings in the Use of Semantic Mapping with Poor Readers. Program Report 85-4.

ERIC Educational Resources Information Center

Pittelman, Susan D.; And Others

A study investigated whether semantic mapping is more effective for poor readers instructed in a small group of poor readers or in a class of students with mixed reading abilities. Students in five fourth-grade classes served as the control, receiving no semantic mapping instruction. Subjects, 39 fourth-grade poor readers, were presented semantic…

Fluorescein angiography

MedlinePlus

... other retinopathy High blood pressure Inflammation or edema Macular degeneration Microaneurysms -- enlargement of capillaries in the retina Tumors ... Eye Problems Read more Eye Diseases Read more Macular Degeneration Read more A.D.A.M., Inc. is ...

Diel Metagenomics and Metatranscriptomics of Elkhorn Slough Hypersaline Microbial Mat

NASA Astrophysics Data System (ADS)

Lee, J.; Detweiler, A. M.; Everroad, R. C.; Bebout, L. E.; Weber, P. K.; Pett-Ridge, J.; Bebout, B.

2014-12-01

To understand the variation in gene expression associated with the daytime oxygenic phototrophic and nighttime fermentation regimes seen in hypersaline microbial mats, a contiguous mat piece was subjected to sampling at regular intervals over a 24-hour diel period. Additionally, to understand the impact of sulfate reduction on biohydrogen consumption, molybdate was added to a parallel experiment in the same run. 4 metagenome and 12 metatranscriptome Illumina HiSeq lanes were completed over day / night, and control / molybdate experiments. Preliminary comparative examination of noon and midnight metatranscriptomic samples mapped using bowtie2 to reference genomes has revealed several notable results about the dominant mat-building cyanobacterium Microcoleus chthonoplastes PCC 7420. Dominant cyanobacterium M. chthonoplastes PCC 7420 shows expression in several pathways for nitrogen scavenging, including nitrogen fixation. Reads mapped to M. chthonoplastes PCC 7420 shows expression of two starch storage and utilization pathways, one as a starch-trehalose-maltose-glucose pathway, another through UDP-glucose-cellulose-β-1,4 glucan-glucose pathway. The overall trend of gene expression was primarily light driven up-regulation followed by down-regulation in dark, while much of the remaining expression profile appears to be constitutive. Co-assembly of quality-controlled reads from 4 metagenomes was performed using Ray Meta with progressively smaller K-mer sizes, with bins identified and filtered using principal component analysis of coverages from all libraries and a %GC filter, followed by reassembly of the remaining co-assembly reads and binned reads. Despite having relatively similar abundance profiles in each metagenome, this binning approach was able to distinctly resolve bins from dominant taxa, but also sulfate reducing bacteria that are desired for understanding molybdate inhibition. Bins generated from this iterative assembly process will be used for downstream mapping of transcriptomic reads as well as isolation efforts for Cyanobacteria-associated bacteria.

Map and Globe Reading Skills.

ERIC Educational Resources Information Center

Georgia State Dept. of Education, Atlanta. Office of Instructional Services.

Although the guide was designed to accompany an instructional television series, it contains teacher-developed activities on map and globe skills which can be selected and adapted to the needs of elementary students independent of the series. Geographic concepts include direction, the globe, boundaries, hemispheres, scale, latitude, longitude, and…

Listening to Students: Modification of a Reading Program Based on the Sources of Foreign Language Reading Anxiety

ERIC Educational Resources Information Center

Aydin, Belgin; Kuru Gonen, Ipek

2012-01-01

This paper is concerned with the modifications implemented in a second year foreign language (FL) reading program with respect to the problems students experience while reading in FL. This research draws on the sources of FL reading anxiety identified in the first year reading program with a motivation to re-design the second year program to help…

Reading difficulties in Spanish adults with dyslexia.

PubMed

Suárez-Coalla, Paz; Cuetos, Fernando

2015-04-01

Recent studies show that dyslexia persists into adulthood, even in highly educated and well-read people. The main characteristic that adults with dyslexia present is a low speed when reading. In Spanish, a shallow orthographic system, no studies about adults with dyslexia are available; and it is possible that the consistency of the orthographic system favours the reading fluency. The aim of this study was to get an insight of the reading characteristics of Spanish adults with dyslexia and also to infer the reading strategies that they are using. For that purpose, a group of 30 dyslexics (M age = 32 years old) and an age-matched group of 30 adults without reading disabilities completed several phonological and reading tasks: phonological awareness tasks, rapid automatic naming, lexical decision, word and pseudoword reading, letter detection and text reading. The results showed that highly educated Spanish dyslexics performed significantly worse than the control group in the majority of the tasks. Specifically, they showed difficulties reading long pseudowords, indicating problems in automating the grapheme-phoneme rules, but they also seem to present difficulties reading words, which indicate problems with the lexical route. It seems that the Spanish dyslexic adults, as in deep orthographies, continue having difficulties in phonological awareness tasks, rapid naming and reading.

Reading and listening comprehension and their relation to inattention and hyperactivity.

PubMed

Cain, Kate; Bignell, Simon

2014-03-01

Children with diagnoses of attention-deficit/hyperactivity disorder (ADHD) frequently have reading problems. To date, it is not clear whether poor reading is associated with both inattention and hyperactivity and also whether poor reading comprehension is the result of poor word reading skills or more general language comprehension weaknesses. We report two studies to examine how reading and listening comprehension skills are related to inattention and hyperactivity/impulsivity. Separate groups of 7- to 11-year-olds participated in each study. In both studies, we used teacher ratings of inattention and hyperactivity/impulsivity to identify three groups at risk of ADHD: poor attention, high hyperactivity, poor attention and high hyperactivity, and also same-age controls. In Study 1, we explored how inattention and hyperactivity predicted reading after controlling for non-verbal IQ and vocabulary. In Study 2, we compared listening and reading comprehension in these groups. Poor attention was related to poor reading comprehension, although the relation was partially mediated by word reading skill (Study 1). Groups with high hyperactivity had weak listening comprehension relative to reading comprehension (Study 2). These results indicate that the reading comprehension problems of children with attention difficulties are related to poor word reading and that listening comprehension is particularly vulnerable in children at risk of ADHD. © 2013 The British Psychological Society.

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.…

Old and New Ways to Study Characteristics of Reading Disability: The Case of the Nonword-Reading Deficit

ERIC Educational Resources Information Center

Van den Broeck, Wim; Geudens, Astrid

2012-01-01

Theoretical and computational models of reading have traditionally been informed by specific characteristics of disabled readers. One of the most frequently studied marker effects of developmental dyslexia is the nonword-reading deficit. Disabled readers are generally believed to show a specific problem in reading nonwords. This study presents a…

An Observational Study of the Relationship between Diagnosis and Remediation in Reading. Research Series No. 72.

ERIC Educational Resources Information Center

Weinshank, Annette B.

A study was conducted to determine whether reading specialists' diagnoses lead directly to remedial recommendations. Eight experienced reading specialists were observed during 24 sessions as they performed a series of tasks using three simulated cases of reading difficulty, two of which were thinly disguised versions of the same reading problem.…

Specificity and Overlap in Skills Underpinning Reading and Arithmetical Fluency

ERIC Educational Resources Information Center

van Daal, Victor; van der Leij, Aryan; Ader, Herman

2013-01-01

The aim of this study was to examine unique and common causes of problems in reading and arithmetic fluency. 13- to 14-year-old students were placed into one of five groups: reading disabled (RD, n = 16), arithmetic disabled (AD, n = 34), reading and arithmetic disabled (RAD, n = 17), reading, arithmetic, and listening comprehension disabled…

Lectura y Vida: Revista Latinoamericana de Lectura, 2000 (Reading and Life: Latin American Reading Magazine, 2000).

ERIC Educational Resources Information Center

Lectura y Vida: Revista Latinoamericana de Lectura, 2001

2001-01-01

Articles in this volume, written in Spanish, focus on the following: reading and writing assessment: Some characteristics of new assessment practices; how to support active participation in the reading of expository texts; argumentative writing as a problem in the written composition of students in teacher training; reading in a workshop…

Using the Networked Peer Support Strategy to Enhance Reading Comprehension for Students with Various Thinking Styles

ERIC Educational Resources Information Center

Lee, Chien I.; Chang, Chih C.

2017-01-01

How to enhance students' reading comprehension as well as reading interest is a currently serious problem for elementary school students. Students can learn various knowledge through reading, as a result of this reason, the advantage and disadvantage of reading ability could directly affect the learning efficiency. This study proposes networked…

After-School Tutoring for Reading Achievement and Urban Middle School Students

ERIC Educational Resources Information Center

Nelson-Royes, Andrea M.; Reglin, Gary L.

2011-01-01

This research study's purpose or theme was to qualitatively investigate the reading component of a private after-school tutoring program that offered academic assistance to eighth-grade students. The problem with reading is many urban middle school students have poor reading skills and do not perform well on reading standardized tests. Relative to…

An interactive method for digitizing zone maps

NASA Technical Reports Server (NTRS)

Giddings, L. E.; Thompson, E. J.

1975-01-01

A method is presented for digitizing maps that consist of zones, such as contour or climatic zone maps. A color-coded map is prepared by any convenient process. The map is then read into memory of an Image 100 computer by means of its table scanner, using colored filters. Zones are separated and stored in themes, using standard classification procedures. Thematic data are written on magnetic tape and these data, appropriately coded, are combined to make a digitized image on tape. Step-by-step procedures are given for digitization of crop moisture index maps with this procedure. In addition, a complete example of the digitization of a climatic zone map is given.

Designing Caregiver-Implemented Shared-Reading Interventions to Overcome Implementation Barriers

PubMed Central

Logan, Jessica R.; Damschroder, Laura

2015-01-01

Purpose This study presents an application of the theoretical domains framework (TDF; Michie et al., 2005), an integrative framework drawing on behavior-change theories, to speech-language pathology. Methods A multistep procedure was used to identify barriers affecting caregivers' implementation of shared-reading interventions with their children with language impairment (LI). The authors examined caregiver-level data corresponding to implementation issues from two randomized controlled trials and mapped these to domains in the TDF as well as empirically validated behavior-change techniques. Results Four barriers to implementation were identified as potentially affecting caregivers' implementation: time pressures, reading difficulties, discomfort with reading, and lack of awareness of benefits. These were mapped to 3 TDF domains: intentions, beliefs about capabilities, and skills. In turn, 4 behavior-change techniques were identified as potential vehicles for affecting these domains: reward, feedback, model, and encourage. An ongoing study is described that is determining the effects of these techniques for improving caregivers' implementation of a shared-reading intervention. Conclusions A description of the steps to identifying barriers to implementation, in conjunction with an ongoing experiment that will explicitly determine whether behavior-change techniques affect these barriers, provides a model for how implementation science can be used to identify and overcome implementation barriers in the treatment of communication disorders. PMID:26262941

Designing Caregiver-Implemented Shared-Reading Interventions to Overcome Implementation Barriers.

PubMed

Justice, Laura M; Logan, Jessica R; Damschroder, Laura

2015-12-01

This study presents an application of the theoretical domains framework (TDF; Michie et al., 2005), an integrative framework drawing on behavior-change theories, to speech-language pathology. A multistep procedure was used to identify barriers affecting caregivers' implementation of shared-reading interventions with their children with language impairment (LI). The authors examined caregiver-level data corresponding to implementation issues from two randomized controlled trials and mapped these to domains in the TDF as well as empirically validated behavior-change techniques. Four barriers to implementation were identified as potentially affecting caregivers' implementation: time pressures, reading difficulties, discomfort with reading, and lack of awareness of benefits. These were mapped to 3 TDF domains: intentions, beliefs about capabilities, and skills. In turn, 4 behavior-change techniques were identified as potential vehicles for affecting these domains: reward, feedback, model, and encourage. An ongoing study is described that is determining the effects of these techniques for improving caregivers' implementation of a shared-reading intervention. A description of the steps to identifying barriers to implementation, in conjunction with an ongoing experiment that will explicitly determine whether behavior-change techniques affect these barriers, provides a model for how implementation science can be used to identify and overcome implementation barriers in the treatment of communication disorders.

Stroma Based Prognosticators Incorporating Differences between African and European Americans

DTIC Science & Technology

2017-10-01

amenable to bisulfite sequencing of more than a few genes. Exploiting the recent three-fold reduction in the cost of sequencing per read , we developed oligo...cards. The ability of the HiSeq 4000 to obtain about three times as many reads as the HiSeq2500, at the same price, means we can stay on track, though...capture, and sequencing (Table 2). We obtain tens of millions of mapped deduplicated reads per sample, while using only 5% of a sequencing lane per sample

Exploring the pros and cons of mechanistic case diagrams for problem-based learning

PubMed Central

2017-01-01

Purpose Mechanistic case diagram (MCD) was recommended for increasing the depth of understanding of disease, but with few articles on its specific methods. We address the experience of making MCD in the fullest depth to identify the pros and cons of using MCDs in such ways. Methods During problem-based learning, we gave guidelines of MCD for its mechanistic exploration from subcellular processes to clinical features, being laid out in as much detail as possible. To understand the students’ attitudes and depth of study using MCDs, we analyzed the results of a questionnaire in an open format about experiencing MCDs and examined the resulting products. Results Through the responses to questionnaire, we found several favorable outcomes, major of which was deeper insight and comprehensive understanding of disease facilitated by the process of making well-organized diagram. The main disadvantages of these guidelines were the feeling of too much workload and difficulty of finding mechanisms. Students gave suggestions to overcome these problems: cautious reading of comprehensive texts, additional guidance from staff about depth and focus of mechanisms, and cooperative group work. From the analysis of maps, we recognized there should be allowance of diversities in the appearance of maps and many hypothetical connections, which could be related to an insufficient understanding of mechanisms in nature. Conclusion The more detailed an MCD task is, the better students can become acquainted with deep knowledges. However, this advantage should be balanced by the results that there are many ensuing difficulties for the work and deliberate help plans should be prepared. PMID:28870018

Reading Improvement in the Secondary School.

ERIC Educational Resources Information Center

Dechant, Emerald

This book, a comprehensive statement about the reading problems of adolescent students, relates the principles of learning and learning theory to the teaching of reading. Using a linguistic orientation, the author guides the teacher through the procedure for developing word recognition skills, comprehension skills, content-area reading skills, and…

Proceedings of the College Reading Association, Volume 6, Fall 1965.

ERIC Educational Resources Information Center

Ketcham, Clay A., Ed.

The proceedings of the eighth annual meeting of the College Reading Association consisted of the following papers: "President's Report" (M. J. Weiss); "What Constitutes a Minimal Program for Clinical Diagnosis of Reading Disabilities?" (G. L. Bond); "Problems in Establishing Developmental Reading Programs in Junior…

T1 and T2 mapping in myocarditis: seeing beyond the horizon of Lake Louise criteria and histopathology.

PubMed

Puntmann, Valentina O; Zeiher, Andreas M; Nagel, Eike

2018-05-01

Myocarditis and its sequelae remain an unconquered clinical problem, disproportionately affecting the young. Several hurdles beset myocarditis, including non-specific symptoms, heterogeneous clinical presentation, dynamic disease stages, underscored by an absence of an easy diagnostic test or a specific treatment. Areas covered: The current diagnostic means are poorly equipped to counter the challenge; the gold standard by invasive endomyocardial biopsy relies on availability of expert procedural and reading skill. The tissue diagnostic criteria were developed to improve readers agreement with clinical diagnosis, and not based on evidence for differential treatment or improved prognosis. The Lake-Louise Criteria represented a first step towards a non-invasive diagnosis. They require extensive imaging, which is insufficiently robust with poor diagnostic confidence and tissue pathophysiological validation; they similarly lack evidence of improved outcome by guiding clinical management. T1 and T2 mapping are a step-change, providing robust, short and quantifiable imaging application, which can veritably reflect the dynamic and heterogeneous underlying disease. Expert commentary: T1 and T2 mapping harbours a unique potential for an objective non-invasive disease recognition and treatment discovery in myocarditis. These measures should enter independently into clinical experimentation, with a high priority for outcome and therapeutic studies.

Reading deficits in very low birthweight children are associated with vocabulary and attention issues at the age of seven.

PubMed

Leijon, Ingemar; Ingemansson, Fredrik; Nelson, Nina; Wadsby, Marie; Samuelsson, Stefan

2016-01-01

This Swedish study compared reading skills between seven-year-old children with a very low birthweight (VLBW) and controls with a normal birthweight, exploring associations between reading variables and cognition, parent-rated behaviour, perinatal factors and family factors. We studied 51 VLBW children, with no major neurodevelopmental impairments and attending their first year at a regular school, and compared them with the 51 sex- and age-matched controls. The test battery, carried out at 7.8 ± 0.4 years of age, included reading skills, the Wechsler Intelligence Scale for Children - III and the Child Behaviour Checklist. Very low birthweight children with a mean birthweight of 1105 g (± 291 g) and a gestational age of 28.8 (± 2.2) weeks scored significantly lower in all reading subtests and cognition and demonstrated more behavioural problems than normal birthweight controls. We also found significant associations between poor vocabulary, combined with attention problems, and phonological awareness, rapid naming and spelling control. Perinatal factors had no association with reading function, and socio-economic factors had very few. Very low birthweight children demonstrated deficits in all reading domains and had poorer cognition and more behavioural problems at the age of seven, with reading ability related to vocabulary and attention. ©2015 The Authors. Acta Paediatrica published by John Wiley & Sons Ltd on behalf of Foundation Acta Paediatrica.

Repetitive DNA and Plant Domestication: Variation in Copy Number and Proximity to Genes of LTR-Retrotransposons among Wild and Cultivated Sunflower (Helianthus annuus) Genotypes.

PubMed

Mascagni, Flavia; Barghini, Elena; Giordani, Tommaso; Rieseberg, Loren H; Cavallini, Andrea; Natali, Lucia

2015-11-24

The sunflower (Helianthus annuus) genome contains a very large proportion of transposable elements, especially long terminal repeat retrotransposons. However, knowledge on the retrotransposon-related variability within this species is still limited. We used next-generation sequencing (NGS) technologies to perform a quantitative and qualitative survey of intraspecific variation of the retrotransposon fraction of the genome across 15 genotypes--7 wild accessions and 8 cultivars--of H. annuus. By mapping the Illumina reads of the 15 genotypes onto a library of sunflower long terminal repeat retrotransposons, we observed considerable variability in redundancy among genotypes, at both superfamily and family levels. In another analysis, we mapped Illumina paired reads to two sets of sequences, that is, long terminal repeat retrotransposons and protein-encoding sequences, and evaluated the extent of retrotransposon proximity to genes in the sunflower genome by counting the number of paired reads in which one read mapped to a retrotransposon and the other to a gene. Large variability among genotypes was also ascertained for retrotransposon proximity to genes. Both long terminal repeat retrotransposon redundancy and proximity to genes varied among retrotransposon families and also between cultivated and wild genotypes. Such differences are discussed in relation to the possible role of long terminal repeat retrotransposons in the domestication of sunflower. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Transcriptome Analysis of Nine Tissues to Discover Genes Involved in the Biosynthesis of Active Ingredients in Sophora flavescens.

PubMed

Han, Rongchun; Takahashi, Hiroki; Nakamura, Michimi; Bunsupa, Somnuk; Yoshimoto, Naoko; Yamamoto, Hirobumi; Suzuki, Hideyuki; Shibata, Daisuke; Yamazaki, Mami; Saito, Kazuki

2015-01-01

Sophora flavescens AITON (kurara) has long been used to treat various diseases. Although several research findings revealed the biosynthetic pathways of its characteristic chemical components as represented by matrine, insufficient analysis of transcriptome data hampered in-depth analysis of the underlying putative genes responsible for the biosynthesis of pharmaceutical chemical components. In this study, more than 200 million fastq format reads were generated by Illumina's next-generation sequencing approach using nine types of tissue from S. flavescens, followed by CLC de novo assembly, ultimately yielding 83,325 contigs in total. By mapping the reads back to the contigs, reads per kilobase of the transcript per million mapped reads values were calculated to demonstrate gene expression levels, and overrepresented gene ontology terms were evaluated using Fisher's exact test. In search of the putative genes relevant to essential metabolic pathways, all 1350 unique enzyme commission numbers were used to map pathways against the Kyoto Encyclopedia of Genes and Genomes. By analyzing expression patterns, we proposed some candidate genes involved in the biosynthesis of isoflavonoids and quinolizidine alkaloids. Adopting RNA-Seq analysis, we obtained substantially credible contigs for downstream work. The preferential expression of the gene for putative lysine/ornithine decarboxylase committed in the initial step of matrine biosynthesis in leaves and stems was confirmed in semi-quantitative polymerase chain reaction (PCR) analysis. The findings in this report may serve as a stepping-stone for further research into this promising medicinal plant.

User Preferences in Image Map Using

NASA Astrophysics Data System (ADS)

Vondráková, A.; Vozenilek, V.

2016-06-01

In the process of map making, the attention is given to the resulting image map (to be accurate, readable, and suit the primary purpose) and its user aspects. Current cartography understands the user issues as all matters relating to user perception, map use and also user preferences. Most commercial cartographic production is strongly connected to economic circumstances. Companies are discovering user's interests and market demands. However, is it sufficient to focus just on the user's preferences? Recent research on user aspects at Palacký University Olomouc addresses a much wider scope of user aspects. The user's preferences are very often distorting - the users think that the particular image map is kind, beautiful, and useful and they wants to buy it (or use it - it depends on the form of the map production). But when the same user gets the task to use practically this particular map (such as finding the shortest way), so the user concludes that initially preferred map is useless, and uses a map, that was worse evaluated according to his preferences. It is, therefore, necessary to evaluate not only the correctness of image maps and their aesthetics but also to assess the user perception and other user issues. For the accomplishment of such testing, eye-tracking technology is a useful tool. The research analysed how users read image maps, or if they prefer image maps over traditional maps. The eye tracking experiment on the comparison of the conventional and image map reading was conducted. The map readers were asked to solve few simple tasks with either conventional or image map. The readers' choice of the map to solve the task was one of investigated aspect of user preferences. Results demonstrate that the user preferences and user needs are often quite different issues. The research outcomes show that it is crucial to implement map user testing into the cartographic production process.

Early language mediates the relations between preschool inattention and school-age reading achievement.

PubMed

O'Neill, Sarah; Thornton, Veronica; Marks, David J; Rajendran, Khushmand; Halperin, Jeffrey M

2016-05-01

Early inattention is associated with later reading problems in children, but the mechanism by which this occurs is unclear. We investigated whether the negative relation between preschoolers' ADHD symptoms and 8-year-old reading achievement is directly related to the severity of inattention or is mediated by early language skills. Children (n = 150; 76% boys) were evaluated at 3 time points: preschool (T1), mean (SD) age = 4.24 (.49) years; 1 year later (T2), mean (SD) age = 5.28 (.50) years; and during school age (T3), mean (SD) age = 8.61 (.31) years. At T1, parents' Kiddie-SADS responses were dimensionalized to reflect ADHD severity. Children completed the Language domain of the NEPSY (i.e., A Developmental Neuropsychological Assessment) at T1 and again at T2. At T3, children completed the Wechsler Individual Achievement Test, Second Edition Word Reading, Pseudoword Decoding, Reading Comprehension, and Spelling subtests, and their teachers completed ratings of Reading and Written Expression performance in school. The mediating effect of T2 Language on the relation between preschool Inattention and age 8 Reading was examined using the nonparametric bootstrapping procedure, while controlling for T1 Language. Language ability at T2 mediated the path from preschool inattention (but not hyperactivity/impulsivity) to 8-year-old reading achievement (both test scores and ratings) after controlling for preschoolers' language ability. Early attentional deficits may negatively impact school-age reading outcomes by compromising the development of language skills, which in turn imperils later reading achievement. Screening children with attentional problems for language impairment, as well as implementing early intervention for both attentional and language problems may be critical to promote reading achievement during school years. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Map-Reading Skill Development with 3D Technologies

ERIC Educational Resources Information Center

Carbonell Carrera, Carlos; Avarvarei, Bogdan Vlad; Chelariu, Elena Liliana; Draghia, Lucia; Avarvarei, Simona Catrinel

2017-01-01

Landforms often are represented on maps using abstract cartographic techniques that the reader must interpret for successful three-dimensional terrain visualization. New technologies in 3D landscape representation, both digital and tangible, offer the opportunity to visualize terrain in new ways. The results of a university student workshop, in…

Map Feature Content and Text Recall of Good and Poor Readers.

ERIC Educational Resources Information Center

Amlund, Jeanne T.; And Others

1985-01-01

Reports two experiments evaluating the effect of map feature content on text recall by subjects of varying reading skill levels. Finds that both experiments support the conjoint retention hypothesis, in which dual-coding of spatial and verbal information and their interaction in memory enhance recall. (MM)

An Inquiry Activity for Genetics Using Chromosome Mapping.

ERIC Educational Resources Information Center

Leonard, William H.; Snodgrass, George

1982-01-01

Concepts to be developed, objectives, and student instructions are provided for an activity useful as an introduction to or review of Mendelian genetics and sex determination. Universal codes (read by optical scanners at supermarket checkout stands) from soup can labels are used as chromosome maps during the activity. (JN)

Essential Map Concepts for Young Children.

ERIC Educational Resources Information Center

Hatcher, Barbara

This paper discusses four key concepts to help preschool and primary grade children develop the ability to read and understand maps. Examples of student activities to develop each of the concepts are provided. The essential concepts are representation, symbolization, perspective, and scale. Representation is vital. Children must perceive that a…

Learning about Global Interdependence: An Area-Value Mapping Exercise.

ERIC Educational Resources Information Center

Crooker, Richard A.

1990-01-01

Presents a lesson for secondary school students that uses an area value map to increase student understanding about the geography of international drug production and consumption. Provides a list of necessary classroom materials, suggested background readings for students, procedures to be followed, and a bibliography of references. (DB)

Interdisciplinary Navigation Unit for Mathematics and Earth Science Using Geospatial Technology

NASA Astrophysics Data System (ADS)

Smaglik, S. M.; Harris, V.

2006-12-01

Central Wyoming College (CWC) is located northeast of the Wind River Mountains. Although many people find recreation in the wilderness and remote areas surrounding the area, people still lose their lives because they become lost or disoriented. Creating an interdisciplinary field-based curriculum unit within mathematics (MATH 1000) and earth science (GEOL 1070) courses for non-science and education majors, provides students an opportunity to develop critical thinking skills and quantitative literacy. It also provides some necessary skills for survival and an understanding of landscape formation and wilderness navigation using geoscience. A brief history of navigation, including the importance of finding latitude and longitude, and the fairly recent implementation of the Global Positioning System, precedes activities in which students learn to use a basic compass. In addition to learning how to adjust for magnetic declination they read topographic maps, specifically USGS quadrangles, and learn how to use the scale in the legend to verify calculations using the Pythagorean Theorem. Students learn how to estimate distance and time required for traveling a pre- determined distance while using dimensional analysis to convert from the English system to metric. They learn how to read and measure latitude and longitude, as well as universal transverse Mercator projection measurements (UTM's), to find their position. The basic mathematical skills are assessed through hands-on activities such as finding their location on a map using a compass, a GPS unit, and Google Earth, and using a combination of maps, compasses, and GPS units to navigate through a course. Our goal is to provide life-saving information to students while incorporating necessary core curriculum from both mathematics and earth science classes. We work to create field-based activities, as well as assessments, to insure that students who complete the course are prepared to safely enjoy the outdoors and are prepared for future courses requiring mathematical problem-solving and/or lab science as a prerequisite.

Coping Strategies Applied to Comprehend Multistep Arithmetic Word Problems by Students with Above-Average Numeracy Skills and Below-Average Reading Skills

ERIC Educational Resources Information Center

Nortvedt, Guri A.

2011-01-01

This article discusses how 13-year-old students with above-average numeracy skills and below-average reading skills cope with comprehending word problems. Compared to other students who are proficient in numeracy and are skilled readers, these students are more disadvantaged when solving single-step and multistep arithmetic word problems. The…

Longitudinal Mediators of Achievement in Mathematics and Reading in Typical and Atypical Development

PubMed Central

Barnes, Marcia A.; Raghubar, Kimberly P.; English, Lianne; Williams, Jeffrey M.; Taylor, Heather; Landry, Susan

2014-01-01

Longitudinal studies of neurodevelopmental disorders that are diagnosed at or before birth and which are associated with specific learning difficulties at school-age provide one method for investigating developmental precursors of later-emerging academic disabilities. Spina bifida myelomeningocele (SBM) is a neurodevelopmental disorder associated with particular problems in mathematics, in contrast to well-developed word reading. Children with SBM (n = 30) and typically developing children (n = 35) were used to determine whether cognitive abilities measured at 36 and 60 months of age mediated the effect of group on mathematical and reading achievement outcomes at 8.5 and 9.5 years of age. A series of multiple mediator models showed that: visual-spatial working memory at 36 months and phonological awareness at 60 months partially mediated the effect of group on math calculations; phonological awareness partially mediated the effect of group on small addition and subtraction problems on a test of math fluency; and visual-spatial working memory mediated the effect of group on a test of math problem solving. Groups did not differ on word reading, and phonological awareness was the only mediator for reading fluency and reading comprehension. The findings are discussed with reference to theories of mathematical development and disability and with respect to both common and differing cognitive correlates of math and reading. PMID:24269579

From "cracking the orthographic code" to "playing with language": toward a usage-based foundation of the reading process.

PubMed

Wallot, Sebastian

2014-01-01

The empirical study of reading dates back more than 125 years. But despite this long tradition, the scientific understanding of reading has made rather heterogeneous progress: many factors that influence the process of text reading have been uncovered, but theoretical explanations remain fragmented; no general theory pulls together the diverse findings. A handful of scholars have noted that properties thought to be at the core of the reading process do not actually generalize across different languages or from situations single-word reading to connected text reading. Such observations cast doubt on many of the traditional conceptions about reading. In this article, I suggest that the observed heterogeneity in the research is due to misguided conceptions about the reading process. Particularly problematic are the unrefined notions about meaning which undergird many reading theories: most psychological theories of reading implicitly assume a kind of elemental token semantics, where words serve as stable units of meaning in a text. This conception of meaning creates major conceptual problems. As an alternative, I argue that reading shoud be rather understood as a form of language use, which circumvents many of the conceptual problems and connects reading to a wider range of linguistic communication. Finally, drawing from Wittgenstein, the concept of "language games" is outlined as an approach to language use that can be operationalized scientifically to provide a new foundation for reading research.

Reading, Writing, and Mapping Our Worlds into Being: Shared Teacher Inquiries into Whose Literacies Count

ERIC Educational Resources Information Center

Cordova, Ralph A.; Matthiesen, Amanda L.

2010-01-01

An inner-city second grade teacher-researcher and her university-based partner examine how she and her inner-city second graders learned to resist and expand the constraints of their mandated, scripted reading curriculum by exploring their neighborhood and classrooms as communities spaces for literacies learning. Drawing on an interactional…

IFLA Section of Libraries for the Blind. Expert Meeting, 1984. Papers.

ERIC Educational Resources Information Center

International Federation of Library Associations, The Hague (Netherlands).

Papers on library services and developments in reading materials for the blind, which were presented at the 1984 Expert Meeting of the IFLA Section of Libraries for the Blind include: (1) "Teaching Map Concepts to the Blind" (R. B. Horsfall and B. Cox, Canada); (2) "Optical Character Recognition 'Reading' for Computerized Braille Production"…

Research Maps New Routes for Reading Success in PLA Early Childhood Initiative.

ERIC Educational Resources Information Center

Meyers, Elaine

2002-01-01

The Public Library Association (PLA) partnered with the National Institute of Child Health and Human Development (NICHD) to develop research-based tools for parents to prepare children for reading. Inherent in the materials is the major role of the public library in formation of readers. Outlines goals and activities (2001-2002) of the PLA/ALSC…

First Impressions Matter: Navigating Graphic Novels Utilizing Linguistic, Visual, and Spatial Resources

ERIC Educational Resources Information Center

Jimenez, Laura M.; Meyer, Carla K.

2016-01-01

Graphic novels in the K-12 classroom are most often used to motivate marginalized readers because of the lower text load and assumption of easy reading. This assumption has thus far been unexplored by reading research. This qualitative multiple-case study utilized think-aloud protocols in a new attention-mapping activity to better understand how…

Diagnostic Accuracy of Multivariate Universal Screening Procedures for Reading in Upper Elementary Grades

ERIC Educational Resources Information Center

Klingbeil, David A.; Nelson, Peter M.; Van Norman, Ethan R.; Birr, Chris

2017-01-01

We examined the diagnostic accuracy and efficiency of three approaches to universal screening for reading difficulties using retrospective data from 1,307 students in Grades 3 through 5. School staff collected screening data using the Measures of Academic Progress (MAP), a curriculum-based measure (CBM), and running records (RR). The criterion…

Linking Pupil and Teacher Competence in Reading and Mathematics in Vietnam

ERIC Educational Resources Information Center

Griffin, Patrick

2008-01-01

This article reports results derived from the national study of Grade 5 in Vietnamese primary schools in which teachers and pupils took tests in reading and mathematics. The test data were calibrated so that teacher and pupil results could be mapped onto the same continuum. Results showed that the overlapping tests for teachers and pupils were…

The Great Debate in Reading Instruction

ERIC Educational Resources Information Center

Ediger, Marlow

2012-01-01

The reading curriculum receives more attention than any other academic discipline. It is true that individuals engage in much reading in school subjects such as word problems in mathematics as well as reading numerals and symbols, science content in doing experiments and demonstrations, social studies with its emphasis upon diverse social science…

The Effects of Comprehension Monitoring Training on the Reading Competence of Learning Disabled and Regular Class Students.

ERIC Educational Resources Information Center

Chan, Lorna K. S.; Cole, Peter G.

1986-01-01

A study involving 36 (10-12 years) learning disabled (LD) students with reading problems and 36 regular class students matched with LD subjects for reading age demonstrated the benefit of training LD students to use metacognitive activities in reading comprehension. (Author/CL)

The "RAP" on Reading Comprehension

ERIC Educational Resources Information Center

Hagaman, Jessica L.; Luschen, Kati; Reid, Robert

2010-01-01

Reading problems are one of the most frequent reasons students are referred for special education services and the disparity between students with reading difficulties and those who read successfully appears to be increasing. As a result, there is now an emphasis on early intervention programs such as RTI. In many cases, early intervention in…

Investigating Patterns of Errors for Specific Comprehension and Fluency Difficulties

ERIC Educational Resources Information Center

Koriakin, Taylor A.; Kaufman, Alan S.

2017-01-01

Although word reading has traditionally been viewed as a foundational skill for development of reading fluency and comprehension, some children demonstrate "specific" reading comprehension problems, in the context of intact word reading. The purpose of this study was to identify specific patterns of errors associated with reading…

Lectura y Vida. Revista Latinoamericana de Lectura (Reading and Life. Latinamerican Reading Magazine). 1990-1995.

ERIC Educational Resources Information Center

International Reading Association, Newark, DE.

This series of 24 magazines offers readings in Spanish on literacy, education problems, psycholinguistics, expository writing, and reading behavior. The magazine's editorial committee includes representatives from Colombia, Brazil, Argentina, Chile, the United States, Uruguay, Mexico, Venezuela, and Spain. Articles concern literacy issues of both…

Reading in the Social Studies Classroom.

ERIC Educational Resources Information Center

Bullock, Terry L.; Hesse, Karl D.

This publication examines reading instruction techniques that can be used by teachers to diagnose and remedy students' weaknesses in reading social studies materials. There are four chapters. Chapter one discusses issues, including trends related to reading in the social studies and problems presented by social studies textbooks. Chapters two and…

Reading to Preschoolers Exposed: Is the Emperor Really Naked?

ERIC Educational Resources Information Center

Lonigan, Christopher J.

1994-01-01

Argues there is reason for more optimism concerning the effects of reading to preschoolers than suggested by the Scarborough and Dobrich review in this issue (PS522390). Discusses methodological problems in many studies; cites studies indicating direct and indirect links between reading to preschoolers and reading achievement, suggesting that…

Anticipation Guides: Reading for Mathematics Understanding

ERIC Educational Resources Information Center

Adams, Anne E.; Pegg, Jerine; Case, Melissa

2015-01-01

With the acceptance by many states of the Common Core State Standards for Mathematics, new emphasis is being placed on students' ability to engage in mathematical practices such as understanding problems (including word problems), reading and critiquing arguments, and making explicit use of definitions (CCSSI 2010). Engaging students in…

Partnerships to Support Reading Comprehension for Students with Language Impairment

ERIC Educational Resources Information Center

Ehren, Barbara J.

2006-01-01

Students with language impairment often experience serious and far-reaching effects of reading comprehension problems on their academic performance. The complexity of the problems and the characteristics of effective intervention necessitate a collaborative approach among general education teachers, special education teachers, and speech-language…

Evaluation of focal cartilage lesions of the knee using MRI T2 mapping and delayed Gadolinium Enhanced MRI of Cartilage (dGEMRIC).

PubMed

Årøen, Asbjørn; Brøgger, Helga; Røtterud, Jan Harald; Sivertsen, Einar Andreas; Engebretsen, Lars; Risberg, May Arna

2016-02-11

Assessment of degenerative changes of the cartilage is important in knee cartilage repair surgery. Magnetic Resonance Imaging (MRI) T2 mapping and delayed Gadolinium Enhanced MRI of Cartilage (dGEMRIC) are able to detect early degenerative changes. The hypothesis of the study was that cartilage surrounding a focal cartilage lesion in the knee does not possess degenerative changes. Twenty-eight consecutive patients included in a randomized controlled trial on cartilage repair were evaluated using MRI T2 mapping and dGEMRIC before cartilage treatment was initiated. Inclusion was based on disabling knee problems (Lysholm score of ≤ 75) due to an arthroscopically verified focal femoral condyle cartilage lesion. Furthermore, no major malalignments or knee ligament injuries were accepted. Mean patient age was 33 ± 9.6 years, and the mean duration of knee symptoms was 49 ± 60 months. The MRI T2 mapping and the dGEMRIC measurements were performed at three standardized regions of interest (ROIs) at the medial and lateral femoral condyle, avoiding the cartilage lesion The MRI T2 mapping of the cartilage did not demonstrate significant differences between condyles with or without cartilage lesions. The dGEMRIC results did not show significantly lower values of the affected condyle compared with the opposite condyle and the contra-lateral knee in any of the ROIs. The intraclass correlation coefficient (ICC) of the dGEMRIC readings was 0.882. The MRI T2 mapping and the dGEMRIC confirmed the arthroscopic findings that normal articular cartilage surrounded the cartilage lesion, reflecting normal variation in articular cartilage quality. NCT00885729 , registered April 17 2009.

Iterative framework radiation hybrid mapping

USDA-ARS?s Scientific Manuscript database

Building comprehensive radiation hybrid maps for large sets of markers is a computationally expensive process, since the basic mapping problem is equivalent to the traveling salesman problem. The mapping problem is also susceptible to noise, and as a result, it is often beneficial to remove markers ...

Instructor-Led Approach to Integrating an Augmented Reality Sandbox into a Large-Enrollment Introductory Geoscience Course for Nonmajors Produces No Gains

ERIC Educational Resources Information Center

Giorgis, Scott; Mahlen, Nancy; Anne, Kirk

2017-01-01

The augmented reality (AR) sandbox bridges the gap between two-dimensional (2D) and three-dimensional (3D) visualization by projecting a digital topographic map onto a sandbox landscape. As the landscape is altered, the map dynamically adjusts, providing an opportunity to discover how to read topographic maps. We tested the hypothesis that the AR…

Method and system for progressive mesh storage and reconstruction using wavelet-encoded height fields

NASA Technical Reports Server (NTRS)

Baxes, Gregory A. (Inventor); Linger, Timothy C. (Inventor)

2011-01-01

Systems and methods are provided for progressive mesh storage and reconstruction using wavelet-encoded height fields. A method for progressive mesh storage includes reading raster height field data, and processing the raster height field data with a discrete wavelet transform to generate wavelet-encoded height fields. In another embodiment, a method for progressive mesh storage includes reading texture map data, and processing the texture map data with a discrete wavelet transform to generate wavelet-encoded texture map fields. A method for reconstructing a progressive mesh from wavelet-encoded height field data includes determining terrain blocks, and a level of detail required for each terrain block, based upon a viewpoint. Triangle strip constructs are generated from vertices of the terrain blocks, and an image is rendered utilizing the triangle strip constructs. Software products that implement these methods are provided.

Method and system for progressive mesh storage and reconstruction using wavelet-encoded height fields

NASA Technical Reports Server (NTRS)

Baxes, Gregory A. (Inventor)

2010-01-01

Systems and methods are provided for progressive mesh storage and reconstruction using wavelet-encoded height fields. A method for progressive mesh storage includes reading raster height field data, and processing the raster height field data with a discrete wavelet transform to generate wavelet-encoded height fields. In another embodiment, a method for progressive mesh storage includes reading texture map data, and processing the texture map data with a discrete wavelet transform to generate wavelet-encoded texture map fields. A method for reconstructing a progressive mesh from wavelet-encoded height field data includes determining terrain blocks, and a level of detail required for each terrain block, based upon a viewpoint. Triangle strip constructs are generated from vertices of the terrain blocks, and an image is rendered utilizing the triangle strip constructs. Software products that implement these methods are provided.

Mapping RNA-seq Reads with STAR

PubMed Central

Dobin, Alexander; Gingeras, Thomas R.

2015-01-01

Mapping of large sets of high-throughput sequencing reads to a reference genome is one of the foundational steps in RNA-seq data analysis. The STAR software package performs this task with high levels of accuracy and speed. In addition to detecting annotated and novel splice junctions, STAR is capable of discovering more complex RNA sequence arrangements, such as chimeric and circular RNA. STAR can align spliced sequences of any length with moderate error rates providing scalability for emerging sequencing technologies. STAR generates output files that can be used for many downstream analyses such as transcript/gene expression quantification, differential gene expression, novel isoform reconstruction, signal visualization, and so forth. In this unit we describe computational protocols that produce various output files, use different RNA-seq datatypes, and utilize different mapping strategies. STAR is Open Source software that can be run on Unix, Linux or Mac OS X systems. PMID:26334920

Mapping RNA-seq Reads with STAR.

PubMed

Dobin, Alexander; Gingeras, Thomas R

2015-09-03

Mapping of large sets of high-throughput sequencing reads to a reference genome is one of the foundational steps in RNA-seq data analysis. The STAR software package performs this task with high levels of accuracy and speed. In addition to detecting annotated and novel splice junctions, STAR is capable of discovering more complex RNA sequence arrangements, such as chimeric and circular RNA. STAR can align spliced sequences of any length with moderate error rates, providing scalability for emerging sequencing technologies. STAR generates output files that can be used for many downstream analyses such as transcript/gene expression quantification, differential gene expression, novel isoform reconstruction, and signal visualization. In this unit, we describe computational protocols that produce various output files, use different RNA-seq datatypes, and utilize different mapping strategies. STAR is open source software that can be run on Unix, Linux, or Mac OS X systems. Copyright © 2015 John Wiley & Sons, Inc.

Audiovisual communication of object-names improves the spatial accuracy of recalled object-locations in topographic maps.

PubMed

Lammert-Siepmann, Nils; Bestgen, Anne-Kathrin; Edler, Dennis; Kuchinke, Lars; Dickmann, Frank

2017-01-01

Knowing the correct location of a specific object learned from a (topographic) map is fundamental for orientation and navigation tasks. Spatial reference systems, such as coordinates or cardinal directions, are helpful tools for any geometric localization of positions that aims to be as exact as possible. Considering modern visualization techniques of multimedia cartography, map elements transferred through the auditory channel can be added easily. Audiovisual approaches have been discussed in the cartographic community for many years. However, the effectiveness of audiovisual map elements for map use has hardly been explored so far. Within an interdisciplinary (cartography-cognitive psychology) research project, it is examined whether map users remember object-locations better if they do not just read the corresponding place names, but also listen to them as voice recordings. This approach is based on the idea that learning object-identities influences learning object-locations, which is crucial for map-reading tasks. The results of an empirical study show that the additional auditory communication of object names not only improves memory for the names (object-identities), but also for the spatial accuracy of their corresponding object-locations. The audiovisual communication of semantic attribute information of a spatial object seems to improve the binding of object-identity and object-location, which enhances the spatial accuracy of object-location memory.

Audiovisual communication of object-names improves the spatial accuracy of recalled object-locations in topographic maps

PubMed Central

Bestgen, Anne-Kathrin; Edler, Dennis; Kuchinke, Lars; Dickmann, Frank

2017-01-01

Knowing the correct location of a specific object learned from a (topographic) map is fundamental for orientation and navigation tasks. Spatial reference systems, such as coordinates or cardinal directions, are helpful tools for any geometric localization of positions that aims to be as exact as possible. Considering modern visualization techniques of multimedia cartography, map elements transferred through the auditory channel can be added easily. Audiovisual approaches have been discussed in the cartographic community for many years. However, the effectiveness of audiovisual map elements for map use has hardly been explored so far. Within an interdisciplinary (cartography-cognitive psychology) research project, it is examined whether map users remember object-locations better if they do not just read the corresponding place names, but also listen to them as voice recordings. This approach is based on the idea that learning object-identities influences learning object-locations, which is crucial for map-reading tasks. The results of an empirical study show that the additional auditory communication of object names not only improves memory for the names (object-identities), but also for the spatial accuracy of their corresponding object-locations. The audiovisual communication of semantic attribute information of a spatial object seems to improve the binding of object-identity and object-location, which enhances the spatial accuracy of object-location memory. PMID:29059237

Data communications in a parallel active messaging interface of a parallel computer

DOEpatents

Blocksome, Michael A.; Ratterman, Joseph D.; Smith, Brian E.

2014-09-02

Eager send data communications in a parallel active messaging interface (`PAMI`) of a parallel computer, the PAMI composed of data communications endpoints that specify a client, a context, and a task, including receiving an eager send data communications instruction with transfer data disposed in a send buffer characterized by a read/write send buffer memory address in a read/write virtual address space of the origin endpoint; determining for the send buffer a read-only send buffer memory address in a read-only virtual address space, the read-only virtual address space shared by both the origin endpoint and the target endpoint, with all frames of physical memory mapped to pages of virtual memory in the read-only virtual address space; and communicating by the origin endpoint to the target endpoint an eager send message header that includes the read-only send buffer memory address.

Data communications in a parallel active messaging interface of a parallel computer

DOEpatents

Blocksome, Michael A.; Ratterman, Joseph D.; Smith, Brian E.

2014-09-16

Eager send data communications in a parallel active messaging interface (`PAMI`) of a parallel computer, the PAMI composed of data communications endpoints that specify a client, a context, and a task, including receiving an eager send data communications instruction with transfer data disposed in a send buffer characterized by a read/write send buffer memory address in a read/write virtual address space of the origin endpoint; determining for the send buffer a read-only send buffer memory address in a read-only virtual address space, the read-only virtual address space shared by both the origin endpoint and the target endpoint, with all frames of physical memory mapped to pages of virtual memory in the read-only virtual address space; and communicating by the origin endpoint to the target endpoint an eager send message header that includes the read-only send buffer memory address.

Digital map databases in support of avionic display systems

NASA Astrophysics Data System (ADS)

Trenchard, Michael E.; Lohrenz, Maura C.; Rosche, Henry, III; Wischow, Perry B.

1991-08-01

The emergence of computerized mission planning systems (MPS) and airborne digital moving map systems (DMS) has necessitated the development of a global database of raster aeronautical chart data specifically designed for input to these systems. The Naval Oceanographic and Atmospheric Research Laboratory''s (NOARL) Map Data Formatting Facility (MDFF) is presently dedicated to supporting these avionic display systems with the development of the Compressed Aeronautical Chart (CAC) database on Compact Disk Read Only Memory (CDROM) optical discs. The MDFF is also developing a series of aircraft-specific Write-Once Read Many (WORM) optical discs. NOARL has initiated a comprehensive research program aimed at improving the pilots'' moving map displays current research efforts include the development of an alternate image compression technique and generation of a standard set of color palettes. The CAC database will provide digital aeronautical chart data in six different scales. CAC is derived from the Defense Mapping Agency''s (DMA) Equal Arc-second (ARC) Digitized Raster Graphics (ADRG) a series of scanned aeronautical charts. NOARL processes ADRG to tailor the chart image resolution to that of the DMS display while reducing storage requirements through image compression techniques. CAC is being distributed by DMA as a library of CDROMs.

Evidence-based interventions for reading and language difficulties: creating a virtuous circle.

PubMed

Snowling, Margaret J; Hulme, Charles

2011-03-01

BACKGROUND. Children may experience two very different forms of reading problem: decoding difficulties (dyslexia) and reading comprehension difficulties. Decoding difficulties appear to be caused by problems with phonological (speech sound) processing. Reading comprehension difficulties in contrast appear to be caused by problems with 'higher level' language difficulties including problems with semantics (including deficient knowledge of word meanings) and grammar (knowledge of morphology and syntax). AIMS. We review evidence concerning the nature, causes of, and treatments for children's reading difficulties. We argue that any well-founded educational intervention must be based on a sound theory of the causes of a particular form of learning difficulty, which in turn must be based on an understanding of how a given skill is learned by typically developing children. Such theoretically motivated interventions should in turn be evaluated in randomized controlled trials (RCTs) to establish whether they are effective, and for whom. RESULTS. There is now considerable evidence showing that phonologically based interventions are effective in ameliorating children's word level decoding difficulties, and a smaller evidence base showing that reading and oral language (OL) comprehension difficulties can be ameliorated by suitable interventions to boost vocabulary and broader OL skills. CONCLUSIONS. The process of developing theories about the origins of children's educational difficulties and evaluating theoretically motivated treatments in RCTs, produces a 'virtuous circle' whereby theory informs practice, and the evaluation of effective interventions in turn feeds back to inform and refine theories about the nature and causes of children's reading and language difficulties. ©2010 The British Psychological Society.

Cognitive processes in children's reading and attention: the role of working memory, divided attention, and response inhibition.

PubMed

Savage, Robert; Cornish, Kim; Manly, Tom; Hollis, Chris

2006-08-01

Children experiencing attention difficulties have documented cognitive deficits in working memory (WM), response inhibition and dual tasks. Recent evidence suggests however that these same cognitive processes are also closely associated with reading acquisition. This paper therefore explores whether these variables predicted attention difficulties or reading among 123 children with and without significant attention problems sampled from the school population. Children were screened using current WM and attention task measures. Three factors explained variance in WM and attention tasks. Response inhibition tasks loaded mainly with central executive measures, but a dual processing task loaded with the visual-spatial WM measures. Phonological loop measures loaded independently of attention measures. After controls for age, IQ and attention-group membership, phonological loop and 'central processing' measures both predicted reading ability. A 'visual memory/dual-task' factor predicted attention group membership after controls for age, IQ and reading ability. Results thus suggest that some of the processes previously assumed to be predictive of attention problems may reflect processes involved in reading acquisition. Visual memory and dual-task functioning are, however, purer indices of cognitive difficulty in children experiencing attention problems.

Computerization in industry causes problems for people with reading and writing difficulties (dyslexia).

PubMed

Knutsson, A

1986-01-01

For 10 years computerization in industry has advanced at a rapid pace. A problem which has not received attention is that of people with reading and writing difficulties who experience severe problems when they have to communicate with a computer monitor screen. These individuals are often embarrassed by their difficulties and conceal them from their fellow workers. A number of case studies are described which show the form the problems can take. In one case, an employee was compelled to move from department to department as each was computerized in turn. Computers transform a large number of manual tasks in industry into jobs which call for reading and writing skills. Better education at elementary school and at the workplace in connection with computerization are the most important means of overcoming this problem. Moreover, computer programs could be written in a more human way.

Therapeutic effects of problem-solving training and play-reading groups.

PubMed

Coché, E; Douglas, A A

1977-07-01

Twenty-five adult patients of a private psychiatric hospital participated in small groups that convened for eight sessions in order to increase skills in interpersonal problem solving. The groups repeatedly went through the steps of (a) bringing up a problem; (b) clarifying it; (c) proposing solutions; and(d) weighing the solutions. A control grop of 29 patients did not receive problem-solving training. A "placebo" sample of 21 Ss also met in small groups, but their task was to read comedies together. The results obtained through a series of analyses of covariance showed that the experimental condition was more successful than the other two in improving people's impulse control, self-esteem and feeling of competence. The play-reading condition was found to be as helpful as the problem-solving groups in reducing depression and general psychopathology. Control patients showed significantly less improvement than did patients in the other conditions.

Reading, Writing, … and Arithmetic?

ERIC Educational Resources Information Center

Sussman, Dan

2017-01-01

How can the best of mathematical problem-based learning be applied toward literature classes? Daniel Sussman, an English teacher at Moorestown Friends School in New Jersey, discusses how he uses problem solving tactics to encourage close, critical reading of fiction texts in his Jewish literature and poetry classes. He explores the challenges of…

Aliteracy: What Teachers Can Do to Keep Johnny Reading.

ERIC Educational Resources Information Center

Decker, Barbara Cooper

Aliteracy, the ability to read but the unwillingness to do so, is a growing problem in American society. Aliteracy crosses all socioeconomic levels, thereby allowing autocratic, charismatic leaders to influence thinking and decision-making. Social changes that have contributed to the problem of aliteracy include the influence of television on…

The Cumulative Effect of Hyperactivity and Peer Relationships on Reading Comprehension

ERIC Educational Resources Information Center

Johnson, Kaprea F.

2014-01-01

The impact of hyperactivity and peer relationships on academic achievement has long been highlighted in the professional literature. This study highlights how much variation in reading comprehension scores, an indicator of academic achievement, are accounted for by hyperactivity, conduct problems, and peer problems. The participants included 129…

Home Environmental and Behavioral Risk Indices for Reading Achievement.

PubMed

Taylor, Jeanette; Ennis, Chelsea R; Hart, Sara A; Mikolajewski, Amy J; Schatschneider, Christopher

2017-07-01

The goal of this study was to identify home environmental and temperament/behavior variables that best predict standardized reading comprehension scores among school-aged children. Data from 269 children aged 9-16 ( M = 12.08; SD = 1.62) were used in discriminant function analyses to create the Home and Behavior indices. Family income was controlled in each index. The final Home and Behavior models each classified around 75% of cases correctly (reading comprehension at grade level vs. not). Each index was then used to predict other outcomes related to reading. Results showed that Home and/or Behavior accounted for 4-7% of the variance in reading fluency and spelling and 20-35% of the variance in parent-rated problems in math, social anxiety, and other dimensions. These metrics show promise as environmental and temperament/behavior risk scores that could be used to predict and potentially screen for further assessment of reading related problems.

Expertise and age differences in pilot decision making.

PubMed

Morrow, Daniel G; Miller, Lisa M Soederberg; Ridolfo, Heather E; Magnor, Clifford; Fischer, Ute M; Kokayeff, Nina K; Stine-Morrow, Elizabeth A L

2009-01-01

We examined the influence of age and expertise on pilot decision making. Older and younger expert and novice pilots read at their own pace scenarios describing simpler or more complex flight situations. Then in a standard interview they discussed the scenario problem and how they would respond. Protocols were coded for identification of problem and solutions to this problem, and frequency of elaborations on problem and solution. Scenario comprehension was measured as differential reading time allocation to problem-critical information and scenario memory by the accuracy of answering questions about the scenarios after the interview. All groups accurately identified the problems, but experts elaborated problem descriptions more than novices did. Experts also spent more time reading critical information in the complex scenarios, which may reflect time needed to develop elaborate situation models of the problems. Expertise comprehension benefits were similar for older and younger pilots. Older experts were especially likely to elaborate the problem compared to younger experts, while older novices were less likely to elaborate the problem and to identify appropriate solutions compared to their younger counterparts. The findings suggest age invariance in knowledge-based comprehension relevant to pilot decision making.

Characteristics of Students at Risk for Mathematics Difficulties Predicting Arithmetic Word Problem Solving Performance: The Role of Attention, Behavior, and Reading

ERIC Educational Resources Information Center

Jitendra, Asha K.; Corroy, Kelly Cozine; Dupuis, Danielle N.

2013-01-01

The purposes of this study were (a) to evaluate differences in arithmetic word problem solving between high and low at-risk students for mathematics difficulties (MD) and (b) to assess the influence of attention, behavior, reading, and socio-economic status (SES) in predicting the word problem solving performance of third-grade students with MD.…

The Comprehension Problems for Second-Language Learners with Poor Reading Comprehension despite Adequate Decoding: A Meta-Analysis

PubMed Central

Spencer, Mercedes; Wagner, Richard K.

2016-01-01

We conducted a meta-analysis of 16 existing studies to examine the nature of the comprehension problems for children who were second-language learners with poor reading comprehension despite adequate decoding. Results indicated that these children had deficits in oral language (d = −0.80), but these deficits were not as severe as their reading comprehension deficit (d = −2.47). Second-language learners also had weaker oral language skills compared to native-speaking children regardless of comprehension status (d = −0.84). We discuss theoretical and practical implications of the finding that second-language learners who are poor at reading comprehension despite adequate decoding have deficits in oral language but the deficit is not sufficient to explain their deficit in reading comprehension. PMID:28461711

The Comprehension Problems for Second-Language Learners with Poor Reading Comprehension despite Adequate Decoding: A Meta-Analysis.

PubMed

Spencer, Mercedes; Wagner, Richard K

2017-05-01

We conducted a meta-analysis of 16 existing studies to examine the nature of the comprehension problems for children who were second-language learners with poor reading comprehension despite adequate decoding. Results indicated that these children had deficits in oral language ( d = -0.80), but these deficits were not as severe as their reading comprehension deficit ( d = -2.47). Second-language learners also had weaker oral language skills compared to native-speaking children regardless of comprehension status ( d = -0.84). We discuss theoretical and practical implications of the finding that second-language learners who are poor at reading comprehension despite adequate decoding have deficits in oral language but the deficit is not sufficient to explain their deficit in reading comprehension.

Keratometry obtained by corneal mapping versus the IOLMaster in the prediction of postoperative refraction in routine cataract surgery.

PubMed

Dulku, Simon; Smith, Henry B; Antcliff, Richard J

2013-01-01

To establish whether simulated keratometry values obtained by corneal mapping (videokeratography) would provide a superior refractive outcome to those obtained by Zeiss IOLMaster (partial coherence interferometry) in routine cataract surgery. Prospective, non-randomized, single-surgeon study set at the The Royal United Hospital, Bath, UK, District General Hospital. Thirty-three patients undergoing routine cataract surgery in the absence of significant ocular comorbidity. Conventional biometry was recorded using the Zeiss IOLMaster. Postoperative refraction was calculated using the SRK/T formula and the most appropriate power of lens implanted. Preoperative keratometry values were also obtained using Humphrey Instruments Atlas Version A6 corneal mapping. Achieved refraction was compared with predicted refraction for the two methods of keratometry after the A-constants were optimized to obtain a mean arithmetic error of zero dioptres for each device. The mean absolute prediction error was 0.39 dioptres (standard deviation 0.29) for IOLMaster and 0.48 dioptres (standard deviation 0.31) for corneal mapping (P = 0.0015). Keratometry readings between the devices were highly correlated by Spearman correlation (0.97). The Bland-Altman plot demonstrated close agreement between keratometers, with a bias of 0.0079 dioptres and 95% limits of agreement of -0.48-0.49 dioptres. The IOLMaster was superior to Humphrey Atlas A6 corneal mapping in the prediction of postoperative refraction. This difference could not have been predicted from the keratometry readings alone. When comparing biometry devices, close agreement between readings should not be considered a substitute for actual postoperative refraction data. © 2012 The Authors. Clinical and Experimental Ophthalmology © 2012 Royal Australian and New Zealand College of Ophthalmologists.

College and Adult Reading X: The Tenth Yearbook of the North Central Reading Association.

ERIC Educational Resources Information Center

Fisher, Joseph A., Ed.

Including sections on research, programs, and professional problems and issues, this yearbook contains presentations given at the 1978 and 1979 meetings of the North Central Reading Association. Papers include: "The Effects of Anxiety on Reading Comprehension" (David Wark and others); "Some Effects of Anxiety on University Students" (J. Michael…

The Affects of Not Reading: Hating Characters, Being Bored, Feeling Stupid

ERIC Educational Resources Information Center

Poletti, Anna; Seaboyer, Judith; Kennedy, Rosanne; Barnett, Tully; Douglas, Kate

2016-01-01

This article brings recent debates in literary studies regarding the practice of close reading into conversation with Derek Attridge's idea of "readerly hospitality" (2004) to diagnose the problem of students in undergraduate literary studies programme not completing set reading. We argue that the method of close reading depends on…

Reading and the Aged: A Statement of the Problem.

ERIC Educational Resources Information Center

Kingston, Albert J., Jr.

A review of studies concerning the reading habits of people 65 years old or older shows that females spend more time reading then do males; senior citizens do not suddenly develop new or extensive reading habits; they prefer light romance with no sex, biographies, westerns, and mysteries; intellectual and physical disabilities are not major…

Text-to-Speech and Reading While Listening: Reading Support for Individuals with Severe Traumatic Brain Injury

ERIC Educational Resources Information Center

Harvey, Judy

2013-01-01

Individuals with severe traumatic brain injury (TBI) often have reading challenges. They maintain or reestablish basic decoding and word recognition skills following injury, but problems with reading comprehension often persist. Practitioners have the potential to accommodate struggling readers by changing the presentational mode of text in a…

Epilogue: Reading Comprehension Is Not a Single Ability--Implications for Assessment and Instruction

ERIC Educational Resources Information Center

Kamhi, Alan G.; Catts, Hugh W.

2017-01-01

Purpose: In this epilogue, we review the 4 response articles and highlight the implications of a multidimensional view of reading for the assessment and instruction of reading comprehension. Method: We reiterate the problems with standardized tests of reading comprehension and discuss the advantages and disadvantages of recently developed…

Reading and Comprehension Levels in a Sample of Urban, Low-Income Persons

ERIC Educational Resources Information Center

Delgado, Cheryl; Weitzel, Marilyn

2013-01-01

Objective: Because health literacy is related to healthcare outcomes, this study looked at reading and comprehension levels in a sample of urban, low-income persons. Design: This was a descriptive exploration of reading comprehension levels, controlled for medical problems that could impact on vision and therefore ability to read. Setting: Ninety…

The Effect of Text-to-Self Reading Strategies on Reading Comprehension

ERIC Educational Resources Information Center

Cutright, Cathy Arlene

2010-01-01

Middle-school male students currently face a disadvantage in reading comprehension compared to female students. Research suggests the problem is that more male students score below grade level in reading comprehension because they require more cognitive scaffolding. The purpose of this study was to evaluate the effectiveness of text-to-self…

Complex Word Reading in Dutch Deaf Children and Adults

ERIC Educational Resources Information Center

van Hoogmoed, Anne H.; Knoors, Harry; Schreuder, Robert; Verhoeven, Ludo

2013-01-01

Children who are deaf are often delayed in reading comprehension. This delay could be due to problems in morphological processing during word reading. In this study, we investigated whether 6th grade deaf children and adults are delayed in comparison to their hearing peers in reading complex derivational words and compounds compared to…

PigGIS: Pig Genomic Informatics System

PubMed Central

Ruan, Jue; Guo, Yiran; Li, Heng; Hu, Yafeng; Song, Fei; Huang, Xin; Kristiensen, Karsten; Bolund, Lars; Wang, Jun

2007-01-01

Pig Genomic Information System (PigGIS) is a web-based depository of pig (Sus scrofa) genomic learning mainly engineered for biomedical research to locate pig genes from their human homologs and position single nucleotide polymorphisms (SNPs) in different pig populations. It utilizes a variety of sequence data, including whole genome shotgun (WGS) reads and expressed sequence tags (ESTs), and achieves a successful mapping solution to the low-coverage genome problem. With the data presently available, we have identified a total of 15 700 pig consensus sequences covering 18.5 Mb of the homologous human exons. We have also recovered 18 700 SNPs and 20 800 unique 60mer oligonucleotide probes for future pig genome analyses. PigGIS can be freely accessed via the web at and . PMID:17090590

Robustness of controllability and observability of linear time-varying systems with application to the emergency control of power systems

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

Sastry, S. S.; Desoer, C. A.

1980-01-01

Fixed point methods from nonlinear anaysis are used to establish conditions under which the uniform complete controllability of linear time-varying systems is preserved under non-linear perturbations in the state dynamics and the zero-input uniform complete observability of linear time-varying systems is preserved under non-linear perturbation in the state dynamics and output read out map. Algorithms for computing the specific input to steer the perturbed systems from a given initial state to a given final state are also presented. As an application, a very specific emergency control of an interconnected power system is formulated as a steering problem and it ismore » shown that this emergency control is indeed possible in finite time.« less

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…

The Effects of Guided Reading Instruction on the Reading Comprehension and Reading Attitudes of Fourth-Grade At-Risk Students

ERIC Educational Resources Information Center

Bruce, Laquanda T.

2010-01-01

America's public schools have faced challenges in educating students, particularly those identified as at risk. According to the No Child Left Behind Act, nearly 70% of 4th grade students are unable to perform on a basic level on national reading tests. The research problem in this study addressed the significance of guided reading instruction,…

High School Students with Reading Comprehension Difficulties: Results of a Randomized Control Trial of a Two-Year Reading Intervention

ERIC Educational Resources Information Center

Vaughn, Sharon; Roberts, Greg; Wexler, Jade; Vaughn, Michael G.; Fall, Anna-Mária; Schnakenberg, Jennifer B.

2015-01-01

A 2-year, randomized control trial with 9th to 10th grade students with significant reading problems was provided for 50 minutes a day in small groups. Comparison students were provided an elective class and treatment students the reading intervention. Students were identified as demonstrating reading difficulties through failure on their state…

Effects of An Integrated Format for Reading Instruction on the Comprehension and Word-Recognition Performance of Fourth- and Fifth-Grade Students Who Exhibit Severe Reading Problems.

ERIC Educational Resources Information Center

Parmer, Lavada Jacumin; Thames, Dana G.; Kazelskis, Richard

A study examined the effectiveness of an integrated language arts instructional format for teaching reading compared with the effectiveness of the typical traditional reading program. The study investigated the effectiveness of approaches that are representative of both viewpoints of the reading process (i.e., word recognition and the construction…

Introduction to the Clinical Forum: Reading Comprehension Is Not a Single Ability.

PubMed

Gray, Shelley

2017-04-20

In this introduction to the clinical forum on reading comprehension, the Editor-in-Chief of Language, Speech, and Hearing Services in Schools provides data on our national reading comprehension problem, resources for increasing our understanding of reading comprehension, and a call to action for speech-language pathologists to work with educational teams to address poor reading comprehension in school-age children.

UGbS-Flex, a novel bioinformatics pipeline for imputation-free SNP discovery in polyploids without a reference genome: finger millet as a case study.

PubMed

Qi, Peng; Gimode, Davis; Saha, Dipnarayan; Schröder, Stephan; Chakraborty, Debkanta; Wang, Xuewen; Dida, Mathews M; Malmberg, Russell L; Devos, Katrien M

2018-06-15

Research on orphan crops is often hindered by a lack of genomic resources. With the advent of affordable sequencing technologies, genotyping an entire genome or, for large-genome species, a representative fraction of the genome has become feasible for any crop. Nevertheless, most genotyping-by-sequencing (GBS) methods are geared towards obtaining large numbers of markers at low sequence depth, which excludes their application in heterozygous individuals. Furthermore, bioinformatics pipelines often lack the flexibility to deal with paired-end reads or to be applied in polyploid species. UGbS-Flex combines publicly available software with in-house python and perl scripts to efficiently call SNPs from genotyping-by-sequencing reads irrespective of the species' ploidy level, breeding system and availability of a reference genome. Noteworthy features of the UGbS-Flex pipeline are an ability to use paired-end reads as input, an effective approach to cluster reads across samples with enhanced outputs, and maximization of SNP calling. We demonstrate use of the pipeline for the identification of several thousand high-confidence SNPs with high representation across samples in an F 3 -derived F 2 population in the allotetraploid finger millet. Robust high-density genetic maps were constructed using the time-tested mapping program MAPMAKER which we upgraded to run efficiently and in a semi-automated manner in a Windows Command Prompt Environment. We exploited comparative GBS with one of the diploid ancestors of finger millet to assign linkage groups to subgenomes and demonstrate the presence of chromosomal rearrangements. The paper combines GBS protocol modifications, a novel flexible GBS analysis pipeline, UGbS-Flex, recommendations to maximize SNP identification, updated genetic mapping software, and the first high-density maps of finger millet. The modules used in the UGbS-Flex pipeline and for genetic mapping were applied to finger millet, an allotetraploid selfing species without a reference genome, as a case study. The UGbS-Flex modules, which can be run independently, are easily transferable to species with other breeding systems or ploidy levels.

Development and evaluation of a specialized task taxonomy for spatial planning - A map literacy experiment with topographic maps

NASA Astrophysics Data System (ADS)

Rautenbach, Victoria; Coetzee, Serena; Çöltekin, Arzu

2017-05-01

Topographic maps are among the most commonly used map types, however, their complex and information-rich designs depicting natural, human-made and cultural features make them difficult to read. Regardless of their complexity, spatial planners make extensive use of topographic maps in their work. On the other hand, various studies suggest that map literacy among the development planning professionals in South Africa is not very high. The widespread use of topographic maps combined with the low levels of map literacy presents challenges for effective development planning. In this paper we address some of these challenges by developing a specialized task taxonomy based on systematically assessed map literacy levels; and conducting an empirical experiment with topographic maps to evaluate our task taxonomy. In such empirical studies if non-realistic tasks are used, the results of map literacy tests may be skewed. Furthermore, experience and familiarity with the studied map type play a role in map literacy. There is thus a need to develop map literacy tests aimed at planners specifically. We developed a taxonomy of realistic map reading tasks typically executed during the planning process. The taxonomy defines six levels tasks of increasing difficulty and complexity, ranging from recognising symbols to extracting knowledge. We hypothesized that competence in the first four levels indicates functional map literacy. In this paper, we present results from an empirical experiment with 49 map literate participants solving a subset of tasks from the first four levels of the taxonomy with a topographic map. Our findings suggest that the proposed taxonomy is a good reference for evaluating topographic map literacy. Participants solved the tasks on all four levels as expected and we therefore conclude that the experiment based on the first four levels of the taxonomy successfully determined the functional map literacy of the participants. We plan to continue the study for the remaining levels, repeat the experiments with a group of map illiterate participants to confirm that the taxonomy can also be used to determine map illiteracy.

In situ data analytics and indexing of protein trajectories.

PubMed

Johnston, Travis; Zhang, Boyu; Liwo, Adam; Crivelli, Silvia; Taufer, Michela

2017-06-15

The transition toward exascale computing will be accompanied by a performance dichotomy. Computational peak performance will rapidly increase; I/O performance will either grow slowly or be completely stagnant. Essentially, the rate at which data are generated will grow much faster than the rate at which data can be read from and written to the disk. MD simulations will soon face the I/O problem of efficiently writing to and reading from disk on the next generation of supercomputers. This article targets MD simulations at the exascale and proposes a novel technique for in situ data analysis and indexing of MD trajectories. Our technique maps individual trajectories' substructures (i.e., α-helices, β-strands) to metadata frame by frame. The metadata captures the conformational properties of the substructures. The ensemble of metadata can be used for automatic, strategic analysis within a trajectory or across trajectories, without manually identify those portions of trajectories in which critical changes take place. We demonstrate our technique's effectiveness by applying it to 26.3k helices and 31.2k strands from 9917 PDB proteins and by providing three empirical case studies. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Spatial Cognition and Map Interpretation

DTIC Science & Technology

1987-09-01

Terrain association Spatial cognition Map reading Videogames aa mldm II naeaaaaiy and Hontlty by block numbor) Spatial memory span Orientation...ability. Finally, field and classroom performance was compared to wayfinding in a simulated ( videogame ) environment in which position coordinates were...a simulated ( videogame ) environment. Findings: MITAC instruction significantly improved the experimental group’s ability to perform terrain

27 CFR 9.128 - Seneca Lake.

Code of Federal Regulations, 2012 CFR

2012-04-01

... bridge over the New York State Barge Canal, follow the Canal south approximately 0.2 miles to the mouth... the Reading Center, N.Y. map; (5) Proceed west approximately 0.7 miles on County Road 23 to its... Yan, N.Y. and Dresden, N.Y. maps, for approximately 18 miles to its junction with an unnamed light...

27 CFR 9.128 - Seneca Lake.

Code of Federal Regulations, 2013 CFR

2013-04-01

... bridge over the New York State Barge Canal, follow the Canal south approximately 0.2 miles to the mouth... the Reading Center, N.Y. map; (5) Proceed west approximately 0.7 miles on County Road 23 to its... Yan, N.Y. and Dresden, N.Y. maps, for approximately 18 miles to its junction with an unnamed light...

27 CFR 9.128 - Seneca Lake.

Code of Federal Regulations, 2010 CFR

2010-04-01

... bridge over the New York State Barge Canal, follow the Canal south approximately 0.2 miles to the mouth... the Reading Center, N.Y. map; (5) Proceed west approximately 0.7 miles on County Road 23 to its... Yan, N.Y. and Dresden, N.Y. maps, for approximately 18 miles to its junction with an unnamed light...

27 CFR 9.128 - Seneca Lake.

Code of Federal Regulations, 2011 CFR

2011-04-01

... bridge over the New York State Barge Canal, follow the Canal south approximately 0.2 miles to the mouth... the Reading Center, N.Y. map; (5) Proceed west approximately 0.7 miles on County Road 23 to its... Yan, N.Y. and Dresden, N.Y. maps, for approximately 18 miles to its junction with an unnamed light...

27 CFR 9.128 - Seneca Lake.

Code of Federal Regulations, 2014 CFR

2014-04-01

... bridge over the New York State Barge Canal, follow the Canal south approximately 0.2 miles to the mouth... the Reading Center, N.Y. map; (5) Proceed west approximately 0.7 miles on County Road 23 to its... Yan, N.Y. and Dresden, N.Y. maps, for approximately 18 miles to its junction with an unnamed light...

Computer Games versus Maps before Reading Stories: Priming Readers' Spatial Situation Models

ERIC Educational Resources Information Center

Smith, Glenn Gordon; Majchrzak, Dan; Hayes, Shelley; Drobisz, Jack

2011-01-01

The current study investigated how computer games and maps compare as preparation for readers to comprehend and retain spatial relations in text narratives. Readers create situation models of five dimensions: spatial, temporal, causal, goal, and protagonist (Zwaan, Langston, & Graesser 1995). Of these five, readers mentally model the spatial…

Back to the Basics: Birmingham, Alabama, Measurement and Scale

ERIC Educational Resources Information Center

Handley, Lawrence R.; Lockwood, Catherine M.; Handley, Nathan

2005-01-01

"Back to the Basics: Birmingham, Alabama" is the fourth in a series of workshops that focus on teaching foundational map reading and spatial differentiation skills. It is the second published exercise from the Back to the Basics series developed by the Wetland Education through Maps and Aerial Photography (WETMAAP) Program (see…

Back to the Basics: Lake Tahoe, California/Nevada--Spatial Measurement

ERIC Educational Resources Information Center

Handley, Lawrence R.; Lockwood, Catherine M.; Handley, Nathan

2006-01-01

"Back to the Basics: South Lake Tahoe, California/Nevada" continues the series of exercises on teaching foundational map reading and spatial differentiation skills. It is the third published exercise from the Back to the Basics series developed by the Wetland Education through Maps and Aerial Photography (WETMAAP) Program. The current…

Differences in Information Mapping Strategies in Left and Right Brain Learners.

ERIC Educational Resources Information Center

Hauck, LaVerne S., Jr.

The Information Mapping technique was used to present a learning packet, and its usefulness in helping right-brain cerebrally dominant students to achieve the same level of subject mastery as their left-brain counterparts was examined. Reading level, grade point average, and gender were also analyzed. Torrance's "Your Style of Learning and…