The RNA profile of porcine parvovirus 4, a Boca-like virus, is unique among the Parvoviruses

USDA-ARS?s Scientific Manuscript database

Phylogenetically, porcine parvovirus 4 (PPV4) is most related to bovine parvovirus 2 that has two open reading frames (ORFs), but its genome organization resembles that of members of the Bocavirus genus that has three ORFs. Although PPV4 transcribes its genome from a single promoter and the transcri...

A local duplication of the Melanocortin receptor 1 locus in Astyanax

PubMed Central

Gross, Joshua B.; Weagley, James; Stahl, Bethany A.; Ma, Li; Espinasa, Luis; McGaugh, Suzanne E.

2017-01-01

In this study, we report evidence of a novel duplication of Melanocortin receptor 1 (Mc1r) in the cavefish genome. This locus was discovered following the observation of excessive allelic diversity in a ~820 bp fragment of Mc1r amplified via degenerate PCR from a natural population of Astyanax aeneus fish from Guerrero, Mexico. The cavefish genome reveals the presence of two closely related Mc1r open reading frames separated by a 1.46 kb intergenic region. One open reading frame corresponds to the previously reported Mc1r receptor, and the other open reading frame (duplicate copy) is 975 bp in length, encoding a receptor of 325 amino acids. Sequence similarity analyses position both copies in the syntenic region of the single Mc1r locus in 16 representative craniate genomes spanning bony fish (including Astyanax) to mammals, suggesting we discovered tandem duplicates of this important gene. The two Mc1r copies share ~89% sequence similarity, and, within Astyanax, are more similar to one another compared to other melanocortin family members. Future studies will inform the precise functional significance of the duplicated Mc1r locus, and if this novel copy number variant may have adaptive significance for the Astyanax lineage. PMID:28738163

Ribosome rearrangements at the onset of translational bypassing

PubMed Central

Agirrezabala, Xabier; Samatova, Ekaterina; Klimova, Mariia; Zamora, Miguel; Gil-Carton, David; Rodnina, Marina V.; Valle, Mikel

2017-01-01

Bypassing is a recoding event that leads to the translation of two distal open reading frames into a single polypeptide chain. We present the structure of a translating ribosome stalled at the bypassing take-off site of gene 60 of bacteriophage T4. The nascent peptide in the exit tunnel anchors the P-site peptidyl-tRNAGly to the ribosome and locks an inactive conformation of the peptidyl transferase center (PTC). The mRNA forms a short dynamic hairpin in the decoding site. The ribosomal subunits adopt a rolling conformation in which the rotation of the small subunit around its long axis causes the opening of the A-site region. Together, PTC conformation and mRNA structure safeguard against premature termination and read-through of the stop codon and reconfigure the ribosome to a state poised for take-off and sliding along the noncoding mRNA gap. PMID:28630923

Photon-HDF5: An Open File Format for Timestamp-Based Single-Molecule Fluorescence Experiments.

PubMed

Ingargiola, Antonino; Laurence, Ted; Boutelle, Robert; Weiss, Shimon; Michalet, Xavier

2016-01-05

We introduce Photon-HDF5, an open and efficient file format to simplify exchange and long-term accessibility of data from single-molecule fluorescence experiments based on photon-counting detectors such as single-photon avalanche diode, photomultiplier tube, or arrays of such detectors. The format is based on HDF5, a widely used platform- and language-independent hierarchical file format for which user-friendly viewers are available. Photon-HDF5 can store raw photon data (timestamp, channel number, etc.) from any acquisition hardware, but also setup and sample description, information on provenance, authorship and other metadata, and is flexible enough to include any kind of custom data. The format specifications are hosted on a public website, which is open to contributions by the biophysics community. As an initial resource, the website provides code examples to read Photon-HDF5 files in several programming languages and a reference Python library (phconvert), to create new Photon-HDF5 files and convert several existing file formats into Photon-HDF5. To encourage adoption by the academic and commercial communities, all software is released under the MIT open source license. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Photon-HDF5: An Open File Format for Timestamp-Based Single-Molecule Fluorescence Experiments

PubMed Central

Ingargiola, Antonino; Laurence, Ted; Boutelle, Robert; Weiss, Shimon; Michalet, Xavier

2016-01-01

We introduce Photon-HDF5, an open and efficient file format to simplify exchange and long-term accessibility of data from single-molecule fluorescence experiments based on photon-counting detectors such as single-photon avalanche diode, photomultiplier tube, or arrays of such detectors. The format is based on HDF5, a widely used platform- and language-independent hierarchical file format for which user-friendly viewers are available. Photon-HDF5 can store raw photon data (timestamp, channel number, etc.) from any acquisition hardware, but also setup and sample description, information on provenance, authorship and other metadata, and is flexible enough to include any kind of custom data. The format specifications are hosted on a public website, which is open to contributions by the biophysics community. As an initial resource, the website provides code examples to read Photon-HDF5 files in several programming languages and a reference Python library (phconvert), to create new Photon-HDF5 files and convert several existing file formats into Photon-HDF5. To encourage adoption by the academic and commercial communities, all software is released under the MIT open source license. PMID:26745406

Photon-HDF5: an open file format for single-molecule fluorescence experiments using photon-counting detectors

DOE PAGES

Ingargiola, A.; Laurence, T. A.; Boutelle, R.; ...

2015-12-23

We introduce Photon-HDF5, an open and efficient file format to simplify exchange and long term accessibility of data from single-molecule fluorescence experiments based on photon-counting detectors such as single-photon avalanche diode (SPAD), photomultiplier tube (PMT) or arrays of such detectors. The format is based on HDF5, a widely used platform- and language-independent hierarchical file format for which user-friendly viewers are available. Photon-HDF5 can store raw photon data (timestamp, channel number, etc) from any acquisition hardware, but also setup and sample description, information on provenance, authorship and other metadata, and is flexible enough to include any kind of custom data. Themore » format specifications are hosted on a public website, which is open to contributions by the biophysics community. As an initial resource, the website provides code examples to read Photon-HDF5 files in several programming languages and a reference python library (phconvert), to create new Photon-HDF5 files and convert several existing file formats into Photon-HDF5. As a result, to encourage adoption by the academic and commercial communities, all software is released under the MIT open source license.« less

The ferredoxin-thioredoxin reductase variable subunit gene from Anacystis nidulans.

PubMed

Szekeres, M; Droux, M; Buchanan, B B

1991-03-01

The ferredoxin-thioredoxin reductase variable subunit gene of Anacystis nidulans was cloned, and its nucleotide sequence was determined. A single-copy 219-bp open reading frame encoded a protein of 73 amino acid residues, with a calculated Mr of 8,400. The monocistronic transcripts were represented in a 400-base and a less abundant 300-base mRNA form.

Production of foot-and-mouth disease virus capsid proteins by the TEV protease.

PubMed

Puckette, Michael; Smith, Justin D; Gabbert, Lindsay; Schutta, Christopher; Barrera, José; Clark, Benjamin A; Neilan, John G; Rasmussen, Max

2018-06-10

Protective immunity to viral pathogens often includes production of neutralizing antibodies to virus capsid proteins. Many viruses produce capsid proteins by expressing a precursor polyprotein and related protease from a single open reading frame. The foot-and-mouth disease virus (FMDV) expresses a 3C protease (3Cpro) that cleaves a P1 polyprotein intermediate into individual capsid proteins, but the FMDV 3Cpro also degrades many host cell proteins and reduces the viability of host cells, including subunit vaccine production cells. To overcome the limitations of using the a wild-type 3Cpro in FMDV subunit vaccine expression systems, we altered the protease restriction sequences within a FMDV P1 polyprotein to enable production of FMDV capsid proteins by the Tobacco Etch Virus NIa protease (TEVpro). Separate TEVpro and modified FMDV P1 proteins were produced from a single open reading frame by an intervening FMDV 2A sequence. The modified FMDV P1 polyprotein was successfully processed by the TEVpro in both mammalian and bacterial cells. More broadly, this method of polyprotein production and processing may be adapted to other recombinant expression systems, especially plant-based expression. Published by Elsevier B.V.

Death of a dogma: eukaryotic mRNAs can code for more than one protein

PubMed Central

Mouilleron, Hélène; Delcourt, Vivian; Roucou, Xavier

2016-01-01

mRNAs carry the genetic information that is translated by ribosomes. The traditional view of a mature eukaryotic mRNA is a molecule with three main regions, the 5′ UTR, the protein coding open reading frame (ORF) or coding sequence (CDS), and the 3′ UTR. This concept assumes that ribosomes translate one ORF only, generally the longest one, and produce one protein. As a result, in the early days of genomics and bioinformatics, one CDS was associated with each protein-coding gene. This fundamental concept of a single CDS is being challenged by increasing experimental evidence indicating that annotated proteins are not the only proteins translated from mRNAs. In particular, mass spectrometry (MS)-based proteomics and ribosome profiling have detected productive translation of alternative open reading frames. In several cases, the alternative and annotated proteins interact. Thus, the expression of two or more proteins translated from the same mRNA may offer a mechanism to ensure the co-expression of proteins which have functional interactions. Translational mechanisms already described in eukaryotic cells indicate that the cellular machinery is able to translate different CDSs from a single viral or cellular mRNA. In addition to summarizing data showing that the protein coding potential of eukaryotic mRNAs has been underestimated, this review aims to challenge the single translated CDS dogma. PMID:26578573

Double versus single reading of mammograms in a breast cancer screening programme: a cost-consequence analysis.

PubMed

Posso, Margarita C; Puig, Teresa; Quintana, Ma Jesus; Solà-Roca, Judit; Bonfill, Xavier

2016-09-01

To assess the costs and health-related outcomes of double versus single reading of digital mammograms in a breast cancer screening programme. Based on data from 57,157 digital screening mammograms from women aged 50-69 years, we compared costs, false-positive results, positive predictive value and cancer detection rate using four reading strategies: double reading with and without consensus and arbitration, and single reading with first reader only and second reader only. Four highly trained radiologists read the mammograms. Double reading with consensus and arbitration was 15 % (Euro 334,341) more expensive than single reading with first reader only. False-positive results were more frequent at double reading with consensus and arbitration than at single reading with first reader only (4.5 % and 4.2 %, respectively; p < 0.001). The positive predictive value (9.3 % and 9.1 %; p = 0.812) and cancer detection rate were similar for both reading strategies (4.6 and 4.2 per 1000 screens; p = 0.283). Our results suggest that changing to single reading of mammograms could produce savings in breast cancer screening. Single reading could reduce the frequency of false-positive results without changing the cancer detection rate. These results are not conclusive and cannot be generalized to other contexts with less trained radiologists. • Double reading of digital mammograms is more expensive than single reading. • Compared to single reading, double reading yields a higher proportion of false-positive results. • The cancer detection rate was similar for double and single readings. • Single reading may be a cost-effective strategy in breast cancer screening programmes.

Complete sequence of Tvv1, a family of Ty 1 copia-like retrotransposons of Vitis vinifera L., reconstituted by chromosome walking.

PubMed

Pelsy, F.; Merdinoglu, D.

2002-09-01

A chromosome-walking strategy was used to sequence and characterize retrotransposons in the grapevine genome. The reconstitution of a family of retroelements, named Tvv1, was achieved by six successive steps. These elements share a single, highly conserved open reading frame 4,153 nucleotides-long, putatively encoding the gag, pro, int, rt and rh proteins. Comparison of the Tvv1 open reading frame coding potential with those of drosophila copia and tobacco Tnt1, revealed that Tvv1 is closely related to Ty 1 copia-like retrotransposons. A highly variable untranslated leader region, upstream of the open reading frame, allowed us to differentiate Tvv1 variants, which represent a family of at least 28 copies, in varying sizes. This internal region is flanked by two long terminal repeats in direct orientation, sized between 149 and 157 bp. Among elements theoretically sized from 4,970 to 5,550 bp, we describe the full-length sequence of a reference element Tvv1-1, 5,343 nucleotides-long. The full-length sequence of Tvv1-1 compared to pea PDR1 shows a 53.3% identity. In addition, both elements contain long terminal repeats of nearly the same size in which the U5 region could be entirely absent. Therefore, we assume that Tvv1 and PDR1 could constitute a particular class of short LTRs retroelements.

The ferredoxin-thioredoxin reductase variable subunit gene from Anacystis nidulans.

PubMed Central

Szekeres, M; Droux, M; Buchanan, B B

1991-01-01

The ferredoxin-thioredoxin reductase variable subunit gene of Anacystis nidulans was cloned, and its nucleotide sequence was determined. A single-copy 219-bp open reading frame encoded a protein of 73 amino acid residues, with a calculated Mr of 8,400. The monocistronic transcripts were represented in a 400-base and a less abundant 300-base mRNA form. Images PMID:1705544

Complete genome sequence of Flavobacterium psychrophilum strain CSF259-93 used to select rainbow trout for increased genetic resistance against bacterial cold water disease

USDA-ARS?s Scientific Manuscript database

The genome sequence of Flavobacterium psychrophilum strain CSF259-93, isolated from rainbow trout (Oncorhynchus mykiss), consists of a single circular genome of 2,900,735 bp and 2,701 predicted open reading frames (ORFs). Strain CSF259-93 has been used to select a line of rainbow trout with increase...

Cost-Effectiveness of Double Reading versus Single Reading of Mammograms in a Breast Cancer Screening Programme

PubMed Central

Posso, Margarita; Carles, Misericòrdia; Rué, Montserrat; Puig, Teresa; Bonfill, Xavier

2016-01-01

Objectives The usual practice in breast cancer screening programmes for mammogram interpretation is to perform double reading. However, little is known about its cost-effectiveness in the context of digital mammography. Our purpose was to evaluate the cost-effectiveness of double reading versus single reading of digital mammograms in a population-based breast cancer screening programme. Methods Data from 28,636 screened women was used to establish a decision-tree model and to compare three strategies: 1) double reading; 2) double reading for women in their first participation and single reading for women in their subsequent participations; and 3) single reading. We calculated the incremental cost-effectiveness ratio (ICER), which was defined as the expected cost per one additionally detected cancer. We performed a deterministic sensitivity analysis to test the robustness of the ICER. Results The detection rate of double reading (5.17‰) was similar to that of single reading (4.78‰; P = .768). The mean cost of each detected cancer was €8,912 for double reading and €8,287 for single reading. The ICER of double reading versus single reading was €16,684. The sensitivity analysis showed variations in the ICER according to the sensitivity of reading strategies. The strategy that combines double reading in first participation with single reading in subsequent participations was ruled out due to extended dominance. Conclusions From our results, double reading appears not to be a cost-effective strategy in the context of digital mammography. Double reading would eventually be challenged in screening programmes, as single reading might entail important net savings without significantly changing the cancer detection rate. These results are not conclusive and should be confirmed in prospective studies that investigate long-term outcomes like quality adjusted life years (QALYs). PMID:27459663

[Reading ability of junior high school students in relation to self-evaluation and depression].

PubMed

Yamashita, Toshiya; Hayashi, Takashi

2012-01-01

Guidelines for the diagnosis of reading disorders in elementary school students were published recently in Japan. On the basis of these guidelines, we administrated reading test batteries to 43 Japanese junior high-school students from grade two. The reading test consisted of single sounds, single words, and single sentences. We evaluated the reading speed and the number of reading errors made by the test takers; their performance was compared with the normal value for elementary school students in grade six, as stated in the guidelines. The reading ability of the junior high-school students was not higher than that of the elementary school students. Seven students (16.3%) were found to have reading difficulties (RD group) and they met the criterion for diagnosis of reading disorder as per the guidelines. Three students had difficulties in reading single sounds and single words, but they faced no problems when reading single sentences. It was supposed that the strategies used by the students for reading sentences may have differed from those used for reading single sounds or single words. No significant differences were found between the RD and non-RD group students on scores of scholastic self-evaluation, self-esteem, and depressive symptoms. Therefore, reading difficulty did not directly influence the level of self-evaluation or depression.

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

PubMed Central

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

2014-01-01

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

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

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

PubMed

Kisand, Veljo; Lettieri, Teresa

2013-04-01

De novo genome sequencing of previously uncharacterized microorganisms has the potential to open up new frontiers in microbial genomics by providing insight into both functional capabilities and biodiversity. Until recently, Roche 454 pyrosequencing was the NGS method of choice for de novo assembly because it generates hundreds of thousands of long reads (<450 bps), which are presumed to aid in the analysis of uncharacterized genomes. The array of tools for processing NGS data are increasingly free and open source and are often adopted for both their high quality and role in promoting academic freedom. The error rate of pyrosequencing the Alcanivorax borkumensis genome was such that thousands of insertions and deletions were artificially introduced into the finished genome. Despite a high coverage (~30 fold), it did not allow the reference genome to be fully mapped. Reads from regions with errors had low quality, low coverage, or were missing. The main defect of the reference mapping was the introduction of artificial indels into contigs through lower than 100% consensus and distracting gene calling due to artificial stop codons. No assembler was able to perform de novo assembly comparable to reference mapping. Automated annotation tools performed similarly on reference mapped and de novo draft genomes, and annotated most CDSs in the de novo assembled draft genomes. Free and open source software (FOSS) tools for assembly and annotation of NGS data are being developed rapidly to provide accurate results with less computational effort. Usability is not high priority and these tools currently do not allow the data to be processed without manual intervention. Despite this, genome assemblers now readily assemble medium short reads into long contigs (>97-98% genome coverage). A notable gap in pyrosequencing technology is the quality of base pair calling and conflicting base pairs between single reads at the same nucleotide position. Regardless, using draft whole genomes that are not finished and remain fragmented into tens of contigs allows one to characterize unknown bacteria with modest effort.

Open Court Reading©. What Works Clearinghouse Intervention Report. Updated October 2014

ERIC Educational Resources Information Center

What Works Clearinghouse, 2014

2014-01-01

"Open Court Reading©" is a reading program for grades K-6 published by McGraw-Hill Education that is designed to teach decoding, comprehension, inquiry, and writing in a three-part logical progression. Part One of each unit, Preparing to Read, focuses on phonemic awareness, sounds and letters, phonics, fluency, and word knowledge. Part…

Open Court Reading[c]. What Works Clearinghouse Intervention Report

ERIC Educational Resources Information Center

What Works Clearinghouse, 2012

2012-01-01

"Open Court Reading"[c] is a core reading program for grades K-6 developed by SRA/McGraw-Hill that is designed to teach decoding, comprehension, inquiry, and writing in a logical progression. Part 1 of each unit, Preparing to Read, focuses on phonemic awareness, sounds and letters, phonics, fluency, and word knowledge. Part 2, Reading…

Open Court Reading[c]. What Works Clearinghouse Intervention Report

ERIC Educational Resources Information Center

What Works Clearinghouse, 2008

2008-01-01

"Open Court Reading"[c] is an elementary basal reading program for grades K-6 developed by SRA/McGraw-Hill. The program is designed to systematically teach decoding, comprehension, inquiry and investigation, and writing in a logical progression. Part 1 of each unit, Preparing to Read, focuses on phonemic awareness, sounds and letters, phonics,…

Death of a dogma: eukaryotic mRNAs can code for more than one protein.

PubMed

Mouilleron, Hélène; Delcourt, Vivian; Roucou, Xavier

2016-01-08

mRNAs carry the genetic information that is translated by ribosomes. The traditional view of a mature eukaryotic mRNA is a molecule with three main regions, the 5' UTR, the protein coding open reading frame (ORF) or coding sequence (CDS), and the 3' UTR. This concept assumes that ribosomes translate one ORF only, generally the longest one, and produce one protein. As a result, in the early days of genomics and bioinformatics, one CDS was associated with each protein-coding gene. This fundamental concept of a single CDS is being challenged by increasing experimental evidence indicating that annotated proteins are not the only proteins translated from mRNAs. In particular, mass spectrometry (MS)-based proteomics and ribosome profiling have detected productive translation of alternative open reading frames. In several cases, the alternative and annotated proteins interact. Thus, the expression of two or more proteins translated from the same mRNA may offer a mechanism to ensure the co-expression of proteins which have functional interactions. Translational mechanisms already described in eukaryotic cells indicate that the cellular machinery is able to translate different CDSs from a single viral or cellular mRNA. In addition to summarizing data showing that the protein coding potential of eukaryotic mRNAs has been underestimated, this review aims to challenge the single translated CDS dogma. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Openness to Experience and Night-Sky Watching Interest as Predictors of Reading for Pleasure: Path Analysis of a Mediation Model

ERIC Educational Resources Information Center

Kelly, William E.

2010-01-01

The relation between reading for pleasure, night-sky watching interest, and openness to experience were examined in a sample of 129 college students. Results of a path analysis examining a mediation model indicated that the influence of night-sky interest on reading for pleasure was not mediated by the broad personality domain openness to…

Activation of RNA polymerase III transcription of human Alu repetitive elements by adenovirus type 5: Requirement for the E1b 58-Kilodalton protein and the products of E4 open reading frames 3 and 6

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

Panning, B.; Smiley, J.R.

1993-06-01

Alu elements are the single most abundant class of dispersed repeated sequences in the human genome, comprising 5-10% of the mass of human DNA. This report demonstrates that Ad5 infection strongly stimulates Pol III transcription of human Alu elements in HeLa and 293 cells. In contrast to the cases of Ad5-induced Pol III transcriptional activation, this process requires the E1b 58-kDa protein and the products of E4 open reading frames (ORFs) 3 and 6 in addition to the E1a 289-residue product. These findings suggest novel regulatory properties of the Ad5 E1b and E4 proteins and raise the possibility that analogousmore » cellular trans-acting factors serve to modulate Alu expression in vivo.« less

Deletion of a Single-Copy Trna Affects Microtubule Function in Saccharomyces Cerevisiae

PubMed Central

Reijo, R. A.; Cho, D. S.; Huffaker, T. C.

1993-01-01

rts1-1 was identified as an extragenic suppressor of tub2-104, a cold-sensitive allele of the sole gene encoding β-tubulin in the yeast, Saccharomyces cerevisiae. In addition, rts1-1 cells are heat sensitive and resistant to the microtubule-destabilizing drug, benomyl. The rts1-1 mutation is a deletion of approximately 5 kb of genomic DNA on chromosome X that includes one open reading frame and three tRNA genes. Dissection of this region shows that heat sensitivity is due to deletion of the open reading frame (HIT1). Suppression and benomyl resistance are caused by deletion of the gene encoding a tRNA(AGG)(Arg) (HSX1). Northern analysis of rts1-1 cells indicates that HSX1 is the only gene encoding this tRNA. Deletion of HSX1 does not suppress the tub2-104 mutation by misreading at the AGG codons in TUB2. It also does not suppress by interfering with the protein arginylation that targets certain proteins for degradation. These results leave open the prospect that this tRNA(AGG)(Arg) plays a novel role in the cell. PMID:8307335

Identification, cloning, and sequencing of a fragment of Amsacta moorei entomopoxvirus DNA containing the spheroidin gene and three vaccinia virus-related open reading frames.

PubMed Central

Hall, R L; Moyer, R W

1991-01-01

Entomopoxvirus virions are frequently contained within crystalline occlusion bodies, which are composed of primarily a single protein, spheroidin, which is analogous to the polyhedrin protein of baculovirus. The spheroidin gene of Amsacta moorei entomopoxvirus was identified following the microsequencing of polypeptides generated from cyanogen bromide treatment of spheroidin and the subsequent synthesis of oligonucleotide hybridization probes. DNA sequencing of a 6.8-kb region of DNA containing the spheroidin gene showed that the spheroidin protein is derived from a 3.0-kb open reading frame potentially encoding a protein of 115 kDa. Three copies of the heptanucleotide, TTTTTNT, a sequence associated with early gene transcription in the vertebrate poxviruses, and four in-frame translational termination signals were found within 60 bp upstream of the putative spheroidin gene promoter (TAAATG). The spheroidin gene promoter region contains the sequence TAAATG, which is found in many late promoters of the vertebrate poxviruses and which serves as the site of transcriptional initiation, as shown by primer extension. Primer extension experiments also showed that spheroidin gene transcripts contain 5' poly(A) sequences typical of vertebrate poxvirus late transcripts. The 92 bases upstream of the initiating TAAATG are unusually A + T rich and contain only 7 G or C residues. An analysis of open reading frames around the spheroidin gene suggests that the colinear core of "essential genes" typical of the vertebrate poxviruses is absent in A. moorei entomopoxvirus. Images PMID:1942245

Precise detection of de novo single nucleotide variants in human genomes.

PubMed

Gómez-Romero, Laura; Palacios-Flores, Kim; Reyes, José; García, Delfino; Boege, Margareta; Dávila, Guillermo; Flores, Margarita; Schatz, Michael C; Palacios, Rafael

2018-05-22

The precise determination of de novo genetic variants has enormous implications across different fields of biology and medicine, particularly personalized medicine. Currently, de novo variations are identified by mapping sample reads from a parent-offspring trio to a reference genome, allowing for a certain degree of differences. While widely used, this approach often introduces false-positive (FP) results due to misaligned reads and mischaracterized sequencing errors. In a previous study, we developed an alternative approach to accurately identify single nucleotide variants (SNVs) using only perfect matches. However, this approach could be applied only to haploid regions of the genome and was computationally intensive. In this study, we present a unique approach, coverage-based single nucleotide variant identification (COBASI), which allows the exploration of the entire genome using second-generation short sequence reads without extensive computing requirements. COBASI identifies SNVs using changes in coverage of exactly matching unique substrings, and is particularly suited for pinpointing de novo SNVs. Unlike other approaches that require population frequencies across hundreds of samples to filter out any methodological biases, COBASI can be applied to detect de novo SNVs within isolated families. We demonstrate this capability through extensive simulation studies and by studying a parent-offspring trio we sequenced using short reads. Experimental validation of all 58 candidate de novo SNVs and a selection of non-de novo SNVs found in the trio confirmed zero FP calls. COBASI is available as open source at https://github.com/Laura-Gomez/COBASI for any researcher to use. Copyright © 2018 the Author(s). Published by PNAS.

Reading and Reality. Proceedings of the Annual Reading Conference (14th, Terre Haute, Indiana, June 14, 1984).

ERIC Educational Resources Information Center

Gibbs, Vanita M., Comp.; Waterman, David C., Comp.

Intended for reading teachers, this pamphlet contains the presentations of the 14th annual reading conference at Indiana State University, beginning with opening remarks by David C. Waterman and welcoming comments by J. Stephen Hazlett. In the opening address, "What Good is Comprehension without Composition?" by Sharon and David Moore, the role of…

Drosophila Nora virus capsid proteins differ from those of other picorna-like viruses.

PubMed

Ekström, Jens-Ola; Habayeb, Mazen S; Srivastava, Vaibhav; Kieselbach, Thomas; Wingsle, Gunnar; Hultmark, Dan

2011-09-01

The recently discovered Nora virus from Drosophila melanogaster is a single-stranded RNA virus. Its published genomic sequence encodes a typical picorna-like cassette of replicative enzymes, but no capsid proteins similar to those in other picorna-like viruses. We have now done additional sequencing at the termini of the viral genome, extending it by 455 nucleotides at the 5' end, but no more coding sequence was found. The completeness of the final 12,333-nucleotide sequence was verified by the production of infectious virus from the cloned genome. To identify the capsid proteins, we purified Nora virus particles and analyzed their proteins by mass spectrometry. Our results show that the capsid is built from three major proteins, VP4A, B and C, encoded in the fourth open reading frame of the viral genome. The viral particles also contain traces of a protein from the third open reading frame, VP3. VP4A and B are not closely related to other picorna-like virus capsid proteins in sequence, but may form similar jelly roll folds. VP4C differs from the others and is predicted to have an essentially α-helical conformation. In a related virus, identified from EST database sequences from Nasonia parasitoid wasps, VP4C is encoded in a separate open reading frame, separated from VP4A and B by a frame-shift. This opens a possibility that VP4C is produced in non-equimolar quantities. Altogether, our results suggest that the Nora virus capsid has a different protein organization compared to the order Picornavirales. Copyright © 2011 Elsevier B.V. All rights reserved.

Patients' Positive and Negative Responses to Reading Mental Health Clinical Notes Online.

PubMed

Denneson, Lauren M; Chen, Jason I; Pisciotta, Maura; Tuepker, Anais; Dobscha, Steven K

2018-05-01

This study describes responses to OpenNotes, clinical notes available online, among patients receiving mental health care and explores whether responses vary by patient demographic or clinical characteristics. Survey data from 178 veterans receiving mental health treatment at a large Veterans Affairs medical center included patient-reported health self-efficacy, health knowledge, alliance with clinicians, and negative emotional responses after reading OpenNotes. Health care data were extracted from the patient care database. Reading OpenNotes helped many participants feel in control of their health care (49%) and have more trust in clinicians (45%), although a few (8%) frequently felt upset after reading their notes. In multivariate models, posttraumatic stress disorder was associated with increased patient-clinician alliance (p=.046) but also with negative emotional responses (p<.01). Patients receiving mental health care frequently reported benefits from reading OpenNotes, yet some experienced negative responses.

Efficient radiologic reading environment by using an open-source macro program as connection software.

PubMed

Lee, Young Han

2012-01-01

The objectives are (1) to introduce an easy open-source macro program as connection software and (2) to illustrate the practical usages in radiologic reading environment by simulating the radiologic reading process. The simulation is a set of radiologic reading process to do a practical task in the radiologic reading room. The principal processes are: (1) to view radiologic images on the Picture Archiving and Communicating System (PACS), (2) to connect the HIS/EMR (Hospital Information System/Electronic Medical Record) system, (3) to make an automatic radiologic reporting system, and (4) to record and recall information of interesting cases. This simulation environment was designed by using open-source macro program as connection software. The simulation performed well on the Window-based PACS workstation. Radiologists practiced the steps of the simulation comfortably by utilizing the macro-powered radiologic environment. This macro program could automate several manual cumbersome steps in the radiologic reading process. This program successfully acts as connection software for the PACS software, EMR/HIS, spreadsheet, and other various input devices in the radiologic reading environment. A user-friendly efficient radiologic reading environment could be established by utilizing open-source macro program as connection software. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

A feasibility study to determine if there is a market for automatic meter-reading devices

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

Hilberg, G.R.

1996-08-01

For many utilities the cost of manually reading meters is increasing due to personnel expenses and equipment costs. The current system of manual meters provides little ability for the utility to reduce costs. To reduce meter reading costs the utility must automate the manual system and reduce personnel expenses. A water utility in San Diego county was studied to calculate the cost of reading individual water meters. This would allow for the selective replacement of {open_quotes}high-cost{close_quotes} meters to quickly reduce meter-reading costs while limiting the necessary capital investments. As the {open_quotes}high-cost{close_quotes} meters are selectively replaced, a utility with a significantmore » difference in individual meter reading costs could save three to five dollars per meter per year. This study showed that the {open_quotes}high-cost{close_quotes} meters were six times more expensive to read than the average meter. Additionally, AMR systems increase the information available to consumers and to the utility on usage patterns and problems. The challenge was to cost effectively identify the {open_quotes}high-cost{close_quotes} meters. The costs to collect these data were less than $500.« less

[Effects of reading difficulties on scholastic self-evaluation and mental health in elementary school children].

PubMed

Yamashita, Toshiya; Hayashi, Takashi

2014-05-01

We aimed to examine the effects of reading difficulties on scholastic self-evaluation and mental health in elementary school students. Following guidelines for diagnosing reading disorders in elementary school students, we administered reading test batteries consisting of single sounds, single words, and single sentences to 41 fifth-grade elementary school students in Japan. The students' levels of scholastic self-evaluation, self-esteem, and depressive symptoms were assessed using self-rating questionnaires. By evaluating students' reading speed and the number of reading errors they made, we found that six students (14.6%) had reading difficulties (RD group) as per the guidelines for diagnosing reading disorders. The scholastic self-evaluation scores of this RD group were significantly lower than that of the non-RD group. No significant differences were found between the groups on self-esteem or depressive symptoms scores, which we considered to be indicators of mental health, Speed in reading single sounds and single words, and the number of reading errors in reading single sounds had significant negative correlations with scholastic self-evaluation scores. We found that reading difficulties might result in decreased scholastic self-evaluation in elementary school students; however, reading difficulties did not directly influence self-esteem or depression.

Hybrid-denovo: a de novo OTU-picking pipeline integrating single-end and paired-end 16S sequence tags.

PubMed

Chen, Xianfeng; Johnson, Stephen; Jeraldo, Patricio; Wang, Junwen; Chia, Nicholas; Kocher, Jean-Pierre A; Chen, Jun

2018-03-01

Illumina paired-end sequencing has been increasingly popular for 16S rRNA gene-based microbiota profiling. It provides higher phylogenetic resolution than single-end reads due to a longer read length. However, the reverse read (R2) often has significant low base quality, and a large proportion of R2s will be discarded after quality control, resulting in a mixture of paired-end and single-end reads. A typical 16S analysis pipeline usually processes either paired-end or single-end reads but not a mixture. Thus, the quantification accuracy and statistical power will be reduced due to the loss of a large amount of reads. As a result, rare taxa may not be detectable with the paired-end approach, or low taxonomic resolution will result in a single-end approach. To have both the higher phylogenetic resolution provided by paired-end reads and the higher sequence coverage by single-end reads, we propose a novel OTU-picking pipeline, hybrid-denovo, that can process a hybrid of single-end and paired-end reads. Using high-quality paired-end reads as a gold standard, we show that hybrid-denovo achieved the highest correlation with the gold standard and performed better than the approaches based on paired-end or single-end reads in terms of quantifying the microbial diversity and taxonomic abundances. By applying our method to a rheumatoid arthritis (RA) data set, we demonstrated that hybrid-denovo captured more microbial diversity and identified more RA-associated taxa than a paired-end or single-end approach. Hybrid-denovo utilizes both paired-end and single-end 16S sequencing reads and is recommended for 16S rRNA gene targeted paired-end sequencing data.

Open Reading Frame Phylogenetic Analysis on the Cloud

PubMed Central

2013-01-01

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

De Novo Genome and Transcriptome Assembly of the Canadian Beaver (Castor canadensis).

PubMed

Lok, Si; Paton, Tara A; Wang, Zhuozhi; Kaur, Gaganjot; Walker, Susan; Yuen, Ryan K C; Sung, Wilson W L; Whitney, Joseph; Buchanan, Janet A; Trost, Brett; Singh, Naina; Apresto, Beverly; Chen, Nan; Coole, Matthew; Dawson, Travis J; Ho, Karen; Hu, Zhizhou; Pullenayegum, Sanjeev; Samler, Kozue; Shipstone, Arun; Tsoi, Fiona; Wang, Ting; Pereira, Sergio L; Rostami, Pirooz; Ryan, Carol Ann; Tong, Amy Hin Yan; Ng, Karen; Sundaravadanam, Yogi; Simpson, Jared T; Lim, Burton K; Engstrom, Mark D; Dutton, Christopher J; Kerr, Kevin C R; Franke, Maria; Rapley, William; Wintle, Richard F; Scherer, Stephen W

2017-02-09

The Canadian beaver ( Castor canadensis ) is the largest indigenous rodent in North America. We report a draft annotated assembly of the beaver genome, the first for a large rodent and the first mammalian genome assembled directly from uncorrected and moderate coverage (< 30 ×) long reads generated by single-molecule sequencing. The genome size is 2.7 Gb estimated by k-mer analysis. We assembled the beaver genome using the new Canu assembler optimized for noisy reads. The resulting assembly was refined using Pilon supported by short reads (80 ×) and checked for accuracy by congruency against an independent short read assembly. We scaffolded the assembly using the exon-gene models derived from 9805 full-length open reading frames (FL-ORFs) constructed from the beaver leukocyte and muscle transcriptomes. The final assembly comprised 22,515 contigs with an N50 of 278,680 bp and an N50-scaffold of 317,558 bp. Maximum contig and scaffold lengths were 3.3 and 4.2 Mb, respectively, with a combined scaffold length representing 92% of the estimated genome size. The completeness and accuracy of the scaffold assembly was demonstrated by the precise exon placement for 91.1% of the 9805 assembled FL-ORFs and 83.1% of the BUSCO (Benchmarking Universal Single-Copy Orthologs) gene set used to assess the quality of genome assemblies. Well-represented were genes involved in dentition and enamel deposition, defining characteristics of rodents with which the beaver is well-endowed. The study provides insights for genome assembly and an important genomics resource for Castoridae and rodent evolutionary biology. Copyright © 2017 Lok et al.

De Novo Genome and Transcriptome Assembly of the Canadian Beaver (Castor canadensis)

PubMed Central

Lok, Si; Paton, Tara A.; Wang, Zhuozhi; Kaur, Gaganjot; Walker, Susan; Yuen, Ryan K. C.; Sung, Wilson W. L.; Whitney, Joseph; Buchanan, Janet A.; Trost, Brett; Singh, Naina; Apresto, Beverly; Chen, Nan; Coole, Matthew; Dawson, Travis J.; Ho, Karen; Hu, Zhizhou; Pullenayegum, Sanjeev; Samler, Kozue; Shipstone, Arun; Tsoi, Fiona; Wang, Ting; Pereira, Sergio L.; Rostami, Pirooz; Ryan, Carol Ann; Tong, Amy Hin Yan; Ng, Karen; Sundaravadanam, Yogi; Simpson, Jared T.; Lim, Burton K.; Engstrom, Mark D.; Dutton, Christopher J.; Kerr, Kevin C. R.; Franke, Maria; Rapley, William; Wintle, Richard F.; Scherer, Stephen W.

2017-01-01

The Canadian beaver (Castor canadensis) is the largest indigenous rodent in North America. We report a draft annotated assembly of the beaver genome, the first for a large rodent and the first mammalian genome assembled directly from uncorrected and moderate coverage (< 30 ×) long reads generated by single-molecule sequencing. The genome size is 2.7 Gb estimated by k-mer analysis. We assembled the beaver genome using the new Canu assembler optimized for noisy reads. The resulting assembly was refined using Pilon supported by short reads (80 ×) and checked for accuracy by congruency against an independent short read assembly. We scaffolded the assembly using the exon–gene models derived from 9805 full-length open reading frames (FL-ORFs) constructed from the beaver leukocyte and muscle transcriptomes. The final assembly comprised 22,515 contigs with an N50 of 278,680 bp and an N50-scaffold of 317,558 bp. Maximum contig and scaffold lengths were 3.3 and 4.2 Mb, respectively, with a combined scaffold length representing 92% of the estimated genome size. The completeness and accuracy of the scaffold assembly was demonstrated by the precise exon placement for 91.1% of the 9805 assembled FL-ORFs and 83.1% of the BUSCO (Benchmarking Universal Single-Copy Orthologs) gene set used to assess the quality of genome assemblies. Well-represented were genes involved in dentition and enamel deposition, defining characteristics of rodents with which the beaver is well-endowed. The study provides insights for genome assembly and an important genomics resource for Castoridae and rodent evolutionary biology. PMID:28087693

Comparing Students With and Without Reading Difficulties on Reading Comprehension Assessments: A Meta-Analysis.

PubMed

Collins, Alyson A; Lindström, Esther R; Compton, Donald L

Researchers have increasingly investigated sources of variance in reading comprehension test scores, particularly with students with reading difficulties (RD). The purpose of this meta-analysis was to determine if the achievement gap between students with RD and typically developing (TD) students varies as a function of different reading comprehension response formats (e.g., multiple choice, cloze). A systematic literature review identified 82 eligible studies. All studies administered reading comprehension assessments to students with RD and TD students in Grades K-12. Hedge's g standardized mean difference effect sizes were calculated, and random effects robust variance estimation techniques were used to aggregate average weighted effect sizes for each response format. Results indicated that the achievement gap between students with RD and TD students was larger for some response formats (e.g., picture selection ES g = -1.80) than others (e.g., retell ES g = -0.60). Moreover, for multiple-choice, cloze, and open-ended question response formats, single-predictor metaregression models explored potential moderators of heterogeneity in effect sizes. No clear patterns, however, emerged in regard to moderators of heterogeneity in effect sizes across response formats. Findings suggest that the use of different response formats may lead to variability in the achievement gap between students with RD and TD students.

Types of Aphasia

MedlinePlus

... Auditory Overload Aphasia vs Apraxia Reading, Writing and Math Reading Rehab (PDF opens in new window) Putting ... on Paper (PDF opens in new window) Acalculia - Math Challenges After Stroke Maximizing Communication Recovery & Independence Talking ...

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

Ingargiola, A.; Laurence, T. A.; Boutelle, R.

We introduce Photon-HDF5, an open and efficient file format to simplify exchange and long term accessibility of data from single-molecule fluorescence experiments based on photon-counting detectors such as single-photon avalanche diode (SPAD), photomultiplier tube (PMT) or arrays of such detectors. The format is based on HDF5, a widely used platform- and language-independent hierarchical file format for which user-friendly viewers are available. Photon-HDF5 can store raw photon data (timestamp, channel number, etc) from any acquisition hardware, but also setup and sample description, information on provenance, authorship and other metadata, and is flexible enough to include any kind of custom data. Themore » format specifications are hosted on a public website, which is open to contributions by the biophysics community. As an initial resource, the website provides code examples to read Photon-HDF5 files in several programming languages and a reference python library (phconvert), to create new Photon-HDF5 files and convert several existing file formats into Photon-HDF5. As a result, to encourage adoption by the academic and commercial communities, all software is released under the MIT open source license.« less

Oral Language and Reading; Proceedings of the Annual Reading Conference of the Department of Elementary Education at Indiana State University (3rd, Terre Haute, June 14-15, 1973).

ERIC Educational Resources Information Center

Waterman, David C., Ed.; Gibbs, Vanita M., Ed.

This pamphlet is a collection of the speeches given at the Third Annual Reading Conference at Indiana State University, Terre Haute. The theme of the conference was "Oral Language and Reading." The contents include: "Official Program"; opening remarks, "They Led and Followed," by William G. McCarthy; opening address, "Strategies for Reading…

Structure, sequence and expression of the hepatitis delta (δ) viral genome

NASA Astrophysics Data System (ADS)

Wang, Kang-Sheng; Choo, Qui-Lim; Weiner, Amy J.; Ou, Jing-Hsiung; Najarian, Richard C.; Thayer, Richard M.; Mullenbach, Guy T.; Denniston, Katherine J.; Gerin, John L.; Houghton, Michael

1986-10-01

Biochemical and electron microscopic data indicate that the human hepatitis δ viral agent contains a covalently closed circular and single-stranded RNA genome that has certain similarities with viroid-like agents from plants. The sequence of the viral genome (1,678 nucleotides) has been determined and an open reading frame within the complementary strand has been shown to encode an antigen that binds specifically to antisera from patients with chronic hepatitis δ viral infections.

Teaching in an Open Classroom: Informal Checks, Diagnoses, and Learning Strategies for Beginning Reading and Math.

ERIC Educational Resources Information Center

Langstaff, Nancy

This book, intended for use by inservice teachers, preservice teachers, and parents interested in open classrooms, contains three chapters. "Beginning Reading in an Open Classroom" discusses language development, sight vocabulary, visual discrimination, auditory discrimination, directional concepts, small muscle control, and measurement of…

Origins of Media Exposure: Linking Personality Traits to TV, Radio, Print, and Film Use.

ERIC Educational Resources Information Center

Finn, Seth

1997-01-01

Investigates the five-factor model of personality (neuroticism, extroversion, openness, agreeableness, and conscientiousness) as a correlate of mass media use. Shows strongest relationships for mass media use between openness and pleasure reading, extroversion and negative pleasure reading, and openness and negative TV viewing. Finds that…

An evaluation of emergency medicine investigators' views on open access to medical literature.

PubMed

Rodriguez, R M; Wong, J; Hardy, J; Frankel, E

2006-12-01

Scientists and governmental agencies have called for free universal access to research publications via the internet--open access. To examine the current medical literature reading practices of emergency medicine investigators (EMIs) and their views towards open access. Surveys were mailed to the 212 corresponding authors of all original research articles published in years 2002 and 2003 in the Annals of Emergency Medicine, Academic Emergency Medicine and The Journal of Emergency Medicine. The most commonly read forms of medical literature reported by the 129 (61%) EMI respondents were hard-copy medical journals and online literature review services. 59% of EMIs were in favour of open access; 58% stated they would read a wider variety of medical literature; 21% believed open access would improve the quality of publications and 39% thought it would decrease the quality. When asked how a US 1500 dollars fee for open access would affect their ability to publish research, 69% said it would greatly impede and 19% said it would slightly impede their research. Despite concerns that open access may impede their ability to publish research and decrease the quality of publications, most EMIs surveyed favoured open access. They believed open access would increase and broaden their medical literature reading.

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.

Large diversity of the piggyBac-like elements in the genome of Tribolium castaneum

PubMed Central

Wang, Jianjun; Du, Yuzhou; Wang, Suzhi; Brown, Sue; Park, Yoonseong

2011-01-01

The piggyBac transposable element, originally discovered in the cabbage looper, Trichoplusia ni, has been widely used in insect transgenesis including the red flour beetle Tribolium castaneum. We surveyed piggyBac-like (PLE) sequences in the genome of Tribolium castaneum by homology searches using as queries the diverse PLE sequences that have been described previously. The search yielded a total of 32 piggyBac-like elements (TcPLEs) which were classified into 14 distinct groups. Most of the TcPLEs contain defective functional motifs in that they are lacking inverted terminal repeats or have disrupted open reading frames. Only one single copy of TcPLE1 appears to be intact with imperfect 16 bp inverted terminal repeats flanking an open reading frame encoding a transposase of 571 amino acid residues. Many copies of TcPLEs were found to be inserted into or close to other transposon-like sequences. This large diversity of TcPLEs with generally low copy numbers suggests multiple invasions of the TcPLEs over a long evolutionary time without extensive multiplications or occurrence of rapid loss of TcPLEs copies. PMID:18342253

Demonstration of retrotransposition of the Tf1 element in fission yeast.

PubMed

Levin, H L; Boeke, J D

1992-03-01

Tf1, a retrotransposon from fission yeast, has LTRs and coding sequences resembling the protease, reverse transcriptase and integrase domains of retroviral pol genes. A unique aspect of Tf1 is that it contains a single open reading frame whereas other retroviruses and retrotransposons usually possess two or more open reading frames. To determine whether Tf1 can transpose, we overproduced Tf1 transcripts encoded by a plasmid copy of the element marked with a neo gene. Approximately 0.1-4.0% of the cell population acquired chromosomally inherited resistance to G418. DNA blot analysis demonstrated that such strains had acquired both Tf1 and neo specific sequences within a restriction fragment of the same size; the size of this restriction fragment varied between different isolates. Structural analysis of the cloned DNA flanking the Tf1-neo element of two transposition candidates with the same regions in the parent strain showed that the ability to grow on G418 was due to transposition of Tf1-neo and not other types of recombination events.

Orthographic units in the absence of visual processing: Evidence from sublexical structure in braille.

PubMed

Fischer-Baum, Simon; Englebretson, Robert

2016-08-01

Reading relies on the recognition of units larger than single letters and smaller than whole words. Previous research has linked sublexical structures in reading to properties of the visual system, specifically on the parallel processing of letters that the visual system enables. But whether the visual system is essential for this to happen, or whether the recognition of sublexical structures may emerge by other means, is an open question. To address this question, we investigate braille, a writing system that relies exclusively on the tactile rather than the visual modality. We provide experimental evidence demonstrating that adult readers of (English) braille are sensitive to sublexical units. Contrary to prior assumptions in the braille research literature, we find strong evidence that braille readers do indeed access sublexical structure, namely the processing of multi-cell contractions as single orthographic units and the recognition of morphemes within morphologically-complex words. Therefore, we conclude that the recognition of sublexical structure is not exclusively tied to the visual system. However, our findings also suggest that there are aspects of morphological processing on which braille and print readers differ, and that these differences may, crucially, be related to reading using the tactile rather than the visual sensory modality. Copyright © 2016 Elsevier B.V. All rights reserved.

Developmental rearrangement of cyanobacterial nif genes: nucleotide sequence, open reading frames, and cytochrome P-450 homology of the Anabaena sp. strain PCC 7120 nifD element.

PubMed Central

Lammers, P J; McLaughlin, S; Papin, S; Trujillo-Provencio, C; Ryncarz, A J

1990-01-01

An 11-kbp DNA element of unknown function interrupts the nifD gene in vegetative cells of Anabaena sp. strain PCC 7120. In developing heterocysts the nifD element excises from the chromosome via site-specific recombination between short repeat sequences that flank the element. The nucleotide sequence of the nifH-proximal half of the element was determined to elucidate the genetic potential of the element. Four open reading frames with the same relative orientation as the nifD element-encoded xisA gene were identified in the sequenced region. Each of the open reading frames was preceded by a reasonable ribosome-binding site and had biased codon utilization preferences consistent with low levels of expression. Open reading frame 3 was highly homologous with three cytochrome P-450 omega-hydroxylase proteins and showed regional homology to functionally significant domains common to the cytochrome P-450 superfamily. The sequence encoding open reading frame 2 was the most highly conserved portion of the sequenced region based on heterologous hybridization experiments with three genera of heterocystous cyanobacteria. Images PMID:2123860

Publisher's Note: EPL and Open Access Articles

NASA Astrophysics Data System (ADS)

Ancarani, Barbara; Brassac, Catherine; Burr, Frédéric; Dose, Volker; King, Caroline

2008-01-01

In May 2007 the EPLA Board of Directors welcomed the CERN initiative for the creation of a Sponsoring Consortium for Open Access Publishing in Particle Physics (SCOAP3) and agreed to enter into negotiations to enable high energy physics papers to be published in EPL with selective open access. At a subsequent meeting in August 2007, the Board decided to offer substantial initial discount while open access remained a small fraction of the content of EPL. A necessary precursor to negotiation with SCOAP3 is a general open access policy. The Directors agreed that this policy should offer a free-to-read option for all authors in all sections of EPL and so provide fair opportunities across the broad range of physics covered by EPL. The policy for the journal should allow individual authors, their institutions, funding agencies or sponsoring consortia to pay for published articles to be freely available to all, permanently. The Board stressed the importance of maintaining EPL as a refereed journal with robust and reliable content, in contrast to a repository or preprint server. EPL would remain a subscription journal for content that is not free to read and authors, institutions or funding agencies may choose to pay for their articles to be open access. As an initial step in this open access venture, a single-article fee of € 1000 ( 1330) can now be paid by individuals who choose to have their article published free to all. This pricing, which is substantially discounted, ensures that EPL remains competitive with other similar journals. EPL will continue to ensure this policy is sustainable although the journal must remain financially viable and the pricing scheme will be under continual review. At this stage we welcome enquires concerning an institutional membership fee that would allow that institute to pay in advance for open access publications in EPL for authors from that institute. The fee would follow a band structure, based on the number of articles that institute expects to publish over the coming year. Meanwhile we would like to thank all Authors for their submissions, all Referees for their reviews, all Co-Editors for their editorial processing throughout 2007 and we look forward to developing and expanding EPL activities during 2008. Please visit the website regularly (http://www.epljournal.org) to remain up-to-date with the latest developments with EPL and to read the most recently published articles. Remember all articles are already free to read for 30 days from their online publication date. If you have comments or questions about changes taking place in 2008, please e-mail us at info@epljournal.org or editorial.office@epletters.net. With our best wishes for 2008!

Cultural Awareness and Reading. Proceedings of the Annual Reading Conference (12th, Terre Haute, Indiana, June 17-18, 1982).

ERIC Educational Resources Information Center

Gibbs, Vanita M., Comp.; Pabst, Robert L., Comp.

Reflecting the expertise of the speakers and providing a rich resource of information within the conference theme, the articles in these proceedings explore the relationship between cultural awareness and reading. The proceedings begin with a copy of the conference program and opening remarks by the conference cochair. Following an opening address…

Reading Disabilities of Chinese Elementary School Students: Beyond the Phonological Deficits of Single-Character Identification

ERIC Educational Resources Information Center

Jin, Hua; Lin, Dan; Zhang, Dake; Wen, Hongbo; Zhu, Huohong; He, Xianyou; Mo, Lei

2010-01-01

This study investigated the contributions of single-word identification and compound word categorization to Chinese students' reading achievement among 31 students with reading difficulties and 20 students without reading difficulties. The results suggested that, deficiency in single characters identification is not the primarily reason for…

Single-Word Reading: Behavioral and Biological Perspectives. New Directions in Communication Disorders Research

ERIC Educational Resources Information Center

Grigorenko, Elena L., Ed.; Naples, Adam J., Ed.

2007-01-01

As the first title in the new series, "New Directions in Communication Disorders Research: Integrative Approaches", this volume discusses a unique phenomenon in cognitive science, single-word reading, which is an essential element in successful reading competence. Single-word reading is an interdisciplinary area of research that incorporates…

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

Predicted secondary structure similarity in the absence of primary amino acid sequence homology: hepatitis B virus open reading frames.

PubMed Central

Schaeffer, E; Sninsky, J J

1984-01-01

Proteins that are related evolutionarily may have diverged at the level of primary amino acid sequence while maintaining similar secondary structures. Computer analysis has been used to compare the open reading frames of the hepatitis B virus to those of the woodchuck hepatitis virus at the level of amino acid sequence, and to predict the relative hydrophilic character and the secondary structure of putative polypeptides. Similarity is seen at the levels of relative hydrophilicity and secondary structure, in the absence of sequence homology. These data reinforce the proposal that these open reading frames encode viral proteins. Computer analysis of this type can be more generally used to establish structural similarities between proteins that do not share obvious sequence homology as well as to assess whether an open reading frame is fortuitous or codes for a protein. PMID:6585835

76 FR 4659 - Science Advisory Board Staff Office; Notification of a Public Teleconference of the Science...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-26

...://yosemite.epa.gov/sab/ sabproduct.nsf/fedrgstr--activities/ FL%20Estuaries%20TSD?OpenDocument'' should read ``http:// yosemite.epa.gov/sab/sabproduct.nsf/fedrgstr--activites/ FL%20Estuaries%20TSD?OpenDocument.'' 2.../sabproduct.nsf/fedrgstr--activities/ FL%20Estuaries%20TSD?OpenDocument'' should read ``http:// yosemite.epa...

Findings from a Multiyear Scale-Up Effectiveness Trial of Open Court Reading

ERIC Educational Resources Information Center

Vaden-Kiernan, Michael; Borman, Geoffrey; Caverly, Sarah; Bell, Nance; Sullivan, Kate; Ruiz de Castilla, Veronica; Fleming, Grace; Rodriguez, Debra; Henry, Chad; Long, Tracy; Hughes Jones, Debra

2018-01-01

This multiyear scale-up effectiveness study of Open Court Reading (OCR) involved approximately 4,500 students and more than 1,000 teachers per year in Grades K-5 from 49 elementary schools in seven districts across the country. Using a school-level cluster randomized trial design, we assessed the implementation and effectiveness of Open Court…

A simplified financial model for automatic meter reading

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

Ward, S.M.

1994-01-15

The financial model proposed here (which can be easily adapted for electric, gas, or water) combines aspects of [open quotes]life cycle,[close quotes] [open quotes]consumer value[close quotes] and [open quotes]revenue based[close quotes] approaches and addresses intangible benefits. A simple value tree of one-word descriptions clarifies the relationship between level of investment and level of value, visually relating increased value to increased cost. The model computes the numerical present values of capital costs, recurring costs, and revenue benefits over a 15-year period for the seven configurations: manual reading of existing or replacement standard meters (MMR), manual reading using electronic, hand-held retrievers (EMR),more » remote reading of inaccessible meters via hard-wired receptacles (RMR), remote reading of meters adapted with pulse generators (RMR-P), remote reading of meters adapted with absolute dial encoders (RMR-E), offsite reading over a few hundred feet with mobile radio (OMR), and fully automatic reading using telephone or an equivalent network (AMR). In the model, of course, the costs of installing the configurations are clearly listed under each column. The model requires only four annualized inputs and seven fixed-cost inputs that are rather easy to obtain.« less

Construction of a restriction map and gene map of the lettuce chloroplast small single-copy region using Southern cross-hybridization.

PubMed

Mitchelson, K R

1996-01-01

The small single-copy region (SSCR) of the chloroplast genome of many higher plants typically contain ndh genes encoding proteins that share homology with subunits of the respiratory-chain reduced nicotinamide adenine dinucleotide (NADH) dehydrogenase complex of mitochondria. A map of the lettuce chloroplast SSCR has been determined by Southern cross-hybridization, taking advantage of the high degree of homology between a tobacco small single-copy fragment and a corresponding lettuce chloroplast fragment. The gene order of the SSCR of lettuce and tobacco chloroplasts is similar. The cross-hybridization method can rapidly create a primary gene map of unknown chloroplast fragments, thus providing detailed information of the localization and arrangement of genes and conserved open reading frame regions.

39 CFR 3004.12 - Reading room.

Code of Federal Regulations, 2010 CFR

2010-07-01

... reading room at its offices is open during business hours. (b) The records available for public inspection... Reading room. (a) The Commission maintains a public reading room at its offices (901 New York Avenue, NW...

Increase in Middle East Respiratory Syndrome-Coronavirus Cases in Saudi Arabia Linked to Hospital Outbreak With Continued Circulation of Recombinant Virus, July 1–August 31, 2015

PubMed Central

Assiri, Abdullah M.; Biggs, Holly M.; Abedi, Glen R.; Lu, Xiaoyan; Bin Saeed, Abdulaziz; Abdalla, Osman; Mohammed, Mutaz; Al-Abdely, Hail M.; Algarni, Homoud S.; Alhakeem, Raafat F.; Almasri, Malak M.; Alsharef, Ali A.; Nooh, Randa; Erdman, Dean D.; Gerber, Susan I.; Watson, John T.

2016-01-01

During July–August 2015, the number of cases of Middle East respiratory syndrome (MERS) reported from Saudi Arabia increased dramatically. We reviewed the 143 confirmed cases from this period and classified each based upon likely transmission source. We found that the surge in cases resulted predominantly (90%) from secondary transmission largely attributable to an outbreak at a single healthcare facility in Riyadh. Genome sequencing of MERS coronavirus from 6 cases demonstrated continued circulation of the recently described recombinant virus. A single unique frameshift deletion in open reading frame 5 was detected in the viral sequence from 1 case. PMID:27704019

Electrophysiological Correlates of Reading the Single- and Interactive-Mind

PubMed Central

Wang, Yi-Wen; Zheng, Yu-Wei; Lin, Chong-De; Wu, Jie; Shen, De-Li

2011-01-01

Understanding minds is the cognitive basis of successful social interaction. In everyday life, human mental activity often happens at the moment of social interaction among two or multiple persons instead of only one-person. Understanding the interactive mind of two- or multi-person is more complex and higher than understanding the single-person mind in the hierarchical structure of theory of mind. Understanding the interactive mind maybe differentiate from understanding the single mind. In order to examine the dissociative electrophysiological correlates of reading the single mind and reading the interactive mind, the 64 channels event-related potentials were recorded while 16 normal adults were observing three kinds of Chinese idioms depicted physical scenes, one-person with mental activity, and two- or multi-person with mental interaction. After the equivalent N400, in the 500- to 700-ms epoch, the mean amplitudes of late positive component (LPC) over frontal for reading the single mind and reading the interactive mind were significantly more positive than for physical representation, while there was no difference between the former two. In the 700- to 800-ms epoch, the mean amplitudes of LPC over frontal–central for reading the interactive mind were more positive than for reading the single mind and physical representation, while there was no difference between the latter two. The present study provides electrophysiological signature of the dissociations between reading the single mind and reading the interactive mind. PMID:21845178

Termination and read-through proteins encoded by genome segment 9 of Colorado tick fever virus.

PubMed

Mohd Jaafar, Fauziah; Attoui, Houssam; De Micco, Philippe; De Lamballerie, Xavier

2004-08-01

Genome segment 9 (Seg-9) of Colorado tick fever virus (CTFV) is 1884 bp long and contains a large open reading frame (ORF; 1845 nt in length overall), although a single in-frame stop codon (at nt 1052-1054) reduces the ORF coding capacity by approximately 40 %. However, analyses of highly conserved RNA sequences in the vicinity of the stop codon indicate that it belongs to a class of 'leaky terminators'. The third nucleotide positions in codons situated both before and after the stop codon, shows the highest variability, suggesting that both regions are translated during virus replication. This also suggests that the stop signal is functionally leaky, allowing read-through translation to occur. Indeed, both the truncated 'termination' protein and the full-length 'read-through' protein (VP9 and VP9', respectively) were detected in CTFV-infected cells, in cells transfected with a plasmid expressing only Seg-9 protein products, and in the in vitro translation products from undenatured Seg-9 ssRNA. The ratios of full-length and truncated proteins generated suggest that read-through may be down-regulated by other viral proteins. Western blot analysis of infected cells and purified CTFV showed that VP9 is a structural component of the virion, while VP9' is a non-structural protein.

The positive regulatory function of the 5'-proximal open reading frames in GCN4 mRNA can be mimicked by heterologous, short coding sequences.

PubMed Central

Williams, N P; Mueller, P P; Hinnebusch, A G

1988-01-01

Translational control of GCN4 expression in the yeast Saccharomyces cerevisiae is mediated by multiple AUG codons present in the leader of GCN4 mRNA, each of which initiates a short open reading frame of only two or three codons. Upstream AUG codons 3 and 4 are required to repress GCN4 expression in normal growth conditions; AUG codons 1 and 2 are needed to overcome this repression in amino acid starvation conditions. We show that the regulatory function of AUG codons 1 and 2 can be qualitatively mimicked by the AUG codons of two heterologous upstream open reading frames (URFs) containing the initiation regions of the yeast genes PGK and TRP1. These AUG codons inhibit GCN4 expression when present singly in the mRNA leader; however, they stimulate GCN4 expression in derepressing conditions when inserted upstream from AUG codons 3 and 4. This finding supports the idea that AUG codons 1 and 2 function in the control mechanism as translation initiation sites and further suggests that suppression of the inhibitory effects of AUG codons 3 and 4 is a general consequence of the translation of URF 1 and 2 sequences upstream. Several observations suggest that AUG codons 3 and 4 are efficient initiation sites; however, these sequences do not act as positive regulatory elements when placed upstream from URF 1. This result suggests that efficient translation is only one of the important properties of the 5' proximal URFs in GCN4 mRNA. We propose that a second property is the ability to permit reinitiation following termination of translation and that URF 1 is optimized for this regulatory function. Images PMID:3065626

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

PubMed Central

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

2013-01-01

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

Facilitating text reading in posterior cortical atrophy.

PubMed

Yong, Keir X X; Rajdev, Kishan; Shakespeare, Timothy J; Leff, Alexander P; Crutch, Sebastian J

2015-07-28

We report (1) the quantitative investigation of text reading in posterior cortical atrophy (PCA), and (2) the effects of 2 novel software-based reading aids that result in dramatic improvements in the reading ability of patients with PCA. Reading performance, eye movements, and fixations were assessed in patients with PCA and typical Alzheimer disease and in healthy controls (experiment 1). Two reading aids (single- and double-word) were evaluated based on the notion that reducing the spatial and oculomotor demands of text reading might support reading in PCA (experiment 2). Mean reading accuracy in patients with PCA was significantly worse (57%) compared with both patients with typical Alzheimer disease (98%) and healthy controls (99%); spatial aspects of passages were the primary determinants of text reading ability in PCA. Both aids led to considerable gains in reading accuracy (PCA mean reading accuracy: single-word reading aid = 96%; individual patient improvement range: 6%-270%) and self-rated measures of reading. Data suggest a greater efficiency of fixations and eye movements under the single-word reading aid in patients with PCA. These findings demonstrate how neurologic characterization of a neurodegenerative syndrome (PCA) and detailed cognitive analysis of an important everyday skill (reading) can combine to yield aids capable of supporting important everyday functional abilities. This study provides Class III evidence that for patients with PCA, 2 software-based reading aids (single-word and double-word) improve reading accuracy. © 2015 American Academy of Neurology.

Facilitating text reading in posterior cortical atrophy

PubMed Central

Rajdev, Kishan; Shakespeare, Timothy J.; Leff, Alexander P.; Crutch, Sebastian J.

2015-01-01

Objective: We report (1) the quantitative investigation of text reading in posterior cortical atrophy (PCA), and (2) the effects of 2 novel software-based reading aids that result in dramatic improvements in the reading ability of patients with PCA. Methods: Reading performance, eye movements, and fixations were assessed in patients with PCA and typical Alzheimer disease and in healthy controls (experiment 1). Two reading aids (single- and double-word) were evaluated based on the notion that reducing the spatial and oculomotor demands of text reading might support reading in PCA (experiment 2). Results: Mean reading accuracy in patients with PCA was significantly worse (57%) compared with both patients with typical Alzheimer disease (98%) and healthy controls (99%); spatial aspects of passages were the primary determinants of text reading ability in PCA. Both aids led to considerable gains in reading accuracy (PCA mean reading accuracy: single-word reading aid = 96%; individual patient improvement range: 6%–270%) and self-rated measures of reading. Data suggest a greater efficiency of fixations and eye movements under the single-word reading aid in patients with PCA. Conclusions: These findings demonstrate how neurologic characterization of a neurodegenerative syndrome (PCA) and detailed cognitive analysis of an important everyday skill (reading) can combine to yield aids capable of supporting important everyday functional abilities. Classification of evidence: This study provides Class III evidence that for patients with PCA, 2 software-based reading aids (single-word and double-word) improve reading accuracy. PMID:26138948

Prologue: Reading Comprehension Is Not a Single Ability

ERIC Educational Resources Information Center

Catts, Hugh W.; Kamhi, Alan G.

2017-01-01

Purpose: In this initial article of the clinical forum on reading comprehension, we argue that reading comprehension is not a single ability that can be assessed by one or more general reading measures or taught by a small set of strategies or approaches. Method: We present evidence for a multidimensional view of reading comprehension that…

Investigation of the Functional Neuroanatomy of Single Word Reading and Its Development

ERIC Educational Resources Information Center

Palmer, Erica D.; Brown, Timothy T.; Petersen, Steven E.; Schlaggar, Bradley L.

2004-01-01

An understanding of the processing underlying single word reading will provide insight into how skilled reading is achieved, with important implications for reading education and impaired reading. Investigation of the functional neuroanatomy of both the mature and the developing systems will be critical for reaching this understanding. To this…

Sustaining Composition: Studying Content-Based, Ecological, and Economical Sustainability of Open-Source Textbooks through "Writing Spaces: Readings on Writing"

ERIC Educational Resources Information Center

Munson, Margaret

2013-01-01

Writing programs in institutions of higher education work to prepare students for real-world writing within any field of study. The composition of "Writing Spaces: Readings on Writing" offers an open-source text for students, teachers, and policy-makers at all levels. Exposure to an open space for learning encourages access to information,…

Separating homeologs by phasing in the tetraploid wheat transcriptome.

PubMed

Krasileva, Ksenia V; Buffalo, Vince; Bailey, Paul; Pearce, Stephen; Ayling, Sarah; Tabbita, Facundo; Soria, Marcelo; Wang, Shichen; Akhunov, Eduard; Uauy, Cristobal; Dubcovsky, Jorge

2013-06-25

The high level of identity among duplicated homoeologous genomes in tetraploid pasta wheat presents substantial challenges for de novo transcriptome assembly. To solve this problem, we develop a specialized bioinformatics workflow that optimizes transcriptome assembly and separation of merged homoeologs. To evaluate our strategy, we sequence and assemble the transcriptome of one of the diploid ancestors of pasta wheat, and compare both assemblies with a benchmark set of 13,472 full-length, non-redundant bread wheat cDNAs. A total of 489 million 100 bp paired-end reads from tetraploid wheat assemble in 140,118 contigs, including 96% of the benchmark cDNAs. We used a comparative genomics approach to annotate 66,633 open reading frames. The multiple k-mer assembly strategy increases the proportion of cDNAs assembled full-length in a single contig by 22% relative to the best single k-mer size. Homoeologs are separated using a post-assembly pipeline that includes polymorphism identification, phasing of SNPs, read sorting, and re-assembly of phased reads. Using a reference set of genes, we determine that 98.7% of SNPs analyzed are correctly separated by phasing. Our study shows that de novo transcriptome assembly of tetraploid wheat benefit from multiple k-mer assembly strategies more than diploid wheat. Our results also demonstrate that phasing approaches originally designed for heterozygous diploid organisms can be used to separate the close homoeologous genomes of tetraploid wheat. The predicted tetraploid wheat proteome and gene models provide a valuable tool for the wheat research community and for those interested in comparative genomic studies.

Separating homeologs by phasing in the tetraploid wheat transcriptome

PubMed Central

2013-01-01

Background The high level of identity among duplicated homoeologous genomes in tetraploid pasta wheat presents substantial challenges for de novo transcriptome assembly. To solve this problem, we develop a specialized bioinformatics workflow that optimizes transcriptome assembly and separation of merged homoeologs. To evaluate our strategy, we sequence and assemble the transcriptome of one of the diploid ancestors of pasta wheat, and compare both assemblies with a benchmark set of 13,472 full-length, non-redundant bread wheat cDNAs. Results A total of 489 million 100 bp paired-end reads from tetraploid wheat assemble in 140,118 contigs, including 96% of the benchmark cDNAs. We used a comparative genomics approach to annotate 66,633 open reading frames. The multiple k-mer assembly strategy increases the proportion of cDNAs assembled full-length in a single contig by 22% relative to the best single k-mer size. Homoeologs are separated using a post-assembly pipeline that includes polymorphism identification, phasing of SNPs, read sorting, and re-assembly of phased reads. Using a reference set of genes, we determine that 98.7% of SNPs analyzed are correctly separated by phasing. Conclusions Our study shows that de novo transcriptome assembly of tetraploid wheat benefit from multiple k-mer assembly strategies more than diploid wheat. Our results also demonstrate that phasing approaches originally designed for heterozygous diploid organisms can be used to separate the close homoeologous genomes of tetraploid wheat. The predicted tetraploid wheat proteome and gene models provide a valuable tool for the wheat research community and for those interested in comparative genomic studies. PMID:23800085

Prospective study aiming to compare 2D mammography and tomosynthesis + synthesized mammography in terms of cancer detection and recall. From double reading of 2D mammography to single reading of tomosynthesis.

PubMed

Romero Martín, Sara; Raya Povedano, Jose Luis; Cara García, María; Santos Romero, Ana Luz; Pedrosa Garriguet, Margarita; Álvarez Benito, Marina

2018-06-01

To evaluate tomosynthesis compared with 2D-mammography in cancer detection and recalls in a screening-programme, and assess performing synthesized instead of 2D, and compare double reading of 2D with single reading of tomosynthesis. Women (age 50-69 years) participating in the screening-programme were included. 2D-mammography and tomosynthesis were performed. There were four reading models: 2D-mammography (first); 2D-mammography (second); tomosynthesis + synthesized (third); tomosynthesis + synthesized + 2D (fourth reading). Paired double reading of 2D (first+second) and tomosynthesis (third+fourth) were analysed. In 16,067 participants, there were 98 cancers and 1,196 recalls. Comparing double reading of 2D with single reading of tomosynthesis, there was an increase of 12.6 % in cancer detection with the third reading (p= 0.043) and 6.9 % with the fourth reading (p=0.210), and a decrease in recalls of 40.5 % (p<0.001) and 44.4 % (p<0.001), respectively. With double reading of both techniques, there was an increase in cancer detection of 17.4 % (p = 0.004) and a decrease in recalls of 12.5 % (p = 0.001) with tomosynthesis. Single reading of tomosynthesis plus synthesized increased cancer detection and decreased recalls compared with double reading 2D. 2D did not improve results when added to tomosynthesis. • Tomosynthesis increases cancer detection and decreases recall rates versus 2D mammography. • Synthesized-mammography avoids performing 2D, showing higher cancer detection. • Single reading of tomosynthesis + synthesized is feasible as a new practice.

Accuracy and reading time for six strategies using digital breast tomosynthesis in women with mammographically negative dense breasts.

PubMed

Tagliafico, Alberto Stefano; Calabrese, Massimo; Bignotti, Bianca; Signori, Alessio; Fisci, Erica; Rossi, Federica; Valdora, Francesca; Houssami, Nehmat

2017-12-01

To compare six strategies using digital breast tomosynthesis in women with mammographically negative dense breasts. This is a substudy of the 'ASTOUND' trial. 163 women who underwent tomosynthesis with synthetically reconstructed projection images (S-2D) inclusive of 13 (7.9%) cases diagnosed with breast cancer at histopathology after surgery were evaluated. Accuracy measures and screen-reading time of six reading strategies were assessed: (A) Single reading of S-2D alone, (B) single reading of tomosynthesis alone, (C) single reading of joint interpretation of tomosynthesis + S-2D, (D) double-reading of S-2D alone, (E) double reading of tomosynthesis alone, (F) double reading of joint interpretation of tomosynthesis + S-2D. The median age of the patients was 53 years (range, 36-88 years). The highest global accuracy was obtained with double reading of tomosynthesis + S2D (F) with an AUC of 0.979 (p<0.001) and a mean reading time of 154 s versus 34 s for the fastest strategy (single reading of S-2D alone). The AUCs for the other five strategies did not differ from each other. Double reading of tomosynthesis+ S2D had the best accuracy of six screen-reading strategies although it had the longest reading time. • Tomosynthesis acquisitions are progressively implemented with reconstructed synthesized 2D images • Double reading using S-2D plus tomosynthesis had the highest global accuracy (p<0.001). • Double reading of S-2D plus tomosynthesis increased reading time.

Constructing high complexity synthetic libraries of long ORFs using in vitro selection

NASA Technical Reports Server (NTRS)

Cho, G.; Keefe, A. D.; Liu, R.; Wilson, D. S.; Szostak, J. W.

2000-01-01

We present a method that can significantly increase the complexity of protein libraries used for in vitro or in vivo protein selection experiments. Protein libraries are often encoded by chemically synthesized DNA, in which part of the open reading frame is randomized. There are, however, major obstacles associated with the chemical synthesis of long open reading frames, especially those containing random segments. Insertions and deletions that occur during chemical synthesis cause frameshifts, and stop codons in the random region will cause premature termination. These problems can together greatly reduce the number of full-length synthetic genes in the library. We describe a strategy in which smaller segments of the synthetic open reading frame are selected in vitro using mRNA display for the absence of frameshifts and stop codons. These smaller segments are then ligated together to form combinatorial libraries of long uninterrupted open reading frames. This process can increase the number of full-length open reading frames in libraries by up to two orders of magnitude, resulting in protein libraries with complexities of greater than 10(13). We have used this methodology to generate three types of displayed protein library: a completely random sequence library, a library of concatemerized oligopeptide cassettes with a propensity for forming amphipathic alpha-helical or beta-strand structures, and a library based on one of the most common enzymatic scaffolds, the alpha/beta (TIM) barrel. Copyright 2000 Academic Press.

A Transcriptome Map of Actinobacillus pleuropneumoniae at Single-Nucleotide Resolution Using Deep RNA-Seq

PubMed Central

Su, Zhipeng; Zhu, Jiawen; Xu, Zhuofei; Xiao, Ran; Zhou, Rui; Li, Lu; Chen, Huanchun

2016-01-01

Actinobacillus pleuropneumoniae is the pathogen of porcine contagious pleuropneumoniae, a highly contagious respiratory disease of swine. Although the genome of A. pleuropneumoniae was sequenced several years ago, limited information is available on the genome-wide transcriptional analysis to accurately annotate the gene structures and regulatory elements. High-throughput RNA sequencing (RNA-seq) has been applied to study the transcriptional landscape of bacteria, which can efficiently and accurately identify gene expression regions and unknown transcriptional units, especially small non-coding RNAs (sRNAs), UTRs and regulatory regions. The aim of this study is to comprehensively analyze the transcriptome of A. pleuropneumoniae by RNA-seq in order to improve the existing genome annotation and promote our understanding of A. pleuropneumoniae gene structures and RNA-based regulation. In this study, we utilized RNA-seq to construct a single nucleotide resolution transcriptome map of A. pleuropneumoniae. More than 3.8 million high-quality reads (average length ~90 bp) from a cDNA library were generated and aligned to the reference genome. We identified 32 open reading frames encoding novel proteins that were mis-annotated in the previous genome annotations. The start sites for 35 genes based on the current genome annotation were corrected. Furthermore, 51 sRNAs in the A. pleuropneumoniae genome were discovered, of which 40 sRNAs were never reported in previous studies. The transcriptome map also enabled visualization of 5'- and 3'-UTR regions, in which contained 11 sRNAs. In addition, 351 operons covering 1230 genes throughout the whole genome were identified. The RNA-Seq based transcriptome map validated annotated genes and corrected annotations of open reading frames in the genome, and led to the identification of many functional elements (e.g. regions encoding novel proteins, non-coding sRNAs and operon structures). The transcriptional units described in this study provide a foundation for future studies concerning the gene functions and the transcriptional regulatory architectures of this pathogen. PMID:27018591

Translation of 5′ leaders is pervasive in genes resistant to eIF2 repression

PubMed Central

Fahey, Ciara; Kenny, Elaine M; Terenin, Ilya M; Dmitriev, Sergey E; Cormican, Paul; Morris, Derek W; Shatsky, Ivan N; Baranov, Pavel V

2015-01-01

Eukaryotic cells rapidly reduce protein synthesis in response to various stress conditions. This can be achieved by the phosphorylation-mediated inactivation of a key translation initiation factor, eukaryotic initiation factor 2 (eIF2). However, the persistent translation of certain mRNAs is required for deployment of an adequate stress response. We carried out ribosome profiling of cultured human cells under conditions of severe stress induced with sodium arsenite. Although this led to a 5.4-fold general translational repression, the protein coding open reading frames (ORFs) of certain individual mRNAs exhibited resistance to the inhibition. Nearly all resistant transcripts possess at least one efficiently translated upstream open reading frame (uORF) that represses translation of the main coding ORF under normal conditions. Site-specific mutagenesis of two identified stress resistant mRNAs (PPP1R15B and IFRD1) demonstrated that a single uORF is sufficient for eIF2-mediated translation control in both cases. Phylogenetic analysis suggests that at least two regulatory uORFs (namely, in SLC35A4 and MIEF1) encode functional protein products. DOI: http://dx.doi.org/10.7554/eLife.03971.001 PMID:25621764

Homology between DNA polymerases of poxviruses, herpesviruses, and adenoviruses: nucleotide sequence of the vaccinia virus DNA polymerase gene.

PubMed Central

Earl, P L; Jones, E V; Moss, B

1986-01-01

A 5400-base-pair segment of the vaccinia virus genome was sequenced and an open reading frame of 938 codons was found precisely where the DNA polymerase had been mapped by transfer of a phosphonoacetate-resistance marker. A single nucleotide substitution changing glycine at position 347 to aspartic acid accounts for the drug resistance of the mutant vaccinia virus. The 5' end of the DNA polymerase mRNA was located 80 base pairs before the methionine codon initiating the open reading frame. Correspondence between the predicted Mr 108,577 polypeptide and the 110,000 purified enzyme indicates that little or no proteolytic processing occurs. Extensive homology, extending over 435 amino acids, was found upon comparing the DNA polymerase of vaccinia virus and DNA polymerase of Epstein-Barr virus. A highly conserved sequence of 14 amino acids in the carboxyl-terminal regions of the above DNA polymerases is also present at a similar location in adenovirus DNA polymerase. This structure, which is predicted to form a turn flanked by beta-pleated sheets, may form part of an essential binding or catalytic site that accounts for its presence in DNA polymerases of poxviruses, herpesviruses, and adenoviruses. Images PMID:3012524

Nucleotide sequence of a resistance breaking mutant of southern bean mosaic virus.

PubMed

Lee, L; Anderson, E J

1998-01-01

SBMV-S is a resistance-breaking mutant of an Arkansas isolate of the bean strain of southern bean mosaic virus (SBMV-BARK) that is able to move systemically in Phaseolus vulgaris cvs. Pinto and Great Northern, whereas the wild-type SBMV-BARK causes local necrotic lesions and is restricted to the inoculated leaves of these hosts. Sequence analysis of the 4136 nucleotide genomes of SBMV-BARK and SBMV-S revealed seven nucleotide differences, but only four deduced amino acid changes. A single amino acid change occurred in the C-terminal region of the putative RNA-dependent RNA polymerase and three differences were identified in the N-terminal portion of the virus coat protein. SBMV-BARK and SBMV-S were compared with other sobemoviruses and were found to contain a high level of nucleotide sequence identity (91.3%) to SBMV-B. Unlike SBMV-B however, SBMV-BARK and SBMV-S contained four putative overlapping open reading frames, making them more similar in genome organization to the cowpea strain, SBMV-C. The possibility exists that mutations or even errors, that resulted in mis-identification of open reading frames, occurred in previously published information on nucleotide sequence and genomic organization for SBMV-B.

Accumulation of RNA homologous to human papillomavirus type 16 open reading frames in genital precancers.

PubMed Central

Crum, C P; Nuovo, G; Friedman, D; Silverstein, S J

1988-01-01

The accumulation of human papillomavirus type 16 (HPV-16)-specific RNAs in tissue sections from biopsies of patients with genital precancers was studied by in situ hybridization with single-stranded 35S-labeled RNA. These analyses revealed that the most abundant early-region RNAs were derived from the E4 and E5 open reading frames (ORFs). RNAs homologous to the E6/E7 ORFs were also detected, whereas RNAs homologous to the intervening E1 ORF were not. This suggests that the E4 and E5 mRNAs are derived by splicing to the upstream E6/E7 ORFs, consistent with studies of HPV-11 in condylomata (L. T. Chow et al., Cancer Cells (Cold Spring Harbor) 5:55-72, 1987). Abundant RNAs homologous to the 5' portion of L1 were also detected. These RNAs were localized to the apical strata of the epithelium. HPV-16 RNAs accumulated in discrete regions of these lesions, and when present were most abundant in the upper cell layers of the precancerous epithelium. RNAs homologous to early ORFs were also detected in some germinal cells within the basal layer of the epithelium. Images PMID:2824859

Accumulation of RNA homologous to human papillomavirus type 16 open reading frames in genital precancers.

PubMed

Crum, C P; Nuovo, G; Friedman, D; Silverstein, S J

1988-01-01

The accumulation of human papillomavirus type 16 (HPV-16)-specific RNAs in tissue sections from biopsies of patients with genital precancers was studied by in situ hybridization with single-stranded 35S-labeled RNA. These analyses revealed that the most abundant early-region RNAs were derived from the E4 and E5 open reading frames (ORFs). RNAs homologous to the E6/E7 ORFs were also detected, whereas RNAs homologous to the intervening E1 ORF were not. This suggests that the E4 and E5 mRNAs are derived by splicing to the upstream E6/E7 ORFs, consistent with studies of HPV-11 in condylomata (L. T. Chow et al., Cancer Cells (Cold Spring Harbor) 5:55-72, 1987). Abundant RNAs homologous to the 5' portion of L1 were also detected. These RNAs were localized to the apical strata of the epithelium. HPV-16 RNAs accumulated in discrete regions of these lesions, and when present were most abundant in the upper cell layers of the precancerous epithelium. RNAs homologous to early ORFs were also detected in some germinal cells within the basal layer of the epithelium.

Accumulation of RNA homologous to human papillomavirus type 16 open reading frames in genital precancers

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

Crum, C.P.; Nuovo, G.; Friedman, D.

1988-01-01

The accumulation of human papillomavirus type 16 (HPV-16)-specific RNAs in tissue sections from biopsies of patients with genital precancers was studied by in situ hybridization with single-stranded /sup 35/S-labeled RNA. These analyses revealed that the most abundant early-region RNAs were derived from the E4 and E5 open reading frames (ORFs). RNAs homologous to the E6/E7 ORFs were also detected, whereas RNAs homologous to the intervening E1 ORF were not. This suggest that the E4 and E5 mRNAs are derived by splicing to the upstream E6/E7 ORFs, consistent with studies of HPV-11 in condylomata. Abundant RNAs homologous to the 5' portionmore » of L1 were also detected. These RNAs were localized to the apical strata of the epithelium. HPV-16 RNAs accumulated in discrete regions of these lesions, and when present were most abundant in the upper cell layers of the precancerous epithelium. RNAs homologous to early ORFs were also detected in some germinal cells within the basal layer of the epithelium.« less

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

Page turning system

NASA Technical Reports Server (NTRS)

Kerley, James J. (Inventor); Eklund, Wayne D. (Inventor)

1992-01-01

A device for holding reading materials for use by readers without arm mobility is presented. The device is adapted to hold the reading materials in position for reading with the pages displayed to enable turning by use of a rubber tipped stick that is held in the mouth and has a pair of rectangular frames. The frames are for holding and positioning the reading materials opened in reading posture with the pages displayed at a substantially unobstructed sighting position for reading. The pair of rectangular frames are connected to one another by a hinge so the angle between the frames may be varied thereby varying the inclination of the reading material. A pair of bent spring mounted wires for holding opposing pages of the reading material open for reading without substantial visual interference of the pages is mounted to the base. The wires are also adjustable to the thickness of the reading material and have a variable friction adjustment. This enables the force of the wires against the pages to be varied and permits the reader to manipulate the pages with the stick.

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

PubMed

Pandey, Ram Vinay; Schlötterer, Christian

2013-01-01

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

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

PubMed Central

Pandey, Ram Vinay; Schlötterer, Christian

2013-01-01

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

Vampiremania Sparks Developmental Readers (Open to Suggestion).

ERIC Educational Resources Information Center

Kaiden, Ellen Beth

1994-01-01

Describes how using Anne Rice's vampire novel "The Queen of the Damned" as supplementary reading in a developmental college reading course motivated students to enjoy reading and to improve their skills. (SR)

4 CFR 81.8 - Public reading facility.

Code of Federal Regulations, 2011 CFR

2011-01-01

....8 Public reading facility. GAO maintains a public reading facility in the Law Library at the Government Accountability Office Building, 441 G Street, NW., Washington, DC. The facility shall be open to...

4 CFR 81.8 - Public reading facility.

Code of Federal Regulations, 2010 CFR

2010-01-01

....8 Public reading facility. GAO maintains a public reading facility in the Law Library at the Government Accountability Office Building, 441 G Street, NW., Washington, DC. The facility shall be open to...

Hybrid error correction and de novo assembly of single-molecule sequencing reads

PubMed Central

Koren, Sergey; Schatz, Michael C.; Walenz, Brian P.; Martin, Jeffrey; Howard, Jason; Ganapathy, Ganeshkumar; Wang, Zhong; Rasko, David A.; McCombie, W. Richard; Jarvis, Erich D.; Phillippy, Adam M.

2012-01-01

Emerging single-molecule sequencing instruments can generate multi-kilobase sequences with the potential to dramatically improve genome and transcriptome assembly. However, the high error rate of single-molecule reads is challenging, and has limited their use to resequencing bacteria. To address this limitation, we introduce a novel correction algorithm and assembly strategy that utilizes shorter, high-identity sequences to correct the error in single-molecule sequences. We demonstrate the utility of this approach on Pacbio RS reads of phage, prokaryotic, and eukaryotic whole genomes, including the novel genome of the parrot Melopsittacus undulatus, as well as for RNA-seq reads of the corn (Zea mays) transcriptome. Our approach achieves over 99.9% read correction accuracy and produces substantially better assemblies than current sequencing strategies: in the best example, quintupling the median contig size relative to high-coverage, second-generation assemblies. Greater gains are predicted if read lengths continue to increase, including the prospect of single-contig bacterial chromosome assembly. PMID:22750884

Indel variant analysis of short-read sequencing data with Scalpel

PubMed Central

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

2017-01-01

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

Evaluating Approaches to Rendering Braille Text on a High-Density Pin Display.

PubMed

Morash, Valerie S; Russomanno, Alexander; Gillespie, R Brent; OModhrain, Sile

2017-10-13

Refreshable displays for tactile graphics are typically composed of pins that have smaller diameters and spacing than standard braille dots. We investigated configurations of high-density pins to form braille text on such displays using non-refreshable stimuli produced with a 3D printer. Normal dot braille (diameter 1.5 mm) was compared to high-density dot braille (diameter 0.75 mm) wherein each normal dot was rendered by high-density simulated pins alone or in a cluster of pins configured in a diamond, X, or square; and to "blobs" that could result from covering normal braille and high-density multi-pin configurations with a thin membrane. Twelve blind participants read MNREAD sentences displayed in these conditions. For high-density simulated pins, single pins were as quickly and easily read as normal braille, but diamond, X, and square multi-pin configurations were slower and/or harder to read than normal braille. We therefore conclude that as long as center-to-center dot spacing and dot placement is maintained, the dot diameter may be open to variability for rendering braille on a high density tactile display.

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

Accurate Reading with Sequential Presentation of Single Letters

PubMed Central

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

2012-01-01

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

Moving from Recitation to Open-Format Literature Discussion in Chinese Classrooms

ERIC Educational Resources Information Center

Cheng, Yahua; Zhang, Jie; Li, Hong; Anderson, Richard; Ding, Fengjiao; Nguyen-Jahiel, Kim; Shu, Hua; Wu, Xinchun

2015-01-01

A study involving 106 fourth graders and two teachers from a school in Beijing investigated the impact of a peer-led, open-format discussion approach, called collaborative reasoning (CR), on students' reading comprehension and teacher's professional learning. Mixed results of effects of CR on children's reading comprehension were found. After…

Results with Open Court Reading.

ERIC Educational Resources Information Center

McGraw-Hill Companies, New York, NY. Educational and Professional Publishing Group.

This publication tells the stories of eight schools from around the nation that have used the Open Court Reading program, describing the history of the schools, the challenges they faced, and their attempts to meet those challenges. The schools are located in California, Florida, Texas, and New York. Each of the school stories includes a focus on…

Is computer aided detection (CAD) cost effective in screening mammography? A model based on the CADET II study

PubMed Central

2011-01-01

Background Single reading with computer aided detection (CAD) is an alternative to double reading for detecting cancer in screening mammograms. The aim of this study is to investigate whether the use of a single reader with CAD is more cost-effective than double reading. Methods Based on data from the CADET II study, the cost-effectiveness of single reading with CAD versus double reading was measured in terms of cost per cancer detected. Cost (Pound (£), year 2007/08) of single reading with CAD versus double reading was estimated assuming a health and social service perspective and a 7 year time horizon. As the equipment cost varies according to the unit size a separate analysis was conducted for high, average and low volume screening units. One-way sensitivity analyses were performed by varying the reading time, equipment and assessment cost, recall rate and reader qualification. Results CAD is cost increasing for all sizes of screening unit. The introduction of CAD is cost-increasing compared to double reading because the cost of CAD equipment, staff training and the higher assessment cost associated with CAD are greater than the saving in reading costs. The introduction of single reading with CAD, in place of double reading, would produce an additional cost of £227 and £253 per 1,000 women screened in high and average volume units respectively. In low volume screening units, the high cost of purchasing the equipment will results in an additional cost of £590 per 1,000 women screened. One-way sensitivity analysis showed that the factors having the greatest effect on the cost-effectiveness of CAD with single reading compared with double reading were the reading time and the reader's professional qualification (radiologist versus advanced practitioner). Conclusions Without improvements in CAD effectiveness (e.g. a decrease in the recall rate) CAD is unlikely to be a cost effective alternative to double reading for mammography screening in UK. This study provides updated estimates of CAD costs in a full-field digital system and assessment cost for women who are re-called after initial screening. However, the model is highly sensitive to various parameters e.g. reading time, reader qualification, and equipment cost. PMID:21241473

Book reading styles in dual-parent and single-mother families.

PubMed

Blake, Joanna; Macdonald, Silvana; Bayrami, Lisa; Agosta, Vanessa; Milian, Andrea

2006-09-01

Whereas many studies have investigated quantitative aspects of book reading (frequency), few have examined qualitative aspects, especially in very young children and through direct observations of shared reading. The purpose of this study was to determine possible differences in book-reading styles between mothers and fathers and between mothers from single- and dual-parent families. It also related types of parental verbalizations during book reading to children's reported language measures. Dual-parent (29) and single-parent (24) families were observed in shared book reading with their toddlers (15-month-olds) or young preschoolers (27-month-olds). Parent-child dyads were videotaped while book reading. The initiator of each book-reading episode was coded. Parents' verbalizations were exhaustively coded into 10 categories. Mothers completed the MacArthur Communicative Development Inventory, and the children were given the Bayley scales. All parents differentiated their verbalizations according to the age rather than the gender of the child, but single mothers imitated female children more than males. Few differences in verbalizations were found between mothers and fathers or between mothers from single- and dual-parent families. Fathers allowed younger children to initiate book-reading episodes more than mothers. For both age groups of children, combined across families, verbalizations that related the book to the child's experience were correlated with reported language measures. Questions and imitations were related to language measures for the older age group. The important types of parental verbalizations during shared book reading for children's language acquisition are relating, questions and imitations.

High-capacity optical long data memory based on enhanced Young's modulus in nanoplasmonic hybrid glass composites.

PubMed

Zhang, Qiming; Xia, Zhilin; Cheng, Yi-Bing; Gu, Min

2018-03-22

Emerging as an inevitable outcome of the big data era, long data are the massive amount of data that captures changes in the real world over a long period of time. In this context, recording and reading the data of a few terabytes in a single storage device repeatedly with a century-long unchanged baseline is in high demand. Here, we demonstrate the concept of optical long data memory with nanoplasmonic hybrid glass composites. Through the sintering-free incorporation of nanorods into the earth abundant hybrid glass composite, Young's modulus is enhanced by one to two orders of magnitude. This discovery, enabling reshaping control of plasmonic nanoparticles of multiple-length allows for continuous multi-level recording and reading with a capacity over 10 terabytes with no appreciable change of the baseline over 600 years, which opens new opportunities for long data memory that affects the past and future.

Development of an Action Plan for the Creation of a Capacity Building Cell within the National Institute of Open Schooling, India. Contract No. C10A-159

ERIC Educational Resources Information Center

Mishra, Sanjaya

2010-01-01

In order to understand the Open Schooling system in India, the National Institute of Open Schooling (NIOS), and its operations, the author scanned and read a large number of documents in a short span of time. These readings formed the basis of his discussions with a range of stakeholders with whom he conducted interviews/interaction to gather…

Open the Door for Reading (Motivational Activities).

ERIC Educational Resources Information Center

Voorhees, Roxy

Designed to help elementary teachers motivate students to read, this illustrated booklet presents a store of classroom ideas that promote and enrich reading. Materials presented include (1) instructions for making a "bookworm" bookmark for each student; (2) various animated bulletin board games intended to accompany the reading process and to help…

Open to Suggestion.

ERIC Educational Resources Information Center

Journal of Reading, 1987

1987-01-01

Recounts the use of: (1) a game of reading trivia to review a unit in reading, (2) a reading-related art activity that emphasized the importance of following directions, and (3) the assignment of a research paper in a remedial curriculum. (NKA)

EFL Learners' Multiple Documents Literacy: Effects of a Strategy-Directed Intervention Program

ERIC Educational Resources Information Center

Karimi, Mohammad Nabi

2015-01-01

There is a substantial body of L2 research documenting the central role of strategy instruction in reading comprehension. However, this line of research has been conducted mostly within the single text paradigm of reading research. With reading literacy undergoing a marked shift from single source reading to multiple documents literacy, little is…

Pre- and post-head processing for single- and double-scrambled sentences of a head-final language as measured by the eye tracking method.

PubMed

Tamaoka, Katsuo; Asano, Michiko; Miyaoka, Yayoi; Yokosawa, Kazuhiko

2014-04-01

Using the eye-tracking method, the present study depicted pre- and post-head processing for simple scrambled sentences of head-final languages. Three versions of simple Japanese active sentences with ditransitive verbs were used: namely, (1) SO₁O₂V canonical, (2) SO₂O₁V single-scrambled, and (3) O₁O₂SV double-scrambled order. First pass reading times indicated that the third noun phrase just before the verb in both single- and double-scrambled sentences required longer reading times compared to canonical sentences. Re-reading times (the sum of all fixations minus the first pass reading) showed that all noun phrases including the crucial phrase before the verb in double-scrambled sentences required longer re-reading times than those required for single-scrambled sentences; single-scrambled sentences had no difference from canonical ones. Therefore, a single filler-gap dependency can be resolved in pre-head anticipatory processing whereas two filler-gap dependencies require much greater cognitive loading than a single case. These two dependencies can be resolved in post-head processing using verb agreement information.

High-Fidelity Rapid Initialization and Read-Out of an Electron Spin via the Single Donor D(-) Charge State.

PubMed

Watson, T F; Weber, B; House, M G; Büch, H; Simmons, M Y

2015-10-16

We demonstrate high-fidelity electron spin read-out of a precision placed single donor in silicon via spin selective tunneling to either the D(+) or D(-) charge state of the donor. By performing read-out at the stable two electron D(0)↔D(-) charge transition we can increase the tunnel rates to a nearby single electron transistor charge sensor by nearly 2 orders of magnitude, allowing faster qubit read-out (1 ms) with minimum loss in read-out fidelity (98.4%) compared to read-out at the D(+)↔D(0) transition (99.6%). Furthermore, we show that read-out via the D(-) charge state can be used to rapidly initialize the electron spin qubit in its ground state with a fidelity of F(I)=99.8%.

Findings from a Multi-Year Scale-Up Effectiveness Trial of Open-Court Reading (Imagine It!)

ERIC Educational Resources Information Center

Vaden-Kiernan, Michael; Borman, Geoffrey; Caverly, Sarah; Bell, Nance; de Castilla, Veronica Ruiz; Sullivan, Kate; Fleming, Grace

2016-01-01

This study addresses the effectiveness of a widely used core reading program that reflects the research-based practices recommended by the National Reading Panel. This and other similar programs are increasingly used to prevent reading difficulties and ensure that all children are reading at or above grade level by the end of third grade.…

Beach Books: 2014-2016. What Do Colleges and Universities Want Students to Read outside Class?

ERIC Educational Resources Information Center

Randall, David

2016-01-01

Hundreds of American colleges and universities continue to assign a summer reading to entering freshmen--typically one book, which the students are asked to read outside their courses. Many institutions embed the common reading in a larger program of campus activities: typically, they invite the common reading author to help open the academic year…

Emerging Concerns in Reading; Highlights of the 21st Annual Reading Conference of Lehigh University.

ERIC Educational Resources Information Center

Kender, Joseph P., Ed.

Addressing the question, "How can we teach all educable children to read effectively?" the papers in the first part of this volume look at several topical concerns in reading: "On Relocating the Reading Program: Finding a Better Barn for Our Sacred Cow,""The Transitional Open Classroom,""A Computer Program for Initial Screening of Problem…

Preliminary Findings from a Multi-Year Scale-Up Effectiveness Trial of Open-Court Reading (Imagine It!)

ERIC Educational Resources Information Center

Borman, Geoffrey; Vaden-Kiernan, Michael; Caverly, Sarah; Bell, Nance; de Castilla, Veronica Ruiz; Sullivan, Kate

2015-01-01

This study addresses the effectiveness of a nationally used core reading program that reflects the research-based practices recommended by the National Reading Panel. This and other similar programs are increasingly used to prevent reading difficulties and ensure that all children are reading at or above grade level by the end of third grade. The…

The Reading Environment; Proceedings of the Annual Reading Conference (8th, Terre Haute, Indiana, June 15-16, 1978).

ERIC Educational Resources Information Center

Waterman, David C., Comp.; Gibbs, Vanita M., Comp.

The papers presented in this annual reading conference report focus on various aspects of the topic, "The Reading Environment." The opening address advocates establishing reading programs that correspond to the developmental stages of individual children--programs that consider the needs of the whole child. The other papers delivered at the…

A mechanism for exon skipping caused by nonsense or missense mutations in BRCA1 and other genes.

PubMed

Liu, H X; Cartegni, L; Zhang, M Q; Krainer, A R

2001-01-01

Point mutations can generate defective and sometimes harmful proteins. The nonsense-mediated mRNA decay (NMD) pathway minimizes the potential damage caused by nonsense mutations. In-frame nonsense codons located at a minimum distance upstream of the last exon-exon junction are recognized as premature termination codons (PTCs), targeting the mRNA for degradation. Some nonsense mutations cause skipping of one or more exons, presumably during pre-mRNA splicing in the nucleus; this phenomenon is termed nonsense-mediated altered splicing (NAS), and its underlying mechanism is unclear. By analyzing NAS in BRCA1, we show here that inappropriate exon skipping can be reproduced in vitro, and results from disruption of a splicing enhancer in the coding sequence. Enhancers can be disrupted by single nonsense, missense and translationally silent point mutations, without recognition of an open reading frame as such. These results argue against a nuclear reading-frame scanning mechanism for NAS. Coding-region single-nucleotide polymorphisms (cSNPs) within exonic splicing enhancers or silencers may affect the patterns or efficiency of mRNA splicing, which may in turn cause phenotypic variability and variable penetrance of mutations elsewhere in a gene.

Prologue: Reading Comprehension Is Not a Single Ability.

PubMed

Catts, Hugh W; Kamhi, Alan G

2017-04-20

In this initial article of the clinical forum on reading comprehension, we argue that reading comprehension is not a single ability that can be assessed by one or more general reading measures or taught by a small set of strategies or approaches. We present evidence for a multidimensional view of reading comprehension that demonstrates how it varies as a function of reader ability, text, and task. The implications of this view for instruction of reading comprehension are considered. Reading comprehension is best conceptualized with a multidimensional model. The multidimensionality of reading comprehension means that instruction will be more effective when tailored to student performance with specific texts and tasks.

19 CFR 145.3 - Opening of letter class mail; reading of correspondence prohibited.

Code of Federal Regulations, 2011 CFR

2011-04-01

... letter class mail subject to Customs examination which appears to contain matter in addition to, or other... 19 Customs Duties 2 2011-04-01 2011-04-01 false Opening of letter class mail; reading of correspondence prohibited. 145.3 Section 145.3 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF...

19 CFR 145.3 - Opening of letter class mail; reading of correspondence prohibited.

Code of Federal Regulations, 2014 CFR

2014-04-01

... letter class mail subject to Customs examination which appears to contain matter in addition to, or other... 19 Customs Duties 2 2014-04-01 2014-04-01 false Opening of letter class mail; reading of correspondence prohibited. 145.3 Section 145.3 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF...

19 CFR 145.3 - Opening of letter class mail; reading of correspondence prohibited.

Code of Federal Regulations, 2013 CFR

2013-04-01

... letter class mail subject to Customs examination which appears to contain matter in addition to, or other... 19 Customs Duties 2 2013-04-01 2013-04-01 false Opening of letter class mail; reading of correspondence prohibited. 145.3 Section 145.3 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF...

19 CFR 145.3 - Opening of letter class mail; reading of correspondence prohibited.

Code of Federal Regulations, 2012 CFR

2012-04-01

... letter class mail subject to Customs examination which appears to contain matter in addition to, or other... 19 Customs Duties 2 2012-04-01 2012-04-01 false Opening of letter class mail; reading of correspondence prohibited. 145.3 Section 145.3 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF...

Identification of a non-LTR retrotransposon from the gypsy moth

Treesearch

K.J. Garner; J.M. Slavicek

1999-01-01

A family of highly repetitive elements, named LDT1, has been identified in the gypsy moth, Lymantria dispar. The complete element is 5.4 kb in length and lacks long-terminal repeats, The element contains two open reading frames with a significant amino acid sequence similarity to several non-LTR retrotransposons. The first open reading frame contains...

Expression and strain variation of the novel “Small Open Reading Frame” 3 (smorf) multigene family in Babesia bovis

USDA-ARS?s Scientific Manuscript database

Small open reading frame (smorf) genes comprise the second largest Babesia bovis multigene family. All known 44 variant smorf genes are located in close chromosomal proximity to ves1 genes, which encode proteins that mediate cytoadhesion and contribute to immune evasion. In this study, we characte...

A Multisite Cluster Randomized Field Trial of Open Court Reading

ERIC Educational Resources Information Center

Borman, Geoffrey D.; Dowling, N. Maritza; Schneck, Carrie

2008-01-01

In this article, the authors report achievement outcomes of a multisite cluster randomized field trial of Open Court Reading 2005 (OCR), a K-6 literacy curriculum published by SRA/McGraw-Hill. The participants are 49 first-grade through fifth-grade classrooms from predominantly minority and poor contexts across the nation. Blocking by grade level…

U.S. Global Change Research Program

MedlinePlus

... Announcing... Read more The Deepening Story of How Climate Change Threatens Human Health Read more Celebrating the 25th Anniversary of the U.S. Global Change Research... Read more Nomination Period Open for ... more Connecting America’s Communities with Actionable Climate ...

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline

PubMed Central

2013-01-01

We describe MetAMOS, an open source and modular metagenomic assembly and analysis pipeline. MetAMOS represents an important step towards fully automated metagenomic analysis, starting with next-generation sequencing reads and producing genomic scaffolds, open-reading frames and taxonomic or functional annotations. MetAMOS can aid in reducing assembly errors, commonly encountered when assembling metagenomic samples, and improves taxonomic assignment accuracy while also reducing computational cost. MetAMOS can be downloaded from: https://github.com/treangen/MetAMOS. PMID:23320958

Readings and Experiences of Multimodality

ERIC Educational Resources Information Center

Leander, Kevin M.; Aziz, Seemi; Botzakis, Stergios; Ehret, Christian; Landry, David; Rowsell, Jennifer

2017-01-01

Our understanding of reading--including reading multimodal texts--is always constrained or opened up by what we consider to be a text, what aspects of a reader's embodied activity we focus on, and how we draw a boundary around a reading event. This article brings together five literacy researchers who respond to a human-scale graphic novel,…

A tapeworm molecule manipulates vitellogenin expression in the beetle Tenebrio molitor

PubMed Central

Warr, E.; Meredith, J. M.; Nimmo, D. D.; Basu, S.; Hurd, H.; Eggleston, P.

2006-01-01

Metacestodes of Hymenolepis diminuta secrete a molecule that decreases vitellogenin (Vg) synthesis in the beetle host, Tenebrio molitor. The 5608 bp T. molitor Vg cDNA represents a single-copy gene encoding a single open reading frame of 1821 amino acids with a predicted molecular mass of 206 kDa. Northern blot analysis revealed detectable levels of transcripts only in adult females. In vivo, Vg mRNA abundance was significantly higher in fat bodies from infected females compared with control females at all but the earliest time point. In vitro, Vg mRNA abundance was significantly increased in fat bodies incubated with live stage I–II parasites. The apparent conflict between increased Vg mRNA abundance and decreased Vg protein in fat bodies from infected females is discussed. PMID:16907836

Verification of 2A peptide cleavage.

PubMed

Szymczak-Workman, Andrea L; Vignali, Kate M; Vignali, Dario A A

2012-02-01

The need for reliable, multicistronic vectors for multigene delivery is at the forefront of biomedical technology. It is now possible to express multiple proteins from a single open reading frame (ORF) using 2A peptide-linked multicistronic vectors. These small sequences, when cloned between genes, allow for efficient, stoichiometric production of discrete protein products within a single vector through a novel "cleavage" event within the 2A peptide sequence. The easiest and most effective way to assess 2A cleavage is to perform transient transfection of 293T cells (human embryonic kidney cells) followed by western blot analysis, as described in this protocol. 293T cells are easy to grow and can be efficiently transfected with a variety of vectors. Cleavage can be assessed by detection with antibodies against the target proteins or anti-2A serum.

Using Serial and Discrete Digit Naming to Unravel Word Reading Processes

PubMed Central

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

2018-01-01

During reading acquisition, word recognition is assumed to undergo a developmental shift from slow serial/sublexical processing of letter strings to fast parallel processing of whole word forms. This shift has been proposed to be detected by examining the size of the relationship between serial- and discrete-trial versions of word reading and rapid naming tasks. Specifically, a strong association between serial naming of symbols and single word reading suggests that words are processed serially, whereas a strong association between discrete naming of symbols and single word reading suggests that words are processed in parallel as wholes. In this study, 429 Grade 1, 3, and 5 English-speaking Canadian children were tested on serial and discrete digit naming and word reading. Across grades, single word reading was more strongly associated with discrete naming than with serial naming of digits, indicating that short high-frequency words are processed as whole units early in the development of reading ability in English. In contrast, serial naming was not a unique predictor of single word reading across grades, suggesting that within-word sequential processing was not required for the successful recognition for this set of words. Factor mixture analysis revealed that our participants could be clustered into two classes, namely beginning and more advanced readers. Serial naming uniquely predicted single word reading only among the first class of readers, indicating that novice readers rely on a serial strategy to decode words. Yet, a considerable proportion of Grade 1 students were assigned to the second class, evidently being able to process short high-frequency words as unitized symbols. We consider these findings together with those from previous studies to challenge the hypothesis of a binary distinction between serial/sublexical and parallel/lexical processing in word reading. We argue instead that sequential processing in word reading operates on a continuum, depending on the level of reading proficiency, the degree of orthographic transparency, and word-specific characteristics. PMID:29706918

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

PubMed

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

2018-01-01

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

Defense Threat Reduction Agency > Research > DTRIAC > FAQ Sheet

Science.gov Websites

FOIA Electronic Reading Room Privacy Impact Assessment DTRA No Fear Act Reporting Nuclear Test . Q: Does DTRIAC have a public reading room? A: No, DTRIAC does not have a reading room open to the

Sacred Cows That Should Be Put to Pasture.

ERIC Educational Resources Information Center

Artley, A. Sterl

This paper examines some of the problems associated with unquestioned teaching practices and theories ("sacred cows") in the field of reading. Topics discussed include phonics, pronunciation, oral reading, teacher accountability and behavioral objectives, individualized reading, and the open classroom. (KS)

Passive UHF RFID Tag with Multiple Sensing Capabilities

PubMed Central

Fernández-Salmerón, José; Rivadeneyra, Almudena; Martínez-Martí, Fernando; Capitán-Vallvey, Luis Fermín; Palma, Alberto J.; Carvajal, Miguel A.

2015-01-01

This work presents the design, fabrication, and characterization of a printed radio frequency identification tag in the ultra-high frequency band with multiple sensing capabilities. This passive tag is directly screen printed on a cardboard box with the aim of monitoring the packaging conditions during the different stages of the supply chain. This tag includes a commercial force sensor and a printed opening detector. Hence, the force applied to the package can be measured as well as the opening of the box can be detected. The architecture presented is a passive single-chip RFID tag. An electronic switch has been implemented to be able to measure both sensor magnitudes in the same access without including a microcontroller or battery. Moreover, the chip used here integrates a temperature sensor and, therefore, this tag provides three different parameters in every reading. PMID:26506353

Targeted Fluoro Positioning for the Discovery of a Potent and Highly Selective Matrix Metalloproteinase Inhibitor.

PubMed

Fischer, Thomas; Riedl, Rainer

2017-04-01

Invited for this month's cover picture is the group of Professor Rainer Riedl from the Institute of Chemistry and Biotechnology at the Zurich University of Applied Sciences (ZHAW), Switzerland. The cover picture depicts the structure-based design of a drug-like small molecule inhibitor of matrix metalloproteinase-13 (MMP-13) with a combined dual binding motif. The targeted introduction of a single fluoro atom was of vital importance for the optimization of the inhibitor. For more details, read the full text of the Communication at 10.1002/open.201600158.

Quantum-dot based nanothermometry in optical plasmonic recording media

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

Maestro, Laura Martinez; Centre for Micro-Photonics, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, Victoria 3122; Zhang, Qiming

2014-11-03

We report on the direct experimental determination of the temperature increment caused by laser irradiation in a optical recording media constituted by a polymeric film in which gold nanorods have been incorporated. The incorporation of CdSe quantum dots in the recording media allowed for single beam thermal reading of the on-focus temperature from a simple analysis of the two-photon excited fluorescence of quantum dots. Experimental results have been compared with numerical simulations revealing an excellent agreement and opening a promising avenue for further understanding and optimization of optical writing processes and media.

Ninety-six haploid yeast strains with individual disruptions of open reading frames between YOR097C and YOR192C, constructed for the Saccharomyces genome deletion project, have an additional mutation in the mismatch repair gene MSH3.

PubMed

Lehner, Kevin R; Stone, Megan M; Farber, Rosann A; Petes, Thomas D

2007-11-01

As part of the Saccharomyces Genome Deletion Project, sets of presumably isogenic haploid and diploid strains that differed only by single gene deletions were constructed. We found that one set of 96 strains (containing deletions of ORFs located between YOR097C and YOR192C) in the collection, which was derived from the haploid BY4741, has an additional mutation in the MSH3 mismatch repair gene.

Nucleotide sequence of the gene determining plasmid-mediated citrate utilization.

PubMed Central

Ishiguro, N; Sato, G

1985-01-01

The citrate utilization determinant from transposon Tn3411 has been cloned and sequenced, and its polypeptide products have been characterized in minicell experiments. The nucleotide sequence was determined for a 2,047-base-pair BglII restriction endonuclease fragment that includes the citrate determinant. This region contains an open reading frame that would encode a 431-amino-acid very hydrophobic polypeptide and which is preceded by a reasonable ribosomal binding site. However, the single polypeptide found in minicell experiments had an apparent molecular weight of 35,000 on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Images PMID:2999087

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

PubMed

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

2018-03-09

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

78 FR 21120 - Registration Review; Pesticide Dockets Opened for Review and Comment and Other Docket Acts...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-09

... Constitution Ave. NW., Washington, DC 20460-0001. The Public Reading Room is open from 8:30 a.m. to 4:30 p.m., Monday through Friday, excluding legal holidays. The telephone number for the Public Reading Room is (202... the visitor instructions and additional information about the docket available at http://www.epa.gov...

Regulation of hTERT Expression and Function in Newly Immortalized p53(+) Human Mammary Epithelial Cell Lines

DTIC Science & Technology

2008-06-01

proteins during embryogene- sis, neurodevelopment and cancer. Part of their function is through the repression of CKIs, including p16. Some functions...protein 2 Other AUTS2 autism susceptibility candidate 2 C1orf24 chromosome 1 open reading frame 24 C20orf97 chromosome 20 open reading frame 97

Regulation of hTERT Expression and Function in Newly Immortalized p53(+) Human Mammary Epithelial Cell Lines

DTIC Science & Technology

2007-06-01

embryogene- sis, neurodevelopment and cancer. Part of their function is through the repression of CKIs, including p16. Some functions have been attributed to...AUTS2 autism susceptibility candidate 2 C1orf24 chromosome 1 open reading frame 24 C20orf97 chromosome 20 open reading frame 97 DKFZP566B183

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

PubMed

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

2013-10-01

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

The isolation of cDNAs from OATL1 at Xp11.2 using a 480-kb YAC

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

Geraghty, M.T.; Brody, L.C.; Martin, L.S.

1993-05-01

Using an ornithine-{delta}-aminotransferase (OAT) cDNA, the authors identified five YACs that cover two nonadjacent OAT-related loci in Xp11.2-p11.3, designated OATL1 (distal) and OATL2 (proximal). Because several retinal degenerative disorders map to this region, they used YAC2 (480 kb), which covers the most distal part of OATL1, as a probe to screen a retinal cDNA library. From 8 {times} 10{sup 4} plaques screened, they isolated 13 clones. Two were OAT cDNAs. The remaining 11 were divided into eight groups by cross-hybridization. Groups 1-4 contain cDNAs that originate from single-copy X-linked genes in YAC2. Each has an open reading frame of >500more » bp and detects one or more transcripts on a Northern blot. The gene for each was sublocalized and ordered in YAC2. The cDNAs in groups 5-8 contained two or more Alu sequences, had no open reading frames, and did not detect transcripts. The cDNAs from groups 1-4 provide expressed sequence tags and identify candidate genes for the genetic disorders that map to this region. 28 refs., 5 figs., 1 tab.« less

Cytoplasmic Male Sterility-Associated Chimeric Open Reading Frames Identified by Mitochondrial Genome Sequencing of Four Cajanus Genotypes

PubMed Central

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

2013-01-01

The hybrid pigeonpea (Cajanus cajan) breeding technology based on cytoplasmic male sterility (CMS) is currently unique among legumes and displays major potential for yield increase. CMS is defined as a condition in which a plant is unable to produce functional pollen grains. The novel chimeric open reading frames (ORFs) produced as a results of mitochondrial genome rearrangements are considered to be the main cause of CMS. To identify these CMS-related ORFs in pigeonpea, we sequenced the mitochondrial genomes of three C. cajan lines (the male-sterile line ICPA 2039, the maintainer line ICPB 2039, and the hybrid line ICPH 2433) and of the wild relative (Cajanus cajanifolius ICPW 29). A single, circular-mapping molecule of length 545.7 kb was assembled and annotated for the ICPA 2039 line. Sequence annotation predicted 51 genes, including 34 protein-coding and 17 RNA genes. Comparison of the mitochondrial genomes from different Cajanus genotypes identified 31 ORFs, which differ between lines within which CMS is present or absent. Among these chimeric ORFs, 13 were identified by comparison of the related male-sterile and maintainer lines. These ORFs display features that are known to trigger CMS in other plant species and to represent the most promising candidates for CMS-related mitochondrial rearrangements in pigeonpea. PMID:23792890

Single-Word Recognition Need Not Depend on Single-Word Features: Narrative Coherence Counteracts Effects of Single-Word Features that Lexical Decision Emphasizes.

PubMed

Teng, Dan W; Wallot, Sebastian; Kelty-Stephen, Damian G

2016-12-01

Research on reading comprehension of connected text emphasizes reliance on single-word features that organize a stable, mental lexicon of words and that speed or slow the recognition of each new word. However, the time needed to recognize a word might not actually be as fixed as previous research indicates, and the stability of the mental lexicon may change with task demands. The present study explores the effects of narrative coherence in self-paced story reading to single-word feature effects in lexical decision. We presented single strings of letters to 24 participants, in both lexical decision and self-paced story reading. Both tasks included the same words composing a set of adjective-noun pairs. Reading times revealed that the tasks, and the order of the presentation of the tasks, changed and/or eliminated familiar effects of single-word features. Specifically, experiencing the lexical-decision task first gradually emphasized the role of single-word features, and experiencing the self-paced story-reading task afterwards counteracted the effect of single-word features. We discuss the implications that task-dependence and narrative coherence might have for the organization of the mental lexicon. Future work will need to consider what architectures suit the apparent flexibility with which task can accentuate or diminish effects of single-word features.

Children's Literature in the Basals.

ERIC Educational Resources Information Center

O'Brien, Maureen A.

Three basal reading series, levels kindergarten through grade three, were studied to categorize the types of literature each contained. The following series were analyzed: "The Headway Program" (Open Court Publishing Company), "Series r Macmillan Reading," and "Basics in Reading" (Scott, Foresman and Company). It was…

Photon-HDF5: Open Data Format and Computational Tools for Timestamp-based Single-Molecule Experiments

PubMed Central

Ingargiola, Antonino; Laurence, Ted; Boutelle, Robert; Weiss, Shimon; Michalet, Xavier

2017-01-01

Archival of experimental data in public databases has increasingly become a requirement for most funding agencies and journals. These data-sharing policies have the potential to maximize data reuse, and to enable confirmatory as well as novel studies. However, the lack of standard data formats can severely hinder data reuse. In photon-counting-based single-molecule fluorescence experiments, data is stored in a variety of vendor-specific or even setup-specific (custom) file formats, making data interchange prohibitively laborious, unless the same hardware-software combination is used. Moreover, the number of available techniques and setup configurations make it difficult to find a common standard. To address this problem, we developed Photon-HDF5 (www.photon-hdf5.org), an open data format for timestamp-based single-molecule fluorescence experiments. Building on the solid foundation of HDF5, Photon-HDF5 provides a platform- and language-independent, easy-to-use file format that is self-describing and supports rich metadata. Photon-HDF5 supports different types of measurements by separating raw data (e.g. photon-timestamps, detectors, etc) from measurement metadata. This approach allows representing several measurement types and setup configurations within the same core structure and makes possible extending the format in backward-compatible way. Complementing the format specifications, we provide open source software to create and convert Photon-HDF5 files, together with code examples in multiple languages showing how to read Photon-HDF5 files. Photon-HDF5 allows sharing data in a format suitable for long term archival, avoiding the effort to document custom binary formats and increasing interoperability with different analysis software. We encourage participation of the single-molecule community to extend interoperability and to help defining future versions of Photon-HDF5. PMID:28649160

Photon-HDF5: Open Data Format and Computational Tools for Timestamp-based Single-Molecule Experiments.

PubMed

Ingargiola, Antonino; Laurence, Ted; Boutelle, Robert; Weiss, Shimon; Michalet, Xavier

2016-02-13

Archival of experimental data in public databases has increasingly become a requirement for most funding agencies and journals. These data-sharing policies have the potential to maximize data reuse, and to enable confirmatory as well as novel studies. However, the lack of standard data formats can severely hinder data reuse. In photon-counting-based single-molecule fluorescence experiments, data is stored in a variety of vendor-specific or even setup-specific (custom) file formats, making data interchange prohibitively laborious, unless the same hardware-software combination is used. Moreover, the number of available techniques and setup configurations make it difficult to find a common standard. To address this problem, we developed Photon-HDF5 (www.photon-hdf5.org), an open data format for timestamp-based single-molecule fluorescence experiments. Building on the solid foundation of HDF5, Photon-HDF5 provides a platform- and language-independent, easy-to-use file format that is self-describing and supports rich metadata. Photon-HDF5 supports different types of measurements by separating raw data (e.g. photon-timestamps, detectors, etc) from measurement metadata. This approach allows representing several measurement types and setup configurations within the same core structure and makes possible extending the format in backward-compatible way. Complementing the format specifications, we provide open source software to create and convert Photon-HDF5 files, together with code examples in multiple languages showing how to read Photon-HDF5 files. Photon-HDF5 allows sharing data in a format suitable for long term archival, avoiding the effort to document custom binary formats and increasing interoperability with different analysis software. We encourage participation of the single-molecule community to extend interoperability and to help defining future versions of Photon-HDF5.

Photon-HDF5: open data format and computational tools for timestamp-based single-molecule experiments

NASA Astrophysics Data System (ADS)

Ingargiola, Antonino; Laurence, Ted; Boutelle, Robert; Weiss, Shimon; Michalet, Xavier

2016-02-01

Archival of experimental data in public databases has increasingly become a requirement for most funding agencies and journals. These data-sharing policies have the potential to maximize data reuse, and to enable confirmatory as well as novel studies. However, the lack of standard data formats can severely hinder data reuse. In photon-counting-based single-molecule fluorescence experiments, data is stored in a variety of vendor-specific or even setup-specific (custom) file formats, making data interchange prohibitively laborious, unless the same hardware-software combination is used. Moreover, the number of available techniques and setup configurations make it difficult to find a common standard. To address this problem, we developed Photon-HDF5 (www.photon-hdf5.org), an open data format for timestamp-based single-molecule fluorescence experiments. Building on the solid foundation of HDF5, Photon- HDF5 provides a platform- and language-independent, easy-to-use file format that is self-describing and supports rich metadata. Photon-HDF5 supports different types of measurements by separating raw data (e.g. photon-timestamps, detectors, etc) from measurement metadata. This approach allows representing several measurement types and setup configurations within the same core structure and makes possible extending the format in backward-compatible way. Complementing the format specifications, we provide open source software to create and convert Photon- HDF5 files, together with code examples in multiple languages showing how to read Photon-HDF5 files. Photon- HDF5 allows sharing data in a format suitable for long term archival, avoiding the effort to document custom binary formats and increasing interoperability with different analysis software. We encourage participation of the single-molecule community to extend interoperability and to help defining future versions of Photon-HDF5.

Applying Research in Reading Instruction for Adults: First Steps for Teachers

ERIC Educational Resources Information Center

McShane, Susan

2005-01-01

Reading is the most basic of skills. Reading provides access to other skills and knowledge, facilitates life-long learning, and opens doors to opportunity. The National Institute for Literacy is authorized by the U.S. Congress to collect and disseminate information on the components of reading and the findings from scientific research. The…

Cloning and identification of bacteriophage T4 gene 2 product gp2 and action of gp2 on infecting DNA in vivo.

PubMed Central

Lipinska, B; Rao, A S; Bolten, B M; Balakrishnan, R; Goldberg, E B

1989-01-01

We sequenced bacteriophage T4 genes 2 and 3 and the putative C-terminal portion of gene 50. They were found to have appropriate open reading frames directed counterclockwise on the T4 map. Mutations in genes 2 and 64 were shown to be in the same open reading frame, which we now call gene 2. This gene codes for a protein of 27,068 daltons. The open reading frame corresponding to gene 3 codes for a protein of 20,634 daltons. Appropriate bands on polyacrylamide gels were identified at 30 and 20 kilodaltons, respectively. We found that the product of the cloned gene 2 can protect T4 DNA double-stranded ends from exonuclease V action. Images PMID:2644202

Transient replication of BPV-1 requires two viral polypeptides encoded by the E1 and E2 open reading frames.

PubMed

Ustav, M; Stenlund, A

1991-02-01

Bovine papillomavirus (BPV) DNA is maintained as an episome with a constant copy number in transformed cells and is stably inherited. To study BPV replication we have developed a transient replication assay based on a highly efficient electroporation procedure. Using this assay we have determined that in the context of the viral genome two of the viral open reading frames, E1 and E2, are required for replication. Furthermore we show that when produced from expression vectors in the absence of other viral gene products, the full length E2 transactivator polypeptide and a 72 kd polypeptide encoded by the E1 open reading frame in its entirety, are both necessary and sufficient for replication BPV in C127 cells.

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

PubMed Central

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

2014-01-01

The wide availability of whole-genome sequencing (WGS) and an abundance of open-source software have made detection of single-nucleotide polymorphisms (SNPs) in bacterial genomes an increasingly accessible and effective tool for comparative analyses. Thus, ensuring that real nucleotide differences between genomes (i.e., true SNPs) are detected at high rates and that the influences of errors (such as false positive SNPs, ambiguously called sites, and gaps) are mitigated is of utmost importance. The choices researchers make regarding the generation and analysis of WGS data can greatly influence the accuracy of short-read sequence alignments and, therefore, the efficacy of such experiments. We studied the effects of some of these choices, including: i) depth of sequencing coverage, ii) choice of reference-guided short-read sequence assembler, iii) choice of reference genome, and iv) whether to perform read-quality filtering and trimming, on our ability to detect true SNPs and on the frequencies of errors. We performed benchmarking experiments, during which we assembled simulated and real Listeria monocytogenes strain 08-5578 short-read sequence datasets of varying quality with four commonly used assemblers (BWA, MOSAIK, Novoalign, and SMALT), using reference genomes of varying genetic distances, and with or without read pre-processing (i.e., quality filtering and trimming). We found that assemblies of at least 50-fold coverage provided the most accurate results. In addition, MOSAIK yielded the fewest errors when reads were aligned to a nearly identical reference genome, while using SMALT to align reads against a reference sequence that is ∼0.82% distant from 08-5578 at the nucleotide level resulted in the detection of the greatest numbers of true SNPs and the fewest errors. Finally, we show that whether read pre-processing improves SNP detection depends upon the choice of reference sequence and assembler. In total, this study demonstrates that researchers should test a variety of conditions to achieve optimal results. PMID:25144537

Effectiveness and cost-effectiveness of double reading in digital mammography screening: A systematic review and meta-analysis.

PubMed

Posso, Margarita; Puig, Teresa; Carles, Misericòrdia; Rué, Montserrat; Canelo-Aybar, Carlos; Bonfill, Xavier

2017-11-01

Double reading is the strategy of choice for mammogram interpretation in screening programmes. It remains, however, unknown whether double reading is still the strategy of choice in the context of digital mammography. Our aim was to determine the effectiveness and cost-effectiveness of double reading versus single reading of digital mammograms in screening programmes. We performed a systematic review by searching the PubMed, Embase, and Cochrane Library databases up to April 2017. We used the QUADAS-2 (Quality Assessment of Diagnostic Accuracy Studies) tool and CHEERS (Consolidated Health Economic Evaluation Reporting Standards) checklist to assess the methodological quality of the diagnostic studies and economic evaluations, respectively. A proportion's meta-analysis approach, 95% Confidence Intervals (95% CI) and test of heterogeneity (P values) were used for pooled results. Costs are expressed US$ PPP (United States Dollar purchasing power parities). The PROSPERO ID of this Systematic Review's protocol is CRD42014013804. Of 1473 potentially relevant hits, four high-quality studies were included. The pooled cancer detection rate of double reading was 6.01 per 1000 screens (CI: 4.47‰-7.77‰), and it was 5.65 per 1000 screens (CI: 3.95‰-7.65‰) for single reading (P=0.76). The pooled proportion of false-positives of double reading was 47.03 per 1000 screens (CI: 39.13‰-55.62‰) and it was 40.60 per 1000 screens (CI: 38.58‰-42.67‰) for single reading (P=0.12). One study reported, for double reading, an ICER (Incremental Cost-Effectiveness Ratio) of 16,684 Euros (24,717 US$ PPP; 2015 value) per detected cancer. Single reading+CAD (computer-aided-detection) was cost-effective in Japan. The evidence of benefit for double reading compared to single reading for digital mammography interpretation is scarce. Double reading seems to increase operational costs, have a not significantly higher false-positive rate, and a similar cancer detection rate. Copyright © 2017 Elsevier B.V. All rights reserved.

Motivating Remedial Readers (Open to Suggestion).

ERIC Educational Resources Information Center

Glowacki, Joan

1990-01-01

Describes the effect on remedial reading students of engaging in reading activities with trainable mentally handicapped children. Reports that the students requested additional opportunities to share reading activities with the mentally handicapped students. Notes that students developed a Big Book that described their experiences during the…

Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics

PubMed Central

Ardui, Simon; Ameur, Adam; Vermeesch, Joris R; Hestand, Matthew S

2018-01-01

Abstract Short read massive parallel sequencing has emerged as a standard diagnostic tool in the medical setting. However, short read technologies have inherent limitations such as GC bias, difficulties mapping to repetitive elements, trouble discriminating paralogous sequences, and difficulties in phasing alleles. Long read single molecule sequencers resolve these obstacles. Moreover, they offer higher consensus accuracies and can detect epigenetic modifications from native DNA. The first commercially available long read single molecule platform was the RS system based on PacBio's single molecule real-time (SMRT) sequencing technology, which has since evolved into their RSII and Sequel systems. Here we capsulize how SMRT sequencing is revolutionizing constitutional, reproductive, cancer, microbial and viral genetic testing. PMID:29401301

Characterization of two distinct dual specificity phosphatases encoded in alternative open reading frames of a single gene located on human chromosome 10q22.2.

PubMed

Chen, Hsu-Hsin; Luche, Ralf; Wei, Bo; Tonks, Nicholas K

2004-10-01

Dual specificity phosphatases (DSPs) are members of the protein-tyrosine phosphatase superfamily that dephosphorylate both phosphotyrosine and phosphoserine/threonine residues in vitro. Many DSPs have been found to play important roles in various aspects of cellular function and to be involved in human disease. We have identified a gene located on human chromosome 10q22.2, which utilizes alternative open reading frames (ORFs) to encode the following two distinct DSPs: the previously described testis and skeletal muscle-specific dual specificity phosphatase (TMDP) and a novel DSP, muscle-restricted dual specificity phosphatase (MDSP). Use of alternative ORFs encoding distinct proteins from a single gene is extremely rare in eukaryotes, and in all previously reported cases the two proteins produced from one gene are unrelated. To our knowledge this is the first example of a gene from which two distinct proteins of the same family are expressed using alternative ORFs. Here we provide evidence that both MDSP and TMDP proteins are expressed in vivo and are restricted to specific tissues, skeletal muscle and testis, respectively. Most interestingly, the protein expression profiles of both MDSP and TMDP during mouse postnatal development are strikingly similar. MDSP is expressed at very low levels in myotubes and early postnatal muscle. TMDP is not detectable in testis lysate in the first 3 weeks of life. The expression of both MDSP and TMDP proteins was markedly increased at approximately the 3rd week after birth and continued to increase gradually into adulthood, implying that the physiological functions of both DSPs are specific to the mature/late-developing organs. The conserved gene structure and the similarity in postnatal expression profile of these two proteins suggest biological significance of the unusual gene arrangement.

Improving Reading Comprehension in Reading and Listening Settings: The Effect of Two Training Programmes Focusing on Metacognition and Working Memory

ERIC Educational Resources Information Center

Carretti, Barbara; Caldarola, Nadia; Tencati, Chiara; Cornoldi, Cesare

2014-01-01

Background: Metacognition and working memory (WM) have been found associated with success in reading comprehension, but no studies have examined their combined effect on the training of reading comprehension. Another open question concerns the role of listening comprehension: In particular, it is not clear whether training to improve reading…

Factors That Facilitate or Hinder the Use of Computer-Assisted Reading in the L2 Reading Classroom

ERIC Educational Resources Information Center

Al-Seghayer, Khalid

2016-01-01

This study examined factors associated with whether instructors of English as a second or foreign language (ESL/EFL) incorporate computer-assisted reading (CAR) into their second-language (L2) reading classrooms. To achieve this goal, 70 ESL/EFL instructors completed a survey containing 37 items and 1 open-ended question concerning their…

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

PubMed

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

2010-01-01

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

A randomised open-label cross-over study of inhaler errors, preference and time to achieve correct inhaler use in patients with COPD or asthma: comparison of ELLIPTA with other inhaler devices.

PubMed

van der Palen, Job; Thomas, Mike; Chrystyn, Henry; Sharma, Raj K; van der Valk, Paul Dlpm; Goosens, Martijn; Wilkinson, Tom; Stonham, Carol; Chauhan, Anoop J; Imber, Varsha; Zhu, Chang-Qing; Svedsater, Henrik; Barnes, Neil C

2016-11-24

Errors in the use of different inhalers were investigated in patients naive to the devices under investigation in a multicentre, single-visit, randomised, open-label, cross-over study. Patients with chronic obstructive pulmonary disease (COPD) or asthma were assigned to ELLIPTA vs DISKUS (Accuhaler), metered-dose inhaler (MDI) or Turbuhaler. Patients with COPD were also assigned to ELLIPTA vs Handihaler or Breezhaler. Patients demonstrated inhaler use after reading the patient information leaflet (PIL). A trained investigator assessed critical errors (i.e., those likely to result in the inhalation of significantly reduced, minimal or no medication). If the patient made errors, the investigator demonstrated the correct use of the inhaler, and the patient demonstrated inhaler use again. Fewer COPD patients made critical errors with ELLIPTA after reading the PIL vs: DISKUS, 9/171 (5%) vs 75/171 (44%); MDI, 10/80 (13%) vs 48/80 (60%); Turbuhaler, 8/100 (8%) vs 44/100 (44%); Handihaler, 17/118 (14%) vs 57/118 (48%); Breezhaler, 13/98 (13%) vs 45/98 (46%; all P<0.001). Most patients (57-70%) made no errors using ELLIPTA and did not require investigator instruction. Instruction was required for DISKUS (65%), MDI (85%), Turbuhaler (71%), Handihaler (62%) and Breezhaler (56%). Fewer asthma patients made critical errors with ELLIPTA after reading the PIL vs: DISKUS (3/70 (4%) vs 9/70 (13%), P=0.221); MDI (2/32 (6%) vs 8/32 (25%), P=0.074) and significantly fewer vs Turbuhaler (3/60 (5%) vs 20/60 (33%), P<0.001). More asthma and COPD patients preferred ELLIPTA over the other devices (all P⩽0.002). Significantly, fewer COPD patients using ELLIPTA made critical errors after reading the PIL vs other inhalers. More asthma and COPD patients preferred ELLIPTA over comparator inhalers.

A randomised open-label cross-over study of inhaler errors, preference and time to achieve correct inhaler use in patients with COPD or asthma: comparison of ELLIPTA with other inhaler devices

PubMed Central

van der Palen, Job; Thomas, Mike; Chrystyn, Henry; Sharma, Raj K; van der Valk, Paul DLPM; Goosens, Martijn; Wilkinson, Tom; Stonham, Carol; Chauhan, Anoop J; Imber, Varsha; Zhu, Chang-Qing; Svedsater, Henrik; Barnes, Neil C

2016-01-01

Errors in the use of different inhalers were investigated in patients naive to the devices under investigation in a multicentre, single-visit, randomised, open-label, cross-over study. Patients with chronic obstructive pulmonary disease (COPD) or asthma were assigned to ELLIPTA vs DISKUS (Accuhaler), metered-dose inhaler (MDI) or Turbuhaler. Patients with COPD were also assigned to ELLIPTA vs Handihaler or Breezhaler. Patients demonstrated inhaler use after reading the patient information leaflet (PIL). A trained investigator assessed critical errors (i.e., those likely to result in the inhalation of significantly reduced, minimal or no medication). If the patient made errors, the investigator demonstrated the correct use of the inhaler, and the patient demonstrated inhaler use again. Fewer COPD patients made critical errors with ELLIPTA after reading the PIL vs: DISKUS, 9/171 (5%) vs 75/171 (44%); MDI, 10/80 (13%) vs 48/80 (60%); Turbuhaler, 8/100 (8%) vs 44/100 (44%); Handihaler, 17/118 (14%) vs 57/118 (48%); Breezhaler, 13/98 (13%) vs 45/98 (46%; all P<0.001). Most patients (57–70%) made no errors using ELLIPTA and did not require investigator instruction. Instruction was required for DISKUS (65%), MDI (85%), Turbuhaler (71%), Handihaler (62%) and Breezhaler (56%). Fewer asthma patients made critical errors with ELLIPTA after reading the PIL vs: DISKUS (3/70 (4%) vs 9/70 (13%), P=0.221); MDI (2/32 (6%) vs 8/32 (25%), P=0.074) and significantly fewer vs Turbuhaler (3/60 (5%) vs 20/60 (33%), P<0.001). More asthma and COPD patients preferred ELLIPTA over the other devices (all P⩽0.002). Significantly, fewer COPD patients using ELLIPTA made critical errors after reading the PIL vs other inhalers. More asthma and COPD patients preferred ELLIPTA over comparator inhalers. PMID:27883002

Perceived Effects of Earning a Reading Endorsement in a Single-District Sponsored Reading Cohort

ERIC Educational Resources Information Center

Atwood, Bonny L.

2011-01-01

This grounded theory study examined the perceived effects of a cohort of seven secondary-level teachers earning a reading endorsement in a single-district sponsored professional development program. The researcher collected data through semi-structured personal interviews with the teachers, their principal, and the director of special services for…

Transient replication of BPV-1 requires two viral polypeptides encoded by the E1 and E2 open reading frames.

PubMed Central

Ustav, M; Stenlund, A

1991-01-01

Bovine papillomavirus (BPV) DNA is maintained as an episome with a constant copy number in transformed cells and is stably inherited. To study BPV replication we have developed a transient replication assay based on a highly efficient electroporation procedure. Using this assay we have determined that in the context of the viral genome two of the viral open reading frames, E1 and E2, are required for replication. Furthermore we show that when produced from expression vectors in the absence of other viral gene products, the full length E2 transactivator polypeptide and a 72 kd polypeptide encoded by the E1 open reading frame in its entirety, are both necessary and sufficient for replication BPV in C127 cells. Images PMID:1846806

New Insights on Developmental Dyslexia Subtypes: Heterogeneity of Mixed Reading Profiles

PubMed Central

Zoubrinetzky, Rachel; Bielle, Frédérique; Valdois, Sylviane

2014-01-01

We examined whether classifications based on reading performance are relevant to identify cognitively homogeneous subgroups of dyslexic children. Each of the 71 dyslexic participants was selected to have a mixed reading profile, i.e. poor irregular word and pseudo-word reading performance (accuracy and speed). Despite their homogeneous reading profile, the participants were found to split into four distinct cognitive subgroups, characterized by a single phonological disorder, a single visual attention span disorder, a double deficit or none of these disorders. The two subgroups characterized by single and contrasted cognitive disorders were found to exhibit a very similar reading pattern but more contrasted spelling performance (quantitative analysis). A qualitative analysis of the error types produced in reading and spelling provided some cues about the participants' underlying cognitive deficit. The overall findings disqualify subtyping based on reading profiles as a classification method to identify cognitively homogeneous subgroups of dyslexic children. They rather show an opaque relationship between the cognitive underpinnings of developmental dyslexia and their behavioral manifestations in reading and spelling. Future neuroimaging and genetic studies should take this issue into account since synthesizing over cognitively heterogeneous children would entail potential pitfalls. PMID:24918441

Keeping It Simple: The Case for E-Mail.

ERIC Educational Resources Information Center

Haimovic, Gila

The Open University of Israel (OUI) is a distance education institution that offers over 250 computer-mediated courses through the Internet. All OUI students must pass an English reading comprehension exemption exam or take the University's English reading comprehension courses. Because reading instruction differs from content instruction,…

Viewing Reading Recovery as a Restructuring Phenomenon

ERIC Educational Resources Information Center

Rinehart, James S.; Short, Paula Myrick

2010-01-01

This study investigated components of Reading Recovery that relate to a restructuring paradigm. Specifically, Reading Recovery was analyzed as a way to redesign teachers' work, empower teachers, and affect the core technology of teaching. Data were collected by a survey that consisted of open-ended questions and of categorical response items.…

The Development of Wireless Body Area Network for Motion Sensing Application

NASA Astrophysics Data System (ADS)

Puspitaningayu, P.; Widodo, A.; Yundra, E.; Ramadhany, F.; Arianto, L.; Habibie, D.

2018-04-01

The information era has driven the society into the digitally-controlled lifestyle. Wireless body area networks (WBAN) as the specific scope of wireless sensor networks (WSN) is consistently growing into bigger applications. Currently, people are able to monitor their medical parameters by simply using small electronics devices attached to their body and connected to the authorities. On top of that, this time, smart phones are typically equipped with sensors such as accelerometer, gyroscope, barometric pressure, heart rate monitor, etc. It means that the sensing yet the signal processing can be performed by a single device. Moreover, Android opens lot wider opportunities for new applications as the most popular open-sourced smart phone platform. This paper is intended to show the development of motion sensing application which focused on analysing data from accelerometer and gyroscope. Beside reads the sensors, this application also has the ability to convert the sensors’ numerical value into graphs.

Reading with Love: Reading of Life Narrative of a Mother of a Child with Cerebral Palsy

ERIC Educational Resources Information Center

Mercieca, Daniela; Mercieca, Duncan P.

2014-01-01

This paper draws upon Deleuze and Guattari's ideas to suggest a different kind of reading of a narrative of a mother of a child with severe disability, and thus a different kind of ethical response to them. This reading gives readers the possibility of opening up experiences of parents and children with disability, rather than…

Consensus generation and variant detection by Celera Assembler.

PubMed

Denisov, Gennady; Walenz, Brian; Halpern, Aaron L; Miller, Jason; Axelrod, Nelson; Levy, Samuel; Sutton, Granger

2008-04-15

We present an algorithm to identify allelic variation given a Whole Genome Shotgun (WGS) assembly of haploid sequences, and to produce a set of haploid consensus sequences rather than a single consensus sequence. Existing WGS assemblers take a column-by-column approach to consensus generation, and produce a single consensus sequence which can be inconsistent with the underlying haploid alleles, and inconsistent with any of the aligned sequence reads. Our new algorithm uses a dynamic windowing approach. It detects alleles by simultaneously processing the portions of aligned reads spanning a region of sequence variation, assigns reads to their respective alleles, phases adjacent variant alleles and generates a consensus sequence corresponding to each confirmed allele. This algorithm was used to produce the first diploid genome sequence of an individual human. It can also be applied to assemblies of multiple diploid individuals and hybrid assemblies of multiple haploid organisms. Being applied to the individual human genome assembly, the new algorithm detects exactly two confirmed alleles and reports two consensus sequences in 98.98% of the total number 2,033311 detected regions of sequence variation. In 33,269 out of 460,373 detected regions of size >1 bp, it fixes the constructed errors of a mosaic haploid representation of a diploid locus as produced by the original Celera Assembler consensus algorithm. Using an optimized procedure calibrated against 1 506 344 known SNPs, it detects 438 814 new heterozygous SNPs with false positive rate 12%. The open source code is available at: http://wgs-assembler.cvs.sourceforge.net/wgs-assembler/

Comparing comprehension measured by multiple-choice and open-ended questions.

PubMed

Ozuru, Yasuhiro; Briner, Stephen; Kurby, Christopher A; McNamara, Danielle S

2013-09-01

This study compared the nature of text comprehension as measured by multiple-choice format and open-ended format questions. Participants read a short text while explaining preselected sentences. After reading the text, participants answered open-ended and multiple-choice versions of the same questions based on their memory of the text content. The results indicated that performance on open-ended questions was correlated with the quality of self-explanations, but performance on multiple-choice questions was correlated with the level of prior knowledge related to the text. These results suggest that open-ended and multiple-choice format questions measure different aspects of comprehension processes. The results are discussed in terms of dual process theories of text comprehension. PsycINFO Database Record (c) 2013 APA, all rights reserved

ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition.

PubMed

Koslicki, David; Chatterjee, Saikat; Shahrivar, Damon; Walker, Alan W; Francis, Suzanna C; Fraser, Louise J; Vehkaperä, Mikko; Lan, Yueheng; Corander, Jukka

2015-01-01

Estimation of bacterial community composition from high-throughput sequenced 16S rRNA gene amplicons is a key task in microbial ecology. Since the sequence data from each sample typically consist of a large number of reads and are adversely impacted by different levels of biological and technical noise, accurate analysis of such large datasets is challenging. There has been a recent surge of interest in using compressed sensing inspired and convex-optimization based methods to solve the estimation problem for bacterial community composition. These methods typically rely on summarizing the sequence data by frequencies of low-order k-mers and matching this information statistically with a taxonomically structured database. Here we show that the accuracy of the resulting community composition estimates can be substantially improved by aggregating the reads from a sample with an unsupervised machine learning approach prior to the estimation phase. The aggregation of reads is a pre-processing approach where we use a standard K-means clustering algorithm that partitions a large set of reads into subsets with reasonable computational cost to provide several vectors of first order statistics instead of only single statistical summarization in terms of k-mer frequencies. The output of the clustering is then processed further to obtain the final estimate for each sample. The resulting method is called Aggregation of Reads by K-means (ARK), and it is based on a statistical argument via mixture density formulation. ARK is found to improve the fidelity and robustness of several recently introduced methods, with only a modest increase in computational complexity. An open source, platform-independent implementation of the method in the Julia programming language is freely available at https://github.com/dkoslicki/ARK. A Matlab implementation is available at http://www.ee.kth.se/ctsoftware.

The Relation between Executive Functioning, Reaction Time, Naming Speed, and Single Word Reading in Children with Typical Development and Language Impairments

ERIC Educational Resources Information Center

Messer, David; Henry, Lucy A.; Nash, Gilly

2016-01-01

Background: Few investigations have examined the relationship between a comprehensive range of executive functioning (EF) abilities and reading. Aims: Our investigation identified components of EF that independently predicted single word reading, and determined whether their predictive role remained when additional variables were included in the…

Commentary on "Reading Comprehension Is Not a Single Ability": Implications for Child Language Intervention

ERIC Educational Resources Information Center

Ukrainetz, Teresa A.

2017-01-01

Purpose: This commentary responds to the implications for child language intervention of Catts and Kamhi's (2017) call to move from viewing reading comprehension as a single ability to recognizing it as a complex constellation of reader, text, and activity. Method: Reading comprehension, as Catts and Kamhi explain, is very complicated. In this…

Working Memory Deficits in Children with Reading Difficulties: Memory Span and Dual Task Coordination

ERIC Educational Resources Information Center

Wang, Shinmin; Gathercole, Susan E.

2013-01-01

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…

Open to Suggestion.

ERIC Educational Resources Information Center

Journal of Reading, 1981

1981-01-01

Contributors offer teaching ideas, including: using Sherlock Holmes mysteries to teach character and plot development, using materials supplied by the athletic coaches in the reading laboratory, and using individualized reading in the content areas. (AEA)

MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit

PubMed Central

Li, Junhua; Chen, Weineng; Chen, Hua; Mende, Daniel R.; Arumugam, Manimozhiyan; Pan, Qi; Liu, Binghang; Qin, Junjie; Wang, Jun; Bork, Peer

2012-01-01

MOCAT is a highly configurable, modular pipeline for fast, standardized processing of single or paired-end sequencing data generated by the Illumina platform. The pipeline uses state-of-the-art programs to quality control, map, and assemble reads from metagenomic samples sequenced at a depth of several billion base pairs, and predict protein-coding genes on assembled metagenomes. Mapping against reference databases allows for read extraction or removal, as well as abundance calculations. Relevant statistics for each processing step can be summarized into multi-sheet Excel documents and queryable SQL databases. MOCAT runs on UNIX machines and integrates seamlessly with the SGE and PBS queuing systems, commonly used to process large datasets. The open source code and modular architecture allow users to modify or exchange the programs that are utilized in the various processing steps. Individual processing steps and parameters were benchmarked and tested on artificial, real, and simulated metagenomes resulting in an improvement of selected quality metrics. MOCAT can be freely downloaded at http://www.bork.embl.de/mocat/. PMID:23082188

Ub-ISAP: a streamlined UNIX pipeline for mining unique viral vector integration sites from next generation sequencing data.

PubMed

Kamboj, Atul; Hallwirth, Claus V; Alexander, Ian E; McCowage, Geoffrey B; Kramer, Belinda

2017-06-17

The analysis of viral vector genomic integration sites is an important component in assessing the safety and efficiency of patient treatment using gene therapy. Alongside this clinical application, integration site identification is a key step in the genetic mapping of viral elements in mutagenesis screens that aim to elucidate gene function. We have developed a UNIX-based vector integration site analysis pipeline (Ub-ISAP) that utilises a UNIX-based workflow for automated integration site identification and annotation of both single and paired-end sequencing reads. Reads that contain viral sequences of interest are selected and aligned to the host genome, and unique integration sites are then classified as transcription start site-proximal, intragenic or intergenic. Ub-ISAP provides a reliable and efficient pipeline to generate large datasets for assessing the safety and efficiency of integrating vectors in clinical settings, with broader applications in cancer research. Ub-ISAP is available as an open source software package at https://sourceforge.net/projects/ub-isap/ .

Spliced RNA of woodchuck hepatitis virus.

PubMed

Ogston, C W; Razman, D G

1992-07-01

Polymerase chain reaction was used to investigate RNA splicing in liver of woodchucks infected with woodchuck hepatitis virus (WHV). Two spliced species were detected, and the splice junctions were sequenced. The larger spliced RNA has an intron of 1300 nucleotides, and the smaller spliced sequence shows an additional downstream intron of 1104 nucleotides. We did not detect singly spliced sequences from which the smaller intron alone was removed. Control experiments showed that spliced sequences are present in both RNA and DNA in infected liver, showing that the viral reverse transcriptase can use spliced RNA as template. Spliced sequences were detected also in virion DNA prepared from serum. The upstream intron produces a reading frame that fuses the core to the polymerase polypeptide, while the downstream intron causes an inframe deletion in the polymerase open reading frame. Whereas the splicing patterns in WHV are superficially similar to those reported recently in hepatitis B virus, we detected no obvious homology in the coding capacity of spliced RNAs from these two viruses.

MarDRe: efficient MapReduce-based removal of duplicate DNA reads in the cloud.

PubMed

Expósito, Roberto R; Veiga, Jorge; González-Domínguez, Jorge; Touriño, Juan

2017-09-01

This article presents MarDRe, a de novo cloud-ready duplicate and near-duplicate removal tool that can process single- and paired-end reads from FASTQ/FASTA datasets. MarDRe takes advantage of the widely adopted MapReduce programming model to fully exploit Big Data technologies on cloud-based infrastructures. Written in Java to maximize cross-platform compatibility, MarDRe is built upon the open-source Apache Hadoop project, the most popular distributed computing framework for scalable Big Data processing. On a 16-node cluster deployed on the Amazon EC2 cloud platform, MarDRe is up to 8.52 times faster than a representative state-of-the-art tool. Source code in Java and Hadoop as well as a user's guide are freely available under the GNU GPLv3 license at http://mardre.des.udc.es . rreye@udc.es. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

MOCAT: a metagenomics assembly and gene prediction toolkit.

PubMed

Kultima, Jens Roat; Sunagawa, Shinichi; Li, Junhua; Chen, Weineng; Chen, Hua; Mende, Daniel R; Arumugam, Manimozhiyan; Pan, Qi; Liu, Binghang; Qin, Junjie; Wang, Jun; Bork, Peer

2012-01-01

MOCAT is a highly configurable, modular pipeline for fast, standardized processing of single or paired-end sequencing data generated by the Illumina platform. The pipeline uses state-of-the-art programs to quality control, map, and assemble reads from metagenomic samples sequenced at a depth of several billion base pairs, and predict protein-coding genes on assembled metagenomes. Mapping against reference databases allows for read extraction or removal, as well as abundance calculations. Relevant statistics for each processing step can be summarized into multi-sheet Excel documents and queryable SQL databases. MOCAT runs on UNIX machines and integrates seamlessly with the SGE and PBS queuing systems, commonly used to process large datasets. The open source code and modular architecture allow users to modify or exchange the programs that are utilized in the various processing steps. Individual processing steps and parameters were benchmarked and tested on artificial, real, and simulated metagenomes resulting in an improvement of selected quality metrics. MOCAT can be freely downloaded at http://www.bork.embl.de/mocat/.

Integrated electronics for time-resolved array of single-photon avalanche diodes

NASA Astrophysics Data System (ADS)

Acconcia, G.; Crotti, M.; Rech, I.; Ghioni, M.

2013-12-01

The Time Correlated Single Photon Counting (TCSPC) technique has reached a prominent position among analytical methods employed in a great variety of fields, from medicine and biology (fluorescence spectroscopy) to telemetry (laser ranging) and communication (quantum cryptography). Nevertheless the development of TCSPC acquisition systems featuring both a high number of parallel channels and very high performance is still an open challenge: to satisfy the tight requirements set by the applications, a fully parallel acquisition system requires not only high efficiency single photon detectors but also a read-out electronics specifically designed to obtain the highest performance in conjunction with these sensors. To this aim three main blocks have been designed: a gigahertz bandwidth front-end stage to directly read the custom technology SPAD array avalanche current, a reconfigurable logic to route the detectors output signals to the acquisition chain and an array of time measurement circuits capable of recording the photon arrival times with picoseconds time resolution and a very high linearity. An innovative architecture based on these three circuits will feature a very high number of detectors to perform a truly parallel spatial or spectral analysis and a smaller number of high performance time-to-amplitude converter offering very high performance and a very high conversion frequency while limiting the area occupation and power dissipation. The routing logic will make the dynamic connection between the two arrays possible in order to guarantee that no information gets lost.

Cloning and characterization of an RNase-related protein gene preferentially expressed in rice stems.

PubMed

Wei, Jun-Ya; Li, An-Ming; Li, Yin; Wang, Jing; Liu, Xiao-Bin; Liu, Liang-Shi; Xu, Zeng-Fu

2006-04-01

RNase-related proteins (RRPs) are S- and S-like RNase homologs lacking the active site required for RNase activity. Here we describe the cloning and characterization of the rice (Oryza sativa) RRP gene (OsRRP). A single copy of OsRRP occurs in the rice genome. OsRRP contains three introns and an open reading frame encoding 252 amino acids, with the replacement of two histidines involved in the active site of RNase by lysine and tyrosine respectively. OsRRP is preferentially expressed in stems of wild-type rice and is significantly down-regulated in an increased tillering dwarf mutant ext37.

Reading Every Single Day: A Journey to Authentic Reading

ERIC Educational Resources Information Center

Hudson, Alida K.; Williams, Joan A.

2015-01-01

This article details one teacher's implementation of reading workshop in her second grade classroom. She provided a framework for authentic reading using the five components of reading workshop: time, choice, response, community, and structure. She found that reading workshop is a highly effective practice for not only increasing students'…

MutScan: fast detection and visualization of target mutations by scanning FASTQ data.

PubMed

Chen, Shifu; Huang, Tanxiao; Wen, Tiexiang; Li, Hong; Xu, Mingyan; Gu, Jia

2018-01-22

Some types of clinical genetic tests, such as cancer testing using circulating tumor DNA (ctDNA), require sensitive detection of known target mutations. However, conventional next-generation sequencing (NGS) data analysis pipelines typically involve different steps of filtering, which may cause miss-detection of key mutations with low frequencies. Variant validation is also indicated for key mutations detected by bioinformatics pipelines. Typically, this process can be executed using alignment visualization tools such as IGV or GenomeBrowse. However, these tools are too heavy and therefore unsuitable for validating mutations in ultra-deep sequencing data. We developed MutScan to address problems of sensitive detection and efficient validation for target mutations. MutScan involves highly optimized string-searching algorithms, which can scan input FASTQ files to grab all reads that support target mutations. The collected supporting reads for each target mutation will be piled up and visualized using web technologies such as HTML and JavaScript. Algorithms such as rolling hash and bloom filter are applied to accelerate scanning and make MutScan applicable to detect or visualize target mutations in a very fast way. MutScan is a tool for the detection and visualization of target mutations by only scanning FASTQ raw data directly. Compared to conventional pipelines, this offers a very high performance, executing about 20 times faster, and offering maximal sensitivity since it can grab mutations with even one single supporting read. MutScan visualizes detected mutations by generating interactive pile-ups using web technologies. These can serve to validate target mutations, thus avoiding false positives. Furthermore, MutScan can visualize all mutation records in a VCF file to HTML pages for cloud-friendly VCF validation. MutScan is an open source tool available at GitHub: https://github.com/OpenGene/MutScan.

Frozen shoulder

MedlinePlus

... Changes in your hormones, such as during menopause Shoulder injury Shoulder surgery Open heart surgery Cervical disk disease ... and the A.D.A.M. Editorial team. Shoulder Injuries and Disorders Read more NIH MedlinePlus Magazine Read ...

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

RADAR: A novel fast-screening method for reading difficulties with special focus on dyslexia.

PubMed

Smyrnakis, Ioannis; Andreadakis, Vassilios; Selimis, Vassilios; Kalaitzakis, Michail; Bachourou, Theodora; Kaloutsakis, Georgios; Kymionis, George D; Smirnakis, Stelios; Aslanides, Ioannis M

2017-01-01

Dyslexia is a developmental learning disorder of single word reading accuracy and/or fluency, with compelling research directed towards understanding the contributions of the visual system. While dyslexia is not an oculomotor disease, readers with dyslexia have shown different eye movements than typically developing students during text reading. Readers with dyslexia exhibit longer and more frequent fixations, shorter saccade lengths, more backward refixations than typical readers. Furthermore, readers with dyslexia are known to have difficulty in reading long words, lower skipping rate of short words, and high gaze duration on many words. It is an open question whether it is possible to harness these distinctive oculomotor scanning patterns observed during reading in order to develop a screening tool that can reliably identify struggling readers, who may be candidates for dyslexia. Here, we introduce a novel, fast, objective, non-invasive method, named Rapid Assessment of Difficulties and Abnormalities in Reading (RADAR) that screens for features associated with the aberrant visual scanning of reading text seen in dyslexia. Eye tracking parameter measurements that are stable under retest and have high discriminative power, as indicated by their ROC (receiver operating characteristic) curves, were obtained during silent text reading. These parameters were combined to derive a total reading score (TRS) that can reliably separate readers with dyslexia from typical readers. We tested TRS in a group of school-age children ranging from 8.5 to 12.5 years of age. TRS achieved 94.2% correct classification of children tested. Specifically, 35 out of 37 control (specificity 94.6%) and 30 out of 32 readers with dyslexia (sensitivity 93.8%) were classified correctly using RADAR, under a circular validation condition (see section Results/Total Reading Score) where the individual evaluated was not included in the test construction group. In conclusion, RADAR is a novel, automated, fast and reliable way to identify children at high risk of dyslexia that is amenable to large-scale screening. Moreover, analysis of eye movement parameters obtained with RADAR during reading will likely be useful for implementing individualized treatment strategies and for monitoring objectively the success of chosen interventions. We envision that it will be possible to use RADAR as a sensitive, objective, and quantitative first pass screen to identify individuals with reading disorders that manifest with abnormal oculomotor reading strategies, like dyslexia.

RADAR: A novel fast-screening method for reading difficulties with special focus on dyslexia

PubMed Central

Smyrnakis, Ioannis; Andreadakis, Vassilios; Selimis, Vassilios; Kalaitzakis, Michail; Bachourou, Theodora; Kaloutsakis, Georgios; Kymionis, George D.; Smirnakis, Stelios; Aslanides, Ioannis M.

2017-01-01

Dyslexia is a developmental learning disorder of single word reading accuracy and/or fluency, with compelling research directed towards understanding the contributions of the visual system. While dyslexia is not an oculomotor disease, readers with dyslexia have shown different eye movements than typically developing students during text reading. Readers with dyslexia exhibit longer and more frequent fixations, shorter saccade lengths, more backward refixations than typical readers. Furthermore, readers with dyslexia are known to have difficulty in reading long words, lower skipping rate of short words, and high gaze duration on many words. It is an open question whether it is possible to harness these distinctive oculomotor scanning patterns observed during reading in order to develop a screening tool that can reliably identify struggling readers, who may be candidates for dyslexia. Here, we introduce a novel, fast, objective, non-invasive method, named Rapid Assessment of Difficulties and Abnormalities in Reading (RADAR) that screens for features associated with the aberrant visual scanning of reading text seen in dyslexia. Eye tracking parameter measurements that are stable under retest and have high discriminative power, as indicated by their ROC (receiver operating characteristic) curves, were obtained during silent text reading. These parameters were combined to derive a total reading score (TRS) that can reliably separate readers with dyslexia from typical readers. We tested TRS in a group of school-age children ranging from 8.5 to 12.5 years of age. TRS achieved 94.2% correct classification of children tested. Specifically, 35 out of 37 control (specificity 94.6%) and 30 out of 32 readers with dyslexia (sensitivity 93.8%) were classified correctly using RADAR, under a circular validation condition (see section Results/Total Reading Score) where the individual evaluated was not included in the test construction group. In conclusion, RADAR is a novel, automated, fast and reliable way to identify children at high risk of dyslexia that is amenable to large-scale screening. Moreover, analysis of eye movement parameters obtained with RADAR during reading will likely be useful for implementing individualized treatment strategies and for monitoring objectively the success of chosen interventions. We envision that it will be possible to use RADAR as a sensitive, objective, and quantitative first pass screen to identify individuals with reading disorders that manifest with abnormal oculomotor reading strategies, like dyslexia. PMID:28800632

The Right to Read: An Open Letter to the Citizens of Our Country from the National Council of Teachers of English.

ERIC Educational Resources Information Center

National Council of Teachers of English, Champaign, IL.

Democracy can exist only in a climate in which teachers are free to teach and students are free to learn, a climate conducive to open inquiry and responsible discussion of any and all questions related to the ethical and cultural welfare of mankind. The right of an individual to read rests on the fundamental democratic assumption that an educated…

Reading Quizzes Improve Exam Scores for Community College Students

ERIC Educational Resources Information Center

Pape-Lindstrom, Pamela; Eddy, Sarah; Freeman, Scott

2018-01-01

To test the hypothesis that adding course structure may encourage self-regulated learning skills resulting in an increase in student exam performance in the community college setting, we added daily preclass online, open-book reading quizzes to an introductory biology course. We compared three control terms without reading quizzes and three…

Tobacco chloroplast tRNALys(UUU) gene contains a 2.5-kilobase-pair intron: An open reading frame and a conserved boundary sequence in the intron

PubMed Central

Sugita, Mamoru; Shinozaki, Kazuo; Sugiura, Masahiro

1985-01-01

The nucleotide sequence of a tRNALys(UUU) gene on tobacco (Nicotiana tabacum) chloroplast DNA has been determined. This gene is located 215 base pairs upstream from the gene for the 32,000-dalton thylakoid membrane protein on the same DNA strand and has a 2526-base-pair intron in the anticodon loop. The intron boundary sequence does not follow the G-U/A-G rule but is similar to those of tobacco chloroplast split genes for tRNAGly(UCC) and ribosomal proteins L2 and S12. The intron contains one major open reading frame of 509 codons. The codon usage in the open reading frame resembles those observed in the genes for tobacco chloroplast proteins so far analyzed. The primary transcript of this tRNA gene is 2.7 kilobases long. Images PMID:16593561

Tobacco chloroplast tRNA(UUU) gene contains a 2.5-kilobase-pair intron: An open reading frame and a conserved boundary sequence in the intron.

PubMed

Sugita, M; Shinozaki, K; Sugiura, M

1985-06-01

The nucleotide sequence of a tRNA(Lys)(UUU) gene on tobacco (Nicotiana tabacum) chloroplast DNA has been determined. This gene is located 215 base pairs upstream from the gene for the 32,000-dalton thylakoid membrane protein on the same DNA strand and has a 2526-base-pair intron in the anticodon loop. The intron boundary sequence does not follow the G-U/A-G rule but is similar to those of tobacco chloroplast split genes for tRNA(Gly)(UCC) and ribosomal proteins L2 and S12. The intron contains one major open reading frame of 509 codons. The codon usage in the open reading frame resembles those observed in the genes for tobacco chloroplast proteins so far analyzed. The primary transcript of this tRNA gene is 2.7 kilobases long.

High-fidelity projective read-out of a solid-state spin quantum register.

PubMed

Robledo, Lucio; Childress, Lilian; Bernien, Hannes; Hensen, Bas; Alkemade, Paul F A; Hanson, Ronald

2011-09-21

Initialization and read-out of coupled quantum systems are essential ingredients for the implementation of quantum algorithms. Single-shot read-out of the state of a multi-quantum-bit (multi-qubit) register would allow direct investigation of quantum correlations (entanglement), and would give access to further key resources such as quantum error correction and deterministic quantum teleportation. Although spins in solids are attractive candidates for scalable quantum information processing, their single-shot detection has been achieved only for isolated qubits. Here we demonstrate the preparation and measurement of a multi-spin quantum register in a low-temperature solid-state system by implementing resonant optical excitation techniques originally developed in atomic physics. We achieve high-fidelity read-out of the electronic spin associated with a single nitrogen-vacancy centre in diamond, and use this read-out to project up to three nearby nuclear spin qubits onto a well-defined state. Conversely, we can distinguish the state of the nuclear spins in a single shot by mapping it onto, and subsequently measuring, the electronic spin. Finally, we show compatibility with qubit control: we demonstrate initialization, coherent manipulation and single-shot read-out in a single experiment on a two-qubit register, using techniques suitable for extension to larger registers. These results pave the way for a test of Bell's inequalities on solid-state spins and the implementation of measurement-based quantum information protocols. © 2011 Macmillan Publishers Limited. All rights reserved

The attentional blink is related to phonemic decoding, but not sight-word recognition, in typically reading adults.

PubMed

Tyson-Parry, Maree M; Sailah, Jessica; Boyes, Mark E; Badcock, Nicholas A

2015-10-01

This research investigated the relationship between the attentional blink (AB) and reading in typical adults. The AB is a deficit in the processing of the second of two rapidly presented targets when it occurs in close temporal proximity to the first target. Specifically, this experiment examined whether the AB was related to both phonological and sight-word reading abilities, and whether the relationship was mediated by accuracy on a single-target rapid serial visual processing task (single-target accuracy). Undergraduate university students completed a battery of tests measuring reading ability, non-verbal intelligence, and rapid automatised naming, in addition to rapid serial visual presentation tasks in which they were required to identify either two (AB task) or one (single target task) target/s (outlined shapes: circle, square, diamond, cross, and triangle) in a stream of random-dot distractors. The duration of the AB was related to phonological reading (n=41, β=-0.43): participants who exhibited longer ABs had poorer phonemic decoding skills. The AB was not related to sight-word reading. Single-target accuracy did not mediate the relationship between the AB and reading, but was significantly related to AB depth (non-linear fit, R(2)=.50): depth reflects the maximal cost in T2 reporting accuracy in the AB. The differential relationship between the AB and phonological versus sight-word reading implicates common resources used for phonemic decoding and target consolidation, which may be involved in cognitive control. The relationship between single-target accuracy and the AB is discussed in terms of cognitive preparation. Copyright © 2015 Elsevier Ltd. All rights reserved.

Read-Aloud Accommodations, Expository Text, and Adolescents with Learning Disabilities

ERIC Educational Resources Information Center

Meyer, Nancy K.; Bouck, Emily C.

2017-01-01

Adolescents with learning disabilities in reading have difficulties with reading and understanding difficult gradelevel curricular material. One frequently used method of support is using read-aloud accommodations, which can be live read-alouds or text-to-speech (TTS) read-alouds. A single case alternating treatment design was used to examine the…

Treatment for Alexia With Agraphia Following Left Ventral Occipito-Temporal Damage: Strengthening Orthographic Representations Common to Reading and Spelling

PubMed Central

Rising, Kindle; Rapcsak, Steven Z.; Beeson, Pélagie M.

2015-01-01

Purpose Damage to left ventral occipito-temporal cortex can give rise to written language impairment characterized by pure alexia/letter-by-letter (LBL) reading, as well as surface alexia and agraphia. The purpose of this study was to examine the therapeutic effects of a combined treatment approach to address concurrent LBL reading with surface alexia/agraphia. Method Simultaneous treatment to address slow reading and errorful spelling was administered to 3 individuals with reading and spelling impairments after left ventral occipito-temporal damage due to posterior cerebral artery stroke. Single-word reading/spelling accuracy, reading latencies, and text reading were monitored as outcome measures for the combined effects of multiple oral re-reading treatment and interactive spelling treatment. Results After treatment, participants demonstrated faster and more accurate single-word reading and improved text-reading rates. Spelling accuracy also improved, particularly for untrained irregular words, demonstrating generalization of the trained interactive spelling strategy. Conclusion This case series characterizes concomitant LBL with surface alexia/agraphia and demonstrates a successful treatment approach to address both the reading and spelling impairment. PMID:26110814

Treatment for Alexia With Agraphia Following Left Ventral Occipito-Temporal Damage: Strengthening Orthographic Representations Common to Reading and Spelling.

PubMed

Kim, Esther S; Rising, Kindle; Rapcsak, Steven Z; Beeson, Pélagie M

2015-10-01

Damage to left ventral occipito-temporal cortex can give rise to written language impairment characterized by pure alexia/letter-by-letter (LBL) reading, as well as surface alexia and agraphia. The purpose of this study was to examine the therapeutic effects of a combined treatment approach to address concurrent LBL reading with surface alexia/agraphia. Simultaneous treatment to address slow reading and errorful spelling was administered to 3 individuals with reading and spelling impairments after left ventral occipito-temporal damage due to posterior cerebral artery stroke. Single-word reading/spelling accuracy, reading latencies, and text reading were monitored as outcome measures for the combined effects of multiple oral re-reading treatment and interactive spelling treatment. After treatment, participants demonstrated faster and more accurate single-word reading and improved text-reading rates. Spelling accuracy also improved, particularly for untrained irregular words, demonstrating generalization of the trained interactive spelling strategy. This case series characterizes concomitant LBL with surface alexia/agraphia and demonstrates a successful treatment approach to address both the reading and spelling impairment.

Single Parenthood and Children's Reading Performance in Asia

ERIC Educational Resources Information Center

Park, Hyunjoon

2007-01-01

Using the data from Program for International Student Assessment, I examine the gap in reading performance between 15-year-old students in single-parent and intact families in 5 Asian countries in comparison to the United States. The ordinary least square regression analyses show negligible disadvantages of students with a single parent in Hong…

Why Should I Read?--A Cross-Cultural Investigation into Adolescents' Reading Socialisation and Reading Attitude

ERIC Educational Resources Information Center

Broeder, Peter; Stokmans, Mia

2013-01-01

While reading behaviour of adolescents is a frequent object of research, most studies in this field are restricted to a single country. This study investigates reading as a leisure-time activity across social groups from three regions differing in reading tradition as well as in the facilities available for reading. The authors analyse the reading…

Exploring the association between visual perception abilities and reading of musical notation.

PubMed

Lee, Horng-Yih

2012-06-01

In the reading of music, the acquisition of pitch information depends primarily upon the spatial position of notes as well as upon an individual's spatial processing ability. This study investigated the relationship between the ability to read single notes and visual-spatial ability. Participants with high and low single-note reading abilities were differentiated based upon differences in musical notation-reading abilities and their spatial processing; object recognition abilities were then assessed. It was found that the group with lower note-reading abilities made more errors than did the group with a higher note-reading abilities in the mental rotation task. In contrast, there was no apparent significant difference between the two groups in the object recognition task. These results suggest that note-reading may be related to visual spatial processing abilities, and not to an individual's ability with object recognition.

Production of Candida antaractica Lipase B Gene Open Reading Frame using Automated PCR Gene Assembly Protocol on Robotic Workcell & Expression in Ethanologenic Yeast for use as Resin-Bound Biocatalyst in Biodiesel Production

USDA-ARS?s Scientific Manuscript database

A synthetic Candida antarctica lipase B (CALB) gene open reading frame (ORF) for expression in yeast was produced using an automated PCR assembly and DNA purification protocol on an integrated robotic workcell. The lycotoxin-1 (Lyt-1) C3 variant gene ORF was added in-frame with the CALB ORF to pote...

Effects of Single-Gender Education on the Reading Achievement of Third through Fifth Grade Boys

ERIC Educational Resources Information Center

Brown, Michael Shane

2013-01-01

It is said repeatedly, boys can't read. However, the statement should be boys "can" read they just don't. Understanding there is a need for action is the first step educators must take in helping boys emerge as confident and successful readers. Single-gender classrooms can be successful tools when seeking new ways in which to engage boys…

Measuring College Students' Reading Comprehension Ability Using Cloze Tests

ERIC Educational Resources Information Center

Williams, Rihana Shiri; Ari, Omer; Santamaria, Carmen Nicole

2011-01-01

Recent investigations challenge the construct validity of sustained silent reading tests. Performance of two groups of post-secondary students (e.g. struggling and non-struggling) on a sustained silent reading test and two types of cloze test (i.e. maze and open-ended) was compared in order to identify the test format that contributes greater…

Rose City Reading: Towards an Open Educational Resource with a Place-Based Curriculum

ERIC Educational Resources Information Center

Twenge-Jinings, Fidelia; Sullivan, Joanna

2016-01-01

Realizing that ESOL students often do not integrate naturally into their new communities, we developed a reading class that focuses only on topics such as history, culture, arts, nature and entertainment that pertain to Portland or Oregon. In addition to readings, we asked that students go out and "live" what they learned through a…

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

PubMed Central

Benjamin, Christopher F. A.; Gaab, Nadine

2012-01-01

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

Rearrangement of Influenza Virus Spliced Segments for the Development of Live-Attenuated Vaccines

PubMed Central

Nogales, Aitor; DeDiego, Marta L.; Topham, David J.

2016-01-01

ABSTRACT Influenza viral infections represent a serious public health problem, with influenza virus causing a contagious respiratory disease which is most effectively prevented through vaccination. Segments 7 (M) and 8 (NS) of the influenza virus genome encode mRNA transcripts that are alternatively spliced to express two different viral proteins. This study describes the generation, using reverse genetics, of three different recombinant influenza A/Puerto Rico/8/1934 (PR8) H1N1 viruses containing M or NS viral segments individually or modified M or NS viral segments combined in which the overlapping open reading frames of matrix 1 (M1)/M2 for the modified M segment and the open reading frames of nonstructural protein 1 (NS1)/nuclear export protein (NEP) for the modified NS segment were split by using the porcine teschovirus 1 (PTV-1) 2A autoproteolytic cleavage site. Viruses with an M split segment were impaired in replication at nonpermissive high temperatures, whereas high viral titers could be obtained at permissive low temperatures (33°C). Furthermore, viruses containing the M split segment were highly attenuated in vivo, while they retained their immunogenicity and provided protection against a lethal challenge with wild-type PR8. These results indicate that influenza viruses can be effectively attenuated by the rearrangement of spliced segments and that such attenuated viruses represent an excellent option as safe, immunogenic, and protective live-attenuated vaccines. Moreover, this is the first time in which an influenza virus containing a restructured M segment has been described. Reorganization of the M segment to encode M1 and M2 from two separate, nonoverlapping, independent open reading frames represents a useful tool to independently study mutations in the M1 and M2 viral proteins without affecting the other viral M product. IMPORTANCE Vaccination represents our best therapeutic option against influenza viral infections. However, the efficacy of current influenza vaccines is suboptimal, and novel approaches are necessary for the prevention of disease caused by this important human respiratory pathogen. In this work, we describe a novel approach to generate safer and more efficient live-attenuated influenza virus vaccines (LAIVs) based on recombinant viruses whose genomes encode nonoverlapping and independent M1/M2 (split M segment [Ms]) or both M1/M2 and NS1/NEP (Ms and split NS segment [NSs]) open reading frames. Viruses containing a modified M segment were highly attenuated in mice but were able to confer, upon a single intranasal immunization, complete protection against a lethal homologous challenge with wild-type virus. Notably, the protection efficacy conferred by our viruses with split M segments was better than that conferred by the current temperature-sensitive LAIV. Altogether, these results open a new avenue for the development of safer and more protective LAIVs on the basis of the reorganization of spliced viral RNA segments in the genome. PMID:27122587

Nasalance and nasality at experimental velopharyngeal openings in palatal prosthesis: a case study

PubMed Central

LIMA-GREGIO, Aveliny Mantovan; MARINO, Viviane Cristina de Castro; PEGORARO-KROOK, Maria Inês; BARBOSA, Plinio Almeida; AFERRI, Homero Carneiro; DUTKA, Jeniffer de Cassia Rillo

2011-01-01

The use of prosthetic devices for correction of velopharyngeal insufficiency (VPI) is an alternative treatment for patients with conditions that preclude surgery and for those individuals with a hypofunctional velopharynx (HV) with a poor prognosis for the surgical repair of VPI. Understanding the role and measuring the outcome of prosthetic treatment of velopharyngeal dysfunction requires the use of tools that allow for documenting pre- and post-treatment outcomes. Experimental openings in speech bulbs have been used for simulating VPI in studies documenting changes in aerodynamic, acoustic and kinematics aspects of speech associated with the use of palatal prosthetic devices. The use of nasometry to document changes in speech associated with experimental openings in speech bulbs, however, has not been described in the literature. Objective This single-subject study investigated nasalance and nasality at the presence of experimental openings drilled through the speech bulb of a patient with HV. Material and Methods Nasometric recordings of the word "pato" were obtained under 4 velopharyngeal conditions: no-opening (control condition), no speech bulb, speech bulb with a 20 mm2 opening, and speech bulb with 30 mm2 opening. Five speech-language pathologists performed auditory-perceptual ratings while the subject read an oral passage under all conditions. Results Kruskal-Wallis test showed significant difference among conditions (p=0.0002), with Scheffé post hoc test indicating difference from the no-opening condition. Conclusion The changes in nasalance observed after drilling holes of known sizes in a speech bulb suggest that nasometry reflect changes in transfer of sound energy related to different sizes of velopharyngeal opening. PMID:22230996

Oximetry in children recovering from deep hypothermia for cardiac surgery.

PubMed

Macnab, A J; Baker-Brown, G; Anderson, E E

1990-10-01

Although pulse oximetry is a potentially useful diagnostic tool in the treatment of children after major open heart surgery, there are concerns regarding its reliability for measuring oxygen saturation (SaO2) in hypothermic or low perfusion states. To test pulse oximeter reliability in children under these conditions, our study compared 187 SaO2 pulse oximeter readings (Biox 3700) with simultaneous hemoximeter (OSM2, Radiometer) readings from 56 children rewarming after open heart surgery. Ages ranged from 4 months to 18 yr; temperatures ranged from 23.5 degrees to 38 degrees C (toe) and 31.3 degrees to 40.8 degrees C (core). The mean pulse oximeter SaO2 reading was 94.90% (SD 7.18, range 54% to 100%), mean hemoximeter reading was 96.07% (SD 7.06; minimum 54%; maximum 100%). The correlation between the readings was high (r = .88, p less than .005), and was not affected by low core temperature. When oximeter and cardiac monitor pulse rates coincided, the oximeter SaO2 value was within +/- 5% (p less than .05). We conclude that the Biox 3700 oximeter is reliable for noninvasive SaO2 monitoring in mild to moderately hypothermic children after open heart surgery, particularly when oximeter and cardiac heart rates coincide. Further studies are needed to confirm our findings in children with core temperatures less than 31.3 degrees C, and when other oximeters are used.

[Development of a training program for Japanese dyslexic children and its short-term efficacy].

PubMed

Wakamiya, Eiji; Takeshita, Takashi; Nakanishi, Makoto; Mizuta, Mekumi; Kurimoto, Naoko; Okumura, Tomohito; Tamai, Hiroshi; Koeda, Tatsuya; Inagaki, Masumi

2013-07-01

The purpose of this study is to develop a computer training program of reading for the Japanese dyslexic children and to examine its short-term efficacy on their reading and writing abilities. Fifteen dyslexic children underwent two sets of training programs, one for single-hiragana and non-word reading, and the other for the reading of real words, in which each hiragana was followed by the correctly read sound. Subjects were required to use a given program for five minutes a day for three weeks, switching to the other program after a three-week interval. Four kinds of reading test and one writing test were done at the beginning and end of each program period. The averages reading speeds increased, and the single-hiragana reading error average was lower after the training. Hiragana-writing errors also decreased, even though no writing procedure was involved in the programs. The results indicate the usefulness of these training programs as an early intervention of reading and writing for the Japanese dyslexic children.

Federal Reading Rooms for Risk Management Plans (RMP)

EPA Pesticide Factsheets

Reading Rooms, listed here by state, are open to the public by either appointment or walk-in. You may access Off-Site Consequence Analysis (scenarios) portions of RMPs, and take notes but not remove or reproduce materials.

Breast screening using 2D-mammography or integrating digital breast tomosynthesis (3D-mammography) for single-reading or double-reading--evidence to guide future screening strategies.

PubMed

Houssami, Nehmat; Macaskill, Petra; Bernardi, Daniela; Caumo, Francesca; Pellegrini, Marco; Brunelli, Silvia; Tuttobene, Paola; Bricolo, Paola; Fantò, Carmine; Valentini, Marvi; Ciatto, Stefano

2014-07-01

We compared detection measures for breast screening strategies comprising single-reading or double-reading using standard 2D-mammography or 2D/3D-mammography, based on the 'screening with tomosynthesis or standard mammography' (STORM) trial. STORM prospectively examined screen-reading in two sequential phases, 2D-mammography alone and integrated 2D/3D-mammography, in asymptomatic women participating in Trento and Verona (Northern Italy) population-based screening services. Outcomes were ascertained from assessment and/or excision histology or follow-up. For each screen-reading strategy we calculated the number of detected and non-detected (including interval) cancers, cancer detection rates (CDRs), false positive recall (FPR) measures and incremental CDR relative to a comparator strategy. We estimated the false:true positive (FP:TP) ratio and sensitivity of each mammography screening strategy. Paired binary data were compared using McNemar's test. Amongst 7292 screening participants, there were 65 (including six interval) breast cancers; estimated first-year interval cancer rate was 0.82/1000 screens (95% confidence interval (CI): 0.30-1.79/1000). For single-reading, 35 cancers were detected at both 2D and 2D/3D-mammography, 20 cancers were detected only with 2D/3D-mammography compared with none at 2D-mammography alone (p<0.001) and 10 cancers were not detected. For double-reading, 39 cancers were detected at 2D-mammography and 2D/3D-mammography, 20 were detected only with 2D/3D-mammography compared with none detected at 2D-mammography alone (p<0.001) and six cancers were not detected. The incremental CDR attributable to 2D/3D-mammography (versus 2D-mammography) of 2.7/1000 screens (95% CI: 1.6-4.2) was evident for single and for double-reading. Incremental CDR attributable to double-reading (versus single-reading) of 0.55/1000 screens (95% CI: -0.02-1.4) was evident for 2D-mammography and for 2D/3D-mammography. Estimated FP:TP ratios showed that 2D/3D-mammography screening strategies had more favourable FP to TP trade-off and higher sensitivity, applying single-reading or double-reading, relative to 2D-mammography screening. The evidence we report warrants rethinking of breast screening strategies and should be used to inform future evaluations of 2D/3D-mammography that assess whether or not the estimated incremental detection translates into improved screening outcomes such as a reduction in interval cancer rates. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Single chip camera device having double sampling operation

NASA Technical Reports Server (NTRS)

Fossum, Eric R. (Inventor); Nixon, Robert (Inventor)

2002-01-01

A single chip camera device is formed on a single substrate including an image acquisition portion for control portion and the timing circuit formed on the substrate. The timing circuit also controls the photoreceptors in a double sampling mode in which are reset level is first read and then after an integration time a charged level is read.

The Distribution of Fixation Durations during Reading: Effects of Stimulus Quality

ERIC Educational Resources Information Center

White, Sarah J.; Staub, Adrian

2012-01-01

Participants' eye movements were recorded as they read single sentences presented normally, presented entirely in faint text, or presented normally except for a single faint word. Fixations were longer when the entire sentence was faint than when the sentence was presented normally. In addition, fixations were much longer on a single faint word…

Designing robust watermark barcodes for multiplex long-read sequencing.

PubMed

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

2017-03-15

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

The Community Intercomparison Suite (CIS)

NASA Astrophysics Data System (ADS)

Watson-Parris, Duncan; Schutgens, Nick; Cook, Nick; Kipling, Zak; Kershaw, Phil; Gryspeerdt, Ed; Lawrence, Bryan; Stier, Philip

2017-04-01

Earth observations (both remote and in-situ) create vast amounts of data providing invaluable constraints for the climate science community. Efficient exploitation of these complex and highly heterogeneous datasets has been limited however by the lack of suitable software tools, particularly for comparison of gridded and ungridded data, thus reducing scientific productivity. CIS (http://cistools.net) is an open-source, command line tool and Python library which allows the straight-forward quantitative analysis, intercomparison and visualisation of remote sensing, in-situ and model data. The CIS can read gridded and ungridded remote sensing, in-situ and model data - and many other data sources 'out-of-the-box', such as ESA Aerosol and Cloud CCI product, MODIS, Cloud CCI, Cloudsat, AERONET. Perhaps most importantly however CIS also employs a modular plugin architecture to allow for the reading of limitless different data types. Users are able to write their own plugins for reading the data sources which they are familiar with, and share them within the community, allowing all to benefit from their expertise. To enable the intercomparison of this data the CIS provides a number of operations including: the aggregation of ungridded and gridded datasets to coarser representations using a number of different built in averaging kernels; the subsetting of data to reduce its extent or dimensionality; the co-location of two distinct datasets onto a single set of co-ordinates; the visualisation of the input or output data through a number of different plots and graphs; the evaluation of arbitrary mathematical expressions against any number of datasets; and a number of other supporting functions such as a statistical comparison of two co-located datasets. These operations can be performed efficiently on local machines or large computing clusters - and is already available on the JASMIN computing facility. A case-study using the GASSP collection of in-situ aerosol observations will demonstrate the power of using CIS to perform model evaluations. The use of an open-source, community developed tool in this way opens up a huge amount of data which would previously have been inaccessible to many users, while also providing replicable, repeatable analysis which scientists and policy-makers alike can trust and understand.

Recombinant expression of the alternate reading frame protein (ARFP) of hepatitis C virus genotype 4a (HCV-4a) and detection of ARFP and anti-ARFP antibodies in HCV-infected patients.

PubMed

Shehat, Michael G; Bahey-El-Din, Mohammed; Kassem, Mervat A; Farghaly, Faten A; Abdul-Rahman, Medhat H; Fanaki, Nourhan H

2015-08-01

HCV is a single-stranded RNA virus with a single open reading frame (ORF) that is translated into a polyprotein that is then processed to form 10 viral proteins. An additional eleventh viral protein, the alternative reading frame protein (ARFP), was discovered relatively recently. This protein results from a translational frameshift in the core region during the expression of the viral proteins. Recombinant expression of different forms of ARFP was previously done for HCV genotypes 1 and 2, and more recently, genotype 3. However, none of the previous studies addressed the expression of ARFP of HCV genotype 4a, which is responsible for 80 % of HCV infections in the Middle East and Africa. Moreover, the direct detection of the ARFP antigen in HCV-infected patients was never studied before for any HCV genotype. In the present study, recombinant ARFP derived from HCV genotype 4a was successfully expressed in E. coli and purified using metal affinity chromatography. The recombinant ARFP protein and anti-ARFP antibodies were used for detection of ARFP antigen in patients' sera, employing competitive enzyme-linked immunosorbent assay (ELISA) procedures. Furthermore, the recombinant antigen was also used to detect and quantify anti-ARFP antibodies in HCV-infected Egyptian patients at different stages of pegylated interferon/ribavirin therapy, using an ELISA assay. The ARFP antigen was detectable in 69.4 % of RNA-positive sera, indicating that ARFP antigen is produced during the natural course of HCV infection. In addition, significant levels of anti-ARFP antibodies were present in 41 % of the serum samples tested. The important diagnostic value of the recombinant ARFP antigen was also demonstrated.

Test Performance Vis a Vis Test-Taking Strategies in Reading Comprehension of English as a Second Language.

ERIC Educational Resources Information Center

Roizen, Merle A.

A study of students' self-expressed test-taking strategies for reading comprehension tests in English as a second language (ESL) had as subjects 86 Hebrew-speaking university students in Israel. The students were given a reading comprehension test, half with open-ended questions and half with multiple choice. Half the responses were anonymous and…

The Stickybear Reading Comprehension Series: Science. School Version with Lesson Plans for Ages 7-10. Volume 1. Stickybear Software.

ERIC Educational Resources Information Center

1996

This software product presents multi-level stories to capture the interest of children in grades two through five, while teaching them crucial reading comprehension skills. With stories touching on everything from the invention of velcro to the journey of food through the digestive system, the open-ended reading comprehension program is versatile…

Processing and Memory of Central versus Peripheral Information as a Function of Reading Goals: Evidence from Eye-Movements

ERIC Educational Resources Information Center

Yeari, Menahem; van den Broek, Paul; Oudega, Marja

2015-01-01

The present study examined the effect of reading goals on the processing and memory of central and peripheral textual information. Using eye-tracking methodology, we compared the effect of four common reading goals--entertainment, presentation, studying for a close-ended (multiple-choice) questions test, and studying for an open-ended questions…

Rhythm, Rhyme, and Reason; Proceedings of the Annual Reading Conference (9th, Terre Haute, Indiana, June 14, 1979).

ERIC Educational Resources Information Center

Waterman, David C., Comp.; Gibbs, Vanita M., Comp.

Part of a series on selected aspects of curriculum development, this monograph contains reading conference proceedings that include an opening address by author Marguerite Henry in which she shares personal experiences in her evolution as a writer and six papers on remedial reading and language arts. The first paper describes the neurological…

Multidimensional Aspects of Literacy Research, Theory, and Practice. Forty-Third Yearbook of the National Reading Conference.

ERIC Educational Resources Information Center

Kinzer, Charles K., Ed.; Leu, Donald J., Ed.

The 55 conference papers, the annual review of research, and the student-award-winning paper in this yearbook cover such diverse topics in the field of reading as assessment, content-area reading, early literacy, teacher education, teacher behavior, and construction of meaning through writing. The yearbook opens with the presidential address to…

Thinking outside the boxes: Using current reading models to assess and treat developmental surface dyslexia.

PubMed

Law, Caroline; Cupples, Linda

2017-03-01

Improving the reading performance of children with developmental surface dyslexia has proved challenging, with limited generalisation of reading skills typically reported after intervention. The aim of this study was to provide tailored, theoretically motivated intervention to two children with developmental surface dyslexia. Our objectives were to improve their reading performance, and to evaluate the utility of current reading models in therapeutic practice. Detailed reading and cognitive profiles for two male children with developmental surface dyslexia were compared to the results obtained by age-matched control groups. The specific area of single-word reading difficulty for each child was identified within the dual route model (DRM) of reading, following which a theoretically motivated intervention programme was devised. Both children showed significant improvements in single-word reading ability after training, with generalisation effects observed for untrained words. However, the assessment and intervention results also differed for each child, reinforcing the view that the causes and consequences of developmental dyslexia, even within subtypes, are not homogeneous. Overall, the results of the interventions corresponded more closely with the DRM than other current reading models, in that real word reading improved in the absence of enhanced nonword reading for both children.

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.

Using Repeated Reading to Improve Reading Speed and Comprehension in Students with Visual Impairments

ERIC Educational Resources Information Center

Savaiano, Mackenzie E.; Hatton, Deborah D.

2013-01-01

Introduction: This study evaluated whether children with visual impairments who receive repeated reading instruction exhibit an increase in their oral reading rate and comprehension and a decrease in oral reading error rates. Methods: A single-subject, changing-criterion design replicated across three participants was used to demonstrate the…

Open Admissions: A Bibliography for Research and Application.

ERIC Educational Resources Information Center

Shrier, Irene; Lavin, David E.

This bibliography presents materials for research and application of open admissions policies in higher education. Sections cover: open admissions; factors influencing high school graduates to attend college; disadvantaged and minority students; precollege and special programs; English and reading skills; general compensatory programs; dropouts;…

The relations between reading and spelling: an examination of subtypes of reading disability.

PubMed

Bar-Kochva, Irit; Amiel, Meirav

2016-07-01

Three groups of reading-disabled children were found in studies of English, German, and French: a group with a double deficit in reading and spelling, a group with a single spelling deficit, and a more rarely reported group presenting a single reading deficit. This study set out to examine whether these groups can be found in adults, readers and spellers of Hebrew, which differs from the previously studied orthographies in many aspects. To this end, Hebrew-speaking adults with or without reading disability were administered various literacy and literacy-related tests. Results confirm the existence of the same three groups. While all shared a phonological deficit, subtle differences in phonological decoding ability and in speed of processing distinguished between the groups. The study therefore suggests that the previously reported associations and dissociations between reading and spelling are not restricted to English, German, or French and may not be only developmental in nature.

Genomic and Phylogenetic Characterization of Brazilian Yellow Fever Virus Strains

PubMed Central

Palacios, Gustavo; Cardoso, Jedson F.; Martins, Livia C.; Sousa, Edivaldo C.; de Lima, Clayton P. S.; Medeiros, Daniele B. A.; Savji, Nazir; Desai, Aaloki; Rodrigues, Sueli G.; Carvalho, Valeria L.; Lipkin, W. Ian

2012-01-01

Globally, yellow fever virus infects nearly 200,000 people, leading to 30,000 deaths annually. Although the virus is endemic to Latin America, only a single genome from this region has been sequenced. Here, we report 12 Brazilian yellow fever virus complete genomes, their genetic traits, phylogenetic characterization, and phylogeographic dynamics. Variable 3′ noncoding region (3′NCR) patterns and specific mutations throughout the open reading frame altered predicted secondary structures. Our findings suggest that whereas the introduction of yellow fever virus in Brazil led to genotype I-predominant dispersal throughout South and Central Americas, genotype II remained confined to Bolivia, Peru, and the western Brazilian Amazon. PMID:23015713

DR-78, a novel Drosophila melanogaster genomic DNA fragment highly homologous to the DNA-binding domain of thyroid hormone-retinoic acid-vitamin D receptor subfamily.

PubMed

Martín-Blanco, E; Kornberg, T B

1993-11-16

Degenerate oligodeoxyribonucleotides were designed for both ends of the DNA-binding domain of members of the nuclear receptor superfamily. PCR amplified Drosophila melanogaster DNA was purified and cloned (DR plasmids). Genomic lambda DASH clones were identified at high stringency with an amplified DR-78 plasmid DNA and isolated. The partial sequence shows a very probable open reading frame which would encode a peptide highly homologous to members of the thyroid hormone-retinoic acid-vitamin D receptor subfamily. The fragment corresponds to a single copy gene and was mapped at position 78D of chromosome three by in situ hybridization.

A Pilot Comparison of 18F-fluorocholine PET/CT, Ultrasonography and 123I/99mTc-sestaMIBI Dual-Phase Dual-Isotope Scintigraphy in the Preoperative Localization of Hyperfunctioning Parathyroid Glands in Primary or Secondary Hyperparathyroidism

PubMed Central

Michaud, Laure; Balogova, Sona; Burgess, Alice; Ohnona, Jessica; Huchet, Virginie; Kerrou, Khaldoun; Lefèvre, Marine; Tassart, Marc; Montravers, Françoise; Périé, Sophie; Talbot, Jean-Noël

2015-01-01

Abstract We compared 18F-fluorocholine hybrid positron emission tomography/X-ray computed tomography (FCH-PET/CT) with ultrasonography (US) and scintigraphy in patients with hyperparathyroidism and discordant, or equivocal results of US and 123I/99mTc-sesta-methoxyisobutylisonitrile (sestaMIBI) dual-phase parathyroid scintigraphy. FCH-PET/CT was performed in 17 patients with primary (n = 11) lithium induced (n = 1) or secondary hyperparathyroidism (1 dialyzed, 4 renal-transplanted). The reference standard was based on results of surgical exploration and histopathological examination. The results of imaging modalities were evaluated, on site and by masked reading, on per-patient and per-lesion bases. In a first approach, equivocal images/foci were considered as negative. On a per-patient level, the sensitivity was for US 38%, for scintigraphy 69% by open and 94% by masked reading, and for FCH-PET/CT 88% by open and 94% by masked reading. On a per-lesion level, sensitivity was for US 42%, for scintigraphy 58% by open and 83% by masked reading, and for FCH-PET/CT 88% by open and 96% by masked reading. One ectopic adenoma was missed by the 3 imaging modalities. Considering equivocal images/foci as positive increased the accuracy of the open reading of scintigraphy or of FCH-PET/CT, but not of US. FCH-PET/CT was significantly superior to US in all approaches, whereas it was more sensitive than scintigraphy only for open reading considering equivocal images/foci as negative (P = 0.04). FCH uptake was more intense in adenomas than in hyperplastic parathyroid glands. Thyroid lesions were suspected in 9 patients. They may induce false-positive results as in one case of oncocytic thyroid adenoma, or false-negative results as in one case of intrathyroidal parathyroid adenoma. Thyroid cancer (4 cases) can be visualized with FCH as with 99mTc-sestaMIBI, but the intensity of uptake was moderate, similar to that of parathyroid hyperplasia. This pilot study confirmed that FCH-PET/CT is an adequate imaging tool in patients with primary or secondary hyperparathyroidism, since both adenomas and hyperplastic parathyroid glands can be detected. The sensitivity of FCH-PET/CT was better than that of US and was not inferior to that of dual-phase dual-isotope 123I/99mTc-scintigraphy. Further studies should evaluate whether FCH could replace 99mTc-sestaMIBI as the functional agent for parathyroid imaging, but US would still be useful to identify thyroid lesions. PMID:26469908

Single-Sex Classrooms and Reading Achievement: An Exploratory Study

ERIC Educational Resources Information Center

Stotsky, Sandra; Denny, George

2012-01-01

Gendered schooling is growing in the United States, but little research exists on single-sex classes in public elementary schools. This study sought to find out if single-sex classes in two elementary schools made a difference in boys' reading gains in 2008-2009, as judged by scores on the state's annual literacy test. In one school, boys in the…

Transposition of an intron in yeast mitochondria requires a protein encoded by that intron.

PubMed

Macreadie, I G; Scott, R M; Zinn, A R; Butow, R A

1985-06-01

The optional 1143 bp intron in the yeast mitochondrial 21S rRNA gene (omega +) is nearly quantitatively inserted in genetic crosses into 21S rRNA alleles that lack it (omega -). The intron contains an open reading frame that can encode a protein of 235 amino acids, but no function has been ascribed to this sequence. We previously found an in vivo double-strand break in omega - DNA at or close to the intron insertion site only in zygotes of omega + X omega - crosses that appears with the same kinetics as intron insertion. We now show that mutations in the intron open reading frame that would alter the translation product simultaneously inhibit nonreciprocal omega recombination and the in vivo double-strand break in omega - DNA. These results provide evidence that the open reading frame encodes a protein required for intron transposition and support the role of the double-strand break in the process.

A 21.7 kb DNA segment on the left arm of yeast chromosome XIV carries WHI3, GCR2, SPX18, SPX19, an homologue to the heat shock gene SSB1 and 8 new open reading frames of unknown function.

PubMed

Jonniaux, J L; Coster, F; Purnelle, B; Goffeau, A

1994-12-01

We report the amino acid sequence of 13 open reading frames (ORF > 299 bp) located on a 21.7 kb DNA segment from the left arm of chromosome XIV of Saccharomyces cerevisiae. Five open reading frames had been entirely or partially sequenced previously: WHI3, GCR2, SPX19, SPX18 and a heat shock gene similar to SSB1. The products of 8 other ORFs are new putative proteins among which N1394 is probably a membrane protein. N1346 contains a leucine zipper pattern and the corresponding ORF presents an HAP (global regulator of respiratory genes) upstream activating sequence in the promoting region. N1386 shares homologies with the DNA structure-specific recognition protein family SSRPs and the corresponding ORF is preceded by an MCB (MluI cell cycle box) upstream activating factor.

Protein expression of preferred human codon-optimized Gaussia luciferase genes with an artificial open-reading frame in mammalian and bacterial cells.

PubMed

Inouye, Satoshi; Suzuki, Takahiro

2016-12-01

The protein expressions of three preferred human codon-optimized Gaussia luciferase genes (pGLuc, EpGLuc, and KpGLuc) were characterized in mammalian and bacterial cells by comparing them with those of wild-type Gaussia luciferase gene (wGLuc) and human codon-optimized Gaussia luciferase gene (hGLuc). Two synthetic genes of EpGLuc and KpGLuc containing the complete preferred human codons have an artificial open-reading frame; however, they had the similar protein expression levels to those of pGLuc and hGLuc in mammalian cells. In bacterial cells, the protein expressions of pGLuc, EpGLuc, and KpGLuc with approximately 65% GC content were the same and showed approximately 60% activities of wGLuc and hGLuc. The artificial open-reading frame in EpGLuc and KpGLuc did not affect the protein expression in mammalian and bacterial cells. Copyright © 2016 Elsevier Inc. All rights reserved.

Reducing assembly complexity of microbial genomes with single-molecule sequencing.

PubMed

Koren, Sergey; Harhay, Gregory P; Smith, Timothy P L; Bono, James L; Harhay, Dayna M; Mcvey, Scott D; Radune, Diana; Bergman, Nicholas H; Phillippy, Adam M

2013-01-01

The short reads output by first- and second-generation DNA sequencing instruments cannot completely reconstruct microbial chromosomes. Therefore, most genomes have been left unfinished due to the significant resources required to manually close gaps in draft assemblies. Third-generation, single-molecule sequencing addresses this problem by greatly increasing sequencing read length, which simplifies the assembly problem. To measure the benefit of single-molecule sequencing on microbial genome assembly, we sequenced and assembled the genomes of six bacteria and analyzed the repeat complexity of 2,267 complete bacteria and archaea. Our results indicate that the majority of known bacterial and archaeal genomes can be assembled without gaps, at finished-grade quality, using a single PacBio RS sequencing library. These single-library assemblies are also more accurate than typical short-read assemblies and hybrid assemblies of short and long reads. Automated assembly of long, single-molecule sequencing data reduces the cost of microbial finishing to $1,000 for most genomes, and future advances in this technology are expected to drive the cost lower. This is expected to increase the number of completed genomes, improve the quality of microbial genome databases, and enable high-fidelity, population-scale studies of pan-genomes and chromosomal organization.

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

DOE PAGES

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

2016-03-15

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

Pteros: fast and easy to use open-source C++ library for molecular analysis.

PubMed

Yesylevskyy, Semen O

2012-07-15

An open-source Pteros library for molecular modeling and analysis of molecular dynamics trajectories for C++ programming language is introduced. Pteros provides a number of routine analysis operations ranging from reading and writing trajectory files and geometry transformations to structural alignment and computation of nonbonded interaction energies. The library features asynchronous trajectory reading and parallel execution of several analysis routines, which greatly simplifies development of computationally intensive trajectory analysis algorithms. Pteros programming interface is very simple and intuitive while the source code is well documented and easily extendible. Pteros is available for free under open-source Artistic License from http://sourceforge.net/projects/pteros/. Copyright © 2012 Wiley Periodicals, Inc.

Commentary on "Reading Comprehension Is Not a Single Ability": Implications for Child Language Intervention.

PubMed

Ukrainetz, Teresa A

2017-04-20

This commentary responds to the implications for child language intervention of Catts and Kamhi's (2017) call to move from viewing reading comprehension as a single ability to recognizing it as a complex constellation of reader, text, and activity. Reading comprehension, as Catts and Kamhi explain, is very complicated. In this commentary, I consider how comprehension has been taught and the directions in which it is moving. I consider how speech-language pathologists (SLPs), with their distinctive expertise and resources, can contribute to effective reading comprehension instruction. I build from Catts and Kamhi's emphasis on the importance of context and knowledge, using the approaches of staying on topic, close reading, and incorporating quality features of intervention. I consider whether and how SLPs should treat language skills and comprehension strategies to achieve noticeable changes in their students' reading comprehension. Within this multidimensional view of reading comprehension, SLPs can make strategic, meaningful contributions to improving the reading comprehension of students with language impairments.

Does a single session of reading literary fiction prime enhanced mentalising performance? Four replication experiments of Kidd and Castano (2013).

PubMed

Samur, Dalya; Tops, Mattie; Koole, Sander L

2018-02-01

Prior experiments indicated that reading literary fiction improves mentalising performance relative to reading popular fiction, non-fiction, or not reading. However, the experiments had relatively small sample sizes and hence low statistical power. To address this limitation, the present authors conducted four high-powered replication experiments (combined N = 1006) testing the causal impact of reading literary fiction on mentalising. Relative to the original research, the present experiments used the same literary texts in the reading manipulation; the same mentalising task; and the same kind of participant samples. Moreover, one experiment was pre-registered as a direct replication. In none of the experiments did reading literary fiction have any effect on mentalising relative to control conditions. The results replicate earlier findings that familiarity with fiction is positively correlated with mentalising. Taken together, the present findings call into question whether a single session of reading fiction leads to immediate improvements in mentalising.

75 FR 39528 - Farm Credit Administration Board; Amendment to Sunshine Act Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-09

... item to the open session to read as follows: Open Session B. New Business Proposed Bookletter--Farm... amend the agenda by adding an item to the open session of that meeting. FOR FURTHER INFORMATION CONTACT... INFORMATION: Parts of this meeting of the Board will be open to the public (limited space available), and...

10 CFR 1703.103 - Requests for board records available through the public reading room.

Code of Federal Regulations, 2011 CFR

2011-01-01

... Public Reading Room will be maintained at the Board's headquarters and will be open between 8:30 a.m. and... interested person's comments, data, views, or arguments to the Board concerning its recommendations and the...

Does the PMSP Connectionist Model of Single Word Reading Learn to Read in the Same Way as a Child?

ERIC Educational Resources Information Center

Powell, Daisy; Plaut, David; Funnell, Elaine

2006-01-01

The Plaut, McClelland, Seidenberg and Patterson (1996) connectionist model of reading was evaluated at two points early in its training against reading data collected from British children on two occasions during their first year of literacy instruction. First, the network's non-word reading was poor relative to word reading when compared with the…

Segtor: Rapid Annotation of Genomic Coordinates and Single Nucleotide Variations Using Segment Trees

PubMed Central

Renaud, Gabriel; Neves, Pedro; Folador, Edson Luiz; Ferreira, Carlos Gil; Passetti, Fabio

2011-01-01

Various research projects often involve determining the relative position of genomic coordinates, intervals, single nucleotide variations (SNVs), insertions, deletions and translocations with respect to genes and their potential impact on protein translation. Due to the tremendous increase in throughput brought by the use of next-generation sequencing, investigators are routinely faced with the need to annotate very large datasets. We present Segtor, a tool to annotate large sets of genomic coordinates, intervals, SNVs, indels and translocations. Our tool uses segment trees built using the start and end coordinates of the genomic features the user wishes to use instead of storing them in a database management system. The software also produces annotation statistics to allow users to visualize how many coordinates were found within various portions of genes. Our system currently can be made to work with any species available on the UCSC Genome Browser. Segtor is a suitable tool for groups, especially those with limited access to programmers or with interest to analyze large amounts of individual genomes, who wish to determine the relative position of very large sets of mapped reads and subsequently annotate observed mutations between the reads and the reference. Segtor (http://lbbc.inca.gov.br/segtor/) is an open-source tool that can be freely downloaded for non-profit use. We also provide a web interface for testing purposes. PMID:22069465

Use of an E-Reader as a Compensatory Strategy among University Students with Reading Disabilities

ERIC Educational Resources Information Center

Tanners, Adam

2010-01-01

This study investigated the impact of a Kindle e-book reader on the reading rate, comprehension and e-reader acceptance of five postsecondary students with reading disabilities. A single-case Alternating Treatments Design was employed to measure reading rates and reading comprehension. Students were exposed to a series of controlled reading…

Effects of Assisted-Repeated Reading on Students of Varying Reading Ability: A Single-Subject Experimental Research Study

ERIC Educational Resources Information Center

Hapstak, Jo-Ann; Tracey, Diane H.

2007-01-01

This study examined the effects of assisted-repeated reading on four first-grade students whose reading ability varied (a special education student, a non-classified poor reader, an English Language Learner (ELL) student, and a general education student) to determine if an assisted-repeated reading intervention is differentially effective for…

Automaticity in reading and the Stroop task: testing the limits of involuntary word processing.

PubMed

Brown, Tracy L; Joneleit, Kelly; Robinson, Cathy S; Brown, Carli Rose

2002-01-01

We investigated the parameters of involuntary word reading in the Stroop task in 7 experiments. Experiments 1-4 varied response modality and the presence of congruent word trials in a test of the claim that presenting a Stroop color word with only one letter in the target color eliminates the Stroop effect. Experiments 5 and 6 addressed the roles of spatial attention and orthographic processing as possible mechanisms behind the reduction of Stroop effects with the single-letter format. Experiment 7 investigated the limits of involuntary reading under optimal conditions for selective processing of rectangular color patch targets. We found that the single-letter format reduced but never eliminated Stroop effects, spatial attention but not orthographic processing plays a role in the effect of the single-letter format, and word reading is not completely prevented even with austere presentation conditions. We conclude with a defense of the involuntariness criterion for automaticity in the Stroop task, particularly when word reading is viewed in the context of a skilled performance.

The Stickybear Reading Comprehension Series: Sports. School Version with Lesson Plans. For Ages 7-10. Volume 2. Stickybear Software.

ERIC Educational Resources Information Center

1996

This software product presents multi-level stories to capture the interest of children in grades two through five, while teaching them crucial reading comprehension skills. With stories touching on everything from superstars to sports facts, the open-ended reading comprehension program is versatile and easy to use for educators and children alike.…

Is the orthographic/phonological onset a single unit in reading aloud?

PubMed

Mousikou, Petroula; Coltheart, Max; Saunders, Steven; Yen, Lisa

2010-02-01

Two main theories of visual word recognition have been developed regarding the way orthographic units in printed words map onto phonological units in spoken words. One theory suggests that a string of single letters or letter clusters corresponds to a string of phonemes (Coltheart, 1978; Venezky, 1970), while the other suggests that a string of single letters or letter clusters corresponds to coarser phonological units, for example, onsets and rimes (Treiman & Chafetz, 1987). These theoretical assumptions were critical for the development of coding schemes in prominent computational models of word recognition and reading aloud. In a reading-aloud study, we tested whether the human reading system represents the orthographic/phonological onset of printed words and nonwords as single units or as separate letters/phonemes. Our results, which favored a letter and not an onset-coding scheme, were successfully simulated by the dual-route cascaded (DRC) model (Coltheart, Rastle, Perry, Langdon, & Ziegler, 2001). A separate experiment was carried out to further adjudicate between 2 versions of the DRC model.

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

PubMed

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

2017-10-06

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

Nucleotide sequence of soybean chloroplast DNA regions which contain the psb A and trn H genes and cover the ends of the large single copy region and one end of the inverted repeats.

PubMed

Spielmann, A; Stutz, E

1983-10-25

The soybean chloroplast psb A gene (photosystem II thylakoid membrane protein of Mr 32 000, lysine-free) and the trn H gene (tRNAHisGUG), which both map in the large single copy region adjacent to one of the inverted repeat structures (IR1), have been sequenced including flanking regions. The psb A gene shows in its structural part 92% sequence homology with the corresponding genes of spinach and N. debneyi and contains also an open reading frame for 353 aminoacids. The aminoacid sequence of a potential primary translation product (calculated Mr, 38 904, no lysine) diverges from that of spinach and N. debneyi in only two positions in the C-terminal part. The trn H gene has the same polarity as the psb A gene and the coding region is located at the very end of the large single copy region. The deduced sequence of the soybean chloroplast tRNAHisGUG is identical with that of Zea mays chloroplasts. Both ends of the large single copy region were sequenced including a small segment of the adjacent IR1 and IR2.

deFUME: Dynamic exploration of functional metagenomic sequencing data.

PubMed

van der Helm, Eric; Geertz-Hansen, Henrik Marcus; Genee, Hans Jasper; Malla, Sailesh; Sommer, Morten Otto Alexander

2015-07-31

Functional metagenomic selections represent a powerful technique that is widely applied for identification of novel genes from complex metagenomic sources. However, whereas hundreds to thousands of clones can be easily generated and sequenced over a few days of experiments, analyzing the data is time consuming and constitutes a major bottleneck for experimental researchers in the field. Here we present the deFUME web server, an easy-to-use web-based interface for processing, annotation and visualization of functional metagenomics sequencing data, tailored to meet the requirements of non-bioinformaticians. The web-server integrates multiple analysis steps into one single workflow: read assembly, open reading frame prediction, and annotation with BLAST, InterPro and GO classifiers. Analysis results are visualized in an online dynamic web-interface. The deFUME webserver provides a fast track from raw sequence to a comprehensive visual data overview that facilitates effortless inspection of gene function, clustering and distribution. The webserver is available at cbs.dtu.dk/services/deFUME/and the source code is distributed at github.com/EvdH0/deFUME.

GaN Nanowire Arrays for Efficient Optical Read-Out and Optoelectronic Control of NV Centers in Diamond.

PubMed

Hetzl, Martin; Wierzbowski, Jakob; Hoffmann, Theresa; Kraut, Max; Zuerbig, Verena; Nebel, Christoph E; Müller, Kai; Finley, Jonathan J; Stutzmann, Martin

2018-06-13

Solid-state quantum emitters embedded in a semiconductor crystal environment are potentially scalable platforms for quantum optical networks operated at room temperature. Prominent representatives are nitrogen-vacancy (NV) centers in diamond showing coherent entanglement and interference with each other. However, these emitters suffer from inefficient optical outcoupling from the diamond and from fluctuations of their charge state. Here, we demonstrate the implementation of regular n-type gallium nitride nanowire arrays on diamond as photonic waveguides to tailor the emission direction of surface-near NV centers and to electrically control their charge state in a p-i-n nanodiode. We show that the electrical excitation of single NV centers in such a diode can efficiently replace optical pumping. By the engineering of the array parameters, we find an optical read-out efficiency enhanced by a factor of 10 and predict a lateral NV-NV coupling 3 orders of magnitude stronger through evanescently coupled nanowire antennas compared to planar diamond not covered by nanowires, which opens up new possibilities for large-scale on-chip quantum-computing applications.

Functional analysis of human foamy virus accessory reading frames.

PubMed Central

Baunach, G; Maurer, B; Hahn, H; Kranz, M; Rethwilm, A

1993-01-01

Foamy viruses belong to the retroviruses which possess a complex genome structure. The human foamy virus (HFV) isolate bears three open reading frames (the so-called bel genes) in the 3' region of the genome which have been reported to give rise to possibly six different proteins via alternative splicing (W. Muranyi and R. M. Flügel, J. Virol. 65:727-735, 1991). In order to analyze the requirements of these proteins for HFV replication in vitro, we constructed a set of single and combinatory bel gene mutants of an infectious molecular clone of HFV. The mutant which lacked the transacting activator, bel-1, was found to be replication incompetent. All other mutants replicated equally well and gave rise to comparable titers of infectious cell-free virus. When HFV proviruses were put under the control of a heterologous promoter (simian virus 40), none of the accessory gene products was found to be required for expression of structural (gag) proteins. There was no evidence for a posttranscriptional regulatory protein that is present in other complex retroviruses. Images PMID:8394455

IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis

PubMed Central

Safonova, Yana; Bonissone, Stefano; Kurpilyansky, Eugene; Starostina, Ekaterina; Lapidus, Alla; Stinson, Jeremy; DePalatis, Laura; Sandoval, Wendy; Lill, Jennie; Pevzner, Pavel A.

2015-01-01

The analysis of concentrations of circulating antibodies in serum (antibody repertoire) is a fundamental, yet poorly studied, problem in immunoinformatics. The two current approaches to the analysis of antibody repertoires [next generation sequencing (NGS) and mass spectrometry (MS)] present difficult computational challenges since antibodies are not directly encoded in the germline but are extensively diversified by somatic recombination and hypermutations. Therefore, the protein database required for the interpretation of spectra from circulating antibodies is custom for each individual. Although such a database can be constructed via NGS, the reads generated by NGS are error-prone and even a single nucleotide error precludes identification of a peptide by the standard proteomics tools. Here, we present the IgRepertoireConstructor algorithm that performs error-correction of immunosequencing reads and uses mass spectra to validate the constructed antibody repertoires. Availability and implementation: IgRepertoireConstructor is open source and freely available as a C++ and Python program running on all Unix-compatible platforms. The source code is available from http://bioinf.spbau.ru/igtools. Contact: ppevzner@ucsd.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26072509

An experimental study on the effect of wind load around tall towers of square and hexagonal shapes in staggered form

NASA Astrophysics Data System (ADS)

Anwar, Proma; Islam, Md. Quamrul; Ali, Mohammad

2017-06-01

In this research work an experiment is conducted to observe the effect of wind load around square and hexagonal shaped cylinders in staggered form. The experiment is performed in an open circuit wind tunnel at a Reynolds number of 4.23×104 based on the face width of the cylinder across the flow direction. The flow velocity has been kept uniform at 14.3 m/s throughout the experiment. The test is conducted for single cylinders first and then in staggered form. The cylinders are rotated to create different angles of attack and the angles are chosen at a definite interval. The static pressure readings are taken at different locations of the cylinder by inclined multi-manometers. From the surface static pressure readings pressure coefficients, drag coefficients and lift coefficients are calculated using numerical integration method. These results will surely help engineers to design buildings more stable against wind load. All the results are expressed in non-dimensional form, so that they can be applied for prototype structures.

Design and construction of 2A peptide-linked multicistronic vectors.

PubMed

Szymczak-Workman, Andrea L; Vignali, Kate M; Vignali, Dario A A

2012-02-01

The need for reliable, multicistronic vectors for multigene delivery is at the forefront of biomedical technology. This article describes the design and construction of 2A peptide-linked multicistronic vectors, which can be used to express multiple proteins from a single open reading frame (ORF). The small 2A peptide sequences, when cloned between genes, allow for efficient, stoichiometric production of discrete protein products within a single vector through a novel "cleavage" event within the 2A peptide sequence. Expression of more than two genes using conventional approaches has several limitations, most notably imbalanced protein expression and large size. The use of 2A peptide sequences alleviates these concerns. They are small (18-22 amino acids) and have divergent amino-terminal sequences, which minimizes the chance for homologous recombination and allows for multiple, different 2A peptide sequences to be used within a single vector. Importantly, separation of genes placed between 2A peptide sequences is nearly 100%, which allows for stoichiometric and concordant expression of the genes, regardless of the order of placement within the vector.

Complete coherent control of silicon vacancies in diamond nanopillars containing single defect centers

DOE PAGES

Zhang, Jingyuan Linda; Lagoudakis, Konstantinos G.; Tzeng, Yan -Kai; ...

2017-10-23

Arrays of identical and individually addressable qubits lay the foundation for the creation of scalable quantum hardware such as quantum processors and repeaters. Silicon-vacancy (SiV) centers in diamond offer excellent physical properties such as low inhomogeneous broadening, fast photon emission, and a large Debye–Waller factor. The possibility for all-optical ultrafast manipulation and techniques to extend the spin coherence times makes them promising candidates for qubits. Here, we have developed arrays of nanopillars containing single (SiV) centers with high yield, and we demonstrate ultrafast all-optical complete coherent control of the excited state population of a single SiV center at the opticalmore » transition frequency. The high quality of the chemical vapor deposition (CVD) grown SiV centers provides excellent spectral stability, which allows us to coherently manipulate and quasi-resonantly read out the excited state population of individual SiV centers on picosecond timescales using ultrafast optical pulses. Furthermore, this work opens new opportunities to create a scalable on-chip diamond platform for quantum information processing and scalable nanophotonics applications.« less

Complete coherent control of silicon vacancies in diamond nanopillars containing single defect centers

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

Zhang, Jingyuan Linda; Lagoudakis, Konstantinos G.; Tzeng, Yan -Kai

Arrays of identical and individually addressable qubits lay the foundation for the creation of scalable quantum hardware such as quantum processors and repeaters. Silicon-vacancy (SiV) centers in diamond offer excellent physical properties such as low inhomogeneous broadening, fast photon emission, and a large Debye–Waller factor. The possibility for all-optical ultrafast manipulation and techniques to extend the spin coherence times makes them promising candidates for qubits. Here, we have developed arrays of nanopillars containing single (SiV) centers with high yield, and we demonstrate ultrafast all-optical complete coherent control of the excited state population of a single SiV center at the opticalmore » transition frequency. The high quality of the chemical vapor deposition (CVD) grown SiV centers provides excellent spectral stability, which allows us to coherently manipulate and quasi-resonantly read out the excited state population of individual SiV centers on picosecond timescales using ultrafast optical pulses. Furthermore, this work opens new opportunities to create a scalable on-chip diamond platform for quantum information processing and scalable nanophotonics applications.« less

Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R.

PubMed

McCarthy, Davis J; Campbell, Kieran R; Lun, Aaron T L; Wills, Quin F

2017-04-15

Single-cell RNA sequencing (scRNA-seq) is increasingly used to study gene expression at the level of individual cells. However, preparing raw sequence data for further analysis is not a straightforward process. Biases, artifacts and other sources of unwanted variation are present in the data, requiring substantial time and effort to be spent on pre-processing, quality control (QC) and normalization. We have developed the R/Bioconductor package scater to facilitate rigorous pre-processing, quality control, normalization and visualization of scRNA-seq data. The package provides a convenient, flexible workflow to process raw sequencing reads into a high-quality expression dataset ready for downstream analysis. scater provides a rich suite of plotting tools for single-cell data and a flexible data structure that is compatible with existing tools and can be used as infrastructure for future software development. The open-source code, along with installation instructions, vignettes and case studies, is available through Bioconductor at http://bioconductor.org/packages/scater . davis@ebi.ac.uk. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

Identification of a Linked Set of Genes in Serpulina hyodysenteriae (B204) Predicted To Encode Closely Related 39-Kilodalton Extracytoplasmic Proteins

PubMed Central

Gabe, Jeffrey D.; Dragon, Elizabeth; Chang, Ray-Jen; McCaman, Michael T.

1998-01-01

A tandem pair of nearly identical genes from Serpulina hyodysenteriae (B204) were cloned and sequenced. The full open reading frame of one gene and the partial open reading frame of the neighboring gene appear to encode secreted proteins which are homologous to, yet distinct from, the 39-kDa extracytoplasmic protein purified from the membrane fraction of S. hyodysenteriae. We have designated these newly identified genes vspA and vspB (for variable surface protein). PMID:9440540

An Expert System Interfaced with a Database System to Perform Troubleshooting of Aircraft Carrier Piping Systems

DTIC Science & Technology

1988-12-01

interval of four feet, and are numbered sequentially bow to stem. * "wing tank" is a tank or void, outboard of the holding bulkhead, away from the center...system and DBMS simultaneously with a multi-processor, allowing queries to the DBMS without terminating the expert system. This method was judged...RECIRC). eductor -strip("Y"):- ask _ques _read_ans(OVBD,"ovbd dis open"),ovbd dis-open(OVBD). eductor-strip("N"):- ask_ques read_ans( LINEUP , "strip lineup

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

Treesearch

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

2012-01-01

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

Increasing Fluency in Disabled Middle School Readers: Repeated Reading Utilizing above Grade Level Reading Passages

ERIC Educational Resources Information Center

Paige, David D.

2006-01-01

This study examined the effects of repeated reading using above grade level narrative passages on: (a) reading rate as measured in words per minute (wpm) and (b) reading miscues. A single group, pretest-posttest design was used to measure the treatment effects. The study group consisted of 11, sixth grade African-American students with learning…

Characterization and gene cloning of the rice (Oryza sativa L.) dwarf and narrow-leaf mutant dnl3.

PubMed

Shi, L; Wei, X J; Adedze, Y M N; Sheng, Z H; Tang, S Q; Hu, P S; Wang, J L

2016-09-16

The dwarf and narrow-leaf rice (Oryza sativa L.) mutant dnl3 was isolated from the Japonica cultivar Zhonghua 11 (wild-type). dnl3 exhibited pleiotropic developmental defects. The narrow-leaf phenotype resulted from a marked reduction in the number of vascular bundles, while the dwarf stature was caused by the formation of foreshortened internodes and a reduced number of parenchyma cells. The suggestion that cell division is impaired in the mutant was consistent with the transcriptional behavior of various genes associated with cell division. The mutant was less responsive to exogenously supplied gibberellic acid than the wild-type, and profiling the transcription of genes involved in gibberellin synthesis and response revealed that a lesion in the mutant affected gibberellin signal transduction. The dnl3 phenotype was inherited as a single-dominant gene, mapping within a 19.1-kb region of chromosome 12, which was found to harbor three open reading frames. Resequencing the open reading frames revealed that the mutant carried an allele at one of the three genes that differed from the wild-type sequence by 2-bp deletions; this gene encoded a cellulose synthase-like D4 (CSLD4) protein. Therefore, OsCSLD4 is a candidate gene for DNL3. DNL3 was expressed in all of the rice organs tested at the heading stage, particularly in the leaves, roots, and culms. These results suggest that DNL3 plays important roles in rice leaf morphogenesis and vegetative development.

Cloning and expression analysis of phytoene desaturase and ζ-carotene desaturase genes in Carica papaya.

PubMed

Yan, P; Gao, X Z; Shen, W T; Zhou, P

2011-02-01

The fruit flesh color of papaya is an important nutritional quality trait and is due to the accumulation of carotenoid. To elucidate the carotenoid biosynthesis pathway in Carica papaya, the phytoene desaturase (PDS) and the ζ-carotene desaturase (ZDS) genes were isolated from papaya (named CpPDS and CpZDS) using the rapid amplification of cDNA ends (RACE) approach, and their expression levels were investigated in red- and yellow-fleshed papaya varieties. CpPDS contains a 1749 bp open reading frame coding for 583 amino acids, while CpZDS contains a 1716 bp open reading frame coding for 572 amino acids. The deduced CpPDS and CpZDS proteins contain a conserved dinucleotide-binding site at the N-terminus and a carotenoid-binding domain at the C-terminus. Papaya genome sequence analysis revealed that CpPDS and CpZDS are single copy; the CpPDS was mapped to papaya chromosome LG6, and the CpZDS was mapped to chromosome LG3. Quantitative PCR showed that both CpPDS and CpZDS were expressed in all tissues examined with the highest expression in maturing fruits, and that the expression of CpPDS and CpZDS were higher in red-fleshed fruits than in yellow-fleshed fruits. These results indicated that the differential accumulation of carotenoids in red- and yellow-fleshed papaya varieties might be partly explained by the transcriptional level of CpPDS and CpZDS.

Intracellular modifications induced by poliovirus reduce the requirement for structural motifs in the 5' noncoding region of the genome involved in internal initiation of protein synthesis.

PubMed Central

Percy, N; Belsham, G J; Brangwyn, J K; Sullivan, M; Stone, D M; Almond, J W

1992-01-01

A series of genetic deletions based partly on two RNA secondary structure models (M. A. Skinner, V. R. Racaniello, G. Dunn, J. Cooper, P. D. Minor, and J. W. Almond, J. Mol. Biol. 207:379-392, 1989; E. V. Pilipenko, V. M. Blinov, L. I. Romanova, A. N. Sinyakov, S. V. Maslova, and V. I. Agol, Virology 168:201-209, 1989) was made in the cDNA encoding the 5' noncoding region (5' NCR) of the poliovirus genome in order to study the sequences that direct the internal entry of ribosomes. The modified cDNAs were placed between two open reading frames in a single transcriptional unit and used to transfect cells in culture. Internal entry of ribosomes was detected by measuring translation from the second open reading frame in the bicistronic mRNA. When assayed alone, a large proportion of the poliovirus 5' NCR superstructure including several well-defined stem-loops was required for ribosome entry and efficient translation. However, in cells cotransfected with a complete infectious poliovirus cDNA, the requirement for the stem-loops in this large superstructure was reduced. The results suggest that virus infection modifies the cellular translational machinery, so that shortened forms of the 5' NCR are sufficient for cap-independent translation, and that the internal entry of ribosomes occurs by two distinct modes during the virus replication cycle. Images PMID:1310772

Bioinformatic analysis suggests that the Orbivirus VP6 cistron encodes an overlapping gene

PubMed Central

Firth, Andrew E

2008-01-01

Background The genus Orbivirus includes several species that infect livestock – including Bluetongue virus (BTV) and African horse sickness virus (AHSV). These viruses have linear dsRNA genomes divided into ten segments, all of which have previously been assumed to be monocistronic. Results Bioinformatic evidence is presented for a short overlapping coding sequence (CDS) in the Orbivirus genome segment 9, overlapping the VP6 cistron in the +1 reading frame. In BTV, a 77–79 codon AUG-initiated open reading frame (hereafter ORFX) is present in all 48 segment 9 sequences analysed. The pattern of base variations across the 48-sequence alignment indicates that ORFX is subject to functional constraints at the amino acid level (even when the constraints due to coding in the overlapping VP6 reading frame are taken into account; MLOGD software). In fact the translated ORFX shows greater amino acid conservation than the overlapping region of VP6. The ORFX AUG codon has a strong Kozak context in all 48 sequences. Each has only one or two upstream AUG codons, always in the VP6 reading frame, and (with a single exception) always with weak or medium Kozak context. Thus, in BTV, ORFX may be translated via leaky scanning. A long (83–169 codon) ORF is present in a corresponding location and reading frame in all other Orbivirus species analysed except Saint Croix River virus (SCRV; the most divergent). Again, the pattern of base variations across sequence alignments indicates multiple coding in the VP6 and ORFX reading frames. Conclusion At ~9.5 kDa, the putative ORFX product in BTV is too small to appear on most published protein gels. Nonetheless, a review of past literature reveals a number of possible detections. We hope that presentation of this bioinformatic analysis will stimulate an attempt to experimentally verify the expression and functional role of ORFX, and hence lead to a greater understanding of the molecular biology of these important pathogens. PMID:18489030

Marco Said I Look like Charcoal: A Puerto Rican's Exploration of Her Ethnic Identity

ERIC Educational Resources Information Center

Vargas, Yarma Velazquez

2008-01-01

When race is so self-evident that it becomes "unspoken," it becomes a text that can be arbitrarily read or not read at all. When race is thought of as shades or textures of color that paint the already loaded canvas of our ethnicities, it is the reader who has the power of interpretation, opening the possibility for multiple readings that will…

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

PubMed

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

2013-06-01

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

Terrain - Umbra Package v. 1.0

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

Oppel, Fred; Hart, Brian; Rigdon, James Brian

This library contains modules that read terrain files (e.g., OpenFlight, Open Scene Graph IVE, GeoTIFF Image) and to read and manage ESRI terrain datasets. All data is stored and managed in Open Scene Graph (OSG). Terrain system accesses OSG and provides elevation data, access to meta-data such as soil types and enables linears, areals and buildings to be placed in a terrain, These geometry objects include boxes, point, path, and polygon (region), and sector modules. Utilities have been made available for clamping objects to the terrain and accessing LOS information. This assertion includes a managed C++ wrapper code (TerrainWrapper) tomore » enable C# applications, such as OpShed and UTU, to incorporate this library.« less

An eye movement corpus study of the age-of-acquisition effect.

PubMed

Dirix, Nicolas; Duyck, Wouter

2017-12-01

In the present study, we investigated the effects of word-level age of acquisition (AoA) on natural reading. Previous studies, using multiple language modalities, showed that earlier-learned words are recognized, read, spoken, and responded to faster than words learned later in life. Until now, in visual word recognition the experimental materials were limited to single-word or sentence studies. We analyzed the data of the Ghent Eye-tracking Corpus (GECO; Cop, Dirix, Drieghe, & Duyck, in press), an eyetracking corpus of participants reading an entire novel, resulting in the first eye movement megastudy of AoA effects in natural reading. We found that the ages at which specific words were learned indeed influenced reading times, above other important (correlated) lexical variables, such as word frequency and length. Shorter fixations for earlier-learned words were consistently found throughout the reading process, in both early (single-fixation durations, first-fixation durations, gaze durations) and late (total reading times) measures. Implications for theoretical accounts of AoA effects and eye movements are discussed.

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…

Book Reading Styles in Dual-Parent and Single-Mother Families

ERIC Educational Resources Information Center

Blake, Joanna; Macdonald, Silvana; Bayrami, Lisa; Agosta, Vanessa; Milian, Andrea

2006-01-01

Background: Whereas many studies have investigated quantitative aspects of book reading (frequency), few have examined qualitative aspects, especially in very young children and through direct observations of shared reading. Aim: The purpose of this study was to determine possible differences in book-reading styles between mothers and fathers and …

Perceived Challenges to Integrating Reading Strategies in Content Areas: A Single Case Study

ERIC Educational Resources Information Center

Pezzolla, Karen

2017-01-01

An alarming percentage of middle and high school students find themselves unable to read their textbooks at grade level proficiency; lacking the necessary skills to access and process information, and read critically. The Common Core State Standards require students to apply reading strategies across the curriculum, therefore requiring teachers to…

Literature Especially with Remedial Readers (Open to Suggestion).

ERIC Educational Resources Information Center

Glowacki, Joan

1990-01-01

Argues that incorporating literature into daily reading instruction opens up avenues that junior high remedial students may never think exist for them. Presents eight techniques to help teachers get started using literature in the remedial classroom. (RS)

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

PubMed

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

2017-07-03

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

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.

Examinations and Grading: The System of Open-Book Examination is Excellent

ERIC Educational Resources Information Center

Ching-yen, Chang

1973-01-01

Positive support for the system of open-book examination is presented. A case study of an open-book examination in organic chemistry is cited as a basis for theories that testing method improves capacity for analyzing and solving problems, deepens knowledge, and helps to overcome shortcomings of casual readings. (SM)

The Impact of Open Licensing on the Early Reader Ecosystem

ERIC Educational Resources Information Center

Butcher, Neil; Hoosen, Sarah; Levey, Lisbeth; Moore, Derek

2016-01-01

The Impact of Open Licensing on the Early Reader Ecosystem examines how to use open licensing to promote quality learning resources for young children that are relevant and interesting. Research in early reading tends to focus on traditional publishing value and supply chains, without taking much consideration of new approaches and solutions…

Balancing Open Access with Academic Standards: Implications for Community College Faculty

ERIC Educational Resources Information Center

Gabbard, Anita; Mupinga, Davison M.

2013-01-01

Community colleges act as the gateway for students to higher education. Many of these colleges realize this mission through open-door policies where students lacking in basic reading, writing, and mathematics skills can enroll. But, this open-access policy often creates challenges when meeting academic standards. Based on data collected from…

Liberty Centennial Student Campaign Manual.

ERIC Educational Resources Information Center

Statue of Liberty-Ellis Island Foundation, New York, NY.

Background readings and project ideas to involve elementary and secondary school students in fundraising for the restoration of the Statue of Liberty are provided. Materials can be divided into two sections. The first section, background readings, contains President Ronald Reagan's opening remarks at the ceremony introducing the Statue of…

Continuing Literacy.

ERIC Educational Resources Information Center

Clarke, Ronald F., Ed.

The aim of this conference was to stimulate joint action among organizations involved with adult education in east and central Africa, as well as publishers, journalists, librarians and book distributors; it focused on the problems of keeping people reading and improving their ability to read in any language. Opening addresses covered reading…

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

PubMed

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

2018-02-01

Recent models suggest that face and word recognition may rely on overlapping cognitive processes and neural regions. In support of this notion, face recognition deficits have been demonstrated in developmental dyslexia. Here we test whether the opposite association can also be found, that is, impaired reading in developmental prosopagnosia. We tested 10 adults with developmental prosopagnosia and 20 matched controls. All participants completed the Cambridge Face Memory Test, the Cambridge Face Perception test and a Face recognition questionnaire used to quantify everyday face recognition experience. Reading was measured in four experimental tasks, testing different levels of letter, word, and text reading: (a) single word reading with words of varying length,(b) vocal response times in single letter and short word naming, (c) recognition of single letters and short words at brief exposure durations (targeting the word superiority effect), and d) text reading. Participants with developmental prosopagnosia performed strikingly similar to controls across the four reading tasks. Formal analysis revealed a significant dissociation between word and face recognition, as the difference in performance with faces and words was significantly greater for participants with developmental prosopagnosia than for controls. Adult developmental prosopagnosics read as quickly and fluently as controls, while they are seemingly unable to learn efficient strategies for recognizing faces. We suggest that this is due to the differing demands that face and word recognition put on the perceptual system. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Teachers' Perceptions of the Efficacy of the Open Court Program for English Proficient and English Language Learners

ERIC Educational Resources Information Center

Lee, Steven K.; Ajayi, Lasisi; Richards, Rachel

2007-01-01

The purpose of the study is to examine teachers' perceptions of the Open Court language program. Open Court is published by McGraw Hill and has been approved by the "No Child Left Behind Act" as an appropriate research-based reading program. The Open Court program was adopted as part of the efforts to provide all elementary school…

Reading Quizzes Improve Exam Scores for Community College Students.

PubMed

Pape-Lindstrom, Pamela; Eddy, Sarah; Freeman, Scott

2018-06-01

To test the hypothesis that adding course structure may encourage self-regulated learning skills resulting in an increase in student exam performance in the community college setting, we added daily preclass online, open-book reading quizzes to an introductory biology course. We compared three control terms without reading quizzes and three experimental terms with online, open-book reading quizzes; the instructor of record, class size, and instructional time did not vary. Analyzing the Bloom's taxonomy level of a random sample of exam questions indicated a similar cognitive level of high-stakes assessments across all six terms in the study. To control for possible changes in student preparation or ability over time, we calculated each student's grade point average in courses other than biology during the term under study and included it as a predictor variable in our regression models. Our final model showed that students in the experimental terms had significantly higher exam scores than students in the control terms. This result shows that online reading quizzes can boost achievement in community college students. We also comment on the importance of discipline-based education research in community college settings and the structure of our community college/4-year institution collaboration.

Upstream open reading frames regulate the expression of the nuclear Wnt13 isoforms

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

Tang Tao; Rector, Kyle; Barnett, Corey D.

2008-02-22

Wnt proteins control cell survival and cell fate during development. Although Wnt expression is tightly regulated in a spatio-temporal manner, the mechanisms involved both at the transcriptional and translational levels are poorly defined. We have identified a downstream translation initiation codon, AUG(+74), in Wnt13B and Wnt13C mRNAs responsible for the expression of Wnt13 nuclear forms. In this report, we demonstrate that the expression of the nuclear Wnt13C form is translationally regulated in response to stress and apoptosis. Though the 5'-leaders of both Wnt13C and Wnt13B mRNAs have an inhibitory effect on translation, they did not display an internal ribosome entrymore » site activity as demonstrated by dicistronic reporter assays. However, mutations or deletions of the upstream AUG(-99) and AUG(+1) initiation codons abrogate these translation inhibitory effects, demonstrating that Wnt13C expression is controlled by upstream open reading frames. Since long 5'-untranslated region with short upstream open reading frames characterize other Wnt transcripts, our present data on the translational control of Wnt13 expression open the way to further studies on the translation control of Wnt expression as a modulator of their subcellular localization and activity.« less

A comparative analysis of minimally invasive and open spine surgery patient education resources.

PubMed

Agarwal, Nitin; Feghhi, Daniel P; Gupta, Raghav; Hansberry, David R; Quinn, John C; Heary, Robert F; Goldstein, Ira M

2014-09-01

The Internet has become a widespread source for disseminating health information to large numbers of people. Such is the case for spine surgery as well. Given the complexity of spinal surgeries, an important point to consider is whether these resources are easily read and understood by most Americans. The average national reading grade level has been estimated to be at about the 7th grade. In the present study the authors strove to assess the readability of open spine surgery resources and minimally invasive spine surgery resources to offer suggestions to help improve the readability of patient resources. Online patient education resources were downloaded in 2013 from 50 resources representing either traditional open back surgery or minimally invasive spine surgery. Each resource was assessed using 10 scales from Readability Studio Professional Edition version 2012.1. Patient education resources representing traditional open back surgery or minimally invasive spine surgery were all found to be written at a level well above the recommended 6th grade level. In general, minimally invasive spine surgery materials were written at a higher grade level. The readability of patient education resources from spine surgery websites exceeds the average reading ability of an American adult. Revisions may be warranted to increase quality and patient comprehension of these resources to effectively reach a greater patient population.

A retrotransposable element from the mosquito Anopheles gambiae .

PubMed Central

Besansky, N J

1990-01-01

A family of middle repetitive elements from the African malaria vector Anopheles gambiae is described. Approximately 100 copies of the element, designated T1Ag, are dispersed in the genome. Full-length elements are 4.6 kilobase pairs in length, but truncation of the 5' end is common. Nucleotide sequences of one full-length, two 5'-truncated, and two 5' ends of T1Ag elements were determined and aligned to define a consensus sequence. Sequence analysis revealed two long, overlapping open reading frames followed by a polyadenylation signal, AATAAA, and a tail consisting of tandem repetitions of the motif TGAAA. No direct or inverted long terminal repeats (LTRs) were detected. The first open reading frame, 442 amino acids in length, includes a domain resembling that of nucleic acid-binding proteins. The second open reading frame, 975 amino acids long, resembles the reverse transcriptases of a category of retrotransposable elements without LTRs, variously termed class II retrotransposons, class III elements or non-LTR retrotransposons. Similarity at the sequence and structural levels places T1Ag in this category. Images PMID:1689457

An open reading frame in intron seven of the sea urchin DNA-methyltransferase gene codes for a functional AP1 endonuclease.

PubMed

Cioffi, Anna Valentina; Ferrara, Diana; Cubellis, Maria Vittoria; Aniello, Francesco; Corrado, Marcella; Liguori, Francesca; Amoroso, Alessandro; Fucci, Laura; Branno, Margherita

2002-08-01

Analysis of the genome structure of the Paracentrotus lividus (sea urchin) DNA methyltransferase (DNA MTase) gene showed the presence of an open reading frame, named METEX, in intron 7 of the gene. METEX expression is developmentally regulated, showing no correlation with DNA MTase expression. In fact, DNA MTase transcripts are present at high concentrations in the early developmental stages, while METEX is expressed at late stages of development. Two METEX cDNA clones (Met1 and Met2) that are different in the 3' end have been isolated in a cDNA library screening. The putative translated protein from Met2 cDNA clone showed similarity with Escherichia coli endonuclease III on the basis of sequence and predictive three-dimensional structure. The protein, overexpressed in E. coli and purified, had functional properties similar to the endonuclease specific for apurinic/apyrimidinic (AP) sites on the basis of the lyase activity. Therefore the open reading frame, present in intron 7 of the P. lividus DNA MTase gene, codes for a functional AP endonuclease designated SuAP1.

Reading Comprehension Interventions for Students with Autism Spectrum Disorders: A Synthesis of Research

ERIC Educational Resources Information Center

El Zein, Farah; Solis, Michael; Vaughn, Sharon; McCulley, Lisa

2014-01-01

The authors synthesized reading intervention studies conducted between 1980 and 2012 with K-12 students identified with autism spectrum disorders (ASD). Nine single-subject design studies, one quasi-experimental study, and two single-group design studies met the criteria for inclusion. Findings from the studies indicate that modifying…

Nucleotide sequence and transcriptional start site of the Methylobacterium organophilum XX methanol dehydrogenase structural gene

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

Machlin, S.M.; Hanson, R.S.

The nucleotide sequence of a cloned 2.5-kilobase-pair SmaI fragment containing the methanol dehydrogenase (MDH) structural gene from Methylobacterium organophilum XX was determined. A single open reading frame with a coding capacity of 626 amino acids (molecular weight, 66,000) was identified on one stand, and N-terminal sequencing of purified MDH revealed that 27 of these residues constituted a putative signal peptide. Primer extension mapping of in vivo transcripts indicated that the start of mRNA synthesis was 160 to 170 base pairs upstream of the ATG codon. Northern (RNA) blot analysis further demonstrated that the transcript was 2.1 kilobase pairs in lengthmore » and therefore appeared to encode only MDH.« less

Cymbidium chlorotic mosaic virus, a new sobemovirus isolated from a spring orchid (Cymbidium goeringii) in Japan.

PubMed

Kondo, Hideki; Takemoto, Shogo; Maruyama, Kazuyuki; Chiba, Sotaro; Andika, Ida Bagus; Suzuki, Nobuhiro

2015-08-01

Cymbidium chlorotic mosaic virus (CyCMV), isolated from a spring orchid (Cymbidium goeringii), was characterized molecularly. CyCMV isometric virions comprise a single, positive-strand RNA genome of 4,083 nucleotides and 30-kDa coat protein. The virus genome contains five overlapping open reading frames with a genomic organization similar to that of sobemoviruses. BLAST searches and phylogenetic analysis revealed that CyCMV is most closely related to papaya lethal yellowing virus, a proposed dicot-infecting sobemovirus (58.8 % nucleotide sequence identity), but has a relatively distant relationship to monocot-infecting sobemoviruses, with only modest sequence identities. This suggests that CyCMV is a new monocot-infecting member of the floating genus Sobemovirus.

Genetically improved BarraCUDA.

PubMed

Langdon, W B; Lam, Brian Yee Hong

2017-01-01

BarraCUDA is an open source C program which uses the BWA algorithm in parallel with nVidia CUDA to align short next generation DNA sequences against a reference genome. Recently its source code was optimised using "Genetic Improvement". The genetically improved (GI) code is up to three times faster on short paired end reads from The 1000 Genomes Project and 60% more accurate on a short BioPlanet.com GCAT alignment benchmark. GPGPU BarraCUDA running on a single K80 Tesla GPU can align short paired end nextGen sequences up to ten times faster than bwa on a 12 core server. The speed up was such that the GI version was adopted and has been regularly downloaded from SourceForge for more than 12 months.

Cloning and characterization of the human 5,10-methenyltetrahydrofolate synthetase-encoding cDNA.

PubMed

Dayan, A; Bertrand, R; Beauchemin, M; Chahla, D; Mamo, A; Filion, M; Skup, D; Massie, B; Jolivet, J

1995-11-20

Methenyltetrahydrofolate synthetase (MTHFS) catalyses the obligatory initial metabolic step in the intracellular conversion of 5-formyltetrahydrofolate to other reduced folates. We have isolated and sequenced a human MTHFS cDNA which is 872-bp long and codes for a 203-amino-acid protein of 23,229 Da. Escherichia coli BL21(DE3), transfected with pET11c plasmids containing an open reading frame encoding MTHFS, showed a 100-fold increase in MTHFS activity in bacterial extracts after IPTG induction. Northern blot studies of human tissues determined that the MTHFS mRNA was expressed preferentially in the liver and Southern blot analysis of human genomic DNA suggested the presence of a single-copy gene.

An All-School Library Challenge

ERIC Educational Resources Information Center

Quirk, Connie

2005-01-01

The library media center is hosting an all-school team challenge, designed to celebrate reading and library skills. Students could choose from the contest categories like "Lord of the Rings", "Harry Potter", Author Facts Challenge and Opening Lines Challenge for the competition and those students who read more challenging books show their…

Connecting Libraries and Schools with CLASP.

ERIC Educational Resources Information Center

Del Vecchio, Stephen

1993-01-01

Describes the Dewitt Wallace-Reader's Digest Connecting Libraries and Schools Project (CLASP) of the New York Public Library, a cooperative pilot project to encourage reading among children and youth. Sample projects described include summer reading lists, open school night outreach, and outreach to parents. The importance of materials support is…

75 FR 77697 - Action To Ensure Authority To Issue Permits Under the Prevention of Significant Deterioration...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-13

... Reading Room is open from 8:30 a.m. to 4:30 p.m., Monday through Friday, excluding legal holidays. The telephone number for the Public Reading Room is (202) 566-1744, and the telephone number for the Air Docket...

Developing Literacy for the Vocational-Technical Trades.

ERIC Educational Resources Information Center

Penisten, John

The University of Hawaii at Hilo offers a vocational-technical occupational reading curriculum that encourages literacy for technology. The program is geared to meet the special needs of enrollees in the university's trade and industry division, most of whom are postsecondary open-admission students. Most have poor reading skills, averaging a…

Opening a Window into Reading Development: Eye Movements' Role within a Broader Literacy Research Framework

ERIC Educational Resources Information Center

Miller, Brett; O'Donnell, Carol

2013-01-01

insight into how readers process text. The heart of this work spans roughly 40 years reflecting the maturity of both the topics under study and experimental approaches used to investigate reading. Recent technological advancements offer increased flexibility to the field, providing…

Functional neuroanatomy of arithmetic and word reading and its relationship to age

PubMed Central

Evans, Tanya M.; Flowers, D. Lynn; Luetje, Megan M.; Napoliello, Eileen; Eden, Guinevere F.

2016-01-01

Arithmetic and written language are uniquely human skills acquired during early schooling and used daily. While prior studies have independently characterized the neural bases for arithmetic and reading, here we examine both skills in a single study to capture their shared and unique cognitive mechanisms, as well as the role of age/experience in modulating their neural representations. We used functional MRI in 7- to 29-year-olds who performed single-digit subtraction, single-digit addition, and single-word reading. Using a factorial design, we examined the main effects of Task (subtraction, addition, reading) and Age (as a continuous variable), and their interactions. A main effect of Task revealed preferential activation for subtraction in bilateral intraparietal sulci and supramarginal gyri, right insula, inferior frontal gyrus, and cingulate. The right middle temporal gyrus and left superior temporal gyrus were preferentially active for both addition and reading, and left fusiform gyrus was preferentially active for reading. A main effect of Age revealed increased activity in older participants in right angular gyrus, superior temporal sulcus, and putamen, and less activity in left supplementary motor area, suggesting a left frontal to right temporo-parietal shift of activity with increasing age/experience across all tasks. Interactions for Task by Age were found in right hippocampus and left middle frontal gyrus, with older age invoking greater activity for addition and at the same time less activity for subtraction and reading. Together, in a study conducted in the same participants using similar task and acquisition parameters, the results reveal the neural substrates of these educationally relevant cognitive skills in typical participants in the context of age/experience. PMID:27566261

WWC Review of the Report "The Impact of Collaborative Strategic Reading on the Reading Comprehension of Grade 5 Students in Linguistically Diverse Schools." What Works Clearinghouse Single Study Review

ERIC Educational Resources Information Center

What Works Clearinghouse, 2013

2013-01-01

The study reviewed in this paper examined the impact of "Collaborative Strategic Reading" ("CSR"), a set of instructional strategies used to build reading proficiency, on the reading comprehension of fifth-grade students. The analysis included 1,355 students from 74 social studies classrooms within 26 linguistically diverse…

A Meta-Analysis of Self-Monitoring on Reading Performance of K-12 Students

ERIC Educational Resources Information Center

Guzman, Guadalupe; Goldberg, Taryn S.; Swanson, H. Lee

2018-01-01

The published single-case design (SCD) research (N = 19 articles) on self-monitoring and reading performance was synthesized. The following inclusion criteria were used: (a) the study must have been peer-reviewed, (b) implemented an intervention targeting student self-monitoring of reading skills, (c) included data on at least 1 reading outcome,…

Multicomponent Treatment of Rapid Naming, Reading Rate, and Visual Attention in Single and Double Deficit Dyslexics

ERIC Educational Resources Information Center

Johnson, Kary A.

2013-01-01

While the relationship between rapid automatic naming (RAN) deficiencies and dyslexia (reading disability) is well developed and supported in the behavioral and medical research literature to date, direct treatment of the specific RAN deficiency in addition to subsequently poor reading outcomes in the lexical skill of reading rate and the…

The Impact of Past Language Arts Teachers on the Reading Motivation of Twelfth Grade Students

ERIC Educational Resources Information Center

Shepard, Courtney A.

2017-01-01

Adolescents' motivation to read continues to decline. The purpose of this embedded single case study was to explore adolescent reading motivation to determine some ways in which adolescents are motivated to read. Through purposeful sampling, the participants included seven twelfth grade students and three English Language Arts teachers in grades…

Impaired Oral Reading in Two Atypical Dyslexics: A Comparison with a Computational Lexical-Analogy Model

ERIC Educational Resources Information Center

Marchand, Y.; Friedman, R.B.

2005-01-01

A computational model of reading was developed based upon the notion that the structural relationship between orthography and phonology is of greater importance than the dimension of semantics for the reading aloud of single words. Degradation of this model successfully simulated the reading performance of two patients with atypical acquired…

Nucleotide sequencing and characterization of the genes encoding benzene oxidation enzymes of Pseudomonas putida.

PubMed Central

Irie, S; Doi, S; Yorifuji, T; Takagi, M; Yano, K

1987-01-01

The nucleotide sequence of the genes from Pseudomonas putida encoding oxidation of benzene to catechol was determined. Five open reading frames were found in the sequence. Four corresponding protein molecules were detected by a DNA-directed in vitro translation system. Escherichia coli cells containing the fragment with the four open reading frames transformed benzene to cis-benzene glycol, which is an intermediate of the oxidation of benzene to catechol. The relation between the product of each cistron and the components of the benzene oxidation enzyme system is discussed. Images PMID:3667527

Canine RD3 mutation establishes rod cone dysplasia type 2 (rcd2) as ortholog of human and murine rd3

PubMed Central

Kukekova, Anna V.; Goldstein, Orly; Johnson, Jennifer L.; Richardson, Malcolm A.; Pearce-Kelling, Susan E.; Swaroop, Anand; Friedman, James S.; Aguirre, Gustavo D.; Acland, Gregory M.

2009-01-01

Rod cone dysplasia type 2 (rcd2) is an autosomal recessive disorder that segregates in collie dogs. Linkage disequilibrium and meiotic linkage mapping were combined to take advantage of population structure within this breed, and to fine map rcd2 to a 230 kb candidate region that included the gene C1orf36 responsible for human and murine rd3, and within which all affected dogs were homozygous for one haplotype. In one of three identified canine retinal RD3 splice variants, an insertion was found that cosegregates with rcd2, and is predicted to alter the last 61 codons of the normal open reading frame and further extend the ORF. Thus combined meiotic linkage and LD mapping within a single canine breed can yield critical reduction of the disease interval when appropriate advantage is taken of within breed population structure. This should permit a similar approach to tackle other hereditary traits that segregate in single closed populations. PMID:19130129

Characterization of novel avian paramyxovirus strain APMV/Shimane67 isolated from migratory wild geese in Japan.

PubMed

Yamamoto, Eiji; Ito, Hiroshi; Tomioka, Yukiko; Ito, Toshihiro

2015-09-01

An avian paramyxovirus (APMV) isolated from goose feces (APMV/Shimane67) was biologically, serologically and genetically characterized. APMV/Shimane67 showed typical paramyxovirus morphology on electron microscopy. On hemagglutination inhibition test, antiserum against APMV/Shimane67 revealed low reactivity with other APMV serotypes and vice versa. The fusion (F) protein gene of APMV/Shimane67 contained 1,638 nucleotides in a single open reading frame encoding a protein of 545 amino acids. The cleavage site of F protein contained a pair of single basic amino acid (VRENR/L). The nucleotide and deduced amino acid sequences of the F gene of APMV/Shimane67 had relatively low identities (42.9-62.7% and 28.9-67.3%, respectively) with those of other APMVs. Phylogenetic analysis showed that APMV/Shimane67 was related to NDV, APMV-9 and APMV-12, but was distinct from those APMV serotypes. These results suggest that APMV/Shimane67 is a new APMV serotype, APMV-13.

Overview on Sobemoviruses and a Proposal for the Creation of the Family Sobemoviridae

PubMed Central

Sõmera, Merike; Sarmiento, Cecilia; Truve, Erkki

2015-01-01

The genus Sobemovirus, unassigned to any family, consists of viruses with single-stranded plus-oriented single-component RNA genomes and small icosahedral particles. Currently, 14 species within the genus have been recognized by the International Committee on Taxonomy of Viruses (ICTV) but several new species are to be recognized in the near future. Sobemovirus genomes are compact with a conserved structure of open reading frames and with short untranslated regions. Several sobemoviruses are important pathogens. Moreover, over the last decade sobemoviruses have become important model systems to study plant virus evolution. In the current review we give an overview of the structure and expression of sobemovirus genomes, processing and functions of individual proteins, particle structure, pathology and phylogenesis of sobemoviruses as well as of satellite RNAs present together with these viruses. Based on a phylogenetic analysis we propose that a new family Sobemoviridae should be recognized including the genera Sobemovirus and Polemovirus. Finally, we outline the future perspectives and needs for the research focusing on sobemoviruses. PMID:26083319

Mutational analysis of the transcriptional activator VirG of Agrobacterium tumefaciens.

PubMed Central

Scheeren-Groot, E P; Rodenburg, K W; den Dulk-Ras, A; Turk, S C; Hooykaas, P J

1994-01-01

To find VirG proteins with altered properties, the virG gene was mutagenized. Random chemical mutagenesis of single-stranded DNA containing the Agrobacterium tumefaciens virG gene led with high frequency to the inactivation of the gene. Sequence analysis showed that 29% of the mutants contained a virG gene with one single-base-pair substitution somewhere in the open reading frame. Thirty-nine different mutations that rendered the VirG protein inactive were mapped. Besides these inactive mutants, two mutants in which the vir genes were active even in the absence of acetosyringone were found on indicator plates. A VirG protein with an N54D substitution turned out to be able to induce a virB-lacZ reporter gene to a high level even in the absence of the inducer acetosyringone. A VirG protein with an I77V substitution exhibited almost no induction in the absence of acetosyringone but showed a maximum induction level already at low concentrations of acetosyringone. Images PMID:7961391

Single-Event Effect Performance of a Conductive-Bridge Memory EEPROM

NASA Technical Reports Server (NTRS)

Chen, Dakai; Wilcox, Edward; Berg, Melanie; Kim, Hak; Phan, Anthony; Figueiredo, Marco; Seidleck, Christina; LaBel, Kenneth

2015-01-01

We investigated the heavy ion SEE characteristics of an EEPROM based on CBRAM technology. SEFI is the dominant type of SEE for each operating mode (standby, read-only, write/read). We also observed single bit upsets in the CBRAM cell, during write/read tests. the SEULET threshold is between 10 and 20 MeV * sq cm/mg, with an upper fluence limit of 3 × 10(exp 6) cm(exp -2) at 10 MeV * sq cm/mg. In the stand by mode, the CBRAM array appears immune to bit upsets.

Photometry Using Kepler "Superstamps" of Open Clusters NGC 6791 & NGC 6819

NASA Astrophysics Data System (ADS)

Kuehn, Charles A.; Drury, Jason A.; Bellamy, Beau R.; Stello, Dennis; Bedding, Timothy R.; Reed, Mike; Quick, Breanna

2015-09-01

The Kepler space telescope has proven to be a gold mine for the study of variable stars. Usually, Kepler only reads out a handful of pixels around each pre-selected target star, omitting a large number of stars in the Kepler field. Fortunately, for the open clusters NGC 6791 and NGC 6819, Kepler also read out larger "superstamps" which contained complete images of the central region of each cluster. These cluster images can be used to study additional stars in the open clusters that were not originally on Kepler's target list. We discuss our work on using two photometric techniques to analyze these superstamps and present sample results from this project to demonstrate the value of this technique for a wide variety of variable stars.

Comparing the use of open and closed questions for Web-based measures of the continued-influence effect.

PubMed

Connor Desai, Saoirse; Reimers, Stian

2018-06-25

Open-ended questions, in which participants write or type their responses, are used in many areas of the behavioral sciences. Although effective in the lab, they are relatively untested in online experiments, and the quality of responses is largely unexplored. Closed-ended questions are easier to use online because they generally require only single key- or mouse-press responses and are less cognitively demanding, but they can bias the responses. We compared the data quality obtained using open and closed response formats using the continued-influence effect (CIE), in which participants read a series of statements about an unfolding event, one of which is unambiguously corrected later. Participants typically continue to refer to the corrected misinformation when making inferential statements about the event. We implemented this basic procedure online (Exp. 1A, n = 78), comparing standard open-ended responses to an alternative procedure using closed-ended responses (Exp. 1B, n = 75). Finally, we replicated these findings in a larger preregistered study (Exps. 2A and 2B, n = 323). We observed the CIE in all conditions: Participants continued to refer to the misinformation following a correction, and their references to the target misinformation were broadly similar in number across open- and closed-ended questions. We found that participants' open-ended responses were relatively detailed (including an average of 75 characters for inference questions), and almost all responses attempted to address the question. The responses were faster, however, for closed-ended questions. Overall, we suggest that with caution it may be possible to use either method for gathering CIE data.

Review of Single Subject Research Examining the Effectiveness of Interventions for At-Risk English Learners

ERIC Educational Resources Information Center

Baker, Doris Luft; Richards-Tutor, Catherine; Sparks, Anthony; Canges, Rebecca

2018-01-01

We review published single subject design (SSD) studies that examine the effects of interventions for English learners at-risk or with learning disabilities. Results of our literature search yielded 10 studies, five in reading, one in reading and behavior, and four in mathematics that met our inclusion criteria. Seven studies targeted…

The read-write Linked Data Web.

PubMed

Berners-Lee, Tim; O'Hara, Kieron

2013-03-28

This paper discusses issues that will affect the future development of the Web, either increasing its power and utility, or alternatively suppressing its development. It argues for the importance of the continued development of the Linked Data Web, and describes the use of linked open data as an important component of that. Second, the paper defends the Web as a read-write medium, and goes on to consider how the read-write Linked Data Web could be achieved.

A Protocol for Functional Assessment of Whole-Protein Saturation Mutagenesis Libraries Utilizing High-Throughput Sequencing.

PubMed

Stiffler, Michael A; Subramanian, Subu K; Salinas, Victor H; Ranganathan, Rama

2016-07-03

Site-directed mutagenesis has long been used as a method to interrogate protein structure, function and evolution. Recent advances in massively-parallel sequencing technology have opened up the possibility of assessing the functional or fitness effects of large numbers of mutations simultaneously. Here, we present a protocol for experimentally determining the effects of all possible single amino acid mutations in a protein of interest utilizing high-throughput sequencing technology, using the 263 amino acid antibiotic resistance enzyme TEM-1 β-lactamase as an example. In this approach, a whole-protein saturation mutagenesis library is constructed by site-directed mutagenic PCR, randomizing each position individually to all possible amino acids. The library is then transformed into bacteria, and selected for the ability to confer resistance to β-lactam antibiotics. The fitness effect of each mutation is then determined by deep sequencing of the library before and after selection. Importantly, this protocol introduces methods which maximize sequencing read depth and permit the simultaneous selection of the entire mutation library, by mixing adjacent positions into groups of length accommodated by high-throughput sequencing read length and utilizing orthogonal primers to barcode each group. Representative results using this protocol are provided by assessing the fitness effects of all single amino acid mutations in TEM-1 at a clinically relevant dosage of ampicillin. The method should be easily extendable to other proteins for which a high-throughput selection assay is in place.

Clustering single cells: a review of approaches on high-and low-depth single-cell RNA-seq data.

PubMed

Menon, Vilas

2017-12-11

Advances in single-cell RNA-sequencing technology have resulted in a wealth of studies aiming to identify transcriptomic cell types in various biological systems. There are multiple experimental approaches to isolate and profile single cells, which provide different levels of cellular and tissue coverage. In addition, multiple computational strategies have been proposed to identify putative cell types from single-cell data. From a data generation perspective, recent single-cell studies can be classified into two groups: those that distribute reads shallowly over large numbers of cells and those that distribute reads more deeply over a smaller cell population. Although there are advantages to both approaches in terms of cellular and tissue coverage, it is unclear whether different computational cell type identification methods are better suited to one or the other experimental paradigm. This study reviews three cell type clustering algorithms, each representing one of three broad approaches, and finds that PCA-based algorithms appear most suited to low read depth data sets, whereas gene clustering-based and biclustering algorithms perform better on high read depth data sets. In addition, highly related cell classes are better distinguished by higher-depth data, given the same total number of reads; however, simultaneous discovery of distinct and similar types is better served by lower-depth, higher cell number data. Overall, this study suggests that the depth of profiling should be determined by initial assumptions about the diversity of cells in the population, and that the selection of clustering algorithm(s) is subsequently based on the depth of profiling will allow for better identification of putative transcriptomic cell types. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Reading Development in Upper Elementary Language Minority Readers of Hebrew: The Specific Challenge of Fluency

ERIC Educational Resources Information Center

Shahar-Yames, Daphna; Prior, Anat

2017-01-01

We examined reading proficiency, focusing on fluency, in 56 Russian-speaking language minority (LM) students and 56 native Hebrew-speaking (NH) peers. Fifth-grade students completed measures of Hebrew reading accuracy and fluency from word to text level as well as phonological awareness (PA), RAN and vocabulary. LM students read single words less…

Concurrent and Longitudinal Predictors of Reading for Deaf and Hearing Children in Primary School

ERIC Educational Resources Information Center

Harris, Margaret; Terlektsi, Emmanouela; Kyle, Fiona Elizabeth

2017-01-01

Forty-one children with severe-profound prelingual hearing loss were assessed on single word reading, reading comprehension, English vocabulary, phonological awareness and speechreading at three time points, 1 year apart (T1-T3). Their progress was compared with that of a group of hearing children of similar nonverbal IQ, initially reading at the…

Comprehension and Time Expended for a Doctoral Student with a Learning Disability when Reading with and without an Accommodation

ERIC Educational Resources Information Center

Tanners, Adam; McDougall, Dennis; Skouge, Jim; Narkon, Drue

2012-01-01

The purpose of this alternating treatment, single-case research study was to compare reading comprehension and time expended reading, of a doctoral student with learning disabilities, under two reading conditions. In condition one, the student used a self-discovered accommodation, that is, listening, on an iPod, to an audiobook version…

Using Text-to-Speech Reading Support for an Adult with Mild Aphasia and Cognitive Impairment

ERIC Educational Resources Information Center

Harvey, Judy; Hux, Karen; Snell, Jeffry

2013-01-01

This single case study served to examine text-to-speech (TTS) effects on reading rate and comprehension in an individual with mild aphasia and cognitive impairment. Findings showed faster reading, given TTS presented at a normal speaking rate, but no significant comprehension changes. TTS may support reading in people with aphasia when time…

Integrating Scenario-Based and Component Reading Skill Measures to Understand the Reading Behavior of Struggling Readers

ERIC Educational Resources Information Center

Sabatini, John P.; O'Reilly, Tenaha; Halderman, Laura K.; Bruce, Kelly

2014-01-01

In recent years, researchers, educators, and policy makers have called for a new generation of reading comprehension assessments (e.g., Partnership for 21st Century Skills, 2008). Advocates of this movement argue for a deeper type of reading assessment, one that captures students' ability to not only understand single texts in isolation but also…

Phrasing in the speech and reading of the hearing impaired.

PubMed

Gregory, J F

1986-08-01

The study reported here explored a partial explanation for the fourth-grade "bottleneck" in literacy advancement by hearing-impaired students. Speech samples from 21 deaf subjects were rated for degree of evident phrasal quality. Likewise, reading comprehension scores for each student were obtained under four reading conditions: reading in whole sentences, in phrases, in fragmented word groups, and in single words. Degree of rated speech phrasality was found to relate significantly and positively to correct recall answers to questions based upon silent reading of passages typed in meaningful word groups (but not when the passages were typed in whole sentences, fragmented word groups, or in single words). The results were taken to suggest that--whereas staccato-speaking deaf students may lack a sense of the phrase altogether--phrasal-speaking deaf youngsters fail to independently apply their phrase sense in the normal reading situation. Thus, both types of deaf youngsters have difficulty affecting the transition to phrase reading that is common for hearing students at or about the fourth-grade level. Finally, I argue that this phrase sense can be instilled in hearing-impaired students and that they can be trained to use it in reading.

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

PubMed

Lassmann, Timo

2015-01-28

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

Single-shot readout of accumulation mode Si/SiGe spin qubits using RF reflectometry

NASA Astrophysics Data System (ADS)

Volk, Christian; Martins, Frederico; Malinowski, Filip; Marcus, Charles M.; Kuemmeth, Ferdinand

Spin qubits based on gate-defined quantum dots are promising systems for realizing quantum computation. Due to their low concentration of nuclear-spin-carrying isotopes, Si/SiGe heterostructures are of particular interest. While high fidelities have been reported for single-qubit and two-qubit gate operations, qubit initialization and measurement times are relatively slow. In order to develop fast read-out techniques compatible with the operation of spin qubits, we characterize double and triple quantum dots confined in undoped Si/Si0.7Ge0.3 heterostructures using accumulation and depletion gates and a nearby RF charge sensor dot. We implement a RF reflectometry technique that allows single-shot charge read-out at integration times on the order of a few μs. We show our recent advancement towards implementing spin qubits in these structures, including spin-selective single-shot read-out.

76 FR 9988 - Improving EPA Regulations

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-23

...., Washington, DC. The Public Reading Room is open from 8:30 a.m. to 4:30 p.m., Monday through Friday, excluding legal holidays. The telephone number for the Public Reading Room is (202) 566-1744, and the telephone... key considerations in mind: EPA must uphold its mission to protect human health and the environment...

Attention Process Training-3 to improve reading comprehension in mild aphasia: A single-case experimental design study.

PubMed

Lee, Jaime B; Sohlberg, McKay Moore; Harn, Beth; Horner, Robert; Cherney, Leora R

2018-06-04

People with aphasia frequently present with nonlinguistic deficits, in addition to their compromised language abilities, which may contribute to their problems with reading comprehension. Treatment of attention, working memory and executive control may improve reading comprehension in individuals with aphasia, particularly those with mild reading problems. This single-case experimental design study evaluated the efficacy of Attention Process Training-3, an intervention combining direct attention training and metacognitive facilitation, for improving reading comprehension in individuals with mild aphasia. A multiple baseline design across six participants was used to evaluate treatment effects. The primary outcome measure was a maze reading task. Cognitive measures were administered pre- and post-treatment. Visual inspection of graphed maze reading performance data indicated a basic effect between APT-3 and improved maze reading for three of the six participants. Quantitative analyses, using Tau-U, corroborated findings identified through visual analysis. The overall effect size was significant (Tau = .48, p = .01). Results suggest that APT-3 has the potential to improve reading in individuals with aphasia, but that it may be more efficacious under certain conditions. Treatment and participant variables, including intensity of treatment and metacognitive strategy usage, are discussed as potential influences on participants' responsiveness to APT-3.

The classification of normal screening mammograms

NASA Astrophysics Data System (ADS)

Ang, Zoey Z. Y.; Rawashdeh, Mohammad A.; Heard, Robert; Brennan, Patrick C.; Lee, Warwick; Lewis, Sarah J.

2016-03-01

Rationale and objectives: To understand how breast screen readers classify the difficulty of normal screening mammograms using common lexicon describing normal appearances. Cases were also assessed on their suitability for a single reader strategy. Materials and Methods: 15 breast readers were asked to interpret a test set of 29 normal screening mammogram cases and classify them by rating the difficulty of the case on a five-point Likert scale, identifying the salient features and assessing their suitability for single reading. Using the False Positive Fractions from a previous study, the 29 cases were classified into 10 "low", 10 "medium" and nine "high" difficulties. Data was analyzed with descriptive statistics. Spearman's correlation was used to test the strength of association between the difficulty of the cases and the readers' recommendation for single reading strategy. Results: The ratings from readers in this study corresponded to the known difficulty level of cases for the 'low' and 'high' difficulty cases. Uniform ductal pattern and density, symmetrical mammographic features and the absence of micro-calcifications were the main reasons associated with 'low' difficulty cases. The 'high' difficulty cases were described as having `dense breasts'. There was a statistically significant negative correlation between the difficulty of the cases and readers' recommendation for single reading (r = -0.475, P = 0.009). Conclusion: The findings demonstrated potential relationships between certain mammographic features and the difficulty for readers to classify mammograms as 'normal'. The standard Australian practice of double reading was deemed more suitable for most cases. There was an inverse moderate association between the difficulty of the cases and the recommendations for single reading.

A dual-route cascaded model of reading by deaf adults: evidence for grapheme to viseme conversion.

PubMed

Elliott, Eeva A; Braun, Mario; Kuhlmann, Michael; Jacobs, Arthur M

2012-01-01

There is an ongoing debate whether deaf individuals access phonology when reading, and if so, what impact the ability to access phonology might have on reading achievement. However, the debate so far has been theoretically unspecific on two accounts: (a) the phonological units deaf individuals may have of oral language have not been specified and (b) there seem to be no explicit cognitive models specifying how phonology and other factors operate in reading by deaf individuals. We propose that deaf individuals have representations of the sublexical structure of oral-aural language which are based on mouth shapes and that these sublexical units are activated during reading by deaf individuals. We specify the sublexical units of deaf German readers as 11 "visemes" and incorporate the viseme set into a working model of single-word reading by deaf adults based on the dual-route cascaded model of reading aloud by Coltheart, Rastle, Perry, Langdon, and Ziegler (2001. DRC: A dual route cascaded model of visual word recognition and reading aloud. Psychological Review, 108, 204-256. doi: 10.1037//0033-295x.108.1.204). We assessed the indirect route of this model by investigating the "pseudo-homoviseme" effect using a lexical decision task in deaf German reading adults. We found a main effect of pseudo-homovisemy, suggesting that at least some deaf individuals do automatically access sublexical structure during single-word reading.

A Frameshift Mutation in the Cubilin Gene (CUBN) in Border Collies with Imerslund-Gräsbeck Syndrome (Selective Cobalamin Malabsorption)

PubMed Central

Owczarek-Lipska, Marta; Jagannathan, Vidhya; Drögemüller, Cord; Lutz, Sabina; Glanemann, Barbara

2013-01-01

Imerslund-Gräsbeck syndrome (IGS) or selective cobalamin malabsorption has been described in humans and dogs. IGS occurs in Border Collies and is inherited as a monogenic autosomal recessive trait in this breed. Using 7 IGS cases and 7 non-affected controls we mapped the causative mutation by genome-wide association and homozygosity mapping to a 3.53 Mb interval on chromosome 2. We re-sequenced the genome of one affected dog at ∼10× coverage and detected 17 non-synonymous variants in the critical interval. Two of these non-synonymous variants were in the cubilin gene (CUBN), which is known to play an essential role in cobalamin uptake from the ileum. We tested these two CUBN variants for association with IGS in larger cohorts of dogs and found that only one of them was perfectly associated with the phenotype. This variant, a single base pair deletion (c.8392delC), is predicted to cause a frameshift and premature stop codon in the CUBN gene. The resulting mutant open reading frame is 821 codons shorter than the wildtype open reading frame (p.Q2798Rfs*3). Interestingly, we observed an additional nonsense mutation in the MRC1 gene encoding the mannose receptor, C type 1, which was in perfect linkage disequilibrium with the CUBN frameshift mutation. Based on our genetic data and the known role of CUBN for cobalamin uptake we conclude that the identified CUBN frameshift mutation is most likely causative for IGS in Border Collies. PMID:23613799

Genomic analysis of the symbiotic marine crenarchaeon, Cenarchaeumsymbiosum

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

Hallam, Steven J.; Konstantinidis, Konstantinos T.; Brochier,Celine

2006-06-24

Crenarchaea are ubiquitous and abundant microbial constituents of soils, sediments, lakes and ocean waters, yet relatively little is known about their fundamental evolutionary, ecological, and physiological properties. To better describe the ubiquitous nonthermophilic Crenarchaea, we analyzed the genome sequence of one representative, the uncultivated sponge symbiont, Cenarchaeum symbiosum. C. symbiosum genotypes coinhabiting the same host partitioned into two dominant populations, corresponding to previously described a- and b-type ribosomal RNA variants. Although synthetic, overlapping a- and b-type ribotypes harbored significant genetic variability. A single tiling path comprising the dominant a-type genotype was assembled, and used to explore the biological properties ofmore » C. symbiosum and its planktonic relatives. Out of a total of 2,066 predicted open reading frames, 36% were more highly conserved with other Archaea. The remainder partitioned between bacteria (18%), eukaryotes (1.5%) and viruses (0.1%). A total of 525 open reading frames were more highly conserved with sequences derived from marine environmental genomic surveys, most probably representing orthologous genes found in free-living planktonic Crenarchaea. The remaining genes partitioned between functional RNAs (2.4%), and hypotheticals (42%) with limited homology to known functional genes. The latter category likely contains genes specifically involved in mediated archaeal-sponge symbiosis. Phylogenetic analyses placed C. symbiosum as a basal crenarchaeon, sharing specific genomic features in common with either Crenarchaea, Euryarchaea, or both. The genome sequence of C. symbiosum reflect a unique and unusual evolutionary, physiological, and ecological history, one remarkably distinct from that of any other previously known microbial lineage.« less

Alterations of the three short open reading frames in the Rous sarcoma virus leader RNA modulate viral replication and gene expression.

PubMed Central

Moustakas, A; Sonstegard, T S; Hackett, P B

1993-01-01

The Rous sarcoma virus (RSV) leader RNA has three short open reading frames (ORF1 to ORF3) which are conserved in all avian sarcoma-leukosis retroviruses. Effects on virus propagation were determined following three types of alterations in the ORFs: (i) replacement of AUG initiation codons in order to prohibit ORF translation, (ii) alterations of the codon context around the AUG initiation codon to enhance translation of the normally silent ORF3, and (iii) elongation of the ORF coding sequences. Mutagenesis of the AUG codons for ORF1 and ORF2 (AUG1 and AUG2) singly or together delayed the onset of viral replication and cell transformation. In contrast, mutagenesis of AUG3 almost completely suppressed these viral activities. Mutagenesis of ORF3 to enhance its translation inhibited viral propagation. When the mutant ORF3 included an additional frameshift mutation which extended the ORF beyond the initiation site for the gag, gag-pol, and env proteins, host cells were initially transformed but died soon thereafter. Elongation of ORF1 from 7 to 62 codons led to the accumulation of transformation-defective virus with a delayed onset of replication. In contrast, viruses with elongation of ORF1 from 7 to 30 codons, ORF2 from 16 to 48 codons, or ORF3 from 9 to 64 codons, without any alterations in the AUG context, exhibited wild-type phenotypes. These results are consistent with a model that translation of the ORFs is necessary to facilitate virus production. Images PMID:7685415

The Impact of Gloss Types on Iranian EFL Students' Reading Comprehension and Lexical Retention

ERIC Educational Resources Information Center

Farvardin, Mohammad Taghi; Biria, Reza

2012-01-01

Research has shown that the effect of marginal glosses on reading comprehension and vocabulary retention is a controversial issue. The purpose of this study was to investigate this issue among Iranian university EFL students. Three types of glosses were applied in this study: single gloss in participants' first language (SL1G), single gloss in…

Tackling Ambulatory Safety Risks Through Patient Engagement: What 10,000 Patients and Families Say About Safety-Related Knowledge, Behaviors, and Attitudes After Reading Visit Notes.

PubMed

Bell, Sigall K; Folcarelli, Patricia; Fossa, Alan; Gerard, Macda; Harper, Marvin; Leveille, Suzanne; Moore, Caroline; Sands, Kenneth E; Sarnoff Lee, Barbara; Walker, Jan; Bourgeois, Fabienne

2018-04-27

Ambulatory safety risks including delayed diagnoses or missed abnormal test results are difficult for clinicians to see, because they often occur in the space between visits. Experts advocate greater patient engagement to improve safety, but strategies are limited. Patient access to clinical notes ("OpenNotes") may help close the safety gap between visits. We surveyed patients and families who logged on to the patient portal and had at least one ambulatory note available in the past 12 months at two academic hospitals during June to September 2016, focusing on patient-reported effects of OpenNotes on safety knowledge, behaviors, and attitudes. A total of 6913 (28%) of 24,722 patients at an adult hospital and 3672 (17%) of 21,579 participants at the children's hospital submitted surveys. Approximately 75% of patients and parents each reported that reading notes helped them understand the reason for both tests and referrals, and approximately 50% felt that it helped them complete tests and referrals. Roughly 75% of participants were more likely to check and understand test results. Overall, 97% of participants reported that trust in the provider, activation, patient-provider goal alignment, and teamwork were each better or the same after reading 1 note or more. Nonwhite participants and those with high school education or less were 30% to 50% more likely to report that reading notes helped them complete tests compared with white and more educated respondents, respectively. Overall, the majority of more than 10,000 patients and parents reported reading notes helped them understand and follow through on tests and referrals. As information transparency spreads, OpenNotes can help activate patients and families, facilitate safety behaviors, and forge stronger partnerships with clinicians.

The organisation and interviral homologies of genes at the 3' end of tobacco rattle virus RNA1

PubMed Central

Boccara, Martine; Hamilton, William D. O.; Baulcombe, David C.

1986-01-01

The RNA1 of tobacco rattle virus (TRV) has been cloned as cDNA and the nucleotide sequence determined of 2 kb from the 3'-terminal region. The sequence contains three long open reading frames. One of these starts 5' of the cDNA and probably corresponds to the carboxy-terminal sequence of a 170-K protein encoded on RNA1. The deduced protein sequence from this reading frame shows homology with the putative replicases of tobacco mosaic virus (TMV) and tricornaviruses. The location of the second open reading frame, which encodes a 29-K polypeptide, was shown by Northern blot analysis to coincide with a 1.6-kb subgenomic RNA. The validity of this reading frame was confirmed by showing that the cDNA extending over this region could be transcribed and translated in vitro to produce a polypeptide of the predicted size which co-migrates in electrophoresis with a translation product of authentic viral RNA. The sequence of this 29-K polypeptide showed homology with two regions in the 30-K protein of TMV. This homology includes positions in the TMV 30-K protein where mutations have been identified which affect the transport of virus between cells. The third open reading frame encodes a potential 16-K protein and was shown by Northern blot hybridisation to be contained within the region of a 0.7-kb subgenomic RNA which is found in cellular RNA of infected cells but not virus particles. The many similarities between TRV and TMV in viral morphology, gene organisation and sequence suggest that these two viral groups may share a common viral ancestor. ImagesFig. 2.Fig. 3. PMID:16453668

Nucleotide sequence of soybean chloroplast DNA regions which contain the psb A and trn H genes and cover the ends of the large single copy region and one end of the inverted repeats.

PubMed Central

Spielmann, A; Stutz, E

1983-01-01

The soybean chloroplast psb A gene (photosystem II thylakoid membrane protein of Mr 32 000, lysine-free) and the trn H gene (tRNAHisGUG), which both map in the large single copy region adjacent to one of the inverted repeat structures (IR1), have been sequenced including flanking regions. The psb A gene shows in its structural part 92% sequence homology with the corresponding genes of spinach and N. debneyi and contains also an open reading frame for 353 aminoacids. The aminoacid sequence of a potential primary translation product (calculated Mr, 38 904, no lysine) diverges from that of spinach and N. debneyi in only two positions in the C-terminal part. The trn H gene has the same polarity as the psb A gene and the coding region is located at the very end of the large single copy region. The deduced sequence of the soybean chloroplast tRNAHisGUG is identical with that of Zea mays chloroplasts. Both ends of the large single copy region were sequenced including a small segment of the adjacent IR1 and IR2. PMID:6314279

Useful Bicistronic Reporter System for Studying Poly(A) Site-Defining cis Elements and Regulation of Alternative Polyadenylation.

PubMed

Deng, Zhongyuan; Zhang, Shen; Gu, Shaohua; Ni, Xinzhi; Zeng, Wenxian; Li, Xianchun

2018-01-17

The link between polyadenylation (pA) and various biological, behavioral, and pathological events of eukaryotes underlines the need to develop in vivo polyadenylation assay methods for characterization of the cis -acting elements, trans -acting factors and environmental stimuli that affect polyadenylation efficiency and/or relative usage of two alternative polyadenylation (APA) sites. The current protein-based CAT or luciferase reporter systems can measure the polyadenylation efficiency of a single pA site or candidate cis element but not the choice of two APA sites. To address this issue, we developed a set of four new bicistronic reporter vectors that harbor either two luciferase or fluorescence protein open reading frames connected with one Internal Ribosome Entry Site (IRES). Transfection of single or dual insertion constructs of these vectors into mammalian cells demonstrated that they could be utilized not only to quantify the strength of a single candidate pA site or cis element, but also to accurately measure the relative usage of two APA sites at both the mRNA (qRT-PCR) and protein levels. This represents the first reporter system that can study polyadenylation efficiency of a single pA site or element and regulation of two APA sites at both the mRNA and protein levels.

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

North, Michael J.

SchemaOnRead provides tools for implementing schema-on-read including a single function call (e.g., schemaOnRead("filename")) that reads text (TXT), comma separated value (CSV), raster image (BMP, PNG, GIF, TIFF, and JPG), R data (RDS), HDF5, NetCDF, spreadsheet (XLS, XLSX, ODS, and DIF), Weka Attribute-Relation File Format (ARFF), Epi Info (REC), Pajek network (PAJ), R network (NET), Hypertext Markup Language (HTML), SPSS (SAV), Systat (SYS), and Stata (DTA) files. It also recursively reads folders (e.g., schemaOnRead("folder")), returning a nested list of the contained elements.

Processing Time and Cognitive Effort of Longhand Note Taking When Reading and Summarizing a Structured or Linear Text

ERIC Educational Resources Information Center

Olive, Thierry; Barbier, Marie-Laure

2017-01-01

We examined longhand note taking strategies when reading and summarizing a source text that was formatted with bullets or that was presented in a single paragraph. We analyzed cognitive effort when reading the source text, when jotting notes, when reading the notes, and when composing the summary, as well as time spent in these activities and the…

The Effect of an Enrichment Reading Program on the Cognitive Processes and Neural Structures of Children Having Reading Difficulties

ERIC Educational Resources Information Center

Kuruyer, Hayriye Gül; Akyol, Hayati; Karli Oguz, Kader; Has, Arzu Ceylan

2017-01-01

The main purpose of the current study is to explain the effect of an enrichment reading program on the cognitive processes and neural structures of children experiencing reading difficulties. The current study was carried out in line with a single-subject research method and the between-subjects multiple probe design belonging to this method. This…

National Reading Tests in Denmark, Norway, and Sweden: A Comparison of Construct Definitions, Cognitive Targets, and Response Formats

ERIC Educational Resources Information Center

Tengberg, Michael

2017-01-01

Reading comprehension tests are often assumed to measure the same, or at least similar, constructs. Yet, reading is not a single but a multidimensional form of processing, which means that variations in terms of reading material and item design may emphasize one aspect of the construct at the cost of another. The educational systems in Denmark,…

The Effects of a Dog Reading Visitation Program on Academic Engagement Behavior in Three Elementary Students with Emotional and Behavioral Disabilities: A Single Case Design

ERIC Educational Resources Information Center

Bassette, Laura A.; Taber-Doughty, Teresa

2013-01-01

Background: Children with emotional and behavioral disabilities (EBD) struggle with behavioral problems during reading activities in school. One way to address these concerns may be through dog reading programs which are increasing in popularity in schools and libraries. Preliminary anecdotal research suggests dog reading programs may improve…

High-coverage sequencing and annotated assembly of the genome of the Australian dragon lizard Pogona vitticeps.

PubMed

Georges, Arthur; Li, Qiye; Lian, Jinmin; O'Meally, Denis; Deakin, Janine; Wang, Zongji; Zhang, Pei; Fujita, Matthew; Patel, Hardip R; Holleley, Clare E; Zhou, Yang; Zhang, Xiuwen; Matsubara, Kazumi; Waters, Paul; Graves, Jennifer A Marshall; Sarre, Stephen D; Zhang, Guojie

2015-01-01

The lizards of the family Agamidae are one of the most prominent elements of the Australian reptile fauna. Here, we present a genomic resource built on the basis of a wild-caught male ZZ central bearded dragon Pogona vitticeps. The genomic sequence for P. vitticeps, generated on the Illumina HiSeq 2000 platform, comprised 317 Gbp (179X raw read depth) from 13 insert libraries ranging from 250 bp to 40 kbp. After filtering for low-quality and duplicated reads, 146 Gbp of data (83X) was available for assembly. Exceptionally high levels of heterozygosity (0.85 % of single nucleotide polymorphisms plus sequence insertions or deletions) complicated assembly; nevertheless, 96.4 % of reads mapped back to the assembled scaffolds, indicating that the assembly included most of the sequenced genome. Length of the assembly was 1.8 Gbp in 545,310 scaffolds (69,852 longer than 300 bp), the longest being 14.68 Mbp. N50 was 2.29 Mbp. Genes were annotated on the basis of de novo prediction, similarity to the green anole Anolis carolinensis, Gallus gallus and Homo sapiens proteins, and P. vitticeps transcriptome sequence assemblies, to yield 19,406 protein-coding genes in the assembly, 63 % of which had intact open reading frames. Our assembly captured 99 % (246 of 248) of core CEGMA genes, with 93 % (231) being complete. The quality of the P. vitticeps assembly is comparable or superior to that of other published squamate genomes, and the annotated P. vitticeps genome can be accessed through a genome browser available at https://genomics.canberra.edu.au.

Use of Schema on Read in Earth Science Data Archives

NASA Astrophysics Data System (ADS)

Petrenko, M.; Hegde, M.; Smit, C.; Pilone, P.; Pham, L.

2017-12-01

Traditionally, NASA Earth Science data archives have file-based storage using proprietary data file formats, such as HDF and HDF-EOS, which are optimized to support fast and efficient storage of spaceborne and model data as they are generated. The use of file-based storage essentially imposes an indexing strategy based on data dimensions. In most cases, NASA Earth Science data uses time as the primary index, leading to poor performance in accessing data in spatial dimensions. For example, producing a time series for a single spatial grid cell involves accessing a large number of data files. With exponential growth in data volume due to the ever-increasing spatial and temporal resolution of the data, using file-based archives poses significant performance and cost barriers to data discovery and access. Storing and disseminating data in proprietary data formats imposes an additional access barrier for users outside the mainstream research community. At the NASA Goddard Earth Sciences Data Information Services Center (GES DISC), we have evaluated applying the "schema-on-read" principle to data access and distribution. We used Apache Parquet to store geospatial data, and have exposed data through Amazon Web Services (AWS) Athena, AWS Simple Storage Service (S3), and Apache Spark. Using the "schema-on-read" approach allows customization of indexing—spatial or temporal—to suit the data access pattern. The storage of data in open formats such as Apache Parquet has widespread support in popular programming languages. A wide range of solutions for handling big data lowers the access barrier for all users. This presentation will discuss formats used for data storage, frameworks with support for "schema-on-read" used for data access, and common use cases covering data usage patterns seen in a geospatial data archive.

Use of Schema on Read in Earth Science Data Archives

NASA Technical Reports Server (NTRS)

Hegde, Mahabaleshwara; Smit, Christine; Pilone, Paul; Petrenko, Maksym; Pham, Long

2017-01-01

Traditionally, NASA Earth Science data archives have file-based storage using proprietary data file formats, such as HDF and HDF-EOS, which are optimized to support fast and efficient storage of spaceborne and model data as they are generated. The use of file-based storage essentially imposes an indexing strategy based on data dimensions. In most cases, NASA Earth Science data uses time as the primary index, leading to poor performance in accessing data in spatial dimensions. For example, producing a time series for a single spatial grid cell involves accessing a large number of data files. With exponential growth in data volume due to the ever-increasing spatial and temporal resolution of the data, using file-based archives poses significant performance and cost barriers to data discovery and access. Storing and disseminating data in proprietary data formats imposes an additional access barrier for users outside the mainstream research community. At the NASA Goddard Earth Sciences Data Information Services Center (GES DISC), we have evaluated applying the schema-on-read principle to data access and distribution. We used Apache Parquet to store geospatial data, and have exposed data through Amazon Web Services (AWS) Athena, AWS Simple Storage Service (S3), and Apache Spark. Using the schema-on-read approach allows customization of indexing spatially or temporally to suit the data access pattern. The storage of data in open formats such as Apache Parquet has widespread support in popular programming languages. A wide range of solutions for handling big data lowers the access barrier for all users. This presentation will discuss formats used for data storage, frameworks with This presentation will discuss formats used for data storage, frameworks with support for schema-on-read used for data access, and common use cases covering data usage patterns seen in a geospatial data archive.

Reading fluency: implications for the assessment of children with reading disabilities.

PubMed

Meisinger, Elizabeth B; Bloom, Juliana S; Hynd, George W

2010-06-01

The current investigation explored the diagnostic utility of reading fluency measures in the identification of children with reading disabilities. Participants were 50 children referred to a university-based clinic because of suspected reading problems and/or a prior diagnosis of dyslexia, where children completed a battery of standardized intellectual, reading achievement, and processing measures. Within this clinical sample, a group of children were identified that exhibited specific deficits in their reading fluency skills with concurrent deficits in rapid naming speed and reading comprehension. This group of children would not have been identified as having a reading disability according to assessment of single word reading skills alone, suggesting that it is essential to assess reading fluency in addition to word reading because failure to do so may result in the under-identification of children with reading disabilities.

Slower saccadic reading in Parkinson’s disease

PubMed Central

Jehangir, Naz; Yu, Caroline Yizhu; Song, Jeehey; Shariati, Mohammad Ali; Binder, Steven; Beyer, Jill; Santini, Veronica; Poston, Kathleen

2018-01-01

Idiopathic Parkinson’s Disease (PD) is characterized by degeneration of dopaminergic and other neurons, leading to motor and non-motor deficits. Abnormal eye movements in PD, including fixations, saccades, and convergence, are well described. However, saccadic reading, which requires serial and alternating saccades and fixations, is not well studied, despite its obvious impact on the quality of life. In this study, we assessed saccadic reading using variations of the King-Devick (KD) test, a rapid single digit number naming test, as a way to assess the ability to make serial left-to-right ocular motor movements necessary for reading. We recruited 42 treated PD patients and 80 age-matched controls and compared their reading times with a variety of measures, including age, duration of disease, Unified Parkinson’s Disease Rating Scale (UPDRS), the National Eye Institute 25-Item Visual Functioning Questionnaire 25 (VFQ-25), and Montreal Cognitive assessment (MoCA) test. The subjects performed 4 trials of reading 120 single digit numbers aloud as fast as possible without making errors. In each trial, they read 3 pages (KD1, KD2, and KD3), and each page contained 40 numbers per page in 8 lines with 5 numbers/line. We found that PD patients read about 20% slower than controls on all tests (KD1, 2, and 3 tests) (p < 0.02), and both groups read irregularly spaced numbers slower than regularly spaced numbers. Having lines between numbers to guide reading (KD1 tests) did not impact reading time in both PD and controls, but increased visual crowding as a result of decreased spacing between numbers (KD3 tests) was associated with significantly slower reading times in both PD and control groups. Our study revealed that saccadic reading is slower in PD, but controls and PD patients are both impacted by visuospatial planning challenges posed by increased visual crowding and irregularity of number spacing. Reading time did not correlate with UPDRS or MoCA scores in PD patients but significantly correlated with age, duration of disease, and VFQ-25 scores. The presence of convergence insufficiency did not significantly correlate with reading time in PD patients, although on average there was slower reading time in those with convergence insufficiency by 8 s (p = 0.2613). We propose that a simple reading task using 120 single-digit numbers can be used as a screening tool in the clinical setting to assess functional ocular motor difficulties in Parkinson’s disease that can have a profound impact on quality of life. PMID:29364897

Slower saccadic reading in Parkinson's disease.

PubMed

Jehangir, Naz; Yu, Caroline Yizhu; Song, Jeehey; Shariati, Mohammad Ali; Binder, Steven; Beyer, Jill; Santini, Veronica; Poston, Kathleen; Liao, Yaping Joyce

2018-01-01

Idiopathic Parkinson's Disease (PD) is characterized by degeneration of dopaminergic and other neurons, leading to motor and non-motor deficits. Abnormal eye movements in PD, including fixations, saccades, and convergence, are well described. However, saccadic reading, which requires serial and alternating saccades and fixations, is not well studied, despite its obvious impact on the quality of life. In this study, we assessed saccadic reading using variations of the King-Devick (KD) test, a rapid single digit number naming test, as a way to assess the ability to make serial left-to-right ocular motor movements necessary for reading. We recruited 42 treated PD patients and 80 age-matched controls and compared their reading times with a variety of measures, including age, duration of disease, Unified Parkinson's Disease Rating Scale (UPDRS), the National Eye Institute 25-Item Visual Functioning Questionnaire 25 (VFQ-25), and Montreal Cognitive assessment (MoCA) test. The subjects performed 4 trials of reading 120 single digit numbers aloud as fast as possible without making errors. In each trial, they read 3 pages (KD1, KD2, and KD3), and each page contained 40 numbers per page in 8 lines with 5 numbers/line. We found that PD patients read about 20% slower than controls on all tests (KD1, 2, and 3 tests) (p < 0.02), and both groups read irregularly spaced numbers slower than regularly spaced numbers. Having lines between numbers to guide reading (KD1 tests) did not impact reading time in both PD and controls, but increased visual crowding as a result of decreased spacing between numbers (KD3 tests) was associated with significantly slower reading times in both PD and control groups. Our study revealed that saccadic reading is slower in PD, but controls and PD patients are both impacted by visuospatial planning challenges posed by increased visual crowding and irregularity of number spacing. Reading time did not correlate with UPDRS or MoCA scores in PD patients but significantly correlated with age, duration of disease, and VFQ-25 scores. The presence of convergence insufficiency did not significantly correlate with reading time in PD patients, although on average there was slower reading time in those with convergence insufficiency by 8 s (p = 0.2613). We propose that a simple reading task using 120 single-digit numbers can be used as a screening tool in the clinical setting to assess functional ocular motor difficulties in Parkinson's disease that can have a profound impact on quality of life.

Influences of Visual Attention and Reading Time on Children and Adults

ERIC Educational Resources Information Center

Wei, Chun-Chun; Ma, Min-Yuan

2017-01-01

This study investigates the relationship between visual attention and reading time using a mobile electroencephalography device. The mobile electroencephalography device uses a single channel dry sensor, which easily measures participants' attention in the real-world reading environment. The results reveal that age significantly influences visual…

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...

Single or Dual Representations for Reading and Spelling?

ERIC Educational Resources Information Center

Holmes, Virginia M.; Babauta, Mariko L.

2005-01-01

Neuropsychological models postulate that the memory representation acquired for use in reading words is separate from the one acquired for use in spelling, while developmental models assume that the same representation is developed for access in both reading and spelling. The dual-representation model contends that there is often more precise…

Evaluation of Attention Training and Metacognitive Facilitation to Improve Reading Comprehension in Aphasia

ERIC Educational Resources Information Center

Lee, Jaime B.; Sohlberg, McKay Moore

2013-01-01

Purpose: This pilot study investigated the impact of direct attention training combined with metacognitive facilitation on reading comprehension in individuals with aphasia. Method: A single-subject, multiple baseline design was employed across 4 participants to evaluate potential changes in reading comprehension resulting from an 8-week…

Word Reading Fluency as a Serial Naming Task

ERIC Educational Resources Information Center

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

2018-01-01

Word list reading fluency is theoretically expected to depend on single word reading speed. Yet the correlation between the two diminishes with increasing fluency, while fluency remains strongly correlated to serial digit naming. We hypothesized that multi-element sequence processing is an important component of fluency. We used confirmatory…

Phonological Priming and Orthographic Analogies in Reading.

ERIC Educational Resources Information Center

Goswami, Usha

1990-01-01

Findings of two experiments involving young children at a reading level of six years to six years, nine months suggest that phonological priming is an insufficient explanation of the analogy effect at the single word level. Phonological priming plays no role in the use of analogies in story reading. (RH)

Basic Reading Instruction for Students in Automotive Occupations. Student's Handbook.

ERIC Educational Resources Information Center

General Behavioral Systems, Inc., Torrance, CA.

The basic reading course outlined in this student handbook emphasizes the decoding process. The contents consist of a letter-and-sound spelling chart and 87 course modules which are based on single-letter and letter-combination sounds. Many of the modules include exercises, and some contain reading material. (JM)

Basic Processes in Reading: The Effect of Interletter Spacing

ERIC Educational Resources Information Center

Risko, Evan F.; Lanthier, Sophie N.; Besner, Derek

2011-01-01

Reading is acutely sensitive to the amount of space between letters within a string. In the present investigation, we explore the impairment caused by increasing interletter spacing when reading single words and nonwords aloud. Specifically, 2 hypotheses are tested: (a) whether increasing interletter spacing induces serial processing while reading…

Research-Based Integrated Reading and Writing Course Development

ERIC Educational Resources Information Center

Pierce, Calisa A.

2017-01-01

With the continuing national emphases on acceleration and completion, an integrated reading and writing course (a combined developmental reading and developmental writing course, with all levels compressed into a single course) is one way to move students more quickly and efficiently through the developmental sequence while still maintaining…

Using Noldus Observer XT for research on deaf signers learning to read: an innovative methodology.

PubMed

Ducharme, Daphne A; Arcand, Isabelle

2009-08-01

Despite years of research on the reading problems of deaf students, we still do not know how deaf signers who read well actually crack the code of print. How connections are made between sign language and written language is still an open question. In this article, we show how the Noldus Observer XT software can be used to conduct an in-depth analysis of the online behavior of deaf readers. First, we examine factors that may have an impact on reading behavior. Then, we describe how we videotaped teachers with their deaf student signers of langue des signes québécoise during a reading task, how we conducted a recall activity to better understand the students' reading behavior, and how we used this innovative software to analyze the taped footage. Finally, we discuss the contribution this type of research can have on the future reading behavior of deaf students.

Effects of text-to-speech software use on the reading proficiency of high school struggling readers.

PubMed

Park, Hye Jin; Takahashi, Kiriko; Roberts, Kelly D; Delise, Danielle

2017-01-01

The literature highlights the benefits of text-to-speech (TTS) software when used as an assistive technology facilitating struggling readers' access to print. However, the effects of TTS software use, upon students' unassisted reading proficiency, have remained relatively unexplored. The researchers utilized an experimental design to investigate whether 9th grade struggling readers who use TTS software to read course materials demonstrate significant improvements in unassisted reading performance. A total of 164 students of 30 teachers in Hawaii participated in the study. Analyses of covariance results indicated that the TTS intervention had a significant, positive effect on student reading vocabulary and reading comprehension after 10 weeks of TTS software use (average 582 minutes). There are several limitations to the study; however, the current study opens up for discussions and need for further studies investigating TTS software as a viable reading intervention for adolescent struggling readers.

Reading and Literacy Initiatives. Hearing on Examining Proposal To Improve the Reading and Literacy Skills of Children and Families, Focusing on S.1596 and H.R.2614, Bills To Provide for Reading Excellence by Improving In-Service Instructional Practices for Teachers Who Teach Reading, To Stimulate the Development of More High-Quality Family Literacy Programs, To Support Extended Learning-Time Opportunities for Children, and To Ensure That Children Can Read Well and Independently not Later than Third Grade of the Committee on Labor and Human Resources. United States Senate. One Hundred Fifth Congress, Second Session.

ERIC Educational Resources Information Center

Congress of the U.S., Washington, DC. Senate Committee on Labor and Human Resources.

The U.S. Senate conducted a hearing consisting of two panels: the first panel discussed overcoming reading difficulties with a primary focus on children and the second panel focused on reading and literacy outreach activities that are ongoing in the U.S. After opening statements of the Hon. James M. Jeffords, the Hon. Edward M. Kennedy, and the…

Open Oncology Notes: A Qualitative Study of Oncology Patients' Experiences Reading Their Cancer Care Notes.

PubMed

Kayastha, Neha; Pollak, Kathryn I; LeBlanc, Thomas W

2018-04-01

Electronic medical records increasingly allow patients access to clinician notes. Although most believe that open notes benefits patients, some suggest negative consequences. Little is known about the experiences of patients with cancer reading their medical notes; thus we aimed to describe this qualitatively. We interviewed 20 adults with metastatic or incurable cancer receiving cancer treatment. The semistructured qualitative interviews included four segments: assessing their overall experience reading notes, discussing how notes affected their cancer care experiences, reading a real note with the interviewer, and making suggestions for improvement. We used a constant comparison approach to analyze these qualitative data. We found four themes. Patients reported that notes resulted in the following: (1) increased comprehension; (2) ameliorated uncertainty, relieved anxiety, and facilitated control; (3) increased trust; and (4) for a subset of patients, increased anxiety. Patients described increased comprehension because notes refreshed their memory and clarified their understanding of visits. This helped mitigate the unfamiliarity of cancer, addressing uncertainty and relieving anxiety. Notes facilitated control, empowering patients to ask clinicians more questions. The transparency of notes also increased trust in clinicians. For a subset of patients, however, notes were emotionally difficult to read and raised concerns. Patients identified medical jargon and repetition in notes as areas for improvement. Most patients thought that reading notes improved their care experiences. A small subset of patients experienced increased distress. As reading notes becomes a routine part of the patient experience, physicians might want to elicit and address concerns that arise from notes, thereby further engaging patients in their care.

Uncovering Information Hidden in Web Archives: Glimpse at Web Analysis Building on Data Warehouses; Towards Continuous Web Archiving: First Results and an Agenda for the Future; The Open Video Digital Library; After Migration to an Electronic Journal Collection: Impact on Faculty and Doctoral Students; Who Is Reading On-Line Education Journals? Why? And What Are They Reading?; Report on eLibrary@UBC4: Research, Collaboration and the Digital Library - Visions for 2010.

ERIC Educational Resources Information Center

Rauber, Andreas; Bruckner, Robert M.; Aschenbrenner, Andreas; Witvoet, Oliver; Kaiser, Max; Masanes, Julien; Marchionini, Gary; Geisler, Gary; King, Donald W.; Montgomery, Carol Hansen; Rudner, Lawrence M.; Gellmann, Jennifer S.; Miller-Whitehead, Marie; Iverson, Lee

2002-01-01

These six articles discuss Web archives and Web analysis building on data warehouses; international efforts at continuous Web archiving; the Open Video Digital Library; electronic journal collections in academic libraries; online education journals; and an electronic library symposium at the University of British Columbia. (LRW)

An intronic open reading frame was released from one of group II introns in the mitochondrial genome of the haptophyte Chrysochromulina sp. NIES-1333

PubMed Central

Nishimura, Yuki; Kamikawa, Ryoma; Hashimoto, Tetsuo; Inagaki, Yuji

2014-01-01

Mitochondrial (mt) genome sequences, which often bear introns, have been sampled from phylogenetically diverse eukaryotes. Thus, we can anticipate novel insights into intron evolution from previously unstudied mt genomes. We here investigated the origins and evolution of three introns in the mt genome of the haptophyte Chrysochromulina sp. NIES-1333, which was sequenced completely in this study. All the three introns were characterized as group II, on the basis of predicted secondary structure, and the conserved sequence motifs at the 5′ and 3′ termini. Our comparative studies on diverse mt genomes prompt us to propose that the Chrysochromulina mt genome laterally acquired the introns from mt genomes in distantly related eukaryotes. Many group II introns harbor intronic open reading frames for the proteins (intron-encoded proteins or IEPs), which likely facilitate the splicing of their host introns. However, we propose that a “free-standing,” IEP-like protein, which is not encoded within any introns in the Chrysochromulina mt genome, is involved in the splicing of the first cox1 intron that lacks any open reading frames. PMID:25054084

Genome sequences of a mouse-avirulent and a mouse-virulent strain of Ross River virus.

PubMed

Faragher, S G; Meek, A D; Rice, C M; Dalgarno, L

1988-04-01

The nucleotide sequence of the genomic RNA of a mouse-avirulent strain of Ross River virus, RRV NB5092 (isolated in 1969), has been determined and the corresponding sequence for the prototype mouse-virulent strain, RRV T48 (isolated in 1959), has been completed. The RRV NB5092 genome is approximately 11,674 nucleotides in length, compared with 11,853 nucleotides for RRV T48. RRV NB5092 and RRV T48 have the same genome organization. For both viruses an untranslated region of 80 nucleotides at the 5' end of the genome is followed by a 7440-nucleotide open reading frame which is interrupted after 5586 nucleotides by a single opal termination codon. By homology with other alphaviruses, the 5586-nucleotide open reading frame encodes the nonstructural proteins nsP1, nsP2, and nsP3; a fourth nonstructural protein, nsP4, is produced by read-through of the opal codon. The RRV nonstructural proteins show strong homology with the corresponding proteins of Sindbis virus and Semliki Forest virus in terms of size, net charge, and hydropathy characteristics. However, homology is not uniform between or within the proteins; nsP1, nsP2, and nsP4 contain extended domains which are highly conserved between alphaviruses, while the C-terminal region of nsP3 shows little conservation in sequence or length between alphaviruses. An untranslated "junction" region of 44 nucleotides (for RRV NB5092) or 47 nucleotides (for RRV T48) separates the nonstructural and structural protein coding regions. The structural proteins (capsid-E3-E2-6K-E1) are translated from an open reading frame of 3762 nucleotides which is followed by a 3'-untranslated region of approximately 348 nucleotides (for RRV NB5092) or 524 nucleotides (for RRV T48). Excluding deletions and insertions, the genomes of RRV NB5092 and RRV T48 differ at 284 nucleotides, representing a sequence divergence of 2.38%. Sequence deletions or insertions were found only in the noncoding regions and include a 173-nucleotide deletion in the 3'-untranslated region of RRV NB5092, compared with RRV T48. In the coding regions, most of the nucleotide differences are silent; there are 36 amino acid differences in the nonstructural proteins and 12 in the structural proteins. The distribution of amino acid differences between the two RRV strains correlates with the location of domains which are poorly conserved in sequence between alphaviruses. The possible role of amino acid differences in envelope glycoproteins E1 and E2 in determining the different antigenic and biological properties of RRV NB5092 and RRV T48 is discussed.

Generation of 2A-linked multicistronic cassettes by recombinant PCR.

PubMed

Szymczak-Workman, Andrea L; Vignali, Kate M; Vignali, Dario A A

2012-02-01

The need for reliable, multicistronic vectors for multigene delivery is at the forefront of biomedical technology. It is now possible to express multiple proteins from a single open reading frame (ORF) using 2A peptide-linked multicistronic vectors. These small sequences, when cloned between genes, allow for efficient, stoichiometric production of discrete protein products within a single vector through a novel "cleavage" event within the 2A peptide sequence. Expression of more than two genes using conventional approaches has several limitations, most notably imbalanced protein expression and large size. The use of 2A peptide sequences alleviates these concerns. They are small (18-22 amino acids) and have divergent amino-terminal sequences, which minimizes the chance for homologous recombination and allows for multiple, different 2A peptide sequences to be used within a single vector. Importantly, separation of genes placed between 2A peptide sequences is nearly 100%, which allows for stoichiometric and concordant expression of the genes, regardless of the order of placement within the vector. This protocol describes the use of recombinant polymerase chain reaction (PCR) to connect multiple 2A-linked protein sequences. The final construct is subcloned into an expression vector.

IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis.

PubMed

Safonova, Yana; Bonissone, Stefano; Kurpilyansky, Eugene; Starostina, Ekaterina; Lapidus, Alla; Stinson, Jeremy; DePalatis, Laura; Sandoval, Wendy; Lill, Jennie; Pevzner, Pavel A

2015-06-15

The analysis of concentrations of circulating antibodies in serum (antibody repertoire) is a fundamental, yet poorly studied, problem in immunoinformatics. The two current approaches to the analysis of antibody repertoires [next generation sequencing (NGS) and mass spectrometry (MS)] present difficult computational challenges since antibodies are not directly encoded in the germline but are extensively diversified by somatic recombination and hypermutations. Therefore, the protein database required for the interpretation of spectra from circulating antibodies is custom for each individual. Although such a database can be constructed via NGS, the reads generated by NGS are error-prone and even a single nucleotide error precludes identification of a peptide by the standard proteomics tools. Here, we present the IgRepertoireConstructor algorithm that performs error-correction of immunosequencing reads and uses mass spectra to validate the constructed antibody repertoires. IgRepertoireConstructor is open source and freely available as a C++ and Python program running on all Unix-compatible platforms. The source code is available from http://bioinf.spbau.ru/igtools. ppevzner@ucsd.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

Remaining Mysteries of Molecular Biology: The Role of Polyamines in the Cell.

PubMed

Miller-Fleming, Leonor; Olin-Sandoval, Viridiana; Campbell, Kate; Ralser, Markus

2015-10-23

The polyamines (PAs) spermidine, spermine, putrescine and cadaverine are an essential class of metabolites found throughout all kingdoms of life. In this comprehensive review, we discuss their metabolism, their various intracellular functions and their unusual and conserved regulatory features. These include the regulation of translation via upstream open reading frames, the over-reading of stop codons via ribosomal frameshifting, the existence of an antizyme and an antizyme inhibitor, ubiquitin-independent proteasomal degradation, a complex bi-directional membrane transport system and a unique posttranslational modification-hypusination-that is believed to occur on a single protein only (eIF-5A). Many of these features are broadly conserved indicating that PA metabolism is both concentration critical and evolutionary ancient. When PA metabolism is disrupted, a plethora of cellular processes are affected, including transcription, translation, gene expression regulation, autophagy and stress resistance. As a result, the role of PAs has been associated with cell growth, aging, memory performance, neurodegenerative diseases, metabolic disorders and cancer. Despite comprehensive studies addressing PAs, a unifying concept to interpret their molecular role is missing. The precise biochemical function of polyamines is thus one of the remaining mysteries of molecular cell biology. Copyright © 2015. Published by Elsevier Ltd.

Local restoration of dystrophin expression with the morpholino oligomer AVI-4658 in Duchenne muscular dystrophy: a single-blind, placebo-controlled, dose-escalation, proof-of-concept study

PubMed Central

Kinali, Maria; Arechavala-Gomeza, Virginia; Feng, Lucy; Cirak, Sebahattin; Hunt, David; Adkin, Carl; Guglieri, Michela; Ashton, Emma; Abbs, Stephen; Nihoyannopoulos, Petros; Garralda, Maria Elena; Rutherford, Mary; Mcculley, Caroline; Popplewell, Linda; Graham, Ian R; Dickson, George; Wood, Matthew JA; Wells, Dominic J; Wilton, Steve D; Kole, Ryszard; Straub, Volker; Bushby, Kate; Sewry, Caroline; Morgan, Jennifer E; Muntoni, Francesco

2009-01-01

Summary Background Mutations that disrupt the open reading frame and prevent full translation of DMD, the gene that encodes dystrophin, underlie the fatal X-linked disease Duchenne muscular dystrophy. Oligonucleotides targeted to splicing elements (splice switching oligonucleotides) in DMD pre-mRNA can lead to exon skipping, restoration of the open reading frame, and the production of functional dystrophin in vitro and in vivo, which could benefit patients with this disorder. Methods We did a single-blind, placebo-controlled, dose-escalation study in patients with DMD recruited nationally, to assess the safety and biochemical efficacy of an intramuscular morpholino splice-switching oligonucleotide (AVI-4658) that skips exon 51 in dystrophin mRNA. Seven patients with Duchenne muscular dystrophy with deletions in the open reading frame of DMD that are responsive to exon 51 skipping were selected on the basis of the preservation of their extensor digitorum brevis (EDB) muscle seen on MRI and the response of cultured fibroblasts from a skin biopsy to AVI-4658. AVI-4658 was injected into the EDB muscle; the contralateral muscle received saline. Muscles were biopsied between 3 and 4 weeks after injection. The primary endpoint was the safety of AVI-4658 and the secondary endpoint was its biochemical efficacy. This trial is registered, number NCT00159250. Findings Two patients received 0·09 mg AVI-4658 in 900 μL (0·9%) saline and five patients received 0·9 mg AVI-4658 in 900 μL saline. No adverse events related to AVI-4658 administration were reported. Intramuscular injection of the higher-dose of AVI-4658 resulted in increased dystrophin expression in all treated EDB muscles, although the results of the immunostaining of EDB-treated muscle for dystrophin were not uniform. In the areas of the immunostained sections that were adjacent to the needle track through which AVI-4658 was given, 44–79% of myofibres had increased expression of dystrophin. In randomly chosen sections of treated EDB muscles, the mean intensity of dystrophin staining ranged from 22% to 32% of the mean intensity of dystrophin in healthy control muscles (mean 26·4%), and the mean intensity was 17% (range 11–21%) greater than the intensity in the contralateral saline-treated muscle (one-sample paired t test p=0·002). In the dystrophin-positive fibres, the intensity of dystrophin staining was up to 42% of that in healthy muscle. We showed expression of dystrophin at the expected molecular weight in the AVI-4658-treated muscle by immunoblot. Interpretation Intramuscular AVI-4658 was safe and induced the expression of dystrophin locally within treated muscles. This proof-of-concept study has led to an ongoing systemic clinical trial of AVI-4658 in patients with DMD. Funding UK Department of Health. PMID:19713152

The Detection of Emerging Trends Using Wikipedia Traffic Data and Context Networks.

PubMed

Kämpf, Mirko; Tessenow, Eric; Kenett, Dror Y; Kantelhardt, Jan W

2015-01-01

Can online media predict new and emerging trends, since there is a relationship between trends in society and their representation in online systems? While several recent studies have used Google Trends as the leading online information source to answer corresponding research questions, we focus on the online encyclopedia Wikipedia often used for deeper topical reading. Wikipedia grants open access to all traffic data and provides lots of additional (semantic) information in a context network besides single keywords. Specifically, we suggest and study context-normalized and time-dependent measures for a topic's importance based on page-view time series of Wikipedia articles in different languages and articles related to them by internal links. As an example, we present a study of the recently emerging Big Data market with a focus on the Hadoop ecosystem, and compare the capabilities of Wikipedia versus Google in predicting its popularity and life cycles. To support further applications, we have developed an open web platform to share results of Wikipedia analytics, providing context-rich and language-independent relevance measures for emerging trends.

The Detection of Emerging Trends Using Wikipedia Traffic Data and Context Networks

PubMed Central

Kämpf, Mirko; Tessenow, Eric; Kenett, Dror Y.; Kantelhardt, Jan W.

2015-01-01

Can online media predict new and emerging trends, since there is a relationship between trends in society and their representation in online systems? While several recent studies have used Google Trends as the leading online information source to answer corresponding research questions, we focus on the online encyclopedia Wikipedia often used for deeper topical reading. Wikipedia grants open access to all traffic data and provides lots of additional (semantic) information in a context network besides single keywords. Specifically, we suggest and study context-normalized and time-dependent measures for a topic’s importance based on page-view time series of Wikipedia articles in different languages and articles related to them by internal links. As an example, we present a study of the recently emerging Big Data market with a focus on the Hadoop ecosystem, and compare the capabilities of Wikipedia versus Google in predicting its popularity and life cycles. To support further applications, we have developed an open web platform to share results of Wikipedia analytics, providing context-rich and language-independent relevance measures for emerging trends. PMID:26720074

Underlying Skills of Oral and Silent Reading Fluency in Chinese: Perspective of Visual Rapid Processing

PubMed Central

Zhao, Jing; Kwok, Rosa K. W.; Liu, Menglian; Liu, Hanlong; Huang, Chen

2017-01-01

Reading fluency is a critical skill to improve the quality of our daily life and working efficiency. The majority of previous studies focused on oral reading fluency rather than silent reading fluency, which is a much more dominant reading mode that is used in middle and high school and for leisure reading. It is still unclear whether the oral and silent reading fluency involved the same underlying skills. To address this issue, the present study examined the relationship between the visual rapid processing and Chinese reading fluency in different modes. Fifty-eight undergraduate students took part in the experiment. The phantom contour paradigm and the visual 1-back task were adopted to measure the visual rapid temporal and simultaneous processing respectively. These two tasks reflected the temporal and spatial dimensions of visual rapid processing separately. We recorded the temporal threshold in the phantom contour task, as well as reaction time and accuracy in the visual 1-back task. Reading fluency was measured in both single-character and sentence levels. Fluent reading of single characters was assessed with a paper-and-pencil lexical decision task, and a sentence verification task was developed to examine reading fluency on a sentence level. The reading fluency test in each level was conducted twice (i.e., oral reading and silent reading). Reading speed and accuracy were recorded. The correlation analysis showed that the temporal threshold in the phantom contour task did not correlate with the scores of the reading fluency tests. Although, the reaction time in visual 1-back task correlated with the reading speed of both oral and silent reading fluency, the comparison of the correlation coefficients revealed a closer relationship between the visual rapid simultaneous processing and silent reading. Furthermore, the visual rapid simultaneous processing exhibited a significant contribution to reading fluency in silent mode but not in oral reading mode. These findings suggest that the underlying mechanism between oral and silent reading fluency is different at the beginning of the basic visual coding. The current results also might reveal a potential modulation of the language characteristics of Chinese on the relationship between visual rapid processing and reading fluency. PMID:28119663

Underlying Skills of Oral and Silent Reading Fluency in Chinese: Perspective of Visual Rapid Processing.

PubMed

Zhao, Jing; Kwok, Rosa K W; Liu, Menglian; Liu, Hanlong; Huang, Chen

2016-01-01

Reading fluency is a critical skill to improve the quality of our daily life and working efficiency. The majority of previous studies focused on oral reading fluency rather than silent reading fluency, which is a much more dominant reading mode that is used in middle and high school and for leisure reading. It is still unclear whether the oral and silent reading fluency involved the same underlying skills. To address this issue, the present study examined the relationship between the visual rapid processing and Chinese reading fluency in different modes. Fifty-eight undergraduate students took part in the experiment. The phantom contour paradigm and the visual 1-back task were adopted to measure the visual rapid temporal and simultaneous processing respectively. These two tasks reflected the temporal and spatial dimensions of visual rapid processing separately. We recorded the temporal threshold in the phantom contour task, as well as reaction time and accuracy in the visual 1-back task. Reading fluency was measured in both single-character and sentence levels. Fluent reading of single characters was assessed with a paper-and-pencil lexical decision task, and a sentence verification task was developed to examine reading fluency on a sentence level. The reading fluency test in each level was conducted twice (i.e., oral reading and silent reading). Reading speed and accuracy were recorded. The correlation analysis showed that the temporal threshold in the phantom contour task did not correlate with the scores of the reading fluency tests. Although, the reaction time in visual 1-back task correlated with the reading speed of both oral and silent reading fluency, the comparison of the correlation coefficients revealed a closer relationship between the visual rapid simultaneous processing and silent reading. Furthermore, the visual rapid simultaneous processing exhibited a significant contribution to reading fluency in silent mode but not in oral reading mode. These findings suggest that the underlying mechanism between oral and silent reading fluency is different at the beginning of the basic visual coding. The current results also might reveal a potential modulation of the language characteristics of Chinese on the relationship between visual rapid processing and reading fluency.

Assembly and diploid architecture of an individual human genome via single-molecule technologies

PubMed Central

Pendleton, Matthew; Sebra, Robert; Pang, Andy Wing Chun; Ummat, Ajay; Franzen, Oscar; Rausch, Tobias; Stütz, Adrian M; Stedman, William; Anantharaman, Thomas; Hastie, Alex; Dai, Heng; Fritz, Markus Hsi-Yang; Cao, Han; Cohain, Ariella; Deikus, Gintaras; Durrett, Russell E; Blanchard, Scott C; Altman, Roger; Chin, Chen-Shan; Guo, Yan; Paxinos, Ellen E; Korbel, Jan O; Darnell, Robert B; McCombie, W Richard; Kwok, Pui-Yan; Mason, Christopher E; Schadt, Eric E; Bashir, Ali

2015-01-01

We present the first comprehensive analysis of a diploid human genome that combines single-molecule sequencing with single-molecule genome maps. Our hybrid assembly markedly improves upon the contiguity observed from traditional shotgun sequencing approaches, with scaffold N50 values approaching 30 Mb, and we identified complex structural variants (SVs) missed by other high-throughput approaches. Furthermore, by combining Illumina short-read data with long reads, we phased both single-nucleotide variants and SVs, generating haplotypes with over 99% consistency with previous trio-based studies. Our work shows that it is now possible to integrate single-molecule and high-throughput sequence data to generate de novo assembled genomes that approach reference quality. PMID:26121404

Assembly and diploid architecture of an individual human genome via single-molecule technologies.

PubMed

Pendleton, Matthew; Sebra, Robert; Pang, Andy Wing Chun; Ummat, Ajay; Franzen, Oscar; Rausch, Tobias; Stütz, Adrian M; Stedman, William; Anantharaman, Thomas; Hastie, Alex; Dai, Heng; Fritz, Markus Hsi-Yang; Cao, Han; Cohain, Ariella; Deikus, Gintaras; Durrett, Russell E; Blanchard, Scott C; Altman, Roger; Chin, Chen-Shan; Guo, Yan; Paxinos, Ellen E; Korbel, Jan O; Darnell, Robert B; McCombie, W Richard; Kwok, Pui-Yan; Mason, Christopher E; Schadt, Eric E; Bashir, Ali

2015-08-01

We present the first comprehensive analysis of a diploid human genome that combines single-molecule sequencing with single-molecule genome maps. Our hybrid assembly markedly improves upon the contiguity observed from traditional shotgun sequencing approaches, with scaffold N50 values approaching 30 Mb, and we identified complex structural variants (SVs) missed by other high-throughput approaches. Furthermore, by combining Illumina short-read data with long reads, we phased both single-nucleotide variants and SVs, generating haplotypes with over 99% consistency with previous trio-based studies. Our work shows that it is now possible to integrate single-molecule and high-throughput sequence data to generate de novo assembled genomes that approach reference quality.

78 FR 46333 - Product Cancellation Order for Certain Pesticide Registrations; Correction

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-31

... 20460-0001. The Public Reading Room is open from 8:30 a.m. to 4:30 p.m., Monday through Friday, excluding legal holidays. The telephone number for the Public Reading Room is (202) 566-1744, and the telephone number for the OPP Docket is (703) 305-5805. Please review the visitor instructions and additional...

77 FR 47351 - Notification of Submission to the Secretaries of Agriculture and Health and Human Services...

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78 FR 72879 - Product Cancellation Order for Certain Pesticide Registrations; Correction

Federal Register 2010, 2011, 2012, 2013, 2014

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..., DC 20460-0001. The Public Reading Room is open from 8:30 a.m. to 4:30 p.m., Monday through Friday, excluding legal holidays. The telephone number for the Public Reading Room is (202) 566-1744, and the telephone number for the OPP Docket is (703) 305- 5805. Please review the visitor instructions and...

Analyzing "Inconsistencies" in Practice: Teachers' Continued Use of Round Robin Reading

ERIC Educational Resources Information Center

Ash, Gwynne Ellen; Kuhn, Melanie R.; Walpole, Sharon

2009-01-01

This study analyzed in-service teachers' and literacy coaches' perceptions of Round Robin Reading to begin developing an understanding of the persistence of this practice in public schools in the United States. Surveying 80 teachers and 27 literacy coaches using an open-ended instrument, we found that many teachers continued to use Round Robin…

Dorothy Day: A Love of Fiction and Her Love of the Poor

ERIC Educational Resources Information Center

Brady, Judith Ann

2010-01-01

Dorothy Day's love of the poor originated from reading novels that portrayed the poor as persons worthy of respect. This article explores how Day's reading novels opened her mind and heart to the realities of poverty. The methodology is literature-based. Dorothy Day's autobiography reveals the novelists who captivated her mind and cultivated a…

Influence of Acculturation on Parents' Readings of and Expectations for Physical Education

ERIC Educational Resources Information Center

George, Meredith; Cutner-Smith, Matthew D.

2018-01-01

Purpose: The purpose of this study was to examine the influence of acculturation on parents' readings of and expectations for physical education. Method: Participants were 39 parents of pupils enrolled at one public middle school. Data were collected with an open-ended questionnaire and follow-up formal interviews. They were analyzed using…

75 FR 70241 - Compatibility of Underground Storage Tank Systems With Biofuel Blends

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2010-11-17

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Open-Trial Pilot of "Mind Reading" and in Vivo Rehearsal for Children with HFASD

ERIC Educational Resources Information Center

Thomeer, Marcus L.; Rodgers, Jonathan D.; Lopata, Christopher; McDonald, Christin A.; Volker, Martin A.; Toomey, Jennifer A.; Smith, Rachael A.; Gullo, Gaetano

2011-01-01

In this pilot study, the authors evaluated a manualized administration of the "Mind Reading" (MR) program with in vivo rehearsal to determine the effects on emotion recognition and autism features of eleven 7- to 12-year-old children with High-Functioning Autism Spectrum Disorders (HFASD), and to determine the overall feasibility of the…

36 CFR § 703.7 - Public Reading Facility.

Code of Federal Regulations, 2013 CFR

2013-07-01

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2012-02-08

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49 CFR 325.59 - Measurement procedure; stationary test.

Code of Federal Regulations, 2011 CFR

2011-10-01

... made of the sound level generated by a stationary motor vehicle as follows: (a) Park the motor vehicle... open throttle. Return the engine's speed to idle. (e) Observe the maximum reading on the sound level... this section until the first two maximum sound level readings that are within 2 dB(A) of each other are...

77 FR 13977 - Quality Assurance Requirements for Continuous Opacity Monitoring Systems at Stationary Sources

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Identification of Methyl Halide-Utilizing Genes in the Methyl Bromide-Utilizing Bacterial Strain IMB-1 Suggests a High Degree of Conservation of Methyl Halide-Specific Genes in Gram-Negative Bacteria

USGS Publications Warehouse

Woodall, C.A.; Warner, K.L.; Oremland, R.S.; Murrell, J.C.; McDonald, I.R.

2001-01-01

Strain IMB-1, an aerobic methylotrophic member of the alpha subgroup of the Proteobacteria, can grow with methyl bromide as a sole carbon and energy source. A single cmu gene cluster was identified in IMB-1 that contained six open reading frames: cmuC, cmuA, orf146, paaE, hutI, and partial metF. CmuA from IMB-1 has high sequence homology to the methyltransferase CmuA from Methylobacterium chloromethanicum and Hyphomicrobium chloromethanicum and contains a C-terminal corrinoid-binding motif and an N-terminal methyl-transferase motif. However, cmuB, identified in M. chloromethanicum and H. chloromethanicum, was not detected in IMB-1.

Quetzal: a transposon of the Tc1 family in the mosquito Anopheles albimanus.

PubMed

Ke, Z; Grossman, G L; Cornel, A J; Collins, F H

1996-10-01

A member of the Tc1 family of transposable elements has been identified in the Central and South American mosquito Anopheles albimanus. The full-length Quetzal element is 1680 base pairs (bp) in length, possesses 236 bp inverted terminal repeats (ITRs), and has a single open reading frame (ORF) with the potential of encoding a 341-amino-acid (aa) protein that is similar to the transposases of other members of the Tc1 family, particularly elements described from three different Drosophila species. The approximately 10-12 copies per genome of Quetzal are found in the euchromatin of all three chromosomes of A. albimanus. One full-length clone, Que27, appears capable of encoding a complete transposase and may represent a functional copy of this element.

First complete genome sequence of vanilla mosaic strain of Dasheen mosaic virus isolated from the Cook Islands.

PubMed

Puli'uvea, Christopher; Khan, Subuhi; Chang, Wee-Leong; Valmonte, Gardette; Pearson, Michael N; Higgins, Colleen M

2017-02-01

We present the first complete genome of vanilla mosaic virus (VanMV). The VanMV genomic structure is consistent with that of a potyvirus, containing a single open reading frame (ORF) encoding a polyprotein of 3139 amino acids. Motif analyses indicate the polyprotein can be cleaved into the expected ten individual proteins; other recognised potyvirus motifs are also present. As expected, the VanMV genome shows high sequence similarity to the published Dasheen mosaic virus (DsMV) genome sequences; comparisons with DsMV continue to support VanMV as a vanilla infecting strain of DsMV. Phylogenetic analyses indicate that VanMV and DsMV share a common ancestor, with VanMV having the closest relationship with DsMV strains from the South Pacific.

Illustrations and supporting texts for sound standing waves of air columns in pipes in introductory physics textbooks

NASA Astrophysics Data System (ADS)

Zeng, Liang; Smith, Chris; Poelzer, G. Herold; Rodriguez, Jennifer; Corpuz, Edgar; Yanev, George

2014-12-01

In our pilot studies, we found that many introductory physics textbook illustrations with supporting text for sound standing waves of air columns in open-open, open-closed, and closed-closed pipes inhibit student understanding of sound standing wave phenomena due to student misunderstanding of how air molecules move within these pipes. Based on the construct of meaningful learning from cognitive psychology and semiotics, a quasiexperimental study was conducted to investigate the comparative effectiveness of two alternative approaches to student understanding: a traditional textbook illustration approach versus a newly designed air molecule motion illustration approach. Thirty volunteer students from introductory physics classes were randomly assigned to two groups of 15 each. Both groups were administered a presurvey. Then, group A read the air molecule motion illustration handout, and group B read a traditional textbook illustration handout; both groups were administered postsurveys. Subsequently, the procedure was reversed: group B read the air molecule motion illustration handout and group A read the traditional textbook illustration handout. This was followed by a second postsurvey along with an exit research questionnaire. The study found that the majority of students experienced meaningful learning and stated that they understood sound standing wave phenomena significantly better using the air molecule motion illustration approach. This finding provides a method for physics education researchers to design illustrations for abstract sound standing wave concepts, for publishers to improve their illustrations with supporting text, and for instructors to facilitate deeper learning in their students on sound standing waves.

32 CFR 1285.2 - Policy.

Code of Federal Regulations, 2011 CFR

2011-07-01

... information concerning the activities of its Government. DLA policy is to conduct its activities in an open... activities in an open manner consistent with the need for security and adherence to other requirements of law..., where a public reading room also serves as an activity's library, restricted publications may be...

32 CFR 1285.2 - Policy.

Code of Federal Regulations, 2010 CFR

2010-07-01

... information concerning the activities of its Government. DLA policy is to conduct its activities in an open... activities in an open manner consistent with the need for security and adherence to other requirements of law..., where a public reading room also serves as an activity's library, restricted publications may be...

An Analysis of the Impact of Single-Sex Schools on Seventh Grade Math and Reading Tasks Scores

ERIC Educational Resources Information Center

Groves-Redwood, Tarawa F.

2012-01-01

The purpose of this study was to determine if there is a statistically significant mean difference in math and reading student performance by types of schools. The types of schools were identified as all-male and all-female public middle schools. Specifically, this study examined the impact of public single-sex schools on the mathematics and…

Acquisition of Maternal Education and Its Relation to Single-Word Reading in Middle Childhood: An Analysis of the Millennium Cohort Study

ERIC Educational Resources Information Center

King, Thomas; McKean, Cristina; Rush, Robert; Westrupp, Elizabeth M.; Mensah, Fiona K.; Reilly, Sheena; Law, James

2017-01-01

Maternal education captured at a single time point is commonly employed as a predictor of a child's cognitive development. In this article, we ask what bearing the acquisition of additional qualifications has upon reading performance in middle childhood. This was a secondary analysis of the United Kingdom's Millennium Cohort Study, a cohort of…

The Influence of Visual Word Form in Reading: Single Case Study of an Arabic Patient with Deep Dyslexia

ERIC Educational Resources Information Center

Boumaraf, Assia; Macoir, Joël

2016-01-01

Deep dyslexia is a written language disorder characterized by poor reading of non-words, and advantage for concrete over abstract words with production of semantic, visual and morphological errors. In this single case study of an Arabic patient with input deep dyslexia, we investigated the impact of graphic features of Arabic on manifestations of…

A Comparison of Students in Single-Sex Classes and Coeducational Classes in High Poverty Public Elementary Schools in Mathematics and Reading Achievement

ERIC Educational Resources Information Center

Aldridge, Ashley Elizabeth

2009-01-01

The purpose of this study was to investigate whether any statistically significant differences in mathematics and reading academic achievement and academic gains of male and female students taught in single-sex classes existed when compared to male and female students taught in coeducational classes. This study reported findings from mathematics…

Making Higher Education More Affordable, One Course Reading at a Time: Academic Libraries as Key Advocates for Open Access Textbooks and Educational Resources

ERIC Educational Resources Information Center

Okamoto, Karen

2013-01-01

Open access textbooks (OATs) and educational resources (OERs) are being lauded as a viable alternative to costly print textbooks. Some academic libraries are joining the OER movement by creating guides to open repositories. Others are promoting OATs and OERs, reviewing them, and even helping to create them. This article analyzes how academic…

A dual V t disturb-free subthreshold SRAM with write-assist and read isolation

NASA Astrophysics Data System (ADS)

Bhatnagar, Vipul; Kumar, Pradeep; Pandey, Neeta; Pandey, Sujata

2018-02-01

This paper presents a new dual V t 8T SRAM cell having single bit-line read and write, in addition to Write Assist and Read Isolation (WARI). Also a faster write back scheme is proposed for the half selected cells. A high V t device is used for interrupting the supply to one of the inverters for weakening the feedback loop for assisted write. The proposed cell provides an improved read static noise margin (RSNM) due to the bit-line isolation during the read. Static noise margins for data read (RSNM), write (WSNM), read delay, write delay, data retention voltage (DRV), leakage and average powers have been calculated. The proposed cell was found to operate properly at a supply voltage as small as 0.41 V. A new write back scheme has been suggested for half-selected cells, which uses a single NMOS access device and provides reduced delay, pulse timing hardware requirements and power consumption. The proposed new WARI 8T cell shows better performance in terms of easier write, improved read noise margin, reduced leakage power, and less delay as compared to the existing schemes that have been available so far. It was also observed that with proper adjustment of the cell ratio the supply voltage can further be reduced to 0.2 V.

De novo assembly and phasing of a Korean human genome.

PubMed

Seo, Jeong-Sun; Rhie, Arang; Kim, Junsoo; Lee, Sangjin; Sohn, Min-Hwan; Kim, Chang-Uk; Hastie, Alex; Cao, Han; Yun, Ji-Young; Kim, Jihye; Kuk, Junho; Park, Gun Hwa; Kim, Juhyeok; Ryu, Hanna; Kim, Jongbum; Roh, Mira; Baek, Jeonghun; Hunkapiller, Michael W; Korlach, Jonas; Shin, Jong-Yeon; Kim, Changhoon

2016-10-13

Advances in genome assembly and phasing provide an opportunity to investigate the diploid architecture of the human genome and reveal the full range of structural variation across population groups. Here we report the de novo assembly and haplotype phasing of the Korean individual AK1 (ref. 1) using single-molecule real-time sequencing, next-generation mapping, microfluidics-based linked reads, and bacterial artificial chromosome (BAC) sequencing approaches. Single-molecule sequencing coupled with next-generation mapping generated a highly contiguous assembly, with a contig N50 size of 17.9 Mb and a scaffold N50 size of 44.8 Mb, resolving 8 chromosomal arms into single scaffolds. The de novo assembly, along with local assemblies and spanning long reads, closes 105 and extends into 72 out of 190 euchromatic gaps in the reference genome, adding 1.03 Mb of previously intractable sequence. High concordance between the assembly and paired-end sequences from 62,758 BAC clones provides strong support for the robustness of the assembly. We identify 18,210 structural variants by direct comparison of the assembly with the human reference, identifying thousands of breakpoints that, to our knowledge, have not been reported before. Many of the insertions are reflected in the transcriptome and are shared across the Asian population. We performed haplotype phasing of the assembly with short reads, long reads and linked reads from whole-genome sequencing and with short reads from 31,719 BAC clones, thereby achieving phased blocks with an N50 size of 11.6 Mb. Haplotigs assembled from single-molecule real-time reads assigned to haplotypes on phased blocks covered 89% of genes. The haplotigs accurately characterized the hypervariable major histocompatability complex region as well as demonstrating allele configuration in clinically relevant genes such as CYP2D6. This work presents the most contiguous diploid human genome assembly so far, with extensive investigation of unreported and Asian-specific structural variants, and high-quality haplotyping of clinically relevant alleles for precision medicine.

Precision of Curriculum-Based Measurement Reading Data: Considerations for Multiple-Baseline Designs

ERIC Educational Resources Information Center

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

2017-01-01

Single-case designs provide an established technology for evaluating the effects of academic interventions. Researchers interested in studying the long-term effects of reading interventions often use curriculum-based measures of reading (CBM-R) as they possess many of the desirable characteristics for use in a time-series design. The reliability…

A Modified Dialogic Reading Intervention for Preschool Children with Autism Spectrum Disorder

ERIC Educational Resources Information Center

Fleury, Veronica P.; Schwartz, Ilene S.

2017-01-01

We examined the effect of a modified dialogic reading intervention on levels of verbal participation and vocabulary growth in nine preschool children with autism spectrum disorder (ASD) using single-case design methodology. Baseline book reading resulted in consistently low levels of verbal participation followed by an immediate increase in verbal…

Is There a Vertical Component to Saccade Targeting in Chinese Reading?

ERIC Educational Resources Information Center

Zang, Chuanli; Meng, Hongxia; Liang, Feifei; Bai, Xuejun; Yan, Guoli

2013-01-01

In this study, we examined whether Chinese character structure influenced readers' saccadic targeting in Chinese reading. Readers' eye movements were recorded when they read single sentences containing one-character or two-character target words. Both the one-character words and the two constituent characters of two-character words either had a…

Reading Ability and the Utilization of Orthographic Structure in Reading. Technical Report No. 515.

ERIC Educational Resources Information Center

Massaro, Dominic W.; Taylor, Glen A.

Previous research has demonstrated that readers utilize orthographic structure in their perceptual recognition of letter strings. Two experiments were conducted to assess whether this utilization varied with reading ability. Anagrams of words were made to create strings that orthogonally combined high and low single letter positional frequency and…

Multiple Mediation Analysis of the Relationship between Rapid Naming and Reading

ERIC Educational Resources Information Center

Poulsen, Mads; Juul, Holger; Elbro, Carsten

2015-01-01

It is well established that rapid automatised naming (RAN) correlates with reading ability. Despite several attempts, no single component process (mediator) has been identified that fully accounts for the correlation. The present paper estimated the explanatory value of several mediators for the RAN--reading correlation. One hundred and sixty-nine…

Repeated Reading, Turn Taking, and Augmentative and Alternative Communication (AAC)

ERIC Educational Resources Information Center

Edmister, Evette; Wegner, Jane

2015-01-01

This single participant multiple baseline research design measured the effects of repeatedly reading narrative books to children who used voice output augmentative communication devices to communicate. The study sought to determine if there was a difference observed in the number of turns taken when reading stories repeatedly. Three girls ranging…

Single Photon Counting Performance and Noise Analysis of CMOS SPAD-Based Image Sensors.

PubMed

Dutton, Neale A W; Gyongy, Istvan; Parmesan, Luca; Henderson, Robert K

2016-07-20

SPAD-based solid state CMOS image sensors utilising analogue integrators have attained deep sub-electron read noise (DSERN) permitting single photon counting (SPC) imaging. A new method is proposed to determine the read noise in DSERN image sensors by evaluating the peak separation and width (PSW) of single photon peaks in a photon counting histogram (PCH). The technique is used to identify and analyse cumulative noise in analogue integrating SPC SPAD-based pixels. The DSERN of our SPAD image sensor is exploited to confirm recent multi-photon threshold quanta image sensor (QIS) theory. Finally, various single and multiple photon spatio-temporal oversampling techniques are reviewed.

Conditional Dispersive Readout of a CMOS Single-Electron Memory Cell

NASA Astrophysics Data System (ADS)

Schaal, S.; Barraud, S.; Morton, J. J. L.; Gonzalez-Zalba, M. F.

2018-05-01

Quantum computers require interfaces with classical electronics for efficient qubit control, measurement, and fast data processing. Fabricating the qubit and the classical control layer using the same technology is appealing because it will facilitate the integration process, improving feedback speeds and offering potential solutions to wiring and layout challenges. Integrating classical and quantum devices monolithically, using complementary metal-oxide-semiconductor (CMOS) processes, enables the processor to profit from the most mature industrial technology for the fabrication of large-scale circuits. We demonstrate a CMOS single-electron memory cell composed of a single quantum dot and a transistor that locks charge on the quantum-dot gate. The single-electron memory cell is conditionally read out by gate-based dispersive sensing using a lumped-element L C resonator. The control field-effect transistor (FET) and quantum dot are fabricated on the same chip using fully depleted silicon-on-insulator technology. We obtain a charge sensitivity of δ q =95 ×10-6e Hz-1 /2 when the quantum-dot readout is enabled by the control FET, comparable to results without the control FET. Additionally, we observe a single-electron retention time on the order of a second when storing a single-electron charge on the quantum dot at millikelvin temperatures. These results demonstrate first steps towards time-based multiplexing of gate-based dispersive readout in CMOS quantum devices opening the path for the development of an all-silicon quantum-classical processor.

Student Perceptions of College Faculty Who Use OER

ERIC Educational Resources Information Center

Vojtech, Gabrielle; Grissett, Judy

2017-01-01

Research indicates that students find open educational resources (OER) favorable, but there is no research regarding students' perceptions of faculty who use open textbooks. In the present study we examined this topic experimentally with two undergraduate psychology courses at a small public university. Participants read two passages--one about an…

A method to compute SEU fault probabilities in memory arrays with error correction

NASA Technical Reports Server (NTRS)

Gercek, Gokhan

1994-01-01

With the increasing packing densities in VLSI technology, Single Event Upsets (SEU) due to cosmic radiations are becoming more of a critical issue in the design of space avionics systems. In this paper, a method is introduced to compute the fault (mishap) probability for a computer memory of size M words. It is assumed that a Hamming code is used for each word to provide single error correction. It is also assumed that every time a memory location is read, single errors are corrected. Memory is read randomly whose distribution is assumed to be known. In such a scenario, a mishap is defined as two SEU's corrupting the same memory location prior to a read. The paper introduces a method to compute the overall mishap probability for the entire memory for a mission duration of T hours.

Reading Speed Does Not Benefit from Increased Line Spacing in AMD Patients

PubMed Central

CHUNG, SUSANA T. L.; JARVIS, SAMUEL H.; WOO, STANLEY Y.; HANSON, KARA; JOSE, RANDALL T.

2009-01-01

Purpose Crowding, the adverse spatial interaction due to the proximity of adjacent targets, has been suggested as an explanation for slow reading in peripheral vision. Previously, we showed that increased line spacing, which presumably reduces crowding between adjacent lines of text, improved reading speed in the normal periphery (Chung, Optom Vis Sci 2004;81:525–35). The purpose of this study was to examine whether or not individuals with age-related macular degeneration (AMD) would benefit from increased line spacing for reading. Methods Experiment 1: Eight subjects with AMD read aloud 100-word passages rendered at five line spacings: the standard single spacing, 1.5×, 2×, 3×, and 4× the standard spacing. Print sizes were 1× and 2× of the critical print size. Reading time and number of reading errors for each passage were measured to compute the reading speed. Experiment 2: Four subjects with AMD read aloud sequences of six 4-letter words, presented on a computer monitor using the rapid serial visual presentation (RSVP) paradigm. Target words were presented singly, or flanked above and below by two other words that changed in synchrony with the target word, at various vertical word separations. Print size was 2× the critical print size. Reading speed was calculated based on the RSVP exposure duration that yielded 80% of the words read correctly. Results Averaged across subjects, reading speeds for passages were virtually constant for the range of line spacings tested. For sequences of unrelated words, reading speeds were also virtually constant for the range of vertical word separations tested, except at the smallest (standard) separation at which reading speed was lower. Conclusions Contrary to the previous finding that reading speed improved in normal peripheral vision, increased line spacing in passages, or increased vertical separation between words in RSVP, did not lead to improved reading speed in people with AMD. PMID:18772718

Development open source microcontroller based temperature data logger

NASA Astrophysics Data System (ADS)

Abdullah, M. H.; Che Ghani, S. A.; Zaulkafilai, Z.; Tajuddin, S. N.

2017-10-01

This article discusses the development stages in designing, prototyping, testing and deploying a portable open source microcontroller based temperature data logger for use in rough industrial environment. The 5V powered prototype of data logger is equipped with open source Arduino microcontroller for integrating multiple thermocouple sensors with their module, secure digital (SD) card storage, liquid crystal display (LCD), real time clock and electronic enclosure made of acrylic. The program for the function of the datalogger is programmed so that 8 readings from the thermocouples can be acquired within 3 s interval and displayed on the LCD simultaneously. The recorded temperature readings at four different points on both hydrodistillation show similar profile pattern and highest yield of extracted oil was achieved on hydrodistillation 2 at 0.004%. From the obtained results, this study achieved the objective of developing an inexpensive, portable and robust eight channels temperature measuring module with capabilities to monitor and store real time data.

Short-Term Flooding Effects on Gas Exchange and Quantum Yield of Rabbiteye Blueberry (Vaccinium ashei Reade) 1

PubMed Central

Davies, Frederick S.; Flore, James A.

1986-01-01

Roots of 1.5-year-old `Woodard' rabbiteye blueberry plants (Vaccinium ashei Reade) were flooded in containers or maintained at container capacity over a 5-day period. Carbon assimilation, and stomatal and residual conductances were monitored on one fully expanded shoot/plant using an open flow gas analysis system. Quantum yield was calculated from light response curves. Carbon assimilation and quantum yield of flooded plants decreased to 64 and 41% of control values, respectively, after 1 day of flooding and continued decreasing to 38 and 27% after 4 days. Stomatal and residual conductances to CO2 also decreased after 1 day of flooding compared with those of unflooded plants with residual conductance severely limiting carbon assimilation after 4 days of flooding. Stomatal opening occurred in 75 to 90 minutes and rate of opening was unaffected by flooding. PMID:16664791

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

PubMed Central

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

2016-01-01

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

Single-Event Effect Performance of a Conductive-Bridge Memory EEPROM

NASA Technical Reports Server (NTRS)

Chen, Dakai; Wilcox, Edward; Berg, Melanie; Kim, Hak; Phan, Anthony; Figueiredo, Marco; Seidleck, Christina; LaBel, Kenneth

2015-01-01

We investigated the heavy ion single-event effect (SEE) susceptibility of the industry’s first stand-alone memory based on conductive-bridge memory (CBRAM) technology. The device is available as an electrically erasable programmable read-only memory (EEPROM). We found that single-event functional interrupt (SEFI) is the dominant SEE type for each operational mode (standby, dynamic read, and dynamic write/read). SEFIs occurred even while the device is statically biased in standby mode. Worst case SEFIs resulted in errors that filled the entire memory space. Power cycle did not always clear the errors. Thus the corrupted cells had to be reprogrammed in some cases. The device is also vulnerable to bit upsets during dynamic write/read tests, although the frequency of the upsets are relatively low. The linear energy transfer threshold for cell upset is between 10 and 20 megaelectron volts per square centimeter per milligram, with an upper limit cross section of 1.6 times 10(sup -11) square centimeters per bit (95 percent confidence level) at 10 megaelectronvolts per square centimeter per milligram. In standby mode, the CBRAM array appears invulnerable to bit upsets.

WWC Review of the Report "Evaluation of the i3 Scale-up of Reading Recovery Year One Report, 2011-12." What Works Clearinghouse Single Study Review

ERIC Educational Resources Information Center

What Works Clearinghouse, 2014

2014-01-01

For the 2013 study, "Evaluation of the i3 Scale-up of Reading Recovery Year One Report, 2011-12," researchers examined the Year 1 impacts of the Investing in Innovation (i3) scale-up of "Reading Recovery"®, a short-term intervention for struggling readers, on the reading achievement of first-grade students. The analytic sample…

75 FR 54338 - Agency Information Collection Activities: Submission to OMB for Review and Approval; State Review...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-07

....gov : (our preferred method) Follow the on-line instructions for submitting comments. E-mail..., DC. The EPA Docket Center Public Reading Room is open from 8:30 a.m. to 4:30 p.m., Monday through Friday, excluding legal holidays. The telephone number for the Reading Room is (202) 566-1744, and the...

Examining Central Issues in Literacy Research, Theory, and Practice. Forty-Second Yearbook of the National Reading Conference.

ERIC Educational Resources Information Center

Leu, Donald J., Ed.; Kinzer, Charles K., Ed.

The 43 conference papers in this yearbook cover such diverse topics in the field of reading as the analysis of children's literacy responses, the study of aesthetic literacy, and the investigation of phonemic awareness. The yearbook includes both data-driven studies and conceptual explorations of diverse literacy learners. The yearbook opens with…

75 FR 36650 - Agency Information Collection Activities: Proposed Collection; Comment Request; Recordkeeping...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-28

... Reading Room is open from 8 a.m. to 4:30 p.m., Monday through Friday, excluding legal holidays. The telephone number for the Reading Room is (202) 566-1744, and the telephone number for the Enforcement and... copying as specified in the statute. The regulations at 40 CFR part 169 (Books and Records of Pesticide...

Excitement, Adventure, Indifference: Romance Readers' Perceptions of How Romance Reading Impacts Their Sex Lives

ERIC Educational Resources Information Center

Anderton, Gretchen E.

2009-01-01

This mixed-methods study examined romance readers' perceptions of how reading romance novels has impacted their sex lives, feelings about their sex partners, knowledge of sexuality and their sexual behavior. Fifty-three women romance readers over the age of 18 completed an online survey composed of multiple choice and open-ended essay questions. …

Monster Magic: A Reading Activities Idea Book for Use with Children. A Fun with Reading Book.

ERIC Educational Resources Information Center

Fowler, Zinita

Intended as a usable resource for librarians and teachers in planning and implementing a program for young library users and students, this book was developed to stimulate children to use the library. The introduction contains opening comments--including an explanation of how the theme of "monster magic" inspires creativity, specific goals, and a…

75 FR 13715 - Endangered and Threatened Wildlife and Plants; Revised Designation of Critical Habitat for Bull...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-23

... 1973, as amended. In total, approximately 36,498 kilometers (km) (22,679 miles (mi)) of streams (which... box that reads ``Enter Keyword or ID,'' enter the docket number for the proposed rule, which is FWS-R1-ES-2009-0085. Check the box that reads ``Open for Comment/Submission,'' and then click the Search...

On the Use of the Immediate Recall Task as a Measure of Second Language Reading Comprehension

ERIC Educational Resources Information Center

Chang, Yuh-Fang

2006-01-01

The immediate written recall task, a widely used measure of both first language (L1) and second language (L2) reading comprehension, has been advocated over traditional test methods such as multiple choice, cloze tests and open-ended questions because it is a direct and integrative assessment task. It has been, however, criticized as requiring…

Characterization of the 5’- and 3’-terminal subgenomic RNAs produced by a capillovirus: evidence for a CP subgenomic RNA

USDA-ARS?s Scientific Manuscript database

The members of Capillovirus genus encode two overlapping open reading frames (ORFs): ORF1 encodes a large polyprotein containing the domains of replication-associated proteins plus a coat protein (CP), and ORF2 encodes a movement protein, located within ORF1 in a different reading frame. Organizatio...

77 FR 13997 - Quality Assurance Requirements for Continuous Opacity Monitoring Systems at Stationary Sources

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-08

... comments. Email: [email protected] . Fax: (202) 566-9744. Mail: Attention Docket ID No. EPA-HQ-OAR...., Washington, DC. The Docket Facility and Public Reading Room are open from 8:30 a.m. to 4:30 p.m., Monday... the telephone number for the Public Reading Room is (202) 566-1744. FOR FURTHER INFORMATION CONTACT...

Visionary leader 2009: Deborah Kumar.

PubMed

Zuppa, Barbara

2010-01-01

The following manuscript is the winning Visionary Leader 2009 entry submitted to Nursing Management in recognition of Deborah Kumar, MSN, RN, NEA-BC, Director, Medical Division, The Reading Hospital and Medical Center, West Reading, Pa. Deborah was formally recognized for her achievements during the opening ceremony of Congress 2009, September 9, in Chicago, Ill. There, she received the award, sponsored this year by B.E. Smith.

Identification of the initiation site of poliovirus polyprotein synthesis

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

Dorner, A.J.; Dorner, L.F.; Larsen, G.R.

1982-06-01

The complete nucleotide sequence of poliovirus RNA has a long open reading frame capable of encoding the precursor polyprotein NCVPOO. The first AUG codon in this reading frame is located 743 nucleotides from the 5' end of the RNA and is preceded by eight AUG codons in all three reading frames. Because all proteins that map at the amino terminus of the polyprotein (P1-1a, VPO, and VP4) are blocked at their amino termini and previous studies of ribosome binding have been inconclusive, direct identification of the initiation site of protein synthesis was difficult. We separated and identified all of themore » tryptic peptides of capsid protein VP4 and correlated these peptides with the amino acid sequence predicted to follow the AUG codon at nucleotide 743. Our data indicate that VP4 begins with a blocked glycine that is encoded immediately after the AUG codon at nucleotide 743. An S1 nuclease analysis of poliovirus mRNA failed to reveal a splice in the 5' region. We concluded that synthesis of poliovirus polyprotein is initiated at nucleotide 743, the first AUG codon in the long open reading frame.« less

Agreement and reading time for differently-priced devices for the digital capture of X-ray films.

PubMed

Salazar, Antonio José; Camacho, Juan Camilo; Aguirre, Diego Andrés

2012-03-01

We assessed the reliability of three digital capture devices: a film digitizer (which cost US $15,000), a flat-bed scanner (US $1800) and a digital camera (US $450). Reliability was measured as the agreement between six observers when reading images acquired from a single device and also in terms of the pair-device agreement. The images were 136 chest X-ray cases. The variables measured were the interstitial opacities distribution, interstitial patterns, nodule size and percentage pneumothorax size. The agreement between the six readers when reading images acquired from a single device was similar for the three devices. The pair-device agreements were moderate for all variables. There were significant differences in reading-time between devices: the mean reading-time for the film digitizer was 93 s, it was 59 s for the flat-bed scanner and 70 s for the digital camera. Despite the differences in their cost, there were no substantial differences in the performance of the three devices.

An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing.

PubMed

Zimin, Aleksey V; Stevens, Kristian A; Crepeau, Marc W; Puiu, Daniela; Wegrzyn, Jill L; Yorke, James A; Langley, Charles H; Neale, David B; Salzberg, Steven L

2017-01-01

The 22-gigabase genome of loblolly pine (Pinus taeda) is one of the largest ever sequenced. The draft assembly published in 2014 was built entirely from short Illumina reads, with lengths ranging from 100 to 250 base pairs (bp). The assembly was quite fragmented, containing over 11 million contigs whose weighted average (N50) size was 8206 bp. To improve this result, we generated approximately 12-fold coverage in long reads using the Single Molecule Real Time sequencing technology developed at Pacific Biosciences. We assembled the long and short reads together using the MaSuRCA mega-reads assembly algorithm, which produced a substantially better assembly, P. taeda version 2.0. The new assembly has an N50 contig size of 25 361, more than three times as large as achieved in the original assembly, and an N50 scaffold size of 107 821, 61% larger than the previous assembly. © The Author 2017. Published by Oxford University Press.

Erratum to: An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing.

PubMed

Zimin, Aleksey V; Stevens, Kristian A; Crepeau, Marc W; Puiu, Daniela; Wegrzyn, Jill L; Yorke, James A; Langley, Charles H; Neale, David B; Salzberg, Steven L

2017-10-01

The 22-gigabase genome of loblolly pine (Pinus taeda) is one of the largest ever sequenced. The draft assembly published in 2014 was built entirely from short Illumina reads, with lengths ranging from 100 to 250 base pairs (bp). The assembly was quite fragmented, containing over 11 million contigs whose weighted average (N50) size was 8206 bp. To improve this result, we generated approximately 12-fold coverage in long reads using the Single Molecule Real Time sequencing technology developed at Pacific Biosciences. We assembled the long and short reads together using the MaSuRCA mega-reads assembly algorithm, which produced a substantially better assembly, P. taeda version 2.0. The new assembly has an N50 contig size of 25 361, more than three times as large as achieved in the original assembly, and an N50 scaffold size of 107 821, 61% larger than the previous assembly. © The Authors 2017. Published by Oxford University Press.

AN ADA NAMELIST PACKAGE

NASA Technical Reports Server (NTRS)

Klumpp, A. R.

1994-01-01

The Ada Namelist Package, developed for the Ada programming language, enables a calling program to read and write FORTRAN-style namelist files. A namelist file consists of any number of assignment statements in any order. Features of the Ada Namelist Package are: the handling of any combination of user-defined types; the ability to read vectors, matrices, and slices of vectors and matrices; the handling of mismatches between variables in the namelist file and those in the programmed list of namelist variables; and the ability to avoid searching the entire input file for each variable. The principle user benefits of this software are the following: the ability to write namelist-readable files, the ability to detect most file errors in the initialization phase, a package organization that reduces the number of instantiated units to a few packages rather than to many subprograms, a reduced number of restrictions, and an increased execution speed. The Ada Namelist reads data from an input file into variables declared within a user program. It then writes data from the user program to an output file, printer, or display. The input file contains a sequence of assignment statements in arbitrary order. The output is in namelist-readable form. There is a one-to-one correspondence between namelist I/O statements executed in the user program and variables read or written. Nevertheless, in the input file, mismatches are allowed between assignment statements in the file and the namelist read procedure statements in the user program. The Ada Namelist Package itself is non-generic. However, it has a group of nested generic packages following the nongeneric opening portion. The opening portion declares a variety of useraccessible constants, variables and subprograms. The subprograms are procedures for initializing namelists for reading, reading and writing strings. The subprograms are also functions for analyzing the content of the current dataset and diagnosing errors. Two nested generic packages follow the opening portion. The first generic package contains procedures that read and write objects of scalar type. The second contains subprograms that read and write one and two-dimensional arrays whose components are of scalar type and whose indices are of either of the two discrete types (integer or enumeration). Subprograms in the second package also read and write vector and matrix slices. The Ada Namelist ASCII text files are available on a 360k 5.25" floppy disk written on an IBM PC/AT running under the PC DOS operating system. The largest subprogram in the package requires 150k of memory. The package was developed using VAX Ada v. 1.5 under DEC VMS v. 4.5. It should be portable to any validated Ada compiler. The software was developed in 1989, and is a copyrighted work with all copyright vested in NASA.

Reading and deaf individuals: perspectives on the qualitative similarity hypothesis.

PubMed

Wang, Ye; Andrews, Jean

2014-01-01

In this, the first article in the American Annals of the Deaf special issue on English reading development for individuals who are d/Deaf and hard of hearing, the coeditors aim to promote interdisciplinary dialogue among researchers regarding literacy research with d/Deaf and hard of hearing (d/Dhh) students by setting the tone for an open and inclusive forum. Researchers from various disciplines are invited to discuss the similarities and differences between students who are d/Dhh and their typically developing hearing peers in terms of aspects such as reading process, reading development, and reading assessment. Challenges related to the acquisition of language and literacy by d/Dhh students are described. The article highlights the purpose of the special issue, which is to explore what works where, when, why, and for whom.

Initial cloning and sequencing of hydHG, an operon homologous to ntrBC and regulating the labile hydrogenase activity in Escherichia coli K-12.

PubMed Central

Stoker, K; Reijnders, W N; Oltmann, L F; Stouthamer, A H

1989-01-01

To isolate genes from Escherichia coli which regulate the labile hydrogenase activity, a plasmid library was used to transform hydL mutants lacking the labile hydrogenase. A single type of gene, designated hydG, was isolated. This gene also partially restored the hydrogenase activity in hydF mutants (which are defective in all hydrogenase isoenzymes), although the low hydrogenase 1 and 2 levels were not induced. Therefore, hydG apparently regulates, specifically, the labile hydrogenase activity. Restoration of this latter activity in hydF mutants was accompanied by a proportional increase of the H2 uptake activity, suggesting a functional relationship. H2:fumarate oxidoreductase activity was not restored in complemented hydL mutants. These latter strains may therefore lack, in addition to the labile hydrogenase, a second component (provisionally designated component R), possibly an electron carrier coupling H2 oxidation to the anerobic respiratory chain. Sequence analysis showed an open reading frame of 1,314 base pairs for hydG. It was preceded by a ribosome-binding site but apparently lacked a promoter. Minicell experiments revealed a single polypeptide of approximately 50 kilodaltons. Comparison of the predicted amino acid sequence with a protein sequence data base revealed strong homology to NtrC from Klebsiella pneumoniae, a DNA-binding transcriptional activator. The 411 base pairs upstream from pHG40 contained a second open reading frame overlapping hydG by four bases. The deduced amino acid sequence showed considerable homology with the C-terminal part of NtrB. This sequence was therefore assumed to be part of a second gene, encoding the NtrB-like component, and was designated hydH. The labile hydrogenase activity in E. coli is apparently regulated by a multicomponent system analogous to the NtrB-NtrC system. This conclusion is in agreement with the results of Birkmann et al. (A. Birkmann, R. G. Sawers, and A. Böck, Mol. Gen. Genet. 210:535-542, 1987), who demonstrated ntrA dependence for the labile hydrogenase activity. Images PMID:2666400

Beyond open access: open discourse, the next great equalizer.

PubMed

Dayton, Andrew I

2006-08-30

The internet is expanding the realm of scientific publishing to include free and open public debate of published papers. Journals are beginning to support web posting of comments on their published articles and independent organizations are providing centralized web sites for posting comments about any published article. The trend promises to give one and all access to read and contribute to cutting edge scientific criticism and debate.

Assessing the performance of the Oxford Nanopore Technologies MinION

PubMed Central

Laver, T.; Harrison, J.; O’Neill, P.A.; Moore, K.; Farbos, A.; Paszkiewicz, K.; Studholme, D.J.

2015-01-01

The Oxford Nanopore Technologies (ONT) MinION is a new sequencing technology that potentially offers read lengths of tens of kilobases (kb) limited only by the length of DNA molecules presented to it. The device has a low capital cost, is by far the most portable DNA sequencer available, and can produce data in real-time. It has numerous prospective applications including improving genome sequence assemblies and resolution of repeat-rich regions. Before such a technology is widely adopted, it is important to assess its performance and limitations in respect of throughput and accuracy. In this study we assessed the performance of the MinION by re-sequencing three bacterial genomes, with very different nucleotide compositions ranging from 28.6% to 70.7%; the high G + C strain was underrepresented in the sequencing reads. We estimate the error rate of the MinION (after base calling) to be 38.2%. Mean and median read lengths were 2 kb and 1 kb respectively, while the longest single read was 98 kb. The whole length of a 5 kb rRNA operon was covered by a single read. As the first nanopore-based single molecule sequencer available to researchers, the MinION is an exciting prospect; however, the current error rate limits its ability to compete with existing sequencing technologies, though we do show that MinION sequence reads can enhance contiguity of de novo assembly when used in conjunction with Illumina MiSeq data. PMID:26753127

A new open reading frame in the genome of the cyanobacterium Synechocystis sp. PCC 6803

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

Lysenko, E.S.; Ogarkova, O.A.; Tarasov, V.A.

1995-02-01

A new open reading frame ORF242, coding for a 26.47-kDa polypeptide, was found in a DNA fragment of the cyanobacterium Synechocystis 6803, transforming a photosynthetic mutant to photoautotrophy and having homology with plant chloroplast DNA. In the 5{prime} flanking region of ORF242, consensus sequences characteristic of a functioning gene were found. One copy of ORF242 is present in the Synechocystis 6803 genome. Insertion inactivation of ORF242 does not lead to a decrease in photosynthetic activity in cells of cyanobacteria but may influence the ratio between active complexes of photosystems I and II. 22 refs., 6 figs., 2 tabs.

When left-hemisphere reading is compromised: Comparing reading ability in participants after left cerebral hemispherectomy and participants with developmental dyslexia.

PubMed

Katzir, Tami; Christodoulou, Joanna A; de Bode, Stella

2016-10-01

We investigated reading skills in individuals who have undergone left cerebral hemispherectomy and in readers with developmental dyslexia to understand diverse characteristics contributing to reading difficulty. Although dyslexia is a developmental disorder, left hemispherectomy requires that patients (re)establish the language process needed to perform the language-based tasks in the nondominant (right) hemisphere to become readers. Participants with developmental dyslexia (DD; n = 11) and participants who had undergone left hemispherectomy (HEMI; n = 11) were matched on age and gender, and were compared on timed and untimed measures of single word and pseudo-word reading. The hemispherectomy group was subdivided into prenatal (in utero) and postnatal (>3 years) insult groups, indicating the timing of the primary lesion that ultimately required surgical intervention. On an untimed reading measure, the readers with DD were comparable to individuals who had undergone left hemispherectomy due to prenatal insult, but both scored higher than the postnatal hemispherectomy group. Timed word reading differed across groups. The hemispherectomy prenatal subgroup had low average scores on both timed and untimed tests. The group with dyslexia had average scores on untimed measures and below average scores on timed reading. The hemispherectomy postnatal group had the lowest scores among the groups by a significant margin, and the most pronounced reading difficulty. Patients with prenatal lesions leading to an isolated right hemisphere (RH) have the potential to develop reading to a degree comparable to that in persons with dyslexia for single word reading. This potential sharply diminishes in individuals who undergo hemispherectomy due to postnatal insult. The higher scores of the prenatal hemispherectomy group on timed reading suggest that under these conditions, individuals with an isolated RH can compensate to a significant degree. Wiley Periodicals, Inc. © 2016 International League Against Epilepsy.

Transcription-associated mutational pressure in the Parvovirus B19 genome: Reactivated genomes contribute to the variability of viral populations.

PubMed

Khrustalev, Vladislav Victorovich; Ermalovich, Marina Anatolyevna; Hübschen, Judith M; Khrustaleva, Tatyana Aleksandrovna

2017-12-21

In this study we used non-overlapping parts of the two long open reading frames coding for nonstructural (NS) and capsid (VP) proteins of all available sequences of the Parvovirus B19 subgenotype 1a genome and found out that the rates of A to G, C to T and A to T mutations are higher in the first long reading frame (NS) of the virus than in the second one (VP). This difference in mutational pressure directions for two parts of the same viral genome can be explained by the fact of transcription of just the first long reading frame during the lifelong latency in nonerythroid cells. Adenine deamination (producing A to G and A to T mutations) and cytosine deamination (producing C to T mutations) occur more frequently in transcriptional bubbles formed by DNA "plus" strand of the first open reading frame. These mutations can be inherited only in case of reactivation of the infectious virus due to the help of Adenovirus that allows latent Parvovirus B19 to start transcription of the second reading frame and then to replicate its genome by the rolling circle mechanism using the specific origin. Results of this study provide evidence that the genomes reactivated from latency make significant contributions to the variability of Parvovirus B19. Copyright © 2017 Elsevier Ltd. All rights reserved.

"Serial" Effects in Parallel Models of Reading

ERIC Educational Resources Information Center

Chang, Ya-Ning; Furber, Steve; Welbourne, Stephen

2012-01-01

There is now considerable evidence showing that the time to read a word out loud is influenced by an interaction between orthographic length and lexicality. Given that length effects are interpreted by advocates of dual-route models as evidence of serial processing this would seem to pose a serious challenge to models of single word reading which…

Phonological Processing Skills as Predictors of Literacy amongst Arabic Speaking Bahraini Children

ERIC Educational Resources Information Center

al Mannai, Haya; Everatt, John

2005-01-01

This paper reports a study of the reading and spelling skills of grades 1-3 Arabic-speaking children in Bahrain. Children were tested on their literacy skills (single word reading and spelling), their ability to decode letter strings (non-word reading) and measures of phonological awareness, short-term memory, speed of processing and non-verbal…

The Effects of Audiotaped Progressive Muscle Relaxation Training on the Reading Performance of Emotionally Disturbed Adolescents.

ERIC Educational Resources Information Center

Margolis, Howard; Pica, Louis, Jr.

A study examined the degree to which audiotaped progressive muscle relaxation training influenced the oral and silent reading performance of eight adolescents who were legally classified as emotionally disturbed. A single-case ABAB withdrawal design was used to examine the effects of relaxation training on oral reading. In addition, a…

A Developmental Study of Chinese Children's Word and Character Reading

ERIC Educational Resources Information Center

Li, Tong; Wang, Ying; Tong, Xiuhong; McBride, Catherine

2017-01-01

To investigate the relationship between Chinese children's character and word reading, 62 third and 50 fifth grade children in Hong Kong were asked to read single characters and words that were comprised of these characters. Results showed that words helped children to recognize characters for both grades of children. Compared to older children,…

Beyond the Single Text: Nurturing Young Children's Interest in Reading and Writing for Multiple Purposes.

ERIC Educational Resources Information Center

Donovan, Carol A.; Milewicz, Elizabeth J.; Smolkin, Laura B.

2003-01-01

Describes children's early use of oral and written language for different purposes. Advocates fostering early appreciation of a variety of texts to cultivate children's disposition to read and write for enjoyment, information, and communication. Presents ideas for using the talking, reading, and writing done every day by young children to develop…

What Multilevel Parallel Programs do when you are not Watching: A Performance Analysis Case Study Comparing MPI/OpenMP, MLP, and Nested OpenMP

NASA Technical Reports Server (NTRS)

Jost, Gabriele; Labarta, Jesus; Gimenez, Judit

2004-01-01

With the current trend in parallel computer architectures towards clusters of shared memory symmetric multi-processors, parallel programming techniques have evolved that support parallelism beyond a single level. When comparing the performance of applications based on different programming paradigms, it is important to differentiate between the influence of the programming model itself and other factors, such as implementation specific behavior of the operating system (OS) or architectural issues. Rewriting-a large scientific application in order to employ a new programming paradigms is usually a time consuming and error prone task. Before embarking on such an endeavor it is important to determine that there is really a gain that would not be possible with the current implementation. A detailed performance analysis is crucial to clarify these issues. The multilevel programming paradigms considered in this study are hybrid MPI/OpenMP, MLP, and nested OpenMP. The hybrid MPI/OpenMP approach is based on using MPI [7] for the coarse grained parallelization and OpenMP [9] for fine grained loop level parallelism. The MPI programming paradigm assumes a private address space for each process. Data is transferred by explicitly exchanging messages via calls to the MPI library. This model was originally designed for distributed memory architectures but is also suitable for shared memory systems. The second paradigm under consideration is MLP which was developed by Taft. The approach is similar to MPi/OpenMP, using a mix of coarse grain process level parallelization and loop level OpenMP parallelization. As it is the case with MPI, a private address space is assumed for each process. The MLP approach was developed for ccNUMA architectures and explicitly takes advantage of the availability of shared memory. A shared memory arena which is accessible by all processes is required. Communication is done by reading from and writing to the shared memory.

Reading apps for children: Readability from the design perspective

NASA Astrophysics Data System (ADS)

Mohammed, Wasan Abdulwahab; Husni, Husniza

2017-10-01

Electronic reading for young children opens new avenues especially with the advance of modern reading devices. The readability of mobile learning applications has received extensive attention by the designers and developers. The reason for such concern is due to its importance in determining usability related issues especially in the design context for children. In many cases, children find it difficult to interact with mobile reading apps. This is because apps for reading and for entertainment require different features. As such, this study sets out three objectives: 1) to evaluate five reading apps for young children from design perspectives; 2) to examine the readability for current existing mobile apps for reading and 3) to propose and evaluate mobile apps UI guideline for readability. Readability indices, observation and interview were conducted on 6 - 8 years old students. The obtained result showed that certain reading apps provide better reading experience for children than others. Some of the reasons are mostly related to the design characteristics embedded within the app. In addition, the use of animation was found to stimulate children reading experience as it is believed to offer the interactivity elements to gain their interest and willingness to read. These findings are believed to provide the recommendations and insights for designers of reading apps for children.

An Upstream Open Reading Frame Is Essential for Feedback Regulation of Ascorbate Biosynthesis in Arabidopsis

PubMed Central

Laing, William A.; Martínez-Sánchez, Marcela; Wright, Michele A.; Bulley, Sean M.; Brewster, Di; Dare, Andrew P.; Rassam, Maysoon; Wang, Daisy; Storey, Roy; Macknight, Richard C.; Hellens, Roger P.

2015-01-01

Ascorbate (vitamin C) is an essential antioxidant and enzyme cofactor in both plants and animals. Ascorbate concentration is tightly regulated in plants, partly to respond to stress. Here, we demonstrate that ascorbate concentrations are determined via the posttranscriptional repression of GDP-l-galactose phosphorylase (GGP), a major control enzyme in the ascorbate biosynthesis pathway. This regulation requires a cis-acting upstream open reading frame (uORF) that represses the translation of the downstream GGP open reading frame under high ascorbate concentration. Disruption of this uORF stops the ascorbate feedback regulation of translation and results in increased ascorbate concentrations in leaves. The uORF is predicted to initiate at a noncanonical codon (ACG rather than AUG) and encode a 60- to 65-residue peptide. Analysis of ribosome protection data from Arabidopsis thaliana showed colocation of high levels of ribosomes with both the uORF and the main coding sequence of GGP. Together, our data indicate that the noncanonical uORF is translated and encodes a peptide that functions in the ascorbate inhibition of translation. This posttranslational regulation of ascorbate is likely an ancient mechanism of control as the uORF is conserved in GGP genes from mosses to angiosperms. PMID:25724639

An upstream open reading frame is essential for feedback regulation of ascorbate biosynthesis in Arabidopsis.

PubMed

Laing, William A; Martínez-Sánchez, Marcela; Wright, Michele A; Bulley, Sean M; Brewster, Di; Dare, Andrew P; Rassam, Maysoon; Wang, Daisy; Storey, Roy; Macknight, Richard C; Hellens, Roger P

2015-03-01

Ascorbate (vitamin C) is an essential antioxidant and enzyme cofactor in both plants and animals. Ascorbate concentration is tightly regulated in plants, partly to respond to stress. Here, we demonstrate that ascorbate concentrations are determined via the posttranscriptional repression of GDP-l-galactose phosphorylase (GGP), a major control enzyme in the ascorbate biosynthesis pathway. This regulation requires a cis-acting upstream open reading frame (uORF) that represses the translation of the downstream GGP open reading frame under high ascorbate concentration. Disruption of this uORF stops the ascorbate feedback regulation of translation and results in increased ascorbate concentrations in leaves. The uORF is predicted to initiate at a noncanonical codon (ACG rather than AUG) and encode a 60- to 65-residue peptide. Analysis of ribosome protection data from Arabidopsis thaliana showed colocation of high levels of ribosomes with both the uORF and the main coding sequence of GGP. Together, our data indicate that the noncanonical uORF is translated and encodes a peptide that functions in the ascorbate inhibition of translation. This posttranslational regulation of ascorbate is likely an ancient mechanism of control as the uORF is conserved in GGP genes from mosses to angiosperms. © 2015 American Society of Plant Biologists. All rights reserved.

Identification and characterization of Kaposi's sarcoma-associated herpesvirus open reading frame 11 promotor activation

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

Chen, Lei

2008-01-01

Open reading frame 11 (ORF11) of Kaposi's sarcoma-associated herpesvirus belongs to a herpesviral homologous protein family shared by some members of the gamma- herpesvirus subfamily. Little is known about this ORF11 homologous protein family. We have characterized an unknown open reading frame, ORF11, located adjacent and in the opposite orientation to a well-characterized viral IL-6 gene. Northern blot analysis reveals that ORF11 is expressed during the KSHV lytic cycle with delayed-early transcription kinetics. We have determined the 5{prime} and 3{prime} untranslated region of the unspliced ORF11 transcript and identified both the transcription start site and the transcription termination site. Coremore » promoter region, representing ORF11 promoter activity, was mapped to a 159nt fragment 5{prime} most proximal to the transcription start site. A functional TATA box was identified in the core promoter region. Interestingly, we found that ORF11 transcriptional activation is not responsive to Rta, the KSHV lytic switch protein. We also discovered that part of the ORF11 promoter region, the 209nt fragment upstream of the transcription start site, was repressed by phorbol esters. Our data help to understand transcription regulation of ORF11 and to elucidate roles of ORF11 in KSHV pathogenesis and life cycle.« less

The TGA codons are present in the open reading frame of selenoprotein P cDNA

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

Hill, K.E.; Lloyd, R.S.; Read, R.

1991-03-11

The TGA codon in DNA has been shown to direct incorporation of selenocysteine into protein. Several proteins from bacteria and animals contain selenocysteine in their primary structures. Each of the cDNA clones of these selenoproteins contains one TGA codon in the open reading frame which corresponds to the selenocysteine in the protein. A cDNA clone for selenoprotein P (SeP), obtained from a {gamma}ZAP rat liver library, was sequenced by the dideoxy termination method. The correct reading frame was determined by comparison of the deduced amino acid sequence with the amino acid sequence of several peptides from SeP. Using SeP labelledmore » with {sup 75}Se in vivo, the selenocysteine content of the peptides was verified by the collection of carboxymethylated {sup 77}Se-selenocysteine as it eluted from the amino acid analyzer and determination of the radioactivity contained in the collected samples. Ten TGA codons are present in the open reading frame of the cDNA. Peptide fragmentation studies and the deduced sequence indicate that selenium-rich regions are located close to the carboxy terminus. Nine of the 10 selenocysteines are located in the terminal 26% of the sequence with four in the terminal 15 amino acids. The deduced sequence codes for a protein of 385 amino acids. Cleavage of the signal peptide gives the mature protein with 366 amino acids and a calculated mol wt of 41,052 Da. Searches of PIR and SWISSPROT protein databases revealed no similarity with glutathione peroxidase or other selenoproteins.« less

JingleBells: A Repository of Immune-Related Single-Cell RNA-Sequencing Datasets.

PubMed

Ner-Gaon, Hadas; Melchior, Ariel; Golan, Nili; Ben-Haim, Yael; Shay, Tal

2017-05-01

Recent advances in single-cell RNA-sequencing (scRNA-seq) technology increase the understanding of immune differentiation and activation processes, as well as the heterogeneity of immune cell types. Although the number of available immune-related scRNA-seq datasets increases rapidly, their large size and various formats render them hard for the wider immunology community to use, and read-level data are practically inaccessible to the non-computational immunologist. To facilitate datasets reuse, we created the JingleBells repository for immune-related scRNA-seq datasets ready for analysis and visualization of reads at the single-cell level (http://jinglebells.bgu.ac.il/). To this end, we collected the raw data of publicly available immune-related scRNA-seq datasets, aligned the reads to the relevant genome, and saved aligned reads in a uniform format, annotated for cell of origin. We also added scripts and a step-by-step tutorial for visualizing each dataset at the single-cell level, through the commonly used Integrated Genome Viewer (www.broadinstitute.org/igv/). The uniform scRNA-seq format used in JingleBells can facilitate reuse of scRNA-seq data by computational biologists. It also enables immunologists who are interested in a specific gene to visualize the reads aligned to this gene to estimate cell-specific preferences for splicing, mutation load, or alleles. Thus JingleBells is a resource that will extend the usefulness of scRNA-seq datasets outside the programming aficionado realm. Copyright © 2017 by The American Association of Immunologists, Inc.

Single Photon Counting Performance and Noise Analysis of CMOS SPAD-Based Image Sensors

PubMed Central

Dutton, Neale A. W.; Gyongy, Istvan; Parmesan, Luca; Henderson, Robert K.

2016-01-01

SPAD-based solid state CMOS image sensors utilising analogue integrators have attained deep sub-electron read noise (DSERN) permitting single photon counting (SPC) imaging. A new method is proposed to determine the read noise in DSERN image sensors by evaluating the peak separation and width (PSW) of single photon peaks in a photon counting histogram (PCH). The technique is used to identify and analyse cumulative noise in analogue integrating SPC SPAD-based pixels. The DSERN of our SPAD image sensor is exploited to confirm recent multi-photon threshold quanta image sensor (QIS) theory. Finally, various single and multiple photon spatio-temporal oversampling techniques are reviewed. PMID:27447643

Identification and molecular characterization of a novel circular single-stranded DNA virus associated with yerba mate in Argentina.

PubMed

Bejerman, Nicolás; de Breuil, Soledad; Nome, Claudia

2018-06-06

A single-stranded DNA (ssDNA) virus was detected in Yerba mate samples showing chlorotic linear patterns, chlorotic rings and vein yellowing. The full-genome sequences of six different isolates of this ssDNA circular virus were obtained, which share > 99% sequence identity with each other. The newly identified virus has been tentatively named as yerba mate-associated circular DNA virus (YMaCV). The 2707 nt-long viral genome has two and three open reading frame on its complementary and virion-sense strands, respectively. The coat protein is more similar to that of mastreviruses (44% identity), whereas the replication-associated protein of YMaCV is more similar (49% identity) to that encoded by a recently described, unclassified ssDNA virus isolated on trees in Brazil. This is the first report of a circular DNA virus associated with yerba mate. Its unique genome organization and phylogenetic relationships indicates that YMaCV represents a distinct evolutionary lineage within the ssDNA viruses and therefore this virus should be classified as a member of a new species within an unassigned genus or family.

Comprehensive analysis of single molecule sequencing-derived complete genome and whole transcriptome of Hyposidra talaca nuclear polyhedrosis virus.

PubMed

Nguyen, Thong T; Suryamohan, Kushal; Kuriakose, Boney; Janakiraman, Vasantharajan; Reichelt, Mike; Chaudhuri, Subhra; Guillory, Joseph; Divakaran, Neethu; Rabins, P E; Goel, Ridhi; Deka, Bhabesh; Sarkar, Suman; Ekka, Preety; Tsai, Yu-Chih; Vargas, Derek; Santhosh, Sam; Mohan, Sangeetha; Chin, Chen-Shan; Korlach, Jonas; Thomas, George; Babu, Azariah; Seshagiri, Somasekar

2018-06-12

We sequenced the Hyposidra talaca NPV (HytaNPV) double stranded circular DNA genome using PacBio single molecule sequencing technology. We found that the HytaNPV genome is 139,089 bp long with a GC content of 39.6%. It encodes 141 open reading frames (ORFs) including the 37 baculovirus core genes, 25 genes conserved among lepidopteran baculoviruses, 72 genes known in baculovirus, and 7 genes unique to the HytaNPV genome. It is a group II alphabaculovirus that codes for the F protein and lacks the gp64 gene found in group I alphabaculovirus viruses. Using RNA-seq, we confirmed the expression of the ORFs identified in the HytaNPV genome. Phylogenetic analysis showed HytaNPV to be closest to BusuNPV, SujuNPV and EcobNPV that infect other tea pests, Buzura suppressaria, Sucra jujuba, and Ectropis oblique, respectively. We identified repeat elements and a conserved non-coding baculovirus element in the genome. Analysis of the putative promoter sequences identified motif consistent with the temporal expression of the genes observed in the RNA-seq data.

General Open Systems Theory and the Substrata-Factor Theory of Reading.

ERIC Educational Resources Information Center

Kling, Martin

This study was designed to extend the generality of the Substrata-Factor Theory by two methods of investigation: (1) theoretically, to establish the validity of the hypothesis that an isomorphic relationship exists between the Substrata-Factor Theory and the General Open Systems Theory, and (2) experimentally, to discover through a series of…

General Open Systems Theory and the Substrata-Factor Theory of Reading.

ERIC Educational Resources Information Center

Kling, Martin

This study was designed to extend the generality of the Substrata-Factor Theory by two methods of investigation: (1) theoretically, to est"blish the validity of the hypothesis that an isomorphic relationship exists between the Substrata-Factor Theory and the General Open Systems Theory, and (2) experimentally, to disc"ver through a…

Correction to: CYP79 P450 monooxygenases in gymnosperms: CYP79A118 is associated with the formation of taxiphyllin in Taxus baccata.

PubMed

Luck, Katrin; Jia, Qidong; Huber, Meret; Handrick, Vinzenz; Wong, Gane Ka-Shu; Nelson, David R; Chen, Feng; Gershenzon, Jonathan; Köllner, Tobias G

2017-12-01

Due to an unfortunate turn of events, the funding note for Open Access publication was not properly provided in the original publication. Hence, the original article has been corrected. The opening line of the Acknowledgement section should read.

Washington Headquarters Services

Science.gov Websites

Status OPM Status: Open Open Main Navigation Home Our Services Our Customers Our People Our Leaders Our Organization Contact Us CAC Site Navigation Customers Employees Our Services Our Customers Our People Our facilities in the Washington, DC area. Read more about Our Customers Our People A picture with the left edge

19 CFR 145.3 - Opening of letter class mail; reading of correspondence prohibited.

Code of Federal Regulations, 2010 CFR

2010-04-01

... correspondence prohibited. 145.3 Section 145.3 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF... correspondence. Except as provided in paragraph (e), Customs officers and employees may open and examine sealed... than, correspondence, provided they have reasonable cause to suspect the presence of merchandise or...

4 Massive Open Online Courses and How They Work

ERIC Educational Resources Information Center

Gose, Ben

2012-01-01

Massive open online courses (MOOC's) are the latest development in online education. Over the past decade, millions of students have taken free online versions of existing courses at well-known universities like the Massachusetts Institute of Technology, but such courses often offered little more than reading lists and lecture notes. MOOC's are…

Vertical bloch line memory

NASA Technical Reports Server (NTRS)

Katti, R.; Wu, J.; Stadler, H.

1990-01-01

Vertical Bloch Line (VBL) memory is a recently conceived, integrated, solid-state, block-access, VLSI memory which offers the potential of 1Gbit/sq cm real storage density, gigabit per second data rates, and sub-millisecond average access times simultaneously at relatively low mass, volume, and power values when compared to alternative technologies. VBL's are micromagnetic structures within magnetic domain walls which can be manipulated using magnetic fields from integrated conductors. The presence or absence of VBL pairs are used to store binary information. At present, efforts are being directed at developing a single-chip memory using 25Mbit/sq cm technology in magnetic garnet material which integrates, at a single operating point, the writing, storage, reading, and amplification functions needed in a memory. This paper describes the current design architecture, functional elements, and supercomputer simulation results which are used to assist the design process. The current design architecture uses three metal layers, two ion implantation steps for modulating the thickness of the magnetic layer, one ion implantation step for assisting propagation in the major line track, one NiFe soft magnetic layer, one CoPt hard magnetic layer, and one reflective Cr layer for facilitating magneto-optic observation of magnetic structure. Data are stored in a series of elongated magnetic domains, called stripes, which serve as storage sites for arrays of VBL pairs. The ends of these stripes are placed near conductors which serve as VBL read/write gates. A major line track is present to provide a source and propagation path for magnetic bubbles. Writing and reading, respectively, are achieved by converting magnetic bubbles to VBL's and vice versa. The output function is effected by stretching a magnetic bubble and detecting it magnetoresistively. Experimental results from the past design cycle created four design goals for the current design cycle. First, the bias field ranges for the stripes and the major line needed to be matched. Second, the magnetic field barrier between the stripe and the read/write gates needed to be reduced. Third, current conductor routing needed to be improved to reduce occurrences of open-circuiting, short-circuiting, and eddy-current shielding. Fourth, a modified Co-alloy was needed with an increased coercivity and controlled magnetization to allow VBL stabilization to occur without affecting stripe stability.

Detection and assessment of copy number variation using PacBio long-read and Illumina sequencing in New Zealand dairy cattle.

PubMed

Couldrey, C; Keehan, M; Johnson, T; Tiplady, K; Winkelman, A; Littlejohn, M D; Scott, A; Kemper, K E; Hayes, B; Davis, S R; Spelman, R J

2017-07-01

Single nucleotide polymorphisms have been the DNA variant of choice for genomic prediction, largely because of the ease of single nucleotide polymorphism genotype collection. In contrast, structural variants (SV), which include copy number variants (CNV), translocations, insertions, and inversions, have eluded easy detection and characterization, particularly in nonhuman species. However, evidence increasingly shows that SV not only contribute a substantial proportion of genetic variation but also have significant influence on phenotypes. Here we present the discovery of CNV in a prominent New Zealand dairy bull using long-read PacBio (Pacific Biosciences, Menlo Park, CA) sequencing technology and the Sniffles SV discovery tool (version 0.0.1; https://github.com/fritzsedlazeck/Sniffles). The CNV identified from long reads were compared with CNV discovered in the same bull from Illumina sequencing using CNVnator (read depth-based tool; Illumina Inc., San Diego, CA) as a means of validation. Subsequently, further validation was undertaken using whole-genome Illumina sequencing of 556 cattle representing the wider New Zealand dairy cattle population. Very limited overlap was observed in CNV discovered from the 2 sequencing platforms, in part because of the differences in size of CNV detected. Only a few CNV were therefore able to be validated using this approach. However, the ability to use CNVnator to genotype the 557 cattle for copy number across all regions identified as putative CNV allowed a genome-wide assessment of transmission level of copy number based on pedigree. The more highly transmissible a putative CNV region was observed to be, the more likely the distribution of copy number was multimodal across the 557 sequenced animals. Furthermore, visual assessment of highly transmissible CNV regions provided evidence supporting the presence of CNV across the sequenced animals. This transmission-based approach was able to confirm a subset of CNV that segregates in the New Zealand dairy cattle population. Genome-wide identification and validation of CNV is an important step toward their inclusion in genomic selection strategies. The Authors. Published by the Federation of Animal Science Societies and Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/).

Hot Spots of Recombination in Fission Yeast: Inactivation of the M26 Hot Spot by Deletion of the Ade6 Promoter and the Novel Hotspot Ura4-Aim

PubMed Central

Zahn-Zabal, M.; Lehmann, E.; Kohli, J.

1995-01-01

The M26 mutation in the ade6 gene of Schizosaccharomyces pombe creates a hot spot of meiotic recombination. A single base substitution, the M26 mutation is situated within the open reading frame, near the 5' end. It has previously been shown that the heptanucleotide sequence 5' ATGACGT 3', which includes the M26 mutation, is required for hot spot activity. The 510-bp ade6-delXB deletion encompasses the promoter and the first 23 bp of the open reading frame, ending 112 bp upstream of M26. Deletion of the promoter in cis to M26 abolishes hot spot activity, while deletion in trans to M26 has no effect. Homozygous deletion of the promoter also eliminates M26 hot spot activity, indicating that the heterology created through deletion of the promoter per se is not responsible for the loss of hot spot activity. Thus, DNA sequences other than the heptanucleotide 5' ATGACGT 3', which must be located at the 5' end of the ade6 gene, appear to be required for hot spot activity. While the M26 hotspot stimulates crossovers associated with M26 conversion, it does not affect the crossover frequency in the intervals adjacent to ade6. The flanking marker ura4-aim, a heterology created by insertion of the ura4(+) gene upstream of ade6, turned out to be a hot spot itself. It shows disparity of conversion with preferential loss of the insertion. The frequency of conversion at ura4-aim is reduced when the M26 hot spot is active 15 kb away, indicating competition for recombination factors by hot spots in close proximity. PMID:7498729

Structural and functional analyses of Saccharomyces cerevisiae wild-type and mutant RNA1 genes.

PubMed Central

Traglia, H M; Atkinson, N S; Hopper, A K

1989-01-01

The yeast gene RNA1 has been defined by the thermosensitive rna1-1 lesion. This lesion interferes with the processing and production of all major classes of RNA. Each class of RNA is affected at a distinct and presumably unrelated step. Furthermore, RNA does not appear to exit the nucleus. To investigate how the RNA1 gene product can pleiotropically affect disparate processes, we undertook a structural analysis of wild-type and mutant RNA1 genes. The wild-type gene was found to contain a 407-amino-acid open reading frame that encodes a hydrophilic protein. No clue regarding the function of the RNA1 protein was obtained by searching banks for similarity to other known gene products. Surprisingly, the rna1-1 lesion was found to code for two amino acid differences from wild type. We found that neither single-amino-acid change alone resulted in temperature sensitivity. The carboxy-terminal region of the RNA1 open reading frame contains a highly acidic domain extending from amino acids 334 to 400. We generated genomic deletions that removed C-terminal regions of this protein. Deletion of amino acids 397 to 407 did not appear to affect cell growth. Removal of amino acids 359 to 397, a region containing 24 acidic residues, caused temperature-sensitive growth. This allele, rna1-delta 359-397, defines a second conditional lesion of the RNA1 locus. We found that strains possessing the rna1-delta 359-397 allele did not show thermosensitive defects in pre-rRNA or pre-tRNA processing. Removal of amino acids 330 to 407 resulted in loss of viability. Images PMID:2674676

The site-specific ribosomal insertion element type II of Bombyx mori (R2Bm) contains the coding sequence for a reverse transcriptase-like enzyme.

PubMed Central

Burke, W D; Calalang, C C; Eickbush, T H

1987-01-01

Two classes of DNA elements interrupt a fraction of the rRNA repeats of Bombyx mori. We have analyzed by genomic blotting and sequence analysis one class of these elements which we have named R2. These elements occupy approximately 9% of the rDNA units of B. mori and appear to be homologous to the type II rDNA insertions detected in Drosophila melanogaster. Approximately 25 copies of R2 exist within the B. mori genome, of which at least 20 are located at a precise location within otherwise typical rDNA units. Nucleotide sequence analysis has revealed that the 4.2-kilobase-pair R2 element has a single large open reading frame, occupying over 82% of the total length of the element. The central region of this 1,151-amino-acid open reading frame shows homology to the reverse transcriptase enzymes found in retroviruses and certain transposable elements. Amino acid homology of this region is highest to the mobile line 1 elements of mammals, followed by the mitochondrial type II introns of fungi, and the pol gene of retroviruses. Less homology exists with transposable elements of D. melanogaster and Saccharomyces cerevisiae. Two additional regions of sequence homology between L1 and R2 elements were also found outside the reverse transcriptase region. We suggest that the R2 elements are retrotransposons that are site specific in their insertion into the genome. Such mobility would enable these elements to occupy a small fraction of the rDNA units of B. mori despite their continual elimination from the rDNA locus by sequence turnover. Images PMID:2439905

An empirical assessment of the short-term impacts of a reading of Deborah Zoe Laufer's drama Informed Consent on attitudes and intentions to participate in genetic research.

PubMed

Rothwell, Erin; Botkin, Jeffrey R; Cheek-O'Donnell, Sydney; Wong, Bob; Case, Gretchen A; Johnson, Erin; Matheson, Trent; Wilson, Alena; Robinson, Nicole R; Rawlings, Jared; Horejsi, Brooke; Lopez, Ana Maria; Byington, Carrie L

2018-01-01

This study assessed the short-term impact of the play "Informed Consent" by Deborah Zoe Laufer (a fictionalized look at the controversy over specimens collected from the Havasupai Tribe for diabetes research in 1989) on perceptions of trust, willingness to donate biospecimens, and attitudes toward harm and privacy among the medical and undergraduate students, faculty, and the public in the Intermountain West. Surveys were administered before and after a staged reading of the play by professional actors. Survey items included the short form Trust in Medical Researchers, and single-item questions about group identity, ethics of genetic testing in children, and willingness to donate biospecimens. In addition, respondents were given the option to answer open-ended questions through e-mail. Out of the 481 who attended the play, 421 completed both the pre and post surveys, and 166 participants completed open-ended questions online approximately 1 week after the play. Across all participants, there were significant declines for trust in medical researchers and for the survey item "is it ethical for investigators to test children for adult onset diseases" (p < .001 for both) following the play. There was a significant increase in agreement to improve group identity protections (p < .001) and there were no differences on willingness to donate biospecimens to research (p = .777). Qualitative data provided extensive contextual data supporting these perspectives. This is one of the first studies to document short-term impacts of a theatrical performance on both attitudes and behavioral intentions toward research ethics and clinical research participation. Future research should continue to explore the impact of theatrical performances among public and investigators on the ethical issues and complexities in clinical research.

Molecular cloning and nucleotide sequence of the alpha and beta subunits of allophycocyanin from the cyanelle genome of Cyanophora paradoxa.

PubMed Central

Bryant, D A; de Lorimier, R; Lambert, D H; Dubbs, J M; Stirewalt, V L; Stevens, S E; Porter, R D; Tam, J; Jay, E

1985-01-01

The genes for the alpha- and beta-subunit apoproteins of allophycocyanin (AP) were isolated from the cyanelle genome of Cyanophora paradoxa and subjected to nucleotide sequence analysis. The AP beta-subunit apoprotein gene was localized to a 7.8-kilobase-pair Pst I restriction fragment from cyanelle DNA by hybridization with a tetradecameric oligonucleotide probe. Sequence analysis using that oligonucleotide and its complement as primers for the dideoxy chain-termination sequencing method confirmed the presence of both AP alpha- and beta-subunit genes on this restriction fragment. Additional oligonucleotide primers were synthesized as sequencing progressed and were used to determine rapidly the nucleotide sequence of a 1336-base-pair region of this cloned fragment. This strategy allowed the sequencing to be completed without a detailed restriction map and without extensive and time-consuming subcloning. The sequenced region contains two open reading frames whose deduced amino acid sequences are 81-85% homologous to cyanobacterial and red algal AP subunits whose amino acid sequences have been determined. The two open reading frames are in the same orientation and are separated by 39 base pairs. AP alpha is 5' to AP beta and both coding sequences are preceded by a polypurine, Shine-Dalgarno-type sequence. Sequences upstream from AP alpha closely resemble the Escherichia coli consensus promoter sequences and also show considerable homology to promoter sequences for several chloroplast-encoded psbA genes. A 56-base-pair palindromic sequence downstream from the AP beta gene could play a role in the termination of transcription or translation. The allophycocyanin apoprotein subunit genes are located on the large single-copy region of the cyanelle genome. PMID:2987916

A near full-length open reading frame next generation sequencing assay for genotyping and identification of resistance-associated variants in hepatitis C virus.

PubMed

Pedersen, M S; Fahnøe, U; Hansen, T A; Pedersen, A G; Jenssen, H; Bukh, J; Schønning, K

2018-06-01

The current treatment options for hepatitis C virus (HCV), based on direct acting antivirals (DAA), are dependent on virus genotype and previous treatment experience. Treatment failures have been associated with detection of resistance-associated substitutions (RASs) in the DAA targets of HCV, the NS3, NS5A and NS5 B proteins. To develop a next generation sequencing based method that provides genotype and detection of HCV NS3, NS5A, and NS5 B RASs without prior knowledge of sample genotype. In total, 101 residual plasma samples from patients with HCV covering 10 different viral subtypes across 4 genotypes with viral loads of 3.84-7.61 Log IU/mL were included. All samples were de-identified and consequently prior treatment status for patients was unknown. Almost full open reading frame amplicons (∼ 9 kb) were generated using RT-PCR with a single primer set. The resulting amplicons were sequenced with high throughput sequencing and analysed using an in-house developed script for detecting RASs. The method successfully amplified and sequenced 94% (95/101) of samples with an average coverage of 14,035; four of six failed samples were genotype 4a. Samples analysed twice yielded reproducible nucleotide frequencies across all sites. RASs were detected in 21/95 (22%) samples at a 15% threshold. The method identified one patient infected with two genotype 2b variants, and the presence of subgenomic deletion variants in 8 (8.4%) of 95 successfully sequenced samples. The presented method may provide identification of HCV genotype, RASs detection, and detect multiple HCV infection without prior knowledge of sample genotype. Copyright © 2018 Elsevier B.V. All rights reserved.

Co-infection with human polyomavirus BK enhances gene expression and replication of human adenovirus.

PubMed

Bil-Lula, Iwona; Woźniak, Mieczysław

2018-03-26

Immunocompromised patients are susceptible to multiple viral infections. Relevant interactions between co-infecting viruses might result from viral regulatory genes which trans-activate or repress the expression of host cell genes as well as the genes of any co-infecting virus. The aim of the current study was to show that the replication of human adenovirus 5 is enhanced by co-infection with BK polyomavirus and is associated with increased expression of proteins including early region 4 open reading frame 1 and both the large tumor antigen and small tumor antigen. Clinical samples of whole blood and urine from 156 hematopoietic stem cell transplant recipients were tested. We also inoculated adenocarcinomic human alveolar basal epithelial cells with both human adenovirus 5 and BK polyomavirus to evaluate if co-infection of viruses affected their replication. Data showed that adenovirus load was significantly higher in the plasma (mean 7.5 x 10 3  ± 8.5 x 10 2 copies/ml) and urine (mean 1.9 x 10 3  ± 8.0 x 10 2 copies/ml) of samples from patients with co-infections, in comparison to samples from patients with isolated adenovirus infection. In vitro co-infection led to an increased (8.6 times) expression of the adenovirus early region 4 open reading frame gene 48 hours post-inoculation. The expression of the early region 4 open reading frame gene positively correlated with the expression of BK polyomavirus large tumor antigen (r = 0.90, p < 0.0001) and small tumor antigen (r = 0.83, p < 0.001) genes. The enhanced expression of the early region 4 open reading frame gene due to co-infection with BK polyomavirus was associated with enhanced adenovirus, but not BK polyomavirus, replication. The current study provides evidence that co-infection of adenovirus and BK polyomavirus contributes to enhanced adenovirus replication. Data obtained from this study may have significant importance in the clinical setting.

Human milk metagenome: a functional capacity analysis

PubMed Central

2013-01-01

Background Human milk contains a diverse population of bacteria that likely influences colonization of the infant gastrointestinal tract. Recent studies, however, have been limited to characterization of this microbial community by 16S rRNA analysis. In the present study, a metagenomic approach using Illumina sequencing of a pooled milk sample (ten donors) was employed to determine the genera of bacteria and the types of bacterial open reading frames in human milk that may influence bacterial establishment and stability in this primal food matrix. The human milk metagenome was also compared to that of breast-fed and formula-fed infants’ feces (n = 5, each) and mothers’ feces (n = 3) at the phylum level and at a functional level using open reading frame abundance. Additionally, immune-modulatory bacterial-DNA motifs were also searched for within human milk. Results The bacterial community in human milk contained over 360 prokaryotic genera, with sequences aligning predominantly to the phyla of Proteobacteria (65%) and Firmicutes (34%), and the genera of Pseudomonas (61.1%), Staphylococcus (33.4%) and Streptococcus (0.5%). From assembled human milk-derived contigs, 30,128 open reading frames were annotated and assigned to functional categories. When compared to the metagenome of infants’ and mothers’ feces, the human milk metagenome was less diverse at the phylum level, and contained more open reading frames associated with nitrogen metabolism, membrane transport and stress response (P < 0.05). The human milk metagenome also contained a similar occurrence of immune-modulatory DNA motifs to that of infants’ and mothers’ fecal metagenomes. Conclusions Our results further expand the complexity of the human milk metagenome and enforce the benefits of human milk ingestion on the microbial colonization of the infant gut and immunity. Discovery of immune-modulatory motifs in the metagenome of human milk indicates more exhaustive analyses of the functionality of the human milk metagenome are warranted. PMID:23705844

76 FR 2677 - Request Facilities To Report Toxics Release Inventory Information Electronically or Complete Fill...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-14

... through Friday, excluding legal holidays. The EPA Docket Center Public Reading Room is open from 8:30 a.m... Reading Room is (202) 566-1744, and the telephone number for the OEI Docket is (202) 566-1752. 2... data faster than when the data are submitted on hard-copy forms. In light of the features and tools TRI...

How the Science versus Religion Debate Has Missed the Point of Genesis 1 and 2: Jacques Ellul (1912-1994)

ERIC Educational Resources Information Center

Vanderburg, Willem H.

2010-01-01

From a social and historical perspective, the conflict between science and religion regarding the opening chapters of Genesis in the Jewish and Christian Bibles may have more to do with uncritically reading these texts through our "cultural glasses" than with what these texts actually say. Within the context of his work, Jacques Ellul read these…

Measurement of Toe-Brachial Indices in People with Subnormal Toe Pressures Complexities and Revelations.

PubMed

McAra, Sylvia; Trevethan, Robert

2018-03-01

Insufficient information exists about the nature of toe-brachial indices (TBIs) and how best to obtain them, yet their validity may be particularly important for the identification and management of peripheral artery disease and cardiovascular disease risk. We explore ways in which valid TBI measurements might be obtained. The TBI data were recorded from 97 people with subnormal toe pressures. Most people provided three TBI readings from each foot on six different occasions over a 6-month period. The foot with the lower baseline TBI was noted. For most people, only small inconsistencies existed among the three readings taken from each foot on a single occasion, and there were no consistent differences based on sequence. However, for some people there were noticeable and unsystematic differences among the measures. Selecting any specific one of the three readings based on its sequential position, or averaging specific readings, did not yield TBIs that were unequivocally typical for a person, and taking the lowest reading of each set seemed to offer the most expedient solution in this context. That permitted baseline descriptive statistics to be produced for both the higher and lower pressure feet, between which there was a statistically significant TBI difference. Accurate and consistent TBI readings cannot be assumed for people with subnormal toe pressures, and taking only a single reading or indiscriminately averaging readings seems inadvisable. Two readings and, if they are discrepant, additional readings, are recommended for each foot, ideally on several occasions, and careful consideration should be given to determine the most representative reading for each foot. Cuff sizes and other sources of inaccuracy or distortion should not be ignored, and standardized protocols for obtaining TBIs are recommended.

A combination of green tea extract and l-theanine improves memory and attention in subjects with mild cognitive impairment: a double-blind placebo-controlled study.

PubMed

Park, Sang-Ki; Jung, In-Chul; Lee, Won Kyung; Lee, Young Sun; Park, Hyoung Kook; Go, Hyo Jin; Kim, Kiseong; Lim, Nam Kyoo; Hong, Jin Tae; Ly, Sun Yung; Rho, Seok Seon

2011-04-01

A combination of green tea extract and l-theanine (LGNC-07) has been reported to have beneficial effects on cognition in animal studies. In this randomized, double-blind, placebo-controlled study, the effect of LGNC-07 on memory and attention in subjects with mild cognitive impairment (MCI) was investigated. Ninety-one MCI subjects whose Mini Mental State Examination-K (MMSE-K) scores were between 21 and 26 and who were in either stage 2 or 3 on the Global Deterioration Scale were enrolled in this study. The treatment group (13 men, 32 women; 57.58 ± 9.45 years) took 1,680 mg of LGNC-07, and the placebo group (12 men, 34 women; 56.28 ± 9.92 years) received an equivalent amount of maltodextrin and lactose for 16 weeks. Neuropsychological tests (Rey-Kim memory test and Stroop color-word test) and electroencephalography were conducted to evaluate the effect of LGNC-07 on memory and attention. Further analyses were stratified by baseline severity to evaluate treatment response on the degree of impairment (MMSE-K 21-23 and 24-26). LGNC-07 led to improvements in memory by marginally increasing delayed recognition in the Rey-Kim memory test (P = .0572). Stratified analyses showed that LGNC-07 improved memory and selective attention by significantly increasing the Rey-Kim memory quotient and word reading in the subjects with MMSE-K scores of 21-23 (LGNC-07, n = 11; placebo, n = 9). Electroencephalograms were recorded in 24 randomly selected subjects hourly for 3 hours in eye-open, eye-closed, and reading states after a single dose of LGNC-07 (LGNC-07, n = 12; placebo, n = 12). Brain theta waves, an indicator of cognitive alertness, were increased significantly in the temporal, frontal, parietal, and occipital areas after 3 hours in the eye-open and reading states. Therefore, this study suggests that LGNC-07 has potential as an intervention for cognitive improvement.

Reading comprehension and reading related abilities in adolescents with reading disabilities and attention-deficit/hyperactivity disorder.

PubMed

Ghelani, Karen; Sidhu, Robindra; Jain, Umesh; Tannock, Rosemary

2004-11-01

Reading comprehension is a very complex task that requires different cognitive processes and reading abilities over the life span. There are fewer studies of reading comprehension relative to investigations of word reading abilities. Reading comprehension difficulties, however, have been identified in two common and frequently overlapping childhood disorders: reading disability (RD) and attention-deficit/hyperactivity disorder (ADHD). The nature of reading comprehension difficulties in these groups remains unclear. The performance of four groups of adolescents (RD, ADHD, comorbid ADHD and RD, and normal controls) was compared on reading comprehension tasks as well as on reading rate and accuracy tasks. Adolescents with RD showed difficulties across most reading tasks, although their comprehension scores were average. Adolescents with ADHD exhibited adequate single word reading abilities. Subtle difficulties were observed, however, on measures of text reading rate and accuracy as well as on silent reading comprehension, but scores remained in the average range. The comorbid group demonstrated similar difficulties to the RD group on word reading accuracy and on reading rate but experienced problems on only silent reading comprehension. Implications for reading interventions are outlined, as well as the clinical relevance for diagnosis.

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

PubMed Central

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

2015-01-01

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

The Effects of a Peer-Mediated Reading Intervention on Juvenile Offenders' Main Idea Statements about Informational Text

ERIC Educational Resources Information Center

Wexler, Jade; Reed, Deborah K.; Barton, Erin E.; Mitchell, Marisa; Clancy, Erin

2018-01-01

Many youth in the juvenile justice system with or at risk for emotional and behavioral disorders struggle with reading. A multiple-baseline-across-participants single-case research design was used to examine the relationship between a supplemental peer-mediated reading intervention and juvenile offenders' generation of main idea statements about…

The Influence of Parents' Backgrounds, Beliefs about English Learning, and a Dialogic Reading Program on Thai Kindergarteners' English Lexical Development

ERIC Educational Resources Information Center

Petchprasert, Anongnad

2014-01-01

This study investigated parents' backgrounds and their beliefs about English language learning, and compared the receptive English vocabulary development of three to six year-old-Thai children before and after participating in a parent-child reading program with the dialogic reading (DR) method. Fifty-four single parents of 54 children voluntarily…

Effects of Head Rotation on Space- and Word-Based Reading Errors in Spatial Neglect

ERIC Educational Resources Information Center

Reinhart, Stefan; Keller, Ingo; Kerkhoff, Georg

2010-01-01

Patients with right hemisphere lesions often omit or misread words on the left side of a text or the beginning letters of single words which is termed neglect dyslexia (ND). Two types of reading errors are typically observed in ND: omissions and word-based reading errors. The prior are considered as space-based omission errors on the…

The effects of antecedent color on reading for students with learning disabilities and co-occurring attention-deficit/ hyperactivity disorder.

PubMed

Belfiore, P J; Grskovic, J A; Murphy, A M; Zentall, S S

1996-07-01

The effects of color on the reading recognition and comprehension of 3 students with learning disabilities and attention-deficit/hyperactivity disorder were assessed in a single-subject design. Color did not enhance sight-word learning; for longer reading comprehension tasks, color had an immediate effect across and within sessions.

EFFECT OF METHOD OF READING TRAINING ON INITIAL LEARNING AND TRANSFER.

ERIC Educational Resources Information Center

JEFFREY, W.E.; SAMUELS, S. JAY

IN A THREE-STAGE STUDY OF THE EFFECTS OF THE PHONIC AND LOOK-SAY METHODS OF READING ON THE TRANSFER OF READING SKILLS, 60 KINDERGARTEN CHILDREN WERE DIVIDED INTO A LETTER GROUP, A WORD GROUP, AND A CONTROL GROUP. MATERIALS USED WERE SIX GRAPHEMES DESIGNED DIFFERENTLY FROM ENGLISH LETTERS AND ASSIGNED TO SIX SINGLE ENGLISH PHONEMES. DURING STAGE…

Highly flexible SRAM cells based on novel tri-independent-gate FinFET

NASA Astrophysics Data System (ADS)

Liu, Chengsheng; Zheng, Fanglin; Sun, Yabin; Li, Xiaojin; Shi, Yanling

2017-10-01

In this paper, a novel tri-independent-gate (TIG) FinFET is proposed for highly flexible SRAM cells design. To mitigate the read-write conflict, two kinds of SRAM cells based on TIG FinFETs are designed, and high tradeoff are obtained between read stability and speed. Both cells can offer multi read operations for frequency requirement with single voltage supply. In the first TIG FinFET SRAM cell, the strength of single-fin access transistor (TIG FinFET) can be flexibly adjusted by selecting five different modes to meet the needs of dynamic frequency design. Compared to the previous double-independent-gate (DIG) FinFET SRAM cell, 12.16% shorter read delay can be achieved with only 1.62% read stability decrement. As for the second TIG FinFET SRAM cell, pass-gate feedback technology is applied and double-fin TIG FinFETs are used as access transistors to solve the severe write-ability degradation. Three modes exist to flexibly adjust read speed and stability, and 68.2% larger write margin and 51.7% shorter write delay are achieved at only the expense of 26.2% increase in leakage power, with the same layout area as conventional FinFET SRAM cell.

Quantum-dot-tagged microbeads for multiplexed optical coding of biomolecules.

PubMed

Han, M; Gao, X; Su, J Z; Nie, S

2001-07-01

Multicolor optical coding for biological assays has been achieved by embedding different-sized quantum dots (zinc sulfide-capped cadmium selenide nanocrystals) into polymeric microbeads at precisely controlled ratios. Their novel optical properties (e.g., size-tunable emission and simultaneous excitation) render these highly luminescent quantum dots (QDs) ideal fluorophores for wavelength-and-intensity multiplexing. The use of 10 intensity levels and 6 colors could theoretically code one million nucleic acid or protein sequences. Imaging and spectroscopic measurements indicate that the QD-tagged beads are highly uniform and reproducible, yielding bead identification accuracies as high as 99.99% under favorable conditions. DNA hybridization studies demonstrate that the coding and target signals can be simultaneously read at the single-bead level. This spectral coding technology is expected to open new opportunities in gene expression studies, high-throughput screening, and medical diagnostics.

Functional discovery via a compendium of expression profiles.

PubMed

Hughes, T R; Marton, M J; Jones, A R; Roberts, C J; Stoughton, R; Armour, C D; Bennett, H A; Coffey, E; Dai, H; He, Y D; Kidd, M J; King, A M; Meyer, M R; Slade, D; Lum, P Y; Stepaniants, S B; Shoemaker, D D; Gachotte, D; Chakraburtty, K; Simon, J; Bard, M; Friend, S H

2000-07-07

Ascertaining the impact of uncharacterized perturbations on the cell is a fundamental problem in biology. Here, we describe how a single assay can be used to monitor hundreds of different cellular functions simultaneously. We constructed a reference database or "compendium" of expression profiles corresponding to 300 diverse mutations and chemical treatments in S. cerevisiae, and we show that the cellular pathways affected can be determined by pattern matching, even among very subtle profiles. The utility of this approach is validated by examining profiles caused by deletions of uncharacterized genes: we identify and experimentally confirm that eight uncharacterized open reading frames encode proteins required for sterol metabolism, cell wall function, mitochondrial respiration, or protein synthesis. We also show that the compendium can be used to characterize pharmacological perturbations by identifying a novel target of the commonly used drug dyclonine.

Delimitation of essential genes of cassava latent virus DNA 2.

PubMed Central

Etessami, P; Callis, R; Ellwood, S; Stanley, J

1988-01-01

Insertion and deletion mutagenesis of both extended open reading frames (ORFs) of cassava latent virus DNA 2 destroys infectivity. Infectivity is restored by coinoculating constructs that contain single mutations within different ORFs. Although frequent intermolecular recombination produces dominant parental-type virus, mutants can be retained within the virus population indicating that they are competent for replication and suggesting that rescue can occur by complementation of trans acting gene products. By cloning specific fragments into DNA 1 coat protein deletion vectors we have delimited the DNA 2 coding regions and provide substantive evidence that both are essential for virus infection. Although a DNA 2 component is unique to whitefly-transmitted geminiviruses, the results demonstrate that neither coding region is involved solely in insect transmission. The requirement for a bipartite genome for whitefly-transmitted geminiviruses is discussed. Images PMID:3387209