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Sample records for additional open reading

  1. 19 CFR 145.3 - Opening of letter class mail; reading of correspondence prohibited.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 19 Customs Duties 2 2010-04-01 2010-04-01 false Opening of letter class mail; reading of... HOMELAND SECURITY; DEPARTMENT OF THE TREASURY (CONTINUED) MAIL IMPORTATIONS General Provisions § 145.3 Opening of letter class mail; reading of correspondence prohibited. (a) Matter in addition...

  2. 19 CFR 145.3 - Opening of letter class mail; reading of correspondence prohibited.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 19 Customs Duties 2 2012-04-01 2012-04-01 false Opening of letter class mail; reading of... HOMELAND SECURITY; DEPARTMENT OF THE TREASURY (CONTINUED) MAIL IMPORTATIONS General Provisions § 145.3 Opening of letter class mail; reading of correspondence prohibited. (a) Matter in addition...

  3. 19 CFR 145.3 - Opening of letter class mail; reading of correspondence prohibited.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 19 Customs Duties 2 2011-04-01 2011-04-01 false Opening of letter class mail; reading of... HOMELAND SECURITY; DEPARTMENT OF THE TREASURY (CONTINUED) MAIL IMPORTATIONS General Provisions § 145.3 Opening of letter class mail; reading of correspondence prohibited. (a) Matter in addition...

  4. 19 CFR 145.3 - Opening of letter class mail; reading of correspondence prohibited.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 19 Customs Duties 2 2013-04-01 2013-04-01 false Opening of letter class mail; reading of... HOMELAND SECURITY; DEPARTMENT OF THE TREASURY (CONTINUED) MAIL IMPORTATIONS General Provisions § 145.3 Opening of letter class mail; reading of correspondence prohibited. (a) Matter in addition...

  5. 19 CFR 145.3 - Opening of letter class mail; reading of correspondence prohibited.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 19 Customs Duties 2 2014-04-01 2014-04-01 false Opening of letter class mail; reading of... HOMELAND SECURITY; DEPARTMENT OF THE TREASURY (CONTINUED) MAIL IMPORTATIONS General Provisions § 145.3 Opening of letter class mail; reading of correspondence prohibited. (a) Matter in addition...

  6. 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…

  7. 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…

  8. Bioprospecting open reading frames for peptide effectors.

    PubMed

    Xiong, Ling; Scott, Charles

    2014-01-01

    Recent successes in the development of small-molecule antagonists of protein-protein interactions designed based on co-crystal structures of peptides bound to their biological targets confirm that short peptides derived from interacting proteins can be high-value ligands for pharmacologic validation of targets and for identification of druggable sites. Evolved sequence space is likely to be enriched for interacting peptides, but identifying minimal peptide effectors within genomic sequence can be labor intensive. Here we describe the use of incremental truncation to diversify genetic material on the scale of open reading frames into comprehensive libraries of constituent peptides. The approach is capable of generating peptides derived from both continuous and discontinuous sequence elements, and is compatible with the expression of free linear or backbone cyclic peptides, with peptides tethered to amino- or carboxyl-terminal fusion partners or with the expression of peptides displayed within protein scaffolds (peptide aptamers). Incremental truncation affords a valuable source of molecular diversity to interrogate the druggable genome or evaluate the therapeutic potential of candidate genes.

  9. Children's patterns of reasoning about reading and addition concepts.

    PubMed

    Farrington-Flint, Lee; Canobi, Katherine H; Wood, Clare; Faulkner, Dorothy

    2010-06-01

    Children's reasoning was examined within two educational contexts (word reading and addition) so as to understand the factors that contribute to relational reasoning in the two domains. Sixty-seven 5- to 7-year-olds were given a series of related words to read or single-digit addition items to solve (interspersed with unrelated items). The frequency, accuracy, and response times of children's self-reports on the conceptually related items provided a measure of relational reasoning, while performance on the unrelated addition and reading items provided a measure of procedural skill. The results indicated that the children's ability to use conceptual relations to solve both reading and addition problems enhanced speed and accuracy levels, increased with age, and was related to procedural skill. However, regression analyses revealed that domain-specific competencies can best explain the use of conceptual relations in both reading and addition. Moreover, a cluster analysis revealed that children differ according to the academic domain in which they first apply conceptual relations and these differences are related to individual variation in their procedural skills within these particular domains. These results highlight the developmental significance of relational reasoning in the context of reading and addition and underscore the importance of concept-procedure links in explaining children's literacy and arithmetical development.

  10. 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

  11. 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…

  12. Translational control of Nrf2 within the open reading frame

    SciTech Connect

    Perez-Leal, Oscar Barrero, Carlos A.; Merali, Salim

    2013-07-19

    Highlights: •Identification of a novel Nrf2 translational repression mechanism. •The repressor is within the 3′ portion of the Nrf2 ORF. •The translation of Nrf2 or eGFP is reduced by the regulatory element. •The translational repression can be reversed with synonymous codon substitutions. •The molecular mechanism requires the mRNA sequence, but not the encoded amino acids. -- Abstract: Nuclear Factor Erythroid 2-Related Factor 2 (Nrf2) is a transcription factor that is essential for the regulation of an effective antioxidant and detoxifying response. The regulation of its activity can occur at transcription, translation and post-translational levels. Evidence suggests that under environmental stress conditions, new synthesis of Nrf2 is required – a process that is regulated by translational control and is not fully understood. Here we described the identification of a novel molecular process that under basal conditions strongly represses the translation of Nrf2 within the open reading frame (ORF). This mechanism is dependent on the mRNA sequence within the 3′ portion of the ORF of Nrf2 but not in the encoded amino acid sequence. The Nrf2 translational repression can be reversed with the use of synonymous codon substitutions. This discovery suggests an additional layer of control to explain the reason for the low Nrf2 concentration under quiescent state.

  13. 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…

  14. The Effect of Noise in an Open Space School on Reading Comprehension.

    ERIC Educational Resources Information Center

    Weinstein, Carol S.; Weinstein, Neil D.

    Parents and educators have expressed fears that high noise levels in open space schools may interfere with academic achievement. This investigation compared the reading comprehension of 60 fourth grade students in an open space school during periods both of quiet and of naturally occurring background noise. The reading tasks resembled normal…

  15. Computational discovery of small open reading frames in Bacillus lehensis

    NASA Astrophysics Data System (ADS)

    Zainuddin, Nurhafizhoh; Illias, Rosli Md.; Mahadi, Nor Muhammad; Firdaus-Raih, Mohd

    2015-09-01

    Bacillus lehensis is a Gram-positive and endospore-forming alkalitolerant bacterial strain. In recent years there has been increasing interest in alkaliphilic bacteria and their ability to grow under extreme conditions as well as their ability to serve various important functions in industrial biology especially enzyme production. Small open reading frames (sORFs) have emerged as important regulators in various biological roles such as tumor progression, hormone signalling and stress response. Over the past decade, many biocomputational tools have been developed to predict genes in bacterial genomes. In this study, three softwares were used to predict sORF (≤ 80 aa) in B. lehensis by using whole genome sequence. We used comparative analysis to identify the sORFs in B. lehensis that conserved across all other bacterial genomes. We extended the analysis by doing the homology analysis against protein database. This study established the sORFs in B. lehensis that are conserved across bacteria which might has important biological function which still remain elusive in biological field.

  16. Cloning and sequencing of a putative Escherichia coli [NiFe] hydrogenase-1 operon containing six open reading frames.

    PubMed Central

    Menon, N K; Robbins, J; Peck, H D; Chatelus, C Y; Choi, E S; Przybyla, A E

    1990-01-01

    DNA encompassing the structural genes of an Escherichia coli [NiFe] hydrogenase has been cloned and sequenced. The genes were identified as those encoding the large and small subunits of hydrogenase isozyme 1 based on NH2-terminal sequences of purified subunits (kindly provided by K. Francis and K. T. Shanmugam). The structural genes formed part of a putative operon that contained four additional open reading frames. We have designated the operon hya and the six open reading frames hyaA through F. hyaA and hyaB encode the small and large structural subunits, respectively. The nucleotide-derived amino acid sequence of hyaC has a calculated molecular mass of 27.6 kilodaltons, contains 20% aromatic residues, and has four potential membrane-spanning regions. Open reading frames hyaD through F could encode polypeptides of 21.5, 14.9, and 31.5 kilodaltons, respectively. These putative peptides have no homology to other reported protein sequences, and their functions are unknown. Images FIG. 2 FIG. 3 PMID:2180913

  17. An Investigation of the Additive Benefits of Parent Dialogic Reading Techniques in Older Preschool Children

    ERIC Educational Resources Information Center

    Switalski, Sarah O'Neill

    2012-01-01

    This study examined the additive benefit of parent dialogic reading techniques in older, high-risk preschool children using multiple baseline design across participants, a single subject research design, as was as well as pre-test and post-test measures. Five preschoolers age-eligible to begin kindergarten the following school year participated.…

  18. Translational control of protein kinase Ceta by two upstream open reading frames.

    PubMed

    Raveh-Amit, Hadas; Maissel, Adva; Poller, Jonathan; Marom, Liraz; Elroy-Stein, Orna; Shapira, Michal; Livneh, Etta

    2009-11-01

    Protein kinase C (PKC) represents a family of serine/threonine kinases that play a central role in the regulation of cell growth, differentiation, and transformation. Posttranslational control of the PKC isoforms and their activation have been extensively studied; however, not much is known about their translational regulation. Here we report that the expression of one of the PKC isoforms, PKCeta, is regulated at the translational level both under normal growth conditions and during stress imposed by amino acid starvation, the latter causing a marked increase in its protein levels. The 5' untranslated region (5' UTR) of PKCeta is unusually long and GC rich, characteristic of many oncogenes and growth regulatory genes. We have identified two conserved upstream open reading frames (uORFs) in its 5' UTR and show their effect in suppressing the expression of PKCeta in MCF-7 growing cells. While the two uORFs function as repressive elements that maintain low basal levels of PKCeta in growing cells, they are required for its enhanced expression upon amino acid starvation. We show that the translational regulation during stress involves leaky scanning and is dependent on eIF-2alpha phosphorylation by GCN2. Our work further suggests that translational regulation could provide an additional level for controlling the expression of PKC family members, being more common than currently recognized.

  19. The use of Open Reading frame ESTs (ORESTES) for analysis of the honey bee transcriptome

    PubMed Central

    Nunes, Francis MF; Valente, Valeria; Sousa, Josane F; Cunha, Marco AV; Pinheiro, Daniel G; Maia, Rafaela M; Araujo, Daniela D; Costa, Maria CR; Martins, Waleska K; Carvalho, Alex F; Monesi, Nadia; Nascimento, Adriana M; Peixoto, Pablo MV; Silva, Maria FR; Ramos, Ricardo GP; Reis, Luis FL; Dias-Neto, Emmanuel; Souza, Sandro J; Simpson, Andrew JG; Zago, Marco A; Soares, Ademilson EE; Bitondi, Marcia MG; Espreafico, Enilza M; Espindola, Foued S; Paco-Larson, Maria L; Simoes, Zila LP; Hartfelder, Klaus; Silva, Wilson A

    2004-01-01

    Background The ongoing efforts to sequence the honey bee genome require additional initiatives to define its transcriptome. Towards this end, we employed the Open Reading frame ESTs (ORESTES) strategy to generate profiles for the life cycle of Apis mellifera workers. Results Of the 5,021 ORESTES, 35.2% matched with previously deposited Apis ESTs. The analysis of the remaining sequences defined a set of putative orthologs whose majority had their best-match hits with Anopheles and Drosophila genes. CAP3 assembly of the Apis ORESTES with the already existing 15,500 Apis ESTs generated 3,408 contigs. BLASTX comparison of these contigs with protein sets of organisms representing distinct phylogenetic clades revealed a total of 1,629 contigs that Apis mellifera shares with different taxa. Most (41%) represent genes that are in common to all taxa, another 21% are shared between metazoans (Bilateria), and 16% are shared only within the Insecta clade. A set of 23 putative genes presented a best match with human genes, many of which encode factors related to cell signaling/signal transduction. 1,779 contigs (52%) did not match any known sequence. Applying a correction factor deduced from a parallel analysis performed with Drosophila melanogaster ORESTES, we estimate that approximately half of these no-match ESTs contigs (22%) should represent Apis-specific genes. Conclusions The versatile and cost-efficient ORESTES approach produced minilibraries for honey bee life cycle stages. Such information on central gene regions contributes to genome annotation and also lends itself to cross-transcriptome comparisons to reveal evolutionary trends in insect genomes. PMID:15527499

  20. Comprehensive translational control of tyrosine kinase expression by upstream open reading frames.

    PubMed

    Wethmar, K; Schulz, J; Muro, E M; Talyan, S; Andrade-Navarro, M A; Leutz, A

    2016-03-31

    Post-transcriptional control has emerged as a major regulatory event in gene expression and often occurs at the level of translation initiation. Although overexpression or constitutive activation of tyrosine kinases (TKs) through gene amplification, translocation or mutation are well-characterized oncogenic events, current knowledge about translational mechanisms of TK activation is scarce. Here, we report the presence of translational cis-regulatory upstream open reading frames (uORFs) in the majority of transcript leader sequences of human TK mRNAs. Genetic ablation of uORF initiation codons in TK transcripts resulted in enhanced translation of the associated downstream main protein-coding sequences (CDSs) in all cases studied. Similarly, experimental removal of uORF start codons in additional non-TK proto-oncogenes, and naturally occurring loss-of-uORF alleles of the c-met proto-oncogene (MET) and the kinase insert domain receptor (KDR), was associated with increased CDS translation. Based on genome-wide sequence analyses we identified polymorphisms in 15.9% of all human genes affecting uORF initiation codons, associated Kozak consensus sequences or uORF-related termination codons. Together, these data suggest a comprehensive role of uORF-mediated translational control and delineate how aberrant induction of proto-oncogenes through loss-of-function mutations at uORF initiation codons may be involved in the etiology of cancer. We provide a detailed map of uORFs across the human genome to stimulate future research on the pathogenic role of uORFs.

  1. Open reading frame 176 in the photosynthesis gene cluster of Rhodobacter capsulatus encodes idi, a gene for isopentenyl diphosphate isomerase.

    PubMed Central

    Hahn, F M; Baker, J A; Poulter, C D

    1996-01-01

    Isopentenyl diphosphate (IPP) isomerase catalyzes an essential activation step in the isoprenoid biosynthetic pathway. A database search based on probes from the highly conserved regions in three eukaryotic IPP isomerases revealed substantial similarity with ORF176 in the photosynthesis gene cluster in Rhodobacter capsulatus. The open reading frame was cloned into an Escherichia coli expression vector. The encoded 20-kDa protein, which was purified in two steps by ion exchange and hydrophobic interaction chromatography, catalyzed the interconversion of IPP and dimethylallyl diphosphate. Thus, the photosynthesis gene cluster encodes all of the enzymes required to incorporate IPP into the ultimate carotenoid and bacteriochlorophyll metabolites in R. capsulatus. More recent searches uncovered additional putative open reading frames for IPP isomerase in seed-bearing plants (Oryza sativa, Arabadopsis thaliana, and Clarkia breweri), a worm (Caenorhabiditis elegans), and another eubacterium (Escherichia coli). The R. capsulatus enzyme is the smallest of the IPP isomerases to be identified thus far and may consist mostly of a fundamental catalytic core for the enzyme. PMID:8550491

  2. Identification of small open reading frames in the Glaciozyma antarctica genome

    NASA Astrophysics Data System (ADS)

    Mat-Sharani, Shuhaila; Bharudin, Izwan; Zainuddin, Nursyafiqi; Abdul-Murad, Abdul-Munir; Abu-Bakar, Farah-Diba; Najimuddin, Nazalan; Mahadi, Nor-Muhammad; Firdaus-Raih, Mohd

    2015-09-01

    Glaciozyma antarctica is an obligate psychrophilic yeast that was isolated from Casey Research Station, Antarctica. The objective of this study was to identify small Open Reading Frames (sORFs) in the G. antarctica genome. Small ORFs have been found in other organisms including Saccharomyces cerevisiae and human and they have been known to partake in a diverse variety of functions. In this study, ORFs were searched from the existing G. antarctica genome annotations and this resulted 294 sORFs (of at most 100 amino acids) which represented 4% of the 7857 annotated ORFs. Several of these sORFs were validated by mapping to EST and transcriptome of G. antarctica.

  3. Engineering ribosomal leaky scanning and upstream open reading frames for precise control of protein translation

    PubMed Central

    Ferreira, Joshua P; Noderer, William L; Diaz de Arce, Alexander J; Wang, Clifford L

    2014-01-01

    We have employed upstream open reading frames (uORFs) to systematically tune the translation levels of recombinant proteins. We present the design principles that guided the development of this technology and provide information that may help others in implementing synthetic uORFs for their own applications. We also report on recent applications to our own research projects, including the coupling of uORF and translation initiation site (TIS) engineering with small molecule-inducible post-translational control. Finally, we discuss opportunities to investigate and potentially engineer gene-specific translational responses to cellular stress. PMID:24637490

  4. Reading.

    ERIC Educational Resources Information Center

    Mulford, Jeremy, Ed.

    1971-01-01

    A collection of articles reflecting the underlying concern of British contributors with continuity--conceiving reading and learning as a whole throughout the school years--comprises this special issue of "English in Education." Specific topics treated are: "What Children Learn in Learning to Read" by R. Morris; "Reading without Primers" by W.…

  5. Evaluation of Contrast Sensitivity, Chromatic Vision, and Reading Ability in Patients with Primary Open Angle Glaucoma

    PubMed Central

    Güerri, Noemi; Cameo, Beatriz; Polo, Vicente; Larrosa, Jose M.

    2016-01-01

    Purpose. To compare contrast sensitivity, acquired color vision deficiency, and reading ability in patients with glaucoma at different stages of the disease and to establish correlations between visual field parameters and visual function scores. Methods. This prospective cross-sectional study included 121 glaucoma patients. Subjects with a diagnosis of chronic open angle glaucoma were recruited and classified according to Hodapp-Parrish-Anderson criteria. Patients with severe visual field defects were excluded because they were older, which could bias the interpretation of visual function tests. Contrast sensitivity was measured using the Pelli-Robson Chart and the CSV1000E test. Chromatic vision was evaluated using the Farnsworth-panel D15 and the L'Anthony D15 tests of Vision Color Recorder software. Reading ability was measured using Radner-Vissum test. Results. Contrast sensitivity (with photopic and mesopic luminance with glare) differed significantly between patients with early and moderate visual field defects (p < 0.05). Reading ability scores and results of the chromatic vision tests did not differ significantly between the two groups. Significant and moderate Spearman correlations between visual field indexes and contrast sensitivity tests were detected. Conclusions. Contrast sensitivity was significantly worse in patients with moderate glaucoma compared to those with early-stage glaucoma. Evaluation of visual function in clinical practice provides important information to address a glaucoma patient's vision complaints. PMID:27872754

  6. 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.

  7. Identification and characterization of Kaposi's sarcoma-associated herpesvirus open reading frame 11 promotor activation

    SciTech Connect

    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. Core 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.

  8. Direct Detection of Alternative Open Reading Frames Translation Products in Human Significantly Expands the Proteome

    PubMed Central

    Vanderperre, Benoît; Lucier, Jean-François; Bissonnette, Cyntia; Motard, Julie; Tremblay, Guillaume; Vanderperre, Solène; Wisztorski, Maxence; Salzet, Michel; Boisvert, François-Michel; Roucou, Xavier

    2013-01-01

    A fully mature mRNA is usually associated to a reference open reading frame encoding a single protein. Yet, mature mRNAs contain unconventional alternative open reading frames (AltORFs) located in untranslated regions (UTRs) or overlapping the reference ORFs (RefORFs) in non-canonical +2 and +3 reading frames. Although recent ribosome profiling and footprinting approaches have suggested the significant use of unconventional translation initiation sites in mammals, direct evidence of large-scale alternative protein expression at the proteome level is still lacking. To determine the contribution of alternative proteins to the human proteome, we generated a database of predicted human AltORFs revealing a new proteome mainly composed of small proteins with a median length of 57 amino acids, compared to 344 amino acids for the reference proteome. We experimentally detected a total of 1,259 alternative proteins by mass spectrometry analyses of human cell lines, tissues and fluids. In plasma and serum, alternative proteins represent up to 55% of the proteome and may be a potential unsuspected new source for biomarkers. We observed constitutive co-expression of RefORFs and AltORFs from endogenous genes and from transfected cDNAs, including tumor suppressor p53, and provide evidence that out-of-frame clones representing AltORFs are mistakenly rejected as false positive in cDNAs screening assays. Functional importance of alternative proteins is strongly supported by significant evolutionary conservation in vertebrates, invertebrates, and yeast. Our results imply that coding of multiple proteins in a single gene by the use of AltORFs may be a common feature in eukaryotes, and confirm that translation of unconventional ORFs generates an as yet unexplored proteome. PMID:23950983

  9. AN ATTEMPT TO SECURE ADDITIONAL EVIDENCE CONCERNING FACTORS AFFECTING LEARNING TO READ.

    ERIC Educational Resources Information Center

    HAYES, ROBERT B.; NEMETH, JOSEPH S.

    A COMPARISON WAS MADE OF FOUR DIFFERENT METHODS OF TEACHING BEGINNING READING. THE PROGRAMS STUDIED WERE (1) AN ECLECTIC, "WHOLE WORD" READING PROGRAM PRESENTED IN SCOTT, FORESMAN PUBLICATIONS, (2) A "PHONIC" READING PROGRAM PUBLISHED BY J.B. LIPPINCOTT, (3) A COMBINATION ECLECTIC, "WHOLE WORD - PHONIC" READING…

  10. Small Open Reading Frames, Non-Coding RNAs and Repetitive Elements in Bradyrhizobium japonicum USDA 110

    PubMed Central

    Hahn, Julia; Tsoy, Olga V.; Thalmann, Sebastian; Čuklina, Jelena; Gelfand, Mikhail S.

    2016-01-01

    Small open reading frames (sORFs) and genes for non-coding RNAs are poorly investigated components of most genomes. Our analysis of 1391 ORFs recently annotated in the soybean symbiont Bradyrhizobium japonicum USDA 110 revealed that 78% of them contain less than 80 codons. Twenty-one of these sORFs are conserved in or outside Alphaproteobacteria and most of them are similar to genes found in transposable elements, in line with their broad distribution. Stabilizing selection was demonstrated for sORFs with proteomic evidence and bll1319_ISGA which is conserved at the nucleotide level in 16 alphaproteobacterial species, 79 species from other taxa and 49 other Proteobacteria. Further we used Northern blot hybridization to validate ten small RNAs (BjsR1 to BjsR10) belonging to new RNA families. We found that BjsR1 and BjsR3 have homologs outside the genus Bradyrhizobium, and BjsR5, BjsR6, BjsR7, and BjsR10 have up to four imperfect copies in Bradyrhizobium genomes. BjsR8, BjsR9, and BjsR10 are present exclusively in nodules, while the other sRNAs are also expressed in liquid cultures. We also found that the level of BjsR4 decreases after exposure to tellurite and iron, and this down-regulation contributes to survival under high iron conditions. Analysis of additional small RNAs overlapping with 3’-UTRs revealed two new repetitive elements named Br-REP1 and Br-REP2. These REP elements may play roles in the genomic plasticity and gene regulation and could be useful for strain identification by PCR-fingerprinting. Furthermore, we studied two potential toxin genes in the symbiotic island and confirmed toxicity of the yhaV homolog bll1687 but not of the newly annotated higB homolog blr0229_ISGA in E. coli. Finally, we revealed transcription interference resulting in an antisense RNA complementary to blr1853, a gene induced in symbiosis. The presented results expand our knowledge on sORFs, non-coding RNAs and repetitive elements in B. japonicum and related bacteria. PMID

  11. Minimum probe length for unique identification of all open reading frames in a microbial genome

    SciTech Connect

    Sokhansanj, B A; Ng, J; Fitch, J P

    2000-03-05

    In this paper, we determine the minimum hybridization probe length to uniquely identify at least 95% of the open reading frame (ORF) in an organism. We analyze the whole genome sequences of 17 species, 11 bacteria, 4 archaea, and 2 eukaryotes. We also present a mathematical model for minimum probe length based on assuming that all ORFs are random, of constant length, and contain an equal distribution of bases. The model accurately predicts the minimum probe length for all species, but it incorrectly predicts that all ORFs may be uniquely identified. However, a probe length of just 9 bases is adequate to identify over 95% of the ORFs for all 15 prokaryotic species we studied. Using a minimum probe length, while accepting that some ORFs may not be identified and that data will be lost due to hybridization error, may result in significant savings in microarray and oligonucleotide probe design.

  12. Expression of antibodies using single open reading frame (sORF) vector design

    PubMed Central

    Gion, Wendy R.; Davis-Taber, Rachel A.; Regier, Dean A.; Fung, Emma; Medina, Limary; Santora, Ling C.; Bose, Sahana; Ivanov, Alexander V.; Perilli-Palmer, Barbara A.; Chumsae, Chris M.; Matuck, Joseph G.; Kunes, Yune Z.; Carson, Gerald R.

    2013-01-01

    Efficient production of large quantities of therapeutic antibodies is becoming a major goal of the pharmaceutical industry. We developed a proprietary expression system using a polyprotein precursor-based approach to antibody expression in mammalian cells. In this approach, the coding regions for heavy and light chains are included within a single open reading frame (sORF) separated by an in-frame intein gene. A single mRNA and subsequent polypeptide are produced upon transient and stable transfection into HEK293 and CHO cells, respectively. Heavy and light chains are separated by the autocatalytic action of the intein and antibody processing proceeds to produce active, secreted antibody. Here, we report advances in sORF technology toward establishment of a viable manufacturing platform for therapeutic antibodies in CHO cells. Increasing expression levels and improving antibody processing by intein and signal peptide selection are discussed. PMID:23774760

  13. VIDA: a virus database system for the organization of animal virus genome open reading frames.

    PubMed

    Albà, M M; Lee, D; Pearl, F M; Shepherd, A J; Martin, N; Orengo, C A; Kellam, P

    2001-01-01

    VIDA is a new virus database that organizes open reading frames (ORFs) from partial and complete genomic sequences from animal viruses. Currently VIDA includes all sequences from GenBank for Herpesviridae, Coronaviridae and Arteriviridae. The ORFs are organized into homologous protein families, which are identified on the basis of sequence similarity relationships. Conserved sequence regions of potential functional importance are identified and can be retrieved as sequence alignments. We use a controlled taxonomical and functional classification for all the proteins and protein families in the database. When available, protein structures that are related to the families have also been included. The database is available for online search and sequence information retrieval at http://www.biochem.ucl.ac.uk/bsm/virus_database/ VIDA.html.

  14. VIDA: a virus database system for the organization of animal virus genome open reading frames

    PubMed Central

    Albà, M. Mar; Lee, David; Pearl, Frances M. G.; Shepherd, Adrian J.; Martin, Nigel; Orengo, Christine A.; Kellam, Paul

    2001-01-01

    VIDA is a new virus database that organizes open reading frames (ORFs) from partial and complete genomic sequences from animal viruses. Currently VIDA includes all sequences from GenBank for Herpesviridae, Coronaviridae and Arteriviridae. The ORFs are organized into homologous protein families, which are identified on the basis of sequence similarity relationships. Conserved sequence regions of potential functional importance are identified and can be retrieved as sequence alignments. We use a controlled taxonomical and functional classification for all the proteins and protein families in the database. When available, protein structures that are related to the families have also been included. The database is available for online search and sequence information retrieval at http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html. PMID:11125070

  15. Mutational Analysis of the Open Reading Frames in the Transposable Element Is1

    PubMed Central

    Jakowec, M.; Prentki, P.; Chandler, M.; Galas, D. J.

    1988-01-01

    IS1 is one of the smallest transposable elements found in bacteria (768 bp). It contains eight overlapping open-reading-frames (ORFs) greater than 50 codons, designated insA to insG and insB'. To determine which of the ORFs actually code for proteins involved in transposition, we have introduced amber codons into each ORF by site-directed mutagenesis which make neutral changes in the overlapping ORFs. Each mutant IS1 was then tested for its ability to mediate cointegrate formation in Su(+) and Su(-) backgrounds. The mutant elements were also tested for trans-complementation in an IS1-free Salmonella background. Our results show that the products of the insA and insB genes are the only ones essential for cointegrate formation. We suggest that other ORFs may, however, encode accessory proteins. PMID:2851480

  16. Expression studies of the HCV-1a core+1 open reading frame in mammalian cells.

    PubMed

    Vassilaki, Niki; Boleti, Haralabia; Mavromara, Penelope

    2008-05-01

    The hepatitis C virus (HCV) genome possesses an open reading frame overlapping the core gene in the +1 frame (core+1 ORF). Initial studies, mainly in rabbit reticulocyte lysates, indicated that the HCV-1 core+1 ORF is expressed by a -2/+1 frameshift at codons 8-11 during translation elongation of the viral polyprotein, resulting in a protein known as alternative reading frame protein (ARFP), frameshift (F), or core+1. However, subsequent investigation, based on reporter constructs carrying portions of the core+1 ORF, suggested the function of alternative mechanisms for core+1 expression in mammalian cells, including translation initiation from internal codons 85/87 or 26. Because results from these studies have been variable, we sought to re-evaluate expression of the core+1 ORF using constructs carrying the complete core+1 coding sequence fused to GFP or LUC. We showed here that codons 85/87 serve as the predominant initiation sites for internal translation initiation of core+1 ORF in Huh-7 and Huh-7/T7 mammalian cells, which support nuclear or cytoplasmic transcription, respectively. We also showed that internal translation initiation can occur concomitantly with the expression of the core+1/F protein that is produced artificially in Huh-7 or naturally in Huh-7/T7 cells. Furthermore, translation of core+1 ORF is not significantly affected by the presence of the HCV IRES element. The core+1/S-GFP protein is cytoplasmic and exhibits an ER distribution similar to that of the core+1/F-GFP protein.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  18. Implementation Work at Scale: An Examination of the Fidelity of Implementation Study of the Scale-Up Effectiveness Trial of Open Court Reading

    ERIC Educational Resources Information Center

    Sullivan, Kate; Bell, Nance; Jones, Debra Hughes; Caverly, Sarah; Vaden-Kiernan, Michael

    2016-01-01

    The Fidelity of Implementation (FOI) study that is the focus of this report was conducted as a component of a scale-up effectiveness trial of the SRA/McGraw-Hill Open Court Reading program. The overall purpose of the FOI study was to support and provide context for findings from the larger experimental impact study of Open Court Reading (OCR). To…

  19. 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…

  20. Mining antimicrobial peptides from small open reading frames in Ciona intestinalis.

    PubMed

    Lu, Yongzhong; Zhuang, Yu; Liu, Jie

    2014-01-01

    Though being able to encode various kinds of bioactive peptides, small open reading frames (sORFs) are poorly annotated in many genomic data. The present study was conducted to evaluate the potential of sORFs in encoding antimicrobial peptides (AMPs) in the basal chordate model Ciona intestinalis. About 4.8 m genomic sequence was first retrieved for sORFs mining by the program sORF finder, then the sORFs were translated into amino acid sequences for AMP prediction via CAMP server, and thereafter, ten putative AMPs were selected for expression and antimicrobial activity validation. In total, over 180 peptides deduced from the sORFs were predicted to be AMPs. Among the ten tested peptides, six were found to have significant expressed sequence tag matches, providing strong evidence for gene expression; five were proved to be active against the bacterial strains. These results indicate that many sORFs in C. intestinalis genome contain AMP information. This work can serve as an important initial step to investigate the role of sORFs in the innate defense of C. intestinalis.

  1. Adenovirus Type 5 E4 Open Reading Frame 4 Protein Induces Apoptosis in Transformed Cells

    PubMed Central

    Shtrichman, Ronit; Kleinberger, Tamar

    1998-01-01

    Adenovirus type 5 E4 open reading frame 4 (E4orf4) protein has been previously shown to counteract transactivation of the junB and c-fos genes by cyclic AMP plus E1A protein and to interact with protein phosphatase 2A (PP2A). Here, we show that the wild-type E4orf4 protein induces apoptosis in the E1A-expressing 293 cells, in NIH 3T3 cells transformed with v-Ras, and in the lung carcinoma cell line H1299. The induction of apoptosis is not accompanied by enhanced levels of p53 in 293 cells and occurs in the absence of p53 in H1299 cells, indicating involvement of a p53-independent pathway. A mutant E4orf4 protein that had lost the ability to induce apoptosis also lost its ability to bind PP2A. We suggest that E4orf4 antagonizes continuous signals to proliferate, like those given by E1A or v-Ras, and that the conflicting signals lead to the induction of cell death. PMID:9525619

  2. HER-2 UPSTREAM OPEN READING FRAME EFFECTS ON THE USE OF DOWNSTREAM INITIATION CODONS

    PubMed Central

    Spevak, Christina C.; Park, Eun-Hee; Geballe, Adam P.; Pelletier, Jerry; Sachs, Matthew S.

    2006-01-01

    The her-2 (neu, erbB-2) oncogene encodes a 185-kDa transmembrane receptor tyrosine kinase. HER2 overexpression occurs in numerous primary human tumors and contributes to 25–30% of breast and ovarian carcinomas. Synthesis of HER2 is controlled in part by an upstream open reading frame (uORF) present in the transcript. We used synthetic capped and polyadenylated mRNAs containing sequences derived from the 5′ region of the her-2 transcript fused to firefly luciferase (LUC) reporter to examine this ORF’s effect on translation in cell-free systems derived from reticulocytes, wheat germ and Neurospora crassa, and in RNA-transfected HeLa cells. The uORF reduced translation of the downstream cistron in all systems. [35S]Met-labeling of in vitro translation products obtained indicated that the uORF also affected downstream start-site selection. Primer extension inhibition (toeprint) assays of ribosomes loaded at initiation codons in reticulocyte lysates indicated that the uORF affected the interaction of ribosomes with the primary her-2 AUG codon. PMID:17045969

  3. Flatworms have lost the right open reading frame kinase 3 gene during evolution

    PubMed Central

    Breugelmans, Bert; Ansell, Brendan R. E.; Young, Neil D.; Amani, Parisa; Stroehlein, Andreas J.; Sternberg, Paul W.; Jex, Aaron R.; Boag, Peter R.; Hofmann, Andreas; Gasser, Robin B.

    2015-01-01

    All multicellular organisms studied to date have three right open reading frame kinase genes (designated riok-1, riok-2 and riok-3). Current evidence indicates that riok-1 and riok-2 have essential roles in ribosome biosynthesis, and that the riok-3 gene assists this process. In the present study, we conducted a detailed bioinformatic analysis of the riok gene family in 25 parasitic flatworms (platyhelminths) for which extensive genomic and transcriptomic data sets are available. We found that none of the flatworms studied have a riok-3 gene, which is unprecedented for multicellular organisms. We propose that, unlike in other eukaryotes, the loss of RIOK-3 from flatworms does not result in an evolutionary disadvantage due to the unique biology and physiology of this phylum. We show that the loss of RIOK-3 coincides with a loss of particular proteins associated with essential cellular pathways linked to cell growth and apoptosis. These findings indicate multiple, key regulatory functions of RIOK-3 in other metazoan species. Taking advantage of a known partial crystal structure of human RIOK-1, molecular modelling revealed variability in nucleotide binding sites between flatworm and human RIOK proteins. PMID:25976756

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

    SciTech Connect

    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 /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' 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.

  5. Transcriptional regulation of the open reading frame 35 encoded by Kaposi's sarcoma-associated herpesvirus.

    PubMed

    Masa, Shiri-Rivka; Lando, Revital; Sarid, Ronit

    2008-02-05

    Kaposi's sarcoma-associated herpesvirus (KSHV) is a member of the Gammaherpesvirinae and is causally associated with Kaposi's sarcoma, primary effusion lymphoma, and multicentric Castleman's disease. The KSHV genome encodes over 85 genes; the function of some is entirely unknown. We have characterized the transcriptional regulation of a conserved and uncharacterized Gammaherpesvirinae open reading frame, orf35, which lies in a cluster of several overlapping genes, orf34 to orf38. We identified the transcription start site and analyzed upstream sequences. We found that expression of the KSHV lytic replication and transcription activator (RTA) strongly increased the orf35 promoter activity through a 46-nucleotide region which includes a conserved AP-1 binding site. Electrophoretic mobility shift assay demonstrated direct binding of cJUN and cFOS to the predicted AP-1 binding site. Finally, using a mutated promoter lacking the AP-1 site and dominant-negative cFOS, we established that the RTA-mediated orf35 transactivation is AP-1-dependent.

  6. A Study of the Effect of Additional Reading Assistance on Student Achievement

    ERIC Educational Resources Information Center

    Gillan-Sanderson, Nicole A.

    2012-01-01

    This study describes a procedure one school district used to increase students' reading abilities through reviewing data and adjusting the instruction to give students intensive services, as needed. This school worked in a problem-solving team approach to develop a comprehensive team that followed the progression of student achievement.…

  7. DNA sequencing and analysis of a 24.7 kb segment encompassing centromere CEN11 of Saccharomyces cerevisiae reveals nine previously unknown open reading frames.

    PubMed

    Düsterhöft, A; Philippsen, P

    1992-09-01

    A 24.7 kb segment of the cosmid clone pUKG047 containing a Sau3AI-partial fragment from the centromere region of Saccharomyces cerevisiae chromosome XI was sequenced and analysed. A mixed strategy of directed methods including exonuclease III nested deletion, restriction fragment subcloning and oligonucleotide-directed sequences was carried out. Exclusive use was made of the Applied Biosystems Taq DyeDeoxy Terminator Cycle technology and a laser-based AB1373A sequencing system for reactions, gel electrophoresis and automated reading. A total of 12 open reading frames (ORFs) was found. Nine new ORFs (YK102 to YK110) were identified, three of which (YK102, YK107, YK108) showed homologies to proteins of known function from other organisms. In addition, sequence analysis revealed three recently functionally characterized genes (MET14, VPS/SPO15, PAP1), which could be joined to the earlier published CEN11 region.

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

    PubMed Central

    Liang, Yanchun

    2016-01-01

    More and more studies have demonstrated that long noncoding RNAs (lncRNAs) play critical roles in diversity of biological process and are also associated with various types of disease. How to rapidly identify lncRNAs and messenger RNA is the fundamental step to uncover the function of lncRNAs identification. Here, we present a novel method for rapid identification of lncRNAs utilizing sequence intrinsic composition features and open reading frame information based on support vector machine model, named as Lncident (LncRNAs identification). The 10-fold cross-validation and ROC curve are used to evaluate the performance of Lncident. The main advantage of Lncident is high speed without the loss of accuracy. Compared with the exiting popular tools, Lncident outperforms Coding-Potential Calculator, Coding-Potential Assessment Tool, Coding-Noncoding Index, and PLEK. Lncident is also much faster than Coding-Potential Calculator and Coding-Noncoding Index. Lncident presents an outstanding performance on microorganism, which offers a great application prospect to the analysis of microorganism. In addition, Lncident can be trained by users' own collected data. Furthermore, R package and web server are simultaneously developed in order to maximize the convenience for the users. The R package “Lncident” can be easily installed on multiple operating system platforms, as long as R is supported. PMID:28116287

  9. Tying Down Loose Ends in the Chlamydomonas Genome: Functional Significance of Abundant Upstream Open Reading Frames

    PubMed Central

    Cross, Frederick R.

    2015-01-01

    The Chlamydomonas genome has been sequenced, assembled, and annotated to produce a rich resource for genetics and molecular biology in this well-studied model organism. The annotated genome is very rich in open reading frames upstream of the annotated coding sequence (‘uORFs’): almost three quarters of the assigned transcripts have at least one uORF, and frequently more than one. This is problematic with respect to the standard ‘scanning’ model for eukaryotic translation initiation. These uORFs can be grouped into three classes: class 1, initiating in-frame with the coding sequence (CDS) (thus providing a potential in-frame N-terminal extension); class 2, initiating in the 5′ untranslated sequences (5UT) and terminating out-of-frame in the CDS; and class 3, initiating and terminating within the 5UT. Multiple bioinformatics criteria (including analysis of Kozak consensus sequence agreement and BLASTP comparisons to the closely related Volvox genome, and statistical comparison to cds and to random sequence controls) indicate that of ∼4000 class 1 uORFs, approximately half are likely in vivo translation initiation sites. The proposed resulting N-terminal extensions in many cases will sharply alter the predicted biochemical properties of the encoded proteins. These results suggest significant modifications in ∼2000 of the ∼20,000 transcript models with respect to translation initiation and encoded peptides. In contrast, class 2 uORFs may be subject to purifying selection, and the existent ones (surviving selection) are likely inefficiently translated. Class 3 uORFs are found in more than half of transcripts, frequently multiple times per transcript; however, they are remarkably similar to random sequence expectations with respect to size, number, and composition, and therefore may in most cases be selectively neutral. PMID:26701783

  10. Bovine herpesvirus 1 U(s) open reading frame 4 encodes a glycoproteoglycan.

    PubMed Central

    Keil, G M; Engelhardt, T; Karger, A; Enz, M

    1996-01-01

    Sequence analysis of the short unique (Us) segment of the bovine herpesvirus 1 (BHV-1) genome predicted that the Us open reading frame (ORF) 4 encodes a protein with homology to glycoprotein G (gG) of other alpha-herpesviruses (P. Leung-Tack, J.-C. Audonnet, and M. Riviere, Virology 199:409-421, 1994). RNA analysis showed that the Us ORF4 is contained within two transcripts of 3.5 and 1.8 kb. The 3.5 kb RNA represents a structurally bicistronic RNA which encompasses the Us ORF3 and Us ORF4, whereas the 1.8-kb RNA constitutes the monocistronic Us ORF4 mRNA. To identify the predicted BHV-I gG, recombinant vaccinia virus expressing the Us ORF4 was used to raise specific antibodies in rabbits. The antiserum recognized a 65-kDa polypeptide and a very diffusely migrating species of proteins with an apparent molecular mass of between 90 and greater than 240 kDa in supernatants of BHV-1-infected cells which was also precipitated together with 61- and 70-kDa polypeptides from cell-associated proteins. The specificity of the reaction was demonstrated by the absence of these proteins from the supernatant of cells infected with the Us ORF4 deletion mutant BHV-l/gp1-8. Treatment of the immunoprecipitated proteins with glycosidases and chondroitinase AC showed that the 65-kDa protein constitutes gG, which contains both N- and O-linked carbohydrates, and that the high-molecular-mass proteins contain glycosaminoglycans linked to a 65-kDa glycoprotein that is antigenically related to gG. These molecules were therefore named glycoproteoglycan C (gpgG). Pulse chase experiments indicated that gG and gpgG were processed from a common precursor molecule with an apparent molecular mass of 61 kDa via a 70-kDa intermediate. Both gG and gpgG could not be found associated with purified virions. In summary, our results identify the BHV-I gG protein and demonstrate the presence of a form of posttranslational modification, glycosamino-glycosylation, that has not yet been described for a

  11. Prazosin addition to fluvoxamine: A preclinical study and open clinical trial in OCD.

    PubMed

    Feenstra, Matthijs G P; Klompmakers, André; Figee, Martijn; Fluitman, Sjoerd; Vulink, Nienke; Westenberg, Herman G M; Denys, Damiaan

    2016-02-01

    The efficacy of selective serotonin reuptake inhibitors (SRIs) in psychiatric disorders may be "augmented" through the addition of atypical antipsychotic drugs. A synergistic increase in dopamine (DA) release in the prefrontal cortex has been suggested to underlie this augmentation effect, though the mechanism of action is not clear yet. We used in vivo microdialysis in rats to study DA release following the administration of combinations of fluvoxamine (10 mg/kg) and quetiapine (10 mg/kg) with various monoamine-related drugs. The results confirmed that the selective 5-HT1A antagonist WAY-100635 (0.05 mg/kg) partially blocked the fluvoxamine-quetiapine synergistic effect (maximum DA increase dropped from 325% to 214%). A novel finding is that the α1-adrenergic blocker prazosin (1 mg/kg), combined with fluvoxamine, partially mimicked the effect of augmentation (maximum DA increase 205%; area-under-the-curve 163%). As this suggested that prazosin augmentation might be tested in a clinical study, we performed an open clinical trial of prazosin 20 mg addition to SRI in therapy-resistant patients with obsessive-compulsive disorder applying for neurosurgery. A small, non-significant reduction in Yale Brown Obsessive Compulsive Scale (Y-BOCS) scores was observed in 10 patients and one patient was classified as a responder with a reduction in Y-BOCS scores of more than 25%. We suggest that future clinical studies augmenting SRIs with an α1-adrenergic blocker in less treatment resistant cases should be considered. The clinical trial "Prazosin in combination with a serotonin reuptake inhibitor for patients with Obsessive Compulsive disorder: an open label study" was registered at 24/05/2011 under trial number ISRCTN61562706: http://www.controlled-trials.com/ISRCTN61562706.

  12. Additives

    NASA Technical Reports Server (NTRS)

    Smalheer, C. V.

    1973-01-01

    The chemistry of lubricant additives is discussed to show what the additives are chemically and what functions they perform in the lubrication of various kinds of equipment. Current theories regarding the mode of action of lubricant additives are presented. The additive groups discussed include the following: (1) detergents and dispersants, (2) corrosion inhibitors, (3) antioxidants, (4) viscosity index improvers, (5) pour point depressants, and (6) antifouling agents.

  13. Tutoring Opened My Eyes: Tutor Experiences in the America Reads Challenge

    ERIC Educational Resources Information Center

    Lane, Holly B.; Hudson, Roxanne F.; McCray, Erica D.; Tragash, Jennifer R.; Zeig, Jacqueline L.

    2011-01-01

    The America Reads Challenge offers colleges and universities an opportunity to make a contribution to the community while enhancing the education of their students, employing tutoring as a service learning experience. At the same time, their efforts will help the institution develop and sustain community partnerships. This paper reports an…

  14. 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…

  15. 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…

  16. Additive Effects of Stimulus Quality and Word Frequency on Eye Movements during Chinese Reading

    ERIC Educational Resources Information Center

    Liu, Pingping; Li, Xingshan; Han, Buxin

    2015-01-01

    Eye movements of Chinese readers were recorded for sentences in which high- and low-frequency target words were presented normally or with reduced stimulus quality in two experiments. We found stimulus quality and word frequency produced strong additive effects on fixation durations for target words. The results demonstrate that stimulus quality…

  17. 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,…

  18. A cis-acting element present within the Gag open reading frame negatively impacts on the activity of the HIV-1 IRES.

    PubMed

    Valiente-Echeverría, Fernando; Vallejos, Maricarmen; Monette, Anne; Pino, Karla; Letelier, Alejandro; Huidobro-Toro, J Pablo; Mouland, Andrew J; López-Lastra, Marcelo

    2013-01-01

    Translation initiation from the human immunodeficiency virus type-1 (HIV-1) mRNA can occur through a cap or an IRES dependent mechanism. Cap-dependent translation initiation of the HIV-1 mRNA can be inhibited by the instability element (INS)-1, a cis-acting regulatory element present within the gag open reading frame (ORF). In this study we evaluated the impact of the INS-1 on HIV-1 IRES-mediated translation initiation. Using heterologous bicistronic mRNAs, we show that the INS-1 negatively impact on HIV-1 IRES-driven translation in in vitro and in cell-based experiments. Additionally, our results show that the inhibitory effect of the INS-1 is not general to all IRESes since it does not hinder translation driven by the HCV IRES. The inhibition by the INS-1 was partially rescued in cells by the overexpression of the viral Rev protein or hnRNPA1.

  19. A cis-Acting Element Present within the gag Open Reading Frame Negatively Impacts on the Activity of the HIV-1 IRES

    PubMed Central

    Valiente-Echeverría, Fernando; Vallejos, Maricarmen; Monette, Anne; Pino, Karla; Letelier, Alejandro; Huidobro-Toro, J. Pablo; Mouland, Andrew J.; López-Lastra, Marcelo

    2013-01-01

    Translation initiation from the human immunodeficiency virus type-1 (HIV-1) mRNA can occur through a cap or an IRES dependent mechanism. Cap-dependent translation initiation of the HIV-1 mRNA can be inhibited by the instability element (INS)-1, a cis-acting regulatory element present within the gag open reading frame (ORF). In this study we evaluated the impact of the INS-1 on HIV-1 IRES-mediated translation initiation. Using heterologous bicistronic mRNAs, we show that the INS-1 negatively impact on HIV-1 IRES-driven translation in in vitro and in cell-based experiments. Additionally, our results show that the inhibitory effect of the INS-1 is not general to all IRESes since it does not hinder translation driven by the HCV IRES. The inhibition by the INS-1 was partially rescued in cells by the overexpression of the viral Rev protein or hnRNPA1. PMID:23451120

  20. Evolution of rbcL group IA introns and intron open reading frames within the colonial Volvocales (Chlorophyceae).

    PubMed

    Nozaki, Hisayoshi; Takahara, Manabu; Nakazawa, Atsushi; Kita, Yoko; Yamada, Takashi; Takano, Hiroyoshi; Kawano, Shigeyuki; Kato, Masahiro

    2002-06-01

    Mobile group I introns sometimes contain an open reading frame (ORF) possibly encoding a site-specific DNA endonuclease. However, previous phylogenetic studies have not clearly deduced the evolutionary roles of the group I intron ORFs. In this paper, we examined the phylogeny of group IA2 introns inserted in the position identical to that of the chloroplast-encoded rbcL coding region (rbcL-462 introns) and their ORFs from 13 strains of five genera (Volvox, Pleodorina, Volvulina, Astrephomene, and Gonium) of the colonial Volvocales (Chlorophyceae) and a related unicellular green alga, Vitreochlamys. The rbcL-462 introns contained an intact or degenerate ORF of various sizes except for the Gonium multicoccum rbcL-462 intron. Partial amino acid sequences of some rbcL-462 intron ORFs exhibited possible homology to the endo/excinuclease amino acid terminal domain. The distribution of the rbcL-462 introns is sporadic in the phylogenetic trees of the colonial Volvocales based on the five chloroplast exon sequences (6021 bp). Phylogenetic analyses of the conserved intron sequences resolved that the G. multicoccum rbcL-462 intron had a phylogenetic position separate from those of other colonial volvocalean rbcL-462 introns, indicating the recent horizontal transmission of the intron in the G. multicoccum lineage. However, the combined data set from conserved intron sequences and ORFs from most of the rbcL-462 introns resolved robust phylogenetic relationships of the introns that were consistent with those of the host organisms. Therefore, most of the extant rbcL-462 introns may have been vertically inherited from the common ancestor of their host organisms, whereas such introns may have been lost in other lineages during evolution of the colonial Volvocales. In addition, apparently higher synonymous substitutions than nonsynonymous substitutions in the rbcL-462 intron ORFs indicated that the ORFs might evolve under functional constraint, which could result in homing of the

  1. Quantity, Quality, and Variety of Pupil Responses during an Open-Communication Structured Group Directed Reading-Thinking Activity and a Closed Communication Structured Group Directed Reading Activity.

    ERIC Educational Resources Information Center

    Petre, Richard M.

    The quality, quantity, and variety of pupil responses while using two different group directed reading activities, the Directed Reading Activity (DRA), and the Directed Reading-Thinking Activity (DRTA) were investigated in this study. The subjects, all fourth graders in two nearby communities, were grouped into above-grade-level, at-grade-level,…

  2. Computer-Assisted Reading and Discovery for Student-Generated Text in Massive Open Online Courses

    ERIC Educational Resources Information Center

    Reich, Justin; Tingley, Dustin; Leder-Luis, Jetson; Roberts, Margaret E.; Stewart, Brandon M.

    2015-01-01

    Dealing with the vast quantities of text that students generate in Massive Open Online Courses (MOOCs) and other large-scale online learning environments is a daunting challenge. Computational tools are needed to help instructional teams uncover themes and patterns as students write in forums, assignments, and surveys. This paper introduces to the…

  3. 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…

  4. 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…

  5. A Meta-Analysis of Test Format Effects on Reading and Listening Test Performance: Focus on Multiple-Choice and Open-Ended Formats

    ERIC Educational Resources Information Center

    In'nami, Yo; Koizumi, Rie

    2009-01-01

    A meta-analysis was conducted on the effects of multiple-choice and open-ended formats on L1 reading, L2 reading, and L2 listening test performance. Fifty-six data sources located in an extensive search of the literature were the basis for the estimates of the mean effect sizes of test format effects. The results using the mixed effects model of…

  6. Incorrect Procedures Used by Primary Grade Pupils in Solving Open Addition and Subtraction Sentences.

    ERIC Educational Resources Information Center

    Lindvall, C. Mauritz; Ibarra, Cheryl Gibbons

    1980-01-01

    An exploratory investigation of various incorrect solution procedures used by students attempting to solve a variety of forms of open sentences is reported. The study identifies specific incorrect strategies, indicates their relative frequency of occurrence, and attempts to offer some explanation for certain of the incorrect procedures used. (MK)

  7. UL69 of human cytomegalovirus, an open reading frame with homology to ICP27 of herpes simplex virus, encodes a transactivator of gene expression.

    PubMed Central

    Winkler, M; Rice, S A; Stamminger, T

    1994-01-01

    The UL69 open reading frame of human cytomegalovirus (HCMV) is homologous to the immediate-early protein ICP27 of herpes simplex virus, an essential viral regulatory protein involved in the transition from early to late gene expression. Genes with homology to ICP27 have been detected in all subclasses of herpesviruses so far. While the respective proteins in alpha- and gammaherpesviruses have been defined as trans-regulatory molecules, nothing is known about these genes in betaherpesviruses. This study was therefore undertaken in order to investigate expression from the UL69 gene locus of HCMV. Northern (RNA) blot experiments revealed a complex pattern of transcripts that changed during the time course of the HCMV replicative cycle: two transcripts of 2.7 and 3.5 kb that were regulated differentially could be detected as early as 7 h after infection. However, these transcripts could not be detected in the presence of cycloheximide. Additional, larger transcripts were present exclusively at late times after infection. To analyze protein expression from the UL69 gene region, the UL69 open reading frame was expressed as a histidine-tagged protein in Escherichia coli. A specific antiserum was generated and used to detect the UL69 protein in HCMV-infected cells which revealed its localization within the intranuclear inclusions that are characteristic for HCMV infection. In cotransfection experiments, an HCMV true late promoter could not be activated by UL69, whereas an early promoter and several heterologous promoters were stimulated about 10-fold. Complementation studies showed that the UL69 protein cannot substitute for ICP27 in the context of the HSV infection, suggesting functional differences between these two proteins. In summary, these experiments define a novel regulatory protein encoded by HCMV that is expressed as an early-late gene and appears to exert a broad stimulatory effect on gene expression. Images PMID:8189530

  8. Role of a short open reading frame in ribosome shunt on the cauliflower mosaic virus RNA leader.

    PubMed

    Pooggin, M M; Hohn, T; Fütterer, J

    2000-06-09

    The pregenomic 35 S RNA of cauliflower mosaic virus (CaMV) belongs to the growing number of mRNAs known to have a complex leader sequence. The 612-nucleotide leader contains several short open reading frames (sORFs) and forms an extended hairpin structure. Downstream translation of 35 S RNA is nevertheless possible due to the ribosome shunt mechanism, by which ribosomes are directly transferred from a take-off site near the capped 5' end of the leader to a landing site near its 3' end. There they resume scanning and reach the first long open reading frame. We investigated in detail how the multiple sORFs influence ribosome migration either via shunting or linear scanning along the CaMV leader. The sORFs together constituted a major barrier for the linear ribosome migration, whereas the most 5'-proximal sORF, sORF A, in combination with sORFs B and C, played a positive role in translation downstream of the leader by diverting scanning ribosomes to the shunt route. A simplified, shunt-competent leader was constructed with the most part of the hairpin including all the sORFs except sORF A replaced by a scanning-inhibiting structure. In this leader as well as in the wild type leader, proper translation and termination of sORF A was required for efficient shunt and also for the level of shunt enhancement by a CaMV-encoded translation transactivator. sORF A could be replaced by heterologous sORFs, but a one-codon (start/stop) sORF was not functional. The results implicate that in CaMV, shunt-mediated translation requires reinitiation. The efficiency of the shunt process is influenced by translational properties of the sORF.

  9. Characterization of a second open reading frame in genome segment 10 of bluetongue virus

    PubMed Central

    Stewart, Meredith; Hardy, Alexandra; Barry, Gerald; Pinto, Rute Maria; Caporale, Marco; Melzi, Eleonora; Hughes, Joseph; Taggart, Aislynn; Janowicz, Anna; Varela, Mariana

    2015-01-01

    Viruses have often evolved overlapping reading frames in order to maximize their coding capacity. Until recently, the segmented dsRNA genome of viruses of the Orbivirus genus was thought to be monocistronic, but the identification of the bluetongue virus (BTV) NS4 protein changed this assumption. A small ORF in segment 10, overlapping the NS3 ORF in the +1 position, is maintained in more than 300 strains of the 27 different BTV serotypes and in more than 200 strains of the phylogenetically related African horse sickness virus (AHSV). In BTV, this ORF (named S10-ORF2 in this study) encodes a putative protein 50–59 residues in length and appears to be under strong positive selection. HA- or GFP-tagged versions of S10-ORF2 expressed from transfected plasmids localized within the nucleoli of transfected cells, unless a putative nucleolar localization signal was mutated. S10-ORF2 inhibited gene expression, but not RNA translation, in transient transfection reporter assays. In both mammalian and insect cells, BTV S10-ORF2 deletion mutants (BTV8ΔS10-ORF2) displayed similar replication kinetics to wt virus. In vivo, S10-ORF2 deletion mutants were pathogenic in mouse models of disease. Although further evidence is required for S10-ORF2 expression during infection, the data presented provide an initial characterization of this ORF. PMID:26290332

  10. 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…

  11. 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.…

  12. An Analysis of Incorrect Procedures Used by Primary Grade Pupils in Solving Open Addition and Subtraction Sentences.

    ERIC Educational Resources Information Center

    Lindvall, C. Mauritz; Ibarra, Cheryl Gibbons

    This study involved the extensive testing and interviewing of 102 primary grade pupils, representing a sampling from diverse school environments, to study the capabilities and difficulties evidenced by primary-grade pupils in solving open addition and subtraction sentences. Phase 1 of the study identified the specific incorrect procedures commonly…

  13. Increasing Word-Reading Speed in Poor Readers: No Additional Benefits of Explicit Letter-Cluster Training

    ERIC Educational Resources Information Center

    Marinus, Eva; de Jong, Peter; van der Leij, Aryan

    2012-01-01

    The present study examined whether explicit training of letter-clusters leads to more gains in word-reading speed than training of the separate letters of the same clusters. Ninety-nine poor reading second-grade children were randomly assigned to a cluster-training, a parallel letter-training, or a no-training condition. The cluster-training…

  14. 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

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

    1990-12-01

    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.

  15. 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

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

    PubMed Central

    2002-01-01

    Background Functional genomics involves the parallel experimentation with large sets of proteins. This requires management of large sets of open reading frames as a prerequisite of the cloning and recombinant expression of these proteins. Results A Java program was developed for retrieval of protein and nucleic acid sequences and annotations from NCBI GenBank, using the XML sequence format. Annotations retrieved by ORFer include sequence name, organism and also the completeness of the sequence. The program has a graphical user interface, although it can be used in a non-interactive mode. For protein sequences, the program also extracts the open reading frame sequence, if available, and checks its correct translation. ORFer accepts user input in the form of single or lists of GenBank GI identifiers or accession numbers. It can be used to extract complete sets of open reading frames and protein sequences from any kind of GenBank sequence entry, including complete genomes or chromosomes. Sequences are either stored with their features in a relational database or can be exported as text files in Fasta or tabulator delimited format. The ORFer program is freely available at http://www.proteinstrukturfabrik.de/orfer. Conclusion The ORFer program allows for fast retrieval of DNA sequences, protein sequences and their open reading frames and sequence annotations from GenBank. Furthermore, storage of sequences and features in a relational database is supported. Such a database can supplement a laboratory information system (LIMS) with appropriate sequence information. PMID:12493080

  17. The expression of the open reading frame of "Arabidopsis" CAX1, but not its cDNA, confers metal tolerance in yeast

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The biochemical properties and regulation of several plant CAX (CAtion eXchanger)-type vacuolar Ca (2+)/H (+) exchangers have been extensively analyzed in yeast expression assays. In the present study, we compare and contrast the phenotypes of yeast cells expressing the CAX1 cDNA and open reading fr...

  18. The Development and Implementation of an Applied Psychology Course Utilizing Behavior Modification Procedures to Supplement a Community College Reading Program for Open Enrollment Students.

    ERIC Educational Resources Information Center

    Kahn, Gloria Batkin

    This study attempted to assess the effect of behavior modification techniques on community college open enrollment students with severe educational deficits. Of 30 suburban New York members of a reading class, half were exposed to direct teaching, instructor praise, peer partners, self and peer ratings, role playing, Premack contracts,…

  19. Human herpesvirus 8 open reading frame 26 and open reading frame 65 sequences from multiple myeloma patients: a shared pattern not found in Kaposi's sarcoma or primary effusion lymphoma.

    PubMed

    Ma, H J; Sjak-Shie, N N; Vescio, R A; Kaminsky, M; Mikail, A; Pold, M; Parker, K; Beksac, M; Belson, D; Moss, T J; Wu, C H; Zhou, J; Zhang, L; Chen, G; Said, J W; Berenson, J R

    2000-11-01

    Human herpesvirus 8 (HHV-8), also known as Kaposi's sarcoma-associated herpesvirus, has been implicated in the pathogenesis of Kaposi's sarcoma (KS), primary effusion lymphoma (PEL), multicentric Castleman's disease, and recently multiple myeloma (MM). DNA sequence analyses of HHV-8 suggest that multiple HHV-8 strains exist. We extracted DNA from 24 patients with MM and 3 patients with monoclonal gammopathy of undetermined significance and compared HHV-8 open reading frames (ORFs) 26 and 65 sequences with those derived from patients with KS, PEL, and two HHV-8-positive PEL cell lines KS-1 and BC-1. ORF26 sequence data suggest that MM patients are consistently carriers of HHV-8 strain subtype C3. All MM patients also consistently revealed either a single bp deletion or substitution at position 112197 in ORF65. This unique alteration is not present in patients with KS or PEL or in PEL cell lines. It occurs in the portion of ORF65 that is known to be responsible for a serological response to HHV-8.

  20. Upstream Open Reading Frames Located in the Leader of Protein Kinase Mζ mRNA Regulate Its Translation

    PubMed Central

    Bal, Natalia V.; Susorov, Denis; Chesnokova, Ekaterina; Kasianov, Artem; Mikhailova, Tatiana; Alkalaeva, Elena; Balaban, Pavel M.; Kolosov, Peter

    2016-01-01

    For protein synthesis that occurs locally in dendrites, the translational control mechanisms are much more important for neuronal functioning than the transcription levels. Here, we show that uORFs (upstream open reading frames) in the 5′ untranslated region (5′UTR) play a critical role in regulation of the translation of protein kinase Mζ (PKMζ). Elimination of these uORFs activates translation of the reporter protein in vitro and in primary cultures of rat hippocampal neurons. Using cell-free translation systems, we demonstrate that translational initiation complexes are formed only on uORFs. Further, we address the mechanism of translational repression of PKMζ translation, by uORFs. We observed an increase in translation of the reporter protein under the control of PKMζ leader in neuronal culture during non-specific activation by picrotoxin. We also show that such a mechanism is similar to the mechanism seen in cell stress, as application of sodium arsenite to neuron cultures induced translation of mRNA carrying PKMζ 5′UTR similarly to picrotoxin activation. Therefore, we suppose that phosphorylation of eIF2a, like in cell stress, is a main regulator of PKMζ translation. Altogether, our findings considerably extend our understanding of the role of uORF in regulation of PKMζ translation in activated neurons, important at early stages of LTP. PMID:27790092

  1. 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

  2. Translational control of the Xenopus laevis connexin-41 5'-untranslated region by three upstream open reading frames.

    PubMed

    Meijer, H A; Dictus, W J; Keuning, E D; Thomas, A A

    2000-10-06

    The Xenopus laevis Connexin-41 (Cx41) mRNA contains three upstream open reading frames (uORFs) in the 5'-untranslated region (UTR). We analyzed the translation efficiency of constructs containing the Cx41 5'-UTR linked to the green fluorescent protein reporter after injection of transcripts into one-cell stage Xenopus embryos. The translational efficiency of the wild-type Cx41 5'-UTR was only 2% compared with that of the beta-globin 5'-UTR. Mutation of each of the three uAUGs into AAG codons enhanced translation 82-, 9-, and 4-fold compared with the wild-type Cx41 5'-UTR. Based on these increased translation efficiencies, the percentages of ribosomes that recognized the uAUGs were calculated. Only 0.03% of the ribosomes that entered at the cap structure scanned the entire 5'-UTR and translated the main ORF. The results indicate that all uAUGs are recognized by the majority of the scanning ribosomes and that the three uAUGs strongly modulate translation efficiency in Xenopus laevis embryos. Based on these data, a model of ribosomal flow along the mRNA is postulated. We conclude that the three uORFs may play an important role in the regulation of Cx41 expression.

  3. In vitro translation of the upstream open reading frame in the mammalian mRNA encoding S-adenosylmethionine decarboxylase.

    PubMed

    Raney, A; Baron, A C; Mize, G J; Law, G L; Morris, D R

    2000-08-11

    The upstream open reading frame (uORF) in the mRNA encoding S-adenosylmethionine decarboxylase is a polyamine-responsive element that suppresses translation of the associated downstream cistron in vivo. In this paper, we provide the first direct evidence of peptide synthesis from the S-adenosylmethionine decarboxylase uORF using an in vitro translation system. We examine both the influence of cation concentration on peptide synthesis and the effect of altering the uORF sequence on peptide synthesis. Synthesis of wild type and altered peptides was similar at all concentrations of magnesium tested. In contrast, synthesis of the wild type peptide was more sensitive than that of altered peptides to elevated concentrations of the naturally occurring polyamines, spermidine and spermine, as well as several polyamine analogs. The sensitivity of in vitro synthesis to spermidine was influenced by both the amino acid sequence and the length of the peptide product of the uORF. Findings from the present study correlate with the effects of the uORF and polyamines on translation of a downstream cistron in vivo and support the hypothesis that polyamines and the structure of the nascent peptide create a rate-limiting step in uORF translation, perhaps through a ribosome stalling mechanism.

  4. The Development of Comprehension and Reading-Related Skills in Children Learning English as an Additional Language and Their Monolingual, English-Speaking Peers

    ERIC Educational Resources Information Center

    Burgoyne, K.; Whiteley, H. E.; Hutchinson, J. M.

    2011-01-01

    Background: A significant number of pupils in UK schools learn English as an additional language (EAL). Relative differences between the educational attainment of this group and monolingual, English-speaking pupils call for an exploration of the literacy needs of EAL learners. Aims: This study explores the developmental progression of reading and…

  5. High Temperature Thermoplastic Additive Manufacturing Using Low-Cost, Open-Source Hardware

    NASA Technical Reports Server (NTRS)

    Gardner, John M.; Stelter, Christopher J.; Yashin, Edward A.; Siochi, Emilie J.

    2016-01-01

    Additive manufacturing (or 3D printing) via Fused Filament Fabrication (FFF), also known as Fused Deposition Modeling (FDM), is a process where material is placed in specific locations layer-by-layer to create a complete part. Printers designed for FFF build parts by extruding a thermoplastic filament from a nozzle in a predetermined path. Originally developed for commercial printers, 3D printing via FFF has become accessible to a much larger community of users since the introduction of Reprap printers. These low-cost, desktop machines are typically used to print prototype parts or novelty items. As the adoption of desktop sized 3D printers broadens, there is increased demand for these machines to produce functional parts that can withstand harsher conditions such as high temperature and mechanical loads. Materials meeting these requirements tend to possess better mechanical properties and higher glass transition temperatures (Tg), thus requiring printers with high temperature printing capability. This report outlines the problems and solutions, and includes a detailed description of the machine design, printing parameters, and processes specific to high temperature thermoplastic 3D printing.

  6. Identification and characterization of upstream open reading frames (uORF) in the 5' untranslated regions (UTR) of genes in Saccharomyces cerevisiae.

    PubMed

    Zhang, Zhihong; Dietrich, Fred S

    2005-08-01

    We have taken advantage of recently sequenced hemiascomycete fungal genomes to computationally identify additional genes potentially regulated by upstream open reading frames (uORFs). Our approach is based on the observation that the structure, including the uORFs, of the post-transcriptionally uORF regulated Saccharomyces cerevisiae genes GCN4 and CPA1 is conserved in related species. Thirty-eight candidate genes for which uORFs were found in multiple species were identified and tested. We determined by 5' RACE that 15 of these 38 genes are transcribed. Most of these 15 genes have only a single uORF in their 5' UTR, and the length of these uORFs range from 3 to 24 codons. We cloned seven full-length UTR sequences into a luciferase (LUC) reporter system. Luciferase activity and mRNA level were compared between the wild-type UTR construct and a construct where the uORF start codon was mutated. The translational efficiency index (TEI) of each construct was calculated to test the possible regulatory function on translational level. We hypothesize that uORFs in the UTR of RPC11, TPK1, FOL1, WSC3, and MKK1 may have translational regulatory roles while uORFs in the 5' UTR of ECM7 and IMD4 have little effect on translation under the conditions tested.

  7. Inactivation of a Synechocystis sp strain PCC 6803 gene with homology to conserved chloroplast open reading frame 184 increases the photosystem II-to-photosystem I ratio.

    PubMed Central

    Wilde, A; Härtel, H; Hübschmann, T; Hoffmann, P; Shestakov, S V; Börner, T

    1995-01-01

    A gene of the unicellular cyanobacterium Synechocystis sp strain PCC 6803 that is homologous to the conserved chloroplast open reading frame orf184 has been cloned and sequenced. The nucleotide sequence of the gene predicts a protein of 184 amino acids with a calculated molecular mass of 21.5 kD and two membrane-spanning regions. Amino acid sequence analysis showed 46 to 37% homology of the cyanobacterial orf184 with tobacco orf184, rice orf185, liverwort orf184, and Euglena gracilis orf206 sequences. Two orf184-specific mutants of Synechocystis sp PCC 6803 were constructed by insertion mutagenesis. Cells of mutants showed growth characteristics similar to those of the wild type. Their pigment composition was distinctly different from the wild type, as indicated by an increase in the phycocyanin-to-chlorophyll ratio. In addition, mutants also had a two- to threefold increase in photosynthetic electron transfer rates as well as in photosystem II-to-photosystem I ratio-a phenomenon hitherto not reported for mutants with altered photosynthetic characteristics. The observed alterations in the orf184-specific mutants provide strong evidence for a functional role of the orf184 gene product in photosynthetic processes. PMID:7780311

  8. Evolutionary dynamics of introns and their open reading frames in the U7 region of the mitochondrial rnl gene in species of Ceratocystis.

    PubMed

    Sethuraman, Jyothi; Rudski, Shelly M; Wosnitza, Kari; Hafez, Mohamed; Guppy, Brent; Hausner, Georg

    2013-01-01

    The mtDNA rnl-U7 region has been examined for the presence of introns in selected species of the genus Ceratocystis. Comparative sequence analysis identified group I and group II introns encoding single and double motif LAGLIDADG open reading frames (ORFs) at the following positions L1671, L1787, and L1923. In addition downstream of the rnl-U7 region group I introns were detected at positions L1971 and L2231, and a group II intron at L2059. A GIY-YIG type ORF was located within one mL1923 LAGLIDADG type ORF and a degenerated GIY-YIG ORF fused to a nad2 gene fragment was found in association with the mL1971 group I intron. The diversity of composite elements that appear to be sporadically distributed among closely related species of Ceratocystis illustrates the potential for homing endonucleases and their associated introns to invade new sites. Phylogenetic analysis showed that single motif LADGLIDADG ORFs related to the mL1923 ORFs have invaded the L1787 group II intron and the L1671 group I intron. Phylogenetic analysis of intron encoded single and double motif LAGLIDADG ORFs also showed that these ORFs transferred four times from group I into group II B1 type introns.

  9. Identification of an alternative open reading frame ("hidden gene"?) stringently required for infectivity of poliovirus cDNA clones.

    PubMed

    Pierangeli, A; Bucci, M; Forzan, M; Pagnotti, P; Equestre, M; Pérez Bercoff, R

    1998-10-01

    Translation of the uncapped poliovirus RNA starts at the AUG triplet spanning positions 741-743, and proceeds uninterrupted for almost the entire length of the genome. Such a cap-independent mechanism of internal initiation of translation determines that a long, extra-cistronic region extends between the 5'-end and the main open reading frame (ORF). We have identified 10 short ORFs initiated by the alternative translation initiation codons ACG, AUA, and GUG in the 5'-terminal extra-cistronic region (5'-ECR) of poliovirus RNA. Mutations introduced in all but one of these mini-cistrons had no effect on the infectivity of full-length cDNA clones, except when they modified a "hidden frame" spanning between nucleotides 157-192 (starting triplet: ACG). The mini cistron 157-192 is conserved in position, length and sequence in the genome of all types and strains of poliovirus. Adaptation to rat (Lansing) or mouse (variant of Sabin 2) is accompanied by a consistent pattern of changes in the primary sequence of this "hidden frame". The substitutions that abrogated the infectivity of cDNA clones were not expected to modify the predicted secondary structure of the 5'-ECR, and they did not alter the ability of the IRES to direct internal initiation of translation in bi-cistronic mRNAs. The infectivity of the mutated poliovirus cDNAs could be complemented in trans by co-transfecting the target COS-1 cells with an expression vector containing just the 5'-ECR of poliovirus type 2 (Lansing strain). The infectivity of poliovirus cDNA could be restored by co-transfecting short RNA transcripts of the wt 5'-ECR (Lansing), suggesting that the complementation in trans indeed requires the expression of the helper cDNA clone.

  10. Reselection of a genomic upstream open reading frame in mouse hepatitis coronavirus 5'-untranslated-region mutants.

    PubMed

    Wu, Hung-Yi; Guan, Bo-Jhih; Su, Yu-Pin; Fan, Yi-Hsin; Brian, David A

    2014-01-01

    An AUG-initiated upstream open reading frame (uORF) encoding a potential polypeptide of 3 to 13 amino acids (aa) is found within the 5' untranslated region (UTR) of >75% of coronavirus genomes based on 38 reference strains. Potential CUG-initiated uORFs are also found in many strains. The AUG-initiated uORF is presumably translated following genomic 5'-end cap-dependent ribosomal scanning, but its function is unknown. Here, in a reverse-genetics study with mouse hepatitis coronavirus, the following were observed. (i) When the uORF AUG-initiating codon was replaced with a UAG stop codon along with a U112A mutation to maintain a uORF-harboring stem-loop 4 structure, an unimpaired virus with wild-type (WT) growth kinetics was recovered. However, reversion was found at all mutated sites within five virus passages. (ii) When the uORF was fused with genomic (main) ORF1 by converting three in-frame stop codons to nonstop codons, a uORF-ORF1 fusion protein was made, and virus replicated at WT levels. However, a frameshifting G insertion at virus passage 7 established a slightly 5'-extended original uORF. (iii) When uAUG-eliminating deletions of 20, 30, or 51 nucleotides (nt) were made within stem-loop 4, viable but debilitated virus was recovered. However, a C80U mutation in the first mutant and an A77G mutation in the second appeared by passage 10, which generated alternate uORFs that correlated with restored WT growth kinetics. In vitro, the uORF-disrupting nondeletion mutants showed enhanced translation of the downstream ORF1 compared with the WT. These results together suggest that the uORF represses ORF1 translation yet plays a beneficial but nonessential role in coronavirus replication in cell culture.

  11. A phylogenetically conserved RNA structure in the poliovirus open reading frame inhibits the antiviral endoribonuclease RNase L.

    PubMed

    Han, Jian-Qiu; Townsend, Hannah L; Jha, Babal Kant; Paranjape, Jayashree M; Silverman, Robert H; Barton, David J

    2007-06-01

    RNase L is an antiviral endoribonuclease that cleaves viral mRNAs after single-stranded UA and UU dinucleotides. Poliovirus (PV) mRNA is surprisingly resistant to cleavage by RNase L due to an RNA structure in the 3C(Pro) open reading frame (ORF). The RNA structure associated with the inhibition of RNase L is phylogenetically conserved in group C enteroviruses, including PV type 1 (PV1), PV2, PV3, coxsackie A virus 11 (CAV11), CAV13, CAV17, CAV20, CAV21, and CAV24. The RNA structure is not present in other human enteroviruses (group A, B, or D enteroviruses). Coxsackievirus B3 mRNA and hepatitis C virus mRNA were fully sensitive to cleavage by RNase L. HeLa cells expressing either wild-type RNase L or a dominant-negative mutant RNase L were used to examine the effects of RNase L on PV replication. PV replication was not inhibited by RNase L activity, but rRNA cleavage characteristic of RNase L activity was detected late during the course of PV infection, after assembly of intracellular virus. Rather than inhibiting PV replication, RNase L activity was associated with larger plaques and better cell-to-cell spread. Mutations in the RNA structure associated with the inhibition of RNase L did not affect the magnitude of PV replication in HeLa cells expressing RNase L, consistent with the absence of observed RNase L activity until after virus assembly. Thus, PV carries an RNA structure in the 3C protease ORF that potently inhibits the endonuclease activity of RNase L, but this RNA structure does not prevent RNase L activity late during the course of infection, as virus assembly nears completion.

  12. Quantification of mRNA stability of stress-responsive yeast genes following conditional excision of open reading frames.

    PubMed

    Talarek, Nicolas; Bontron, Séverine; De Virgilio, Claudio

    2013-08-01

    Eukaryotic cells rapidly adjust the levels of mRNAs in response to environmental stress primarily by controlling transcription and mRNA turnover. How different stress conditions influence the fate of stress-responsive mRNAs, however, is relatively poorly understood. This is largely due to the fact that mRNA half-life assays are traditionally based on interventions (e.g., temperature-shifts using temperature-sensitive RNA polymerase II alleles or treatment with general transcription inhibitory drugs), which, rather than blocking, specifically induce transcription of stress-responsive genes. To study the half-lives of the latter suite of mRNAs, we developed and describe here a minimally perturbing alternative method, coined CEO, which is based on discontinuance of transcription following the conditional excision of open reading frames. Using CEO, we confirm that the target of rapamycin complex I (TORC1), a nutrient-activated, central stimulator of eukaryotic cell growth, favors the decay of mRNAs that depend on the stress- and/or nutrient-regulated transcription factors Msn2/4 and Gis1 for their transcription. We further demonstrate that TORC1 controls the stability of these mRNAs via the Rim15-Igo1/2-PP2A(Cdc55) effector branch, which reportedly also controls Gis1 promoter recruitment. These data pinpoint PP2A(Cdc55) as a central node in homo-directional coordination of transcription and post-transcriptional mRNA stabilization of a specific array of nutrient-regulated genes.

  13. The hepatitis E virus open reading frame 3 product interacts with microtubules and interferes with their dynamics.

    PubMed

    Kannan, Harilakshmi; Fan, Sumin; Patel, Deendayal; Bossis, Ioannis; Zhang, Yan-Jin

    2009-07-01

    Hepatitis E virus (HEV) is the causative agent of hepatitis E, a major form of viral hepatitis in developing countries. The open reading frame 3 (ORF3) of HEV encodes a phosphoprotein with a molecular mass of approximately 13 kDa (hereinafter called vp13). vp13 is essential for establishing HEV infections in animals, yet its exact functions are still obscure. Our current study found evidence showing interaction between vp13 and microtubules. Live-cell confocal fluorescence microscopy revealed both filamentous and punctate distribution patterns of vp13 in cells transfected with recombinant ORF3 reporter plasmids. The filamentous pattern of vp13 was altered by a microtubule-destabilizing drug. The vp13 expression led to elevation of acetylated alpha-tubulin, indicating increased microtubule stability. Its association with microtubules was further supported by its presence in microtubule-containing pellets in microtubule isolation assays. Exposure of these pellets to a high-salt buffer caused release of the vp13 to the supernatant, suggesting an electrostatic interaction. Inclusion of ATP and GTP in the lysis buffer during microtubule isolation also disrupted the interaction, indicating its sensitivity to the nucleotides. Further assays showed that motor proteins are needed for the vp13 association with the microtubules because disruption of dynein function abolished the vp13 filamentous pattern. Analysis of ORF3 deletion constructs found that both of the N-terminal hydrophobic domains of vp13 are needed for the interaction. Thus, our findings suggest that the vp13 interaction with microtubules might be needed for establishment of an HEV infection.

  14. Open-reading-frame sequence tags (OSTs) support the existence of at least 17,300 genes in C. elegans.

    PubMed

    Reboul, J; Vaglio, P; Tzellas, N; Thierry-Mieg, N; Moore, T; Jackson, C; Shin-i, T; Kohara, Y; Thierry-Mieg, D; Thierry-Mieg, J; Lee, H; Hitti, J; Doucette-Stamm, L; Hartley, J L; Temple, G F; Brasch, M A; Vandenhaute, J; Lamesch, P E; Hill, D E; Vidal, M

    2001-03-01

    The genome sequences of Caenorhabditis elegans, Drosophila melanogaster and Arabidopsis thaliana have been predicted to contain 19,000, 13,600 and 25,500 genes, respectively. Before this information can be fully used for evolutionary and functional studies, several issues need to be addressed. First, the gene number estimates obtained in silico and not yet supported by any experimental data need to be verified. For example, it seems biologically paradoxical that C. elegans would have 50% more genes than Drosophilia. Second, intron/exon predictions need to be tested experimentally. Third, complete sets of open reading frames (ORFs), or "ORFeomes," need to be cloned into various expression vectors. To address these issues simultaneously, we have designed and applied to C. elegans the following strategy. Predicted ORFs are amplified by PCR from a highly representative cDNA library using ORF-specific primers, cloned by Gateway recombination cloning and then sequenced to generate ORF sequence tags (OSTs) as a way to verify identity and splicing. In a sample (n=1,222) of the nearly 10,000 genes predicted ab initio (that is, for which no expressed sequence tag (EST) is available so far), at least 70% were verified by OSTs. We also observed that 27% of these experimentally confirmed genes have a structure different from that predicted by GeneFinder. We now have experimental evidence that supports the existence of at least 17,300 genes in C. elegans. Hence we suggest that gene counts based primarily on ESTs may underestimate the number of genes in human and in other organisms.

  15. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

    SciTech Connect

    Lee, Jumin; Cheng, Xi; Swails, Jason M.; Yeom, Min Sun; Eastman, Peter K.; Lemkul, Justin A.; Wei, Shuai; Buckner, Joshua; Jeong, Jong Cheol; Qi, Yifei; Jo, Sunhwan; Pande, Vijay S.; Case, David A.; Brooks, Charles L.; MacKerell, Alexander D.; Klauda, Jeffery B.; Im, Wonpil

    2015-11-12

    Here we report that proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. The use of the CHARMM36 force field (C36 FF) in different MD simulation programs can result in disagreements with published simulations performed with CHARMM due to differences in the protocols used to treat the long-range and 1-4 nonbonded interactions. In this study, we systematically test the use of the C36 lipid FF in NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM. A wide range of Lennard-Jones (LJ) cutoff schemes and integrator algorithms were tested to find the optimal simulation protocol to best match bilayer properties of six lipids with varying acyl chain saturation and head groups. MD simulations of a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer were used to obtain the optimal protocol for each program. MD simulations with all programs were found to reasonably match the DPPC bilayer properties (surface area per lipid, chain order parameters, and area compressibility modulus) obtained using the standard protocol used in CHARMM as well as from experiments. The optimal simulation protocol was then applied to the other five lipid simulations and resulted in excellent agreement between results from most simulation programs as well as with experimental data. AMBER compared least favorably with the expected membrane properties, which appears to be due to its use of the hard-truncation in the LJ potential versus a force-based switching function used to smooth the LJ potential as it approaches the cutoff distance. The optimal simulation protocol for each program has been implemented in CHARMM-GUI. This protocol is expected to be applicable to the remainder of the additive C36 FF including the proteins, nucleic acids, carbohydrates, and small molecules.

  16. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

    DOE PAGES

    Lee, Jumin; Cheng, Xi; Swails, Jason M.; ...

    2015-11-12

    Here we report that proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. The use of the CHARMM36 force field (C36 FF) in different MD simulation programs can result in disagreements with published simulations performed with CHARMM due to differences in the protocols used to treat the long-range and 1-4 nonbonded interactions. In this study, we systematically test the use of the C36 lipid FF in NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM. A wide range of Lennard-Jones (LJ) cutoff schemes and integrator algorithms were tested to find themore » optimal simulation protocol to best match bilayer properties of six lipids with varying acyl chain saturation and head groups. MD simulations of a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer were used to obtain the optimal protocol for each program. MD simulations with all programs were found to reasonably match the DPPC bilayer properties (surface area per lipid, chain order parameters, and area compressibility modulus) obtained using the standard protocol used in CHARMM as well as from experiments. The optimal simulation protocol was then applied to the other five lipid simulations and resulted in excellent agreement between results from most simulation programs as well as with experimental data. AMBER compared least favorably with the expected membrane properties, which appears to be due to its use of the hard-truncation in the LJ potential versus a force-based switching function used to smooth the LJ potential as it approaches the cutoff distance. The optimal simulation protocol for each program has been implemented in CHARMM-GUI. This protocol is expected to be applicable to the remainder of the additive C36 FF including the proteins, nucleic acids, carbohydrates, and small molecules.« less

  17. Open reading frame UL26 of human cytomegalovirus encodes a novel tegument protein that contains a strong transcriptional activation domain.

    PubMed

    Stamminger, Thomas; Gstaiger, Matthias; Weinzierl, Konstanze; Lorz, Kerstin; Winkler, Michael; Schaffner, Walter

    2002-05-01

    A selection strategy, the activator trap, was used in order to identify genes of human cytomegalovirus (HCMV) that encode strong transcriptional activation domains in mammalian cells. This approach is based on the isolation of activation domains from a GAL4 fusion library by means of selective plasmid replication, which is mediated in transfected cells by a GAL4-inducible T antigen gene. With this screening strategy, we were able to isolate two types of plasmids encoding transactivating fusion proteins from a library of random HCMV DNA inserts. One plasmid contained the exon 3 of the HCMV IE-1/2 gene region, which has previously been identified as a strong transcriptional activation domain. In the second type of plasmid, the open reading frame (ORF) UL26 of HCMV was fused to the GAL4 DNA-binding domain. By quantitative RNA mapping using S1 nuclease analysis, we were able to classify UL26 as a strong enhancer-type activation domain with no apparent homology to characterized transcriptional activators. Western blot analysis with a specific polyclonal antibody raised against a prokaryotic UL26 fusion protein revealed that two protein isoforms of 21 and 27 kDa are derived from the UL26 ORF in both infected and transfected cells. Both protein isoforms, which arise via alternative usage of two in-frame translational start codons, showed a nuclear localization and could be detected as early as 6 h after infection of primary human fibroblasts. By performing Western blot analysis with purified virions combined with fractionation experiments, we provide evidence that pUL26 is a novel tegument protein of HCMV that is imported during viral infection. Furthermore, we observed transactivation of the HCMV major immediate-early enhancer-promoter by pUL26, whereas several early and late promoters were not affected. Our data suggest that pUL26 is a novel tegument protein of HCMV with a strong transcriptional activation domain that could play an important role during initiation of

  18. Mystery of 1-Vinylpropargyl Formation from Acetylene Addition to the Propargyl Radical: An Open-and-Shut Case.

    PubMed

    da Silva, Gabriel

    2017-03-16

    The addition of acetylene (C2H2) to the propargyl radical (C3H3) initiates a cascade of molecular weight growth reactions that result in the production of polycyclic aromatic hydrocarbons (PAHs) in flames. Although it is well-established that the first reaction step produces the cyclic C5H5 radical cyclopentadienyl (c-C5H5), recent studies have also detected significant quantities of the open-chain form, 1-vinylpropargyl (l-C5H5). This work presents a mechanism for the C3H3 + C2H2 reaction from ab initio calculations, which includes pathways for the formation of both the open and shut isomers as well as for their interconversion. Formation of both isomers proceeds from the initial HCCCH2CHCH(•) reaction adduct with similar barriers, both well below the entrance channel energy. Subsequent isomerization of l-C5H5 with c-C5H5 also transpires at below the energy of the reactants, although this process connects two deep wells (being resonance stabilized radicals), and must compete with collisional energy transfer. An RRKM theory/master equation model is developed for the reported C5H5 reaction mechanism. Master equation simulations suggest that both cyclic and open-chain isomers are expected to form from the C3H3 + C2H2 reaction across a range of temperatures, although the lifetime of l-C5H5 is relatively short for rearrangement to c-C5H5.

  19. Selection pressure on the hepatitis B virus pre-S/S and P open reading frames in Tongan subjects with a chronic hepatitis B virus infection.

    PubMed

    Abbott, William G H; Tsai, Peter; Ross, Howard A; 'Ofanoa, Malakai; Trevarton, Alexander J; Hornell, John; Munn, Stephen R; Gane, Edward J

    2012-11-01

    Identification of the full repertoire of hepatitis B virus (HBV) peptides that are presented to CD8+ T cells by common HLA class I alleles will be useful for designing immunotherapies for chronic hepatitis B. One hundred and seventy five cloned sequences containing the pre-S/S and P open reading frames (ORF) of the HBV were obtained from serum HBV-DNA of HBeAg-positive (n=4) and HBeAg-negative (inactive healthy carriers (IHC), n=16) Tongan subjects with an inactive chronic HBV infection. In addition, 34 and 32 sequences were obtained 5.2±1.4 (mean±SD) years apart from eight subjects. PAML was used to identify codons in the pre-S/S and P ORFs that were under positive selection pressure (ω>1). The number of non-synonymous substitutions in these codons was compared in IHC who were homozygous for either HLA-B∗4001 (n=9) or HLA-B*5602 (n=7), and who were either positive (n=6) or negative (n=10) for HLA-A*02. 34 codons in the pre-S/S and 11 codons in the P ORFs were under positive selection pressure. There was a higher number of non-synonymous substitutions in these codons in HBeAg-negative versus HBeAg-positive subjects in the P (p=0.02) but not the pre-S/S (p=0.64) ORF. There was no association between any HLA class I allele and non-synonymous substitutions in these codons. There was no increase in positive selection pressure on the pre-S/S and P ORFs with time. In conclusion, we could not find HLA class I-restricted selection pressure on any pre-S/S or P ORF amino acid; raising the possibility that peptide-based immunotherapies for chronic hepatitis B may not require peptides from these ORFs.

  20. Translation of the open reading frame encoded by comS, a gene of the srf operon, is necessary for the development of genetic competence, but not surfactin biosynthesis, in Bacillus subtilis.

    PubMed Central

    D'Souza, C; Nakano, M M; Frisby, D L; Zuber, P

    1995-01-01

    A small open reading frame, comS of the srf operon, is the site of mutations that impair competence development in Bacillus subtilis. comS open reading frame translation was required for competence, as was confirmed by the suppression of a comS amber mutation [comS(Am)] by the nonsense suppressor sup-3. comS(Am), when introduced into the srf operon, eliminated late competence gene expression but had no significant effect on surfactin production. PMID:7608091

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

    ERIC Educational Resources Information Center

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

    2015-01-01

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

  2. Open Your Cupboards to Learning Center Games: Activities for Reinforcing Math and Reading Skills for Teacher and Parent Involvement.

    ERIC Educational Resources Information Center

    Langham, Martha A.; Peterson, Nancy M.

    This book has been developed to furnish teachers and parents with ideas for activities and games which aid children in the transition from oral language to printed language for reading and math. These games are designed to provide children with activities and experiences that increase vocabularies and make them useful in communication, language…

  3. Reading First: States Report Improvements in Reading Instruction, but Additional Procedures Would Clarify Education's Role in Ensuring Proper Implementation by States. Report to Congressional Requesters. GAO-07-161

    ERIC Educational Resources Information Center

    Ashby, Cornelia M.

    2007-01-01

    The Reading First program was designed to help students in kindergarten through third grade develop stronger reading skills. This report examines the implementation of the Reading First program, including: (1) changes that have occurred to reading instruction; (2) criteria states have used to award sub-grants to districts, and the difficulties, if…

  4. Re(de)fining the Orthographic Neighborhood: The Role of Addition and Deletion Neighbors in Lexical Decision and Reading

    ERIC Educational Resources Information Center

    Davis, Colin J.; Perea, Manuel; Acha, Joana

    2009-01-01

    The influence of addition and deletion neighbors on visual word identification was investigated in four experiments. Experiments 1 and 2 used Spanish stimuli. In Experiment 1, lexical decision latencies were slower and less accurate for words and nonwords with higher-frequency deletion neighbors (e.g., "jugar" in "juzgar"),…

  5. Purified recombinant hypothetical protein coded by open reading frame Rv1885c of Mycobacterium tuberculosis exhibits a monofunctional AroQ class of periplasmic chorismate mutase activity.

    PubMed

    Prakash, Prachee; Aruna, Bandi; Sardesai, Abhijit A; Hasnain, Seyed E

    2005-05-20

    Naturally occurring variants of the enzyme chorismate mutase are known to exist that exhibit diversity in enzyme structure, regulatory properties, and association with other proteins. Chorismate mutase was not annotated in the initial genome sequence of Mycobacterium tuberculosis (Mtb) because of low sequence similarity between known chorismate mutases. Recombinant protein coded by open reading frame Rv1885c of Mtb exhibited chorismate mutase activity in vitro. Biochemical and biophysical characterization of the recombinant protein suggests its resemblance to the AroQ class of chorismate mutases, prototype examples of which include the Escherichia coli and yeast chorismate mutases. We also demonstrate that unlike the corresponding proteins of E. coli, Mtb chorismate mutase does not have any associated prephenate dehydratase or dehydrogenase activity, indicating its monofunctional nature. The Rv1885c-encoded chorismate mutase showed allosteric regulation by pathway-specific as well as cross-pathway-specific ligands, as evident from proteolytic cleavage protection and enzyme assays. The predicted N-terminal signal sequence of Mtb chorismate mutase was capable of functioning as one in E. coli, suggesting that Mtb chorismate mutase belongs to the AroQ class of chorismate mutases. It was evident that Rv1885c may not be the only enzyme with chorismate mutase enzyme function within Mtb, based on our observation of the presence of chorismate mutase activity displayed by another hypothetical protein coded by open reading frame Rv0948c, a novel instance of the existence of two monofunctional chorismate mutases ever reported in any pathogenic bacterium.

  6. Suppression of ribosomal reinitiation at upstream open reading frames in amino acid-starved cells forms the basis for GCN4 translational control.

    PubMed Central

    Abastado, J P; Miller, P F; Jackson, B M; Hinnebusch, A G

    1991-01-01

    GCN4 encodes a transcriptional activator of amino acid-biosynthetic genes in Saccharomyces cerevisiae that is regulated at the translational level by upstream open reading frames (uORFs) in its mRNA leader. uORF4 (counting from the 5' end) is sufficient to repress GCN4 under nonstarvation conditions; uORF1 is required to overcome the inhibitory effect of uORF4 and stimulate GCN4 translation in amino acid-starved cells. Insertions of sequences with the potential to form secondary structure around uORF4 abolish derepression, indicating that ribosomes reach GCN4 by traversing uORF4 sequences rather than by binding internally to the GCN4 start site. By showing that wild-type regulation occurred even when uORF4 was elongated to overlap GCN4 by 130 nucleotides, we provide strong evidence that those ribosomes which translate GCN4 do so by ignoring the uORF4 AUG start codon. This conclusion is in accord with the fact that translation of a uORF4-lacZ fusion was lower in a derepressed gcd1 mutant than in a nonderepressible gcn2 strain. We also show that increasing the distance between uORF1 and uORF4 to the wild-type spacing that separates uORF1 from GCN4 specifically impaired the ability of uORF1 to derepress GCN4 translation. As expected, this alteration led to increased uORF4-lacZ translation in gcd1 cells. Our results suggest that under starvation conditions, a substantial fraction of ribosomes that translate uORF1 fail to reassemble the factors needed for reinitiation by the time they scan to uORF4, but become competent to reinitiate after scanning the additional sequences to GCN4. Under nonstarvation conditions, ribosomes would recover more rapidly from uORF1 translation, causing them all to reinitiate at uORF4 rather than at GCN4. Images PMID:1986242

  7. Inviting patients and care partners to read doctors' notes: OpenNotes and shared access to electronic medical records.

    PubMed

    Wolff, Jennifer L; Darer, Jonathan D; Berger, Andrea; Clarke, Deserae; Green, Jamie A; Stametz, Rebecca A; Delbanco, Tom; Walker, Jan

    2016-08-07

    We examined the acceptability and effects of delivering doctors' visit notes electronically (via OpenNotes) to patients and care partners with authorized access to patients' electronic medical records. Adult patients and care partners at Geisinger Health System were surveyed at baseline and after 12 months of exposure to OpenNotes. Reporting on care partner access to OpenNotes, patients and care partners stated that they had better agreement about patient treatment plans and more productive discussions about their care. At follow-up, patients were more confident in their ability to manage their health, felt better prepared for office visits, and reported understanding their care better than at baseline. Care partners were more likely to access and use patient portal functionality and reported improved communication with patients' providers at follow-up. Our findings suggest that offering patients and care partners access to doctors' notes is acceptable and improves communication and patients' confidence in managing their care.

  8. Identification of novel proteins binding the AU-rich element of α-prothymosin mRNA through the selection of open reading frames (RIDome).

    PubMed

    Patrucco, Laura; Peano, Clelia; Chiesa, Andrea; Guida, Filomena; Luisi, Imma; Boria, Ilenia; Mignone, Flavio; De Bellis, Gianluca; Zucchelli, Silvia; Gustincich, Stefano; Santoro, Claudio; Sblattero, Daniele; Cotella, Diego

    2015-01-01

    We describe here a platform for high-throughput protein expression and interaction analysis aimed at identifying the RNA-interacting domainome. This approach combines the selection of a phage library displaying "filtered" open reading frames with next-generation DNA sequencing. The method was validated using an RNA bait corresponding to the AU-rich element of α-prothymosin, an RNA motif that promotes mRNA stability and translation through its interaction with the RNA-binding protein ELAVL1. With this strategy, we not only confirmed known RNA-binding proteins that specifically interact with the target RNA (such as ELAVL1/HuR and RBM38) but also identified proteins not previously known to be ARE-binding (R3HDM2 and RALY). We propose this technology as a novel approach for studying the RNA-binding proteome.

  9. Isolation and expression of human cytokine synthesis inhibitory factor cDNA clones: Homology to Epstein-Barr virus open reading frame BCRFI

    SciTech Connect

    Vieira, P.; De Waal-Malefyt, R.; Dang, M.N.; Johnson, K.E.; Kastelein, R.; Fiorentino, D.F.; DeVries, J.E.; Roncarolo, M.G.; Mosmann, T.R.; Moore, K.W. )

    1991-02-15

    The authors demonstrated the existence of human cytokine synthesis inhibitory factor (DSIF) (interleukin 10 (IL-10)). cDNA clones encoding human IL-10 (hIL-10) were isolated from a tetanus toxin-specific human T-cell clone. Like mouse IL-10, hIL-10 exhibits strong DNA and amino acid sequence homology to an open reading frame in the Epstein-Barr virus, BDRFL. hIL-10 and the BCRFI product inhibit cytokine synthesis by activated human peripheral blood mononuclear cells and by a mouse Th1 clone. Both hIL-10 and mouse IL-10 sustain the viability of a mouse mast cell line in culture, but BCRFI lacks comparable activity in this way, suggesting that BCRFI may have conserved only a subset of hIL-10 activities.

  10. Novel Endorna-like viruses, including three with two open reading frames, challenge the membership criteria and taxonomy of the Endornaviridae.

    PubMed

    Ong, Jamie W L; Li, Hua; Sivasithamparam, Krishnapillai; Dixon, Kingsley W; Jones, Michael G K; Wylie, Stephen J

    2016-12-01

    Viruses associated with wild orchids and their mycorrhizal fungi are poorly studied. Using a shotgun sequencing approach, we identified eight novel endornavirus-like genome sequences from isolates of Ceratobasidium fungi isolated from pelotons within root cortical cells of wild indigenous orchid species Microtis media, Pterostylis sanguinea and an undetermined species of Pterostylis in Western Australia. They represent the first endornaviruses to be described from orchid mycorrhizal fungi and from the Australian continent. Five of the novel endornaviruses were detected from one Ceratobasidium isolate collected from one Pterostylis plant. The partial and complete viral replicases shared low (9-30%) identities with one another and with endornaviruses described from elsewhere. Four had genome lengths greater than those of previously described endornaviruses, two resembled ascomycete-infecting endornaviruses, and unlike currently described endornaviruses, three had two open reading frames. The unusual features of these new viruses challenge current taxonomic criteria for membership of the family Endornaviridae.

  11. 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

  12. Open reading frame sequencing and structure-based alignment of polypeptides encoded by RT1-Bb, RT1-Ba, RT1-Db, and RT1-Da alleles.

    PubMed

    Ettinger, Ruth A; Moustakas, Antonis K; Lobaton, Suzanne D

    2004-11-01

    MHC class II genes are major genetic components in rats developing autoimmunity. The majority of rat MHC class II sequencing has focused on exon 2, which forms the first external domain. Sequence of the complete open reading frame for rat MHC class II haplotypes and structure-based alignment is lacking. Herein, the complete open reading frame for RT1-Bbeta, RT1-Balpha, RT1-Dbeta, and RT1-Dalpha was sequenced from ten different rat strains, covering eight serological haplotypes, namely a, b, c, d, k, l, n, and u. Each serological haplotype was unique at the nucleotide level of the sequenced RT1-B/D region. Within individual genes, the number of alleles identified was seven, seven, six, and three and the degree of amino-acid polymorphism between allotypes for each gene was 22%, 16%, 19%, and 0.4% for RT1-Bbeta, RT1-Balpha, RT1-Dbeta, and RT1-Dalpha, respectively. The extent and distribution of amino-acid polymorphism was comparable with mouse and human MHC class II. Structure-based alignment identified the beta65-66 deletion, the beta84a insertion, the alpha9a insertion, and the alpha1a-1c insertion in RT1-B previously described for H2-A. Rat allele-specific deletions were found at RT1-Balpha76 and RT1-Dbeta90-92. The mature RT1-Dbeta polypeptide was one amino acid longer than HLA-DRB1 due to the position of the predicted signal peptide cleavage site. These data are important to a comprehensive understanding of MHC class II structure-function and for mechanistic studies of rat models of autoimmunity.

  13. Combination Antisense Treatment for Destructive Exon Skipping of Myostatin and Open Reading Frame Rescue of Dystrophin in Neonatal mdx Mice

    PubMed Central

    Lu-Nguyen, Ngoc B; Jarmin, Susan A; Saleh, Amer F; Popplewell, Linda; Gait, Michael J; Dickson, George

    2015-01-01

    The fatal X-linked Duchenne muscular dystrophy (DMD), characterized by progressive muscle wasting and muscle weakness, is caused by mutations within the DMD gene. The use of antisense oligonucleotides (AOs) modulating pre-mRNA splicing to restore the disrupted dystrophin reading frame, subsequently generating a shortened but functional protein has emerged as a potential strategy in DMD treatment. AO therapy has recently been applied to induce out-of-frame exon skipping of myostatin pre-mRNA, knocking-down expression of myostatin protein, and such an approach is suggested to enhance muscle hypertrophy/hyperplasia and to reduce muscle necrosis. Within this study, we investigated dual exon skipping of dystrophin and myostatin pre-mRNAs using phosphorodiamidate morpholino oligomers conjugated with an arginine-rich peptide (B-PMOs). Intraperitoneal administration of B-PMOs was performed in neonatal mdx males on the day of birth, and at weeks 3 and 6. At week 9, we observed in treated mice (as compared to age-matched, saline-injected controls) normalization of muscle mass, a recovery in dystrophin expression, and a decrease in muscle necrosis, particularly in the diaphragm. Our data provide a proof of concept for antisense therapy combining dystrophin restoration and myostatin inhibition for the treatment of DMD. PMID:25959011

  14. Sensitization to Food Additives in Patients with Allergy: A Study Based on Skin Test and Open Oral Challenge.

    PubMed

    Moghtaderi, Mozhgan; Hejrati, Zinatosadat; Dehghani, Zahra; Dehghani, Faranak; Kolahi, Niloofar

    2016-06-01

    There has been a great increase in the consumption of various food additives in recent years. The purpose of this study was to identify the incidence of sensitization to food additives by using skin prick test in patients with allergy and to determine the concordance rate between positive skin tests and oral challenge in hypersensitivity to additives. This cross-sectional study included 125 (female 71, male 54) patients aged 2-76 years with allergy and 100 healthy individuals. Skin tests were performed in both patient and control groups with 25 fresh food additives. Among patients with allergy, 22.4% showed positive skin test at least to one of the applied materials. Skin test was negative to all tested food additives in control group. Oral food challenge was done in 28 patients with positive skin test, in whom 9 patients showed reaction to culprit (Concordance rate=32.1%). The present study suggested that about one-third of allergic patients with positive reaction to food additives showed positive oral challenge; it may be considered the potential utility of skin test to identify the role of food additives in patients with allergy.

  15. Open Education Revisited.

    ERIC Educational Resources Information Center

    Bough, Max, Ed.

    1979-01-01

    This journal provides 12 brief articles focused on open education. Topics explored include (1) open education and reading, (2) mainstreaming, (3) characteristics of an open teacher, (4) administration of an open concept school, (5) an existential methodology in the language arts, (6) social studies in open education, (7) open education in early…

  16. A unique open reading frame within the comX gene of Streptococcus mutans regulates genetic competence and oxidative stress tolerance

    PubMed Central

    Kaspar, Justin; Ahn, Sang-Joon; Palmer, Sara R.; Choi, Sang Chul; Stanhope, Michael J.; Burne, Robert A.

    2015-01-01

    Streptococcus mutans displays complex regulation of genetic competence, with ComX controlling late competence gene transcription. The rcrRPQ operon has been shown to link oxidative stress tolerance, (p)ppGpp metabolism and competence in S. mutans. Importantly, an rcrR polar (ΔrcrR-P) mutant is hyper-transformable, but an rcrR non-polar (ΔrcrR-NP) mutant cannot be transformed. Transcriptome comparisons of the rcrR mutants using RNA-Seq and quantitative real-time polymerase chain reaction revealed little expression in the 5′ region of comX in ΔrcrR-NP, but high level expression in the 3′ region. Northern blotting with comX probes revealed two distinct transcripts in the ΔrcrR-P and ΔrcrR-NP strains, and 5′ Rapid Amplification of cDNA Ends mapped the 5′ terminus of the shorter transcript to nt +140 of the comX structural gene, where a unique 69-aa open reading frame, termed XrpA, was encoded in a different reading frame than ComX. Two single-nucleotide substitution mutants (comX::T162C; comX::T210A) were introduced to disrupt XrpA without affecting the sequence of ComX. When the mutations were in the ΔrcrR-NP genetic background, ComX production and transformation were restored. Overexpression of xrpA led to impaired growth in aerobic conditions and decreased transformability. These results reveal an unprecedented mechanism for competence regulation and stress tolerance by a gene product encoded within the comX gene that appears unique to S. mutans. PMID:25620525

  17. 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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  18. Recent Additions in the Modeling Capabilities of an Open-Source Wave Energy Converter Design Tool: Preprint

    SciTech Connect

    Tom, N.; Lawson, M.; Yu, Y. H.

    2015-04-20

    WEC-Sim is a midfidelity numerical tool for modeling wave energy conversion devices. The code uses the MATLAB SimMechanics package to solve multibody dynamics and models wave interactions using hydrodynamic coefficients derived from frequency-domain boundary-element methods. This paper presents the new modeling features introduced in the latest release of WEC-Sim. The first feature discussed conversion of the fluid memory kernel to a state-space form. This enhancement offers a substantial computational benefit after the hydrodynamic body-to-body coefficients are introduced and the number of interactions increases exponentially with each additional body. Additional features include the ability to calculate the wave-excitation forces based on the instantaneous incident wave angle, allowing the device to weathervane, as well as import a user-defined wave elevation time series. A review of the hydrodynamic theory for each feature is provided and the successful implementation is verified using test cases.

  19. The anticentre old open clusters Berkeley 27, Berkeley 34 and Berkeley 36: new additions to the BOCCE project

    NASA Astrophysics Data System (ADS)

    Donati, P.; Bragaglia, A.; Cignoni, M.; Cocozza, G.; Tosi, M.

    2012-08-01

    In this paper, we present the investigation of the evolutionary status of three open clusters: Berkeley 27, Berkeley 34 and Berkeley 36, all located in the Galactic anticentre direction. All of them were observed with SUperb Seeing Imager 2 at the New Technology Telescope using the Bessel B, V and I filters. The cluster parameters have been obtained using the synthetic colour-magnitude diagram (CMD) method, i.e. the direct comparison of the observational CMDs with a library of synthetic CMDs generated with different evolutionary sets (Padova, FRANEC and FST). This analysis shows that Berkeley 27 has an age between 1.5 and 1.7 Gyr, a reddening E(B-V) in the range 0.40-0.50 and a distance modulus (m-M)0 between 13.1 and 13.3; Berkeley 34 is older with an age in the range 2.1-2.5 Gyr, E(B-V) between 0.57 and 0.64 and (m-M)0 between 14.1 and 14.3; Berkeley 36, with an age between 7.0 and 7.5 Gyr, has a reddening of E(B-V) ˜ 0.50 and a distance modulus (m-M)0 between 13.1 and 13.2. For all the clusters, our analysis suggests a subsolar metallicity in accord with their position in the outer Galactic disc. This work is based on data collected at the European Southern Observatory (ESO) telescopes under programme 076.D-0119.

  20. A novel mutation in the upstream open reading frame of the CDKN1B gene causes a MEN4 phenotype.

    PubMed

    Occhi, Gianluca; Regazzo, Daniela; Trivellin, Giampaolo; Boaretto, Francesca; Ciato, Denis; Bobisse, Sara; Ferasin, Sergio; Cetani, Filomena; Pardi, Elena; Korbonits, Márta; Pellegata, Natalia S; Sidarovich, Viktoryia; Quattrone, Alessandro; Opocher, Giuseppe; Mantero, Franco; Scaroni, Carla

    2013-03-01

    The CDKN1B gene encodes the cyclin-dependent kinase inhibitor p27(KIP1), an atypical tumor suppressor playing a key role in cell cycle regulation, cell proliferation, and differentiation. Impaired p27(KIP1) expression and/or localization are often observed in tumor cells, further confirming its central role in regulating the cell cycle. Recently, germline mutations in CDKN1B have been associated with the inherited multiple endocrine neoplasia syndrome type 4, an autosomal dominant syndrome characterized by varying combinations of tumors affecting at least two endocrine organs. In this study we identified a 4-bp deletion in a highly conserved regulatory upstream ORF (uORF) in the 5'UTR of the CDKN1B gene in a patient with a pituitary adenoma and a well-differentiated pancreatic neoplasm. This deletion causes the shift of the uORF termination codon with the consequent lengthening of the uORF-encoded peptide and the drastic shortening of the intercistronic space. Our data on the immunohistochemical analysis of the patient's pancreatic lesion, functional studies based on dual-luciferase assays, site-directed mutagenesis, and on polysome profiling show a negative influence of this deletion on the translation reinitiation at the CDKN1B starting site, with a consequent reduction in p27(KIP1) expression. Our findings demonstrate that, in addition to the previously described mechanisms leading to reduced p27(KIP1) activity, such as degradation via the ubiquitin/proteasome pathway or non-covalent sequestration, p27(KIP1) activity can also be modulated by an uORF and mutations affecting uORF could change p27(KIP1) expression. This study adds the CDKN1B gene to the short list of genes for which mutations that either create, delete, or severely modify their regulatory uORFs have been associated with human diseases.

  1. A Novel Mutation in the Upstream Open Reading Frame of the CDKN1B Gene Causes a MEN4 Phenotype

    PubMed Central

    Occhi, Gianluca; Regazzo, Daniela; Trivellin, Giampaolo; Boaretto, Francesca; Ciato, Denis; Bobisse, Sara; Ferasin, Sergio; Cetani, Filomena; Pardi, Elena; Korbonits, Márta; Pellegata, Natalia S.; Sidarovich, Viktoryia; Quattrone, Alessandro; Opocher, Giuseppe; Mantero, Franco; Scaroni, Carla

    2013-01-01

    The CDKN1B gene encodes the cyclin-dependent kinase inhibitor p27KIP1, an atypical tumor suppressor playing a key role in cell cycle regulation, cell proliferation, and differentiation. Impaired p27KIP1 expression and/or localization are often observed in tumor cells, further confirming its central role in regulating the cell cycle. Recently, germline mutations in CDKN1B have been associated with the inherited multiple endocrine neoplasia syndrome type 4, an autosomal dominant syndrome characterized by varying combinations of tumors affecting at least two endocrine organs. In this study we identified a 4-bp deletion in a highly conserved regulatory upstream ORF (uORF) in the 5′UTR of the CDKN1B gene in a patient with a pituitary adenoma and a well-differentiated pancreatic neoplasm. This deletion causes the shift of the uORF termination codon with the consequent lengthening of the uORF–encoded peptide and the drastic shortening of the intercistronic space. Our data on the immunohistochemical analysis of the patient's pancreatic lesion, functional studies based on dual-luciferase assays, site-directed mutagenesis, and on polysome profiling show a negative influence of this deletion on the translation reinitiation at the CDKN1B starting site, with a consequent reduction in p27KIP1 expression. Our findings demonstrate that, in addition to the previously described mechanisms leading to reduced p27KIP1 activity, such as degradation via the ubiquitin/proteasome pathway or non-covalent sequestration, p27KIP1 activity can also be modulated by an uORF and mutations affecting uORF could change p27KIP1 expression. This study adds the CDKN1B gene to the short list of genes for which mutations that either create, delete, or severely modify their regulatory uORFs have been associated with human diseases. PMID:23555276

  2. Differential regulation of hepatitis B virus core protein expression and genome replication by a small upstream open reading frame and naturally occurring mutations in the precore region.

    PubMed

    Zong, Li; Qin, Yanli; Jia, Haodi; Ye, Lei; Wang, Yongxiang; Zhang, Jiming; Wands, Jack R; Tong, Shuping; Li, Jisu

    2017-05-01

    Hepatitis B virus (HBV) transcribes two subsets of 3.5-kb RNAs: precore RNA for hepatitis B e antigen (HBeAg) expression, and pregenomic RNA for core and P protein translation as well as genome replication. HBeAg expression could be prevented by mutations in the precore region, while an upstream open reading frame (uORF) has been proposed as a negative regulator of core protein translation. We employed replication competent HBV DNA constructs and transient transfection experiments in Huh7 cells to verify the uORF effect and to explore the alternative function of precore RNA. Optimized Kozak sequence for the uORF or extra ATG codons as present in some HBV genotypes reduced core protein expression. G1896A nonsense mutation promoted more efficient core protein expression than mutated precore ATG, while a +1 frameshift mutation was ineffective. In conclusion, various HBeAg-negative precore mutations and mutations affecting uORF differentially regulate core protein expression and genome replication.

  3. Varicella-zoster virus (VZV) open reading frame 10 protein, the homolog of the essential herpes simplex virus protein VP16, is dispensable for VZV replication in vitro.

    PubMed Central

    Cohen, J I; Seidel, K

    1994-01-01

    Varicella-zoster virus (VZV) open reading frame 10 (ORF10) protein in the homolog of the herpes simplex virus type 1 (HSV-1) protein VP16. VZV ORF10 transactivates the VZV IE62 gene and is a tegument protein present in the virion. HSV-1 VP16, a potent transactivator of HSV-1 immediate-early genes and tegument protein, is essential for HSV-1 replication in vitro. To determine whether VZV ORF10 is required for viral replication in vitro, we constructed two VZV mutants which were unable to express ORF10. One mutant had a stop codon after the 61st codon of the ORF10 gene, and the other mutant was deleted for all but the last five codons of the gene. Both VZV mutants grew in cell culture to titers similar to that of the parental virus. To determine whether HSV-1 VP16 alters the growth of VZV, we constructed a VZV mutant in which VP16 was inserted in place of ORF10. Using immune electron microscopy, we found that HSV-1 VP16 was present in the tegument of the recombinant VZV virions. The VZV VP16 substitution mutant produced smaller plaques and grew to a lower titer than parental virus. Thus, VZV ORF10 is not required for growth of the virus in vitro, and substitution of HSV-1 VP16 for VZV ORF10 impairs the growth of VZV. Images PMID:7966575

  4. Expression, nucleotide sequence and mutational analysis of two open reading frames in the nif gene region of Anabaena sp. strain PCC7120.

    PubMed

    Borthakur, D; Basche, M; Buikema, W J; Borthakur, P B; Haselkorn, R

    1990-04-01

    A 1.8 kb transcript corresponding to a region of the Anabaena 7120 chromosome 4 kb downstream of the nifHDK operon appears 12-18 h after heterocyst induction. The DNA corresponding to this transcript was sequenced and found to contain two open reading frames, designated ORF 1 and ORF 2. Two polypeptides, of 30 kDa and 13 kDa, encoded by these ORFs were expressed in Escherichia coli. An apparent start site for the transcript, detected by S1 nuclease protection, was located 42 bp upstream of the ATG start codon of ORF 1. ORF 2 shows strong sequence similarity to ORF 6 in the nif gene region of Azotobacter vinelandii. ORF 1 was interrupted using a 1.4 kb neomycin resistance cassette and the resulting mutant grew very slowly on medium lacking combined nitrogen. The mutant had 45% of wild-type acetylene reduction activity, which could be complemented by a 2.8 kb EcoRI fragment of wild-type Anabaena DNA containing only ORF 1 and ORF 2. Thus, one or both of these ORFs is required for efficient nitrogen fixation in Anabaena.

  5. Open reading frame 94 of Helicoverpa armigera single nucleocapsid nucleopolyhedrovirus encodes a novel conserved occlusion-derived virion protein, ODV-EC43.

    PubMed

    Fang, Minggang; Wang, Hanzhong; Wang, Hualin; Yuan, Li; Chen, Xinwen; Vlak, Just M; Hu, Zhihong

    2003-11-01

    Open reading frame 94 (Ha94) of Helicoverpa armigera single nucleocapsid nucleopolyhedrovirus (HaSNPV) is 1086 bp long and a homologue of Autographa californica multiple NPV ORF109. The gene is conserved among all baculoviruses whose genomes have been completely sequenced so far and is thus considered a baculovirus core gene. Ha94 transcripts were detected from 24 to 96 h post-infection (p.i.) of HzAM1 cells with HaSNPV. Polyclonal antiserum raised to a GST-HA94 fusion protein recognized a 43 kDa protein, HA94, in infected cell lysates from 36 to 96 h p.i., suggesting that Ha94 is a late gene. Western blot analysis of proteins present in budded virus and occlusion-derived virus (ODV) showed that Ha94 encodes a structural component of ODV. When ODVs were fractionated further into nucleocapsid and envelope components, Western blot analysis indicated that the encoded protein was associated with both the nucleocapsid and the envelope. In summary, data available indicated that Ha94 encodes a novel ODV-specific protein of HaSNPV, designated ODV-EC43.

  6. Open reading frames 1a and 1b of the porcine reproductive and respiratory syndrome virus (PRRSV) collaboratively initiate viral minus-strand RNA synthesis.

    PubMed

    Tang, Yan-Dong; Fang, Qiong-Qiong; Liu, Ji-Ting; Wang, Tong-Yun; Wang, Yu; Tao, Ye; Liu, Yong-Gang; Cai, Xue-Hui

    2016-09-02

    The porcine reproductive and respiratory syndrome virus (PRRSV) causes a persistent threat to the swine industry, especially when highly pathogenic PRRSV (HP-PRRSV) emerges. Previous studies have indicated that PRRSV RNA synthesis was correlated with HP-PRRSV virulence. PRRSV RNA synthesis includes genomic RNA and sub-genomic mRNA, and these processes require minus-strand RNA as a template. However, the mechanisms involved in PRRSV minus-strand RNA synthesis are not fully understood. A mini-genome system can be used to assess viral replication mechanisms and to evaluate the effects of potential antiviral drugs on viral replicase activities. In this study, we developed a mini-genome system that uses firefly luciferase as a reporter. Based on this system, we found that PRRSV RNA-dependent RNA polymerase nsp9 alone failed to activate virus minus-strand RNA synthesis. We also demonstrated that combinations of open reading frames 1a (ORF1a) and ORF1b are necessary for viral minus-strand RNA synthesis.

  7. Rapid expression screening of Caenorhabditis elegans homeobox open reading frames using a two-step polymerase chain reaction promoter-gfp reporter construction technique.

    PubMed

    Cassata, G; Kagoshima, H; Prétôt, R F; Aspöck, G; Niklaus, G; Bürglin, T R

    1998-05-28

    In this paper a description is given of the expression pattern of the Caenorhabditis elegans homeobox gene ceh-38 using GFP reporter constructs, which were generated using a two-step polymerase chain reaction (PCR) procedure. This method allows fast analysis of genes of interest by looking at their expression in vivo using their putative promoter region to control the expression of a reporter gene. In this case the method was applied to screen C. elegans homeobox-containing genes to identify those that are expressed in the head and nervous system. The C. elegans genome project has made rapid progress, and more than 79 megabases of genomic data with several thousand open reading frames are available. This information can be used to design primers from putative promoter regions, which are amplified using long-range PCR. The long-range PCR product is then directly joined to the vector in a long-range Fill-in PCR. Since many genome projects are advancing rapidly, this approach should also be applicable for other model systems, and the method lends itself to automation, since no gel-purification steps are necessary. ceh-38 is a member of the ONECUT class of homeobox genes. Expression of ceh-38 starts during embryogenesis. In larvae and adults, expression was seen in many different types of tissues, such as the pharynx, gut, hypodermis and many nerve cells.

  8. Kaposi's Sarcoma-Associated Herpesvirus Open Reading Frame 50/Rta Protein Activates the Entire Viral Lytic Cycle in the HH-B2 Primary Effusion Lymphoma Cell Line†

    PubMed Central

    Gradoville, Lyndle; Gerlach, Jennifer; Grogan, Elizabeth; Shedd, Duane; Nikiforow, Sarah; Metroka, Craig; Miller, George

    2000-01-01

    Rta, the gene product of Kaposi's sarcoma-associated herpesvirus (KSHV) encoded mainly in open reading frame 50 (ORF50), is capable of activating expression of viral lytic cycle genes. What was not demonstrated in previous studies was whether KSHV Rta was competent to initiate the entire viral lytic life cycle including lytic viral DNA replication, late-gene expression with appropriate kinetics, and virus release. In HH-B2, a newly established primary effusion lymphoma (PEL) cell line, KSHV ORF50 behaved as an immediate-early gene and autostimulated its own expression. Expression of late genes, ORF65, and K8.1 induced by KSHV Rta was eliminated by phosphonoacetic acid, an inhibitor of viral DNA polymerase. Transfection of KSHV Rta increased the production of encapsidated DNase-resistant viral DNA from HH-B2 cells. Thus, introduction of an ORF50 expression plasmid is sufficient to drive the lytic cycle to completion in cultured PEL cells. PMID:10846108

  9. Transgenic mouse model expressing P53R172H, luciferase, EGFP, and KRASG12D in a single open reading frame for live imaging of tumor

    PubMed Central

    Ju, Hye-Lim; Calvisi, Diego F.; Moon, Hyuk; Baek, Sinhwa; Ribback, Silvia; Dombrowski, Frank; Cho, Kyung Joo; Chung, Sook In; Han, Kwang-Hyub; Ro, Simon Weonsang

    2015-01-01

    Genetically engineered mouse cancer models allow tumors to be imaged in vivo via co-expression of a reporter gene with a tumor-initiating gene. However, differential transcriptional and translational regulation between the tumor-initiating gene and the reporter gene can result in inconsistency between the actual tumor size and the size indicated by the imaging assay. To overcome this limitation, we developed a transgenic mouse in which two oncogenes, encoding P53R172H and KRASG12D, are expressed together with two reporter genes, encoding enhanced green fluorescent protein (EGFP) and firefly luciferase, in a single open reading frame following Cre-mediated DNA excision. Systemic administration of adenovirus encoding Cre to these mice induced specific transgene expression in the liver. Repeated bioluminescence imaging of the mice revealed a continuous increase in the bioluminescent signal over time. A strong correlation was found between the bioluminescent signal and actual tumor size. Interestingly, all liver tumors induced by P53R172H and KRASG12D in the model were hepatocellular adenomas. The mouse model was also used to trace cell proliferation in the epidermis via live fluorescence imaging. We anticipate that the transgenic mouse model will be useful for imaging tumor development in vivo and for investigating the oncogenic collaboration between P53R172H and KRASG12D. PMID:25623590

  10. Virions of Pariacoto virus contain a minor protein translated from the second AUG codon of the capsid protein open reading frame.

    PubMed

    Johnson, Karyn N; Ball, L Andrew

    2003-10-01

    Virions of the alphanodavirus Pariacoto virus (PaV) have T=3 icosahedral symmetry and are assembled from multiple copies of a precursor protein that is cleaved into two mature capsid proteins after assembly. The crystal structure of PaV shows that the N-terminal approximately 30 amino acid residues of the subunits surrounding the 5-fold axes interact extensively with icosahedrally ordered regions of the encapsidated positive-sense genomic RNAs. We found that wild-type PaV particles also contain a minor capsid protein that is truncated by 24 residues at its N terminus. Reverse genetic experiments showed that translation of this protein initiated at the second AUG of the capsid protein open reading frame. When either the longer or shorter version of the capsid protein was expressed independently of the other, it assembled into virus particles and underwent maturational cleavage. Virions that lacked the shorter capsid protein retained infectivity for cultured insect cells and Galleria mellonella larvae.

  11. E2 of cottontail rabbit papillomavirus is a nuclear phosphoprotein translated from an mRNA encoding multiple open reading frames.

    PubMed Central

    Barbosa, M S; Wettstein, F O

    1988-01-01

    The papillomavirus E2 protein is a transcription trans-activator and as such as a paramount effect on viral functions. We have identified and characterized the cottontail rabbit papillomavirus E2 protein expressed from the late simian virus 40 promoter in COS-7 cells. E2 was shown to be a highly phosphorylated 49-kilodalton protein. Subcellular fractionation and indirect immunofluorescent staining indicated that E2 was located in the nuclei. E2 was expressed from a vector which contained just the open reading frame. ORF E2 and also from vectors which extended farther upstream and also expressed E7 or the short E6 protein. However, the level of E2 was very low in cells transfected with a vector expressing the long E6 protein. Mapping of transcripts with nuclease S1 and exonuclease ExoVII in cells expressing the short E6 and E2 proteins showed that E2 was translated from an RNA which encoded the short E6, E7, and E2 proteins but served as mRNA for only the short E6 and E2 proteins. Images PMID:2841476

  12. Alternative splicing within the elk-1 5' untranslated region serves to modulate initiation events downstream of the highly conserved upstream open reading frame 2.

    PubMed

    Rahim, Gwendoline; Araud, Tanguy; Jaquier-Gubler, Pascale; Curran, Joseph

    2012-05-01

    The 5' untranslated region (UTR) plays a central role in the regulation of mammalian translation initiation. Key components include RNA structure, upstream AUGs (uAUGs), upstream open reading frames (uORFs), and internal ribosome entry site elements that can interact to modulate the readout. We previously reported the characterization of two alternatively spliced 5' UTR isoforms of the human elk-1 gene. Both contain two uAUGs and a stable RNA stem-loop, but the long form (5' UTR(L)) was more repressive than the short form (5' UTR(S)) for initiation at the ELK-1 AUG. We now demonstrate that ELK-1 expression arises by a combination of leaky scanning and reinitiation, with the latter mediated by the small uORF2 conserved in both spliced isoforms. In HEK293T cells, a considerable fraction of ribosomes scans beyond the ELK-1 AUG in a reinitiation mode. These are sequestered by a series of out-of-frame AUG codons that serve to prevent access to a second in-frame AUG start site used to express short ELK-1 (sELK-1), an N-terminally truncated form of ELK-1 that has been observed only in neuronal cells. We present evidence that all these events are fine-tuned by the nature of the 5' UTR and the activity of the α subunit of eukaryotic initiation factor 2 and provide insights into the neuronal specificity of sELK-1 expression.

  13. Functional analysis of naturally occurring mutations in the open reading frame of CCR5 in HIV-infected Chinese patients and healthy controls.

    PubMed

    Zhao, Xiu-Ying; Lee, Shui-Shan; Wong, Ka-Hing; Chan, Kenny C W; Ng, Fai; Chan, Chris C S; Han, Dan; Yam, Wing-Cheong; Yuen, Kwok-Yung; Ng, Mun-Hon; Zheng, Bo-Jian

    2005-04-15

    We studied polymorphism of the HIV coreceptor CC chemokine receptor (CCR) 5 in 1099 Chinese adults residing in Hong Kong, including 785 HIV-negative healthy donors and 314 HIV-positive patients. Ten mutants in the CCR5 open reading frame were identified, 7 of which were nonsynonymous. The frequencies of these alleles did not show a significant difference between HIV patients and healthy controls. G106R, Delta32, R223Q, 299(FS), and S336I were cloned from prevalent mutant genes, and their effects on HIV infection were analyzed by a series of in vitro experiments to determine their transcription levels, expression levels, conformational changes, and HIV coreceptor function. R223Q is the most prevalent CCR5 mutant in ethnic Chinese, with a frequency of 0.046, which does not affect HIV infection in vitro, however. The S336I mutant also does not affect its transcription, expression, or HIV coreceptor function. Similar to 299(FS), the mutant G106R located in the third transmembrane domain results in diminished HIV coreceptor function in vitro through conformation changes in ECL2.

  14. The nucleotide sequence of a 39 kb segment of yeast chromosome IV: 12 new open reading frames, nine known genes and one genes for Gly-tRNA.

    PubMed

    Bahr, A; Möller-Rieker, S; Hankeln, T; Kraemer, C; Protin, U; Schmidt, E R

    1997-02-01

    The complete nucleotide sequence of a 39,090 bp segment from the left arm of yeast chromosome IV was determined. Twenty-one open reading frames (ORFs) longer than 100 amino acids and a Gly-tRNA gene were discovered. Nine of the 21 ORFs (D0892, D1022, D1037, D1045, D1057, D1204, D1209, D1214, D1219) correspond to the previously sequenced Saccharomyces cerevisiae genes for the NAD-dependent glutamate dehydrogenase (GDH), the secretory component (SHR3), the GABA transport protein (UGA4), the high mobility group-like protein (NHP2), the hydroxymethylbilane synthase (HEM3), the methylated DNA protein-cysteine S-methyltransferase (MGT1), a putative sugar transport protein, the Shm1 protein (SHM1) and the anti-silencing protein (ASF2). The inferred amino acid sequences of 11 ORFs show significant similarity with known proteins from various organisms, whereas the remaining ORF does not share any similarity with known proteins.

  15. Fine mapping of the latency-related gene of herpes simplex virus type 1: alternative splicing produces distinct latency-related RNAs containing open reading frames

    SciTech Connect

    Wechsler, S.L.; Nesburn, A.B.; Watson, R.; Slanina, S.M.; Ghiasi, H.

    1988-11-01

    The latency-related (LR) gene of herpes simplex virus type 1 (HSV-1) is transcriptionally active during HSV-1 latency, producing at least two LR-RNAs. The LR gene partially overlaps the immediate-early gene ICP0 and is transcribed in the opposite direction from ICP0, producing LR-RNAs that are complementary (antisense) to ICP0 mRNA. The LR gene is thought to be involved in HSV-1 latency. The authors report here the time mapping and partial sequence analysis of this HSV-1 LR gene. /sup 32/P-labeled genomic DNA restriction fragments and synthetic oligonucleotides were used as probes for in situ hybridizations and Northern (RNA) blot hybridizations of RNA from trigeminal ganglia of rabbits latently infected with HSV-1. The two most abundant LR-RNAs appeared to share their 5' and 3' ends and to be produced by alternative splicing. These LR-RNAs were approximately 2 and 1.3 to 1.5 kilobases in length and were designated LR-RNA 1 and LF-RNA 2, respectively. LR-RNA 1 appeared to have at least one intron removed, while LR-RNA 2 appeared to have at least two introns removed. The LR-RNAs contained two potential long open reading frames, suggesting the possibility that one or more of the LR-RNAs may be a functional mRNA.

  16. The Effects of Extensive Reading and Reading Strategies on Reading Self-Efficacy

    ERIC Educational Resources Information Center

    Burrows, Lance

    2012-01-01

    This study is a quasi-experimental, longitudinal investigation into the role that extensive reading and reading strategies play in the cultivation of reading self-efficacy. Conducted over the course of one academic year, how changes in reading self-efficacy translate into changes in reading comprehension was examined. In addition, the…

  17. Open reading frame 5 (ORF5), encoding a ferredoxinlike protein, and nifQ are cotranscribed with nifE, nifN, nifX, and ORF4 in Rhodobacter capsulatus.

    PubMed

    Moreno-Vivian, C; Hennecke, S; Pühler, A; Klipp, W

    1989-05-01

    DNA sequence analysis of a 1,600-base-pair fragment located downstream of nifENX in nif region A of Rhodobacter capsulatus revealed two additional open reading frames (ORFs): ORF5, encoding a ferredoxinlike protein, and nifQ. The ferredoxinlike gene product contained two cysteine motifs, typical of ferredoxins coordinating two 4Fe-4S clusters, but the distance between these two motifs was unusual for low-molecular-weight ferredoxins. The R. capsulatus nifQ gene product shared a high degree of homology with Klebsiella pneumoniae and Azotobacter vinelandii NifQ, including a typical cysteine motif located in the C-terminal part. nifQ insertion mutants and also an ORF5-nifQ double deletion mutant showed normal diazotrophic growth only in the presence of high concentrations of molybdate. This demonstrated that the gene encoding the ferredoxinlike protein is not essential for nitrogen fixation. No NifA-activated consensus promoter could be found in the intergenic region between nifENX-ORF4 and ORF5-nifQ. Analyses of a nifQ-lacZYA fusion revealed that transcription of nifQ was initiated at a promoter in front of nifE. In contrast to other nitrogen-fixing organisms, R. capsulatus nifE, nifN, nifX, ORF4, ORF5, and nifQ were organized in one transcriptional unit.

  18. [Reading Teacher Education.

    ERIC Educational Resources Information Center

    Palmatier, Robert A., Ed.

    1976-01-01

    This issue of "Epistle," the publication forum of Professors of Reading Teacher Educators, contains three papers as well as the regular features on job openings and on miscellaneous facts. Titles and authors of the articles are: "Doctoral Education in Reading: The State of the Art," by Richard Allington; "The Virtues of Being a Toad and What That…

  19. Immunogenicity of a Multi-Epitope DNA Vaccine Encoding Epitopes from Cu–Zn Superoxide Dismutase and Open Reading Frames of Brucella abortus in Mice

    PubMed Central

    Escalona, Emilia; Sáez, Darwin; Oñate, Angel

    2017-01-01

    Brucellosis is a bacterial zoonotic disease affecting several mammalian species that is transmitted to humans by direct or indirect contact with infected animals or their products. In cattle, brucellosis is almost invariably caused by Brucella abortus. Live, attenuated Brucella vaccines are commonly used to prevent illness in cattle, but can cause abortions in pregnant animals. It is, therefore, desirable to design an effective and safer vaccine against Brucella. We have used specific Brucella antigens that induce immunity and protection against B. abortus. A novel recombinant multi-epitope DNA vaccine specific for brucellosis was developed. To design the vaccine construct, we employed bioinformatics tools to predict epitopes present in Cu–Zn superoxide dismutase and in the open reading frames of the genomic island-3 (BAB1_0260, BAB1_0270, BAB1_0273, and BAB1_0278) of Brucella. We successfully designed a multi-epitope DNA plasmid vaccine chimera that encodes and expresses 21 epitopes. This DNA vaccine induced a specific humoral and cellular immune response in BALB/c mice. It induced a typical T-helper 1 response, eliciting production of immunoglobulin G2a and IFN-γ particularly associated with the Th1 cell subset of CD4+ T cells. The production of IL-4, an indicator of Th2 activation, was not detected in splenocytes. Therefore, it is reasonable to suggest that the vaccine induced a predominantly Th1 response. The vaccine induced a statistically significant level of protection in BALB/c mice when challenged with B. abortus 2308. This is the first use of an in silico strategy to a design a multi-epitope DNA vaccine against B. abortus. PMID:28232837

  20. 1-Deoxy-d-Xylulose 5-Phosphate Synthase, the Gene Product of Open Reading Frame (ORF) 2816 and ORF 2895 in Rhodobacter capsulatus

    PubMed Central

    Hahn, Frederick M.; Eubanks, Lisa M.; Testa, Charles A.; Blagg, Brian S. J.; Baker, Jonathan A.; Poulter, C. Dale

    2001-01-01

    In eubacteria, green algae, and plant chloroplasts, isopentenyl diphosphate, a key intermediate in the biosynthesis of isoprenoids, is synthesized by the methylerythritol phosphate pathway. The five carbons of the basic isoprenoid unit are assembled by joining pyruvate and d-glyceraldehyde 3-phosphate. The reaction is catalyzed by the thiamine diphosphate-dependent enzyme 1-deoxy-d-xylulose 5-phosphate synthase. In Rhodobacter capsulatus, two open reading frames (ORFs) carry the genes that encode 1-deoxy-d-xylulose 5-phosphate synthase. ORF 2816 is located in the photosynthesis-related gene cluster, along with most of the genes required for synthesis of the photosynthetic machinery of the bacterium, whereas ORF 2895 is located elsewhere in the genome. The proteins encoded by ORF 2816 and ORF 2895, 1-deoxy-d-xylulose 5-phosphate synthase A and B, containing a His6 tag, were synthesized in Escherichia coli and purified to greater than 95% homogeneity in two steps. 1-Deoxy-d-xylulose 5-phosphate synthase A appears to be a homodimer with 68 kDa subunits. A new assay was developed, and the following steady-state kinetic constants were determined for 1-deoxy-d-xylulose 5-phosphate synthase A and B: Kmpyruvate = 0.61 and 3.0 mM, Kmd-glyceraldehyde 3-phosphate = 150 and 120 μM, and Vmax = 1.9 and 1.4 μmol/min/mg in 200 mM sodium citrate (pH 7.4). The ORF encoding 1-deoxy-d-xylulose 5-phosphate synthase B complemented the disrupted essential dxs gene in E. coli strain FH11. PMID:11114895

  1. Implementation and assessment of a yeast orphan gene research project: involving undergraduates in authentic research experiences and progressing our understanding of uncharacterized open reading frames.

    PubMed

    Bowling, Bethany V; Schultheis, Patrick J; Strome, Erin D

    2016-02-01

    Saccharomyces cerevisiae was the first eukaryotic organism to be sequenced; however, little progress has been made in recent years in furthering our understanding of all open reading frames (ORFs). From October 2012 to May 2015 the number of verified ORFs had only risen from 75.31% to 78%, while the number of uncharacterized ORFs had decreased from 12.8% to 11% (representing > 700 genes still left in this category; http://www.yeastgenome.org/genomesnapshot). Course-based research has been shown to increase student learning while providing experience with real scientific investigation; however, implementation in large, multi-section courses presents many challenges. This study sought to test the feasibility and effectiveness of incorporating authentic research into a core genetics course, with multiple instructors, to increase student learning and progress our understanding of uncharacterized ORFs. We generated a module-based annotation toolkit and utilized easily accessible bioinformatics tools to predict gene function for uncharacterized ORFs within the Saccharomyces Genome Database (SGD). Students were each assigned an uncharacterized ORF, which they annotated using contemporary comparative genomics methodologies, including multiple sequence alignment, conserved domain identification, signal peptide prediction and cellular localization algorithms. Student learning outcomes were measured by quizzes, project reports and presentations, as well as a post-project questionnaire. Our results indicate that the authentic research experience had positive impacts on students' perception of their learning and their confidence to conduct future research. Furthermore, we believe that creation of an online repository and adoption and/or adaptation of this project across multiple researchers and institutions could speed the process of gene function prediction.

  2. Human T-cell leukemia virus open reading frame II encodes a posttranscriptional repressor that is recruited at the level of transcription.

    PubMed

    Younis, Ihab; Boris-Lawrie, Kathleen; Green, Patrick L

    2006-01-01

    Human T-cell leukemia virus (HTLV) infection is a chronic, lifelong infection that is associated with the development of leukemia and neurological disease after a long latency period, and the mechanism by which the virus is able to evade host immune surveillance is elusive. Besides the structural and enzymatic proteins, HTLV encodes regulatory (Tax and Rex) and accessory (open reading frame I [ORF I] and ORF II) proteins. Tax activates viral and cellular transcription and promotes T-cell growth and malignant transformation. Rex acts posttranscriptionally to facilitate cytoplasmic expression of incompletely spliced viral mRNAs. Recently, we reported that the accessory gene products of HTLV-1 and HTLV-2 ORF II (p30II and p28II, respectively) are able to restrict viral replication. These proteins act as negative regulators of both Tax and Rex by binding to and retaining their mRNA in the nucleus, leading to reduced protein expression and virion production. Here, we show that p28II is recruited to the viral promoter in a Tax-dependent manner. After recruitment to the promoter, p28II or p30II then travels with the transcription elongation machinery until its target mRNA is synthesized. Experiments artificially directing these proteins to the promoter indicate that p28II, unlike HTLV-1 p30II, displays no transcriptional activity. Furthermore, the tethering of p28II directly to tax/rex mRNA resulted in repression of Tax function, which could be attributed to the ability of p28II to block TAP/p15-mediated enhancement of Tax expression. p28II-mediated reduction of viral replication in infected cells may permit survival of the cells by allowing escape from immune recognition, which is consistent with the critical role of HTLV accessory proteins in viral persistence in vivo.

  3. Roles of genomic island 3 (GI-3) BAB1_0267 and BAB1_0270 open reading frames (ORFs) in the virulence of Brucella abortus 2308.

    PubMed

    Ortiz-Román, Luisa; Riquelme-Neira, Roberto; RobertoVidal; Oñate, Angel

    2014-08-06

    One of the properties of bacteria is their capacity to acquire large fragments of genomic DNA from other bacteria or to loose important parts of their own genome. Such fragments include genomic islands (GIs); nine GIs are present in Brucella, including genomic island 3 (GI-3), present in B. abortus, B. melitensis and B. ovis. The GI-3 have 29 open reading frames (ORFs) most of them with unknown function. Within the GI-3, the ORFs BAB1_0267 encodes a hypothetical protein sharing a SH3 domain and BAB1_270 a zinc-dependent metallopeptidase. We have obtained deletion mutants for BAB1_0267 and BAB1_0270 ORFs present within GI-3, which have been named the Δ0267 and Δ0270, respectively; in both cases the mutation did not affect the growth of bacteria. Both mutants were evaluated with respect to their growth rates, their ability to invade and replicate in the non-professional and professional phagocytes, HeLa and J774.A1 cells, respectively. Their persistence in the spleens of mice was also evaluated. The mutants efficiently invaded HeLa and J774.A1 cells but both mutants showed a decreased intracellular survival in macrophages and HeLa cells 72 and 96 h post-infection, respectively, and were non-detected in J774.A1 cells 120 h post infection. With respect to in vivo persistence Δ0267 was detected through the fourth week while Δ0270 decreased at 7 days disappearing the second week. Our results indicated that deletion of BAB1_0267 and BAB1_270 are necessary to establish an optimal infectious process in B. abortus 2308, having more effect the deletion of ORF BAB1_0270. Therefore these ORFs, principally BAB1_0270 are important virulent of B. abortus.

  4. The gag gene products of human immunodeficiency virus type 1: alignment within the gag open reading frame, identification of posttranslational modifications, and evidence for alternative gag precursors.

    PubMed

    Mervis, R J; Ahmad, N; Lillehoj, E P; Raum, M G; Salazar, F H; Chan, H W; Venkatesan, S

    1988-11-01

    Seven human immunodeficiency virus gag polypeptides were identified in the purified virus and in infected CD4+ lymphocytes by peptide mapping and limited amino acid sequencing of immune-purified proteins. Two gag polyproteins of 55,000 (p55) and 41,000 (p41) daltons were rapidly labeled and readily processed into the major internal gag proteins that were aligned within the gag open reading frame (ORF) as NH2-p16 (MA)-p24 (CA)-p9 (NC)-p7-COOH. The myristoylated p16 (matrix, MA) protein was processed from the myristoylated p55 gag precursor protein. The immunoreactivity of the p16 (MA) protein with region-specific gag antisera and the conservation of the N-terminal myristyl group of the p55 precursor protein in p16 (MA) confirmed its position as the N-terminal-most protein. The p9 (nucleocapsid, NC) protein was localized to residue 378 of the gag ORF, next to the C terminus of the p24/p25 (core antigen, CA) protein. The p9 protein had a repeating Cys residue containing motif which is found in the nucleic acid-binding Cys residue-containing proteins of retroviruses. The p24 (CA) protein, which was localized to residue 133 of the gag ORF, was apparently derived by C-terminal processing of an intermediate polypeptide, p25. Both the mature p24 (CA) and p16 (MA) proteins were phosphorylated at Ser residue(s). We also identified two forms of gag p41 species, one resulting from the C-terminal processing of p55 and the other originating either from N-terminal processing of p55 or from de novo synthesis.

  5. Varicella-zoster virus open reading frame 4 encodes a transcriptional activator that is functionally distinct from that of herpes simplex virus homology ICP27.

    PubMed Central

    Perera, L P; Kaushal, S; Kinchington, P R; Mosca, J D; Hayward, G S; Straus, S E

    1994-01-01

    Varicella-zoster virus is the etiological agent of chickenpox and zoster in humans and belongs to the Alphaherpesvirinae subfamily within the family Herpesviridae. Much of the current understanding of gene regulation in alphaherpesviruses has been derived from studies of the prototype herpes simplex virus (HSV). In HSV, two virus-encoded, trans-regulatory proteins, ICP4 and ICP27, are essential for the replicative cycle of the virus. ICP4 is important in modulating HSV genes of all three kinetic classes, whereas the trans-regulatory effects of ICP27 are primarily associated with the expression of late genes. Recent evidence indicates that the trans-regulatory effects of ICP27 involve posttranscriptional processing of target gene transcripts (R. M. Sandri-Golding and G. E. Mendoza, Genes Dev. 6:848-863, 1992). The ICP27 homolog in varicella-zoster virus is a 452-amino-acid polypeptide encoded by the open reading frame 4 (ORF4) gene. Contrary to what is found with ICP27, we show that the ORF4 polypeptide is a transcriptional activator of diverse target promoters and has a critical requirement for the presence of upstream elements within these promoters to mediate its transcriptional effects. Evidence is also presented to implicate a critical role for the cysteine-rich, C-terminal region of the ORF4 polypeptide in its trans-regulatory functions. Specifically, by oligonucleotide-directed site-specific mutagenesis, we demonstrate that of 10 cysteine residues in the ORF4 polypeptide, only C-421 and C-426 are essential for transactivator function and suggest that these cysteine residues may participate in critical protein-protein interactions rather than protein-nucleic acid interactions to mediate ORF4 inducibility. Images PMID:8139031

  6. Partial Restoration of Antibacterial Activity of the Protein Encoded by a Cryptic Open Reading Frame (cyt1Ca) from Bacillus thuringiensis subsp. israelensis by Site-Directed Mutagenesis

    PubMed Central

    Itsko, Mark; Manasherob, Robert; Zaritsky, Arieh

    2005-01-01

    Insecticidal crystal proteins of Bacillus thuringiensis belong to two unrelated toxin families: receptor-specific Cry toxins against insects and Cyt toxins that lyse a broad range of cells, including bacteria, via direct binding to phospholipids. A new cyt-like open reading frame (cyt1Ca) encoding a 60-kDa protein, has recently been discovered (C. Berry et al., Appl. Environ. Microbiol. 68:5082-5095, 2002). Cyt1Ca displays the structure of a two-domain fusion protein: the N-terminal moiety resembles the full-length Cyt toxins, and the C-terminal moiety is similar to the receptor-binding domains of several ricin-like toxins, such as Mtx1. Neither the larvicidal activity of cyt1Ca expressed in Escherichia coli nor the hemolytic effect of His-tagged purified Cyt1Ca has been observed (R. Manasherob et al., unpublished). This was attributed to five amino acid differences between the sequences of its N-terminal moiety and Cyt1Aa. The 3′ end of cyt1Ca was truncated (removing the ricin-binding domain of Cyt1Ca), and six single bases were appropriately changed by site-directed mutagenesis, sequentially replacing the noncharged amino acids by charged ones, according to Cyt1Aa, to form several versions. Expression of these mutated cyt1Ca versions caused loss of the colony-forming ability of the corresponding E. coli cells to different extents compared with the original gene. In some mutants this antibacterial effect was associated by significant distortion of cell morphology and in others by generation of multiple inclusion bodies spread along the cell envelope. The described deleterious effects of mutated cyt1Ca versions against E. coli may reflect an evolutionary relationship between Cyt1Aa and Cyt1Ca. PMID:16159771

  7. Two Subclasses of Kaposi's Sarcoma-Associated Herpesvirus Lytic Cycle Promoters Distinguished by Open Reading Frame 50 Mutant Proteins That Are Deficient in Binding to DNA

    PubMed Central

    Chang, Pey-Jium; Shedd, Duane; Miller, George

    2005-01-01

    A transcriptional activator encoded in open reading frame 50 (ORF50) of the Kaposi's sarcoma-associated herpesvirus (KSHV) genome initiates the viral lytic cycle. Here we classify four lytic cycle genes on the basis of several characteristics of the ORF50 response elements (ORF50 REs) in their promoters: nucleotide sequence homology, the capacity to bind ORF50 protein in vitro, the ability to bind the cellular protein RBP-Jκ in vitro, and the capacity to confer activation by DNA binding-deficient mutants of ORF50 protein. ORF50 expressed in human cells binds the promoters of PAN and K12 but does not bind ORF57 or vMIP-1 promoters. Conversely, the RBP-Jκ protein binds ORF57 and vMIP-1 but not PAN or K12 promoters. DNA binding-deficient mutants of ORF50 protein differentiate these two subclasses of promoters in reporter assays; the PAN and K12 promoters cannot be activated, while the ORF57 and vMIP-1 promoters are responsive. Although DNA binding-deficient mutants of ORF50 protein are defective in activating direct targets, they are nonetheless capable of activating the lytic cascade of KSHV. Significantly, DNA binding-deficient ORF50 mutants are competent to autostimulate expression of endogenous ORF50 and to autoactivate ORF50 promoter reporters. The experiments show that ORF50 protein activates downstream targets by at least two distinct mechanisms: one involves direct binding of ORF50 REs in promoter DNA; the other mechanism employs interactions with the RBP-Jκ cellular protein bound to promoter DNA in the region of the ORF50 RE. The DNA binding-deficient mutants allow classification of ORF50-responsive genes and will facilitate study of the several distinct mechanisms of activation of KSHV lytic cycle genes that are under the control of ORF50 protein. PMID:15994769

  8. Implementation and assessment of a yeast orphan gene research project; involving undergraduates in authentic research experiences and progressing our understanding of uncharacterized open reading frames

    PubMed Central

    Bowling, Bethany V.; Schultheis, Patrick J.

    2015-01-01

    Saccharomyces cerevisiae was the first eukaryotic organism to be sequenced, however little progress has been made in recent years in furthering our understanding of all open reading frames (ORFs). From October 2012 to May 2015 the number of verified ORFs has only risen from 75.31% to 78% while the number of uncharacterized ORFs have decreased from 12.8% to 11% (representing more than 700 genes still left in this category) [http://www.yeastgenome.org/genomesnapshot]. Course-based research has been shown to increase student learning while providing experience with real scientific investigation; however, implementation in large, multi-section courses presents many challenges. This study sought to test the feasibility and effectiveness of incorporating authentic research into a core genetics course with multiple instructors to increase student learning and progress our understanding of uncharacterized ORFs. We generated a module-based annotation toolkit and utilized easily accessible bioinformatics tools to predict gene function for uncharacterized ORFs within the Saccharomyces Genome Database (SGD). Students were each assigned an uncharacterized ORF which they annotated using contemporary comparative genomics methodologies including multiple sequence alignment, conserved domain identification, signal peptide prediction and cellular localization algorithms. Student learning outcomes were measured by quizzes, project reports and presentations, as well as a post-project questionnaire. Our results indicate the authentic research experience had positive impacts on student's perception of their learning and their confidence to conduct future research. Furthermore we believe that creation of an online repository and adoption and/or adaptation of this project across multiple researchers and institutions could speed the process of gene function prediction. PMID:26460164

  9. Detection of a group II intron without an open reading frame in the alpha-toxin gene of Clostridium perfringens isolated from a broiler chicken.

    PubMed

    Ma, Menglin; Ohtani, Kaori; Shimizu, Tohru; Misawa, Naoaki

    2007-03-01

    A DNA insertion of 834 bp, designated CPF-G2Im, was identified within the alpha toxin gene (cpa) of Clostridium perfringens strain CPBC16ML, isolated from a broiler chicken. Sequence analysis of CPF-G2Im indicated that it was integrated 340 nucleotides downstream of the start codon of cpa. However, the insertion did not abolish the phospholipase C and hemolytic activities of CPBC16ML. To investigate the expression of its alpha toxin, the intact copy of cpa was cloned into an expression vector and transformed into Escherichia coli M15 cells. Immunoblotting analysis showed that the protein expressed from the transformant as well as in the culture supernatant of C. perfringens strain CPBC16ML had the expected molecular weight detected in reference strains of C. perfringens. Northern hybridization and reverse transcriptase PCR (RT-PCR) analysis revealed that the entire CPF-G2Im insertion was completely spliced from the cpa precursor mRNA transcripts. The sequence of the insertion fragment has 95% and 97% identity to two noncoding regions corresponding to sequences that flank a predicted group II RT gene present in the pCPF4969 plasmid of C. perfringens. However, an RT was not encoded by the CPF-G2Im fragment. Based on the secondary structure prediction analysis, CPF-G2Im revealed typical features of group II introns. The present study shows that CPF-G2Im is capable of splicing in both C. perfringens and E. coli. To our knowledge, this is the first report that a group II intron without an open reading frame (ORF) is located in the cpa ORF of C. perfringens.

  10. Neither the RNA nor the proteins of open reading frames 3a and 3b of the coronavirus infectious bronchitis virus are essential for replication.

    PubMed

    Hodgson, Teri; Britton, Paul; Cavanagh, Dave

    2006-01-01

    Gene 3 of infectious bronchitis virus is tricistronic; open reading frames (ORFs) 3a and 3b encode two small nonstructural (ns) proteins, 3a and 3b, of unknown function, and a third, structural protein E, is encoded by ORF 3c. To determine if either the 3a or the 3b protein is required for replication, we first modified their translation initiation codons to prevent translation of the 3a and 3b proteins from recombinant infectious bronchitis viruses (rIBVs). Replication in primary chick kidney (CK) cells and in chicken embryos was not affected. In chicken tracheal organ cultures (TOCs), the recombinant rIBVs reached titers similar to those of the wild-type virus, but in the case of viruses lacking the 3a protein, the titer declined reproducibly earlier. Translation of the IBV E protein is believed to be initiated by internal entry of ribosomes at a structure formed by the sequences corresponding to ORFs 3a and 3b. To assess the necessity of this mechanism, we deleted most of the sequence representing 3a and 3b to produce a gene in which ORF 3c (E) was adjacent to the gene 3 transcription-associated sequence. Western blot analysis revealed that the recombinant IBV produced fivefold less E protein. Nevertheless, titers produced in CK cells, embryos, and TOCs were similar to those of the wild-type virus, although they declined earlier in TOCs, probably due to the absence of the 3a protein. Thus, neither the tricistronic arrangement of gene 3, the internal initiation of translation of E protein, nor the 3a and 3b proteins are essential for replication per se, suggesting that these proteins are accessory proteins that may have roles in vivo.

  11. Immunogenicity of a Multi-Epitope DNA Vaccine Encoding Epitopes from Cu-Zn Superoxide Dismutase and Open Reading Frames of Brucella abortus in Mice.

    PubMed

    Escalona, Emilia; Sáez, Darwin; Oñate, Angel

    2017-01-01

    Brucellosis is a bacterial zoonotic disease affecting several mammalian species that is transmitted to humans by direct or indirect contact with infected animals or their products. In cattle, brucellosis is almost invariably caused by Brucella abortus. Live, attenuated Brucella vaccines are commonly used to prevent illness in cattle, but can cause abortions in pregnant animals. It is, therefore, desirable to design an effective and safer vaccine against Brucella. We have used specific Brucella antigens that induce immunity and protection against B. abortus. A novel recombinant multi-epitope DNA vaccine specific for brucellosis was developed. To design the vaccine construct, we employed bioinformatics tools to predict epitopes present in Cu-Zn superoxide dismutase and in the open reading frames of the genomic island-3 (BAB1_0260, BAB1_0270, BAB1_0273, and BAB1_0278) of Brucella. We successfully designed a multi-epitope DNA plasmid vaccine chimera that encodes and expresses 21 epitopes. This DNA vaccine induced a specific humoral and cellular immune response in BALB/c mice. It induced a typical T-helper 1 response, eliciting production of immunoglobulin G2a and IFN-γ particularly associated with the Th1 cell subset of CD4(+) T cells. The production of IL-4, an indicator of Th2 activation, was not detected in splenocytes. Therefore, it is reasonable to suggest that the vaccine induced a predominantly Th1 response. The vaccine induced a statistically significant level of protection in BALB/c mice when challenged with B. abortus 2308. This is the first use of an in silico strategy to a design a multi-epitope DNA vaccine against B. abortus.

  12. SARS-coronavirus open reading frame-9b suppresses innate immunity by targeting mitochondria and the MAVS/TRAF3/TRAF6 signalosome.

    PubMed

    Shi, Chong-Shan; Qi, Hai-Yan; Boularan, Cedric; Huang, Ning-Na; Abu-Asab, Mones; Shelhamer, James H; Kehrl, John H

    2014-09-15

    Coronaviruses (CoV) have recently emerged as potentially serious pathogens that can cause significant human morbidity and death. The severe acute respiratory syndrome (SARS)-CoV was identified as the etiologic agent of the 2002-2003 international SARS outbreak. Yet, how SARS evades innate immune responses to cause human disease remains poorly understood. In this study, we show that a protein encoded by SARS-CoV designated as open reading frame-9b (ORF-9b) localizes to mitochondria and causes mitochondrial elongation by triggering ubiquitination and proteasomal degradation of dynamin-like protein 1, a host protein involved in mitochondrial fission. Also, acting on mitochondria, ORF-9b targets the mitochondrial-associated adaptor molecule MAVS signalosome by usurping PCBP2 and the HECT domain E3 ligase AIP4 to trigger the degradation of MAVS, TRAF3, and TRAF 6. This severely limits host cell IFN responses. Reducing either PCBP2 or AIP4 expression substantially reversed the ORF-9b-mediated reduction of MAVS and the suppression of antiviral transcriptional responses. Finally, transient ORF-9b expression led to a strong induction of autophagy in cells. The induction of autophagy depended upon ATG5, a critical autophagy regulator, but the inhibition of MAVS signaling did not. These results indicate that SARS-CoV ORF-9b manipulates host cell mitochondria and mitochondrial function to help evade host innate immunity. This study has uncovered an important clue to the pathogenesis of SARS-CoV infection and illustrates the havoc that a small ORF can cause in cells.

  13. Zm908p11, encoded by a short open reading frame (sORF) gene, functions in pollen tube growth as a profilin ligand in maize

    PubMed Central

    Dong, Xue; Wang, Dongxue; Liu, Peng; Li, Chengxia; Zhao, Qian; Zhu, Dengyun; Yu, Jingjuan

    2013-01-01

    Double fertilization of flowering plants depends on the targeted transportation of sperm to the embryo sac by the pollen tube. Currently, little is known about the underlying molecular mechanisms that regulate pollen germination and pollen tube growth in maize (Zea mays). Here, a maize pollen-predominant gene Zm908, with several putative short open reading frames (sORFs), was isolated and characterized. The longest ORF of Zm908 encodes a small protein of 97 amino acids. This was designated as Zm908p11 and is distributed throughout the maize pollen tube. Western blot detected the small peptide in mature pollen. Quantitative reverse transcription–PCR and northern blot analysis revealed that Zm908p11 was expressed predominantly in mature pollen grains. Ectopic overexpression of full-length Zm908 and Zm908p11 in tobacco resulted in defective pollen, while transgenic tobacco plants with a site-specific mutation or a frameshift mutation of Zm908p11 showed normal pollen development. Overexpression of Zm908p11 in maize decreased pollen germination efficiency. Maize pollen cDNA library screening and protein–protein interaction assays demonstrated that Zm908p11 interacts with maize profilin 1 (ZmPRO1). A microarray analysis identified 273 up-regulated and 203 down-regulated genes in the overexpressing transgenic Zm908p11 pollen. Taken together, these results indicate that Zm908 functions as Zm908p11, and binds to profilins as a novel ligand, with a required role during pollen tube growth in maize. Accordingly, a model is proposed for the role of Zm908p11 during pollen tube growth in maize. PMID:23676884

  14. Two subclasses of Kaposi's sarcoma-associated herpesvirus lytic cycle promoters distinguished by open reading frame 50 mutant proteins that are deficient in binding to DNA.

    PubMed

    Chang, Pey-Jium; Shedd, Duane; Miller, George

    2005-07-01

    A transcriptional activator encoded in open reading frame 50 (ORF50) of the Kaposi's sarcoma-associated herpesvirus (KSHV) genome initiates the viral lytic cycle. Here we classify four lytic cycle genes on the basis of several characteristics of the ORF50 response elements (ORF50 REs) in their promoters: nucleotide sequence homology, the capacity to bind ORF50 protein in vitro, the ability to bind the cellular protein RBP-Jkappa in vitro, and the capacity to confer activation by DNA binding-deficient mutants of ORF50 protein. ORF50 expressed in human cells binds the promoters of PAN and K12 but does not bind ORF57 or vMIP-1 promoters. Conversely, the RBP-Jkappa protein binds ORF57 and vMIP-1 but not PAN or K12 promoters. DNA binding-deficient mutants of ORF50 protein differentiate these two subclasses of promoters in reporter assays; the PAN and K12 promoters cannot be activated, while the ORF57 and vMIP-1 promoters are responsive. Although DNA binding-deficient mutants of ORF50 protein are defective in activating direct targets, they are nonetheless capable of activating the lytic cascade of KSHV. Significantly, DNA binding-deficient ORF50 mutants are competent to autostimulate expression of endogenous ORF50 and to autoactivate ORF50 promoter reporters. The experiments show that ORF50 protein activates downstream targets by at least two distinct mechanisms: one involves direct binding of ORF50 REs in promoter DNA; the other mechanism employs interactions with the RBP-Jkappa cellular protein bound to promoter DNA in the region of the ORF50 RE. The DNA binding-deficient mutants allow classification of ORF50-responsive genes and will facilitate study of the several distinct mechanisms of activation of KSHV lytic cycle genes that are under the control of ORF50 protein.

  15. An Sp1 response element in the Kaposi's sarcoma-associated herpesvirus open reading frame 50 promoter mediates lytic cycle induction by butyrate.

    PubMed

    Ye, Jianjiang; Shedd, Duane; Miller, George

    2005-02-01

    Kaposi's sarcoma-associated herpesvirus (KSHV) can be driven into the lytic cycle in vitro by phorbol esters and sodium butyrate. This report begins to analyze the process by which butyrate activates the promoter of KSHV open reading frame 50 (ORF50), the key viral regulator of the KSHV latency to lytic cycle switch. A short fragment of the promoter, 134 nucleotides upstream of the translational start of ORF50, retained basal uninduced activity and conferred maximal responsiveness to sodium butyrate. The butyrate response element was mapped to a consensus Sp1-binding site. By means of electrophoretic mobility shift assays, both Sp1 and Sp3 were shown to form complexes in vitro with the ORF50 promoter at the Sp1 site. Butyrate induced the formation of a group of novel complexes, including several Sp3-containing complexes, one Sp1-containing complex, and several other complexes that were not identified with antibodies to Sp1 or Sp3. Formation of all butyrate-induced DNA-protein complexes was mediated by the consensus Sp1 site. In insect and mammalian cell lines, Sp1 significantly activated the ORF50 promoter linked to luciferase. Chromatin immunoprecipitation experiments in a PEL cell line showed that butyrate induced Sp1, CBP, and p300 binding to the ORF50 promoter in vivo in an on-off manner. The results suggest that induction of the KSHV lytic cycle by butyrate is mediated through interactions at the Sp1/Sp3 site located 103 to 112 nucleotides upstream of the translational initiation of ORF50 presumably by enhancing the binding of Sp1 to this site.

  16. The Role of Speech Prosody and Text Reading Prosody in Children's Reading Comprehension

    ERIC Educational Resources Information Center

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

    2014-01-01

    Background: Text reading prosody has been associated with reading comprehension. However, text reading prosody is a reading-dependent measure that relies heavily on decoding skills. Investigation of the contribution of speech prosody--which is independent from reading skills--in addition to text reading prosody, to reading comprehension could…

  17. Implementation of the Realized Genomic Relationship Matrix to Open-Pollinated White Spruce Family Testing for Disentangling Additive from Nonadditive Genetic Effects

    PubMed Central

    Gamal El-Dien, Omnia; Ratcliffe, Blaise; Klápště, Jaroslav; Porth, Ilga; Chen, Charles; El-Kassaby, Yousry A.

    2016-01-01

    The open-pollinated (OP) family testing combines the simplest known progeny evaluation and quantitative genetics analyses as candidates’ offspring are assumed to represent independent half-sib families. The accuracy of genetic parameter estimates is often questioned as the assumption of “half-sibling” in OP families may often be violated. We compared the pedigree- vs. marker-based genetic models by analysing 22-yr height and 30-yr wood density for 214 white spruce [Picea glauca (Moench) Voss] OP families represented by 1694 individuals growing on one site in Quebec, Canada. Assuming half-sibling, the pedigree-based model was limited to estimating the additive genetic variances which, in turn, were grossly overestimated as they were confounded by very minor dominance and major additive-by-additive epistatic genetic variances. In contrast, the implemented genomic pairwise realized relationship models allowed the disentanglement of additive from all nonadditive factors through genetic variance decomposition. The marker-based models produced more realistic narrow-sense heritability estimates and, for the first time, allowed estimating the dominance and epistatic genetic variances from OP testing. In addition, the genomic models showed better prediction accuracies compared to pedigree models and were able to predict individual breeding values for new individuals from untested families, which was not possible using the pedigree-based model. Clearly, the use of marker-based relationship approach is effective in estimating the quantitative genetic parameters of complex traits even under simple and shallow pedigree structure. PMID:26801647

  18. Implementation of the Realized Genomic Relationship Matrix to Open-Pollinated White Spruce Family Testing for Disentangling Additive from Nonadditive Genetic Effects.

    PubMed

    Gamal El-Dien, Omnia; Ratcliffe, Blaise; Klápště, Jaroslav; Porth, Ilga; Chen, Charles; El-Kassaby, Yousry A

    2016-01-22

    The open-pollinated (OP) family testing combines the simplest known progeny evaluation and quantitative genetics analyses as candidates' offspring are assumed to represent independent half-sib families. The accuracy of genetic parameter estimates is often questioned as the assumption of "half-sibling" in OP families may often be violated. We compared the pedigree- vs. marker-based genetic models by analysing 22-yr height and 30-yr wood density for 214 white spruce [Picea glauca (Moench) Voss] OP families represented by 1694 individuals growing on one site in Quebec, Canada. Assuming half-sibling, the pedigree-based model was limited to estimating the additive genetic variances which, in turn, were grossly overestimated as they were confounded by very minor dominance and major additive-by-additive epistatic genetic variances. In contrast, the implemented genomic pairwise realized relationship models allowed the disentanglement of additive from all nonadditive factors through genetic variance decomposition. The marker-based models produced more realistic narrow-sense heritability estimates and, for the first time, allowed estimating the dominance and epistatic genetic variances from OP testing. In addition, the genomic models showed better prediction accuracies compared to pedigree models and were able to predict individual breeding values for new individuals from untested families, which was not possible using the pedigree-based model. Clearly, the use of marker-based relationship approach is effective in estimating the quantitative genetic parameters of complex traits even under simple and shallow pedigree structure.

  19. Evaluation and validity of a polymerase chain reaction-based open reading frame typing method to dissect the molecular epidemiology for Acinetobacter baumannii in an epidemiologic study of a hospital outbreak.

    PubMed

    Fujikura, Yuji; Yuki, Atsushi; Hamamoto, Takaaki; Ichimura, Sadahiro; Kawana, Akihiko; Ohkusu, Kiyofumi; Matsumoto, Tetsuya

    2016-11-01

    Acinetobacter baumannii is regarded as one of the most important pathogens in hospital outbreaks. To obtain an efficient and simple epidemiologic method of surveillance during outbreaks, we assessed the applicability of the polymerase chain reaction-based open reading frames typing (POT) method and compared it with pulsed-field gel electrophoresis. The POT method was found to have sufficient discriminatory power to identify the strains and would be widely applicable to epidemiologic surveillance during hospital outbreaks.

  20. Reading(s).

    ERIC Educational Resources Information Center

    Summerfield, Geoffrey; Summerfield, Judith

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

  1. A Special Chinese Reading Acceleration Training Paradigm: To Enhance the Reading Fluency and Comprehension of Chinese Children with Reading Disabilities

    PubMed Central

    Dai, Li; Zhang, Chenchen; Liu, Xiangping

    2016-01-01

    According to a number of studies, use of a Reading Acceleration Program as reading intervention training has been demonstrated to improve reading speed and comprehension level effectively in most languages and countries. The objective of the current study was to provide further evidence of the effectiveness of a Reading Acceleration Program for Chinese children with reading disabilities using a distinctive Chinese reading acceleration training paradigm. The reading acceleration training paradigm is divided into a non-accelerated reading paradigm, a Character-accelerated reading paradigm and a Words-accelerated reading paradigm. The results of training Chinese children with reading disabilities indicate that the acceleration reading paradigm applies to children with Chinese-reading disabilities. In addition, compared with other reading acceleration paradigms, Words-accelerated reading training is more effective in helping children with reading disabilities read at a high speed while maintaining superior comprehension levels. PMID:28018272

  2. Reading Ourselves.

    ERIC Educational Resources Information Center

    Sherriff, Dawn

    2001-01-01

    Describes how reading and art have taught the author to slow down. Discusses how she wants her students to leave the third-grade classroom reading--reading words, reading pictures, and reading their world. Considers how one student slows down her reading, pays attention to her thinking, and begins to see the pictures and connections that poems…

  3. Microstructural architecture developed in the fabrication of solid and open-cellular copper components by additive manufacturing using electron beam melting

    NASA Astrophysics Data System (ADS)

    Ramirez, Diana Alejandra

    The fabrication of Cu components were first built by additive manufacturing using electron beam melting (EBM) from low-purity, atomized Cu powder containing a high density of Cu2O precipitates leading to a novel example of precipitate-dislocation architecture. These microstructures exhibit cell-like arrays (1-3microm) in the horizontal reference plane perpendicular to the build direction with columnar-like arrays extending from ~12 to >60 microm in length and corresponding spatial dimensions of 1-3 microm. These observations were observed by the use of optical metallography, and scanning and transmission electron microscopy. The hardness measurements were taken both on the atomized powder and the Cu components. The hardness for these architectures ranged from ~HV 83 to 88, in contrast to the original Cu powder microindentation hardness of HV 72 and the commercial Cu base plate hardness of HV 57. These observations were utilized for the fabrication of open-cellular copper structures by additive manufacturing using EBM and illustrated the ability to fabricate some form of controlled microstructural architecture by EBM parameter alteration or optimizing. The fabrication of these structures ranged in densities from 0.73g/cm3 to 6.67g/cm3. These structures correspond to four different articulated mesh arrays. While these components contained some porosity as a consequence of some unmelted regions, the Cu2O precipitates also contributed to a reduced density. Using X-ray Diffraction showed the approximate volume fraction estimated to be ~2%. The addition of precipitates created in the EBM melt scan formed microstructural arrays which contributed to hardening contributing to the strength of mesh struts and foam ligaments. The measurements of relative stiffness versus relative density plots for Cu compared very closely with Ti-6Al-4V open cellular structures - both mesh and foams. The Cu reticulated mesh structures exhibit a slope of n = 2 in contrast to a slope of n = 2

  4. Methods for generating precise deletions and insertions in the genome of wild-type Escherichia coli: application to open reading frame characterization.

    PubMed

    Link, A J; Phillips, D; Church, G M

    1997-10-01

    We have developed a new system of chromosomal mutagenesis in order to study the functions of uncharacterized open reading frames (ORFs) in wild-type Escherichia coli. Because of the operon structure of this organism, traditional methods such as insertional mutagenesis run the risk of introducing polar effects on downstream genes or creating secondary mutations elsewhere in the genome. Our system uses crossover PCR to create in-frame, tagged deletions in chromosomal DNA. These deletions are placed in the E. coli chromosome by using plasmid pKO3, a gene replacement vector that contains a temperature-sensitive origin of replication and markers for positive and negative selection for chromosomal integration and excision. Using kanamycin resistance (Kn(r)) insertional alleles of the essential genes pepM and rpsB cloned into the replacement vector, we calibrated the system for the expected results when essential genes are deleted. Two poorly understood genes, hdeA and yjbJ, encoding highly abundant proteins were selected as targets for this approach. When the system was used to replace chromosomal hdeA with insertional alleles, we observed vastly different results that were dependent on the exact nature of the insertions. When a Kn(r) gene was inserted into hdeA at two different locations and orientations, both essential and nonessential phenotypes were seen. Using PCR-generated deletions, we were able to make in-frame deletion strains of both hdeA and yjbJ. The two genes proved to be nonessential in both rich and glucose-minimal media. In competition experiments using isogenic strains, the strain with the insertional allele of yjbJ showed growth rates different from those of the strain with the deletion allele of yjbJ. These results illustrate that in-frame, unmarked deletions are among the most reliable types of mutations available for wild-type E. coli. Because these strains are isogenic with the exception of their deleted ORFs, they may be used in competition with

  5. Molecular identification and genetic diversity of open reading frame 7 field isolated porcine reproductive and respiratory syndrome in North Sumatera, Indonesia, in the period of 2008-2014

    PubMed Central

    Faisal, Faisal; Widayanti, Rini; Haryanto, Aris; Tabu, Charles Rangga

    2015-01-01

    Aim: Molecular identification and genetic diversity of open reading frame 7 (ORF7) of field isolated porcine reproductive and respiratory syndrome virus (PRRSV) in North Sumatera, Indonesia, in the period of 2008-2014. Materials and Methods: A total of 47 PRRSV samples were collected from the death case of pigs. The samples were collected from different districts in the period of 2008-2014 from North Sumatera province. Two pairs of primer were designed to amplify ORF7 of Type 1 and 2 PRRSV based on the sequence of reference viruses VR2332 and Lelystad. Viral RNAs were extracted from samples using PureLink™ micro-to-Midi total RNA purification system (Invitrogen). To amplify the ORF7 of PRRSV, the synthesis cDNA and DNA amplification were performed by reverse transcription polymerase chain reaction (RT-PCR) and nested PCR method. Then the DNA sequencing of PCR products and phylogenetic analysis were accomplished by molecular evolutionary genetics analysis version 6.0 software program. Results: RT-: PCR and nested PCR used in this study had successfully detected of 18 samples positive PRRS virus with the amplification products at 703bp and 508bp, respectively. Sequencing of the ORF7 shows that 18 PRRS viruses isolated from North Sumatera belonged to North American (NA). JXA1 Like and classic NA type viruses. Several mutations were detected, particularly in the area of nuclear localization signal (NLS1) and in NLS2. In the local viruses, which were related closed to JXA1 virus; there are two differences in amino acids in position 12 and 43 of ORF7. Our tested viruses showed that the amino acid positions 12 and 43 are Asparagine and Arginine, while the reference virus (VR2332, Lelystad, and JXA1) occupied both by Lysine. Based on differences in two amino acids at position 12 and 43 showed that viruses from North Sumatera has its own uniqueness and related closed to highly pathogenic PRRS (HP-PRRS) virus (JXA1). Conclusion: The results demonstrated that North Sumatera

  6. Reading Laboratories: The Conversion of the Speed Reading Lab into an ESL Reading Lab.

    ERIC Educational Resources Information Center

    Novak, Sigrid Scholtz

    It is proposed that the reading-machine laboratory provides a means for the classroom ESL instructor to continue using his present method in the classroom (intensive, theoretical-grammatical instruction) while providing additional extensive reading and learning practice with the machines in the reading laboratory. Two speed reading systems…

  7. Reading Faster

    ERIC Educational Resources Information Center

    Nation, Paul

    2009-01-01

    This article describes the visual nature of the reading process as it relates to reading speed. It points out that there is a physical limit on normal reading speed and beyond this limit the reading process will be different from normal reading where almost every word is attended to. The article describes a range of activities for developing…

  8. From linked open data to molecular interaction: studying selectivity trends for ligands of the human serotonin and dopamine transporter† †The authors declare no competing interests. ‡ ‡Electronic supplementary information (ESI) available. See DOI: 10.1039/c6md00207b Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file.

    PubMed Central

    Hellsberg, Eva; Viereck, Michael; Ecker, Gerhard F.

    2016-01-01

    Retrieval of congeneric and consistent SAR data sets for protein targets of interest is still a laborious task to do if no appropriate in-house data set is available. However, combining integrated open data sources (such as the Open PHACTS Discovery Platform) with workflow tools now offers the possibility of querying across multiple domains and tailoring the search to the given research question. Starting from two phylogenetically related protein targets of interest (the human serotonin and dopamine transporters), the whole chemical compound space was explored by implementing a scaffold-based clustering of compounds possessing biological measurements for both targets. In addition, potential hERG blocking liabilities were included. The workflow allowed studying the selectivity trends of scaffold series, identifying potentially harmful compound series, and performing SAR, docking studies and molecular dynamics (MD) simulations for a consistent data set of 56 cathinones. This delivered useful insights into driving determinants for hDAT selectivity over hSERT. With respect to the scaffold-based analyses it should be noted that the cathinone data set could be retrieved only when Murcko scaffold analyses were combined with similarity searches such as a common substructure search. PMID:27891211

  9. 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…

  10. Synthesis in Escherichia coli of two smaller enzymically active analogues of Coxiella burnetii macrophage infectivity potentiator (CbMip) protein utilizing a single open reading frame from the cbmip gene.

    PubMed Central

    Mo, Y Y; Seshu, J; Wang, D; Mallavia, L P

    1998-01-01

    FK506-binding proteins (FKBPs) have been identified in a variety of eukaryotic and prokaryotic organisms. Macrophage infectivity potentiator (CbMip, 23.5 kDa) protein of the obligate intracellular bacterium, Coxiella burnetii, was shown previously to belong to the family of FKBPs based on sequence homology and peptidyl-prolyl cis/trans isomerase (PPIase) activity. Further characterization of the cbmip gene has identified two additional proteins with molecular masses of 15.5 and 15.0 kDa that are synthesized, in addition to the 23.5 kDa CbMip, when expressed in Escherichia coli. Amino acid sequencing at the N-terminus combined with transcription and translation fusion expression revealed that the two proteins were synthesized from the same open reading frame of the cbmip gene, but starting at different internal translation start codons, probably by translational reinitiation. When the internal methionines serving as start sites were replaced with lysine by site-directed mutagenesis, the synthesis of 15.5 and 15.0 kDa proteins was abolished even though the synthesis of 23.5 kDa CbMip was intact. This confirmed that the 15.5 and 15.0 kDa proteins are indeed generated by translational reinitiation and are not degradation products of the 23.5 kDa protein. Like other FKBPs, both 15.5 and 15.0 kDa proteins exhibit PPIase activity. Because they share significant sequence homology with FKBPs and have a similar PPIase activity, 15.5 and 15. 0 kDa proteins are designated as C. burnetii FKBP (Cb-FKBP) analogues I and II, respectively. TnphoA mutagenesis demonstrated that whereas the large protein (CbMip) is secreted, Cb-FKBP analogues I and II are cytoplasmic, indicating that structural variations could allow for different subcellular compartmentalization of similar proteins. Western-blot analysis of lysates of purified C. burnetii using a CbMip-specific monoclonal antibody revealed the presence of a protein migrating at approximately 15 kDa, indicating the presence of smaller

  11. Reading Comics

    ERIC Educational Resources Information Center

    Tilley, Carol L.

    2008-01-01

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

  12. Reading Recovery.

    ERIC Educational Resources Information Center

    Jones, Joanna R., Ed.

    1992-01-01

    This issue of the Arizona Reading Journal focuses on the theme "reading recovery" and includes the following articles: "Why Is an Inservice Programme for Reading Recovery Teachers Necessary?" (Marie M. Clay); "What Is Reading Recovery?" (Gay Su Pinnell); "Teaching a Hard To Teach Child" (Constance A.…

  13. Reading Rituals

    ERIC Educational Resources Information Center

    Manzo, Kathleen Kennedy

    2007-01-01

    The Ogden, Utah schools have used the mandates of the federal Reading First grant program to transform reading instruction and student achievement in low-performing schools. Reading First was approved by Congress in 2001 under the No Child Left Behind Act to bring scientifically based reading methods and materials to struggling schools. The $1…

  14. Entrepreneurship Education: Supplementary Readings.

    ERIC Educational Resources Information Center

    Scanlan, Thomas J.; And Others

    This third volume in the Entrepreneurship Education curriculum materials includes readings and suggested additional resources which complement the instructional strategies contained in the first two volumes. Three sections are included in the guide: critical incidents, readings in entrepreneurial skills, and management skill area resources.…

  15. Bridging and Reading Proficiency.

    ERIC Educational Resources Information Center

    Philbin, Margaret M.; Rubenstein, Herbert

    A study was conducted for additional support of the view that bridging--drawing inferences to relate a sentence to a preceding sentence--occurs during reading rather than at the time of testing. Subjects were 88 third and 67 fifth grade students whose reading proficiency was measured by performance on the Metropolitan Achievement Test. The…

  16. Organization and partial sequence of a DNA region of the Rhizobium leguminosarum symbiotic plasmid pRL6JI containing the genes fixABC, nifA, nifB and a novel open reading frame.

    PubMed Central

    Grönger, P; Manian, S S; Reiländer, H; O'Connell, M; Priefer, U B; Pühler, A

    1987-01-01

    By hybridization and heteroduplex studies the fixABC and nifA genes of the Rhizobium leguminosarum symbiotic plasmid pRL6JI have been identified. DNA sequencing of the region containing nifA showed an open reading frame of 1557 bp encoding a protein of 56, 178 D. Based on sequence homology, this ORF was confirmed to correspond to the nifA gene. Comparison of three nifA proteins (Klebsiella pneumoniae, Rhizobium meliloti, Rhizobium leguminosarum) revealed only a weak relationship in their N-terminal regions, whereas the C-terminal parts exhibited strong homology. Sequence analysis also showed that the R. leguminosarum nifA gene is followed by nifB and preceded by fixC with an open reading frame inserted in between. This novel ORF of 294 bp was found to be highly conserved also in R. meliloti. No known promoter and termination signals could be defined on the sequenced R. leguminosarum fragment. Images PMID:3029674

  17. Protective effect of a DNA vaccine containing an open reading frame with homology to an ABC-type transporter present in the genomic island 3 of Brucella abortus in BALB/c mice.

    PubMed

    Riquelme-Neira, Roberto; Retamal-Díaz, Angello; Acuña, Francisca; Riquelme, Pablo; Rivera, Alejandra; Sáez, Darwin; Oñate, Angel

    2013-08-12

    The immunogenicity of a DNA vaccine containing an open reading frame (ORF) of genomic island 3 (GI-3), specific for Brucella abortus and Brucella melitensis, has been examined. Intramuscular injection of plasmid DNA carrying the open reading frame with homology to an ABC-type transporter (pV278a) into BALB/c mice elicited both humoral and cellular immune responses. Mice injected with pV278a had a dominant immunoglobulin G2a (IgG2a) response. This DNA vaccine elicited a T-cell-proliferative response and induced significant levels of interferon gamma (INF-γ) upon restimulation with recombinant 278a protein. Upon stimulation with an appropriate recombinant protein or crude Brucella protein, the vaccine did not induce IL-4, suggesting a typical T-helper (TH1) response. Furthermore, the vaccine induced protection in BALB/c mice when challenged with the virulent strain Brucella abortus 2308. Taken together, these data suggest that DNA vaccination offers an improved delivery of the homologous of an ABC-type transporter antigen, and provides the first evidence of a protective effect of this antigen in the construction of vaccines against B. abortus.

  18. Who's Reading and Why: Reading Habits of 1st Grade through Graduate Students

    ERIC Educational Resources Information Center

    Camp, Deanne

    2007-01-01

    The habit of reading develops over a period of time. This study explored reading habits across a wide range of students. An open-ended survey of reading habits involved 242 participants from grades 1, 4, 6, 8, 11, undergraduate non-education majors, undergraduate elementary majors, and graduate reading majors. As data were analyzed, themes emerged…

  19. 19 CFR 103.1 - Public reading rooms.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 19 Customs Duties 1 2013-04-01 2013-04-01 false Public reading rooms. 103.1 Section 103.1 Customs... reading rooms. Each office listed below will maintain a public reading room or public reading area where... Angeles Street, Los Angeles, California 90012. The reading rooms are open to the public during...

  20. 19 CFR 103.1 - Public reading rooms.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 19 Customs Duties 1 2012-04-01 2012-04-01 false Public reading rooms. 103.1 Section 103.1 Customs... reading rooms. Each office listed below will maintain a public reading room or public reading area where... Angeles Street, Los Angeles, California 90012. The reading rooms are open to the public during...

  1. 19 CFR 103.1 - Public reading rooms.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 19 Customs Duties 1 2011-04-01 2011-04-01 false Public reading rooms. 103.1 Section 103.1 Customs... reading rooms. Each office listed below will maintain a public reading room or public reading area where... Angeles Street, Los Angeles, California 90012. The reading rooms are open to the public during...

  2. 19 CFR 103.1 - Public reading rooms.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 19 Customs Duties 1 2014-04-01 2014-04-01 false Public reading rooms. 103.1 Section 103.1 Customs... reading rooms. Each office listed below will maintain a public reading room or public reading area where... Angeles Street, Los Angeles, California 90012. The reading rooms are open to the public during...

  3. 19 CFR 103.1 - Public reading rooms.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 19 Customs Duties 1 2010-04-01 2010-04-01 false Public reading rooms. 103.1 Section 103.1 Customs... reading rooms. Each office listed below will maintain a public reading room or public reading area where... Angeles Street, Los Angeles, California 90012. The reading rooms are open to the public during...

  4. Rekindle the Love of Reading

    ERIC Educational Resources Information Center

    Isero, Mark

    2014-01-01

    This author describes a reading project using Kindles that was designed to increase the reading habits of 9th graders. With a selection of 500 titles for classroom usage, students were encouraged to read any book they chose--in addition to those required for their school term. Isero states that, in the past, many of his students would not risk…

  5. Getting Along With Reading Teachers

    ERIC Educational Resources Information Center

    Fenwick, Sara Innis

    1970-01-01

    Some of the stated needs of reading teachers include: more books where students can find them at arm's length, more open Door" hours, more help and time for individual students, more flexibility in borrowing rules, more books and other media relevant to the reading specialists, and more storytelling by librarians. (MF)

  6. The ubiquitous cellular transcriptional factor USF targets the varicella-zoster virus open reading frame 10 promoter and determines virulence in human skin xenografts in SCIDhu mice in vivo.

    PubMed

    Che, Xibing; Berarducci, Barbara; Sommer, Marvin; Ruyechan, William T; Arvin, Ann M

    2007-04-01

    Varicella-zoster virus (VZV) open reading frame 10 (ORF10) is a determinant of virulence in SCIDhu skin xenografts but not in human T cells in vivo. In this analysis of the regulation of ORF10 transcription, we have identified four ORF10-related transcripts, including a major 1.3-kb RNA spanning ORF10 only and three other read-through transcripts. Rapid-amplification-of-cDNA-ends experiments indicated that the 1.3-kb transcript of ORF10 has single initiation and termination sites. In transient expression assays, the ORF10 promoter was strongly stimulated by the major VZV transactivator, IE62. Deletion analyses revealed approximate boundaries for the full ORF10 promoter activity between -75 and -45 and between +5 and -8, relative to the ORF10 transcription start site. The recombinant virus POKA10-Deltapro, with the ORF10 promoter deletion, blocked transcription of ORF10 and also of ORF9A and ORF9 mRNAs, whereas expression of read-through ORF9A/9/10 and ORF9/10 transcripts was increased, compensating for the loss of the monocistronic mRNAs. The cellular factor USF bound specifically to its consensus site within the ORF10 promoter and was required for IE62 transactivation, whereas disrupting the predicted TATA boxes or Oct-1 binding elements had no effect. The USF binding site was disrupted in the recombinant virus, POKA10-proDeltaUSF, and no ORF10 protein was produced. Both ORF10 promoter mutants reduced VZV replication in SCIDhu skin xenografts. These observations provided further evidence of the contribution of the ORF10 protein to VZV pathogenesis in skin and demonstrated that VZV depends upon the cellular transcriptional factor USF to support its virulence in human skin in vivo.

  7. The complete sequence of a 10.8 kb segment distal of SUF2 on the right arm of chromosome III from Saccharomyces cerevisiae reveals seven open reading frames including the RVS161, ADP1 and PGK genes.

    PubMed

    Skala, J; Purnelle, B; Goffeau, A

    1992-05-01

    We have entirely sequenced a 10,835 bp segment of the right arm from chromosome III contained in the J11D and J11D-K3B GF clones. The segment contains seven open reading frames longer then 100 amino acids. Three of them, RVS161 (Urdaci et al., 1990; Crouzet et al., 1991), ADP1 (Purnelle et al., 1991) and PGK1 (Hitzeman et al., 1982) have been described previously. YCR10C encodes a putative membrane protein. YCR8W (encoding a putative protein kinase) and YCR14C extend inside the D10H (Skala et al., 1991) and 62B5-2D clones respectively. Four ARS elements previously reported by Palzkill et al. (1986) are located between RVS161 and YCR10C.

  8. Learning to Read through Reading.

    ERIC Educational Resources Information Center

    Sierra Conservation Center, Jamestown, CA.

    One of the twelve exemplary programs summarized in the Introduction to Right to Read's "Effective Reading Programs: Summaries of 222 Selected Programs" (CS001934), this program attempts to raise the reading skills of inmates of the Sierra Conservation Center to the level needed for training in conservation work while in prison, or for…

  9. A Stereoselective Route to Tetrahydrobenzoxazepines and Tetrahydrobenzodiazepines via Ring-Opening and Aza-Michael Addition of Activated Aziridines with 2-Hydroxyphenyl and 2-Aminophenyl Acrylates.

    PubMed

    Shahi, Chandan Kumar; Bhattacharyya, Aditya; Nanaji, Yerramsetti; Ghorai, Manas K

    2017-01-06

    A simple and efficient synthetic route to 2,3,4,5-tetrahydrobenzoxazepines and -benzodiazepines bearing easily functionalizable appendages has been developed by ring-opening of activated aziridines with 2-hydroxyphenyl acrylates and 2-aminophenyl acrylate, respectively, and subsequent intramolecular C-N bond formation through palladium-catalyzed aza-Michael reaction. The straightforward synthetic approach delivers the desired molecular scaffolds in high yields (up to 82%) with excellent stereoselectivity (ee up to 94%).

  10. Kentucky Performance Assessment of Reading: Valid?

    ERIC Educational Resources Information Center

    Strong, Sue; Sexton, Larry C.

    1996-01-01

    Researchers surveyed Kentucky high school seniors to collect data on and compare the results of the Kentucky Instructional Results Information System (KIRIS) open-response reading results and ACT reading multiple-choice format. Results found a great deal of disagreement between the KIRIS and ACT reading results. (SM)

  11. Role of the Hepatitis C Virus Core+1 Open Reading Frame and Core cis-Acting RNA Elements in Viral RNA Translation and Replication▿ †

    PubMed Central

    Vassilaki, Niki; Friebe, Peter; Meuleman, Philipe; Kallis, Stephanie; Kaul, Artur; Paranhos-Baccalà, Glaucia; Leroux-Roels, Geert; Mavromara, Penelope; Bartenschlager, Ralf

    2008-01-01

    Four conserved RNA stem-loop structures designated SL47, SL87, SL248, and SL443 have been predicted in the hepatitis C virus (HCV) core encoding region. Moreover, alternative translation products have been detected from a reading frame overlapping the core gene (core+1/ARFP/F). To study the importance of the core+1 frame and core-RNA structures for HCV replication in cell culture and in vivo, a panel of core gene silent mutations predicted to abolish core+1 translation and affecting core-RNA stem-loops were introduced into infectious-HCV genomes of the isolate JFH1. A mutation disrupting translation of all known forms of core+1 and affecting SL248 did not alter virus production in Huh7 cells and in mice xenografted with human liver tissue. However, a combination of mutations affecting core+1 at multiple codons and at the same time, SL47, SL87, and SL248, delayed RNA replication kinetics and substantially reduced virus titers. The in vivo infectivity of this mutant was impaired, and in virus genomes recovered from inoculated mice, SL87 was restored by reversion and pseudoreversion. Mutations disrupting the integrity of this stem-loop, as well as that of SL47, were detrimental for virus viability, whereas mutations disrupting SL248 and SL443 had no effect. This phenotype was not due to impaired RNA stability but to reduced RNA translation. Thus, SL47 and SL87 are important RNA elements contributing to HCV genome translation and robust replication in cell culture and in vivo. PMID:18799568

  12. A Social Status Hierarchy: Reading Groups.

    ERIC Educational Resources Information Center

    Bayer, Ann

    1981-01-01

    A study was done to determine the social status and hierarchy attached to reading achievement in a first grade class. In addition to learning to read, children are tacitly learning that reading is the most important subject to be mastered in school and that both group and individual status is determined by the reading group to which one belongs.…

  13. Required Reading

    ERIC Educational Resources Information Center

    Janko, Edmund

    2002-01-01

    In this article, the author insists that those seeking public office prove their literary mettle. As an English teacher, he does have a litmus test for all public officials, judges and senators included--a reading litmus test. He would require that all candidates and nominees have read and reflected on a nucleus of works whose ideas and insights…

  14. Against Readings

    ERIC Educational Resources Information Center

    Edmundson, Mark

    2009-01-01

    Edmundson states that if he could make one wish for the members of his profession, college and university professors of literature, he would wish that for one year, two, three, or five, they would give up readings. By "a reading," he means the application of an analytical vocabulary to describe and (usually) to judge a work of literary art.…

  15. Bilingual Reading.

    ERIC Educational Resources Information Center

    Garganta, Soledad; Ramirez, Inez

    This report discusses the importance of bilingual reading instruction for limited English speaking ability (LESA) students, and careful testing of their language dominance and reading levels. Bilingual students, and English- and Spanish-dominant students from the Fabens Independent School District, Grades K-13, were tested for the data reported…

  16. Teaching Reading.

    ERIC Educational Resources Information Center

    Ricketts, Mary

    1980-01-01

    Described are five approaches to teaching reading: Language Experience, Modified Alphabet, Linguistic, Programmed, and Basal. It is suggested that a good teacher, well trained, certified in his or her profession, an active participant in professional organizations, can teach reading successfully using almost any approach. (KC)

  17. Reading Remixed

    ERIC Educational Resources Information Center

    Valenza, Joyce Kasman; Stephens, Wendy

    2012-01-01

    Critics claim that digital technologies are killing reading, but these teacher-librarians have observed that teens are as excited about reading as they ever were. Online communities give these readers opportunities to get to know authors, communicate with other fans, and learn more about books of interest. Publishers and authors are responding to…

  18. Read Arizona.

    ERIC Educational Resources Information Center

    Arizona State Dept. of Library, Archives and Public Records, Phoenix.

    This manual, designed to help public libraries in Arizona to plan their summer reading programs for children, celebrates the 25th anniversary of the Arizona Reading Program. The material in the manual is prepared for libraries to adapt for their own uses. Chapters of the manual include: (1) Introductory Materials; (2) Goals, Objectives and…

  19. NGSI student activities in open source information analysis in support of the training program of the U.S. DOE laboratories for the entry into force of the additional protocol

    SciTech Connect

    Sandoval, M Analisa; Uribe, Eva C; Sandoval, Marisa N; Boyer, Brian D; Stevens, Rebecca S

    2009-01-01

    In 2008 a joint team from Los Alamos National Laboratory (LANL) and Brookhaven National Laboratory (BNL) consisting of specialists in training of IAEA inspectors in the use of complementary access activities formulated a training program to prepare the U.S. Doe laboratories for the entry into force of the Additional Protocol. As a major part of the support of the activity, LANL summer interns provided open source information analysis to the LANL-BNL mock inspection team. They were a part of the Next Generation Safeguards Initiative's (NGSI) summer intern program aimed at producing the next generation of safeguards specialists. This paper describes how they used open source information to 'backstop' the LANL-BNL team's effort to construct meaningful Additional Protocol Complementary Access training scenarios for each of the three DOE laboratories, Lawrence Livermore National Laboratory, Idaho National Laboratory, and Oak Ridge National Laboratory.

  20. Interruptions disrupt reading comprehension.

    PubMed

    Foroughi, Cyrus K; Werner, Nicole E; Barragán, Daniela; Boehm-Davis, Deborah A

    2015-06-01

    Previous research suggests that being interrupted while reading a text does not disrupt the later recognition or recall of information from that text. This research is used as support for Ericsson and Kintsch's (1995) long-term working memory (LT-WM) theory, which posits that disruptions while reading (e.g., interruptions) do not impair subsequent text comprehension. However, to fully comprehend a text, individuals may need to do more than recognize or recall information that has been presented in the text at a later time. Reading comprehension often requires individuals to connect and synthesize information across a text (e.g., successfully identifying complex topics such as themes and tones) and not just make a familiarity-based decision (i.e., recognition). The goal for this study was to determine whether interruptions while reading disrupt reading comprehension when the questions assessing comprehension require participants to connect and synthesize information across the passage. In Experiment 1, interruptions disrupted reading comprehension. In Experiment 2, interruptions disrupted reading comprehension but not recognition of information from the text. In Experiment 3, the addition of a 15-s time-out prior to the interruption successfully removed these negative effects. These data suggest that the time it takes to process the information needed to successfully comprehend text when reading is greater than that required for recognition. Any interference (e.g., an interruption) that occurs during the comprehension process may disrupt reading comprehension. This evidence supports the need for transient activation of information in working memory for successful text comprehension and does not support LT-WM theory.

  1. 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…

  2. Young People and Reading: A School Study Conducted by the National Literacy Trust for the Reading Champions Initiative

    ERIC Educational Resources Information Center

    Clark, Christina; Torsi, Stephen; Strong, Julia

    2005-01-01

    Imagine what a difference it would make if every child loved to read. Every teacher knows the difference that a love of reading makes to a child's performance; reading opens so many doors. However, research has long shown not only that men and boys in the developed world lag behind women and girls when it comes to engaging with reading. Thus…

  3. Translation Regulation of the Glutamyl-prolyl-tRNA Synthetase Gene EPRS through Bypass of Upstream Open Reading Frames with Noncanonical Initiation Codons.

    PubMed

    Young, Sara K; Baird, Thomas D; Wek, Ronald C

    2016-05-13

    In the integrated stress response, phosphorylation of eIF2α (eIF2α-P) reduces protein synthesis while concomitantly promoting preferential translation of specific transcripts associated with stress adaptation. Translation of the glutamyl-prolyl-tRNA synthetase gene EPRS is enhanced in response to eIF2α-P. To identify the underlying mechanism of translation control, we employed biochemical approaches to determine the regulatory features by which upstream ORFs (uORFs) direct downstream translation control and expression of the EPRS coding region. Our findings reveal that translation of two inhibitory uORFs encoded by noncanonical CUG and UUG initiation codons in the EPRS mRNA 5'-leader serve to dampen levels of translation initiation at the EPRS coding region. By a mechanism suggested to involve increased translation initiation stringency during stress-induced eIF2α-P, we observed facilitated ribosome bypass of these uORFs, allowing for increased translation of the EPRS coding region. Importantly, EPRS protein expression is enhanced through this preferential translation mechanism in response to multiple known activators of eIF2α-P and likely serves to facilitate stress adaptation in response to a variety of cellular stresses. The rules presented here for the regulated ribosome bypass of noncanonical initiation codons in the EPRS 5'-leader add complexity into the nature of uORF-mediated translation control mechanisms during eIF2α-P and additionally illustrate the roles that previously unexamined uORFs with noncanonical initiation codons can play in modulating gene expression.

  4. Oral Reading Fluency and Comprehension in Kenya: Reading Acquisition in a Multilingual Environment

    ERIC Educational Resources Information Center

    Piper, Benjamin; Schroeder, Leila; Trudell, Barbara

    2016-01-01

    Reading research has shown that variable relationships exist between measures of oral reading fluency and reading comprehension, depending on whether the language of the text is the reader's first language or an additional language. This paper explores this phenomenon, using reading assessment data for 2,000 Kenyan children in two or three…

  5. How Does Speed and Accuracy in Reading Relate to Reading Comprehension in Arabic?

    ERIC Educational Resources Information Center

    Abu-Leil, Aula Khateeb; Share, David L.; Ibrahim, Raphiq

    2014-01-01

    The purpose of this study was to investigate the potential contribution of decoding efficiency to the development of reading comprehension among skilled adult native Arabic speakers. In addition, we tried to investigate the influence of Arabic vowels on reading accuracy, reading speed, and therefore to reading comprehension. Seventy-five Arabic…

  6. The primary structure and expression of the second open reading frame of the polymerase gene of the coronavirus MHV-A59; a highly conserved polymerase is expressed by an efficient ribosomal frameshifting mechanism.

    PubMed Central

    Bredenbeek, P J; Pachuk, C J; Noten, A F; Charité, J; Luytjes, W; Weiss, S R; Spaan, W J

    1990-01-01

    Sequence analysis of a substantial part of the polymerase gene of the murine coronavirus MHV-A59 revealed the 3' end of an open reading frame (ORF1a) overlapping with a large ORF (ORF1b; 2733 amino acids) which covers the 3' half of the polymerase gene. The expression of ORF1b occurs by a ribosomal frameshifting mechanism since the ORF1a/ORF1b overlapping nucleotide sequence is capable of inducing ribosomal frameshifting in vitro as well as in vivo. A stem-loop structure and a pseudoknot are predicted in the nucleotide sequence involved in ribosomal frameshifting. Comparison of the predicted amino acid sequence of MHV ORF1b with the amino acid sequence deduced from the corresponding gene of the avian coronavirus IBV demonstrated that in contrast to the other viral genes this ORF is extremely conserved. Detailed analysis of the predicted amino acid sequence revealed sequence elements which are conserved in many DNA and RNA polymerases. Images PMID:2159623

  7. Immunogenicity and Protective Response Induced by Recombinant Plasmids Based on the BAB1_0267 and BAB1_0270 Open Reading Frames of Brucella abortus 2308 in BALB/c Mice

    PubMed Central

    Gómez, Leonardo A.; Alvarez, Francisco I.; Fernández, Pablo A.; Flores, Manuel R.; Molina, Raúl E.; Coloma, Roberto F.; Oñate, Angel A.

    2016-01-01

    Immunogenicity induced by recombinant plasmids based on the BAB1_0267 and BAB1_0270 open reading frames (ORFs) of Brucella abortus 2308 was evaluated. Bioinformatics analyses indicate that the BAB1_0267 and BAB1_0270 ORFs encode a protein with a SH3 domain and a Zn-dependent metalloproteinase, respectively. Both ORFs have important effects on intracellular survival and replication of B. abortus 2308, mediated via professional and non-professional phagocytic cells. Our results show that immunization with the recombinant plasmid based on the BAB1_0267 ORF significantly increases the production of IgG1, levels of IFN-γ and the lymphoproliferative response of splenocytes. However, BAB1_0267 did not provide significant levels of protection. The plasmid based on the BAB1_0270 significantly increased IgG2a production, levels of IFN-γ and TNF-α, and the lymphoproliferative response of splenocytes. These results demonstrate that immunization with the BAB1_0270 derived recombinant plasmid induce a Th1-type immune response, correlated with a heightened resistance to B. abortus 2308 infection in mice. It is concluded that the Th1-type immune response against bacterial Zn-dependent metalloproteinase induces a protective response in mice, and that pV270 recombinant plasmid is an effective candidate microbicide against brucellosis. PMID:27747197

  8. Translational and Structural Requirements of the Early Nodulin Gene enod40, a Short-Open Reading Frame-Containing RNA, for Elicitation of a Cell-Specific Growth Response in the Alfalfa Root Cortex

    PubMed Central

    Sousa, Carolina; Johansson, Christina; Charon, Celine; Manyani, Hamid; Sautter, Christof; Kondorosi, Adam; Crespi, Martin

    2001-01-01

    A diversity of mRNAs containing only short open reading frames (sORF-RNAs; encoding less than 30 amino acids) have been shown to be induced in growth and differentiation processes. The early nodulin gene enod40, coding for a 0.7-kb sORF-RNA, is expressed in the nodule primordium developing in the root cortex of leguminous plants after infection by symbiotic bacteria. Ballistic microtargeting of this gene into Medicago roots induced division of cortical cells. Translation of two sORFs (I and II, 13 and 27 amino acids, respectively) present in the conserved 5′ and 3′ regions of enod40 was required for this biological activity. These sORFs may be translated in roots via a reinitiation mechanism. In vitro translation products starting from the ATG of sORF I were detectable by mutating enod40 to yield peptides larger than 38 amino acids. Deletion of a Medicago truncatula enod40 region between the sORFs, spanning a predicted RNA structure, did not affect their translation but resulted in significantly decreased biological activity. Our data reveal a complex regulation of enod40 action, pointing to a role of sORF-encoded peptides and structured RNA signals in developmental processes involving sORF-RNAs. PMID:11113209

  9. Human T-cell leukemia virus type 1 reverse transcriptase (RT) originates from the pro and pol open reading frames and requires the presence of RT-RNase H (RH) and RT-RH-integrase proteins for its activity.

    PubMed

    Trentin, B; Rebeyrotte, N; Mamoun, R Z

    1998-08-01

    The first description of an active form of a recombinant human T-cell leukemia virus type 1 (HTLV-1) reverse transcriptase (RT) and subsequent predictions of its amino acid sequence and quaternary structure are reported here. By using amino acid alignment methods, the NH2 and COOH termini of the RT, RNase H (RH), and integrase (IN) domains of the Pol polyprotein were determined. The HTLV-1 RT seems to be unique since its NH2 terminus is probably encoded by the pro open reading frame (ORF) fused downstream, via a transframe peptide, to the polypeptide encoded by the pol ORF. The HTLV-1 Pol amino acid sequence was revealed to be highly similar to that of Rous sarcoma virus (RSV), particularly at the RT-RH hinge region. These two domains remain linked for RSV; this may also be the case for HTLV-1. In light of these results, RT, RT-RH, and RT-RH-IN genes were constructed and introduced into His-tagged protein expression vectors. The corresponding proteins were synthesized in vitro, and the DNA polymerase activities of different protein combinations were tested. Solely the RT-RH-RT-RH-IN combination was found to have a significant activity level. Velocity sedimentation analysis suggested that the HTLV-1 RT-RH and RT-RH-IN monomers are likely associated in an oligomeric structure, probably of the alpha3/beta type.

  10. Differential Expression of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) Open Reading Frame 5, but not Apoptogenic Cytokines, Contribute to Severe Respiratory Disease in Pigs Infected with Type 2 PRRSV Compared with Pigs Infected with Type 1 PRRSV.

    PubMed

    Han, K; Lee, J; Park, C; Choi, K; Jeong, J; Park, S-J; Kang, I; Chae, C

    2016-01-01

    The aim of this study was to compare the expression of open reading frame 5 (ORF5) of porcine reproductive and respiratory syndrome virus (PRRSV) and apoptogenic cytokines in the lungs from pigs infected with type 1 and type 2 PRRSV. Microscopical lung lesion scores and the mean number of apoptotic cells were significantly (P <0.05) higher in pigs with type 2 PRRSV infection than in those with type 1 PRRSV infection. The score for the mean number of PRRSV ORF5-positive cells per unit area of lung was significantly (P <0.05) higher in pigs with type 2 PRRSV infection. There were no significant differences in the expression of tumour necrosis factor-α and interleukin-1 in lung tissues between type 1 and type 2 PRRSV-infected pigs. The severity of microscopical lung lesions and the number of apoptotic cells correlated well with the number of PRRSV ORF5-positive cells. Therefore, differential expression of PRRSV ORF5, but not apoptogenic cytokines, may attribute to the severity of lung lesions and apoptosis in lungs in PRRSV infection. These results suggest that expression of PRRSV ORF5 may be a critical determinant for different virulence between PRRSV genotypes in terms of respiratory disease.

  11. Network-based reading system for lung cancer screening CT

    NASA Astrophysics Data System (ADS)

    Fujino, Yuichi; Fujimura, Kaori; Nomura, Shin-ichiro; Kawashima, Harumi; Tsuchikawa, Megumu; Matsumoto, Toru; Nagao, Kei-ichi; Uruma, Takahiro; Yamamoto, Shinji; Takizawa, Hotaka; Kuroda, Chikazumi; Nakayama, Tomio

    2006-03-01

    This research aims to support chest computed tomography (CT) medical checkups to decrease the death rate by lung cancer. We have developed a remote cooperative reading system for lung cancer screening over the Internet, a secure transmission function, and a cooperative reading environment. It is called the Network-based Reading System. A telemedicine system involves many issues, such as network costs and data security if we use it over the Internet, which is an open network. In Japan, broadband access is widespread and its cost is the lowest in the world. We developed our system considering human machine interface and security. It consists of data entry terminals, a database server, a computer aided diagnosis (CAD) system, and some reading terminals. It uses a secure Digital Imaging and Communication in Medicine (DICOM) encrypting method and Public Key Infrastructure (PKI) based secure DICOM image data distribution. We carried out an experimental trial over the Japan Gigabit Network (JGN), which is the testbed for the Japanese next-generation network, and conducted verification experiments of secure screening image distribution, some kinds of data addition, and remote cooperative reading. We found that network bandwidth of about 1.5 Mbps enabled distribution of screening images and cooperative reading and that the encryption and image distribution methods we proposed were applicable to the encryption and distribution of general DICOM images via the Internet.

  12. extendFromReads

    SciTech Connect

    Williams, Kelly P.

    2013-10-03

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

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

    ERIC Educational Resources Information Center

    Allington, Richard L.

    2014-01-01

    Long overlooked, reading volume is actually central to the development of reading proficiencies, especially in the development of fluent reading proficiency. Generally no one in schools monitors the actual volume of reading that children engage in. We know that the commonly used commercial core reading programs provide only material that requires…

  14. Iconic Prosody in Story Reading

    ERIC Educational Resources Information Center

    Perlman, Marcus; Clark, Nathaniel; Falck, Marlene Johansson

    2015-01-01

    Recent experiments have shown that people iconically modulate their prosody corresponding with the meaning of their utterance (e.g., Shintel et al., 2006). This article reports findings from a story reading task that expands the investigation of iconic prosody to abstract meanings in addition to concrete ones. Participants read stories that…

  15. FACTORS AFFECTING LEARNING TO READ.

    ERIC Educational Resources Information Center

    HAYES, ROBERT B.; WUEST, RICHARD C.

    FOUR DIFFERENT READING PROGRAMS WERE EVALUATED USING 302 SECOND-GRADE PUPILS WHO HAD PARTICIPATED IN THE SAME PROGRAMS IN GRADE 1. IN ADDITION TO THE STUDY CONDUCTED IN THE SECOND GRADE, A PILOT STUDY WAS CONTINUED INTO GRADE 3, AND A MODIFIED VERSION OF THE GRADE 1 STUDY WAS MADE AGAIN IN GRADE 1. THE FOUR READING PROGRAMS INVOLVED WERE (1) A…

  16. How Close Is Close Reading?

    ERIC Educational Resources Information Center

    Saccomano, Doreen

    2014-01-01

    Close Reading is a strategy that can be used when reading challenging text. This strategy requires teachers to provide scaffolding, and create opportunities for think-alouds and rereading of text in order to help students become active readers who focus on finding text-based support for their answers. In addition, teachers must also be aware of…

  17. Accurate reading comprehension rate as an indicator of broad reading in students in first, second, and third grades.

    PubMed

    Ciancio, Dennis; Thompson, Kelly; Schall, Megan; Skinner, Christopher; Foorman, Barbara

    2015-10-01

    The relationship between reading comprehension rate measures and broad reading skill development was examined using data from approximately 1425 students (grades 1-3). Students read 3 passages, from a pool of 30, and answered open-ended comprehension questions. Accurate reading comprehension rate (ARCR) was calculated by dividing the percentage of questions answered correctly (%QC) by seconds required to read the passage. Across all 30 passages, ARCR and its two components, %QC correct and time spent reading (1/seconds spent reading the passage), were significantly correlated with broad reading scores, with %QC resulting in the lowest correlations. Two sequential regressions supported previous findings which suggest that ARCR measures consistently produced meaningful incremental increases beyond %QC in the amount of variance explained in broad reading skill; however, ARCR produced small or no incremental increases beyond reading time. Discussion focuses on the importance of the measure of reading time embedded in brief accurate reading rate measures and directions for future research.

  18. The Effects of Combining Repeated Reading with "Reading Mastery" on First Graders' Oral Reading Fluency

    ERIC Educational Resources Information Center

    Nanda, Alice O.; Fredrick, Laura D.

    2007-01-01

    The present study replicates and extends the work of Frankhauser, Tso, and Martella (2001) using 6 first-grade students in a multiple baseline design across participants to determine if the addition of three repeated readings following "Reading Mastery I and II" (Engelmann & Bruner, 1995) lessons improves student fluency beyond that expected…

  19. Opening the Gates: Reading "The Gulag"

    ERIC Educational Resources Information Center

    Iannone, Carol

    2009-01-01

    The year 2008 saw the death of one of the towering figures of the twentieth century, Aleksandr Solzhenitsyn. More than any other single man, Solzhenitsyn helped morally delegitimize what had seemed the unchallengeable monolith that was the Union of Soviet Socialist Republics. His life is a standing example and inspiration to those American…

  20. Reading Disorders:

    PubMed Central

    Seaber, Emma

    2016-01-01

    This article explores the relationship between eating disorders and reading behaviors, arguing that there is a meaningful difference in a minority of readers' approach to and understanding of anorexia life-writing, and of literary texts more broadly. To illuminate this distinction, this article begins by considering the reported deleterious influence of Marya Hornbacher’s anorexia memoir, Wasted, elaborating the ways Hornbacher offers a positive presentation of anorexia nervosa that may, intentionally or not, induce certain readers to “try it” themselves. This is followed by an exploration of how Hornbacher’s own reading praxis is implicated in a discursive feedback loop around anorexia narratives. It concludes with a discussion of disordered reading attitudes in relation to the emergence of the “pro-anorexia” phenomenon.

  1. The Effects of L2 Reading Skills on L1 Reading Skills through Transfer

    ERIC Educational Resources Information Center

    Altmisdort, Gonca

    2016-01-01

    This study investigated whether transfer from L2 to L1 in reading occurs, and if so, which reading sub-skills are transferred into L1 reading. The aim is to identify the role of second language reading skills in L1 reading skills by means of transfer. In addition, the positive effects of the second language transfer to the first language in the…

  2. The Effects of Extensive Reading via E-Books on Tertiary Level EFL Students' Reading Attitude, Reading Comprehension, and Vocabulary

    ERIC Educational Resources Information Center

    Chen, Chin-Neng; Chen, Shu-Chu; Chen, Shu-Hui Eileen; Wey, Shyh-Chyi

    2013-01-01

    This study investigates the effects of extensive reading of e-books on tertiary level EFL students' English reading attitude, reading comprehension and vocabulary. Eighty-nine participants were assigned in two groups, with 46 students in the experimental group and the other 43 students in the control group. In addition to a traditional curriculum…

  3. Introducing point mutations into the ATGs of the putative open reading frames of the HSV-1 gene encoding the latency associated transcript (LAT) reduces its anti-apoptosis activity.

    PubMed

    Carpenter, Dale; Henderson, Gail; Hsiang, Chinhui; Osorio, Nelson; BenMohamed, Lbachir; Jones, Clinton; Wechsler, Steven L

    2008-02-01

    The herpes simplex virus type 1 (HSV-1) latency associated transcript (LAT) gene has anti-apoptosis activity that directly or indirectly enhances the virus's reactivation phenotype in small animal models. The first 1.5 kb of the primary 8.3 kb LAT is sufficient and some or all of it is necessary for LAT's anti-apoptosis in transient transfection assays and for LAT's ability to enhance the reactivation phenotype. Based on LAT's genomic sequence, the first 1.5 kb contains eight potential open reading frames (ORFs) defined as an ATG followed by an in frame termination codon. In this study, point mutations were introduced into the ATGs of ORFs present in the 1.5 kb fragment of LAT. Mutagenesis of all eight ATGs in LAT ORFs consistently reduced the anti-apoptotic activity of LAT in transiently transfected mouse neuroblastoma cells regardless of whether apoptosis was induced by caspase 8 or caspase 9. Mutation of the six ATGs located in the stable intron sequences within the 1.5 kb LAT had a dramatic effect on caspase 9, but not caspase 8, induced apoptosis. For both caspase 8 and caspase 9 induced apoptosis, mutating the two ATGs in the exon of the LAT 1.5 kb fragment reduced, but did not eliminate the anti-apoptotic activity of LAT. These studies suggest that altering the fine structure of regulatory RNA or expression of a putative LAT ORF regulates the anti-apoptosis activity of LAT. These studies also indicate that more than one function is present in the 1.5 kb LAT fragment.

  4. Does Extensive Reading Promote Reading Speed?

    ERIC Educational Resources Information Center

    He, Mu

    2014-01-01

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

  5. Oral Reading Fluency in Second Language Reading

    ERIC Educational Resources Information Center

    Jeon, Eun Hee

    2012-01-01

    This study investigated the role of oral reading fluency in second language reading. Two hundred and fifty-five high school students in South Korea were assessed on three oral reading fluency (ORF) variables and six other reading predictors. The relationship between ORF and other reading predictors was examined through an exploratory factor…

  6. Reading Transformation

    ERIC Educational Resources Information Center

    Reeves, Melinda

    2006-01-01

    The parents of students who attend Decatur High School thought that there was little hope of their kids going on to college. After a year or so in Decatur's reading program, their sons and daughters were both transformed and college bound. In this article, the author describes how Decatur was able to successfully transform their students. Seven…

  7. Reading Poverty.

    ERIC Educational Resources Information Center

    Shannon, Patrick

    The central purpose of this book is to challenge current social constructions of poverty, reading education, and the putative relationship between the two. It explores how official and popular representations of poverty are bound to specific historical, social, and economic conditions of their own production. The book offers four stances of…

  8. Dyslexia (specific reading disability).

    PubMed

    Shaywitz, Sally E; Shaywitz, Bennett A

    2005-06-01

    Converging evidence from a number of lines of investigation indicates that dyslexia represents a disorder within the language system and more specifically within a particular subcomponent of that system, phonological processing. Recent advances in imaging technology, particularly the development of functional magnetic resonance imaging, provide evidence of a neurobiological signature for dyslexia, specifically a disruption of two left hemisphere posterior brain systems, one parieto-temporal, the other occipito-temporal, with compensatory engagement of anterior systems around the inferior frontal gyrus and a posterior (right occipito-temporal) system. Furthermore, good evidence indicates a computational role for the left occipito-temporal system: the development of fluent (automatic) reading. The brain systems for reading are malleable and their disruption in dyslexic children may be remediated by provision of an evidence-based, effective reading intervention. In addition, functional magnetic resonance imaging studies of young adults with reading difficulties followed prospectively and longitudinally from age 5 through their mid twenties suggests that there may be two types of reading difficulties, one primarily on a genetic basis, the other, and far more common, reflecting environmental influences. These studies offer the promise for more precise identification and effective management of dyslexia in children, adolescents and adults.

  9. Emerson, Reading, and Democracy: Reading as Engaged Democratic Citizenship

    ERIC Educational Resources Information Center

    Boatright, Michael D.; Faust, Mark A.

    2013-01-01

    "What is the right use of books?" Responding to the question he famously raised, Ralph Waldo Emerson wrote that "books are for nothing but to inspire," which we take as endorsing a pragmatic and pluralistic view of reading literature and other kinds of texts in a manner that keeps books open to a flow of continual questioning and renewal. The…

  10. Reading Aloud to Fourth Grade Students.

    ERIC Educational Resources Information Center

    Forte, Frances

    A study determined if regular listening to oral reading by the teacher affected fourth-grade students' level of comprehension. Subjects were 47 students from an elementary school in central New Jersey. Twenty-five students were read to for 30 minutes daily for 8 weeks in addition to their regular classroom reading instruction. The remaining 22…

  11. A Reading Profile of Functionally Illiterate Adults.

    ERIC Educational Resources Information Center

    Roberts, Bette H.; Russell, Sheldon Noel

    In order to identify the reading behavior and instructional needs of functionally illiterate adults reading below fourth grade level, 50 adults were identified and diagnosed on the Durrell Analysis of Reading Difficulty test and the Slosson Intelligence Test for Children and Adults. In addition, a questionnaire was administered to Oklahoma City…

  12. An "All Right" High School Reading Program.

    ERIC Educational Resources Information Center

    Condas, Anastasia C.

    Noting the importance of a relaxed atmosphere, the availability of all kinds of reading materials, and an unpressured, out-in-the-open approach to measuring student progress, this paper describes the activities and resources that constitute a successful high school reading program. The discussion focuses on the types of books, diagnosis,…

  13. The Reading & Writing for Critical Thinking Project.

    ERIC Educational Resources Information Center

    International Reading Association, Newark, DE.

    An initiative of the Open Society Institute (OSI) and the International Reading Association (IRA), Reading and Writing for Critical Thinking (RWCT) promotes classroom teaching practices that help students learn actively, think critically, and work cooperatively. It offers an integrated program of staff development, activities for teachers of the…

  14. Case Studies in Reading: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Trela, Thaddeus M., Comp.; Becker, George J., Comp.

    Descriptions of individual diagnosis and remediation of reading problems experienced by students at all levels are included in this annotated bibliography. Included are books, texts having case study sections, and journal reports which together comprise useful sources of case studies of reading disabilities. An opening section lists nine "first…

  15. Kindergarten Reading Curriculum: Reading Abilities, Not Reading Readiness.

    ERIC Educational Resources Information Center

    Stewart, Ida Santos

    1985-01-01

    Addresses attitudes toward reading resulting in beginning reading instruction in the kindergarten and preschool curriculum. Argues that previously accepted notions of the necessity of reading readiness are no longer viable and encourages home and classroom support for the acquisition of reading abilities through written and oral language. (DST)

  16. Reading Words and Reading Text.

    ERIC Educational Resources Information Center

    Leong, Che Kan

    The research and practical questions about the internal lexicon, the associated network of internal representation basic to word meaning, boil down to whether in reading English the phonological route is obligatory or optional. Since the English writing system is morphophonemic, not phonetic, access to the internal lexicon cannot and should not…

  17. Hermeneutic reading of classic texts.

    PubMed

    Koskinen, Camilla A-L; Lindström, Unni Å

    2013-09-01

    The purpose of this article is to broaden the understandinfg of the hermeneutic reading of classic texts. The aim is to show how the choice of a specific scientific tradition in conjunction with a methodological approach creates the foundation that clarifies the actual realization of the reading. This hermeneutic reading of classic texts is inspired by Gadamer's notion that it is the researcher's own research tradition and a clearly formulated theoretical fundamental order that shape the researcher's attitude towards texts and create the starting point that guides all reading, uncovering and interpretation. The researcher's ethical position originates in a will to openness towards what is different in the text and which constantly sets the researcher's preunderstanding and research tradition in movement. It is the researcher's attitude towards the text that allows the text to address, touch and arouse wonder. Through a flexible, lingering and repeated reading of classic texts, what is different emerges with a timeless value. The reading of classic texts is an act that may rediscover and create understanding for essential dimensions and of human beings' reality on a deeper level. The hermeneutic reading of classic texts thus brings to light constantly new possibilities of uncovering for a new envisioning and interpretation for a new understanding of the essential concepts and phenomena within caring science.

  18. Reading Science

    ERIC Educational Resources Information Center

    Carlson, Kenneth

    2005-01-01

    Reading the average science textbook, one is struck with a question: Why would people devote their lives to the study of a subject as dry as the Sahara Desert? Students in science classes only need to be let in on the great secret of science. It is fun and full of the stuff in page-turner novels--intrigue, mystery, romance, and sometimes just dumb…

  19. Redesigning Reading Instruction.

    ERIC Educational Resources Information Center

    Ivey, Gay

    2000-01-01

    All students, including struggling readers, need opportunities to make choices in their reading. Schools should shun round-robin oral reading and basal readers, prioritize reading time, allocate resources for varied reading materials keyed to student interests, and develop better reading teachers, not better reading programs. (Contains 20…

  20. Reading Research 1975.

    ERIC Educational Resources Information Center

    Goodacre, Elizabeth J.

    The reading research contributions discussed in this survey are arranged under the following headings: reading standards and tests, dyslexia and specific reading retardation, remedial and reading provision, reading development, and materials and reading interests. Each section summarizes research and findings in that area of study during 1975.…

  1. Open reading frame 3 of genotype 1 hepatitis E virus inhibits nuclear factor-κappa B signaling induced by tumor necrosis factor-α in human A549 lung epithelial cells.

    PubMed

    Xu, Jian; Wu, Fan; Tian, Deying; Wang, Jingjing; Zheng, Zizheng; Xia, Ningshao

    2014-01-01

    Hepatitis E virus (HEV) is one of the primary causative agents of acute hepatitis, and represents a major cause of severe public health problems in developing countries. The pathogenesis of HEV is not well characterized, however, primarily due to the lack of well-defined cell and animal models. Here, we investigated the effects of genotype 1 HEV open reading frame 3 (ORF3) on TNF-α-induced nucleus factor-κappa B (NF-κB) signaling. Human lung epithelial cells (A549) were transiently transfected with ORF3 containing plasmids. These cells were then stimulated with TNF-α and the nucleus translocation of the p65 NF-κB subunit was assessed using western blot and laser confocal microscopy. DNA-binding activity of p65 was also examined using electrophoretic mobility shift assay (EMSA), and the suppression of NF-κB target genes were detected using real-time RT-PCR and ELISA. These results enabled us to identify the decreased phosphorylation levels of IKBα. We focused on the gene of negative regulation of NF-κB, represented by TNF-α-induced protein 3 (TNFAIP3, also known as A20). Reducing the levels of A20 with siRNAs significantly enhances luciferase activation of NF-κB. Furthermore, HEV ORF3 regulated A20 primarily via activating transcription factor 6 (ATF6), involved in unfolded protein response (UPR), resulting in the degradation or inactivation of the receptor interacting protein 1 (RIP1), a major upstream activator of IKB kinase compounds (IKKs). Consequently, the phosphorylation of IKBα and the nucleus translocation of p65 are blocked, which contributes to diminished NF-κB DNA-binding activation and NF-κB-dependent gene expression. The findings suggest that genotype 1 HEV, through ORF3, may transiently activate NF-κB through UPR in early stage, and subsequently inhibit TNF-α-induced NF-κB signaling in late phase so as to create a favorable virus replication environment.

  2. The Reading First Controversy: Promises and Perils of Federal Leadership

    ERIC Educational Resources Information Center

    Barbash, Shepard

    2008-01-01

    "Reading First is the most effective federal program in history." So reads the opening line of a report that Alabama superintendent of education Joseph Morton sent to his congressional delegation last June, in which he recounts how the program has raised reading achievement for poor students in his charge. Morton's view is shared by…

  3. Slow Reading: Reading along "Lectio" Lines

    ERIC Educational Resources Information Center

    Badley, K. Jo-Ann; Badley, Ken

    2011-01-01

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

  4. Reading Together: A Successful Reading Fluency Intervention

    ERIC Educational Resources Information Center

    Young, Chase; Mohr, Kathleen A. J.; Rasinski, Timothy

    2015-01-01

    The article describes a reading fluency intervention called Reading Together that combines the method of repeated readings (Samuels, 1979) and the Neurological Impress Method (Heckelman, 1969). Sixteen volunteers from various backgrounds were recruited and trained to deliver the Reading Together intervention to struggling readers in third through…

  5. Rehearsed Oral Reading: Providing Authentic Reading Experiences.

    ERIC Educational Resources Information Center

    Matz, Karl A.

    A two-part study investigated the prevalence of unrehearsed oral reading and compared reading fluency for rehearsed and unrehearsed reading passages. In the first part of the study, a total of 21 teachers were interviewed and 24 classrooms were observed. Results indicated that by far the most prevalent practice in basal reading programs is the…

  6. Is Oral/Text Reading Fluency a “Bridge” to Reading Comprehension?

    PubMed Central

    Kim, Young-Suk Grace; Park, Chea Hyeong; Wagner, Richard K.

    2015-01-01

    In the present study we investigated developmental relations among word reading fluency, listening comprehension, and text reading fluency to reading comprehension in a relatively transparent language, Korean. A total of 98 kindergartners and 170 first graders in Korea were assessed on a series of tasks involving listening comprehension, word reading fluency, text reading fluency, and reading comprehension. Results from multigroup structural equation models showed that text reading fluency was a dissociable construct for both kindergartners and first graders. In addition, a developmental pattern emerged: listening comprehension was not uniquely related to text reading fluency for first graders, but not for kindergartners, over and above word reading fluency. In addition, text reading fluency was uniquely related to reading comprehension for kindergartners, but not for first graders, after accounting for word reading fluency and listening comprehension. For first graders, listening comprehension dominated the relations. There were no differences in the pattern of relations for skilled and less skilled readers in first grade. Results are discussed from a developmental perspective for reading comprehension component skills including text reading fluency. PMID:25653474

  7. The Open University Opens.

    ERIC Educational Resources Information Center

    Tunstall, Jeremy, Ed.

    Conceived by the British Labor Government in the 1960's the Open University was viewed as a way to extend higher education to Britain's working class, but enrollment figures in classes that represent traditional academic disciplines show that the student population is predominantly middle class. Bringing education into the home presents numerous…

  8. Cognitive flexibility predicts early reading skills

    PubMed Central

    Colé, Pascale; Duncan, Lynne G.; Blaye, Agnès

    2014-01-01

    An important aspect of learning to read is efficiency in accessing different kinds of linguistic information (orthographic, phonological, and semantic) about written words. The present study investigates whether, in addition to the integrity of such linguistic skills, early progress in reading may require a degree of cognitive flexibility in order to manage the coordination of this information effectively. Our study will look for evidence of a link between flexibility and both word reading and passage reading comprehension, and examine whether any such link involves domain-general or reading-specific flexibility. As the only previous support for a predictive relationship between flexibility and early reading comes from studies of reading comprehension in the opaque English orthography, another possibility is that this relationship may be largely orthography-dependent, only coming into play when mappings between representations are complex and polyvalent. To investigate these questions, 60 second-graders learning to read the more transparent French orthography were presented with two multiple classification tasks involving reading-specific cognitive flexibility (based on words) and non-specific flexibility (based on pictures). Reading skills were assessed by word reading, pseudo-word decoding, and passage reading comprehension measures. Flexibility was found to contribute significant unique variance to passage reading comprehension even in the less opaque French orthography. More interestingly, the data also show that flexibility is critical in accounting for one of the core components of reading comprehension, namely, the reading of words in isolation. Finally, the results constrain the debate over whether flexibility has to be reading-specific to be critically involved in reading. PMID:24966842

  9. Phonological Awareness and Reading Speed Deficits in Reading Disabled Greek-Speaking Children

    ERIC Educational Resources Information Center

    Constantinidou, Maria; Stainthorp, Rhona

    2009-01-01

    There is evidence that phonological awareness skills secure decoding ability and that phonological deficits underlie failure to acquire adequate word recognition. Slow word-reading rate may be an additional defining characteristic of reading disability. The present study aimed to investigate whether: (1) reading disabled (RD) Greek-speaking…

  10. The Impact of Technology-Based Reading Programs on Lower Achievers' State Reading Assessment

    ERIC Educational Resources Information Center

    Jacobs, Rhonda Suzanne

    2012-01-01

    Research concerning technology-based reading intervention is limited and additional studies are needed in this area of study. This study examined the individual intervention programs (Read 180 and Thinking Reader) for diverse 6th, 7th, and 8th graders in order to determine the gains per grade level on state standardized reading tests. This study…

  11. Successful Idiom Solving Strategies While Reading and Reading Time with Trained and Untrained Learners

    ERIC Educational Resources Information Center

    Angel, Rosalina Domínguez

    2014-01-01

    The present article examines the outcomes derived from a task on intensive reading carried out by university students. The main goal is to analyze the frequency of use and the success of idiom solving strategies used by the subjects while reading. Additionally, our interest is to compare the above outcomes and the reading time scores of a group of…

  12. Additional insights. Commentary on “the musical stroop effect: opening a new avenue to research on automatisms” by l. Grégoire, P. Perruchet, and B. Poulin-Charronnat (Experimental Psychology, 2013, vol. 60, pp. 269–278).

    PubMed

    Akiva-Kabiri, Lilach; Henik, Avishai

    2014-01-01

    In their paper "The Musical Stroop Effect: Opening a New Avenue to Research on Automatisms," Grégoire, Perruchet, and Poulin-Charronnat (2013) use a musical Stroop-like task to demonstrate the automaticity of musical note naming in musicians. In addition, the authors suggest that music training can serve as a tool in order to study the acquisition of automaticity. In the following commentary, we aim to address three main issues concerning the paper by Grégoire et al. (2013). First, we will suggest some additional interpretations of the results; specifically, we will relate to the association between music and space. Second, we will discuss a methodological issue dealing with interference, facilitation, and the role of the neutral condition. We suggest that the study by Grégoire et al. (2013) lacks a proper neutral condition and thus it is impossible to assert that the congruency effect is interference based. Third, we will discuss the authors' suggestion of using the musical Stroop effect as a tool for studying automatism. We consider the practical relevance of music training as a tool for studying the acquisition of automaticity by pointing out that music training is highly heterogeneous.

  13. 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…

  14. From Decoding to Reading Comprehension: An Assessment of the Effectiveness of the Training of Intervention Providers to Teach Reading Comprehension

    ERIC Educational Resources Information Center

    Gold, Carol

    2010-01-01

    Research indicates that the most effective instruction in basic reading skills and reading comprehension should take place in the classroom. For some students, however, additional reading instruction outside of the regular classroom may be needed and should begin early in a student's educational career. Since reading comprehension is the goal of…

  15. 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…

  16. Beyond Cognition: Reading Motivation and Reading Comprehension.

    PubMed

    Wigfield, Allan; Gladstone, Jessica; Turci, Lara

    2016-09-01

    The authors review research on children's reading motivation and its relation to their reading comprehension. They begin by discussing work on the development of school motivation in general and reading motivation in particular, reviewing work showing that many children's reading motivation declines over the school years. Girls tend to have more positive motivation for reading than do boys, and there are ethnic differences in children's reading motivation. Over the last 15 years researchers have identified in both laboratory and classroom-based research instructional practices that positively impact students' reading motivation and ultimately their reading comprehension. There is a strong need for researchers to build on this work and develop and study in different age groups of children effective classroom-based reading motivation instructional programs for a variety of narrative and informational materials.

  17. Reading Workshop Survival Kit.

    ERIC Educational Resources Information Center

    Muschla, Gary Robert

    Intended for reading and classroom teachers, this book, organized in two parts, is a complete, step-by-step guide to setting up and running a reading workshop for grades 5-12 where reading is "the" priority. Part 1, "Management of the Reading Workshop," shows how to create a reading workshop, offers specific tools and…

  18. Parents Teach Reading, Too.

    ERIC Educational Resources Information Center

    Clary, Linda Mixon

    Parents and teachers need to be involved in teaching children to read and to enjoy reading. There are three planks in a platform that will help all parents become involved in their children's learning to read. First, parents must set the example. If they want their children to read, parents must read around them and to them. Secondly, they must…

  19. Multisyllabic word reading as a moderator of morphological awareness and reading comprehension.

    PubMed

    Gilbert, Jennifer K; Goodwin, Amanda P; Compton, Donald L; Kearns, Devin M

    2014-01-01

    The purpose of this study was to investigate whether the relation between morphological awareness on reading comprehension is moderated by multisyllabic word reading ability in fifth-grade students (N = 169, 53.7% female, 65.2% minority status, 69.2% free/reduced lunch status), oversampled for poor reading skill, when controlling for general knowledge and vocabulary. Based on the lexical quality hypothesis, it was expected that morphological awareness would have a stronger effect on comprehension for children with poor word reading skills, suggesting possible use of morphological awareness for word identification support. Results indicated that neither morphological awareness nor word reading was uniquely associated with reading comprehension when both were included in the model along with vocabulary and general knowledge. Instead, the interaction between word reading and morphological awareness explained significant additional variance in reading comprehension. By probing this interaction, it was determined that the effect of morphological awareness on reading comprehension was significant for the 39% of the sample that had more difficulty reading multisyllabic words but not for students at the higher end of the multisyllabic word reading continuum. We conclude from these results that the relation between morphological awareness and reading comprehension is moderated by multisyllabic word reading ability, providing support for the lexical quality hypothesis. Although we have only correlational data, we suggest tentative instructional practices for improving the reading skill of upper elementary struggling readers.

  20. Mapping RNA-seq Reads with STAR

    PubMed Central

    Dobin, Alexander; Gingeras, Thomas R.

    2015-01-01

    Mapping of large sets of high-throughput sequencing reads to a reference genome is one of the foundational steps in RNA-seq data analysis. The STAR software package performs this task with high levels of accuracy and speed. In addition to detecting annotated and novel splice junctions, STAR is capable of discovering more complex RNA sequence arrangements, such as chimeric and circular RNA. STAR can align spliced sequences of any length with moderate error rates providing scalability for emerging sequencing technologies. STAR generates output files that can be used for many downstream analyses such as transcript/gene expression quantification, differential gene expression, novel isoform reconstruction, signal visualization, and so forth. In this unit we describe computational protocols that produce various output files, use different RNA-seq datatypes, and utilize different mapping strategies. STAR is Open Source software that can be run on Unix, Linux or Mac OS X systems. PMID:26334920

  1. Mapping RNA-seq Reads with STAR.

    PubMed

    Dobin, Alexander; Gingeras, Thomas R

    2015-09-03

    Mapping of large sets of high-throughput sequencing reads to a reference genome is one of the foundational steps in RNA-seq data analysis. The STAR software package performs this task with high levels of accuracy and speed. In addition to detecting annotated and novel splice junctions, STAR is capable of discovering more complex RNA sequence arrangements, such as chimeric and circular RNA. STAR can align spliced sequences of any length with moderate error rates, providing scalability for emerging sequencing technologies. STAR generates output files that can be used for many downstream analyses such as transcript/gene expression quantification, differential gene expression, novel isoform reconstruction, and signal visualization. In this unit, we describe computational protocols that produce various output files, use different RNA-seq datatypes, and utilize different mapping strategies. STAR is open source software that can be run on Unix, Linux, or Mac OS X systems.

  2. Open Source: Everyone Becomes a Printer.

    ERIC Educational Resources Information Center

    Bruce, Bertram

    2000-01-01

    Discusses "open source": a method of distributing software in which programmers make available to all the actual text of their programs. Notes that this makes possible "open-source" writing in the same way that the printing press made possible "open-source" reading, enabling mass literacy. Examines implications of…

  3. Children Can Love Reading.

    ERIC Educational Resources Information Center

    Zibart, Rosemary

    1980-01-01

    Describes the Reading Is Fundamental Program (RIF), whose reading motivation concept is simple: young people who get the opportunity to freely choose and to own books may begin to experience reading as a pleasurable activity. (Author/LLS)

  4. Cosmetology Reading Strategies. 1980 Vocational Reading Series.

    ERIC Educational Resources Information Center

    Thornton, L. Jay; And Others

    Cosmetology Reading Strategies is one of five instructional guides in the Reading Strategies in Vocational Education Series. Developed to assist teachers working with students considered disadvantaged because of reading deficiency, the guide contains several strategies, suitable for adaptation, specifically related to cosmetology instruction. Each…

  5. Promoting Reading Motivation by Reading Together

    ERIC Educational Resources Information Center

    Monteiro, Vera

    2013-01-01

    In the present project we tested the hypothesis that tutorial situations with peers would benefit children's reading motivation. Participants were from elementary school--80 fourth-graders and 80 second-graders. We used a questionnaire to assess reading motivation. In the tutorial sessions we developed a Paired Reading Program. The children who…

  6. Teaching Reading Comprehension through Collaborative Strategic Reading.

    ERIC Educational Resources Information Center

    Vaughn, Sharon; Klingner, Janette Kettman

    1999-01-01

    Provides an overview of collaborative strategic reading (CSR) as an approach to enhancing the reading-comprehension skills of students with learning disabilities. Procedures for implementing CSR with collaborative groups and techniques for teaching reading-comprehension skills are provided. The role of the teacher is described and sample teaching…

  7. Food additives

    PubMed Central

    Spencer, Michael

    1974-01-01

    Food additives are discussed from the food technology point of view. The reasons for their use are summarized: (1) to protect food from chemical and microbiological attack; (2) to even out seasonal supplies; (3) to improve their eating quality; (4) to improve their nutritional value. The various types of food additives are considered, e.g. colours, flavours, emulsifiers, bread and flour additives, preservatives, and nutritional additives. The paper concludes with consideration of those circumstances in which the use of additives is (a) justified and (b) unjustified. PMID:4467857

  8. Talker-specific auditory imagery during reading

    NASA Astrophysics Data System (ADS)

    Nygaard, Lynne C.; Duke, Jessica; Kawar, Kathleen; Queen, Jennifer S.

    2004-05-01

    The present experiment was designed to determine if auditory imagery during reading includes talker-specific characteristics such as speaking rate. Following Kosslyn and Matt (1977), participants were familiarized with two talkers during a brief prerecorded conversation. One talker spoke at a fast speaking rate and one spoke at a slow speaking rate. During familiarization, participants were taught to identify each talker by name. At test, participants were asked to read two passages and told that either the slow or fast talker wrote each passage. In one condition, participants were asked to read each passage aloud, and in a second condition, they were asked to read each passage silently. Participants pressed a key when they had completed reading the passage, and reading times were collected. Reading times were significantly slower when participants thought they were reading a passage written by the slow talker than when reading a passage written by the fast talker. However, the effects of speaking rate were only present in the reading-aloud condition. Additional experiments were conducted to investigate the role of attention to talker's voice during familiarization. These results suggest that readers may engage in auditory imagery while reading that preserves perceptual details of an author's voice.

  9. Psychometric Research in Reading.

    ERIC Educational Resources Information Center

    Davis, Frederick B.

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

  10. Reading Assessment: Looking Ahead

    ERIC Educational Resources Information Center

    Afflerbach, Peter

    2016-01-01

    In this article, I focus on three areas of reading assessment that I believe to be crucial for students' reading development: developing comprehensive formative assessments, assessing the wide array of factors that contribute to students' reading development, and fostering student independence by helping students learn to use reading assessment on…

  11. Roads to Reading.

    ERIC Educational Resources Information Center

    Staiger, Ralph C.

    This book is a collection of ideas that have been used in many countries for the encouragement of reading. Its purposes are to provide information about reading and the reading habit; to put forward examples of local, national, and international reading promotion activities selected as useful, representative of different approaches, and adaptable…

  12. Big Read, Big ROI

    ERIC Educational Resources Information Center

    Dempsey, Beth

    2008-01-01

    In 2004, the National Endowment for the Arts (NEA) released a grim report on the state of literary reading in America. "Reading at Risk" (www.nea.gov/pub/ReadingAtRisk.pdf) detailed a dramatic decline in recreational reading across all segments of the American population--young and old, black, brown, and white. It also included the projected…

  13. Some Approaches to Reading.

    ERIC Educational Resources Information Center

    Smith, Nila Banton; Strickland, Ruth

    This pamphlet discusses some beginning approaches and technological approaches to reading instruction, and the relationship between children's language and reading. The first section looks at several approaches to reading instruction: "The Language Experience Approach,""The Initial Teaching Alphabet,""Linguistic Approaches to Reading,""Programed…

  14. Approaches to Beginning Reading.

    ERIC Educational Resources Information Center

    Aukerman, Robert C.

    The more than one hundred approaches to initial reading instruction can be grouped under ten headings: basal reader, phonemics, phonemic reading, "linguistics," total language arts, language-experience, one-to-one sound symbol, individualized reading, early reading, and perceptual discrimination. Although the basal reader approach is used in more…

  15. Reading with Purpose

    ERIC Educational Resources Information Center

    Linderholm, Tracy

    2006-01-01

    In college-level courses, the vast majority of students read expository textbooks with a primary purpose in mind: to memorize and, hopefully, understand enough information to receive a particular grade on a course exam. Intuitively, this kind of reading is different than the kind of reading that these same students do when reading a novel while…

  16. Individual and group sensitivity to remedial reading program design: Examining reading gains across three middle school reading projects

    PubMed Central

    Calhoon, Mary Beth; Petscher, Yaacov

    2015-01-01

    The purpose of this project was to examine group- and individual-level responses by struggling adolescents readers (6th – 8th grades; N = 155) to three different modalities of the same reading program, Reading Achievement Multi-Component Program (RAMP-UP). The three modalities differ in the combination of reading components (phonological decoding, spelling, fluency, comprehension) that are taught and their organization. Latent change scores were used to examine changes in phonological decoding, fluency, and comprehension for each modality at the group level. In addition, individual students were classified as gainers versus non-gainers (a reading level increase of a year or more vs. less than one year) so that characteristics of gainers and differential sensitivity to instructional modality could be investigated. Findings from both group and individual analyses indicated that reading outcomes were related to modalities of reading instruction. Furthermore, differences in reading gains were seen between students who began treatment with higher reading scores than those with lower reading scores; dependent on modality of treatment. Results, examining group and individual analyses similarities and differences, and the effect the different modalities have on reading outcomes for older struggling readers will be discussed. PMID:25657503

  17. Manual for a Summer Reading Program.

    ERIC Educational Resources Information Center

    Medina, Sue O.

    This manual provides suggestions for materials and projects to carry out a summer reading program for children based on a monster theme. The planning process outlined may be used as a "how-to" guide for developing summer reading programs on other themes as well. In addition to general guidelines, the manual provides information on the following…

  18. The Professional Reading Habits of American Librarians.

    ERIC Educational Resources Information Center

    Weaver, Susan M.

    This research project studied the perceived quality of the library and information science literature and asked questions regarding international librarianship. Additionally, it questioned what librarians read, how they choose their reading material, and how they use the literature for their decision making. The sample consisted of librarians from…

  19. Opening Address

    NASA Astrophysics Data System (ADS)

    Crovini, L.

    1994-01-01

    Ladies and Gentlemen To quote Mr Jean Terrien: "Physics must be one step ahead of metrology". A long-serving Director of the BIPM, he said these words when visiting the IMGC in 1970 as a member of the scientific board of our Institute. At that time it was still an open question whether the IMGC should start research work on the absolute measurement of silicon lattice spacing. Mr Terrien underlined the revolutionary character of x-ray interferometry and, eventually, he caused the balance needle to lean towards the ... right direction. Mr Terrien correctly foresaw that, like Michelson's interferometer of 1880, x-ray interferometry could have a prominent place in today's science and technology. And while, in the first case, after more than a century we can see instruments based on electromagnetic wave interaction within every one's reach in laboratories and, sometimes, in workshops, in the second case, twenty-five years since the first development of an x-ray interferometer we can witness its role in nanometrology. Today and tomorrow we meet to discuss how to go beyond the sixth decimal place in the value of the Avogadro constant. We are aware that the quest for this achievement requires the cooperation of scientists with complementary capabilities. I am sure that the present workshop is a very good opportunity to present and discuss results and to improve and extend existing cooperation. The new adjustment of fundamental constants envisaged by the CODATA Task Group is redoubling scientists' efforts to produce competitive values of NA. The results of the measurements of the silicon lattice spacing in terms of an optical wavelength, which were available for the 1986 adjustment, combined with the determination of silicon molar volume, demonstrate how such an NA determination produces a consistent set of other constants and opens the way to a possible redefinition of the kilogram. We shall see in these two days how far we have progressed along this road. For us at the

  20. Food additives

    MedlinePlus

    ... or natural. Natural food additives include: Herbs or spices to add flavor to foods Vinegar for pickling ... Certain colors improve the appearance of foods. Many spices, as well as natural and man-made flavors, ...

  1. Aggressive assembly of pyrosequencing reads with mates

    PubMed Central

    Miller, Jason R.; Delcher, Arthur L.; Koren, Sergey; Venter, Eli; Walenz, Brian P.; Brownley, Anushka; Johnson, Justin; Li, Kelvin; Mobarry, Clark; Sutton, Granger

    2008-01-01

    Motivation: DNA sequence reads from Sanger and pyrosequencing platforms differ in cost, accuracy, typical coverage, average read length and the variety of available paired-end protocols. Both read types can complement one another in a ‘hybrid’ approach to whole-genome shotgun sequencing projects, but assembly software must be modified to accommodate their different characteristics. This is true even of pyrosequencing mated and unmated read combinations. Without special modifications, assemblers tuned for homogeneous sequence data may perform poorly on hybrid data. Results: Celera Assembler was modified for combinations of ABI 3730 and 454 FLX reads. The revised pipeline called CABOG (Celera Assembler with the Best Overlap Graph) is robust to homopolymer run length uncertainty, high read coverage and heterogeneous read lengths. In tests on four genomes, it generated the longest contigs among all assemblers tested. It exploited the mate constraints provided by paired-end reads from either platform to build larger contigs and scaffolds, which were validated by comparison to a finished reference sequence. A low rate of contig mis-assembly was detected in some CABOG assemblies, but this was reduced in the presence of sufficient mate pair data. Availability: The software is freely available as open-source from http://wgs-assembler.sf.net under the GNU Public License. Contact: jmiller@jcvi.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:18952627

  2. Reading without Nonsense. Second Edition.

    ERIC Educational Resources Information Center

    Smith, Frank

    Intended for reading teachers, this book is concerned with the process of reading, with the perceptual and language skills involved in reading, and with the nature of the task confronting children learning to read. It shows that it is only through reading that children learn to read, and that a teacher's role must therefore be to make reading easy…

  3. Revisiting the "simple view of reading" in a group of children with poor reading comprehension.

    PubMed

    Georgiou, George K; Das, J P; Hayward, Denyse

    2009-01-01

    According to Gough and Tunmer's Simple View of Reading, Reading Comprehension = Decoding (D) x Listening Comprehension (C). The purpose of this study was to evaluate the model with a sample of First Nations children, known to have average decoding and listening comprehension but poor reading comprehension. In addition, the authors examined the contribution of naming speed and phonological awareness to reading comprehension beyond the effects of D and C. Consistent with the findings of previous studies, the children exhibited poor reading comprehension despite average performance in decoding and listening comprehension, a finding that challenges the simple view of reading. The results also revealed that an additive model (D + C) fitted the data equally well as a product model (D x C). Neither naming speed nor phonological awareness accounted for unique variance.

  4. Open Content in Open Context

    ERIC Educational Resources Information Center

    Kansa, Sarah Whitcher; Kansa, Eric C.

    2007-01-01

    This article presents the challenges and rewards of sharing research content through a discussion of Open Context, a new open access data publication system for field sciences and museum collections. Open Context is the first data repository of its kind, allowing self-publication of research data, community commentary through tagging, and clear…

  5. Reading Disabilities and PASS Reading Enhancement Programme

    ERIC Educational Resources Information Center

    Mahapatra, Shamita

    2016-01-01

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

  6. Potlining Additives

    SciTech Connect

    Rudolf Keller

    2004-08-10

    In this project, a concept to improve the performance of aluminum production cells by introducing potlining additives was examined and tested. Boron oxide was added to cathode blocks, and titanium was dissolved in the metal pool; this resulted in the formation of titanium diboride and caused the molten aluminum to wet the carbonaceous cathode surface. Such wetting reportedly leads to operational improvements and extended cell life. In addition, boron oxide suppresses cyanide formation. This final report presents and discusses the results of this project. Substantial economic benefits for the practical implementation of the technology are projected, especially for modern cells with graphitized blocks. For example, with an energy savings of about 5% and an increase in pot life from 1500 to 2500 days, a cost savings of $ 0.023 per pound of aluminum produced is projected for a 200 kA pot.

  7. Phosphazene additives

    DOEpatents

    Harrup, Mason K; Rollins, Harry W

    2013-11-26

    An additive comprising a phosphazene compound that has at least two reactive functional groups and at least one capping functional group bonded to phosphorus atoms of the phosphazene compound. One of the at least two reactive functional groups is configured to react with cellulose and the other of the at least two reactive functional groups is configured to react with a resin, such as an amine resin of a polycarboxylic acid resin. The at least one capping functional group is selected from the group consisting of a short chain ether group, an alkoxy group, or an aryloxy group. Also disclosed are an additive-resin admixture, a method of treating a wood product, and a wood product.

  8. The Long-Term Effects of Remedial Reading Instruction.

    ERIC Educational Resources Information Center

    Brightbill, Mary

    The long-term effects (after 3 to 5 years) of remedial reading instruction were examined. Comparison was made on reading achievement scores and on achievement ratios between a group of 16 former remedial reading clinic students, aged 12 to 20, and a matched group which did not receive remedial instruction. In addition, 45 former remedial readers…

  9. Close Readings and Children's Literature

    ERIC Educational Resources Information Center

    Serafini, Frank

    2014-01-01

    The concept of close reading is an important consideration when addressing the Common Core State Standards. In addition, "close reading" permeates the CCSS and suggests a particular way of reading and responding to texts. Trying to help students become successful readers in both school based settings and in the world outside of school is…

  10. Administration and the Challenge of Open Enrollment.

    ERIC Educational Resources Information Center

    Mirabeau, Roch L.

    The many problems connected with successful implementation of community college open enrollment involve students, faculty, college resources and basic processes. Together they constitute the challenge posed by open enrollment to administrators. Problems relative to students include low reading and writing abilities, low levels of preparedness and…

  11. 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.

  12. Can Reading Help?

    ERIC Educational Resources Information Center

    Crowe, Chris

    2003-01-01

    Ponders the effect of September 11th on teenagers. Proposes that reading books can help teenagers sort out complicated issues. Recommends young adult novels that offer hope for overcoming tragedy. Lists 50 short story collections worth reading. (PM)

  13. Assessing Motivation to Read.

    ERIC Educational Resources Information Center

    Gambrell, Linda B.; And Others

    1996-01-01

    Describes the Motivation to Read Profile (MRP), which assesses children's self-concepts as readers and the value they see in reading. Discusses its development and offers suggestions for its use with elementary students. Includes the MRP. (SR)

  14. Reading a Research Article.

    ERIC Educational Resources Information Center

    Schantz, Donna; Lindeman, Carol A.

    1982-01-01

    The authors present guidelines for reading a research report. They discuss the format for research reports and point out critical questions to keep in mind when critiquing a research study or reading published research reports. (Editor)

  15. 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…

  16. FIRST-YEAR REPORT ON THE HEGELER PROJECT READING STUDY.

    ERIC Educational Resources Information Center

    HUGHES, ANN; THOMAS, NELLIE

    IN SEPTEMBER 1964 THE HEGELER FOUNDATION CONDUCTED A WIDESCALE READING STUDY TO DETERMINE WHETHER OR NOT THE CORRELATED LANGUAGE ARTS PROGRAM BASED ON THE "OPEN COURT BASIC READERS" WOULD PRODUCE SUPERIOR RESULTS IN READING AND WRITING ACHIEVEMENT. THE FIRST-YEAR RESULTS ARE PRESENTED. THIRTY-TWO EXPERIMENTAL CLASSES AND 32 CONTROL…

  17. Investigating the Relationship between Connectives and Readers' Reading Comprehension Level

    ERIC Educational Resources Information Center

    Gençer, Yusuf; ÇetiInkaya, Gökhan

    2015-01-01

    The purpose of this study is to investigate the relationship between connectives in Turkish texts and readers' reading comprehension. Research was conducted with a total of 50 teachers. In the study group, readers' reading comprehension was determined through 10 descriptive texts by using open-ended questions. The results of the analysis revealed…

  18. 45 CFR 612.2 - Public reading room.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... Welfare Regulations Relating to Public Welfare (Continued) NATIONAL SCIENCE FOUNDATION AVAILABILITY OF RECORDS AND INFORMATION § 612.2 Public reading room. (a) The Foundation maintains a public reading room located in the NSF Library at 4201 Wilson Boulevard, Suite 225, Arlington, Virginia, open during...

  19. Student Perceptions of a Summer School Reading Program.

    ERIC Educational Resources Information Center

    Dewalt, Mark; Bartle, Phil

    A study by researchers in Hickory, North Carolina, examined student perceptions of a summer school reading program used in two Alexander County elementary schools. Surveys were completed by each second and third grade student participating in the summer school reading program. Content analysis was used to examine student responses to open-ended…

  20. A Comparison of Perceptual Motor Skill with Auditory Comprehension as Correlates of Word Recognition, Oral Reading, and Silent Reading.

    ERIC Educational Resources Information Center

    Tillman, Chester E.

    A study was conducted to examine the relationship of perceptual motor skills as measured by the Bender Visual Motor Gestalt Test to word recognition, oral reading, and silent reading. In addition, perceptual motor skill and auditory comprehension were compared as correlates of the three reading variables. Subjects were 60 primary grade students in…

  1. Formal Specification of the OpenMP Memory Model

    SciTech Connect

    Bronevetsky, G; de Supinski, B

    2006-12-19

    OpenMP [2] is an important API for shared memory programming, combining shared memory's potential for performance with a simple programming interface. Unfortunately, OpenMP lacks a critical tool for demonstrating whether programs are correct: a formal memory model. Instead, the current official definition of the OpenMP memory model (the OpenMP 2.5 specification [2]) is in terms of informal prose. As a result, it is impossible to verify OpenMP applications formally since the prose does not provide a formal consistency model that precisely describes how reads and writes on different threads interact. We expand on our previous work that focused on the formal verification of OpenMP programs through a formal memory model [?]. As in that work, our formalization, which is derived from the existing prose model [2], provides a two-step process to verify whether an observed OpenMP execution is conformant. This paper extends the model to cover the entire specification. In addition to this formalization, our contributions include a discussion of ambiguities in the current prose-based memory model description. Although our formal model may not capture the current informal memory model perfectly, in part due to these ambiguities, our model reflects our understanding of the informal model's intent. We conclude with several examples that may indicate areas of the OpenMP memory model that need further refinement, however it is specified. Our goal is to motivate the OpenMP community to adopt those refinements eventually, ideally through a formal model, in later OpenMP specifications.

  2. Doors Open

    ERIC Educational Resources Information Center

    Melia, Ed

    2008-01-01

    Not all of crime writer Ian Rankin's inspiration comes from Edinburgh's mean streets. When it came to writing a Quick Read--one of the short, fast-paced books for reluctant, returning or emergent readers--the Beach Boys provided the unlikely germ for an idea. Despite his success and obvious delight and energy for writing, Rankin admits to being a…

  3. openPMD-viewer

    SciTech Connect

    Lehe, Remi

    2015-10-01

    Many simulation software produce data in the form of a set of field values or of a set of particle positions. (one such example is that of particle-in-cell codes, which produce data on the electromagnetic fields that they simulate.) However, each particular software uses its own particular format and layout, for the output data. This makes it difficult to compare the results of different simulation software, or to have a common visualization tool for these results. However, a standardized layout for fields and particles has recently been developed: the openPMD format ( HYPERLINK "http://www.openpmd.org/"www.openpmd.org) This format is open- source, and specifies a standard way in which field data and particle data should be written. The openPMD format is already implemented in the particle-in-cell code Warp (developed at LBL) and in PIConGPU (developed at HZDR, Germany). In this context, the proposed software (openPMD-viewer) is a Python package, which allows to access and visualize any data which has been formatted according to the openPMD standard. This package contains two main components: - a Python API, which allows to read and extract the data from a openPMD file, so as to be able to work with it within the Python environment. (e.g. plot the data and reprocess it with particular Python functions) - a graphical interface, which works with the ipython notebook, and allows to quickly visualize the data and browse through a set of openPMD files. The proposed software will be typically used when analyzing the results of numerical simulations. It will be useful to quickly extract scientific meaning from a set of numerical data.

  4. Writing Workshops and the Teaching of Reading.

    ERIC Educational Resources Information Center

    Shuman, R. Baird

    This paper discusses three types of writing experiences, "Writing Roulette,""The Even-Steven Swap Game," and "The Open-Ended Story with a Slant," that can be used in a writing workshop for disabled readers at the secondary level. Each activity emphasizes writing but provides motivation for students to read each other's work. Students will have…

  5. Reading and Writing Connections.

    ERIC Educational Resources Information Center

    Mason, Jana M., Ed.

    This collection of papers, from a conference on reading and writing connections held at the University of Illinois in October 1986, reflects the value of demonstrating connections between reading instruction and writing. The book shows practitioners how writing can be blended with reading instruction and how writing activities can be used not just…

  6. Oral Communication in Reading.

    ERIC Educational Resources Information Center

    Ediger, Marlow

    Noting that oral communication skills need continuous refinement, this document outlines various methods of practicing these skills, such as literature circles in reading; a reader's theater; presentations of book reports; story telling; a poetry reading club; and choral reading. The document describes literature circles as small groups of readers…

  7. The Future of Reading

    ERIC Educational Resources Information Center

    Peters, Tom

    2009-01-01

    The future of reading is very much in doubt. In this century, reading could soar to new heights or crash and burn. Some educators and librarians fear that sustained reading for learning, for work, and for pleasure may be slowly dying out as a widespread social practice. Several social and technological developments of the 20th century, such as…

  8. Foreign Language Reading Anxiety.

    ERIC Educational Resources Information Center

    Saito, Yoshiko; Horwitz, Elaine K.; Garza, Thomas J.

    1999-01-01

    Discusses the possibility of anxiety in response to foreign- or second-language reading. Introduces the construct of foreign-language reading anxiety, offers a scale for its measurement, and reports on a preliminary study of reading anxiety in 30 intact first-semester classes of Spanish, Russian, and Japanese. (VWL)

  9. Free Reading Is UTOPIA

    ERIC Educational Resources Information Center

    LeCrone, Nancy

    2010-01-01

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

  10. Reading and Empathy

    ERIC Educational Resources Information Center

    McCreary, John J.; Marchant, Gregory J.

    2017-01-01

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

  11. Guidelines for Reading.

    ERIC Educational Resources Information Center

    New Hampshire Supervisory Union 40, Milford.

    A reading program should stimulate intellectual curiosity. This philosophy is expressed in a 1967 reading guide for primary and secondary schools prepared by the Reading Committee of the Union 40 Curriculum Council of Milford, New Hampshire. It was developed as a result of the 1966 curriculum study by the Union 40 Curriculum Council. While it is…

  12. Current Issues in Reading.

    ERIC Educational Resources Information Center

    French, Michael P., Ed.

    1985-01-01

    Articles in this journal issue focus on reading acquisition and instruction. The titles and authors are as follows: (1) "10 Good Ways to Involve Parents in the Reading Program," by Nickolas Criscuolo; (2) "A Parent Guide for Helping the Child with A Reading Disability," by Frederick Duffelmeyer and Dale Baum; (3)…

  13. ELLs' Perceptions of Reading

    ERIC Educational Resources Information Center

    Howard, Rachael M.

    2012-01-01

    This research investigated reading support and book preferences of fourth grade English language learners (ELLs) who were struggling readers. This qualitative research focused on three case studies. Interviews were conducted to explore ELLs' perceptions on reading motivation, reading programs, and types of support they received. Descriptions of…

  14. Staff Development and Reading.

    ERIC Educational Resources Information Center

    Ediger, Marlow

    Much is being emphasized in staff development in the area of reading instruction. It is important for teachers to study and think reflectively about what can be done to improve the elementary reading curriculum. One procedure that can be used is to hold a quality workshop based on the needs of reading teachers. Teachers might volunteer to serve on…

  15. Prose reading in neglect.

    PubMed

    Beschin, Nicoletta; Cisari, Carlo; Cubelli, Roberto; Della Sala, Sergio

    2014-02-01

    Prose reading has been shown to be a very sensitive measure of Unilateral Spatial Neglect. However, little is known about the relationship between prose reading and other measures of neglect and its severity, or between prose reading and single word reading. Thirty participants with a first stroke in the right hemisphere and clear symptoms of spatial neglect in everyday life were assessed with tests of prose reading (text in one column book-like, and in two columns magazine-like), single words reading, and a battery of 13 tests investigating neglect. Seventy percent of these participants omitted words at the beginning of the text (left end), showing Prose Reading Neglect (PRN). The participants showing PRN differed from those not showing PRN only for the overall severity of neglect, and had a lesion centred on the insula, putamen and superior temporal gyrus. Double dissociations emerged between PRN and single word reading neglect, suggesting different cognitive requirements between the two tests: parallel processing in single word reading vs. serial analysis in text reading. Notably, the pattern of neglected text varied dramatically across participants presenting with PRN, including dissociations between reading performance of one and two columns text. Prose reading proved a complex and unique task which should be directly investigated to predict the effects of unilateral neglect. The outcome of this study should also inform clinical assessment and advises given to patients and care-givers.

  16. Reading as a Whole.

    ERIC Educational Resources Information Center

    Weaver, Constance

    Underlying virtually all of the basal reading series available in the United States today is the assumption that learning to read is a skill-by-skill and word-by-word process. This part-to-whole approach to teaching reading is based on principles of behavioral psychology and "scientific management" developed a half century ago and treats…

  17. Reading is Thinking.

    ERIC Educational Resources Information Center

    Winkeljohann, Rosemary

    1979-01-01

    The focus article in this newsletter contains a discussion of the theory of reading as a thinking process and offers practical suggestions for implementing instruction in teaching reading as a thinking process. The section on theory is based on observations of the reading process as perceived by psycholinguists such as Frank Smith and Kenneth…

  18. Reading/Language Arts.

    ERIC Educational Resources Information Center

    Illinois State Office of Education, Springfield.

    These seven projects comprise the reading and language arts section of a report on Elementary Secondary Education Act Title IV programs for the state of Illinois. Complete descriptions are furnished for the following: a multi-text, individualized reading skills program for grades four through eight; a reading program which stresses phonetic and…

  19. Monster Moose Reading.

    ERIC Educational Resources Information Center

    Finney, Frank

    Monster Moose (MM) Reading is a program specifically aimed at improving children's language, beginning reading, and self-concept development through the creation and utilization of student-authored reading materials which feature a series of wordless picture books about a magical moose. The MM Program is based on the following general principles…

  20. Early Bilingual Reading.

    ERIC Educational Resources Information Center

    Titone, Renzo

    1985-01-01

    This discussion reviews literature on early bilingualism and early reading in two languages and summarizes a research project aimed at developing the experimental conditions for teaching early bilingual reading in institutional settings. The review notes positive effects of early reading generally and of early bilingual literacy on intellectual…

  1. Reading in Mathematics.

    ERIC Educational Resources Information Center

    Taschow, Horst G.

    Difficulties inherent in the reading of mathematics at secondary and college levels are discussed. Special emphasis is placed on the reading of arithmetic numerals, literal numbers, operational symbols, and expressions of relationships, as well as the reading of technical vocabularies and specialized meanings of general words. While each…

  2. Gifted and Reading.

    ERIC Educational Resources Information Center

    Shaughnessy, Michael F.; And Others

    This article reviews the literature and practice (especially in New Mexico) concerning reading instruction of gifted children. It considers early or "precocious" reading, instruction in the early grades, and identification of the gifted in New Mexico. Reading teachers in New Mexico are urged to be aware of specific conflicts in the area…

  3. The Teaching of Reading.

    ERIC Educational Resources Information Center

    Staiger, Ralph C., Ed.

    Designed as a sourcebook, this volume considers reading instruction as a complex, intellectual task rather than as just a matter of pronunciation of words. It is designed for both teachers and parents interested in developing the language and concepts of children. Contents include "Reading in Today's World" by Ralph C. Staiger, "Learning to Read"…

  4. Reading and Writing Connections.

    ERIC Educational Resources Information Center

    Fleming, Margaret, Ed.

    1985-01-01

    Drawing from both research and practice, the articles in this collection address a number of issues related to the reading and writing connection. The 24 articles are grouped into five sections: "Reading, Writing, and Thinking"; "The Parts and the Whole"; "Reading for Writing"; "Contexts for Literacy"; and…

  5. FOUR PATHS TO READING.

    ERIC Educational Resources Information Center

    HOYT, HOMER

    FOUR DIFFERENT APPROACHES TO BEGINNING READING--THE BASIC READING PROGRAM, SELF-SELECTION IN READING, LANGUAGE EXPERIENCE APPROACH, AND PROGRAMED INSTRUCTION ARE EXPLAINED. THE FOLLOWING QUESTIONS ABOUT EACH METHOD ARE ANSWERED--WHAT IS MEANT BY THIS METHOD. WHY IS THIS METHOD CONSIDERED A SOUND APPROACH. HOW DOES THE TEACHER BEGIN. HOW DOES THE…

  6. Summer Library Reading Programs

    ERIC Educational Resources Information Center

    Fiore, Carole D.

    2007-01-01

    Virtually all public libraries in the United States provide some type of summer library reading program during the traditional summer vacation period. Summer library reading programs provide opportunities for students of many ages and abilities to practice their reading skills and maintain skills that are developed during the school year. Fiore…

  7. THE TEACHING OF READING.

    ERIC Educational Resources Information Center

    WARDEBERG, HELEN L.

    CONTAINED IN THE GUIDE IS INFORMATION ON THE BASIC SKILLS TO BE INCLUDED IN ANY INSTRUCTIONAL PROGRAM IN READING, ON THE DEVELOPMENT OF A GUIDED PROGRAM FOR INDIVIDUAL AND PERSONAL READING, AND ON THE EVALUATION OF A READING PROGRAM. THE OBJECTIVE IS TO HELP EACH CHILD BECOME AS EFFICIENT AND DIVERSIFIED A READER AS HIS ABILITIES PERMIT. NO LESSON…

  8. Reading to Learn

    ERIC Educational Resources Information Center

    Herman, Phillip; Wardrip, Peter

    2012-01-01

    Science teachers expect high school students to know how to read, understand, and learn from texts at the core of the curriculum. But though students learn to read in grade school, many do not know how to "read to learn" science. And science teachers are often too busy teaching science to actively help students increase their science reading…

  9. Reading and the Student.

    ERIC Educational Resources Information Center

    Ediger, Marlow

    For each student to achieve optimally, a quality reading program must provide for individual differences. To guide students to learn as much as possible individually, selected philosophies of reading instruction may be used. These include: (1) experimentalism with its stress placed upon students reading to solve problems; (2) measurably stated…

  10. Goals of Reading Instruction.

    ERIC Educational Resources Information Center

    Ediger, Marlow

    The reading teacher needs to choose students' reading goals carefully. This paper considers some of these possible goals, and states that, in the reading curriculum, the teacher needs to guide pupils to move upward on the cognitive level of objectives. The paper also states that pupils need to achieve well in the affective dimension of objectives,…

  11. Reading, Language Arts & Literacy.

    ERIC Educational Resources Information Center

    Matthew, Kathy, Ed.

    This document contains the following papers on educational technology issues related to reading, language arts, and literacy: (1) "The Infusion of Technology into a Teacher Education Course: Issues and Strategies" (Mary Ann Kolloff); (2) "Project READ: Developing Online Course Materials for a Reading Methods Class" (Judith A.…

  12. 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…

  13. Do reading and spelling share a lexicon?

    PubMed

    Jones, Angela C; Rawson, Katherine A

    2016-05-01

    In the reading and spelling literature, an ongoing debate concerns whether reading and spelling share a single orthographic lexicon or rely upon independent lexica. Available evidence tends to support a single lexicon account over an independent lexica account, but evidence is mixed and open to alternative explanation. In the current work, we propose another, largely ignored account--separate-but-shared lexica--according to which reading and spelling have separate orthographic lexica, but information can be shared between them. We report three experiments designed to competitively evaluate these three theoretical accounts. In each experiment, participants learned new words via reading training and/or spelling training. The key manipulation concerned the amount of reading versus spelling practice a given item received. Following training, we assessed both response time and accuracy on final outcome measures of reading and spelling. According to the independent lexica account, final performance in one modality will not be influenced by the level of practice in the other modality. According to the single lexicon account, final performance will depend on the overall amount of practice regardless of modality. According to the separate-but-shared account, final performance will be influenced by the level of practice in both modalities but will benefit more from same-modality practice. Results support the separate-but-shared account, indicating that reading and spelling rely upon separate lexica, but information can be shared between them.

  14. High School Science Teachers' Perceptions of Teaching Content-Related Reading Comprehension Instruction

    NASA Astrophysics Data System (ADS)

    Williams, Theresa

    In order to achieve academic success, students must be able to comprehend written material in content-area textbooks. However, a large number of high school students struggle to comprehend science content. Research findings have demonstrated that students make measurable gains in comprehending content-area textbooks when provided quality reading comprehension instruction. The purpose of this study was to gain an understanding of how high school science teachers perceived their responsibility to provide content-related comprehension instruction and 10 high school science teachers were interviewed for this study. Data analysis consisted of open, axial, and selective coding. The findings revealed that 8 out of the 10 participants believed that it is their responsibility to provide reading comprehension. However, the findings also revealed that the participants provided varying levels of reading comprehension instruction as an integral part of their science instruction. The potential for positive social change could be achieved by teachers and administrators. Teachers may use the findings to reflect upon their own personal feelings and beliefs about providing explicit reading comprehension. In addition to teachers' commitment to reading comprehension instruction, administrators could deliberate about professional development opportunities that might improve necessary skills, eventually leading to better comprehension skills for students and success in their education.

  15. Standardized Reading Tests and the Postsecondary Reading Curriculum.

    ERIC Educational Resources Information Center

    Wood, Nancy V.

    To help college reading teachers develop an awareness of what standardized reading tests do and do not reveal about students' reading abilities, a study examined the testing of reading and criticized four major standardized tests. Results indicated that reading is tested through (1) reading passages accompanied by multiple choice questions, (2)…

  16. Braille Reading Is Less Efficient Than Visual Reading.

    ERIC Educational Resources Information Center

    Williamson, Leon E.; And Others

    The reading performances of fifteen blind readers and fifteen sighted readers were compared by evaluating the reading performances of each reader reading at instructional level from Lippincott's "Basic Reading Series" and from Form A of the "Gray Oral Reading Test." Nine matched pairs of subjects read at grade one first reader level and six pairs…

  17. TELEMETRY EQUIPMENT WITH DIGITAL READING,

    DTIC Science & Technology

    Contents: Basic peculiarities of telemetry equipment with digital reading ; Elements of pulse technology applied in telemetry equipment with digital... reading ; Digital reading systems; Telemetry systems with digital reading . (Author)

  18. Open Access

    ERIC Educational Resources Information Center

    Suber, Peter

    2012-01-01

    The Internet lets us share perfect copies of our work with a worldwide audience at virtually no cost. We take advantage of this revolutionary opportunity when we make our work "open access": digital, online, free of charge, and free of most copyright and licensing restrictions. Open access is made possible by the Internet and copyright-holder…

  19. Examining Reading Development and Reading Disability in English Language Learners: Potential Contributions from Functional Neuroimaging

    ERIC Educational Resources Information Center

    Pugh, Kenneth R.; Sandak, Rebecca; Frost, Stephen J.; Moore, Dina; Mencl, W. Einar

    2005-01-01

    Neuroimaging studies have suggested that across different written languages, skilled reading behavior is supported by similar, largely left hemisphere (LH), networks. In addition, recent studies of reading disability (RD) in monolingual readers, conducted in several languages, suggest a common neurobiological signature for this syndrome…

  20. What, Why, and How They Read: Reading Preferences and Patterns of Rural Young Adults

    ERIC Educational Resources Information Center

    Becnel, Kim; Moeller, Robin A.

    2015-01-01

    The purpose of this study is to better understand the reading patterns and preferences of rural teen readers and the cultures of reading that do or do not exist in the rural communities in which the teens reside. In addition, the researchers sought to discover, by conducting a series of focus groups, whether rural teen readers felt connected to…

  1. Pre-Service Teachers' Use of Reading Strategies in Their Own Readings and Future Classrooms

    ERIC Educational Resources Information Center

    Akyol, Hayati; Ulusoy, Mustafa

    2010-01-01

    The main purpose of this study was to determine pre-service teachers' use of reading strategies in their own readings. In addition, pre-service teachers' use of these strategies in their future teaching practices was also investigated. The subjects for this study were 505 pre-service teachers enrolled in one of the major universities in Ankara.…

  2. 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

  3. A Machine that Reads (Reading Technology).

    ERIC Educational Resources Information Center

    Rickelman, Robert J.; Henk, William A.

    1990-01-01

    Discusses the Xerox/Kurzweil Personal Reader which is an advanced optical scanner that reads a greater range of typeset or typewritten text than its predecessors, and converts it into highly naturalistic speech. (MG)

  4. Using a New Reading Comprehension Assessment to Measure Discourse Representations and Identify Types of Comprehenders

    ERIC Educational Resources Information Center

    Carlson, Sarah; Seipel, Ben; McMaster, Kristen

    2011-01-01

    Many researchers focus on assessing the cognitive components of reading comprehension. However, researchers are challenged to find the best way to measure the cognitive components of reading comprehension because many reading comprehension assessments differ in terms of format (i.e., cloze, multiple-chose, open-ended); presentation (i.e., print);…

  5. 10 CFR 1703.103 - Requests for board records available through the public reading room.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... reading room. 1703.103 Section 1703.103 Energy DEFENSE NUCLEAR FACILITIES SAFETY BOARD PUBLIC INFORMATION AND REQUESTS § 1703.103 Requests for board records available through the public reading room. (a) A Public Reading Room will be maintained at the Board's headquarters and will be open between 8:30 a.m....

  6. 10 CFR 1703.103 - Requests for board records available through the public reading room.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... reading room. 1703.103 Section 1703.103 Energy DEFENSE NUCLEAR FACILITIES SAFETY BOARD PUBLIC INFORMATION AND REQUESTS § 1703.103 Requests for board records available through the public reading room. (a) A Public Reading Room will be maintained at the Board's headquarters and will be open between 8:30 a.m....

  7. 10 CFR 1703.103 - Requests for board records available through the public reading room.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... reading room. 1703.103 Section 1703.103 Energy DEFENSE NUCLEAR FACILITIES SAFETY BOARD PUBLIC INFORMATION AND REQUESTS § 1703.103 Requests for board records available through the public reading room. (a) A Public Reading Room will be maintained at the Board's headquarters and will be open between 8:30 a.m....

  8. 10 CFR 1703.103 - Requests for board records available through the public reading room.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... reading room. 1703.103 Section 1703.103 Energy DEFENSE NUCLEAR FACILITIES SAFETY BOARD PUBLIC INFORMATION AND REQUESTS § 1703.103 Requests for board records available through the public reading room. (a) A Public Reading Room will be maintained at the Board's headquarters and will be open between 8:30 a.m....

  9. 10 CFR 1703.103 - Requests for board records available through the public reading room.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... reading room. 1703.103 Section 1703.103 Energy DEFENSE NUCLEAR FACILITIES SAFETY BOARD PUBLIC INFORMATION AND REQUESTS § 1703.103 Requests for board records available through the public reading room. (a) A Public Reading Room will be maintained at the Board's headquarters and will be open between 8:30 a.m....

  10. College Students' Self-Perceptions on Factors Which Have Influenced Their Reading Ability.

    ERIC Educational Resources Information Center

    Nieratka, Ernest; Epstein, Ira

    A pilot study was designed to develop an instrument to examine students' self-perceptions regarding their own reading. An open survey was conducted in which 300 college students in a compensatory reading program listed those factors which might influence a person's reading ability. In all, 163 responses were listed, and these were reduced to 10…

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

    ERIC Educational Resources Information Center

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

    2015-01-01

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

  12. 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.

  13. Reading Skill Levels in the Navy.

    DTIC Science & Technology

    1978-04-01

    reading tasks. Additionally, the material has likely grown more d i f f i cu l t due to the increasing use of high technology pervading the Navy . Not all...were fa i r ly comparable up to the 8th grade level. For purposes of this report , we derived a general index of reading abi lity by taking the average...Chisom , B. S. Derivation of new readability formulas for Navy enlisted personnel (Automated Readability Index , Fog Count, and Flesch Reading Ease

  14. Reading and General Cognitive Ability: A Multivariate Analysis of 7-Year-Old Twins

    ERIC Educational Resources Information Center

    Harlaar, Nicole; Hayiou-Thomas, Marianna E.; Plomin, Robert

    2005-01-01

    We examined the association between reading and general cognitive ability (g) in a population-based sample of 6,476 pairs of 7-year-old twins. Additive genetic influences largely accounted for individual differences in reading and the covariation between reading and g. Furthermore, both genetic and shared environmental influences on reading and g…

  15. Can Read, Can Write

    ERIC Educational Resources Information Center

    Melia, Ed

    2008-01-01

    Linda Worden always loved books. She liked the way they felt in her hands and the way they smelled. The only problem was she could not read them--until she took part in Channel 4's "Can't Read, Can't Write". This article tells the story of Linda Worden and how learning to read changed her life. Her attempts to learn as an adult are a shocking…

  16. Reading disorders and dyslexia

    PubMed Central

    Hulme, Charles; Snowling, Margaret J.

    2016-01-01

    Purpose of review We review current knowledge about the nature of reading development and disorders, distinguishing between the processes involved in learning to decode print, and the processes involved in reading comprehension. Recent findings Children with decoding difficulties/dyslexia experience deficits in phoneme awareness, letter-sound knowledge and rapid automatized naming in the preschool years and beyond. These phonological/language difficulties appear to be proximal causes of the problems in learning to decode print in dyslexia. We review data from a prospective study of children at high risk of dyslexia to show that being at family risk of dyslexia is a primary risk factor for poor reading and children with persistent language difficulties at school entry are more likely to develop reading problems. Early oral language difficulties are strong predictors of later difficulties in reading comprehension. Summary There are two distinct forms of reading disorder in children: dyslexia (a difficulty in learning to translate print into speech) and reading comprehension impairment. Both forms of reading problem appear to be predominantly caused by deficits in underlying oral language skills. Implications for screening and for the delivery of robust interventions for language and reading are discussed. PMID:27496059

  17. Summer library reading programs.

    PubMed

    Fiore, Carole D

    2007-01-01

    Virtually all public libraries in the United States provide some type of summer library reading program during the traditional summer vacation period. Summer library reading programs provide opportunities for students of many ages and abilities to practice their reading skills and maintain skills that are developed during the school year. Fiore summarizes some of the research in the field and relates it to library programs and usage by students. Several traditional and innovative programs from U.S. and Canadian libraries are described. She concludes with a call for further research related to summer library reading programs.

  18. Assisted Reading with Digital Audiobooks for Students with Reading Disabilities

    ERIC Educational Resources Information Center

    Esteves, Kelli J.; Whitten, Elizabeth

    2011-01-01

    The goal of this study was to compare the efficacy of assisted reading with digital audiobooks with the traditional practice of sustained silent reading (SSR) in terms of reading fluency and reading attitude with upper elementary students with reading disabilities. Treatment group participants selected authentic children's literature and engaged…

  19. Reading Strategy: Tackling Reading through Topic and Main Ideas

    ERIC Educational Resources Information Center

    Naidu, Bharathi; Briewin, Marshal; Embi, Mohamed Amin

    2013-01-01

    Reading comprehension is one of the four skills essential in learning English. In a reading class, students tend to read all the information provided in reading materials, but how much do they actually retain? This study explores whether learners use identification of the topic and main ideas as a reading strategy to assist in reading…

  20. Binocular Coordination during Reading and Non-Reading Tasks

    ERIC Educational Resources Information Center

    Kirkby, Julie A.; Webster, Lisa A. D.; Blythe, Hazel I.; Liversedge, Simon P.

    2008-01-01

    The goal of this review is to evaluate the literature on binocular coordination during reading and non-reading tasks in adult, child, and dyslexic populations. The review begins with a description of the basic characteristics of eye movements during reading. Then, reading and non-reading studies investigating binocular coordination are evaluated.…

  1. Reading Attitudes and Reading Interests of Urban Intermediate Grade Students.

    ERIC Educational Resources Information Center

    Hummel, Jeffrey W.; Fisher, Peter J. L.

    1985-01-01

    Administered Survey of Reading Attitudes and Bundy Reading Preference Survey to 130 fourth- and fifth-grade students. Significant moderate correlation between total score of Bundy Reading Preference Survey and the Reading as Enjoyment Dimension of the Survey of Reading Attitudes contributes to construct validity of both measures. (Author)

  2. 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…

  3. Reduced voltage losses yield 10% efficient fullerene free organic solar cells with >1 V open circuit voltages† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6ee02598f Click here for additional data file.

    PubMed Central

    Wheeler, S.; Dimitrov, S.; Abdelsamie, M.; Gorman, J.; Ashraf, R. S.; Holliday, S.; Wadsworth, A.; Gasparini, N.; Kaienburg, P.; Yan, H.; Amassian, A.; Brabec, C. J.; Durrant, J. R.; McCulloch, I.

    2016-01-01

    Optimization of the energy levels at the donor–acceptor interface of organic solar cells has driven their efficiencies to above 10%. However, further improvements towards efficiencies comparable with inorganic solar cells remain challenging because of high recombination losses, which empirically limit the open-circuit voltage (V oc) to typically less than 1 V. Here we show that this empirical limit can be overcome using non-fullerene acceptors blended with the low band gap polymer PffBT4T-2DT leading to efficiencies approaching 10% (9.95%). We achieve V oc up to 1.12 V, which corresponds to a loss of only E g/q – V oc = 0.5 ± 0.01 V between the optical bandgap E g of the polymer and V oc. This high V oc is shown to be associated with the achievement of remarkably low non-geminate and non-radiative recombination losses in these devices. Suppression of non-radiative recombination implies high external electroluminescence quantum efficiencies which are orders of magnitude higher than those of equivalent devices employing fullerene acceptors. Using the balance between reduced recombination losses and good photocurrent generation efficiencies achieved experimentally as a baseline for simulations of the efficiency potential of organic solar cells, we estimate that efficiencies of up to 20% are achievable if band gaps and fill factors are further optimized. PMID:28066506

  4. Open Education and the Open Science Economy

    ERIC Educational Resources Information Center

    Peters, Michael A.

    2009-01-01

    Openness as a complex code word for a variety of digital trends and movements has emerged as an alternative mode of "social production" based on the growing and overlapping complexities of open source, open access, open archiving, open publishing, and open science. This paper argues that the openness movement with its reinforcing structure of…

  5. Authentic Reading Assessment. ERIC Digest.

    ERIC Educational Resources Information Center

    Dutcher, Peggy

    Authentic reading assessment is examined, focusing on its implementation within the Michigan Essential Skills Reading Test (MESRT). Authentic reading assessment emerged as a response to research that indicates that reading is not a particular skill but an interaction among reader, text, and the context of the reading situation. Unlike formal…

  6. Reading with a Special Touch.

    ERIC Educational Resources Information Center

    McCool, Mary

    Disadvantaged secondary school students with special reading needs can be motivated in the reading room. The school year can start with "popcorn" reading involving materials that are funny, interesting, and exciting. The teacher reads to the students or the students read silently, using materials on the students' independent rather than…

  7. Title I Reading Center Program.

    ERIC Educational Resources Information Center

    Broward County Schools, Fort Lauderdale, FL.

    One of the twelve exemplary reading programs summarized in the Introduction to Right to Read's "Effective Reading Programs: Summaries of 222 Selected Programs" (CS001934), this program uses a variety of cross-referenced materials and small group instruction to develop students' reading skills, vocabulary, and reading comprehension.…

  8. Nystagmus Does Not Limit Reading Ability in Albinism

    PubMed Central

    Dysli, Muriel; Abegg, Mathias

    2016-01-01

    Purpose Subjects with albinism usually suffer from nystagmus and reduced visual acuity, which may impair reading performance. The contribution of nystagmus to decreased reading ability is not known. Low vision and nystagmus may have an additive effect. We aimed to address this question by motion compensation of the nystagmus in affected subjects and by simulating nystagmus in healthy controls. Methods Reading speed and eye movements were assessed in 9 subjects with nystagmus associated with albinism and in 12 healthy controls. We compared the reading ability with steady word presentation and with words presented on a gaze contingent display where words move in parallel to the nystagmus and thus correct for the nystagmus. As the control, healthy subjects were asked to read words and texts in steady reading conditions as well as text passages that moved in a pattern similar to nystagmus. Results Correcting nystagmus with a gaze contingent display neither improved nor reduced the reading speed for single words. Subjects with nystagmus and healthy participants achieved comparable reading speed when reading steady texts. However, movement of text in healthy controls caused a significantly reduced reading speed and more regressive saccades. Conclusions Our results argue against nystagmus as the rate limiting factor for reading speed when words were presented in high enough magnification and support the notion that other sensory visual impairments associated with albinism (for example reduced visual acuity) might be the primary causes for reading impairment. PMID:27391149

  9. Open Babel: An open chemical toolbox

    PubMed Central

    2011-01-01

    Background A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendor-neutral formats. Results We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion. Conclusions Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license from http://openbabel.org. PMID:21982300

  10. Does early reading failure decrease children's reading motivation?

    PubMed

    Morgan, Paul L; Fuchs, Douglas; Compton, Donald L; Cordray, David S; Fuchs, Lynn S

    2008-01-01

    The authors used a pretest-posttest control group design with random assignment to evaluate whether early reading failure decreases children's motivation to practice reading. First, they investigated whether 60 first-grade children would report substantially different levels of interest in reading as a function of their relative success or failure in learning to read. Second, they evaluated whether increasing the word reading ability of 15 at-risk children would lead to gains in their motivation to read. Multivariate analyses of variance suggest marked differences in both motivation and reading practice between skilled and unskilled readers. However, bolstering at-risk children's word reading ability did not yield evidence of a causal relationship between early reading failure and decreased motivation to engage in reading activities. Instead, hierarchical regression analyses indicate a covarying relationship among early reading failure, poor motivation, and avoidance of reading.

  11. Toddler Reading Time

    MedlinePlus

    ... mother's lap and moves over to her stuffed animals. Her mom knows better than to try to finish the book. For Gabrielle and lots of other toddlers, these little bits of reading are just right. Reasons to Read to Toddlers Studies show that ...

  12. Reading Where It Counts

    ERIC Educational Resources Information Center

    Miller, Harry

    2014-01-01

    In this article, teachers are reminded that their content subject areas require acquainting children with special words or symbols related to that subject area (e.g. mathematics or social studies). Because children can read well does not mean they would be understanding of any special reading skill required in a content subject area; that the…

  13. Reading and Postmodernism.

    ERIC Educational Resources Information Center

    Alexander, James C.

    One of the main differences between the whole language position and the more traditional views lies in the epistemological base upon which whole language is rooted. Although whole language proponents may not have clearly put forth an epistemology upon which their views of reading acquisition and the reading process are based, still a careful…

  14. Philosophy of Reading Instruction.

    ERIC Educational Resources Information Center

    Ediger, Marlow

    Reading teachers need to provide for individual differences so that each pupil might attain optimally. Methods of teaching reading should be varied and thus reflect diverse philosophies of instruction. These philosophies should be analyzed and used to guide optimal pupil achievement. A philosophy of phoneme/grapheme relationships should be…

  15. Anything but Reading

    ERIC Educational Resources Information Center

    Krashen, Stephen

    2009-01-01

    Both the popular media and professional literature are filled with suggestions on how to improve reading, but the one approach that always works is rarely mentioned: provide readers with a supply of interesting and comprehensible books. Instead, people are given advice that is dead wrong as a means of improving reading (e.g., roller skating and…

  16. Improving Students' Reading Fluency.

    ERIC Educational Resources Information Center

    Goldstein, Amy

    This report describes a program for improving students' reading fluency in order to become more proficient readers. The targeted population consists of first and second grade students in a growing middle class community located in the Midwest. The lack of fluent reading was documented through teacher observation and the calculation of how many…

  17. Supporting Older Students' Reading

    ERIC Educational Resources Information Center

    Gutchewsky, Kim; Curran, Joanne

    2012-01-01

    According to a 2010 report by ACT, "Only 31 percent of students are performing at a college-and-career reading level with respect to successfully understanding complex text" (p. 5). This statistic demonstrates what educators know: Middle and high school students face numerous challenges in reading, understanding, connecting to, and…

  18. Reading with an Infant.

    ERIC Educational Resources Information Center

    Lamme, Linda Leonard

    1980-01-01

    Emphasizes that parents' reading to infants fosters interest in literature and provides foundation for basic reading skills. Titles of musical books, point-and-say books, touch and smell books, cardboard books, cloth books, plastic books, and early stories are provided. (Author/DB)

  19. Reading, Writing, and Computing.

    ERIC Educational Resources Information Center

    Adams, Dennis M.; And Others

    Reading, writing, and computing, which are interrelated and can thrive on each other for literacy and intellectual growth, are in the process of becoming linked in instructional practice. As reading and writing become more demanding, their task is eased with computer use. The computer seems to provide the connection between composing,…

  20. The Roots of Reading.

    ERIC Educational Resources Information Center

    Montoya, Colleen, Ed.

    2002-01-01

    This newsletter covers educational issues affecting schools in the Western Regional Educational Laboratory's 4-state region (Arizona, California, Nevada, and Utah) and nationwide. The following articles appear in the Volume 4, Number 1 issue: (1) "The Roots of Reading"; (2) "Breaking the Code: Reading Literacy in K-3"; (3)…

  1. An Individualized Reading Program.

    ERIC Educational Resources Information Center

    Davis, Nancy B.

    The operating procedures of a university reading and study skills center for completely individualized reading instruction are described. The program is offered as a student service (no fee) on a voluntary, noncredit basis. A prepared set of instructional tapes is used whereby students can largely serve themselves, proceeding at their own rates,…

  2. Superheroes and Summer Reading.

    ERIC Educational Resources Information Center

    Meyer, Ron; Buckner, Joyce

    1980-01-01

    To combat summer learning loss among remedial readers, teachers and consultants in the Omaha, Nebraska, Title I program designed a series of comic-book reading units and mailed them to students' homes. Parents were pleased with the project and it appeared that less reading skill had been lost by September. (SJL)

  3. Beginning Reading in Italy.

    ERIC Educational Resources Information Center

    Tutolo, Daniel

    Teaching practices in Italy, where teachers combine three different methods for teaching reading, may provide insight into ways to improve methodologies in the United States. The first method is the natural method, which, unlike American methods, teaches reading and writing simultaneously with the emphasis on writing. The teacher writes as…

  4. Measuring Reading Performance Informally.

    ERIC Educational Resources Information Center

    Powell, William R.

    To improve the accuracy of the informal reading inventory (IRI), a differential set of criteria is necessary for both word recognition and comprehension scores for different levels and reading conditions. In initial evaluation, word recognition scores should reflect only errors of insertions, omissions, mispronunciations, substitiutions, unkown…

  5. Reading Is Fundamental, 1977.

    ERIC Educational Resources Information Center

    Smithsonian Institution, Washington, DC. National Reading is Fun-damental Program.

    Reading Is Fundamental (RIF) is a national, nonprofit organization designed to motivate children to read by making a wide variety of inexpensive books available to them and allowing the children to choose and keep books that interest them. This annual report for 1977 contains the following information on the RIF project: an account of the…

  6. Why I Read.

    ERIC Educational Resources Information Center

    Mori, Kyoko

    2002-01-01

    Notes that the author was struck by the "self-centered" readers she encountered in her classroom and at professional conferences--readers who respond to reading by thinking of their own life and experiences. Argues that reading is so much more than a trip into the self. Presents two brief responses, by Lauren L. Wohl and Daniel Hade. (RS)

  7. Keep Them Reading

    ERIC Educational Resources Information Center

    Vanneman, Susan

    2010-01-01

    The relentless quest of the school librarian is finding the right book for each student, searching for the home-run book for every child, and keeping students reading book after book after book. A considerable amount of the school librarian's time, effort, and creativity are devoted not only to motivating students to read, but to keeping them…

  8. Using Collaborative Strategic Reading.

    ERIC Educational Resources Information Center

    Klingner, Janette K.; Vaughn, Sharon

    1998-01-01

    Describes collaborative strategic reading (CSR), a technique for teaching students, such as those with learning disabilities, reading comprehension and vocabulary skills in a cooperative setting. Covers teaching the four strategies of CSR (preview, click and clunk, get the gist, and wrap up), as well as teaching students cooperative learning group…

  9. Appalachian Reading Survey.

    ERIC Educational Resources Information Center

    Pennsylvania State Univ., University Park.

    The impact of ESEA Title I programs on reading competencies of elementary and secondary students in Northern Appalachia was examined. Fourth- and seventh-grade reading programs were assessed through samples taken from 74 different schools involving 1,429 students in 16 school districts within the Northern Appalachia area of Maryland, Ohio,…

  10. Lippincott Basic Reading Program.

    ERIC Educational Resources Information Center

    Monterey Peninsula Unified School District, Monterey, CA.

    This program, included in "Effective Reading Programs...," serves 459 students in grades 1-3 at 15 elementary schools. The program employs a diagnostic-prescriptive approach to instruction in a nongraded setting through the use of the Lippincott Basic Reading program. When a child enters the program, he is introduced to a decoding…

  11. Reading: Process and Program.

    ERIC Educational Resources Information Center

    Goodman, Kenneth S.; Niles, Olive S.

    Broad and major concerns dealing with reading are set forth in this monograph to provoke discussion and examination by both researchers and practitioners. In Part 1, Kenneth S. Goodman presents a psycholinguistic view of language and reading (within a transformational-generative framework) as essentially a set of processes of recoding, decoding,…

  12. Reading and Math.

    ERIC Educational Resources Information Center

    Baldwin, Anna; And Others

    This publication contains materials used in the three phases of the reading and mathematics components of work-specific classes. Each section begins with an overview of developments in that phase. Section 1 focuses on Phase 1 during which math and reading were taught as separate components. It contains a math placement appraisal, worksheets and…

  13. Motivating Interest in Reading.

    ERIC Educational Resources Information Center

    International Reading Association. Utah Council.

    This yearbook is a collection of articles on the topic of motivating interest in reading. The articles are: "An Introduction to Recreational Reading in the Classroom" by Floyd Sucher, which discusses objectives, materials, setting, scheduling, and sharing activities; "New Words and New Meaning for Old Words" by Vermont Harward, Dan Bird, and Edith…

  14. Against Reading Lists

    ERIC Educational Resources Information Center

    Davis, Lennard J.

    2012-01-01

    A course's reading list is the skeleton of a semester's body of thought, the inventory that a professor writes up for the departmental Web site and the schedule of courses that lists the goods. Despite the obvious utility of fixed reading lists, one should jettison them when possible. The author has been conducting an informal experiment using a…

  15. Reading Rate and Comprehension

    ERIC Educational Resources Information Center

    Jodai, Hojat

    2011-01-01

    Reading fluency is one of the most important signs of language proficiency both for native and foreign language speakers (Grabe, 2010; Macalister, 2010; Winston, 2010; Hasbrouck, 2008; Rasinski, 2004; Oakley, 2003; Waldman, 1985; Cited in: Sayenko, 2010, Introduction Para 1). This paper is in the area of reading fluency and tries to investigate…

  16. Basic Blueprint Reading.

    ERIC Educational Resources Information Center

    Deieso, Angie; Meier, Jean

    This workbook, designed for workplace literacy courses, contains materials for a basic course in blueprint reading. The course provides a review of mathematics, information about using measuring tools to read blueprints, an explanation of the principles of blueprint drawing, and instructions on interpreting blueprint specifications. Introductory…

  17. Books for Summer Reading.

    ERIC Educational Resources Information Center

    Phi Delta Kappan, 1996

    1996-01-01

    Suggests several novels for educators' summer reading enjoyment, including classics by Robert Pirsig, Robertson Davies, John Steinbeck, Albert Camus, and Charles Dickens. Educators might also read Alex Kotlowitz's "There Are No Children Here" (Doubleday, 1991) and Sharon Quint's "Schooling Homeless Children" (Teachers College Press, 1994) to gain…

  18. Reading Skill Retention.

    ERIC Educational Resources Information Center

    Rude, Robert L.

    There is mixed evidence regarding the ability of students to retain reading ability over long, non-instructional periods such as the summer recess. In some instances there are significant losses in reading ability, while in other cases the losses fail to reach significance. However, in some cases, such as with basic visual discrimination tasks,…

  19. Teaching Reading in Homeschool.

    ERIC Educational Resources Information Center

    Yambo, Idalia

    This paper discusses the home-schooling trend and identifies reading instructional methods used by home-schooling parents. Interviews were conducted with 5 home-schooling families of children ranging in age from 1 to 14 years. Parents reported that they began reading instruction with their child at about age 5 and agreed that instruction in…

  20. Reading Stars. 2013 Report

    ERIC Educational Resources Information Center

    National Literacy Trust, 2013

    2013-01-01

    The National Literacy Trust's Premier League Reading Stars has now been running for 10 years. During this time, hundreds of thousands of children and families have been inspired by the power of football to develop a love of reading. Although the programme has grown and evolved over this period, the premise remains the same: harnessing the…

  1. TRENDS IN ADULT READING.

    ERIC Educational Resources Information Center

    MILLER, JUSTIN H.

    TRENDS EVIDENT IN ADULT READING DURING THE 1960'S IN THE AREAS OF ADMINISTRATION, PROGRAMS, TEACHING, TECHNIQUES, RESEARCH PROJECTS, AND METHODS OF PROMOTION OF READING PROGRAMS ARE DISCUSSED. TWO INSTANCES OF COMMERCIAL EXPLOITATION BASED ON INTENSE AND OFTEN FALLACIOUS ADVERTISING AND ON PUBLIC IGNORANCE ARE CITED. A POSITIVE TREND IN THE AREA…

  2. Processes in Reading Comprehension.

    ERIC Educational Resources Information Center

    Ransom, Grayce A.

    This examination of the processes in reading comprehension is divided into seven categories. "Theoretical Foundations" reviews some of the research conducted by Bruner, Piaget, and Bloom in the areas of cognition or comprehension processes of young children. "Development of a Spiraling Reading Curriculum" examines a spiraling taxonomy of reading…

  3. Motivation in Content Reading.

    ERIC Educational Resources Information Center

    Tutolo, Daniel

    Motivational devices are useful in content-area reading because the content load of most content textbooks is so extensive that few if any students can be expected to understand all that an author intends to communicate. Many students who are inexperienced with the subject matter are unable to read the assignments independently. The recognition of…

  4. How Knowledge Powers Reading

    ERIC Educational Resources Information Center

    Lemov, Doug

    2017-01-01

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

  5. Opening remarks

    SciTech Connect

    Hildebrand, S.G.

    1994-09-01

    Included in this paper are the opening remarks of S.G. Hildebrand, from Environmental Science Division, ORNL, to a conference on water resources and water resource issues. Wetlands are the focus of this talk, with an emphasis on conservation and land use to conserve wetland functions and values.

  6. Open Adoption

    ERIC Educational Resources Information Center

    Baran, Annette; And Others

    1976-01-01

    Adult adoptees are increasingly challenging the practice of sealing their birth records. The authors examine the historical roots of adoptive practices in this country and suggest that the time has come for open adoption to gain acceptance as an alternative. (Author)

  7. Opening Address

    NASA Astrophysics Data System (ADS)

    Yamada, T.

    2014-12-01

    Ladies and Gentlemen, it is my great honor and pleasure to present an opening address of the 3rd International Workshop on "State of the Art in Nuclear Cluster Physics"(SOTANCP3). On the behalf of the organizing committee, I certainly welcome all your visits to KGU Kannai Media Center belonging to Kanto Gakuin University, and stay in Yokohama. In particular, to whom come from abroad more than 17 countries, I would appreciate your participations after long long trips from your homeland to Yokohama. The first international workshop on "State of the Art in Nuclear Cluster Physics", called SOTANCP, was held in Strasbourg, France, in 2008, and the second one was held in Brussels, Belgium, in 2010. Then the third workshop is now held in Yokohama. In this period, we had the traditional 10th cluster conference in Debrecen, Hungary, in 2012. Thus we have the traditional cluster conference and SOTANCP, one after another, every two years. This obviously shows our field of nuclear cluster physics is very active and flourishing. It is for the first time in about 10 years to hold the international workshop on nuclear cluster physics in Japan, because the last cluster conference held in Japan was in Nara in 2003, about 10 years ago. The president in Nara conference was Prof. K. Ikeda, and the chairpersons were Prof. H. Horiuchi and Prof. I. Tanihata. I think, quite a lot of persons in this room had participated at the Nara conference. Since then, about ten years passed. So, this workshop has profound significance for our Japanese colleagues. The subjects of this workshop are to discuss "the state of the art in nuclear cluster physics" and also discuss the prospect of this field. In a couple of years, we saw significant progresses of this field both in theory and in experiment, which have brought better and new understandings on the clustering aspects in stable and unstable nuclei. I think, the concept of clustering has been more important than ever. This is true also in the

  8. Science Fiction: Serious Reading, Critical Reading

    ERIC Educational Resources Information Center

    Zigo, Diane; Moore, Michael T.

    2004-01-01

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

  9. Integrating Reading and Writing through Extensive Reading

    ERIC Educational Resources Information Center

    Park, Jeongyeon

    2016-01-01

    This study explores whether an extensive reading (ER) approach can enhance L2 learners' writing performance in an English for Academic Purposes context. Two classes were compared in terms of writing improvement after one semester: a 'traditional' writing class primarily focused on writing practice and grammar instruction, and an ER class in which…

  10. 75 FR 30863 - Nixon Presidential Historical Materials: Opening of Materials

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-02

    ... RECORDS ADMINISTRATION Nixon Presidential Historical Materials: Opening of Materials AGENCY: National Archives and Records Administration. ACTION: Notice of opening of additional materials. SUMMARY: This notice announces the opening of additional Nixon Presidential Historical Materials by the Richard...

  11. 76 FR 35918 - Nixon Presidential Historical Materials; Opening of Materials

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-20

    ... Materials; Opening of Materials AGENCY: National Archives and Records Administration. ACTION: Notice of Opening of Additional Materials. SUMMARY: This notice announces the opening of additional Nixon Presidential Historical Materials by the Richard Nixon Presidential Library and Museum, a division of...

  12. Forecasting Reading Anxiety for Promoting English-Language Reading Performance Based on Reading Annotation Behavior

    ERIC Educational Resources Information Center

    Chen, Chih-Ming; Wang, Jung-Ying; Chen, Yong-Ting; Wu, Jhih-Hao

    2016-01-01

    To reduce effectively the reading anxiety of learners while reading English articles, a C4.5 decision tree, a widely used data mining technique, was used to develop a personalized reading anxiety prediction model (PRAPM) based on individual learners' reading annotation behavior in a collaborative digital reading annotation system (CDRAS). In…

  13. Effects of Differentiated Reading on Elementary Students' Reading Comprehension and Attitudes toward Reading

    ERIC Educational Resources Information Center

    Shaunessy-Dedrick, Elizabeth; Evans, Linda; Ferron, John; Lindo, Myriam

    2015-01-01

    In this investigation, we examined the effects of a differentiated reading approach on fourth grade students' reading comprehension and attitudes toward reading. Eight Title I schools within one urban district were randomly assigned to treatment (Schoolwide Enrichment Model-Reading [SEM-R]) or control (district reading curriculum) conditions.…

  14. The Effects of Sustained Silent Reading on Reading Achievement and Reading Attitudes of Fourth Grade Students

    ERIC Educational Resources Information Center

    Gray, Holly Lynn

    2012-01-01

    This study tested the effects of a Sustained Silent Reading program on reading achievement and reading attitude. The study accessed scores from the DIBELS Oral Reading Fluency (Good, Kaminski, & Dill, 2007) to measure reading achievement. This measure was given before and after a twelve week period, during which the treatment group…

  15. The Relationships between Korean University Students' Reading Attitude, Reading Strategy Use, and Reading Proficiency

    ERIC Educational Resources Information Center

    Kim, Hyangil

    2016-01-01

    This present study investigated the relationships among L2 readers' reading attitude, reading strategy use, and reading proficiency in order to identify patterns caused by individuals' differences. For this study, 153 Korean university students replied to a reading attitude and reading strategy questionnaire. An ANOVA and frequency analysis were…

  16. Role of Reading Engagement in Mediating Effects of Reading Comprehension Instruction on Reading Outcomes

    ERIC Educational Resources Information Center

    Wigfield, Allan; Guthrie, John T.; Perencevich, Kathleen C.; Taboada, Ana; Klauda, Susan Lutz; McRae, Angela; Barbosa, Pedro

    2008-01-01

    The engagement model of reading development suggests that instruction improves students' reading comprehension to the extent that it increases students' engagement processes in reading. We compared how Concept-Oriented Reading Instruction (CORI) (support for cognitive and motivational processes in reading), strategy instruction (support for…

  17. Student-Centered Reading Activities.

    ERIC Educational Resources Information Center

    Moffett, James; Wagner, Betty Jane

    1991-01-01

    Offers student-centered reading activities designed to bring students to reading maturity and involvement in literature. Discusses partner reading, dramatizing and performing texts, transforming texts, journal writing, discussion, and writing. (PRA)

  18. Transcription of Two Adjacent Carbohydrate Utilization Gene Clusters in Bifidobacterium breve UCC2003 Is Controlled by LacI- and Repressor Open Reading Frame Kinase (ROK)-Type Regulators

    PubMed Central

    O'Connell, Kerry Joan; O'Connell Motherway, Mary; Liedtke, Andrea; Fitzgerald, Gerald F.; Ross, R. Paul; Stanton, Catherine; Zomer, Aldert

    2014-01-01

    Members of the genus Bifidobacterium are commonly found in the gastrointestinal tracts of mammals, including humans, where their growth is presumed to be dependent on various diet- and/or host-derived carbohydrates. To understand transcriptional control of bifidobacterial carbohydrate metabolism, we investigated two genetic carbohydrate utilization clusters dedicated to the metabolism of raffinose-type sugars and melezitose. Transcriptomic and gene inactivation approaches revealed that the raffinose utilization system is positively regulated by an activator protein, designated RafR. The gene cluster associated with melezitose metabolism was shown to be subject to direct negative control by a LacI-type transcriptional regulator, designated MelR1, in addition to apparent indirect negative control by means of a second LacI-type regulator, MelR2. In silico analysis, DNA-protein interaction, and primer extension studies revealed the MelR1 and MelR2 operator sequences, each of which is positioned just upstream of or overlapping the correspondingly regulated promoter sequences. Similar analyses identified the RafR binding operator sequence located upstream of the rafB promoter. This study indicates that transcriptional control of gene clusters involved in carbohydrate metabolism in bifidobacteria is subject to conserved regulatory systems, representing either positive or negative control. PMID:24705323

  19. The Contribution of Segmental and Suprasegmental Phonology to Reading Comprehension.

    PubMed

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

    2016-01-01

    The aim of the present study was to examine the relation between decoding and segmental and suprasegmental phonology, and their contribution to reading comprehension, in the upper primary grades. Following a longitudinal design, the performance of 99 Dutch primary school children on phonological awareness (segmental phonology) and text reading prosody (suprasegmental phonology) in fourth-grade and fifth-grade, and reading comprehension in sixth-grade were examined. In addition, decoding efficiency as a general assessment of reading was examined. Structural path modeling firstly showed that the relation between decoding efficiency and both measures of phonology from fourth- to fifth grade was unidirectional. Secondly, the relation between decoding in fourth- and fifth-grade and reading comprehension in sixth-grade became indirect when segmental and suprasegmental phonology were added to the model. Both factors independently exerted influence on later reading comprehension. This leads to the conclusion that not only segmental, but also suprasegmental phonology, contributes substantially to children's reading development.

  20. Opening education.

    PubMed

    Smith, Marshall S

    2009-01-02

    Spurred by the publication of Massachusetts Institute of Technology OpenCourseWare in 2002, the open educational resources (OER) movement, which has rapidly expanded and captured the imagination and energy of millions of creators and users throughout the world, now faces many opportunities and substantial challenges as it moves to become an integral part of the world's educational environment. The confluence of the Web and a spirit of sharing intellectual property have fueled a worldwide movement to make knowledge and education materials open to all for use. OER are content (courses, books, lesson plans, articles, etc.), tools (virtual laboratories, simulations, and games), and software that support learning and educational practice. OER are free on the Web, and most have licenses that allow copyright holders to retain ownership while providing specified rights for use in original and modified forms. At the least, OER have helped to level the distribution of knowledge across the world. A second promise of OER is to help transform educational practices. This article explores the history of and promises and challenges for OER.

  1. 32 CFR 296.6 - Reading room.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...″ Floppy diskette $0.50 (2) 3.5″ Floppy diskette $0.50 (3) CD-R Media $3.75 (4) Video Tape $4.00. (b) The NRO FOIA Electronic Reading Room is located on the NRO Home Page: www.nro.odci.gov. ... at 14675 Lee Road, Chantilly VA, 20151-1715 and is open weekdays only from 8:00 am until 4:00...

  2. 32 CFR 296.6 - Reading room.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...″ Floppy diskette $0.50 (2) 3.5″ Floppy diskette $0.50 (3) CD-R Media $3.75 (4) Video Tape $4.00. (b) The NRO FOIA Electronic Reading Room is located on the NRO Home Page: www.nro.odci.gov. ... at 14675 Lee Road, Chantilly VA, 20151-1715 and is open weekdays only from 8:00 am until 4:00...

  3. Metalinguistic awareness and reading performance: a cross language comparison.

    PubMed

    Ibrahim, Raphiq; Eviatar, Zohar; Aharon-Peretz, Judith

    2007-07-01

    The study examined two questions: (1) do the greater phonological awareness skills of billinguals affect reading performance; (2) to what extent do the orthographic characteristics of a language influence reading performance and how does this interact with the effects of phonological awareness. We estimated phonological metalinguistic abilities and reading measures in three groups of first graders: monolingual Hebrew speakers, bilingual Russian-Hebrew speakers, and Arabic-speaking children. We found that language experience affects phonological awareness, as both Russian-Hebrew bilinguals and the Arabic speakers achieved higher scores on metalinguistic tests than Hebrew speakers. Orthography affected reading measures and their correlation with phonological abilitites. Children reading Hebrew showed better text reading ability and significant correlations between phonological awareness and reading scores. Children reading Arabic showed a slight advantage in single word and nonword reading over the two Hebrew reading groups, and very weak relationships between phonological abilities and reading performance. We conclude that native Arabic speakers have more difficulty in processing Arabic orthography than Hebrew monolinguals and bilinguals have in processing Hebrew orthography, and suggest that this is due to the additional visual complexity of Arabic orthography.

  4. Opening the Dutch Open Telescope

    NASA Astrophysics Data System (ADS)

    Rutten, R. J.; de Wijn, A. G.; Sütterlin, P.; Bettonvil, F. C. M.; Hammerschlag, R. H.

    2002-10-01

    We hope to "open the DOT" to the international solar physics community as a facility for high-resolution tomography of the solar atmosphere. Our aim is to do so combining peer-review time allocation with service-mode operation in a "hands-on-telescope" education program bringing students to La Palma to assist in the observing and processing. The largest step needed is considerable speedup of the DOT speckle processing.

  5. Teen Summer Reading Program, 1999. Read around the World.

    ERIC Educational Resources Information Center

    Virginia State Library, Richmond.

    This guide for the 1999 Virginia teen summer reading program for public libraries, "Read around the World," includes the following chapters: (1) "Reading and Teens," including serving the underserved, tips for teens, and a recipe for choosing a book to read for fun; (2) "Programming and Teens," including "The Why…

  6. Improving EFL Learners' Reading Levels through Extensive Reading

    ERIC Educational Resources Information Center

    Mermelstein, Aaron David

    2014-01-01

    Today there is an increasing amount of research promoting the effectiveness of extensive reading (ER) towards increasing learners' vocabulary, comprehension, reading speed, and motivation towards reading. However, little has been done to measure the effects of ER on learners' reading levels. This quantitative study examined the effects of ER on…

  7. Reading Motivation and Reading Engagement: Clarifying Commingled Conceptions

    ERIC Educational Resources Information Center

    Unrau, Norman J.; Quirk, Matthew

    2014-01-01

    The constructs of motivation for reading and reading engagement have frequently become blurred and ambiguous in both research and discussions of practice. To address this commingling of constructs, the authors provide a concise review of the literature on motivation for reading and reading engagement and illustrate the blurring of those concepts…

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

    ERIC Educational Resources Information Center

    Bastug, Muhammet; Demirtas, Gonca

    2016-01-01

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

  9. When Reading Gets Ruff: Canine-Assisted Reading Programs

    ERIC Educational Resources Information Center

    Lane, Holly B.; Zavada, Shannon D. W.

    2013-01-01

    Canine-assisted reading programs show promise as an innovative method for engaging reluctant readers and motivating them to practice. In such programs, specially trained dogs visit classrooms and libraries, and children read to them. Children who struggle with reading may be motivated to read more because they find dogs to be calming and…

  10. Improving Reading Rates and Comprehension through Timed Repeated Reading

    ERIC Educational Resources Information Center

    Chang, Anna C-S.; Millett, Sonia

    2013-01-01

    Thirteen English as a foreign language students read 26 passages during a 13-week period. Each passage was read five times, and students answered comprehension questions after the first and the fifth reading. Another 13 students read the same number of passages but without repetition and only answered the comprehension questions once. All students…

  11. Children's Reading Problems. Reading Education Report No. 8.

    ERIC Educational Resources Information Center

    Collins, Allan; Haviland, Susan E.

    This paper reviews recent research to determine why children encounter problems understanding what they read. Four points are discussed as especially relevant to children's problems in reading comprehension: (1) reading differs from early language experiences, and an analysis of these differences can indicate likely sources of reading difficulty;…

  12. The Potency of "READS" to Inform Students' Reading Ability

    ERIC Educational Resources Information Center

    Mohamed, Abdul Rashid; Eng, Lin Siew; Mohamed Ismail, Shaik Abdul Malik

    2012-01-01

    This paper shares an initiative conducted in Malaysia in terms of knowledge to gauge students' Reading Age and to inform teachers of their students' reading progress and learning. Ensuring teachers understand the needs of students' reading ability and preparing students to read and comprehend texts are the two most fundamental parallel tasks in…

  13. 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'…

  14. Sources of Individual Differences in Reading Comprehension and Reading Fluency.

    ERIC Educational Resources Information Center

    Jenkins, Joseph R.; Fuchs, Lynn S.; van den Broek, Paul; Espin, Christine; Deno, Stanley L.

    2003-01-01

    Examines the common and distinct contributions of context-free and context reading skill to reading comprehension and the contributions of context-free reading skill and reading comprehension to context fluency. Results support the conclusion that word level processes contribute relatively more to fluency at lower levels while comprehension…

  15. "Read Naturally": A Strategy To Increase Oral Reading Fluency.

    ERIC Educational Resources Information Center

    Hasbrouck, Jan E.; Ihnot, Candyce; Rogers, Ginger H.

    1999-01-01

    Describes the Read Naturally (RN) strategy to improve reading fluency that combines reading from a model, repeated readings, and progress-monitoring. Suggests positive results found in data collected from classroom implementations with K-3 remedial and special education students and 6th-grade special education students. (NH)

  16. Reading Acts: An Inquiry into Reading and Teaching

    ERIC Educational Resources Information Center

    Sams, Brandon L.

    2012-01-01

    This text performs reading for teaching in an audit culture. Two teachers, myself and Steven, read the memoir "Hole in My Life" by Jack Gantos and, while reading, recorded our experiences as readers and planned to teach the book to Steven's English class. This study is an inquiry into the phenomenon of "reading to teach,"…

  17. Teachers' Role in Fostering Reading Skill: Effective and Successful Reading

    ERIC Educational Resources Information Center

    Jose, G. Rexlin; Raja, B. William Dharma

    2011-01-01

    Reading bestows enjoyment and enlightenment. It unlocks the unknown. It is a complex cognitive activity that is indispensable for the kind of knowledge society. So the students of today's world must know how to learn from reading and to enter the present literate society. One who reads can lead others to light. People who read can be free because…

  18. CALIPSO Data Read Software

    Atmospheric Science Data Center

    2017-01-04

    ... Callable routines in Interactive Data Language (IDL) provide basic read access to CALIPSO science data files. ... in both Microsoft Word and PDF formats. Interactive Data Language (IDL) is available from  Exelis Visual Information Solutions . ...

  19. Reading: Ave Atque Vale.

    ERIC Educational Resources Information Center

    Donovan, Ann

    1984-01-01

    Although basic literacy will continue to be necessary for survival, mass communications and information technology are bringing about an inevitable and lamentable decline in reading for pleasure and in the love of literature for its own sake. (TE)

  20. What Are Reading Disorders?

    MedlinePlus

    ... and language-based learning disabilities are commonly called dyslexia . These disorders are present from a young age ... information about these problems. Types of Reading Disorders Dyslexia is a brain-based type of learning disability ...

  1. Speed- Reading Made Easy

    ERIC Educational Resources Information Center

    Brown, W. S.

    1970-01-01

    Illustrates a compromise between vertical and horizontal typographies which should make speed reading faster and more reliable, and suggests that computers could prepare text according to this arrangement. (MB)

  2. Developmental reading disorder

    MedlinePlus

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

  3. Art Criticism and Reading.

    ERIC Educational Resources Information Center

    Feldman, Edmund Burke; Woods, Don

    1981-01-01

    The authors review a body of theory and accumulating evidence which suggests that critical study of the arts facilitates the development of cognitive skills, including those essential to reading. (Author/SJL)

  4. Can India's ``literate'' read?

    NASA Astrophysics Data System (ADS)

    Kothari, Brij; Bandyopadhyay, Tathagata

    2010-12-01

    This paper takes a close look at India's literacy rate by exploring whether the officially "literate" can read and at what level. In a large sample, aged 7+, drawn from four Hindi-speaking states, two methods were used to measure literacy. One was the standard Census Method (CM) which relies on self-reporting and the other was a Reading Method (RM) which required the same individuals to actually read a simple text at grade 2 level. The findings revealed a substantial difference between the reading literacy rates obtained by CM and RM. CM over-reported RM by 16%. The overestimation was higher for males. Decoding skills were found to erode in most cases after completion of primary schooling, assuming no further education. A minimum grade 8-9 education was required for decoding skills to not deteriorate after schooling.

  5. The cold reading technique.

    PubMed

    Dutton, D L

    1988-04-15

    For many people, belief in the paranormal derives from personal experience of face-to-face interviews with astrologers, palm readers, aura and Tarot readers, and spirit mediums. These encounters typically involve cold reading, a process in which a reader makes calculated guesses about a client's background and problems and, depending on the reaction, elaborates a reading which seems to the client so uniquely appropriate that it carries with it the illusion of having been produced by paranormal means. The cold reading process is shown to depend initially on the Barnum effect, the tendency for people to embrace generalized personality descriptions as idiosyncratically their own. Psychological research into the Barnum effect is critically reviewed, and uses of the effect by a professional magician are described. This is followed by detailed analysis of the cold reading performances of a spirit medium. Future research should investigate the degree to which cold readers may have convinced themselves that they actually possess psychic or paranormal abilities.

  6. The "Enigma" Reading Program.

    ERIC Educational Resources Information Center

    Sachs, Frances Greenberg; Banas, Norma

    1985-01-01

    Approaches are discussed for constructing and implementing the ENIGMA (Engineering Individual Growth Through Manipulative Associations) reading program, a language-based activity using teacher-made puzzles and stories in a manipulative-associative manner. (CL)

  7. Open University

    ScienceCinema

    None

    2016-07-12

    Michel Pentz est née en Afrique du Sud et venu au Cern en 1957 comme physicien et président de l'associaion du personnel. Il est également fondateur du mouvement Antiapartheid de Genève et a participé à la fondation de l'Open University en Grande-Bretagne. Il nous parle des contextes pédagogiques, culturels et nationaux dans lesquels la méthode peut s'appliquer.

  8. Reading Interventions With Behavioral and Social Skill Outcomes: A Synthesis of Research

    PubMed Central

    Roberts, Garrett J.; Solis, Michael; Ciullo, Stephen; McKenna, John W.; Vaughn, Sharon

    2015-01-01

    Research findings have suggested that reading deficits and problem behaviors are positively related. This synthesis investigated how reading interventions impact behavioral/social skill outcomes by reviewing studies that included (a) a reading intervention without behavioral/social skill components, (b) behavioral/social skill dependent variables, and (c) students in Grades K-12. Fifteen articles were evaluated by the type of reading intervention, associations between positive reading effects and behavioral/social skill outcomes, and The What Works Clearinghouse (WWC) determinants of study ratings. Findings suggested that reading interventions tended to have positive reading outcomes, while behavioral/social skill outcomes were small or negative. Research did not suggest an association between improved reading and behavioral performance, regardless of the WWC study determinants rating. Implications include reading instruction may not be sufficient to improve behavioral and social skill outcomes. Additional research is warranted to investigate the long-term impact of reading on behavioral and social skill outcomes. PMID:25548392

  9. Reading interventions with behavioral and social skill outcomes: a synthesis of research.

    PubMed

    Roberts, Garrett J; Solis, Michael; Ciullo, Stephen; McKenna, John W; Vaughn, Sharon

    2015-01-01

    Research findings have suggested that reading deficits and problem behaviors are positively related. This synthesis investigated how reading interventions impact behavioral/social skill outcomes by reviewing studies that included (a) a reading intervention without behavioral/social skill components, (b) behavioral/social skill dependent variables, and (c) students in Grades K-12. Fifteen articles were evaluated by the type of reading intervention, associations between positive reading effects and behavioral/social skill outcomes, and The What Works Clearinghouse (WWC) determinants of study ratings. Findings suggested that reading interventions tended to have positive reading outcomes, while behavioral/social skill outcomes were small or negative. Research did not suggest an association between improved reading and behavioral performance, regardless of the WWC study determinants rating. Implications include reading instruction may not be sufficient to improve behavioral and social skill outcomes. Additional research is warranted to investigate the long-term impact of reading on behavioral and social skill outcomes.

  10. The Open Data Repositorys Data Publisher

    NASA Technical Reports Server (NTRS)

    Stone, N.; Lafuente, B.; Downs, R. T.; Blake, D.; Bristow, T.; Fonda, M.; Pires, A.

    2015-01-01

    Data management and data publication are becoming increasingly important components of researcher's workflows. The complexity of managing data, publishing data online, and archiving data has not decreased significantly even as computing access and power has greatly increased. The Open Data Repository's Data Publisher software strives to make data archiving, management, and publication a standard part of a researcher's workflow using simple, web-based tools and commodity server hardware. The publication engine allows for uploading, searching, and display of data with graphing capabilities and downloadable files. Access is controlled through a robust permissions system that can control publication at the field level and can be granted to the general public or protected so that only registered users at various permission levels receive access. Data Publisher also allows researchers to subscribe to meta-data standards through a plugin system, embargo data publication at their discretion, and collaborate with other researchers through various levels of data sharing. As the software matures, semantic data standards will be implemented to facilitate machine reading of data and each database will provide a REST application programming interface for programmatic access. Additionally, a citation system will allow snapshots of any data set to be archived and cited for publication while the data itself can remain living and continuously evolve beyond the snapshot date. The software runs on a traditional LAMP (Linux, Apache, MySQL, PHP) server and is available on GitHub (http://github.com/opendatarepository) under a GPLv2 open source license. The goal of the Open Data Repository is to lower the cost and training barrier to entry so that any researcher can easily publish their data and ensure it is archived for posterity.

  11. The Open Data Repository's Data Publisher

    NASA Astrophysics Data System (ADS)

    Stone, N.; Lafuente, B.; Downs, R. T.; Bristow, T.; Blake, D. F.; Fonda, M.; Pires, A.

    2015-12-01

    Data management and data publication are becoming increasingly important components of research workflows. The complexity of managing data, publishing data online, and archiving data has not decreased significantly even as computing access and power has greatly increased. The Open Data Repository's Data Publisher software (http://www.opendatarepository.org) strives to make data archiving, management, and publication a standard part of a researcher's workflow using simple, web-based tools and commodity server hardware. The publication engine allows for uploading, searching, and display of data with graphing capabilities and downloadable files. Access is controlled through a robust permissions system that can control publication at the field level and can be granted to the general public or protected so that only registered users at various permission levels receive access. Data Publisher also allows researchers to subscribe to meta-data standards through a plugin system, embargo data publication at their discretion, and collaborate with other researchers through various levels of data sharing. As the software matures, semantic data standards will be implemented to facilitate machine reading of data and each database will provide a REST application programming interface for programmatic access. Additionally, a citation system will allow snapshots of any data set to be archived and cited for publication while the data itself can remain living and continuously evolve beyond the snapshot date. The software runs on a traditional LAMP (Linux, Apache, MySQL, PHP) server and is available on GitHub (http://github.com/opendatarepository) under a GPLv2 open source license. The goal of the Open Data Repository is to lower the cost and training barrier to entry so that any researcher can easily publish their data and ensure it is archived for posterity. We gratefully acknowledge the support for this study by the Science-Enabling Research Activity (SERA), and NASA NNX11AP82A

  12. Reading in the Secondary School.

    ERIC Educational Resources Information Center

    Teaching English, 1976

    1976-01-01

    The topic of discussion of this issue of the journal "Teaching English" is reading instruction in the secondary school. Articles include "Reading in the Primary School" (Alastair Hendry), "Patterns of Progress" (Fergus McBride), "Teaching Reading--Whose Business?" (James Maxwell), "A Reading Policy for the Secondary School" (Iain McGillivray),…

  13. Who Reads Novels? A Symposium.

    ERIC Educational Resources Information Center

    American Scholar, 1979

    1979-01-01

    Seven scholars respond individually to these questions: Do you read many contemporary novels? If you do, whose novels do you read and for what reasons? If you no longer read many contemporary novels, why have you ceased to do so and what kinds of reading have supplanted them? (Editor/SJL)

  14. [Weldon Elementary School Reading Program.

    ERIC Educational Resources Information Center

    Clovis Unified School District, CA.

    This program, included in "Effective Reading Programs...," serves 485 white and Spanish-speaking students in K-6. In the program, begun in 1970, state-mandated basal reading series are supplemented by four locally developed programs: Levels Design Letter Readiness, Rebus Reading, Project Read, and Great Studies. The Levels Design Letter…

  15. In Defense of Reading Quizzes

    ERIC Educational Resources Information Center

    Tropman, Elizabeth

    2014-01-01

    Many students fail to read the assigned material before class. A failure to read is detrimental to both student learning and course engagement. This paper considers the often-neglected teaching technique of giving frequent quizzes on the reading. Drawing on the author's experiences assigning reading quizzes, together with student opinions…

  16. Dyslexia: Problems of Reading Disabilities.

    ERIC Educational Resources Information Center

    Goldberg, Herman K.; Schiffman, Gilbert B.

    The purpose of this book is to provide an understanding of both the educational and medical aspects of reading and to show how they are interrelated in reading disabilities. The various aspects of reading disabilities are presented in the following chapters: Introduction to the Reading Problem; Early Predictive Studies; Psychological Evaluation;…

  17. Reading and the Special Learner.

    ERIC Educational Resources Information Center

    Hedley, Carolyn N., Ed.; Hicks, John S., Ed.

    Compiled from papers presented at the annual Reading/Special Education Institute at Fordham University, this collection of essays addresses reading problems of special education students. The book is divided into three sections. The first section covers reading assessment and reading intervention; section 2 addresses the specific learner and the…

  18. Classics in Reading: A Survey.

    ERIC Educational Resources Information Center

    Froese, Victor

    1982-01-01

    Frank Smith and Kenneth Goodman were the most frequently cited authors; Bond and Dykstra's "The Cooperative Research Program in First Grade Reading Instruction" and Chall's "Learning to Read: The Great Debate" the most frequently cited works in a survey that asked graduate faculty in reading to name "classics" in reading research. (FL)

  19. Acquisition of a Reading Repertoire.

    ERIC Educational Resources Information Center

    Powell, William R.

    Drawing on results from informal reading inventories and studies of oral reading behavior, a theory is presented to describe the process of learning to read. Reading is seen to be broader than a skill and more like a repertoire with many abilities, aptitudes, and special accomplishments performing in concert. This repertoire is acquired in four…

  20. What Is a Reading Error?

    ERIC Educational Resources Information Center

    Labov, William; Baker, Bettina

    2010-01-01

    Early efforts to apply knowledge of dialect differences to reading stressed the importance of the distinction between differences in pronunciation and mistakes in reading. This study develops a method of estimating the probability that a given oral reading that deviates from the text is a true reading error by observing the semantic impact of the…

  1. Patterns of Thinking in Reading.

    ERIC Educational Resources Information Center

    Ediger, Marlow

    The reading teacher needs to be well versed in the teaching of reading, which includes different patterns of thinking in each student. A skilled reader develops patterns of thinking pertaining to content read. Identified patterns of thinking need to be analyzed and incorporated as objectives for student attainment in reading. This paper discusses…

  2. Explorations in Second Language Reading

    ERIC Educational Resources Information Center

    Cohen, Roger, Ed.

    2009-01-01

    The chapters in "Explorations in Second Language Reading" reveal the importance of reading in the classroom and how instructors can use reading as a bridge to improve learners' other linguistic and interpersonal skills. Most significantly, each author prompts us to rediscover how enjoyable ESOL reading can be and how it can increase learner…

  3. Improving Reading to Improve Math

    ERIC Educational Resources Information Center

    Glenberg, Arthur; Willford, Jonathan; Gibson, Bryan; Goldberg, Andrew; Zhu, Xiaojin

    2012-01-01

    Reading provides information across the curriculum. Thus, to the extent that fundamental (i.e., generalizable) reading comprehension strategies can be taught, the benefits should be found in multiple domains. To test this claim, children in the third and fourth grades read by simulating text content using the two-part, embodied "Moved by Reading"…

  4. When Do Children Read Books?

    ERIC Educational Resources Information Center

    van Ours, Jan C.

    2008-01-01

    This paper investigates the reading of fiction books by 15 year olds in 18 OECD countries. It appears that girls read fiction books more often than boys, whereas boys read comic books more often than girls. Parental education, family structure, and the number of books and televisions at home influence the intensity with which children read fiction…

  5. The Philosophical Arena and Reading.

    ERIC Educational Resources Information Center

    Ediger, Marlow

    Each plan for guiding pupils to read emphasizes an inherent philosophy or philosophies of education. Existentialism encourages reading by promoting free choice of reading material and relating decisions to results. A reading curriculum based on the tenets of realism would give the learner a view of the world as it actually exists. Experimentalism…

  6. Using OpenGL for imaging

    NASA Astrophysics Data System (ADS)

    Rost, Randi J.

    1996-04-01

    Although OpenGL is not usually thought of as a library for imaging, it was designed to expose the capabilities of modern frame buffer hardware. The emphasis in OpenGL is on 3D graphics (i.e., geometry), but OpenGL also includes a fairly rich set of capabilities for 2D imaging. This paper describes the capabilities of OpenGL for imaging applications, including pixel transfer operations (draw, read, copy); color lookup tables; linear transformation of color values; pixel conversion capabilities; and pixel operations such as blending, masking, and clipping. Several recently proposed extensions to OpenGL add significant capabilities to the core imaging model, including convolution, window level mapping, and image transformation and resampling. These capabilities are discussed in the context of the pixel processing pipeline defined by OpenGL.

  7. Open Enrollment: Challenge to the College Reading/Skills Program.

    ERIC Educational Resources Information Center

    Kerstiens, Gene

    The procedure for determining, by computer-programing, English sections according to test results at El Camino College, California, is described. El Camino College is a large community college in the Los Angeles area, admission to which is based solely on a high school diploma and residence in the district. As a result of entrance test scores on…

  8. OpenMDAO Framework Status

    NASA Technical Reports Server (NTRS)

    Naiman, Cynthia Gutierrez

    2010-01-01

    Advancing and exploring the science of Multidisciplinary Analysis & Optimization (MDAO) capabilities are high-level goals in the Fundamental Aeronautics Program s Subsonic Fixed Wing (SFW) project. The OpenMDAO team has made significant progress toward completing the Alpha OpenMDAO deliverable due in September 2010. Included in the presentation are: details of progress on developing the OpenMDAO framework, example usage of OpenMDAO, technology transfer plans, near term plans, progress toward establishing partnerships with external parties, and discussion of additional potential collaborations.

  9. Reading Recovery Program Evaluation. Report 1992-93.

    ERIC Educational Resources Information Center

    Salinas, Analida; And Others

    A study evaluated the effectiveness of the first two years of the Reading Recovery program at the McAllen Independent School District, Texas. Thirteen campuses participated in the first year (1991-92) while 16 campuses participated in 1993. In addition, the Literacy Program, designed to expand the positive effects of Reading Recovery strategies in…

  10. Readings in Public School Collective Bargaining. Volume 2.

    ERIC Educational Resources Information Center

    Educational Service Bureau, Inc., Washington, DC.

    This report contains a variety of readings related to different aspects of collective negotiations in public education. Subject areas covered include (1) State labor laws, (2) emerging roles of educators, (3) teacher militancy, (4) impasse resolution, and (5) public policy on teacher strikes. For additional readings on collective negotiations see…

  11. Updated Perspectives on Educational Diagnosticians' Understanding of Reading Assessments

    ERIC Educational Resources Information Center

    Rueter, Jessica A.; McWhorter, Rochell R.; Lamb, John H.; Dykes, Frank O.

    2016-01-01

    Chappell, Stephens, Kinnison, and Pettigrew (2009) conducted a study investigating educational diagnosticians knowledge of early reading development. Our study replicated the work of Chappell et al. through a mixed methods design that investigated educational diagnosticians' perceptions and knowledge of early reading development. Additionally, our…

  12. The Fluid Reading Primer: Animated Decoding Support for Emergent Readers.

    ERIC Educational Resources Information Center

    Zellweger, Polle T.; Mackinlay, Jock D.

    A prototype application called the Fluid Reading Primer was developed to help emergent readers with the process of decoding written words into their spoken forms. The Fluid Reading Primer is part of a larger research project called Fluid Documents, which is exploring the use of interactive animation of typography to show additional information in…

  13. Helping Your Child in Reading in the Social Studies.

    ERIC Educational Resources Information Center

    Ediger, Marlow

    There are numerous ways in which parents can assist students in social studies. Parents can read aloud library books that deal with social studies; older peers can also read aloud, providing practice to the older student as well. Parents can relate current events to a nearby globe, locating places mentioned in newscasts. In addition, parents and…

  14. Physical and Psychological Decrements Affecting Reading in the Aged.

    ERIC Educational Resources Information Center

    Wilson, Molly M.

    While reading has been recognized as a potentially useful and enjoyable pastime for the elderly, physical and psychological decrements affect the ability of the elderly to read. As the eyes age, near-point tasks become more difficult. In addition to reduced sensory intake, perceptual changes occur. The central nervous system slows, and data travel…

  15. Developing Reading Fluency in EFL: How Assisted Repeated Reading and Extensive Reading Affect Fluency Development

    ERIC Educational Resources Information Center

    Taguchi, Etsuo; Takayasu-Maass, Miyoko; Gorsuch, Greta J.

    2004-01-01

    Extensive research on reading in a first language has shown the critical role fluency plays in successful reading. Fluency alone, however, does not guarantee successful reading. Cognitive and metacognitive reading strategies and schemata that readers utilize also play important roles in constructing meaning from text. Most research, however,…

  16. Students' Self-Perception of Reading Ability, Enjoyment of Reading and Reading Achievement

    ERIC Educational Resources Information Center

    Smith, Jeffrey K.; Smith, Lisa F.; Gilmore, Alison; Jameson, Madgerie

    2012-01-01

    Using data from New Zealand's National Education Monitoring Project, a light sampling, low stakes performance based national school assessment program, reading self-efficacy, reading enjoyment, and reading achievement were examined in samples of 8 and 12 year old children. Sample sizes were n = 480 for each group. While reading achievement…

  17. Reading Improvement in English- and Hebrew-Speaking Children with Reading Difficulties after Reading Acceleration Training

    ERIC Educational Resources Information Center

    Horowitz-Kraus, Tzipi; Cicchino, Nicole; Amiel, Merav; Holland, Scott K.; Breznitz, Zvia

    2014-01-01

    A reading acceleration program known to improve reading fluency in Hebrew-speaking adults was tested for its effect on children. Eighty-nine Hebrew- and English-speaking children with reading difficulties were divided into a waiting list group and two training groups (Hebrew and English) and underwent 4 weeks of reading acceleration training.…

  18. What Are Teenagers Reading? Adolescent Fiction Reading Habits and Reading Choices

    ERIC Educational Resources Information Center

    Hopper, Rosemary

    2005-01-01

    What are adolescents choosing to read? This is an important question because of potential divergence between school students' reading interests and reading expectations in school. This article considers the findings from a study of the reading over one week in May 2002 of 707 school students aged between 11 and 15, undertaken in 30 schools in the…

  19. Reading to Speak: Integrating Oral Communication Skills

    ERIC Educational Resources Information Center

    Zhang, Yun

    2009-01-01

    According to Ur (1996, 120), "of all the four skills (listening, speaking, reading and writing), speaking seems intuitively the most important." Indeed, whether for business or pleasure, a primary motivation to learn a second language is to be able to converse with speakers of that language. However, in addition to being an important…

  20. ReadXplorer 2—detailed read mapping analysis and visualization from one single source

    PubMed Central

    Hilker, Rolf; Stadermann, Kai Bernd; Schwengers, Oliver; Anisiforov, Evgeny; Jaenicke, Sebastian; Weisshaar, Bernd; Zimmermann, Tobias; Goesmann, Alexander

    2016-01-01

    Motivation: The vast amount of already available and currently generated read mapping data requires comprehensive visualization, and should benefit from bioinformatics tools offering a wide spectrum of analysis functionality from just one source. Appropriate handling of multiple mapped reads during mapping analyses remains an issue that demands improvement. Results: The capabilities of the read mapping analysis and visualization tool ReadXplorer were vastly enhanced. Here, we present an even finer granulated read mapping classification, improving the level of detail for analyses and visualizations. The spectrum of automatic analysis functions has been broadened to include genome rearrangement detection as well as correlation analysis between two mapping data sets. Existing functions were refined and enhanced, namely the computation of differentially expressed genes, the read count and normalization analysis and the transcription start site detection. Additionally, ReadXplorer 2 features a highly improved support for large eukaryotic data sets and a command line version, enabling its integration into workflows. Finally, the new version is now able to display any kind of tabular results from other bioinformatics tools. Availability and Implementation: http://www.readxplorer.org Contact: readxplorer@computational.bio.uni-giessen.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27540267

  1. OpenER, a Dutch Initiative in Open Educational Resources

    ERIC Educational Resources Information Center

    Schuwer, Robert; Mulder, Fred

    2009-01-01

    Over the period 2006-2008, the Dutch Open Universiteit Nederland conducted an experiment in which Open Educational Resources (OER) were offered in an effort to bridge the gap between informal and formal learning and to establish a new style of entry portal to higher education with no barriers at all. OpenER received considerable attention both in…

  2. Reading visual braille with a retinal prosthesis.

    PubMed

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

    2012-01-01

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

  3. Reading performance is predicted by more than phonological processing

    PubMed Central

    Kibby, Michelle Y.; Lee, Sylvia E.; Dyer, Sarah M.

    2014-01-01

    We compared three phonological processing components (phonological awareness, rapid automatized naming and phonological memory), verbal working memory, and attention control in terms of how well they predict the various aspects of reading: word recognition, pseudoword decoding, fluency and comprehension, in a mixed sample of 182 children ages 8–12 years. Participants displayed a wide range of reading ability and attention control. Multiple regression was used to determine how well the phonological processing components, verbal working memory, and attention control predict reading performance. All equations were highly significant. Phonological memory predicted word identification and decoding. In addition, phonological awareness and rapid automatized naming predicted every aspect of reading assessed, supporting the notion that phonological processing is a core contributor to reading ability. Nonetheless, phonological processing was not the only predictor of reading performance. Verbal working memory predicted fluency, decoding and comprehension, and attention control predicted fluency. Based upon our results, when using Baddeley’s model of working memory it appears that the phonological loop contributes to basic reading ability, whereas the central executive contributes to fluency and comprehension, along with decoding. Attention control was of interest as some children with ADHD have poor reading ability even if it is not sufficiently impaired to warrant diagnosis. Our finding that attention control predicts reading fluency is consistent with prior research which showed sustained attention plays a role in fluency. Taken together, our results suggest that reading is a highly complex skill that entails more than phonological processing to perform well. PMID:25285081

  4. Analysis of physiological impact while reading stereoscopic radiographs

    NASA Astrophysics Data System (ADS)

    Unno, Yasuko Y.; Tajima, Takashi; Kuwabara, Takao; Hasegawa, Akira; Natsui, Nobutaka; Ishikawa, Kazuo; Hatada, Toyohiko

    2011-03-01

    A stereoscopic viewing technology is expected to improve diagnostic performance in terms of reading efficiency by adding one more dimension to the conventional 2D images. Although a stereoscopic technology has been applied to many different field including TV, movies and medical applications, physiological fatigue through reading stereoscopic radiographs has been concerned although no established physiological fatigue data have been provided. In this study, we measured the α-amylase concentration in saliva, heart rates and normalized tissue hemoglobin index (nTHI) in blood of frontal area to estimate physiological fatigue through reading both stereoscopic radiographs and the conventional 2D radiographs. In addition, subjective assessments were also performed. As a result, the pupil contraction occurred just after the reading of the stereoscopic images, but the subjective assessments regarding visual fatigue were nearly identical for the reading the conventional 2D and stereoscopic radiographs. The α-amylase concentration and the nTHI continued to decline while examinees read both 2D and stereoscopic images, which reflected the result of subjective assessment that almost half of the examinees reported to feel sleepy after reading. The subjective assessments regarding brain fatigue showed that there were little differences between 2D and stereoscopic reading. In summary, this study shows that the physiological fatigue caused by stereoscopic reading is equivalent to the conventional 2D reading including ocular fatigue and burden imposed on brain.

  5. The Experimental Effects of the Strategic Adolescent Reading Intervention (STARI) on a Scenarios-Based Reading Comprehension Assessment

    ERIC Educational Resources Information Center

    Kim, James; Hemphill, Lowry; Troyer, Margaret; Jones, Stephanie; LaRusso, Maria; Kim, Ha-Yeon; Donovan, Suzanne; Snow, Catherine

    2016-01-01

    Nearly one-quarter of U.S. eighth graders score below basic on national assessments of reading (NCES, 2013) and are poorly equipped for the reading demands of secondary school. Struggling adolescent readers cannot summarize a simple passage, use context to determine word meanings, and have difficulties making text-based inferences. In addition,…

  6. Exploring How Nature and Nurture Affect the Development of Reading: An Analysis of the Florida Twin Project on Reading

    ERIC Educational Resources Information Center

    Hart, Sara A.; Logan, Jessica A. R.; Soden-Hensler, Brooke; Kershaw, Sarah; Taylor, Jeanette; Schatschneider, Christopher

    2013-01-01

    Research on the development of reading skills through the primary school years has pointed to the importance of individual differences in initial ability as well as the growth of those skills. Additionally, it has been theorized that reading skills develop incrementally. The present study examined the genetic and environmental influences on 2…

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

    PubMed Central

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

    2012-01-01

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

  8. [Reading research articles].

    PubMed

    van der Graaf, Yolanda; Zaat, Joost

    2015-01-01

    Keeping up with the latest developments is not easy, but neither is reading articles on research. There are too many medical journals that contain information that is irrelevant to clinical practice. From this mass of articles you have to decide which are important for your own clinical practice and which are not. Most articles naturally fall into the latter category as spectacular findings with important consequences for medical practice do not occur every week. The most important thing in a research article is the research question. If you begin with this, then you can put aside much scientific literature. The methodology section is essential; reading this can save you a lot of time. In this article we take you step-by-step through the process of reading research articles. The articles in our Methodology series can be used as background information. These articles have been combined in a tablet app, which is available via www.ntvg.nl/methodologie.

  9. Openness initiative

    SciTech Connect

    Duncan, S.S.

    1995-12-31

    Although antinuclear campaigns seem to be effective, public communication and education efforts on low-level radioactive waste have mixed results. Attempts at public information programs on low-level radioactive waste still focus on influencing public opinion. A question then is: {open_quotes}Is it preferable to have a program focus on public education that will empower individuals to make informed decisions rather than trying to influence them in their decisions?{close_quotes} To address this question, a case study with both quantitative and qualitative data will be used. The Ohio Low-Level Radioactive Waste Education Program has a goal to provide people with information they want/need to make their own decisions. The program initiated its efforts by conducting a statewide survey to determine information needed by people and where they turned for that information. This presentation reports data from the survey and then explores the program development process in which programs were designed and presented using the information. Pre and post data from the programs reveal attitude and knowledge shifts.

  10. 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)

  11. Drugstore Reading Glasses

    NASA Astrophysics Data System (ADS)

    Erlichson, Herman

    2006-03-01

    The occasion for this paper was my reading of a paper in the February 2005 issue of TPT. As one gets older the near point of the eye begins to recede.2 This is called presbyopia.3 An alternative to purchasing glasses from an optometrist is to purchase an inexpensive pair of reading glasses in a pharmacy. The pharmacy has these glasses ordered by diopters corresponding to the strength of the lens needed for a particular presbyopic eye. The glasses are, of course, not available for myopic eyes.

  12. 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

  13. 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…

  14. SchemaOnRead Manual

    SciTech Connect

    North, Michael J.

    2015-09-30

    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.

  15. Knowledge, its Application, and Attitudes Associated with the Reading of Diverse Genres of Science Texts

    NASA Astrophysics Data System (ADS)

    Gonçalves Nigro, Rogerio; Frateschi Trivelato, Silvia

    2012-11-01

    The purpose of this article is to assess the knowledge, application of knowledge, and attitudes associated with the reading of different genres of expository science texts. We assigned approximately half of a sample consisting of 220 students 14-15 years of age, chosen at random, to read an excerpt from a popular scientific text, and the other half to read an excerpt from a textbook addressing the same topic. Readers took knowledge and application tests immediately after the reading and again 15 days later. Students also took knowledge and reading proficiency pre-tests, and attitude tests related to the selected texts. Overall, girls scored higher than boys and readers of the popular scientific text scored higher than their colleagues who read the textbook excerpt. We noted interaction between 'reader gender' and 'genre of the text read' in terms of long-term learning based on the reading. Attitude regarding the text read appears as an important factor in explaining behavior of boys who read the popular scientific text. Surprisingly, knowledge and application test scores were not statistically different among girls with different degrees of reading proficiency who read the textbook excerpt. In addition, on the application tests, among the boys who read the popular scientific text, good readers scored lower than their colleagues who read the textbook excerpt. In our opinion, this study can serve to show that 'reading in science education' is not a trivial matter and we feel that the subject merits more in-depth investigation.

  16. Parents' reading-related knowledge and children's reading acquisition.

    PubMed

    Ladd, Megan; Martin-Chang, Sandra; Levesque, Kyle

    2011-12-01

    Teacher reading-related knowledge (phonological awareness and phonics knowledge) predicts student reading, however little is known about the reading-related knowledge of parents. Participants comprised 70 dyads (children from kindergarten and grade 1 and their parents). Parents were administered a questionnaire tapping into reading-related knowledge, print exposure, storybook reading, and general cultural knowledge. Children were tested on measures of letter-word knowledge, sound awareness, receptive vocabulary, oral expression, and mathematical skill. Parent reading-related knowledge showed significant positive links with child letter-word knowledge and sound awareness, but showed no correlations with child measures of mathematical skill or vocabulary. Furthermore, parent reading-related knowledge was not associated with parents' own print exposure or cultural knowledge, indicating that knowledge about English word structure may be separate from other cognitive skills. Implications are discussed in terms of improving parent reading-related knowledge to promote child literacy.

  17. A Read-Aloud for Science (Read It Aloud).

    ERIC Educational Resources Information Center

    Richardson, Judy S.; Breen, Margaret

    1996-01-01

    Recommends a young adult read-aloud selection for science classes on endangered species. Describes listening, writing, discussing, investigating, and debating activities capitalizing on this read-aloud. (SR)

  18. The Use of Computer-Automated Reading in Reading Instruction.

    ERIC Educational Resources Information Center

    Leton, Donald A.; Pertz, Dorothy A.

    1984-01-01

    Evaluated the use of computer-automated reading in reading instruction for primary students. Results indicated that compared to controls, students in the experimental group experienced significant achievement gains. The resource role of the school psychologist is also discussed. (JAC)

  19. Reading improvement in English- and Hebrew-speaking children with reading difficulties after reading acceleration training.

    PubMed

    Horowitz-Kraus, Tzipi; Cicchino, Nicole; Amiel, Merav; Holland, Scott K; Breznitz, Zvia

    2014-10-01

    A reading acceleration program known to improve reading fluency in Hebrew-speaking adults was tested for its effect on children. Eighty-nine Hebrew- and English-speaking children with reading difficulties were divided into a waiting list group and two training groups (Hebrew and English) and underwent 4 weeks of reading acceleration training. Results of pre- and post-testing of reading abilities point to a significant main effect of the test, demonstrating improvements in silent contextual reading speed, reading comprehension, and speed of processing in both Hebrew and English training groups as compared to their performance before the intervention. This study indicates that the Reading Acceleration Program might be an effective program for improving reading abilities in children, independent of language.

  20. Reading Knee-Deep

    ERIC Educational Resources Information Center

    Jewett, Pamela

    2007-01-01

    Freire told his audience at a seminar at the University of Massachusetts, "You need to read knee-deep in texts, for deeper than surface meanings, and you need to know the words to be able to do it" (quoted in Cleary, 2003). In a children's literature class, fifteen teachers and I traveled along a path that moved us toward reading…