Sample records for small open reading

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

    USDA-ARS?s Scientific Manuscript database

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

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

    ERIC Educational Resources Information Center

    Langstaff, Nancy

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

  3. Student Perceptions of College Faculty Who Use OER

    ERIC Educational Resources Information Center

    Vojtech, Gabrielle; Grissett, Judy

    2017-01-01

    Research indicates that students find open educational resources (OER) favorable, but there is no research regarding students' perceptions of faculty who use open textbooks. In the present study we examined this topic experimentally with two undergraduate psychology courses at a small public university. Participants read two passages--one about an…

  4. Identification of very small open reading frames in the genomes of Holmes Jungle virus, Ord River virus, and Wongabel virus of the genus Hapavirus, family Rhabdoviridae.

    PubMed

    Gubala, Aneta; Walsh, Susan; McAllister, Jane; Weir, Richard; Davis, Steven; Melville, Lorna; Mitchell, Ian; Bulach, Dieter; Gauci, Penny; Skvortsov, Alex; Boyle, David

    2017-01-01

    Viruses of the family Rhabdoviridae infect a broad range of hosts from a variety of ecological and geographical niches, including vertebrates, arthropods, and plants. The arthropod-transmitted members of this family display considerable genetic diversity and remarkable genomic flexibility that enable coding for various accessory proteins in different locations of the genome. Here, we describe the genome of Holmes Jungle virus, isolated from Culex annulirostris mosquitoes collected in northern Australia, and make detailed comparisons with the closely related Ord River and Wongabel viruses, with a focus on identifying very small open reading frames (smORFs) in their genomes. This is the first systematic prediction of smORFs in rhabdoviruses, emphasising the intricacy of the rhabdovirus genome and the knowledge gaps. We speculate that these smORFs may be of importance to the life cycle of the virus in the arthropod vector.

  5. Co-infection with human polyomavirus BK enhances gene expression and replication of human adenovirus.

    PubMed

    Bil-Lula, Iwona; Woźniak, Mieczysław

    2018-03-26

    Immunocompromised patients are susceptible to multiple viral infections. Relevant interactions between co-infecting viruses might result from viral regulatory genes which trans-activate or repress the expression of host cell genes as well as the genes of any co-infecting virus. The aim of the current study was to show that the replication of human adenovirus 5 is enhanced by co-infection with BK polyomavirus and is associated with increased expression of proteins including early region 4 open reading frame 1 and both the large tumor antigen and small tumor antigen. Clinical samples of whole blood and urine from 156 hematopoietic stem cell transplant recipients were tested. We also inoculated adenocarcinomic human alveolar basal epithelial cells with both human adenovirus 5 and BK polyomavirus to evaluate if co-infection of viruses affected their replication. Data showed that adenovirus load was significantly higher in the plasma (mean 7.5 x 10 3  ± 8.5 x 10 2 copies/ml) and urine (mean 1.9 x 10 3  ± 8.0 x 10 2 copies/ml) of samples from patients with co-infections, in comparison to samples from patients with isolated adenovirus infection. In vitro co-infection led to an increased (8.6 times) expression of the adenovirus early region 4 open reading frame gene 48 hours post-inoculation. The expression of the early region 4 open reading frame gene positively correlated with the expression of BK polyomavirus large tumor antigen (r = 0.90, p < 0.0001) and small tumor antigen (r = 0.83, p < 0.001) genes. The enhanced expression of the early region 4 open reading frame gene due to co-infection with BK polyomavirus was associated with enhanced adenovirus, but not BK polyomavirus, replication. The current study provides evidence that co-infection of adenovirus and BK polyomavirus contributes to enhanced adenovirus replication. Data obtained from this study may have significant importance in the clinical setting.

  6. Identification of very small open reading frames in the genomes of Holmes Jungle virus, Ord River virus, and Wongabel virus of the genus Hapavirus, family Rhabdoviridae

    PubMed Central

    Gubala, Aneta; Walsh, Susan; McAllister, Jane; Weir, Richard; Davis, Steven; Melville, Lorna; Mitchell, Ian; Bulach, Dieter; Gauci, Penny; Skvortsov, Alex; Boyle, David

    2017-01-01

    Viruses of the family Rhabdoviridae infect a broad range of hosts from a variety of ecological and geographical niches, including vertebrates, arthropods, and plants. The arthropod-transmitted members of this family display considerable genetic diversity and remarkable genomic flexibility that enable coding for various accessory proteins in different locations of the genome. Here, we describe the genome of Holmes Jungle virus, isolated from Culex annulirostris mosquitoes collected in northern Australia, and make detailed comparisons with the closely related Ord River and Wongabel viruses, with a focus on identifying very small open reading frames (smORFs) in their genomes. This is the first systematic prediction of smORFs in rhabdoviruses, emphasising the intricacy of the rhabdovirus genome and the knowledge gaps. We speculate that these smORFs may be of importance to the life cycle of the virus in the arthropod vector. PMID:28747815

  7. 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.

  8. ReprDB and panDB: minimalist databases with maximal microbial representation.

    PubMed

    Zhou, Wei; Gay, Nicole; Oh, Julia

    2018-01-18

    Profiling of shotgun metagenomic samples is hindered by a lack of unified microbial reference genome databases that (i) assemble genomic information from all open access microbial genomes, (ii) have relatively small sizes, and (iii) are compatible to various metagenomic read mapping tools. Moreover, computational tools to rapidly compile and update such databases to accommodate the rapid increase in new reference genomes do not exist. As a result, database-guided analyses often fail to profile a substantial fraction of metagenomic shotgun sequencing reads from complex microbiomes. We report pipelines that efficiently traverse all open access microbial genomes and assemble non-redundant genomic information. The pipelines result in two species-resolution microbial reference databases of relatively small sizes: reprDB, which assembles microbial representative or reference genomes, and panDB, for which we developed a novel iterative alignment algorithm to identify and assemble non-redundant genomic regions in multiple sequenced strains. With the databases, we managed to assign taxonomic labels and genome positions to the majority of metagenomic reads from human skin and gut microbiomes, demonstrating a significant improvement over a previous database-guided analysis on the same datasets. reprDB and panDB leverage the rapid increases in the number of open access microbial genomes to more fully profile metagenomic samples. Additionally, the databases exclude redundant sequence information to avoid inflated storage or memory space and indexing or analyzing time. Finally, the novel iterative alignment algorithm significantly increases efficiency in pan-genome identification and can be useful in comparative genomic analyses.

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

    PubMed

    Eren, A Murat; Vineis, Joseph H; Morrison, Hilary G; Sogin, Mitchell L

    2013-01-01

    Consensus between independent reads improves the accuracy of genome and transcriptome analyses, however lack of consensus between very similar sequences in metagenomic studies can and often does represent natural variation of biological significance. The common use of machine-assigned quality scores on next generation platforms does not necessarily correlate with accuracy. Here, we describe using the overlap of paired-end, short sequence reads to identify error-prone reads in marker gene analyses and their contribution to spurious OTUs following clustering analysis using QIIME. Our approach can also reduce error in shotgun sequencing data generated from libraries with small, tightly constrained insert sizes. The open-source implementation of this algorithm in Python programming language with user instructions can be obtained from https://github.com/meren/illumina-utils.

  10. Type 2 NADH Dehydrogenases in the Cyanobacterium Synechocystis sp. Strain PCC 6803 Are Involved in Regulation Rather Than Respiration

    PubMed Central

    Howitt, Crispin A.; Udall, Pacer K.; Vermaas, Wim F. J.

    1999-01-01

    Analysis of the genome of Synechocystis sp. strain PCC 6803 reveals three open reading frames (slr0851, slr1743, and sll1484) that may code for type 2 NAD(P)H dehydrogenases (NDH-2). The sequence similarity between the translated open reading frames and NDH-2s from other organisms is low, generally not exceeding 30% identity. However, NAD(P)H and flavin adenine dinucleotide binding motifs are conserved in all three putative NDH-2s in Synechocystis sp. strain PCC 6803. The three open reading frames were cloned, and deletion constructs were made for each. An expression construct containing one of the three open reading frames, slr1743, was able to functionally complement an Escherichia coli mutant lacking both NDH-1s and NDH-2s. Therefore, slr0851, slr1743, and sll1484 have been designated ndbA, ndbB, and ndbC, respectively. Strains that lacked one or more of the ndb genes were created in wild-type and photosystem (PS) I-less backgrounds. Deletion of ndb genes led to small changes in photoautotrophic growth rates and respiratory activities. Electron transfer rates into the plastoquinone pool in thylakoids in darkness were consistent with the presence of a small amount of NDH-2 activity in thylakoids. No difference was observed between wild-type and the Ndb-less strains in the banding patterns seen on native gels when stained for either NADH or NADPH dehydrogenase activity, indicating that the Ndb proteins do not accumulate to high levels. A striking phenotype of the PS I-less background strains lacking one or more of the NDH-2s is that they were able to grow at high light intensities that were lethal to the control strain but they retained normal PS II activity. We suggest that the Ndb proteins in Synechocystis sp. strain PCC 6803 are redox sensors and that they play a regulatory role responding to the redox state of the plastoquinone pool. PMID:10383967

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

    PubMed

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

    2015-01-01

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

  12. Complete Genome Sequence of the Mesoplasma florum W37 Strain

    PubMed Central

    Baby, Vincent; Matteau, Dominick; Knight, Thomas F.

    2013-01-01

    Mesoplasma florum is a small-genome fast-growing mollicute that is an attractive model for systems and synthetic genomics studies. We report the complete 825,824-bp genome sequence of a second representative of this species, M. florum strain W37, which contains 733 predicted open reading frames and 35 stable RNAs. PMID:24285658

  13. Computational Fluids Domain Reduction to a Simplified Fluid Network

    DTIC Science & Technology

    2012-04-19

    readily available read/ write software library. Code components from the open source projects OpenFoam and Paraview were explored for their adaptability...to the project. Both Paraview and OpenFoam read polyhedral mesh. OpenFoam does not read results data. Paraview actually allows for user “filters

  14. Open Oncology Notes: A Qualitative Study of Oncology Patients' Experiences Reading Their Cancer Care Notes.

    PubMed

    Kayastha, Neha; Pollak, Kathryn I; LeBlanc, Thomas W

    2018-04-01

    Electronic medical records increasingly allow patients access to clinician notes. Although most believe that open notes benefits patients, some suggest negative consequences. Little is known about the experiences of patients with cancer reading their medical notes; thus we aimed to describe this qualitatively. We interviewed 20 adults with metastatic or incurable cancer receiving cancer treatment. The semistructured qualitative interviews included four segments: assessing their overall experience reading notes, discussing how notes affected their cancer care experiences, reading a real note with the interviewer, and making suggestions for improvement. We used a constant comparison approach to analyze these qualitative data. We found four themes. Patients reported that notes resulted in the following: (1) increased comprehension; (2) ameliorated uncertainty, relieved anxiety, and facilitated control; (3) increased trust; and (4) for a subset of patients, increased anxiety. Patients described increased comprehension because notes refreshed their memory and clarified their understanding of visits. This helped mitigate the unfamiliarity of cancer, addressing uncertainty and relieving anxiety. Notes facilitated control, empowering patients to ask clinicians more questions. The transparency of notes also increased trust in clinicians. For a subset of patients, however, notes were emotionally difficult to read and raised concerns. Patients identified medical jargon and repetition in notes as areas for improvement. Most patients thought that reading notes improved their care experiences. A small subset of patients experienced increased distress. As reading notes becomes a routine part of the patient experience, physicians might want to elicit and address concerns that arise from notes, thereby further engaging patients in their care.

  15. Ribosome rearrangements at the onset of translational bypassing

    PubMed Central

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

    2017-01-01

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

  16. Deletion of Marek’s disease virus large subunit of ribonucleotide reductase (RR) impairs virus growth in vitro and in vivo

    USDA-ARS?s Scientific Manuscript database

    Marek’s disease virus (MDV), a highly cell-associated lymphotropic alphaherpesvirus, is the causative agent of a neoplastic disease in domestic chickens, called Marek’s disease (MD). In the unique long region of the MDV genome, open reading frames UL39 and UL40 encode the large and small subunits o...

  17. Marek’s Disease Virus Encoded Ribonucleotide Reductase Large Subunit is not Essential for In Vitro Replication

    USDA-ARS?s Scientific Manuscript database

    Marek’s disease virus (MDV) infected cells express a viral ribonucleotide reductase (RR) that is distinguishable from that present in uninfected cells by monoclonal antibody T81. Open reading frames UL39 and UL40 of the MDV genome encode the large (RR1) and small (RR2) subunits of RR enzyme, respe...

  18. Fiber-optics couple arthroscope to TV

    NASA Technical Reports Server (NTRS)

    Franke, J. M.; Rhodes, D. B.

    1981-01-01

    Convenient, hand-held coupler images output of arthroscope onto coherent fiber bundle. Arthroscope allows surgeons to examine internal organs through any small opening in body. Coupler is also used for engine inspection, instrument repair, and around-corner visual inspection. Image from arthroscope travels along flexible bundle and appears at other cable end where it is recollimated by lens. Image is read from lens or projected on color TV camera.

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

    PubMed Central

    2011-01-01

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

  20. 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

  1. Meter reading for smaller customers in an open-access environment

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

    NONE

    1995-05-01

    As the ability to buy gas and transportation services directly from suppliers becomes available to small commercial and residential customers, local distribution companies (LDCs) are evaluating how to measure and track their consumption. The LDCs often measure the gas use of large commercial and industrial customers with remote, automated meter-reading (AMR) devices, many of which provide real-time data. The utility can justify the expense of installing these devices because of the customers` considerable gas consumption. But for customers who already contribute very little to margins, AMR investments by LDCs are more problematic. The paper discusses some options for remote meteringmore » and forecasts future trends in the industry.« less

  2. 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…

  3. 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…

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

    ERIC Educational Resources Information Center

    What Works Clearinghouse, 2008

    2008-01-01

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

  5. 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…

  6. 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…

  7. The effect of a specialized dyslexia font, OpenDyslexic, on reading rate and accuracy.

    PubMed

    Wery, Jessica J; Diliberto, Jennifer A

    2017-07-01

    A single-subject alternating treatment design was used to investigate the extent to which a specialized dyslexia font, OpenDyslexic, impacted reading rate or accuracy compared to two commonly used fonts when used with elementary students identified as having dyslexia. OpenDyslexic was compared to Arial and Times New Roman in three reading tasks: (a) letter naming, (b) word reading, and (c) nonsense word reading. Data were analyzed through visual analysis and improvement rate difference, a nonparametric measure of nonoverlap for comparing treatments. Results from this alternating treatment experiment show no improvement in reading rate or accuracy for individual students with dyslexia, as well as the group as a whole. While some students commented that the font was "new" or "different", none of the participants reported preferring to read material presented in that font. These results indicate there may be no benefit for translating print materials to this font.

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

    PubMed

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

    2018-05-01

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

  9. [Organization and expression of poliovirus genome].

    PubMed

    Vevcherenko, S G

    1984-01-01

    In the present paper on the basis of analysis of literary data it is postulated that along with the AUG codon at N743 there exists a second initiation codon in the poliovirus RNA (the AUG codon at N586). The translation initiated at N586 can be transferred to the phase of the major reading frame by removing the small hairpin N732-N744 formed near the first initiation site, or by removing the small region N739-N745. In the first case at the boundary between the hypothetical leader peptide encoded by the 5'-terminus of the long, open reading frame of the spliced poliovirus RNA and the capsid protein VP4 must be the Gln-Gly proteolytic cleavage signal, and in the second case--the Tyr-Gly signal. In both cases the leader peptide can be chipped off by the virus specific proteinase. It is supposed that the exon-intronic structure of the poliovirus genome is needed for coordination of translation and transcription during the poliovirus reproduction cycle.

  10. Identification of a Mg2+-sensitive ORF in the 5′-leader of TRPM7 magnesium channel mRNA

    PubMed Central

    Nikonorova, Inna A.; Kornakov, Nikolay V.; Dmitriev, Sergey E.; Vassilenko, Konstantin S.; Ryazanov, Alexey G.

    2014-01-01

    TRPM7 is an essential and ubiquitous channel-kinase regulating cellular influx of Mg2+. Although TRPM7 mRNA is highly abundant, very small amount of the protein is detected in cells, suggesting post-transcriptional regulation of trpm7 gene expression. We found that TRPM7 mRNA 5′-leader contains two evolutionarily conserved upstream open reading frames that act together to drastically inhibit translation of the TRPM7 reading frame at high magnesium levels and ensure its optimal translation at low magnesium levels, when the activity of the channel-kinase is most required. The study provides the first example of magnesium channel synthesis being controlled by Mg2+ in higher eukaryotes. PMID:25326319

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

    PubMed

    Lee, Young Han

    2012-01-01

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

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

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

    Hilberg, G.R.

    1996-08-01

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

  13. Expression, regulation and functional assessment of the 80 amino acid Small Adipocyte Factor 1 (Smaf1) protein in adipocytes.

    PubMed

    Ren, Gang; Eskandari, Parisa; Wang, Siqian; Smas, Cynthia M

    2016-01-15

    The gene for Small Adipocyte Factor 1, Smaf1 (also known as adipogenin, ADIG), encodes a ∼600 base transcript that is highly upregulated during 3T3-L1 in vitro adipogenesis and markedly enriched in adipose tissues. Based on the lack of an obvious open reading frame in the Smaf1 transcript, it is not known if the Smaf1 gene is protein coding or non-coding RNA. Using a peptide from a putative open reading frame of Smaf1 as antigen, we generated antibodies for western analysis. Our studies prove that Smaf1 encodes an adipose-enriched protein which in western blot analysis migrates at ∼10 kDa. Rapid induction of Smaf1 protein occurs during in vitro adipogenesis and its expression in 3T3-L1 adipocytes is positively regulated by insulin and glucose. Moreover, siRNA studies reveal that expression of Smaf1 in adipocytes is wholly dependent on PPARγ. On the other hand, use of siRNA for Smaf1 to nearly abolish its protein expression in adipocytes revealed that Smaf1 does not have a major role in adipocyte triglyceride accumulation, lipolysis or insulin-stimulated pAkt induction. However, immunolocalization studies using HA-tagged Smaf1 reveal enrichment at adipocyte lipid droplets. Together our findings show that Smaf1 is a novel small protein endogenous to adipocytes and that Smaf1 expression is closely tied to PPARγ-mediated signals and the adipocyte phenotype. Copyright © 2015 Elsevier Inc. All rights reserved.

  14. 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

  15. Types of Aphasia

    MedlinePlus

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

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

    ERIC Educational Resources Information Center

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

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

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

    ERIC Educational Resources Information Center

    Finn, Seth

    1997-01-01

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

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

    PubMed

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

    2006-12-01

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

  19. 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. Copyright © 2017 Elsevier Inc. All rights reserved.

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

    PubMed

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

    2014-01-01

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

  1. Publisher's Note: EPL and Open Access Articles

    NASA Astrophysics Data System (ADS)

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

    2008-01-01

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

  2. 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

  3. Feasibility Study of a Precision Cast Loading Machine for Small Ammunition Items

    DTIC Science & Technology

    1975-05-01

    distribution unlimited. READ INStRUCTIONS BEFORE COMPLETING FORM 1. RECIPIENT’S CATALOG NUMBER S. TYRE OF REPORT « PERIOD COVERED S. PCRFORMINO ORO...through a short length rubber hose into the hemisphere. A clamp actuated by an air cylinder can close or open the rubber hose. Because of unknown... rubber hose in the recess on the face of the fixture, exposing opposite hole for observation by the TV monitor through the TV camera. 8. Release table

  4. The Effect of a Specialized Dyslexia Font, Opendyslexic, on Reading Rate and Accuracy

    ERIC Educational Resources Information Center

    Wery, Jessica J.; Diliberto, Jennifer A.

    2017-01-01

    A single-subject alternating treatment design was used to investigate the extent to which a specialized dyslexia font, OpenDyslexic, impacted reading rate or accuracy compared to two commonly used fonts when used with elementary students identified as having dyslexia. OpenDyslexic was compared to Arial and Times New Roman in three reading tasks:…

  5. 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…

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

    PubMed

    Mitchelson, K R

    1996-01-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

    Schaeffer, E; Sninsky, J J

    1984-01-01

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

  9. 76 FR 4659 - Science Advisory Board Staff Office; Notification of a Public Teleconference of the Science...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-26

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

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

    ERIC Educational Resources Information Center

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

    2018-01-01

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

  11. A simplified financial model for automatic meter reading

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

    Ward, S.M.

    1994-01-15

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

  12. Discovery of numerous novel small genes in the intergenic regions of the Escherichia coli O157:H7 Sakai genome

    PubMed Central

    Hücker, Sarah M.; Ardern, Zachary; Goldberg, Tatyana; Schafferhans, Andrea; Bernhofer, Michael; Vestergaard, Gisle; Nelson, Chase W.; Schloter, Michael; Rost, Burkhard; Scherer, Siegfried

    2017-01-01

    In the past, short protein-coding genes were often disregarded by genome annotation pipelines. Transcriptome sequencing (RNAseq) signals outside of annotated genes have usually been interpreted to indicate either ncRNA or pervasive transcription. Therefore, in addition to the transcriptome, the translatome (RIBOseq) of the enteric pathogen Escherichia coli O157:H7 strain Sakai was determined at two optimal growth conditions and a severe stress condition combining low temperature and high osmotic pressure. All intergenic open reading frames potentially encoding a protein of ≥ 30 amino acids were investigated with regard to coverage by transcription and translation signals and their translatability expressed by the ribosomal coverage value. This led to discovery of 465 unique, putative novel genes not yet annotated in this E. coli strain, which are evenly distributed over both DNA strands of the genome. For 255 of the novel genes, annotated homologs in other bacteria were found, and a machine-learning algorithm, trained on small protein-coding E. coli genes, predicted that 89% of these translated open reading frames represent bona fide genes. The remaining 210 putative novel genes without annotated homologs were compared to the 255 novel genes with homologs and to 250 short annotated genes of this E. coli strain. All three groups turned out to be similar with respect to their translatability distribution, fractions of differentially regulated genes, secondary structure composition, and the distribution of evolutionary constraint, suggesting that both novel groups represent legitimate genes. However, the machine-learning algorithm only recognized a small fraction of the 210 genes without annotated homologs. It is possible that these genes represent a novel group of genes, which have unusual features dissimilar to the genes of the machine-learning algorithm training set. PMID:28902868

  13. 39 CFR 3004.12 - Reading room.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

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

  14. Comparison of the Effectiveness and Efficiency of Text Previewing and Preteaching Keywords as Small-Group Reading Comprehension Strategies with Middle-School Students

    ERIC Educational Resources Information Center

    Burns, Matthew K.; Hodgson, Jennifer; Parker, David C.; Fremont, Kathryn

    2011-01-01

    Reading instruction for middle- and high-school students is focused on vocabulary and comprehension, yet research suggests that comprehension skills among these students are alarmingly low. Small-group reading interventions are becoming more prevalent in schools, but there are few studies regarding small-group reading comprehension interventions.…

  15. Human molybdopterin synthase gene: identification of a bicistronic transcript with overlapping reading frames.

    PubMed Central

    Stallmeyer, B; Drugeon, G; Reiss, J; Haenni, A L; Mendel, R R

    1999-01-01

    A universal molybdenum-containing cofactor (MoCo) is essential for the activity of all human molybdoenzymes, including sulphite oxidase. The free cofactor is highly unstable, and all organisms share a similar biosynthetic pathway. The involved enzymes exhibit homologies, even between bacteria and humans. We have exploited these homologies to isolate a cDNA for the heterodimeric molybdopterin (MPT)-synthase. This enzyme is necessary for the conversion of an unstable precursor into molybdopterin, the organic moiety of MoCo. The corresponding transcript shows a bicistronic structure, encoding the small and large subunits of the MPT-synthase in two different open reading frames (ORFs) that overlap by 77 nucleotides. In various human tissues, only one size of mRNA coinciding with the bicistronic transcript was detected. In vitro translation and mutagenesis experiments demonstrated that each ORF is translated independently, leading to the synthesis of a 10-kDa protein and a 21-kDa protein for the small and large subunits, respectively, and indicated that the 3'-proximal ORF of the bicistronic transcript is translated by leaky scanning. PMID:10053003

  16. 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,…

  17. The Status of Exon Skipping as a Therapeutic Approach to Duchenne Muscular Dystrophy

    PubMed Central

    Lu, Qi-Long; Yokota, Toshifumi; Takeda, Shin'ichi; Garcia, Luis; Muntoni, Francesco; Partridge, Terence

    2011-01-01

    Duchenne muscular dystrophy (DMD) is associated with mutations in the dystrophin gene that disrupt the open reading frame whereas the milder Becker's form is associated with mutations which leave an in-frame mRNA transcript that can be translated into a protein that includes the N- and C- terminal functional domains. It has been shown that by excluding specific exons at, or adjacent to, frame-shifting mutations, open reading frame can be restored to an out-of-frame mRNA, leading to the production of a partially functional Becker-like dystrophin protein. Such targeted exclusion can be achieved by administration of oligonucleotides that are complementary to sequences that are crucial to normal splicing of the exon into the transcript. This principle has been validated in mouse and canine models of DMD with a number of variants of oligonucleotide analogue chemistries and by transduction with adeno-associated virus (AAV)-small nuclear RNA (snRNA) reagents encoding the antisense sequence. Two different oligonucleotide agents are now being investigated in human trials for splicing out of exon 51 with some early indications of success at the biochemical level. PMID:20978473

  18. Using Small-Group Instruction to Improve Students' Reading Fluency: An Evaluation of the Existing Research

    ERIC Educational Resources Information Center

    Begeny, John C.; Levy, Rebecca A.; Field, Stacey A.

    2018-01-01

    Reading fluency is necessary for reading comprehension, but approximately 40% of U.S. fourth-grade students have inadequate reading fluency skills. Because small-group (SG) instruction is often used as a first line of intervention for struggling readers, SG instruction targeting deficiencies in text reading fluency ought to be part of every…

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

    NASA Technical Reports Server (NTRS)

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

    2000-01-01

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

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

    PubMed Central

    2014-01-01

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

  1. Involvement of Antizyme Characterized from the Small Abalone Haliotis diversicolor in Gonadal Development.

    PubMed

    Li, Wei-Dong; Huang, Min; Lü, Wen-Gang; Chen, Xiao; Shen, Ming-Hui; Li, Xiang-Min; Wang, Rong-Xia; Ke, Cai-Huan

    2015-01-01

    The small abalone Haliotis diversicolor is an economically important mollusk that is widely cultivated in Southern China. Gonad precocity may affect the aquaculture of small abalone. Polyamines, which are small cationic molecules essential for cellular proliferation, may affect gonadal development. Ornithine decarboxylase (ODC) and antizyme (AZ) are essential elements of a feedback circuit that regulates cellular polyamines. This paper presents the molecular cloning and characterization of AZ from small abalone. Sequence analysis showed that the cDNA sequence of H. diversicolor AZ (HdiODCAZ) consisted of two overlapping open reading frames (ORFs) and conformed to the +1 frameshift property of the frame. Thin Layer chromatography (TLC) analysis suggested that the expressed protein encoded by +1 ORF2 was the functional AZ that targets ODC to 26S proteasome degradation. The result demonstrated that the expression level of AZ was higher than that of ODC in the ovary of small abalone. In addition, the expression profiles of ODC and AZ at the different development stages of the ovary indicated that these two genes might be involved in the gonadal development of small abalone.

  2. Involvement of Antizyme Characterized from the Small Abalone Haliotis diversicolor in Gonadal Development

    PubMed Central

    Lü, Wen-Gang; Chen, Xiao; Shen, Ming-Hui; Li, Xiang-Min; Wang, Rong-Xia; Ke, Cai-Huan

    2015-01-01

    The small abalone Haliotis diversicolor is an economically important mollusk that is widely cultivated in Southern China. Gonad precocity may affect the aquaculture of small abalone. Polyamines, which are small cationic molecules essential for cellular proliferation, may affect gonadal development. Ornithine decarboxylase (ODC) and antizyme (AZ) are essential elements of a feedback circuit that regulates cellular polyamines. This paper presents the molecular cloning and characterization of AZ from small abalone. Sequence analysis showed that the cDNA sequence of H. diversicolor AZ (HdiODCAZ) consisted of two overlapping open reading frames (ORFs) and conformed to the +1 frameshift property of the frame. Thin Layer chromatography (TLC) analysis suggested that the expressed protein encoded by +1 ORF2 was the functional AZ that targets ODC to 26S proteasome degradation. The result demonstrated that the expression level of AZ was higher than that of ODC in the ovary of small abalone. In addition, the expression profiles of ODC and AZ at the different development stages of the ovary indicated that these two genes might be involved in the gonadal development of small abalone. PMID:26313647

  3. Page turning system

    NASA Technical Reports Server (NTRS)

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

    1992-01-01

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

  4. Vampiremania Sparks Developmental Readers (Open to Suggestion).

    ERIC Educational Resources Information Center

    Kaiden, Ellen Beth

    1994-01-01

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

  5. 4 CFR 81.8 - Public reading facility.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

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

  6. 4 CFR 81.8 - Public reading facility.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

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

  7. Mining for Micropeptides.

    PubMed

    Makarewich, Catherine A; Olson, Eric N

    2017-09-01

    Advances in computational biology and large-scale transcriptome analyses have revealed that a much larger portion of the genome is transcribed than was previously recognized, resulting in the production of a diverse population of RNA molecules with both protein-coding and noncoding potential. Emerging evidence indicates that several RNA molecules have been mis-annotated as noncoding and in fact harbor short open reading frames (sORFs) that encode functional peptides and that have evaded detection until now due to their small size. sORF-encoded peptides (SEPs), or micropeptides, have been shown to have important roles in fundamental biological processes and in the maintenance of cellular homeostasis. These small proteins can act independently, for example as ligands or signaling molecules, or they can exert their biological functions by engaging with and modulating larger regulatory proteins. Given their small size, micropeptides may be uniquely suited to fine-tune complex biological systems. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

    ERIC Educational Resources Information Center

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

    2015-01-01

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

  9. Results with Open Court Reading.

    ERIC Educational Resources Information Center

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

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

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

    PubMed

    Büssow, Konrad; Hoffmann, Steve; Sievert, Volker

    2002-12-19

    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. 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. 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.

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

    ERIC Educational Resources Information Center

    Mishra, Sanjaya

    2010-01-01

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

  12. 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…

  13. New meters open new business opportunities for Blue Earth

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

    Mashaw, R.

    1996-07-01

    Competition in the electric utility industry isn`t a concern only for the big boys. Small utilities, too, are giving increasing attention to measures that will improve their competitiveness through paring costs and improving service. Blue Earth, Minn., Light and Water Department, with approximately 2,200 electric meters, is a prime example of a small utility that thinks big. {open_quotes}We conducted a customer survey to determine what our customers want from us in terms of service,{close_quotes} said General Manager Jeffrey Jansen. {open_quotes}To meet those needs we`ve begun to sell a new fiberglass, high-efficiency electric water heater; offer rent or purchase of uninterruptiblemore » power systems to provide back-up for sensitive electronics if an outage occurs; and we`re even selling bottled water. We`re also going to offer budget billing as of August 1, because our customers wanted that option.{close_quotes} Recognizing that providing excellent customer service is only part of the competitiveness equation, Blue Earth has also looked for ways to cut costs. Its latest effort has been the implementation of a new hand-held meter reading system, which Jansen expects to provide substantial savings, and offer opportunities for adding new services in the future.« less

  14. The Plant Peptidome: An Expanding Repertoire of Structural Features and Biological Functions[OPEN

    PubMed Central

    Tavormina, Patrizia; De Coninck, Barbara; Nikonorova, Natalia; De Smet, Ive; Cammue, Bruno P.A.

    2015-01-01

    Peptides fulfill a plethora of functions in plant growth, development, and stress responses. They act as key components of cell-to-cell communication, interfere with signaling and response pathways, or display antimicrobial activity. Strikingly, both the diversity and amount of plant peptides have been largely underestimated. Most characterized plant peptides to date acting as small signaling peptides or antimicrobial peptides are derived from nonfunctional precursor proteins. However, evidence is emerging on peptides derived from a functional protein, directly translated from small open reading frames (without the involvement of a precursor) or even encoded by primary transcripts of microRNAs. These novel types of peptides further add to the complexity of the plant peptidome, even though their number is still limited and functional characterization as well as translational evidence are often controversial. Here, we provide a comprehensive overview of the reported types of plant peptides, including their described functional and structural properties. We propose a novel, unifying peptide classification system to emphasize the enormous diversity in peptide synthesis and consequent complexity of the still expanding knowledge on the plant peptidome. PMID:26276833

  15. Open to Suggestion.

    ERIC Educational Resources Information Center

    Journal of Reading, 1987

    1987-01-01

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

  16. 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.…

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

    ERIC Educational Resources Information Center

    Randall, David

    2016-01-01

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

  18. 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…

  19. 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…

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

    ERIC Educational Resources Information Center

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

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

  1. Micro-Experimental Analysis of the Small-Group Reading Lesson: Social and Cognitive Consequences of Silent Reading.

    ERIC Educational Resources Information Center

    Wilkinson, Ian A. G.; Anderson, Richard C.

    This study examined a social-organizational hypothesis that explains how silent reading in small-group lessons might influence students' learning. One hundred children in four third-grade classes, each divided into three ability groups, received two silent and two oral reading lessons. Group dynamics were measured from videotapes of the lessons.…

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

    Code of Federal Regulations, 2011 CFR

    2011-04-01

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

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

    Code of Federal Regulations, 2014 CFR

    2014-04-01

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

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

    Code of Federal Regulations, 2013 CFR

    2013-04-01

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

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

    Code of Federal Regulations, 2012 CFR

    2012-04-01

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

  6. Identification of a non-LTR retrotransposon from the gypsy moth

    Treesearch

    K.J. Garner; J.M. Slavicek

    1999-01-01

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

  7. 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…

  8. U.S. Global Change Research Program

    MedlinePlus

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

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

    PubMed Central

    2013-01-01

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

  10. Readings and Experiences of Multimodality

    ERIC Educational Resources Information Center

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

    2017-01-01

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

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

    PubMed

    Fischer, Thomas; Riedl, Rainer

    2017-04-01

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

  12. Assembly of cucumber (Cucumis sativus L.) somaclones

    NASA Astrophysics Data System (ADS)

    Skarzyńska, Agnieszka; Kuśmirek, Wiktor; Pawełkowicz, Magdalena; PlÄ der, Wojciech; Nowak, Robert M.

    2017-08-01

    The development of next generation sequencing opens the possibility of using sequencing in various plant studies, such as finding structural changes and small polymorphisms between species and within them. Most analyzes rely on genomic sequences and it is crucial to use well-assembled genomes of high quality and completeness. Herein we compare commonly available programs for genomic assembling and newly developed software - dnaasm. Assemblies were tested on cucumber (Cucumis sativus L.) lines obtained by in vitro regeneration (somaclones), showing different phenotypes. Obtained results shows that dnaasm assembler is a good tool for short read assembly, which allows obtaining genomes of high quality and completeness.

  13. Defense Threat Reduction Agency > Research > DTRIAC > FAQ Sheet

    Science.gov Websites

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

  14. Sacred Cows That Should Be Put to Pasture.

    ERIC Educational Resources Information Center

    Artley, A. Sterl

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

  15. 78 FR 21120 - Registration Review; Pesticide Dockets Opened for Review and Comment and Other Docket Acts...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-09

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

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

    DTIC Science & Technology

    2008-06-01

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

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

    DTIC Science & Technology

    2007-06-01

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

  18. 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:27788207

  19. Children's Literature in the Basals.

    ERIC Educational Resources Information Center

    O'Brien, Maureen A.

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

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

    ERIC Educational Resources Information Center

    McShane, Susan

    2005-01-01

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

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

    PubMed Central

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

    1989-01-01

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

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

    PubMed

    Ustav, M; Stenlund, A

    1991-02-01

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

  3. Motivating Remedial Readers (Open to Suggestion).

    ERIC Educational Resources Information Center

    Glowacki, Joan

    1990-01-01

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

  4. Analysis of the Mitochondrial Genome in Hypomyces aurantius Reveals a Novel Twintron Complex in Fungi.

    PubMed

    Deng, Youjin; Zhang, Qihui; Ming, Ray; Lin, Longji; Lin, Xiangzhi; Lin, Yiying; Li, Xiao; Xie, Baogui; Wen, Zhiqiang

    2016-06-30

    Hypomyces aurantius is a mycoparasite that causes cobweb disease, a most serious disease of cultivated mushrooms. Intra-species identification is vital for disease control, however the lack of genomic data makes development of molecular markers challenging. Small size, high copy number, and high mutation rate of fungal mitochondrial genome makes it a good candidate for intra and inter species differentiation. In this study, the mitochondrial genome of H. H.a0001 was determined from genomic DNA using Illumina sequencing. The roughly 72 kb genome shows all major features found in other Hypocreales: 14 common protein genes, large and small subunit rRNAs genes and 27 tRNAs genes. Gene arrangement comparison showed conserved gene orders in Hypocreales mitochondria are relatively conserved, with the exception of Acremonium chrysogenum and Acremonium implicatum. Mitochondrial genome comparison also revealed that intron length primarily contributes to mitogenome size variation. Seventeen introns were detected in six conserved genes: five in cox1, four in rnl, three in cob, two each in atp6 and cox3, and one in cox2. Four introns were found to contain two introns or open reading frames: cox3-i2 is a twintron containing two group IA type introns; cox2-i1 is a group IB intron encoding two homing endonucleases; and cox1-i4 and cox1-i3 both contain two open reading frame (ORFs). Analyses combining secondary intronic structures, insertion sites, and similarities of homing endonuclease genes reveal two group IA introns arranged side by side within cox3-i2. Mitochondrial data for H. aurantius provides the basis for further studies relating to population genetics and species identification.

  5. Analysis of the Mitochondrial Genome in Hypomyces aurantius Reveals a Novel Twintron Complex in Fungi

    PubMed Central

    Deng, Youjin; Zhang, Qihui; Ming, Ray; Lin, Longji; Lin, Xiangzhi; Lin, Yiying; Li, Xiao; Xie, Baogui; Wen, Zhiqiang

    2016-01-01

    Hypomyces aurantius is a mycoparasite that causes cobweb disease, a most serious disease of cultivated mushrooms. Intra-species identification is vital for disease control, however the lack of genomic data makes development of molecular markers challenging. Small size, high copy number, and high mutation rate of fungal mitochondrial genome makes it a good candidate for intra and inter species differentiation. In this study, the mitochondrial genome of H. H.a0001 was determined from genomic DNA using Illumina sequencing. The roughly 72 kb genome shows all major features found in other Hypocreales: 14 common protein genes, large and small subunit rRNAs genes and 27 tRNAs genes. Gene arrangement comparison showed conserved gene orders in Hypocreales mitochondria are relatively conserved, with the exception of Acremonium chrysogenum and Acremonium implicatum. Mitochondrial genome comparison also revealed that intron length primarily contributes to mitogenome size variation. Seventeen introns were detected in six conserved genes: five in cox1, four in rnl, three in cob, two each in atp6 and cox3, and one in cox2. Four introns were found to contain two introns or open reading frames: cox3-i2 is a twintron containing two group IA type introns; cox2-i1 is a group IB intron encoding two homing endonucleases; and cox1-i4 and cox1-i3 both contain two open reading frame (ORFs). Analyses combining secondary intronic structures, insertion sites, and similarities of homing endonuclease genes reveal two group IA introns arranged side by side within cox3-i2. Mitochondrial data for H. aurantius provides the basis for further studies relating to population genetics and species identification. PMID:27376282

  6. 13 CFR 107.40 - How to read this part 107.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 13 Business Credit and Assistance 1 2010-01-01 2010-01-01 false How to read this part 107. 107.40 Section 107.40 Business Credit and Assistance SMALL BUSINESS ADMINISTRATION SMALL BUSINESS INVESTMENT COMPANIES Introduction to Part 107 § 107.40 How to read this part 107. (a) Center Headings. All references...

  7. The Effect of Light Level and Small Pupils on Presbyopic Reading Performance.

    PubMed

    Xu, Renfeng; Gil, Daniel; Dibas, Mohammed; Hare, William; Bradley, Arthur

    2016-10-01

    To examine the impact of small pupils and light levels on reading performance of distance-corrected presbyopes. To determine whether small pupils would enable presbyopes to read at near even at low light levels. To establish the lower range of text luminances, we quantified the space-averaged luminance of text in nine different artificially lit interior environments, and examined the impact of the text characters on space-averaged luminance of electronic and printed displays. Distance and near reading speeds of 20 presbyopes (ages 40-60 years) were measured while viewing through artificial pupils (diameters 1-4.5 mm), natural pupils, or with a multifocal contact lens. Space-averaged text luminance levels varied from 0.14 to 140 cd/m2 (including the range of measured environmental text luminances). Adding black text to a white computer display or paper reduces luminance by approximately 15% to 31%, and the lowest encountered environmental text luminance was approximately 2 to 3 cd/m2. For both distance and near reading performance, the 2- to 3-mm small pupil yielded the best overall reading acuity for space-averaged text light levels ≥ 2 cd/m2. The 2- to 3-mm artificial pupils and the multifocal contact lenses both enabled maximum or near-maximum reading speeds for 0.5 logMAR characters at distance and near, but with natural pupils, reading speeds were significantly reduced at near. Although photon noise at low luminance reduces the visual benefits of small pupils, the benefits of 2- to 3-mm artificial pupils are sufficient to enable >80% of distance-corrected presbyopes to read proficiently at near, even at the lowest text luminances found in interior environments.

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

    ERIC Educational Resources Information Center

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

    2014-01-01

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

  9. 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…

  10. Global shape mimicry of tRNA within a viral internal ribosome entry site mediates translational reading frame selection

    PubMed Central

    Au, Hilda H.; Cornilescu, Gabriel; Mouzakis, Kathryn D.; Ren, Qian; Burke, Jordan E.; Lee, Seonghoon; Butcher, Samuel E.; Jan, Eric

    2015-01-01

    The dicistrovirus intergenic region internal ribosome entry site (IRES) adopts a triple-pseudoknotted RNA structure and occupies the core ribosomal E, P, and A sites to directly recruit the ribosome and initiate translation at a non-AUG codon. A subset of dicistrovirus IRESs directs translation in the 0 and +1 frames to produce the viral structural proteins and a +1 overlapping open reading frame called ORFx, respectively. Here we show that specific mutations of two unpaired adenosines located at the core of the three-helical junction of the honey bee dicistrovirus Israeli acute paralysis virus (IAPV) IRES PKI domain can uncouple 0 and +1 frame translation, suggesting that the structure adopts distinct conformations that contribute to 0 or +1 frame translation. Using a reconstituted translation system, we show that ribosomes assembled on mutant IRESs that direct exclusive 0 or +1 frame translation lack reading frame fidelity. Finally, a nuclear magnetic resonance/small-angle X-ray scattering hybrid approach reveals that the PKI domain of the IAPV IRES adopts an RNA structure that resembles a complete tRNA. The tRNA shape-mimicry enables the viral IRES to gain access to the ribosome tRNA-binding sites and form intermolecular contacts with the ribosome that are necessary for initiating IRES translation in a specific reading frame. PMID:26554019

  11. The Development of Wireless Body Area Network for Motion Sensing Application

    NASA Astrophysics Data System (ADS)

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

    2018-04-01

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

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

    PubMed Central

    Ustav, M; Stenlund, A

    1991-01-01

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

  13. A Description of Contrasting Discourse Patterns Used in Differentiated Reading Instruction

    ERIC Educational Resources Information Center

    Ankrum, Julie; Genest, Maria; Morewood, Aimee

    2017-01-01

    The purpose of this article is to provide a description of contrasting discourse patterns during small-group reading instruction. The authors report on case studies conducted in two 1st-grade classrooms in different school districts in Pennsylvania. Small-group reading instruction was observed over the course of one year in each classroom, and…

  14. Helping Low-Achieving First-Grade Readers: A Program Combining Reading Recovery Tutoring and Small-Group Instruction.

    ERIC Educational Resources Information Center

    Dorn, Linda; Allen, Anne

    1995-01-01

    Evaluates an approach that supplemented existing Reading Recovery programs with small-group, early literacy instruction in 28 Arkansas public schools. The program enabled many children to receive timely support. When space became available in Reading Recovery, these children made accelerated progress and were discontinued earlier than children who…

  15. The Effect of Guided Reading Instruction on Reading Achievement

    ERIC Educational Resources Information Center

    Underwood, Vanda Lea

    2010-01-01

    Although reading achievement correlates highly with a student's ability to do well in school, not all children achieve in reading. The purpose of this mixed-method study was to investigate whether reading instruction provided in small groups at the child's own reading level, known as "guided reading instruction," would result in…

  16. Effects of Different Text Display Types on Reading Comprehension, Sustained Attention and Cognitive Load in Mobile Reading Contexts

    ERIC Educational Resources Information Center

    Chen, Chih-Ming; Lin, Yu-Ju

    2016-01-01

    Despite the popularity of mobile reading devices, many studies have indicated that small screens restrict information transmission, adversely affecting reading performance on mobile devices. Moreover, mobile reading typically occurs in different reading contexts. Therefore, suitable text display type for mobile reading in different reading…

  17. Keeping It Simple: The Case for E-Mail.

    ERIC Educational Resources Information Center

    Haimovic, Gila

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

  18. Viewing Reading Recovery as a Restructuring Phenomenon

    ERIC Educational Resources Information Center

    Rinehart, James S.; Short, Paula Myrick

    2010-01-01

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

  19. 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…

  20. Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins

    PubMed Central

    Delcourt, Vivian; Lucier, Jean-François; Gagnon, Jules; Beaudoin, Maxime C; Vanderperre, Benoît; Breton, Marc-André; Motard, Julie; Jacques, Jean-François; Brunelle, Mylène; Gagnon-Arsenault, Isabelle; Fournier, Isabelle; Ouangraoua, Aida; Hunting, Darel J; Cohen, Alan A; Landry, Christian R; Scott, Michelle S

    2017-01-01

    Recent functional, proteomic and ribosome profiling studies in eukaryotes have concurrently demonstrated the translation of alternative open-reading frames (altORFs) in addition to annotated protein coding sequences (CDSs). We show that a large number of small proteins could in fact be coded by these altORFs. The putative alternative proteins translated from altORFs have orthologs in many species and contain functional domains. Evolutionary analyses indicate that altORFs often show more extreme conservation patterns than their CDSs. Thousands of alternative proteins are detected in proteomic datasets by reanalysis using a database containing predicted alternative proteins. This is illustrated with specific examples, including altMiD51, a 70 amino acid mitochondrial fission-promoting protein encoded in MiD51/Mief1/SMCR7L, a gene encoding an annotated protein promoting mitochondrial fission. Our results suggest that many genes are multicoding genes and code for a large protein and one or several small proteins. PMID:29083303

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

    PubMed

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

    2013-09-01

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

  2. Exploring Reading with a Small Group of Fourth Grade Readers and Their Teachers through Collaborative Retrospective Miscue Analysis

    ERIC Educational Resources Information Center

    Poock, William Henry

    2017-01-01

    Literacy educators hold different beliefs about the best approaches to teach students how to read and about the reading process including a skills view of reading and learning to read versus a transactional, sociopsycholinguistic view of reading and learning to read (Weaver, 2002). Reading for understanding is an important skill to develop in…

  3. Functions and impact of tal-like genes in animals with regard to applied aspects.

    PubMed

    Zhu, Min; Hu, Xiaolong; Cao, Guangli; Xue, Renyu; Gong, Chengliang

    2018-06-16

    A large number of DNAs in eukaryote genomes can code for atypical transcripts, and their functions are controversial. It has been reported that the transcripts contain many small open reading frames (sORFs), which were originally considered as non-translatable RNAs. However, increasing evidence has suggested that some of these sORFs can encode for small peptides and some are conserved across large evolutionary distances. It has been reported that the small peptides have functions and may be involved in varieties of cellular processes, playing important roles in development, physiology, and metabolism. Among the sORFs, studies of the non-canonical gene polished rice/tarsal-less (pri/tal) in Drosophila and mille-pattes(mlpt) in Tribolium have been more thoroughly studied. The genes similar to pri/tal in other species have been defined as the tarsal-less-related gene family, tal-like gene. In this review, we described recent progress in the discovery and functional characterization of the small peptides encoded by the tal-like gene and their possible functional potentials.

  4. Multicenter prospective evaluation of the express view reading mode for small-bowel capsule endoscopy studies.

    PubMed

    Saurin, Jean-Christophe; Jacob, Philippe; Heyries, Laurent; Pesanti, Christian; Cholet, Franck; Fassler, Isaac; Boulant, James; Bramli, Slim; De Leusse, Antoin; Rahmi, Gabriel

    2018-05-01

     Reducing the reading time of capsule endoscopy films is of high priority for gastroenterologists. We report a prospective multicenter evaluation of an "express view" reading mode (Intromedic capsule system).  Eighty-three patients with obscure gastrointestinal bleeding were prospectively included in 10 centers. All patients underwent small-bowel capsule endoscopy (Intromedic, Seoul, Republic of Korea). Films were read in standard mode, then a second reading was performed in express view mode at a second center. For each lesion, the precise location, nature, and relevance were collected. A consensus reading and review were done by three experts, and considered to be the gold standard.  The mean reading time of capsule films was 39.7 minutes (11 - 180 minutes) and 19.7 minutes (4 - 40 minutes) by standard and express view mode, respectively ( P  < 1 × 10  - 4 ). The consensus review identified a significant lesion in 44/83 patients (53.0 %). Standard reading and express view reading had a 93.3 % and 82.2 % sensitivity, respectively (NS). Consensus review identified 70 significant images from which standard reading and express view reading detected 58 (82.9 %) and 55 (78.6 %), respectively. The informatics algorithm detected 66/70 images (94.3 %) thus missing four small-bowel angiodysplasia.  The express view algorithm allows an important shortening of Intromedic capsule film reading time with a high sensitivity.

  5. Evidence for the recent origin of a bacterial protein-coding, overlapping orphan gene by evolutionary overprinting.

    PubMed

    Fellner, Lea; Simon, Svenja; Scherling, Christian; Witting, Michael; Schober, Steffen; Polte, Christine; Schmitt-Kopplin, Philippe; Keim, Daniel A; Scherer, Siegfried; Neuhaus, Klaus

    2015-12-18

    Gene duplication is believed to be the classical way to form novel genes, but overprinting may be an important alternative. Overprinting allows entirely novel proteins to evolve de novo, i.e., formerly non-coding open reading frames within functional genes become expressed. Only three cases have been described for Escherichia coli. Here, a fourth example is presented. RNA sequencing revealed an open reading frame weakly transcribed in cow dung, coding for 101 residues and embedded completely in the -2 reading frame of citC in enterohemorrhagic E. coli. This gene is designated novel overlapping gene, nog1. The promoter region fused to gfp exhibits specific activities and 5' rapid amplification of cDNA ends indicated the transcriptional start 40-bp upstream of the start codon. nog1 was strand-specifically arrested in translation by a nonsense mutation silent in citC. This Nog1-mutant showed a phenotype in competitive growth against wild type in the presence of MgCl2. Small differences in metabolite concentrations were also found. Bioinformatic analyses propose Nog1 to be inner membrane-bound and to possess at least one membrane-spanning domain. A phylogenetic analysis suggests that the orphan gene nog1 arose by overprinting after Escherichia/Shigella separated from the other γ-proteobacteria. Since nog1 is of recent origin, non-essential, short, weakly expressed and only marginally involved in E. coli's central metabolism, we propose that this gene is in an initial stage of evolution. While we present specific experimental evidence for the existence of a fourth overlapping gene in enterohemorrhagic E. coli, we believe that this may be an initial finding only and overlapping genes in bacteria may be more common than is currently assumed by microbiologists.

  6. 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)

  7. Small Schools Reading Curriculum, 7-8: Reading, Language Arts, Mathematics, Science, Social Studies. Scope, Objectives, Activities, Resources, Monitoring Procedures.

    ERIC Educational Resources Information Center

    Hartl, David, Ed.; And Others

    Designed to assist teachers in small schools with the improvement of curriculum and instruction and to help smaller districts which do not have curriculum personnel to comply with Washington's Student Learning Objectives (SLO) Law, this guide contains reading curriculum materials for grades 7 and 8. The objectives listed are correlated to the…

  8. Small Schools Reading Curriculum, 4-6: Reading, Language Arts, Mathematics, Science, Social Studies. Scope, Objectives, Activities, Resources, Monitoring Procedures.

    ERIC Educational Resources Information Center

    Hartl, David, Ed.; And Others

    Designed to assist teachers in small schools with the improvement of curriculum and instruction and to help smaller districts which do not have curriculum personnel to comply with Washington's Student Learning Objectives (SLO) Law, this guide contains reading curriculum materials for grades 4-6. The objectives listed are correlated to the Goals…

  9. Small Schools Reading Curriculum, K-3: Reading, Language Arts, Mathematics, Science, Social Studies. Scope, Objectives, Activities, Resources, Monitoring Procedures.

    ERIC Educational Resources Information Center

    Hartl, David, Ed.; And Others

    Designed to assist teachers in small schools with the improvement of curriculum and instruction and to help smaller districts which do not have curriculum personnel to comply with Washington's Student Learning Objectives (SLO) Law, this guide contains reading curriculum materials for grades K-3. The objectives listed are correlated to the Goals…

  10. libgapmis: extending short-read alignments

    PubMed Central

    2013-01-01

    Background A wide variety of short-read alignment programmes have been published recently to tackle the problem of mapping millions of short reads to a reference genome, focusing on different aspects of the procedure such as time and memory efficiency, sensitivity, and accuracy. These tools allow for a small number of mismatches in the alignment; however, their ability to allow for gaps varies greatly, with many performing poorly or not allowing them at all. The seed-and-extend strategy is applied in most short-read alignment programmes. After aligning a substring of the reference sequence against the high-quality prefix of a short read--the seed--an important problem is to find the best possible alignment between a substring of the reference sequence succeeding and the remaining suffix of low quality of the read--extend. The fact that the reads are rather short and that the gap occurrence frequency observed in various studies is rather low suggest that aligning (parts of) those reads with a single gap is in fact desirable. Results In this article, we present libgapmis, a library for extending pairwise short-read alignments. Apart from the standard CPU version, it includes ultrafast SSE- and GPU-based implementations. libgapmis is based on an algorithm computing a modified version of the traditional dynamic-programming matrix for sequence alignment. Extensive experimental results demonstrate that the functions of the CPU version provided in this library accelerate the computations by a factor of 20 compared to other programmes. The analogous SSE- and GPU-based implementations accelerate the computations by a factor of 6 and 11, respectively, compared to the CPU version. The library also provides the user the flexibility to split the read into fragments, based on the observed gap occurrence frequency and the length of the read, thereby allowing for a variable, but bounded, number of gaps in the alignment. Conclusions We present libgapmis, a library for extending pairwise short-read alignments. We show that libgapmis is better-suited and more efficient than existing algorithms for this task. The importance of our contribution is underlined by the fact that the provided functions may be seamlessly integrated into any short-read alignment pipeline. The open-source code of libgapmis is available at http://www.exelixis-lab.org/gapmis. PMID:24564250

  11. Frozen shoulder

    MedlinePlus

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

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

    ERIC Educational Resources Information Center

    National Council of Teachers of English, Champaign, IL.

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

  13. Reading Quizzes Improve Exam Scores for Community College Students

    ERIC Educational Resources Information Center

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

    2018-01-01

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

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

    PubMed Central

    Sugita, Mamoru; Shinozaki, Kazuo; Sugiura, Masahiro

    1985-01-01

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

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

    PubMed

    Sugita, M; Shinozaki, K; Sugiura, M

    1985-06-01

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

  16. Combination of Bottom-up 2D-LC-MS and Semi-top-down GelFree-LC-MS Enhances Coverage of Proteome and Low Molecular Weight Short Open Reading Frame Encoded Peptides of the Archaeon Methanosarcina mazei.

    PubMed

    Cassidy, Liam; Prasse, Daniela; Linke, Dennis; Schmitz, Ruth A; Tholey, Andreas

    2016-10-07

    The recent discovery of an increasing number of small open reading frames (sORF) creates the need for suitable analytical technologies for the comprehensive identification of the corresponding gene products. For biological and functional studies the knowledge of the entire set of proteins and sORF gene products is essential. Consequently in the present study we evaluated analytical approaches that will allow for simultaneous analysis of widest parts of the proteome together with the predicted sORF. We performed a full proteome analysis of the methane producing archaeon Methanosarcina mazei strain Gö1 cytosolic proteome using a high/low pH reversed phase LC-MS bottom-up approach. The second analytical approach was based on semi-top-down strategy, encompassing a separation at intact protein level using a GelFree system, followed by digestion and LC-MS analysis. A high overlap in identified proteins was found for both approaches yielding the most comprehensive coverage of the cytosolic proteome of this organism achieved so far. The application of the second approach in combination with an adjustment of the search criteria for database searches further led to a significant increase of sORF peptide identifications, finally allowing to detect and identify 28 sORF gene products.

  17. Identification, Characterization and Full-Length Sequence Analysis of a Novel Polerovirus Associated with Wheat Leaf Yellowing Disease

    PubMed Central

    Zhang, Peipei; Liu, Yan; Liu, Wenwen; Cao, Mengji; Massart, Sebastien; Wang, Xifeng

    2017-01-01

    To identify the pathogens responsible for leaf yellowing symptoms on wheat samples collected from Jinan, China, we tested for the presence of three known barley/wheat yellow dwarf viruses (BYDV-GAV, -PAV, WYDV-GPV) (most likely pathogens) using RT-PCR. A sample that tested negative for the three viruses was selected for small RNA sequencing. Twenty-five million sequences were generated, among which 5% were of viral origin. A novel polerovirus was discovered and temporarily named wheat leaf yellowing-associated virus (WLYaV). The full genome of WLYaV corresponds to 5,772 nucleotides (nt), with six AUG-initiated open reading frames, one non-AUG-initiated open reading frame, and three untranslated regions, showing typical features of the family Luteoviridae. Sequence comparison and phylogenetic analyses suggested that WLYaV had the closest relationship with sugarcane yellow leaf virus (ScYLV), but the identities of full genomic nucleotides and deduced amino acid sequence of coat protein (CP) were 64.9 and 86.2%, respectively, below the species demarcation thresholds (90%) in the family Luteoviridae. Furthermore, agroinoculation of Nicotiana benthamiana leaves with a cDNA clone of WLYaV caused yellowing symptoms on the plant. Our study adds a new polerovirus that is associated with wheat leaf yellowing disease, which would help to identify and control pathogens of wheat. PMID:28932215

  18. Identification, Characterization and Full-Length Sequence Analysis of a Novel Polerovirus Associated with Wheat Leaf Yellowing Disease.

    PubMed

    Zhang, Peipei; Liu, Yan; Liu, Wenwen; Cao, Mengji; Massart, Sebastien; Wang, Xifeng

    2017-01-01

    To identify the pathogens responsible for leaf yellowing symptoms on wheat samples collected from Jinan, China, we tested for the presence of three known barley/wheat yellow dwarf viruses (BYDV-GAV, -PAV, WYDV-GPV) (most likely pathogens) using RT-PCR. A sample that tested negative for the three viruses was selected for small RNA sequencing. Twenty-five million sequences were generated, among which 5% were of viral origin. A novel polerovirus was discovered and temporarily named wheat leaf yellowing-associated virus (WLYaV). The full genome of WLYaV corresponds to 5,772 nucleotides (nt), with six AUG-initiated open reading frames, one non-AUG-initiated open reading frame, and three untranslated regions, showing typical features of the family Luteoviridae . Sequence comparison and phylogenetic analyses suggested that WLYaV had the closest relationship with sugarcane yellow leaf virus (ScYLV), but the identities of full genomic nucleotides and deduced amino acid sequence of coat protein (CP) were 64.9 and 86.2%, respectively, below the species demarcation thresholds (90%) in the family Luteoviridae . Furthermore, agroinoculation of Nicotiana benthamiana leaves with a cDNA clone of WLYaV caused yellowing symptoms on the plant. Our study adds a new polerovirus that is associated with wheat leaf yellowing disease, which would help to identify and control pathogens of wheat.

  19. Reduction of CMOS Image Sensor Read Noise to Enable Photon Counting.

    PubMed

    Guidash, Michael; Ma, Jiaju; Vogelsang, Thomas; Endsley, Jay

    2016-04-09

    Recent activity in photon counting CMOS image sensors (CIS) has been directed to reduction of read noise. Many approaches and methods have been reported. This work is focused on providing sub 1 e(-) read noise by design and operation of the binary and small signal readout of photon counting CIS. Compensation of transfer gate feed-through was used to provide substantially reduced CDS time and source follower (SF) bandwidth. SF read noise was reduced by a factor of 3 with this method. This method can be applied broadly to CIS devices to reduce the read noise for small signals to enable use as a photon counting sensor.

  20. Multiperspective smFRET reveals rate-determining late intermediates of ribosomal translocation.

    PubMed

    Wasserman, Michael R; Alejo, Jose L; Altman, Roger B; Blanchard, Scott C

    2016-04-01

    Directional translocation of the ribosome through the mRNA open reading frame is a critical determinant of translational fidelity. This process entails a complex interplay of large-scale conformational changes within the actively translating particle, which together coordinate the movement of tRNA and mRNA substrates with respect to the large and small ribosomal subunits. Using pre-steady state, single-molecule fluorescence resonance energy transfer imaging, we tracked the nature and timing of these conformational events within the Escherichia coli ribosome from five structural perspectives. Our investigations revealed direct evidence of structurally and kinetically distinct late intermediates during substrate movement, whose resolution determines the rate of translocation. These steps involve intramolecular events within the EF-G-GDP-bound ribosome, including exaggerated, reversible fluctuations of the small-subunit head domain, which ultimately facilitate peptidyl-tRNA's movement into its final post-translocation position.

  1. Multi-perspective smFRET reveals rate-determining late intermediates of ribosomal translocation

    PubMed Central

    Wasserman, Michael R.; Alejo, Jose L.; Altman, Roger B.; Blanchard, Scott C.

    2016-01-01

    Directional translocation of the ribosome through the messenger RNA open reading frame is a critical determinant of translational fidelity. This process entails a complex interplay of large-scale conformational changes within the actively translating particle, which together coordinate the movement of transfer and messenger RNA substrates with respect to the large and small ribosomal subunits. Using pre-steady state, single-molecule fluorescence resonance energy transfer imaging, we have tracked the nature and timing of these conformational events within the Escherichia coli ribosome from five structural perspectives. Our investigations reveal direct evidence of structurally and kinetically distinct, late intermediates during substrate movement, whose resolution is rate-determining to the translocation mechanism. These steps involve intra-molecular events within the EFG(GDP)-bound ribosome, including exaggerated, reversible fluctuations of the small subunit head domain, which ultimately facilitate peptidyl-tRNA’s movement into its final post-translocation position. PMID:26926435

  2. Decoding sORF translation - from small proteins to gene regulation.

    PubMed

    Cabrera-Quio, Luis Enrique; Herberg, Sarah; Pauli, Andrea

    2016-11-01

    Translation is best known as the fundamental mechanism by which the ribosome converts a sequence of nucleotides into a string of amino acids. Extensive research over many years has elucidated the key principles of translation, and the majority of translated regions were thought to be known. The recent discovery of wide-spread translation outside of annotated protein-coding open reading frames (ORFs) came therefore as a surprise, raising the intriguing possibility that these newly discovered translated regions might have unrecognized protein-coding or gene-regulatory functions. Here, we highlight recent findings that provide evidence that some of these newly discovered translated short ORFs (sORFs) encode functional, previously missed small proteins, while others have regulatory roles. Based on known examples we will also speculate about putative additional roles and the potentially much wider impact that these translated regions might have on cellular homeostasis and gene regulation.

  3. Read 180®. What Works Clearinghouse Intervention Report

    ERIC Educational Resources Information Center

    What Works Clearinghouse, 2016

    2016-01-01

    "READ 180®" is a reading program designed for struggling readers who are reading 2 or more years below grade level. It combines online and direct instruction, student assessment, and teacher professional development. "READ 180®" is delivered in 90-minute sessions that include whole-group instruction, three small-group…

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

    USDA-ARS?s Scientific Manuscript database

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

  5. UK Naval Dockyards Asbestosis Study: radiological methods in the surveillance of workers exposed to asbestos

    PubMed Central

    Sheers, G.; Rossiter, C. E.; Gilson, J. C.; Mackenzie, F. A. F.

    1978-01-01

    ABSTRACT In a survey of the effects of exposure to asbestos in the UK Naval Dockyards, small- and large-film chest radiographs of 674 men have been examined. These films have been read under survey conditions by two readers using a simple screening classification, and also in a controlled trial by five readers using the full ILO U/C classification. Comparison between the reading methods showed a deficiency, independent of the size of film, of at least 30% in the detection of asbestos-related radiographic abnormalities when the screening classification was used. For adequate diagnostic sensitivity the ILO U/C classification appears to be essential. There was a deficiency of 43% in significant abnormalities observed by a majority of readers in the small films when directly compared with large film readings. This deficiency could be reduced to 7% by using readings of the small films at any level of abnormality by any of the five readers. When the ILO U/C readings were related to the clinical diagnoses, the only abnormality missed was a small pleural plaque. Films with previously agreed coding were inserted at intervals during the reading trial and helped to maintain the consistency of reading. Right oblique views were taken for 1884 men, in addition to the full-sized postero-anterior view, but the contribution provided by this view proved insufficient to justify its use in large surveys. The cost of a survey when small films are used as a screening method is reduced to between one-third and one-half of the cost when large films are used, assuming that the abnormality rate is not more than 5%. However, this cost advantage for small films is likely to be overtaken by the development of automatic large-film units. The radiation dose when small films are used is increased by a factor of about 20, but is within the prescribed safety level. It is concluded that at least three readers should be involved, using the full ILO U/C classification. Small films may be of particular use in a large-scale survey, in which the abnormality rate is expected to be low, and which might otherwise be too expensive. A sensitive reading method and a high standard of film quality are essential factors in the use of this technique. PMID:698132

  6. 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…

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

    ERIC Educational Resources Information Center

    Twenge-Jinings, Fidelia; Sullivan, Joanna

    2016-01-01

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

  8. CD8 T cell response and evolutionary pressure to HIV-1 cryptic epitopes derived from antisense transcription

    PubMed Central

    Carlson, Jonathan; Yan, Jiyu; Akinsiku, Olusimidele T.; Schaefer, Malinda; Sabbaj, Steffanie; Bet, Anne; Levy, David N.; Heath, Sonya; Tang, Jianming; Kaslow, Richard A.; Walker, Bruce D.; Ndung’u, Thumbi; Goulder, Philip J.; Heckerman, David; Hunter, Eric; Goepfert, Paul A.

    2010-01-01

    Retroviruses pack multiple genes into relatively small genomes by encoding several genes in the same genomic region with overlapping reading frames. Both sense and antisense HIV-1 transcripts contain open reading frames for known functional proteins as well as numerous alternative reading frames (ARFs). At least some ARFs have the potential to encode proteins of unknown function, and their antigenic properties can be considered as cryptic epitopes (CEs). To examine the extent of active immune response to virally encoded CEs, we analyzed human leukocyte antigen class I–associated polymorphisms in HIV-1 gag, pol, and nef genes from a large cohort of South Africans with chronic infection. In all, 391 CEs and 168 conventional epitopes were predicted, with the majority (307; 79%) of CEs derived from antisense transcripts. In further evaluation of CD8 T cell responses to a subset of the predicted CEs in patients with primary or chronic infection, both sense- and antisense-encoded CEs were immunogenic at both stages of infection. In addition, CEs often mutated during the first year of infection, which was consistent with immune selection for escape variants. These findings indicate that the HIV-1 genome might encode and deploy a large potential repertoire of unconventional epitopes to enhance vaccine-induced antiviral immunity. PMID:20065064

  9. Oximetry in children recovering from deep hypothermia for cardiac surgery.

    PubMed

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

    1990-10-01

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

  10. 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.

  11. Identification of Small RNAs in Desulfovibrio vulgaris Hildenborough

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

    Burns, Andrew; Joachimiak, Marcin; Deutschbauer, Adam

    2010-05-17

    Desulfovibrio vulgaris is an anaerobic sulfate-reducing bacterium capable of facilitating the removal of toxic metals such as uranium from contaminated sites via reduction. As such, it is essential to understand the intricate regulatory cascades involved in how D. vulgaris and its relatives respond to stressors in such sites. One approach is the identification and analysis of small non-coding RNAs (sRNAs); molecules ranging in size from 20-200 nucleotides that predominantly affect gene regulation by binding to complementary mRNA in an anti-sense fashion and therefore provide an immediate regulatory response. To identify sRNAs in D. vulgaris, a bacterium that does not possessmore » an annotated hfq gene, RNA was pooled from stationary and exponential phases, nitrate exposure, and biofilm conditions. The subsequent RNA was size fractionated, modified, and converted to cDNA for high throughput transcriptomic deep sequencing. A computational approach to identify sRNAs via the alignment of seven separate Desulfovibrio genomes was also performed. From the deep sequencing analysis, 2,296 reads between 20 and 250 nt were identified with expression above genome background. Analysis of those reads limited the number of candidates to ~;;87 intergenic, while ~;;140 appeared to be antisense to annotated open reading frames (ORFs). Further BLAST analysis of the intergenic candidates and other Desulfovibrio genomes indicated that eight candidates were likely portions of ORFs not previously annotated in the D. vulgaris genome. Comparison of the intergenic and antisense data sets to the bioinformatical predicted candidates, resulted in ~;;54 common candidates. Current approaches using Northern analysis and qRT-PCR are being used toverify expression of the candidates and to further develop the role these sRNAs play in D. vulgaris regulation.« less

  12. Reduction of CMOS Image Sensor Read Noise to Enable Photon Counting

    PubMed Central

    Guidash, Michael; Ma, Jiaju; Vogelsang, Thomas; Endsley, Jay

    2016-01-01

    Recent activity in photon counting CMOS image sensors (CIS) has been directed to reduction of read noise. Many approaches and methods have been reported. This work is focused on providing sub 1 e− read noise by design and operation of the binary and small signal readout of photon counting CIS. Compensation of transfer gate feed-through was used to provide substantially reduced CDS time and source follower (SF) bandwidth. SF read noise was reduced by a factor of 3 with this method. This method can be applied broadly to CIS devices to reduce the read noise for small signals to enable use as a photon counting sensor. PMID:27070625

  13. Prologue: Reading Comprehension Is Not a Single Ability

    ERIC Educational Resources Information Center

    Catts, Hugh W.; Kamhi, Alan G.

    2017-01-01

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

  14. Highly Motivated Children's Perceptions of Reading

    ERIC Educational Resources Information Center

    Carney, Kelli Ann

    2013-01-01

    The purpose of this interpretive case study was to explore the reading perceptions and attitudes of children who exhibited high levels of motivation to read. The study explored the extent to which the highly motivated children read and the extent to which they enjoy reading. Seven children enrolled in the fifth grade at a small, rural elementary…

  15. Promoting Reading Comprehension, Content Learning, and English Acquisition through Collaborative Strategic Reading (CSR).

    ERIC Educational Resources Information Center

    Klingner, Janette K.; Vaughn, Sharon

    1999-01-01

    Describes procedures for teaching Collaborative Strategic Reading (CSR), in which students of mixed reading and achievement levels work in small, cooperative groups to assist one another in applying reading strategies to facilitate their comprehension of content-area text. Discusses whole-class instruction of CSR strategies, implementing CSR in…

  16. Interactive Shared Book Reading. What Works Clearinghouse Intervention Report

    ERIC Educational Resources Information Center

    What Works Clearinghouse, 2007

    2007-01-01

    "Interactive Shared Book Reading" is a general practice that adults may use when reading with children and is intended to enhance young children's language and literacy skills. Typically, "Interactive Shared Book Reading" involves an adult reading a book to a child or a small group of children and using a variety of techniques…

  17. Encouraging Reading and Language Development in Cultural Minority Children.

    ERIC Educational Resources Information Center

    Kawakami, Alice J.; Au, Kathryn Hu-pei

    1986-01-01

    The article reviews approaches used in the Kamehameha Elementary Education Program (KEEP) in Hawaii to increase reading skills of educationally at-risk Polynesian-Hawaiian children (K-grade 3). Whole class story reading lessons and small group reading comprehension lessons are described. (CL)

  18. Complete genome sequence of keunjorong mosaic virus, a potyvirus from Cynanchum wilfordii.

    PubMed

    Nam, Moon; Lee, Joo-Hee; Choi, Hong Soo; Lim, Hyoun-Sub; Moon, Jae Sun; Lee, Su-Heon

    2013-08-01

    We have determined the complete genome sequence of keunjorong mosaic virus (KjMV). The KjMV genome is composed of 9,611 nucleotides, excluding the 3'-terminal poly(A) tail. It contains two open reading frames (ORFs), with the large one encoding a polyprotein of 3,070 amino acids and the small overlapping ORF encoding a PIPO protein of 81 amino acids. The KjMV genome shared the highest nucleotide sequence identity (57.5  %) with pepper mottle virus and freesia mosaic virus, two members of the genus Potyvirus. Based on the phylogenetic relatedness to known potyviruses, KjMV appears to be a member of a new species in the genus Potyvirus.

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

    ERIC Educational Resources Information Center

    Roizen, Merle A.

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

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

    ERIC Educational Resources Information Center

    1996

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

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

    ERIC Educational Resources Information Center

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

    2015-01-01

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

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

    ERIC Educational Resources Information Center

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

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

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

    ERIC Educational Resources Information Center

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

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

  4. Fiction reading has a small positive impact on social cognition: A meta-analysis.

    PubMed

    Dodell-Feder, David; Tamir, Diana I

    2018-02-26

    Scholars from both the social sciences and the humanities have credited fiction reading with a range of positive real-world social effects. Research in psychology has suggested that readers may make good citizens because fiction reading is associated with better social cognition. But does fiction reading causally improve social cognition? Here, we meta-analyze extant published and unpublished experimental data to address this question. Multilevel random-effects meta-analysis of 53 effect sizes from 14 studies demonstrated that it does: compared to nonfiction reading and no reading, fiction reading leads to a small, statistically significant improvement in social-cognitive performance (g = .15-.16). This effect is robust across sensitivity analyses and does not appear to be the result of publication bias. We recommend that in future work, researchers use more robust reading manipulations, assess whether the effects transfer to improved real-world social functioning, and investigate mechanisms. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

  5. Open Admissions: A Bibliography for Research and Application.

    ERIC Educational Resources Information Center

    Shrier, Irene; Lavin, David E.

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    1985-06-01

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

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

    PubMed

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

    1994-12-01

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

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

    PubMed

    Inouye, Satoshi; Suzuki, Takahiro

    2016-12-01

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

  10. Reading for Pleasure in Paradise: Paired Reading in Antigua and Barbuda

    ERIC Educational Resources Information Center

    Warrington, Molly J.; George, Patricia

    2014-01-01

    Reading for pleasure is essential in the development of literacy. This paper reports on findings from a paired reading strategy introduced into primary schools in Antigua and Barbuda in order to foster children's pleasure in reading. This programme of cross-age peer tutoring intervention began with the training of teachers in a small group of…

  11. Jumping from the Highest Graded Readers to Ungraded Novels: Four Case Studies

    ERIC Educational Resources Information Center

    Uden, Jez; Schmitt, Diane; Schmitt, Norbert

    2014-01-01

    This study follows a small group of learners in the UK to the end of a graded reading program using the Cambridge Readers and investigates whether this particular graded reading series provides a bridge to reading unsimplified novels for pleasure. The participants' reading comprehension, reading rates, vocabulary text coverage, and overall affect…

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

    PubMed

    Yesylevskyy, Semen O

    2012-07-15

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

  13. A Small Learning Community's Impact on Students' Success Assessed by State Test Scores in Reading and Math

    ERIC Educational Resources Information Center

    Smith, Christiana Helen Croson

    2013-01-01

    Drastic reform measures have taken place at Howard High School of Technology to incorporate a 10th grade small learning community. Due to the costs and resources associated with implementing small learning communities, it is important to examine if the 10th graders' achievement on the state tests in reading and math were significantly different…

  14. 75 FR 39528 - Farm Credit Administration Board; Amendment to Sunshine Act Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-09

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

  15. 10 CFR 1703.103 - Requests for board records available through the public reading room.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

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

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

    ERIC Educational Resources Information Center

    1996

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

  17. Factors Predicting READ 180 18-Week Grades among Middle School Students: The Role of Self-Efficacy, Ethnicity, Reading and Language Skills and Socioeconomic Indicators

    ERIC Educational Resources Information Center

    Brown, Rhonda M.

    2014-01-01

    Middle school students who struggle in reading are likely to also experience difficulty in their other subjects in school. A variety of reading intervention programs exist for schools to utilize to increase reading comprehension. The Scholastic READ 180 program is used as part of this study. This small, focused study of 160 students examined the…

  18. Targeting the r(CGG) repeats that cause FXTAS with modularly assembled small molecules and oligonucleotides.

    PubMed

    Tran, Tuan; Childs-Disney, Jessica L; Liu, Biao; Guan, Lirui; Rzuczek, Suzanne; Disney, Matthew D

    2014-04-18

    We designed small molecules that bind the structure of the RNA that causes fragile X-associated tremor ataxia syndrome (FXTAS), an incurable neuromuscular disease. FXTAS is caused by an expanded r(CGG) repeat (r(CGG)(exp)) that inactivates a protein regulator of alternative pre-mRNA splicing. Our designed compounds modulate r(CGG)(exp) toxicity in cellular models of FXTAS, and pull-down experiments confirm that they bind r(CGG)(exp) in vivo. Importantly, compound binding does not affect translation of the downstream open reading frame (ORF). We compared molecular recognition properties of our optimal compound to oligonucleotides. Studies show that r(CGG)(exp)'s self-structure is a significant energetic barrier for oligonucleotide binding. A fully modified 2'-OMethyl phosphorothioate is incapable of completely reversing an FXTAS-associated splicing defect and inhibits translation of the downstream ORF, which could have deleterious effects. Taken together, these studies suggest that a small molecule that recognizes structure may be more well suited for targeting highly structured RNAs that require strand invasion by a complementary oligonucleotide.

  19. Targeting the r(CGG) Repeats That Cause FXTAS with Modularly Assembled Small Molecules and Oligonucleotides

    PubMed Central

    2015-01-01

    We designed small molecules that bind the structure of the RNA that causes fragile X-associated tremor ataxia syndrome (FXTAS), an incurable neuromuscular disease. FXTAS is caused by an expanded r(CGG) repeat (r(CGG)exp) that inactivates a protein regulator of alternative pre-mRNA splicing. Our designed compounds modulate r(CGG)exp toxicity in cellular models of FXTAS, and pull-down experiments confirm that they bind r(CGG)expin vivo. Importantly, compound binding does not affect translation of the downstream open reading frame (ORF). We compared molecular recognition properties of our optimal compound to oligonucleotides. Studies show that r(CGG)exp’s self-structure is a significant energetic barrier for oligonucleotide binding. A fully modified 2′-OMethyl phosphorothioate is incapable of completely reversing an FXTAS-associated splicing defect and inhibits translation of the downstream ORF, which could have deleterious effects. Taken together, these studies suggest that a small molecule that recognizes structure may be more well suited for targeting highly structured RNAs that require strand invasion by a complementary oligonucleotide. PMID:24506227

  20. Now We Get It! Boosting Comprehension with Collaborative Strategic Reading

    ERIC Educational Resources Information Center

    Klingner, Janette K.; Vaughn, Sharon; Boardman, Alison; Swanson, Elizabeth

    2012-01-01

    Collaborative Strategic Reading is an innovative new approach to teaching reading that weaves together two instructional programs: cooperative learning and reading comprehension strategy instruction. In small groups, students work through the four main steps-Preview, "Click and Clunk," Get the Gist, and Wrap Up-helping each other improve…

  1. The Right to Be a Fan

    ERIC Educational Resources Information Center

    Gutierrez, Peter

    2011-01-01

    Reading experts have consistently cited the importance of independent reading, reading for pleasure, and fostering "a love of reading." Unfortunately, fanning the fire of fan readership is not so easy in the service of our clear-cut and standards-aligned curricula, except perhaps in small, carefully channeled doses. Moreover, the impetus for such…

  2. Nonword Reading across Orthographies: How Flexible Is the Choice of Reading Units?

    ERIC Educational Resources Information Center

    Goswami, Usha; Ziegler, Johannes C.; Dalton, Louise; Schnieder, Wolfgang

    2003-01-01

    Used cross-language blocking experiments to test the hypothesis that children learning to read inconsistent orthographies would show considerable flexibility in making use of spelling-sound correspondences at different unit sizes, whereas children learning to read consistent orthographies should mainly employ small-size grapheme-phoneme…

  3. Response to Intervention (RTI) Effectiveness in Kindergarten Reading Achievement

    ERIC Educational Resources Information Center

    Whittaker, Susan

    2013-01-01

    The purpose of this quantitative study was to determine whether kindergarten-reading achievement could be increased by implementing Response to Intervention (RtI) strategies. Kindergarten children (N = 290) who were identified as at-risk for reading difficulties were assigned to receive intervention through a) small reading groups (SRG), b)…

  4. Preschoolers' Reading Skills Benefit from One Modest Change by Teachers

    ERIC Educational Resources Information Center

    Grabmeier, Jeff

    2012-01-01

    A small change in how teachers and parents read aloud to preschoolers may provide a big boost to their reading skills later on, a new study found. That change involves making specific references to print in books while reading--such as pointing out letters and words on the pages, showing capital letters, and showing how they read from left to…

  5. The Early Years: Parents and Young Deaf Children Reading Together

    ERIC Educational Resources Information Center

    Lutz, Lori

    2017-01-01

    Research is just beginning to describe the role of reading in the lives of families with deaf children. While the time that deaf children spend reading or being read to represents only a small part of their lives at home, research highlights its importance for young children--hearing as well as deaf. Children whose parents read to them at home…

  6. Comprehension Questioning Small Group Reading Instruction for Urban Students with Learning Disabilities

    ERIC Educational Resources Information Center

    Jones, Valerie

    2012-01-01

    It is evident from reading research that students with learning disabilities (LD) greatly benefit from teacher-student interactions during small group comprehension instruction (e.g., Berkeley, Scruggs, & Mastropieri, 2010). Given that questioning takes up the vast majority of instructional interactions between teachers and students (Chin,…

  7. MRI roadmap-guided transendocardial delivery of exon-skipping recombinant adeno-associated virus restores dystrophin expression in a canine model of Duchenne muscular dystrophy.

    PubMed

    Barbash, I M; Cecchini, S; Faranesh, A Z; Virag, T; Li, L; Yang, Y; Hoyt, R F; Kornegay, J N; Bogan, J R; Garcia, L; Lederman, R J; Kotin, R M

    2013-03-01

    Duchenne muscular dystrophy (DMD) cardiomyopathy patients currently have no therapeutic options. We evaluated catheter-based transendocardial delivery of a recombinant adeno-associated virus (rAAV) expressing a small nuclear U7 RNA (U7smOPT) complementary to specific cis-acting splicing signals. Eliminating specific exons restores the open reading frame resulting in translation of truncated dystrophin protein. To test this approach in a clinically relevant DMD model, golden retriever muscular dystrophy (GRMD) dogs received serotype 6 rAAV-U7smOPT via the intracoronary or transendocardial route. Transendocardial injections were administered with an injection-tipped catheter and fluoroscopic guidance using X-ray fused with magnetic resonance imaging (XFM) roadmaps. Three months after treatment, tissues were analyzed for DNA, RNA, dystrophin protein, and histology. Whereas intracoronary delivery did not result in effective transduction, transendocardial injections, XFM guidance, enabled 30±10 non-overlapping injections per animal. Vector DNA was detectable in all samples tested and ranged from <1 to >3000 vector genome copies per cell. RNA analysis, western blot analysis, and immunohistology demonstrated extensive expression of skipped RNA and dystrophin protein in the treated myocardium. Left ventricular function remained unchanged over a 3-month follow-up. These results demonstrated that effective transendocardial delivery of rAAV-U7smOPT was achieved using XFM. This approach restores an open reading frame for dystrophin in affected dogs and has potential clinical utility.

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

    PubMed Central

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

    1998-01-01

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

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

    DTIC Science & Technology

    1988-12-01

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

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

    PubMed Central

    Firth, Andrew E

    2008-01-01

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

  11. Meeting the Reading Challenges of Science Textbooks in the Primary Grades

    ERIC Educational Resources Information Center

    Bryce, Nadine

    2011-01-01

    Four primary grade teachers overcame challenges of textbook-based science reading through a focus on reading strategies and an emphasis on making meaning. Teachers used whole-class and small-group guided reading instruction to focus students on organizational and textual features of the science textbooks. They also used teacher-guided talk and…

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

    ERIC Educational Resources Information Center

    Vargas, Yarma Velazquez

    2008-01-01

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

  13. High School Students with Reading Comprehension Difficulties: Results of a Randomized Control Trial of a Two-Year Reading Intervention

    ERIC Educational Resources Information Center

    Vaughn, Sharon; Roberts, Greg; Wexler, Jade; Vaughn, Michael G.; Fall, Anna-Mária; Schnakenberg, Jennifer B.

    2015-01-01

    A 2-year, randomized control trial with 9th to 10th grade students with significant reading problems was provided for 50 minutes a day in small groups. Comparison students were provided an elective class and treatment students the reading intervention. Students were identified as demonstrating reading difficulties through failure on their state…

  14. Terrain - Umbra Package v. 1.0

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

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

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

  15. Tech Reading/Small Engines: Performance Package, Minnesota Profile of Learning.

    ERIC Educational Resources Information Center

    Minnesota State Dept. of Children, Families, and Learning, St. Paul.

    Developed by classroom teachers during the development phase of Minnesota's Graduation Standards, this performance package is made up of locally designed assignments that, taken together, show whether a student has learned and can apply the knowledge and skills related to technical reading regarding small engines. It begins with reference to the…

  16. Small Schools Student Learning Objectives, K-3: Reading, Language Arts, Mathematics, Science, Social Studies.

    ERIC Educational Resources Information Center

    Hartl, David, Ed.; And Others

    Developed by primary teachers and elementary principals from small districts in Snohomish and Island counties in Washington, this handbook contains sequenced student learning objectives for grades K-3 in the curriculum areas of reading, language arts, mathematics, science, and social studies. Each student learning objective is correlated to the…

  17. Enhancing Preschool Educators' Ability to Facilitate Conversations during Shared Book Reading

    ERIC Educational Resources Information Center

    Milburn, Trelani F.; Girolametto, Luigi; Weitzman, Elaine; Greenberg, Janice

    2014-01-01

    The purpose of this study was to investigate whether professional development enhanced educators' use of conversational strategies during shared book reading with small groups of preschoolers. Twenty preschool educators and small groups of children from each of their classrooms were randomly assigned to the experimental or control group. The 10…

  18. Microcontrollers for data logging in Environmental Physics

    NASA Astrophysics Data System (ADS)

    Harrison, R. Giles; Westbrook, Christopher. D.

    2016-04-01

    Methods for obtaining reliable environmental measurements are central in developing a quantitative understanding of the natural world [1]. In the environmental sciences, data is usually obtained through planned experimental work, by collaborators in large field experiments or merely from others downloaded through the internet. Careful appreciation of the provenance and reliability of measurements has traditionally been a central aspect of physics education, and a similar physics-centred approach to measurements has been embedded in the new Environmental Physics BSc programme at the University of Reading [2]. Through the use of practical classes, students are educated in using small programmable microcontroller devices to obtain environmental data. The classes are based around exploring the open source Arduino, to which a range of analogue and digital sensors are connected and evaluated. A simplified prototyping system has been developed to help emphasise the measurement aspects over the electronics considerations. The practical classes work towards deployment of a miniature data logger based on the Arduino's microcontroller but optimised for low power, from which the environmental measurements are compared with co-located standard data obtained at the Reading University Atmospheric Observatory. [1] R.G. Harrison, Meteorological Measurements and Instrumentation, Wiley, 2014. (http://eu.wiley.com/WileyCDA/WileyTitle/productCd-1118745809.html) [2] Environmental Physics BSc (https://www.reading.ac.uk/ready-to-study/study/subject-area/environment-ug/bsc-environmental-physics.aspx)

  19. Literature Especially with Remedial Readers (Open to Suggestion).

    ERIC Educational Resources Information Center

    Glowacki, Joan

    1990-01-01

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

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

    ERIC Educational Resources Information Center

    Ching-yen, Chang

    1973-01-01

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

  1. 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…

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

    ERIC Educational Resources Information Center

    Gabbard, Anita; Mupinga, Davison M.

    2013-01-01

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

  3. Liberty Centennial Student Campaign Manual.

    ERIC Educational Resources Information Center

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

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

  4. Continuing Literacy.

    ERIC Educational Resources Information Center

    Clarke, Ronald F., Ed.

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

  5. Identification of herpes simplex virus type 1 proteins encoded within the first 1.5 kb of the latency-associated transcript.

    PubMed

    Henderson, Gail; Jaber, Tareq; Carpenter, Dale; Wechsler, Steven L; Jones, Clinton

    2009-09-01

    Expression of the first 1.5 kb of the latency-associated transcript (LAT) that is encoded by herpes simplex virus type 1 (HSV-1) is sufficient for wild-type (wt) levels of reactivation from latency in small animal models. Peptide-specific immunoglobulin G (IgG) was generated against open reading frames (ORFs) that are located within the first 1.5 kb of LAT coding sequences. Cells stably transfected with LAT or trigeminal ganglionic neurons of mice infected with a LAT expressing virus appeared to express the L2 or L8 ORF. Only L2 ORF expression was readily detected in trigeminal ganglionic neurons of latently infected mice.

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

    ERIC Educational Resources Information Center

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

    2007-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  8. Does Supplemental Instruction Support the Transition from Spanish to English Reading Instruction for First-Grade English Learners at Risk of Reading Difficulties?

    ERIC Educational Resources Information Center

    Baker, Doris Luft; Burns, Darci; Kame'enui, Edward J.; Smolkowski, Keith; Baker, Scott King

    2016-01-01

    This study examines the effect of 30 min of small group explicit instruction on reading outcomes for first-grade Spanish-speaking English learners (ELs) at risk of reading difficulties. Participants were 78 ELs from seven schools who were receiving Spanish only, or Spanish and English, whole group reading instruction in first grade. Students were…

  9. Reading Quizzes Improve Exam Scores for Community College Students.

    PubMed

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

    2018-06-01

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

  10. Improving the Reading Scores of Students Who Fall below Grade Level Expectations.

    ERIC Educational Resources Information Center

    Varcadipane, Vincent N.

    This report describes the process used by a small, one-building kindergarten-through-grade-six school district in New Jersey to improve the reading scores of students who had fallen below their current grade in reading. Areas of need included improving the reading scores of students in regular education, special education, and…

  11. When Guided Reading Isn't Working: Strategies for Effective Instruction

    ERIC Educational Resources Information Center

    Wall, Heather

    2014-01-01

    Guided reading is widespread as a small group reading instructional approach, and yet in some cases the original intent of guided reading as a method for encouraging readers' independent strategic thinking has been lost. This article describes one group of teachers' discoveries as they searched for a way to improve their instruction by…

  12. Are Teenagers "Really" Keen Digital Readers? Adolescent Engagement in Ebook Reading and the Relevance of Paper Books Today

    ERIC Educational Resources Information Center

    Merga, Margaret K.

    2014-01-01

    Digital reading technologies may be intuitively appealing. They offer many possibilities, including great potential for interactivity around books, portability of whole libraries in one small reading unit, and almost instant satisfaction of demand for a particular book. Though there is limited research exploring the appeal of digital reading for…

  13. Eye Movement Monitoring in the Study of Silent Reading.

    ERIC Educational Resources Information Center

    McConkie, George W.

    Eye movement monitoring is useful both in the control of experiments on reading and as a source of data. Experiments using eye monitoring techniques have helped develop the following conclusions about the reading process: the region of text read during a fixation is quite small and asymmetric to the right of the center of vision, successive…

  14. Why University Students Don't Read: What Professors Can Do to Increase Compliance

    ERIC Educational Resources Information Center

    Hoeft, Mary E.

    2012-01-01

    This article reports findings from two studies assessing reading compliance among first semester freshmen at a small Midwestern two-year liberal arts university. The first study assessed reading compliance of students enrolled in two sections of First Year Seminar, finding that 46% of students reported that they read assignments, yet only 55% of…

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

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

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

    2008-02-22

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

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

    PubMed

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

    2014-09-01

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

  17. A retrotransposable element from the mosquito Anopheles gambiae .

    PubMed Central

    Besansky, N J

    1990-01-01

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

  18. A versatile and efficient high-throughput cloning tool for structural biology.

    PubMed

    Geertsma, Eric R; Dutzler, Raimund

    2011-04-19

    Methods for the cloning of large numbers of open reading frames into expression vectors are of critical importance for challenging structural biology projects. Here we describe a system termed fragment exchange (FX) cloning that facilitates the high-throughput generation of expression constructs. The method is based on a class IIS restriction enzyme and negative selection markers. FX cloning combines attractive features of established recombination- and ligation-independent cloning methods: It allows the straightforward transfer of an open reading frame into a variety of expression vectors and is highly efficient and very economic in its use. In addition, FX cloning avoids the common but undesirable feature of significantly extending target open reading frames with cloning related sequences, as it leaves a minimal seam of only a single extra amino acid to either side of the protein. The method has proven to be very robust and suitable for all common pro- and eukaryotic expression systems. It considerably speeds up the generation of expression constructs compared to traditional methods and thus facilitates a broader expression screening.

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

    PubMed

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

    2002-08-01

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

  20. An All-School Library Challenge

    ERIC Educational Resources Information Center

    Quirk, Connie

    2005-01-01

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

  1. Connecting Libraries and Schools with CLASP.

    ERIC Educational Resources Information Center

    Del Vecchio, Stephen

    1993-01-01

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

  2. 75 FR 77697 - Action To Ensure Authority To Issue Permits Under the Prevention of Significant Deterioration...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-13

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

  3. Developing Literacy for the Vocational-Technical Trades.

    ERIC Educational Resources Information Center

    Penisten, John

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

  4. 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…

  5. Invented Spelling Activities in Small Groups and Early Spelling and Reading

    ERIC Educational Resources Information Center

    Martins, Margarida Alves; Salvador, Liliana; Albuquerque, Ana; Silva, Cristina

    2016-01-01

    Our aim was to assess the impact of an invented spelling programme conducted in small groups on children's written language acquisition in Portuguese. We expected the experimental group to have better post-test results than the control group in spelling and reading. Participants were 160 preschool-age children who were randomly divided into an…

  6. Teachers' Responses to Using a Small-Group Delivery Method during Reading Instruction: A Qualitative Approach

    ERIC Educational Resources Information Center

    Reynolds, Dorothy M. Valentine

    2010-01-01

    The purpose of this research was to examine teachers' perspectives on transitioning from a predominately whole to small-group delivery method during reading instruction. This study used a qualitative approach and nested itself in an epistemology of constructivism. The research operated under the umbrella of practice ethnography as it closely…

  7. Small Schools Student Learning Objectives, 9-12: Mathematics, Reading, Reading in the Content Areas, Language Arts.

    ERIC Educational Resources Information Center

    Nelson, JoAnne, Ed.; Hartl, David, Ed.

    Designed by Washington curriculum specialists and secondary teachers to assist teachers in small schools with the improvement of curriculum and instruction and to aid smaller districts lacking curriculum personnel to comply with Washington's Student Learning Objectives Law, this handbook contains learning objectives in the areas of language arts,…

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

    PubMed Central

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

    1987-01-01

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

  9. Characterization of the Tupaia rhabdovirus genome reveals a long open reading frame overlapping with P and a novel gene encoding a small hydrophobic protein.

    PubMed

    Springfeld, Christoph; Darai, Gholamreza; Cattaneo, Roberto

    2005-06-01

    Rhabdoviruses are negative-stranded RNA viruses of the order Mononegavirales and have been isolated from vertebrates, insects, and plants. Members of the genus Lyssavirus cause the invariably fatal disease rabies, and a member of the genus Vesiculovirus, Chandipura virus, has recently been associated with acute encephalitis in children. We present here the complete genome sequence and transcription map of a rhabdovirus isolated from cultivated cells of hepatocellular carcinoma tissue from a moribund tree shrew. The negative-strand genome of tupaia rhabdovirus is composed of 11,440 nucleotides and encodes six genes that are separated by one or two intergenic nucleotides. In addition to the typical rhabdovirus genes in the order N-P-M-G-L, a gene encoding a small hydrophobic putative type I transmembrane protein of approximately 11 kDa was identified between the M and G genes, and the corresponding transcript was detected in infected cells. Similar to some Vesiculoviruses and many Paramyxovirinae, the P gene has a second overlapping reading frame that can be accessed by ribosomal choice and encodes a protein of 26 kDa, predicted to be the largest C protein of these virus families. Phylogenetic analyses of the tupaia rhabdovirus N and L genes show that the virus is distantly related to the Vesiculoviruses, Ephemeroviruses, and the recently characterized Flanders virus and Oita virus and further extends the sequence territory occupied by animal rhabdoviruses.

  10. Characterization of the Tupaia Rhabdovirus Genome Reveals a Long Open Reading Frame Overlapping with P and a Novel Gene Encoding a Small Hydrophobic Protein

    PubMed Central

    Springfeld, Christoph; Darai, Gholamreza; Cattaneo, Roberto

    2005-01-01

    Rhabdoviruses are negative-stranded RNA viruses of the order Mononegavirales and have been isolated from vertebrates, insects, and plants. Members of the genus Lyssavirus cause the invariably fatal disease rabies, and a member of the genus Vesiculovirus, Chandipura virus, has recently been associated with acute encephalitis in children. We present here the complete genome sequence and transcription map of a rhabdovirus isolated from cultivated cells of hepatocellular carcinoma tissue from a moribund tree shrew. The negative-strand genome of tupaia rhabdovirus is composed of 11,440 nucleotides and encodes six genes that are separated by one or two intergenic nucleotides. In addition to the typical rhabdovirus genes in the order N-P-M-G-L, a gene encoding a small hydrophobic putative type I transmembrane protein of approximately 11 kDa was identified between the M and G genes, and the corresponding transcript was detected in infected cells. Similar to some Vesiculoviruses and many Paramyxovirinae, the P gene has a second overlapping reading frame that can be accessed by ribosomal choice and encodes a protein of 26 kDa, predicted to be the largest C protein of these virus families. Phylogenetic analyses of the tupaia rhabdovirus N and L genes show that the virus is distantly related to the Vesiculoviruses, Ephemeroviruses, and the recently characterized Flanders virus and Oita virus and further extends the sequence territory occupied by animal rhabdoviruses. PMID:15890917

  11. 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.

  12. Effect of Common Visual Dysfunctions on Reading.

    ERIC Educational Resources Information Center

    McPartland, Brian P.

    1985-01-01

    Six common visual dysfunctions are briefly explained and their relationships to reading noted: (1) ametropia, refractive error; (2) inaccurate saccades, the small jumping eye movements used in reading; (3) inefficient binocularity/fusion; (4) insufficient convergence/divergence; (5) heterophoria, imbalance in extra-ocular muscles; and (6)…

  13. Sex Differences in Learning Rate in an Intensive Summer Reading Clinic.

    ERIC Educational Resources Information Center

    Cahn, Lorynne, D.

    1988-01-01

    Examines whether sex differences in reading learning rate occurred when female instructors worked with small groups of elementary school boys and girls on an individualized basis in an intensive summer reading clinic program. Reports that girls outperformed boys on all measures. (RAE)

  14. The Effects of Implementing a Reading Workshop in Middle School Language Arts Classrooms

    ERIC Educational Resources Information Center

    Thomas, Angela Falter

    2012-01-01

    Two language arts teachers in a small, rural middle school set a goal of improving their reading instruction and ultimately their students' learning. The two teachers implemented Reading Workshop as their new methodology for teaching reading to all six of their 7th and 8th grade classes. Interviews and classroom observations, over the course of…

  15. Extensive Reading in EFL Classroom at Secondary Schools in Bangladesh: Current Practices and Future Possibilities

    ERIC Educational Resources Information Center

    Haider, Md. Zulfeqar; Akhter, Elina

    2012-01-01

    Extensive reading is being practiced in many EFL and ESL classrooms as an effective means for developing learners' reading as well as other related skills. This paper is based on a small-scale study that explores the current practices and future possibilities of using extensive reading in the EFL classrooms at the junior secondary schools in…

  16. Does Repeated Reading Improve Reading Fluency and Comprehension for Struggling Adolescent Readers?

    ERIC Educational Resources Information Center

    Still, Kristine Lynn; Flynt, Christine A.

    2012-01-01

    This was a 12-week study that explored the effects of repeated peer readings on struggling adolescent readers. It was a quasi-experimental design with one treatment group and one control group. There were two small group English classes that were consistently using the repeated reading strategy (the treatment group) and students in the co-teach…

  17. The read-write Linked Data Web.

    PubMed

    Berners-Lee, Tim; O'Hara, Kieron

    2013-03-28

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

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

    PubMed

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

    2018-03-15

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

  19. Small Schools Student Learning Objectives, K-8: Reading, Language Arts, Mathematics. K-3; Science, Social Studies.

    ERIC Educational Resources Information Center

    Hartl, David, Ed.; And Others

    Developed by 40 primary teachers and 10 elementary principals from small school districts in Washington, this handbook contains sequenced student learning objectives for grades K-3 in science and social studies and for grades K-8 in reading, language arts, and mathematics. The handbook is designed to assist teachers with the improvement of…

  20. Prologue: Reading Comprehension Is Not a Single Ability.

    PubMed

    Catts, Hugh W; Kamhi, Alan G

    2017-04-20

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

  1. Tracing children's vocabulary development from preschool through the school-age years: An 8-year longitudinal study

    PubMed Central

    Kang, Cuiping; Liu, Hongyun; Zhang, Yuping; McBride-Chang, Catherine; Tardif, Twila; Li, Hong; Liang, Weilan; Zhang, Zhixiang; Shu, Hua

    2014-01-01

    In this 8-year longitudinal study, we traced the vocabulary growth of Chinese children, explored potential precursors of vocabulary knowledge, and investigated how vocabulary growth predicted future reading skills. Two hundred sixty-four (264) native Chinese children from Beijing were measured on a variety of reading and language tasks over 8 years. Between the ages of 4 to 10 years, they were administered tasks of vocabulary and related cognitive skills. At age 11, comprehensive reading skills, including character recognition, reading fluency, and reading comprehension were examined. Individual differences in vocabulary developmental profiles were estimated using the intercept-slope cluster method. Vocabulary development was then examined in relation to later reading outcomes. Three subgroups of lexical growth were classified, namely high-high (with a large initial vocabulary size and a fast growth rate), low-high (with a small initial vocabulary size and a fast growth rate) and low-low (with a small initial vocabulary size and a slow growth rate) groups. Low-high and low-low groups were distinguishable mostly through phonological skills, morphological skills and other reading-related cognitive skills. Childhood vocabulary development (using intercept and slope) explained subsequent reading skills. Findings suggest that language-related and reading-related cognitive skills differ among groups with different developmental trajectories of vocabulary, and the initial size and growth rate of vocabulary may be two predictors for later reading development. PMID:24962559

  2. Discovery and small RNA profile of Pecan mosaic-associated virus, a novel potyvirus of pecan trees.

    PubMed

    Su, Xiu; Fu, Shuai; Qian, Yajuan; Zhang, Liqin; Xu, Yi; Zhou, Xueping

    2016-05-26

    A novel potyvirus was discovered in pecan (Carya illinoensis) showing leaf mosaic symptom through the use of deep sequencing of small RNAs. The complete genome of this virus was determined to comprise of 9,310 nucleotides (nt), and shared 24.0% to 58.9% nucleotide similarities with that of other Potyviridae viruses. The genome was deduced to encode a single open reading frame (polyprotein) on the plus strand. Phylogenetic analysis based on the whole genome sequence and coat protein amino acid sequence showed that this virus is most closely related to Lettuce mosaic virus. Using electron microscopy, the typical Potyvirus filamentous particles were identified in infected pecan leaves with mosaic symptoms. Our results clearly show that this virus is a new member of the genus Potyvirus in the family Potyviridae. The virus is tentatively named Pecan mosaic-associated virus (PMaV). Additionally, profiling of the PMaV-derived small RNA (PMaV-sRNA) showed that the most abundant PMaV-sRNAs were 21-nt in length. There are several hotspots for small RNA production along the PMaV genome; two 21-nt PMaV-sRNAs starting at 811 nt and 610 nt of the minus-strand genome were highly repeated.

  3. Discovery and small RNA profile of Pecan mosaic-associated virus, a novel potyvirus of pecan trees

    PubMed Central

    Su, Xiu; Fu, Shuai; Qian, Yajuan; Zhang, Liqin; Xu, Yi; Zhou, Xueping

    2016-01-01

    A novel potyvirus was discovered in pecan (Carya illinoensis) showing leaf mosaic symptom through the use of deep sequencing of small RNAs. The complete genome of this virus was determined to comprise of 9,310 nucleotides (nt), and shared 24.0% to 58.9% nucleotide similarities with that of other Potyviridae viruses. The genome was deduced to encode a single open reading frame (polyprotein) on the plus strand. Phylogenetic analysis based on the whole genome sequence and coat protein amino acid sequence showed that this virus is most closely related to Lettuce mosaic virus. Using electron microscopy, the typical Potyvirus filamentous particles were identified in infected pecan leaves with mosaic symptoms. Our results clearly show that this virus is a new member of the genus Potyvirus in the family Potyviridae. The virus is tentatively named Pecan mosaic-associated virus (PMaV). Additionally, profiling of the PMaV-derived small RNA (PMaV-sRNA) showed that the most abundant PMaV-sRNAs were 21-nt in length. There are several hotspots for small RNA production along the PMaV genome; two 21-nt PMaV-sRNAs starting at 811 nt and 610 nt of the minus-strand genome were highly repeated. PMID:27226228

  4. Repression of small toxic protein synthesis by the Sib and OhsC small RNAs.

    PubMed

    Fozo, Elizabeth M; Kawano, Mitsuoki; Fontaine, Fanette; Kaya, Yusuf; Mendieta, Kathy S; Jones, Kristi L; Ocampo, Alejandro; Rudd, Kenneth E; Storz, Gisela

    2008-12-01

    The sequences encoding the QUAD1 RNAs were initially identified as four repeats in Escherichia coli. These repeats, herein renamed SIB, are conserved in closely related bacteria, although the number of repeats varies. All five Sib RNAs in E. coli MG1655 are expressed, and no phenotype was observed for a five-sib deletion strain. However, a phenotype reminiscent of plasmid addiction was observed for overexpression of the Sib RNAs, and further examination of the SIB repeat sequences revealed conserved open reading frames encoding highly hydrophobic 18- to 19-amino-acid proteins (Ibs) opposite each sib gene. The Ibs proteins were found to be toxic when overexpressed and this toxicity could be prevented by coexpression of the corresponding Sib RNA. Two other RNAs encoded divergently in the yfhL-acpS intergenic region were similarly found to encode a small hydrophobic protein (ShoB) and an antisense RNA regulator (OhsC). Overexpression of both IbsC and ShoB led to immediate changes in membrane potential suggesting both proteins affect the cell envelope. Whole genome expression analysis showed that overexpression of IbsC and ShoB, as well as the small hydrophobic LdrD and TisB proteins, has both overlapping and unique consequences for the cell.

  5. Repression of small toxic protein synthesis by the Sib and OhsC small RNAs

    PubMed Central

    Fozo, Elizabeth M.; Kawano, Mitsuoki; Fontaine, Fanette; Kaya, Yusuf; Mendieta, Kathy S.; Jones, Kristi L.; Ocampo, Alejandro; Rudd, Kenneth E.; Storz, Gisela

    2008-01-01

    Summary The sequences encoding the QUAD1 RNAs were initially identified as four repeats in Escherichia coli. These repeats, herein renamed SIB, are conserved in closely related bacteria, though the number of repeats varies. All five Sib RNAs in E. coli MG1655 are expressed, and no phenotype was observed for a five sib deletion strain. However, a phenotype reminiscent of plasmid addiction was observed for overexpression of the Sib RNAs, and further examination of the SIB repeat sequences revealed conserved open reading frames encoding highly hydrophobic 18–19 amino acid proteins (Ibs) opposite each sib gene. The Ibs proteins were found to be toxic when overexpressed and this toxicity could be prevented by co-expression of the corresponding Sib RNA. Two other RNAs encoded divergently in the yfhL-acpS intergenic region were similarly found to encode a small hydrophobic protein (ShoB) and an antisense RNA regulator (OhsC). Overexpression of both IbsC and ShoB led to immediate changes in membrane potential suggesting both proteins affect the cell envelope. Whole genome expression analysis showed that overexpression of IbsC and ShoB, as well as the small hydrophobic LdrD and TisB proteins, has both overlapping and unique consequences for the cell. PMID:18710431

  6. 76 FR 9988 - Improving EPA Regulations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-23

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

  7. Layers of reading intervention in kindergarten through third grade: changes in teaching and student outcomes.

    PubMed

    O'Connor, Rollanda E; Fulmer, Deborah; Harty, Kristin R; Bell, Kathryn M

    2005-01-01

    In this study, students and their teachers participated in a layered approach to reading intervention in kindergarten through third grade that included professional development for teachers in scientifically based reading instruction, ongoing measurement of reading progress, and additional small-group or individual instruction for students whose progress was insufficient to maintain grade-level reading achievement. Reading outcomes were compared with historical control groups of students in the same schools. The findings revealed overall improvements in reading, improved reading for students who began the study in high-risk categories, and decreases in the incidence of reading disability at the end of third grade. Implications for scaling up are discussed.

  8. Biochemical and genetic characterization of enterocin A from Enterococcus faecium, a new antilisterial bacteriocin in the pediocin family of bacteriocins.

    PubMed Central

    Aymerich, T; Holo, H; Håvarstein, L S; Hugas, M; Garriga, M; Nes, I F

    1996-01-01

    A new bacteriocin has been isolated from an Enterococcus faecium strain. The bacteriocin, termed enterocin A, was purified to homogeneity as judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, N-terminal amino acid sequencing, and mass spectrometry analysis. By combining the data obtained from amino acid and DNA sequencing, the primary structure of enterocin A was determined. It consists of 47 amino acid residues, and the molecular weight was calculated to be 4,829, assuming that the four cysteine residues form intramolecular disulfide bridges. This molecular weight was confirmed by mass spectrometry analysis. The amino acid sequence of enterocin A shared significant homology with a group of bacteriocins (now termed pediocin-like bacteriocins) isolated from a variety of lactic acid-producing bacteria, which include members of the genera Lactobacillus, Pediococcus, Leuconostoc, and Carnobacterium. Sequencing of the structural gene of enterocin A, which is located on the bacterial chromosome, revealed an N-terminal leader sequence of 18 amino acid residues, which was removed during the maturation process. The enterocin A leader belongs to the double-glycine leaders which are found among most other small nonlantibiotic bacteriocins, some lantibiotics, and colicin V. Downstream of the enterocin A gene was located a second open reading frame, encoding a putative protein of 103 amino acid residues. This gene may encode the immunity factor of enterocin A, and it shares 40% identity with a similar open reading frame in the operon of leucocin AUL 187, another pediocin-like bacteriocin. PMID:8633865

  9. Transcriptionally active PCR for antigen identification and vaccine development: in vitro genome-wide screening and in vivo immunogenicity

    PubMed Central

    Regis, David P.; Dobaño, Carlota; Quiñones-Olson, Paola; Liang, Xiaowu; Graber, Norma L.; Stefaniak, Maureen E.; Campo, Joseph J.; Carucci, Daniel J.; Roth, David A.; He, Huaping; Felgner, Philip L.; Doolan, Denise L.

    2009-01-01

    We have evaluated a technology called Transcriptionally Active PCR (TAP) for high throughput identification and prioritization of novel target antigens from genomic sequence data using the Plasmodium parasite, the causative agent of malaria, as a model. First, we adapted the TAP technology for the highly AT-rich Plasmodium genome, using well-characterized P. falciparum and P. yoelii antigens and a small panel of uncharacterized open reading frames from the P. falciparum genome sequence database. We demonstrated that TAP fragments encoding six well-characterized P. falciparum antigens and five well-characterized P. yoelii antigens could be amplified in an equivalent manner from both plasmid DNA and genomic DNA templates, and that uncharacterized open reading frames could also be amplified from genomic DNA template. Second, we showed that the in vitro expression of the TAP fragments was equivalent or superior to that of supercoiled plasmid DNA encoding the same antigen. Third, we evaluated the in vivo immunogenicity of TAP fragments encoding a subset of the model P. falciparum and P. yoelii antigens. We found that antigen-specific antibody and cellular immune responses induced by the TAP fragments in mice were equivalent or superior to those induced by the corresponding plasmid DNA vaccines. Finally, we developed and demonstrated proof-of-principle for an in vitro humoral immunoscreening assay for down-selection of novel target antigens. These data support the potential of a TAP approach for rapid high throughput functional screening and identification of potential candidate vaccine antigens from genomic sequence data. PMID:18164079

  10. 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.

  11. Transcriptionally active PCR for antigen identification and vaccine development: in vitro genome-wide screening and in vivo immunogenicity.

    PubMed

    Regis, David P; Dobaño, Carlota; Quiñones-Olson, Paola; Liang, Xiaowu; Graber, Norma L; Stefaniak, Maureen E; Campo, Joseph J; Carucci, Daniel J; Roth, David A; He, Huaping; Felgner, Philip L; Doolan, Denise L

    2008-03-01

    We have evaluated a technology called transcriptionally active PCR (TAP) for high throughput identification and prioritization of novel target antigens from genomic sequence data using the Plasmodium parasite, the causative agent of malaria, as a model. First, we adapted the TAP technology for the highly AT-rich Plasmodium genome, using well-characterized P. falciparum and P. yoelii antigens and a small panel of uncharacterized open reading frames from the P. falciparum genome sequence database. We demonstrated that TAP fragments encoding six well-characterized P. falciparum antigens and five well-characterized P. yoelii antigens could be amplified in an equivalent manner from both plasmid DNA and genomic DNA templates, and that uncharacterized open reading frames could also be amplified from genomic DNA template. Second, we showed that the in vitro expression of the TAP fragments was equivalent or superior to that of supercoiled plasmid DNA encoding the same antigen. Third, we evaluated the in vivo immunogenicity of TAP fragments encoding a subset of the model P. falciparum and P. yoelii antigens. We found that antigen-specific antibody and cellular immune responses induced by the TAP fragments in mice were equivalent or superior to those induced by the corresponding plasmid DNA vaccines. Finally, we developed and demonstrated proof-of-principle for an in vitro humoral immunoscreening assay for down-selection of novel target antigens. These data support the potential of a TAP approach for rapid high throughput functional screening and identification of potential candidate vaccine antigens from genomic sequence data.

  12. The Impact of Reading Recovery on the Reading Achievement of First Grade Students

    ERIC Educational Resources Information Center

    Case, Marguerite

    2015-01-01

    There are so many different intervention programs for educators to use to increase the reading achievement of below grade level students, that it can often be difficult to choose the appropriate one for the students. Most programs are scripted and are used with small groups of students. Reading Recovery is not a scripted program and is taught in a…

  13. The Efficacy of "Chunking" Reading Materials. Final Report.

    ERIC Educational Resources Information Center

    Carver, Ronald P.

    In a series of three experiments involving 104 individuals, the effect of chunking sentences (the spatial separation of sentences into small groups of meaningfully related words) upon the reading rate and comprehension of mature readers was investigated. Passages and questions from a standardized reading test were displayed via an…

  14. Odyssey Reading. What Works Clearinghouse Intervention Report

    ERIC Educational Resources Information Center

    What Works Clearinghouse, 2012

    2012-01-01

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

  15. Herman Method[TM]. What Works Clearinghouse Intervention Report

    ERIC Educational Resources Information Center

    What Works Clearinghouse, 2010

    2010-01-01

    The "Herman Method"[TM] teaches reading in small groups of up to three students. The curriculum provides instruction in phonemic awareness, phonics, fluency, vocabulary, and reading comprehension, while also teaching spelling and writing. It contains 20 modules of instruction through a fifth grade level. Each module includes a reading,…

  16. Corrective Strategies in Reading for At-Risk Community College Students.

    ERIC Educational Resources Information Center

    Yevoli, Carole

    Focusing on corrective strategies for improving reading skills of at-risk community college students, this document reviews the history of such strategies, highlights current efforts, and assesses future needs. The first section traces the history of remedial reading programs at community colleges, beginning with small individualized sections…

  17. Improving Reading Achievement in High Poverty, Rural Schools

    ERIC Educational Resources Information Center

    Tufts, Janet

    2017-01-01

    Purpose: The purpose of this quantitative study was to determine what correlation exists between a student's poverty coefficient and the daily number of minutes provided for independent reading and third grade reading achievement level as measured by California Assessment of Student Performance and Progress (CAASPP) in small, rural school…

  18. Integrated Language Experience Approach--Using Research Unit.

    ERIC Educational Resources Information Center

    Warren City Schools, OH.

    This program, included in "Effective Reading Programs...," is the result of the efforts of a small team of teachers who desired an alternative method for teaching efficient reading and study skills to underachieving high school students and for supplementing remedial reading classes. Begun in 1972, the program serves 130 ninth graders…

  19. A Synthesis of Read-Aloud Interventions on Early Reading Outcomes Among Preschool through Third Graders at Risk for Reading Difficulties

    PubMed Central

    Swanson, Elizabeth A.; Wanzek, Jeanne; Petscher, Yaacov; Vaughn, Sharon; Heckert, Jennifer; Cavanaugh, Christie; Kraft, Guliz; Tackett, Katie

    2012-01-01

    A synthesis and meta-analysis of the extant research on the effects of storybook read aloud interventions for children at-risk for reading difficulties ages 3–8 is provided. A total of 29 studies met criteria for the synthesis, with 18 studies providing sufficient data for inclusion in the meta-analysis. Read aloud instruction has been examined using dialogic reading, repeated reading of stories, story reading with limited questioning before, during, and/or after reading, computer assisted story reading, and story reading with extended vocabulary activities. Significant, positive effects on children’s language, phonological awareness, print concepts, comprehension, and vocabulary outcomes were found. Despite the positive effects for read aloud interventions, only a small amount of outcome variance was accounted for by intervention type. PMID:21521868

  20. Cloning and expression of a small heat and salt tolerant protein (Hsp22) from Chaetomium globosum.

    PubMed

    Aggarwal, Rashmi; Gupta, Sangeeta; Sharma, Sapna; Banerjee, Sagar; Singh, Priyanka

    2012-11-01

    The present study reports molecular characterization of small heat shock protein gene in Indian isolates of Chaetomium globosum, C. perlucidum, C. reflexum, C. cochlioides and C. cupreum. Six isolates of C. globosum and other species showed a band of 630bp using specific primers. Amplified cDNA product of C. globosum (Cg 1) cloned and sequenced showed 603bp open reading frame encoding 200 amino-acids. The protein sequence had a molecular mass of 22 kDa and was therefore, named Hsp22. BlastX analysis revealed that the gene codes for a protein homologous to previously characterized Hsp22.4 gene from C. globosum (AAR36902.1, XP 001229241.1) and shared 95% identity in amino acid sequence. It also showed varying degree of similarities with small Hsp protein from Neurospora spp. (60%), Myceliophthora sp. (59%), Glomerella sp. (50%), Hypocrea sp. (52%), and Fusarium spp. (51%). This gene was further cloned into pET28a (+) and transformed E. coli BL21 cells were induced by IPTG, and the expressed protein of 30 kDa was analyzed by SDS-PAGE. The IPTG induced transformants displayed significantly greater resistance to NaCl and Na2CO3 stresses.

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

    PubMed

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

    2018-04-27

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

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

    PubMed Central

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

    1986-01-01

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

  3. Case nine. Two hospitals struggling to survive in a small rural community.

    PubMed

    Gaidos, H A

    1990-01-01

    St. Luke's Hospital was the only hospital in town until 26 years before the time of the case. In the late 1950s St. Luke's Hospital was overcrowded and in dire need of renovation and expansion. Plans were devised and the hospital applied for Hill-Burton money to expand. At the same time, a group of local citizens decided to also apply for Hill-Burton money to build another hospital, County Memorial, in the community. The Hill-Burton money was divided and both received money. Both facilities opened within months of each other. For about 10 to 12 years, both hospitals prospered. At the time of the case, competition has heated up between the two facilities. Attempts at collaboration fail; the story is one of wasted resources and community pain because of the lack of ability of two competitors to put aside differences for mutual benefit. The case ends with there being only one hospital in town. Read alone, the case is instructive in terms of the difficulties created when organizations value survival in a known form above all else. Read and considered in concert with Case Eight, it encourages contemplation of the pros and cons of head-on competition versus collaboration.

  4. Using Noldus Observer XT for research on deaf signers learning to read: an innovative methodology.

    PubMed

    Ducharme, Daphne A; Arcand, Isabelle

    2009-08-01

    Despite years of research on the reading problems of deaf students, we still do not know how deaf signers who read well actually crack the code of print. How connections are made between sign language and written language is still an open question. In this article, we show how the Noldus Observer XT software can be used to conduct an in-depth analysis of the online behavior of deaf readers. First, we examine factors that may have an impact on reading behavior. Then, we describe how we videotaped teachers with their deaf student signers of langue des signes québécoise during a reading task, how we conducted a recall activity to better understand the students' reading behavior, and how we used this innovative software to analyze the taped footage. Finally, we discuss the contribution this type of research can have on the future reading behavior of deaf students.

  5. Effects of text-to-speech software use on the reading proficiency of high school struggling readers.

    PubMed

    Park, Hye Jin; Takahashi, Kiriko; Roberts, Kelly D; Delise, Danielle

    2017-01-01

    The literature highlights the benefits of text-to-speech (TTS) software when used as an assistive technology facilitating struggling readers' access to print. However, the effects of TTS software use, upon students' unassisted reading proficiency, have remained relatively unexplored. The researchers utilized an experimental design to investigate whether 9th grade struggling readers who use TTS software to read course materials demonstrate significant improvements in unassisted reading performance. A total of 164 students of 30 teachers in Hawaii participated in the study. Analyses of covariance results indicated that the TTS intervention had a significant, positive effect on student reading vocabulary and reading comprehension after 10 weeks of TTS software use (average 582 minutes). There are several limitations to the study; however, the current study opens up for discussions and need for further studies investigating TTS software as a viable reading intervention for adolescent struggling readers.

  6. Reading and Literacy Initiatives. Hearing on Examining Proposal To Improve the Reading and Literacy Skills of Children and Families, Focusing on S.1596 and H.R.2614, Bills To Provide for Reading Excellence by Improving In-Service Instructional Practices for Teachers Who Teach Reading, To Stimulate the Development of More High-Quality Family Literacy Programs, To Support Extended Learning-Time Opportunities for Children, and To Ensure That Children Can Read Well and Independently not Later than Third Grade of the Committee on Labor and Human Resources. United States Senate. One Hundred Fifth Congress, Second Session.

    ERIC Educational Resources Information Center

    Congress of the U.S., Washington, DC. Senate Committee on Labor and Human Resources.

    The U.S. Senate conducted a hearing consisting of two panels: the first panel discussed overcoming reading difficulties with a primary focus on children and the second panel focused on reading and literacy outreach activities that are ongoing in the U.S. After opening statements of the Hon. James M. Jeffords, the Hon. Edward M. Kennedy, and the…

  7. The sequence, and its evolutionary implications, of a Thermococcus celer protein associated with transcription

    NASA Technical Reports Server (NTRS)

    Kaine, B. P.; Mehr, I. J.; Woese, C. R.

    1994-01-01

    Through random search, a gene from Thermococcus celer has been identified and sequenced that appears to encode a transcription-associated protein (110 amino acid residues). The sequence has clear homology to approximately the last half of an open reading frame reported previously for Sulfolobus acidocaldarius [Langer, D. & Zillig, W. (1993) Nucleic Acids Res. 21, 2251]. The protein translations of these two archaeal genes in turn are homologs of a small subunit found in eukaryotic RNA polymerase I (A12.2) and the counterpart of this from RNA polymerase II (B12.6). Homology is also seen with the eukaryotic transcription factor TFIIS, but it involves only the terminal 45 amino acids of the archaeal proteins. Evolutionary implications of these homologies are discussed.

  8. Verification of 2A peptide cleavage.

    PubMed

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

    2012-02-01

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

  9. Uncovering Information Hidden in Web Archives: Glimpse at Web Analysis Building on Data Warehouses; Towards Continuous Web Archiving: First Results and an Agenda for the Future; The Open Video Digital Library; After Migration to an Electronic Journal Collection: Impact on Faculty and Doctoral Students; Who Is Reading On-Line Education Journals? Why? And What Are They Reading?; Report on eLibrary@UBC4: Research, Collaboration and the Digital Library - Visions for 2010.

    ERIC Educational Resources Information Center

    Rauber, Andreas; Bruckner, Robert M.; Aschenbrenner, Andreas; Witvoet, Oliver; Kaiser, Max; Masanes, Julien; Marchionini, Gary; Geisler, Gary; King, Donald W.; Montgomery, Carol Hansen; Rudner, Lawrence M.; Gellmann, Jennifer S.; Miller-Whitehead, Marie; Iverson, Lee

    2002-01-01

    These six articles discuss Web archives and Web analysis building on data warehouses; international efforts at continuous Web archiving; the Open Video Digital Library; electronic journal collections in academic libraries; online education journals; and an electronic library symposium at the University of British Columbia. (LRW)

  10. An intronic open reading frame was released from one of group II introns in the mitochondrial genome of the haptophyte Chrysochromulina sp. NIES-1333

    PubMed Central

    Nishimura, Yuki; Kamikawa, Ryoma; Hashimoto, Tetsuo; Inagaki, Yuji

    2014-01-01

    Mitochondrial (mt) genome sequences, which often bear introns, have been sampled from phylogenetically diverse eukaryotes. Thus, we can anticipate novel insights into intron evolution from previously unstudied mt genomes. We here investigated the origins and evolution of three introns in the mt genome of the haptophyte Chrysochromulina sp. NIES-1333, which was sequenced completely in this study. All the three introns were characterized as group II, on the basis of predicted secondary structure, and the conserved sequence motifs at the 5′ and 3′ termini. Our comparative studies on diverse mt genomes prompt us to propose that the Chrysochromulina mt genome laterally acquired the introns from mt genomes in distantly related eukaryotes. Many group II introns harbor intronic open reading frames for the proteins (intron-encoded proteins or IEPs), which likely facilitate the splicing of their host introns. However, we propose that a “free-standing,” IEP-like protein, which is not encoded within any introns in the Chrysochromulina mt genome, is involved in the splicing of the first cox1 intron that lacks any open reading frames. PMID:25054084

  11. An Examination of a Small-Group Decoding Intervention for Struggling Readers: Comparing Accuracy and Automaticity Criteria

    ERIC Educational Resources Information Center

    Hudson, Roxanne F.; Isakson, Carole; Richman, Taylor; Lane, Holly B.; Arriaza-Allen, Stephanie

    2011-01-01

    In this study, we compared methods to improve the decoding and reading fluency of struggling readers. Second-grade poor readers were randomly assigned to one of the two practice conditions within a repeated reading intervention. Both interventions were in small groups, were 20-28 min long, took place 2-4 days per week, and consisted of phonemic…

  12. Using Video Self-Modelling to Increase Active Learning Responses during Small-Group Reading Instruction for Primary School Pupils with Social Emotional and Mental Health Difficulties

    ERIC Educational Resources Information Center

    Young-Pelton, Cheryl A.; Bushman, Samantha L.

    2015-01-01

    Effectiveness of a video self-modelling (VSM) intervention was examined with primary schoolchildren who attended a full-time special education programme for pupils with social emotional and behavioural difficulties and who exhibited inappropriate behaviour during small-group reading instruction. A randomised multiple-probe baseline design was used…

  13. Collective Beer Brand Identity: A Semiotic Analysis of the Websites Representing Small and Medium Enterprises in the Brewing Industry of Western PA

    ERIC Educational Resources Information Center

    Cincotta, Dominic

    2014-01-01

    This research studies how brand identities, individually and communally, as read through websites are created among small and medium-sized enterprise breweries in western Pennsylvania. Content analysis through the frame of Kress and van Leeuwen was used as the basis for the codebook that reads each brand identity for the researcher. The…

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

    PubMed

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

    2015-01-01

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

  15. Applicability of the Compensatory Encoding Model in Foreign Language Reading: An Investigation with Chinese College English Language Learners

    PubMed Central

    Han, Feifei

    2017-01-01

    While some first language (L1) reading models suggest that inefficient word recognition and small working memory tend to inhibit higher-level comprehension processes; the Compensatory Encoding Model maintains that slow word recognition and small working memory do not normally hinder reading comprehension, as readers are able to operate metacognitive strategies to compensate for inefficient word recognition and working memory limitation as long as readers process a reading task without time constraint. Although empirical evidence is accumulated for support of the Compensatory Encoding Model in L1 reading, there is lack of research for testing of the Compensatory Encoding Model in foreign language (FL) reading. This research empirically tested the Compensatory Encoding Model in English reading among Chinese college English language learners (ELLs). Two studies were conducted. Study one focused on testing whether reading condition varying time affects the relationship between word recognition, working memory, and reading comprehension. Students were tested on a computerized English word recognition test, a computerized Operation Span task, and reading comprehension in time constraint and non-time constraint reading. The correlation and regression analyses showed that the strength of association was much stronger between word recognition, working memory, and reading comprehension in time constraint than that in non-time constraint reading condition. Study two examined whether FL readers were able to operate metacognitive reading strategies as a compensatory way of reading comprehension for inefficient word recognition and working memory limitation in non-time constraint reading. The participants were tested on the same computerized English word recognition test and Operation Span test. They were required to think aloud while reading and to complete the comprehension questions. The think-aloud protocols were coded for concurrent use of reading strategies, classified into language-oriented strategies, content-oriented strategies, re-reading, pausing, and meta-comment. The correlation analyses showed that while word recognition and working memory were only significantly related to frequency of language-oriented strategies, re-reading, and pausing, but not with reading comprehension. Jointly viewed, the results of the two studies, complimenting each other, supported the applicability of the Compensatory Encoding Model in FL reading with Chinese college ELLs. PMID:28522984

  16. Applicability of the Compensatory Encoding Model in Foreign Language Reading: An Investigation with Chinese College English Language Learners.

    PubMed

    Han, Feifei

    2017-01-01

    While some first language (L1) reading models suggest that inefficient word recognition and small working memory tend to inhibit higher-level comprehension processes; the Compensatory Encoding Model maintains that slow word recognition and small working memory do not normally hinder reading comprehension, as readers are able to operate metacognitive strategies to compensate for inefficient word recognition and working memory limitation as long as readers process a reading task without time constraint. Although empirical evidence is accumulated for support of the Compensatory Encoding Model in L1 reading, there is lack of research for testing of the Compensatory Encoding Model in foreign language (FL) reading. This research empirically tested the Compensatory Encoding Model in English reading among Chinese college English language learners (ELLs). Two studies were conducted. Study one focused on testing whether reading condition varying time affects the relationship between word recognition, working memory, and reading comprehension. Students were tested on a computerized English word recognition test, a computerized Operation Span task, and reading comprehension in time constraint and non-time constraint reading. The correlation and regression analyses showed that the strength of association was much stronger between word recognition, working memory, and reading comprehension in time constraint than that in non-time constraint reading condition. Study two examined whether FL readers were able to operate metacognitive reading strategies as a compensatory way of reading comprehension for inefficient word recognition and working memory limitation in non-time constraint reading. The participants were tested on the same computerized English word recognition test and Operation Span test. They were required to think aloud while reading and to complete the comprehension questions. The think-aloud protocols were coded for concurrent use of reading strategies, classified into language-oriented strategies, content-oriented strategies, re-reading, pausing, and meta-comment. The correlation analyses showed that while word recognition and working memory were only significantly related to frequency of language-oriented strategies, re-reading, and pausing, but not with reading comprehension. Jointly viewed, the results of the two studies, complimenting each other, supported the applicability of the Compensatory Encoding Model in FL reading with Chinese college ELLs.

  17. 78 FR 46333 - Product Cancellation Order for Certain Pesticide Registrations; Correction

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-31

    ... 20460-0001. The Public Reading Room is open from 8:30 a.m. to 4:30 p.m., Monday through Friday, excluding legal holidays. The telephone number for the Public Reading Room is (202) 566-1744, and the telephone number for the OPP Docket is (703) 305-5805. Please review the visitor instructions and additional...

  18. 77 FR 47351 - Notification of Submission to the Secretaries of Agriculture and Health and Human Services...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-08

    ... Bldg., Rm. 3334, 1301 Constitution Ave. NW., Washington, DC 20460-0001. The Public Reading Room is open... the Public Reading Room is (202) 566-1744, and the telephone number for the OPP Docket is (703) 305- 5805. Please review the visitor instructions and additional information about the docket available at...

  19. 78 FR 72879 - Product Cancellation Order for Certain Pesticide Registrations; Correction

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-04

    ..., DC 20460-0001. The Public Reading Room is open from 8:30 a.m. to 4:30 p.m., Monday through Friday, excluding legal holidays. The telephone number for the Public Reading Room is (202) 566-1744, and the telephone number for the OPP Docket is (703) 305- 5805. Please review the visitor instructions and...

  20. Analyzing "Inconsistencies" in Practice: Teachers' Continued Use of Round Robin Reading

    ERIC Educational Resources Information Center

    Ash, Gwynne Ellen; Kuhn, Melanie R.; Walpole, Sharon

    2009-01-01

    This study analyzed in-service teachers' and literacy coaches' perceptions of Round Robin Reading to begin developing an understanding of the persistence of this practice in public schools in the United States. Surveying 80 teachers and 27 literacy coaches using an open-ended instrument, we found that many teachers continued to use Round Robin…

  1. Dorothy Day: A Love of Fiction and Her Love of the Poor

    ERIC Educational Resources Information Center

    Brady, Judith Ann

    2010-01-01

    Dorothy Day's love of the poor originated from reading novels that portrayed the poor as persons worthy of respect. This article explores how Day's reading novels opened her mind and heart to the realities of poverty. The methodology is literature-based. Dorothy Day's autobiography reveals the novelists who captivated her mind and cultivated a…

  2. Influence of Acculturation on Parents' Readings of and Expectations for Physical Education

    ERIC Educational Resources Information Center

    George, Meredith; Cutner-Smith, Matthew D.

    2018-01-01

    Purpose: The purpose of this study was to examine the influence of acculturation on parents' readings of and expectations for physical education. Method: Participants were 39 parents of pupils enrolled at one public middle school. Data were collected with an open-ended questionnaire and follow-up formal interviews. They were analyzed using…

  3. 75 FR 70241 - Compatibility of Underground Storage Tank Systems With Biofuel Blends

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-17

    ..., Room 3334, 1301 Constitution Ave., NW., Washington, DC. The Public Reading Room is open from 8:30 a.m... Reading Room is (202) 566-1744, and the telephone number for the UST Docket is (202) 566-0270. FOR FURTHER... that there are other reasonable ways to demonstrate compatibility. With that in mind, EPA is...

  4. 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…

  5. 36 CFR § 703.7 - Public Reading Facility.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...§ 703.7 Section § 703.7 Parks, Forests, and Public Property LIBRARY OF CONGRESS DISCLOSURE OR PRODUCTION OF RECORDS OR INFORMATION Availability of Library of Congress Records § 703.7 Public Reading... Library records. This facility shall be open to the public from 8:30 a.m. to 4:30 p.m., except Saturdays...

  6. 77 FR 6557 - Agency Information Collection Activities: Request for Comments on One Proposed Information...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-08

    ... Compliance Docket and Information Center (ECDIC), in the EPA Docket Center (EPA/DC), EPA West, Room 3334, 1301 Constitution Avenue NW., Washington, DC. The EPA/DC Public Reading Room is open from 8 a.m. to 4:30 p.m., Monday through Friday, excluding legal holidays. The telephone number for the Reading Room...

  7. 49 CFR 325.59 - Measurement procedure; stationary test.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... made of the sound level generated by a stationary motor vehicle as follows: (a) Park the motor vehicle... open throttle. Return the engine's speed to idle. (e) Observe the maximum reading on the sound level... this section until the first two maximum sound level readings that are within 2 dB(A) of each other are...

  8. 77 FR 13977 - Quality Assurance Requirements for Continuous Opacity Monitoring Systems at Stationary Sources

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-08

    ... instructions for submitting comments. Email: [email protected] . Fax: (202) 566-9744. Mail: Attention... Constitution Ave. NW., Washington, DC. The Docket Facility and Public Reading Room are open from 8:30 a.m. to 4... (202) 566-1742, and the telephone number for the Public Reading Room is (202) 566-1744. FOR FURTHER...

  9. Illustrations and supporting texts for sound standing waves of air columns in pipes in introductory physics textbooks

    NASA Astrophysics Data System (ADS)

    Zeng, Liang; Smith, Chris; Poelzer, G. Herold; Rodriguez, Jennifer; Corpuz, Edgar; Yanev, George

    2014-12-01

    In our pilot studies, we found that many introductory physics textbook illustrations with supporting text for sound standing waves of air columns in open-open, open-closed, and closed-closed pipes inhibit student understanding of sound standing wave phenomena due to student misunderstanding of how air molecules move within these pipes. Based on the construct of meaningful learning from cognitive psychology and semiotics, a quasiexperimental study was conducted to investigate the comparative effectiveness of two alternative approaches to student understanding: a traditional textbook illustration approach versus a newly designed air molecule motion illustration approach. Thirty volunteer students from introductory physics classes were randomly assigned to two groups of 15 each. Both groups were administered a presurvey. Then, group A read the air molecule motion illustration handout, and group B read a traditional textbook illustration handout; both groups were administered postsurveys. Subsequently, the procedure was reversed: group B read the air molecule motion illustration handout and group A read the traditional textbook illustration handout. This was followed by a second postsurvey along with an exit research questionnaire. The study found that the majority of students experienced meaningful learning and stated that they understood sound standing wave phenomena significantly better using the air molecule motion illustration approach. This finding provides a method for physics education researchers to design illustrations for abstract sound standing wave concepts, for publishers to improve their illustrations with supporting text, and for instructors to facilitate deeper learning in their students on sound standing waves.

  10. Syntactical Complexity and Vocabulary Diversity in Two Groups of Children's Books.

    ERIC Educational Resources Information Center

    McCormick, Sandra

    This study compared syntactic complexity and vocabulary diversity in two groups of books that can be used for reading aloud to preschool children: books recommended by authorities in reading and children's literature for reading aloud and "grocery store" books (small, inexpensive picture books that can be purchased in grocery stores). Trade names…

  11. Enhancing Literacy Instruction for Grade Level Readers in the Early Elementary Grades

    ERIC Educational Resources Information Center

    Warren, Marie

    2010-01-01

    Local school districts are under pressure to have elementary reading teachers understand how phonics, during teacher-led small group literacy instruction, can help students who read below grade level. Elementary teachers need research-based strategies regarding which reading instructions of letter-sound components are necessary to help students…

  12. Systems for Teaching Complex Texts: A Proof-of-Concept Investigation

    ERIC Educational Resources Information Center

    Fisher, Douglas; Frey, Nancy

    2016-01-01

    In this article we investigate the systems that need to be in place for students to learn from increasingly complex texts. Our concept, drawn from past research, includes clear learning targets, teacher modeling, collaborative conversations, close reading, small group reading, and wide reading. Using a "proof of concept" model, we follow…

  13. Adolescent Literacy: Learning and Understanding Content

    ERIC Educational Resources Information Center

    Goldman, Susan R.

    2012-01-01

    Learning to read--amazing as it is to small children and their parents--is one thing. Reading to learn, explains Susan Goldman of the University of Illinois at Chicago, is quite another. Are today's students able to use reading and writing to acquire knowledge, solve problems, and make decisions in academic, personal, and professional arenas? Do…

  14. Links between Early Rhythm Skills, Musical Training, and Phonological Awareness

    ERIC Educational Resources Information Center

    Moritz, Catherine; Yampolsky, Sasha; Papadelis, Georgios; Thomson, Jennifer; Wolf, Maryanne

    2013-01-01

    A small number of studies show that music training is associated with improvements in reading or in its component skills. A central question underlying this present research is whether musical activity can enhance the acquisition of reading skill, potentially before formal reading instruction begins. We explored two dimensions of this question: an…

  15. Reciprocal Peer Tutoring and Repeated Reading: Increasing Practicality Using Student Groups

    ERIC Educational Resources Information Center

    Oddo, Maria; Barnett, David W.; Hawkins, Renee O.; Musti-Rao, Shobana

    2010-01-01

    Previous research has investigated the efficacy of peer-mediated repeated reading (RR) interventions carried out by student dyads. This research extends the existing research by investigating the impact of RR on oral reading fluency and comprehension when carried out by a teacher in small groups of fourth-grade students. Outcomes were analyzed…

  16. Retooling the Reading Lesson: Matching the Right Tools to the Job.

    ERIC Educational Resources Information Center

    Short, Ruth A.; Kane, Mary; Peeling, Tammy

    2000-01-01

    Describes a year long literacy improvement project in two third-grade classrooms that focused on struggling readers. Describes small-group reading instruction in the classrooms that focused on 3 components: rereading familiar texts; shared and guided reading, incorporating strategy use in decoding unfamiliar words; and shared and guided writing.…

  17. Strategy Instruction Shifts Teacher and Student Interactions during Text-Based Discussions

    ERIC Educational Resources Information Center

    Boardman, Alison G.; Boelé, Amy L.; Klingner, Janette K.

    2018-01-01

    This study examined how teacher and student interactions were influenced by a multistrategy reading model, Collaborative Strategic Reading (CSR), where students learn to apply before-, during-, and after-reading strategies in small cooperative learning groups. Five middle school English language arts teachers and their students (N = 184)…

  18. 4th-Grade Readers . . . Not Too Old to Snuggle

    ERIC Educational Resources Information Center

    Gutshall, Anne

    2009-01-01

    Although parents and teachers appreciate the value of reading aloud to early elementary children, they often forget that upper elementary children can still benefit from individual attention during reading. A small pilot study in a South Carolina elementary school demonstrates the value of pairing adults and children for regular reading time.…

  19. A Computer Program for Training Eccentric Reading in Persons with Central Scotoma

    ERIC Educational Resources Information Center

    Kasten, Erich; Haschke, Peggy; Meinhold, Ulrike; Oertel-Verweyen, Petra

    2010-01-01

    This article explores the effectiveness of a computer program--Xcentric viewing--for training eccentric reading in persons with central scotoma. The authors conducted a small study to investigate whether this program increases the reading capacities of individuals with age-related macular degeneration (AMD). Instead of a control group, they…

  20. Coding System for the First Grade Reading Group Study.

    ERIC Educational Resources Information Center

    Brophy, Jere; And Others

    The First-Grade Reading Group Study is an experimental examination of teaching behaviors and their effects in first-grade reading groups. The specific teaching behaviors of interest are defined by a model for small group instruction which describes organization and management of the class, and ways of responding to children's answers that are…

  1. 32 CFR 1285.2 - Policy.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... information concerning the activities of its Government. DLA policy is to conduct its activities in an open... activities in an open manner consistent with the need for security and adherence to other requirements of law..., where a public reading room also serves as an activity's library, restricted publications may be...

  2. 32 CFR 1285.2 - Policy.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... information concerning the activities of its Government. DLA policy is to conduct its activities in an open... activities in an open manner consistent with the need for security and adherence to other requirements of law..., where a public reading room also serves as an activity's library, restricted publications may be...

  3. 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…

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

    PubMed

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

    2016-06-15

    Deep sequencing of the transcripts of regulatory non-coding RNA generates footprints of post-transcriptional processes. After obtaining sequence reads, the short reads are mapped to a reference genome, and specific mapping patterns can be detected called read mapping profiles, which are distinct from random non-functional degradation patterns. These patterns reflect the maturation processes that lead to the production of shorter RNA sequences. Recent next-generation sequencing studies have revealed not only the typical maturation process of miRNAs but also the various processing mechanisms of small RNAs derived from tRNAs and snoRNAs. We developed an algorithm termed SHARAKU to align two read mapping profiles of next-generation sequencing outputs for non-coding RNAs. In contrast with previous work, SHARAKU incorporates the primary and secondary sequence structures into an alignment of read mapping profiles to allow for the detection of common processing patterns. Using a benchmark simulated dataset, SHARAKU exhibited superior performance to previous methods for correctly clustering the read mapping profiles with respect to 5'-end processing and 3'-end processing from degradation patterns and in detecting similar processing patterns in deriving the shorter RNAs. Further, using experimental data of small RNA sequencing for the common marmoset brain, SHARAKU succeeded in identifying the significant clusters of read mapping profiles for similar processing patterns of small derived RNA families expressed in the brain. The source code of our program SHARAKU is available at http://www.dna.bio.keio.ac.jp/sharaku/, and the simulated dataset used in this work is available at the same link. Accession code: The sequence data from the whole RNA transcripts in the hippocampus of the left brain used in this work is available from the DNA DataBank of Japan (DDBJ) Sequence Read Archive (DRA) under the accession number DRA004502. yasu@bio.keio.ac.jp Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  5. But it's doctor recommended and I read the fine print: antecedents to drug companies' perceived credibility.

    PubMed

    Park, Jin Seong; Hoy, Mariea Grubbs

    2013-01-01

    Using 2009 National Consumer Survey data from Experian Simmons, the authors found that dependence on doctor recommendations to assess the integrity of advertised drugs and the extent of reading small print in direct-to-consumer prescription drug advertising positively related to consumers' perceived credibility of health information from pharmaceutical companies, which in turn positively influenced willingness to ask their doctor for a specific medicine they saw or heard advertised. The potential effect of small print reading on willingness to request prescription was partially mediated by perceived credibility of information from drug companies. The findings are discussed in light of their practical implications.

  6. The Open Global Glacier Model

    NASA Astrophysics Data System (ADS)

    Marzeion, B.; Maussion, F.

    2017-12-01

    Mountain glaciers are one of the few remaining sub-systems of the global climate system for which no globally applicable, open source, community-driven model exists. Notable examples from the ice sheet community include the Parallel Ice Sheet Model or Elmer/Ice. While the atmospheric modeling community has a long tradition of sharing models (e.g. the Weather Research and Forecasting model) or comparing them (e.g. the Coupled Model Intercomparison Project or CMIP), recent initiatives originating from the glaciological community show a new willingness to better coordinate global research efforts following the CMIP example (e.g. the Glacier Model Intercomparison Project or the Glacier Ice Thickness Estimation Working Group). In the recent past, great advances have been made in the global availability of data and methods relevant for glacier modeling, spanning glacier outlines, automatized glacier centerline identification, bed rock inversion methods, and global topographic data sets. Taken together, these advances now allow the ice dynamics of glaciers to be modeled on a global scale, provided that adequate modeling platforms are available. Here, we present the Open Global Glacier Model (OGGM), developed to provide a global scale, modular, and open source numerical model framework for consistently simulating past and future global scale glacier change. Global not only in the sense of leading to meaningful results for all glaciers combined, but also for any small ensemble of glaciers, e.g. at the headwater catchment scale. Modular to allow combinations of different approaches to the representation of ice flow and surface mass balance, enabling a new kind of model intercomparison. Open source so that the code can be read and used by anyone and so that new modules can be added and discussed by the community, following the principles of open governance. Consistent in order to provide uncertainty measures at all realizable scales.

  7. Evaluation of a Two-Phase Implementation of a Tier-2 (Small Group) Reading Intervention for Young Low-Progress Readers

    ERIC Educational Resources Information Center

    Buckingham, Jennifer; Wheldall, Kevin; Beaman-Wheldall, Robyn

    2014-01-01

    In a response to intervention (RtI) model, reading is taught in increasingly intensive tiers of instruction. The aim of the study was to examine the efficacy of a Tier-2 (small group) literacy intervention for young struggling readers. This article focuses on the second phase of a randomised control trial involving 14 students in kindergarten as…

  8. miRge - A Multiplexed Method of Processing Small RNA-Seq Data to Determine MicroRNA Entropy

    PubMed Central

    Myers, Jason R.; Gupta, Simone; Weng, Lien-Chun; Ashton, John M.; Cornish, Toby C.; Pandey, Akhilesh; Halushka, Marc K.

    2015-01-01

    Small RNA RNA-seq for microRNAs (miRNAs) is a rapidly developing field where opportunities still exist to create better bioinformatics tools to process these large datasets and generate new, useful analyses. We built miRge to be a fast, smart small RNA-seq solution to process samples in a highly multiplexed fashion. miRge employs a Bayesian alignment approach, whereby reads are sequentially aligned against customized mature miRNA, hairpin miRNA, noncoding RNA and mRNA sequence libraries. miRNAs are summarized at the level of raw reads in addition to reads per million (RPM). Reads for all other RNA species (tRNA, rRNA, snoRNA, mRNA) are provided, which is useful for identifying potential contaminants and optimizing small RNA purification strategies. miRge was designed to optimally identify miRNA isomiRs and employs an entropy based statistical measurement to identify differential production of isomiRs. This allowed us to identify decreasing entropy in isomiRs as stem cells mature into retinal pigment epithelial cells. Conversely, we show that pancreatic tumor miRNAs have similar entropy to matched normal pancreatic tissues. In a head-to-head comparison with other miRNA analysis tools (miRExpress 2.0, sRNAbench, omiRAs, miRDeep2, Chimira, UEA small RNA Workbench), miRge was faster (4 to 32-fold) and was among the top-two methods in maximally aligning miRNAs reads per sample. Moreover, miRge has no inherent limits to its multiplexing. miRge was capable of simultaneously analyzing 100 small RNA-Seq samples in 52 minutes, providing an integrated analysis of miRNA expression across all samples. As miRge was designed for analysis of single as well as multiple samples, miRge is an ideal tool for high and low-throughput users. miRge is freely available at http://atlas.pathology.jhu.edu/baras/miRge.html. PMID:26571139

  9. Development open source microcontroller based temperature data logger

    NASA Astrophysics Data System (ADS)

    Abdullah, M. H.; Che Ghani, S. A.; Zaulkafilai, Z.; Tajuddin, S. N.

    2017-10-01

    This article discusses the development stages in designing, prototyping, testing and deploying a portable open source microcontroller based temperature data logger for use in rough industrial environment. The 5V powered prototype of data logger is equipped with open source Arduino microcontroller for integrating multiple thermocouple sensors with their module, secure digital (SD) card storage, liquid crystal display (LCD), real time clock and electronic enclosure made of acrylic. The program for the function of the datalogger is programmed so that 8 readings from the thermocouples can be acquired within 3 s interval and displayed on the LCD simultaneously. The recorded temperature readings at four different points on both hydrodistillation show similar profile pattern and highest yield of extracted oil was achieved on hydrodistillation 2 at 0.004%. From the obtained results, this study achieved the objective of developing an inexpensive, portable and robust eight channels temperature measuring module with capabilities to monitor and store real time data.

  10. Short-Term Flooding Effects on Gas Exchange and Quantum Yield of Rabbiteye Blueberry (Vaccinium ashei Reade) 1

    PubMed Central

    Davies, Frederick S.; Flore, James A.

    1986-01-01

    Roots of 1.5-year-old `Woodard' rabbiteye blueberry plants (Vaccinium ashei Reade) were flooded in containers or maintained at container capacity over a 5-day period. Carbon assimilation, and stomatal and residual conductances were monitored on one fully expanded shoot/plant using an open flow gas analysis system. Quantum yield was calculated from light response curves. Carbon assimilation and quantum yield of flooded plants decreased to 64 and 41% of control values, respectively, after 1 day of flooding and continued decreasing to 38 and 27% after 4 days. Stomatal and residual conductances to CO2 also decreased after 1 day of flooding compared with those of unflooded plants with residual conductance severely limiting carbon assimilation after 4 days of flooding. Stomatal opening occurred in 75 to 90 minutes and rate of opening was unaffected by flooding. PMID:16664791

  11. Expression, purification and biochemical characterization of a single-stranded DNA binding protein from Herbaspirillum seropedicae.

    PubMed

    Vernal, Javier; Serpa, Viviane I; Tavares, Carolina; Souza, Emanuel M; Pedrosa, Fábio O; Terenzi, Hernán

    2007-05-01

    An open reading frame encoding a protein similar in size and sequence to the Escherichia coli single-stranded DNA binding protein (SSB protein) was identified in the Herbaspirillum seropedicae genome. This open reading frame was cloned into the expression plasmid pET14b. The SSB protein from H. seropedicae, named Hs_SSB, was overexpressed in E. coli strain BL21(DE3) and purified to homogeneity. Mass spectrometry data confirmed the identity of this protein. The apparent molecular mass of the native Hs_SSB was estimated by gel filtration, suggesting that the native protein is a tetramer made up of four similar subunits. The purified protein binds to single-stranded DNA (ssDNA) in a similar manner to other SSB proteins. The production of this recombinant protein in good yield opens up the possibility of obtaining its 3D-structure and will help further investigations into DNA metabolism.

  12. ReadXplorer—visualization and analysis of mapped sequences

    PubMed Central

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

    2014-01-01

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

  13. Increasing Literacy Skills for Students with Intellectual and Developmental Disabilities: Effects of Integrating Comprehensive Reading Instruction with Sign Language

    ERIC Educational Resources Information Center

    Beecher, Larissa; Childre, Amy

    2012-01-01

    This study evaluated the impact of a comprehensive reading program enhanced with sign language on the literacy and language skills of three elementary school students with intellectual and developmental disabilities. Students received individual and small group comprehensive reading instruction for approximately 55 minutes per session. Reading…

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

    ERIC Educational Resources Information Center

    Lin, Lu-Fang

    2017-01-01

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

  15. Patterson Road Elementary School Formula Phonics Reading Chain.

    ERIC Educational Resources Information Center

    Orcutt Union School District, CA.

    This program, included in "Effective Reading Programs...," serves 320 students in grades 2-6. The majority of the students are white and come from low- and middle-income homes in the sururbs of a small city. Staggered scheduling allows two ungraded reading chains of 12 groups each to meet 45 minutes daily. Grouping is determined not by…

  16. Close Reading of Literary Nonfiction: The Three-Column Journal

    ERIC Educational Resources Information Center

    McConn, Matthew

    2018-01-01

    The Common Core State Standards have placed more emphasis on the close reading of all texts, and have made a point of increasing the use of nonfiction in secondary English classrooms. In this article, the author describes an approach for implementing close reading of literary nonfiction. The approach comes from a small-scale classroom-based…

  17. Does It Say That? Tensions in Teacher Questions When the Text Has the Final Say

    ERIC Educational Resources Information Center

    Boelé, Amy L.

    2017-01-01

    Using sociocultural concepts of authoritative and dialogic discourse, I sought to examine 5th-grade teachers' questioning practices during small-group reading instruction to understand the differences between groups reading text on grade level and groups reading texts below grade level. The purpose was also to examine how questions functioned for…

  18. Strategic Reading Groups: Guiding Readers in the Middle Grades

    ERIC Educational Resources Information Center

    Berne, Jennifer; Degener, Sophie C.

    2012-01-01

    Strategic grouping can transform reading instruction in the middle grades from a hit-or-miss learning experience to a targeted, responsive one. This book features a practical and field-tested model for small-group differentiated reading instruction in Grades 4-8. Jennifer Berne and Sophie C. Degener offer a clear, detailed discussion of how to…

  19. Going Blended with a Triple-Entry Activity: Students' Online Discussions of Assigned Readings Using "Marginalia"

    ERIC Educational Resources Information Center

    Kanevsky, Lannie; Xin, Cindy; Ram, Ilana

    2016-01-01

    In this paper, we describe and investigate small group discussions of assigned readings in an online version of a "triple-entry activity" in a blended course used an annotation tool, "Marginalia". We wondered if students would interact in this structured, critical, reflective reading activity as effectively online as they had…

  20. Jottings: An Approach to Guiding Reading in the Elementary Classroom

    ERIC Educational Resources Information Center

    Knight, Jennifer A.; Justesen, Hilary A.

    2018-01-01

    Comprehension is the overall goal of reading. One approach to help students increase their comprehension is to discuss a text in small-group settings. Yet, many students struggle to fully engage in meaningful discussions within these groups. Students' ability to retain and share what they read is one reason for this lack of discussion. Teaching…

  1. Effects of Reciprocal Teaching on Reading Comprehension of Low-Achieving Adolescents. The Importance of Specific Teacher Skills

    ERIC Educational Resources Information Center

    Okkinga, Mariska; van Steensel, Roel; van Gelderen, Amos J. S.; Sleegers, Peter J. C.

    2018-01-01

    Low-achieving adolescents are known to have difficulties with reading comprehension. This article discusses how reciprocal teaching can improve low-achieving adolescents' reading comprehension in whole-classroom settings (as opposed to small-group settings) and to what extent intervention effects are dependent on teacher behaviour. Over the course…

  2. 13 CFR 108.40 - How to read this part 108.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 13 Business Credit and Assistance 1 2010-01-01 2010-01-01 false How to read this part 108. 108.40 Section 108.40 Business Credit and Assistance SMALL BUSINESS ADMINISTRATION NEW MARKETS VENTURE CAPITAL (âNMVCâ) PROGRAM Introduction to Part 108 § 108.40 How to read this part 108. (a) Center headings. All...

  3. Web-Based Text Structure Strategy Instruction Improves Seventh Graders' Content Area Reading Comprehension

    ERIC Educational Resources Information Center

    Wijekumar, Kausalai; Meyer, Bonnie J. F.; Lei, Puiwa

    2017-01-01

    Reading comprehension in the content areas is a challenge for many middle grade students. Text structure-based instruction has yielded positive outcomes in reading comprehension at all grade levels in small and large studies. The text structure strategy delivered via the web, called Intelligent Tutoring System for the Text Structure Strategy…

  4. An Evaluation of an Implementation of the Reading Recovery Program.

    ERIC Educational Resources Information Center

    Denton, Carolyn A.

    The effectiveness of the Reading Recovery Program, a literacy intervention for at-risk first-grade students, as it was implemented in 1995-96 in a small rural school district in Texas was studied. Reading Recovery consists of daily individual literacy tutoring sessions taught by a specially trained teacher, and emphasizes active engagement of the…

  5. 75 FR 54338 - Agency Information Collection Activities: Submission to OMB for Review and Approval; State Review...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-07

    ....gov : (our preferred method) Follow the on-line instructions for submitting comments. E-mail..., DC. The EPA Docket Center Public Reading Room is open from 8:30 a.m. to 4:30 p.m., Monday through Friday, excluding legal holidays. The telephone number for the Reading Room is (202) 566-1744, and the...

  6. Examining Central Issues in Literacy Research, Theory, and Practice. Forty-Second Yearbook of the National Reading Conference.

    ERIC Educational Resources Information Center

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

    The 43 conference papers in this yearbook cover such diverse topics in the field of reading as the analysis of children's literacy responses, the study of aesthetic literacy, and the investigation of phonemic awareness. The yearbook includes both data-driven studies and conceptual explorations of diverse literacy learners. The yearbook opens with…

  7. 75 FR 36650 - Agency Information Collection Activities: Proposed Collection; Comment Request; Recordkeeping...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-28

    ... Reading Room is open from 8 a.m. to 4:30 p.m., Monday through Friday, excluding legal holidays. The telephone number for the Reading Room is (202) 566-1744, and the telephone number for the Enforcement and... copying as specified in the statute. The regulations at 40 CFR part 169 (Books and Records of Pesticide...

  8. Excitement, Adventure, Indifference: Romance Readers' Perceptions of How Romance Reading Impacts Their Sex Lives

    ERIC Educational Resources Information Center

    Anderton, Gretchen E.

    2009-01-01

    This mixed-methods study examined romance readers' perceptions of how reading romance novels has impacted their sex lives, feelings about their sex partners, knowledge of sexuality and their sexual behavior. Fifty-three women romance readers over the age of 18 completed an online survey composed of multiple choice and open-ended essay questions. …

  9. Monster Magic: A Reading Activities Idea Book for Use with Children. A Fun with Reading Book.

    ERIC Educational Resources Information Center

    Fowler, Zinita

    Intended as a usable resource for librarians and teachers in planning and implementing a program for young library users and students, this book was developed to stimulate children to use the library. The introduction contains opening comments--including an explanation of how the theme of "monster magic" inspires creativity, specific goals, and a…

  10. 75 FR 13715 - Endangered and Threatened Wildlife and Plants; Revised Designation of Critical Habitat for Bull...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-23

    ... 1973, as amended. In total, approximately 36,498 kilometers (km) (22,679 miles (mi)) of streams (which... box that reads ``Enter Keyword or ID,'' enter the docket number for the proposed rule, which is FWS-R1-ES-2009-0085. Check the box that reads ``Open for Comment/Submission,'' and then click the Search...

  11. On the Use of the Immediate Recall Task as a Measure of Second Language Reading Comprehension

    ERIC Educational Resources Information Center

    Chang, Yuh-Fang

    2006-01-01

    The immediate written recall task, a widely used measure of both first language (L1) and second language (L2) reading comprehension, has been advocated over traditional test methods such as multiple choice, cloze tests and open-ended questions because it is a direct and integrative assessment task. It has been, however, criticized as requiring…

  12. Characterization of the 5’- and 3’-terminal subgenomic RNAs produced by a capillovirus: evidence for a CP subgenomic RNA

    USDA-ARS?s Scientific Manuscript database

    The members of Capillovirus genus encode two overlapping open reading frames (ORFs): ORF1 encodes a large polyprotein containing the domains of replication-associated proteins plus a coat protein (CP), and ORF2 encodes a movement protein, located within ORF1 in a different reading frame. Organizatio...

  13. 77 FR 13997 - Quality Assurance Requirements for Continuous Opacity Monitoring Systems at Stationary Sources

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-08

    ... comments. Email: [email protected] . Fax: (202) 566-9744. Mail: Attention Docket ID No. EPA-HQ-OAR...., Washington, DC. The Docket Facility and Public Reading Room are open from 8:30 a.m. to 4:30 p.m., Monday... the telephone number for the Public Reading Room is (202) 566-1744. FOR FURTHER INFORMATION CONTACT...

  14. Visionary leader 2009: Deborah Kumar.

    PubMed

    Zuppa, Barbara

    2010-01-01

    The following manuscript is the winning Visionary Leader 2009 entry submitted to Nursing Management in recognition of Deborah Kumar, MSN, RN, NEA-BC, Director, Medical Division, The Reading Hospital and Medical Center, West Reading, Pa. Deborah was formally recognized for her achievements during the opening ceremony of Congress 2009, September 9, in Chicago, Ill. There, she received the award, sponsored this year by B.E. Smith.

  15. Identification of the initiation site of poliovirus polyprotein synthesis

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

    Dorner, A.J.; Dorner, L.F.; Larsen, G.R.

    1982-06-01

    The complete nucleotide sequence of poliovirus RNA has a long open reading frame capable of encoding the precursor polyprotein NCVPOO. The first AUG codon in this reading frame is located 743 nucleotides from the 5' end of the RNA and is preceded by eight AUG codons in all three reading frames. Because all proteins that map at the amino terminus of the polyprotein (P1-1a, VPO, and VP4) are blocked at their amino termini and previous studies of ribosome binding have been inconclusive, direct identification of the initiation site of protein synthesis was difficult. We separated and identified all of themore » tryptic peptides of capsid protein VP4 and correlated these peptides with the amino acid sequence predicted to follow the AUG codon at nucleotide 743. Our data indicate that VP4 begins with a blocked glycine that is encoded immediately after the AUG codon at nucleotide 743. An S1 nuclease analysis of poliovirus mRNA failed to reveal a splice in the 5' region. We concluded that synthesis of poliovirus polyprotein is initiated at nucleotide 743, the first AUG codon in the long open reading frame.« less

  16. AN ADA NAMELIST PACKAGE

    NASA Technical Reports Server (NTRS)

    Klumpp, A. R.

    1994-01-01

    The Ada Namelist Package, developed for the Ada programming language, enables a calling program to read and write FORTRAN-style namelist files. A namelist file consists of any number of assignment statements in any order. Features of the Ada Namelist Package are: the handling of any combination of user-defined types; the ability to read vectors, matrices, and slices of vectors and matrices; the handling of mismatches between variables in the namelist file and those in the programmed list of namelist variables; and the ability to avoid searching the entire input file for each variable. The principle user benefits of this software are the following: the ability to write namelist-readable files, the ability to detect most file errors in the initialization phase, a package organization that reduces the number of instantiated units to a few packages rather than to many subprograms, a reduced number of restrictions, and an increased execution speed. The Ada Namelist reads data from an input file into variables declared within a user program. It then writes data from the user program to an output file, printer, or display. The input file contains a sequence of assignment statements in arbitrary order. The output is in namelist-readable form. There is a one-to-one correspondence between namelist I/O statements executed in the user program and variables read or written. Nevertheless, in the input file, mismatches are allowed between assignment statements in the file and the namelist read procedure statements in the user program. The Ada Namelist Package itself is non-generic. However, it has a group of nested generic packages following the nongeneric opening portion. The opening portion declares a variety of useraccessible constants, variables and subprograms. The subprograms are procedures for initializing namelists for reading, reading and writing strings. The subprograms are also functions for analyzing the content of the current dataset and diagnosing errors. Two nested generic packages follow the opening portion. The first generic package contains procedures that read and write objects of scalar type. The second contains subprograms that read and write one and two-dimensional arrays whose components are of scalar type and whose indices are of either of the two discrete types (integer or enumeration). Subprograms in the second package also read and write vector and matrix slices. The Ada Namelist ASCII text files are available on a 360k 5.25" floppy disk written on an IBM PC/AT running under the PC DOS operating system. The largest subprogram in the package requires 150k of memory. The package was developed using VAX Ada v. 1.5 under DEC VMS v. 4.5. It should be portable to any validated Ada compiler. The software was developed in 1989, and is a copyrighted work with all copyright vested in NASA.

  17. Reading and deaf individuals: perspectives on the qualitative similarity hypothesis.

    PubMed

    Wang, Ye; Andrews, Jean

    2014-01-01

    In this, the first article in the American Annals of the Deaf special issue on English reading development for individuals who are d/Deaf and hard of hearing, the coeditors aim to promote interdisciplinary dialogue among researchers regarding literacy research with d/Deaf and hard of hearing (d/Dhh) students by setting the tone for an open and inclusive forum. Researchers from various disciplines are invited to discuss the similarities and differences between students who are d/Dhh and their typically developing hearing peers in terms of aspects such as reading process, reading development, and reading assessment. Challenges related to the acquisition of language and literacy by d/Dhh students are described. The article highlights the purpose of the special issue, which is to explore what works where, when, why, and for whom.

  18. Beyond open access: open discourse, the next great equalizer.

    PubMed

    Dayton, Andrew I

    2006-08-30

    The internet is expanding the realm of scientific publishing to include free and open public debate of published papers. Journals are beginning to support web posting of comments on their published articles and independent organizations are providing centralized web sites for posting comments about any published article. The trend promises to give one and all access to read and contribute to cutting edge scientific criticism and debate.

  19. A new open reading frame in the genome of the cyanobacterium Synechocystis sp. PCC 6803

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

    Lysenko, E.S.; Ogarkova, O.A.; Tarasov, V.A.

    1995-02-01

    A new open reading frame ORF242, coding for a 26.47-kDa polypeptide, was found in a DNA fragment of the cyanobacterium Synechocystis 6803, transforming a photosynthetic mutant to photoautotrophy and having homology with plant chloroplast DNA. In the 5{prime} flanking region of ORF242, consensus sequences characteristic of a functioning gene were found. One copy of ORF242 is present in the Synechocystis 6803 genome. Insertion inactivation of ORF242 does not lead to a decrease in photosynthetic activity in cells of cyanobacteria but may influence the ratio between active complexes of photosystems I and II. 22 refs., 6 figs., 2 tabs.

  20. The open reading frames in the 3' long terminal repeats of several mouse mammary tumor virus integrants encode V beta 3-specific superantigens

    PubMed Central

    1992-01-01

    Mice expressing the minor lymphocyte stimulation antigens, Mls-1a, -2a, or -3a, singly on the B10.BR background have been generated. Mls phenotypes correlate with the integration of mouse mammary tumor viruses (MTV) in the mouse genome. The open reading frames within the 3' long terminal repeats of the integrated MTVs 1, 3, 6, and 13 encode V beta 3-specific superantigens. Sequence data for these viral superantigens is presented, indicating that it is the COOH-terminal portion of the viral superantigen that interacts with the T cell receptor V beta element. PMID:1309854

  1. Transcription-associated mutational pressure in the Parvovirus B19 genome: Reactivated genomes contribute to the variability of viral populations.

    PubMed

    Khrustalev, Vladislav Victorovich; Ermalovich, Marina Anatolyevna; Hübschen, Judith M; Khrustaleva, Tatyana Aleksandrovna

    2017-12-21

    In this study we used non-overlapping parts of the two long open reading frames coding for nonstructural (NS) and capsid (VP) proteins of all available sequences of the Parvovirus B19 subgenotype 1a genome and found out that the rates of A to G, C to T and A to T mutations are higher in the first long reading frame (NS) of the virus than in the second one (VP). This difference in mutational pressure directions for two parts of the same viral genome can be explained by the fact of transcription of just the first long reading frame during the lifelong latency in nonerythroid cells. Adenine deamination (producing A to G and A to T mutations) and cytosine deamination (producing C to T mutations) occur more frequently in transcriptional bubbles formed by DNA "plus" strand of the first open reading frame. These mutations can be inherited only in case of reactivation of the infectious virus due to the help of Adenovirus that allows latent Parvovirus B19 to start transcription of the second reading frame and then to replicate its genome by the rolling circle mechanism using the specific origin. Results of this study provide evidence that the genomes reactivated from latency make significant contributions to the variability of Parvovirus B19. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. "Sponge" Up that Time for Reading.

    ERIC Educational Resources Information Center

    Clary, Linda Mixon

    1989-01-01

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

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

    PubMed

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

    2012-02-01

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

  4. Pathobiologic Roles of Epstein–Barr Virus-Encoded MicroRNAs in Human Lymphomas

    PubMed Central

    Navari, Mohsen; Etebari, Maryam; Ibrahimi, Mostafa; Leoncini, Lorenzo

    2018-01-01

    Epstein–Barr virus (EBV) is a human γ-herpesvirus implicated in several human malignancies, including a wide range of lymphomas. Several molecules encoded by EBV in its latent state are believed to be related to EBV-induced lymphomagenesis, among which microRNAs—small RNAs with a posttranscriptional regulating role—are of great importance. The genome of EBV encodes 44 mature microRNAs belonging to two different classes, including BamHI-A rightward transcript (BART) and Bam HI fragment H rightward open reading frame 1 (BHRF1), with different expression levels in different EBV latency types. These microRNAs might contribute to the pathogenetic effects exerted by EBV through targeting self mRNAs and host mRNAs and interfering with several important cellular mechanisms such as immunosurveillance, cell proliferation, and apoptosis. In addition, EBV microRNAs can regulate the surrounding microenvironment of the infected cells through exosomal transportation. Moreover, these small molecules could be potentially used as molecular markers. In this review, we try to present an updated and extensive view of the role of EBV-encoded miRNAs in human lymphomas. PMID:29649101

  5. Nucleotide sequence of the Varkud mitochondrial plasmid of Neurospora and synthesis of a hybrid transcript with a 5' leader derived from mitochondrial RNA.

    PubMed

    Akins, R A; Grant, D M; Stohl, L L; Bottorff, D A; Nargang, F E; Lambowitz, A M

    1988-11-05

    The Mauriceville and Varkud mitochondrial plasmids of Neurospora are closely related, closed circular DNAs (3.6 and 3.7 kb, respectively; 1 kb = 10(3) bases or base-pairs), whose characteristics suggest relationships to mitochondrial DNA introns and retrotransposons. Here, we characterized the structure of the Varkud plasmid, determined its complete nucleotide sequence and mapped its major transcripts. The Mauriceville and Varkud plasmids have more than 97% positional identity. Both plasmids contain a 710 amino acid open reading frame that encodes a reverse transcriptase-like protein. The amino acid sequence of this open reading frame is strongly conserved between the two plasmids (701/710 amino acids) as expected for a functionally important protein. Both plasmids have a 0.4 kb region that contains five PstI palindromes and a direct repeat of approximately 160 base-pairs. Comparison of sequences in this region suggests that the Varkud plasmid has diverged less from a common ancestor than has the Mauriceville plasmid. Two major transcripts of the Varkud plasmid were detected by Northern hybridization experiments: a full-length linear RNA of 3.7 kb and an additional prominent transcript of 4.9 kb, 1.2 kb longer than monomer plasmid. Remarkably, we find that the 4.9 kb transcript is a hybrid RNA consisting of the full-length 3.7 kb Varkud plasmid transcript plus a 5' leader of 1.2 kb that is derived from the 5' end of the mitochondrial small rRNA. This and other findings suggest that the Varkud plasmid, like certain RNA viruses, has a mechanism for joining heterologous RNAs to the 5' end of its major transcript, and that, under some circumstances, nucleotide sequences in mitochondria may be recombined at the RNA level.

  6. The site-specific ribosomal insertion element type II of Bombyx mori (R2Bm) contains the coding sequence for a reverse transcriptase-like enzyme.

    PubMed Central

    Burke, W D; Calalang, C C; Eickbush, T H

    1987-01-01

    Two classes of DNA elements interrupt a fraction of the rRNA repeats of Bombyx mori. We have analyzed by genomic blotting and sequence analysis one class of these elements which we have named R2. These elements occupy approximately 9% of the rDNA units of B. mori and appear to be homologous to the type II rDNA insertions detected in Drosophila melanogaster. Approximately 25 copies of R2 exist within the B. mori genome, of which at least 20 are located at a precise location within otherwise typical rDNA units. Nucleotide sequence analysis has revealed that the 4.2-kilobase-pair R2 element has a single large open reading frame, occupying over 82% of the total length of the element. The central region of this 1,151-amino-acid open reading frame shows homology to the reverse transcriptase enzymes found in retroviruses and certain transposable elements. Amino acid homology of this region is highest to the mobile line 1 elements of mammals, followed by the mitochondrial type II introns of fungi, and the pol gene of retroviruses. Less homology exists with transposable elements of D. melanogaster and Saccharomyces cerevisiae. Two additional regions of sequence homology between L1 and R2 elements were also found outside the reverse transcriptase region. We suggest that the R2 elements are retrotransposons that are site specific in their insertion into the genome. Such mobility would enable these elements to occupy a small fraction of the rDNA units of B. mori despite their continual elimination from the rDNA locus by sequence turnover. Images PMID:2439905

  7. Reading apps for children: Readability from the design perspective

    NASA Astrophysics Data System (ADS)

    Mohammed, Wasan Abdulwahab; Husni, Husniza

    2017-10-01

    Electronic reading for young children opens new avenues especially with the advance of modern reading devices. The readability of mobile learning applications has received extensive attention by the designers and developers. The reason for such concern is due to its importance in determining usability related issues especially in the design context for children. In many cases, children find it difficult to interact with mobile reading apps. This is because apps for reading and for entertainment require different features. As such, this study sets out three objectives: 1) to evaluate five reading apps for young children from design perspectives; 2) to examine the readability for current existing mobile apps for reading and 3) to propose and evaluate mobile apps UI guideline for readability. Readability indices, observation and interview were conducted on 6 - 8 years old students. The obtained result showed that certain reading apps provide better reading experience for children than others. Some of the reasons are mostly related to the design characteristics embedded within the app. In addition, the use of animation was found to stimulate children reading experience as it is believed to offer the interactivity elements to gain their interest and willingness to read. These findings are believed to provide the recommendations and insights for designers of reading apps for children.

  8. An Upstream Open Reading Frame Is Essential for Feedback Regulation of Ascorbate Biosynthesis in Arabidopsis

    PubMed Central

    Laing, William A.; Martínez-Sánchez, Marcela; Wright, Michele A.; Bulley, Sean M.; Brewster, Di; Dare, Andrew P.; Rassam, Maysoon; Wang, Daisy; Storey, Roy; Macknight, Richard C.; Hellens, Roger P.

    2015-01-01

    Ascorbate (vitamin C) is an essential antioxidant and enzyme cofactor in both plants and animals. Ascorbate concentration is tightly regulated in plants, partly to respond to stress. Here, we demonstrate that ascorbate concentrations are determined via the posttranscriptional repression of GDP-l-galactose phosphorylase (GGP), a major control enzyme in the ascorbate biosynthesis pathway. This regulation requires a cis-acting upstream open reading frame (uORF) that represses the translation of the downstream GGP open reading frame under high ascorbate concentration. Disruption of this uORF stops the ascorbate feedback regulation of translation and results in increased ascorbate concentrations in leaves. The uORF is predicted to initiate at a noncanonical codon (ACG rather than AUG) and encode a 60- to 65-residue peptide. Analysis of ribosome protection data from Arabidopsis thaliana showed colocation of high levels of ribosomes with both the uORF and the main coding sequence of GGP. Together, our data indicate that the noncanonical uORF is translated and encodes a peptide that functions in the ascorbate inhibition of translation. This posttranslational regulation of ascorbate is likely an ancient mechanism of control as the uORF is conserved in GGP genes from mosses to angiosperms. PMID:25724639

  9. An upstream open reading frame is essential for feedback regulation of ascorbate biosynthesis in Arabidopsis.

    PubMed

    Laing, William A; Martínez-Sánchez, Marcela; Wright, Michele A; Bulley, Sean M; Brewster, Di; Dare, Andrew P; Rassam, Maysoon; Wang, Daisy; Storey, Roy; Macknight, Richard C; Hellens, Roger P

    2015-03-01

    Ascorbate (vitamin C) is an essential antioxidant and enzyme cofactor in both plants and animals. Ascorbate concentration is tightly regulated in plants, partly to respond to stress. Here, we demonstrate that ascorbate concentrations are determined via the posttranscriptional repression of GDP-l-galactose phosphorylase (GGP), a major control enzyme in the ascorbate biosynthesis pathway. This regulation requires a cis-acting upstream open reading frame (uORF) that represses the translation of the downstream GGP open reading frame under high ascorbate concentration. Disruption of this uORF stops the ascorbate feedback regulation of translation and results in increased ascorbate concentrations in leaves. The uORF is predicted to initiate at a noncanonical codon (ACG rather than AUG) and encode a 60- to 65-residue peptide. Analysis of ribosome protection data from Arabidopsis thaliana showed colocation of high levels of ribosomes with both the uORF and the main coding sequence of GGP. Together, our data indicate that the noncanonical uORF is translated and encodes a peptide that functions in the ascorbate inhibition of translation. This posttranslational regulation of ascorbate is likely an ancient mechanism of control as the uORF is conserved in GGP genes from mosses to angiosperms. © 2015 American Society of Plant Biologists. All rights reserved.

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

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

    Chen, Lei

    2008-01-01

    Open reading frame 11 (ORF11) of Kaposi's sarcoma-associated herpesvirus belongs to a herpesviral homologous protein family shared by some members of the gamma- herpesvirus subfamily. Little is known about this ORF11 homologous protein family. We have characterized an unknown open reading frame, ORF11, located adjacent and in the opposite orientation to a well-characterized viral IL-6 gene. Northern blot analysis reveals that ORF11 is expressed during the KSHV lytic cycle with delayed-early transcription kinetics. We have determined the 5{prime} and 3{prime} untranslated region of the unspliced ORF11 transcript and identified both the transcription start site and the transcription termination site. Coremore » promoter region, representing ORF11 promoter activity, was mapped to a 159nt fragment 5{prime} most proximal to the transcription start site. A functional TATA box was identified in the core promoter region. Interestingly, we found that ORF11 transcriptional activation is not responsive to Rta, the KSHV lytic switch protein. We also discovered that part of the ORF11 promoter region, the 209nt fragment upstream of the transcription start site, was repressed by phorbol esters. Our data help to understand transcription regulation of ORF11 and to elucidate roles of ORF11 in KSHV pathogenesis and life cycle.« less

  11. A local duplication of the Melanocortin receptor 1 locus in Astyanax

    PubMed Central

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

    2017-01-01

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

  12. The TGA codons are present in the open reading frame of selenoprotein P cDNA

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

    Hill, K.E.; Lloyd, R.S.; Read, R.

    1991-03-11

    The TGA codon in DNA has been shown to direct incorporation of selenocysteine into protein. Several proteins from bacteria and animals contain selenocysteine in their primary structures. Each of the cDNA clones of these selenoproteins contains one TGA codon in the open reading frame which corresponds to the selenocysteine in the protein. A cDNA clone for selenoprotein P (SeP), obtained from a {gamma}ZAP rat liver library, was sequenced by the dideoxy termination method. The correct reading frame was determined by comparison of the deduced amino acid sequence with the amino acid sequence of several peptides from SeP. Using SeP labelledmore » with {sup 75}Se in vivo, the selenocysteine content of the peptides was verified by the collection of carboxymethylated {sup 77}Se-selenocysteine as it eluted from the amino acid analyzer and determination of the radioactivity contained in the collected samples. Ten TGA codons are present in the open reading frame of the cDNA. Peptide fragmentation studies and the deduced sequence indicate that selenium-rich regions are located close to the carboxy terminus. Nine of the 10 selenocysteines are located in the terminal 26% of the sequence with four in the terminal 15 amino acids. The deduced sequence codes for a protein of 385 amino acids. Cleavage of the signal peptide gives the mature protein with 366 amino acids and a calculated mol wt of 41,052 Da. Searches of PIR and SWISSPROT protein databases revealed no similarity with glutathione peroxidase or other selenoproteins.« less

  13. Experts and Novices Reading Literature: An Analysis of Disciplinary Literacy in English Language Arts

    ERIC Educational Resources Information Center

    Reynolds, Todd; Rush, Leslie S.

    2017-01-01

    The purpose of this pilot study is to examine how experts and novices in the study of literary texts read those texts, and to make suggestions for an English Language Arts (ELA) disciplinary literacy based on those findings. A small sample of experts and novices, four professors of literature and four college freshmen, participated in read-alouds…

  14. An Experimental Study of Scheduling and Duration of "Tier 2" First-Grade Reading Intervention

    ERIC Educational Resources Information Center

    Denton, Carolyn A.; Cirino, Paul T.; Barth, Amy E.; Romain, Melissa; Vaughn, Sharon; Wexler, Jade; Francis, David J.; Fletcher, Jack M.

    2011-01-01

    This study compared the effects on reading outcomes of delivering supplemental, small-group intervention to first-grade students at risk for reading difficulties randomly assigned to one of three different treatment schedules: extended (4 sessions per week, 16 weeks; n = 66), concentrated (4 sessions per week, 8 weeks; n = 64), or distributed (2…

  15. Developmental Reading and Nursing Program Partnerships: Helping Students Succeed in Reading-Intensive Coursework

    ERIC Educational Resources Information Center

    Costanzo, Ryan D.; Fitzpatrick, Amanda

    2012-01-01

    While clinical competence and hands-on ability are crucial to nursing, students in college-based nursing programs face almost certain failure if they lack skills and strategies for textbook reading. Faculty and staff at a small liberal arts college with a two-year nursing program used focus groups consisting of first-semester and final-semester…

  16. Lessons Learned in Dreamland: How a Small Urban Charter School Overcame Start-Up Woes to Increase Reading Scores 28 Percent

    ERIC Educational Resources Information Center

    Carter, Carolyn J.

    2011-01-01

    Charter school administrators weathered start-up woes, among them challenging students with unmet needs, verbal assaults, dwindling student enrollment, and a first-year budget deficit exceeding $200,000 to implement a reading improvement strategy that holds promise for helping at-risk students read better, a point particularly underscored…

  17. The Relationship between Bible Reading and Attitude toward Substance Use among 13-15 Year Olds

    ERIC Educational Resources Information Center

    Francis, Leslie J.

    2002-01-01

    The relationship between Bible reading and attitude toward drug use is examined among a sample of 25,888 teenagers, 13-15 year olds, throughout England and Wales. Information about sex, age, personality, belief in God, and church attendance was also considered. The conclusion is that Bible reading makes a small but significant contribution to…

  18. 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…

  19. 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…

  20. Correction to: CYP79 P450 monooxygenases in gymnosperms: CYP79A118 is associated with the formation of taxiphyllin in Taxus baccata.

    PubMed

    Luck, Katrin; Jia, Qidong; Huber, Meret; Handrick, Vinzenz; Wong, Gane Ka-Shu; Nelson, David R; Chen, Feng; Gershenzon, Jonathan; Köllner, Tobias G

    2017-12-01

    Due to an unfortunate turn of events, the funding note for Open Access publication was not properly provided in the original publication. Hence, the original article has been corrected. The opening line of the Acknowledgement section should read.

  1. Washington Headquarters Services

    Science.gov Websites

    Status OPM Status: Open Open Main Navigation Home Our Services Our Customers Our People Our Leaders Our Organization Contact Us CAC Site Navigation Customers Employees Our Services Our Customers Our People Our facilities in the Washington, DC area. Read more about Our Customers Our People A picture with the left edge

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

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... correspondence prohibited. 145.3 Section 145.3 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF... correspondence. Except as provided in paragraph (e), Customs officers and employees may open and examine sealed... than, correspondence, provided they have reasonable cause to suspect the presence of merchandise or...

  3. 4 Massive Open Online Courses and How They Work

    ERIC Educational Resources Information Center

    Gose, Ben

    2012-01-01

    Massive open online courses (MOOC's) are the latest development in online education. Over the past decade, millions of students have taken free online versions of existing courses at well-known universities like the Massachusetts Institute of Technology, but such courses often offered little more than reading lists and lecture notes. MOOC's are…

  4. Quantitative and Qualitative Involvement of P3N-PIPO in Overcoming Recessive Resistance against Clover Yellow Vein Virus in Pea Carrying the cyv1 Gene

    PubMed Central

    Choi, Sun Hee; Hagiwara-Komoda, Yuka; Atsumi, Go; Shimada, Ryoko; Hisa, Yusuke; Naito, Satoshi

    2013-01-01

    In pea carrying cyv1, a recessive gene for resistance to Clover yellow vein virus (ClYVV), ClYVV isolate Cl-no30 was restricted to the initially infected cells, whereas isolate 90-1 Br2 overcame this resistance. We mapped the region responsible for breaking of cyv1-mediated resistance by examining infection of cyv1 pea with chimeric viruses constructed from parts of Cl-no30 and 90-1 Br2. The breaking of resistance was attributed to the P3 cistron, which is known to produce two proteins: P3, from the main open reading frame (ORF), and P3N-PIPO, which has the N-terminal part of P3 fused to amino acids encoded by a small open reading frame (ORF) called PIPO in the +2 reading frame. We introduced point mutations that were synonymous with respect to the P3 protein but nonsynonymous with respect to the P3N-PIPO protein, and vice versa, into the chimeric viruses. Infection of plants with these mutant viruses revealed that both P3 and P3N-PIPO were involved in overcoming cyv1-mediated resistance. Moreover, P3N-PIPO quantitatively affected the virulence of Cl-no30 in cyv1 pea. Additional expression in trans of the P3N-PIPO derived from Cl-no30, using White clover mosaic virus as a vector, enabled Cl-no30 to move to systemic leaves in cyv1 pea. Susceptible pea plants infected with chimeric ClYVV possessing the P3 cistron of 90-1 Br2, and which were therefore virulent toward cyv1 pea, accumulated more P3N-PIPO than did those infected with Cl-no30, suggesting that the higher level of P3N-PIPO in infected cells contributed to the breaking of resistance by 90-1 Br2. This is the first report showing that P3N-PIPO is a virulence determinant in plants resistant to a potyvirus. PMID:23616656

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

    PubMed

    Kisand, Veljo; Lettieri, Teresa

    2013-04-01

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

  6. Human milk metagenome: a functional capacity analysis

    PubMed Central

    2013-01-01

    Background Human milk contains a diverse population of bacteria that likely influences colonization of the infant gastrointestinal tract. Recent studies, however, have been limited to characterization of this microbial community by 16S rRNA analysis. In the present study, a metagenomic approach using Illumina sequencing of a pooled milk sample (ten donors) was employed to determine the genera of bacteria and the types of bacterial open reading frames in human milk that may influence bacterial establishment and stability in this primal food matrix. The human milk metagenome was also compared to that of breast-fed and formula-fed infants’ feces (n = 5, each) and mothers’ feces (n = 3) at the phylum level and at a functional level using open reading frame abundance. Additionally, immune-modulatory bacterial-DNA motifs were also searched for within human milk. Results The bacterial community in human milk contained over 360 prokaryotic genera, with sequences aligning predominantly to the phyla of Proteobacteria (65%) and Firmicutes (34%), and the genera of Pseudomonas (61.1%), Staphylococcus (33.4%) and Streptococcus (0.5%). From assembled human milk-derived contigs, 30,128 open reading frames were annotated and assigned to functional categories. When compared to the metagenome of infants’ and mothers’ feces, the human milk metagenome was less diverse at the phylum level, and contained more open reading frames associated with nitrogen metabolism, membrane transport and stress response (P < 0.05). The human milk metagenome also contained a similar occurrence of immune-modulatory DNA motifs to that of infants’ and mothers’ fecal metagenomes. Conclusions Our results further expand the complexity of the human milk metagenome and enforce the benefits of human milk ingestion on the microbial colonization of the infant gut and immunity. Discovery of immune-modulatory motifs in the metagenome of human milk indicates more exhaustive analyses of the functionality of the human milk metagenome are warranted. PMID:23705844

  7. 76 FR 2677 - Request Facilities To Report Toxics Release Inventory Information Electronically or Complete Fill...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-14

    ... through Friday, excluding legal holidays. The EPA Docket Center Public Reading Room is open from 8:30 a.m... Reading Room is (202) 566-1744, and the telephone number for the OEI Docket is (202) 566-1752. 2... data faster than when the data are submitted on hard-copy forms. In light of the features and tools TRI...

  8. How the Science versus Religion Debate Has Missed the Point of Genesis 1 and 2: Jacques Ellul (1912-1994)

    ERIC Educational Resources Information Center

    Vanderburg, Willem H.

    2010-01-01

    From a social and historical perspective, the conflict between science and religion regarding the opening chapters of Genesis in the Jewish and Christian Bibles may have more to do with uncritically reading these texts through our "cultural glasses" than with what these texts actually say. Within the context of his work, Jacques Ellul read these…

  9. Comprehension of Health-related Written Materials by Older Adults

    PubMed Central

    Liu, Chiung-ju; Kemper, Susan; Bovaird, James A.

    2008-01-01

    This study examined how Flesch Reading Ease and text cohesion affect older adults' comprehension of common health texts. All older adults benefited when high Flesh Reading Ease was combined with high cohesion. Older adults with small working memories had more difficulty understanding texts high in Flesch Reading Ease. Additionally, older adults with low verbal ability or older than 77 years of age had difficulty understanding texts high in text cohesion but low in Flesch Reading Ease. These results imply that writers must increase Flesch Reading Ease without disrupting text cohesion to ensure comprehension of health-related texts. PMID:19543546

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2014-08-01

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

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

    PubMed Central

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

    2014-01-01

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

  13. High School Students With Reading Comprehension Difficulties: Results of a Randomized Control Trial of a Two-Year Reading Intervention.

    PubMed

    Vaughn, Sharon; Roberts, Greg; Wexler, Jade; Vaughn, Michael G; Fall, Anna-Mária; Schnakenberg, Jennifer B

    2015-01-01

    A 2-year, randomized control trial with 9th to 10th grade students with significant reading problems was provided for 50 minutes a day in small groups. Comparison students were provided an elective class and treatment students the reading intervention. Students were identified as demonstrating reading difficulties through failure on their state accountability test and were randomly assigned to one of three treatment conditions and a business as usual (BAU) condition: reading without dropout prevention, reading with dropout prevention, dropout prevention without reading, or a BAU condition. Findings from the 2-year reading intervention (reading with and without dropout prevention combined and BAU) are reported in this article. Students in reading treatment compared to students in BAU demonstrated significant gains on reading comprehension (effect size = .43), and improved reading was associated with better grades in social studies. Findings from this study provide a rationale for further implementation and investigation of intensive intervention for high school students with reading difficulties. © Hammill Institute on Disabilities 2014.

  14. Assessing the Promise of a Supplemental Reading Intervention for At-Risk First Grade Students in a Public School Setting

    ERIC Educational Resources Information Center

    Mokhtari, Kouider; Neel, Joanna L.; Kaiser, Forrest; Le, Hong-Hai

    2015-01-01

    In this exploratory quasi-experimental case study, we assessed the promise of a yearlong supplemental reading intervention with a small pilot group of at-risk first grade readers in an elementary school setting. Using standardized measures of reading proficiency, we found that after 47 hours of one-on-one tutoring instruction, students read…

  15. Reading Habits of Secondary School Teachers: A Study of Selected Secondary Schools in Addis Ababa and Dessie

    ERIC Educational Resources Information Center

    Hassen, Rukya

    2016-01-01

    This study is a small-scale study of an exploration of reading habit of high school teachers. Fifty-four teachers from five schools who teach in different schools in Addis Ababa and Dessie participated in this study. Data were collected through questionnaire and in-depth interview. The result of the study shows that reading is poorly developed…

  16. Report on Phase I (Interest, Comprehension, & Readability) Prepublication Learner Verification of "Reading Basics Plus," Harper & Row, Publishers, Inc.

    ERIC Educational Resources Information Center

    Ball, Edward H.

    "Reading Basics Plus" consists of an integrated set of texts, workbooks, duplicating masters, word cards, charts, and teacher's guidebooks. By a process of small group trials, students' and teachers' reactions to the proposed content of the "Reading Basics Plus" program for grades four, five, and six were obtained in order to provide editors and…

  17. Fission yeast retrotransposon Tf1 integration is targeted to 5' ends of open reading frames.

    PubMed

    Behrens, R; Hayles, J; Nurse, P

    2000-12-01

    Target site selection of transposable elements is usually not random but involves some specificity for a DNA sequence or a DNA binding host factor. We have investigated the target site selection of the long terminal repeat-containing retrotransposon Tf1 from the fission yeast Schizosaccharomyces pombe. By monitoring induced transposition events we found that Tf1 integration sites were distributed throughout the genome. Mapping these insertions revealed that Tf1 did not integrate into open reading frames, but occurred preferentially in longer intergenic regions with integration biased towards a region 100-420 bp upstream of the translation start site. Northern blot analysis showed that transcription of genes adjacent to Tf1 insertions was not significantly changed.

  18. Fission yeast retrotransposon Tf1 integration is targeted to 5′ ends of open reading frames

    PubMed Central

    Behrens, Ralf; Hayles, Jacky; Nurse, Paul

    2000-01-01

    Target site selection of transposable elements is usually not random but involves some specificity for a DNA sequence or a DNA binding host factor. We have investigated the target site selection of the long terminal repeat-containing retrotransposon Tf1 from the fission yeast Schizosaccharomyces pombe. By monitoring induced transposition events we found that Tf1 integration sites were distributed throughout the genome. Mapping these insertions revealed that Tf1 did not integrate into open reading frames, but occurred preferentially in longer intergenic regions with integration biased towards a region 100–420 bp upstream of the translation start site. Northern blot analysis showed that transcription of genes adjacent to Tf1 insertions was not significantly changed. PMID:11095681

  19. The prevalence of specific reading disability in an amblyopic population. A preliminary report.

    PubMed

    Koklanis, Konstandina; Georgievski, Zoran; Brassington, Kate; Bretherton, Lesley

    2006-01-01

    To investigate the prevalence of specific reading disability in children with functional amblyopia and to explore the relationship between the two. In this prospective study, 20 consecutive children, aged 6 to 15 years (mean 8 +/-1.99 years), and diagnosed with amblyopia underwent a vision and reading assessment. The orthoptic examination included the assessment of participants' visual acuity, ocular motility and binocular functions. Specific reading disability was diagnosed using the Wide Range Achievement Test (WRAT III Reading Subtest). Intelligence, phonological awareness, rapid automatized naming (RAN), and the ability to read pseudo or nonsense words was also assessed using various psycho-linguistic reading tests. The prevalence of specific reading disability in this small series of amblyopic children was found to be 5% (n=1/20). This was even less than that reported in the local Victoria general population (16%). The type of amblyopia appeared related to phonological awareness (p=0.018) and decoding words (p=0.024), those with anisometropic amblyopia performing significantly better on these tasks than the strabismic amblyopes. The presence of binocular vision functions was also related to decoding words; those with binocular single vision performed better than those with suppression and lacking single binocular vision (p=0.007). Generally, amblyopic children also showed a lower RAN score when compared to phonological awareness score. There was no statistically significant difference for the severity of amblyopia (p=>0.05). In this very small pilot series, reading disorders were relatively rare in children with amblyopia. However, strabismic amblyopia and presence of suppression may have an adverse effect on phonological skills. In addition, amblyopia may be associated with a deficit in RAN. Further research is needed and planned to gain a better understanding about the relationship between amblyopia and reading ability.

  20. Low-voltage-operated organic one-time programmable memory using printed organic thin-film transistors and antifuse capacitors.

    PubMed

    Jung, Soon-Won; Na, Bock Soon; Park, Chan Woo; Koo, Jae Bon

    2014-11-01

    We demonstrate an organic one-time programmable memory cell formed entirely at plastic-compatible temperatures. All the processes are performed at below 130 degrees C. Our memory cell consists of a printed organic transistor and an organic capacitor. Inkjet-printed organic transistors are fabricated by using high-k polymer dielectric blends comprising poly(vinylidenefluoride-trifluoroethylene) [P(VDF-TrFE)] and poly(methyl methacrylate) (PMMA) for low-voltage operation. P(NDI2OD-T2) transistors have a high field-effect mobility of 0.2 cm2/Vs and a low operation gate voltage of less than 10 V. The operation voltage effectively decreases owing to the high permittivity of the P(VDF-TrFE):PMMA blended film. The data in the memory cell are programmed by electrically breaking the organic capacitor. The organic capacitor acts like an antifuse capacitor, because it is initially open, and it becomes permanently short-circuited by applying a high voltage. The organic memory cells are programmed with 4 V, and they are read out with 2 V. The memory data are read out by sensing the current in the memory cell. The printed organic one-time programmable memory is suitable for applications storing small amount of data, such as low-cost radio-frequency identification (RFID) tag.

  1. Production and pathogenicity of hepatitis C virus core gene products

    PubMed Central

    Li, Hui-Chun; Ma, Hsin-Chieh; Yang, Chee-Hing; Lo, Shih-Yen

    2014-01-01

    Hepatitis C virus (HCV) is a major cause of chronic liver diseases, including steatosis, cirrhosis and hepatocellular carcinoma, and its infection is also associated with insulin resistance and type 2 diabetes mellitus. HCV, belonging to the Flaviviridae family, is a small enveloped virus whose positive-stranded RNA genome encoding a polyprotein. The HCV core protein is cleaved first at residue 191 by the host signal peptidase and further cleaved by the host signal peptide peptidase at about residue 177 to generate the mature core protein (a.a. 1-177) and the cleaved peptide (a.a. 178-191). Core protein could induce insulin resistance, steatosis and even hepatocellular carcinoma through various mechanisms. The peptide (a.a. 178-191) may play a role in the immune response. The polymorphism of this peptide is associated with the cellular lipid drop accumulation, contributing to steatosis development. In addition to the conventional open reading frame (ORF), in the +1 frame, an ORF overlaps with the core protein-coding sequence and encodes the alternative reading frame proteins (ARFP or core+1). ARFP/core+1/F protein could enhance hepatocyte growth and may regulate iron metabolism. In this review, we briefly summarized the current knowledge regarding the production of different core gene products and their roles in viral pathogenesis. PMID:24966583

  2. 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. © The Author(s) 2014.

  3. nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data.

    PubMed

    Schober, Daniel; Jacob, Daniel; Wilson, Michael; Cruz, Joseph A; Marcu, Ana; Grant, Jason R; Moing, Annick; Deborde, Catherine; de Figueiredo, Luis F; Haug, Kenneth; Rocca-Serra, Philippe; Easton, John; Ebbels, Timothy M D; Hao, Jie; Ludwig, Christian; Günther, Ulrich L; Rosato, Antonio; Klein, Matthias S; Lewis, Ian A; Luchinat, Claudio; Jones, Andrew R; Grauslys, Arturas; Larralde, Martin; Yokochi, Masashi; Kobayashi, Naohiro; Porzel, Andrea; Griffin, Julian L; Viant, Mark R; Wishart, David S; Steinbeck, Christoph; Salek, Reza M; Neumann, Steffen

    2018-01-02

    NMR is a widely used analytical technique with a growing number of repositories available. As a result, demands for a vendor-agnostic, open data format for long-term archiving of NMR data have emerged with the aim to ease and encourage sharing, comparison, and reuse of NMR data. Here we present nmrML, an open XML-based exchange and storage format for NMR spectral data. The nmrML format is intended to be fully compatible with existing NMR data for chemical, biochemical, and metabolomics experiments. nmrML can capture raw NMR data, spectral data acquisition parameters, and where available spectral metadata, such as chemical structures associated with spectral assignments. The nmrML format is compatible with pure-compound NMR data for reference spectral libraries as well as NMR data from complex biomixtures, i.e., metabolomics experiments. To facilitate format conversions, we provide nmrML converters for Bruker, JEOL and Agilent/Varian vendor formats. In addition, easy-to-use Web-based spectral viewing, processing, and spectral assignment tools that read and write nmrML have been developed. Software libraries and Web services for data validation are available for tool developers and end-users. The nmrML format has already been adopted for capturing and disseminating NMR data for small molecules by several open source data processing tools and metabolomics reference spectral libraries, e.g., serving as storage format for the MetaboLights data repository. The nmrML open access data standard has been endorsed by the Metabolomics Standards Initiative (MSI), and we here encourage user participation and feedback to increase usability and make it a successful standard.

  4. Retention of Text Material under Cued and Uncued Recall and Open and Closed Book Conditions

    ERIC Educational Resources Information Center

    Nevid, Jeffrey S.; Pyun, Yea Seul; Cheney, Brianna

    2016-01-01

    Evidence supports the benefits of effortful processing in strengthening retention of newly learned material. The present study compared two forms of effortful processing, uncued (free) recall and cued recall, under both open and closed book conditions, on both immediate and delayed (one-week) test performance. Participants read a section of a…

  5. "Predatory" Online Journals Lure Scholars Who Are Eager to Publish

    ERIC Educational Resources Information Center

    Stratford, Michael

    2012-01-01

    OMICS Publishing Group is an open-access publisher operating under an author-pays model. Unlike traditional journal subscriptions in which readers or institutions pay to read content, OMICS relies on its contributors for financial support. Although the author-pays model is not a new phenomenon in the realm of open access, its recent popularity has…

  6. An Open Letter to President Barack Obama from C. Frederick Risinger

    ERIC Educational Resources Information Center

    Risinger, C. Frederick

    2010-01-01

    This article presents an open letter to President Barack Obama written by the author to express his concerns about the increasing emphasis on mathematics and science education along with the continued emphasis on reading/language arts while a fourth major curriculum area--social studies--is being marginalized by lack of funding and reduced…

  7. Meteorology and Climate Inspire Secondary Science Students

    ERIC Educational Resources Information Center

    Charlton-Perez, Andrew; Dacre, Helen; Maskell, Kathy; Reynolds, Ross; South, Rachel; Wood, Curtis

    2010-01-01

    As part of its National Science and Engineering Week activities in 2009 and 2010, the University of Reading organised two open days for 60 local key stage 4 pupils. The theme of both open days was "How do we predict weather and climate?" Making use of the students' familiarity with weather and climate, several concepts of relevance to secondary…

  8. A History of the City of Sydney Public Library.

    ERIC Educational Resources Information Center

    Hinsch, Neil

    The Sydney Public Library began as the Australian Subscription Library and Reading Room which opened in Sydney on December 1, 1827, with 1,000 volumes. The Municipal Council of Sydney took possession of the library in 1909. The library evolved from a closed access, fixed shelf position library to an open access system in 1910. A complete…

  9. Open access and beyond

    PubMed Central

    Mathur, Shawn; Schmidt, Christian; Das, Chhaya; Tucker, Philip W

    2006-01-01

    Uncensored exchange of scientific results hastens progress. Open Access does not stop at the removal of price and permission barriers; still, censorship and reading disabilities, to name a few, hamper access to information. Here, we invite the scientific community and the public to discuss new methods to distribute, store and manage literature in order to achieve unfettered access to literature. PMID:16956402

  10. Open Access and beyond.

    PubMed

    Mathur, Shawn; Schmidt, Christian; Das, Chhaya; Tucker, Philip W

    2006-09-06

    Uncensored exchange of scientific results hastens progress. Open Access does not stop at the removal of price and permission barriers; still, censorship and reading disabilities, to name a few, hamper access to information. Here, we invite the scientific community and the public to discuss new methods to distribute, store and manage literature in order to achieve unfettered access to literature.

  11. Nurturing a lexical legacy: reading experience is critical for the development of word reading skill

    NASA Astrophysics Data System (ADS)

    Nation, Kate

    2017-12-01

    The scientific study of reading has taught us much about the beginnings of reading in childhood, with clear evidence that the gateway to reading opens when children are able to decode, or `sound out' written words. Similarly, there is a large evidence base charting the cognitive processes that characterise skilled word recognition in adults. Less understood is how children develop word reading expertise. Once basic reading skills are in place, what factors are critical for children to move from novice to expert? This paper outlines the role of reading experience in this transition. Encountering individual words in text provides opportunities for children to refine their knowledge about how spelling represents spoken language. Alongside this, however, reading experience provides much more than repeated exposure to individual words in isolation. According to the lexical legacy perspective, outlined in this paper, experiencing words in diverse and meaningful language environments is critical for the development of word reading skill. At its heart is the idea that reading provides exposure to words in many different contexts, episodes and experiences which, over time, sum to a rich and nuanced database about their lexical history within an individual's experience. These rich and diverse encounters bring about local variation at the word level: a lexical legacy that is measurable during word reading behaviour, even in skilled adults.

  12. Drift Rates of Three Micro-g LaCoste Turnkey Airborne Gravity Systems (TAGS) Used for the GRAV-D Project

    NASA Astrophysics Data System (ADS)

    Preaux, S. A.; Crump, B.; Damiani, T.

    2015-12-01

    The Gravity for the Redefinition of the American Vertical Datum (GRAV-D) project of NOAA's National Geodetic Survey has been collecting airborne gravity data since 2008 using 3 TAGS gravimeters, S-137, S-160 and S-161 (Table 1). The 38 surveys contain 1697 gravimeter calibration readings taken when the aircraft is parked on the ground before and after each flight, called still readings. This dataset is uniquely suited to examine the drift characteristics of these instruments. This study is broken into 3 parts: re-computation of individual still reading values; examination of drift rates during flights and surveys; and examination of long term drift rates. Re-computation of still readings was accomplished by isolating the least-noisy 10-minute segment of gravity data while the aircraft was parked and the beam unclamped. This automated method worked in most cases, but a small number of readings required further examination. This method improved the consistency of pre- and post-flight still readings as compared to those recorded in the field. Preliminary results indicate that the drift rate for these 3 instruments during a typical survey period is both small (95% smaller than 0.35 mGal/day) and linear. The average drift rate during a survey is -0.11 mGal/day with a standard deviation of 0.12 mGal/day (Figure 1). Still readings for most surveys were well represented by a linear trend, but a small number have curvature or discontinuities. The nature and cause of this non-linearity will be investigated. Early results show a long term linear drift rate for these 3 gravimeters between 0.01 and 0.04 mGal/day. There also appears to be significant non-linear variability. Comparing the 1.5-2 year time series of still readings from S-160 and S-161 with the 7.5 year time series for S-137, indicates that data from more than two years are needed to accurately characterize the long-term behavior. Instrumentation and processing causes for this non-linearity will be explored. Table1. Number of surveys and still reading and duration of use for each Gravimeter Meter # of surveys # still readings Duration of use S-137 27 1205 7.5 years S-160 4 288 1.5 years S-161 7 204 2 years

  13. 77 FR 14459 - Notice of Request for Renewal of a Previously Approved Collection

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-09

    ... guarantee applicants. The revised STLP application is a single, consolidated document that is easier to read... other certified Small Businesses (8a, women-owned, small disadvantaged, HUBZone, veteran owned, and... Small Businesses (8a, women-owned, small disadvantaged, HUBZone, veteran owned, and service disabled...

  14. Biomechanical ToolKit: Open-source framework to visualize and process biomechanical data.

    PubMed

    Barre, Arnaud; Armand, Stéphane

    2014-04-01

    C3D file format is widely used in the biomechanical field by companies and laboratories to store motion capture systems data. However, few software packages can visualize and modify the integrality of the data in the C3D file. Our objective was to develop an open-source and multi-platform framework to read, write, modify and visualize data from any motion analysis systems using standard (C3D) and proprietary file formats (used by many companies producing motion capture systems). The Biomechanical ToolKit (BTK) was developed to provide cost-effective and efficient tools for the biomechanical community to easily deal with motion analysis data. A large panel of operations is available to read, modify and process data through C++ API, bindings for high-level languages (Matlab, Octave, and Python), and standalone application (Mokka). All these tools are open-source and cross-platform and run on all major operating systems (Windows, Linux, MacOS X). Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  15. ATLAS (Automatic Tool for Local Assembly Structures) - A Comprehensive Infrastructure for Assembly, Annotation, and Genomic Binning of Metagenomic and Metaranscripomic Data

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

    White, Richard A.; Brown, Joseph M.; Colby, Sean M.

    ATLAS (Automatic Tool for Local Assembly Structures) is a comprehensive multiomics data analysis pipeline that is massively parallel and scalable. ATLAS contains a modular analysis pipeline for assembly, annotation, quantification and genome binning of metagenomics and metatranscriptomics data and a framework for reference metaproteomic database construction. ATLAS transforms raw sequence data into functional and taxonomic data at the microbial population level and provides genome-centric resolution through genome binning. ATLAS provides robust taxonomy based on majority voting of protein coding open reading frames rolled-up at the contig level using modified lowest common ancestor (LCA) analysis. ATLAS provides robust taxonomy based onmore » majority voting of protein coding open reading frames rolled-up at the contig level using modified lowest common ancestor (LCA) analysis. ATLAS is user-friendly, easy install through bioconda maintained as open-source on GitHub, and is implemented in Snakemake for modular customizable workflows.« less

  16. Low power test architecture for dynamic read destructive fault detection in SRAM

    NASA Astrophysics Data System (ADS)

    Takher, Vikram Singh; Choudhary, Rahul Raj

    2018-06-01

    Dynamic Read Destructive Fault (dRDF) is the outcome of resistive open defects in the core cells of static random-access memories (SRAMs). The sensitisation of dRDF involves either performing multiple read operations or creation of number of read equivalent stress (RES), on the core cell under test. Though the creation of RES is preferred over the performing multiple read operation on the core cell, cell dissipates more power during RES than during the read or write operation. This paper focuses on the reduction in power dissipation by optimisation of number of RESs, which are required to sensitise the dRDF during test mode of operation of SRAM. The novel pre-charge architecture has been proposed in order to reduce the power dissipation by limiting the number of RESs to an optimised number of two. The proposed low power architecture is simulated and analysed which shows reduction in power dissipation by reducing the number of RESs up to 18.18%.

  17. Update on Healthy Aging: Reading Material on Health Topics for the New Reader and Tutor. Literacy Education for the Elderly Project.

    ERIC Educational Resources Information Center

    Jacobs, Bella; Ventura-Merkel, Catherine

    Fifteen lessons contain low-vocabulary, high interest reading materials on health issues to enhance the learning of the new older reader. Each lesson is preceded by tutor guidelines with specific goals and objectives and review exercises. The materials are useful in either one-to-one or small-group tutoring. Reading selections in the lessons,…

  18. UK Preparatory School Librarians' and Teachers' Design and Use of Reading Lists: A Qualitative Study of Approaches, Perceptions, and Content

    ERIC Educational Resources Information Center

    Scott, Rebecca; Inskip, Charles

    2017-01-01

    This paper reports the findings of a small-scale qualitative study that explored the perceptions of and approaches used by UK school librarians and teachers in the design and use of reading lists. The research question was: "What is the best way to construct reading lists to maximize their benefit in the school library or classroom?" The…

  19. Early Intervention for Children at Risk for Reading Disabilities: The Impact of Grade at Intervention and Individual Differences on Intervention Outcomes

    ERIC Educational Resources Information Center

    Lovett, Maureen W.; Frijters, Jan C.; Wolf, Maryanne; Steinbach, Karen A.; Sevcik, Rose A.; Morris, Robin D.

    2017-01-01

    Across multiple schools and sites, the impact of grade-at-intervention was evaluated for children at risk or meeting criteria for reading disabilities. A multiple-component reading intervention with demonstrated efficacy was offered to small groups of children in 1st, 2nd, or 3rd grade. In a quasi-experimental design, 172 children received the…

  20. Using expected sequence features to improve basecalling accuracy of amplicon pyrosequencing data.

    PubMed

    Rask, Thomas S; Petersen, Bent; Chen, Donald S; Day, Karen P; Pedersen, Anders Gorm

    2016-04-22

    Amplicon pyrosequencing targets a known genetic region and thus inherently produces reads highly anticipated to have certain features, such as conserved nucleotide sequence, and in the case of protein coding DNA, an open reading frame. Pyrosequencing errors, consisting mainly of nucleotide insertions and deletions, are on the other hand likely to disrupt open reading frames. Such an inverse relationship between errors and expectation based on prior knowledge can be used advantageously to guide the process known as basecalling, i.e. the inference of nucleotide sequence from raw sequencing data. The new basecalling method described here, named Multipass, implements a probabilistic framework for working with the raw flowgrams obtained by pyrosequencing. For each sequence variant Multipass calculates the likelihood and nucleotide sequence of several most likely sequences given the flowgram data. This probabilistic approach enables integration of basecalling into a larger model where other parameters can be incorporated, such as the likelihood for observing a full-length open reading frame at the targeted region. We apply the method to 454 amplicon pyrosequencing data obtained from a malaria virulence gene family, where Multipass generates 20 % more error-free sequences than current state of the art methods, and provides sequence characteristics that allow generation of a set of high confidence error-free sequences. This novel method can be used to increase accuracy of existing and future amplicon sequencing data, particularly where extensive prior knowledge is available about the obtained sequences, for example in analysis of the immunoglobulin VDJ region where Multipass can be combined with a model for the known recombining germline genes. Multipass is available for Roche 454 data at http://www.cbs.dtu.dk/services/MultiPass-1.0 , and the concept can potentially be implemented for other sequencing technologies as well.

  1. Subtle increases in interletter spacing facilitate the encoding of words during normal reading.

    PubMed

    Perea, Manuel; Gomez, Pablo

    2012-01-01

    Several recent studies have revealed that words presented with a small increase in interletter spacing are identified faster than words presented with the default interletter spacing (i.e., w a t e r faster than water). Modeling work has shown that this advantage occurs at an early encoding level. Given the implications of this finding for the ease of reading in the new digital era, here we examined whether the beneficial effect of small increases in interletter spacing can be generalized to a normal reading situation. We conducted an experiment in which the participant's eyes were monitored when reading sentences varying in interletter spacing: i) sentences were presented with the default (0.0) interletter spacing; ii) sentences presented with a +1.0 interletter spacing; and iii) sentences presented with a +1.5 interletter spacing. Results showed shorter fixation duration times as an inverse function of interletter spacing (i.e., fixation durations were briefest with +1.5 spacing and slowest with the default spacing). Subtle increases in interletter spacing facilitate the encoding of the fixated word during normal reading. Thus, interletter spacing is a parameter that may affect the ease of reading, and it could be adjustable in future implementations of e-book readers.

  2. Subtle Increases in Interletter Spacing Facilitate the Encoding of Words during Normal Reading

    PubMed Central

    Perea, Manuel; Gomez, Pablo

    2012-01-01

    Background Several recent studies have revealed that words presented with a small increase in interletter spacing are identified faster than words presented with the default interletter spacing (i.e., w a t e r faster than water). Modeling work has shown that this advantage occurs at an early encoding level. Given the implications of this finding for the ease of reading in the new digital era, here we examined whether the beneficial effect of small increases in interletter spacing can be generalized to a normal reading situation. Methodology We conducted an experiment in which the participant’s eyes were monitored when reading sentences varying in interletter spacing: i) sentences were presented with the default (0.0) interletter spacing; ii) sentences presented with a +1.0 interletter spacing; and iii) sentences presented with a +1.5 interletter spacing. Principal Findings Results showed shorter fixation duration times as an inverse function of interletter spacing (i.e., fixation durations were briefest with +1.5 spacing and slowest with the default spacing). Conclusions Subtle increases in interletter spacing facilitate the encoding of the fixated word during normal reading. Thus, interletter spacing is a parameter that may affect the ease of reading, and it could be adjustable in future implementations of e-book readers. PMID:23082178

  3. Atropos: specific, sensitive, and speedy trimming of sequencing reads.

    PubMed

    Didion, John P; Martin, Marcel; Collins, Francis S

    2017-01-01

    A key step in the transformation of raw sequencing reads into biological insights is the trimming of adapter sequences and low-quality bases. Read trimming has been shown to increase the quality and reliability while decreasing the computational requirements of downstream analyses. Many read trimming software tools are available; however, no tool simultaneously provides the accuracy, computational efficiency, and feature set required to handle the types and volumes of data generated in modern sequencing-based experiments. Here we introduce Atropos and show that it trims reads with high sensitivity and specificity while maintaining leading-edge speed. Compared to other state-of-the-art read trimming tools, Atropos achieves significant increases in trimming accuracy while remaining competitive in execution times. Furthermore, Atropos maintains high accuracy even when trimming data with elevated rates of sequencing errors. The accuracy, high performance, and broad feature set offered by Atropos makes it an appropriate choice for the pre-processing of Illumina, ABI SOLiD, and other current-generation short-read sequencing datasets. Atropos is open source and free software written in Python (3.3+) and available at https://github.com/jdidion/atropos.

  4. Atropos: specific, sensitive, and speedy trimming of sequencing reads

    PubMed Central

    Collins, Francis S.

    2017-01-01

    A key step in the transformation of raw sequencing reads into biological insights is the trimming of adapter sequences and low-quality bases. Read trimming has been shown to increase the quality and reliability while decreasing the computational requirements of downstream analyses. Many read trimming software tools are available; however, no tool simultaneously provides the accuracy, computational efficiency, and feature set required to handle the types and volumes of data generated in modern sequencing-based experiments. Here we introduce Atropos and show that it trims reads with high sensitivity and specificity while maintaining leading-edge speed. Compared to other state-of-the-art read trimming tools, Atropos achieves significant increases in trimming accuracy while remaining competitive in execution times. Furthermore, Atropos maintains high accuracy even when trimming data with elevated rates of sequencing errors. The accuracy, high performance, and broad feature set offered by Atropos makes it an appropriate choice for the pre-processing of Illumina, ABI SOLiD, and other current-generation short-read sequencing datasets. Atropos is open source and free software written in Python (3.3+) and available at https://github.com/jdidion/atropos. PMID:28875074

  5. Expression of a non-coding RNA in ectromelia virus is required for normal plaque formation.

    PubMed

    Esteban, David J; Upton, Chris; Bartow-McKenney, Casey; Buller, R Mark L; Chen, Nanhai G; Schriewer, Jill; Lefkowitz, Elliot J; Wang, Chunlin

    2014-02-01

    Poxviruses are dsDNA viruses with large genomes. Many genes in the genome remain uncharacterized, and recent studies have demonstrated that the poxvirus transcriptome includes numerous so-called anomalous transcripts not associated with open reading frames. Here, we characterize the expression and role of an apparently non-coding RNA in orthopoxviruses, which we call viral hairpin RNA (vhRNA). Using a bioinformatics approach, we predicted expression of a transcript not associated with an open reading frame that is likely to form a stem-loop structure due to the presence of a 21 nt palindromic sequence. Expression of the transcript as early as 2 h post-infection was confirmed by northern blot and analysis of publicly available vaccinia virus infected cell transcriptomes. The transcription start site was determined by RACE PCE and transcriptome analysis, and early and late promoter sequences were identified. Finally, to test the function of the transcript we generated an ectromelia virus knockout, which failed to form plaques in cell culture. The important role of the transcript in viral replication was further demonstrated using siRNA. Although the function of the transcript remains unknown, our work contributes to evidence of an increasingly complex poxvirus transcriptome, suggesting that transcripts such as vhRNA not associated with an annotated open reading frame can play an important role in viral replication.

  6. The Saccharomyces cerevisiae LOS1 gene involved in pre-tRNA splicing encodes a nuclear protein that behaves as a component of the nuclear matrix.

    PubMed

    Shen, W C; Selvakumar, D; Stanford, D R; Hopper, A K

    1993-09-15

    Mutations of the Saccharomyces cerevisiae LOS1 gene cause the accumulation of end matured intron-containing pre-tRNAs at elevated temperatures. In an effort to decipher the role of the LOS1 protein in pre-tRNA splicing, we have analyzed the LOS1 gene and its protein product. The LOS1 gene is located on the left arm of chromosome XI and the order of genes in this area of the chromosome is .... URA1 ... SAC1 TRP3 UBA1 STE6 LOS1 .... FAS1..... The LOS1 open reading frame encodes a putative protein of 1100 amino acids that shows no significant homology to other genes. The LOS1 open reading frame was tagged with the influenza virus hemagglutinin epitope recognized by the 12CA5 antibody. The 12CA5 antibody recognizes an epitope-tagged protein of the size predicted by the LOS1 open reading frame. Using this antibody for indirect immunofluorescence and cell fractionation studies we show that the LOS1 protein is located in nuclei. Los1p cannot be extracted from nuclei by treatment with nucleases, salts, or Triton X-100. This insolubility suggests that Los1p is a component of the nucleoskeleton. We propose that LOS1 mutations may affect pre-tRNA processing via alteration of the nuclear matrix.

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

    PubMed

    Pelsy, F.; Merdinoglu, D.

    2002-09-01

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

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

    PubMed

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

    2014-02-01

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

  9. The Genetic and Environmental Etiologies of the Relations between Cognitive Skills and Components of Reading Ability

    PubMed Central

    Christopher, Micaela E.; Keenan, Janice M.; Hulslander, Jacqueline; DeFries, John C.; Miyake, Akira; Wadsworth, Sally J.; Willcutt, Erik; Pennington, Bruce; Olson, Richard K.

    2016-01-01

    While previous research has shown cognitive skills to be important predictors of reading ability in children, the respective roles for genetic and environmental influences on these relations is an open question. The present study explored the genetic and environmental etiologies underlying the relations between selected executive functions and cognitive abilities (working memory, inhibition, processing speed, and naming speed) with three components of reading ability (word reading, reading comprehension, and listening comprehension). Twin pairs drawn from the Colorado Front Range (n = 676; 224 monozygotic pairs; 452 dizygotic pairs) between the ages of eight and 16 (M = 11.11) were assessed on multiple measures of each cognitive and reading-related skill. Each cognitive and reading-related skill was modeled as a latent variable, and behavioral genetic analyses estimated the portions of phenotypic variance on each latent variable due to genetic, shared environmental, and nonshared environmental influences. The covariance between the cognitive skills and reading-related skills was driven primarily by genetic influences. The cognitive skills also shared large amounts of genetic variance, as did the reading-related skills. The common cognitive genetic variance was highly correlated with the common reading genetic variance, suggesting that genetic influences involved in general cognitive processing are also important for reading ability. Skill-specific genetic variance in working memory and processing speed also predicted components of reading ability. Taken together, the present study supports a genetic association between children’s cognitive ability and reading ability. PMID:26974208

  10. Pushing Traditional Publishing Boundaries in the Journal of Astronomy & Earth Science Education JAESE

    NASA Astrophysics Data System (ADS)

    Slater, T. F.

    2017-12-01

    Responding to the community's need for an archival journal to document program evaluation and educational impact of programs and innovations, the Journal of Astronomy & Earth Science Education (JAESE.org) is a scholarly, peer-reviewed journal designed to serve the discipline-based astronomy, planetary, and geosciences education research community. JAESE's first issue was published on December 31, 2014 and has published four volumes and seven issues since that time. By far, the median article topic has been focused on planetarium education research, while there have only been a few articles on conventional solid-Earth geosciences education research. Although there is not yet an even distribution of topics across the field, there is a relatively even distribution among author demographics. Authors include a range of both junior and senior members of the field. There have been significantly more female authors than male authors. Submissions are distributed as blind-copies to two or three peer reviewers with authors' names and identifying information redacted from the manuscript. The average time to complete the first round of peer-review reviewers is 6.2-weeks. There have been too few manuscripts to reliably publish a "percentage acceptance rate." Taken together, JAESE's guiding Editorial Advisory Board judges this to be a successful first few years. In a purposeful effort to make JAESE authors' scholarly works as widely accessible as possible, JAESE adopted an open-access business model. JAESE articles are available to read free-of-charge over the Internet, delivered as PDFs. To date, the most common way articles are downloaded by readers is through Google Scholar. Instead of charging readers and libraries recurring subscription fees, JAESE charges authors a nominal submission fee and a small open-access fee, averaging about $700 USD. These charges are far lower than the traditional page charges and gold-package open-access fees typically charged to authors or their institutions by typical scientific journals, making JAESE an attractive publishing venue for many scholars to make their work as widely read as possible. Author guidelines and Reviewer Applications are available at http://www.jaese.org

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

    PubMed

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

    2018-01-01

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

  12. RNA editing makes mistakes in plant mitochondria: editing loses sense in transcripts of a rps19 pseudogene and in creating stop codons in coxI and rps3 mRNAs of Oenothera.

    PubMed Central

    Schuster, W; Brennicke, A

    1991-01-01

    An intact gene for the ribosomal protein S19 (rps19) is absent from Oenothera mitochondria. The conserved rps19 reading frame found in the mitochondrial genome is interrupted by a termination codon. This rps19 pseudogene is cotranscribed with the downstream rps3 gene and is edited on both sides of the translational stop. Editing, however, changes the amino acid sequence at positions that were well conserved before editing. Other strange editings create translational stops in open reading frames coding for functional proteins. In coxI and rps3 mRNAs CGA codons are edited to UGA stop codons only five and three codons, respectively, downstream to the initiation codon. These aberrant editings in essential open reading frames and in the rps19 pseudogene appear to have been shifted to these positions from other editing sites. These observations suggest a requirement for a continuous evolutionary constraint on the editing specificities in plant mitochondria. Images PMID:1762921

  13. Citing and Reading Behaviors of High-Energy Physics or How a Community Stopped Worrying about Journals and Learned to Love Repositories

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

    Gentil-Beccot, Anne; Mele, Salvatore; /CERN

    Contemporary scholarly discourse follows many alternative routes in addition to the three-century old tradition of publication in peer-reviewed journals. The field of High-Energy Physics (HEP) has explored alternative communication strategies for decades, initially via the mass mailing of paper copies of preliminary manuscripts, then via the inception of the first online repositories and digital libraries. This field is uniquely placed to answer recurrent questions raised by the current trends in scholarly communication: is there an advantage for scientists to make their work available through repositories, often in preliminary form? Is there an advantage to publishing in Open Access journals? Domore » scientists still read journals or do they use digital repositories? The analysis of citation data demonstrates that free and immediate online dissemination of preprints creates an immense citation advantage in HEP, whereas publication in Open Access journals presents no discernible advantage. In addition, the analysis of clickstreams in the leading digital library of the field shows that HEP scientists seldom read journals, preferring preprints instead.« less

  14. Superlative Model Using Word Cloud for Short Answers Evaluation in eLearning

    ERIC Educational Resources Information Center

    Jayashankar, Shailaja; Sridaran, R.

    2017-01-01

    Teachers are thrown open to abundance of free text answers which are very daunting to read and evaluate. Automatic assessments of open ended answers have been attempted in the past but none guarantees 100% accuracy. In order to deal with the overload involved in this manual evaluation, a new tool becomes necessary. The unique superlative model…

  15. 76 FR 3536 - Defense Federal Acquisition Regulation Supplement; Technical Amendments

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-20

    ... concerns, HUBZone small business concerns, small disadvantaged business concerns, women-owned small... date, and revising paragraph (a)(10) to read as follows: 252.225-7009 Restriction on Acqusition of Certain Articles Containing Specialty Metals. * * * * * RESTRICTION ON ACQUISITION OF CERTAIN ARTICLES...

  16. AstroVis: Visualizing astronomical data cubes

    NASA Astrophysics Data System (ADS)

    Finniss, Stephen; Tyler, Robin; Questiaux, Jacques

    2016-08-01

    AstroVis enables rapid visualization of large data files on platforms supporting the OpenGL rendering library. Radio astronomical observations are typically three dimensional and stored as data cubes. AstroVis implements a scalable approach to accessing these files using three components: a File Access Component (FAC) that reduces the impact of reading time, which speeds up access to the data; the Image Processing Component (IPC), which breaks up the data cube into smaller pieces that can be processed locally and gives a representation of the whole file; and Data Visualization, which implements an approach of Overview + Detail to reduces the dimensions of the data being worked with and the amount of memory required to store it. The result is a 3D display paired with a 2D detail display that contains a small subsection of the original file in full resolution without reducing the data in any way.

  17. CMS Use of a Data Federation

    NASA Astrophysics Data System (ADS)

    Bloom, Kenneth; Cms Collaboration

    2014-06-01

    CMS is in the process of deploying an Xrootd based infrastructure to facilitate a global data federation. The services of the federation are available to export data from half the physical capacity and the majority of sites are configured to read data over the federation as a back-up. CMS began with a relatively modest set of use-cases for recovery of failed local file opens, debugging and visualization. CMS is finding that the data federation can be used to support small scale analysis and load balancing. Looking forward we see potential in using the federation to provide more flexibility in the location workflows are executed as the difference between local access and wide area access are diminished by optimization and improved networking. In this presentation we discuss the application development work and the facility deployment work, the use-cases currently in production, and the potential for the technology moving forward.

  18. Viral Evasion and Manipulation of Host RNA Quality Control Pathways

    PubMed Central

    2016-01-01

    Viruses have evolved diverse strategies to maximize the functional and coding capacities of their genetic material. Individual viral RNAs are often used as substrates for both replication and translation and can contain multiple, sometimes overlapping open reading frames. Further, viral RNAs engage in a wide variety of interactions with both host and viral proteins to modify the activities of important cellular factors and direct their own trafficking, packaging, localization, stability, and translation. However, adaptations increasing the information density of small viral genomes can have unintended consequences. In particular, viral RNAs have developed features that mark them as potential targets of host RNA quality control pathways. This minireview focuses on ways in which viral RNAs run afoul of the cellular mRNA quality control and decay machinery, as well as on strategies developed by viruses to circumvent or exploit cellular mRNA surveillance. PMID:27226372

  19. Viral Evasion and Manipulation of Host RNA Quality Control Pathways.

    PubMed

    Hogg, J Robert

    2016-08-15

    Viruses have evolved diverse strategies to maximize the functional and coding capacities of their genetic material. Individual viral RNAs are often used as substrates for both replication and translation and can contain multiple, sometimes overlapping open reading frames. Further, viral RNAs engage in a wide variety of interactions with both host and viral proteins to modify the activities of important cellular factors and direct their own trafficking, packaging, localization, stability, and translation. However, adaptations increasing the information density of small viral genomes can have unintended consequences. In particular, viral RNAs have developed features that mark them as potential targets of host RNA quality control pathways. This minireview focuses on ways in which viral RNAs run afoul of the cellular mRNA quality control and decay machinery, as well as on strategies developed by viruses to circumvent or exploit cellular mRNA surveillance. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  20. An intron within the 16S ribosomal RNA gene of the archaeon Pyrobaculum aerophilum

    NASA Technical Reports Server (NTRS)

    Burggraf, S.; Larsen, N.; Woese, C. R.; Stetter, K. O.

    1993-01-01

    The 16S rRNA genes of Pyrobaculum aerophilum and Pyrobaculum islandicum were amplified by the polymerase chain reaction, and the resulting products were sequenced directly. The two organisms are closely related by this measure (over 98% similar). However, they differ in that the (lone) 16S rRNA gene of Pyrobaculum aerophilum contains a 713-bp intron not seen in the corresponding gene of Pyrobaculum islandicum. To our knowledge, this is the only intron so far reported in the small subunit rRNA gene of a prokaryote. Upon excision the intron is circularized. A secondary structure model of the intron-containing rRNA suggests a splicing mechanism of the same type as that invoked for the tRNA introns of the Archaea and Eucarya and 23S rRNAs of the Archaea. The intron contains an open reading frame whose protein translation shows no certain homology with any known protein sequence.

  1. The complete nucleotide sequence and genome organization of a novel betaflexivirus infecting Citrullus lanatus.

    PubMed

    Xin, Min; Zhang, Peipei; Liu, Wenwen; Ren, Yingdang; Cao, Mengji; Wang, Xifeng

    2017-10-01

    The complete nucleotide sequence of a novel positive single-stranded (+ss) RNA virus, tentatively named watermelon virus A (WVA), was determined using a combination of three methods: RNA sequencing, small RNA sequencing, and Sanger sequencing. The full genome of WVA is comprised of 8,372 nucleotides (nt), excluding the poly (A) tail, and contains four open reading frames (ORFs). The largest ORF, ORF1 encodes a putative replication-associated polyprotein (RP) with three conserved domains. ORF2 and ORF4 encode a movement protein (MP) and coat protein (CP), respectively. The putative product encoded by ORF3, of an estimated molecular mass of 25 kDa, has no significant similarity with other proteins. Identity and phylogenetic analysis indicate that WVA is a new virus, closely related to members of the family Betaflexiviridae. However, the final taxonomic allocation of WVA within the family is yet to be determined.

  2. ORFeome Phage Display.

    PubMed

    Zantow, Jonas; Moreira, Gustavo Marçal Schmidt Garcia; Dübel, Stefan; Hust, Michael

    2018-01-01

    ORFeome phage display allows the efficient functional screening of entire proteomes or even metaproteomes to identify immunogenic proteins. For this purpose, randomly fragmented, whole genomes or metagenomes are cloned into a phage-display vector allowing positive selection for open reading frames (ORF) to improve the library quality. These libraries display all possible proteins encoded by a pathogen or a microbiome on the phage surface. Consequently, immunogenic proteins can be selected from these libraries using disease-related immunoglobulins from patient serum. ORFeome phage display in particular allows the identification of immunogenic proteins that are only expressed in the host-pathogen interaction but not in cultivation, as well as the detection of very low expressed and very small immunogens and immunogenic proteins of non-cultivable organisms. The identified immunogenic proteins are potential biomarkers for the development of diagnostic assays or vaccines. These articles will give an introduction to ORFeome phage-display technology and give detailed protocols to identify immunogenic proteins by phage display.

  3. Plant genomes enclose footprints of past infections by giant virus relatives.

    PubMed

    Maumus, Florian; Epert, Aline; Nogué, Fabien; Blanc, Guillaume

    2014-06-27

    Nucleocytoplasmic large DNA viruses (NCLDVs) are eukaryotic viruses with large genomes (100 kb-2.5 Mb), which include giant Mimivirus, Megavirus and Pandoravirus. NCLDVs are known to infect animals, protists and phytoplankton but were never described as pathogens of land plants. Here, we show that the bryophyte Physcomitrella patens and the lycophyte Selaginella moellendorffii have open reading frames (ORFs) with high phylogenetic affinities to NCLDV homologues. The P. patens genes are clustered in DNA stretches (up to 13 kb) containing up to 16 NCLDV-like ORFs. Molecular evolution analysis suggests that the NCLDV-like regions were acquired by horizontal gene transfer from distinct but closely related viruses that possibly define a new family of NCLDVs. Transcriptomics and DNA methylation data indicate that the NCLDV-like regions are transcriptionally inactive and are highly cytosine methylated through a mechanism not relying on small RNAs. Altogether, our data show that members of NCLDV have infected land plants.

  4. Role of eIF2α Kinases in Translational Control and Adaptation to Cellular Stress.

    PubMed

    Wek, Ronald C

    2018-02-12

    A central mechanism regulating translation initiation in response to environmental stress involves phosphorylation of the α subunit of eukaryotic initiation factor 2 (eIF2α). Phosphorylation of eIF2α causes inhibition of global translation, which conserves energy and facilitates reprogramming of gene expression and signaling pathways that help to restore protein homeostasis. Coincident with repression of protein synthesis, many gene transcripts involved in the stress response are not affected or are even preferentially translated in response to increased eIF2α phosphorylation by mechanisms involving upstream open reading frames (uORFs). This review highlights the mechanisms regulating eIF2α kinases, the role that uORFs play in translational control, and the impact that alteration of eIF2α phosphorylation by gene mutations or small molecule inhibitors can have on health and disease. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

  5. Shotgun mitogenomics across body size classes in a local assemblage of tropical Diptera: Phylogeny, species diversity and mitochondrial abundance spectrum.

    PubMed

    Choo, Le Qin; Crampton-Platt, Alex; Vogler, Alfried P

    2017-10-01

    Mitochondrial genomes can be assembled readily from shotgun-sequenced DNA mixtures of mass-trapped arthropods ("mitochondrial metagenomics"), speeding up the taxonomic characterization. Bulk sequencing was conducted on some 800 individuals of Diptera obtained by canopy fogging of a single tree in Borneo dominated by small (<1.5 mm) individuals. Specimens were split into five body size classes for DNA extraction, to equalize read numbers across specimens and to study how body size, a key ecological trait, interacts with species and phylogenetic diversity. Genome assembly produced 304 orthologous mitochondrial contigs presumed to each represent a different species. The small-bodied fraction was the by far most species-rich (187 contigs). Identification of contigs was through phylogenetic analysis together with 56 reference mitogenomes, which placed most of the Bornean community into seven clades of small-bodied species, indicating phylogenetic conservation of body size. Mapping of shotgun reads against the mitogenomes showed wide ranges of read abundances within each size class. Ranked read abundance plots were largely log-linear, indicating a uniformly filled abundance spectrum, especially for small-bodied species. Small-bodied species differed greatly from other size classes in neutral metacommunity parameters, exhibiting greater levels of immigration, besides greater total community size. We suggest that the established uses of mitochondrial metagenomics for analysis of species and phylogenetic diversity can be extended to parameterize recent theories of community ecology and biodiversity, and by focusing on the number mitochondria, rather than individuals, a new theoretical framework for analysis of mitochondrial abundance spectra can be developed that incorporates metabolic activity approximated by the count of mitochondria. © 2017 John Wiley & Sons Ltd.

  6. Capabilities, methodologies, and use of the cambio file-translation application.

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

    Lasche, George P.

    2007-03-01

    This report describes the capabilities, methodologies, and uses of the Cambio computer application, designed to automatically read and display nuclear spectral data files of any known format in the world and to convert spectral data to one of several commonly used analysis formats. To further assist responders, Cambio incorporates an analysis method based on non-linear fitting techniques found in open literature and implemented in openly published source code in the late 1980s. A brief description is provided of how Cambio works, of what basic formats it can currently read, and how it can be used. Cambio was developed at Sandiamore » National Laboratories and is provided as a free service to assist nuclear emergency response analysts anywhere in the world in the fight against nuclear terrorism.« less

  7. Euglena gracilis chloroplast DNA: analysis of a 1.6 kb intron of the psb C gene containing an open reading frame of 458 codons.

    PubMed

    Montandon, P E; Vasserot, A; Stutz, E

    1986-01-01

    We retrieved a 1.6 kbp intron separating two exons of the psb C gene which codes for the 44 kDa reaction center protein of photosystem II. This intron is 3 to 4 times the size of all previously sequenced Euglena gracilis chloroplast introns. It contains an open reading frame of 458 codons potentially coding for a basic protein of 54 kDa of yet unknown function. The intron boundaries follow consensus sequences established for chloroplast introns related to class II and nuclear pre-mRNA introns. Its 3'-terminal segment has structural features similar to class II mitochondrial introns with an invariant base A as possible branch point for lariat formation.

  8. A Microanalysis of the Small-Group Guided Reading Lesson: Effects of an Emphasis on Global Story Meaning. Technical Report No. 519.

    ERIC Educational Resources Information Center

    Anderson, Richard C.; And Others

    A study sought to replicate and extend previous research which found that an emphasis on meaning in reading leads to better recall of lesson material than does an emphasis on accurate oral reading, and that the child who is taking an active turn recalls more of the lesson material than do the children who are following along. Six third-grade…

  9. A bill to require the Small Business Administration to submit a regular National Small Business Index to Congress to assess how policies provide incentives or impediments to small business development.

    THOMAS, 112th Congress

    Sen. Landrieu, Mary L. [D-LA

    2012-05-17

    Senate - 05/17/2012 Read twice and referred to the Committee on Small Business and Entrepreneurship. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  10. Productive extension of semantic memory in school-aged children: Relations with reading comprehension and deployment of cognitive resources.

    PubMed

    Bauer, Patricia J; Blue, Shala N; Xu, Aoxiang; Esposito, Alena G

    2016-07-01

    We investigated 7- to 10-year-old children's productive extension of semantic memory through self-generation of new factual knowledge derived through integration of separate yet related facts learned through instruction or through reading. In Experiment 1, an experimenter read the to-be-integrated facts. Children successfully learned and integrated the information and used it to further extend their semantic knowledge, as evidenced by high levels of correct responses in open-ended and forced-choice testing. In Experiment 2, on half of the trials, the to-be-integrated facts were read by an experimenter (as in Experiment 1) and on half of the trials, children read the facts themselves. Self-generation performance was high in both conditions (experimenter- and self-read); in both conditions, self-generation of new semantic knowledge was related to an independent measure of children's reading comprehension. In Experiment 3, the way children deployed cognitive resources during reading was predictive of their subsequent recall of newly learned information derived through integration. These findings indicate self-generation of new semantic knowledge through integration in school-age children as well as relations between this productive means of extension of semantic memory and cognitive processes engaged during reading. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

  11. Productive Extension of Semantic Memory in School-aged Children: Relations with Reading Comprehension and Deployment of Cognitive Resources

    PubMed Central

    Bauer, Patricia J.; Blue, Shala N.; Xu, Aoxiang; Esposito, Alena G.

    2016-01-01

    We investigated 7- to 10-year-old children’s productive extension of semantic memory through self-generation of new factual knowledge derived through integration of separate yet related facts learned through instruction or through reading. In Experiment 1, an experimenter read the to-be-integrated facts. Children successfully learned and integrated the information and used it to further extend their semantic knowledge, as evidenced by high levels of correct responses in open-ended and forced-choice testing. In Experiment 2, on half of the trials, the to-be-integrated facts were read by an experimenter (as in Experiment 1) and on half of the trials, children read the facts themselves. Self-generation performance was high in both conditions (experimenter- and self-read); in both conditions, self-generation of new semantic knowledge was related to an independent measure of children’s reading comprehension. In Experiment 3, the way children deployed cognitive resources during reading was predictive of their subsequent recall of newly learned information derived through integration. These findings indicate self-generation of new semantic knowledge through integration in school-age children as well as relations between this productive means of extension of semantic memory and cognitive processes engaged during reading. PMID:27253263

  12. Developing Reading Comprehension with Moving Image Narratives

    ERIC Educational Resources Information Center

    Maine, Fiona; Shields, Robin

    2015-01-01

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

  13. Improving Reading in Culturally Situated Contexts

    ERIC Educational Resources Information Center

    Bennet, Maria; Lancaster, Julie

    2012-01-01

    This article explores second year pre-service teachers' ability to work with Indigenous students and their families during a small-scale project conducted in an Indigenous community. Supported field placements offered the pre-service teachers valuable opportunities to engage with the teaching of reading to Indigenous students "on their…

  14. The Impact of Early Classroom Inattention on Phonological Processing and Word-Reading Development.

    PubMed

    Dittman, Cassandra K

    2016-08-01

    The present study investigated the longitudinal relationships between inattention, phonological processing and word reading across the first 2 years of formal reading instruction. In all, 136 school entrants were administered measures of letter knowledge, phonological awareness, phonological memory, rapid naming, and word reading at the start and end of their 1st year of school, and the end of their 2nd year, while teachers completed rating scales of inattention. School entry inattentiveness predicted unique variance in word reading at the end of first grade, after controlling for verbal ability, letter knowledge, and phonological processing. End-of-first-grade inattention predicted a small but significant amount of unique variance in second-grade word reading and word-reading efficiency. Inattention, however, was not a reliable predictor of phonological processing in either first or second grade. Early classroom inattentiveness influences learning to read independent of critical developmental precursors of word-reading development. © The Author(s) 2013.

  15. 78 FR 7849 - Interagency Task Force on Veterans Small Business Development

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-04

    ... SMALL BUSINESS ADMINISTRATION Interagency Task Force on Veterans Small Business Development AGENCY: U.S. Small Business Administration. ACTION: Notice of open Federal Interagency Task Force Meeting... meeting of the Interagency Task Force on Veterans Small Business Development. The meeting will be open to...

  16. 78 FR 70087 - Interagency Task Force on Veterans Small Business Development

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-22

    ... SMALL BUSINESS ADMINISTRATION Interagency Task Force on Veterans Small Business Development AGENCY: U.S. Small Business Administration. ACTION: Notice of open Federal Interagency Task Force meeting... meeting of the Interagency Task Force on Veterans Small Business Development. The meeting will be open to...

  17. 78 FR 45996 - Interagency Task Force on Veterans Small Business Development

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-30

    ... SMALL BUSINESS ADMINISTRATION Interagency Task Force on Veterans Small Business Development AGENCY: U.S. Small Business Administration. ACTION: Notice of open Federal Interagency Task Force meeting... meeting of the Interagency Task Force on Veterans Small Business Development. The meeting will be open to...

  18. 78 FR 21492 - Interagency Task Force on Veterans Small Business Development

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-10

    ... SMALL BUSINESS ADMINISTRATION Interagency Task Force on Veterans Small Business Development AGENCY: U.S. Small Business Administration. ACTION: Notice of open Federal Interagency Task Force Meeting... meeting of the Interagency Task Force on Veterans Small Business Development. The meeting will be open to...

  19. Open America's Waters Act

    THOMAS, 111th Congress

    Sen. McCain, John [R-AZ

    2010-06-23

    Senate - 06/23/2010 Read twice and referred to the Committee on Commerce, Science, and Transportation. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  20. Small wins big: analytic pinyin skills promote Chinese word reading.

    PubMed

    Lin, Dan; McBride-Chang, Catherine; Shu, Hua; Zhang, Yuping; Li, Hong; Zhang, Juan; Aram, Dorit; Levin, Iris

    2010-08-01

    The present study examined invented spelling of pinyin (a phonological coding system for teaching and learning Chinese words) in relation to subsequent Chinese reading development. Among 296 Chinese kindergartners in Beijing, independent invented pinyin spelling was found to be uniquely predictive of Chinese word reading 12 months later, even with Time 1 syllable deletion, phoneme deletion, and letter knowledge, in addition to the autoregressive effects of Time 1 Chinese word reading, statistically controlled. These results underscore the importance of children's early pinyin representations for Chinese reading acquisition, both theoretically and practically. The findings further support the idea of a universal phonological principle and indicate that pinyin is potentially an ideal measure of phonological awareness in Chinese.

  1. Development of a measuring system of contact force during braille reading using an optical 6-axis force sensor.

    PubMed

    Watanabe, T; Oouchi, S; Yamaguchi, T; Shimojo, M; Shimada, S

    2006-01-01

    A system with an optical 6-axis force sensor was developed to measure contact force during braille reading. In using this system, we encountered two problems. One is a variability of output values depending on the contact point. This was solved by using two transformation techniques. The other is that subjects read braille in a different manner from the usual. We compared two manners of braille reading, one-handed vs two-handed, and found a small reduction in reading speed. Using this system, we collected data from four braille readers and quantitatively showed more minute contact force trajectories than those in earlier studies.

  2. Regulation Costs to Small Business Act

    THOMAS, 113th Congress

    Sen. Rubio, Marco [R-FL

    2013-03-12

    Senate - 03/12/2013 Read twice and referred to the Committee on Small Business and Entrepreneurship. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  3. Women's Small Business Procurement Parity Act

    THOMAS, 113th Congress

    Sen. Shaheen, Jeanne [D-NH

    2014-06-17

    Senate - 06/17/2014 Read twice and referred to the Committee on Small Business and Entrepreneurship. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  4. Small Business Innovation Act of 2013

    THOMAS, 113th Congress

    Sen. Baldwin, Tammy [D-WI

    2013-07-11

    Senate - 07/11/2013 Read twice and referred to the Committee on Small Business and Entrepreneurship. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  5. Transparency in Small Business Assistance Act

    THOMAS, 113th Congress

    Sen. Heller, Dean [R-NV

    2013-05-14

    Senate - 05/14/2013 Read twice and referred to the Committee on Small Business and Entrepreneurship. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  6. Small Business Goaling Act of 2012

    THOMAS, 112th Congress

    Sen. Cardin, Benjamin L. [D-MD

    2012-05-22

    Senate - 05/22/2012 Read twice and referred to the Committee on Small Business and Entrepreneurship. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  7. Small Business Fairness Act of 2011

    THOMAS, 112th Congress

    Sen. Enzi, Michael B. [R-WY

    2011-05-26

    Senate - 05/26/2011 Read twice and referred to the Committee on Small Business and Entrepreneurship. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  8. Small Business Fairness Act of 2013

    THOMAS, 113th Congress

    Sen. Enzi, Michael B. [R-WY

    2013-06-19

    Senate - 06/19/2013 Read twice and referred to the Committee on Small Business and Entrepreneurship. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

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

    PubMed

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

    2011-09-01

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

  10. Tiers of intervention in kindergarten through third grade.

    PubMed

    O'Connor, Rollanda E; Harty, Kristin R; Fulmer, Deborah

    2005-01-01

    This study measured the effects of increasing levels of intervention in reading for a cohort of children in Grades K through 3 to determine whether the severity of reading disability (RD) could be significantly reduced in the catchment schools. Tier 1 consisted of professional development for teachers of reading. The focus of this study is on additional instruction that was provided as early as kindergarten for children whose achievement fell below average. Tier 2 intervention consisted of small-group reading instruction 3 times per week, and Tier 3 of daily instruction delivered individually or in groups of two. A comparison of the reading achievement of third-grade children who were at risk in kindergarten showed moderate to large differences favoring children in the tiered interventions in decoding, word identification, fluency, and reading comprehension.

  11. SU-F-T-445: Effect of Triaxial Cables and Microdetectors in Small Field Dosimetry

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

    Das, I; Andersen, A

    2016-06-15

    Purpose: Advances in radiation treatment especially with smaller fields used in SRS, Gamma knife, Tomotherapy, Cyberknife, and IMRT, require a high degree of precision especially with microdetectors for small field dosimetry (Das et al, Med Ph, 35, 206, 2008; Alfonso et al, Med Phys, 35, 5179, 2008). Due to small signal, the triaxial cable becomes critical in terms of signal to noise ratio (SNR) which is studied with microdetectors. Methods: Six high quality triaxial cables, 9.1 meters long from different manufacturers without any defects were acquired along with 5 most popular microdetectors (microdiamond, plastic scintillators, SRS-diode, edge-diode and pinpoint). Amore » dedicated electrometer was used for each combination except W1 which has its own supermax electrometer. A 6MV photon beam from Varian True beam with 100 MU at a 600 MU/min was used. Measurements were made at a depth of 5 cm in water phantom. Field sizes were varied from 0.5 cm to 10 cm square fields. Readings were taken with combination of cables and microdetectors. Results: Signal is dependent on the quality of the connectors, cables and types of microdetector. The readings varied from nC to pC depending on the type of microdetector. The net signal, S, (Sc-Sn), where Sc is signal with chamber and Sn is without chamber is a linear function of sensitive volume, v; (S = α+β•V), where α and β are constants. The standard deviation (SD) in 3 sets of reading with each combination of cable-detector was extremely low <0.02%. As expected the SD is higher in small fields (<3cm). Maximum estimated error was only ±0.2% in cables-detector combinations. Conclusion: The choice of cables has relatively small effect (±0.2%) with microdosimeter and should be accounted in overall error estimation in k value that is needed to convert ratio of reading to dose in small field dosimetry.« less

  12. STEP UP for American Small Businesses Act

    THOMAS, 113th Congress

    Sen. Cantwell, Maria [D-WA

    2014-12-09

    Senate - 12/09/2014 Read twice and referred to the Committee on Small Business and Entrepreneurship. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  13. Small Business Export Opportunity Development Act of 2009

    THOMAS, 111th Congress

    Sen. Snowe, Olympia J. [R-ME

    2009-06-08

    Senate - 06/08/2009 Read twice and referred to the Committee on Small Business and Entrepreneurship. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  14. Small Business Common Application Act of 2012

    THOMAS, 112th Congress

    Sen. Hagan, Kay R. [D-NC

    2012-05-16

    Senate - 05/16/2012 Read twice and referred to the Committee on Small Business and Entrepreneurship. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  15. Small Business Additional Temporary Extension Act of 2011

    THOMAS, 112th Congress

    Sen. Landrieu, Mary L. [D-LA

    2011-05-25

    Senate - 05/25/2011 Read twice and referred to the Committee on Small Business and Entrepreneurship. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  16. Small Business Venture Capital Act of 2009

    THOMAS, 111th Congress

    Sen. Kerry, John F. [D-MA

    2009-10-21

    Senate - 10/21/2009 Read twice and referred to the Committee on Small Business and Entrepreneurship. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  17. SCORE for Small Business Act of 2012

    THOMAS, 112th Congress

    Sen. Landrieu, Mary L. [D-LA

    2012-08-02

    Senate - 08/02/2012 Read twice and referred to the Committee on Small Business and Entrepreneurship. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  18. Lung surgery - discharge

    MedlinePlus

    ... Read More Bronchiectasis Chronic obstructive pulmonary disease Lung cancer Lung cancer - non-small cell Lung cancer - small cell ... team. Related MedlinePlus Health Topics COPD Emphysema Lung Cancer Lung Diseases Pleural Disorders Browse the Encyclopedia A.D. ...

  19. Increasing Small Business Lending Act of 2011

    THOMAS, 112th Congress

    Sen. Kerry, John F. [D-MA

    2011-11-08

    Senate - 11/08/2011 Read twice and referred to the Committee on Small Business and Entrepreneurship. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  20. Women's Small Business Ownership Act of 2014

    THOMAS, 113th Congress

    Sen. Cantwell, Maria [D-WA

    2014-07-30

    Senate - 07/30/2014 Read twice and referred to the Committee on Small Business and Entrepreneurship. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  1. Veterans Small Business Enhancement Act of 2014

    THOMAS, 113th Congress

    Sen. Durbin, Richard J. [D-IL

    2014-09-11

    Senate - 09/11/2014 Read twice and referred to the Committee on Small Business and Entrepreneurship. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  2. Small Business Community Partner Relief Act of 2010

    THOMAS, 111th Congress

    Sen. Landrieu, Mary L. [D-LA

    2010-03-25

    Senate - 03/25/2010 Read twice and referred to the Committee on Small Business and Entrepreneurship. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  3. SCORE for Small Business Act of 2014

    THOMAS, 113th Congress

    Sen. Landrieu, Mary L. [D-LA

    2014-02-10

    Senate - 02/10/2014 Read twice and referred to the Committee on Small Business and Entrepreneurship. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  4. Small Business Emergency Loan Relief Act of 2009

    THOMAS, 111th Congress

    Sen. Brown, Sherrod [D-OH

    2009-10-20

    Senate - 10/20/2009 Read twice and referred to the Committee on Small Business and Entrepreneurship. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  5. Small Business Contracting Programs Parity Act of 2009

    THOMAS, 111th Congress

    Sen. Snowe, Olympia J. [R-ME

    2009-07-21

    Senate - 07/21/2009 Read twice and referred to the Committee on Small Business and Entrepreneurship. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  6. Native Small Business Conformity Act of 2013

    THOMAS, 113th Congress

    Sen. Schatz, Brian [D-HI

    2013-10-29

    Senate - 10/29/2013 Read twice and referred to the Committee on Small Business and Entrepreneurship. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  7. Small Business Disaster Assistance Act of 2011

    THOMAS, 112th Congress

    Sen. Casey, Robert P., Jr. [D-PA

    2011-10-13

    Senate - 10/13/2011 Read twice and referred to the Committee on Small Business and Entrepreneurship. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  8. Small Business Environmental Stewardship Assistance Act of 2010

    THOMAS, 111th Congress

    Sen. Wyden, Ron [D-OR

    2010-04-29

    Senate - 04/29/2010 Read twice and referred to the Committee on Small Business and Entrepreneurship. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  9. Women's Small Business Ownership Act of 2012

    THOMAS, 112th Congress

    Sen. Snowe, Olympia J. [R-ME

    2012-05-17

    Senate - 05/17/2012 Read twice and referred to the Committee on Small Business and Entrepreneurship. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  10. Small Business Investment and Innovation Act of 2010

    THOMAS, 111th Congress

    Sen. Landrieu, Mary L. [D-LA

    2010-11-18

    Senate - 11/18/2010 Read twice and referred to the Committee on Small Business and Entrepreneurship. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  11. Small Business International Trade Enhancements Act of 2009

    THOMAS, 111th Congress

    Sen. Landrieu, Mary L. [D-LA

    2009-06-08

    Senate - 06/08/2009 Read twice and referred to the Committee on Small Business and Entrepreneurship. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  12. Small Business Programs Parity Act of 2010

    THOMAS, 111th Congress

    Sen. Landrieu, Mary L. [D-LA

    2010-03-26

    Senate - 03/26/2010 Read twice and referred to the Committee on Small Business and Entrepreneurship. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  13. 33 CFR 125.43 - Hearing procedure.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... support of such reasons. (e) Hearings shall be opened by the reading of the Notice of the Commandant and... membership cards, petitions bearing the applicant's or holder's signature, books, treatises or articles...

  14. 33 CFR 125.43 - Hearing procedure.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... support of such reasons. (e) Hearings shall be opened by the reading of the Notice of the Commandant and... membership cards, petitions bearing the applicant's or holder's signature, books, treatises or articles...

  15. Open to Suggestion.

    ERIC Educational Resources Information Center

    Rivard, Joseph D; Bieske, Gordon B.

    1993-01-01

    Offers (1) a teaching strategy using contemporary music themes to increase adolescents' confidence and reading fluency; and (2) a brief description of four literacy programs from around the world which were UNESCO prize winners. (SR)

  16. Generation of 2A-linked multicistronic cassettes by recombinant PCR.

    PubMed

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

    2012-02-01

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

  17. Small interfering RNAs based on huntingtin trinucleotide repeats are highly toxic to cancer cells.

    PubMed

    Murmann, Andrea E; Gao, Quan Q; Putzbach, William E; Patel, Monal; Bartom, Elizabeth T; Law, Calvin Y; Bridgeman, Bryan; Chen, Siquan; McMahon, Kaylin M; Thaxton, C Shad; Peter, Marcus E

    2018-03-01

    Trinucleotide repeat (TNR) expansions in the genome cause a number of degenerative diseases. A prominent TNR expansion involves the triplet CAG in the huntingtin (HTT) gene responsible for Huntington's disease (HD). Pathology is caused by protein and RNA generated from the TNR regions including small siRNA-sized repeat fragments. An inverse correlation between the length of the repeats in HTT and cancer incidence has been reported for HD patients. We now show that siRNAs based on the CAG TNR are toxic to cancer cells by targeting genes that contain long reverse complementary TNRs in their open reading frames. Of the 60 siRNAs based on the different TNRs, the six members in the CAG/CUG family of related TNRs are the most toxic to both human and mouse cancer cells. siCAG/CUG TNR-based siRNAs induce cell death in vitro in all tested cancer cell lines and slow down tumor growth in a preclinical mouse model of ovarian cancer with no signs of toxicity to the mice. We propose to explore TNR-based siRNAs as a novel form of anticancer reagents. © 2018 The Authors.

  18. A novel glutamine-rich putative transcriptional adaptor protein (TIG-1), preferentially expressed in placental and bone-marrow tissues.

    PubMed

    Abraham, S; Solomon, W B

    2000-09-19

    We used a subtractive hybridization protocol to identify novel expressed sequence tags (ESTs) corresponding to mRNAs whose expression was induced upon exposure of the human leukemia cell line K562 to the phorbol ester 12-O-tetradecanolyphorbol-13-acetate (TPA). The complete open reading frame of one of the novel ESTs, named TIG-1, was obtained by screening K562 cell and placental cDNA libraries. The deduced open reading frame of the TIG-1 cDNA encodes for a glutamine repeat-rich protein with a predicted molecular weight of 63kDa. The predicted open reading frame also contains a consensus bipartite nuclear localization signal, though no specific DNA-binding domain is found. The corresponding TIG-1 mRNA is ubiquitously expressed. Placental tissue expresses the TIG-1 mRNA 200 times more than the lowest expressing tissues such as kidney and lung. There is also preferential TIG-1 mRNA expression in cells of bone-marrow lineage.In-vitro transcription/translation of the TIG-1 cDNA yielded a polypeptide with an apparent molecular weight of 97kDa. Using polyclonal antibodies obtained from a rabbit immunized with the carboxy-terminal portion of bacterially expressed TIG-1 protein, a polypeptide with molecular weight of 97kDa was identified by Western blot analyses of protein lysates obtained from K562 cells. Cotransfection assays of K562 cells, using a GAL4-TIG-1 fusion gene and GAL4 operator-CAT, indicate that the TIG-1 protein may have transcriptional regulatory activity when tethered to DNA. We hypothesize that this novel glutamine-rich protein participates in a protein complex that regulates gene transcription. It has been demonstrated by Naar et al. (Naar, A.M., Beaurang, P.A., Zhou, S., Abraham, S., Solomon, W.B., Tjian, R., 1999, Composite co-activator ARC mediates chromatin-directed transcriptional activation. Nature 398, 828-830) that the amino acid sequences of peptide fragments obtained from a polypeptide found in a complex of proteins that alters chromatin structure (ARC) are identical to portions of the deduced open reading frame of TIG-1 mRNA.

  19. Strategies for Improving Non-Fiction Reading Comprehension.

    ERIC Educational Resources Information Center

    Bell, Karen; Caspari, Amy

    This report describes a program for introducing students to strategies for improving their comprehension of non-fiction materials. The targeted population consisted of students of one third grade class in a small, middle class suburb, northwest of a large, midwestern city. Difficulty reading and comprehending non-fiction material was documented…

  20. Big Books and Small Marvels

    ERIC Educational Resources Information Center

    Stanistreet, Paul

    2012-01-01

    The Reader Organisation's Get into Reading programme is all about getting people together in groups to engage with serious books. The groups are mixed and the participants sometimes challenging, but the outcomes are often remarkable. Jane Davis, who founded the Reader Organisation and continues to oversee Get into Reading, has witnessed a massive…

  1. Television, Dialogue Journals, and Feedback in the EFL Classroom.

    ERIC Educational Resources Information Center

    Ennis, Mark

    1997-01-01

    An approach used to teach English as a foreign language (EFL) and American culture that addresses the four language skills (listening, speaking, reading writing) in a complementary, non-contrived way is described. Classroom activities combine television viewing, discussion, writing, and reading journal entries. Students watch small segments of…

  2. English Language Learning: Revaluing Language as Resource. NCTE Reading Initiative.

    ERIC Educational Resources Information Center

    Whitmore, Kathryn F.; Martinez-Roldan, Carmen

    In this inquiry study, teachers will explore the concept of English Language Learning and its implications for classrooms. Individually and in small groups, teachers will have opportunities to read, talk, and reflect about current issues regarding linguistic diversity in classrooms and schools, including bilingual/multilingual, ESL, and language…

  3. Using the Film JFK To Teach Critical Thinking.

    ERIC Educational Resources Information Center

    Bassham, Gregory; Nardone, Henry

    1997-01-01

    A college instructional module uses the film "JFK" and related reading materials to convince even the less motivated students that reasoning abilities can be of significant personal and public value. Small groups are assigned presentations based on research and readings. Student response has been enthusiastic and the technique has been…

  4. Information Processing Abilities and Reading.

    ERIC Educational Resources Information Center

    Samuels, S. Jay

    1987-01-01

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

  5. Understanding Ocean Acidification

    ERIC Educational Resources Information Center

    National Oceanic and Atmospheric Administration, 2011

    2011-01-01

    This curriculum module is designed for students who are taking high school chemistry. Students should already have some experience with the following: (1) Understanding and reading the pH scale; (2) Knowledge of the carbon cycle; (3) Using scientific notation to express large and small values; and (4) Reading chemical equations. This curriculum…

  6. Emotion: A Critical Analysis for Children.

    ERIC Educational Resources Information Center

    Shibles, Warren

    Part of the "Teaching Young People to be Critical Series," this booklet defines and analyzes emotions and emotional terms for children in light of theories of philosophers Ludwig Wittgenstein and John Dewey. Intended for individual or small group work, the objectives are threefold: reading improvement, reading enjoyment, and student involvement in…

  7. Teachers' Perceptions of Georgia's Early Reading Intervention Program: A Qualitative Study

    ERIC Educational Resources Information Center

    Hobby, Patti Tennant

    2012-01-01

    This qualitative study used an ethnographic method to investigate teachers' perceptions of reading interventions delivered in a state-funded early intervention program (EIP). Academically at-risk students struggle to meet grade-level standards year after year, even with interventions involving small group, targeted assistance. Teacher perceptions…

  8. Psycholinguistic Approach to Reading (PAR).

    ERIC Educational Resources Information Center

    Cajon Valley Union School District, El Cajon, CA.

    This program, included in "Effective Reading Programs...," sees 1675 children in kindergarten through grade eight, most of whom are white middle-class children from a small city. The emphasis in this program is on increasing comprehension by teaching words in context. The strategies require the children to use their intuitive knowledge…

  9. Detection of microRNAs in color space.

    PubMed

    Marco, Antonio; Griffiths-Jones, Sam

    2012-02-01

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

  10. Life Writing Lite: Judy Garland and Reparative Rhetorics of Celebrity Life Writing

    ERIC Educational Resources Information Center

    Janangelo, Joseph

    2010-01-01

    This essay offers a rhetorical reading of entertainer Judy Garland's early life writing projects. The author focuses on two open letters Garland published in 1950, in which she talks to the public and press to let them know "the truth" ("Open") about her life and how much her audience means to her. As a troubled celebrity, Garland had for years…

  11. Open Fuels Standard Act of 2011

    THOMAS, 112th Congress

    Sen. Cantwell, Maria [D-WA

    2011-09-22

    Senate - 09/22/2011 Read twice and referred to the Committee on Commerce, Science, and Transportation. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  12. Open Internet Preservation Act of 2014

    THOMAS, 113th Congress

    Sen. Markey, Edward J. [D-MA

    2014-02-03

    Senate - 02/03/2014 Read twice and referred to the Committee on Commerce, Science, and Transportation. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  13. KID Project: an internet-based digital video atlas of capsule endoscopy for research purposes.

    PubMed

    Koulaouzidis, Anastasios; Iakovidis, Dimitris K; Yung, Diana E; Rondonotti, Emanuele; Kopylov, Uri; Plevris, John N; Toth, Ervin; Eliakim, Abraham; Wurm Johansson, Gabrielle; Marlicz, Wojciech; Mavrogenis, Georgios; Nemeth, Artur; Thorlacius, Henrik; Tontini, Gian Eugenio

    2017-06-01

     Capsule endoscopy (CE) has revolutionized small-bowel (SB) investigation. Computational methods can enhance diagnostic yield (DY); however, incorporating machine learning algorithms (MLAs) into CE reading is difficult as large amounts of image annotations are required for training. Current databases lack graphic annotations of pathologies and cannot be used. A novel database, KID, aims to provide a reference for research and development of medical decision support systems (MDSS) for CE.  Open-source software was used for the KID database. Clinicians contribute anonymized, annotated CE images and videos. Graphic annotations are supported by an open-access annotation tool (Ratsnake). We detail an experiment based on the KID database, examining differences in SB lesion measurement between human readers and a MLA. The Jaccard Index (JI) was used to evaluate similarity between annotations by the MLA and human readers.  The MLA performed best in measuring lymphangiectasias with a JI of 81 ± 6 %. The other lesion types were: angioectasias (JI 64 ± 11 %), aphthae (JI 64 ± 8 %), chylous cysts (JI 70 ± 14 %), polypoid lesions (JI 75 ± 21 %), and ulcers (JI 56 ± 9 %).  MLA can perform as well as human readers in the measurement of SB angioectasias in white light (WL). Automated lesion measurement is therefore feasible. KID is currently the only open-source CE database developed specifically to aid development of MDSS. Our experiment demonstrates this potential.

  14. Southeast Hurricanes Small Business Disaster Relief Act of 2011

    THOMAS, 112th Congress

    Sen. Landrieu, Mary L. [D-LA

    2011-03-28

    Senate - 03/28/2011 Read twice and referred to the Committee on Small Business and Entrepreneurship. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  15. Small Business Administration Disaster Recovery and Reform Act of 2009

    THOMAS, 111th Congress

    Sen. Landrieu, Mary L. [D-LA

    2009-11-05

    Senate - 11/05/2009 Read twice and referred to the Committee on Small Business and Entrepreneurship. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  16. Southeast Hurricanes Small Business Disaster Relief Act of 2010

    THOMAS, 111th Congress

    Sen. Landrieu, Mary L. [D-LA

    2010-02-04

    Senate - 02/04/2010 Read twice and referred to the Committee on Small Business and Entrepreneurship. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  17. Small Business Health Information Technology Financing Act of 2009

    THOMAS, 111th Congress

    Sen. Kerry, John F. [D-MA

    2009-11-10

    Senate - 11/10/2009 Read twice and referred to the Committee on Small Business and Entrepreneurship. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  18. Strengthening Our Economy Through Small Business Innovation Act of 2009

    THOMAS, 111th Congress

    Sen. Feingold, Russell D. [D-WI

    2009-01-08

    Senate - 01/08/2009 Read twice and referred to the Committee on Small Business and Entrepreneurship. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  19. A bill to extend the small business loan enhancements.

    THOMAS, 111th Congress

    Sen. Snowe, Olympia J. [R-ME

    2010-07-15

    Senate - 07/15/2010 Read twice and referred to the Committee on Small Business and Entrepreneurship. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  20. Small Business Training in Federal Contracting Certification Act of 2010

    THOMAS, 111th Congress

    Sen. Snowe, Olympia J. [R-ME

    2010-05-27

    Senate - 05/27/2010 Read twice and referred to the Committee on Small Business and Entrepreneurship. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

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