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,…

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…

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…

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.

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

PubMed

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

2018-05-01

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

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

PubMed

Lee, Young Han

2012-01-01

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

Chemical Safety Assessment Using Read-Across: Assessing the Use of Novel Testing Methods to Strengthen the Evidence Base for Decision Making.

PubMed

Berggren, Elisabet; Amcoff, Patric; Benigni, Romualdo; Blackburn, Karen; Carney, Edward; Cronin, Mark; Deluyker, Hubert; Gautier, Francoise; Judson, Richard S; Kass, Georges E N; Keller, Detlef; Knight, Derek; Lilienblum, Werner; Mahony, Catherine; Rusyn, Ivan; Schultz, Terry; Schwarz, Michael; Schüürmann, Gerrit; White, Andrew; Burton, Julien; Lostia, Alfonso M; Munn, Sharon; Worth, Andrew

2015-12-01

Safety assessment for repeated dose toxicity is one of the largest challenges in the process to replace animal testing. This is also one of the proof of concept ambitions of SEURAT-1, the largest ever European Union research initiative on alternative testing, co-funded by the European Commission and Cosmetics Europe. This review is based on the discussion and outcome of a workshop organized on initiative of the SEURAT-1 consortium joined by a group of international experts with complementary knowledge to further develop traditional read-across and include new approach data. The aim of the suggested strategy for chemical read-across is to show how a traditional read-across based on structural similarities between source and target substance can be strengthened with additional evidence from new approach data--for example, information from in vitro molecular screening, "-omics" assays and computational models--to reach regulatory acceptance. We identified four read-across scenarios that cover typical human health assessment situations. For each such decision context, we suggested several chemical groups as examples to prove when read-across between group members is possible, considering both chemical and biological similarities. We agreed to carry out the complete read-across exercise for at least one chemical category per read-across scenario in the context of SEURAT-1, and the results of this exercise will be completed and presented by the end of the research initiative in December 2015.

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

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

Brain-based individual difference measures of reading skill in deaf and hearing adults.

PubMed

Mehravari, Alison S; Emmorey, Karen; Prat, Chantel S; Klarman, Lindsay; Osterhout, Lee

2017-07-01

Most deaf children and adults struggle to read, but some deaf individuals do become highly proficient readers. There is disagreement about the specific causes of reading difficulty in the deaf population, and consequently, disagreement about the effectiveness of different strategies for teaching reading to deaf children. Much of the disagreement surrounds the question of whether deaf children read in similar or different ways as hearing children. In this study, we begin to answer this question by using real-time measures of neural language processing to assess if deaf and hearing adults read proficiently in similar or different ways. Hearing and deaf adults read English sentences with semantic, grammatical, and simultaneous semantic/grammatical errors while event-related potentials (ERPs) were recorded. The magnitude of individuals' ERP responses was compared to their standardized reading comprehension test scores, and potentially confounding variables like years of education, speechreading skill, and language background of deaf participants were controlled for. The best deaf readers had the largest N400 responses to semantic errors in sentences, while the best hearing readers had the largest P600 responses to grammatical errors in sentences. These results indicate that equally proficient hearing and deaf adults process written language in different ways, suggesting there is little reason to assume that literacy education should necessarily be the same for hearing and deaf children. The results also show that the most successful deaf readers focus on semantic information while reading, which suggests aspects of education that may promote improved literacy in the deaf population. Copyright © 2017 Elsevier Ltd. All rights reserved.

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 ...

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…

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

ERIC Educational Resources Information Center

Langstaff, Nancy

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

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

ERIC Educational Resources Information Center

Finn, Seth

1997-01-01

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

The impact of a science-based integrated instructional protocol on the motivation, reading comprehension, and science achievement of fourth and fifth graders

NASA Astrophysics Data System (ADS)

Stephens, Kathy E.

The purpose of this study was to determine the impact of implementing an integrated instructional protocol of science-based informational texts as teacher read alouds, student independent reading, and written journal responses on motivation, reading comprehension, and science achievement of fourth- and fifth-grade students with attention to specific student groups, including gender and ethnicities. A mixed methods research design included a 12-week intervention conducted with 68 fourth and fifth graders and 30 nonintervention fourth and fifth graders. Participating fourth and fifth graders completed the comprehension subtest of the Gates-MacGinitie Reading Test ([GMRT] MacGinitie, MacGinitie, Maria, & Dreyer, 2000) and the Texas Assessment of Knowledge and Skills ([TAKS] Texas Education Agency [TEA], 2005a). The Reading Survey of the Motivation to Read Profile ([MRP], Gambrell, Palmer, Codling, & Mazzoni, 1996) served as another quantitative data source. Qualitative data sources included classroom observations, key informant interviews, and student journal entries. The GMRT results indicated that the intervention fourth graders demonstrated the largest growth in reading comprehension achievement. Significant differences were noted by GMRT results between the intervention and nonintervention fourth graders. A significant difference was found between fourth-grade males and females on the GMRT, with a larger gain posted by the females. No significant differences were found on the GMRT in fifth grade Reading TAKS results indicated a significant difference between intervention fourth-grade Hispanic and African American students, while fifth-grade Science TAKS results indicated no significant differences. The MRP Reading Survey results indicated no significant differences; however, fourth-grade Hispanic and fifth-grade male students demonstrated significant growth. Classroom observations documented the progress of the 12-week intervention; 9 primary instructional and behavioral themes with 40 subcategories were discovered using open coding (Berg, 2004). Data were collected from the MRP Conversational Interview (Gambrell et al., 1996) with 12 key informants, and their journal entries provided evidence of the impact of the instructional protocol. Findings from this study seemed to confirm that students may experience improvement in reading comprehension after participation in an integrated instructional protocol. Findings also suggested gaps in minority ethnicities may be minimized, while female students continued to outscore male students.

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

PubMed

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

2006-12-01

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

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

PubMed

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

2014-01-01

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

[Random Variable Read Me File

NASA Technical Reports Server (NTRS)

Teubert, Christopher; Sankararaman, Shankar; Cullo, Aiden

2017-01-01

Readme for the Random Variable Toolbox usable manner. is a Web-based Git version control repository hosting service. It is mostly used for computer code. It offers all of the distributed version control and source code management (SCM) functionality of Git as well as adding its own features. It provides access control and several collaboration features such as bug tracking, feature requests, task management, and wikis for every project.[3] GitHub offers both plans for private and free repositories on the same account[4] which are commonly used to host open-source software projects.[5] As of April 2017, GitHub reports having almost 20 million users and 57 million repositories,[6] making it the largest host of source code in the world.[7] GitHub has a mascot called Octocat, a cat with five tentacles and a human-like face

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

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:…

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…

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

PubMed Central

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

2014-01-01

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

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

PubMed Central

Schaeffer, E; Sninsky, J J

1984-01-01

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

Exploring the Inconsistent Labels and Definitions of Texts Used in Informational Reading and Writing

ERIC Educational Resources Information Center

Watkins, Naomi M.; Liang, Lauren Aimonette

2014-01-01

This article discusses the various labels and definitions given for texts used for informational reading and writing and the confusion caused by the inconsistency of terms. An EBSCO search on articles published from 2006 to 2011 in the three largest literacy-related professional organizations' journals produced a total of 59 articles.…

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

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-26

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

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

ERIC Educational Resources Information Center

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

2018-01-01

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

A simplified financial model for automatic meter reading

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

Ward, S.M.

1994-01-15

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

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...

Sex Differences in Mathematics and Reading Achievement Are Inversely Related: Within- and Across-Nation Assessment of 10 Years of PISA Data

PubMed Central

Stoet, Gijsbert; Geary, David C.

2013-01-01

We analyzed one decade of data collected by the Programme for International Student Assessment (PISA), including the mathematics and reading performance of nearly 1.5 million 15 year olds in 75 countries. Across nations, boys scored higher than girls in mathematics, but lower than girls in reading. The sex difference in reading was three times as large as in mathematics. There was considerable variation in the extent of the sex differences between nations. There are countries without a sex difference in mathematics performance, and in some countries girls scored higher than boys. Boys scored lower in reading in all nations in all four PISA assessments (2000, 2003, 2006, 2009). Contrary to several previous studies, we found no evidence that the sex differences were related to nations’ gender equality indicators. Further, paradoxically, sex differences in mathematics were consistently and strongly inversely correlated with sex differences in reading: Countries with a smaller sex difference in mathematics had a larger sex difference in reading and vice versa. We demonstrate that this was not merely a between-nation, but also a within-nation effect. This effect is related to relative changes in these sex differences across the performance continuum: We did not find a sex difference in mathematics among the lowest performing students, but this is where the sex difference in reading was largest. In contrast, the sex difference in mathematics was largest among the higher performing students, and this is where the sex difference in reading was smallest. The implication is that if policy makers decide that changes in these sex differences are desired, different approaches will be needed to achieve this for reading and mathematics. Interventions that focus on high-achieving girls in mathematics and on low achieving boys in reading are likely to yield the strongest educational benefits. PMID:23516422

Sex differences in mathematics and reading achievement are inversely related: within- and across-nation assessment of 10 years of PISA data.

PubMed

Stoet, Gijsbert; Geary, David C

2013-01-01

We analyzed one decade of data collected by the Programme for International Student Assessment (PISA), including the mathematics and reading performance of nearly 1.5 million 15 year olds in 75 countries. Across nations, boys scored higher than girls in mathematics, but lower than girls in reading. The sex difference in reading was three times as large as in mathematics. There was considerable variation in the extent of the sex differences between nations. There are countries without a sex difference in mathematics performance, and in some countries girls scored higher than boys. Boys scored lower in reading in all nations in all four PISA assessments (2000, 2003, 2006, 2009). Contrary to several previous studies, we found no evidence that the sex differences were related to nations' gender equality indicators. Further, paradoxically, sex differences in mathematics were consistently and strongly inversely correlated with sex differences in reading: Countries with a smaller sex difference in mathematics had a larger sex difference in reading and vice versa. We demonstrate that this was not merely a between-nation, but also a within-nation effect. This effect is related to relative changes in these sex differences across the performance continuum: We did not find a sex difference in mathematics among the lowest performing students, but this is where the sex difference in reading was largest. In contrast, the sex difference in mathematics was largest among the higher performing students, and this is where the sex difference in reading was smallest. The implication is that if policy makers decide that changes in these sex differences are desired, different approaches will be needed to achieve this for reading and mathematics. Interventions that focus on high-achieving girls in mathematics and on low achieving boys in reading are likely to yield the strongest educational benefits.

The Influence of Technology Usage on Academic Achievement (Reading and Math) from a Teacher's Perspective

ERIC Educational Resources Information Center

White-Harris, Kimberly L.

2017-01-01

The purpose of this study was to examine the perceptions of technology implementation of middle school teachers in one of the largest school districts in Alabama. This study examined if the use of technology had a positive influence on students' academic performance (reading and mathematics). Although several other studies are equivalent to this…

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

ERIC Educational Resources Information Center

Munson, Margaret

2013-01-01

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

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.

Characterization of a Novel Orthomyxo-like Virus Causing Mass Die-Offs of Tilapia

PubMed Central

Bacharach, Eran; Mishra, Nischay; Briese, Thomas; Zody, Michael C.; Kembou Tsofack, Japhette Esther; Zamostiano, Rachel; Berkowitz, Asaf; Ng, James; Nitido, Adam; Corvelo, André; Toussaint, Nora C.; Abel Nielsen, Sandra Cathrine; Hornig, Mady; Del Pozo, Jorge; Bloom, Toby; Ferguson, Hugh

2016-01-01

ABSTRACT Tilapia are an important global food source due to their omnivorous diet, tolerance for high-density aquaculture, and relative disease resistance. Since 2009, tilapia aquaculture has been threatened by mass die-offs in farmed fish in Israel and Ecuador. Here we report evidence implicating a novel orthomyxo-like virus in these outbreaks. The tilapia lake virus (TiLV) has a 10-segment, negative-sense RNA genome. The largest segment, segment 1, contains an open reading frame with weak sequence homology to the influenza C virus PB1 subunit. The other nine segments showed no homology to other viruses but have conserved, complementary sequences at their 5′ and 3′ termini, consistent with the genome organization found in other orthomyxoviruses. In situ hybridization indicates TiLV replication and transcription at sites of pathology in the liver and central nervous system of tilapia with disease. PMID:27048802

AMBER instrument control software

NASA Astrophysics Data System (ADS)

Le Coarer, Etienne P.; Zins, Gerard; Gluck, Laurence; Duvert, Gilles; Driebe, Thomas; Ohnaka, Keiichi; Heininger, Matthias; Connot, Claus; Behrend, Jan; Dugue, Michel; Clausse, Jean Michel; Millour, Florentin

2004-09-01

AMBER (Astronomical Multiple BEam Recombiner) is a 3 aperture interferometric recombiner operating between 1 and 2.5 um, for the Very Large Telescope Interferometer (VLTI). The control software of the instrument, based on the VLT Common Software, has been written to comply with specific features of the AMBER hardware, such as the Infrared detector read out modes or piezo stage drivers, as well as with the very specific operation modes of an interferomtric instrument. In this respect, the AMBER control software was designed to insure that all operations, from the preparation of the observations to the control/command of the instrument during the observations, would be kept as simple as possible for the users and operators, opening the use of an interferometric instrument to the largest community of astronomers. Peculiar attention was given to internal checks and calibration procedures both to evaluate data quality in real time, and improve the successes of long term UV plane coverage observations.

Gene repertoire of amoeba-associated giant viruses.

PubMed

Colson, Philippe; Raoult, Didier

2010-01-01

Acanthamoeba polyphaga mimivirus, Marseillevirus, and Sputnik, a virophage, are intra-amoebal viruses that have been isolated from water collected in cooling towers. They have provided fascinating data and have raised exciting questions about viruses definition and evolution. Mimivirus and Marseillevirus have been classified in the nucleo-cytoplasmic large DNA viruses (NCLDVs) class. Their genomes are the largest and fifth largest viral genomes sequenced so far. The gene repertoire of these amoeba-associated viruses can be divided into four groups: the core genome, genes acquired by lateral gene transfer, duplicated genes, and ORFans. Open reading frames (ORFs) that have homologs in the NCLDVs core gene set represent 2.9 and 6.1% of the Mimivirus and Marseillevirus gene contents, respectively. A substantial proportion of the Mimivirus, Marseillevirus and Sputnik ORFs exhibit sequence similarities to homologs found in bacteria, archaea, eukaryotes or viruses. The large amount of chimeric genes in these viral genomes might have resulted from acquisitions by lateral gene transfers, implicating sympatric bacteria and viruses with an intra-amoebal lifestyle. In addition, lineage-specific gene expansion may have played a major role in the genome shaping. Altogether, the data so far accumulated on amoeba-associated giant viruses are a powerful incentive to isolate and study additional strains to gain better understanding of their pangenome. Copyright 2010 S. Karger AG, Basel.

TIMEDELN: A programme for the detection and parametrization of overlapping resonances using the time-delay method

NASA Astrophysics Data System (ADS)

Little, Duncan A.; Tennyson, Jonathan; Plummer, Martin; Noble, Clifford J.; Sunderland, Andrew G.

2017-06-01

TIMEDELN implements the time-delay method of determining resonance parameters from the characteristic Lorentzian form displayed by the largest eigenvalues of the time-delay matrix. TIMEDELN constructs the time-delay matrix from input K-matrices and analyses its eigenvalues. This new version implements multi-resonance fitting and may be run serially or as a high performance parallel code with three levels of parallelism. TIMEDELN takes K-matrices from a scattering calculation, either read from a file or calculated on a dynamically adjusted grid, and calculates the time-delay matrix. This is then diagonalized, with the largest eigenvalue representing the longest time-delay experienced by the scattering particle. A resonance shows up as a characteristic Lorentzian form in the time-delay: the programme searches the time-delay eigenvalues for maxima and traces resonances when they pass through different eigenvalues, separating overlapping resonances. It also performs the fitting of the calculated data to the Lorentzian form and outputs resonance positions and widths. Any remaining overlapping resonances can be fitted jointly. The branching ratios of decay into the open channels can also be found. The programme may be run serially or in parallel with three levels of parallelism. The parallel code modules are abstracted from the main physics code and can be used independently.

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.

The association between arithmetic and reading performance in school: A meta-analytic study.

PubMed

Singer, Vivian; Strasser, Kathernie

2017-12-01

Many studies of school achievement find a significant association between reading and arithmetic achievement. The magnitude of the association varies widely across the studies, but the sources of this variation have not been identified. The purpose of this paper is to examine the magnitude and determinants of the relation between arithmetic and reading performance during elementary and middle school years. We meta-analyzed 210 correlations between math and reading measures, coming from 68 independent samples (the overall sample size was 58923 participants). The meta-analysis yielded an average correlation of 0.55 between math and reading measures. Among the moderators tested, only transparency of orthography and use of timed or untimed tests were significant in explaining the size of the correlation, with the largest correlations observed between timed measures of arithmetic and reading and between math and reading in opaque orthographies. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

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.

Vampiremania Sparks Developmental Readers (Open to Suggestion).

ERIC Educational Resources Information Center

Kaiden, Ellen Beth

1994-01-01

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

4 CFR 81.8 - Public reading facility.

Code of Federal Regulations, 2011 CFR

2011-01-01

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

4 CFR 81.8 - Public reading facility.

Code of Federal Regulations, 2010 CFR

2010-01-01

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

Plastomes of the green algae Hydrodictyon reticulatum and Pediastrum duplex (Sphaeropleales, Chlorophyceae).

PubMed

McManus, Hilary A; Sanchez, Daniel J; Karol, Kenneth G

2017-01-01

Comparative studies of chloroplast genomes (plastomes) across the Chlorophyceae are revealing dynamic patterns of size variation, gene content, and genome rearrangements. Phylogenomic analyses are improving resolution of relationships, and uncovering novel lineages as new plastomes continue to be characterized. To gain further insight into the evolution of the chlorophyte plastome and increase the number of representative plastomes for the Sphaeropleales, this study presents two fully sequenced plastomes from the green algal family Hydrodictyaceae (Sphaeropleales, Chlorophyceae), one from Hydrodictyon reticulatum and the other from Pediastrum duplex . Genomic DNA from Hydrodictyon reticulatum and Pediastrum duplex was subjected to Illumina paired-end sequencing and the complete plastomes were assembled for each. Plastome size and gene content were characterized and compared with other plastomes from the Sphaeropleales. Homology searches using BLASTX were used to characterize introns and open reading frames (orfs) ≥ 300 bp. A phylogenetic analysis of gene order across the Sphaeropleales was performed. The plastome of Hydrodictyon reticulatum is 225,641 bp and Pediastrum duplex is 232,554 bp. The plastome structure and gene order of H. reticulatum and P. duplex are more similar to each other than to other members of the Sphaeropleales. Numerous unique open reading frames are found in both plastomes and the plastome of P. duplex contains putative viral protein genes, not found in other Sphaeropleales plastomes. Gene order analyses support the monophyly of the Hydrodictyaceae and their sister relationship to the Neochloridaceae. The complete plastomes of Hydrodictyon reticulatum and Pediastrum duplex , representing the largest of the Sphaeropleales sequenced thus far, once again highlight the variability in size, architecture, gene order and content across the Chlorophyceae. Novel intron insertion sites and unique orfs indicate recent, independent invasions into each plastome, a hypothesis testable with an expanded plastome investigation within the Hydrodictyaceae.

The importance of leisure reading to health sciences students: results of a survey.

PubMed

Watson, Erin M

2016-03-01

To determine what value health sciences students place on leisure reading, whether they prefer to read online or in print, what the principal barriers are to their reading and whether they wish to have a leisure reading collection at their health sciences library. In October 2010, a link to a survey was sent to all 1800 students in health sciences professional programmes at the author's institution. Two hundred and thirteen students (11.8%) responded. Most felt that leisure reading had helped in their development as health professionals and increased their empathy. They listed many benefits of reading, such as improved understanding of minority groups, reduced stress, and improved thinking and communication skills. The majority preferred to read books and magazines in print, while the largest number preferred reading newspapers in print as well. Lack of time, fatigue and the expense of purchasing reading materials were the greatest barriers to reading. A majority of students were in favour of having a leisure reading collection set up at their library. Leisure reading was valued by the respondents, who felt it provided personal and professional benefits. However, many indicated that circumstances made it difficult to participate in leisure reading. © 2015 Health Libraries Group.

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

ERIC Educational Resources Information Center

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

2015-01-01

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

Results with Open Court Reading.

ERIC Educational Resources Information Center

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

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

Variations in Reading Achievement Across 14 Southern African School Systems: Which Factors Matter?

NASA Astrophysics Data System (ADS)

Hungi, Njora; Thuku, Florence W.

2010-02-01

In this study the authors employed a multilevel analysis procedure in order to examine the pupil and school levels factors that contributed to variation in reading achievement among Grade 6 primary school pupils in 14 southern African school systems (Botswana, Kenya, Lesotho, Malawi, Mauritius, Mozambique, Namibia, Seychelles, South Africa, Swaziland, Tanzania, Uganda, Zambia, and Zanzibar). The data for this study were collected in 2002 as part of a major project known as the Southern and Eastern Africa Consortium for Monitoring Educational Quality (SACMEQ) that sought to examine the quality of education offered in primary schools in these countries. The most important factors affecting variation in pupil achievement across most of these school systems were grade repetition, pupil socioeconomic background, speaking the language of instruction at home, and Pupil age. South Africa, Uganda and Namibia were among the school systems with the largest between-school variation while Seychelles and Mauritius had the largest within-school variation. Low social equity in reading achievement was evident in Mauritius, Seychelles and Tanzania. Policy implications of the findings are discussed.

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.

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

ERIC Educational Resources Information Center

Mishra, Sanjaya

2010-01-01

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

Open the Door for Reading (Motivational Activities).

ERIC Educational Resources Information Center

Voorhees, Roxy

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

Open to Suggestion.

ERIC Educational Resources Information Center

Journal of Reading, 1987

1987-01-01

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

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

ERIC Educational Resources Information Center

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

2016-01-01

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

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

ERIC Educational Resources Information Center

Randall, David

2016-01-01

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

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

ERIC Educational Resources Information Center

Kender, Joseph P., Ed.

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

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

ERIC Educational Resources Information Center

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

2015-01-01

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

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

ERIC Educational Resources Information Center

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

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

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

Code of Federal Regulations, 2011 CFR

2011-04-01

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

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

Code of Federal Regulations, 2014 CFR

2014-04-01

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

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

Code of Federal Regulations, 2013 CFR

2013-04-01

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

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

Code of Federal Regulations, 2012 CFR

2012-04-01

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

Identification of a non-LTR retrotransposon from the gypsy moth

Treesearch

K.J. Garner; J.M. Slavicek

1999-01-01

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

A Multisite Cluster Randomized Field Trial of Open Court Reading

ERIC Educational Resources Information Center

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

2008-01-01

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

U.S. Global Change Research Program

MedlinePlus

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

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

PubMed Central

2013-01-01

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

Readings and Experiences of Multimodality

ERIC Educational Resources Information Center

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

2017-01-01

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

Defense Threat Reduction Agency > Research > DTRIAC > FAQ Sheet

Science.gov Websites

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

Sacred Cows That Should Be Put to Pasture.

ERIC Educational Resources Information Center

Artley, A. Sterl

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

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

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-09

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

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

DTIC Science & Technology

2008-06-01

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

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

DTIC Science & Technology

2007-06-01

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

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…

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

ERIC Educational Resources Information Center

McShane, Susan

2005-01-01

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

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

PubMed Central

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

1989-01-01

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

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

PubMed

Ustav, M; Stenlund, A

1991-02-01

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

Chemical Safety Assessment Using Read-Across: Assessing the Use of Novel Testing Methods to Strengthen the Evidence Base for Decision Making

PubMed Central

Amcoff, Patric; Benigni, Romualdo; Blackburn, Karen; Carney, Edward; Cronin, Mark; Deluyker, Hubert; Gautier, Francoise; Judson, Richard S.; Kass, Georges E.N.; Keller, Detlef; Knight, Derek; Lilienblum, Werner; Mahony, Catherine; Rusyn, Ivan; Schultz, Terry; Schwarz, Michael; Schüürmann, Gerrit; White, Andrew; Burton, Julien; Lostia, Alfonso M.; Munn, Sharon; Worth, Andrew

2015-01-01

Background Safety assessment for repeated dose toxicity is one of the largest challenges in the process to replace animal testing. This is also one of the proof of concept ambitions of SEURAT-1, the largest ever European Union research initiative on alternative testing, co-funded by the European Commission and Cosmetics Europe. This review is based on the discussion and outcome of a workshop organized on initiative of the SEURAT-1 consortium joined by a group of international experts with complementary knowledge to further develop traditional read-across and include new approach data. Objectives The aim of the suggested strategy for chemical read-across is to show how a traditional read-across based on structural similarities between source and target substance can be strengthened with additional evidence from new approach data—for example, information from in vitro molecular screening, “-omics” assays and computational models—to reach regulatory acceptance. Methods We identified four read-across scenarios that cover typical human health assessment situations. For each such decision context, we suggested several chemical groups as examples to prove when read-across between group members is possible, considering both chemical and biological similarities. Conclusions We agreed to carry out the complete read-across exercise for at least one chemical category per read-across scenario in the context of SEURAT-1, and the results of this exercise will be completed and presented by the end of the research initiative in December 2015. Citation Berggren E, Amcoff P, Benigni R, Blackburn K, Carney E, Cronin M, Deluyker H, Gautier F, Judson RS, Kass GE, Keller D, Knight D, Lilienblum W, Mahony C, Rusyn I, Schultz T, Schwarz M, Schüürmann G, White A, Burton J, Lostia AM, Munn S, Worth A. 2015. Chemical safety assessment using read-across: assessing the use of novel testing methods to strengthen the evidence base for decision making. Environ Health Perspect 123:1232–1240; http://dx.doi.org/10.1289/ehp.1409342 PMID:25956009

ObsPy - A Python Toolbox for Seismology - and Applications

NASA Astrophysics Data System (ADS)

Krischer, L.; Megies, T.; Barsch, R.; MacCarthy, J.; Lecocq, T.; Koymans, M. R.; Carothers, L.; Eulenfeld, T.; Reyes, C. G.; Falco, N.; Sales de Andrade, E.

2017-12-01

Recent years witnessed the evolution of Python's ecosystem into one of the most powerful and productive scientific environments across disciplines. ObsPy (https://www.obspy.org) is a fully community driven, open-source project dedicated to provide a bridge for seismology into that ecosystem. It is a Python toolbox offering: Read and write support for essentially every commonly used data format in seismology with a unified interface and automatic format detection. This includes waveform data (MiniSEED, SAC, SEG-Y, Reftek, …) as well as station (SEED, StationXML, SC3ML, …) and event meta information (QuakeML, ZMAP, …). Integrated access to the largest data centers, web services, and real-time data streams (FDSNWS, ArcLink, SeedLink, ...). A powerful signal processing toolbox tuned to the specific needs of seismologists. Utility functionality like travel time calculations with the TauP method, geodetic functions, and data visualizations. ObsPy has been in constant development for more than eight years and is developed and used by scientists around the world with successful applications in all branches of seismology. Additionally it nowadays serves as the foundation for a large number of more specialized packages. Newest features include: Full interoperability of SEED and StationXML/Inventory objects Access to the Nominal Response Library (NRL) for easy and quick creation of station metadata from scratch Support for the IRIS Federated Catalog Service Improved performance of the EarthWorm client Several improvements to MiniSEED read/write module Improved plotting capabilities for PPSD (spectrograms, PSD of discrete frequencies over time, ..) Support for.. Reading ArcLink Inventory XML Reading Reftek data format Writing SeisComp3 ML (SC3ML) Writing StationTXT format This presentation will give a short overview of the capabilities of ObsPy and point out several representative or new use cases and show-case some projects that are based on ObsPy, e.g.: seismo-live.org Seedlink-plotter MSNoise, and others..

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…

Ngaingan virus, a macropod-associated rhabdovirus, contains a second glycoprotein gene and seven novel open reading frames.

PubMed

Gubala, Aneta; Davis, Steven; Weir, Richard; Melville, Lorna; Cowled, Chris; Walker, Peter; Boyle, David

2010-03-30

Ngaingan virus (NGAV) was isolated from a pool of biting midges that were collected in the tropics of northern Australia. Reported here is the full-length sequence of the NGAV genome, which, at over 15.7 kb, is the largest in any rhabdovirus described to date and contains 13 genes, the highest number of genes observed in any (-) ssRNA virus. Seven of these putative genes show no significant homology to known proteins. Like viruses in the genus Ephemerovirus, NGAV possesses a second glycoprotein gene (G(NS)). Phylogenetic analyses, however, place NGAV within the yet to be classified "Hart Park" group containing Wongabel and Flanders viruses, which do not contain a second glycoprotein gene. Screening of various animal sera from northern Australia has indicated that NGAV is currently circulating in macropods (wallabies, wallaroos and kangaroos), highlighting the need for further studies to determine its potential to cause disease in these species. Crown Copyright 2009. Published by Elsevier Inc. All rights reserved.

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

ERIC Educational Resources Information Center

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

2014-01-01

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

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

ERIC Educational Resources Information Center

Al-Seghayer, Khalid

2016-01-01

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

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

Keeping It Simple: The Case for E-Mail.

ERIC Educational Resources Information Center

Haimovic, Gila

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

Viewing Reading Recovery as a Restructuring Phenomenon

ERIC Educational Resources Information Center

Rinehart, James S.; Short, Paula Myrick

2010-01-01

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

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…

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

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)

Page mode reading with simulated scotomas: a modest effect of interline spacing on reading speed.

PubMed

Bernard, Jean-Baptiste; Scherlen, Anne-Catherine; Anne-Catherine, Scherlen; Castet, Eric; Eric, Castet

2007-12-01

Crowding is thought to be one potent limiting factor of reading in peripheral vision. While several studies investigated how crowding between horizontally adjacent letters or words can influence eccentric reading, little attention has been paid to the influence of vertically adjacent lines of text. The goal of this study was to examine the dependence of page mode reading performance (speed and accuracy) on interline spacing. A gaze-contingent visual display was used to simulate a visual central scotoma while normally sighted observers read meaningful French sentences following MNREAD principles. The sensitivity of this new material to low-level factors was confirmed by showing strong effects of perceptual learning, print size and scotoma size on reading performance. In contrast, reading speed was only slightly modulated by interline spacing even for the largest range tested: a 26% gain for a 178% increase in spacing. This modest effect sharply contrasts with the dramatic influence of vertical word spacing found in a recent RSVP study. This discrepancy suggests either that vertical crowding is minimized when reading meaningful sentences, or that the interaction between crowding and other factors such as attention and/or visuo-motor control is dependent on the paradigm used to assess reading speed (page vs. RSVP mode).

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 ...

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

ERIC Educational Resources Information Center

National Council of Teachers of English, Champaign, IL.

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

Reading Quizzes Improve Exam Scores for Community College Students

ERIC Educational Resources Information Center

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

2018-01-01

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

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

PubMed Central

Sugita, Mamoru; Shinozaki, Kazuo; Sugiura, Masahiro

1985-01-01

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

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

PubMed

Sugita, M; Shinozaki, K; Sugiura, M

1985-06-01

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

UNED OER Experience: From OCW to Open UNED

ERIC Educational Resources Information Center

Ros, Salvador; Hernández, Roberto; Read, Timothy; Artacho, Miguel Rodriguez; Pastor, Rafael; Orueta, Gabriel Diaz

2014-01-01

Much has happened with open software, there has been a global attitude shift in the education community toward the open sharing of educational courses and resources. As the largest public distance education university in Spain, Universidad Nacional de Educacio´n a Distancia (UNED) has had a clear commitment to open learning and content since its…

Effectiveness of Different Medium of Education to Imparting Knowledge at Bangladesh Open University

ERIC Educational Resources Information Center

Islam, Anwarul; Islam, Nasirul

2008-01-01

Open and distance learning system meanly based on different types of media to impart education to the learners. Bangladesh Open University (BOU) offered education through open and distance learning system. There are two largest programs one is Secondary School Certificate (SSC) and another one is Higher Secondary Certificate (HSC) offered by BOU…

Comparing the Open University Systems of China and India: Origins, Developments and Prospects

ERIC Educational Resources Information Center

Perris, Kirk

2015-01-01

The national open universities of China and India are unique adaptations of the open university model that emanated from the UK. These institutions have expanded to become the largest universities in the world as measured by current enrollment of approximately four million each. This article comparatively analyzes how these open universities have…

77 FR 13324 - Fresenius Medical Care AG & Co. KGaA; Analysis of Agreement Containing Consent Orders To Aid...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-06

... site at http://www.ftc.gov to read this Notice and the news release describing it. The FTC Act and... services. The Parties Headquartered in Bad Homburg, Germany, Fresenius is the largest provider of...

Energy monitoring in gins

USDA-ARS?s Scientific Manuscript database

Energy costs are the second largest source of variable costs for cotton gins, accounting for 27% of variable costs. Energy use has typically not been a major consideration in gin design, and previous studies of energy use have utilized instantaneous readings or aggregated season-long values. In this...

Energy Monitoring in Gins - 2011

USDA-ARS?s Scientific Manuscript database

Energy costs are the second largest source of variable costs for gins, accounting for 27% of variable costs. Energy use has typically not been a major consideration in gin design and previous studies of energy use have utilized instantaneous readings or aggregated season-long values. Electricity u...

Electricity use patterns in cotton gins

USDA-ARS?s Scientific Manuscript database

Energy costs are the second largest source of variable costs for cotton gins, with electricity accounting for 18% of variable costs. Energy use has typically not been a major consideration in gin design and previous studies of energy use have utilized instantaneous readings or aggregated season-lon...

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...

Measuring College Students' Reading Comprehension Ability Using Cloze Tests

ERIC Educational Resources Information Center

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

2011-01-01

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

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

ERIC Educational Resources Information Center

Twenge-Jinings, Fidelia; Sullivan, Joanna

2016-01-01

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

An information propagation model considering incomplete reading behavior in microblog

NASA Astrophysics Data System (ADS)

Su, Qiang; Huang, Jiajia; Zhao, Xiande

2015-02-01

Microblog is one of the most popular communication channels on the Internet, and has already become the third largest source of news and public opinions in China. Although researchers have studied the information propagation in microblog using the epidemic models, previous studies have not considered the incomplete reading behavior among microblog users. Therefore, the model cannot fit the real situations well. In this paper, we proposed an improved model entitled Microblog-Susceptible-Infected-Removed (Mb-SIR) for information propagation by explicitly considering the user's incomplete reading behavior. We also tested the effectiveness of the model using real data from Sina Microblog. We demonstrate that the new proposed model is more accurate in describing the information propagation in microblog. In addition, we also investigate the effects of the critical model parameters, e.g., reading rate, spreading rate, and removed rate through numerical simulations. The simulation results show that, compared with other parameters, reading rate plays the most influential role in the information propagation performance in microblog.

An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing.

PubMed

Zimin, Aleksey V; Stevens, Kristian A; Crepeau, Marc W; Puiu, Daniela; Wegrzyn, Jill L; Yorke, James A; Langley, Charles H; Neale, David B; Salzberg, Steven L

2017-01-01

The 22-gigabase genome of loblolly pine (Pinus taeda) is one of the largest ever sequenced. The draft assembly published in 2014 was built entirely from short Illumina reads, with lengths ranging from 100 to 250 base pairs (bp). The assembly was quite fragmented, containing over 11 million contigs whose weighted average (N50) size was 8206 bp. To improve this result, we generated approximately 12-fold coverage in long reads using the Single Molecule Real Time sequencing technology developed at Pacific Biosciences. We assembled the long and short reads together using the MaSuRCA mega-reads assembly algorithm, which produced a substantially better assembly, P. taeda version 2.0. The new assembly has an N50 contig size of 25 361, more than three times as large as achieved in the original assembly, and an N50 scaffold size of 107 821, 61% larger than the previous assembly. © The Author 2017. Published by Oxford University Press.

Erratum to: An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing.

PubMed

Zimin, Aleksey V; Stevens, Kristian A; Crepeau, Marc W; Puiu, Daniela; Wegrzyn, Jill L; Yorke, James A; Langley, Charles H; Neale, David B; Salzberg, Steven L

2017-10-01

The 22-gigabase genome of loblolly pine (Pinus taeda) is one of the largest ever sequenced. The draft assembly published in 2014 was built entirely from short Illumina reads, with lengths ranging from 100 to 250 base pairs (bp). The assembly was quite fragmented, containing over 11 million contigs whose weighted average (N50) size was 8206 bp. To improve this result, we generated approximately 12-fold coverage in long reads using the Single Molecule Real Time sequencing technology developed at Pacific Biosciences. We assembled the long and short reads together using the MaSuRCA mega-reads assembly algorithm, which produced a substantially better assembly, P. taeda version 2.0. The new assembly has an N50 contig size of 25 361, more than three times as large as achieved in the original assembly, and an N50 scaffold size of 107 821, 61% larger than the previous assembly. © The Authors 2017. Published by Oxford University Press.

The association between semantic dementia and surface dyslexia in Japanese.

PubMed

Fushimi, Takao; Komori, Kenjiro; Ikeda, Manabu; Lambon Ralph, Matthew A; Patterson, Karalyn

2009-03-01

One theory about reading suggests that producing the correct pronunciations of written words, particularly less familiar words with an atypical spelling-sound relationship, relies in part on knowledge of the word's meaning. This hypothesis has been supported by reports of surface dyslexia in large case-series studies of English-speaking/reading patients with semantic dementia (SD), but would have increased credibility if it applied to other languages and writing systems as well. The hypothesis predicts that, of the two systems used to write Japanese, SD patients should be unimpaired at oral reading of kana because of its invariant relationship between orthography and phonology. By contrast, oral reading of kanji should be impaired in a graded fashion depending on the consistency characteristics of the kanji target words, with worst performance on words whose component characters take 'minority' (atypical) pronunciations, especially if the words are of lower frequency. Errors in kanji reading should primarily reflect assignment of more typical readings to the component characters in these atypical words. In the largest-ever-reported case series of Japanese patients with semantic dementia, we tested and confirmed this hypothesis.

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.

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

Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution

PubMed Central

Díez, Beatriz; Nylander, Johan A. A.; Ininbergs, Karolina; Dupont, Christopher L.; Allen, Andrew E.; Yooseph, Shibu; Rusch, Douglas B.; Bergman, Birgitta

2016-01-01

Unicellular cyanobacteria are ubiquitous photoautotrophic microbes that contribute substantially to global primary production. Picocyanobacteria such as Synechococcus and Prochlorococcus depend on chlorophyll a-binding protein complexes to capture light energy. In addition, Synechococcus has accessory pigments organized into phycobilisomes, and Prochlorococcus contains chlorophyll b. Across a surface water transect spanning the sparsely studied tropical Indian Ocean, we examined Synechococcus and Prochlorococcus occurrence, taxonomy and habitat preference in an evolutionary context. Shotgun sequencing of size fractionated microbial communities from 0.1 μm to 20 μm and subsequent phylogenetic analysis indicated that cyanobacteria account for up to 15% of annotated reads, with the genera Prochlorococcus and Synechococcus comprising 90% of the cyanobacterial reads, even in the largest size fraction (3.0–20 mm). Phylogenetic analyses of cyanobacterial light-harvesting genes (chl-binding pcb/isiA, allophycocyanin (apcAB), phycocyanin (cpcAB) and phycoerythin (cpeAB)) mostly identified picocyanobacteria clades comprised of overlapping sequences obtained from Indian Ocean, Atlantic and/or Pacific Oceans samples. Habitat reconstructions coupled with phylogenetic analysis of the Indian Ocean samples suggested that large Synechococcus-like ancestors in coastal waters expanded their ecological niche towards open oligotrophic waters in the Indian Ocean through lineage diversification and associated streamlining of genomes (e.g. loss of phycobilisomes and acquisition of Chl b); resulting in contemporary small celled Prochlorococcus. Comparative metagenomic analysis with picocyanobacteria populations in other oceans suggests that this evolutionary scenario may be globally important. PMID:27196065

Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution

DOE PAGES

Diez, Beatriz; Nylander, Johan A. A.; Ininbergs, Karolina; ...

2016-05-19

Unicellular cyanobacteria are ubiquitous photoautotrophic microbes that contribute substantially to global primary production. Picocyanobacteria such as Synechococcus and Prochlorococcus depend on chlorophyll a-binding protein complexes to capture light energy. In addition, Synechococcus has accessory pigments organized into phycobilisomes, and Prochlorococcus contains chlorophyll b. Across a surface water transect spanning the sparsely studied tropical Indian Ocean, we examined Synechococcus and Prochlorococcus occurrence, taxonomy and habitat preference in an evolutionary context. Shotgun sequencing of size fractionated microbial communities from 0.1 μm to 20 μm and subsequent phylogenetic analysis indicated that cyanobacteria account for up to 15% of annotated reads, with the generamore » Prochlorococcus and Synechococcus comprising 90% of the cyanobacterial reads, even in the largest size fraction (3.0–20 mm). Phylogenetic analyses of cyanobacterial light-harvesting genes (chl-binding pcb/isiA, allophycocyanin ( apcAB), phycocyanin ( cpcAB) and phycoerythin ( cpeAB)) mostly identified picocyanobacteria clades comprised of overlapping sequences obtained from Indian Ocean, Atlantic and/or Pacific Oceans samples. Habitat reconstructions coupled with phylogenetic analysis of the Indian Ocean samples suggested that large Synechococcus-like ancestors in coastal waters expanded their ecological niche towards open oligotrophic waters in the Indian Ocean through lineage diversification and associated streamlining of genomes (e.g. loss of phycobilisomes and acquisition of Chl b); resulting in contemporary small celled Prochlorococcus. As a result, comparative metagenomic analysis with picocyanobacteria populations in other oceans suggests that this evolutionary scenario may be globally important.« less

Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution

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

Diez, Beatriz; Nylander, Johan A. A.; Ininbergs, Karolina

Unicellular cyanobacteria are ubiquitous photoautotrophic microbes that contribute substantially to global primary production. Picocyanobacteria such as Synechococcus and Prochlorococcus depend on chlorophyll a-binding protein complexes to capture light energy. In addition, Synechococcus has accessory pigments organized into phycobilisomes, and Prochlorococcus contains chlorophyll b. Across a surface water transect spanning the sparsely studied tropical Indian Ocean, we examined Synechococcus and Prochlorococcus occurrence, taxonomy and habitat preference in an evolutionary context. Shotgun sequencing of size fractionated microbial communities from 0.1 μm to 20 μm and subsequent phylogenetic analysis indicated that cyanobacteria account for up to 15% of annotated reads, with the generamore » Prochlorococcus and Synechococcus comprising 90% of the cyanobacterial reads, even in the largest size fraction (3.0–20 mm). Phylogenetic analyses of cyanobacterial light-harvesting genes (chl-binding pcb/isiA, allophycocyanin ( apcAB), phycocyanin ( cpcAB) and phycoerythin ( cpeAB)) mostly identified picocyanobacteria clades comprised of overlapping sequences obtained from Indian Ocean, Atlantic and/or Pacific Oceans samples. Habitat reconstructions coupled with phylogenetic analysis of the Indian Ocean samples suggested that large Synechococcus-like ancestors in coastal waters expanded their ecological niche towards open oligotrophic waters in the Indian Ocean through lineage diversification and associated streamlining of genomes (e.g. loss of phycobilisomes and acquisition of Chl b); resulting in contemporary small celled Prochlorococcus. As a result, comparative metagenomic analysis with picocyanobacteria populations in other oceans suggests that this evolutionary scenario may be globally important.« less

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.

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.

ObsPy: A Python Toolbox for Seismology

NASA Astrophysics Data System (ADS)

Krischer, Lion; Megies, Tobias; Sales de Andrade, Elliott; Barsch, Robert; MacCarthy, Jonathan

2017-04-01

In recent years the Python ecosystem evolved into one of the most powerful and productive scientific environments across disciplines. ObsPy (https://www.obspy.org) is a fully community-driven, open-source project dedicated to providing a bridge for seismology into that ecosystem. It does so by offering Read and write support for essentially every commonly used data format in seismology with a unified interface and automatic format detection. This includes waveform data (MiniSEED, SAC, SEG-Y, Reftek, …) as well as station (SEED, StationXML, …) and event meta information (QuakeML, ZMAP, …). Integrated access to the largest data centers, web services, and real-time data streams (FDSNWS, ArcLink, SeedLink, ...). A powerful signal processing toolbox tuned to the specific needs of seismologists. Utility functionality like travel time calculations with the TauP method, geodetic functions, and data visualizations. ObsPy has been in constant development for more than seven years and is developed and used by scientists around the world with successful applications in all branches of seismology. Additionally it nowadays serves as the foundation for a large number of more specialized packages. This presentation will give a short overview of the capabilities of ObsPy and point out several representative or new use cases. Additionally we will discuss the road ahead as well as the long-term sustainability of open-source scientific software.

76 FR 3077 - Notice of Decision To Revise a Heat Treatment Schedule for Emerald Ash Borer

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-19

... faster than in any of the other experiments. The heating rates in all of the Myers et al. (2009... core temperature reading to be at least 160 [deg]F for 75 minutes on the largest pieces of firewood...

Chinese Open Universities: Opportunities and Challenges

ERIC Educational Resources Information Center

Li, Xiaobin

2017-01-01

Chinese education has a long history, and the Chinese higher education system is the largest in the world, but open universities in China are not at the same level as they are in developed countries. This article provides an overview of the recent development in the open universities system in China. Specifically, the article discusses the…

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

ERIC Educational Resources Information Center

Roizen, Merle A.

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

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

ERIC Educational Resources Information Center

1996

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

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

ERIC Educational Resources Information Center

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

2015-01-01

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

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

ERIC Educational Resources Information Center

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

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

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

ERIC Educational Resources Information Center

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

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

Participation Rates in a Worksite Wellness Program Using E-Mail Wellness Messages

ERIC Educational Resources Information Center

Anenson, Larry W.; Brunt, Ardith; Terbizan, Donna J.; Christensen, Bryan

2014-01-01

The purpose of this study was to determine which days of the work week had the largest rate of opened e-health messages, whether detailed or basic e-health messages were more likely to be opened, if motivation influenced the rate of message opening, and if the rate of opening messages declined over time. Ninety-one city employees (52 male and 39…

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;…

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

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

PubMed

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

1985-06-01

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

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

PubMed

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

1994-12-01

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

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

PubMed

Inouye, Satoshi; Suzuki, Takahiro

2016-12-01

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

Commercial Literacy Software.

ERIC Educational Resources Information Center

Balajthy, Ernest

1997-01-01

Presents the first year's results of a continuing project to monitor the availability of software of relevance for literacy education purposes. Concludes there is an enormous amount of software available for use by teachers of reading and literacy--whereas drill-and-practice software is the largest category of software available, large numbers of…

Ethics and Study Abroad

ERIC Educational Resources Information Center

Hoffa, William W.

2007-01-01

It came as a great surprise recently to read in "The New York Times" that the New York attorney general's office had launched an investigation into possible financial improprieties between colleges and outside organizations that provide study-abroad programs. Subpoenas had been issued to five of the largest program providers, "with more to come."…

English Learners' (ELs') Trends from the Nation's Report Card. Fast Facts

ERIC Educational Resources Information Center

Office of English Language Acquisition, US Department of Education, 2016

2016-01-01

The National Assessment of Educational Progress (NAEP), also known as the Nation's Report Card, is the largest continuing and nationally representative assessment of what students know about mathematics, reading, science, writing, the arts, civics, economics, geography, U.S. history, and technology and engineering literacy. This fact sheet reports…

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.

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

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-09

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

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

Code of Federal Regulations, 2011 CFR

2011-01-01

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

Employment-Driven Online Student Attrition and the Assessment Policy Divide: An Australian Open-Access Higher Education Perspective

ERIC Educational Resources Information Center

Moore, Catherine; Greenland, Steven

2017-01-01

Two hundred and twenty-six qualitative interviews with students studying at Australia's largest online tertiary education organisation, Open Universities Australia (OUA), found that failure to complete assessments due to unexpected and unavoidable employment commitments was the standout reason for dropping out of its open-access courses. The…

Needs for and Utilization of OER in Distance Education: A Chinese Survey

ERIC Educational Resources Information Center

Chen, Qing; Panda, Santosh

2013-01-01

The recent developments within open educational resources (OERs) and open licensing have generated considerable interest among distance educators since open and distance learning is supposed to be the largest consumer/user of and contributor to OER. In China, given the policy of development and use of elaborate courses, conversion of radio and…

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.…

OpenMP Performance on the Columbia Supercomputer

NASA Technical Reports Server (NTRS)

Haoqiang, Jin; Hood, Robert

2005-01-01

This presentation discusses Columbia World Class Supercomputer which is one of the world's fastest supercomputers providing 61 TFLOPs (10/20/04). Conceived, designed, built, and deployed in just 120 days. A 20-node supercomputer built on proven 512-processor nodes. The largest SGI system in the world with over 10,000 Intel Itanium 2 processors and provides the largest node size incorporating commodity parts (512) and the largest shared-memory environment (2048) with 88% efficiency tops the scalar systems on the Top500 list.

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

PubMed Central

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

1998-01-01

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

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

DTIC Science & Technology

1988-12-01

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

Reading skills among students with intellectual disabilities.

PubMed

Ratz, Christoph; Lenhard, Wolfgang

2013-05-01

Students with intellectual disabilities (ID) display an extremely wide variety of skills in the field of literacy, and the ability to read and write are central learning aims in the education of students with ID. It is vital to gain detailed knowledge on the literacy skills of students with ID in order to plan instruction, create learning environments, implement educational policies or funding models and specify future fields of research. However, there has been little research into the prevalence and variation of their reading skills. The present study assessed the reading stages of 1629 school-aged students with ID regardless of aetiology (age 6-21) in Bavaria, one of the largest regions in Germany within a randomly chosen and representative sample. Teachers described the reading and writing stages of their students in a questionnaire following the developmental model of Frith. Results indicate that 29.3% do not read at all, 6.8% read at a logographic stage, 31.9% at an alphabetic and 32% at an orthographic level. Writing achievements are lower on average. We analyze and discuss the determinants of literacy in this sample with regard to the sociocultural background of students with ID and draw conclusions for teaching and school policies. Copyright © 2013 Elsevier Ltd. All rights reserved.

The different time courses of reading different levels of Chinese characters: an ERP study.

PubMed

Lu, Qilin; Tang, Yi-Yuan; Zhou, Li; Yu, Qingbao

2011-07-12

The dual route processing was generally accepted in the reading of alphabetic languages, which suggests alphabetic words can be read by either addressed pathway or assembled pathway. However, it was still unclear whether there was a particular 'dual route mechanism' during reading Chinese characters. In our previous fMRI study, the result showed that there might be a particular 'dual route mechanism', and its addressed pathway was similar between Chinese and English, whereas for the need of spatial analysis, the assembled pathway of Chinese was different from that of English which involved grapheme-to-phoneme correspondences. The present study, using event-related potential, which provide more temporal information, aimed to further support our previous view, and peered inside the different time courses of reading different types of Chinese characters. It was found that reading high frequency Chinese characters increased the N170 component which was believed to enhance attention to the addressed pathway in the left occipital-temporal area. Pseudo Chinese characters could be read by a particular assembled pathway, which caused the largest amplitude of P320 component in the right occipital-temporal area, which considered as a key brain area for radical analysis. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

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…

Will Mayor De Blasio Turn Back the School Reform Clock?

ERIC Educational Resources Information Center

Meyer, Peter

2014-01-01

While heads were spinning, policy watchers seemed genuinely perplexed by New York City's Mayor de Blasio's education opinions. De Blasio opposed many of Bloomberg's reform efforts despite the achievement gains realized by the nation's largest school district during the last 12 years. Yet on close reading, de Blasio's nine-page education plan…

Biliteracy and Trilingual Practices in the Home Context: Case Studies of Chinese-Canadian Children

ERIC Educational Resources Information Center

Li, Guofang

2006-01-01

Although Chinese has become the third largest mother tongue in both Canada and the USA, Chinese/English biliteracy development has received little attention in educational research. This article explores three Chinese-Canadian first and second graders' biliteracy (Chinese/English reading and writing) and trilingual (Mandarin, Cantonese, and…

Kindergarten Readiness in Wisconsin. WCER Working Paper No. 2017-3

ERIC Educational Resources Information Center

Grodsky, Eric; Yiyue, Huangfu,; Miesner, H. Rose; Packard, Chiara

2017-01-01

Wisconsin's gaps between Black and White student high school graduation rates (Richards, 2016) and Black and White fourth-grade math and reading scores (U.S. Department of Education, 2015) are the largest in the nation. These inequalities have led to criticisms of Wisconsin's schools and teachers as ineffective in bolstering the success of…

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

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)

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

ERIC Educational Resources Information Center

Ching-yen, Chang

1973-01-01

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

The Impact of Open Licensing on the Early Reader Ecosystem

ERIC Educational Resources Information Center

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

2016-01-01

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

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

ERIC Educational Resources Information Center

Gabbard, Anita; Mupinga, Davison M.

2013-01-01

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

Liberty Centennial Student Campaign Manual.

ERIC Educational Resources Information Center

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

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

Continuing Literacy.

ERIC Educational Resources Information Center

Clarke, Ronald F., Ed.

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

Genovo: De Novo Assembly for Metagenomes

NASA Astrophysics Data System (ADS)

Laserson, Jonathan; Jojic, Vladimir; Koller, Daphne

Next-generation sequencing technologies produce a large number of noisy reads from the DNA in a sample. Metagenomics and population sequencing aim to recover the genomic sequences of the species in the sample, which could be of high diversity. Methods geared towards single sequence reconstruction are not sensitive enough when applied in this setting. We introduce a generative probabilistic model of read generation from environmental samples and present Genovo, a novel de novo sequence assembler that discovers likely sequence reconstructions under the model. A Chinese restaurant process prior accounts for the unknown number of genomes in the sample. Inference is made by applying a series of hill-climbing steps iteratively until convergence. We compare the performance of Genovo to three other short read assembly programs across one synthetic dataset and eight metagenomic datasets created using the 454 platform, the largest of which has 311k reads. Genovo's reconstructions cover more bases and recover more genes than the other methods, and yield a higher assembly score.

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

ERIC Educational Resources Information Center

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

2007-01-01

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

Reading Quizzes Improve Exam Scores for Community College Students.

PubMed

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

2018-06-01

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

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

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

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

2008-02-22

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

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

PubMed

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

2014-09-01

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

A retrotransposable element from the mosquito Anopheles gambiae .

PubMed Central

Besansky, N J

1990-01-01

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

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.

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.

Open University Courses in Science and Technology Applicable to the Education of Teachers of Integrated Science.

ERIC Educational Resources Information Center

Pentz, M. J.

The Open University, founded in 1969, has already become the largest university in Britain in terms of the number of undergraduate students, with an enrollment of 41,000 in 1973. This paper is concerned with three areas of discussion: (1) the number of teachers studying Open University courses; (2) the courses available or planned in science and…

An All-School Library Challenge

ERIC Educational Resources Information Center

Quirk, Connie

2005-01-01

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

Connecting Libraries and Schools with CLASP.

ERIC Educational Resources Information Center

Del Vecchio, Stephen

1993-01-01

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

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

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-13

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

Developing Literacy for the Vocational-Technical Trades.

ERIC Educational Resources Information Center

Penisten, John

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

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

ERIC Educational Resources Information Center

Miller, Brett; O'Donnell, Carol

2013-01-01

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

Emission factors for open and domestic biomass burning for use in atmospheric models

Treesearch

S. K. Akagi; R. J. Yokelson; C. Wiedinmyer; M. J. Alvarado; J. S. Reid; T. Karl; J. D. Crounse; P. O. Wennberg

2010-01-01

Biomass burning (BB) is the second largest source of trace gases and the largest source of primary fine carbonaceous particles in the global troposphere. Many recent BB studies have provided new emission factor (EF) measurements. This is especially 5 true for non methane organic compounds (NMOC), which influence secondary organic aerosol (SOA) and ozone formation. New...

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

Supporting Latinx Student Success via Family-School Partnerships: Preliminary Effects of Conjoint Behavioral Consultation on Student and Parent Outcomes

ERIC Educational Resources Information Center

Clarke, Brandy L.; Wheeler, Lorey A.; Sheridan, Susan M.; Witte, Amanda L.; Sommerhalder, Mackenzie S.; Svoboda, Elizabeth A.

2017-01-01

Latinx students are the largest ethnic minority school-age population, yet they have some of the lowest reading proficiency levels and highest rates of school dropout and experience significant unmet behavioral health needs. School-based interventions addressing behavioral challenges and parent engagement are recommended to support Latinx…

Effects of Extended Time Allotments on Reading Comprehension Performance of College Students with and without Learning Disabilities

ERIC Educational Resources Information Center

Lewandowski, Lawrence; Cohen, Justin; Lovett, Benjamin J.

2013-01-01

Students with disabilities often receive test accommodations in schools and on high-stakes tests. Students with learning disabilities (LD) represent the largest disability group in schools, and extended time the most common test accommodation requested by such students. This pairing persists despite controversy over the validity of extended time…

National Board Certification and Teacher Effectiveness: Evidence from Washington State

ERIC Educational Resources Information Center

Cowan, James; Goldhaber, Dan

2016-01-01

We study the effectiveness of teachers certified by the National Board for Professional Teaching Standards (NBPTS) in Washington State, which has one of the largest populations of National Board-Certified Teachers (NBCTs) in the nation. Based on value-added models in math and reading, we find that NBPTS-certified teachers are about 0.01-0.05…

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.

Cognitive function in women with HIV

PubMed Central

Rubin, Leah H.; Valcour, Victor; Martin, Eileen; Crystal, Howard; Young, Mary; Weber, Kathleen M.; Manly, Jennifer; Richardson, Jean; Alden, Christine; Anastos, Kathryn

2015-01-01

Objective: In the largest cohort study of neuropsychological outcomes among HIV-infected women to date, we examined the association between HIV status and cognition in relation to other determinants of cognitive function (aim 1) and the pattern and magnitude of impairment across cognitive outcomes (aim 2). Methods: From 2009 to 2011, 1,521 (1,019 HIV-infected) participants from the Women's Interagency HIV Study (WIHS) completed a comprehensive neuropsychological test battery. We used multivariable regression on raw test scores for the first aim and normative regression-based analyses (t scores) for the second aim. The design was cross-sectional. Results: The effect sizes for HIV status on cognition were very small, accounting for only 0.05 to 0.09 SD units. The effect of HIV status was smaller than that of years of education, age, race, income, and reading level. In adjusted analyses, HIV-infected women performed worse than uninfected women on verbal learning, delayed recall and recognition, and psychomotor speed and attention. The largest deficit was observed in delayed memory. The association of low reading level with cognition was greater in HIV-infected compared to HIV-uninfected women. HIV biomarkers (CD4 count, history of AIDS-defining illness, viral load) were associated with cognitive dysfunction. Conclusions: The effect of HIV on cognition in women is very small except among women with low reading level or HIV-related comorbidities. Direct comparisons of rates of impairment in well-matched groups of HIV-infected men and women are needed to evaluate possible sex differences in cognition. PMID:25540304

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.

Comparison of neurological healthcare oriented educational resources for patients on the internet.

PubMed

Punia, Vineet; Dagar, Anjali; Agarwal, Nitin; He, Wenzhuan; Hillen, Machteld

2014-12-01

The internet has become a major contributor to health literacy promotion. The average American reads at 7th-8th grade level and it is recommended to write patient education materials at or below 6th grade reading level. We tried to assess the level of literacy required to read and understand online patient education materials (OPEM) for neurological diseases from various internet resources. We then compared those to an assumed reference OPEM source, namely the patient education brochures from the American Academy of Neurology (AAN), the world's largest professional association of neurologists. Disease specific patient education brochures were downloaded from the AAN website. OPEM for these diseases were also accessed from other common online sources determined using a predefined criterion. All OPEM were converted to Microsoft Word (Microsoft Corp., Redmond, WA, USA) and their reading level was analyzed using Readability Studio Professional Edition version 2012.1 (Oleander Software, Vandalia, OH, USA). Descriptive analysis and analysis of variance were used to compare reading levels of OPEM from different resources. Medline Plus, Mayo clinic and Wikipedia qualified for OPEM analysis. All OPEM from these resources, including the AAN, were written above the recommended 6th grade reading level. They were also found to be "fairly difficult", "difficult" or "confusing" on the Flesch Reading Ease scale. AAN OPEM on average needed lower reading level, with Wikipedia OPEM being significantly (p<0.01) more difficult to read compared to the other three resources. OPEM on neurological diseases are being written at a level of reading complexity higher than the average American and the recommended reading levels. This may be undermining the utility of these resources. Copyright © 2014 Elsevier Ltd. All rights reserved.

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...

Dystrophin quantification and clinical correlations in Becker muscular dystrophy: implications for clinical trials.

PubMed

Anthony, Karen; Cirak, Sebahattin; Torelli, Silvia; Tasca, Giorgio; Feng, Lucy; Arechavala-Gomeza, Virginia; Armaroli, Annarita; Guglieri, Michela; Straathof, Chiara S; Verschuuren, Jan J; Aartsma-Rus, Annemieke; Helderman-van den Enden, Paula; Bushby, Katherine; Straub, Volker; Sewry, Caroline; Ferlini, Alessandra; Ricci, Enzo; Morgan, Jennifer E; Muntoni, Francesco

2011-12-01

Duchenne muscular dystrophy is caused by mutations in the DMD gene that disrupt the open reading frame and prevent the full translation of its protein product, dystrophin. Restoration of the open reading frame and dystrophin production can be achieved by exon skipping using antisense oligonucleotides targeted to splicing elements. This approach aims to transform the Duchenne muscular dystrophy phenotype to that of the milder disorder, Becker muscular dystrophy, typically caused by in-frame dystrophin deletions that allow the production of an internally deleted but partially functional dystrophin. There is ongoing debate regarding the functional properties of the different internally deleted dystrophins produced by exon skipping for different mutations; more insight would be valuable to improve and better predict the outcome of exon skipping clinical trials. To this end, we have characterized the clinical phenotype of 17 patients with Becker muscular dystrophy harbouring in-frame deletions relevant to on-going or planned exon skipping clinical trials for Duchenne muscular dystrophy and correlated it to the levels of dystrophin, and dystrophin-associated protein expression. The cohort of 17 patients, selected exclusively on the basis of their genotype, included 4 asymptomatic, 12 mild and 1 severe patient. All patients had dystrophin levels of >40% of control and significantly higher dystrophin (P = 0.013), β-dystroglycan (P = 0.025) and neuronal nitric oxide synthase (P = 0.034) expression was observed in asymptomatic individuals versus symptomatic patients with Becker muscular dystrophy. Furthermore, grouping the patients by deletion, patients with Becker muscular dystrophy with deletions with an end-point of exon 51 (the skipping of which could rescue the largest group of Duchenne muscular dystrophy deletions) showed significantly higher dystrophin levels (P = 0.034) than those with deletions ending with exon 53. This is the first quantitative study on both dystrophin and dystrophin-associated protein expression in patients with Becker muscular dystrophy with deletions relevant for on-going exon skipping trials in Duchenne muscular dystrophy. Taken together, our results indicate that all varieties of internally deleted dystrophin assessed in this study have the functional capability to provide a substantial clinical benefit to patients with Duchenne muscular dystrophy.

Dystrophin quantification and clinical correlations in Becker muscular dystrophy: implications for clinical trials

PubMed Central

Anthony, Karen; Cirak, Sebahattin; Torelli, Silvia; Tasca, Giorgio; Feng, Lucy; Arechavala-Gomeza, Virginia; Armaroli, Annarita; Guglieri, Michela; Straathof, Chiara S.; Verschuuren, Jan J.; Aartsma-Rus, Annemieke; Helderman-van den Enden, Paula; Bushby, Katherine; Straub, Volker; Sewry, Caroline; Ferlini, Alessandra; Ricci, Enzo; Morgan, Jennifer E.

2011-01-01

Duchenne muscular dystrophy is caused by mutations in the DMD gene that disrupt the open reading frame and prevent the full translation of its protein product, dystrophin. Restoration of the open reading frame and dystrophin production can be achieved by exon skipping using antisense oligonucleotides targeted to splicing elements. This approach aims to transform the Duchenne muscular dystrophy phenotype to that of the milder disorder, Becker muscular dystrophy, typically caused by in-frame dystrophin deletions that allow the production of an internally deleted but partially functional dystrophin. There is ongoing debate regarding the functional properties of the different internally deleted dystrophins produced by exon skipping for different mutations; more insight would be valuable to improve and better predict the outcome of exon skipping clinical trials. To this end, we have characterized the clinical phenotype of 17 patients with Becker muscular dystrophy harbouring in-frame deletions relevant to on-going or planned exon skipping clinical trials for Duchenne muscular dystrophy and correlated it to the levels of dystrophin, and dystrophin-associated protein expression. The cohort of 17 patients, selected exclusively on the basis of their genotype, included 4 asymptomatic, 12 mild and 1 severe patient. All patients had dystrophin levels of >40% of control and significantly higher dystrophin (P = 0.013), β-dystroglycan (P = 0.025) and neuronal nitric oxide synthase (P = 0.034) expression was observed in asymptomatic individuals versus symptomatic patients with Becker muscular dystrophy. Furthermore, grouping the patients by deletion, patients with Becker muscular dystrophy with deletions with an end-point of exon 51 (the skipping of which could rescue the largest group of Duchenne muscular dystrophy deletions) showed significantly higher dystrophin levels (P = 0.034) than those with deletions ending with exon 53. This is the first quantitative study on both dystrophin and dystrophin-associated protein expression in patients with Becker muscular dystrophy with deletions relevant for on-going exon skipping trials in Duchenne muscular dystrophy. Taken together, our results indicate that all varieties of internally deleted dystrophin assessed in this study have the functional capability to provide a substantial clinical benefit to patients with Duchenne muscular dystrophy. PMID:22102647

A Multidisciplinary Approach to Open Access Village Telecenter Initiatives: The Case of Akshaya

ERIC Educational Resources Information Center

Pal, Joyojeet; Nedevschi, Sergiu; Patra, Rabin K.; Brewer, Eric A.

2006-01-01

The Akshaya project in the rural Malappuram district of Kerala, India is home to the first and largest district-wide e-literacy project in India, and one of the largest known Internet Protocol-based networks. Through a network of 600 kiosks, the project has been designed to reach computer literacy into over 600,000 households, and bring 3.6…

ObsPy: Establishing and maintaining an open-source community package

NASA Astrophysics Data System (ADS)

Krischer, L.; Megies, T.; Barsch, R.

2017-12-01

Python's ecosystem evolved into one of the most powerful and productive research environment across disciplines. ObsPy (https://obspy.org) is a fully community driven, open-source project dedicated to provide a bridge for seismology into that ecosystem. It does so by offering Read and write support for essentially every commonly used data format in seismology, Integrated access to the largest data centers, web services, and real-time data streams, A powerful signal processing toolbox tuned to the specific needs of seismologists, and Utility functionality like travel time calculations, geodetic functions, and data visualizations. ObsPy has been in constant unfunded development for more than eight years and is developed and used by scientists around the world with successful applications in all branches of seismology. By now around 70 people directly contributed code to ObsPy and we aim to make it a self-sustaining community project.This contributions focusses on several meta aspects of open-source software in science, in particular how we experienced them. During the panel we would like to discuss obvious questions like long-term sustainability with very limited to no funding, insufficient computer science training in many sciences, and gaining hard scientific credits for software development, but also the following questions: How to best deal with the fact that a lot of scientific software is very specialized thus usually solves a complex problem but at the same time can only ever reach a limited pool of developers and users by virtue of it being so specialized? Therefore the "many eyes on the code" approach to develop and improve open-source software only applies in a limited fashion. An initial publication for a significant new scientific software package is fairly straightforward. How to on-board and motivate potential new contributors when they can no longer be lured by a potential co-authorship? When is spending significant time and effort on reusable scientific open-source development a reasonable choice for young researchers? The effort to go from purpose tailored code for a single application resulting in a scientific publication is significantly less compared to generalising and engineering it well enough so it can be used by others.

Physical fitness and academic performance in middle school students.

PubMed

Bass, Ronald W; Brown, Dale D; Laurson, Kelly R; Coleman, Margaret M

2013-08-01

The purpose of this study was to determine whether physical fitness is linked to academic success in middle school students. The FITNESSGRAM test battery assessed students (n = 838) in the five components of health-related fitness. The Illinois Standardized Achievement Test (ISAT) was used to assess academic achievement in reading and math. The largest correlations were seen for aerobic fitness and muscular endurance (ranging from 0.12 to 0.27, all p < 0.05). Boys in the Healthy Fitness Zone (HFZ) for aerobic fitness or muscular endurance were 2.5-3 times more likely to pass their math or reading exams. Girls in the HFZ for aerobic fitness were approximately 2-4 times as likely to meet or exceed reading and math test standards. Aerobic capacity and muscular endurance seem to positively affect academic achievement in middle school students. ©2013 Foundation Acta Paediatrica. Published by John Wiley & Sons Ltd.

Estuarine Vegetation at Rush Ranch Open Space Preserve, San Francisco Bay National Estuarine Research Reserve, California

USDA-ARS?s Scientific Manuscript database

The Rush Ranch Open Space Preserve (Rush Ranch) includes the largest remaining undiked tidal wetland within the Suisun Marsh region of the San Francisco Estuary. The brackish tidal wetlands grade into transitional vegetation and undeveloped grasslands of the Potrero Hills. We present analysis of ...

Tidal wetland vegetation and ecotone profiles: The Rush Ranch Open Space Preserve

USDA-ARS?s Scientific Manuscript database

The Rush Ranch Open Space Preserve (Rush Ranch) is a component site of the San Francisco Bay National Estuarine Research Reserve (SF Bay NERR) that includes one of the largest undiked tidal wetlands in the San Francisco Estuary. The brackish tidal wetlands grade into transitional vegetation and unde...

Characteristics of Open Access Journals in Six Subject Areas

ERIC Educational Resources Information Center

Walters, William H.; Linvill, Anne C.

2011-01-01

We examine the characteristics of 663 Open Access (OA) journals in biology, computer science, economics, history, medicine, and psychology, then compare the OA journals with impact factors to comparable subscription journals. There is great variation in the size of OA journals; the largest publishes more than 2,700 articles per year, but half…

Still Imagining the Future

ERIC Educational Resources Information Center

Baker, Chris

2009-01-01

The Open University, or the OU as it is more familiarly known, has reached middle age. The OU has a lot to celebrate. It has become UK's largest university, pioneered supported open learning, and provided access to a high-quality provision from which more than two million learners have benefitted. Internationally, it has many sister institutions…

Enhancement of brain event-related potentials to speech sounds is associated with compensated reading skills in dyslexic children with familial risk for dyslexia.

PubMed

Lohvansuu, Kaisa; Hämäläinen, Jarmo A; Tanskanen, Annika; Ervast, Leena; Heikkinen, Elisa; Lyytinen, Heikki; Leppänen, Paavo H T

2014-12-01

Specific reading disability, dyslexia, is a prevalent and heritable disorder impairing reading acquisition characterized by a phonological deficit. However, the underlying mechanism of how the impaired phonological processing mediates resulting dyslexia or reading disabilities remains still unclear. Using ERPs we studied speech sound processing of 30 dyslexic children with familial risk for dyslexia, 51 typically reading children with familial risk for dyslexia, and 58 typically reading control children. We found enhanced brain responses to shortening of a phonemic length in pseudo-words (/at:a/ vs. /ata/) in dyslexic children with familial risk as compared to other groups. The enhanced brain responses were associated with better performance in behavioral phonemic length discrimination task, as well as with better reading and writing accuracy. Source analyses revealed that the brain responses of sub-group of dyslexic children with largest responses originated from a more posterior area of the right temporal cortex as compared to the responses of the other participants. This is the first electrophysiological evidence for a possible compensatory speech perception mechanism in dyslexia. The best readers within the dyslexic group have probably developed alternative strategies which employ compensatory mechanisms substituting their possible earlier deficit in phonological processing and might therefore be able to perform better in phonemic length discrimination and reading and writing accuracy tasks. However, we speculate that for reading fluency compensatory mechanisms are not that easily built and dyslexic children remain slow readers during their adult life. Copyright © 2014 Elsevier B.V. All rights reserved.

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

PubMed

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

2018-04-27

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

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

PubMed Central

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

1986-01-01

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

Fugitive methane emissions from natural, urban, agricultural, and energy-production landscapes of eastern Australia

NASA Astrophysics Data System (ADS)

Kelly, Bryce F. J.; Iverach, Charlotte P.; Lowry, Dave; Fisher, Rebecca E.; France, James L.; Nisbet, Euan G.

2015-04-01

Modern cavity ringdown spectroscopy systems (CRDS) enable the continuous measurement of methane concentration. This allows for improved quantification of greenhouse gas emissions associated with various natural and human landscapes. We present a subset of over 4000 km of continuous methane surveying along the east coast of Australia, made using a Picarro G2301 CRDS, deployed in a utility vehicle with an air inlet above the roof at 2.2 mAGL. Measurements were made every 5 seconds to a precision of <0.5 ppb for CH4. These surveys were undertaken during dry daytime hours and all measurements were moisture corrected. We compare the concentration of methane in the near surface atmosphere adjacent to open-cut coal mines, unconventional gas developments (coal seam gas; CSG), and leaks detected in cities and country towns. In areas of dryland crops the median methane concentration was 1.78 ppm, while in the irrigation districts located on vertisol soils the concentration was as low as 1.76 ppm, which may indicate that these soils are a sink for methane. In the Hunter Valley, New South Wales, open-cut coal mining district we mapped a continuous 50 km interval where the concentration of methane exceeded 1.80 ppm. The median concentration in this interval was 2.02 ppm. Peak readings were beyond the range of the reliable measurement (in excess of 3.00 ppm). This extended plume is an amalgamation of plumes from 17 major pits 1 to 10 km in length. Adjacent to CSG developments in the Surat Basin, southeast Queensland, only small anomalies were detected near the well-heads. Throughout the vast majority of the gas fields the concentration of methane was below 1.80 ppm. The largest source of fugitive methane associated with CSG was off-gassing methane from the co-produced water holding ponds. At one location the down wind plume had a cross section of approximately 1 km where the concentration of methane was above 1.80 ppm. The median concentration within this section was 1.82 ppm, with a peak reading of 2.11 ppm. The ambient air methane concentration was always higher in urban environments compared to the surrounding countryside. Along one major road in Sydney we mapped an interval that extended for 6 km where the concentration was greater than 1.80 ppm. The median concentration in this interval was 1.90 ppm, with a peak reading of 1.97 ppm. This high reading in an urban setting is most likely due to leaks from the domestic gas distribution system. Methane leaks were detected in all country towns. Our measurements show that at the point of resource extraction the methane emission footprint of CSG is smaller than that of open-cut coal mining. However, leaking gas from urban centers must be added to the fugitive emissions of CSG to calculate the total fugitive emission footprint of CSG, which may therefore not be as low as claimed in the national greenhouse gas accounts. Our results highlight the need for additional continuous monitoring of methane emissions from all sectors, and for the full life-cycle of energy resources to be considered.

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

PubMed

Ducharme, Daphne A; Arcand, Isabelle

2009-08-01

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

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

PubMed

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

2017-01-01

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

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

ERIC Educational Resources Information Center

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

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

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

PubMed

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

2018-04-01

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

The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data

PubMed Central

Clarke, Laura; Fairley, Susan; Zheng-Bradley, Xiangqun; Streeter, Ian; Perry, Emily; Lowy, Ernesto; Tassé, Anne-Marie; Flicek, Paul

2017-01-01

The International Genome Sample Resource (IGSR; http://www.internationalgenome.org) expands in data type and population diversity the resources from the 1000 Genomes Project. IGSR represents the largest open collection of human variation data and provides easy access to these resources. IGSR was established in 2015 to maintain and extend the 1000 Genomes Project data, which has been widely used as a reference set of human variation and by researchers developing analysis methods. IGSR has mapped all of the 1000 Genomes sequence to the newest human reference (GRCh38), and will release updated variant calls to ensure maximal usefulness of the existing data. IGSR is collecting new structural variation data on the 1000 Genomes samples from long read sequencing and other technologies, and will collect relevant functional data into a single comprehensive resource. IGSR is extending coverage with new populations sequenced by collaborating groups. Here, we present the new data and analysis that IGSR has made available. We have also introduced a new data portal that increases discoverability of our data—previously only browseable through our FTP site—by focusing on particular samples, populations or data sets of interest. PMID:27638885

Cloning and expression analysis of carboxyltransferase of acetyl-coA carboxylase from Jatropha curcas.

PubMed

Xie, Wu-Wei; Gao, Shun; Wang, Sheng-Hua; Zhu, Jin-Qiu; Xu, Ying; Tang, Lin; Chen, Fang

2010-01-01

A full-length cDNA of the carboxyltransferase (accA) gene of acetyl-coenzym A (acetyl-CoA) carboxylase from Jatropha curcas was cloned and sequenced. The gene with an open reading frame (ORF) of 1149 bp encodes a polypeptide of 383 amino acids, with a molecular mass of 41.9 kDa. Utilizing fluorogenic real-time polymerase chain reaction (RT-PCR), the expression levels of the accA gene in leaves and fruits at early, middle and late stages under pH 7.0/8.0 and light/darkness stress were investigated. The expression levels of the accA gene in leaves at early, middle and late stages increased significantly under pH 8.0 stress compared to pH 7.0. Similarly, the expression levels in fruits showed a significant increase under darkness condition compared to the control. Under light stress, the expression levels in the fruits at early, middle and late stages showed the largest fluctuations compared to those of the control. These findings suggested that the expression levels of the accA gene are closely related to the growth conditions and developmental stages in the leaves and fruits of Jatropha curcas.

Genomic sequence of Heliothis virescens ascovirus 3g isolated from Spodoptera exigua.

PubMed

Huang, Guo-Hua; Wang, Yun-Sheng; Wang, Xing; Garretson, Tyler A; Dai, Liang-Ying; Zhang, Chuan-Xi; Cheng, Xiao-Wen

2012-11-01

Heliothis virescens ascovirus 3a (HvAV-3a), a member of the family Ascoviridae, has the highest diversity among ascovirus species that have been reported in Australia, Indonesia, China, and the United States. To understand the diversity and origin of this important ascovirus, the complete genome of the HvAV Indonesia strain (HvAV-3g), isolated from Spodoptera exigua, was determined to be 199,721 bp, with a G+C content of 45.9%. Therefore, HvAV-3g has the largest genome among the reported ascovirus genomes to date. There are 194 predicted open reading frames (ORFs) encoding proteins of 50 or more amino acid residues. In comparison to HvAV-3e reported from Australia, HvAV-3g has all the ORFs in HvAV-3e with 6 additional ORFs unique to HvAV-3g, including 1 peptidase C26 gene with the highest identity to Drosophila spp. and 2 gas vesicle protein U (GvpU) genes with identities to Bacillus megaterium. The five unique homologous regions (hrs) and 25 baculovirus repeat ORFs (bro) of HvAV-3g are highly variable.

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

ERIC Educational Resources Information Center

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

2002-01-01

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

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

PubMed Central

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

2014-01-01

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

Longitudinal associations between reading and mathematics achievement.

PubMed

Grimm, Kevin J

2008-01-01

The association between early reading skills and changes in mathematics was examined in a large, low-income sample to determine whether students who have a greater level of reading skills in early elementary school exhibit more rapid gains in tests of mathematics. The longitudinal associations between third grade reading comprehension and changes in three components of mathematics achievement (Problem Solving and Data Interpretation, Mathematical Concepts and Estimation, Mathematical Computation) from third through eighth grade were examined. Latent growth models were fit to the repeated assessments of each mathematics component and the students' third grade reading and global mathematics scores were included as predictors of the intercept and slope. Gender, poverty status, and ethnicity were included in the models as control variables. The results showed males and African-American students tended to have shallower rates of change than females and non-African-American/non-Hispanic students. In terms of the effect of reading on changes in mathematics, third grade reading comprehension was found to be a positive significant predictor of change for each component of mathematics, suggesting students with a greater level of reading achievement in early elementary school change more rapidly in mathematics skills controlling for prior mathematics skills and student characteristics. The largest effects were shown for the Problem Solving and Data Interpretation test, a test focused on the applications of mathematics knowledge, and the Mathematical Concepts and Estimation test. Negligible effects were found for changes in Mathematical Computation. Thus, early reading comprehension was shown to be related to a conceptual understanding of mathematics and the application of mathematics knowledge. These findings lend support for the notion that early reading skills are important for success in mathematics.

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

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-31

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

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

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...

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...

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

ERIC Educational Resources Information Center

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

2009-01-01

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

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

ERIC Educational Resources Information Center

Brady, Judith Ann

2010-01-01

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

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

ERIC Educational Resources Information Center

George, Meredith; Cutner-Smith, Matthew D.

2018-01-01

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

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

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...

Open-Trial Pilot of "Mind Reading" and in Vivo Rehearsal for Children with HFASD

ERIC Educational Resources Information Center

Thomeer, Marcus L.; Rodgers, Jonathan D.; Lopata, Christopher; McDonald, Christin A.; Volker, Martin A.; Toomey, Jennifer A.; Smith, Rachael A.; Gullo, Gaetano

2011-01-01

In this pilot study, the authors evaluated a manualized administration of the "Mind Reading" (MR) program with in vivo rehearsal to determine the effects on emotion recognition and autism features of eleven 7- to 12-year-old children with High-Functioning Autism Spectrum Disorders (HFASD), and to determine the overall feasibility of the…

36 CFR § 703.7 - Public Reading Facility.

Code of Federal Regulations, 2013 CFR

2013-07-01

...§ 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...

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...

49 CFR 325.59 - Measurement procedure; stationary test.

Code of Federal Regulations, 2011 CFR

2011-10-01

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

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

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...

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

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

32 CFR 1285.2 - Policy.

Code of Federal Regulations, 2011 CFR

2011-07-01

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

32 CFR 1285.2 - Policy.

Code of Federal Regulations, 2010 CFR

2010-07-01

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

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…

Online Library Accessibility Support: A Case Study within the Open University Library

ERIC Educational Resources Information Center

Mears, Wendy; Clough, Helen

2015-01-01

The Open University (OU) is the UK's largest distance education provider and has a large and growing disabled student population. Disabled user support presents particular challenges for an online library service in the distance learning environment. The OU introduced guidelines for working with non-OU--authored content (external content) in 2011…

Open Educational Resources and Student Course Outcomes: A Multilevel Analysis

ERIC Educational Resources Information Center

Winitzky-Stephens, Jessie; Pickavance, Jason

2017-01-01

Salt Lake Community College (SLCC) is Utah's largest open enrollment college, and as an institution, is concerned about the expense associated with attaining a degree. All students face challenges in paying for their education, but SLCC students tend to have fewer resources to dedicate to school than students at other institutions in the state.…

AmpuBase: a transcriptome database for eight species of apple snails (Gastropoda: Ampullariidae).

PubMed

Ip, Jack C H; Mu, Huawei; Chen, Qian; Sun, Jin; Ituarte, Santiago; Heras, Horacio; Van Bocxlaer, Bert; Ganmanee, Monthon; Huang, Xin; Qiu, Jian-Wen

2018-03-05

Gastropoda, with approximately 80,000 living species, is the largest class of Mollusca. Among gastropods, apple snails (family Ampullariidae) are globally distributed in tropical and subtropical freshwater ecosystems and many species are ecologically and economically important. Ampullariids exhibit various morphological and physiological adaptations to their respective habitats, which make them ideal candidates for studying adaptation, population divergence, speciation, and larger-scale patterns of diversity, including the biogeography of native and invasive populations. The limited availability of genomic data, however, hinders in-depth ecological and evolutionary studies of these non-model organisms. Using Illumina Hiseq platforms, we sequenced 1220 million reads for seven species of apple snails. Together with the previously published RNA-Seq data of two apple snails, we conducted de novo transcriptome assembly of eight species that belong to five genera of Ampullariidae, two of which represent Old World lineages and the other three New World lineages. There were 20,730 to 35,828 unigenes with predicted open reading frames for the eight species, with N50 (shortest sequence length at 50% of the unigenes) ranging from 1320 to 1803 bp. 69.7% to 80.2% of these unigenes were functionally annotated by searching against NCBI's non-redundant, Gene Ontology database and the Kyoto Encyclopaedia of Genes and Genomes. With these data we developed AmpuBase, a relational database that features online BLAST functionality for DNA/protein sequences, keyword searching for unigenes/functional terms, and download functions for sequences and whole transcriptomes. In summary, we have generated comprehensive transcriptome data for multiple ampullariid genera and species, and created a publicly accessible database with a user-friendly interface to facilitate future basic and applied studies on ampullariids, and comparative molecular studies with other invertebrates.

Reading comprehension and its underlying components in second-language learners: A meta-analysis of studies comparing first- and second-language learners.

PubMed

Melby-Lervåg, Monica; Lervåg, Arne

2014-03-01

We report a systematic meta-analytic review of studies comparing reading comprehension and its underlying components (language comprehension, decoding, and phonological awareness) in first- and second-language learners. The review included 82 studies, and 576 effect sizes were calculated for reading comprehension and underlying components. Key findings were that, compared to first-language learners, second-language learners display a medium-sized deficit in reading comprehension (pooled effect size d = -0.62), a large deficit in language comprehension (pooled effect size d = -1.12), but only small differences in phonological awareness (pooled effect size d = -0.08) and decoding (pooled effect size d = -0.12). A moderator analysis showed that characteristics related to the type of reading comprehension test reliably explained the variation in the differences in reading comprehension between first- and second-language learners. For language comprehension, studies of samples from low socioeconomic backgrounds and samples where only the first language was used at home generated the largest group differences in favor of first-language learners. Test characteristics and study origin reliably contributed to the variations between the studies of language comprehension. For decoding, Canadian studies showed group differences in favor of second-language learners, whereas the opposite was the case for U.S. studies. Regarding implications, unless specific decoding problems are detected, interventions that aim to ameliorate reading comprehension problems among second-language learners should focus on language comprehension skills.

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…

Parachute Opening During Tests for Mars Science Laboratory

NASA Image and Video Library

2009-04-22

Testing during March and April 2009 inside the world largest wind tunnel, at NASA Ames Research Center, Moffett Field, Calif., qualified the parachute for NASA next Mars rover. The parachute for NASA's Mars Science Laboratory mission, to be launched in 2011 and land on Mars in 2012, is the largest ever built to fly on an extraterrestrial mission. This image shows the qualification-test parachute beginning to open a few seconds after it was launched from a mortar into an 80-mile-per-hour (36-meter-per-second) wind. The parachute uses a configuration called disk-gap-band. It has 80 suspension lines, measures more than 50 meters (165 feet) in length, and opens to a diameter of nearly 16 meters (51 feet). Most of the orange and white fabric is nylon, though a small disk of heavier polyester is used near the vent in the apex of the canopy due to higher stresses there. http://photojournal.jpl.nasa.gov/catalog/PIA11992

Parachute Opening During Tests for Mars Science Laboratory

NASA Image and Video Library

2009-04-22

Testing during March and April 2009 inside the world largest wind tunnel, at NASA Ames Research Center, Moffett Field, Calif., qualified the parachute for NASA next Mars rover. The parachute for NASA's Mars Science Laboratory mission, to be launched in 2011 and land on Mars in 2012, is the largest ever built to fly on an extraterrestrial mission. This image shows the qualification-test parachute beginning to open a few seconds after it was launched from a mortar into an 80-mile-per-hour (36-meter-per-second) wind. The parachute uses a configuration called disk-gap-band. It has 80 suspension lines, measures more than 50 meters (165 feet) in length, and opens to a diameter of nearly 16 meters (51 feet). Most of the orange and white fabric is nylon, though a small disk of heavier polyester is used near the vent in the apex of the canopy due to higher stresses there. http://photojournal.jpl.nasa.gov/catalog/PIA11993

Development open source microcontroller based temperature data logger

NASA Astrophysics Data System (ADS)

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

2017-10-01

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

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

PubMed Central

Davies, Frederick S.; Flore, James A.

1986-01-01

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

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.

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

NAEP 2009 Year in Review: A Compilation of Results from the 2009 Mathematics, Reading, Science, and High School Transcript Study Reports. NCES 2011-471

ERIC Educational Resources Information Center

National Center for Education Statistics, 2011

2011-01-01

The Nation's Report Card[TM] informs the public about the academic achievement of elementary and secondary students in the United States. Report cards communicate the findings of the National Assessment of Educational Progress (NAEP), the largest continuing and nationally representative assessment of what the nation's students know and can do.…

Giant Sunspot Erupts with 4th Substantial Flare

NASA Image and Video Library

2017-12-08

The sun emitted a significant solar flare, peaking at 5:40 p.m. EDT on Oct. 24, 2014. The flare erupted from a particularly large active region -- labeled AR 12192 -- on the sun that is the largest in 24 years. This is the fourth substantial flare from this active region since Oct. 19. Read more: www.nasa.gov/content/goddard/giant-sunspot-erupts-with-4t...

National Board Certification and Teacher Effectiveness: Evidence from Washington. CEDR Working Paper. WP #2015-3

ERIC Educational Resources Information Center

Cowan, James; Goldhaber, Dan

2015-01-01

We study the effectiveness of teachers certified by the National Board for Professional Teaching Standards (NBPTS) in Washington State, which has one of the largest populations of National Board Certified Teachers (NBCTs) in the nation. Based on value-added models in math and reading, we find that NBPTS certified teachers are about 0.01-0.05…

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

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-07

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

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

ERIC Educational Resources Information Center

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

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

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

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-28

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

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

ERIC Educational Resources Information Center

Anderton, Gretchen E.

2009-01-01

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

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

ERIC Educational Resources Information Center

Fowler, Zinita

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

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

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-23

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

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

ERIC Educational Resources Information Center

Chang, Yuh-Fang

2006-01-01

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

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

USDA-ARS?s Scientific Manuscript database

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

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

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-08

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

Visionary leader 2009: Deborah Kumar.

PubMed

Zuppa, Barbara

2010-01-01

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

Identification of the initiation site of poliovirus polyprotein synthesis

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

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

1982-06-01

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

Astronomy for Astronomical Numbers: a Worldwide Massive Open Online Class

NASA Astrophysics Data System (ADS)

Austin, Carmen; Impey, Chris David; Wenger, Matthew

2015-01-01

Astronomy: State of the Art is a massive, open, online class (MOOC) offered through Udemy by an instructional team at the University of Arizona. With over 18,000 enrolled, it is the largest astronomy MOOC available. The astronomical numbers enrolled do not translate into a similar level of engagement. The content consists of 14 hours of video lecture, nearly 1000 PowerPoint slides, 250 pages of background readings, and 20 podcast interviews with leading researchers. Perhaps in part because of the large amount of course content, the overall completion rate is low, about 3%. However, this number was four times higher for an early cohort of learners who were selected to have a prior interest in astronomy and who took the class in synchronous mode, with new content being added every week. Completion correlates with engagement as measured by posts to the online discussion board. For a subset of learners, social media like Facebook and Twitter provide an additional, important mode of engagement. For the asynchronous learners who have continuously enrolled for the past 15 months, those who complete the course do so quickly, with few persisting longer than two months. The availability of a completion certificate had no impact of completion rates. This experiment informs a future offering of this MOOC via Coursera, along with a co-convened 'flipped' introductory astronomy class at the University of Arizona, where the video lectures will be online and class time will be used exclusively for small group labs and hands-on activities. Despite their typically low completion rates, MOOCs have the potential to add significantly to public engagement with science.

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.

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.

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.

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

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.

Astronomy for Astronomical Numbers: A Worldwide Massive Open Online Class

ERIC Educational Resources Information Center

Impey, Chris D.; Wenger, Matthew C.; Austin, Carmen L.

2015-01-01

Astronomy: State of the Art is a massive, open, online class (MOOC) offered through Udemy by an instructional team at the University of Arizona. With nearly 24,000 enrolled as of early 2015, it is the largest astronomy MOOC available. The astronomical numbers enrolled do not translate into a similar level of engagement. The content consists of 14…

The Legacy and Impact of Open University Women's/Gender Studies: 30 Years On

ERIC Educational Resources Information Center

Kirkup, Gill; Whitelegg, Elizabeth

2013-01-01

In 1983, the UK Open University (OU) offered its first women's/gender studies (WGS) course. Although a late entrant to the area, OU WGS courses were influential nationally and internationally for many feminists and WGS teachers and scholars. Not only did OU WGS courses have the largest WGS student cohort of any UK institution with over 8000…

Meat Processing and Garden City, KS: Boom and Bust

ERIC Educational Resources Information Center

Broadway, Michael J.; Stull, Donald D.

2006-01-01

In December 1980, the world's largest beef processing plant opened 10 miles west of Garden City, KS. Three years later another beef plant opened on Garden City's eastern edge. Full employment in the surrounding region meant that most of the 4000 workers needed to run these plants had to come from elsewhere--and they did. Garden City grew by…

The Open Education System, Anadolu University, Turkey: E-Transformation in a Mega-University

ERIC Educational Resources Information Center

Latchem, Colin; Ozkul, Ali Ekrem; Aydin, Cengiz Hakan; Mutlu, Mehmet Emin

2006-01-01

Anadolu University in Turkey is one of the world's largest and least known mega-universities. Well over one million students in Turkey, the European Union and Northern Cyprus are enrolled in its Open Education System and yet few accounts of this dual-mode provider appear in the international literature. This article describes the evolution of the…

The Open Academic Model for the Systems Engineering Graduate Program at Stevens Institute of Technology

ERIC Educational Resources Information Center

Lasfer, Kahina

2012-01-01

The Systems Engineering Program at Stevens Institute of Technology has developed the Open Academic Model (OAM) to guide its strategic planning and operations since its founding in 2001. Guided by OAM, the Stevens Systems Engineering Program (SSEP) has grown from inception in 2001 into one of the largest in the US. The main objectives of the…

Reading apps for children: Readability from the design perspective

NASA Astrophysics Data System (ADS)

Mohammed, Wasan Abdulwahab; Husni, Husniza

2017-10-01

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

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

PubMed Central

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

2015-01-01

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

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

PubMed

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

2015-03-01

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

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

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

Chen, Lei

2008-01-01

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

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

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

General Open Systems Theory and the Substrata-Factor Theory of Reading.

ERIC Educational Resources Information Center

Kling, Martin

This study was designed to extend the generality of the Substrata-Factor Theory by two methods of investigation: (1) theoretically, to establish the validity of the hypothesis that an isomorphic relationship exists between the Substrata-Factor Theory and the General Open Systems Theory, and (2) experimentally, to discover through a series of…

General Open Systems Theory and the Substrata-Factor Theory of Reading.

ERIC Educational Resources Information Center

Kling, Martin

This study was designed to extend the generality of the Substrata-Factor Theory by two methods of investigation: (1) theoretically, to est"blish the validity of the hypothesis that an isomorphic relationship exists between the Substrata-Factor Theory and the General Open Systems Theory, and (2) experimentally, to disc"ver through a…

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

PubMed

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

2017-12-01

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

Washington Headquarters Services

Science.gov Websites

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

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

Code of Federal Regulations, 2010 CFR

2010-04-01

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

4 Massive Open Online Courses and How They Work

ERIC Educational Resources Information Center

Gose, Ben

2012-01-01

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

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.

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.

Human milk metagenome: a functional capacity analysis

PubMed Central

2013-01-01

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

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

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-14

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

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

ERIC Educational Resources Information Center

Vanderburg, Willem H.

2010-01-01

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

A New Culture of Transparency: Industry Payments to Orthopedic Surgeons.

PubMed

Lopez, Joseph; Ahmed, Rizwan; Bae, Sunjae; Hicks, Caitlin W; El Dafrawy, Mostafa; Osgood, Greg M; Segev, Dorry L

2016-11-01

Under the Physician Payments Sunshine Act, "payments or transfers of value" by biomedical companies to physicians must be disclosed through the Open Payments Program. Designed to provide transparency of financial transactions between medication and device manufacturers and health care providers, the Open Payments Program shows financial relationships between industry and health care providers. Awareness of this program is crucial because its interpretation or misinterpretation by patients, physicians, and the general public can affect patient care, clinical practice, and research. This study evaluated nonresearch payments by industry to orthopedic surgeons. A retrospective cross-sectional review of the first wave of Physician Payments Sunshine Act data (August through December 2013) was performed to characterize industry payments to orthopedic surgeons by subspecialty, amount, type, origin, and geographic distribution. During this 5-month period, orthopedic surgeons (n=14,828) received $107,666,826, which included 3% of those listed in the Open Payments Program and 23% of the total amount paid. Of orthopedic surgeons who received payment, 45% received less than $100 and 1% received $100,000 or more. Median payment (interquartile range) was $119 ($34-$636), and mean payment was $7261±95,887. The largest payment to an individual orthopedic surgeon was $7,849,711. The 2 largest payment categories were royalty or license fees (68%) and consulting fees (13%). During the study period, orthopedic surgeons had substantial financial ties to industry. Of orthopedic surgeons who received payments, the largest proportion (45%) received less than $100 and only 1% received large payments (≥$100,000). The Open Payments Program offers insight into industry payments to orthopedic surgeons. [Orthopedics. 2016; 39(6):e1058-e1062.]. Copyright 2016, SLACK Incorporated.

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

Uranium mining wastes, garden exhibition and health risks

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

Schmidt, Gerhard; Schmidt, Peter; Hinz, Wilko

2007-07-01

Available in abstract form only. Full text of publication follows: For more than 40 years the Soviet-German stockholding company SDAG WISMUT mined and milled Uranium in the East of Germany and became up to 1990 the world's third largest Uranium producer. After reunification of Germany, the new found state own company Wismut GmbH was faced with the task of decommissioning and rehabilitation of the mining and milling sites. One of the largest mining areas in the world, that had to be cleaned up, was located close to the municipality of Ronneburg near the City of Gera in Thuringia. After closingmore » the operations of the Ronneburg underground mine and at the 160 m deep open pit mine with a free volume of 84 Mio.m{sup 3}, the open pit and 7 large piles of mine waste, together 112 Mio.m{sup 3} of material, had to be cleaned up. As a result of an optimisation procedure it was chosen to relocate the waste rock piles back into the open pit. After taking this decision and approval of the plan the disposal operation was started. Even though the transport task was done by large trucks, this took 16 years. The work will be finished in 2007, a cover consisting of 40 cm of uncontaminated material will be placed on top of the material, and the re-vegetation of the former open pit area will be established. When in 2002 the City of Gera applied to host the largest garden exhibition in Germany, Bundesgartenschau (BUGA), in 2007, Wismut GmbH supported this plan by offering parts of the territory of the former mining site as an exhibition ground. Finally, it was decided by the BUGA organizers to arrange its 2007 exhibition on grounds in Gera and in the valley adjacent to the former open pit mine, with parts of the remediated area within the fence of the exhibition. (authors)« less

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome.

PubMed

Bickhart, Derek M; Rosen, Benjamin D; Koren, Sergey; Sayre, Brian L; Hastie, Alex R; Chan, Saki; Lee, Joyce; Lam, Ernest T; Liachko, Ivan; Sullivan, Shawn T; Burton, Joshua N; Huson, Heather J; Nystrom, John C; Kelley, Christy M; Hutchison, Jana L; Zhou, Yang; Sun, Jiajie; Crisà, Alessandra; Ponce de León, F Abel; Schwartz, John C; Hammond, John A; Waldbieser, Geoffrey C; Schroeder, Steven G; Liu, George E; Dunham, Maitreya J; Shendure, Jay; Sonstegard, Tad S; Phillippy, Adam M; Van Tassell, Curtis P; Smith, Timothy P L

2017-04-01

The decrease in sequencing cost and increased sophistication of assembly algorithms for short-read platforms has resulted in a sharp increase in the number of species with genome assemblies. However, these assemblies are highly fragmented, with many gaps, ambiguities, and errors, impeding downstream applications. We demonstrate current state of the art for de novo assembly using the domestic goat (Capra hircus) based on long reads for contig formation, short reads for consensus validation, and scaffolding by optical and chromatin interaction mapping. These combined technologies produced what is, to our knowledge, the most continuous de novo mammalian assembly to date, with chromosome-length scaffolds and only 649 gaps. Our assembly represents a ∼400-fold improvement in continuity due to properly assembled gaps, compared to the previously published C. hircus assembly, and better resolves repetitive structures longer than 1 kb, representing the largest repeat family and immune gene complex yet produced for an individual of a ruminant species.

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome

PubMed Central

Bickhart, Derek M.; Rosen, Benjamin D.; Koren, Sergey; Sayre, Brian L.; Hastie, Alex R.; Chan, Saki; Lee, Joyce; Lam, Ernest T.; Liachko, Ivan; Sullivan, Shawn T.; Burton, Joshua N.; Huson, Heather J.; Nystrom, John C.; Kelley, Christy M.; Hutchison, Jana L.; Zhou, Yang; Sun, Jiajie; Crisà, Alessandra; de León, F. Abel Ponce; Schwartz, John C.; Hammond, John A.; Waldbieser, Geoffrey C.; Schroeder, Steven G.; Liu, George E.; Dunham, Maitreya J.; Shendure, Jay; Sonstegard, Tad S.; Phillippy, Adam M.; Van Tassell, Curtis P.; Smith, Timothy P.L.

2018-01-01

The decrease in sequencing cost and increased sophistication of assembly algorithms for short-read platforms has resulted in a sharp increase in the number of species with genome assemblies. However, these assemblies are highly fragmented, with many gaps, ambiguities, and errors, impeding downstream applications. We demonstrate current state of the art for de novo assembly using the domestic goat (Capra hircus), based on long reads for contig formation, short reads for consensus validation, and scaffolding by optical and chromatin interaction mapping. These combined technologies produced the most continuous de novo mammalian assembly to date, with chromosome-length scaffolds and only 649 gaps. Our assembly represents a ~400-fold improvement in continuity due to properly assembled gaps compared to the previously published C. hircus assembly, and better resolves repetitive structures longer than 1 kb, representing the largest repeat family and immune gene complex ever produced for an individual of a ruminant species. PMID:28263316

Scientific Encounters of the Insect World. Reading Activities That Explore Nature's Fascinating Insects. A Good Apple Science Activity Book for Grades 4-7.

ERIC Educational Resources Information Center

Embry, Lynn

Insects comprise the largest group of animals in the world and newly discovered ones are being added to the list every year. The habits of even the most common insects are interesting to observe. This book introduces insects that many children will be able to observe in their environments. Interesting information is presented to help children…

The National Council of Churches' Alleged Leftist Bias: To What Degree Did Two Major Media Set the Agenda for Debate on the Issue?

ERIC Educational Resources Information Center

Gentry, Richard H.

In January 1983, the American public read or saw hard-hitting allegations of leftist bias by the National Council of Churches (NCC) in the largest circulation magazine, "Reader's Digest," and on the top-rated television program, "60 Minutes." A study examined the extent to which the media set the agenda for debate on this…

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!

Abriendo Puertas/Opening Doors Parenting Program: Summary Report of Program Implementation and Impacts. Publication #2014-24

ERIC Educational Resources Information Center

Moore, Kristin A.; Caal, Selma; Lawner, Elizabeth K.; Rojas, Angela; Walker, Karen

2014-01-01

Child Trends conducted a random assignment evaluation of the Abriendo Puertas/Opening Doors program, one of the largest programs in the United States working with low-income Latino parents of children ages zero to five. Since it began in 2007, the program has served over 30,000 parents/families in 34 states. The evaluation study examined the…

Challenges Faced by African International Students at a Metropolitan Research University: A Phenomenological Case Study

ERIC Educational Resources Information Center

Evivie, Loretta Gbemudu

2009-01-01

The number of international students coming to the United States has increased from 48,486 in 1959-1960 to 623,805 in the 2007-2008 academic years (Open Doors, 2008). These students contributed $15.5 billion to the United States economy, making education the nation's fifth largest service export (Open Doors, 2008). The literature has focused on…

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.

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

Osteoblastic lesion screening with an advanced post-processing package enabling in-plane rib reading in CT-images.

PubMed

Seuss, Hannes; Dankerl, Peter; Cavallaro, Alexander; Uder, Michael; Hammon, Matthias

2016-05-20

To evaluate screening and diagnostic accuracy for the detection of osteoblastic rib lesions using an advanced post-processing package enabling in-plane rib reading in CT-images. We retrospectively assessed the CT-data of 60 consecutive prostate cancer patients by applying dedicated software enabling in-plane rib reading. Reading the conventional multiplanar reconstructions was considered to be the reference standard. To simulate clinical practice, the reader was given 10 s to screen for sclerotic rib lesions in each patient applying both approaches. Afterwards, every rib was evaluated individually with both approaches without a time limit. Sensitivities, specificities, positive/negative predictive values and the time needed for detection were calculated depending on the lesion's size (largest diameter < 5 mm, 5-10 mm, > 10 mm). In 53 of 60 patients, all ribs were properly displayed in plane, in five patients ribs were partially displayed correctly, and in two patients none of the ribs were displayed correctly. During the 10-s screening approach all patients with sclerotic rib lesions were correctly identified reading the in-plane images (including the patients without a correct rib segmentation), whereas 14 of 23 patients were correctly identified reading conventional multiplanar images. Overall screening sensitivity, specificity, and positive/negative predictive values were 100/27.0/46.0/100 %, respectively, for in-plane reading and 60.9/100/100/80.4 %, respectively, for multiplanar reading. Overall diagnostic (no time limit) sensitivity, specificity, and positive/negative predictive values of in-plane reading were 97.8/92.8/74.6/99.5 %, respectively. False positive results predominantly occurred for lesions <5 mm in size. In-plane reading of the ribs allows reliable detection of osteoblastic lesions for screening purposes. The limited specificity results from false positives predominantly occurring for small lesions.

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…

"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…

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…

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…

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…

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

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.

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.

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.

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

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.

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%.

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.

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

IceBridge Survey Flight Over Saunders Island and Wolstenholme Fjord

NASA Image and Video Library

2017-12-08

This image of Saunders Island and Wolstenholme Fjord with Kap Atholl in the background was taken during an Operation IceBridge survey flight in April, 2013. Sea ice coverage in the fjord ranges from thicker, white ice seen in the background, to thinner grease ice and leads showing open ocean water in the foreground. In March 2013, NASA's Operation IceBridge scientists began another season of research activity over Arctic ice sheets and sea ice. IceBridge, a six-year NASA mission, is the largest airborne survey of Earth's polar ice ever flown. It will yield an unprecedented three-dimensional view of Arctic and Antarctic ice sheets, ice shelves and sea ice. These flights will provide a yearly, multi-instrument look at the behavior of the rapidly changing features of the Greenland and Antarctic ice. Image Credit: NASA / Michael Studinger Read more about the mission here: www.nasa.gov/mission_pages/icebridge/index.html NASA image use policy. NASA Goddard Space Flight Center enables NASA’s mission through four scientific endeavors: Earth Science, Heliophysics, Solar System Exploration, and Astrophysics. Goddard plays a leading role in NASA’s accomplishments by contributing compelling scientific knowledge to advance the Agency’s mission. Follow us on Twitter Like us on Facebook Find us on Instagram

Broadly targeted human cytomegalovirus-specific CD4+ and CD8+ T cells dominate the memory compartments of exposed subjects

PubMed Central

Sylwester, Andrew W.; Mitchell, Bridget L.; Edgar, John B.; Taormina, Cara; Pelte, Christian; Ruchti, Franziska; Sleath, Paul R.; Grabstein, Kenneth H.; Hosken, Nancy A.; Kern, Florian; Nelson, Jay A.; Picker, Louis J.

2005-01-01

Human cytomegalovirus (HCMV) infections of immunocompetent hosts are characterized by a dynamic, life-long interaction in which host immune responses, particularly of T cells, restrain viral replication and prevent disease but do not eliminate the virus or preclude transmission. Because HCMV is among the largest and most complex of known viruses, the T cell resources committed to maintaining this balance have never been characterized completely. Here, using cytokine flow cytometry and 13,687 overlapping 15mer peptides comprising 213 HCMV open reading frames (ORFs), we found that 151 HCMV ORFs were immunogenic for CD4+ and/or CD8+ T cells, and that ORF immunogenicity was influenced only modestly by ORF expression kinetics and function. We further documented that total HCMV-specific T cell responses in seropositive subjects were enormous, comprising on average ∼10% of both the CD4+ and CD8+ memory compartments in blood, whereas cross-reactive recognition of HCMV proteins in seronegative individuals was limited to CD8+ T cells and was rare. These data provide the first glimpse of the total human T cell response to a complex infectious agent and will provide insight into the rules governing immunodominance and cross-reactivity in complex viral infections of humans. PMID:16147978

The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data.

PubMed

Clarke, Laura; Fairley, Susan; Zheng-Bradley, Xiangqun; Streeter, Ian; Perry, Emily; Lowy, Ernesto; Tassé, Anne-Marie; Flicek, Paul

2017-01-04

The International Genome Sample Resource (IGSR; http://www.internationalgenome.org) expands in data type and population diversity the resources from the 1000 Genomes Project. IGSR represents the largest open collection of human variation data and provides easy access to these resources. IGSR was established in 2015 to maintain and extend the 1000 Genomes Project data, which has been widely used as a reference set of human variation and by researchers developing analysis methods. IGSR has mapped all of the 1000 Genomes sequence to the newest human reference (GRCh38), and will release updated variant calls to ensure maximal usefulness of the existing data. IGSR is collecting new structural variation data on the 1000 Genomes samples from long read sequencing and other technologies, and will collect relevant functional data into a single comprehensive resource. IGSR is extending coverage with new populations sequenced by collaborating groups. Here, we present the new data and analysis that IGSR has made available. We have also introduced a new data portal that increases discoverability of our data-previously only browseable through our FTP site-by focusing on particular samples, populations or data sets of interest. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Travel and Adventure Medicine Resources.

PubMed

Sanford, Christopher A; Pottinger, Paul S

2016-03-01

Given the ever-changing nature of travel medicine, practitioners who provide pretravel and posttravel care are obligatorily students for the duration of their professional careers. A large variety of resources are available for medical practitioners. Providers should join at least one travel or tropical medicine professional association, attend its annual meeting, and read its journal. The largest general travel medicine association is the International Society of Travel Medicine. Copyright © 2016 Elsevier Inc. All rights reserved.

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.

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

Brazil opens its first private research institute

NASA Astrophysics Data System (ADS)

Ivanissevich, Alicia

2017-05-01

The Brazilian filmmaker João Moreira Salles - whose family owns one of the largest banks in Brazil - has established a new institute in Rio de Janeiro that will support basic research across all sciences.

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.

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.

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

PubMed

Pelsy, F.; Merdinoglu, D.

2002-09-01

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

The 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

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.

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

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

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…

Molecular analysis and functional expression of the human type E neuronal Ca2+ channel alpha 1 subunit.

PubMed

Schneider, T; Wei, X; Olcese, R; Costantin, J L; Neely, A; Palade, P; Perez-Reyes, E; Qin, N; Zhou, J; Crawford, G D

1994-01-01

A human brain alpha 1 Ca2+ channel subunit was cloned and expressed in Xenopus laevis oocytes. The open reading frame, encoding 2,312 amino acids, has high homology to the marine ray doe-1, the rat E-type, and the rabbit brain BII alpha 1 subunits. The amino and carboxy termini of this human.E-type alpha 1 subunit (alpha 1E) are most similar to the rabbit BII-1 splice variant, the remainder being colinear with the BII alpha 1 with the exception of two insertions, one of 43 amino acids in the C-terminus and another of 7 amino acids, found also in the rat alpha 1E, between domains II and III. Two potential Ca2+ binding sites are predicted from its primary structure. The expression of inward Ba2+ currents reveals voltage-dependent activation and inactivation measured by the cut-open oocyte vaseline-gap technique, with kinetics that correspond to that of a high-voltage-activated neuronal Ca2+ channel, and pharmacologic properties that resemble those of some low-voltage-activated neuronal Ca2+ currents. The human alpha 1E currents are insensitive to omega-conotoxin-GVIA (1 microM), omega-agatoxin-IVA (200 nM), a synthetic funnel web spider toxin (FTX, 20 microM), and Bay-K8644 (0.5 microM); they are inhibited 20% by high concentrations of methoxyverapamil and diltiazem, 65% by 0.1% crude funnel web spider venom and 100% by Ni2+ (IC50 = 30 nM). Single-channel records show a complex activity pattern with several apparent conductance states, the largest having a conductance of 14 pS.

Identification and Characterization of the Anti-Methicillin-Resistant Staphylococcus aureus WAP-8294A2 Biosynthetic Gene Cluster from Lysobacter enzymogenes OH11 ▿ †

PubMed Central

Zhang, Wei; Li, Yaoyao; Qian, Guoliang; Wang, Yan; Chen, Haotong; Li, Yue-Zhong; Liu, Fengquan; Shen, Yuemao; Du, Liangcheng

2011-01-01

Lysobactor enzymogenes strain OH11 is an emerging biological control agent of fungal and bacterial diseases. We recently completed its genome sequence and found it contains a large number of gene clusters putatively responsible for the biosynthesis of nonribosomal peptides and polyketides, including the previously identified antifungal dihydromaltophilin (HSAF). One of the gene clusters contains two huge open reading frames, together encoding 12 modules of nonribosomal peptide synthetases (NRPS). Gene disruption of one of the NRPS led to the disappearance of a metabolite produced in the wild type and the elimination of its antibacterial activity. The metabolite and antibacterial activity were also affected by the disruption of some of the flanking genes. We subsequently isolated this metabolite and subjected it to spectroscopic analysis. The mass spectrometry and nuclear magnetic resonance data showed that its chemical structure is identical to WAP-8294A2, a cyclic lipodepsipeptide with potent anti-methicillin-resistant Staphylococcus aureus (MRSA) activity and currently in phase I/II clinical trials. The WAP-8294A2 biosynthetic genes had not been described previously. So far, the Gram-positive Streptomyces have been the primary source of anti-infectives. Lysobacter are Gram-negative soil/water bacteria that are genetically amendable and have not been well exploited. The WAP-8294A2 synthetase represents one of the largest NRPS complexes, consisting of 45 functional domains. The identification of these genes sets the foundation for the study of the WAP-8294A2 biosynthetic mechanism and opens the door for producing new anti-MRSA antibiotics through biosynthetic engineering in this new source of Lysobacter. PMID:21930890

Air quality impact assessment of multiple open pit coal mines in northern Colombia.

PubMed

Huertas, José I; Huertas, María E; Izquierdo, Sebastián; González, Enrique D

2012-01-01

The coal mining region in northern Colombia is one of the largest open pit mining regions of the world. In 2009, there were 8 mining companies in operation with an approximate coal production of ∼70 Mtons/year. Since 2007, the Colombian air quality monitoring network has reported readings that exceed the daily and annual air quality standards for total suspended particulate (TSP) matter and particles with an equivalent aerodynamic diameter smaller than 10 μm (PM₁₀) in nearby villages. This paper describes work carried out in order to establish an appropriate clean air program for this region, based on the Colombian national environmental authority requirement for modeling of TSP and PM(10) dispersion. A TSP and PM₁₀ emission inventory was initially developed, and topographic and meteorological information for the region was collected and analyzed. Using this information, the dispersion of TSP was modeled in ISC3 and AERMOD using meteorological data collected by 3 local stations during 2008 and 2009. The results obtained were compared to actual values measured by the air quality monitoring network. High correlation coefficients (>0.73) were obtained, indicating that the models accurately described the main factors affecting particle dispersion in the region. The model was then used to forecast concentrations of particulate matter for 2010. Based on results from the model, areas within the modeling region were identified as highly, fairly, moderately and marginally polluted according to local regulations. Additionally, the contribution particulate matter to the pollution at each village was estimated. Using these predicted values, the Colombian environmental authority imposed new decontamination measures on the mining companies operating in the region. These measures included the relocation of three villages financed by the mine companies based on forecasted pollution levels. Copyright © 2011. Published by Elsevier Ltd.

Time-dependent gravity in Southern California, May 1974 to April 1979

NASA Technical Reports Server (NTRS)

Whitcomb, J. H.; Franzen, W. O.; Given, J. W.; Pechmann, J. C.; Ruff, L. J.

1980-01-01

The Southern California gravity survey, begun in May 1974 to obtain high spatial and temporal density gravity measurements to be coordinated with long-baseline three dimensional geodetic measurements of the Astronomical Radio Interferometric Earth Surveying project, is presented. Gravity data was obtained from 28 stations located in and near the seismically active San Gabriel section of the Southern California Transverse Ranges and adjoining San Andreas Fault at intervals of one to two months using gravity meters relative to a base station standard meter. A single-reading standard deviation of 11 microGal is obtained which leads to a relative deviation of 16 microGal between stations, with data averaging reducing the standard error to 2 to 3 microGal. The largest gravity variations observed are found to correlate with nearby well water variations and smoothed rainfall levels, indicating the importance of ground water variations to gravity measurements. The largest earthquake to occur during the survey, which extended to April, 1979, is found to be accompanied in the station closest to the earthquake by the largest measured gravity changes that cannot be related to factors other than tectonic distortion.

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.

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

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.

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

PubMed

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

2018-06-20

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

A longitudinal study investigating neural processing of speech envelope modulation rates in children with (a family risk for) dyslexia.

PubMed

De Vos, Astrid; Vanvooren, Sophie; Vanderauwera, Jolijn; Ghesquière, Pol; Wouters, Jan

2017-08-01

Recent evidence suggests that a fundamental deficit in the synchronization of neural oscillations to temporal information in speech may underlie phonological processing problems in dyslexia. Since previous studies were performed cross-sectionally in school-aged children or adults, developmental aspects of neural auditory processing in relation to reading acquisition and dyslexia remain to be investigated. The present longitudinal study followed 68 children during development from pre-reader (5 years old) to beginning reader (7 years old) and more advanced reader (9 years old). Thirty-six children had a family risk for dyslexia and 14 children eventually developed dyslexia. EEG recordings of auditory steady-state responses to 4 and 20 Hz modulations, corresponding to syllable and phoneme rates, were collected at each point in time. Our results demonstrate an increase in neural synchronization to phoneme-rate modulations around the onset of reading acquisition. This effect was negatively correlated with later reading and phonological skills, indicating that children who exhibit the largest increase in neural synchronization to phoneme rates, develop the poorest reading and phonological skills. Accordingly, neural synchronization to phoneme-rate modulations was found to be significantly higher in beginning and more advanced readers with dyslexia. We found no developmental effects regarding neural synchronization to syllable rates, nor any effects of a family risk for dyslexia. Altogether, our findings suggest that the onset of reading instruction coincides with an increase in neural responsiveness to phoneme-rate modulations, and that the extent of this increase is related to (the outcome of) reading development. Hereby, dyslexic children persistently demonstrate atypically high neural synchronization to phoneme rates from the beginning of reading acquisition onwards. Copyright © 2017 Elsevier Ltd. All rights reserved.

Effect of preservatives on the accuracy of mid-infrared milk component testing.

PubMed

Barbano, D M; Wojciechowski, K L; Lynch, J M

2010-12-01

Our objective was to determine the effect of commonly used milk preservatives on the accuracy of fat, protein, and lactose content determination in milk by mid-infrared (mid-IR) milk analysis. Two producer raw milks (Holstein and Jersey) and 2 pasteurized modified milks, 1 similar to Holstein milk and 1 similar to Jersey milk were used as the 4 different milk sources. Seven different milk preservative approaches (K(2)Cr(2)O(7) and 6 different bronopol-based preservatives) and a portion of unpreserved milk for each of the 4 different milks sources were tested for fat B, lactose, protein, and fat A. The experiment was replicated 3 times (28 d each) for a total of 84 d. Two mid-infrared (mid-IR) transmittance milk analyzers (an optical and a virtual filter instrument) were used. A large batch of pilot milk was prepared from pasteurized, homogenized, unpreserved whole milk, split into vials, quick frozen by immersion in liquid nitrogen, and transferred into a -80 °C freezer. Pilots were thawed and analyzed on each testing day during the study. Significant increases were observed in all uncorrected readings on the pilot milks over the 84 d of the study, but the increases were gradual and small on each instrument for all components. Results from the study were corrected for these changes. A significant difference in mid-IR fat A readings was observed, whereas no differences were detected for fat B, lactose, or protein between unpreserved and preserved milks containing 0.02% K(2)Cr(2)O(7.) Therefore, K(2)Cr(2)O(7) has little or no effect on mid-IR test results. All bronopol-based preservative approaches in this study differed in mid-IR test results compared with K(2)Cr(2)O(7)-preserved and unpreserved milks, with the largest effect on protein results. Mid-IR uncorrected readings increased with time of refrigerated storage at 4°C for all preservative approaches, with the largest increase for protein. The rate of increase in uncorrected readings with time of storage was always higher for raw milks than for pasteurized milks, and the stability of instrument zero was lower for raw milks than for pasteurized milks. The largest economic effect of a systematic bias caused by a preservative occurs when the milks used for calibration and routine testing for payment do not contain the same preservative or when calibration milks are preserved and milks for routine testing are unpreserved. These effects can create errors in payment for large dairy processing plants ranging from several hundred thousand to over a million dollars annually. Copyright © 2010 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Hillsboro Canal bridge monitoring : [summary].

DOT National Transportation Integrated Search

2011-01-01

Floridas inventory of 148 moveable bridges is : the largest in the nation. Most employ open grid : steel decks, which have important advantages : over solid bridge decks: they can be assembled in : the factory, are lightweight and easy to install;...

Altered Distribution of RNA Polymerase Lacking the Omega Subunit within the Prophages along the Escherichia coli K-12 Genome.

PubMed

Yamamoto, Kaneyoshi; Yamanaka, Yuki; Shimada, Tomohiro; Sarkar, Paramita; Yoshida, Myu; Bhardwaj, Neerupma; Watanabe, Hiroki; Taira, Yuki; Chatterji, Dipankar; Ishihama, Akira

2018-01-01

The RNA polymerase (RNAP) of Escherichia coli K-12 is a complex enzyme consisting of the core enzyme with the subunit structure α 2 ββ'ω and one of the σ subunits with promoter recognition properties. The smallest subunit, omega (the rpoZ gene product), participates in subunit assembly by supporting the folding of the largest subunit, β', but its functional role remains unsolved except for its involvement in ppGpp binding and stringent response. As an initial approach for elucidation of its functional role, we performed in this study ChIP-chip (chromatin immunoprecipitation with microarray technology) analysis of wild-type and rpoZ -defective mutant strains. The altered distribution of RpoZ-defective RNAP was identified mostly within open reading frames, in particular, of the genes inside prophages. For the genes that exhibited increased or decreased distribution of RpoZ-defective RNAP, the level of transcripts increased or decreased, respectively, as detected by reverse transcription-quantitative PCR (qRT-PCR). In parallel, we analyzed, using genomic SELEX (systemic evolution of ligands by exponential enrichment), the distribution of constitutive promoters that are recognized by RNAP RpoD holoenzyme alone and of general silencer H-NS within prophages. Since all 10 prophages in E. coli K-12 carry only a small number of promoters, the altered occupancy of RpoZ-defective RNAP and of transcripts might represent transcription initiated from as-yet-unidentified host promoters. The genes that exhibited transcription enhanced by RpoZ-defective RNAP are located in the regions of low-level H-NS binding. By using phenotype microarray (PM) assay, alterations of some phenotypes were detected for the rpoZ -deleted mutant, indicating the involvement of RpoZ in regulation of some genes. Possible mechanisms of altered distribution of RNAP inside prophages are discussed. IMPORTANCE The 91-amino-acid-residue small-subunit omega (the rpoZ gene product) of Escherichia coli RNA polymerase plays a structural role in the formation of RNA polymerase (RNAP) as a chaperone in folding the largest subunit (β', of 1,407 residues in length), but except for binding of the stringent signal ppGpp, little is known of its role in the control of RNAP function. After analysis of genomewide distribution of wild-type and RpoZ-defective RNAP by the ChIP-chip method, we found alteration of the RpoZ-defective RNAP inside open reading frames, in particular, of the genes within prophages. For a set of the genes that exhibited altered occupancy of the RpoZ-defective RNAP, transcription was found to be altered as observed by qRT-PCR assay. All the observations here described indicate the involvement of RpoZ in recognition of some of the prophage genes. This study advances understanding of not only the regulatory role of omega subunit in the functions of RNAP but also the regulatory interplay between prophages and the host E. coli for adjustment of cellular physiology to a variety of environments in nature.

Altered Distribution of RNA Polymerase Lacking the Omega Subunit within the Prophages along the Escherichia coli K-12 Genome

PubMed Central

Yamamoto, Kaneyoshi; Yamanaka, Yuki; Shimada, Tomohiro; Sarkar, Paramita; Yoshida, Myu; Bhardwaj, Neerupma; Watanabe, Hiroki; Taira, Yuki

2018-01-01

ABSTRACT The RNA polymerase (RNAP) of Escherichia coli K-12 is a complex enzyme consisting of the core enzyme with the subunit structure α2ββ′ω and one of the σ subunits with promoter recognition properties. The smallest subunit, omega (the rpoZ gene product), participates in subunit assembly by supporting the folding of the largest subunit, β′, but its functional role remains unsolved except for its involvement in ppGpp binding and stringent response. As an initial approach for elucidation of its functional role, we performed in this study ChIP-chip (chromatin immunoprecipitation with microarray technology) analysis of wild-type and rpoZ-defective mutant strains. The altered distribution of RpoZ-defective RNAP was identified mostly within open reading frames, in particular, of the genes inside prophages. For the genes that exhibited increased or decreased distribution of RpoZ-defective RNAP, the level of transcripts increased or decreased, respectively, as detected by reverse transcription-quantitative PCR (qRT-PCR). In parallel, we analyzed, using genomic SELEX (systemic evolution of ligands by exponential enrichment), the distribution of constitutive promoters that are recognized by RNAP RpoD holoenzyme alone and of general silencer H-NS within prophages. Since all 10 prophages in E. coli K-12 carry only a small number of promoters, the altered occupancy of RpoZ-defective RNAP and of transcripts might represent transcription initiated from as-yet-unidentified host promoters. The genes that exhibited transcription enhanced by RpoZ-defective RNAP are located in the regions of low-level H-NS binding. By using phenotype microarray (PM) assay, alterations of some phenotypes were detected for the rpoZ-deleted mutant, indicating the involvement of RpoZ in regulation of some genes. Possible mechanisms of altered distribution of RNAP inside prophages are discussed. IMPORTANCE The 91-amino-acid-residue small-subunit omega (the rpoZ gene product) of Escherichia coli RNA polymerase plays a structural role in the formation of RNA polymerase (RNAP) as a chaperone in folding the largest subunit (β′, of 1,407 residues in length), but except for binding of the stringent signal ppGpp, little is known of its role in the control of RNAP function. After analysis of genomewide distribution of wild-type and RpoZ-defective RNAP by the ChIP-chip method, we found alteration of the RpoZ-defective RNAP inside open reading frames, in particular, of the genes within prophages. For a set of the genes that exhibited altered occupancy of the RpoZ-defective RNAP, transcription was found to be altered as observed by qRT-PCR assay. All the observations here described indicate the involvement of RpoZ in recognition of some of the prophage genes. This study advances understanding of not only the regulatory role of omega subunit in the functions of RNAP but also the regulatory interplay between prophages and the host E. coli for adjustment of cellular physiology to a variety of environments in nature. PMID:29468196

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).

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

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:

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.

Students Bring Fresh Perspective and New Technology to Webb Telescope

NASA Image and Video Library

2017-12-08

Matthew Bolcar a graduate student from the University of Rochester, N.Y. now works at Goddard full-time. Credit: NASA/GSFC/Chris Gunn To read more about Matthew go to: www.nasa.gov/topics/technology/features/partnerships.html NASA Goddard Space Flight Center is home to the nation's largest organization of combined scientists, engineers and technologists that build spacecraft, instruments and new technology to study the Earth, the sun, our solar system, and the universe.

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...

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...

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)

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

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.

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…

Using basic statistics on the individual patient's own numeric data.

PubMed

Hart, John

2012-12-01

This theoretical report gives an example for how coefficient of variation (CV) and quartile analysis (QA) to assess outliers might be able to be used to analyze numeric data in practice for an individual patient. A patient was examined for 8 visits using infrared instrumentation for measurement of mastoid fossa temperature differential (MFTD) readings. The CV and QA were applied to the readings. The participant also completed the Short Form-12 health perception survey on each visit, and these findings were correlated with CV to determine if CV had outcomes support (clinical significance). An outlier MFTD reading was observed on the eighth visit according to QA that coincided with the largest CV value for the MFTDs. Correlations between the Short Form-12 and CV were low to negligible, positive, and statistically nonsignificant. This case provides an example of how basic statistical analyses could possibly be applied to numerical data in chiropractic practice for an individual patient. This might add objectivity to analyzing an individual patient's data in practice, particularly if clinical significance of a clinical numerical finding is unknown.

The Longhorn Array Database (LAD): An Open-Source, MIAME compliant implementation of the Stanford Microarray Database (SMD)

PubMed Central

Killion, Patrick J; Sherlock, Gavin; Iyer, Vishwanath R

2003-01-01

Background The power of microarray analysis can be realized only if data is systematically archived and linked to biological annotations as well as analysis algorithms. Description The Longhorn Array Database (LAD) is a MIAME compliant microarray database that operates on PostgreSQL and Linux. It is a fully open source version of the Stanford Microarray Database (SMD), one of the largest microarray databases. LAD is available at Conclusions Our development of LAD provides a simple, free, open, reliable and proven solution for storage and analysis of two-color microarray data. PMID:12930545

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:

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:

The what, why, and how of born-open data.

PubMed

Rouder, Jeffrey N

2016-09-01

Although many researchers agree that scientific data should be open to scrutiny to ferret out poor analyses and outright fraud, most raw data sets are not available on demand. There are many reasons researchers do not open their data, and one is technical. It is often time consuming to prepare and archive data. In response, my laboratory has automated the process such that our data are archived the night they are created without any human approval or action. All data are versioned, logged, time stamped, and uploaded including aborted runs and data from pilot subjects. The archive is GitHub, github.com, the world's largest collection of open-source materials. Data archived in this manner are called born open. In this paper, I discuss the benefits of born-open data and provide a brief technical overview of the process. I also address some of the common concerns about opening data before publication.

Materials and strategies that work in low literacy health communication.

PubMed Central

Plimpton, S; Root, J

1994-01-01

In a Maine Area Health Education Center program some solutions were developed to the well-documented problem of health information material that cannot be read or comprehended by low literacy adults. Professionals in health education and adult education were trained to produce easy-to-read health materials and created dozens of low-cost pamphlets on the nation's year 2000 health objectives. The pamphlets are easily reproducible on a copy machine. Concurrently, a model for teaching oral communication skills to health care providers who deal with low-literacy adults was developed in partnership with Maine's largest rural health center delivery system. The train-the-trainers model reached more than 500 direct health care service providers. Participants in the two programs gained skills useful in all aspects of public communication that are replicable in other cities, States, and regions. PMID:8303020

Development of a Simple Tool for Identifying Alcohol Use Disorder in Female Korean Drinkers from Previous Questionnaires.

PubMed

Seo, Yu Ri; Kim, Jong Sung; Kim, Sung Soo; Yoon, Seok Joon; Suh, Won Yoon; Youn, Kwangmi

2016-01-01

This study aimed to develop a simple tool for identifying alcohol use disorders in female Korean drinkers from previous questionnaires. This research was conducted on 400 women who consumed at least one alcoholic drink during the past month and visited the health promotion center at Chungnam National University Hospital between June 2013 to May 2014. Drinking habits and alcohol use disorders were assessed by structured interviews using the Diagnostic and Statistical Manual of Mental Disorders, 5th Edition diagnostic criteria. The subjects were also asked to answer the Alcohol Use Disorders Identification Test (AUDIT), AUDIT-Consumption, CAGE (Cut down, Annoyed, Guilty, Eye-opener), TWEAK (Tolerance, Worried, Eye-opener, Amnesia, Kut down), TACE (Tolerance, Annoyed, Cut down, Eye-opener), and NET (Normal drinker, Eye-opener, Tolerance) questionnaires. The area under receiver operating characteristic (AUROC) of each question of the questionnaires on alcohol use disorders was assessed. After combining two questions with the largest AUROC, it was compared to other previous questionnaires. Among the 400 subjects, 58 (14.5%) were identified as having an alcohol use disorder. Two questions with the largest AUROC were question no. 7 in AUDIT, "How often during the last year have you had a feeling of guilt or remorse after drinking?" and question no. 5 in AUDIT, "How often during the past year have you failed to do what was normally expected from you because of drinking?" with an AUROC (95% confidence interval [CI]) of 0.886 (0.850-0.915) and 0.862 (0.824-0.894), respectively. The AUROC (95% CI) of the combination of the two questions was 0.958 (0.934-0.976) with no significant difference as compared to the existing AUDIT with the largest AUROC. The above results suggest that the simple tool consisting of questions no. 5 and no. 7 in AUDIT is useful in identifying alcohol use disorders in Korean female drinkers.

Brief report: Multiprogram evaluation of reading habits of primary care internal medicine residents on ambulatory rotations.

PubMed

Lai, Cindy J; Aagaard, Eva; Brandenburg, Suzanne; Nadkarni, Mohan; Wei, Henry G; Baron, Robert

2006-05-01

To assess the reading habits and educational resources of primary care internal medicine residents for their ambulatory medicine education. Cross-sectional, multiprogram survey of primary care internal medicine residents. Second- and third-year residents on ambulatory care rotations at 9 primary care medicine programs (124 eligible residents; 71% response rate). Participants were asked open-ended and 5-point Likert-scaled questions about reading habits: time spent reading, preferred resources, and motivating and inhibiting factors. Participants reported reading medical topics for a mean of 4.3+/-3.0 SD hours weekly. Online-only sources were the most frequently utilized medical resource (mean Likert response 4.16+/-0.87). Respondents most commonly cited specific patients' cases (4.38+/-0.65) and preparation for talks (4.08+/-0.89) as motivating factors, and family responsibilities (3.99+/-0.65) and lack of motivation (3.93+/-0.81) as inhibiting factors. To stimulate residents' reading, residency programs should encourage patient- and case-based learning; require teaching assignments; and provide easy access to online curricula.

Opening a Window into Reading Development: Eye Movements’ Role Within a Broader Literacy Research Framework

PubMed Central

Miller, Brett; O’Donnell, Carol

2013-01-01

The cumulative body of eye movement research provides significant 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 the potential to more concertedly study reading and literacy from an individual differences perspective. Historically, eye movement research focused far less on developmental issues related to individual differences in reading; however, this issue and the broader change it represents signal a meaningful transition inclusive of individual differences. The six papers in this special issue signify the recent, increased attention to and recognition of eye movement research’s transition to emphasize individual differences in reading while appreciating early contributions (e.g., Rayner, 1986) in this direction. We introduce these six papers and provide some historical context for the use of eye movement methodology to examine reading and context for the eye movement field’s early transition to examining individual differences, culminating in future research recommendations. PMID:24391304

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

PubMed

Miller, Brett; O'Donnell, Carol

2013-01-01

The cumulative body of eye movement research provides significant 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 the potential to more concertedly study reading and literacy from an individual differences perspective. Historically, eye movement research focused far less on developmental issues related to individual differences in reading; however, this issue and the broader change it represents signal a meaningful transition inclusive of individual differences. The six papers in this special issue signify the recent, increased attention to and recognition of eye movement research's transition to emphasize individual differences in reading while appreciating early contributions (e.g., Rayner, 1986) in this direction. We introduce these six papers and provide some historical context for the use of eye movement methodology to examine reading and context for the eye movement field's early transition to examining individual differences, culminating in future research recommendations.

Open College Textbook Act of 2009

THOMAS, 111th Congress

Sen. Durbin, Richard J. [D-IL

2009-09-24

Senate - 09/24/2009 Read twice and referred to the Committee on Health, Education, Labor, and Pensions. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

Localization of the lysine epsilon-aminotransferase (lat) and delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine synthetase (pcbAB) genes from Streptomyces clavuligerus and production of lysine epsilon-aminotransferase activity in Escherichia coli.

PubMed Central

Tobin, M B; Kovacevic, S; Madduri, K; Hoskins, J A; Skatrud, P L; Vining, L C; Stuttard, C; Miller, J R

1991-01-01

Lysine epsilon-aminotransferase (LAT) in the beta-lactam-producing actinomycetes is considered to be the first step in the antibiotic biosynthetic pathway. Cloning of restriction fragments from Streptomyces clavuligerus, a beta-lactam producer, into Streptomyces lividans, a nonproducer that lacks LAT activity, led to the production of LAT in the host. DNA sequencing of restriction fragments containing the putative lat gene revealed a single open reading frame encoding a polypeptide with an approximately Mr 49,000. Expression of this coding sequence in Escherichia coli led to the production of LAT activity. Hence, LAT activity in S. clavuligerus is derived from a single polypeptide. A second open reading frame began immediately downstream from lat. Comparison of this partial sequence with the sequences of delta-(L-alpha-aminoadipyl)-L-cysteinyl-D valine (ACV) synthetases from Penicillium chrysogenum and Cephalosporium acremonium and with nonribosomal peptide synthetases (gramicidin S and tyrocidine synthetases) found similarities among the open reading frames. Since mapping of the putative N and C termini of S. clavuligerus pcbAB suggests that the coding region occupies approximately 12 kbp and codes for a polypeptide related in size to the fungal ACV synthetases, the molecular characterization of the beta-lactam biosynthetic cluster between pcbC and cefE (approximately 25 kbp) is nearly complete. Images PMID:1917855

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

PubMed Central

Hall, R L; Moyer, R W

1991-01-01

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

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.

Convergence Insufficiency Symptom Survey Scores for Reading Versus Other Near Visual Activities in School-Age Children.

PubMed

Clark, Tiana Y; Clark, Robert A

2015-11-01

To measure the difference in Convergence Insufficiency Symptom Survey scores for reading vs favorite near visual activities. Comparative validity analysis of diagnostic tools. At a single clinical private practice, 100 children aged 9-18 with normal binocular vision were recruited to receive either the original survey emphasizing reading or a modified survey replacing "reading" with their favorite near activity. Average survey scores and subscores for questions emphasizing fatigue, discomfort, impaired vision, and cognitive performance were compared using t tests, while responses to individual questions were compared using Mann-Whitney U tests. The average reading survey score was significantly greater than the favorite near activity survey score (14.1 ± 11.5 vs 6.7 ± 5.8, P = .0001). The largest difference resulted from questions emphasizing cognitive performance (subscore 5.8 ± 4.3 vs 2.0 ± 2.1, P = .0000002), although significant differences were also found for fatigue (5.4 ± 3.8 vs 3.0 ± 2.7, P = .0003), discomfort (3.9 ± 4.6 vs 1.8 ± 2.2, P = .004), and impaired vision (3.2 ± 3.9 vs 1.8 ± 2.2, P = .02). Significant differences were found for 7 survey questions, with higher symptom scores for the reading survey in every case. Using survey scores ≥16 to diagnose convergence insufficiency, significantly more children taking the reading survey would have been diagnosed with convergence insufficiency than children taking the favorite near activity survey (19 of 50 [38%] vs 5 of 50 [10%], P = .001). By emphasizing reading, the Convergence Insufficiency Symptom Survey score significantly overestimates near visual symptoms in children with normal binocular vision compared with symptoms caused by preferred near activities that require similar amplitudes of accommodation and convergence. Copyright © 2015 Elsevier Inc. All rights reserved.

The Impact of the New US-Canada Aviation Agreement At Its Second Anniversary

DOT National Transportation Integrated Search

1997-04-01

The U.S.- Canada market is the world's largest bilateral passenger market. This : series of graphs and maps highlights the changes brought about since the "open : trans-border" agreement was signed in February 1995. 9p.

Oblique rift opening revealed by reoccurring magma injection in central Iceland.

PubMed

Ruch, Joël; Wang, Teng; Xu, Wenbin; Hensch, Martin; Jónsson, Sigurjón

2016-08-05

Extension deficit builds up over centuries at divergent plate boundaries and is recurrently removed during rifting events, accompanied by magma intrusions and transient metre-scale deformation. However, information on transient near-field deformation has rarely been captured, hindering progress in understanding rifting mechanisms and evolution. Here we show new evidence of oblique rift opening during a rifting event influenced by pre-existing fractures and two centuries of extension deficit accumulation. This event originated from the Bárðarbunga caldera and led to the largest basaltic eruption in Iceland in >200 years. The results show that the opening was initially accompanied by left-lateral shear that ceased with increasing opening. Our results imply that pre-existing fractures play a key role in controlling oblique rift opening at divergent plate boundaries.

Validation of the openEHR archetype library by using OWL reasoning.

PubMed

Menárguez-Tortosa, Marcos; Fernández-Breis, Jesualdo Tomás

2011-01-01

Electronic Health Record architectures based on the dual model architecture use archetypes for representing clinical knowledge. Therefore, ensuring their correctness and consistency is a fundamental research goal. In this work, we explore how an approach based on OWL technologies can be used for such purpose. This method has been applied to the openEHR archetype repository, which is the largest available one nowadays. The results of this validation are also reported in this study.

SCIFIO: an extensible framework to support scientific image formats.

PubMed

Hiner, Mark C; Rueden, Curtis T; Eliceiri, Kevin W

2016-12-07

No gold standard exists in the world of scientific image acquisition; a proliferation of instruments each with its own proprietary data format has made out-of-the-box sharing of that data nearly impossible. In the field of light microscopy, the Bio-Formats library was designed to translate such proprietary data formats to a common, open-source schema, enabling sharing and reproduction of scientific results. While Bio-Formats has proved successful for microscopy images, the greater scientific community was lacking a domain-independent framework for format translation. SCIFIO (SCientific Image Format Input and Output) is presented as a freely available, open-source library unifying the mechanisms of reading and writing image data. The core of SCIFIO is its modular definition of formats, the design of which clearly outlines the components of image I/O to encourage extensibility, facilitated by the dynamic discovery of the SciJava plugin framework. SCIFIO is structured to support coexistence of multiple domain-specific open exchange formats, such as Bio-Formats' OME-TIFF, within a unified environment. SCIFIO is a freely available software library developed to standardize the process of reading and writing scientific image formats.

An upstream open reading frame represses expression of Lc, a member of the R/B family of maize transcriptional activators

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

Damiani, R.D. Jr.; Wessler, S.R.

1993-09-01

The R/B genes of maize encode a family of basic helix-loop-helix proteins that determine where and when the anthocyanin-pigment pathway will be expressed in the plant. Previous studies showed that allelic diversity among family members reflects differences in gene expression, specifically in transcription initiation. The authors present evidence that the R gene Lc is under translational control. They demonstrate that the 235-nt transcript leader of Lc represses expression 25- to 30-fold in an in vivo assay. Repression is mediated by the presence in cis of a 38-codon upstream open reading frame. Furthermore, the coding capacity of the upstream open readingmore » frame influences the magnitude of repression. It is proposed that translational control does not contribute to tissue specificity but prevents overexpression of the Lc protein. The diversity of promoter and 5' untranslated leader sequences among the R/B genes provides an opportunity to study the coevolution of transcriptional and translational mechanisms of gene regulation. 36 refs., 5 figs.« less

The OSG Open Facility: an on-ramp for opportunistic scientific computing

NASA Astrophysics Data System (ADS)

Jayatilaka, B.; Levshina, T.; Sehgal, C.; Gardner, R.; Rynge, M.; Würthwein, F.

2017-10-01

The Open Science Grid (OSG) is a large, robust computing grid that started primarily as a collection of sites associated with large HEP experiments such as ATLAS, CDF, CMS, and DZero, but has evolved in recent years to a much larger user and resource platform. In addition to meeting the US LHC community’s computational needs, the OSG continues to be one of the largest providers of distributed high-throughput computing (DHTC) to researchers from a wide variety of disciplines via the OSG Open Facility. The Open Facility consists of OSG resources that are available opportunistically to users other than resource owners and their collaborators. In the past two years, the Open Facility has doubled its annual throughput to over 200 million wall hours. More than half of these resources are used by over 100 individual researchers from over 60 institutions in fields such as biology, medicine, math, economics, and many others. Over 10% of these individual users utilized in excess of 1 million computational hours each in the past year. The largest source of these cycles is temporary unused capacity at institutions affiliated with US LHC computational sites. An increasing fraction, however, comes from university HPC clusters and large national infrastructure supercomputers offering unused capacity. Such expansions have allowed the OSG to provide ample computational resources to both individual researchers and small groups as well as sizable international science collaborations such as LIGO, AMS, IceCube, and sPHENIX. Opening up access to the Fermilab FabrIc for Frontier Experiments (FIFE) project has also allowed experiments such as mu2e and NOvA to make substantial use of Open Facility resources, the former with over 40 million wall hours in a year. We present how this expansion was accomplished as well as future plans for keeping the OSG Open Facility at the forefront of enabling scientific research by way of DHTC.

The OSG Open Facility: An On-Ramp for Opportunistic Scientific Computing

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

Jayatilaka, B.; Levshina, T.; Sehgal, C.

The Open Science Grid (OSG) is a large, robust computing grid that started primarily as a collection of sites associated with large HEP experiments such as ATLAS, CDF, CMS, and DZero, but has evolved in recent years to a much larger user and resource platform. In addition to meeting the US LHC community’s computational needs, the OSG continues to be one of the largest providers of distributed high-throughput computing (DHTC) to researchers from a wide variety of disciplines via the OSG Open Facility. The Open Facility consists of OSG resources that are available opportunistically to users other than resource ownersmore » and their collaborators. In the past two years, the Open Facility has doubled its annual throughput to over 200 million wall hours. More than half of these resources are used by over 100 individual researchers from over 60 institutions in fields such as biology, medicine, math, economics, and many others. Over 10% of these individual users utilized in excess of 1 million computational hours each in the past year. The largest source of these cycles is temporary unused capacity at institutions affiliated with US LHC computational sites. An increasing fraction, however, comes from university HPC clusters and large national infrastructure supercomputers offering unused capacity. Such expansions have allowed the OSG to provide ample computational resources to both individual researchers and small groups as well as sizable international science collaborations such as LIGO, AMS, IceCube, and sPHENIX. Opening up access to the Fermilab FabrIc for Frontier Experiments (FIFE) project has also allowed experiments such as mu2e and NOvA to make substantial use of Open Facility resources, the former with over 40 million wall hours in a year. We present how this expansion was accomplished as well as future plans for keeping the OSG Open Facility at the forefront of enabling scientific research by way of DHTC.« less

CTIO Image of Carina Nebula

NASA Image and Video Library

2017-12-08

NASA image release April 22, 2010 Object Names: Carina Nebula, NGC 3372 Image Type: Astronomical Credit: NASA/N. Smith (University of California, Berkeley) and NOAO/AURA/NSF To read learn more about this image go to: www.nasa.gov/mission_pages/hubble/science/hubble20th-img.... NASA Goddard Space Flight Center is home to the nation's largest organization of combined scientists, engineers and technologists that build spacecraft, instruments and new technology to study the Earth, the sun, our solar system, and the universe.

Mysterious Roving Rocks of Racetrack Playa

NASA Image and Video Library

2017-12-08

In some cases, the trail starts narrow and gets wider, as in this photo. Photo credit: NASA/GSFC/Leva McIntire/LPSA intern To read a feature story on the Racetrack Playa go to: www.nasa.gov/topics/earth/features/roving-rocks.html NASA Goddard Space Flight Center is home to the nation's largest organization of combined scientists, engineers and technologists that build spacecraft, instruments and new technology to study the Earth, the sun, our solar system, and the universe. Follow us on Twitter Join us on Facebook

Mysterious Roving Rocks of Racetrack Playa

NASA Image and Video Library

2017-12-08

The rocks at Racetrack Playa in Death Valley, Calif., are famous. Photo credit: NASA/GSFC/Maggie McAdam To read a feature story on the Racetrack Playa go to: www.nasa.gov/topics/earth/features/roving-rocks.html NASA Goddard Space Flight Center is home to the nation's largest organization of combined scientists, engineers and technologists that build spacecraft, instruments and new technology to study the Earth, the sun, our solar system, and the universe. Follow us on Twitter Join us on Facebook

High-Resolution Analysis of Coronavirus Gene Expression by RNA Sequencing and Ribosome Profiling

PubMed Central

Jones, Joshua D.; Chung, Betty Y.-W.; Siddell, Stuart G.; Brierley, Ian

2016-01-01

Members of the family Coronaviridae have the largest genomes of all RNA viruses, typically in the region of 30 kilobases. Several coronaviruses, such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV) and Middle East respiratory syndrome-related coronavirus (MERS-CoV), are of medical importance, with high mortality rates and, in the case of SARS-CoV, significant pandemic potential. Other coronaviruses, such as Porcine epidemic diarrhea virus and Avian coronavirus, are important livestock pathogens. Ribosome profiling is a technique which exploits the capacity of the translating ribosome to protect around 30 nucleotides of mRNA from ribonuclease digestion. Ribosome-protected mRNA fragments are purified, subjected to deep sequencing and mapped back to the transcriptome to give a global “snap-shot” of translation. Parallel RNA sequencing allows normalization by transcript abundance. Here we apply ribosome profiling to cells infected with Murine coronavirus, mouse hepatitis virus, strain A59 (MHV-A59), a model coronavirus in the same genus as SARS-CoV and MERS-CoV. The data obtained allowed us to study the kinetics of virus transcription and translation with exquisite precision. We studied the timecourse of positive and negative-sense genomic and subgenomic viral RNA production and the relative translation efficiencies of the different virus ORFs. Virus mRNAs were not found to be translated more efficiently than host mRNAs; rather, virus translation dominates host translation at later time points due to high levels of virus transcripts. Triplet phasing of the profiling data allowed precise determination of translated reading frames and revealed several translated short open reading frames upstream of, or embedded within, known virus protein-coding regions. Ribosome pause sites were identified in the virus replicase polyprotein pp1a ORF and investigated experimentally. Contrary to expectations, ribosomes were not found to pause at the ribosomal frameshift site. To our knowledge this is the first application of ribosome profiling to an RNA virus. PMID:26919232

An Adaptive Resonance Theory account of the implicit learning of orthographic word forms.

PubMed

Glotin, H; Warnier, P; Dandurand, F; Dufau, S; Lété, B; Touzet, C; Ziegler, J C; Grainger, J

2010-01-01

An Adaptive Resonance Theory (ART) network was trained to identify unique orthographic word forms. Each word input to the model was represented as an unordered set of ordered letter pairs (open bigrams) that implement a flexible prelexical orthographic code. The network learned to map this prelexical orthographic code onto unique word representations (orthographic word forms). The network was trained on a realistic corpus of reading textbooks used in French primary schools. The amount of training was strictly identical to children's exposure to reading material from grade 1 to grade 5. Network performance was examined at each grade level. Adjustment of the learning and vigilance parameters of the network allowed us to reproduce the developmental growth of word identification performance seen in children. The network exhibited a word frequency effect and was found to be sensitive to the order of presentation of word inputs, particularly with low frequency words. These words were better learned with a randomized presentation order compared with the order of presentation in the school books. These results open up interesting perspectives for the application of ART networks in the study of the dynamics of learning to read. 2009 Elsevier Ltd. All rights reserved.

Readability of Distance Education Course Material.

ERIC Educational Resources Information Center

Mouli, C. Raja; Ramakrishna, C. Pushpa

1991-01-01

Flesch Reading Ease scores were calculated for 48 books used in distance education courses at Andhra Pradesh Open University (India). Scores ranged from 32 (public administration) to 46 (geology). Scores correlated positively with pass percentages. (SK)

Temporal distribution of favourite books, movies, and records: differential encoding and re-sampling.

PubMed

Janssen, Steve M J; Chessa, Antonio G; Murre, Jaap M J

2007-10-01

The reminiscence bump is the effect that people recall more personal events from early adulthood than from childhood or adulthood. The bump has been examined extensively. However, the question of whether the bump is caused by differential encoding or re-sampling is still unanswered. To examine this issue, participants were asked to name their three favourite books, movies, and records. Furthermore,they were asked when they first encountered them. We compared the temporal distributions and found that they all showed recency effects and reminiscence bumps. The distribution of favourite books had the largest recency effect and the distribution of favourite records had the largest reminiscence bump. We can explain these results by the difference in rehearsal. Books are read two or three times, movies are watched more frequently, whereas records are listened to numerous times. The results suggest that differential encoding initially causes the reminiscence bump and that re-sampling increases the bump further.

Tonic accommodation predicts closed-loop accommodation responses.

PubMed

Liu, Chunming; Drew, Stefanie A; Borsting, Eric; Escobar, Amy; Stark, Lawrence; Chase, Christopher

2016-12-01

The purpose of this study is to examine the potential relationship between tonic accommodation (TA), near work induced TA-adaptation and the steady state closed-loop accommodation response (AR). Forty-two graduate students participated in the study. Various aspects of their accommodation system were objectively measured using an open-field infrared auto-refractor (Grand Seiko WAM-5500). Tonic accommodation was assessed in a completely dark environment. The association between TA and closed-loop AR was assessed using linear regression correlations and t-test comparisons. Initial mean baseline TA was 1.84diopter (D) (SD±1.29D) with a wide distribution range (-0.43D to 5.14D). For monocular visual tasks, baseline TA was significantly correlated with the closed-loop AR. The slope of the best fit line indicated that closed-loop AR varied by approximately 0.3D for every 1D change in TA. This ratio was consistent across a variety of viewing distances and different near work tasks, including both static targets and continuous reading. Binocular reading conditions weakened the correlation between baseline TA and AR, although results remained statistically significant. The 10min near reading task with a 3D demand did not reveal significant near work induced TA-adaptation for either monocular or binocular conditions. Consistently, the TA-adaptation did not show any correlation with AR during reading. This study found a strong association between open-loop TA and closed-loop AR across a variety of viewing distances and different near work tasks. Difference between the correlations under monocular and binocular reading condition suggests a potential role for vergence compensation during binocular closed-loop AR. Copyright © 2016 Elsevier Ltd. All rights reserved.

TagDigger: user-friendly extraction of read counts from GBS and RAD-seq data.

PubMed

Clark, Lindsay V; Sacks, Erik J

2016-01-01

In genotyping-by-sequencing (GBS) and restriction site-associated DNA sequencing (RAD-seq), read depth is important for assessing the quality of genotype calls and estimating allele dosage in polyploids. However, existing pipelines for GBS and RAD-seq do not provide read counts in formats that are both accurate and easy to access. Additionally, although existing pipelines allow previously-mined SNPs to be genotyped on new samples, they do not allow the user to manually specify a subset of loci to examine. Pipelines that do not use a reference genome assign arbitrary names to SNPs, making meta-analysis across projects difficult. We created the software TagDigger, which includes three programs for analyzing GBS and RAD-seq data. The first script, tagdigger_interactive.py, rapidly extracts read counts and genotypes from FASTQ files using user-supplied sets of barcodes and tags. Input and output is in CSV format so that it can be opened by spreadsheet software. Tag sequences can also be imported from the Stacks, TASSEL-GBSv2, TASSEL-UNEAK, or pyRAD pipelines, and a separate file can be imported listing the names of markers to retain. A second script, tag_manager.py, consolidates marker names and sequences across multiple projects. A third script, barcode_splitter.py, assists with preparing FASTQ data for deposit in a public archive by splitting FASTQ files by barcode and generating MD5 checksums for the resulting files. TagDigger is open-source and freely available software written in Python 3. It uses a scalable, rapid search algorithm that can process over 100 million FASTQ reads per hour. TagDigger will run on a laptop with any operating system, does not consume hard drive space with intermediate files, and does not require programming skill to use.

Differences in Optical Coherence Tomography Assessment of Bruch Membrane Opening Compared to Stereoscopic Photography for Estimating Cup-to-Disc Ratio.

PubMed

Mwanza, Jean-Claude; Huang, Linda Y; Budenz, Donald L; Shi, Wei; Huang, Gintien; Lee, Richard K

2017-12-01

To compare the vertical and horizontal cup-to-disc ratio (VCDR, HCDR) by an updated optical coherence tomography (OCT) Bruch membrane opening (BMO) algorithm and stereoscopic optic disc photograph readings by glaucoma specialists. Reliability analysis. A total of 195 eyes (116 glaucoma and 79 glaucoma suspect) of 99 patients with stereoscopic photographs and OCT scans of the optic discs taken during the same visit were compared. Optic disc photographs were read by 2 masked glaucoma specialists for VCDR and HCDR estimation. Intraclass correlation coefficient (ICC) and Bland-Altman plots were used to assess the agreement between photograph reading and OCT in estimating CDR. OCT images computed significantly larger VCDR and HCDR than photograph reading before and after stratifying eyes based on disc size (P < .001). The difference in CDR estimates between the 2 methods was equal to or greater than 0.2 in 29% and 35% of the eyes for VCDR and HCDR, respectively, with a mean difference of 0.3 in each case. The ICCs between the readers and OCT ranged between 0.50 and 0.63. The size of disagreement in VCDR correlated weakly with cup area in eyes with medium (r 2  = 0.10, P = .008) and large (r 2  = 0.09, P = .007) discs. OCT and photograph reading by clinicians agree poorly in CDR assessment. The difference in VCDR between the 2 methods was depended on cup area in medium and large discs. These differences should be considered when making conclusions regarding CDRs in clinical practice. Copyright © 2017 Elsevier Inc. All rights reserved.

Draft sequencing and assembly of the genome of the world's largest fish, the whale shark: Rhincodon typus Smith 1828.

PubMed

Read, Timothy D; Petit, Robert A; Joseph, Sandeep J; Alam, Md Tauqeer; Weil, M Ryan; Ahmad, Maida; Bhimani, Ravila; Vuong, Jocelyn S; Haase, Chad P; Webb, D Harry; Tan, Milton; Dove, Alistair D M

2017-07-14

The whale shark (Rhincodon typus) has by far the largest body size of any elasmobranch (shark or ray) species. Therefore, it is also the largest extant species of the paraphyletic assemblage commonly referred to as fishes. As both a phenotypic extreme and a member of the group Chondrichthyes - the sister group to the remaining gnathostomes, which includes all tetrapods and therefore also humans - its genome is of substantial comparative interest. Whale sharks are also listed as an endangered species on the International Union for Conservation of Nature's Red List of threatened species and are of growing popularity as both a target of ecotourism and as a charismatic conservation ambassador for the pelagic ecosystem. A genome map for this species would aid in defining effective conservation units and understanding global population structure. We characterised the nuclear genome of the whale shark using next generation sequencing (454, Illumina) and de novo assembly and annotation methods, based on material collected from the Georgia Aquarium. The data set consisted of 878,654,233 reads, which yielded a draft assembly of 1,213,200 contigs and 997,976 scaffolds. The estimated genome size was 3.44Gb. As expected, the proteome of the whale shark was most closely related to the only other complete genome of a cartilaginous fish, the holocephalan elephant shark. The whale shark contained a novel Toll-like-receptor (TLR) protein with sequence similarity to both the TLR4 and TLR13 proteins of mammals and TLR21 of teleosts. The data are publicly available on GenBank, FigShare, and from the NCBI Short Read Archive under accession number SRP044374. This represents the first shotgun elasmobranch genome and will aid studies of molecular systematics, biogeography, genetic differentiation, and conservation genetics in this and other shark species, as well as providing comparative data for studies of evolutionary biology and immunology across the jawed vertebrate lineages.

Comparison of routine and unprepped CT colonography augmented by low fiber diet and stool tagging: a pilot study.

PubMed

Dachman, Abraham H; Dawson, Damien O; Lefere, Philippe; Yoshida, Hiro; Khan, Nasreen U; Cipriani, Nicole; Rubin, David T

2007-01-01

We performed a pilot study examining the feasibility of a new unprepped CT colonography (CTC) strategy: low fiber diet and tagging (unprepped) vs. low fiber diet, tagging and a magnesium citrate cleansing preparation (prepped). Prior reports of tagging were limited in that the residual stool was neither measured and stratified by size nor did prior reports subjectively evaluate the ease of interpretation by a reader experienced in interpreting CTC examinations. Prospective randomized to unprepped n = 14 and prepped n = 14. Colonic segments were subjectively evaluated for residual stool that would potentially interfere with interpretation. Scores were given in the following categories: percentage of residual stool that was touching or nearly touching mucosa, the largest piece of retained stool, effectiveness of tagging, height of residual fluid, degree of distention, ease of interpretation, and reading time. Ease of the CT read (scale where 4 = optimal read) averaged 1.3 for the unprepped group and 2.3 for the prepped group. The mean read time averaged 17.5 min for unprepped and 17.9 min for prepped. The degree of distention (scale where 4 = well distended) averaged 3.7 for unprepped and 3.6 for prepped. Supine and prone images combined, the unprepped group had 160 segments with stool; prepped group had 58 segments. The amount of stool covering the mucosa in all segments averaged 1.6 (33%-66% coverage) in the unprepped group and 0.35 (<33% mucosal coverage) in the prepped group. The mean size of the largest piece of stool was 33.67 mm for unprepped and 4.01 mm for prepped. Percentage of tagged stool was not significantly different between the groups (range of 94-98%). The height of residual fluid averaged 8.37 mm for unprepped and 13.4 mm for prepped. Three polyps in three patients were found during optical colonoscopy (OC) in the unprepped group (5, 6, and 10 mm), none of which were prospectively detected at CTC. Three polyps in three patients were detected during OC in the prepped group (5, 10, and 15 mm), two of which were prospectively detected at CTC. Two false-positive lesions were observed at CTC in one patient in the prepped group. There was more stool in the unprepped group and while this factor did not slow down the reading time, it made the examination subjectively harder to interpret and likely caused the three polyps in this group to be missed. We conclude that a truly unprepped strategy that leaves significant residual stool, even if well tagged, is not desirable.

A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome.

PubMed

Allali, Imane; Arnold, Jason W; Roach, Jeffrey; Cadenas, Maria Belen; Butz, Natasha; Hassan, Hosni M; Koci, Matthew; Ballou, Anne; Mendoza, Mary; Ali, Rizwana; Azcarate-Peril, M Andrea

2017-09-13

Advancements in Next Generation Sequencing (NGS) technologies regarding throughput, read length and accuracy had a major impact on microbiome research by significantly improving 16S rRNA amplicon sequencing. As rapid improvements in sequencing platforms and new data analysis pipelines are introduced, it is essential to evaluate their capabilities in specific applications. The aim of this study was to assess whether the same project-specific biological conclusions regarding microbiome composition could be reached using different sequencing platforms and bioinformatics pipelines. Chicken cecum microbiome was analyzed by 16S rRNA amplicon sequencing using Illumina MiSeq, Ion Torrent PGM, and Roche 454 GS FLX Titanium platforms, with standard and modified protocols for library preparation. We labeled the bioinformatics pipelines included in our analysis QIIME1 and QIIME2 (de novo OTU picking [not to be confused with QIIME version 2 commonly referred to as QIIME2]), QIIME3 and QIIME4 (open reference OTU picking), UPARSE1 and UPARSE2 (each pair differs only in the use of chimera depletion methods), and DADA2 (for Illumina data only). GS FLX+ yielded the longest reads and highest quality scores, while MiSeq generated the largest number of reads after quality filtering. Declines in quality scores were observed starting at bases 150-199 for GS FLX+ and bases 90-99 for MiSeq. Scores were stable for PGM-generated data. Overall microbiome compositional profiles were comparable between platforms; however, average relative abundance of specific taxa varied depending on sequencing platform, library preparation method, and bioinformatics analysis. Specifically, QIIME with de novo OTU picking yielded the highest number of unique species and alpha diversity was reduced with UPARSE and DADA2 compared to QIIME. The three platforms compared in this study were capable of discriminating samples by treatment, despite differences in diversity and abundance, leading to similar biological conclusions. Our results demonstrate that while there were differences in depth of coverage and phylogenetic diversity, all workflows revealed comparable treatment effects on microbial diversity. To increase reproducibility and reliability and to retain consistency between similar studies, it is important to consider the impact on data quality and relative abundance of taxa when selecting NGS platforms and analysis tools for microbiome studies.

Chiquicamata Mine, Chile

NASA Image and Video Library

2016-08-24

Chuquicamata, in Chile's Atacama Desert, is the largest open pit copper mine in the world, by excavated volume. The copper deposits were first exploited in pre-Hispanic times. Open pit mining began in the early 20th century when a method was developed to work low grade oxidized copper ores. The image was acquired September 2, 2007, covers an area of 19.5 by 29.3 km, and is located at 22.1 degrees south, 68.9 degrees west. http://photojournal.jpl.nasa.gov/catalog/PIA20973

Frameshifting in the p6 cDNA phage display system.

PubMed

Govarts, Cindy; Somers, Klaartje; Stinissen, Piet; Somers, Veerle

2010-12-20

Phage display is a powerful technique that enables easy identification of targets for any type of ligand. Targets are displayed at the phage surface as a fusion protein to one of the phage coat proteins. By means of a repeated process of affinity selection on a ligand, specific enrichment of displayed targets will occur. In our studies using C-terminal display of cDNA fragments to phage coat protein p6, we noticed the occasional enrichment of targets that do not contain an open reading frame. This event has previously been described in other phage display studies using N-terminal display of targets to phage coat proteins and was due to uncommon translational events like frameshifting. The aim of this study was to examine if C-terminal display of targets to p6 is also subjected to frameshifting. To this end, an enriched target not containing an open reading frame was selected and an E-tag was coupled at the C-terminus in order to measure target display at the surface of the phage. The tagged construct was subsequently expressed in 3 different reading frames and display of both target and E-tag measured to detect the occurrence of frameshifting. As a result, we were able to demonstrate display of the target both in the 0 and in the +1 reading frame indicating that frameshifting can also take place when C-terminal fusion to minor coat protein p6 is applied.

A Wind Tunnel Study on the Mars Pathfinder (MPF) Lander Descent Pressure Sensor

NASA Technical Reports Server (NTRS)

Soriano, J. Francisco; Coquilla, Rachael V.; Wilson, Gregory R.; Seiff, Alvin; Rivell, Tomas

2001-01-01

The primary focus of this study was to determine the accuracy of the Mars Pathfinder lander local pressure readings in accordance with the actual ambient atmospheric pressures of Mars during parachute descent. In order to obtain good measurements, the plane of the lander pressure sensor opening should ideally be situated so that it is parallel to the freestream. However, due to two unfavorable conditions, the sensor was positioned in locations where correction factors are required. One of these disadvantages is due to the fact that the parachute attachment point rotated the lander's center of gravity forcing the location of the pressure sensor opening to be off tangent to the freestream. The second and most troublesome factor was that the lander descends with slight oscillations that could vary the amplitude of the sensor readings. In order to accurately map the correction factors required at each sensor position, an experiment simulating the lander descent was conducted in the Martian Surface Wind Tunnel at NASA Ames Research Center. Using a 115 scale model at Earth ambient pressures, the test settings provided the necessary Reynolds number conditions in which the actual lander was possibly subjected to during the descent. In the analysis and results of this experiment, the readings from the lander sensor were converted to the form of pressure coefficients. With a contour map of pressure coefficients at each lander oscillatory position, this report will provide a guideline to determine the correction factors required for the Mars Pathfinder lander descent pressure sensor readings.

MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping.

PubMed

Lee, Wan-Ping; Stromberg, Michael P; Ward, Alistair; Stewart, Chip; Garrison, Erik P; Marth, Gabor T

2014-01-01

MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT. Indeed, MOSAIK was the only aligner to provide consistent mappings for all the generated data (sequencing technologies, low-coverage and exome) in the 1000 Genomes Project. To provide highly accurate alignments, MOSAIK employs a hash clustering strategy coupled with the Smith-Waterman algorithm. This method is well-suited to capture mismatches as well as short insertions and deletions. To support the growing interest in larger structural variant (SV) discovery, MOSAIK provides explicit support for handling known-sequence SVs, e.g. mobile element insertions (MEIs) as well as generating outputs tailored to aid in SV discovery. All variant discovery benefits from an accurate description of the read placement confidence. To this end, MOSAIK uses a neural-network based training scheme to provide well-calibrated mapping quality scores, demonstrated by a correlation coefficient between MOSAIK assigned and actual mapping qualities greater than 0.98. In order to ensure that studies of any genome are supported, a training pipeline is provided to ensure optimal mapping quality scores for the genome under investigation. MOSAIK is multi-threaded, open source, and incorporated into our command and pipeline launcher system GKNO (http://gkno.me).

MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping

PubMed Central

Lee, Wan-Ping; Stromberg, Michael P.; Ward, Alistair; Stewart, Chip; Garrison, Erik P.; Marth, Gabor T.

2014-01-01

MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT. Indeed, MOSAIK was the only aligner to provide consistent mappings for all the generated data (sequencing technologies, low-coverage and exome) in the 1000 Genomes Project. To provide highly accurate alignments, MOSAIK employs a hash clustering strategy coupled with the Smith-Waterman algorithm. This method is well-suited to capture mismatches as well as short insertions and deletions. To support the growing interest in larger structural variant (SV) discovery, MOSAIK provides explicit support for handling known-sequence SVs, e.g. mobile element insertions (MEIs) as well as generating outputs tailored to aid in SV discovery. All variant discovery benefits from an accurate description of the read placement confidence. To this end, MOSAIK uses a neural-network based training scheme to provide well-calibrated mapping quality scores, demonstrated by a correlation coefficient between MOSAIK assigned and actual mapping qualities greater than 0.98. In order to ensure that studies of any genome are supported, a training pipeline is provided to ensure optimal mapping quality scores for the genome under investigation. MOSAIK is multi-threaded, open source, and incorporated into our command and pipeline launcher system GKNO (http://gkno.me). PMID:24599324

5 CFR 2502.4 - Public reference facilities and current index.

Code of Federal Regulations, 2011 CFR

2011-01-01

... public reading area located in the Executive Office of the President Library, Room G-102, New Executive... of records requested. (c) The FOIA Officer shall also maintain a file open to the public, which shall...

5 CFR 2502.4 - Public reference facilities and current index.

Code of Federal Regulations, 2010 CFR

2010-01-01

... public reading area located in the Executive Office of the President Library, Room G-102, New Executive... of records requested. (c) The FOIA Officer shall also maintain a file open to the public, which shall...

75 FR 40827 - Proposed Consent Decree, Clean Air Act Citizen Suit

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-14

... Foam Production (40 CFR part 63, subpart III); (22) Acrylic and Modacrylic Fibers Production (40 CFR..., 1301 Constitution Ave., NW., Washington, DC. The EPA Docket Center Public Reading Room is open from 8...

Open Book on Equal Access to Justice Act

THOMAS, 113th Congress

Rep. Lummis, Cynthia M. [R-WY-At Large

2013-08-01

Senate - 05/07/2014 Received in the Senate and Read twice and referred to the Committee on the Judiciary. (All Actions) Tracker: This bill has the status Passed HouseHere are the steps for Status of Legislation:

Compare Gene Calls

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

Ecale Zhou, Carol L.

2016-07-05

Compare Gene Calls (CGC) is a Python code used for combining and comparing gene calls from any number of gene callers. A gene caller is a computer program that predicts the extends of open reading frames within genomes of biological organisms.

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

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

Vieira, P.; De Waal-Malefyt, R.; Dang, M.N.

1991-02-15

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

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.

Identification of the psaA Gene, Coding for Pneumococcal Surface Adhesin A, in Viridans Group Streptococci other than Streptococcus pneumoniae

PubMed Central

Jado, Isabel; Fenoll, Asunción; Casal, Julio; Pérez, Amalia

2001-01-01

The gene encoding the pneumococcal surface adhesin A (PsaA) protein has been identified in three different viridans group streptococcal species. Comparative studies of the psaA gene identified in different pneumococcal isolates by sequencing PCR products showed a high degree of conservation among these strains. PsaA is encoded by an open reading frame of 930 bp. The analysis of this fragment in Streptococcus mitis, Streptococcus oralis, and Streptococcus anginosus strains revealed a sequence identity of 95, 94, and 90%, respectively, to the corresponding open reading frame of the previously reported Streptococcus pneumoniae serotype 6B strain. Our results confirm that psaA is present and detectable in heterologous bacterial species. The possible implications of these results for the suitability and potential use of PsaA in the identification and diagnosis of pneumococcal diseases are discussed. PMID:11527799

Flow visualization methods for field test verification of CFD analysis of an open gloveport

DOE PAGES

Strons, Philip; Bailey, James L.

2017-01-01

Anemometer readings alone cannot provide a complete picture of air flow patterns at an open gloveport. Having a means to visualize air flow for field tests in general provides greater insight by indicating direction in addition to the magnitude of the air flow velocities in the region of interest. Furthermore, flow visualization is essential for Computational Fluid Dynamics (CFD) verification, where important modeling assumptions play a significant role in analyzing the chaotic nature of low-velocity air flow. A good example is shown Figure 1, where an unexpected vortex pattern occurred during a field test that could not have been measuredmore » relying only on anemometer readings. Here by, observing and measuring the patterns of the smoke flowing into the gloveport allowed the CFD model to be appropriately updated to match the actual flow velocities in both magnitude and direction.« less

DNA sequence analysis of a 10 624 bp fragment of the left arm of chromosome XV from Saccharomyces cerevisiae reveals a RNA binding protein, a mitochondrial protein, two ribosomal proteins and two new open reading frames.

PubMed

Lafuente, M J; Gamo, F J; Gancedo, C

1996-09-01

We have determined the sequence of a 10624 bp DNA segment located in the left arm of chromosome XV of Saccharomyces cerevisiae. The sequence contains eight open reading frames (ORFs) longer than 100 amino acids. Two of them do not present significant homology with sequences found in the databases. The product of ORF o0553 is identical to the protein encoded by the gene SMF1. Internal to it there is another ORF, o0555 that is apparently expressed. The proteins encoded by ORFs o0559 and o0565 are identical to ribosomal proteins S19.e and L18 respectively. ORF o0550 encodes a protein with an RNA binding signature including RNP motifs and stretches rich in asparagine, glutamine and arginine.

Analysis of the DNA sequence of a 15,500 bp fragment near the left telomere of chromosome XV from Saccharomyces cerevisiae reveals a putative sugar transporter, a carboxypeptidase homologue and two new open reading frames.

PubMed

Gamo, F J; Lafuente, M J; Casamayor, A; Ariño, J; Aldea, M; Casas, C; Herrero, E; Gancedo, C

1996-06-15

We report the sequence of a 15.5 kb DNA segment located near the left telomere of chromosome XV of Saccharomyces cerevisiae. The sequence contains nine open reading frames (ORFs) longer than 300 bp. Three of them are internal to other ones. One corresponds to the gene LGT3 that encodes a putative sugar transporter. Three adjacent ORFs were separated by two stop codons in frame. These ORFs presented homology with the gene CPS1 that encodes carboxypeptidase S. The stop codons were not found in the same sequence derived from another yeast strain. Two other ORFs without significant homology in databases were also found. One of them, O0420, is very rich in serine and threonine and presents a series of repeated or similar amino acid stretches along the sequence.

Determination of the complete genomic sequence and analysis of the gene products of the virus of Spring Viremia of Carp, a fish rhabdovirus.

PubMed

Hoffmann, Bernd; Schütze, Heike; Mettenleiter, Thomas C

2002-03-20

The complete genome of spring viremia of carp virus (SVCV) was cloned and the sequence of 11019 nucleotides was determined. It contains five open reading frames (ORF's) encoding for the nucleoprotein N; phosphoprotein P; matrix protein M; glycoprotein G; and the viral RNA dependent RNA polymerase L. Genes are organised in the order typical for rhabdoviruses: 3'-N-P-M-G-L-5'. The short leader and trailer regions of SVCV exhibit inverse complementarity and are similar to the respective 3' and 5' ends of the genome of vesicular stomatitis virus. To verify the predicted open reading frames proteins were expressed in bacteria and analysed with a polyclonal anti-SVCV serum. Furthermore, monospecific antisera against the distinct viral proteins were generated. Comparison of genome and protein confirm the assignment of SVCV to the genus Vesiculovirus.

Translation of the mRNA of the maize transcriptional activator Opaque-2 is inhibited by upstream open reading frames present in the leader sequence.

PubMed Central

Lohmer, S; Maddaloni, M; Motto, M; Salamini, F; Thompson, R D

1993-01-01

The protein encoded by the Opaque-2 (O2) gene is a transcription factor, translated from an mRNA that possesses an unusually long 5' leader sequence containing three upstream open reading frames (uORFs). The efficiency of translation of O2 mRNA has been tested in vivo by a transient assay in which the level of activation of the b32 promoter, a natural target of O2 protein, is measured. We show that uORF-less O2 alleles possess a higher transactivation value than the wild-type allele and that the reduction in transactivation due to the uORFs is a cis-dominant effect. The data presented indicate that both uORF1 and uORF2 are involved in the reducing effect and suggest that both are likely to be translated. PMID:8439744

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

Partial characterization of the lettuce infectious yellows virus genomic RNAs, identification of the coat protein gene and comparison of its amino acid sequence with those of other filamentous RNA plant viruses.

PubMed

Klaassen, V A; Boeshore, M; Dolja, V V; Falk, B W

1994-07-01

Purified virions of lettuce infectious yellows virus (LIYV), a tentative member of the closterovirus group, contained two RNAs of approximately 8500 and 7300 nucleotides (RNAs 1 and 2 respectively) and a single coat protein species with M(r) of approximately 28,000. LIYV-infected plants contained multiple dsRNAs. The two largest were the correct size for the replicative forms of LIYV virion RNAs 1 and 2. To assess the relationships between LIYV RNAs 1 and 2, cDNAs corresponding to the virion RNAs were cloned. Northern blot hybridization analysis showed no detectable sequence homology between these RNAs. A partial amino acid sequence obtained from purified LIYV coat protein was found to align in the most upstream of four complete open reading frames (ORFs) identified in a LIYV RNA 2 cDNA clone. The identity of this ORF was confirmed as the LIYV coat protein gene by immunological analysis of the gene product expressed in vitro and in Escherichia coli. Computer analysis of the LIYV coat protein amino acid sequence indicated that it belongs to a large family of proteins forming filamentous capsids of RNA plant viruses. The LIYV coat protein appears to be most closely related to the coat proteins of two closteroviruses, beet yellows virus and citrus tristeza virus.

Nonproliferation Test and Evaluation Complex - NPTEC

ScienceCinema

None

2018-01-16

The Nonproliferation Test and Evaluation Complex, or NPTEC, is the world's largest facility for open air testing of hazardous toxic materials and biological simulants. NPTEC is used for testing, experimentation, and training for technologies that require the release of toxic chemicals or biological simulants into the environment.

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

PubMed Central

Pritt, Jacob; Langmead, Ben

2016-01-01

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

Literacy Skills in Children With Cochlear Implants: The Importance of Early Oral Language and Joint Storybook Reading

PubMed Central

Ambrose, Sophie E.; Eisenberg, Laurie S.

2009-01-01

The goal of this study was to longitudinally examine relationships between early factors (child and mother) that may influence children's phonological awareness and reading skills 3 years later in a group of young children with cochlear implants (N = 16). Mothers and children were videotaped during two storybook interactions, and children's oral language skills were assessed using the “Reynell Developmental Language Scales, third edition.” Three years later, phonological awareness, reading skills, and language skills were assessed using the “Phonological Awareness Test,” the “Woodcock–Johnson-III Diagnostic Reading Battery,” and the “Oral Written Language Scales.” Variables included in the data analyses were child (age, age at implant, and language skills) and mother factors (facilitative language techniques) and children's phonological awareness and reading standard scores. Results indicate that children's early expressive oral language skills and mothers’ use of a higher level facilitative language technique (open-ended question) during storybook reading, although related, each contributed uniquely to children's literacy skills. Individual analyses revealed that the children with expressive standard scores below 70 at Time 1 also performed below average (<85) on phonological awareness and total reading tasks 3 years later. Guidelines for professionals are provided to support literacy skills in young children with cochlear implants. PMID:18417463

Evidence for reading improvement following tDCS treatment in children and adolescents with Dyslexia.

PubMed

Costanzo, Floriana; Varuzza, Cristiana; Rossi, Serena; Sdoia, Stefano; Varvara, Pamela; Oliveri, Massimiliano; Giacomo, Koch; Vicari, Stefano; Menghini, Deny

2016-01-01

There is evidence that non-invasive brain stimulation transitorily modulates reading by facilitating the neural pathways underactive in individuals with dyslexia. The study aimed at investigating whether multiple sessions of transcranial direct current stimulation (tDCS) would enhance reading abilities of children and adolescents with dyslexia and whether the effect is long-lasting. Eighteen children and adolescents with dyslexia received three 20-minute sessions a week for 6 weeks (18 sessions) of left anodal/right cathodal tDCS set at 1 mA over parieto-temporal regions combined with a cognitive training. The participants were randomly assigned to the active or the sham treatment; reading tasks (text, high and low frequency words, non-words) were used as outcome measures and collected before treatment, after treatment and one month after the end of treatment. The tolerability of tDCS was evaluated. The active group showed reduced low frequency word reading errors and non-word reading times. These positive effects were stable even one month after the end of treatment. None reported adverse effects. The study shows preliminary evidence of tDCS feasibility and efficacy in improving non-words and low frequency words reading of children and adolescents with dyslexia and it opens new rehabilitative perspectives for the remediation of dyslexia.

Do reading and spelling share a lexicon?

PubMed

Jones, Angela C; Rawson, Katherine A

2016-05-01

In the reading and spelling literature, an ongoing debate concerns whether reading and spelling share a single orthographic lexicon or rely upon independent lexica. Available evidence tends to support a single lexicon account over an independent lexica account, but evidence is mixed and open to alternative explanation. In the current work, we propose another, largely ignored account--separate-but-shared lexica--according to which reading and spelling have separate orthographic lexica, but information can be shared between them. We report three experiments designed to competitively evaluate these three theoretical accounts. In each experiment, participants learned new words via reading training and/or spelling training. The key manipulation concerned the amount of reading versus spelling practice a given item received. Following training, we assessed both response time and accuracy on final outcome measures of reading and spelling. According to the independent lexica account, final performance in one modality will not be influenced by the level of practice in the other modality. According to the single lexicon account, final performance will depend on the overall amount of practice regardless of modality. According to the separate-but-shared account, final performance will be influenced by the level of practice in both modalities but will benefit more from same-modality practice. Results support the separate-but-shared account, indicating that reading and spelling rely upon separate lexica, but information can be shared between them. Copyright © 2016 Elsevier Inc. All rights reserved.

Development of a novel parallel-spool pilot operated high-pressure solenoid valve with high flow rate and high speed

NASA Astrophysics Data System (ADS)

Dong, Dai; Li, Xiaoning

2015-03-01

High-pressure solenoid valve with high flow rate and high speed is a key component in an underwater driving system. However, traditional single spool pilot operated valve cannot meet the demands of both high flow rate and high speed simultaneously. A new structure for a high pressure solenoid valve is needed to meet the demand of the underwater driving system. A novel parallel-spool pilot operated high-pressure solenoid valve is proposed to overcome the drawback of the current single spool design. Mathematical models of the opening process and flow rate of the valve are established. Opening response time of the valve is subdivided into 4 parts to analyze the properties of the opening response. Corresponding formulas to solve 4 parts of the response time are derived. Key factors that influence the opening response time are analyzed. According to the mathematical model of the valve, a simulation of the opening process is carried out by MATLAB. Parameters are chosen based on theoretical analysis to design the test prototype of the new type of valve. Opening response time of the designed valve is tested by verifying response of the current in the coil and displacement of the main valve spool. The experimental results are in agreement with the simulated results, therefore the validity of the theoretical analysis is verified. Experimental opening response time of the valve is 48.3 ms at working pressure of 10 MPa. The flow capacity test shows that the largest effective area is 126 mm2 and the largest air flow rate is 2320 L/s. According to the result of the load driving test, the valve can meet the demands of the driving system. The proposed valve with parallel spools provides a new method for the design of a high-pressure valve with fast response and large flow rate.

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

PubMed Central

2014-01-01

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

Achieving a golden mean: mechanisms by which coronaviruses ensure synthesis of the correct stoichiometric ratios of viral proteins.

PubMed

Plant, Ewan P; Rakauskaite, Rasa; Taylor, Deborah R; Dinman, Jonathan D

2010-05-01

In retroviruses and the double-stranded RNA totiviruses, the efficiency of programmed -1 ribosomal frameshifting is critical for ensuring the proper ratios of upstream-encoded capsid proteins to downstream-encoded replicase enzymes. The genomic organizations of many other frameshifting viruses, including the coronaviruses, are very different, in that their upstream open reading frames encode nonstructural proteins, the frameshift-dependent downstream open reading frames encode enzymes involved in transcription and replication, and their structural proteins are encoded by subgenomic mRNAs. The biological significance of frameshifting efficiency and how the relative ratios of proteins encoded by the upstream and downstream open reading frames affect virus propagation has not been explored before. Here, three different strategies were employed to test the hypothesis that the -1 PRF signals of coronaviruses have evolved to produce the correct ratios of upstream- to downstream-encoded proteins. Specifically, infectious clones of the severe acute respiratory syndrome (SARS)-associated coronavirus harboring mutations that lower frameshift efficiency decreased infectivity by >4 orders of magnitude. Second, a series of frameshift-promoting mRNA pseudoknot mutants was employed to demonstrate that the frameshift signals of the SARS-associated coronavirus and mouse hepatitis virus have evolved to promote optimal frameshift efficiencies. Finally, we show that a previously described frameshift attenuator element does not actually affect frameshifting per se but rather serves to limit the fraction of ribosomes available for frameshifting. The findings of these analyses all support a "golden mean" model in which viruses use both programmed ribosomal frameshifting and translational attenuation to control the relative ratios of their encoded proteins.

De Novo ORFs in Drosophila Are Important to Organismal Fitness and Evolved Rapidly from Previously Non-coding Sequences

PubMed Central

Reinhardt, Josephine A.; Wanjiru, Betty M.; Brant, Alicia T.; Saelao, Perot; Begun, David J.; Jones, Corbin D.

2013-01-01

How non-coding DNA gives rise to new protein-coding genes (de novo genes) is not well understood. Recent work has revealed the origins and functions of a few de novo genes, but common principles governing the evolution or biological roles of these genes are unknown. To better define these principles, we performed a parallel analysis of the evolution and function of six putatively protein-coding de novo genes described in Drosophila melanogaster. Reconstruction of the transcriptional history of de novo genes shows that two de novo genes emerged from novel long non-coding RNAs that arose at least 5 MY prior to evolution of an open reading frame. In contrast, four other de novo genes evolved a translated open reading frame and transcription within the same evolutionary interval suggesting that nascent open reading frames (proto-ORFs), while not required, can contribute to the emergence of a new de novo gene. However, none of the genes arose from proto-ORFs that existed long before expression evolved. Sequence and structural evolution of de novo genes was rapid compared to nearby genes and the structural complexity of de novo genes steadily increases over evolutionary time. Despite the fact that these genes are transcribed at a higher level in males than females, and are most strongly expressed in testes, RNAi experiments show that most of these genes are essential in both sexes during metamorphosis. This lethality suggests that protein coding de novo genes in Drosophila quickly become functionally important. PMID:24146629

Repeats of base oligomers as the primordial coding sequences of the primeval earth and their vestiges in modern genes.

PubMed

Ohno, S

1984-01-01

Three outstanding properties uniquely qualify repeats of base oligomers as the primordial coding sequences of all polypeptide chains. First, when compared with randomly generated base sequences in general, they are more likely to have long open reading frames. Second, periodical polypeptide chains specified by such repeats are more likely to assume either alpha-helical or beta-sheet secondary structures than are polypeptide chains of random sequence. Third, provided that the number of bases in the oligomeric unit is not a multiple of 3, these internally repetitious coding sequences are impervious to randomly sustained base substitutions, deletions, and insertions. This is because the recurring periodicity of their polypeptide chains is given by three consecutive copies of the oligomeric unit translated in three different reading frames. Accordingly, when one reading frame is open, the other two are automatically open as well, all three being capable of coding for polypeptide chains of identical periodicity. Under this circumstance, a frame shift due to the deletion or insertion of a number of bases that is not a multiple of 3 fails to alter the down-stream amino acid sequence, and even a base change causing premature chain-termination can silence only one of the three potential coding units. Newly arisen coding sequences in modern organisms are oligomeric repeats, and most of the older genes retain various vestiges of their original internal repetitions. Some of the genes (e.g., oncogenes) have even inherited the property of being impervious to randomly sustained base changes.

NREL Hosts Consumer Energy Expo

Science.gov Websites

reading room at the NREL's Visitors Center. Saturday, June 16, 9 a.m. - 1 p.m. -- Free hourly tours of special children's activities at the Visitors Center. The Consumer Energy Expo is free and open to the

Efficacy of a reading and language intervention for children with Down syndrome: a randomized controlled trial

PubMed Central

Burgoyne, Kelly; Duff, Fiona J; Clarke, Paula J; Buckley, Sue; Snowling, Margaret J; Hulme, Charles

2012-01-01

Background This study evaluates the effects of a language and literacy intervention for children with Down syndrome. Methods Teaching assistants (TAs) were trained to deliver a reading and language intervention to children in individual daily 40-min sessions. We used a waiting list control design, in which half the sample received the intervention immediately, whereas the remaining children received the treatment after a 20-week delay. Fifty-seven children with Down syndrome in mainstream primary schools in two UK locations (Yorkshire and Hampshire) were randomly allocated to intervention (40 weeks of intervention) and waiting control (20 weeks of intervention) groups. Assessments were conducted at three time points: pre-intervention, after 20 weeks of intervention, and after 40 weeks of intervention. Results After 20 weeks of intervention, the intervention group showed significantly greater progress than the waiting control group on measures of single word reading, letter-sound knowledge, phoneme blending and taught expressive vocabulary. Effects did not transfer to other skills (nonword reading, spelling, standardised expressive and receptive vocabulary, expressive information and grammar). After 40 weeks of intervention, the intervention group remained numerically ahead of the control group on most key outcome measures; but these differences were not significant. Children who were younger, attended more intervention sessions, and had better initial receptive language skills made greater progress during the course of the intervention. Conclusions A TA-delivered intervention produced improvements in the reading and language skills of children with Down syndrome. Gains were largest in skills directly taught with little evidence of generalization to skills not directly taught in the intervention. PMID:22533801

Reading outcomes of children and adolescents with attention-deficit/hyperactivity disorder and dyslexia following atomoxetine treatment.

PubMed

Shaywitz, Bennett A; Williams, David W; Fox, Bethany K; Wietecha, Linda A

2014-10-01

Abstract Objective: This study assessed the efficacy of atomoxetine on attention-deficit/hyperactivity disorder (ADHD) symptoms in children and adolescents having ADHD with comorbid dyslexia (ADHD+D) and the effects of the treatment on reading measures. The analyses in this report used data from a study designed to examine the effects of a nonstimulant pharmacological agent, atomoxetine, on reading in children with ADHD+D. Patients ages 10-16 years with ADHD or ADHD+D received open-label atomoxetine for 16 weeks. The ADHD Rating Scale (ADHD-RS) and reading subtests of the Kaufman Test of Educational Achievement (K-TEA) were assessed. Changes in ADHD symptoms and reading scores were also analyzed by ADHD subtype. Treatment effect sizes and correlations between changes in ADHDRS and K-TEA scores were calculated. After atomoxetine treatment, both ADHD and ADHD+D patient groups showed significant reduction in ADHD symptom and improvements in K-TEA reading scores. The range of treatment effect sizes on K-TEA scores was 0.35-0.53 for the ADHD group and 0.50-0.62 for the ADHD+D group. Pearson's correlation coefficients revealed only a few weak correlations between changes in ADHD symptoms and reading scores, regardless of diagnostic group. ADHD symptoms and K-TEA reading scores improved for both the ADHD and ADHD+D groups following atomoxetine treatment. Correlation analyses indicate that improvements in reading outcomes cannot be explained by a reduction of ADHD symptoms alone. These findings support further exploration of the potential effects of atomoxetine on reading in children with ADHD and dyslexia or dyslexia alone.

Federal Consulting: Strategies and Tools for the Career Development Professional.

ERIC Educational Resources Information Center

Kahnweiler, Jennifer B.; Pressman, Sue

The Federal Government is America's largest employer and is expanding consulting opportunities for career development professionals. Increased Federal mandates for outsourcing have opened wide doors for the entrepreneurial-spirited career counselors and created new challenges for traditional methods of offering career services. As consultants who…

Using image processing technology and mathematical algorithm in the automatic selection of vocal cord opening and closing images from the larynx endoscopy video.

PubMed

Kuo, Chung-Feng Jeffrey; Chu, Yueng-Hsiang; Wang, Po-Chun; Lai, Chun-Yu; Chu, Wen-Lin; Leu, Yi-Shing; Wang, Hsing-Won

2013-12-01

The human larynx is an important organ for voice production and respiratory mechanisms. The vocal cord is approximated for voice production and open for breathing. The videolaryngoscope is widely used for vocal cord examination. At present, physicians usually diagnose vocal cord diseases by manually selecting the image of the vocal cord opening to the largest extent (abduction), thus maximally exposing the vocal cord lesion. On the other hand, the severity of diseases such as vocal palsy, atrophic vocal cord is largely dependent on the vocal cord closing to the smallest extent (adduction). Therefore, diseases can be assessed by the image of the vocal cord opening to the largest extent, and the seriousness of breathy voice is closely correlated to the gap between vocal cords when closing to the smallest extent. The aim of the study was to design an automatic vocal cord image selection system to improve the conventional selection process by physicians and enhance diagnosis efficiency. Also, due to the unwanted fuzzy images resulting from examination process caused by human factors as well as the non-vocal cord images, texture analysis is added in this study to measure image entropy to establish a screening and elimination system to effectively enhance the accuracy of selecting the image of the vocal cord closing to the smallest extent. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Pollination of tomatoes by the stingless bee Melipona quadrifasciata and the honey bee Apis mellifera (Hymenoptera, Apidae).

PubMed

dos Santos, S A Bispo; Roselino, A C; Hrncir, M; Bego, L R

2009-06-30

The pollination effectiveness of the stingless bee Melipona quadrifasciata and the honey bee Apis mellifera was tested in tomato plots. The experiment was conducted in four greenhouses as well as in an external open plot in Ribeirão Preto, SP, Brazil. The tomato plants were exposed to visits by M. quadrifasciata in one greenhouse and to A. mellifera in another; two greenhouses were maintained without bees (controls) and an open field plot was exposed to pollinators in an area where both honey bee and stingless bee colonies are abundant. We counted the number of tomatoes produced in each plot. Two hundred tomatoes from each plot were weighed, their vertical and transversal circumferences were measured, and the seeds were counted. We collected 253 Chrysomelidae, 17 Halictidae, one Paratrigona sp, and one honey bee from the flowers of the tomato plants in the open area. The largest number of fruits (1414 tomatoes), the heaviest and largest tomatoes, and the ones with the most seed were collected from the greenhouse with stingless bees. Fruits cultivated in the greenhouse with honey bees had the same weight and size as those produced in one of the control greenhouses. The stingless bee, M. quadrifasciata, was significantly more efficient than honey bees in pollinating greenhouse tomatoes.

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

PubMed Central

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

2014-01-01

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

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

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

PubMed Central

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

1993-01-01

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

Himalayan optical telescope switches on

NASA Astrophysics Data System (ADS)

Padma, T. V.

2016-05-01

The largest optical telescope in India has turned on, opening up a new era for astronomy in the country. The 3.6 m Devasthal Optical Telescope (DOT) - part of an Indo-Belgian collaboration - was activated remotely on 30 March from Belgium by visiting Indian prime minister Narendra Modi and his Belgian counterpart Charles Michel.

Landing the Chief

ERIC Educational Resources Information Center

Hann, Christopher

2008-01-01

Commercial search consulting firms such as Hazard, Young, Attea & Associates, almost unheard of just a generation ago, today help fill a small but growing number of the more than 2,000 superintendent openings that arise each year in the nation's nearly 14,000 public school districts. It is unlikely that the nation's largest school systems,…

Stealing the Goose: Copyright and Learning

ERIC Educational Resources Information Center

McGreal, Rory

2004-01-01

The Internet is the world's largest knowledge common and the information source of first resort. Much of this information is open and freely available. However, there are organizations and companies today that are trying to close off the Internet commons and make it proprietary. These are the "copyright controllers." The preservation of the…

14 CFR 23.365 - Pressurized cabin loads.

Code of Federal Regulations, 2010 CFR

2010-01-01

... stress concentrations, must be accounted for. (c) If landings may be made with the cabin pressurized... be designed for the effects of sudden release of pressure in any compartment with external doors or windows. This condition must be investigated for the effects of failure of the largest opening in the...

ACCESS America's great outdoors: public lands are for everyone!

Treesearch

Joe Meade; Gregory J. Lais

1995-01-01

With nearly 200 million acres of majestic mountains, deep rugged canyons, pristine high lakes, wild rivers, immense forests, and open meadows, the National Forest System provides the largest variety of outdoor recreation opportunities in the United States. Federal lands encompass a combined total of nearly one-third of this country.

Mitochondrial Intronic Open Reading Frames in Podospora: Mobility and Consecutive Exonic Sequence Variations

PubMed Central

Sellem, C. H.; d'Aubenton-Carafa, Y.; Rossignol, M.; Belcour, L.

1996-01-01

The mitochondrial genome of 23 wild-type strains belonging to three different species of the filamentous fungus Podospora was examined. Among the 15 optional sequences identified are two intronic reading frames, nad1-i4-orf1 and cox1-i7-orf2. We show that the presence of these sequences was strictly correlated with tightly clustered nucleotide substitutions in the adjacent exon. This correlation applies to the presence or absence of closely related open reading frames (ORFs), found at the same genetic locations, in all the Pyrenomycete genera examined. The recent gain of these optional ORFs in the evolution of the genus Podospora probably account for such sequence differences. In the homoplasmic progeny from heteroplasmons constructed between Podospora strains differing by the presence of these optional ORFs, nad1-i4-orf1 and cox1-i7-orf2 appeared highly invasive. Sequence comparisons in the nad1-i4 intron of various strains of the Pyrenomycete family led us to propose a scenario of its evolution that includes several events of loss and gain of intronic ORFs. These results strongly reinforce the idea that group I intronic ORFs are mobile elements and that their transfer, and comcomitant modification of the adjacent exon, could participate in the modular evolution of mitochondrial genomes. PMID:8725226

Mitochondrial intronic open reading frames in Podospora: mobility and consecutive exonic sequence variations.

PubMed

Sellem, C H; d'Aubenton-Carafa, Y; Rossignol, M; Belcour, L

1996-06-01

The mitochondrial genome of 23 wild-type strains belonging to three different species of the filamentous fungus Podospora was examined. Among the 15 optional sequences identified are two intronic reading frames, nad1-i4-orf1 and cox1-i7-orf2. We show that the presence of these sequences was strictly correlated with tightly clustered nucleotide substitutions in the adjacent exon. This correlation applies to the presence or absence of closely related open reading frames (ORFs), found at the same genetic locations, in all the Pyrenomycete genera examined. The recent gain of these optional ORFs in the evolution of the genus Podospora probably account for such sequence differences. In the homoplasmic progeny from heteroplasmons constructed between Podospora strains differing by the presence of these optional ORFs, nad1-i4-orf1 and cox1-i7-orf2 appeared highly invasive. Sequence comparisons in the nad1-i4 intron of various strains of the Pyrenomycete family led us to propose a scenario of its evolution that includes several events of loss and gain of intronic ORFs. These results strongly reinforce the idea that group 1 intronic ORFs are mobile elements and that their transfer, and concomitant modification of the adjacent exon, could participate in the modular evolution of mitochondrial genomes.

Mysterious Roving Rocks of Racetrack Playa

NASA Image and Video Library

2017-12-08

Sometimes, a gunfight breaks out, like this one between (left) Mindy Krzykowski and (right) Leva McIntire. This is the wild West, after all. Photo credit: NASA/GSFC/Maggie McAdam To read a feature story on the Racetrack Playa go to: www.nasa.gov/topics/earth/features/roving-rocks.html NASA Goddard Space Flight Center is home to the nation's largest organization of combined scientists, engineers and technologists that build spacecraft, instruments and new technology to study the Earth, the sun, our solar system, and the universe. Follow us on Twitter Join us on Facebook

Mysterious Roving Rocks of Racetrack Playa

NASA Image and Video Library

2017-12-08

Intern Kyle Yawn marked the boundaries of this trail by placing pushpins into cracks in the clay. Now, he photographs the trail to document it. Photo credit: NASA/GSFC/Maggie McAdam To read a feature story on the Racetrack Playa go to: www.nasa.gov/topics/earth/features/roving-rocks.html NASA Goddard Space Flight Center is home to the nation's largest organization of combined scientists, engineers and technologists that build spacecraft, instruments and new technology to study the Earth, the sun, our solar system, and the universe. Follow us on Twitter Join us on Facebook

Mysterious Roving Rocks of Racetrack Playa

NASA Image and Video Library

2017-12-08

The trails have some curious features. Sometimes the clay gets pushed into a mound at the trail's end, as in this photo. Photo credit: NASA/GSFC/Cynthia Cheung To read a feature story on the Racetrack Playa go to: www.nasa.gov/topics/earth/features/roving-rocks.html NASA Goddard Space Flight Center is home to the nation's largest organization of combined scientists, engineers and technologists that build spacecraft, instruments and new technology to study the Earth, the sun, our solar system, and the universe. Follow us on Twitter Join us on Facebook

Mysterious Roving Rocks of Racetrack Playa

NASA Image and Video Library

2017-12-08

The main mystery on Racetrack Playa is how the rocks move, but another, possibly greater mystery, is why some trails don't have rocks. Photo credit: NASA/GSFC/Mindy Krzykowski/LPSA intern To read a feature story on the Racetrack Playa go to: www.nasa.gov/topics/earth/features/roving-rocks.html NASA Goddard Space Flight Center is home to the nation's largest organization of combined scientists, engineers and technologists that build spacecraft, instruments and new technology to study the Earth, the sun, our solar system, and the universe. Follow us on Twitter Join us on Facebook

Goldstrike Mine, Nevada

NASA Image and Video Library

2017-05-15

This image from NASA Terra spacecraft shows Goldstrike in northeast Nevada, the largest gold mine in North America. The mine complex, (including the Betze-Post-Screamer open-pit, and Meikle and Rodeo underground mines) is owned and operated by the world's largest gold mining company, Barrick Gold. Gold occurs as microscopically fine grains, with an average grade of 0.1 ounces per ton of ore. Estimates of reserves are as high as 35 million ounces of gold. The image was acquired September 25, 2010, covers an area of 15 by 15 km, and is located at 41 degrees north, 116.4 degrees west. https://photojournal.jpl.nasa.gov/catalog/PIA21665

Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit

PubMed Central

O'Boyle, Noel M; Morley, Chris; Hutchison, Geoffrey R

2008-01-01

Background Scripting languages such as Python are ideally suited to common programming tasks in cheminformatics such as data analysis and parsing information from files. However, for reasons of efficiency, cheminformatics toolkits such as the OpenBabel toolkit are often implemented in compiled languages such as C++. We describe Pybel, a Python module that provides access to the OpenBabel toolkit. Results Pybel wraps the direct toolkit bindings to simplify common tasks such as reading and writing molecular files and calculating fingerprints. Extensive use is made of Python iterators to simplify loops such as that over all the molecules in a file. A Pybel Molecule can be easily interconverted to an OpenBabel OBMol to access those methods or attributes not wrapped by Pybel. Conclusion Pybel allows cheminformaticians to rapidly develop Python scripts that manipulate chemical information. It is open source, available cross-platform, and offers the power of the OpenBabel toolkit to Python programmers. PMID:18328109

Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit.

PubMed

O'Boyle, Noel M; Morley, Chris; Hutchison, Geoffrey R

2008-03-09

Scripting languages such as Python are ideally suited to common programming tasks in cheminformatics such as data analysis and parsing information from files. However, for reasons of efficiency, cheminformatics toolkits such as the OpenBabel toolkit are often implemented in compiled languages such as C++. We describe Pybel, a Python module that provides access to the OpenBabel toolkit. Pybel wraps the direct toolkit bindings to simplify common tasks such as reading and writing molecular files and calculating fingerprints. Extensive use is made of Python iterators to simplify loops such as that over all the molecules in a file. A Pybel Molecule can be easily interconverted to an OpenBabel OBMol to access those methods or attributes not wrapped by Pybel. Pybel allows cheminformaticians to rapidly develop Python scripts that manipulate chemical information. It is open source, available cross-platform, and offers the power of the OpenBabel toolkit to Python programmers.

Solar Neutrino flare detection in Hyperkamiokande and SK

NASA Astrophysics Data System (ADS)

Fargion, Daniele

2016-07-01

The possible buid and near activity of a Megaton neutrino detection in HyperKamiokande and the older SK implementation by Gadolinium liqid might open to future detection of largest solar flare (pion trace at tens MeV) electron neutrino and antineutrino. The multiwave detection of X-gamma and neutrino event might offer a deep view of such solar acelleration and of neutrino flavor mix along its flight. The possoble near future discover of such events will open a third neutrino astronomy windows after rarest SN 1987A and persistent Solar nuclear signals.

Comparative assessment of bone pose estimation using Point Cluster Technique and OpenSim.

PubMed

Lathrop, Rebecca L; Chaudhari, Ajit M W; Siston, Robert A

2011-11-01

Estimating the position of the bones from optical motion capture data is a challenge associated with human movement analysis. Bone pose estimation techniques such as the Point Cluster Technique (PCT) and simulations of movement through software packages such as OpenSim are used to minimize soft tissue artifact and estimate skeletal position; however, using different methods for analysis may produce differing kinematic results which could lead to differences in clinical interpretation such as a misclassification of normal or pathological gait. This study evaluated the differences present in knee joint kinematics as a result of calculating joint angles using various techniques. We calculated knee joint kinematics from experimental gait data using the standard PCT, the least squares approach in OpenSim applied to experimental marker data, and the least squares approach in OpenSim applied to the results of the PCT algorithm. Maximum and resultant RMS differences in knee angles were calculated between all techniques. We observed differences in flexion/extension, varus/valgus, and internal/external rotation angles between all approaches. The largest differences were between the PCT results and all results calculated using OpenSim. The RMS differences averaged nearly 5° for flexion/extension angles with maximum differences exceeding 15°. Average RMS differences were relatively small (< 1.08°) between results calculated within OpenSim, suggesting that the choice of marker weighting is not critical to the results of the least squares inverse kinematics calculations. The largest difference between techniques appeared to be a constant offset between the PCT and all OpenSim results, which may be due to differences in the definition of anatomical reference frames, scaling of musculoskeletal models, and/or placement of virtual markers within OpenSim. Different methods for data analysis can produce largely different kinematic results, which could lead to the misclassification of normal or pathological gait. Improved techniques to allow non-uniform scaling of generic models to more accurately reflect subject-specific bone geometries and anatomical reference frames may reduce differences between bone pose estimation techniques and allow for comparison across gait analysis platforms.

Fast-SG: an alignment-free algorithm for hybrid assembly.

PubMed

Di Genova, Alex; Ruz, Gonzalo A; Sagot, Marie-France; Maass, Alejandro

2018-05-01

Long-read sequencing technologies are the ultimate solution for genome repeats, allowing near reference-level reconstructions of large genomes. However, long-read de novo assembly pipelines are computationally intense and require a considerable amount of coverage, thereby hindering their broad application to the assembly of large genomes. Alternatively, hybrid assembly methods that combine short- and long-read sequencing technologies can reduce the time and cost required to produce de novo assemblies of large genomes. Here, we propose a new method, called Fast-SG, that uses a new ultrafast alignment-free algorithm specifically designed for constructing a scaffolding graph using light-weight data structures. Fast-SG can construct the graph from either short or long reads. This allows the reuse of efficient algorithms designed for short-read data and permits the definition of novel modular hybrid assembly pipelines. Using comprehensive standard datasets and benchmarks, we show how Fast-SG outperforms the state-of-the-art short-read aligners when building the scaffoldinggraph and can be used to extract linking information from either raw or error-corrected long reads. We also show how a hybrid assembly approach using Fast-SG with shallow long-read coverage (5X) and moderate computational resources can produce long-range and accurate reconstructions of the genomes of Arabidopsis thaliana (Ler-0) and human (NA12878). Fast-SG opens a door to achieve accurate hybrid long-range reconstructions of large genomes with low effort, high portability, and low cost.

MDMA enhances "mind reading" of positive emotions and impairs "mind reading" of negative emotions.

PubMed

Hysek, Cédric M; Domes, Gregor; Liechti, Matthias E

2012-07-01

3,4-Methylenedioxymethamphetamine (MDMA, ecstasy) increases sociability. The prosocial effects of MDMA may result from the release of the "social hormone" oxytocin and associated alterations in the processing of socioemotional stimuli. We investigated the effects of MDMA (125 mg) on the ability to infer the mental states of others from social cues of the eye region in the Reading the Mind in the Eyes Test. The study included 48 healthy volunteers (24 men, 24 women) and used a double-blind, placebo-controlled, within-subjects design. A choice reaction time test was used to exclude impairments in psychomotor function. We also measured circulating oxytocin and cortisol levels and subjective drug effects. MDMA differentially affected mind reading depending on the emotional valence of the stimuli. MDMA enhanced the accuracy of mental state decoding for positive stimuli (e.g., friendly), impaired mind reading for negative stimuli (e.g., hostile), and had no effect on mind reading for neutral stimuli (e.g., reflective). MDMA did not affect psychomotor performance, increased circulating oxytocin and cortisol levels, and produced subjective prosocial effects, including feelings of being more open, talkative, and closer to others. The shift in the ability to correctly read socioemotional information toward stimuli associated with positive emotional valence, together with the prosocial feelings elicited by MDMA, may enhance social approach behavior and sociability when MDMA is used recreationally and facilitate therapeutic relationships in MDMA-assisted psychotherapeutic settings.

Network-based reading system for lung cancer screening CT

NASA Astrophysics Data System (ADS)

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

2006-03-01

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

4. DETAIL VIEW OF OVEN NO. 7 LOOKING NORTH, SHOWING ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

4. DETAIL VIEW OF OVEN NO. 7 LOOKING NORTH, SHOWING REFRACTORY BRICK OF ARCHED OPENING READING 'H-W 8-61 48 ARCH' (HARBISON-WALKER) - Lucernemines Coke Works, Coke Ovens, 0.5 mile East of Lucerne, adjacent, Lucerne Mines, Indiana County, PA

76 FR 11449 - Agency Information Collection Activities; Submission to OMB for Review and Approval; Comment...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-02

... Reading Room is open from 8 a.m. to 4:30 p.m., Monday through Friday, excluding legal holidays. The...-icers and fire-fighting foams. Safer surfactants are those that break down quickly to non-polluting...

75 FR 66757 - Stakeholder Input; Listening Session Seeking Suggestions for Improving the Next National...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-29

..., 1301 Constitution Ave., NW., Washington, DC. The Public Reading Room is open from 8:30 a.m. to 4:30 p.m... leachate from anti-fouling hull coatings; aqueous film forming foam (AFFF); boiler/economizer blowdown...

Open Access: From Myth to Paradox

ScienceCinema

Ginsparg, Paul [Cornell University, Ithaca, New York, United States

2018-04-19

True open access to scientific publications not only gives readers the possibility to read articles without paying subscription, but also makes the material available for automated ingestion and harvesting by 3rd parties. Once articles and associated data become universally treatable as computable objects, openly available to 3rd party aggregators and value-added services, what new services can we expect, and how will they change the way that researchers interact with their scholarly communications infrastructure? I will discuss straightforward applications of existing ideas and services, including citation analysis, collaborative filtering, external database linkages, interoperability, and other forms of automated markup, and speculate on the sociology of the next generation of users.

The "wh" questions of visual phonics: what, who, where, when, and why.

PubMed

Narr, Rachel F; Cawthon, Stephanie W

2011-01-01

Visual Phonics is a reading instructional tool that has been implemented in isolated classrooms for over 20 years. In the past 5 years, several experimental studies demonstrated its efficacy with students who are deaf or hard of hearing. Through a national survey with 200 participants, this study specifically addresses who, where, how, and why a sample of teachers use Visual Phonics in their everyday reading instruction. Through checklists of teaching practice, rating scales, and open-ended questions, teachers self-reported their use of Visual Phonics, reflected upon its efficacy, and what they think about using it with students with a diverse set of instructional needs. The majority reported that Visual Phonics was easy to use, engaging to students, and easy to integrate into a structured reading curriculum. The majority of respondents agreed that it helps increase phonemic awareness and decoding skills, build vocabulary, as well as increase reading comprehension. The implications of these findings in bridging the research-to-practice gap are discussed.

Poor readers' retrieval mechanism: efficient access is not dependent on reading skill

PubMed Central

Johns, Clinton L.; Matsuki, Kazunaga; Van Dyke, Julie A.

2015-01-01

A substantial body of evidence points to a cue-based direct-access retrieval mechanism as a crucial component of skilled adult reading. We report two experiments aimed at examining whether poor readers are able to make use of the same retrieval mechanism. This is significant in light of findings that poor readers have difficulty retrieving linguistic information (e.g., Perfetti, 1985). Our experiments are based on a previous demonstration of direct-access retrieval in language processing, presented in McElree et al. (2003). Experiment 1 replicates the original result using an auditory implementation of the Speed-Accuracy Tradeoff (SAT) method. This finding represents a significant methodological advance, as it opens up the possibility of exploring retrieval speeds in non-reading populations. Experiment 2 provides evidence that poor readers do use a direct-access retrieval mechanism during listening comprehension, despite overall poorer accuracy and slower retrieval speeds relative to skilled readers. The findings are discussed with respect to hypotheses about the source of poor reading comprehension. PMID:26528212

Wide-Open: Accelerating public data release by automating detection of overdue datasets

PubMed Central

Poon, Hoifung; Howe, Bill

2017-01-01

Open data is a vital pillar of open science and a key enabler for reproducibility, data reuse, and novel discoveries. Enforcement of open-data policies, however, largely relies on manual efforts, which invariably lag behind the increasingly automated generation of biological data. To address this problem, we developed a general approach to automatically identify datasets overdue for public release by applying text mining to identify dataset references in published articles and parse query results from repositories to determine if the datasets remain private. We demonstrate the effectiveness of this approach on 2 popular National Center for Biotechnology Information (NCBI) repositories: Gene Expression Omnibus (GEO) and Sequence Read Archive (SRA). Our Wide-Open system identified a large number of overdue datasets, which spurred administrators to respond directly by releasing 400 datasets in one week. PMID:28594819

Wide-Open: Accelerating public data release by automating detection of overdue datasets.

PubMed

Grechkin, Maxim; Poon, Hoifung; Howe, Bill

2017-06-01

Open data is a vital pillar of open science and a key enabler for reproducibility, data reuse, and novel discoveries. Enforcement of open-data policies, however, largely relies on manual efforts, which invariably lag behind the increasingly automated generation of biological data. To address this problem, we developed a general approach to automatically identify datasets overdue for public release by applying text mining to identify dataset references in published articles and parse query results from repositories to determine if the datasets remain private. We demonstrate the effectiveness of this approach on 2 popular National Center for Biotechnology Information (NCBI) repositories: Gene Expression Omnibus (GEO) and Sequence Read Archive (SRA). Our Wide-Open system identified a large number of overdue datasets, which spurred administrators to respond directly by releasing 400 datasets in one week.

Precision manometer gauge

DOEpatents

McPherson, Malcolm J.; Bellman, Robert A.

1984-01-01

A precision manometer gauge which locates a zero height and a measured height of liquid using an open tube in communication with a reservoir adapted to receive the pressure to be measured. The open tube has a reference section carried on a positioning plate which is moved vertically with machine tool precision. Double scales are provided to read the height of the positioning plate accurately, the reference section being inclined for accurate meniscus adjustment, and means being provided to accurately locate a zero or reference position.

Precision manometer gauge

DOEpatents

McPherson, M.J.; Bellman, R.A.

1982-09-27

A precision manometer gauge which locates a zero height and a measured height of liquid using an open tube in communication with a reservoir adapted to receive the pressure to be measured. The open tube has a reference section carried on a positioning plate which is moved vertically with machine tool precision. Double scales are provided to read the height of the positioning plate accurately, the reference section being inclined for accurate meniscus adjustment, and means being provided to accurately locate a zero or reference position.

Impact of the Freedom of Information Act on the National Intelligence Agencies.

DTIC Science & Technology

1982-04-16

previously placed on the open record. This has led some courts to refuse to even consider in camera evidence until more is stated on the open record. Sworn...read an in camera affidavit and awarded summary judgement to the plaintiff because the government’s proof was not, therefore, in evidence. 5 Courts...which perceive a dilemma in these in camera procedures have been giving serious consideration to solving it by permitting plaintiffs or their attorneys

Slow Reading in Glaucoma: Is it due to the Shrinking Visual Span in Central Vision?

PubMed Central

Liu, Rong; Patel, Bhavika N.; Girkin, Christopher

2017-01-01

Purpose Glaucoma is a leading cause of blindness worldwide, characterized by progressive loss of retinal ganglion cells. Patients with bilateral glaucoma read slower than normal cohorts. Here we examined the factors that may underlie slow reading in glaucoma and determined the best predictor of reading speed in glaucoma. Methods A total of 38 subjects participated in this study: 17 patients with primary open-angle glaucoma (mean age = 64.71 years) and 21 age-similar normal controls (58.24 years). For each subject, we measured binocular visual acuity (BVA); binocular contrast sensitivity (BCS); stereoacuity; visual field mean deviation (MD); and the visual span (i.e., the number of letters recognizable at one glance) known to limit reading speed. The visual span was measured with a trigram letter-recognition task in which subjects identify trigrams flashed at varying letter positions left and right of the fixation. Oral reading speed was measured with short blocks of text. Results Even after controlling for age, glaucoma patients showed significantly slower reading speed (by 19%, P < 0.05) and smaller visual span (by 11 bits, P < 0.001) compared to normal controls. While their BVA was relatively normal (20/20 Snellen equivalent), their BCS (P < 0.001); stereoacuity (P < 0.001); and visual field MD (P < 0.001) showed pronounced deficits. Multiple regression analysis further revealed that reading speed in glaucoma was best predicted by the visual span. Conclusions Our results showed that slower reading speed in glaucoma was closely related to the shrinkage of the visual span. Our findings further support the view that the visual span plays a limiting role in reading speed. PMID:29131903

Slow Reading in Glaucoma: Is it due to the Shrinking Visual Span in Central Vision?

PubMed

Kwon, MiYoung; Liu, Rong; Patel, Bhavika N; Girkin, Christopher

2017-11-01

Glaucoma is a leading cause of blindness worldwide, characterized by progressive loss of retinal ganglion cells. Patients with bilateral glaucoma read slower than normal cohorts. Here we examined the factors that may underlie slow reading in glaucoma and determined the best predictor of reading speed in glaucoma. A total of 38 subjects participated in this study: 17 patients with primary open-angle glaucoma (mean age = 64.71 years) and 21 age-similar normal controls (58.24 years). For each subject, we measured binocular visual acuity (BVA); binocular contrast sensitivity (BCS); stereoacuity; visual field mean deviation (MD); and the visual span (i.e., the number of letters recognizable at one glance) known to limit reading speed. The visual span was measured with a trigram letter-recognition task in which subjects identify trigrams flashed at varying letter positions left and right of the fixation. Oral reading speed was measured with short blocks of text. Even after controlling for age, glaucoma patients showed significantly slower reading speed (by 19%, P < 0.05) and smaller visual span (by 11 bits, P < 0.001) compared to normal controls. While their BVA was relatively normal (20/20 Snellen equivalent), their BCS (P < 0.001); stereoacuity (P < 0.001); and visual field MD (P < 0.001) showed pronounced deficits. Multiple regression analysis further revealed that reading speed in glaucoma was best predicted by the visual span. Our results showed that slower reading speed in glaucoma was closely related to the shrinkage of the visual span. Our findings further support the view that the visual span plays a limiting role in reading speed.

An analysis of mobile genetic elements in three Plasmodium species and their potential impact on the nucleotide composition of the P. falciparum genome.

PubMed

Durand, Pierre M; Oelofse, Andries J; Coetzer, Theresa L

2006-11-04

The completed genome sequences of the malaria parasites P. falciparum, P. y. yoelii and P. vivax have revealed some unusual features. P. falciparum contains the most AT rich genome sequenced so far--over 90% in some regions. In comparison, P. y. yoelii is approximately 77% and P. vivax is approximately 55% AT rich. The evolutionary reasons for these findings are unknown. Mobile genetic elements have a considerable impact on genome evolution but a thorough investigation of these elements in Plasmodium has not been undertaken. We therefore performed a comprehensive genome analysis of these elements and their derivatives in the three Plasmodium species. Whole genome analysis was performed using bioinformatic methods. Forty potential protein encoding sequences with features of transposable elements were identified in P. vivax, eight in P. y. yoelii and only six in P. falciparum. Further investigation of the six open reading frames in P. falciparum revealed that only one is potentially an active mobile genetic element. Most of the open reading frames identified in all three species are hypothetical proteins. Some represent annotated host proteins such as the putative telomerase reverse transcriptase genes in P. y. yoelii and P. falciparum. One of the P. vivax open reading frames identified in this study demonstrates similarity to telomerase reverse transcriptase and we conclude it to be the orthologue of this gene. There is a divergence in the frequencies of mobile genetic elements in the three Plasmodium species investigated. Despite the limitations of whole genome analytical methods, it is tempting to speculate that mobile genetic elements might have been a driving force behind the compositional bias of the P. falciparum genome.

Achieving a Golden Mean: Mechanisms by Which Coronaviruses Ensure Synthesis of the Correct Stoichiometric Ratios of Viral Proteins▿

PubMed Central

Plant, Ewan P.; Rakauskaitė, Rasa; Taylor, Deborah R.; Dinman, Jonathan D.

2010-01-01

In retroviruses and the double-stranded RNA totiviruses, the efficiency of programmed −1 ribosomal frameshifting is critical for ensuring the proper ratios of upstream-encoded capsid proteins to downstream-encoded replicase enzymes. The genomic organizations of many other frameshifting viruses, including the coronaviruses, are very different, in that their upstream open reading frames encode nonstructural proteins, the frameshift-dependent downstream open reading frames encode enzymes involved in transcription and replication, and their structural proteins are encoded by subgenomic mRNAs. The biological significance of frameshifting efficiency and how the relative ratios of proteins encoded by the upstream and downstream open reading frames affect virus propagation has not been explored before. Here, three different strategies were employed to test the hypothesis that the −1 PRF signals of coronaviruses have evolved to produce the correct ratios of upstream- to downstream-encoded proteins. Specifically, infectious clones of the severe acute respiratory syndrome (SARS)-associated coronavirus harboring mutations that lower frameshift efficiency decreased infectivity by >4 orders of magnitude. Second, a series of frameshift-promoting mRNA pseudoknot mutants was employed to demonstrate that the frameshift signals of the SARS-associated coronavirus and mouse hepatitis virus have evolved to promote optimal frameshift efficiencies. Finally, we show that a previously described frameshift attenuator element does not actually affect frameshifting per se but rather serves to limit the fraction of ribosomes available for frameshifting. The findings of these analyses all support a “golden mean” model in which viruses use both programmed ribosomal frameshifting and translational attenuation to control the relative ratios of their encoded proteins. PMID:20164235

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

PubMed Central

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

1988-01-01

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

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

PubMed

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

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

RAMICS: trainable, high-speed and biologically relevant alignment of high-throughput sequencing reads to coding DNA

PubMed Central

Wright, Imogen A.; Travers, Simon A.

2014-01-01

The challenge presented by high-throughput sequencing necessitates the development of novel tools for accurate alignment of reads to reference sequences. Current approaches focus on using heuristics to map reads quickly to large genomes, rather than generating highly accurate alignments in coding regions. Such approaches are, thus, unsuited for applications such as amplicon-based analysis and the realignment phase of exome sequencing and RNA-seq, where accurate and biologically relevant alignment of coding regions is critical. To facilitate such analyses, we have developed a novel tool, RAMICS, that is tailored to mapping large numbers of sequence reads to short lengths (<10 000 bp) of coding DNA. RAMICS utilizes profile hidden Markov models to discover the open reading frame of each sequence and aligns to the reference sequence in a biologically relevant manner, distinguishing between genuine codon-sized indels and frameshift mutations. This approach facilitates the generation of highly accurate alignments, accounting for the error biases of the sequencing machine used to generate reads, particularly at homopolymer regions. Performance improvements are gained through the use of graphics processing units, which increase the speed of mapping through parallelization. RAMICS substantially outperforms all other mapping approaches tested in terms of alignment quality while maintaining highly competitive speed performance. PMID:24861618

Music Training Increases Phonological Awareness and Reading Skills in Developmental Dyslexia: A Randomized Control Trial

PubMed Central

Flaugnacco, Elena; Lopez, Luisa; Terribili, Chiara; Montico, Marcella; Zoia, Stefania; Schön, Daniele

2015-01-01

There is some evidence for a role of music training in boosting phonological awareness, word segmentation, working memory, as well as reading abilities in children with typical development. Poor performance in tasks requiring temporal processing, rhythm perception and sensorimotor synchronization seems to be a crucial factor underlying dyslexia in children. Interestingly, children with dyslexia show deficits in temporal processing, both in language and in music. Within this framework, we test the hypothesis that music training, by improving temporal processing and rhythm abilities, improves phonological awareness and reading skills in children with dyslexia. The study is a prospective, multicenter, open randomized controlled trial, consisting of test, rehabilitation and re-test (ID NCT02316873). After rehabilitation, the music group (N = 24) performed better than the control group (N = 22) in tasks assessing rhythmic abilities, phonological awareness and reading skills. This is the first randomized control trial testing the effect of music training in enhancing phonological and reading abilities in children with dyslexia. The findings show that music training can modify reading and phonological abilities even when these skills are severely impaired. Through the enhancement of temporal processing and rhythmic skills, music might become an important tool in both remediation and early intervention programs. Trial Registration ClinicalTrials.gov NCT02316873 PMID:26407242

Music Training Increases Phonological Awareness and Reading Skills in Developmental Dyslexia: A Randomized Control Trial.

PubMed

Flaugnacco, Elena; Lopez, Luisa; Terribili, Chiara; Montico, Marcella; Zoia, Stefania; Schön, Daniele

2015-01-01

There is some evidence for a role of music training in boosting phonological awareness, word segmentation, working memory, as well as reading abilities in children with typical development. Poor performance in tasks requiring temporal processing, rhythm perception and sensorimotor synchronization seems to be a crucial factor underlying dyslexia in children. Interestingly, children with dyslexia show deficits in temporal processing, both in language and in music. Within this framework, we test the hypothesis that music training, by improving temporal processing and rhythm abilities, improves phonological awareness and reading skills in children with dyslexia. The study is a prospective, multicenter, open randomized controlled trial, consisting of test, rehabilitation and re-test (ID NCT02316873). After rehabilitation, the music group (N = 24) performed better than the control group (N = 22) in tasks assessing rhythmic abilities, phonological awareness and reading skills. This is the first randomized control trial testing the effect of music training in enhancing phonological and reading abilities in children with dyslexia. The findings show that music training can modify reading and phonological abilities even when these skills are severely impaired. Through the enhancement of temporal processing and rhythmic skills, music might become an important tool in both remediation and early intervention programs.Trial Registration: ClinicalTrials.gov NCT02316873

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

NASA Astrophysics Data System (ADS)

Williams, Theresa

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

Technical Note: Statistical dependences between channels in radiochromic film readings. Implications in multichannel dosimetry.

PubMed

González-López, Antonio; Vera-Sánchez, Juan Antonio; Ruiz-Morales, Carmen

2016-05-01

This note studies the statistical relationships between color channels in radiochromic film readings with flatbed scanners. The same relationships are studied for noise. Finally, their implications for multichannel film dosimetry are discussed. Radiochromic films exposed to wedged fields of 6 MV energy were read in a flatbed scanner. The joint histograms of pairs of color channels were used to obtain the joint and conditional probability density functions between channels. Then, the conditional expectations and variances of one channel given another channel were obtained. Noise was extracted from film readings by means of a multiresolution analysis. Two different dose ranges were analyzed, the first one ranging from 112 to 473 cGy and the second one from 52 to 1290 cGy. For the smallest dose range, the conditional expectations of one channel given another channel can be approximated by linear functions, while the conditional variances are fairly constant. The slopes of the linear relationships between channels can be used to simplify the expression that estimates the dose by means of the multichannel method. The slopes of the linear relationships between each channel and the red one can also be interpreted as weights in the final contribution to dose estimation. However, for the largest dose range, the conditional expectations of one channel given another channel are no longer linear functions. Finally, noises in different channels were found to correlate weakly. Signals present in different channels of radiochromic film readings show a strong statistical dependence. By contrast, noise correlates weakly between channels. For the smallest dose range analyzed, the linear behavior between the conditional expectation of one channel given another channel can be used to simplify calculations in multichannel film dosimetry.

Predictors and Outcomes of Early vs. Later English Language Proficiency Among English Language Learners

PubMed Central

Halle, Tamara; Hair, Elizabeth; Wandner, Laura; McNamara, Michelle; Chien, Nina

2011-01-01

The development of English language learners (ELLs) was explored from kindergarten through eighth grade within a nationally representative sample of first-time kindergartners (N = 19,890). Growth curve analyses indicated that, compared to native English speakers, ELLs were rated by teachers more favorably on approaches to learning, self control, and externalizing behaviors in kindergarten and generally continued to grow in a positive direction on these social/behavioral outcomes at a steeper rate compared to their native English-speaking peers, holding other factors constant. Differences in reading and math achievement between ELLs and native English speakers varied based on the grade at which English proficiency is attained. Specifically, ELLs who were proficient in English by kindergarten entry kept pace with native English speakers in both reading and math initially and over time; ELLs who were proficient by first grade had modest gaps in reading and math achievement compared to native English speakers that closed narrowly or persisted over time; and ELLs who were not proficient by first grade had the largest initial gaps in reading and math achievement compared to native speakers but the gap narrowed over time in reading and grew over time in math. Among those whose home language is not English, acquiring English proficiency by kindergarten entry was associated with better cognitive and behavioral outcomes through eighth grade compared to taking longer to achieve proficiency. Multinomial regression analyses indicated that child, family, and school characteristics predict achieving English proficiency by kindergarten entry compared to achieving proficiency later. Results are discussed in terms of policies and practices that can support ELL children’s growth and development. PMID:22389551

Technical Note: Statistical dependences between channels in radiochromic film readings. Implications in multichannel dosimetry

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

González-López, Antonio, E-mail: antonio.gonzalez7@carm.es; Vera-Sánchez, Juan Antonio; Ruiz-Morales, Carmen

Purpose: This note studies the statistical relationships between color channels in radiochromic film readings with flatbed scanners. The same relationships are studied for noise. Finally, their implications for multichannel film dosimetry are discussed. Methods: Radiochromic films exposed to wedged fields of 6 MV energy were read in a flatbed scanner. The joint histograms of pairs of color channels were used to obtain the joint and conditional probability density functions between channels. Then, the conditional expectations and variances of one channel given another channel were obtained. Noise was extracted from film readings by means of a multiresolution analysis. Two different dosemore » ranges were analyzed, the first one ranging from 112 to 473 cGy and the second one from 52 to 1290 cGy. Results: For the smallest dose range, the conditional expectations of one channel given another channel can be approximated by linear functions, while the conditional variances are fairly constant. The slopes of the linear relationships between channels can be used to simplify the expression that estimates the dose by means of the multichannel method. The slopes of the linear relationships between each channel and the red one can also be interpreted as weights in the final contribution to dose estimation. However, for the largest dose range, the conditional expectations of one channel given another channel are no longer linear functions. Finally, noises in different channels were found to correlate weakly. Conclusions: Signals present in different channels of radiochromic film readings show a strong statistical dependence. By contrast, noise correlates weakly between channels. For the smallest dose range analyzed, the linear behavior between the conditional expectation of one channel given another channel can be used to simplify calculations in multichannel film dosimetry.« less

What Patients Value About Reading Visit Notes: A Qualitative Inquiry of Patient Experiences With Their Health Information

PubMed Central

Fossa, Alan; Folcarelli, Patricia H; Walker, Jan; Bell, Sigall K

2017-01-01

Background Patients are increasingly asking for their health data. Yet, little is known about what motivates patients to engage with the electronic health record (EHR). Furthermore, quality-focused mechanisms for patients to comment about their records are lacking. Objective We aimed to learn more about patient experiences with reading and providing feedback on their visit notes. Methods We developed a patient feedback tool linked to OpenNotes as part of a pilot quality improvement initiative focused on patient engagement. Patients who had appointments with members of 2 primary care teams piloting the program between August 2014-2015 were eligible to participate. We asked patients what they liked about reading notes and about using a feedback tool and analyzed all patient reports submitted during the pilot period. Two researchers coded the qualitative responses (κ=.74). Results Patients and care partners submitted 260 reports. Among these, 98.5% (256/260) of reports indicated that the reporting tool was valuable, and 68.8% (179/260) highlighted what patients liked about reading notes and the OpenNotes patient reporting tool process. We identified 4 themes describing what patients value about note content: confirm and remember next steps, quicker access and results, positive emotions, and sharing information with care partners; and 4 themes about both patients’ use of notes and the feedback tool: accuracy and correcting mistakes, partnership and engagement, bidirectional communication and enhanced education, and importance of feedback. Conclusions Patients and care partners who read notes and submitted feedback reported greater engagement and the desire to help clinicians improve note accuracy. Aspects of what patients like about using both notes as well as a feedback tool highlight personal, relational, and safety benefits. Future efforts to engage patients through the EHR may be guided by what patients value, offering opportunities to strengthen care partnerships between patients and clinicians. PMID:28710055

ObsPy: A Python toolbox for seismology - Sustainability, New Features, and Applications

NASA Astrophysics Data System (ADS)

Krischer, L.; Megies, T.; Sales de Andrade, E.; Barsch, R.; MacCarthy, J.

2016-12-01

ObsPy (https://www.obspy.org) is a community-driven, open-source project dedicated to offer a bridge for seismology into the scientific Python ecosystem. Amongst other things, it provides Read and write support for essentially every commonly used data format in seismology with a unified interface. This includes waveform data as well as station and event meta information. A signal processing toolbox tuned to the specific needs of seismologists. Integrated access to the largest data centers, web services, and databases. Wrappers around third party codes like libmseed and evalresp. Using ObsPy enables users to take advantage of the vast scientific ecosystem that has developed around Python. In contrast to many other programming languages and tools, Python is simple enough to enable an exploratory and interactive coding style desired by many scientists. At the same time it is a full-fledged programming language usable by software engineers to build complex and large programs. This combination makes it very suitable for use in seismology where research code often must be translated to stable and production ready environments, especially in the age of big data. ObsPy has seen constant development for more than six years and enjoys a large rate of adoption in the seismological community with thousands of users. Successful applications include time-dependent and rotational seismology, big data processing, event relocations, and synthetic studies about attenuation kernels and full-waveform inversions to name a few examples. Additionally it sparked the development of several more specialized packages slowly building a modern seismological ecosystem around it. We will present a short overview of the capabilities of ObsPy and point out several representative use cases and more specialized software built around ObsPy. Additionally we will discuss new and upcoming features, as well as the sustainability of open-source scientific software.

Vasculature-Specific Adenovirus Vectors for Gene Therapy of Prostate Cancer

DTIC Science & Technology

2007-02-01

reporter gene. To this end, a recombinant replication-deficient retrovirus vector containing an open reading frame of Renilla luciferase (hRLuc...dual-mode reporter gene ( Renilla luciferase and green fluorescent protein) has been designed and produced in a pan- tropic configuration. • Dual

75 FR 2153 - National Fire Academy Board of Visitors

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-14

...] National Fire Academy Board of Visitors AGENCY: Federal Emergency Management Agency, DHS. ACTION: Committee Management; Notice of Open Teleconference Federal Advisory Committee Meeting. SUMMARY: The National Fire.... Docket: For access to the docket to read background documents or comments received by the National Fire...

Interactive Reading on the Secondary Level.

ERIC Educational Resources Information Center

Gross, Patricia A.

A study of two teachers and four secondary level English classes examined how traditional methods of teaching literature were replaced by more interactive and integrated approaches to text, based primarily upon a whole language philosophy. Intervention aspects purposely remained open-ended to accommodate each teacher's understandings and…

Complete genome sequence of a new maize-associated cytorhabdovirus

USDA-ARS?s Scientific Manuscript database

A new 11,877 nt cytorhabdovirus sequence with 6 open reading frames has been identified in a maize sample. It shares 50 and 51% genome-wide nucleotide sequence identity with northern cereal mosaic cytorhabdovirus (NCMV) and barley yellow striate mosaic cytorhabdovirus (BYSMV), respectively....

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

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

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

Panning, B.; Smiley, J.R.

1993-06-01

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

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

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

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

2000-03-05

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

Splicing of a group II intron involved in the conjugative transfer of pRS01 in lactococci.

PubMed

Mills, D A; McKay, L L; Dunny, G M

1996-06-01

Analysis of a region involved in the conjugative transfer of the lactococcal conjugative element pRS01 has revealed a bacteria] group II intron. Splicing of this lactococcal intron (designated Ll.ltrB) in vivo resulted in the ligation of two exon messages (ltrBE1 and ltrBE2) which encoded a putative conjugative relaxase essential for the transfer of pRS01. Like many group II introns, the Ll.ltrB intron possessed an open reading frame (ltrA) with homology to reverse transcriptases. Remarkably, sequence analysis of ltrA suggested a greater similarity to open reading frames encoded by eukaryotic mitochondrial group II introns than to those identified to date from other bacteria. Several insertional mutations within ltrA resulted in plasmids exhibiting a conjugative transfer-deficient phenotype. These results provide the first direct evidence for splicing of a prokaryotic group II intron in vivo and suggest that conjugative transfer is a mechanism for group II intron dissemination in bacteria.

The genome organisation and taxonomy of Sugarcane striate mosaic associated virus.

PubMed

Thompson, N; Randles, J W

2001-08-01

Sugarcane striate mosaic associated virus (SCSMaV) has slightly flexuous 950 nm x 15 nm filamentous particles and is associated with sugarcane striate mosaic disease in central Queensland, Australia. We report the full sequence of its RNA genome, which comprises 5 open reading frames representing the polymerase, movement function proteins encoded in a triple gene block and coat protein. Phylogenetic analyses based on either the full nucleotide sequence, the polymerase protein, or the coat protein all placed SCSMaV in an intermediate position between the genera Foveavirus and Carlavirus, but outside both genera. In addition, the absence of a sixth open reading frame excludes it from the genus Carlavirus, and the coat protein is approximately half the size of the type member for the genus Foveavirus. Although SCSMaV was most closely allied to Cherry green ring mottle virus by genome analysis, the two viruses are morphologically and biologically dissimilar. SCSMaV may therefore represent a new plant virus taxon.

AirShow 1.0 CFD Software Users' Guide

NASA Technical Reports Server (NTRS)

Mohler, Stanley R., Jr.

2005-01-01

AirShow is visualization post-processing software for Computational Fluid Dynamics (CFD). Upon reading binary PLOT3D grid and solution files into AirShow, the engineer can quickly see how hundreds of complex 3-D structured blocks are arranged and numbered. Additionally, chosen grid planes can be displayed and colored according to various aerodynamic flow quantities such as Mach number and pressure. The user may interactively rotate and translate the graphical objects using the mouse. The software source code was written in cross-platform Java, C++, and OpenGL, and runs on Unix, Linux, and Windows. The graphical user interface (GUI) was written using Java Swing. Java also provides multiple synchronized threads. The Java Native Interface (JNI) provides a bridge between the Java code and the C++ code where the PLOT3D files are read, the OpenGL graphics are rendered, and numerical calculations are performed. AirShow is easy to learn and simple to use. The source code is available for free from the NASA Technology Transfer and Partnership Office.

Generating an Open Reading Frame (ORF) Entry Clone and Destination Clone.

PubMed

Reece-Hoyes, John S; Walhout, Albertha J M

2018-01-02

This protocol describes using the Gateway recombinatorial cloning system to create an Entry clone carrying an open reading frame (ORF) and then to transfer the ORF into a Destination vector. In this example, BP recombination is used to clone an ORF from a cDNA source into the Donor vector pDONR 221. The ORF from the resulting Entry clone is then transferred into the Destination vector pDEST-15; the product (the Destination clone) will express the ORF as an amino-terminal GST-fusion. The technique can be used as a guide for cloning any other DNA fragment of interest-a promoter sequence or 3' untranslated region (UTR), for example-with substitutions of different genetic material such as genomic DNA, att sites, and vectors as required. The series of constructions and transformations requires 9-15 d, not including time that may be required for sequence confirmation, if desired/necessary. © 2018 Cold Spring Harbor Laboratory Press.

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.

OMERO and Bio-Formats 5: flexible access to large bioimaging datasets at scale

NASA Astrophysics Data System (ADS)

Moore, Josh; Linkert, Melissa; Blackburn, Colin; Carroll, Mark; Ferguson, Richard K.; Flynn, Helen; Gillen, Kenneth; Leigh, Roger; Li, Simon; Lindner, Dominik; Moore, William J.; Patterson, Andrew J.; Pindelski, Blazej; Ramalingam, Balaji; Rozbicki, Emil; Tarkowska, Aleksandra; Walczysko, Petr; Allan, Chris; Burel, Jean-Marie; Swedlow, Jason

2015-03-01

The Open Microscopy Environment (OME) has built and released Bio-Formats, a Java-based proprietary file format conversion tool and OMERO, an enterprise data management platform under open source licenses. In this report, we describe new versions of Bio-Formats and OMERO that are specifically designed to support large, multi-gigabyte or terabyte scale datasets that are routinely collected across most domains of biological and biomedical research. Bio- Formats reads image data directly from native proprietary formats, bypassing the need for conversion into a standard format. It implements the concept of a file set, a container that defines the contents of multi-dimensional data comprised of many files. OMERO uses Bio-Formats to read files natively, and provides a flexible access mechanism that supports several different storage and access strategies. These new capabilities of OMERO and Bio-Formats make them especially useful for use in imaging applications like digital pathology, high content screening and light sheet microscopy that create routinely large datasets that must be managed and analyzed.

Differentiation of mycoplasmalike organisms (MLOs) in European fruit trees by PCR using specific primers derived from the sequence of a chromosomal fragment of the apple proliferation MLO.

PubMed Central

Jarausch, W; Saillard, C; Dosba, F; Bové, J M

1994-01-01

A 1.8-kb chromosomal DNA fragment of the mycoplasmalike organism (MLO) associated with apple proliferation was sequenced. Three putative open reading frames were observed on this fragment. The protein encoded by open reading frame 2 shows significant homologies with bacterial nitroreductases. From the nucleotide sequence four primer pairs for PCR were chosen to specifically amplify DNA from MLOs associated with European diseases of fruit trees. Primer pairs specific for (i) Malus-affecting MLOs, (ii) Malus- and Prunus-affecting MLOs, and (iii) Malus-, Prunus-, and Pyrus-affecting MLOs were obtained. Restriction enzyme analysis of the amplification products revealed restriction fragment length polymorphisms between Malus-, Prunus, and Pyrus-affecting MLOs as well as between different isolates of the apple proliferation MLO. No amplification with either primer pair could be obtained with DNA from 12 different MLOs experimentally maintained in periwinkle. Images PMID:7916180

Orange County, Yellow History: An Intimate Encounter with Vietnamese American Lives

ERIC Educational Resources Information Center

Tranguyen, Trangdai

2004-01-01

Anchored on the Vietnamese American Project (VAP), this essay presents the documentation of the Vietnamese American Experience through the voices of ethnic Vietnamese in Orange County, California, home to the largest concentration of this ethnic group outside Vietnam. Groundbreaking in its approach and method, VAP is an open forum that enables…

TIAA-CREF Moves Beyond Its Base in Pensions.

ERIC Educational Resources Information Center

Strosnider, Kim

1998-01-01

Teachers Insurance and Annuity Association (TIAA) and College Retirement Equities Fund (CREF), the largest pension system in the country, has lost its tax exemption, a change that has both created problems and opened doors to new ventures. TIAA-CREF is now seeking opportunities to manage state tuition-savings plans, and has also established six…

The Professors behind the MOOC Hype

ERIC Educational Resources Information Center

Kolowich, Steve

2013-01-01

The largest-ever survey of professors who have taught MOOCs, or massive open online courses, shows that the process is time-consuming, but, according to the instructors, often successful. Nearly half of the professors felt their online courses were as rigorous academically as the versions they taught in the classroom. The survey, conducted by "The…

Bioremediation efficiency of the largest scale artificial Porphyra yezoensis cultivation in the open sea in China.

PubMed

Wu, Hailong; Huo, Yuanzi; Zhang, Jianheng; Liu, Yuanyuan; Zhao, Yating; He, Peimin

2015-06-15

The bioremediation efficiency of China's largest scale Porphyra yezoensis cultivation for removing dissolved nutrients and controlling harmful algae was studied in the radial sandbanks waters of Jiangsu Province in the year 2012-2013. Mean nutrient concentration values in the P. yezoensis cultivation area were significantly lower than those in the non-cultivation area, especially during the cultivation season (p<0.05). Tissue nitrogen and phosphorus contents of seaweeds were 5.99-0.80% (dry weight (DW)) and 0.16-0.19% (DW), respectively. Production of P. yezoensis was 58950.87tons DW. Based on these values, 3688.15tons of tissue nitrogen and 105.61tons of tissue phosphorus were removed by harvesting P. yezoensis. The richness index of the red tide species Skeleton emacostatum declined from 0.32 to 0.05 during the P. yezoensis cultivation season. These results indicate that large-scale cultivation of P. yezoensis can be used to efficiently alleviate eutrophication and control harmful algae blooms in open sea. Copyright © 2015 Elsevier Ltd. All rights reserved.

Phonological Awareness and Rapid Automatized Naming Predicting Early Development in Reading and Spelling: Results from a Cross-Linguistic Longitudinal Study

PubMed Central

Furnes, Bjarte; Samuelsson, Stefan

2010-01-01

In this study, the relationship between latent constructs of phonological awareness (PA) and rapid automatized naming (RAN) were investigated and related to later measures of reading and spelling in children learning to read in different alphabetic writing systems (i.e., Norwegian/Swedish vs. English). 750 U.S./Australian children and 230 Scandinavian children were followed longitudinally between kindergarten and 2nd grade. PA and RAN were measured in kindergarten and Grade 1, while word recognition, phonological decoding, and spelling were measured in kindergarten, Grade 1, and Grade 2. In general, high stability was observed for the various reading and spelling measures, such that little additional variance was left open for PA and RAN. However, results demonstrated that RAN was more related to reading than spelling across orthographies, with the opposite pattern shown for PA. In addition, tests of measurement invariance show that the factor loadings of each observed indicator on the latent PA factor was the same across U.S./Australia and Scandinavia. Similar findings were obtained for RAN. In general, tests of structural invariance show that models of early literacy development are highly transferable across languages. PMID:21359098

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

PubMed

Pritt, Jacob; Langmead, Ben

2016-09-19

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

Mars Global Digital Dune Database: MC2-MC29

USGS Publications Warehouse

Hayward, Rosalyn K.; Mullins, Kevin F.; Fenton, L.K.; Hare, T.M.; Titus, T.N.; Bourke, M.C.; Colaprete, Anthony; Christensen, P.R.

2007-01-01

Introduction The Mars Global Digital Dune Database presents data and describes the methodology used in creating the database. The database provides a comprehensive and quantitative view of the geographic distribution of moderate- to large-size dune fields from 65? N to 65? S latitude and encompasses ~ 550 dune fields. The database will be expanded to cover the entire planet in later versions. Although we have attempted to include all dune fields between 65? N and 65? S, some have likely been excluded for two reasons: 1) incomplete THEMIS IR (daytime) coverage may have caused us to exclude some moderate- to large-size dune fields or 2) resolution of THEMIS IR coverage (100m/pixel) certainly caused us to exclude smaller dune fields. The smallest dune fields in the database are ~ 1 km2 in area. While the moderate to large dune fields are likely to constitute the largest compilation of sediment on the planet, smaller stores of sediment of dunes are likely to be found elsewhere via higher resolution data. Thus, it should be noted that our database excludes all small dune fields and some moderate to large dune fields as well. Therefore the absence of mapped dune fields does not mean that such dune fields do not exist and is not intended to imply a lack of saltating sand in other areas. Where availability and quality of THEMIS visible (VIS) or Mars Orbiter Camera narrow angle (MOC NA) images allowed, we classifed dunes and included dune slipface measurements, which were derived from gross dune morphology and represent the prevailing wind direction at the last time of significant dune modification. For dunes located within craters, the azimuth from crater centroid to dune field centroid was calculated. Output from a general circulation model (GCM) is also included. In addition to polygons locating dune fields, the database includes over 1800 selected Thermal Emission Imaging System (THEMIS) infrared (IR), THEMIS visible (VIS) and Mars Orbiter Camera Narrow Angle (MOC NA) images that were used to build the database. The database is presented in a variety of formats. It is presented as a series of ArcReader projects which can be opened using the free ArcReader software. The latest version of ArcReader can be downloaded at http://www.esri.com/software/arcgis/arcreader/download.html. The database is also presented in ArcMap projects. The ArcMap projects allow fuller use of the data, but require ESRI ArcMap? software. Multiple projects were required to accommodate the large number of images needed. A fuller description of the projects can be found in the Dunes_ReadMe file and the ReadMe_GIS file in the Documentation folder. For users who prefer to create their own projects, the data is available in ESRI shapefile and geodatabase formats, as well as the open Geographic Markup Language (GML) format. A printable map of the dunes and craters in the database is available as a Portable Document Format (PDF) document. The map is also included as a JPEG file. ReadMe files are available in PDF and ASCII (.txt) files. Tables are available in both Excel (.xls) and ASCII formats.

Transcriptional analysis of Penaeus stylirostris densovirus genes

USDA-ARS?s Scientific Manuscript database

Penaeus stylirostris densovirus (PstDNV) genome contains three open reading frames (ORFs), left, middle, and right, which encode a non-structural (NS) protein, an unknown protein, and a capsid protein (CP), respectively. Transcription mapping revealed that P2, P11 and P61 promoters transcribe the le...

The Writing Curriculum and the Student.

ERIC Educational Resources Information Center

Ediger, Marlow

Writing must receive major emphasis in teaching-learning situations. There are important differences between creative endeavors and those that involve role learning and exact answers. Creativity emphasizes the novel, the unique, the original, and the open-ended. Creativity should stress writing across the curriculum, and should involve reading and…

44 CFR 80.1 - Purpose and scope.

Code of Federal Regulations, 2014 CFR

2014-10-01

... date, applicable program regulations and guidance in effect for the funding program (available at http... requirements of the funding grant program and must be read in conjunction with the relevant program regulations... oversight, applies to projects for which the funding program application period opens or for which funding...

44 CFR 80.1 - Purpose and scope.

Code of Federal Regulations, 2012 CFR

2012-10-01

... date, applicable program regulations and guidance in effect for the funding program (available at http... requirements of the funding grant program and must be read in conjunction with the relevant program regulations... oversight, applies to projects for which the funding program application period opens or for which funding...

44 CFR 80.1 - Purpose and scope.

Code of Federal Regulations, 2011 CFR

2011-10-01

... date, applicable program regulations and guidance in effect for the funding program (available at http... requirements of the funding grant program and must be read in conjunction with the relevant program regulations... oversight, applies to projects for which the funding program application period opens or for which funding...