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.

Dependency Distance Differences across Interpreting Types: Implications for Cognitive Demand

PubMed Central

Liang, Junying; Fang, Yuanyuan; Lv, Qianxi; Liu, Haitao

2017-01-01

Interpreting is generally recognized as a particularly demanding language processing task for the cognitive system. Dependency distance, the linear distance between two syntactically related words in a sentence, is an index of sentence complexity and is also able to reflect the cognitive constraints during various tasks. In the current research, we examine the difference in dependency distance among three interpreting types, namely, simultaneous interpreting, consecutive interpreting and read-out translated speech based on a treebank comprising these types of interpreting output texts with dependency annotation. Results show that different interpreting renditions yield different dependency distances, and consecutive interpreting texts entail the smallest dependency distance other than those of simultaneous interpreting and read-out translated speech, suggesting that consecutive interpreting bears heavier cognitive demands than simultaneous interpreting. The current research suggests for the first time that interpreting is an extremely demanding cognitive task that can further mediate the dependency distance of output sentences. Such findings may be due to the minimization of dependency distance under cognitive constraints. PMID:29312027

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.

Open versus robotic-assisted transabdominal preperitoneal (R-TAPP) inguinal hernia repair: a multicenter matched analysis of clinical outcomes.

PubMed

Gamagami, R; Dickens, E; Gonzalez, A; D'Amico, L; Richardson, C; Rabaza, J; Kolachalam, R

2018-04-26

To compare the perioperative outcomes of initial, consecutive robotic-assisted transabdominal preperitoneal (R-TAPP) inguinal hernia repair (IHR) cases with consecutive open cases completed by the same surgeons. Multicenter, retrospective, comparative study of perioperative results from open and robotic IHR using standard univariate and multivariate regression analyses for propensity score matched (1:1) cohorts. Seven general surgeons at six institutions contributed 602 consecutive open IHR and 652 consecutive R-TAPP IHR cases. Baseline patient characteristics in the unmatched groups were similar with the exception of previous abdominal surgery and all baseline characteristics were comparable in the matched cohorts. In matched analyses, postoperative complications prior to discharge were comparable. However, from post discharge through 30 days, fewer patients experienced complications in the R-TAPP group than in the open group [4.3% vs 7.7% (p = 0.047)]. The R-TAPP group had no reoperations post discharge through 30 days of follow-up compared with five patients (1.1%) in the open group (p = 0.062), respectively. Multivariate logistic regression analysis which demonstrated patient age > 65 years and the open approach were risk factors for complications within 30 days post discharge in the matched group [age > 65 years: odds ratio (OR) = 3.33 (95% CI 1.89, 5.87; p < 0.0001); open approach: OR = 1.89 (95% CI 1.05, 3.38; p = 0.031)]. In this matched analysis, R-TAPP provides similar postoperative complications prior to discharge and a lower rate of postoperative complications through 30 days compared to open repair. R-TAPP is a promising and reproducible approach, and may facilitate adoption of minimally invasive repairs of inguinal hernias.

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.

Repeated readings and science: Fluency with expository passages

NASA Astrophysics Data System (ADS)

Kostewicz, Douglas E.

The current study investigated the effects of repeated readings to a fluency criterion (RRFC) for seven students with disabilities using science text. The study employed a single subject design, specifically, two multiple probe multiple baselines across subjects, to evaluate the effects of the RRFC intervention. Results indicated that students met criterion (200 or more correct words per minute with 2 or fewer errors) on four consecutive passages. A majority of students displayed accelerations to correct words per minute and decelerations to incorrect words per minute on successive initial, intervention readings suggesting reading transfer. Students' reading scores during posttest and maintenance out performed pre-test and baseline readings provided additional measures of reading transfer. For a relationship to comprehension, students scored higher on oral retell measures after meeting criterion as compared to initial readings. Overall, the research findings suggested that the RRFC intervention improves science reading fluency for students with disabilities, and may also indirectly benefit comprehension.

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

Quality of the blood pressure phenotype in the GEnotipo, Fenotipo y Ambiente de la hipertensión arterial en UruguaY (GEFA-HT-UY) study.

PubMed

Luzardo, Leonella; Sottolano, Mariana; Lujambio, Inés; Robaina, Sebastián; Thijs, Lutgarde; da Rosa, Alicia; Krul, Nadia; Carusso, Florencia; Ríos, Ana C; Olascoaga, Alicia; Noboa, Oscar; Staessen, Jan A; Boggia, José

2014-12-01

In the ongoing GEnotipo, Fenotipo y Ambiente de la HiperTensión Arterial en UruguaY (GEFA-HT-UY) study, we applied standardized epidemiological methods to determine complex phenotypes including blood pressure (BP). In this report, we present the quality control of the conventionally measured BP. Three trained observers measured BP five times consecutively in the seated position at each of two home visits and one clinic visit according to the guidelines of the European Society of Hypertension. On 1 December 2013, 4379 single BP readings in 170 participants were available for analysis. Fewer BP readings than the five planned per contact occurred only at one home visit. Among observers, the frequency of identical consecutive readings for systolic or diastolic BP varied from 0 to 4.2%. The occurrence of odd readings ranged from 0.1 to 0.6%. Only 21.6% of the systolic and diastolic BP readings ended on zero (expected 20%). At home visits, there was a progressive decline in BP from the first to the fifth reading. The average of the five BP readings also decreased from the first to the second home visit (-5.63/-2.34 mmHg). Our study highlighted the necessity to implement a stringent quality control of the conventionally measured BP. The procedures set up in the GEFA-HT-UY study are resulting in a well-defined BP phenotype, which is consistent with that in other population studies.

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…

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.

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

Comparison of the Pentacam equivalent keratometry reading and IOL Master keratometry measurement in intraocular lens power calculations.

PubMed

Karunaratne, Nicholas

2013-12-01

To compare the accuracy of the Pentacam Holladay equivalent keratometry readings with the IOL Master 500 keratometry in calculating intraocular lens power. Non-randomized, prospective clinical study conducted in private practice. Forty-five consecutive normal patients undergoing cataract surgery. Forty-five consecutive patients had Pentacam equivalent keratometry readings at the 2-, 3 and 4.5-mm corneal zone and IOL Master keratometry measurements prior to cataract surgery. For each Pentacam equivalent keratometry reading zone and IOL Master measurement the difference between the observed and expected refractive error was calculated using the Holladay 2 and Sanders, Retzlaff and Kraff theoretic (SRKT) formulas. Mean keratometric value and mean absolute refractive error. There was a statistically significantly difference between the mean keratometric values of the IOL Master, Pentacam equivalent keratometry reading 2-, 3- and 4.5-mm measurements (P < 0.0001, analysis of variance). There was no statistically significant difference between the mean absolute refraction error for the IOL Master and equivalent keratometry readings 2 mm, 3 mm and 4.5 mm zones for either the Holladay 2 formula (P = 0.14) or SRKT formula (P = 0.47). The lowest mean absolute refraction error for Holladay 2 equivalent keratometry reading was the 4.5 mm zone (mean 0.25 D ± 0.17 D). The lowest mean absolute refraction error for SRKT equivalent keratometry reading was the 4.5 mm zone (mean 0.25 D ± 0.19 D). Comparing the absolute refraction error of IOL Master and Pentacam equivalent keratometry reading, best agreement was with Holladay 2 and equivalent keratometry reading 4.5 mm, with mean of the difference of 0.02 D and 95% limits of agreement of -0.35 and 0.39 D. The IOL Master keratometry and Pentacam equivalent keratometry reading were not equivalent when used only for corneal power measurements. However, the keratometry measurements of the IOL Master and Pentacam equivalent keratometry reading 4.5 mm may be similarly effective when used in intraocular lens power calculation formulas, following constant optimization. © 2013 Royal Australian and New Zealand College of Ophthalmologists.

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…

Expressive writing for gay-related stress: psychosocial benefits and mechanisms underlying improvement.

PubMed

Pachankis, John E; Goldfried, Marvin R

2010-02-01

This study tested the effectiveness of an expressive writing intervention for gay men on outcomes related to psychosocial functioning. Seventy-seven gay male college students (mean age = 20.19 years, SD = 1.99) were randomly assigned to write for 20 min a day for 3 consecutive days about either (a) the most stressful or traumatic gay-related event in their lives or (b) a neutral topic. We tested an exposure-based hypothesis of written emotional expression by asking half of the participants who were assigned to write about gay-related stress to read their previous day's narrative before writing, whereas the other half did not. Posttest and 3-month follow-up outcomes were assessed with common measures of overall psychological distress, depression, physical health symptoms, and positive and negative affect. Gay-specific social functioning was assessed with measures of gay-related rejection sensitivity, gay-specific self-esteem, and items regarding openness and comfort with one's sexual orientation. Participants who wrote about gay-related stress, regardless of whether they read their previous day's writing, reported significantly greater openness with their sexual orientation 3 months following writing than participants who wrote about a neutral topic, F(1, 74) = 6.66, p < .05, eta(2) = .08. Additional analyses examined the impact of emotional engagement in the writing, severity of the expressed topic, previous disclosure of writing topic, tendency to conceal, and level of perceived social support on mental health outcomes. The findings suggest that an expressive writing task targeting gay-related stress can improve gay men's psychosocial functioning, especially openness with sexual orientation. The intervention seems to be particularly beneficial for those men who write about more severe topics and for those with lower levels of social support. The findings suggest future tests of expressive writing tasks for different aspects of stigma-related stress.

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

PubMed Central

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

2014-01-01

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

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

PubMed Central

Schaeffer, E; Sninsky, J J

1984-01-01

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

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

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-26

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

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

ERIC Educational Resources Information Center

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

2018-01-01

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

A simplified financial model for automatic meter reading

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

Ward, S.M.

1994-01-15

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

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...

Prevention by cromakalim of spontaneously occurring cardiac necroses in polymyopathic hamsters.

PubMed

Jasmin, G; Proschek, L

1996-11-01

Previous studies on the heart necrotizing process at early stages of the hamster polymyopathy have led us to believe that this hereditary disease derives from a defective transmembrane ion flux resulting in myocardial Ca2+ over-load. On the other hand, certain K+ ATP channel openers were shown to prevent cytosolic Ca2+ accumulation in ischemic hearts. Therefore, we investigated the potential beneficial effect of chronic treatment with cromakalim (CR) on the development of necrotic changes in hamster myopathic hearts. Young cardiomyopathic (CM) hamsters were treated parenterally with CR over 4 consecutive weeks. The K+ ATP opener was dissolved in 5% DMSO and injected twice daily (s.c. and i.p. alternatively) at a dose level of 2.5 mg/kg per injection. Microscopic readings were carried out in staged serial paraffin sections of heart ventricles, the diaphragm, and tongue, will all tissues freshly taken at autopsy. In comparison with control untreated hearts, which exhibit numerous necrotic calcific foci, only minute myolytic lesions were found in 5 of 12 hamsters hearts receiving CR (p < 0.0001). Interestingly, the dystrophic process in the tongue was significantly less severe (p < 0.0004) in CR-treated animals. These observations provide evidence for the first time that in vivo sustained treatment with a K+ ATP opener exerts cardioprotection upon development of the hamster hereditary cardiomyopathy.

42 CFR 417.426 - Open enrollment requirements.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 42 Public Health 3 2013-10-01 2013-10-01 false Open enrollment requirements. 417.426 Section 417... Open enrollment requirements. (a) Basic requirements. (1) HMOs or CMPs must provide open enrollment for Medicare beneficiaries for at least 30 consecutive days during each contract year. (2) During open...

42 CFR 417.426 - Open enrollment requirements.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 42 Public Health 3 2014-10-01 2014-10-01 false Open enrollment requirements. 417.426 Section 417... Open enrollment requirements. (a) Basic requirements. (1) HMOs or CMPs must provide open enrollment for Medicare beneficiaries for at least 30 consecutive days during each contract year. (2) During open...

42 CFR 417.426 - Open enrollment requirements.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 42 Public Health 3 2012-10-01 2012-10-01 false Open enrollment requirements. 417.426 Section 417... Open enrollment requirements. (a) Basic requirements. (1) HMOs or CMPs must provide open enrollment for Medicare beneficiaries for at least 30 consecutive days during each contract year. (2) During open...

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,…

On the relationships between DSM-5 dysfunctional personality traits and social cognition deficits: A study in a sample of consecutively admitted Italian psychotherapy patients.

PubMed

Fossati, Andrea; Somma, Antonella; Krueger, Robert F; Markon, Kristian E; Borroni, Serena

2017-11-01

This study aims at testing the hypothesis that the Diagnostic and Statistical Manual of Mental Disorders fifth edition (DSM-5) alternative model of personality disorder (AMPD) traits may be significantly associated with deficits on 2 different social cognition tasks, namely, the Reading the Mind in the Eyes Test and the Movie for the Assessment of Social Cognition, in a sample of consecutively admitted inpatients and outpatients. The sample was composed of 181 consecutively admitted participants (57.5% women; mean age = 38.58 years). Correlation coefficients and partial correlation coefficients were computed in order to assess the associations among social cognition tasks, DSM-5 AMPD traits, and dimensionally assessed DSM-5 Section II personality disorders. Specific maladaptive traits listed in the DSM-5 AMPD were significantly associated with Reading the Mind in the Eyes Test scores and Movie for the Assessment of Social Cognition scores, even when the effect of selected DSM-5 Section II personality disorders was controlled for. Our results support the relevance of studying social cognitive functioning in subjects suffering from personality disorders. Copyright © 2017 John Wiley & Sons, Ltd.

Bringing functions together with fusion enzymes--from nature's inventions to biotechnological applications.

PubMed

Elleuche, Skander

2015-02-01

It is a mammoth task to develop a modular protein toolbox enabling the production of posttranslational organized multifunctional enzymes that catalyze reactions in complex pathways. However, nature has always guided scientists to mimic evolutionary inventions in the laboratory and, nowadays, versatile methods have been established to experimentally connect enzymatic activities with multiple advantages. Among the oldest known natural examples is the linkage of two or more juxtaposed proteins catalyzing consecutive, non-consecutive, or opposing reactions by a native peptide bond. There are multiple reasons for the artificial construction of such fusion enzymes including improved catalytic activities, enabled substrate channelling by proximity of biocatalysts, higher stabilities, and cheaper production processes. To produce fused proteins, it is either possible to genetically fuse coding open reading frames or to connect proteins in a posttranslational process. Molecular biology techniques that have been established for the production of end-to-end or insertional fusions include overlap extension polymerase chain reaction, cloning, and recombination approaches. Depending on their flexibility and applicability, these methods offer various advantages to produce fusion genes in high throughput, different orientations, and including linker sequences to maximize the flexibility and performance of fusion partners. In this review, practical techniques to fuse genes are highlighted, enzymatic parameters to choose adequate enzymes for fusion approaches are summarized, and examples with biotechnological relevance are presented including a focus on plant biomass-degrading glycosyl hydrolases.

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.

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...

Environmental Mapping by a HERO-1 Robot Using Sonar and a Laser Barcode Scanner.

DTIC Science & Technology

1983-12-01

can be labled with an x-y type coordinate grid allowing the rover to directly read * its location as it moves along. A different approach is to...uses a two-dimensional grid of two character barcodes as reference objects. Since bar codes are designed to be read in either of two orientations (top...Processing Laboratory at AFIT (see Appendix B for listing). Navigation grid codes consist of two digits running consecutively from 00 to FF, yielding 256

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…

Position coding effects in a 2D scenario: the case of musical notation.

PubMed

Perea, Manuel; García-Chamorro, Cristina; Centelles, Arnau; Jiménez, María

2013-07-01

How does the cognitive system encode the location of objects in a visual scene? In the past decade, this question has attracted much attention in the field of visual-word recognition (e.g., "jugde" is perceptually very close to "judge"). Letter transposition effects have been explained in terms of perceptual uncertainty or shared "open bigrams". In the present study, we focus on note position coding in music reading (i.e., a 2D scenario). The usual way to display music is the staff (i.e., a set of 5 horizontal lines and their resultant 4 spaces). When reading musical notation, it is critical to identify not only each note (temporal duration), but also its pitch (y-axis) and its temporal sequence (x-axis). To examine note position coding, we employed a same-different task in which two briefly and consecutively presented staves contained four notes. The experiment was conducted with experts (musicians) and non-experts (non-musicians). For the "different" trials, the critical conditions involved staves in which two internal notes that were switched vertically, horizontally, or fully transposed--as well as the appropriate control conditions. Results revealed that note position coding was only approximate at the early stages of processing and that this encoding process was modulated by expertise. We examine the implications of these findings for models of object position encoding. Copyright © 2013 Elsevier B.V. All rights reserved.

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...

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

USDA-ARS?s Scientific Manuscript database

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

A Multisite Cluster Randomized Field Trial of Open Court Reading

ERIC Educational Resources Information Center

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

2008-01-01

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

U.S. Global Change Research Program

MedlinePlus

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

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

PubMed Central

2013-01-01

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

Readings and Experiences of Multimodality

ERIC Educational Resources Information Center

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

2017-01-01

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

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)

34 CFR 685.217 - Teacher loan forgiveness program.

Code of Federal Regulations, 2014 CFR

2014-07-01

... five consecutive years— (i) At an eligible secondary school as a highly qualified mathematics or science teacher, or by an eligible educational service agency as a highly qualified teacher of mathematics... forgiveness if the borrower— (A) Demonstrated knowledge and teaching skills in reading, writing, mathematics...

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.

34 CFR 682.216 - Teacher loan forgiveness program.

Code of Federal Regulations, 2013 CFR

2013-07-01

... consecutive years— (i) At an eligible secondary school as a highly qualified mathematics or science teacher, or at an eligible educational service agency as a highly qualified teacher of mathematics or science... borrower— (A) Demonstrated knowledge and teaching skills in reading, writing, mathematics, and other areas...

34 CFR 685.217 - Teacher loan forgiveness program.

Code of Federal Regulations, 2013 CFR

2013-07-01

... for five consecutive years— (i) At an eligible secondary school as a highly qualified mathematics or science teacher, or at an eligible educational service agency as a highly qualified teacher of mathematics... forgiveness if the borrower— (A) Demonstrated knowledge and teaching skills in reading, writing, mathematics...

34 CFR 682.216 - Teacher loan forgiveness program.

Code of Federal Regulations, 2014 CFR

2014-07-01

... consecutive years— (i) At an eligible secondary school as a highly qualified mathematics or science teacher, or for an eligible educational service agency as a highly qualified teacher of mathematics or science... borrower— (A) Demonstrated knowledge and teaching skills in reading, writing, mathematics, and other areas...

34 CFR 685.217 - Teacher loan forgiveness program.

Code of Federal Regulations, 2012 CFR

2012-07-01

... for five consecutive years— (i) At an eligible secondary school as a highly qualified mathematics or science teacher, or at an eligible educational service agency as a highly qualified teacher of mathematics... forgiveness if the borrower— (A) Demonstrated knowledge and teaching skills in reading, writing, mathematics...

34 CFR 682.216 - Teacher loan forgiveness program.

Code of Federal Regulations, 2012 CFR

2012-07-01

... consecutive years— (i) At an eligible secondary school as a highly qualified mathematics or science teacher, or at an eligible educational service agency as a highly qualified teacher of mathematics or science... borrower— (A) Demonstrated knowledge and teaching skills in reading, writing, mathematics, and other areas...

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…

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.…

Genetic diversity and potential vectors and reservoirs of Cucurbit aphid-borne yellows virus in southeastern Spain.

PubMed

Kassem, Mona A; Juarez, Miguel; Gómez, Pedro; Mengual, Carmen M; Sempere, Raquel N; Plaza, María; Elena, Santiago F; Moreno, Aranzazu; Fereres, Alberto; Aranda, Miguel A

2013-11-01

The genetic variability of a Cucurbit aphid-borne yellows virus (CABYV) (genus Polerovirus, family Luteoviridae) population was evaluated by determining the nucleotide sequences of two genomic regions of CABYV isolates collected in open-field melon and squash crops during three consecutive years in Murcia (southeastern Spain). A phylogenetic analysis showed the existence of two major clades. The sequences did not cluster according to host, year, or locality of collection, and nucleotide similarities among isolates were 97 to 100 and 94 to 97% within and between clades, respectively. The ratio of nonsynonymous to synonymous nucleotide substitutions reflected that all open reading frames have been under purifying selection. Estimates of the population's genetic diversity were of the same magnitude as those previously reported for other plant virus populations sampled at larger spatial and temporal scales, suggesting either the presence of CABYV in the surveyed area long before it was first described, multiple introductions, or a particularly rapid diversification. We also determined the full-length sequences of three isolates, identifying the occurrence and location of recombination events along the CABYV genome. Furthermore, our field surveys indicated that Aphis gossypii was the major vector species of CABYV and the most abundant aphid species colonizing melon fields in the Murcia (Spain) region. Our surveys also suggested the importance of the weed species Ecballium elaterium as an alternative host and potential virus reservoir.

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)

Visual processing during natural reading

PubMed Central

Weiss, Béla; Knakker, Balázs; Vidnyánszky, Zoltán

2016-01-01

Reading is a unique human ability that plays a pivotal role in the development and functioning of our modern society. However, its neural basis remains poorly understood since previous research was focused on reading words with fixed gaze. Here we developed a methodological framework for single-trial analysis of fixation onset-related EEG activity (FOREA) that enabled us to investigate visual information processing during natural reading. To reveal the effect of reading skills on orthographic processing during natural reading, we measured how altering the configural properties of the written text by modifying inter-letter spacing affects FOREA. We found that orthographic processing is reflected in FOREA in three consecutive time windows (120–175 ms, 230–265 ms, 345–380 ms after fixation onset) and the magnitude of FOREA effects in the two later time intervals showed a close association with the participants’ reading speed: FOREA effects were larger in fast than in slow readers. Furthermore, these expertise-driven configural effects were clearly dissociable from the FOREA signatures of visual perceptual processes engaged to handle the increased crowding (155–220 ms) as a result of decreasing letter spacing. Our findings revealed that with increased reading skills orthographic processing becomes more sensitive to the configural properties of the written text. PMID:27231193

Benefits of double reading of screening mammograms: retrospective study on a consecutive series.

PubMed

Caumo, F; Brunelli, S; Zorzi, M; Baglio, I; Ciatto, S; Montemezzi, S

2011-06-01

The purpose of this study was to assess the performance of delayed second reading of screening mammograms when added to real-time reading plus immediate assessment. The study setting was the mammography screening programme of an Italian Local Health Unit. Recall rate and cancer detection rate at first reading or informed second reading only were assessed in a cohort of 23,629 women aged 50-69 years screened during 2007-2008. Incremental recall rate, incremental cancer detection rate and incremental cost of second reading were determined. Recall rate was 13.0% at first and 2.7% at second reading (incremental recall rate +21.1%). Overall, recalls were more frequent in the younger decade and in the presence of denser breasts. Cancer detection rate was 7.06‰ (n=167) at first and 0.93‰ (n=22) at second reading (incremental cancer detection rate +13.1%). Compared with first reading, second reading detected more cancers depicted as isolated microcalcifications and distortions (40.9% vs. 16.2%, p=0.02) and at a lower stage (stage 0-I 81.8% vs. 69.5%, p=0.34). The cost of adding delayed second reading was + 3.65 per screened individual or 3,926.61 per incremental cancer detected. The study confirms the efficacy of second reading, even as an adjunct to real-time single reading plus immediate assessment. Incremental recall rate is acceptable in view of the incremental cancer detection rate, and both figures are within the range of literature reports on double-reading performance.

SPAX - PAX with Super-Pages

NASA Astrophysics Data System (ADS)

Bößwetter, Daniel

Much has been written about the pros and cons of column-orientation as a means to speed up read-mostly analytic workloads in relational databases. In this paper we try to dissect the primitive mechanisms of a database that help express the coherence of tuples and present a novel way of organizing relational data in order to exploit the advantages of both, the row-oriented and the column-oriented world. As we go, we break with yet another bad habit of databases, namely the equal granularity of reads and writes which leads us to the introduction of consecutive clusters of disk pages called super-pages.

Molecular Characterization of a Chromosomal Determinant Conferring Resistance to Zinc and Cobalt Ions in Staphylococcus aureus

PubMed Central

Xiong, Anming; Jayaswal, Radheshyam K.

1998-01-01

A DNA fragment conferring resistance to zinc and cobalt ions was isolated from a genomic DNA library of Staphylococcus aureus RN450. The DNA sequence analysis revealed two consecutive open reading frames, designated zntR and zntA. The predicted ZntR and ZntA showed significant homology to members of ArsR and cation diffusion families, respectively. A mutant strain containing the null allele of zntA was more sensitive to zinc and cobalt ions than was the parent strain. The metal-sensitive phenotype of the mutant was complemented by a 2.9-kb DNA fragment containing zntR and zntA. An S. aureus strain harboring multiple copies of zntR and zntA showed an increased resistance to zinc. The resistance to zinc in the wild-type strain was inducible. Transcriptional analysis indicated that zntR and zntA genes were cotranscribed. The zinc uptake studies suggested that the zntA product was involved in the export of zinc ions out of cells. PMID:9696746

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.

Effects of a Supplemental Vocabulary Program on Word Knowledge and Passage Comprehension

ERIC Educational Resources Information Center

Apthorp, Helen; Randel, Bruce; Cherasaro, Trudy; Clark, Tedra; McKeown, Margaret; Beck, Isabel

2012-01-01

A cluster randomized trial estimated the effects of a supplemental vocabulary program, Elements of Reading[R]: vocabulary on student vocabulary and passage comprehension in moderate- to high-poverty elementary schools. Forty-four schools participated over a period spanning 2 consecutive school years. At baseline, 1,057 teachers and 16,471 students…

Effects of Emergent Literacy Interventions for Preschoolers with Autism Spectrum Disorder

ERIC Educational Resources Information Center

Hudson, Roxanne F.; Sanders, Elizabeth A.; Greenway, Rosanne; Xie, Sharon; Smith, Maya; Gasamis, Colin; Martini, Jay; Schwartz, Ilene; Hackett, Jacob

2017-01-01

Combining data from a series of three planned consecutive randomized controlled trials, the present study investigates two literacy interventions for preschool children with autism spectrum disorder. For the first cohort, children were randomized to interactive book reading (IBR; treatment) or business as usual (BAU; control); in Cohort 2,…

40 CFR 63.11647 - What are my monitoring requirements?

Code of Federal Regulations, 2011 CFR

2011-07-01

... temperature limit is the highest temperature measured during any run of the initial compliance test or 10... either the highest reading during the test or at 10 °F higher than the average temperature measured... least 11 days apart from other consecutive tests. The mercury concentration must be maintained below the...

40 CFR 63.11647 - What are my monitoring requirements?

Code of Federal Regulations, 2012 CFR

2012-07-01

... temperature limit is the highest temperature measured during any run of the initial compliance test or 10... either the highest reading during the test or at 10 °F higher than the average temperature measured... least 11 days apart from other consecutive tests. The mercury concentration must be maintained below the...

40 CFR 63.11647 - What are my monitoring requirements?

Code of Federal Regulations, 2013 CFR

2013-07-01

... temperature limit is the highest temperature measured during any run of the initial compliance test or 10... either the highest reading during the test or at 10 °F higher than the average temperature measured... least 11 days apart from other consecutive tests. The mercury concentration must be maintained below the...

40 CFR 63.11647 - What are my monitoring requirements?

Code of Federal Regulations, 2014 CFR

2014-07-01

... temperature limit is the highest temperature measured during any run of the initial compliance test or 10... either the highest reading during the test or at 10 °F higher than the average temperature measured... least 11 days apart from other consecutive tests. The mercury concentration must be maintained below the...

Relationship between consecutive deterioration of mean deviation value and progression of visual field defect in open-angle glaucoma.

PubMed

Naito, Tomoko; Yoshikawa, Keiji; Mizoue, Shiro; Nanno, Mami; Kimura, Tairo; Suzumura, Hirotaka; Takeda, Ryuji; Shiraga, Fumio

2015-01-01

To analyze the relationship between consecutive deterioration of mean deviation (MD) value and glaucomatous visual field (VF) progression in open-angle glaucoma (OAG), including primary OAG and normal tension glaucoma. The subjects of the study were patients undergoing treatment for OAG who had performed VF tests at least 10 times with a Humphrey field analyzer (SITA standard, C30-2 program). The VF progression was defined by a significantly negative MD slope (MD slope worsening) at the final VF test during the follow-up period. The relationship between the MD slope worsening and the consecutive deterioration of MD value were retrospectively analyzed. A total of 165 eyes of 165 patients were included in the analysis. Significant progression of VF defects was observed in 72 eyes of 72 patients (43.6%), while no significant progression was evident in 93 eyes of 93 patients (56.4%). There was significant relationship between the frequency of consecutive deterioration of MD value and MD slope worsening (P<0.0001, Cochran-Armitage trend test). A significant association was observed for MD slope worsening in the eyes with three (odds ratio: 2.1, P=0.0224) and four (odds ratio: 3.6, P=0.0008) consecutive deterioration of MD value in multiple logistic regression analysis, but no significant association in the eyes with two consecutive deterioration (odds ratio: 1.1, P=0.8282). The eyes with VF progression had significantly lower intraocular pressure reduction rate (P<0.01). This retrospective study has shown that three or more consecutive deterioration of MD value might be a predictor to future significant MD slope worsening in OAG.

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…

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.

40 CFR 280.43 - Methods of release detection for tanks.

Code of Federal Regulations, 2012 CFR

2012-07-01

... two consecutive stick readings at both the beginning and ending of the period; (3) The equipment used... UNDERGROUND STORAGE TANKS (UST) Release Detection § 280.43 Methods of release detection for tanks. Each method... of the tank is made to the nearest one-eighth of an inch at least once a month. Note: Practices...

40 CFR 280.43 - Methods of release detection for tanks.

Code of Federal Regulations, 2011 CFR

2011-07-01

... two consecutive stick readings at both the beginning and ending of the period; (3) The equipment used... UNDERGROUND STORAGE TANKS (UST) Release Detection § 280.43 Methods of release detection for tanks. Each method... of the tank is made to the nearest one-eighth of an inch at least once a month. Note: Practices...

Reinforcement Schedules in Pacing Reading Rate. Final Report.

ERIC Educational Resources Information Center

Schutz, Richard E.; And Others

Responses of individual fourth-grade children were monitored in daily 30-minute sessions for 10 consecutive school days. Individual subjects were used as their own controls. The child sat before a small table with a surface-mounted button and a wall-mounted screen upon which visual stimuli were rear-view projected, using a filmstrip projector with…

Middle School Student Factors as Predictors of College Readiness

ERIC Educational Resources Information Center

Karnick, Kelley

2013-01-01

In this study, several middle school factors of students from two consecutive graduating classes were analyzed to determine what relation they had to college readiness, as measured by ACT subtest scores. The academic factors included: 8th grade EXPLORE composite score, 7th grade spring reading and math MAP scores, highest math course completed in…

Design of Interrogation Protocols for Radiation Dose Measurements Using Optically-Stimulated Luminescent Dosimeters.

PubMed

Abraham, Sara A; Kearfott, Kimberlee J; Jawad, Ali H; Boria, Andrew J; Buth, Tobias J; Dawson, Alexander S; Eng, Sheldon C; Frank, Samuel J; Green, Crystal A; Jacobs, Mitchell L; Liu, Kevin; Miklos, Joseph A; Nguyen, Hien; Rafique, Muhammad; Rucinski, Blake D; Smith, Travis; Tan, Yanliang

2017-03-01

Optically-stimulated luminescent dosimeters are capable of being interrogated multiple times post-irradiation. Each interrogation removes a fraction of the signal stored within the optically-stimulated luminescent dosimeter. This signal loss must be corrected to avoid systematic errors in estimating the average signal of a series of optically-stimulated luminescent dosimeter interrogations and requires a minimum number of consecutive readings to determine an average signal that is within a desired accuracy of the true signal with a desired statistical confidence. This paper establishes a technical basis for determining the required number of readings for a particular application of these dosimeters when using certain OSL dosimetry systems.

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…

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

Nonword reading and Stroop interference: what differentiates attention-deficit/hyperactivity disorder and reading disability?

PubMed

Stubenrauch, Christa; Freund, Juliane; Alecu de Flers, Simone; DeFlers, Simone; Scharke, Wolfgang; Braun, Mario; Jacobs, Arthur M; Konrad, Kerstin

2014-01-01

Attention deficits and impaired reading performance co-occur more often than expected by chance; however, the underlying mechanism of this association still remains rather unexplored. In two consecutive studies, children aged 8 to 12 years with attention-deficit/hyperactivity disorder (ADHD) and children with reading disability (RD) were examined using a 2 (ADHD versus no ADHD) × 2 (RD versus no RD) factorial design. To further delineate deficient interference control from reading processes, we used a newly developed self-paced word/nonword reading task (Experiment 1, n = 68) and a modified computerized Stroop paradigm, including an orthographic phonological neighbor (OPN) condition (Experiment 2, n = 84). RD (compared to non-RD groups) was associated with impairments in both word and nonword reading, while children with ADHD also showed impaired nonword reading. In the Stroop task, RD, but not ADHD, had a significant impact on task performance. Interestingly, a significant interaction between ADHD, RD, and task condition emerged, which was due to particularly slower reaction times to nonwords in children with RD only, while task performance in children with comorbid ADHD and RD resembled that of ADHD only. Thus, our results demonstrate that impairments in nonword reading were not specific to RD but were also present in children with ADHD. In addition, RD and not ADHD was characterized by poor interference control in the Stroop task. These findings question whether unique cognitive deficits are specific to either ADHD or RD.

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.

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...

Massively Open Online Course for Educators (MOOC-Ed) Network Dataset

ERIC Educational Resources Information Center

Kellogg, Shaun; Edelmann, Achim

2015-01-01

This paper presents the Massively Open Online Course for Educators (MOOC-Ed) network dataset. It entails information on two online communication networks resulting from two consecutive offerings of the MOOC called "The Digital Learning Transition in K-12 Schools" in spring and fall 2013. The courses were offered to educators from the USA…

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.…

Benefits of the quality assured double and arbitration reading of mammograms in the early diagnosis of breast cancer in symptomatic women.

PubMed

Waldmann, Annika; Kapsimalakou, Smaragda; Katalinic, Alexander; Grande-Nagel, Isabell; Stoeckelhuber, Beate M; Fischer, Dorothea; Barkhausen, Joerg; Vogt, Florian M

2012-05-01

To address the benefits of double and arbitration reading regarding tumour detection rates, percentage of in situ tumours, and number (of patients) needed to send for expert reading (number needed to treat; NNT) for one additional tumour finding. QuaMaDi is a quality assured breast cancer diagnosis programme; with two-view mammography (craniocaudal, mediolateral oblique) and, in case of breast density ACR 3 or 4, routine ultrasound imaging; and with independent double reading of all images. A consecutive sample of symptomatic women, i.e. women at risk for breast cancer, women aged 70 and above, and/or women with preceding BI-RADS III findings, was analysed. 28,558 mammograms were performed (mean age of women: 57.3 [standard deviation: 12.3] years). Discordant findings were present in 3,837 double readings and were sent for arbitration reading. After histopathological assessment, 52 carcinomas were found (thereof 32% in situ). These carcinomas accounted for 1.8 tumours per 1,000 examinations in the total cohort and increased the tumour detection rate up to 16.4/1,000. The NNT in discordant cases was 74. Double and arbitration reading appears to be a useful tool to ensure the quality of early detection of breast lesions in symptomatic women during indication-based, standardised mammography. • Quality assured breast cancer diagnosis is feasible outside organised screening structures. • Double and arbitration reading is beneficial for populations ineligible for screening. • Double and arbitration reading increases the tumour detection rate. • Double and arbitration reading increases the percentage of in situ cancers.

Using a Case Study Article on Earwax to Enhance Understanding and Interest in Genetics

ERIC Educational Resources Information Center

Van Hoewyk, Doug

2012-01-01

For four consecutive semesters, students in an Introductory Biology class at Coastal Carolina University were assigned to read a case study article that explores the link between a single gene and earwax type. The case study article, broadly defined as a story with an educational message (Herreid, 2007), was originally published by the "New…

Social Justice Leadership: Advocating Equity, Access and Opportunity for Black Students Attending Urban High-Poverty Elementary Schools

ERIC Educational Resources Information Center

Pounders, Cherise

2017-01-01

The purpose of this qualitative phenomenological study was to explore and describe the lived experiences and perspectives of 4 elementary school principals and 4 instructional leaders committed to social justice practices who have improved and sustained grade level performance in reading with Black students for the duration of 3 consecutive years.…

Characterizing Teaching Effectiveness in the Joint Action Theory in Didactics: An Exploratory Study in Primary School

ERIC Educational Resources Information Center

Sensevy, Gérard

2014-01-01

This paper presents an exploratory study of two consecutive reading sessions conducted in primary school by two different teachers. Our purpose is twofold. From a theoretical viewpoint, we propose a tentative set of conditions of teaching effectiveness by relying on the Joint Action Theory in Didactics. From a methodological viewpoint, drawing on…

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

Dyslexics’ faster decay of implicit memory for sounds and words is manifested in their shorter neural adaptation

PubMed Central

Jaffe-Dax, Sagi; Frenkel, Or; Ahissar, Merav

2017-01-01

Dyslexia is a prevalent reading disability whose underlying mechanisms are still disputed. We studied the neural mechanisms underlying dyslexia using a simple frequency-discrimination task. Though participants were asked to compare the two tones in each trial, implicit memory of previous trials affected their responses. We hypothesized that implicit memory decays faster among dyslexics. We tested this by increasing the temporal intervals between consecutive trials, and by measuring the behavioral impact and ERP responses from the auditory cortex. Dyslexics showed a faster decay of implicit memory effects on both measures, with similar time constants. Finally, faster decay of implicit memory also characterized the impact of sound regularities in benefitting dyslexics' oral reading rate. Their benefit decreased faster as a function of the time interval from the previous reading of the same non-word. We propose that dyslexics’ shorter neural adaptation paradoxically accounts for their longer reading times, since it reduces their temporal window of integration of past stimuli, resulting in noisier and less reliable predictions for both simple and complex stimuli. Less reliable predictions limit their acquisition of reading expertise. DOI: http://dx.doi.org/10.7554/eLife.20557.001 PMID:28115055

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…

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

Risk perception in natalizumab-treated multiple sclerosis patients and their neurologists.

PubMed

Heesen, Christoph; Kleiter, Ingo; Nguyen, Franziska; Schäffler, Nina; Kasper, Jürgen; Köpke, Sascha; Gaissmaier, Wolfgang

2010-12-01

Natalizumab is associated with the potentially life-threatening side-effect progressive multifocal leukoencephalopathy (PML). Little is known about patients' and physicians' risk estimates and attitudes towards natalizumab treatment. Consecutive natalizumab-treated patients (n = 69) and neurologists (n = 66) in two centres and cooperating private practices received an evidence-based three-page information leaflet about natalizumab-associated PML and an evaluation sheet. After reading the information, patients were significantly more likely than physicians to intend continuation of natalizumab treatment and willing to accept higher risks of PML: 49% of physicians would stop treatment at a PML risk of 2:10,000 or lower, while only 17% of patients would do so (p < 0.001). This difference could not be explained by risk calculation abilities or lack of understanding. Both groups overestimated natalizumab treatment effects. Patients had a significantly worse perception of multiple sclerosis as a malignant disease. We conclude that patients were willing to accept a higher risk of PML than neurologists. Coherent with their perception of risks and benefits, patients were also more willing to continue treatment. Open information about treatment-related risks is appreciated and might support shared decision making.

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…

Temporal visual field defects are associated with monocular inattention in chiasmal pathology.

PubMed

Fledelius, Hans C

2009-11-01

Chiasmal lesions have been shown to give rise occasionally to uni-ocular temporal inattention, which cannot be compensated for by volitional eye movement. This article describes the assessments of 46 such patients with chiasmal pathology. It aims to determine the clinical spectrum of this disorder, including interference with reading. Retrospective consecutive observational clinical case study over a 7-year period comprising 46 patients with chiasmal field loss of varying degrees. Observation of reading behaviour during monocular visual acuity testing ascertained from consecutive patients who appeared unable to read optotypes on the temporal side of the chart. Visual fields were evaluated by kinetic (Goldmann) and static (Octopus) techniques. Five patients who clearly manifested this condition are presented in more detail. The results of visual field testing were related to absence or presence of uni-ocular visual inattentive behaviour for distance visual acuity testing and/or reading printed text. Despite normal eye movements, the 46 patients making up the clinical series perceived only optotypes in the nasal part of the chart, in one eye or in both, when tested for each eye in turn. The temporal optotypes were ignored, and this behaviour persisted despite instruction to search for any additional letters temporal to those, which had been seen. This phenomenon of unilateral visual inattention held for both eyes in 18 and was unilateral in the remaining 28 patients. Partial or full reversibility after treatment was recorded in 21 of the 39 for whom reliable follow-up data were available. Reading a text was affected in 24 individuals, and permanently so in six. A neglect-like spatial unawareness and a lack of cognitive compensation for varying degrees of temporal visual field loss were present in all the patients observed. Not only is visual field loss a feature of chiasmal pathology, but the higher visual function of affording attention within the temporal visual field by means of using conscious thought to invoke appropriate compensatory eye movement was also absent. This suggests the possibility of 'trans-synaptic dysfunction' caused by loss of visual input to higher visual centres. When inattention to the temporal side is manifest on monocular visual testing it should raise the suspicion of chiasmal pathology.

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…

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 sentences of uniform word length - II: Very rapid adaptation of the preferred saccade length.

PubMed

Cutter, Michael G; Drieghe, Denis; Liversedge, Simon P

2018-04-25

In the current study we investigated whether readers adjust their preferred saccade length (PSL) during reading on a trial-by-trial basis. The PSL refers to the distance between a saccade launch site and saccade target (i.e., the word center during reading) when participants neither undershoot nor overshoot this target (McConkie, Kerr, Reddix, & Zola in Vision Research, 28, 1107-1118, 1988). The tendency for saccades longer or shorter than the PSL to under or overshoot their target is referred to as the range error. Recent research by Cutter, Drieghe, and Liversedge (Journal of Experimental Psychology: Human Perception and Performance, 2017) has shown that the PSL changes to be shorter when readers are presented with 30 consecutive sentences exclusively made of three-letter words, and longer when presented with 30 consecutive sentences exclusively made of five-letter words. We replicated and extended this work by this time presenting participants with these uniform sentences in an unblocked design. We found that adaptation still occurred across different sentence types despite participants only having one trial to adapt. Our analyses suggested that this effect was driven by the length of the words readers were making saccades away from, rather than the length of the words in the rest of the sentence. We propose an account of the range error in which readers use parafoveal word length information to estimate the length of a saccade between the center of two parafoveal words (termed the Centre-Based Saccade Length) prior to landing on the first of these words.

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.

Preschoolers Have Better Long-Term Memory for Rhyming Text than Adults

ERIC Educational Resources Information Center

Király, Ildikó; Takács, Szilvia; Kaldy, Zsuzsa; Blaser, Erik

2017-01-01

The dominant view of children's memory is that it is slow to develop and is inferior to adults'. Here we pitted 4-year-old children against adults in a test of verbatim recall of verbal material. Parents read a novel rhyming verse (and an integrated word list) as their child's bedtime story on ten consecutive days. A group of young adults listened…

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.

What is the optimal interval between successive home blood pressure readings using an automated oscillometric device?

PubMed

Eguchi, Kazuo; Kuruvilla, Sujith; Ogedegbe, Gbenga; Gerin, William; Schwartz, Joseph E; Pickering, Thomas G

2009-06-01

To clarify whether a shorter interval between three successive home blood pressure (HBP) readings (10 s vs. 1 min) taken twice a day gives a better prediction of the average 24-h BP and better patient compliance. We enrolled 56 patients from a hypertension clinic (mean age: 60 +/- 14 years; 54% female patients). The study consisted of three clinic visits, with two 4-week periods of self-monitoring of HBP between them, and a 24-h ambulatory BP monitoring at the second visit. Using a crossover design, with order randomized, the oscillometric HBP device (HEM-5001) could be programmed to take three consecutive readings at either 10-s or 1-min intervals, each of which was done for 4 weeks. Patients were asked to measure three HBP readings in the morning and evening. All the readings were stored in the memory of the monitors. The analyses were performed using the second-third HBP readings. The average systolic BP/diastolic BP for the 10-s and 1-min intervals at home were 136.1 +/- 15.8/77.5 +/- 9.5 and 133.2 +/- 15.5/76.9 +/- 9.3 mmHg (P = 0.001/0.19 for the differences in systolic BP and diastolic BP), respectively. The 1-min BP readings were significantly closer to the average of awake ambulatory BP (131 +/- 14/79 +/- 10 mmHg) than the 10-s interval readings. There was no significant difference in patients' compliance in taking adequate numbers of readings at the different time intervals. The 1-min interval between HBP readings gave a closer agreement with the daytime average BP than the 10-s interval.

What is the optimal interval between successive home blood pressure readings using an automated oscillometric device?

PubMed Central

Eguchi, Kazuo; Kuruvilla, Sujith; Ogedegbe, Gbenga; Gerin, William; Schwartz, Joseph E.; Pickering, Thomas G.

2010-01-01

Objectives To clarify whether a shorter interval between three successive home blood pressure (HBP) readings (10 s vs. 1 min) taken twice a day gives a better prediction of the average 24-h BP and better patient compliance. Design We enrolled 56 patients from a hypertension clinic (mean age: 60 ±14 years; 54% female patients). The study consisted of three clinic visits, with two 4-week periods of self-monitoring of HBP between them, and a 24-h ambulatory BP monitoring at the second visit. Using a crossover design, with order randomized, the oscillometric HBP device (HEM-5001) could be programmed to take three consecutive readings at either 10-s or 1-min intervals, each of which was done for 4 weeks. Patients were asked to measure three HBP readings in the morning and evening. All the readings were stored in the memory of the monitors. Results The analyses were performed using the second–third HBP readings. The average systolic BP/diastolic BP for the 10-s and 1-min intervals at home were 136.1 ±15.8/77.5 ±9.5 and 133.2 ±15.5/76.9 ±9.3 mmHg (P = 0.001/0.19 for the differences in systolic BP and diastolic BP), respectively. The 1-min BP readings were significantly closer to the average of awake ambulatory BP (131 ±14/79 ±10 mmHg) than the 10-s interval readings. There was no significant difference in patients’ compliance in taking adequate numbers of readings at the different time intervals. Conclusion The 1-min interval between HBP readings gave a closer agreement with the daytime average BP than the 10-s interval. PMID:19462492

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

PubMed

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

2006-01-01

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

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…

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

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.

Print exposure modulates the effects of repetition priming during sentence reading.

PubMed

Lowder, Matthew W; Gordon, Peter C

2017-12-01

Individual readers vary greatly in the quality of their lexical representations, and consequently in how quickly and efficiently they can access orthographic and lexical knowledge. This variability may be explained, at least in part, by individual differences in exposure to printed language, because practice at reading promotes the development of stronger reading skills. In the present eyetracking experiment, we tested the hypothesis that the efficiency of word recognition during reading improves with increases in print exposure, by determining whether the magnitude of the repetition-priming effect is modulated by individual differences in scores on the author recognition test (ART). Lexical repetition of target words was manipulated across pairs of unrelated sentences that were presented on consecutive trials. The magnitude of the repetition effect was modulated by print exposure in early measures of processing, such that the magnitude of the effect was inversely related to scores on the ART. The results showed that low levels of print exposure, and thus lower-quality lexical representations, are associated with high levels of difficulty recognizing words, and thus with the greatest room to benefit from repetition. Furthermore, the interaction between scores on the ART and repetition suggests that print exposure is not simply an index of general reading speed, but rather that higher levels of print exposure are associated with an enhanced ability to access lexical knowledge and recognize words during reading.

Detection of microRNAs in color space.

PubMed

Marco, Antonio; Griffiths-Jones, Sam

2012-02-01

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

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.

Clinical utility of pH paper versus pH meter in the measurement of critical gastric pH in stress ulcer prophylaxis.

PubMed

Bradley, J S; Phillips, J O; Cavanaugh, J E; Metzler, M H

1998-11-01

To evaluate the clinical utility of measuring gastric pH with a pH meter vs. pH paper in critical care patients. Prospective comparison of gastric pH measurements, using both pH meter and pH paper. Surgical intensive care unit (ICU) at a rural Midwestern university medical center. Fifty-one patients who received therapy for prophylaxis of stress ulcers in the surgical ICU. Therapy for stress ulcer prophylaxis was monitored. The pH of 985 gastric samples, taken from 51 patients, was measured with both pH meter and pH paper. The pH meter and pH paper measures demonstrated a concordance correlation coefficient of .896. The mean difference between the two measures (pH paper - pH meter) was estimated to be between -0.4 and 1.4, suggesting a positive bias for the paper. The prevalence of events representing clinically relevant differences between the pH meter and pH paper in the measurement of the same gastric sample was calculated. The frequency with which each of the events occurred consecutively (or, in one case, two nearly consecutive events on the same day) was also calculated. Bias in a clinically relevant range was estimated. A set of "probability profiles" was constructed. A hand-held pH meter and pH paper are not interchangeable measures of gastric pH. The pH paper exhibits an appreciable positive bias compared with a hand-held pH meter in the clinically relevant range of 2 to 6. More research is needed to determine if that bias affects treatment outcomes. We recommend the use of a pH meter for patients who demonstrate pH readings of < or = 4, consecutive with readings of < or = 5.

Blackcurrant Leaf Chlorosis Associated Virus: Evidence of the Presence of Circular RNA during Infections.

PubMed

James, Delano; Phelan, James; Sanderson, Daniel

2018-05-15

Blackcurrant leaf chlorosis associated virus (BCLCaV) was detected recently by next-generation sequencing (NGS) and a new and distinct species in the genus Idaeovirus was proposed. Analysis of NGS-derived paired-end reads revealed the existence of bridge reads encompassing the 3'-terminus and 5'-terminus of RNA-2 or RNA-3 of BCLCaV. The full RNA-2 or RNA-3 could be amplified using outward facing or abutting primers; also, RNA-2/RNA-3 could be detected even after three consecutive RNase R enzyme treatments, with denaturation at 95 °C preceding each digestion. Evidence was obtained indicating that there are circular forms of BCLCaV RNA-2 and RNA-3.

Curvature-Based Environment Description for Robot Navigation Using Laser Range Sensors

PubMed Central

Vázquez-Martín, Ricardo; Núñez, Pedro; Bandera, Antonio; Sandoval, Francisco

2009-01-01

This work proposes a new feature detection and description approach for mobile robot navigation using 2D laser range sensors. The whole process consists of two main modules: a sensor data segmentation module and a feature detection and characterization module. The segmentation module is divided in two consecutive stages: First, the segmentation stage divides the laser scan into clusters of consecutive range readings using a distance-based criterion. Then, the second stage estimates the curvature function associated to each cluster and uses it to split it into a set of straight-line and curve segments. The curvature is calculated using a triangle-area representation where, contrary to previous approaches, the triangle side lengths at each range reading are adapted to the local variations of the laser scan, removing noise without missing relevant points. This representation remains unchanged in translation or rotation, and it is also robust against noise. Thus, it is able to provide the same segmentation results although the scene will be perceived from different viewpoints. Therefore, segmentation results are used to characterize the environment using line and curve segments, real and virtual corners and edges. Real scan data collected from different environments by using different platforms are used in the experiments in order to evaluate the proposed environment description algorithm. PMID:22461732

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...

A patient with phonologic alexia can learn to read "much" from "mud pies"

PubMed Central

Lott, Susan Nitzberg; Sample, Diane M.; Oliver, Robyn T.; Lacey, Elizabeth H.; Friedman, Rhonda B.

2008-01-01

People with phonologic alexia often have difficulty reading functors and verbs, in addition to pseudowords. Friedman et al (2002) reported a successful treatment for phonologic alexia that paired problematic functors and verbs with easily read relays that were homophonous nouns (e.g. "be" paired with "bee"). The current study evaluates the efficacy of pairing problematic grammatical words with relays that share initial phonemes, but vary in the relationship of their final phonemes. Results showed that reading of target grammatical words improved to criterion level (90% accuracy over two consecutive probes) in all experimental conditions with shared phonology, but remained far below criterion level in control conditions. There was a significant correlation between degree of phonologic relatedness and error rate. Maintenance of the treatment effect was poor as assessed by traditional measurement, however a dramatic savings during relearning was demonstrated during a subsequent treatment phase. The finding that reading can be re-organized by pairing target words not only with homophones, but with other phonologically related relays, suggests that this approach could be applied to a wide corpus of words and, therefore, potentially be of great use clinically. We suggest, within a connectionist account, that the treatment effect results from relays priming the initial phonologic units of the targets. PMID:18513760

Enhancing children's vegetable consumption using vegetable-promoting picture books. The impact of interactive shared reading and character-product congruence.

PubMed

de Droog, Simone M; Buijzen, Moniek; Valkenburg, Patti M

2014-02-01

The present study investigated whether and how a picture book promoting carrots can increase young children's carrot consumption. One hundred and four children (aged 4-6years) participated in shared reading sessions using the book on five consecutive days in school. These children were assigned randomly to one of four experimental conditions. In a 2×2 between-subjects design, the reading style and character in the book were manipulated. The reading style was either passive (listening to the story) or interactive (also answering questions about the story). The character in the book fitted either conceptually well with carrots (a rabbit) or not (a turtle). Compared to a baseline group of 56 children who were not exposed to the book, the children in the experimental groups consumed almost twice as much carrots (in proportion to other foods consumed), F(1,159)=7.08, p<.01. Results suggest that picture books are particularly effective when children are actively involved, answering questions about the story. Young children seem to enjoy this interactive shared reading style, triggering positive feelings that increase children's liking and consumption of the healthy food promoted in the book. Copyright © 2013 Elsevier Ltd. 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

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

PubMed

Ducharme, Daphne A; Arcand, Isabelle

2009-08-01

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

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

PubMed

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

2017-01-01

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

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

ERIC Educational Resources Information Center

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

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

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

PubMed

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

2018-04-01

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

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

ERIC Educational Resources Information Center

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

2002-01-01

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

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

PubMed Central

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

2014-01-01

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

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…

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…

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.

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

A writing-intensive course improves biology undergraduates' perception and confidence of their abilities to read scientific literature and communicate science.

PubMed

Brownell, Sara E; Price, Jordan V; Steinman, Lawrence

2013-03-01

Most scientists agree that comprehension of primary scientific papers and communication of scientific concepts are two of the most important skills that we can teach, but few undergraduate biology courses make these explicit course goals. We designed an undergraduate neuroimmunology course that uses a writing-intensive format. Using a mixture of primary literature, writing assignments directed toward a layperson and scientist audience, and in-class discussions, we aimed to improve the ability of students to 1) comprehend primary scientific papers, 2) communicate science to a scientific audience, and 3) communicate science to a layperson audience. We offered the course for three consecutive years and evaluated its impact on student perception and confidence using a combination of pre- and postcourse survey questions and coded open-ended responses. Students showed gains in both the perception of their understanding of primary scientific papers and of their abilities to communicate science to scientific and layperson audiences. These results indicate that this unique format can teach both communication skills and basic science to undergraduate biology students. We urge others to adopt a similar format for undergraduate biology courses to teach process skills in addition to content, thus broadening and strengthening the impact of undergraduate courses.

Accessing Biomedical Literature in the Current Information Landscape

PubMed Central

Khare, Ritu; Leaman, Robert; Lu, Zhiyong

2015-01-01

i. Summary Biomedical and life sciences literature is unique because of its exponentially increasing volume and interdisciplinary nature. Biomedical literature access is essential for several types of users including biomedical researchers, clinicians, database curators, and bibliometricians. In the past few decades, several online search tools and literature archives, generic as well as biomedicine-specific, have been developed. We present this chapter in the light of three consecutive steps of literature access: searching for citations, retrieving full-text, and viewing the article. The first section presents the current state of practice of biomedical literature access, including an analysis of the search tools most frequently used by the users, including PubMed, Google Scholar, Web of Science, Scopus, and Embase, and a study on biomedical literature archives such as PubMed Central. The next section describes current research and the state-of-the-art systems motivated by the challenges a user faces during query formulation and interpretation of search results. The research solutions are classified into five key areas related to text and data mining, text similarity search, semantic search, query support, relevance ranking, and clustering results. Finally, the last section describes some predicted future trends for improving biomedical literature access, such as searching and reading articles on portable devices, and adoption of the open access policy. PMID:24788259

Assessment of student learning associated with tree thinking in an undergraduate introductory organismal biology course.

PubMed

Smith, James J; Cheruvelil, Kendra Spence; Auvenshine, Stacie

2013-01-01

Phylogenetic trees provide visual representations of ancestor-descendant relationships, a core concept of evolutionary theory. We introduced "tree thinking" into our introductory organismal biology course (freshman/sophomore majors) to help teach organismal diversity within an evolutionary framework. Our instructional strategy consisted of designing and implementing a set of experiences to help students learn to read, interpret, and manipulate phylogenetic trees, with a particular emphasis on using data to evaluate alternative phylogenetic hypotheses (trees). To assess the outcomes of these learning experiences, we designed and implemented a Phylogeny Assessment Tool (PhAT), an open-ended response instrument that asked students to: 1) map characters on phylogenetic trees; 2) apply an objective criterion to decide which of two trees (alternative hypotheses) is "better"; and 3) demonstrate understanding of phylogenetic trees as depictions of ancestor-descendant relationships. A pre-post test design was used with the PhAT to collect data from students in two consecutive Fall semesters. Students in both semesters made significant gains in their abilities to map characters onto phylogenetic trees and to choose between two alternative hypotheses of relationship (trees) by applying the principle of parsimony (Occam's razor). However, learning gains were much lower in the area of student interpretation of phylogenetic trees as representations of ancestor-descendant relationships.

Assessment of Student Learning Associated with Tree Thinking in an Undergraduate Introductory Organismal Biology Course

PubMed Central

Smith, James J.; Cheruvelil, Kendra Spence; Auvenshine, Stacie

2013-01-01

Phylogenetic trees provide visual representations of ancestor–descendant relationships, a core concept of evolutionary theory. We introduced “tree thinking” into our introductory organismal biology course (freshman/sophomore majors) to help teach organismal diversity within an evolutionary framework. Our instructional strategy consisted of designing and implementing a set of experiences to help students learn to read, interpret, and manipulate phylogenetic trees, with a particular emphasis on using data to evaluate alternative phylogenetic hypotheses (trees). To assess the outcomes of these learning experiences, we designed and implemented a Phylogeny Assessment Tool (PhAT), an open-ended response instrument that asked students to: 1) map characters on phylogenetic trees; 2) apply an objective criterion to decide which of two trees (alternative hypotheses) is “better”; and 3) demonstrate understanding of phylogenetic trees as depictions of ancestor–descendant relationships. A pre–post test design was used with the PhAT to collect data from students in two consecutive Fall semesters. Students in both semesters made significant gains in their abilities to map characters onto phylogenetic trees and to choose between two alternative hypotheses of relationship (trees) by applying the principle of parsimony (Occam's razor). However, learning gains were much lower in the area of student interpretation of phylogenetic trees as representations of ancestor–descendant relationships. PMID:24006401

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…

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... 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...

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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

AN ADA NAMELIST PACKAGE

NASA Technical Reports Server (NTRS)

Klumpp, A. R.

1994-01-01

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

Effect of EPI-743 on the clinical course of the mitochondrial disease Leber hereditary optic neuropathy.

PubMed

Sadun, Alfredo A; Chicani, Carlos Filipe; Ross-Cisneros, Fred N; Barboni, Piero; Thoolen, Martin; Shrader, William D; Kubis, Kenneth; Carelli, Valerio; Miller, Guy

2012-03-01

To evaluate the safety and efficacy of a new therapeutic agent, EPI-743, in Leber hereditary optic neuropathy (LHON) using standard clinical, anatomic, and functional visual outcome measures. Open-label clinical trial. University medical center. Patients  Five patients with genetically confirmed LHON with acute loss of vision were consecutively enrolled and treated with the experimental therapeutic agent EPI-743 within 90 days of conversion. Intervention  During the course of the study, 5 consecutive patients received EPI-743, by mouth, 3 times daily (100-400 mg per dose). Treatment effect was assessed by serial measurements of anatomic and functional visual indices over 6 to 18 months, including Snellen visual acuity, retinal nerve fiber layer thickness measured by optical coherence tomography, Humphrey visual fields (mean decibels and area with 1-log unit depression), and color vision. Treatment effect in this clinical proof of principle study was assessed by comparison of the prospective open-label treatment group with historical controls. Of 5 subjects treated with EPI-743, 4 demonstrated arrest of disease progression and reversal of visual loss. Two patients exhibited a total recovery of visual acuity. No drug-related adverse events were recorded. In a small open-label trial, EPI-743 arrested disease progression and reversed vision loss in all but 1 of the 5 consecutively treated patients with LHON. Given the known natural history of acute and rapid progression of LHON resulting in chronic and persistent bilateral blindness, these data suggest that the previously described irreversible priming to retinal ganglion cell loss may be reversed.

Crackles and instabilities during lung inflation

NASA Astrophysics Data System (ADS)

Alencar, Adriano M.; Majumdar, Arnab; Hantos, Zoltan; Buldyrev, Sergey V.; Eugene Stanley, H.; Suki, Béla

2005-11-01

In a variety of physico-chemical reactions, the actual process takes place in a reactive zone, called the “active surface”. We define the active surface of the lung as the set of airway segments that are closed but connected to the trachea through an open pathway, which is the interface between closed and open regions in a collapsed lung. To study the active surface and the time interval between consecutive openings, we measured the sound pressure of crackles, associated with the opening of collapsed airway segments in isolated dog lungs, inflating from the collapsed state in 120 s. We analyzed the sequence of crackle amplitudes, inter-crackle intervals, and low frequency energy from acoustic data. The series of spike amplitudes spans two orders of magnitude and the inter-crackle intervals spans over five orders of magnitude. The distribution of spike amplitudes follows a power law for nearly two decades, while the distribution of time intervals between consecutive crackles shows two regimes of power law behavior, where the first region represents crackles coming from avalanches of openings whereas the second region is due to the time intervals between separate avalanches. Using the time interval between measured crackles, we estimated the time evolution of the active surface during lung inflation. In addition, we show that recruitment and instabilities along the pressure-volume curve are associated with airway opening and recruitment. We find a good agreement between the theory of the dynamics of lung inflation and the experimental data which combined with numerical results may prove useful in the clinical diagnosis of lung diseases.

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.

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…

Medication self-management skills and cognitive impairment in older adults hospitalized for heart failure: A cross-sectional study.

PubMed

Howell, Erik H; Senapati, Alpana; Hsich, Eileen; Gorodeski, Eiran Z

2017-01-01

Cognitive impairment is highly prevalent among older adults (aged ≥65 years) hospitalized for heart failure and has been associated with poor outcomes. Poor medication self-management skills have been associated with poor outcomes in this population as well. The presence and extent of an association between cognitive impairment and poor medication self-management skills in this population has not been clearly defined. We assessed the cognition of consecutive older adults hospitalized for heart failure, in relation to their medication self-management skills. We conducted a cross-sectional study of older adults (aged ≥65 years) who were hospitalized for heart failure and were being discharged home. Prior to discharge, we assessed cognition using the Mini-Cog. We also tested patients' ability to read a pill bottle label, open a pill bottle safety cap, and allocate mock pills to a pill box. Pill allocation performance was assessed quantitatively (counts of errors of omission and commission) and qualitatively (patterns suggestive of knowledge-based mistakes, rule-based mistakes, or skill-based slips). Of 55 participants, 22% were found to have cognitive impairment. Patients with cognitive impairment tended to be older as compared to those without cognitive impairment (mean age = 81 vs 76 years, p = NS). Patients with cognitive impairment had a higher prevalence of inability to read pill bottle label (prevalence ratio = 5.8, 95% confidence interval = 3.2-10.5, p = 0.001) and inability to open pill bottle safety cap (prevalence ratio = 3.3, 95% confidence interval = 1.3-8.4, p = 0.03). While most patients (65%) had pill-allocation errors regardless of cognition, those patients with cognitive impairment tended to have more errors of omission (mean number of errors = 48 vs 23, p = 0.006), as well as more knowledge-based mistakes (75% vs 40%, p = 0.03). There is an association between cognitive impairment and poor medication self-management skills. Medication taking failures due to poor medication self-management skills may be part of the pathway linking cognitive impairment to poor post-discharge outcomes among patients with heart failure transitioning from hospital to home.

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…

Can the heartscan be used for diagnosis and monitoring of emergencies in general practice?

PubMed

Renier, Walter; Geelen, Mieke; Steverlynck, Lucas; Wauters, Joost; Aertgeerts, Bert; Verbakel, Jan; Vanbrabant, Peter; Gillet, Jean-Bernard; Sabbe, Marc; Buntinx, Frank

2012-10-01

Mostly, it is impossible to establish the type of arrhythmias, based on signs and symptoms only. An ECG device is not always within reach. We presumed the heartscan, a handheld wireless device, to be of value to a GP in emergency situations. We therefore studied inter- and intra-observer variability and the accuracy of the screen readings. All consecutive patients visiting the emergency department (ED) of the Gasthuisberg University Hospital in Leuven, Belgium, as well as patients hospitalised in three hospital wards on one day, were included. Immediately after the heartscan recording, a standard 12-lead ECG was recorded and read by an experienced hospital-based cardiologist. The recordings were read on the device screen by two general practitioners. All readers were blinded to the 12-lead ECG readings and vice versa, and for each other's ones. We compared both the heartscan reading of the first reader and the automatic reading of the device with the readings of the second GP and to the 12-lead ECG results, used as the gold standard. Intra- and inter-observer agreement was studied using total accuracy and kappa values with their 95% confidence interval (CI). Full data of 177 (73%) patients, 80 men (45%) and 97 women (55%), with a mean age of 55 years (range 18-94 y) were recorded. The specificity of the heartscan reading by a clinician was 88%, the sensitivity between 60 and 69%, PPV < 50% and NPV > 95%. Comparing codes of the heartscan with the ECG readings was difficult but sensitivity for atrial fibrillation was 92.3%. Inter- and intra-observer accuracy were high (> 0.86 and > or = 0.95, respectively), with low kappa values. The detection of rhythm disorders by the device is incomplete. However, the heartscan can be a help for the GP. The performance of the heartscan could probably be improved by increasing screen resolution, but, in the future, more sophisticated heart monitors should become available. They should be small, light and affordable.

Incorporation of the technologist's opinion for arbitration of discrepant assessments among radiologists at screening mammography.

PubMed

Coolen, Angela M P; Lameijer, Joost R C; Voogd, Adri C; Strobbe, Luc J; Louwman, Marieke W J; Tjan-Heijnen, Vivianne C G; Duijm, Lucien E M

2018-05-05

We determined whether the addition of the technologist's opinion may be helpful in deciding if discordant readings at blinded double reading should be recalled. A consecutive series of 99,013 digital screening mammograms, obtained between July 2013 and January 2015, were included. All mammograms were first interpreted by a technologist and then double read in a blinded fashion by a team of 13 screening radiologists. All concordant and discordant positive readings among radiologists were recalled. Out of 3562 recalls, 998 women were recalled after a discordant reading. Of these women, 337 (33.8%) had a positive technologist assessment, of which 40 (11.9%) were diagnosed with breast cancer. Sixty women with a negative technologist assessment (60/661, 9.1%) were diagnosed with breast cancer (p = 0.16). Recall rate would have decreased with technologist arbitration (3.6% vs. 2.9%, p < 0.001). Cancer detection rate decreased with 8.5%, from 7.1/1000 screens to 6.5/1000 screens (p = 0.10). Among women with a positive technologist assessment, the probability of breast cancer was highest in case of suspicious microcalcifications and lowest for suspicious masses (30.4% (17/56) versus 7.0% (16/212), p < 0.001). Breast cancers were diagnosed in all groups of mammographic abnormalities, except in women with a suspicious asymmetry and a negative technologist assessment. Assessment by a technologist does not provide a significant discriminating ability in case of a discordant radiologist reading and, taking into account the decrease in cancer detection rate, does not appear to be a suitable arbitration strategy for discordant recalls at blinded double reading.

Biofuel cell based on direct bioelectrocatalysis.

PubMed

Ramanavicius, Arunas; Kausaite, Asta; Ramanaviciene, Almira

2005-04-15

A biofuel cell, consisting of two 3mm diameter carbon rod electrodes and operating at ambient temperature in aqueous solution, pH 6, is described. Biofuel cell based on enzymes able to exchange directly electrons with carbon electrodes was constructed and characterized. Anode of the biofuel cell was based on immobilized Quino-hemoprotein alcohol dehydrogenase from Gluconobacter sp. 33 (QH-ADH), cathode on co-immobilized glucose oxidase from Aspergilus niger (GO(x)) and microperoxidase 8 from the horse heart (MP-8) acting in the consecutive mode. Two enzymes GO(x) and MP-8 applied in the design of biofuel cell cathode were acting in consecutive mode and by hydrogen peroxide oxidized MP-8 was directly accepting electrons from carbon rod electrode. If ethanol was applied as an energy source the maximal open circuit potential of the biofuel cell was -125 mV. If glucose was applied as energy source the open circuit potential of the cell was +145 mV. The maximal open circuit potential (270 mV) was achieved in the presence of extent concentration (over 2 mM) of both substrates (ethanol and glucose). Operational half-life period (tau(1/2)) of the biofuel cell was found to be 2.5 days.

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

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!

Effects of media stray field on electromigration characteristics in current-perpendicular-to-plane giant magnetoresistance spin-valve read sensors

NASA Astrophysics Data System (ADS)

Gui Zeng, Ding; Lee, Kyoung-il; Chung, Kyung-Won; Bae, Seongtae

2012-05-01

Effects of magnetic stray field retrieved from both longitudinal and perpendicular magnetic recording media (denoted by "media stray field") on electromigration (EM) characteristics of current-perpendicular-to-plane (CPP) giant magnetoresistance spin-valve (GMR SV) read sensors have been numerically studied to explore the electrical and magnetic stability of the read sensor under real operation. The mean-time-to-failure (MTTF) of the CPP GMR SV read sensors was found to have a strong dependence on the physical parameters of the recording media and recorded information status, such as the pulse width of media stray field, the bit length, and the head moving velocity. According to the numerical calculation results, it was confirmed that in the longitudinal media, the shorter the stray field pulse width (i.e., the sharper the media transition) allows for the longer MTTF of the CPP GMR SV read sensors; while in the perpendicular media, the sharper the media transition gives rise to a shorter MTTF. Interestingly, it was also revealed that the MTTF could be improved by reducing the bit length as well as increasing the head velocity in both longitudinal and perpendicular media. Furthermore, the bit distribution patterns, especially the number of consecutive `0' bits strongly affected the MTTF of GMR SV read sensors. The strong dependences of MTTF on the media stray field during CPP GMR SV sensor operation are thought to be mainly attributed to the thermal cycling (temperature rise and fall) caused by the resistance change due to GMR effects.

Performance of a semi-quantitative whole blood test for human heart-type fatty acid-binding protein (H-FABP).

PubMed

Hiura, Masahito; Nakajima, Osamu; Mori, Toshizumi; Kitano, Katsuya

2005-10-01

We evaluated the accuracy of visually reading the whole blood Rapicheck H-FABP panel test using the quantitative plasma H-FABP concentration as the reference. Consecutive patients with chest pain (n = 237) who were suspected of having acute myocardial infarction were recruited. The appearance of an evident test line within 5 min was given a grade of +3 (strongly positive), appearance within 15 min +2 (moderately positive) and the appearance of a weak test line within 15 min +1 (weakly positive). The concordance rates were 91.8% for positive, 70.1% for negative and 80.2% for overall. Plasma H-FABP concentrations were above the cut-off value for 9.2% of negative (0) results. Fifty percent of weakly positive (+1) and 25.0% of moderately positive (+2) results had H-FABP concentrations lower than the cut-off value. All of the strongly positive (+3) were above the cut-off value. These results suggested that the false-positive and false-negative results of Rapicheck H-FABP were caused by over or underestimation in visual reading when the plasma H-FABP concentration was near the cut-off concentration. Low accuracy of visual reading of Rapicheck H-FABP was due to poor estimation by manual reading around the cut-off value.

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

Evaluation of blotchy pigments in the anterior chamber angle as a sign of angle closure

PubMed Central

Rao, Harsha L; Mungale, Sachin C; Kumbar, Tukaram; Parikh, Rajul S; Garudadri, Chandra S

2012-01-01

Background: Blotchy pigments in the anterior chamber (AC) angle are considered diagnostic of primary angle closure (PAC). But there are no reports either on the prevalence of blotchy pigments in AC angles or the validity of this sign. Aims: To determine the prevalence of blotchy pigments in AC angles and to evaluate their relationship with glaucomatous optic neuropathy (GON) in eyes with occludable angles. Setting and Design: Cross-sectional, comparative study. Materials and Methods: Gonioscopy was performed in 1001 eyes of 526 subjects (245 eyes of 148 consecutive, occludable angle subjects and 756 eyes of 378 non-consecutive, open angle subjects), above 35 years of age. Quadrant-wise location of blotchy pigments was documented. Statistical Analysis: Odds of blotchy pigments in occludable angles against that in open angles were evaluated. Relationship of GON with blotchy pigments in occludable angle eyes was evaluated using a multivariate model. Results: Prevalence of blotchy pigments in occludable angles was 28.6% (95% CI, 22.9-34.3) and in open angles was 4.7% (95% CI, 3.2-6.3). Blotchy pigments were more frequently seen in inferior (16%) and superior quadrants (15%) of occludable angles, and inferior quadrant of open angles (4%). Odds of superior quadrant blotchy pigments in occludable angles were 33 times that in open angles. GON was seen in 107 occludable angle eyes. Blotchy pigments were not significantly associated with GON (odds ratio = 0.5; P = 0.1). Conclusions: Blotchy pigments were seen in 28.6% of occludable angle eyes and 4.7% of open angles eyes. Presence of blotchy pigments in the superior quadrant is more common in occludable angles. Presence of GON in occludable angle eyes was not associated with blotchy pigments. PMID:23202393

Proximal Opening Wedge Osteotomy Provides Satisfactory Midterm Results With a Low Complication Rate.

PubMed

Oravakangas, Rami; Leppilahti, Juhana; Laine, Vesa; Niinimäki, Tuukka

2016-01-01

Hallux valgus is one of the most common foot deformities. Proximal opening wedge osteotomy is used for the treatment of moderate and severe hallux valgus with metatarsus primus varus. However, hypermobility of the first tarsometatarsal joint can compromise the results of the operation, and a paucity of midterm results are available regarding proximal open wedge osteotomy surgery. The aim of the present study was to assess the midterm results of proximal open wedge osteotomy in a consecutive series of patients with severe hallux valgus. Thirty-one consecutive adult patients (35 feet) with severe hallux valgus underwent proximal open wedge osteotomy. Twenty patients (35.5%) and 23 feet (34.3%) were available for the final follow-up examination. The mean follow-up duration was 5.8 (range 4.6 to 7.0) years. The radiologic measurements and American Orthopaedic Foot and Ankle Society hallux-metatarsophalangeal-interphalangeal scores were recorded pre- and postoperatively, and subjective questionnaires were completed and foot scan analyses performed at the end of the follow-up period. The mean hallux valgus angle decreased from 38° to 23°, and the mean intermetatarsal angle correction decreased from 17° to 10°. The mean improvement in the American Orthopaedic Foot and Ankle Society hallux metatarsophalangeal-interphalangeal score increased from 52 to 84. Two feet (5.7%) required repeat surgery because of recurrent hallux valgus. No nonunions were identified. Proximal open wedge osteotomy provided satisfactory midterm results in the treatment of severe hallux valgus, with a low complication rate. The potential instability of the first tarsometatarsal joint does not seem to jeopardize the midterm results of the operation. Copyright © 2016 American College of Foot and Ankle Surgeons. Published by Elsevier Inc. All rights reserved.

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

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

Accuracy of reading liquid based cytology slides using the ThinPrep Imager compared with conventional cytology: prospective study

PubMed Central

d'Assuncao, Jefferson; Irwig, Les; Macaskill, Petra; Chan, Siew F; Richards, Adele; Farnsworth, Annabelle

2007-01-01

Objective To compare the accuracy of liquid based cytology using the computerised ThinPrep Imager with that of manually read conventional cytology. Design Prospective study. Setting Pathology laboratory in Sydney, Australia. Participants 55 164 split sample pairs (liquid based sample collected after conventional sample from one collection) from consecutive samples of women choosing both types of cytology and whose specimens were examined between August 2004 and June 2005. Main outcome measures Primary outcome was accuracy of slides for detecting squamous lesions. Secondary outcomes were rate of unsatisfactory slides, distribution of squamous cytological classifications, and accuracy of detecting glandular lesions. Results Fewer unsatisfactory slides were found for imager read cytology than for conventional cytology (1.8% v 3.1%; P<0.001). More slides were classified as abnormal by imager read cytology (7.4% v 6.0% overall and 2.8% v 2.2% for cervical intraepithelial neoplasia of grade 1 or higher). Among 550 patients in whom imager read cytology was cervical intraepithelial neoplasia grade 1 or higher and conventional cytology was less severe than grade 1, 133 of 380 biopsy samples taken were high grade histology. Among 294 patients in whom imager read cytology was less severe than cervical intraepithelial neoplasia grade 1 and conventional cytology was grade 1 or higher, 62 of 210 biopsy samples taken were high grade histology. Imager read cytology therefore detected 71 more cases of high grade histology than did conventional cytology, resulting from 170 more biopsies. Similar results were found when one pathologist reread the slides, masked to cytology results. Conclusion The ThinPrep Imager detects 1.29 more cases of histological high grade squamous disease per 1000 women screened than conventional cytology, with cervical intraepithelial neoplasia grade 1 as the threshold for referral to colposcopy. More imager read slides than conventional slides were satisfactory for examination and more contained low grade cytological abnormalities. PMID:17604301

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.

Primary Sutureless Repair Using Biatrial Incision: Suture-And-Open Technique.

PubMed

Kim, Hyungtae; Sung, Si Chan; Choi, Kwang Ho; Lee, Hyoung Doo; Kim, Geena; Ko, Hoon

2018-06-08

We used a suture-and-open technique with a biatrial incision for primary sutureless repair of total anomalous pulmonary venous connection (TAPVC). With this technique, the common pulmonary venous sinus and its branching pulmonary veins are opened after completion of suturing of the left atrial incision to the pericardium around the common pulmonary venous sinus and its branching veins. The technique allows the primary sutureless repair of TAPVC to be done in a less bloody field under full-flow cardiopulmonary bypass. We have performed this technique in our recent 5 consecutive TAPVC patients without significant complications. Copyright © 2018. Published by Elsevier Inc.

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

Impact of robotics on the outcome of elderly patients with endometrial cancer.

PubMed

Lavoue, Vincent; Zeng, Xing; Lau, Susie; Press, Joshua Z; Abitbol, Jeremie; Gotlieb, Raphael; How, Jeffrey; Wang, Yifan; Gotlieb, Walter H

2014-06-01

To evaluate the impact of introducing a robotics program on clinical outcome of elderly patients with endometrial cancer. Evaluation and comparison of peri-operative morbidity and disease-free interval in 163 consecutive elderly patients (≥70years) with endometrial cancer undergoing staging procedure with traditional open surgery compared to robotic surgery. All consecutive patients ≥70years of age with endometrial cancer who underwent robotic surgery (n=113) were compared with all consecutive patients ≥70years of age (n=50) before the introduction of a robotic program in December 2007. Baseline patient characteristics were similar in both eras. Patients undergoing robotic surgery had longer mean operating times (244 compared with 217minutes, p=0.009) but fewer minor adverse events (17% compared with 60%, p<0.001). The robotics cohort had less estimated mean blood loss (75 vs 334mL, p<0.0001) and shorter mean hospital stay (3 vs 6days, p<0.0001). There was no difference in disease-free survival (p=0.61) during the mean follow-up time of 2years. Transitioning from open surgery to a robotics program for the treatment of endometrial cancer in the elderly has significant benefits, including lower minor complication rate, less operative blood loss and shorter hospitalization without compromising 2-year disease-free survival. Copyright © 2014 Elsevier Inc. All rights reserved.

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…

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.

Error-eliminating rapid ultrasonic firing

DOEpatents

Borenstein, Johann; Koren, Yoram

1993-08-24

A system for producing reliable navigation data for a mobile vehicle, such as a robot, combines multiple range samples to increase the "confidence" of the algorithm in the existence of an obstacle. At higher vehicle speed, it is crucial to sample each sensor quickly and repeatedly to gather multiple samples in time to avoid a collision. Erroneous data is rejected by delaying the issuance of an ultrasonic energy pulse by a predetermined wait-period, which may be different during alternate ultrasonic firing cycles. Consecutive readings are compared, and the corresponding data is rejected if the readings differ by more than a predetermined amount. The rejection rate for the data is monitored and the operating speed of the navigation system is reduced if the data rejection rate is increased. This is useful to distinguish and eliminate noise from the data which truly represents the existence of an article in the field of operation of the vehicle.

Error-eliminating rapid ultrasonic firing

DOEpatents

Borenstein, J.; Koren, Y.

1993-08-24

A system for producing reliable navigation data for a mobile vehicle, such as a robot, combines multiple range samples to increase the confidence'' of the algorithm in the existence of an obstacle. At higher vehicle speed, it is crucial to sample each sensor quickly and repeatedly to gather multiple samples in time to avoid a collision. Erroneous data is rejected by delaying the issuance of an ultrasonic energy pulse by a predetermined wait-period, which may be different during alternate ultrasonic firing cycles. Consecutive readings are compared, and the corresponding data is rejected if the readings differ by more than a predetermined amount. The rejection rate for the data is monitored and the operating speed of the navigation system is reduced if the data rejection rate is increased. This is useful to distinguish and eliminate noise from the data which truly represents the existence of an article in the field of operation of the vehicle.

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

Accurate typing of short tandem repeats from genome-wide sequencing data and its applications.

PubMed

Fungtammasan, Arkarachai; Ananda, Guruprasad; Hile, Suzanne E; Su, Marcia Shu-Wei; Sun, Chen; Harris, Robert; Medvedev, Paul; Eckert, Kristin; Makova, Kateryna D

2015-05-01

Short tandem repeats (STRs) are implicated in dozens of human genetic diseases and contribute significantly to genome variation and instability. Yet profiling STRs from short-read sequencing data is challenging because of their high sequencing error rates. Here, we developed STR-FM, short tandem repeat profiling using flank-based mapping, a computational pipeline that can detect the full spectrum of STR alleles from short-read data, can adapt to emerging read-mapping algorithms, and can be applied to heterogeneous genetic samples (e.g., tumors, viruses, and genomes of organelles). We used STR-FM to study STR error rates and patterns in publicly available human and in-house generated ultradeep plasmid sequencing data sets. We discovered that STRs sequenced with a PCR-free protocol have up to ninefold fewer errors than those sequenced with a PCR-containing protocol. We constructed an error correction model for genotyping STRs that can distinguish heterozygous alleles containing STRs with consecutive repeat numbers. Applying our model and pipeline to Illumina sequencing data with 100-bp reads, we could confidently genotype several disease-related long trinucleotide STRs. Utilizing this pipeline, for the first time we determined the genome-wide STR germline mutation rate from a deeply sequenced human pedigree. Additionally, we built a tool that recommends minimal sequencing depth for accurate STR genotyping, depending on repeat length and sequencing read length. The required read depth increases with STR length and is lower for a PCR-free protocol. This suite of tools addresses the pressing challenges surrounding STR genotyping, and thus is of wide interest to researchers investigating disease-related STRs and STR evolution. © 2015 Fungtammasan et al.; Published by Cold Spring Harbor Laboratory Press.

Intraoperative assessment of intraocular pressure in vitrectomized air-filled and fluid-filled eyes.

PubMed

Moon, Chan Hee; Choi, Kyung Seek; Rhee, Mi Ri; Lee, Sung Jin

2013-11-01

To ascertain the difference of intraocular pressure (IOP) measurement between vitrectomized air-filled and fluid-filled eyes. Thirty-one eyes of 31 consecutive patients who underwent conventional vitrectomy and intraocular gas tamponade were assessed. After vitrectomy, IOP of the fluid-filled eyes was measured by Tono-Pen. Thereafter, fluid-air exchange was performed, and IOP of the air-filled eyes was measured again. The IOP within each fluid- and air-filled eye was varied by selecting settings on the vitrectomy system, from 10 to 50 mmHg with 5-mmHg increments. Postoperatively, IOP was assessed by both Tono-Pen and Goldmann applanation tonometry (GAT). Linear and nonlinear regression analyses were conducted between intraoperatively measured Tono-Pen readings and actual IOPs. Bland-Altman plot was used to assess the agreements between postoperatively measured Tono-Pen readings and GAT readings. The discrepancy between Tono-Pen readings and actual IOP in fluid-filled eyes was not significant, except for the profound high pressures over 45 mmHg. However, Tono-Pen readings in air-filled eyes were significantly lower than actual IOPs in all ranges, and Tono-Pen increasingly underestimates IOP at higher levels. Intraoperative Tono-Pen readings were correlated significantly with actual IOP and a quadratic equation evidenced the best fit (R(2) = 0.996). Postoperatively, difference of the measurements between Tono-Pen and GAT was not significant. Tono-Pen and GAT significantly underestimate actual IOP in air-filled eyes. It should be considered that actual IOP would be greater than the measured IOP in gas-filled eyes, even though the IOP is measured as normal. © 2013 Acta Ophthalmologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

Clonazepam treatment of pathologic childhood aerophagia with psychological stresses.

PubMed

Hwang, Jin Bok; Kim, Jun Sik; Ahn, Byung Hoon; Jung, Chul Ho; Lee, Young Hwan; Kam, Sin

2007-04-01

The treatment of pathologic aerophagia has rarely been discussed in the literature. In this retrospective study, the authors investigated the effects of clonazepam on the management of pathologic childhood aerophagia (PCA) with psychological stresses (PS), but not with mental retardation. Data from 22 consecutive PCA patients with PS (aged 2 to 10 yr), who had been followed up for over 1 yr, were reviewed. On the basis of videolaryngoscopic views, the authors observed that the pathology of aerophagia was the result of reflex-induced swallowing with paroxysmal openings of the upper esophageal sphincter due to unknown factors and also observed that these reflex-induced openings were subsided after intravenous low dose benzodiazepine administration. Hence, clonazepam was administered to treat paroxysmal openings in these PCA patients with PS. Remission positivity was defined as symptom-free for a consecutive 1 month within 6 months of treatment. The results of treatment in 22 PCA patients with PS were analyzed. A remission positive state was documented in 14.3% of PCA patients managed by reassurance, and in 66.7% of PCA patients treated with clonazepam (p=0.032). Thus, clonazepam may produce positive results in PCA with PS. Future studies by randomized and placebo-controlled trials are needed to confirm the favorable effect of clonazepam in PCA.

Clonazepam Treatment of Pathologic Childhood Aerophagia with Psychological Stresses

PubMed Central

Kim, Jun Sik; Ahn, Byung Hoon; Jung, Chul-Ho; Lee, Young Hwan; Kam, Sin

2007-01-01

The treatment of pathologic aerophagia has rarely been discussed in the literature. In this retrospective study, the authors investigated the effects of clonazepam on the management of pathologic childhood aerophagia (PCA) with psychological stresses (PS), but not with mental retardation. Data from 22 consecutive PCA patients with PS (aged 2 to 10 yr), who had been followed up for over 1 yr, were reviewed. On the basis of videolaryngoscopic views, the authors observed that the pathologyof aerophagia was the result of reflex-induced swallowing with paroxysmal openings of the upper esophageal sphincter due to unknown factors and also observed that these reflex-induced openings were subsided after intravenous low dose benzodiazepine administration. Hence, clonazepam was administered to treat paroxysmal openings in these PCA patients with PS. Remission positivity was defined as symptom-free for a consecutive 1 month within 6 months of treatment. The results of treatment in 22 PCA patients with PS were analyzed. A remission positive state was documented in 14.3% of PCA patients managed by reassurance, and in 66.7% of PCA patients treated with clonazepam (p=0.032). Thus, clonazepam may produce positive results in PCA with PS. Future studies by randomized and placebo-controlled trials are needed to confirm the favorable effect of clonazepam in PCA. PMID:17449924

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:

Results of open pararenal abdominal aortic aneurysm repair: single centre series and pooled analysis of literature.

PubMed

van Lammeren, Guus W; Ünlü, Çağdaş; Verschoor, Sjoerd; van Dongen, Eric P; Wille, Jan; van de Pavoordt, Eric Dwm; de Vries-Werson, Debbie Ab; De Vries, Jean-Paul Pm

2017-06-01

Objectives Endovascular treatment of pararenal abdominal aortic aneurysm has gained terrain over the past decade, despite the substantial need for reinterventions during follow-up. However, open repair is still a well-established treatment option. With the current study we report the results of a consecutive series of elective primary open pararenal abdominal aortic aneurysm repair in a tertiary vascular referral centre, combined with an overview of current literature and pooled data analysis of perioperative mortality of open and endovascular pararenal abdominal aortic aneurysm repair. Methods A retrospective analysis of a prospective database of all elective open pararenal abdominal aortic aneurysm repairs in the St. Antonius Hospital between 2005 and 2014 was performed. Primary endpoint was 30-day mortality. Secondary endpoints were 30-day morbidity, new onset dialysis, reintervention free survival, and overall survival during follow-up. Results Between 2005 and 2014, 214 consecutive patients underwent elective open pararenal abdominal aortic aneurysm repair. Mean age was 69.8 (±7.1) years, 82.7% (177/214) were men, and mean abdominal aortic aneurysm diameter was 62 (±11) mm. Thirty-day mortality was 3.4%. Thirty-day morbidity was 27.1%, which predominantly consisted of pneumonia (18.7% (40/214)), cardiac events (3.3% (7/214)), and new onset dialysis (2.8% (6/214)). Estimated five-year overall survival rate was 74.2%. 0.9% (2/214) of patients required abdominal aortic aneurysm-related reintervention, and an additional 2.3% (5/214) required surgical repair of an incisional hernia. Pooled analysis of literature revealed a 30-day mortality of 3.0% for open pararenal repair and 1.9% for fenestrated endovascular repair. Conclusion Open pararenal abdominal aortic aneurysm repair in the era of increasing endovascular options results in acceptable perioperative morbidity and mortality rates. Mid-term reintervention rate is low compared to fenestrated endovascular aneurysm repair. Expertise with open repair still remains essential for treatment of pararenal abdominal aortic aneurysms in the near future, especially for those patients that are declined for endovascular treatment.

Snowblower injuries to the hand.

PubMed

Jardin, E; Uhring, J; Rey, P-B; Ferrier, M; Obert, L

2014-09-01

The aim of this study was to describe the nature and incidence of hand injuries caused by snowblowers, as well as the accident conditions and accident prevention. We conducted a retrospective evaluation over ten consecutive winters. Nine patients were included. All were men with an average age of 49.7 years (17-71). The accidents occurred at home in seven out of nine patients. The machine was running in 50% of the injury events. In most cases, the injuries occurred when the patient tried to unclog snow from the lateral discharge chute. Only four out of the nine patients had read the instructions or received instructions from the salesperson. The dominant hand was injured in 7 out of 9 patients. An average of 2.7 fingers were injured. The longest fingers were most commonly injured: 8 middle fingers, 7 ring fingers, 4 little fingers, 2 indexes and 1 thumb. All the fractures were open. Three patients were operated on several times. In 7 out of 9 cases, the patients had sequelae such as amputation. The mean time off work was 11.4 weeks (3-24). All the patients were experienced snowblower users (9 years and 57th use on average). Snowblower accidents are very mutilating. Prevention must include protected access to blades and better verbal and written safety warnings. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Surface Diversity in Mycoplasma agalactiae Is Driven by Site-Specific DNA Inversions within the vpma Multigene Locus

PubMed Central

Glew, Michelle D.; Marenda, Marc; Rosengarten, Renate; Citti, Christine

2002-01-01

The ruminant pathogen Mycoplasma agalactiae possesses a family of abundantly expressed variable surface lipoproteins called Vpmas. Phenotypic switches between Vpma members have previously been correlated with DNA rearrangements within a locus of vpma genes and are proposed to play an important role in disease pathogenesis. In this study, six vpma genes were characterized in the M. agalactiae type strain PG2. All vpma genes clustered within an 8-kb region and shared highly conserved 5′ untranslated regions, lipoprotein signal sequences, and short N-terminal sequences. Analyses of the vpma loci from consecutive clonal isolates showed that vpma DNA rearrangements were site specific and that cleavage and strand exchange occurred within a minimal region of 21 bp located within the 5′ untranslated region of all vpma genes. This process controlled expression of vpma genes by effectively linking the open reading frame (ORF) of a silent gene to a unique active promoter sequence within the locus. An ORF (xer1) immediately adjacent to one end of the vpma locus did not undergo rearrangement and had significant homology to a distinct subset of genes belonging to the λ integrase family of site-specific xer recombinases. It is proposed that xer1 codes for a site-specific recombinase that is not involved in chromosome dimer resolution but rather is responsible for the observed vpma-specific recombination in M. agalactiae. PMID:12374833

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.

Formation of furan fatty alkyl esters from their bis-epoxide fatty esters

USDA-ARS?s Scientific Manuscript database

Epoxidation of vegetable oils and consecutive epoxide ring-opening reaction is a widely investigated path for producing biobased lubricants and polymers. The reaction mechanism and products are considered well-studied and known. In the current study, the reactions of epoxidized alkyl soyate with fou...

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.

An Empirical Investigation of Variance Design Parameters for Planning Cluster-Randomized Trials of Science Achievement.

PubMed

Westine, Carl D; Spybrook, Jessaca; Taylor, Joseph A

2013-12-01

Prior research has focused primarily on empirically estimating design parameters for cluster-randomized trials (CRTs) of mathematics and reading achievement. Little is known about how design parameters compare across other educational outcomes. This article presents empirical estimates of design parameters that can be used to appropriately power CRTs in science education and compares them to estimates using mathematics and reading. Estimates of intraclass correlations (ICCs) are computed for unconditional two-level (students in schools) and three-level (students in schools in districts) hierarchical linear models of science achievement. Relevant student- and school-level pretest and demographic covariates are then considered, and estimates of variance explained are computed. Subjects: Five consecutive years of Texas student-level data for Grades 5, 8, 10, and 11. Science, mathematics, and reading achievement raw scores as measured by the Texas Assessment of Knowledge and Skills. Results: Findings show that ICCs in science range from .172 to .196 across grades and are generally higher than comparable statistics in mathematics, .163-.172, and reading, .099-.156. When available, a 1-year lagged student-level science pretest explains the most variability in the outcome. The 1-year lagged school-level science pretest is the best alternative in the absence of a 1-year lagged student-level science pretest. Science educational researchers should utilize design parameters derived from science achievement outcomes. © The Author(s) 2014.

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…

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:

Differential Effect of CD4+Foxp3+ T-regulatory Cells on the B and T Helper Cell Responses to Influenza Virus Vaccination

DTIC Science & Technology

2010-01-01

for a suppres- sogenic effect ofT-regs on the anti-viral immune responses (7-1 0 ]. Early studies on the mechanisms by which A/ Puerto Rico /8/34 (Hl...USA). Mice were considered diabetic after two consecutive readings of glycemia higher than 200 mg/dL In some experiments, ]. Surls et al./ Vacdne...interval of confidence. The relevance of differences in survival and diabetes incidence of RAG2 KO, RIP-PR8/HA mice infused with T-cells from

Perioperative and oncologic outcomes of minimally invasive liver resection for colorectal metastases: A case-control study of 130 patients.

PubMed

Karagkounis, Georgios; Akyuz, Muhammet; Guerron, Alfredo Daniel; Yazici, Pinar; Aucejo, Federico N; Quintini, Cristiano; Miller, Charles M; Vogt, David P; Fung, John J; Berber, Eren

2016-10-01

Our aim was to compare the perioperative and oncologic outcomes of open liver resection and minimally invasive liver resection in the management of colorectal liver metastases. Patients who underwent minimally invasive liver resection for colorectal liver metastases between January 2006 and June 2015 at a single center were identified and matched by extent of resection to consecutive open liver resection patients from the same period. Clinicopathologic characteristics, perioperative data, recurrence, and survival outcomes were collected and analyzed based on intention-to-treat. Sixty-five patients underwent minimally invasive liver resection during this period and were matched to 65 consecutive open liver resection patients, with similar baseline demographic, tumor, and chemotherapy parameters. Conversion to open occurred in 5 (7.7%) minimally invasive liver resection patients. R0 resection rates and operative times were comparable, but the estimated blood loss was less in the minimally invasive liver resection group (median 200 mL vs 400 mL, P < .001), as were perioperative transfusion rates (4.6% vs 15.4%, P = .04). The duration of stay was shorter after minimally invasive liver resection (median 4 days vs 6 days, P < .001), while major and minor complication rates were similar and no perioperative mortality was recorded. At a median follow-up of 28 months, there was no difference regarding disease-free (P = .90) or overall survival (P = .37). In selected patients with colorectal liver metastases, minimally invasive liver resection resulted in similar oncologic outcomes, with decreased blood loss and shorter duration of stay compared to patients who underwent open liver resection. Copyright © 2016 Elsevier Inc. All rights reserved.

Uncertainty analysis of gas flow measurements using clearance-sealed piston provers in the range from 0.0012 g min-1 to 60 g min-1

NASA Astrophysics Data System (ADS)

Bobovnik, G.; Kutin, J.; Bajsić, I.

2016-08-01

This paper deals with an uncertainty analysis of gas flow measurements using a compact, high-speed, clearance-sealed realization of a piston prover. A detailed methodology for the uncertainty analysis, covering the components due to the gas density, dimensional and time measurements, the leakage flow, the density correction factor and the repeatability, is presented. The paper also deals with the selection of the isothermal and adiabatic measurement models, the treatment of the leakage flow and discusses the need for averaging multiple consecutive readings of the piston prover. The analysis is prepared for the flow range (50 000:1) covered by the three interchangeable flow cells. The results show that using the adiabatic measurement model and averaging the multiple readings, the estimated expanded measurement uncertainty of the gas mass flow rate is less than 0.15% in the flow range above 0.012 g min-1, whereas it increases for lower mass flow rates due to the leakage flow related effects. At the upper end of the measuring range, using the adiabatic instead of the isothermal measurement model, as well as averaging multiple readings, proves important.

Diagnostic performance of dual-energy contrast-enhanced subtracted mammography in dense breasts compared to mammography alone: interobserver blind-reading analysis.

PubMed

Cheung, Yun-Chung; Lin, Yu-Ching; Wan, Yung-Liang; Yeow, Kee-Min; Huang, Pei-Chin; Lo, Yung-Feng; Tsai, Hsiu-Pei; Ueng, Shir-Hwa; Chang, Chee-Jen

2014-10-01

To analyse the accuracy of dual-energy contrast-enhanced spectral mammography in dense breasts in comparison with contrast-enhanced subtracted mammography (CESM) and conventional mammography (Mx). CESM cases of dense breasts with histological proof were evaluated in the present study. Four radiologists with varying experience in mammography interpretation blindly read Mx first, followed by CESM. The diagnostic profiles, consistency and learning curve were analysed statistically. One hundred lesions (28 benign and 72 breast malignancies) in 89 females were analysed. Use of CESM improved the cancer diagnosis by 21.2 % in sensitivity (71.5 % to 92.7 %), by 16.1 % in specificity (51.8 % to 67.9 %) and by 19.8 % in accuracy (65.9 % to 85.8 %) compared with Mx. The interobserver diagnostic consistency was markedly higher using CESM than using Mx alone (0.6235 vs. 0.3869 using the kappa ratio). The probability of a correct prediction was elevated from 80 % to 90 % after 75 consecutive case readings. CESM provided additional information with consistent improvement of the cancer diagnosis in dense breasts compared to Mx alone. The prediction of the diagnosis could be improved by the interpretation of a significant number of cases in the presence of 6 % benign contrast enhancement in this study. • DE-CESM improves the cancer diagnosis in dense breasts compared with mammography. • DE-CESM shows greater consistency than mammography alone by interobserver blind reading. • Diagnostic improvement of DE-CESM is independent of the mammographic reading experience.

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:

Reading ability and retinal sensitivity after surgery for macular hole and macular pucker.

PubMed

Cappello, Ezio; Virgili, Gianni; Tollot, Luigina; Del Borrello, Michele; Menchini, Ugo; Zemella, Marco

2009-09-01

To assess whether reading ability and microperimetry improve as demonstrated for visual acuity after surgery for macular hole and macular pucker. Fifty-nine consecutive patients underwent pars plana vitrectomy for macular pucker (n = 41) or full-thickness macular holes (n = 18). Functional assessment was made at 3, 6, and 12 months after surgery and included far visual acuity (Early Treatment Diabetic Retinopathy Study charts), retinal sensitivity using the microperimeter (MP1, Nidek Technologies, Padova, Italy), and reading ability (MNRead charts). An improvement was recorded both for macular holes and puckers not only for visual acuity, but also for reading acuity and mean central retinal sensitivity (P < 0.01 for the overall comparisons between baseline and follow-up values). Maximum reading speed was already good at baseline both for puckers and holes overall, and a significant mean improvement was recorded only in patients with macular hole at 6 and 12 months (P < 0.01). Although eyes with macular holes had worse baseline visual function compared with puckers (P < 0.01 for all measures of visual function except for reading speed), they recovered to similar levels thanks to greater improvement (P < 0.05 for the difference in improvement during follow-up between puckers and holes for all measures of visual function). No differences were found among indocyanine green or trypan blue staining compared with no staining for internal limiting membrane removal based on all outcome measures (P > 0.05 for the overall difference of visual function improvement during follow-up). The improvement found for visual acuity after vitrectomy for macular hole and pucker also regards retinal sensitivity and reading ability for up to 12 months. This is reassuring concerning the benefits for the patients, and this shows that visual acuity is a valid functional measure for investigating the efficacy of macular surgery.

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.

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

76 FR 21253 - Drawbridge Operation Regulation; Company Canal, Lockport, LA

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-15

... for twelve consecutive hours each day from Monday through Thursday for three weeks. DATES: This... 10 a.m. the draw opens on signal if at least 4 hours notice is given. This deviation allows the... Canal, mile 0.4, at Lockport, Lafourche Parish, Louisiana. The deviation is necessary to perform...

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)

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.

Consecutive pharmacological activation of PKA and PKC mimics the potent cardioprotection of temperature preconditioning

PubMed Central

Khaliulin, Igor; Parker, Joanna E.; Halestrap, Andrew P.

2010-01-01

Aims Temperature preconditioning (TP) provides very powerful protection against ischaemia/reperfusion. Understanding the signalling pathways involved may enable the development of effective pharmacological cardioprotection. We investigated the interrelationship between activation of protein kinase A (PKA) and protein kinase C (PKC) in the signalling mechanisms of TP and developed a potent pharmacological intervention based on this mechanism. Methods and results Isolated rat hearts were subjected to TP, 30 min global ischaemia, and 60 min reperfusion. Other control and TP hearts were perfused with either sotalol (β-adrenergic blocker) or H-89 (PKA inhibitor). Some hearts were pre-treated with either isoproterenol (β-adrenergic agonist) or adenosine (PKC activator) that were given alone, simultaneously, or sequentially. Pre-treatment with isoproterenol, adenosine, and the consecutive isoproterenol/adenosine treatment was also combined with the PKC inhibitor chelerythrine. Cardioprotection was evaluated by haemodynamic function recovery, lactate dehydrogenase release, measurement of mitochondrial permeability transition pore opening, and protein carbonylation during reperfusion. Cyclic AMP and PKA activity were increased in TP hearts. H-89 and sotalol blocked the cardioprotective effect of TP and TP-induced PKC activation. Isoproterenol, adenosine, and the consecutive treatment increased PKC activity during pre-ischaemia. Isoproterenol significantly reduced myocardial glycogen content. Isoproterenol and adenosine, alone or simultaneously, protected hearts but the consecutive treatment gave the highest protection. Cardioprotective effects of adenosine were completely blocked by chelerythrine but those of the consecutive treatment only attenuated. Conclusion The signal transduction pathway of TP involves PKA activation that precedes PKC activation. Pharmacologically induced consecutive PKA/PKC activation mimics TP and induces extremely potent cardioprotection. PMID:20558443

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

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

Laparoscopic and open subtotal colectomies have similar short-term results.

PubMed

Hoogenboom, Froukje J; Bosker, Robbert J I; Groen, Henk; Meijerink, Wilhelmus J H J; Lamme, Bas; Pierie, Jean Pierre E N

2013-01-01

Laparoscopic subtotal colectomy (STC) is a complex procedure. It is possible that short-term benefits for segmental resections cannot be attributed to this complex procedure. This study aims to assess differences in short-term results for laparoscopic versus open STC during a 15-year single-institute experience. We reviewed consecutive patients undergoing laparoscopic or open elective or subacute STC from January 1997 to December 2012. Fifty-six laparoscopic and 50 open STCs were performed. The operation time was significantly longer in the laparoscopic group, median 266 min (range 121-420 min), compared to 153 min (range 90-408 min) in the open group (p < 0.001). Median hospital stay showed no statistical difference, 14 days (range 1-129 days) in the laparoscopic and 13 days (range 1-85 days) in the open group. Between-group postoperative complications were not statistically different. Laparoscopic STC has short-term results similar to the open procedure, except for a longer operation time. The laparoscopic approach for STC is therefore only advisable in selected patients combined with extensive preoperative counseling. Copyright © 2013 S. Karger AG, Basel.

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.

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

Trans-saccadic parafoveal preview benefits in fluent reading: a study with fixation-related brain potentials.

PubMed

Dimigen, Olaf; Kliegl, Reinhold; Sommer, Werner

2012-08-01

During natural reading, a parafoveal preview of the upcoming word facilitates its subsequent recognition (e.g., shorter fixation durations compared to masked preview) but nothing is known about the neural correlates of this so-called preview benefit. Furthermore, while the evidence is strong that readers preprocess orthographic features of upcoming words, it is controversial whether word meaning can also be accessed parafoveally. We investigated the timing, scope, and electrophysiological correlates of parafoveal information use in reading by simultaneously recording eye movements and fixation-related brain potentials (FRPs) while participants read word lists fluently from left to right. For one word-the target-(e.g., "blade") parafoveal information was manipulated by showing an identical ("blade"), semantically related ("knife"), or unrelated ("sugar") word as preview. In boundary trials, the preview was shown parafoveally but changed to the correct target word during the incoming saccade. Replicating classic findings, target words were fixated shorter after identical previews. In the EEG, this benefit was reflected in an occipitotemporal preview positivity between 200 and 280 ms. In contrast, there was no facilitation from related previews. In parafoveal-on-foveal trials, preview and target were embedded at neighboring list positions without a display change. Consecutive fixation of two related words produced N400 priming effects, but only shortly (160 ms) after the second word was directly fixated. Results demonstrate that neural responses to words are substantially altered by parafoveal preprocessing under normal reading conditions. We found no evidence that word meaning contributes to these effects. Saccade-contingent display manipulations can be combined with EEG recordings to study extrafoveal perception in vision. Copyright © 2012 Elsevier Inc. All rights reserved.

Severity of Vision Loss Interacts With Word-Specific Features to Impact Out-Loud Reading in Glaucoma

PubMed Central

Mathews, Priya M.; Rubin, Gary S.; McCloskey, Michael; Salek, Sherveen; Ramulu, Pradeep Y.

2015-01-01

Purpose. To assess the impact of glaucoma-related vision loss on measures of out-loud reading, including time to say individual words, interval time between consecutive words, lexical errors, skipped words, and repetitions. Methods. Glaucoma subjects (n = 63) with bilateral visual field loss and glaucoma suspect controls (n = 57) were recorded while reading a standardized passage out loud. A masked evaluator determined the start and end of each recorded word and identified reading errors. Results. Glaucoma subjects demonstrated longer durations to recite individual words (265 vs. 243 ms, P < 0.001), longer intervals between words (154 vs. 124 ms, P < 0.001), and longer word/post-word interval complexes (the time spanned by the word and the interval following the word; 419 vs. 367 ms, P < 0.001) than controls. In multivariable analyses, each 0.1 decrement in log contrast sensitivity (logCS) was associated with a 15.0 ms longer word/post-interval complex (95% confidence interval [CI] = 9.6–20.4; P < 0.001). Contrast sensitivity was found to significantly interact with word length, word frequency, and word location at the end of a line with regards to word/post-word interval complex duration (P < 0.05 for all). Glaucoma severity was also associated with more lexical errors (Odds ratio = 1.20 for every 0.1 logCS decrement; 95% CI = 1.02–1.39, P < 0.05), but not with more skipped or repeated words. Conclusions. Glaucoma patients with greater vision loss make more lexical errors, are slower in reciting longer and less frequently used words, and more slowly transition to new lines of text. These problem areas may require special attention when designing methods to rehabilitate reading in patients with glaucoma. PMID:25737150

School Psychology Trainer Shortage in the USA: Current Status and Projections for the Future

ERIC Educational Resources Information Center

Clopton, Kerri L.; Haselhuhn, Charlotte W.

2009-01-01

This study documents the number of school psychology faculty openings, reasons for resignations and the outcome of faculty searches in the United States for three consecutive academic years beginning in 2004. School psychology program training directors in the United States were surveyed about program faculty needs, including resignations and the…

Graduate Medical Education Viewed from the National Intern and Resident Matching Program

ERIC Educational Resources Information Center

Graettinger, John S.

1976-01-01

The total number of applicants for first-year programs in graduate medical education through the National Intern and Resident Matching Program in 1976 exceeded the number of positions offered for the second consecutive year. There were deficits in the number of openings offered in the primary care specialties and surfeits in medical and surgical…

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

Identification and Cloning of gusA, Encoding a New β-Glucuronidase from Lactobacillus gasseri ADH†

PubMed Central

Russell, W. M.; Klaenhammer, T. R.

2001-01-01

The gusA gene, encoding a new β-glucuronidase enzyme, has been cloned from Lactobacillus gasseri ADH. This is the first report of a β-glucuronidase gene cloned from a bacterial source other than Escherichia coli. A plasmid library of L. gasseri chromosomal DNA was screened for complementation of an E. coli gus mutant. Two overlapping clones that restored β-glucuronidase activity in the mutant strain were sequenced and revealed three complete and two partial open reading frames. The largest open reading frame, spanning 1,797 bp, encodes a 597-amino-acid protein that shows 39% identity to β-glucuronidase (GusA) of E. coli K-12 (EC 3.2.1.31). The other two complete open reading frames, which are arranged to be separately transcribed, encode a putative bile salt hydrolase and a putative protein of unknown function with similarities to MerR-type regulatory proteins. Overexpression of GusA was achieved in a β-glucuronidase-negative L. gasseri strain by expressing the gusA gene, subcloned onto a low-copy-number shuttle vector, from the strong Lactobacillus P6 promoter. GusA was also expressed in E. coli from a pET expression system. Preliminary characterization of the GusA protein from crude cell extracts revealed that the enzyme was active across an acidic pH range and a broad temperature range. An analysis of other lactobacilli identified β-glucuronidase activity and gusA homologs in other L. gasseri isolates but not in other Lactobacillus species tested. PMID:11229918

Procedural Learning in Children With Developmental Coordination, Reading, and Attention Disorders.

PubMed

Magallón, Sara; Crespo-Eguílaz, Nerea; Narbona, Juan

2015-10-01

The aim is to assess repetition-based learning of procedures in children with developmental coordination disorder (DCD), reading disorder (RD) and attention-deficit hyperactivity disorder (ADHD). Participants included 187 children, studied in 4 groups: (a) DCD comorbid with RD and ADHD (DCD+RD+ADHD) (n = 30); (b) RD comorbid with ADHD (RD+ADHD) (n = 48); (c) ADHD (n = 19); and typically developing children (control group) (n = 90). Two procedural learning tasks were used: Assembly learning and Mirror drawing. Children were tested on 4 occasions for each task: 3 trials were consecutive and the fourth trial was performed after an interference task. Task performance by DCD+RD+ADHD children improved with training (P < .05); however, the improvement was significantly lower than that achieved by the other groups (RD+ADHD, ADHD and controls) (P < .05). In conclusion, children with DCD+RD+ADHD improve in their use of cognitive-motor procedures over a short training period. Aims of intervention in DCD+RD+ADHD should be based on individual learning abilities. © The Author(s) 2015.

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

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.

Comparison of Fully Automated Computer Analysis and Visual Scoring for Detection of Coronary Artery Disease from Myocardial Perfusion SPECT in a Large Population

PubMed Central

Arsanjani, Reza; Xu, Yuan; Hayes, Sean W.; Fish, Mathews; Lemley, Mark; Gerlach, James; Dorbala, Sharmila; Berman, Daniel S.; Germano, Guido; Slomka, Piotr

2012-01-01

We compared the performance of a fully automated quantification of attenuation-corrected (AC) and non-corrected (NC) myocardial perfusion single photon emission computed tomography (MPS) with the corresponding performance of experienced readers for the detection coronary artery disease (CAD). Methods 995 rest/stress 99mTc-sestamibi MPS studies, [650 consecutive cases with coronary angiography and 345 with likelihood of CAD < 5% (LLk)] were obtained by MPS with AC. Total perfusion deficit (TPD) for AC and NC data were compared to the visual summed stress and rest scores of 2 experienced readers. Visual reads were performed in 4 consecutive steps with the following information progressively revealed: NC data, AC+NC data, computer results, all clinical information. Results The diagnostic accuracy of TPD for detection of CAD was similar to both readers (NC: 82% vs. 84%, AC: 86% vs. 85–87% p = NS) with the exception of second reader when using clinical information (89%, p < 0.05). The Receiver-Operator-Characteristics Areas-Under-Curve (ROC-AUC) for TPD were significantly better than visual reads for NC (0.91 vs. 0.87 and 0.89, p < 0.01) and AC (0.92 vs. 0.90, p < 0.01), and it was comparable to visual reads incorporating all clinical information. Per-vessel accuracy of TPD was superior to one reader for NC (81% vs. 77%, p < 0.05) and AC (83% vs. 78%, p < 0.05) and equivalent to second reader [NC (79%) and AC (81%)]. Per-vessel ROC-AUC for NC (0.83) and AC (0.84) for TPD were better than (0.78–0.80 p < 0.01), and comparable to second reader (0.82–0.84, p = NS), for all steps. Conclusion For the detection of ≥ 70% stenosis based on angiographic criteria, a fully automated computer analysis of NC and AC MPS data is equivalent for per-patient and can be superior for per-vessel analysis, when compared to expert analysis. PMID:23315665

Effects of Prolonged Reading on Dry Eye.

PubMed

Karakus, Sezen; Agrawal, Devika; Hindman, Holly B; Henrich, Claudia; Ramulu, Pradeep Y; Akpek, Esen K

2018-04-25

To demonstrate the effects of prolonged silent reading on tear film and ocular surface parameters. Prospective, observational clinical study. A total of 177 patients with dry eye and 34 normal controls aged 50 years and older. After evaluating symptoms using the Ocular Surface Disease Index (OSDI) questionnaire, the following tests were performed in consecutive order: automated noninvasive tear break-up time (TBUT), surface asymmetry and regularity indices, Schirmer's testing without anesthesia, corneal staining using fluorescein, and conjunctival staining using lissamine green. The participants were then asked to read a 30-minute validated passage silently. The tests were repeated after the reading task. Changes in tear film and ocular surface parameters after reading. All parameters, with the exception of surface asymmetry index, worsened after the reading task in patients with dry eye and in controls. The worsening reached a statistical significance for corneal and conjunctival staining in the dry eye group (P < 0.001) and for corneal staining in the control group (P < 0.01). At baseline, OSDI scores correlated only with corneal and conjunctival staining scores (r = 0.19, P = 0.006 and r = 0.27, P < 0.001). Among postreading measurements, baseline OSDI scores correlated with TBUT (r = -0.15, P = 0.03) in addition to corneal and conjunctival staining (r = 0.25, P < 0.001 and r = 0.22, P = 0.001). Changes in TBUT and Schirmer's test correlated significantly with their respective baseline values (r = -0.61, P < 0.001 and r = -0.44, P < 0.001), indicating that the more unstable the tear film and the lower the aqueous tear secretion, the worse they became after the prolonged reading task. Worsening in corneal staining directly correlated with the baseline conjunctival staining (r = 0.17, P = 0.02) and surface regularity index (r = 0.21, P = 0.01). Evaluating tear film and ocular surface parameters at rest may miss clinical findings brought about by common everyday tasks such as reading, leading to discordance between patient-reported symptoms and clinician-observed signs. Quantifying dry eye after visually straining activities such as prolonged silent reading may help better understand patient symptomatology. Copyright © 2018 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.

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

Readability analysis of internet-based patient information regarding skull base tumors.

PubMed

Misra, Poonam; Kasabwala, Khushabu; Agarwal, Nitin; Eloy, Jean Anderson; Liu, James K

2012-09-01

Readability is an important consideration in assessing healthcare-related literature. In order for a source of information to be the most beneficial to patients, it should be written at a level appropriate for the audience. The National Institute of Health recommends that health literature be written at a maximum level of sixth grade. This is not uniformly found in current health literature, putting patients with lower reading levels at a disadvantage. In February 2012, healthcare-oriented education resources were retrieved from websites obtained using the Google search phrase skull base tumors. Of the first 25 consecutive, unique website hits, 18 websites were found to contain information for patients. Ten different assessment scales were utilized to assess the readability of the patient-specific web pages. Patient-oriented material found online for skull base tumors was written at a significantly higher level than the reading level of the average US patient. The average reading level of this material was found to be at a minimum of eleventh grade across all ten scales. Health related material related to skull base tumors available through the internet can be improved to reach a larger audience without sacrificing the necessary information. Revisions of this material can provide significant benefit for average patients and improve their health care.

Interpreting the biological relevance of bioinformatic analyses with T-DNA sequence for protein allergenicity.

PubMed

Harper, B; McClain, S; Ganko, E W

2012-08-01

Global regulatory agencies require bioinformatic sequence analysis as part of their safety evaluation for transgenic crops. Analysis typically focuses on encoded proteins and adjacent endogenous flanking sequences. Recently, regulatory expectations have expanded to include all reading frames of the inserted DNA. The intent is to provide biologically relevant results that can be used in the overall assessment of safety. This paper evaluates the relevance of assessing the allergenic potential of all DNA reading frames found in common food genes using methods considered for the analysis of T-DNA sequences used in transgenic crops. FASTA and BLASTX algorithms were used to compare genes from maize, rice, soybean, cucumber, melon, watermelon, and tomato using international regulatory guidance. Results show that BLASTX for maize yielded 7254 alignments that exceeded allergen similarity thresholds and 210,772 alignments that matched eight or more consecutive amino acids with an allergen; other crops produced similar results. This analysis suggests that each nontransgenic crop has a much greater potential for allergenic risk than what has been observed clinically. We demonstrate that a meaningful safety assessment is unlikely to be provided by using methods with inherently high frequencies of false positive alignments when broadly applied to all reading frames of DNA sequence. Copyright © 2012 Elsevier Inc. All rights reserved.

Evaluation of the validity and reliability of A-scan ultrasound biometry with a single use disposable cover.

PubMed

Cass, K; Thompson, C M; Tromans, C; Wood, I C J

2002-03-01

The UK Medical Devices Agency has suggested that ophthalmic practitioners should, where practicable and not compromising clinical outcome, restrict corneal contact devices to single patient use to minimise a remote theoretical risk of transmission of new variant Creutzfeldt-Jakob disease (vCJD). This study reports on a modified technique of ultrasound A-scan biometry that complies with the MDA recommendations. The right eyes of 37 consecutive hospital patients had a series of biometry readings taken with a Humphrey 820 A-scan instrument with a plane wave transducer use d conventionally and with the addition of a disposable latex cover. Intrasessional repeatability of axial length measurements was similar for conventional readings--mean difference 0.027 mm, 95% confidence intervals (CI) +/- 0.44 mm and those taken with a disposable cover (0.028 mm, CI +/- 0.38). Intersessional repeatability was equivalent with (0.002 mm, CI +.- 0.51) and without a cover (0.03 mm, CI +/- 0.51). Readings with a cover were not significantly different from those without (paired t test; p >0.05), but tended to be greater (mean difference 0.085 mm, CI +/- 0.60). These findings suggest that corneal contact biometry with a disposable cover is a viable and theoretically safer alternative to the conventional technique.

Development of reading ability is facilitated by intensive exposure to a digital children's picture book.

PubMed

Masataka, Nobuo

2014-01-01

Here the author presents preliminary evidence supporting the possibility that the reading ability of 4-year-old children can be improved as a consequence of intensive exposure to the narrative in a digital picture book over a consecutive 5-day period. When creating the digital version used here, two additional functions were provided with it. First, the entire story was voice-recorded by a professional narrator and programmed so that it was played as narration from the speaker of an iPad. Next, as the narration of each digitized page proceeded, the character exactly corresponding to that pronounced by the narrator at that moment became highlighted in red. When the subjects' literacy capability with respect to the syllabic script of the Japanese language (kana) was evaluated before and after the exposure, their performance score was found to increase after the exposure to the digital book, whereas such a change was not recorded in children who experienced exposure to the printed version of the same picture book read to them by their mother. These effects were confirmed when the children were retested 4 weeks later. Although preliminary, the current study represents the first experimental evidence for a positive effect of exposure to digital books upon any aspect of child development.

Development of reading ability is facilitated by intensive exposure to a digital children's picture book

PubMed Central

Masataka, Nobuo

2014-01-01

Here the author presents preliminary evidence supporting the possibility that the reading ability of 4-year-old children can be improved as a consequence of intensive exposure to the narrative in a digital picture book over a consecutive 5-day period. When creating the digital version used here, two additional functions were provided with it. First, the entire story was voice-recorded by a professional narrator and programmed so that it was played as narration from the speaker of an iPad. Next, as the narration of each digitized page proceeded, the character exactly corresponding to that pronounced by the narrator at that moment became highlighted in red. When the subjects' literacy capability with respect to the syllabic script of the Japanese language (kana) was evaluated before and after the exposure, their performance score was found to increase after the exposure to the digital book, whereas such a change was not recorded in children who experienced exposure to the printed version of the same picture book read to them by their mother. These effects were confirmed when the children were retested 4 weeks later. Although preliminary, the current study represents the first experimental evidence for a positive effect of exposure to digital books upon any aspect of child development. PMID:24822051

Reliability and Usefulness of Intraoperative 3-Dimensional Imaging by Mobile C-Arm With Flat-Panel Detector.

PubMed

Fujimori, Takahito; Iwasaki, Motoki; Nagamoto, Yukitaka; Kashii, Masafumi; Takao, Masaki; Sugiura, Tsuyoshi; Yoshikawa, Hideki

2017-02-01

Reliability and agreement study. To assess the reliability of intraoperative 3-dimensional imaging with a mobile C-arm (3D C-arm) equipped with a flat-panel detector. Pedicle screws are widely used in spinal surgery. Postoperative computed tomography (CT) is the most reliable method to detect screw misplacement. Recent advances in imaging devices have enabled surgeons to acquire 3D images of the spine during surgery. However, the reliability of these imaging devices is not known. A total of 203 screws were used in 22 consecutive patients who underwent surgery for scoliosis. Screw position was read twice with a 3D C-arm and twice with CT in a blinded manner by 2 independent observers. Screw positions were classified into 4 categories at every 2 mm and then into 2 simpler categories of acceptable or unacceptable. The degree of agreement with respect to screw positions between the double readings was evaluated by κ value. With unanimous agreement between 2 observers regarding postoperative CT readings considered the gold standard, the sensitivity of the 3D C-arm for determining screw misplacement was calculated. A total 804 readings were performed. For the 4-category classification, the mean κ value for the 2 interobserver readings was 0.52 for the 3D C-arm and 0.46 for CT. For the 2-category classification, the mean κ value for the 2 interobserver readings was 0.80 for the 3D C-arm and 0.66 for CT. The sensitivity, specificity, positive predictive value, and negative predictive value of intraoperative imaging with the 3D C-arm were 70%, 95%, 44%, and 98%, respectively. With respect to screws with perforation ≥4 mm, the sensitivity was 83%. No revision surgery was performed. Intraoperative imaging with a 3D C-arm was reliable for detecting screw misplacement and helpful in decreasing the rate of revision surgery for screw misplacement.

Development and pilot‐testing of a Decision Aid for use among Chinese women facing breast cancer surgery

PubMed Central

Au, Angel H.Y.; Lam, Wendy W.T.; Chan, Miranda C.M.; Or, Amy Y.M.; Kwong, Ava; Suen, Dacita; Wong, Annie L.; Juraskova, Ilona; Wong, Teresa W.T.; Fielding, Richard

2011-01-01

Abstract Background  Women choosing breast cancer surgery encounter treatment decision‐making (TDM) difficulties, which can cause psychological distress. Decision Aids (DAs) may facilitate TDM, but there are no DAs designed for Chinese populations. We developed a DA for Chinese women newly diagnosed with breast cancer, for use during the initial surgical consultation. Aims  Conduct a pilot study to assess the DA acceptability and utility among Chinese women diagnosed with breast cancer. Methods  Women preferred the DA in booklet format. A booklet was developed and revised and evaluated in two consecutive pilot studies (P1 and P2). On concluding their initial diagnostic consultation, 95 and 38 Chinese women newly diagnosed with breast cancer received the draft and revised draft DA booklet, respectively. Four‐day post‐consultation, women had questionnaires read out to them and to which they responded assessing attitudes towards the DA and their understanding of treatment options. Results  The original DA was read/partially read by 66/22% (n = 84) of women, whilst the revised version was read/partially read by 74/16% (n = 35), including subliterate women (χ2 = 0.76, P = 0.679). Knowledge scores varied with the extent the booklet was read (P1: F = 12.68, d.f. 2, P < 0.001; P2: F = 3.744, d.f. 2, P = 0.034). The revised, shorter version was graphically rich and resulted in improved perceived utility, [except for the ‘treatment options’ (χ2 = 5.50, P = 0.019) and ‘TDM guidance’ (χ2 = 8.19, P = 0.004) sections] without increasing anxiety (F = 0.689, P = 0.408; F = 3.45, P = 0.073). Conclusion  The DA was perceived as acceptable and useful for most women. The DA effectiveness is currently being evaluated using a randomized controlled trial. PMID:21223468

Open tibial fractures grade IIIC treated successfully with external fixation, negative-pressure wound therapy and recombinant human bone morphogenetic protein 7.

PubMed

Babiak, Ireneusz

2014-10-01

The aim of the therapy in open tibial fractures grade III was to cover the bone with soft tissue and achieve healed fracture without persistent infection. Open tibial fractures grade IIIC with massive soft tissue damage require combined orthopaedic, vascular and plastic-reconstructive procedures. Negative-pressure wound therapy (NPWT), used in two consecutive cases with open fracture grade IIIC of the tibia diaphysis, healed extensive soft tissue defect with exposure of the bone. NPWT eventually allowed for wound closure by split skin graft within 21-25 days. Ilizarov external fixator combined with application of recombinant human bone morphogenetic protein-7 at the site of delayed union enhanced definitive bone healing within 16-18 months. © 2012 The Authors. International Wound Journal © 2012 Medicalhelplines.com Inc and John Wiley & Sons Ltd.

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

Mini-open repair of achilles rupture in the national football league.

PubMed

McCullough, Kirk A; Shaw, Christopher M; Anderson, Robert B

2014-01-01

Tears of the Achilles tendon in professional athletes are an infrequent yet devastating injury. Historical studies have demonstrated not only a poor rate of return to competitive play but have also noted significant declines in performance for those able to return. While classic treatment of these injuries in the competitive athlete has been an open, locked suture repair, this article reports on a consecutive series of professional football athletes who underwent mini-open repair. All athletes returned to professional football, with seven out of nine (78%) returning to National Football League (NFL) competition. Average return to play was 273 days (8.9 months), with one athlete returning at 166 days (5.4 months). There have been no reruptures and no sural nerve or wound healing complications. Although limited in number currently, mini-open repair in NFL athletes has allowed successful return to competitive play with no reruptures and a trend toward faster return to play compared with historical open repair outcomes.

Effect of anterior capsule contraction on visual function after cataract surgery.

PubMed

Hayashi, Ken; Hayashi, Hideyuki

2007-11-01

To examine the effect of contraction of the anterior capsule opening after cataract surgery on visual acuity and contrast sensitivity. Hayashi Eye Hospital, Fukuoka, Japan. Thirty-two eyes of 32 consecutive patients who showed marked contraction of the anterior capsule opening after implantation of an intraocular lens were recruited. The area of the anterior capsule opening was measured by Scheimpflug videophotography before and after neodymium:YAG (Nd:YAG) laser anterior capsulotomy and was correlated with visual acuity and contrast sensitivity. After Nd:YAG laser anterior capsulotomy, the mean area of the anterior capsule opening increased significantly from 8.2 mm(2) to 18.0 mm(2) (P<.0001). Contrast sensitivity at most visual angles also improved significantly after Nd:YAG anterior capsulotomy, although visual acuity did not. The area of the anterior capsule opening before anterior capsulotomy was correlated significantly with contrast sensitivity but not with visual acuity, whereas there was no correlation between the opening area after anterior capsulotomy and visual acuity or contrast sensitivity. Contraction of the anterior capsule opening after cataract surgery significantly diminished contrast sensitivity in proportion to the opening area but did not markedly worsen visual acuity. Neodymium:YAG laser anterior capsulotomy improved contrast sensitivity.

Open-field behavior of house mice selectively bred for high voluntary wheel-running.

PubMed

Bronikowski, A M; Carter, P A; Swallow, J G; Girard, I A; Rhodes, J S; Garland, T

2001-05-01

Open-field behavioral assays are commonly used to test both locomotor activity and emotionality in rodents. We performed open-field tests on house mice (Mus domesticus) from four replicate lines genetically selected for high voluntary wheel-running for 22 generations and from four replicate random-bred control lines. Individual mice were recorded by video camera for 3 min in a 1-m2 open-field arena on 2 consecutive days. Mice from selected lines showed no statistical differences from control mice with respect to distance traveled, defecation, time spent in the interior, or average distance from the center of the arena during the trial. Thus, we found little evidence that open-field behavior, as traditionally defined, is genetically correlated with wheel-running behavior. This result is a useful converse test of classical studies that report no increased wheel-running in mice selected for increased open-field activity. However, mice from selected lines turned less in their travel paths than did control-line mice, and females from selected lines had slower travel times (longer latencies) to reach the wall. We discuss these results in the context of the historical open-field test and newly defined measures of open-field activity.

Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences.

PubMed

Rideout, Jai Ram; He, Yan; Navas-Molina, Jose A; Walters, William A; Ursell, Luke K; Gibbons, Sean M; Chase, John; McDonald, Daniel; Gonzalez, Antonio; Robbins-Pianka, Adam; Clemente, Jose C; Gilbert, Jack A; Huse, Susan M; Zhou, Hong-Wei; Knight, Rob; Caporaso, J Gregory

2014-01-01

We present a performance-optimized algorithm, subsampled open-reference OTU picking, for assigning marker gene (e.g., 16S rRNA) sequences generated on next-generation sequencing platforms to operational taxonomic units (OTUs) for microbial community analysis. This algorithm provides benefits over de novo OTU picking (clustering can be performed largely in parallel, reducing runtime) and closed-reference OTU picking (all reads are clustered, not only those that match a reference database sequence with high similarity). Because more of our algorithm can be run in parallel relative to "classic" open-reference OTU picking, it makes open-reference OTU picking tractable on massive amplicon sequence data sets (though on smaller data sets, "classic" open-reference OTU clustering is often faster). We illustrate that here by applying it to the first 15,000 samples sequenced for the Earth Microbiome Project (1.3 billion V4 16S rRNA amplicons). To the best of our knowledge, this is the largest OTU picking run ever performed, and we estimate that our new algorithm runs in less than 1/5 the time than would be required of "classic" open reference OTU picking. We show that subsampled open-reference OTU picking yields results that are highly correlated with those generated by "classic" open-reference OTU picking through comparisons on three well-studied datasets. An implementation of this algorithm is provided in the popular QIIME software package, which uses uclust for read clustering. All analyses were performed using QIIME's uclust wrappers, though we provide details (aided by the open-source code in our GitHub repository) that will allow implementation of subsampled open-reference OTU picking independently of QIIME (e.g., in a compiled programming language, where runtimes should be further reduced). Our analyses should generalize to other implementations of these OTU picking algorithms. Finally, we present a comparison of parameter settings in QIIME's OTU picking workflows and make recommendations on settings for these free parameters to optimize runtime without reducing the quality of the results. These optimized parameters can vastly decrease the runtime of uclust-based OTU picking in QIIME.

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.

[Infrared temperature measurement in the ear canal with the DIATEK 9000 Instatemp and the DIATEK 9000 Thermoguide. Comparison with methods of temperature measurement in other body parts].

PubMed

Fritz, U; Rohrberg, M; Lange, C; Weyland, W; Bräuer, A; Braun, U

1996-11-01

Temperature of the tympanic membrane is recommended as a "gold standard" of core-temperature recording. However, use of temperature probes in the auditory canal may lead to damage of tympanic membrane. Temperature measurement in the auditory canal with infrared thermometry does not pose this risk. Furthermore it is easy to perform and not very time-consuming. For this reason infrared thermometry of the auditory canal is becoming increasingly popular in clinical practice. We evaluated two infrared thermometers-the Diatek 9000 Thermoguide and the Diatek 9000 Instatemp-regarding factors influencing agreement with conventional tympanic temperature measurement and other core-temperature recording sites. In addition, we systematically evaluated user dependent factors that influence the agreement with the tympanic temperature. In 20 volunteers we evaluated the influence of three factors: duration of the devices in the auditory canal before taking temperature (0 or 5 s), interval between two following recordings (30, 60, 90, 120, 180 s) and positioning of the grip relative to the auditory-canal axis (0, 60, 180 and 270 degrees). Agreement with tympanic contact probes (Mon-a-therm tympanic) in the contralateral ear was investigated in 100 postoperative patients. Comparative readings with rectal (YSI series 400) and esophageal (Mon-a-therm esophageal stethoscope with temperature sensor) probes were done in 100 patients in the ICU. The method of Bland and Altman was taken for comparison. Shortening of the interval between two consecutive readings led to increasing differences between the two measurements with the second reading decreasing. A similar effect was seen when positioning the infrared thermometers in the auditory canal before taking temperatures: after 5 s the recorded temperatures were significantly lower than temperature recordings taken immediately. Rotation of the devices out of the telephone handle position led to increasing lack of agreement between infrared thermometry and contact probes. Mean differences between infrared thermometry (Instatemp and Thermoguide, CAL-Mode) and tympanic probes were -0.41 +/- 0.67 degree C (2 SD) and -0.43 +/- 0.70 degree C, respectively. Mean differences between the Thermoquide (Rectal-Mode) and rectal probe were -0.19 +/- 0.72 degree C, and between the Thermoguide (Core Mode) and esophageal probe -0.13 +/- 0.74 degree C. Although easy to use, infrared thermometry requires careful handling. To obtain optimal recordings, the time between two consecutive readings should not be less than two min. Recordings should be taken immediately after positioning the devices in the auditory canal. Best results are obtained in the 60 degrees position with the grip of the devices following the ramus mandibulae (telephone handle position). The lower readings of infrared thermometry compared with tympanic contact probes indicate that the readings obtained represent the temperature of the auditory canal rather than of the tympanic membrane itself. To compensate for underestimation of core temperature by infrared thermometry, the results obtained are corrected and transferred into core-equivalent temperatures. This data correction reduces mean differences between infrared recordings and traditional core-temperature monitoring, but leaves limits of agreement between the two methods uninfluenced.

Opening the pleura during internal mammary artery harvesting: advantages and disadvantages

PubMed Central

Ali, Idris M.; Lau, Peter; Kinley, C. Edwin; Sanalla, Abulkasim

1996-01-01

Objective To evaluate the findings of previous studies that opening of the pleura during internal mammary artery (IMA) dissection might be an important factor in increasing the operative morbidity. Design A randomized control trial. Setting A university hospital. Patients Two hundred and eighty consecutive patients with no significant pulmonary disease. Intervention Harvesting of the IMA with (130 patients) or without (150 patients) opening the pleura. Main Outcome Measures Comparison of the incidence of pleural effusion, cardiac tamponade, postoperative respiratory complications and the hospital stay. Results Pleural effusion occurred more often in the patients who had opening of the pleura (20% versus 5%); however, none of the patients required tapping. Postoperative bleeding with cardiac tamponade occurred in five patients in the closed pleura group. Six patients in the open pleura group had postoperative bleeding but without tamponade. The average postoperative hospital stay was 7 days for both groups. No significant differences were recorded in postoperative respiratory complications. Conclusions Opening of the pleura during IMA harvesting does not increase the operative morbidity. It may have other advantages and is recommended in most cases of IMA harvesting. PMID:8599790

78 FR 57674 - Order Limiting Operations at Newark Liberty International Airport

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-19

... season. This waiver applies only to EWR slots for the following days and local times: (1) March 30... runway 4L/22R. Runway 4L/22R will be open during that period with reduced runway length. Night and... five or more consecutive days. However, the FAA does not routinely grant general waivers to the usage...

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.

GONe: Software for estimating effective population size in species with generational overlap

USGS Publications Warehouse

Coombs, J.A.; Letcher, B.H.; Nislow, K.H.

2012-01-01

GONe is a user-friendly, Windows-based program for estimating effective size (N e) in populations with overlapping generations. It uses the Jorde-Ryman modification to the temporal method to account for age structure in populations. This method requires estimates of age-specific survival and birth rate and allele frequencies measured in two or more consecutive cohorts. Allele frequencies are acquired by reading in genotypic data from files formatted for either GENEPOP or TEMPOFS. For each interval between consecutive cohorts, N e is estimated at each locus and over all loci. Furthermore, N e estimates are output for three different genetic drift estimators (F s, F c and F k). Confidence intervals are derived from a chi-square distribution with degrees of freedom equal to the number of independent alleles. GONe has been validated over a wide range of N e values, and for scenarios where survival and birth rates differ between sexes, sex ratios are unequal and reproductive variances differ. GONe is freely available for download at. ?? 2011 Blackwell Publishing Ltd.

Open cholecystectomy in the laparoscopic era.

PubMed

Jenkins, P J; Paterson, H M; Parks, R W; Garden, O J

2007-11-01

As techniques in laparoscopic cholecystectomy have improved, surgeon experience of open cholecystectomy may be limited. This study examined the current indications for and techniques used in primary open cholecystectomy. Some 3100 consecutive patients undergoing elective or emergency cholecystectomy over a 5-year interval were identified from a prospective surgical audit database. Demographic, diagnostic and procedural data were examined. There were 123 (4.0 per cent) primary and 219 (7.4 per cent) converted open cholecystectomies. Some 48.0 and 45.6 per cent of patients in the primary open cholecystectomy and converted groups respectively were men, compared with 24.0 per cent of 2758 who had a successful laparoscopic procedure. Primary open cholecystectomy was employed principally for previous upper abdominal open surgery (22.7 per cent) and emergency operation for general peritonitis (19.5 per cent). The fundus-first approach was employed in 53.7 per cent of primary open procedures and 53.0 per cent of conversions, with subtotal excision in 4.9 and 13.2 per cent respectively. Primary open cholecystectomy remains a common procedure in the treatment of gallbladder disease despite the success of laparoscopic cholecystectomy. Successful outcome in difficult cases requires familiarity with specific techniques, exposure to which may be limited in current training programmes. Copyright (c) 2007 British Journal of Surgery Society Ltd.

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.

A prospective clinical study evaluating the development of bowel wall edema during laparoscopic and open visceral surgery.

PubMed

Marjanovic, Goran; Kuvendziska, Jasmina; Holzner, Philipp Anton; Glatz, Torben; Sick, Olivia; Seifert, Gabriel; Kulemann, Birte; Küsters, Simon; Fink, Jodok; Timme, Sylvia; Hopt, Ulrich Theodor; Wellner, Ulrich; Keck, Tobias; Karcz, Wojciech Konrad

2014-12-01

To examine bowel wall edema development in laparoscopic and open major visceral surgery. In a prospective study, 47 consecutively operated patients with gastric and pancreatic resections were included. Twenty-seven patients were operated in a conventional open procedure (open group) and 20 in a laparoscopic fashion (lap group). In all procedures, a small jejunal segment was resected during standard preparation, of which we measured the dry-wet ratio. Furthermore, HE staining was performed for measuring of bowel wall thickness and edema assessment. Mean value (±std) of dry-wet ratio was significantly lower in the open than in the lap group (0.169 ± 0.017 versus 0.179 ± 0.015; p = 0.03) with the same amount of fluid administration in both groups and a longer infusion interval during laparoscopic surgery. Subgroup analyses (only pancreatic resections) still showed similar results. Histologic examination depicted a significantly larger bowel wall thickness in the open group. Laparoscopic surgery does not seem to lead to the bowel wall edema observed to occur in open surgery regardless of the degree of intravenous fluid administration, thus supporting its use even in major visceral surgery.

Lateralization of temporal lobe epilepsy and learning disabilities, as defined by disability-related civil rights law.

PubMed

Butterbaugh, Grant; Olejniczak, Piotr; Roques, Betsy; Costa, Richard; Rose, Marcy; Fisch, Bruce; Carey, Michael; Thomson, Jessica; Skinner, John

2004-08-01

Epilepsy research has identified higher rates of learning disorders in patients with temporal lobe epilepsy (TLE). However, most studies have not adequately assessed complex functional adult learning skills, such as reading comprehension and written language. We designed this study to evaluate our predictions that higher rates of reading comprehension, written language, and calculation disabilities would be associated with left TLE versus right TLE. Reading comprehension, written language, and calculation skills were assessed by using selected subtests from the Woodcock-Johnson Psycho-Educational Tests of Achievement-Revised in a consecutive series of 31 presurgical patients with TLE. Learning disabilities were defined by one essential criterion consistent with the Americans with Disabilities Act of 1990. Patients had left hemisphere language dominance based on Wada results, left or right TLE based on inpatient EEG monitoring, and negative magnetic resonance imaging (MRI), other than MRI correlates of mesial temporal sclerosis. Higher rates of reading comprehension, written language, and calculation disabilities were associated with left TLE, as compared with right TLE. Nearly 75% of patients with left TLE, whereas fewer than 10% of those with right TLE, had at least one learning disability. Seizure onset in the language-dominant hemisphere, as compared with the nondominant hemisphere, was associated with higher rates of specific learning disabilities and a history of poor literacy or career development or both. These results support the potential clinical benefits of using lateralization of seizure onset as a predictor of the risk of learning disabilities that, once evaluated, could be accommodated to increase the participation of patients with epilepsy in work and educational settings.

Consistency of blood pressure differences between the left and right arms.

PubMed

Eguchi, Kazuo; Yacoub, Mona; Jhalani, Juhee; Gerin, William; Schwartz, Joseph E; Pickering, Thomas G

2007-02-26

It is unclear to what extent interarm blood pressure (BP) differences are reproducible vs the result of random error. The present study was designed to resolve this issue. We enrolled 147 consecutive patients from a hypertension clinic. Three sets of 3 BP readings were recorded, first using 2 oscillometric devices simultaneously in the 2 arms (set 1); next, 3 readings were taken sequentially for each arm using a standard mercury sphygmomanometer (set 2); finally, the readings as performed for set 1 were repeated (set 3). The protocol was repeated at a second visit for 91 patients. Large interarm systolic BP differences were consistently seen in 2 patients with obstructive arterial disease. In the remaining patients, the systolic BP and the diastolic BP, respectively, were slightly higher in the right arm than in the left arm by 2 to 3 mm Hg and by 1 mm Hg for all 3 sets (P<.01 for all). For the systolic BP and the diastolic BP, respectively, the numbers of patients who had a mean interarm difference of more than 5 mm Hg were 11 (7.5%) and 4 (2.7%) across all 3 sets of readings. Among patients who repeated the test, none had a consistent interarm BP difference of more than 5 mm Hg across the 2 visits. The interarm BP difference was consistent only when obstructive arterial disease was present. Although BP in the right arm tended to be higher than in the left arm, clinically meaningful interarm differences were not reproducible in the absence of obstructive arterial disease and are attributable to random variation.

Occipital and Cingulate Hypometabolism are Significantly Under-Reported on 18-Fluorodeoxyglucose Positron Emission Tomography Scans of Patients with Lewy Body Dementia.

PubMed

Hamed, Moath; Schraml, Frank; Wilson, Jeffrey; Galvin, James; Sabbagh, Marwan N

2018-01-01

To determine whether occipital and cingulate hypometabolism is being under-reported or missed on 18-fluorodeoxyglucose positron emission tomography (FDG-PET) CT scans in patients with Dementia with Lewy Bodies (DLB). Recent studies have reported higher sensitivity and specificity for occipital and cingulate hypometabolism on FDG-PET of DLB patients. This retrospective chart review looked at regions of interest (ROI's) in FDG-PET CT scan reports in 35 consecutive patients with a clinical diagnosis of probable, possible, or definite DLB as defined by the latest DLB Consortium Report. ROI's consisting of glucose hypometabolism in frontal, parietal, temporal, occipital, and cingulate areas were tabulated and charted separately by the authors from the reports. A blinded Nuclear medicine physician read the images independently and marked ROI's separately. A Cohen's Kappa coefficient statistic was calculated to determine agreement between the reports and the blinded reads. On the radiology reports, 25.71% and 17.14% of patients reported occipital and cingulate hypometabolism respectively. Independent reads demonstrated significant disagreement with the proportion of occipital and cingulate hypometabolism being reported on initial reads: 91.43% and 85.71% respectively. Cohen's Kappa statistic determinations demonstrated significant agreement only with parietal hypometabolism (p<0.05). Occipital and cingulate hypometabolism is under-reported and missed frequently on clinical interpretations of FDG-PET scans of patients with DLB, but the frequency of hypometabolism is even higher than previously reported. Further studies with more statistical power and receiver operating characteristic analyses are needed to delineate the sensitivity and specificity of these in vivo biomarkers.

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

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

Central tracker for BM@N experiment based on double side Si-microstrip detectors

NASA Astrophysics Data System (ADS)

Kovalev, Yu.; Kapishin, M.; Khabarov, S.; Shafronovskaia, A.; Tarasov, O.; Makankin, A.; Zamiatin, N.; Zubarev, E.

2017-07-01

Design of central tracker system based on Double-Sided Silicon Detectors (DSSD) for BM@N experiment is described. A coordinate plane with 10240 measuring channels, pitch adapter, reading electronics was developed. Each element was tested and assembled into a coordinate plane. The first tests of the plane with 106Ru source were carried out before installation for the BM@N experiment. The results of the study indicate that noisy channels and inefficient channels are less than 3%. In general, single clusters 87% (one group per module of consecutive strips) and 75% of clusters with a width equal to one strip.

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.

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...

44 CFR 80.1 - Purpose and scope.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 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...

75 FR 39561 - National Fire Academy Board of Visitors

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-09

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

Home | Oregon State University Extension Service

Science.gov Websites

"How To" Communities OSU Open Campus Oregon's Agricultural Progress Magazine Emerging Issues Oregon's Agricultural Progress cover image Oregon's Agricultural Progress, the research magazine for the Oregon State University Agricultural Experiment Station. Read current OAP issue » Bridges logo image

New Perspectives in Special Education: Contemporary Philosophical Debates

ERIC Educational Resources Information Center

Farrell, Michael

2012-01-01

This book should be read by everyone who wants to understand special education today. "New Perspectives in Special Education" opens the door to the fascinating and vitally important world of theory that informs contemporary special education. It examines theoretical and philosophical orientations such as "positivism", "poststructuralism" and…

Problem-Solving Test: Attenuation--A Mechanism to Regulate Bacterial Tryptophan Biosynthesis

ERIC Educational Resources Information Center

Szeberenyi, Jozsef

2010-01-01

Terms to be familiar with before you start to solve the test: tryptophan, transcription unit, operon, "trp" repressor, corepressor, operator, promoter, palindrome, initiation, elongation, and termination of transcription, open reading frame, coupled transcription/translation, chromosome-polysome complex. (Contains 2 figures and 1 footnote.)

Understanding the Requirements for Open Source Software

DTIC Science & Technology

2009-06-17

GNOME and K Development Environment ( KDE ) for end-user interfaces, the Eclipse and NetBeans interactive development environments for Java-based Web...17 4.1. Informal Post-hoc Assertion of OSS Requirements vs . Requirements Elicitation...18 4.2. Requirements Reading, Sense-making, and Accountability vs . Requirements Analysis

Science Teaching in Science Education

ERIC Educational Resources Information Center

Callahan, Brendan E.; Dopico, Eduardo

2016-01-01

Reading the interesting article "Discerning selective traditions in science education" by Per Sund, which is published in this issue of "CSSE," allows us to open the discussion on procedures for teaching science today. Clearly there is overlap between the teaching of science and other areas of knowledge. However, we must…

The Community College Story. Third Edition

ERIC Educational Resources Information Center

Vaughan, George B.

2006-01-01

This concise history of community colleges touches on major themes, including open access and equity, comprehensiveness, community-based philosophy, commitment to teaching, and lifelong learning. The third edition includes revised text as well as updated statistical information, time line, reading list, and Internet resources. In the more than a…

Draft genome sequence of rice orange leaf phytoplasma from Guangdong, China

USDA-ARS?s Scientific Manuscript database

The genome of rice orange leaf phytoplasma strain LD1 from Luoding City, Guangdong, P. R. China, was sequenced. The draft LD1genome is 599,264 bp with GC content of 28.2%, 647 predicted open reading frames and 33 RNA genes....

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

PubMed

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

2015-03-01

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

Auditory Processing in Noise: A Preschool Biomarker for Literacy.

PubMed

White-Schwoch, Travis; Woodruff Carr, Kali; Thompson, Elaine C; Anderson, Samira; Nicol, Trent; Bradlow, Ann R; Zecker, Steven G; Kraus, Nina

2015-07-01

Learning to read is a fundamental developmental milestone, and achieving reading competency has lifelong consequences. Although literacy development proceeds smoothly for many children, a subset struggle with this learning process, creating a need to identify reliable biomarkers of a child's future literacy that could facilitate early diagnosis and access to crucial early interventions. Neural markers of reading skills have been identified in school-aged children and adults; many pertain to the precision of information processing in noise, but it is unknown whether these markers are present in pre-reading children. Here, in a series of experiments in 112 children (ages 3-14 y), we show brain-behavior relationships between the integrity of the neural coding of speech in noise and phonology. We harness these findings into a predictive model of preliteracy, revealing that a 30-min neurophysiological assessment predicts performance on multiple pre-reading tests and, one year later, predicts preschoolers' performance across multiple domains of emergent literacy. This same neural coding model predicts literacy and diagnosis of a learning disability in school-aged children. These findings offer new insight into the biological constraints on preliteracy during early childhood, suggesting that neural processing of consonants in noise is fundamental for language and reading development. Pragmatically, these findings open doors to early identification of children at risk for language learning problems; this early identification may in turn facilitate access to early interventions that could prevent a life spent struggling to read.

Open Access: From Myth to Paradox

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

Ginsparg, Paul

2009-05-06

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 speculatemore » on the sociology of the next generation of users.« less

Agreement between auricular and rectal measurements of body temperature in healthy cats.

PubMed

Sousa, Marlos G; Carareto, Roberta; Pereira-Junior, Valdo A; Aquino, Monally C C

2013-04-01

Measurement of body temperature is a routine part of the clinical assessment of a patient. However, this procedure may be time-consuming and stressful to most animals because the standard site of temperature acquisition remains the rectal mucosa. Although an increasing number of clinicians have been using auricular temperature to estimate core body temperature, evidence is still lacking regarding agreement between these two methods in cats. In this investigation, we evaluated the agreement between temperatures measured in the rectum and ear in 29 healthy cats over a 2-week period. Temperatures were measured in the rectum (using digital and mercury-in-glass thermometers) and ear once a day for 14 consecutive days, producing 406 temperature readings for each thermometer. Mean temperature and confidence intervals were similar between methods, and Bland-Altman plots showed small biases and narrow limits of agreement acceptable for clinical purposes. The interobserver variability was also checked, which indicated a strong correlation between two near-simultaneous temperature readings. Results are consistent with auricular thermometry being a reliable alternative to rectal thermometry for assessing core body temperature in healthy cats.

Teacher–Student Support, Effortful Engagement, and Achievement: A 3-Year Longitudinal Study

PubMed Central

Hughes, Jan N.; Luo, Wen; Kwok, Oi-Man; Loyd, Linda K.

2008-01-01

Measures of teacher–student relationship quality (TSRQ), effortful engagement, and achievement in reading and math were collected once each year for 3 consecutive years, beginning when participants were in 1st grade, for a sample of 671 (53.1% male) academically at-risk children attending 1 of 3 school districts in Texas. In separate latent variable structural equation models, the authors tested the hypothesized model, in which Year 2 effortful engagement mediated the association between Year 1 TSRQ and Year 3 reading and math skills. Conduct engagement was entered as a covariate in these analyses to disentangle the effects of effortful engagement and conduct engagement. Reciprocal effects of effortful engagement on TSRQ and of achievement on effortful engagement were also modeled. Results generally supported the hypothesized model. Year 1 variables had a direct effect on Year 3 variables, above year-to-year stability. Findings suggest that achievement, effortful engagement, and TSRQ form part of a dynamic system of influences in the early grades, such that intervening at any point in this nexus may alter children’s school trajectories. PMID:19578558

Sialoendoscopically assisted open sialolithectomy for removal of large submandibular hilar calculi.

PubMed

Su, Yu-xiong; Liao, Gui-qing; Zheng, Guang-sen; Liu, Hai-chao; Liang, Yu-jie; Ou, De-ming

2010-01-01

The management of large hilar calculi is a technically challenging issue during sialoendoscopic surgery. The aim of the present study was to evaluate the clinical efficacy of sialoendoscopically assisted open sialolithectomy for the removal of large submandibular hilar calculi to avoid sialoadenectomy. The present study was undertaken among patients with sialolithiasis scheduled for sialoendoscopic surgery from August 2005 to October 2008. When we failed to remove large submandibular hilar stones intraductally, we performed sialoendoscopically assisted open sialolithectomy. The clinical characteristics, pre- and intraoperative data, and outcomes were documented in a prospective fashion. Of 78 consecutive patients with submandibular sialolithiasis, 18 were treated with sialoendoscopically assisted open sialolithectomy immediately after failure of intraductal removal of calculi by sialoendoscopy. For 17 patients, large hilar sialoliths were successfully removed using this surgical technique. The surgery failed in 1 patient with multiple sialoliths, and the procedure was converted to open sialoadenectomy. Temporary numbness of the tongue for 1 week postoperatively was documented in 3 patients. The patients were followed up for a median period of 18 months without any symptoms or signs of recurrence. Our results suggest that sialoendoscopically assisted open sialolithectomy is an effective and safe surgical technique to remove large submandibular hilar calculi.

Opening the Gates: Reading "The Gulag"

ERIC Educational Resources Information Center

Iannone, Carol

2009-01-01

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

Academic Work and Performance

ERIC Educational Resources Information Center

Gunter, Helen M.

2012-01-01

Reading current accounts of higher education demonstrates the flux and damage of rapid neoliberal changes to the type and conduct of academic work. Opening the Times Higher Education magazine on the 28 April 2011 shows articles about cuts in staffing and undergraduate provision in England, concerns about the quality of for-profit higher education…

The Apis mellifera filamentous virus genome

USDA-ARS?s Scientific Manuscript database

A complete reference genome of the Apis mellifera Filamentous virus (AmFV) was determined using Illumina Hiseq sequencing. The AmFV genome is a double strand DNA molecule of approximately 498’500 nucleotides with a GC content of 50.8%. It encompasses 251 non overlapping open reading frames (ORFs), e...

Direct enzyme assay evidence confirms aldehyde reductase function of Ydr541cp and Ygl039wp from Saccharomyces cerevisiae

USDA-ARS?s Scientific Manuscript database

Aldehyde reductase gene ARI1 is a recently characterized member of intermediate subfamily under SDR (short-chain dehydrogenase/reductase) superfamily that revealed mechanisms of in situ detoxification of furfural and HMF for tolerance of Saccharomyces cerevisiae. Uncharacterized open reading frames ...

78 FR 60720 - Methyl Parathion; Removal of Expired Tolerances

Federal Register 2010, 2011, 2012, 2013, 2014

2013-10-02

...: This regulation is effective October 2, 2013. ADDRESSES: The docket for this action, identified by... the Office of Pesticide Programs Regulatory Public Docket (OPP Docket) in the Environmental Protection...-0001. The Public Reading Room is open from 8:30 a.m. to 4:30 p.m., Monday through Friday, excluding...

Spontaneous Belief Attribution in Younger Siblings of Children on the Autism Spectrum

ERIC Educational Resources Information Center

Gliga, Teodora; Senju, Atsushi; Pettinato, Michèle; Charman, Tony; Johnson, Mark H.

2014-01-01

The recent development in the measurements of spontaneous mental state understanding, employing eye-movements instead of verbal responses, has opened new opportunities for understanding the developmental origin of "mind-reading" impairments frequently described in autism spectrum disorders (ASDs). Our main aim was to characterize the…

Self-Explanation in the Domain of Statistics: An Expertise Reversal Effect

ERIC Educational Resources Information Center

Leppink, Jimmie; Broers, Nick J.; Imbos, Tjaart; van der Vleuten, Cees P. M.; Berger, Martijn P. F.

2012-01-01

This study investigated the effects of four instructional methods on cognitive load, propositional knowledge, and conceptual understanding of statistics, for low prior knowledge students and for high prior knowledge students. The instructional methods were (1) a reading-only control condition, (2) answering open-ended questions, (3) answering…

76 FR 5826 - Notice Pursuant to the National Cooperative Research and Production Act of 1993-Advanced Media...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-02

... Salvador Villa Vidaller, Madrid, SPAIN, have been added as parties to this venture. Also, 3T Technology, Taipei City, TAIWAN; Blue Order Technologies, Kaiserslautern, GERMANY; Harmonic, Inc., Sunnyvale, CA; Integrated Media Technologies, Hollywood, CA; Open Text Media Group, Reading, Berkshire, UNITED KINGDOM...

Effects of the HN gene c-terminal extensions on the Newcastle disease virus virulence

USDA-ARS?s Scientific Manuscript database

The hemagglutinin-neuraminidase (HN) of Newcastle disease virus (NDV) is a multifunctional protein that has receptor recognition, neuraminidase and fusion promotion activities. Sequence analysis revealed that the HN gene of many extremely low virulence NDV strains encodes a larger open reading frame...

"Abriendo Puertas" (Opening Doors) through Writing

ERIC Educational Resources Information Center

Sarmiento, Lilia E.; Vasquez, Sergio A.

2010-01-01

A Latina college professor describes the family history-writing project she uses in her reading/language arts teacher preparation course. The project provides opportunities for Spanish bilingual teacher candidates to gain greater understanding of their cultural selves and to consider ways to successfully deploy that new insight as teachers in…

PRIMARY STRUCTURE OF THE P450 LANOSTEROL DEMETHYLASE GENE FROM SACCHAROMYCES CEREVISIAE

EPA Science Inventory

We have sequenced the structural gene and flanking regions for lanosterol 14 alpha-demethylase (14DM) from Saccharomyces cerevisiae. An open reading frame of 530 codons encodes a 60.7-kDa protein. When this gene is disrupted by integrative transformation, the resulting strain req...

Celebrating the Freedom To "Read! Learn! Connect! @ the Library."

ERIC Educational Resources Information Center

Symons, Ann K.

1999-01-01

Discusses the importance of librarians being advocates for children and fighting for free and open access to printed and electronic information. Discusses Banned Book Week; intellectual freedom; the American Library Association's four main concerns related to the Internet--access, quality, education, and local control; and the importance of…

Transaction Circles with Digital Texts as a Foundation for Democratic Practices

ERIC Educational Resources Information Center

Brown, Sally

2015-01-01

Transaction circles weave together elements of guided reading and literature circles in an open conversational structure that supports students as agentive learners. Discourse within these circles utilizing digital informational texts assist in the development of democratic practices even in a time when federal mandates limit curricula and…

Three sorghum serpin recombinant proteins inhibit midgut trypsin activity and growth of corn earworm

USDA-ARS?s Scientific Manuscript database

The sorghum (Sorghum bicolor) genome contains at least 17 putative serpin (serine protease inhibitor) open reading frames, some of which are induced by pathogens. Recent transcriptome studies found that most of the putative serpins are expressed but their roles are unknown. Four sorghum serpins were...

Effects of Instructional Condition on Preschool Children's Novel Word Learning

ERIC Educational Resources Information Center

Bass, Lori A.; Barron, Eunice V.

2014-01-01

Converging evidence suggests that children's exposure to complex vocabulary during the preschool years has an impact on their later reading achievement. Yet, the most efficient way to incorporate vocabulary instruction into preschool classrooms remains an open question. The purpose of this preliminary study was to investigate effects of…

Opening the Literature Window

ERIC Educational Resources Information Center

Jago, Carol

2012-01-01

Great literature gives students a window to other places and times, but it often requires students to step outside their comfort zones and take on challenges they wouldn't usually attempt. Unfortunately, research shows that many schools are not assigning literature that pushes students beyond their current reading level. Jago encourages teachers…

From Mosquitos to Humans: Genetic Evolution of Zika Virus

PubMed Central

Wang, Lulan; Valderramos, Stephanie G.; Wu, Aiping; Ouyang, Songying; Li, Chunfeng; Brasil, Patricia; Bonaldo, Myrna; Coates, Thomas; Nielsen-Saines, Karin; Jiang, Taijiao; Aliyari, Roghiyh; Cheng, Genhong

2017-01-01

Initially isolated in 1947, Zika virus (ZIKV) has recently emerged as significant public health concern. Sequence analysis of all 41 known ZIKV RNA open reading frames to date indicates that ZIKV has undergone significant changes in both protein and nucleotide sequences during the past half century. PMID:27091703

Who Has Read the Policy on Plagiarism? Unpacking Students' Understanding of Plagiarism

ERIC Educational Resources Information Center

Gullifer, J. M.; Tyson, G. A.

2014-01-01

Research has established that the term "plagiarism" is open to different interpretations, resulting in confusion among students and staff alike. University policy on academic integrity/misconduct defines the behaviours that all stakeholders must abide by, and the parameters for reporting, investigating and penalising infringements. These…

Flexible model of work-based learning boosts development.

PubMed

Clark, Elisabeth

2011-01-19

I was interested to read your news story, 'Nurses miss out on essential training due to staff shortages' (January 5). As director of the Open University-RCN strategic alliance I would emphasise the importance of investing in continuing professional development (CPD), particularly in times of change and service redesign.

Initial experience with robotic pancreatic surgery in Singapore: single institution experience with 30 consecutive cases.

PubMed

Goh, Brian K P; Low, Tze-Yi; Lee, Ser-Yee; Chan, Chung-Yip; Chung, Alexander Y F; Ooi, London L P J

2018-05-24

Presently, the worldwide experience with robotic pancreatic surgery (RPS) is increasing although widespread adoption remains limited. In this study, we report our initial experience with RPS. This is a retrospective review of a single institution prospective database of 72 consecutive robotic hepatopancreatobiliary surgeries performed between 2013 and 2017. Of these, 30 patients who underwent RPS were included in this study of which 25 were performed by a single surgeon. The most common procedure was robotic distal pancreatectomy (RDP) which was performed in 20 patients. This included eight subtotal pancreatectomies, two extended pancreatecto-splenectomies (en bloc gastric resection) and 10 spleen-saving-RDP. Splenic preservation was successful in 10/11 attempted spleen-saving-RDP. Eight patients underwent pancreaticoduodenectomies (five hybrid with open reconstruction), one patient underwent a modified Puestow procedure and one enucleation of uncinate tumour. Four patients had extended resections including two RDP with gastric resection and two pancreaticoduodenectomies with vascular resection. There was one (3.3%) open conversion and seven (23.3%) major (>Grade II) morbidities. Overall, there were four (13.3%) clinically significant (Grade B) pancreatic fistulas of which three required percutaneous drainage. These occurred after three RDP and one robotic enucleation. There was one reoperation for port-site hernia and no 30-day/in-hospital mortalities. The median post-operative stay was 6.5 (range: 3-36) days and there were six (20%) 30-day readmissions. Our initial experience showed that RPS can be adopted safely with a low open conversion rate for a wide variety of procedures including pancreaticoduodenectomy. © 2018 Royal Australasian College of Surgeons.

Comparison between laparoscopic and open radical nephrectomy for the treatment of primary renal tumors in children: single-center experience over a 5-year period.

PubMed

Romao, R L P; Weber, B; Gerstle, J T; Grant, R; Pippi Salle, J L; Bägli, D J; Figueroa, V H; Braga, L H P; Farhat, W A; Koyle, M A; Lorenzo, A J

2014-06-01

To compare the outcomes of laparoscopic nephrectomy (LN) with open radical nephrectomy (ORN) in the management of consecutive pediatric neoplasms. Retrospective cohort study of consecutive children treated for primary renal tumors between 2006 and 2011, segregated based on surgical modality (LN/ORN). Pre-, intra- and postoperative data and outcomes were collected. Demographics from the 45 patients (13 LN, 32 ORN) were similar, and tumors in the LN group were smaller [6.59 ± 1.8 cm vs. 10.99 ± 2.99 cm ORN (p < 0.05)]. Six patients had preoperative chemotherapy (two LN, four ORN). No tumor ruptures occurred with either technique. Wilms tumor (seven LN, 24 ORN) was the most common diagnosis, followed by renal cell carcinoma (four LN, four ORN). Procedure length was similar between groups (282 ± 79 LN, 263 ± 81 min ORN). Mean length of stay was significantly shorter for LN (2.9 vs. 5.9 days; p = 0.002). Postoperative narcotic requirements and use of nasogastric tube were higher in the ORN group. After a median follow-up of 18 (LN) and 33 months (ORN), 1 and 4 recurrences occurred, respectively. LN is an attractive alternative to open surgery in carefully selected cases of pediatric renal tumors. Procedure length and incidence of intra-operative rupture were not increased, while post-operative recovery and hospital stay were shorter for LN. Longer follow-up is mandatory to confirm comparable oncological outcomes to ORN. Copyright © 2013 Journal of Pediatric Urology Company. Published by Elsevier Ltd. All rights reserved.

New Author Choice for Open Access

NASA Astrophysics Data System (ADS)

2007-04-01

AGU journals now offer authors the opportunity to make their articles open for others to read for free. Authors choosing this option pay a fee based on article length and number of figures; these charges are designed to offset the potential loss of subscription income. This new option, called Author Choice, provides •Unlimited access to the article for all readers from the moment of publication. • Permission to deposit the PDF version in institutional repositories so long as the repository accepts AGU copyright permissions. • Continued copyright protection to prevent unauthorized uses of the author's work.

[Prospects for applications in human health of nanopore-based sequencing].

PubMed

Audebert, Christophe; Hot, David; Caboche, Ségolène

2018-04-01

High throughput sequencing has opened up new clinical opportunities moving towards a medicine of precision. Oncology, infectious diseases or human genomics, many applications have been developed in recent years. The introduction of a third generation of nanopore-based sequencing technology, addressing some of the weaknesses of the previous generation, heralds a new revolution. Portability, real time, long reads and marginal investment costs, these promising new technologies point to a new shift of paradigm. What are the perspectives opened up by nanopores for clinical applications? © 2018 médecine/sciences – Inserm.

Benefits from Vergence Rehabilitation: Evidence for Improvement of Reading Saccades and Fixations.

PubMed

Daniel, François; Morize, Aurélien; Brémond-Gignac, Dominique; Kapoula, Zoï

2016-01-01

We hypothesize that binocular coordination of saccades is based on continuous neuroplasticity involving interactions of saccades and vergence. To test this hypothesis we study reading saccades in young students who were diagnosed for vergence disorders before and after vergence rehabilitation. Following orthoptic evaluation and symptomatology screening, 5 weekly sessions of vergence rehabilitation were applied with the REMOBI vergence double step protocole (see Kapoula et al., 2016). Using the Eyeseecam videoculography device we measured vergence as well as saccades and fixations during a reading test four times: at the beginning and at the end of the first and of the fifth vergence rehabilitation session. The results show elimination of symptoms, improvement of clinical orthoptic scores, and importantly increase of measured vergence gain and reduction of inter-trial variability. Improvement of the vergence was associated to a decrease of the disconjugacy of saccades during reading but also to shortening of fixation durations, to reduction of the number of regressive saccades and to a better correction of the intra-saccadic disconjugacy during the following fixation. The results corroborate the hypothesis of neuroplasticity based on saccade vergence interaction in young adults. It validates the clinical validity of the vergence double-step REMOBI method as a means to improve both, vergence and reading performances. It opens a new research approach on the link between fine binocular coordination of saccades, quality of the vergence response, attention, cognition and reading.

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

PubMed

Wright, Imogen A; Travers, Simon A

2014-07-01

The challenge presented by high-throughput sequencing necessitates the development of novel tools for accurate alignment of reads to reference sequences. Current approaches focus on using heuristics to map reads quickly to large genomes, rather than generating highly accurate alignments in coding regions. Such approaches are, thus, unsuited for applications such as amplicon-based analysis and the realignment phase of exome sequencing and RNA-seq, where accurate and biologically relevant alignment of coding regions is critical. To facilitate such analyses, we have developed a novel tool, RAMICS, that is tailored to mapping large numbers of sequence reads to short lengths (<10 000 bp) of coding DNA. RAMICS utilizes profile hidden Markov models to discover the open reading frame of each sequence and aligns to the reference sequence in a biologically relevant manner, distinguishing between genuine codon-sized indels and frameshift mutations. This approach facilitates the generation of highly accurate alignments, accounting for the error biases of the sequencing machine used to generate reads, particularly at homopolymer regions. Performance improvements are gained through the use of graphics processing units, which increase the speed of mapping through parallelization. RAMICS substantially outperforms all other mapping approaches tested in terms of alignment quality while maintaining highly competitive speed performance. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Antenna-coupled unbiased detectors for LW-IR regime

NASA Astrophysics Data System (ADS)

Tiwari, Badri Nath

At room temperature (300K), the electromagnetic (EM) radiation emitted by humans and other living beings peaks mostly in the long-wavelength infrared (LW-IR) regime. And since the atmosphere shows relatively little absorption in this band, applications such as target detection, tracking, active homing, and navigation in autonomous vehicles extensively use the LW-IR frequency range. The present research work is focused on developing antenna-based, uncooled, and unbiased detectors for the LW-IR regime. In the first part of this research, antenna-coupled metal-oxide-metal diodes (ACMOMD) are investigated. In response to the EM radiation, high-frequency antenna currents are induced in the antenna. An asymmetric-barrier Al-Al2O3-Pt MOM diode rectifies the antenna currents. Two different types of fabrication processes have been developed for ACMOMDs namely one-step lithography and two-step lithography. The major drawbacks of MOM-based devices include hard-to-control fabrication processes, generally very high zero-biased resistances, and vulnerability to electrostatic discharges, leading to unstable electrical characteristics. The second part of this research focuses on the development of unbiased LW-IR sensors based on the Seebeck effect. If two different metals are joined together at one end and their other ends are open-circuited, and if a non-zero temperature difference exists between the joined end and the open ends, then a non-zero open-circuit voltage can be measured between the open ends of the wires. Based on this effect, we have developed antenna-coupled nano-thermocouples (ACNTs) in which radiation-induced antenna currents produce polarization-dependent heating of the joined end of the two metals whereas the open ends remain at substrate temperature. This polarization-dependent heating induces polarization-dependent temperature difference between the joined end and the open ends of the metals leading to a polarization-dependent open-circuit voltage between the open ends of the metals. A CW CO2 laser tuned at 10.6 mum wavelength has been used for infrared characterization of these sensors. For these sensors, average responsivity of 22.7 mV/W, signal-to-noise (SNR) ratio of 29 dB, noise equivalent power (NEP) of 1.55 nW, and specific detectivity (D*) of 1.77x105 cm. Hz .W--1 were measured. ACNTs are expected to operate at frequencies much beyond 400 KHz. The third part of this research focuses on the effect of DC read-out interconnects on polarization characteristics of the planar dipole antennas. Different geometries of the interconnects present different electromagnetic boundary conditions to the antenna, and thus affect the far-field polarization characteristics of the antenna. Four designs of DC read-out interconnects are fabricated and their polarization-dependent IR responses are experimentally measured. The High Frequency Structure Simulator (HFSS) from ANSYS is used to simulate the polarization characteristics of the antenna with different read-out geometries.

Is There Value in Having Radiology Provide a Second Reading in Pediatric Orthopaedic Clinic?

PubMed

Natarajan, Vivek; Bosch, Patrick; Dede, Ozgur; Deeney, Vincent; Mendelson, Stephen; Ward, Timothy; Brooks, Maria; Kenkre, Tanya; Roach, James

2017-06-01

The Joint Commission on Accreditation of Healthcare Organizations specifically mandates the dual interpretation of musculoskeletal radiographs by a radiologist in addition to the orthopaedist in all hospital-based orthopaedic clinics. Previous studies have questioned the utility of this practice. The purpose of this study was to further investigate the clinical significance of having the radiologist provide a second interpretation in a hospital-based pediatric orthopaedic clinic. A retrospective review was performed of all patients who had plain radiographs obtained in the pediatric orthopaedic clinic at an academic children's hospital over a 4-month period. For each radiographic series, the orthopaedist's note and the radiology interpretation were reviewed and a determination was made of whether the radiology read provided new clinically useful information and/or a new diagnosis, whether it recommended further imaging, or if it missed a diagnosis that was reflected in the orthopaedist's note. The hospital charges associated with the radiology read for each study were also quantified. The charts of 1570 consecutive clinic patients who were seen in the pediatric orthopaedic clinic from January to April, 2012 were reviewed. There were 2509 radiographic studies performed, of which 2264 had both a documented orthopaedist's note and radiologist's read. The radiologist's interpretation added new, clinically important information in 1.0% (23/2264) of these studies. In 1.7% (38/2264) of the studies, it was determined that the radiologist missed the diagnosis or clinically important information that could affect treatment. The total amount of the professional fees charged for the radiologists' interpretations was $87,362. On average, the hospital charges for each occurrence in which the radiologist's read provided an additional diagnosis or clinically important information beyond the orthopaedist's note were $3798. The results of this study suggest that eliminating the requirement to have the radiologist interpret radiographs in the pediatric orthopaedic clinic would have few clinical consequences. Level III-This is a diagnostic retrospective cohort study.