A hybrid cloud read aligner based on MinHash and kmer voting that preserves privacy

NASA Astrophysics Data System (ADS)

Popic, Victoria; Batzoglou, Serafim

2017-05-01

Low-cost clouds can alleviate the compute and storage burden of the genome sequencing data explosion. However, moving personal genome data analysis to the cloud can raise serious privacy concerns. Here, we devise a method named Balaur, a privacy preserving read mapper for hybrid clouds based on locality sensitive hashing and kmer voting. Balaur can securely outsource a substantial fraction of the computation to the public cloud, while being highly competitive in accuracy and speed with non-private state-of-the-art read aligners on short read data. We also show that the method is significantly faster than the state of the art in long read mapping. Therefore, Balaur can enable institutions handling massive genomic data sets to shift part of their analysis to the cloud without sacrificing accuracy or exposing sensitive information to an untrusted third party.

A hybrid cloud read aligner based on MinHash and kmer voting that preserves privacy

PubMed Central

Popic, Victoria; Batzoglou, Serafim

2017-01-01

Low-cost clouds can alleviate the compute and storage burden of the genome sequencing data explosion. However, moving personal genome data analysis to the cloud can raise serious privacy concerns. Here, we devise a method named Balaur, a privacy preserving read mapper for hybrid clouds based on locality sensitive hashing and kmer voting. Balaur can securely outsource a substantial fraction of the computation to the public cloud, while being highly competitive in accuracy and speed with non-private state-of-the-art read aligners on short read data. We also show that the method is significantly faster than the state of the art in long read mapping. Therefore, Balaur can enable institutions handling massive genomic data sets to shift part of their analysis to the cloud without sacrificing accuracy or exposing sensitive information to an untrusted third party. PMID:28508884

Fast and sensitive taxonomic classification for metagenomics with Kaiju

PubMed Central

Menzel, Peter; Ng, Kim Lee; Krogh, Anders

2016-01-01

Metagenomics emerged as an important field of research not only in microbial ecology but also for human health and disease, and metagenomic studies are performed on increasingly larger scales. While recent taxonomic classification programs achieve high speed by comparing genomic k-mers, they often lack sensitivity for overcoming evolutionary divergence, so that large fractions of the metagenomic reads remain unclassified. Here we present the novel metagenome classifier Kaiju, which finds maximum (in-)exact matches on the protein-level using the Burrows–Wheeler transform. We show in a genome exclusion benchmark that Kaiju classifies reads with higher sensitivity and similar precision compared with current k-mer-based classifiers, especially in genera that are underrepresented in reference databases. We also demonstrate that Kaiju classifies up to 10 times more reads in real metagenomes. Kaiju can process millions of reads per minute and can run on a standard PC. Source code and web server are available at http://kaiju.binf.ku.dk. PMID:27071849

Fast and sensitive taxonomic classification for metagenomics with Kaiju.

PubMed

Menzel, Peter; Ng, Kim Lee; Krogh, Anders

2016-04-13

Metagenomics emerged as an important field of research not only in microbial ecology but also for human health and disease, and metagenomic studies are performed on increasingly larger scales. While recent taxonomic classification programs achieve high speed by comparing genomic k-mers, they often lack sensitivity for overcoming evolutionary divergence, so that large fractions of the metagenomic reads remain unclassified. Here we present the novel metagenome classifier Kaiju, which finds maximum (in-)exact matches on the protein-level using the Burrows-Wheeler transform. We show in a genome exclusion benchmark that Kaiju classifies reads with higher sensitivity and similar precision compared with current k-mer-based classifiers, especially in genera that are underrepresented in reference databases. We also demonstrate that Kaiju classifies up to 10 times more reads in real metagenomes. Kaiju can process millions of reads per minute and can run on a standard PC. Source code and web server are available at http://kaiju.binf.ku.dk.

Examining the genetic and environmental associations among spelling, reading fluency, reading comprehension and a high stakes reading test in a combined sample of third and fourth grade students

PubMed Central

Little, Callie W.

2015-01-01

The present study is an examination of the genetic and environmental effects on the associations among reading fluency, spelling and earlier reading comprehension on a later reading comprehension outcome (FCAT) in a combined sample of 3rd and 4th grade students using data from the 2011-2012 school year of the Florida Twin project on Reading (Taylor et al., 2013). A genetically sensitive model was applied to the data with results indicating a common genetic component among all four measures, along with shared and non-shared environmental influences common between reading fluency, spelling and FCAT. PMID:26770052

Atrial Fibrillation Detection During 24-Hour Ambulatory Blood Pressure Monitoring: Comparison With 24-Hour Electrocardiography.

PubMed

Kollias, Anastasios; Destounis, Antonios; Kalogeropoulos, Petros; Kyriakoulis, Konstantinos G; Ntineri, Angeliki; Stergiou, George S

2018-07-01

This study assessed the diagnostic accuracy of a novel 24-hour ambulatory blood pressure (ABP) monitor (Microlife WatchBP O3 Afib) with implemented algorithm for automated atrial fibrillation (AF) detection during each ABP measurement. One hundred subjects (mean age 70.6±8.2 [SD] years; men 53%; hypertensives 85%; 17 with permanent AF; 4 paroxysmal AF; and 79 non-AF) had simultaneous 24-hour ABP monitoring and 24-hour Holter monitoring. Among a total of 6410 valid ABP readings, 1091 (17%) were taken in ECG AF rhythm. In reading-to-reading ABP analysis, the sensitivity, specificity, and accuracy of ABP monitoring in detecting AF were 93%, 87%, and 88%, respectively. In non-AF subjects, 12.8% of the 24-hour ABP readings indicated false-positive AF, of whom 27% were taken during supraventricular premature beats. There was a strong association between the proportion of false-positive AF readings and that of supraventricular premature beats ( r =0.67; P <0.001). Receiver operating characteristic curve revealed that in paroxysmal AF and non-AF subjects, AF-positive readings at 26% during 24-hour ABP monitoring had 100%/85% sensitivity/specificity (area under the curve 0.91; P <0.01) for detecting paroxysmal AF. These findings suggest that in elderly hypertensives, a novel 24-hour ABP monitor with AF detector has high sensitivity and moderate specificity for AF screening during routine ABP monitoring. Thus, in elderly hypertensives, a 24-hour ABP recording with at least 26% of the readings suggesting AF indicates a high probability for AF diagnosis and should be regarded as an indication for performing 24-hour Holter monitoring. © 2018 American Heart Association, Inc.

Assessing neglect dyslexia with compound words.

PubMed

Reinhart, Stefan; Schunck, Alexander; Schaadt, Anna Katharina; Adams, Michaela; Simon, Alexandra; Kerkhoff, Georg

2016-10-01

The neglect syndrome is frequently associated with neglect dyslexia (ND), which is characterized by omissions or misread initial letters of single words. ND is usually assessed with standardized reading texts in clinical settings. However, particularly in the chronic phase of ND, patients often report reading deficits in everyday situations but show (nearly) normal performances in test situations that are commonly well-structured. To date, sensitive and standardized tests to assess the severity and characteristics of ND are lacking, although reading is of high relevance for daily life and vocational settings. Several studies found modulating effects of different word features on ND. We combined those features in a novel test to enhance test sensitivity in the assessment of ND. Low-frequency words of different length that contain residual pronounceable words when the initial letter strings are neglected were selected. We compared these words in a group of 12 ND-patients suffering from right-hemispheric first-ever stroke with word stimuli containing no existing residual words. Finally, we tested whether the serially presented words are more sensitive for the diagnosis of ND than text reading. The severity of ND was modulated strongly by the ND-test words and error frequencies in single word reading of ND words were on average more than 10 times higher than in a standardized text reading test (19.8% vs. 1.8%). The novel ND-test maximizes the frequency of specific ND-errors and is therefore more sensitive for the assessment of ND than conventional text reading tasks. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

A hybrid short read mapping accelerator

PubMed Central

2013-01-01

Background The rapid growth of short read datasets poses a new challenge to the short read mapping problem in terms of sensitivity and execution speed. Existing methods often use a restrictive error model for computing the alignments to improve speed, whereas more flexible error models are generally too slow for large-scale applications. A number of short read mapping software tools have been proposed. However, designs based on hardware are relatively rare. Field programmable gate arrays (FPGAs) have been successfully used in a number of specific application areas, such as the DSP and communications domains due to their outstanding parallel data processing capabilities, making them a competitive platform to solve problems that are “inherently parallel”. Results We present a hybrid system for short read mapping utilizing both FPGA-based hardware and CPU-based software. The computation intensive alignment and the seed generation operations are mapped onto an FPGA. We present a computationally efficient, parallel block-wise alignment structure (Align Core) to approximate the conventional dynamic programming algorithm. The performance is compared to the multi-threaded CPU-based GASSST and BWA software implementations. For single-end alignment, our hybrid system achieves faster processing speed than GASSST (with a similar sensitivity) and BWA (with a higher sensitivity); for pair-end alignment, our design achieves a slightly worse sensitivity than that of BWA but has a higher processing speed. Conclusions This paper shows that our hybrid system can effectively accelerate the mapping of short reads to a reference genome based on the seed-and-extend approach. The performance comparison to the GASSST and BWA software implementations under different conditions shows that our hybrid design achieves a high degree of sensitivity and requires less overall execution time with only modest FPGA resource utilization. Our hybrid system design also shows that the performance bottleneck for the short read mapping problem can be changed from the alignment stage to the seed generation stage, which provides an additional requirement for the future development of short read aligners. PMID:23441908

GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly

PubMed Central

Do, Hongdo; Molania, Ramyar

2017-01-01

The identification of genomic rearrangements with high sensitivity and specificity using massively parallel sequencing remains a major challenge, particularly in precision medicine and cancer research. Here, we describe a new method for detecting rearrangements, GRIDSS (Genome Rearrangement IDentification Software Suite). GRIDSS is a multithreaded structural variant (SV) caller that performs efficient genome-wide break-end assembly prior to variant calling using a novel positional de Bruijn graph-based assembler. By combining assembly, split read, and read pair evidence using a probabilistic scoring, GRIDSS achieves high sensitivity and specificity on simulated, cell line, and patient tumor data, recently winning SV subchallenge #5 of the ICGC-TCGA DREAM8.5 Somatic Mutation Calling Challenge. On human cell line data, GRIDSS halves the false discovery rate compared to other recent methods while matching or exceeding their sensitivity. GRIDSS identifies nontemplate sequence insertions, microhomologies, and large imperfect homologies, estimates a quality score for each breakpoint, stratifies calls into high or low confidence, and supports multisample analysis. PMID:29097403

Read-only high accuracy volume holographic optical correlator

NASA Astrophysics Data System (ADS)

Zhao, Tian; Li, Jingming; Cao, Liangcai; He, Qingsheng; Jin, Guofan

2011-10-01

A read-only volume holographic correlator (VHC) is proposed. After the recording of all of the correlation database pages by angular multiplexing, a stand-alone read-only high accuracy VHC will be separated from the VHC recording facilities which include the high-power laser and the angular multiplexing system. The stand-alone VHC has its own low power readout laser and very compact and simple structure. Since there are two lasers that are employed for recording and readout, respectively, the optical alignment tolerance of the laser illumination on the SLM is very sensitive. The twodimensional angular tolerance is analyzed based on the theoretical model of the volume holographic correlator. The experimental demonstration of the proposed read-only VHC is introduced and discussed.

Time and position sensitive single photon detector for scintillator read-out

NASA Astrophysics Data System (ADS)

Schössler, S.; Bromberger, B.; Brandis, M.; Schmidt, L. Ph H.; Tittelmeier, K.; Czasch, A.; Dangendorf, V.; Jagutzki, O.

2012-02-01

We have developed a photon counting detector system for combined neutron and γ radiography which can determine position, time and intensity of a secondary photon flash created by a high-energy particle or photon within a scintillator screen. The system is based on a micro-channel plate photomultiplier concept utilizing image charge coupling to a position- and time-sensitive read-out anode placed outside the vacuum tube in air, aided by a standard photomultiplier and very fast pulse-height analyzing electronics. Due to the low dead time of all system components it can cope with the high throughput demands of a proposed combined fast neutron and dual discrete energy γ radiography method (FNDDER). We show tests with different types of delay-line read-out anodes and present a novel pulse-height-to-time converter circuit with its potential to discriminate γ energies for the projected FNDDER devices for an automated cargo container inspection system (ACCIS).

Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA.

PubMed

Holt, Kathryn E; Teo, Yik Y; Li, Heng; Nair, Satheesh; Dougan, Gordon; Wain, John; Parkhill, Julian

2009-08-15

Here, we present a method for estimating the frequencies of SNP alleles present within pooled samples of DNA using high-throughput short-read sequencing. The method was tested on real data from six strains of the highly monomorphic pathogen Salmonella Paratyphi A, sequenced individually and in a pool. A variety of read mapping and quality-weighting procedures were tested to determine the optimal parameters, which afforded > or =80% sensitivity of SNP detection and strong correlation with true SNP frequency at poolwide read depth of 40x, declining only slightly at read depths 20-40x. The method was implemented in Perl and relies on the opensource software Maq for read mapping and SNP calling. The Perl script is freely available from ftp://ftp.sanger.ac.uk/pub/pathogens/pools/.

Cross-Age Reading Buddies and Cultural-Sensitive Literature: Student-Centered English Language Instruction in an Ethiopian Budget School

ERIC Educational Resources Information Center

Cianca, Sherri

2012-01-01

The Ethiopian government has called for educational improvement, emphasizing the employment of active, student-centered pedagogy. One way of maximizing an interactive learning approach involves blending a cross-age reading buddies program with high-quality, culturally relevant children's literature. Employing descriptive, mixed-method research,…

Efficient visual object and word recognition relies on high spatial frequency coding in the left posterior fusiform gyrus: evidence from a case-series of patients with ventral occipito-temporal cortex damage.

PubMed

Roberts, Daniel J; Woollams, Anna M; Kim, Esther; Beeson, Pelagie M; Rapcsak, Steven Z; Lambon Ralph, Matthew A

2013-11-01

Recent visual neuroscience investigations suggest that ventral occipito-temporal cortex is retinotopically organized, with high acuity foveal input projecting primarily to the posterior fusiform gyrus (pFG), making this region crucial for coding high spatial frequency information. Because high spatial frequencies are critical for fine-grained visual discrimination, we hypothesized that damage to the left pFG should have an adverse effect not only on efficient reading, as observed in pure alexia, but also on the processing of complex non-orthographic visual stimuli. Consistent with this hypothesis, we obtained evidence that a large case series (n = 20) of patients with lesions centered on left pFG: 1) Exhibited reduced sensitivity to high spatial frequencies; 2) demonstrated prolonged response latencies both in reading (pure alexia) and object naming; and 3) were especially sensitive to visual complexity and similarity when discriminating between novel visual patterns. These results suggest that the patients' dual reading and non-orthographic recognition impairments have a common underlying mechanism and reflect the loss of high spatial frequency visual information normally coded in the left pFG.

Writing System Modulates the Association between Sensitivity to Acoustic Cues in Music and Reading Ability: Evidence from Chinese-English Bilingual Children.

PubMed

Zhang, Juan; Meng, Yaxuan; Wu, Chenggang; Zhou, Danny Q

2017-01-01

Music and language share many attributes and a large body of evidence shows that sensitivity to acoustic cues in music is positively related to language development and even subsequent reading acquisition. However, such association was mainly found in alphabetic languages. What remains unclear is whether sensitivity to acoustic cues in music is associated with reading in Chinese, a morphosyllabic language. The present study aimed to answer this question by measuring music (i.e., musical metric perception and pitch discrimination), language (i.e., phonological awareness, lexical tone sensitivity), and reading abilities (i.e., word recognition) among 54 third-grade Chinese-English bilingual children. After controlling for age and non-verbal intelligence, we found that both musical metric perception and pitch discrimination accounted for unique variance of Chinese phonological awareness while pitch discrimination rather than musical metric perception predicted Chinese lexical tone sensitivity. More importantly, neither musical metric perception nor pitch discrimination was associated with Chinese reading. As for English, musical metric perception and pitch discrimination were correlated with both English phonological awareness and English reading. Furthermore, sensitivity to acoustic cues in music was associated with English reading through the mediation of English phonological awareness. The current findings indicate that the association between sensitivity to acoustic cues in music and reading may be modulated by writing systems. In Chinese, the mapping between orthography and phonology is not as transparent as in alphabetic languages such as English. Thus, this opaque mapping may alter the auditory perceptual sensitivity in music to Chinese reading.

Writing System Modulates the Association between Sensitivity to Acoustic Cues in Music and Reading Ability: Evidence from Chinese–English Bilingual Children

PubMed Central

Zhang, Juan; Meng, Yaxuan; Wu, Chenggang; Zhou, Danny Q.

2017-01-01

Music and language share many attributes and a large body of evidence shows that sensitivity to acoustic cues in music is positively related to language development and even subsequent reading acquisition. However, such association was mainly found in alphabetic languages. What remains unclear is whether sensitivity to acoustic cues in music is associated with reading in Chinese, a morphosyllabic language. The present study aimed to answer this question by measuring music (i.e., musical metric perception and pitch discrimination), language (i.e., phonological awareness, lexical tone sensitivity), and reading abilities (i.e., word recognition) among 54 third-grade Chinese–English bilingual children. After controlling for age and non-verbal intelligence, we found that both musical metric perception and pitch discrimination accounted for unique variance of Chinese phonological awareness while pitch discrimination rather than musical metric perception predicted Chinese lexical tone sensitivity. More importantly, neither musical metric perception nor pitch discrimination was associated with Chinese reading. As for English, musical metric perception and pitch discrimination were correlated with both English phonological awareness and English reading. Furthermore, sensitivity to acoustic cues in music was associated with English reading through the mediation of English phonological awareness. The current findings indicate that the association between sensitivity to acoustic cues in music and reading may be modulated by writing systems. In Chinese, the mapping between orthography and phonology is not as transparent as in alphabetic languages such as English. Thus, this opaque mapping may alter the auditory perceptual sensitivity in music to Chinese reading. PMID:29170647

Cultural Literacy Based Critical Reading Teaching Material with Active Reader Strategy for Junior High School

ERIC Educational Resources Information Center

Damaianti, Vismaia S.; Damaianti, Lira Fessia; Mulyati, Yeti

2017-01-01

This article describes the findings of a study aimed at producing a set of cultural literacy-oriented critical reading teaching material. This material is developed as a countermeasure to the increasingly thin sensitivity of society, especially the students toward noble values of religion, custom, and culture. With this material student get a…

Tone matters for Cantonese-English bilingual children's English word reading development: A unified model of phonological transfer.

PubMed

Tong, Xiuli; He, Xinjie; Deacon, S Hélène

2017-02-01

Languages differ considerably in how they use prosodic features, or variations in pitch, duration, and intensity, to distinguish one word from another. Prosodic features include lexical tone in Chinese and lexical stress in English. Recent cross-sectional studies show a surprising result that Mandarin Chinese tone sensitivity is related to Mandarin-English bilingual children's English word reading. This study explores the mechanism underlying this relation by testing two explanations of these effects: the prosodic hypothesis and segmental phonological awareness transfer. We administered multiple measures of Cantonese tone sensitivity, English stress sensitivity, segmental phonological awareness in Cantonese and English, nonverbal ability, and English word reading to 123 Cantonese-English bilingual children ages 7 and 8 years. Structural equation modeling revealed a longitudinal prediction of Cantonese tone sensitivity to English word reading between 8 and 9 years of age. This relation was realized through two parallel routes. In one, Cantonese tone sensitivity predicted English stress sensitivity, and English stress sensitivity, in turn, significantly predicted English word reading, as postulated by the prosodic hypothesis. In the second, Cantonese tone sensitivity predicted English word reading through the transfer of segmental phonological awareness between Cantonese and English, as predicted by segmental phonological transfer. These results support a unified model of phonological transfer, emphasizing the role of tone in English word reading for Cantonese-English bilingual children.

Innovative multi-cantilever array sensor system with MOEMS read-out

NASA Astrophysics Data System (ADS)

Ivaldi, F.; Bieniek, T.; Janus, P.; Grabiec, P.; Majstrzyk, W.; Kopiec, D.; Gotszalk, T.

2016-11-01

Cantilever based sensor system are a well-established sensor family exploited in several every-day life applications as well as in high-end research areas. The very high sensitivity of such systems and the possibility to design and functionalize the cantilevers to create purpose built and highly selective sensors have increased the interest of the scientific community and the industry in further exploiting this promising sensors type. Optical deflection detection systems for cantilever sensors provide a reliable, flexible method for reading information from cantilevers with the highest sensitivity. However the need of using multi-cantilever arrays in several fields of application such as medicine, biology or safety related areas, make the optical method less suitable due to its structural complexity. Working in the frame of a the Joint Undertaking project Lab4MEMS II our group proposes a novel and innovative approach to solve this issue, by integrating a Micro-Opto-Electro-Mechanical-System (MOEMS) with dedicated optics, electronics and software with a MOEMS micro-mirror, ultimately developed in the frame of Lab4MEMSII. In this way we are able to present a closely packed, lightweight solution combining the advantages of standard optical read-out systems with the possibility of recording multiple read-outs from large cantilever arrays quasi simultaneously.

Is a "Phoenician" reading style superior to a "Chinese" reading style? Evidence from fourth graders.

PubMed

Bowey, Judith A

2008-07-01

This study compared normally achieving fourth-grade "Phoenician" readers, who identify nonwords significantly more accurately than they do exception words, with "Chinese" readers, who show the reverse pattern. Phoenician readers scored lower than Chinese readers on word identification, exception word reading, orthographic choice, spelling, reading comprehension, and verbal ability. When compared with normally achieving children who read nonwords and exception words equally well, Chinese readers scored as well as these children on word identification, regular word reading, orthographic choice, spelling, reading comprehension, phonological sensitivity, and verbal ability and scored better on exception word reading. Chinese readers also used rhyme-based analogies to read nonwords derived from high-frequency exception words just as often as did these children. As predicted, Phoenician and Chinese readers adopted somewhat different strategies in reading ambiguous nonwords constructed by analogy to high-frequency exception words. Phoenician readers were more likely than Chinese readers to read ambiguous monosyllabic nonwords via context-free grapheme-phoneme correspondences and were less likely to read disyllabic nonwords by analogy to high-frequency analogues. Although the Chinese reading style was more common than the Phoenician style in normally achieving fourth graders, there were similar numbers of poor readers with phonological dyslexia (identifying nonwords significantly more accurately than exception words) and surface dyslexia (showing the reverse pattern), although surface dyslexia was more common in the severely disabled readers. However, few of the poor readers showed pure patterns of phonological or surface dyslexia.

Sensitivity to Linguistic Stress, Phonological Awareness and Early Reading Ability in Preschoolers

ERIC Educational Resources Information Center

Goodman, Ilana; Libenson, Amanda; Wade-Woolley, Lesly

2010-01-01

Recent research has found that sensitivity to linguistic stress is related to phonological awareness and reading development. This study investigated the roles of two types of linguistic stress sensitivity (lexical and metrical stress) in the phonological awareness and reading development of young children. Forty-five kindergarten children were…

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

PubMed

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

2017-01-01

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

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

PubMed Central

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

2017-01-01

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

The influence of film-screen color sensitivity and type of measurement device on kVp measurements.

PubMed

Lam, R W; Price, S C

1989-01-01

Three methods for evaluating radiographic kVp were studied: the Wisconsin Test Cassette, the Noninvasive Evaluator of Radiation Outputs (NERO), and the Dynalyzer. The Dynalyzer kVp readings were the highest and were followed by NERO and cassette readings in descending order. By film type, the cassette readings ranged from Kodak OG (green sensitive), TMG (green sensitive), XK (blue sensitive), and XRP (blue sensitive) in descending order. The results show that there is significant variation between the methods.

Modeling read counts for CNV detection in exome sequencing data.

PubMed

Love, Michael I; Myšičková, Alena; Sun, Ruping; Kalscheuer, Vera; Vingron, Martin; Haas, Stefan A

2011-11-08

Varying depth of high-throughput sequencing reads along a chromosome makes it possible to observe copy number variants (CNVs) in a sample relative to a reference. In exome and other targeted sequencing projects, technical factors increase variation in read depth while reducing the number of observed locations, adding difficulty to the problem of identifying CNVs. We present a hidden Markov model for detecting CNVs from raw read count data, using background read depth from a control set as well as other positional covariates such as GC-content. The model, exomeCopy, is applied to a large chromosome X exome sequencing project identifying a list of large unique CNVs. CNVs predicted by the model and experimentally validated are then recovered using a cross-platform control set from publicly available exome sequencing data. Simulations show high sensitivity for detecting heterozygous and homozygous CNVs, outperforming normalization and state-of-the-art segmentation methods.

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

High speed magneto-resistive random access memory

NASA Technical Reports Server (NTRS)

Wu, Jiin-Chuan (Inventor); Stadler, Henry L. (Inventor); Katti, Romney R. (Inventor)

1992-01-01

A high speed read MRAM memory element is configured from a sandwich of magnetizable, ferromagnetic film surrounding a magneto-resistive film which may be ferromagnetic or not. One outer ferromagnetic film has a higher coercive force than the other and therefore remains magnetized in one sense while the other may be switched in sense by a switching magnetic field. The magneto-resistive film is therefore sensitive to the amplitude of the resultant field between the outer ferromagnetic films and may be constructed of a high resistivity, high magneto-resistive material capable of higher sensing currents. This permits higher read voltages and therefore faster read operations. Alternate embodiments with perpendicular anisotropy, and in-plane anisotropy are shown, including an embodiment which uses high permeability guides to direct the closing flux path through the magneto-resistive material. High density, high speed, radiation hard, memory matrices may be constructed from these memory elements.

Coherent Motion Sensitivity and Reading Development in the Transition from Prereading to Reading Stage

ERIC Educational Resources Information Center

Boets, Bart; Vandermosten, Maaike; Cornelissen, Piers; Wouters, Jan; Ghesquiere, Pol

2011-01-01

Evidence suggests that sensitivity to coherent motion (CM) is related to reading, but its role in the etiology of developmental dyslexia remains unclear. In this longitudinal study, CM sensitivity was measured in 31 children at family risk for dyslexia and 31 low-risk controls. Children, diagnosed with dyslexia in third grade (mean age = 8 years 3…

The Immediate and Longer-Term Effectiveness of a Speech-Rhythm-Based Reading Intervention for Beginning Readers

ERIC Educational Resources Information Center

Harrison, Emily; Wood, Clare; Holliman, Andrew J.; Vousden, Janet I.

2018-01-01

Despite empirical evidence of a relationship between sensitivity to speech rhythm and reading, there have been few studies that have examined the impact of rhythmic training on reading attainment, and no intervention study has focused on speech rhythm sensitivity specifically to enhance reading skills. Seventy-three typically developing 4- to…

Tactile Sensitivity and Braille Reading in People with Early Blindness and Late Blindness

ERIC Educational Resources Information Center

Oshima, Kensuke; Arai, Tetsuya; Ichihara, Shigeru; Nakano, Yasushi

2014-01-01

Introduction: The inability to read quickly can be a disadvantage throughout life. This study focused on the associations of braille reading fluency and individual factors, such as the age at onset of blindness and number of years reading braille, and the tactile sensitivity of people with early and late blindness. The relationship between reading…

Artifacts Of Spectral Analysis Of Instrument Readings

NASA Technical Reports Server (NTRS)

Wise, James H.

1995-01-01

Report presents experimental and theoretical study of some of artifacts introduced by processing outputs of two nominally identical low-frequency-reading instruments; high-sensitivity servo-accelerometers mounted together and operating, in conjunction with signal-conditioning circuits, as seismometers. Processing involved analog-to-digital conversion with anti-aliasing filtering, followed by digital processing including frequency weighting and computation of different measures of power spectral density (PSD).

Accurate Filtering of Privacy-Sensitive Information in Raw Genomic Data.

PubMed

Decouchant, Jérémie; Fernandes, Maria; Völp, Marcus; Couto, Francisco M; Esteves-Veríssimo, Paulo

2018-04-13

Sequencing thousands of human genomes has enabled breakthroughs in many areas, among them precision medicine, the study of rare diseases, and forensics. However, mass collection of such sensitive data entails enormous risks if not protected to the highest standards. In this article, we follow the position and argue that post-alignment privacy is not enough and that data should be automatically protected as early as possible in the genomics workflow, ideally immediately after the data is produced. We show that a previous approach for filtering short reads cannot extend to long reads and present a novel filtering approach that classifies raw genomic data (i.e., whose location and content is not yet determined) into privacy-sensitive (i.e., more affected by a successful privacy attack) and non-privacy-sensitive information. Such a classification allows the fine-grained and automated adjustment of protective measures to mitigate the possible consequences of exposure, in particular when relying on public clouds. We present the first filter that can be indistinctly applied to reads of any length, i.e., making it usable with any recent or future sequencing technologies. The filter is accurate, in the sense that it detects all known sensitive nucleotides except those located in highly variable regions (less than 10 nucleotides remain undetected per genome instead of 100,000 in previous works). It has far less false positives than previously known methods (10% instead of 60%) and can detect sensitive nucleotides despite sequencing errors (86% detected instead of 56% with 2% of mutations). Finally, practical experiments demonstrate high performance, both in terms of throughput and memory consumption. Copyright © 2018. Published by Elsevier Inc.

Symbol-string sensitivity and children's reading.

PubMed

Pammer, Kristen; Lavis, Ruth; Hansen, Peter; Cornelissen, Piers L

2004-06-01

In this study of primary school children, a novel 'symbol-string' task is used to assess sensitivity to the position of briefly presented non-alphabetic but letter-like symbols. The results demonstrate that sensitivity in the symbol-string task explains a unique proportion of the variability in children's contextual reading accuracy. Moreover, developmental dyslexic readers show reduced sensitivity in this task, compared to chronological age controls. The results suggest that limitations set by visuo-spatial processes and/or attentional iconic memory resources may constrain children's reading accuracy.

Analysis of small-bowel capsule endoscopy reading by using Quickview mode: training assistants for reading may produce a high diagnostic yield and save time for physicians.

PubMed

Shiotani, Akiko; Honda, Keisuke; Kawakami, Makiko; Kimura, Yoshiki; Yamanaka, Yoshiyuki; Fujita, Minoru; Matsumoto, Hiroshi; Tarumi, Ken-ichi; Manabe, Noriaki; Haruma, Ken

2012-01-01

The aim was to investigate the clinical utility of RAPID Access 6.5 Quickview software and to evaluate whether preview of the capsule endoscopy video by a trained nurse could detect significant lesions accurately compared with endoscopists. As reading capsule endoscopy is time consuming, one possible cost-effective strategy could be the use of trained nonphysicians or newly available software to preread and identify potentially important capsule images. The 100 capsule images of a variety of significant lesions from 87 patients were investigated. The minimum percentages for settings of sensitivity that could pick up the selected images and the detection rate for significant lesions by a well-trained nurse, two endoscopists with limited experience in reading, and one well-trained physician were examined. The frequency of the selected lesions picked up by Quickview mode using percentages for sensitivity settings of 5%, 15%, 25%, and 35% were 61%, 74%, 93%, and 98%, respectively. The percentages for sensitivity significantly correlated (r=0.78, P<0.001) with the reading time. The detection rate by the nurse or the well-trained physician was significantly higher than that by the physician with limited capsule experience (87% and 84.1% vs. 62.7%; P<0.01). The clinical use of Quickview at 25% did not significantly improve the detection rate. Quickview mode can reduce reading time but has an unacceptably miss rate for potentially important lesions. Use of a trained nonphysician assistant can reduce physician's time and improve diagnostic yield.

Solid state neutron dosimeter for space applications

NASA Technical Reports Server (NTRS)

Entine, Gerald; Nagargar, Vivek; Sharif, Daud

1990-01-01

Personnel engaged in space flight are exposed to significant flux of high energy neutrons arising from both primary and secondary sources of ionizing radiation. Presently, there exist no compact neutron sensor capable of being integrated in a flight instrument to provide real time measurement of this radiation flux. A proposal was made to construct such an instrument using special PIN silicon diode which has the property of being insensitive to the other forms of ionizing radiation. Studies were performed to determine the design and construction of a better reading system to allow the PIN diode to be read with high precision. The physics of the device was studied, especially with respect to those factors which affect the sensitivity and reproducibility of the neutron response. This information was then used to develop methods to achieve high sensitivity at low neutron doses. The feasibility was shown of enhancing the PIN diode sensitivity to make possible the measurement of the low doses of neutrons encountered in space flights. The new PIN diode will make possible the development of a very compact, accurate, personal neutron dosimeter.

How genome complexity can explain the difficulty of aligning reads to genomes.

PubMed

Phan, Vinhthuy; Gao, Shanshan; Tran, Quang; Vo, Nam S

2015-01-01

Although it is frequently observed that aligning short reads to genomes becomes harder if they contain complex repeat patterns, there has not been much effort to quantify the relationship between complexity of genomes and difficulty of short-read alignment. Existing measures of sequence complexity seem unsuitable for the understanding and quantification of this relationship. We investigated several measures of complexity and found that length-sensitive measures of complexity had the highest correlation to accuracy of alignment. In particular, the rate of distinct substrings of length k, where k is similar to the read length, correlated very highly to alignment performance in terms of precision and recall. We showed how to compute this measure efficiently in linear time, making it useful in practice to estimate quickly the difficulty of alignment for new genomes without having to align reads to them first. We showed how the length-sensitive measures could provide additional information for choosing aligners that would align consistently accurately on new genomes. We formally established a connection between genome complexity and the accuracy of short-read aligners. The relationship between genome complexity and alignment accuracy provides additional useful information for selecting suitable aligners for new genomes. Further, this work suggests that the complexity of genomes sometimes should be thought of in terms of specific computational problems, such as the alignment of short reads to genomes.

Suprasegmental Phonology Development and Reading Acquisition: A Longitudinal Study

ERIC Educational Resources Information Center

Calet, Nuria; Gutiérrez-Palma, Nicolás; Simpson, Ian C.; González-Trujillo, M. Carmen; Defior, Sylvia

2015-01-01

Previous studies implicate suprasegmental phonology in reading acquisition. However, little is known about how suprasegmental sensitivity develops or how it contributes to reading. Here, 130 Spanish primary-school children participated in this 2-year longitudinal study. Nonlinguistic rhythm, lexical-stress sensitivity and metrical-stress…

Sensitivity to Phonological, Morphological, and Semantic Cues in Early Reading and Writing in Hebrew.

ERIC Educational Resources Information Center

Levin, Iris; Korat, Ofra

1993-01-01

Studied emergent literacy in Hebrew by analyzing nursery and kindergarten children's attempts to write and read pairs of nouns. Found that, with age, children's sensitivity to phonology increased and sensitivity to semantics decreased and that these sensitivities played a greater role in literacy acquisition than did sensitivity to morphology. (MM)

Method and Characterization of Pyroelectric Coefficients for Determining Material Figures of Merit for Infrared (IR) Detectors

DTIC Science & Technology

2013-12-01

and the signal is read as a photocurrent or at a photovoltaic p-n junction. These detectors can provide high-sensitivity and fast refresh rates and...Alternative methods can be used to modulate the sample temperature directly; for example, by using modern Peltier devices and thermoelectric ...commercially-available hardware. The setup consist of three main components: (1) A temperature regulated thermoelectric stage; (2) A high-sensitivity

Stress-only myocardial perfusion scintigraphy: a prospective study on the accuracy and observer agreement with quantitative coronary angiography as the gold standard.

PubMed

Ejlersen, June A; May, Ole; Mortensen, Jesper; Nielsen, Gitte L; Lauridsen, Jeppe F; Allan, Johansen

2017-11-01

Patients with normal stress perfusion have an excellent prognosis. Prospective studies on the diagnostic accuracy of stress-only scans with contemporary, independent examinations as gold standards are lacking. A total of 109 patients with typical angina and no previous coronary artery disease underwent a 2-day stress (exercise)/rest, gated, and attenuation-corrected (AC), 99m-technetium-sestamibi perfusion study, followed by invasive coronary angiography. The stress datasets were evaluated twice by four physicians with two different training levels (expert and novice): familiar and unfamiliar with AC. The two experts also made a consensus reading of the integrated stress-rest datasets. The consensus reading and quantitative data from the invasive coronary angiography were applied as reference methods. The sensitivity/specificity were 0.92-1.00/0.73-0.90 (reference: expert consensus reading), 0.93-0.96/0.63-0.82 (reference: ≥1 stenosis>70%), and 0.75-0.88/0.70-0.88 (reference: ≥1 stenosis>50%). The four readers showed a high and fairly equal sensitivity independent of their familiarity with AC. The expert familiar with AC had the highest specificity independent of the reference method. The intraobserver and interobserver agreements on the stress-only readings were good (readers without AC experience) to excellent (readers with AC experience). AC stress-only images yielded a high sensitivity independent of the training level and experience with AC of the nuclear physician, whereas the specificity correlated positively with both. Interobserver and intraobserver agreements tended to be the best for physicians with AC experience.

Subcortical processing of speech regularities underlies reading and music aptitude in children.

PubMed

Strait, Dana L; Hornickel, Jane; Kraus, Nina

2011-10-17

Neural sensitivity to acoustic regularities supports fundamental human behaviors such as hearing in noise and reading. Although the failure to encode acoustic regularities in ongoing speech has been associated with language and literacy deficits, how auditory expertise, such as the expertise that is associated with musical skill, relates to the brainstem processing of speech regularities is unknown. An association between musical skill and neural sensitivity to acoustic regularities would not be surprising given the importance of repetition and regularity in music. Here, we aimed to define relationships between the subcortical processing of speech regularities, music aptitude, and reading abilities in children with and without reading impairment. We hypothesized that, in combination with auditory cognitive abilities, neural sensitivity to regularities in ongoing speech provides a common biological mechanism underlying the development of music and reading abilities. We assessed auditory working memory and attention, music aptitude, reading ability, and neural sensitivity to acoustic regularities in 42 school-aged children with a wide range of reading ability. Neural sensitivity to acoustic regularities was assessed by recording brainstem responses to the same speech sound presented in predictable and variable speech streams. Through correlation analyses and structural equation modeling, we reveal that music aptitude and literacy both relate to the extent of subcortical adaptation to regularities in ongoing speech as well as with auditory working memory and attention. Relationships between music and speech processing are specifically driven by performance on a musical rhythm task, underscoring the importance of rhythmic regularity for both language and music. These data indicate common brain mechanisms underlying reading and music abilities that relate to how the nervous system responds to regularities in auditory input. Definition of common biological underpinnings for music and reading supports the usefulness of music for promoting child literacy, with the potential to improve reading remediation.

Yellow filters can improve magnocellular function: motion sensitivity, convergence, accommodation, and reading.

PubMed

Ray, N J; Fowler, S; Stein, J F

2005-04-01

The magnocellular system plays an important role in visual motion processing, controlling vergence eye movements, and in reading. Yellow filters may boost magnocellular activity by eliminating inhibitory blue input to this pathway. It was found that wearing yellow filters increased motion sensitivity, convergence, and accommodation in many children with reading difficulties, both immediately and after three months using the filters. Motion sensitivity was not increased using control neutral density filters. Moreover, reading-impaired children showed significant gains in reading ability after three months wearing the filters compared with those who had used a placebo. It was concluded that yellow filters can improve magnocellular function permanently. Hence, they should be considered as an alternative to corrective lenses, prisms, or exercises for treating poor convergence and accommodation, and also as an aid for children with reading problems.

Impact of the Ability to Divide Attention on Reading Performance in Glaucoma.

PubMed

Swenor, Bonnielin K; Varadaraj, Varshini; Dave, Paulomi; West, Sheila K; Rubin, Gary S; Ramulu, Pradeep Y

2017-05-01

To determine if the ability to divide attention affects the relationship between glaucoma-related vision loss and reading speed. Better eye mean deviation (MD), contrast sensitivity (CS), and better-eye distance visual acuity (VA) were measured in 28 participants with glaucoma and 21 controls. Reading speeds were assessed using MNRead, IRest, and sustained silent reading tests (words per minute, wpm). The ability to divide attention was measured using the Brief Test of Attention (BTA; scored 0-10). Multivariable linear regression models were used to determine the relationship between visual factors and reading speeds. Effect modification by BTA score (low BTA: <7; high BTA: ≥7) was examined. Worse CS (per 0.1 log unit) was associated with slower maximum reading speed on MNRead test for participants with low BTA scores (β = -9 wpm; 95% confidence interval [CI]: -16, -2), but not for those with high BTA scores (β = -2 wpm; 95% CI: -6, +2). Similarly, for the IRest test, worse CS was associated with slower reading speeds (β = -12 wpm; 95% CI: -20, -4) among those with low, but not high BTA scores (β = -4 wpm; 95% CI: -10, +2). For the sustained silent reading test, glaucoma status (versus controls), worse visual field (VF) MD (per 5 dB), and worse CS were associated with 39%, 21%, and 19% slower reading speeds, respectively, for those with low BTA scores (P < 0.05), but these associations were not significant among those with high BTA scores (P > 0.1 for all). Decreased ability to divide attention, indicated by lower BTA scores, is associated with slower reading speeds in glaucoma with reduced CS and VF defects.

Impact of the Ability to Divide Attention on Reading Performance in Glaucoma

PubMed Central

Swenor, Bonnielin K.; Varadaraj, Varshini; Dave, Paulomi; West, Sheila K.; Rubin, Gary S.; Ramulu, Pradeep Y.

2017-01-01

Purpose To determine if the ability to divide attention affects the relationship between glaucoma-related vision loss and reading speed. Methods Better eye mean deviation (MD), contrast sensitivity (CS), and better-eye distance visual acuity (VA) were measured in 28 participants with glaucoma and 21 controls. Reading speeds were assessed using MNRead, IRest, and sustained silent reading tests (words per minute, wpm). The ability to divide attention was measured using the Brief Test of Attention (BTA; scored 0–10). Multivariable linear regression models were used to determine the relationship between visual factors and reading speeds. Effect modification by BTA score (low BTA: <7; high BTA: ≥7) was examined. Results Worse CS (per 0.1 log unit) was associated with slower maximum reading speed on MNRead test for participants with low BTA scores (β = −9 wpm; 95% confidence interval [CI]: −16, −2), but not for those with high BTA scores (β = −2 wpm; 95% CI: −6, +2). Similarly, for the IRest test, worse CS was associated with slower reading speeds (β = −12 wpm; 95% CI: −20, −4) among those with low, but not high BTA scores (β = −4 wpm; 95% CI: −10, +2). For the sustained silent reading test, glaucoma status (versus controls), worse visual field (VF) MD (per 5 dB), and worse CS were associated with 39%, 21%, and 19% slower reading speeds, respectively, for those with low BTA scores (P < 0.05), but these associations were not significant among those with high BTA scores (P > 0.1 for all). Conclusions Decreased ability to divide attention, indicated by lower BTA scores, is associated with slower reading speeds in glaucoma with reduced CS and VF defects. PMID:28460047

The effects of reading comprehension and launch site on frequency-predictability interactions during paragraph reading.

PubMed

Whitford, Veronica; Titone, Debra

2014-01-01

We used eye movement measures of paragraph reading to examine whether word frequency and predictability interact during the earliest stages of lexical processing, with a specific focus on whether these effects are modulated by individual differences in reading comprehension or launch site (i.e., saccade length between the prior and currently fixated word--a proxy for the amount of parafoveal word processing). The joint impact of frequency and predictability on reading will elucidate whether these variables additively or multiplicatively affect the earliest stages of lexical access, which, in turn, has implications for computational models of eye movements during reading. Linear mixed effects models revealed additive effects during both early- and late-stage reading, where predictability effects were comparable for low- and high-frequency words. Moreover, less cautious readers (e.g., readers who engaged in skimming, scanning, mindless reading) demonstrated smaller frequency effects than more cautious readers. Taken together, our findings suggest that during extended reading, frequency and predictability exert additive influences on lexical and postlexical processing, and that individual differences in reading comprehension modulate sensitivity to the effects of word frequency.

Early Sensitivity to Discourse-Level Anomalies: Evidence from Self-Paced Reading

ERIC Educational Resources Information Center

Stewart, Andrew J.; Kidd, Evan; Haigh, Matthew

2009-01-01

Two word-by-word, self-paced reading experiments investigated the speed with which readers were sensitive to discourse-level anomalies. An account arguing for delayed sensitivity (Guzman & Klin, 2000) was contrasted with one allowing for rapid sensitivity (Myers & O'Brien, 1998). Anomalies related to spatial information (Experiment 1) and…

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

PubMed Central

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

2016-01-01

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

Development and characterization of high-resolution neutron pixel detectors based on Timepix read-out chips

NASA Astrophysics Data System (ADS)

Krejci, F.; Zemlicka, J.; Jakubek, J.; Dudak, J.; Vavrik, D.; Köster, U.; Atkins, D.; Kaestner, A.; Soltes, J.; Viererbl, L.; Vacik, J.; Tomandl, I.

2016-12-01

Using a suitable isotope such as 6Li and 10B semiconductor hybrid pixel detectors can be successfully adapted for position sensitive detection of thermal and cold neutrons via conversion into energetic light ions. The adapted devices then typically provides spatial resolution at the level comparable to the pixel pitch (55 μm) and sensitive area of about few cm2. In this contribution, we describe further progress in neutron imaging performance based on the development of a large-area hybrid pixel detector providing practically continuous neutron sensitive area of 71 × 57 mm2. The measurements characterising the detector performance at the cold neutron imaging instrument ICON at PSI and high-flux imaging beam-line Neutrograph at ILL are presented. At both facilities, high-resolution high-contrast neutron radiography with the newly developed detector has been successfully applied for objects which imaging were previously difficult with hybrid pixel technology (such as various composite materials, objects of cultural heritage etc.). Further, a significant improvement in the spatial resolution of neutron radiography with hybrid semiconductor pixel detector based on the fast read-out Timepix-based detector is presented. The system is equipped with a thin planar 6LiF convertor operated effectively in the event-by-event mode enabling position sensitive detection with spatial resolution better than 10 μm.

Does Sensitivity to Orthographic Regularities Influence Reading and Spelling Acquisition? A 1-Year Prospective Study

ERIC Educational Resources Information Center

Rothe, Josefine; Schulte-Körne, Gerd; Ise, Elena

2014-01-01

Recent studies focused on the influence of orthographic processing on reading and spelling performance. It was found that orthographic processing is an independent predictor of reading and spelling performance in different languages and children of different ages. This study investigated sensitivity to orthographic regularities in German-speaking…

Sensitivity to Speech Rhythm Explains Individual Differences in Reading Ability Independently of Phonological Awareness

ERIC Educational Resources Information Center

Holliman, Andrew J.; Wood, Clare; Sheehy, Kieron

2008-01-01

This study considered whether sensitivity to speech rhythm can predict concurrent variance in reading attainment after individual differences in age, vocabulary, and phonological awareness have been controlled. Five- to six-year-old English-speaking children completed a battery of phonological processing assessments and reading assessments, along…

Making Meaning: Children's Sensitivity to Morphological Information during Word Reading

ERIC Educational Resources Information Center

Mccutchen, Deborah; Logan, Becky; Biangardi-Orpe, Ulrike

2009-01-01

In the present study, 81 fifth grade and 82 eighth grade children completed a continuous lexical decision priming task that examined their reading times for evidence of sensitivity to the morphological structure of words during reading. A lexical decision task measured students' response times to target words preceded by a prime (which children…

The development of cortical sensitivity to visual word forms.

PubMed

Ben-Shachar, Michal; Dougherty, Robert F; Deutsch, Gayle K; Wandell, Brian A

2011-09-01

The ability to extract visual word forms quickly and efficiently is essential for using reading as a tool for learning. We describe the first longitudinal fMRI study to chart individual changes in cortical sensitivity to written words as reading develops. We conducted four annual measurements of brain function and reading skills in a heterogeneous group of children, initially 7-12 years old. The results show age-related increase in children's cortical sensitivity to word visibility in posterior left occipito-temporal sulcus (LOTS), nearby the anatomical location of the visual word form area. Moreover, the rate of increase in LOTS word sensitivity specifically correlates with the rate of improvement in sight word efficiency, a measure of speeded overt word reading. Other cortical regions, including V1, posterior parietal cortex, and the right homologue of LOTS, did not demonstrate such developmental changes. These results provide developmental support for the hypothesis that LOTS is part of the cortical circuitry that extracts visual word forms quickly and efficiently and highlight the importance of developing cortical sensitivity to word visibility in reading acquisition.

The Development of Cortical Sensitivity to Visual Word Forms

PubMed Central

Ben-Shachar, Michal; Dougherty, Robert F.; Deutsch, Gayle K.; Wandell, Brian A.

2011-01-01

The ability to extract visual word forms quickly and efficiently is essential for using reading as a tool for learning. We describe the first longitudinal fMRI study to chart individual changes in cortical sensitivity to written words as reading develops. We conducted four annual measurements of brain function and reading skills in a heterogeneous group of children, initially 7–12 years old. The results show age-related increase in children's cortical sensitivity to word visibility in posterior left occipito-temporal sulcus (LOTS), nearby the anatomical location of the visual word form area. Moreover, the rate of increase in LOTS word sensitivity specifically correlates with the rate of improvement in sight word efficiency, a measure of speeded overt word reading. Other cortical regions, including V1, posterior parietal cortex, and the right homologue of LOTS, did not demonstrate such developmental changes. These results provide developmental support for the hypothesis that LOTS is part of the cortical circuitry that extracts visual word forms quickly and efficiently and highlight the importance of developing cortical sensitivity to word visibility in reading acquisition. PMID:21261451

The Development of Cortical Sensitivity to Visual Word Forms

ERIC Educational Resources Information Center

Ben-Shachar, Michal; Dougherty, Robert F.; Deutsch, Gayle K.; Wandell, Brian A.

2011-01-01

The ability to extract visual word forms quickly and efficiently is essential for using reading as a tool for learning. We describe the first longitudinal fMRI study to chart individual changes in cortical sensitivity to written words as reading develops. We conducted four annual measurements of brain function and reading skills in a heterogeneous…

The Respective Advantages and Disadvantages of Different Ways of Measuring the Instructional Sensitivity of Reading Comprehension Test Items.

ERIC Educational Resources Information Center

Perkins, Kyle

In this paper four classes of procedures for measuring the instructional sensitivity of reading comprehension test items are reviewed. True experimental designs are not recommended because some of the most important reading comprehension variables do not lend themselves to experimental manipulation. "Ex post facto" factorial designs are…

Optimizing EFL Learners' Sensitizing Reading Skill: Development of Local Content-Based Textbook

ERIC Educational Resources Information Center

Arifani, Yudhi

2016-01-01

The development of local wisdom based sensitizing reading material is aimed at penetrating one of the imperishable gaps between authentic and non-authentic reading materials dispute in an EFL teaching context. Promoting EFL learners' needs for the first semester students of English department at university level, who rarely or even never have a…

Effect of text type on near work-induced contrast adaptation in myopic and emmetropic young adults.

PubMed

Yeo, Anna C H; Atchison, David A; Schmid, Katrina L

2013-02-27

Contrast adaptation has been speculated to be an error signal for emmetropization. Myopic children exhibit higher contrast adaptation than emmetropic children. This study aimed to determine whether contrast adaptation varies with the type of text viewed by emmetropic and myopic young adults. Baseline contrast sensitivity was determined in 25 emmetropic and 25 spectacle-corrected myopic young adults for 0.5, 1.2, 2.7, 4.4, and 6.2 cycles per degree (cpd) horizontal sine wave gratings. The adults spent periods looking at a 6.2 cpd high-contrast horizontal grating and reading lines of English and Chinese text (these texts comprised 1.2 cpd row and 6 cpd stroke frequencies). The effects of these near tasks on contrast sensitivity were determined, with decreases in sensitivity indicating contrast adaptation. Contrast adaptation was affected by the near task (F2,672 = 43.0; P < 0.001). Adaptation was greater for the grating task (0.13 ± 0.17 log unit, averaged across all frequencies) than reading tasks, but there was no significant difference between the two reading tasks (English 0.05 ± 0.13 log unit versus Chinese 0.04 ± 0.13 log unit). The myopic group showed significantly greater adaptation (by 0.04, 0.04, and 0.05 log units for English, Chinese, and grating tasks, respectively) than the emmetropic group (F1,48 = 5.0; P = 0.03). In young adults, reading Chinese text induced similar contrast adaptation as reading English text. Myopes exhibited greater contrast adaptation than emmetropes. Contrast adaptation, independent of text type, might be associated with myopia development.

Image enhancement filters significantly improve reading performance for low vision observers

NASA Technical Reports Server (NTRS)

Lawton, T. B.

1992-01-01

As people age, so do their photoreceptors; many photoreceptors in central vision stop functioning when a person reaches their late sixties or early seventies. Low vision observers with losses in central vision, those with age-related maculopathies, were studied. Low vision observers no longer see high spatial frequencies, being unable to resolve fine edge detail. We developed image enhancement filters to compensate for the low vision observer's losses in contrast sensitivity to intermediate and high spatial frequencies. The filters work by boosting the amplitude of the less visible intermediate spatial frequencies. The lower spatial frequencies. These image enhancement filters not only reduce the magnification needed for reading by up to 70 percent, but they also increase the observer's reading speed by 2-4 times. A summary of this research is presented.

Centrifuge: rapid and sensitive classification of metagenomic sequences

PubMed Central

Song, Li; Breitwieser, Florian P.

2016-01-01

Centrifuge is a novel microbial classification engine that enables rapid, accurate, and sensitive labeling of reads and quantification of species on desktop computers. The system uses an indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.2 GB for 4078 bacterial and 200 archaeal genomes) and classifies sequences at very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes. Together, these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers. Because of its space-optimized indexing schemes, Centrifuge also makes it possible to index the entire NCBI nonredundant nucleotide sequence database (a total of 109 billion bases) with an index size of 69 GB, in contrast to k-mer-based indexing schemes, which require far more extensive space. PMID:27852649

Nanothermometer Based on Resonant Tunneling Diodes: From Cryogenic to Room Temperatures.

PubMed

Pfenning, Andreas; Hartmann, Fabian; Rebello Sousa Dias, Mariama; Castelano, Leonardo Kleber; Süßmeier, Christoph; Langer, Fabian; Höfling, Sven; Kamp, Martin; Marques, Gilmar Eugenio; Worschech, Lukas; Lopez-Richard, Victor

2015-06-23

Sensor miniaturization together with broadening temperature sensing range are fundamental challenges in nanothermometry. By exploiting a large temperature-dependent screening effect observed in a resonant tunneling diode in sequence with a GaInNAs/GaAs quantum well, we present a low dimensional, wide range, and high sensitive nanothermometer. This sensor shows a large threshold voltage shift of the bistable switching of more than 4.5 V for a temperature raise from 4.5 to 295 K, with a linear voltage-temperature response of 19.2 mV K(-1), and a temperature uncertainty in the millikelvin (mK) range. Also, when we monitor the electroluminescence emission spectrum, an optical read-out control of the thermometer is provided. The combination of electrical and optical read-outs together with the sensor architecture excel the device as a thermometer with the capability of noninvasive temperature sensing, high local resolution, and sensitivity.

Symbol-String Sensitivity and Children's Reading

ERIC Educational Resources Information Center

Pammer, Kristen; Lavis, Ruth; Hansen, Peter; Cornelissen, Piers L.

2004-01-01

In this study of primary school children, a novel "symbol-string" task is used to assess sensitivity to the position of briefly presented non-alphabetic but letter-like symbols. The results demonstrate that sensitivity in the symbol-string task explains a unique proportion of the variability in children's contextual reading accuracy. Moreover,…

A 90GHz Bolometer Camera Detector System for the Green Bank Telescope

NASA Technical Reports Server (NTRS)

Benford, Dominic J.; Allen, Christine A.; Buchanan, Ernest D.; Chen, Tina C.; Chervenak, James A.; Devlin, Mark J.; Dicker, Simon R.; Forgione, Joshua B.

2004-01-01

We describe a close-packed, two-dimensional imaging detector system for operation at 90GHz (3.3mm) for the 100 m Green Bank Telescope (GBT) This system will provide high sensitivity (<1mjy in 1s rapid imaging (15'x15' to 250 microJy in 1 hr) at the world's largest steerable aperture. The heart of this camera is an 8x8 close packed, Nyquist-sampled array of superconducting transition edge sensor bolometers. We have designed and are producing a functional superconducting bolometer array system using a monolithic planar architecture and high-speed multiplexed readout electronics. With an NEP of approx. 2.10(exp 17) W/square root Hz, the TES bolometers will provide fast linear sensitive response for high performance imaging. The detectors are read out by and 8x8 time domain SQUID multiplexer. A digital/analog electronics system has been designed to enable read out by SQUID multiplexers. First light for this instrument on the GBT is expected within a year.

A 90GHz Bolometer Camera Detector System for the Green

NASA Technical Reports Server (NTRS)

Benford, Dominic J.; Allen, Christine A.; Buchanan, Ernest; Chen, Tina C.; Chervenak, James A.; Devlin, Mark J.; Dicker, Simon R.; Forgione, Joshua B.

2004-01-01

We describe a close-packed, two-dimensional imaging detector system for operation at 90GHz (3.3 mm) for the 100m Green Bank Telescope (GBT). This system will provide high sensitivity (less than 1mJy in 1s) rapid imaging (15'x15' to 150 micron Jy in 1 hr) at the world's largest steerable aperture. The heart of this camera is an 8x8 close-packed, Nyquist-sampled array of superconducting transition edge sensor (TES) bolometers. We have designed and are producing a functional superconducting bolometer array system using a monolithic planar architecture and high-speed multiplexed readout electronics. With an NEP of approximately 2 x 10(exp -17) W/square root of Hz, the TES bolometers will provide fast, linear, sensitive response for high performance imaging. The detectors are read out by an 8x8 time domain SQUID multiplexer. A digital/analog electronics system has been designed to enable read out by SQUID multiplexers. First light for this instrument on the GBT is expected within a year.

Radio-frequency Electrometry Using Rydberg Atoms in Vapor Cells: Towards the Shot Noise Limit

NASA Astrophysics Data System (ADS)

Kumar, Santosh; Fan, Haoquan; Jahangiri, Akbar; Kuebler, Harald; Shaffer, James P.; 5. Physikalisches Institut, Universitat Stuttgart, Germany Collaboration

2016-05-01

Rydberg atoms are a promising candidate for radio frequency (RF) electric field sensing. Our method uses electromagnetically induced transparency with Rydberg atoms in vapor cells to read out the effect that the RF electric field has on the Rydberg atoms. The method has the potential for high sensitivity (pV cm-1 Hz- 1 / 2) and can be self-calibrated. Some of the main factors limiting the sensitivity of RF electric field sensing from reaching the shot noise limit are the residual Doppler effect and the sensitivity of the optical read-out using the probe laser. We present progress on overcoming the residual Doppler effect by using a new multi-photon scheme and reaching the shot noise detection limit using frequency modulated spectroscopy. Our experiments also show promise for studying quantum optical effects such as superradiance in vapor cells using Rydberg atoms. This work is supported by DARPA, ARO, and NRO.

Subcortical processing of speech regularities underlies reading and music aptitude in children

PubMed Central

2011-01-01

Background Neural sensitivity to acoustic regularities supports fundamental human behaviors such as hearing in noise and reading. Although the failure to encode acoustic regularities in ongoing speech has been associated with language and literacy deficits, how auditory expertise, such as the expertise that is associated with musical skill, relates to the brainstem processing of speech regularities is unknown. An association between musical skill and neural sensitivity to acoustic regularities would not be surprising given the importance of repetition and regularity in music. Here, we aimed to define relationships between the subcortical processing of speech regularities, music aptitude, and reading abilities in children with and without reading impairment. We hypothesized that, in combination with auditory cognitive abilities, neural sensitivity to regularities in ongoing speech provides a common biological mechanism underlying the development of music and reading abilities. Methods We assessed auditory working memory and attention, music aptitude, reading ability, and neural sensitivity to acoustic regularities in 42 school-aged children with a wide range of reading ability. Neural sensitivity to acoustic regularities was assessed by recording brainstem responses to the same speech sound presented in predictable and variable speech streams. Results Through correlation analyses and structural equation modeling, we reveal that music aptitude and literacy both relate to the extent of subcortical adaptation to regularities in ongoing speech as well as with auditory working memory and attention. Relationships between music and speech processing are specifically driven by performance on a musical rhythm task, underscoring the importance of rhythmic regularity for both language and music. Conclusions These data indicate common brain mechanisms underlying reading and music abilities that relate to how the nervous system responds to regularities in auditory input. Definition of common biological underpinnings for music and reading supports the usefulness of music for promoting child literacy, with the potential to improve reading remediation. PMID:22005291

Frequency Drives Lexical Access in Reading but not in Speaking: The Frequency-Lag Hypothesis

PubMed Central

Gollan, Tamar H.; Slattery, Timothy J.; Goldenberg, Diane; van Assche, Eva; Duyck, Wouter; Rayner, Keith

2010-01-01

To contrast mechanisms of lexical access in production versus comprehension we compared the effects of word-frequency (high, low), context (none, low-constraining, high-constraining), and level of English proficiency (monolinguals, Spanish-English bilinguals, Dutch-English bilinguals), on picture naming, lexical decision, and eye fixation times. Semantic constraint effects were larger in production than in reading. Frequency effects were larger in production than in reading without constraining context, but larger in reading than in production with constraining context. Bilingual disadvantages were modulated by frequency in production but not in eye fixation times, were not smaller in low-constraining context, and were reduced by high-constraining context only in production and only at the lowest level of English proficiency. These results challenge existing accounts of bilingual disadvantages, and reveal fundamentally different processes during lexical access across modalities, entailing a primarily semantically driven search in production, but a frequency driven search in comprehension. The apparently more interactive process in production than comprehension could simply reflect a greater number of frequency-sensitive processing stages in production. PMID:21219080

Comparison of a triaxial fluxgate magnetometer and Toftness sensometer for body surface EMF measurement.

PubMed

Zhang, John; Toftness, Dave; Snyder, Brian; Nosco, Dennis; Balcavage, Walter; Nindl, Gabi

2004-12-01

The use of magnetic fields to treat disease has intrigued mankind since the time of the ancient Greeks. More recently it has been shown that electromagnetic field (EMF) treatment aids bone healing, and repetitive transcranial magnetic stimulation (rTMS) appears to be beneficial in treating schizophrenia and depression. Since external EMFs influence internal body processes, we hypothesized that measurement of body surface EMFs might be used to detect disease states and direct the course of subsequent therapy. However, measurement of minute body surface EMFs requires use of a sensitive and well documented magnetometer. In this study we evaluated the sensitivity and frequency response of a fluxgate magnetometer with a triaxial probe for use in detecting body surface EMF and we compared the magnetometer readings with a signal from a Toftness Sensometer, operated by an experienced clinician, in the laboratory and in a clinical setting. A Peavy Audio Amplifier and variable power output Telulex signal generator were used to develop 50 microT EMFs in a three coil Merritt coil system. A calibrated magnetometer was used to set a 60 Hz 50 microT field in the coil and an ammeter was used to measure the current required to develop the 50 microT field. At frequencies other than 60 Hz, the field strength was maintained at 50 microT by adjusting the Telulex signal output to keep the current constant. The field generated was monitored using a 10 turn coil connected to an oscilloscope. The oscilloscope reading indicated that the field strength was the same at all frequencies tested. To determine if there was a correspondence between the signals detected by a fluxgate magnetometer (FGM1) and the Toftness Sensometer both devices were placed in the Merritt coil and readings were recorded from the FGM1 and compared with the ability of a highly experienced Toftness operator to detect the 50 microT field. Subsequently, in a clinical setting, FGM1 readings made by an FGM1 technician and Sensometer readings were made by 4 Toftness Sensometer operators, having various degrees of experience with this device. Each examiner obtained instrument readings from 5 different volunteers in separate chiropractic adjusting rooms. Additionally, one of the Toftness Sensometers was equipped with an integrated fluxgate magnetometer (FGM2) and this magnetometer was used to obtain a second set of EMF readings in the clinical setting. The triaxial fluxgate magnetometer was determined to be moderately responsive to changes in magnetic field frequency below 10 Hz. At frequencies above 10 Hz the readings corresponded to that of the ambient static geofield. The practitioner operating the Toftness Sensometer was unable to detect magnetic fields at high frequencies (above 10 Hz) even at very high EMFs. The fluxgate magnetometer was shown to be essentially a DC/static magnetic field detector and like all such devices it has a limited frequency range with some low level of sensitivity at very low field frequencies. The interexaminer reliability of four Toftness practitioners using the Sensometer on 5 patients showed low to moderate correlation. The fluxgate magnetometer although highly sensitive to static (DC) EMFs has only limited sensitivity to EMFs in the range of 1 to 10 Hz and is very insensitive to frequencies above 10 Hz. In laboratory comparisons of the Sensometer and the fluxgate magnetometer there was an occasional correspondence between the two instruments in detecting magnetic fields within the Merritt coil but these occasions were not reproducible. In the clinical studies there was low to moderate agreement between the clinicians using the Sensometer to diagnosing spinal conditions and there was little if any agreement between the Sensometer and the fluxgate magnetometer in detecting EMFs emanating from the volunteers body surface.

Comparison of a triaxial fluxgate magnetometer and Toftness sensometer for body surface EMF measurement

PubMed Central

Zhang, John; Toftness, Dave; Snyder, Brian; Nosco, Dennis; Balcavage, Walter; Nindl, Gabi

2004-01-01

Introduction The use of magnetic fields to treat disease has intrigued mankind since the time of the ancient Greeks. More recently it has been shown that electromagnetic field (EMF) treatment aids bone healing, and repetitive transcranial magnetic stimulation (rTMS) appears to be beneficial in treating schizophrenia and depression. Since external EMFs influence internal body processes, we hypothesized that measurement of body surface EMFs might be used to detect disease states and direct the course of subsequent therapy. However, measurement of minute body surface EMFs requires use of a sensitive and well documented magnetometer. In this study we evaluated the sensitivity and frequency response of a fluxgate magnetometer with a triaxial probe for use in detecting body surface EMF and we compared the magnetometer readings with a signal from a Toftness Sensometer, operated by an experienced clinician, in the laboratory and in a clinical setting. Methods A Peavy Audio Amplifier and variable power output Telulex signal generator were used to develop 50 μT EMFs in a three coil Merritt coil system. A calibrated magnetometer was used to set a 60 Hz 50 μT field in the coil and an ammeter was used to measure the current required to develop the 50 μT field. At frequencies other than 60 Hz, the field strength was maintained at 50 μT by adjusting the Telulex signal output to keep the current constant. The field generated was monitored using a 10 turn coil connected to an oscilloscope. The oscilloscope reading indicated that the field strength was the same at all frequencies tested. To determine if there was a correspondence between the signals detected by a fluxgate magnetometer (FGM1) and the Toftness Sensometer both devices were placed in the Merritt coil and readings were recorded from the FGM1 and compared with the ability of a highly experienced Toftness operator to detect the 50 μT field. Subsequently, in a clinical setting, FGM1 readings made by an FGM1 technician and Sensometer readings were made by 4 Toftness Sensometer operators, having various degrees of experience with this device. Each examiner obtained instrument readings from 5 different volunteers in separate chiropractic adjusting rooms. Additionally, one of the Toftness Sensometers was equipped with an integrated fluxgate magnetometer (FGM2) and this magnetometer was used to obtain a second set of EMF readings in the clinical setting. Results The triaxial fluxgate magnetometer was determined to be moderately responsive to changes in magnetic field frequency below 10 Hz. At frequencies above 10 Hz the readings corresponded to that of the ambient static geofield. The practitioner operating the Toftness Sensometer was unable to detect magnetic fields at high frequencies (above 10 Hz) even at very high EMFs. The fluxgate magnetometer was shown to be essentially a DC/static magnetic field detector and like all such devices it has a limited frequency range with some low level of sensitivity at very low field frequencies. The interexaminer reliability of four Toftness practitioners using the Sensometer on 5 patients showed low to moderate correlation. Conclusions The fluxgate magnetometer although highly sensitive to static (DC) EMFs has only limited sensitivity to EMFs in the range of 1 to 10 Hz and is very insensitive to frequencies above 10 Hz. In laboratory comparisons of the Sensometer and the fluxgate magnetometer there was an occasional correspondence between the two instruments in detecting magnetic fields within the Merritt coil but these occasions were not reproducible. In the clinical studies there was low to moderate agreement between the clinicians using the Sensometer to diagnosing spinal conditions and there was little if any agreement between the Sensometer and the fluxgate magnetometer in detecting EMFs emanating from the volunteers body surface. PMID:17549105

The HEXITEC Hard X-Ray Pixelated CdTe Imager for Fast Solar Observations

NASA Technical Reports Server (NTRS)

Baumgartner, Wayne H.; Christe, Steven D.; Ryan, Daniel; Inglis, Andrew R.; Shih, Albert Y.; Gregory, Kyle; Wilson, Matt; Seller, Paul; Gaskin, Jessica; Wilson-Hodge, Colleen

2016-01-01

There is an increasing demand in solar and astrophysics for high resolution X-ray spectroscopic imaging. Such observations would present ground breaking opportunities to study the poorly understood high energy processes in our solar system and beyond, such as solar flares, X-ray binaries, and active galactic nuclei. However, such observations require a new breed of solid state detectors sensitive to high energy X-rays with fine independent pixels to sub-sample the point spread function (PSF) of the X-ray optics. For solar observations in particular, they must also be capable of handling very high count rates as photon fluxes from solar flares often cause pile up and saturation in present generation detectors. The Rutherford Appleton Laboratory (RAL) has recently developed a new cadmium telluride (CdTe) detector system, called HEXITEC (High Energy X-ray Imaging Technology). It is an 80 x 80 array of 250 micron independent pixels sensitive in the 2-200 keV band and capable of a high full frame read out rate of 10 kHz. HEXITEC provides the smallest independently read out CdTe pixels currently available, and are well matched to the few arcsecond PSF produced by current and next generation hard X-ray focusing optics. NASA's Goddard and Marshall Space Flight Centers are collaborating with RAL to develop these detectors for use on future space borne hard X-ray focusing telescopes. We show the latest results on HEXITEC's imaging capability, energy resolution, high read out rate, and reveal it to be ideal for such future instruments.

Measuring the Instructional Sensitivity of ESL Reading Comprehension Items.

ERIC Educational Resources Information Center

Brutten, Sheila R.; And Others

A study attempted to estimate the instructional sensitivity of items in three reading comprehension tests in English as a second language (ESL). Instructional sensitivity is a test-item construct defined as the tendency for a test item to vary in difficulty as a function of instruction. Similar tasks were given to readers at different proficiency…

Implementation of LED fluorescence microscopy for diagnosis of pulmonary and HIV-associated tuberculosis in a hospital setting in Indonesia.

PubMed

Chaidir, Lidya; Parwati, Ida; Annisa, Jessi; Muhsinin, Soni; Meilana, Intan; Alisjahbana, Bachti; van Crevel, Reinout

2013-01-01

Fluorescence microscopy (FM) has not been implemented widely in TB endemic settings and little evaluation has been done in HIV-infected patients. We evaluated diagnostic performance, time and costs of FM with light-emitting diodes technology (LED-FM), compared with conventional (Zieh-Neelsen) microscopy in a hospital in Indonesia which acts as referral centre for HIV-infected patients. We included pulmonary tuberculosis suspects from the outpatient and HIV clinic. Direct and concentrated sputum smears were examined using LED-FM and ZN microscopy by two technicians who were blinded for the HIV-status and the result of the comparative test. Mean reading time per slide was recorded and cost of each slide was calculated. Mycobacteria culture served as the reference standard. Among 404 tuberculosis suspects from the outpatient clinic and 256 from the HIV clinic, mycobacteria culture was positive in 12.6% and 27%, respectively. The optimal sensitivity of LED-FM was achieved by using a threshold of ≥2 AFB/length. LED-FM had a higher sensitivity (75.5% vs. 54.9%, P<0.01) but lower specificity (90.0% vs 96.6%, P<0.01) compared to ZN microscopy. HIV was associated with a lower sensitivity but similar specificity. The average reading time using LED-FM was significantly shorter (2.23±0.78 vs 5.82±1.60 minutes, P<0.01), while costs per slide were similar. High sensitivity of LED-FM combined with shorter reading time of sputum smear slides make this method a potential alternative to ZN microscopy. Additional data on specificity are needed for effective implementation of this technique in high burden TB laboratories.

Classroom-Based Phonological Sensitivity Intervention (PSI) Using a Narrative Platform: An Experimental Study of First Graders at Risk for a Reading Disability

ERIC Educational Resources Information Center

Ritter, Michaela J.; Saxon, Terrill F.

2011-01-01

The purpose of this study was to assess the effectiveness of classroom-based phonological sensitivity intervention (PSI) using a narrative platform for children in first grade who are at risk for a reading disability. Participants consisted of 59 first graders identified as at risk for later reading impairments. At-risk designation was dictated by…

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

PubMed Central

Calhoon, Mary Beth; Petscher, Yaacov

2015-01-01

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

Sensitive resettable odometer aids roadside census of red-winged blackbirds

USGS Publications Warehouse

Harke, D.T.; Stickley, A.R.

1968-01-01

A sensitive resettable odometer reading to 0.01 mile facilitated censusing breeding male redwinged blackbirds (Agelaius phoeniceus) from a vehicle. Territorial males along roadsides were 'marked' with recorded mileage readings rather than with landmarks of the types employed by Hewitt for censuses based on the Lincoln index principle. Sensitive odometers that can be reset have many potential uses in wildlife investigations.

Visual Perception and Reading: New Clues to Patterns of Dysfunction Across Multiple Visual Channels in Developmental Dyslexia.

PubMed

Pina Rodrigues, Ana; Rebola, José; Jorge, Helena; Ribeiro, Maria José; Pereira, Marcelino; van Asselen, Marieke; Castelo-Branco, Miguel

2017-01-01

The specificity of visual channel impairment in dyslexia has been the subject of much controversy. The purpose of this study was to determine if a differential pattern of impairment can be verified between visual channels in children with developmental dyslexia, and in particular, if the pattern of deficits is more conspicuous in tasks where the magnocellular-dorsal system recruitment prevails. Additionally, we also aimed at investigating the association between visual perception thresholds and reading. In the present case-control study, we compared perception thresholds of 33 children diagnosed with developmental dyslexia and 34 controls in a speed discrimination task, an achromatic contrast sensitivity task, and a chromatic contrast sensitivity task. Moreover, we addressed the correlation between the different perception thresholds and reading performance, as assessed by means of a standardized reading test (accuracy and fluency). Group comparisons were performed by the Mann-Whitney U test, and Spearman's rho was used as a measure of correlation. Results showed that, when compared to controls, children with dyslexia were more impaired in the speed discrimination task, followed by the achromatic contrast sensitivity task, with no impairment in the chromatic contrast sensitivity task. These results are also consistent with the magnocellular theory since the impairment profile of children with dyslexia in the visual threshold tasks reflected the amount of magnocellular-dorsal stream involvement. Moreover, both speed and achromatic thresholds were significantly correlated with reading performance, in terms of accuracy and fluency. Notably, chromatic contrast sensitivity thresholds did not correlate with any of the reading measures. Our evidence stands in favor of a differential visual channel deficit in children with developmental dyslexia and contributes to the debate on the pathophysiology of reading impairments.

BBMerge – Accurate paired shotgun read merging via overlap

DOE PAGES

Bushnell, Brian; Rood, Jonathan; Singer, Esther

2017-10-26

Merging paired-end shotgun reads generated on high-throughput sequencing platforms can substantially improve various subsequent bioinformatics processes, including genome assembly, binning, mapping, annotation, and clustering for taxonomic analysis. With the inexorable growth of sequence data volume and CPU core counts, the speed and scalability of read-processing tools becomes ever-more important. The accuracy of shotgun read merging is crucial as well, as errors introduced by incorrect merging percolate through to reduce the quality of downstream analysis. Thus, we designed a new tool to maximize accuracy and minimize processing time, allowing the use of read merging on larger datasets, and in analyses highlymore » sensitive to errors. We present BBMerge, a new merging tool for paired-end shotgun sequence data. We benchmark BBMerge by comparison with eight other widely used merging tools, assessing speed, accuracy and scalability. Evaluations of both synthetic and real-world datasets demonstrate that BBMerge produces merged shotgun reads with greater accuracy and at higher speed than any existing merging tool examined. BBMerge also provides the ability to merge non-overlapping shotgun read pairs by using k-mer frequency information to assemble the unsequenced gap between reads, achieving a significantly higher merge rate while maintaining or increasing accuracy.« less

BBMerge – Accurate paired shotgun read merging via overlap

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

Bushnell, Brian; Rood, Jonathan; Singer, Esther

Merging paired-end shotgun reads generated on high-throughput sequencing platforms can substantially improve various subsequent bioinformatics processes, including genome assembly, binning, mapping, annotation, and clustering for taxonomic analysis. With the inexorable growth of sequence data volume and CPU core counts, the speed and scalability of read-processing tools becomes ever-more important. The accuracy of shotgun read merging is crucial as well, as errors introduced by incorrect merging percolate through to reduce the quality of downstream analysis. Thus, we designed a new tool to maximize accuracy and minimize processing time, allowing the use of read merging on larger datasets, and in analyses highlymore » sensitive to errors. We present BBMerge, a new merging tool for paired-end shotgun sequence data. We benchmark BBMerge by comparison with eight other widely used merging tools, assessing speed, accuracy and scalability. Evaluations of both synthetic and real-world datasets demonstrate that BBMerge produces merged shotgun reads with greater accuracy and at higher speed than any existing merging tool examined. BBMerge also provides the ability to merge non-overlapping shotgun read pairs by using k-mer frequency information to assemble the unsequenced gap between reads, achieving a significantly higher merge rate while maintaining or increasing accuracy.« less

Early development of letter specialization in left fusiform is associated with better word reading and smaller fusiform face area.

PubMed

Centanni, Tracy M; Norton, Elizabeth S; Park, Anne; Beach, Sara D; Halverson, Kelly; Ozernov-Palchik, Ola; Gaab, Nadine; Gabrieli, John DE

2018-03-05

A functional region of left fusiform gyrus termed "the visual word form area" (VWFA) develops during reading acquisition to respond more strongly to printed words than to other visual stimuli. Here, we examined responses to letters among 5- and 6-year-old early kindergarten children (N = 48) with little or no school-based reading instruction who varied in their reading ability. We used functional magnetic resonance imaging (fMRI) to measure responses to individual letters, false fonts, and faces in left and right fusiform gyri. We then evaluated whether signal change and size (spatial extent) of letter-sensitive cortex (greater activation for letters versus faces) and letter-specific cortex (greater activation for letters versus false fonts) in these regions related to (a) standardized measures of word-reading ability and (b) signal change and size of face-sensitive cortex (fusiform face area or FFA; greater activation for faces versus letters). Greater letter specificity, but not letter sensitivity, in left fusiform gyrus correlated positively with word reading scores. Across children, in the left fusiform gyrus, greater size of letter-sensitive cortex correlated with lesser size of FFA. These findings are the first to suggest that in beginning readers, development of letter responsivity in left fusiform cortex is associated with both better reading ability and also a reduction of the size of left FFA that may result in right-hemisphere dominance for face perception. © 2018 John Wiley & Sons Ltd.

Multivariate Models for Prediction of Human Skin Sensitization ...

EPA Pesticide Factsheets

One of the lnteragency Coordinating Committee on the Validation of Alternative Method's (ICCVAM) top priorities is the development and evaluation of non-animal approaches to identify potential skin sensitizers. The complexity of biological events necessary to produce skin sensitization suggests that no single alternative method will replace the currently accepted animal tests. ICCVAM is evaluating an integrated approach to testing and assessment based on the adverse outcome pathway for skin sensitization that uses machine learning approaches to predict human skin sensitization hazard. We combined data from three in chemico or in vitro assays - the direct peptide reactivity assay (DPRA), human cell line activation test (h-CLAT) and KeratinoSens TM assay - six physicochemical properties and an in silico read-across prediction of skin sensitization hazard into 12 variable groups. The variable groups were evaluated using two machine learning approaches , logistic regression and support vector machine, to predict human skin sensitization hazard. Models were trained on 72 substances and tested on an external set of 24 substances. The six models (three logistic regression and three support vector machine) with the highest accuracy (92%) used: (1) DPRA, h-CLAT and read-across; (2) DPRA, h-CLAT, read-across and KeratinoSens; or (3) DPRA, h-CLAT, read-across, KeratinoSens and log P. The models performed better at predicting human skin sensitization hazard than the murine

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.

Centrifuge: rapid and sensitive classification of metagenomic sequences.

PubMed

Kim, Daehwan; Song, Li; Breitwieser, Florian P; Salzberg, Steven L

2016-12-01

Centrifuge is a novel microbial classification engine that enables rapid, accurate, and sensitive labeling of reads and quantification of species on desktop computers. The system uses an indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.2 GB for 4078 bacterial and 200 archaeal genomes) and classifies sequences at very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes. Together, these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers. Because of its space-optimized indexing schemes, Centrifuge also makes it possible to index the entire NCBI nonredundant nucleotide sequence database (a total of 109 billion bases) with an index size of 69 GB, in contrast to k-mer-based indexing schemes, which require far more extensive space. © 2016 Kim et al.; Published by Cold Spring Harbor Laboratory Press.

Physical measurement with in-line fiber Mach-Zehnder interferometer using differential phase white light interferometry

NASA Astrophysics Data System (ADS)

Aref, Seyed Hashem

2017-11-01

In this letter, the sensitivity to strain, curvature, and temperature of a sensor based on in-line fiber Mach-Zahnder interferometer (IFMZI) is studied and experimentally demonstrated. The sensing structure is simply a section of single mode fiber sandwiched between two abrupt tapers to achieve a compact IFMZI. The phase of interferometer changes with the measurand interaction, which is the basis for considering this structure for sensing. The physical parameter sensitivity of IFMZI sensor has been evaluated using differential white light interferometry (DWLI) technique as a phase read-out system. The differential configuration of the IFMZI sensor is used to achieve a high phase resolving power of ±0.062° for read-out interferometer by means of omission of phase noise of environment perturbations. The sensitivity of the sensor to the strain, curvature, and temperature has been measured 0.0199 degree/με, 757.00 degree/m-1, and 3.25 degree/°C, respectively.

Examining the Independent Contribution of Prosodic Sensitivity to Word Reading and Spelling in Early Readers

ERIC Educational Resources Information Center

Holliman, A. J.; Gutiérrez Palma, N.; Critten, S.; Wood, C.; Cunnane, H.; Pillinger, C.

2017-01-01

This study was designed to examine the independent contribution of prosodic sensitivity--the rhythmic patterning of speech-to word reading and spelling in a sample of early readers. Ninety-three English-speaking children aged 5-6 years old (M = 69.28 months, SD = 3.67) were assessed for their prosodic sensitivity, vocabulary knowledge,…

Analysis and Design of a Long Range PTFE Substrate UHF RFID Tag for Cargo Container Identification

NASA Astrophysics Data System (ADS)

Petrariu, Adrian-Ioan; Popa, Valentin

2016-01-01

In this paper, a high-performances microstrip antenna for UHF (ultra high frequency) RFID (radio frequency identification) tag is designed, prototyped and tested. The antenna consists of two main components: a 1.52 mm RT/duroid 5880 laminate substrate on which the antenna is designed and a 10 mm polytetrafluoroethylene (PTFE) dielectric material placed as a separator between the antenna and the reference ground plane for the microstrip antenna. With this structure, the RFID tag can reach a maximum reading distance of 19 m, although the antenna has a compact size of 80 mm × 50 mm. The long reading distance is obtained by attaching to the antenna an RFID chip that can provide a reading sensitivity of -20.5 dBm. The high bandwidth from 677 MHz to 947 MHz measured at -10 dB, makes the tag being usable worldwide especially for cargo container identification, the main purpose of this research.

Radiation imaging with optically read out GEM-based detectors

NASA Astrophysics Data System (ADS)

Brunbauer, F. M.; Lupberger, M.; Oliveri, E.; Resnati, F.; Ropelewski, L.; Streli, C.; Thuiner, P.; van Stenis, M.

2018-02-01

Modern imaging sensors allow for high granularity optical readout of radiation detectors such as MicroPattern Gaseous Detectors (MPGDs). Taking advantage of the high signal amplification factors achievable by MPGD technologies such as Gaseous Electron Multipliers (GEMs), highly sensitive detectors can be realised and employing gas mixtures with strong scintillation yield in the visible wavelength regime, optical readout of such detectors can provide high-resolution event representations. Applications from X-ray imaging to fluoroscopy and tomography profit from the good spatial resolution of optical readout and the possibility to obtain images without the need for extensive reconstruction. Sensitivity to low-energy X-rays and energy resolution permit energy resolved imaging and material distinction in X-ray fluorescence measurements. Additionally, the low material budget of gaseous detectors and the possibility to couple scintillation light to imaging sensors via fibres or mirrors makes optically read out GEMs an ideal candidate for beam monitoring detectors in high energy physics as well as radiotherapy. We present applications and achievements of optically read out GEM-based detectors including high spatial resolution imaging and X-ray fluorescence measurements as an alternative readout approach for MPGDs. A detector concept for low intensity applications such as X-ray crystallography, which maximises detection efficiency with a thick conversion region but mitigates parallax-induced broadening is presented and beam monitoring capabilities of optical readout are explored. Augmenting high resolution 2D projections of particle tracks obtained with optical readout with timing information from fast photon detectors or transparent anodes for charge readout, 3D reconstruction of particle trajectories can be performed and permits the realisation of optically read out time projection chambers. Combining readily available high performance imaging sensors with compatible scintillating gases and the strong signal amplification factors achieved by MPGDs makes optical readout an attractive alternative to the common concept of electronic readout of radiation detectors. Outstanding signal-to-noise ratios and robustness against electronic noise allow unprecedented imaging capabilities for various applications in fields ranging from high energy physics to medical instrumentation.

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

PubMed Central

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

2013-01-01

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

The Role of Prosodic Sensitivity in Children's Reading Development

ERIC Educational Resources Information Center

Whalley, Karen; Hansen, Julie

2006-01-01

While the critical importance of phonological awareness (segmental phonology) to reading ability is well established, the potential role of prosody (suprasegmental phonology) in reading development has only recently been explored. This study examined the relationship between children's prosodic skills and reading ability. Hierarchical multiple…

Does the Irlen[R] Method Bring about an Increase in Reading Scores on a Specific Test of Reading for Students Found to Have Scotopic Sensitivity Syndrome?

ERIC Educational Resources Information Center

Faraci, Marie Elaine

2009-01-01

The problem. The purpose of this study was to examine the effect of the Irlen[R] method's use of colored overlays on the reading achievement of 3rd-grade students who were identified as having Scotopic Sensitivity Syndrome/Irlen[R] Syndrome. Method. This was a true experimental, pre-test, post-test design. The Irlen[R] overlay, either present…

How Reliable Are ATP Bioluminescence Meters in Assessing Decontamination of Environmental Surfaces in Healthcare Settings?

PubMed Central

Omidbakhsh, Navid; Ahmadpour, Faraz; Kenny, Nicole

2014-01-01

Background Meters based on adenosine triphosphate (ATP) bioluminescence measurements in relative light units (RLU) are often used to rapidly assess the level of cleanliness of environmental surfaces in healthcare and other settings. Can such ATP measurements be adversely affected by factors such as soil and cleaner-disinfectant chemistry? Objective This study tested a number of leading ATP meters for their sensitivity, linearity of the measurements, correlation of the readings to the actual microbial contamination, and the potential disinfectant chemicals’ interference in their readings. Methods First, solutions of pure ATP in various concentrations were used to construct a standard curve and determine linearity and sensitivity. Serial dilutions of a broth culture of Staphylococcus aureus, as a representative nosocomial pathogen, were then used to determine if a given meter’s ATP readings correlated with the actual CFUs. Next, various types of disinfectant chemistries were tested for their potential to interfere with the standard ATP readings. Results All four ATP meters tested herein demonstrated acceptable linearity and repeatability in their readings. However, there were significant differences in their sensitivity to detect the levels of viable microorganisms on experimentally contaminated surfaces. Further, most disinfectant chemistries tested here quenched the ATP readings variably in different ATP meters evaluated. Conclusions Apart from their limited sensitivity in detecting low levels of microbial contamination, the ATP meters tested were also prone to interference by different disinfectant chemistries. PMID:24940751

The utility of kindergarten teacher ratings for predicting low academic achievement in first grade.

PubMed

Teisl, J T; Mazzocco, M M; Myers, G F

2001-01-01

The purpose of this study was to assess the predictive value of kindergarten teachers' ratings of pupils for later first-grade academic achievement. Kindergarten students were rated by their teachers on a variety of variables, including math and reading performance, teacher concerns, and amount of learning relative to peers. These variables were then analyzed with respect to outcome measures for math and reading ability administered in the first grade. The teachers' ratings of academic performance were significantly correlated with scores on the outcome measures. Analyses were also carried out to determine sensitivity, specificity, and predictive values of the different teacher ratings. The results indicated high overall accuracy, sensitivity, specificity, and negative predictive value for the ratings. Positive predictive value tended to be lower. A recommendation to follow from these results is that teacher ratings of this sort be used to determine which children should receive cognitive screening measures to further enhance identification of children at risk for learning disability. However, this recommendation is limited by the lack of empirically supported screening measures for math disability versus well-supported screening tools for reading disability.

COPS: A Sensitive and Accurate Tool for Detecting Somatic Copy Number Alterations Using Short-Read Sequence Data from Paired Samples

PubMed Central

Krishnan, Neeraja M.; Gaur, Prakhar; Chaudhary, Rakshit; Rao, Arjun A.; Panda, Binay

2012-01-01

Copy Number Alterations (CNAs) such as deletions and duplications; compose a larger percentage of genetic variations than single nucleotide polymorphisms or other structural variations in cancer genomes that undergo major chromosomal re-arrangements. It is, therefore, imperative to identify cancer-specific somatic copy number alterations (SCNAs), with respect to matched normal tissue, in order to understand their association with the disease. We have devised an accurate, sensitive, and easy-to-use tool, COPS, COpy number using Paired Samples, for detecting SCNAs. We rigorously tested the performance of COPS using short sequence simulated reads at various sizes and coverage of SCNAs, read depths, read lengths and also with real tumor:normal paired samples. We found COPS to perform better in comparison to other known SCNA detection tools for all evaluated parameters, namely, sensitivity (detection of true positives), specificity (detection of false positives) and size accuracy. COPS performed well for sequencing reads of all lengths when used with most upstream read alignment tools. Additionally, by incorporating a downstream boundary segmentation detection tool, the accuracy of SCNA boundaries was further improved. Here, we report an accurate, sensitive and easy to use tool in detecting cancer-specific SCNAs using short-read sequence data. In addition to cancer, COPS can be used for any disease as long as sequence reads from both disease and normal samples from the same individual are available. An added boundary segmentation detection module makes COPS detected SCNA boundaries more specific for the samples studied. COPS is available at ftp://115.119.160.213 with username “cops” and password “cops”. PMID:23110103

Giant magnetoresistive sensor

DOEpatents

Stearns, Daniel G.; Vernon, Stephen P.; Ceglio, Natale M.; Hawryluk, Andrew M.

1999-01-01

A magnetoresistive sensor element with a three-dimensional micro-architecture is capable of significantly improved sensitivity and highly localized measurement of magnetic fields. The sensor is formed of a multilayer film of alternately magnetic and nonmagnetic materials. The sensor is optimally operated in a current perpendicular to plane mode. The sensor is useful in magnetic read/write heads, for high density magnetic information storage and retrieval.

MAVARIC - a comparison of automation-assisted and manual cervical screening: a randomised controlled trial.

PubMed

Kitchener, H C; Blanks, R; Cubie, H; Desai, M; Dunn, G; Legood, R; Gray, A; Sadique, Z; Moss, S

2011-01-01

The principal objective was to compare automation-assisted reading of cervical cytology with manual reading using the histological end point of cervical intraepithelial neoplasia grade II (CIN2) or worse (CIN2+). Secondary objectives included (i) an assessment of the slide ranking facility of the Becton Dickinson (BD) FocalPoint™ Slide Profiler (Becton Dickinson, Franklin Lakes, NJ, USA), especially 'No Further Review', (ii) a comparison of the two approved automated systems, the ThinPrep® Imaging System (Hologic, Bedford, MA, USA) and the BD FocalPoint Guided Screener Imaging System, and (iii) automated versus manual in terms of productivity and cost-effectiveness. A 1 : 2 randomised allocation of slides to either manual reading or automation-assisted paired with manual reading. Cytoscreeners were blinded to whether samples would be read only manually or manually paired with automated. Slide reading procedures followed real-life laboratory protocol to produce a final result and, for paired readings, the worse result determined the management. Costs per event were estimated and combined with productivity to produce a cost per slide, per woman and per CIN2+ and cervical intraepithelial neoplasia grade III (CIN3) or worse (CIN3+) lesion detected. Cost-effectiveness was estimated using cost per CIN2+ detected. Lifetime cost-effectiveness in terms of life-years and quality-adjusted life-years was estimated using a mathematical model. Liquid-based cytology samples were obtained in primary care, and a small number of abnormal samples were obtained from local colposcopy clinics, from different women, in order to enrich the proportion of abnormals. All of the samples were read in a single large service laboratory. Liquid residues used for human papillomavirus (HPV) triage were tested (with Hybrid Capture 2, Qiagen, Crawley, UK) in a specialist virology laboratory in Edinburgh, UK. Histopathology was read by a specialist gynaecological pathology team blinded to HPV results and type of reading. Samples were obtained from women aged 25-64 years undergoing primary cervical screening in Greater Manchester, UK, with small proportions from women outside this age range and from women undergoing colposcopy. The principal intervention was automation-assisted reading of cervical cytology slides which was paired with a manual reading of the same slide. Low-grade cytological abnormalities (borderline and mild dyskaryosis) were triaged with HPV testing to direct colposcopy referral. Women with high-grade cytology were referred for colposcopy and those with negative cytology were returned to recall. The principal outcome measure was the sensitivity of automation-assisted reading relative to manual for the detection of CIN2+. A secondary outcome measure was cost-effectiveness of each type of reading to detect CIN2+. The study was powered to detect a relative sensitivity difference equivalent to an absolute difference of 5%. The principal finding was that automated reading was 8% less sensitive relative to manual, 6.3% in absolute terms. 'No further review' was very reliable and, if restricted to routine screening samples, < 1% of CIN2+ would have been missed. Automated and manual were very similar in terms of cost-effectiveness despite a 60%-80% increase in productivity for automation-assisted reading. The significantly reduced sensitivity of automated reading, combined with uncertainty over cost-effectiveness, suggests no justification at present to recommend its introduction. The reliability of 'no further review' warrants further consideration as a means of saving staff time. Current Controlled Trials ISRCTN66377374. This project was funded by the NIHR Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 15, No. 3. See the HTA programme website for further project information.

Effects of Retinal Morphology on Contrast Sensitivity and Reading Ability in Neovascular Age-Related Macular Degeneration

PubMed Central

Keane, Pearse A.; Patel, Praveen J.; Ouyang, Yanling; Chen, Fred K.; Ikeji, Felicia; Walsh, Alexander C.; Tufail, Adnan

2010-01-01

Purpose. To investigate the effect of changes in retinal morphology on contrast sensitivity and reading ability in patients with neovascular age-related macular degeneration (AMD) in the Avastin (bevacizumab; Genentech, South San Francisco, CA) for choroidal neovascularization (ABC) Trial. Methods. Contrast sensitivity obtained with Pelli-Robson charts, reading ability assessed with Minnesota Reading charts, and Early Treatment Diabetic Retinopathy Study (ETDRS) visual acuity (VA) obtained by protocol refraction, were recorded. Raw Stratus optical coherence tomography (OCT; Carl Zeiss Meditec, Inc., Dublin, CA) images were analyzed with the publicly available software OCTOR, which allows precise delineation of any retinal compartment of interest. Thickness and volume were calculated for neurosensory retina, subretinal fluid (SRF), subretinal tissue, and pigment epithelium detachment, and the resulting measurements were correlated with each visual function parameter. Results. One hundred twenty-two patients with newly diagnosed neovascular AMD and enrolled in the ABC Trial, were evaluated. Increased subretinal tissue volume correlated with decreased contrast sensitivity (Pearson's correlation coefficient, r = −0.4944, P = 0.001). A modest correlation was detected between SRF volume and contrast sensitivity (r = −0.2562, P = 0.004). Increased retinal thickness at the foveal center also correlated with decreased visual function (ETDRS VA: r = −0.4530, P < 0.001). Conclusions. The strongest correlation detected between the functional parameters assessed and any of the OCT-derived morphologic parameters was that between decreased contrast sensitivity and increased subretinal tissue. In the future, assessment of contrast sensitivity and reading ability, in combination with quantitative subanalysis of retinal compartments, may lead to the identification of parameters relevant to functional improvement and ultimate prognosis in patients with newly diagnosed neovascular AMD (www.controlled-trials.com number, ISRCTN83325075). PMID:20554607

Identifying At-Risk Students for Early Reading Intervention: Challenges and Possible Solutions

ERIC Educational Resources Information Center

McAlenney, Athena Lentini; Coyne, Michael D.

2011-01-01

Accurate identification of at-risk kindergarten and 1st-grade students through early reading screening is an essential element of responsiveness to intervention models of reading instruction. The authors consider predictive validity and classification accuracy of early reading screening assessments with attention to sensitivity and specificity.…

Differential cognitive and perceptual correlates of print reading versus braille reading.

PubMed

Veispak, Anneli; Boets, Bart; Ghesquière, Pol

2013-01-01

The relations between reading, auditory, speech, phonological and tactile spatial processing are investigated in a Dutch speaking sample of blind braille readers as compared to sighted print readers. Performance is assessed in blind and sighted children and adults. Regarding phonological ability, braille readers perform equally well compared to print readers on phonological awareness, better on verbal short-term memory and significantly worse on lexical retrieval. The groups do not differ on speech perception or auditory processing. Braille readers, however, have more sensitive fingers than print readers. Investigation of the relations between these cognitive and perceptual skills and reading performance indicates that in the group of braille readers auditory temporal processing has a longer lasting and stronger impact not only on phonological abilities, which have to satisfy the high processing demands of the strictly serial language input, but also directly on the reading ability itself. Print readers switch between grapho-phonological and lexical reading modes depending on the familiarity of the items. Furthermore, the auditory temporal processing and speech perception, which were substantially interrelated with phonological processing, had no direct associations with print reading measures. Copyright © 2012 Elsevier Ltd. All rights reserved.

Multivariate Models for Prediction of Human Skin Sensitization Hazard

PubMed Central

Strickland, Judy; Zang, Qingda; Paris, Michael; Lehmann, David M.; Allen, David; Choksi, Neepa; Matheson, Joanna; Jacobs, Abigail; Casey, Warren; Kleinstreuer, Nicole

2016-01-01

One of ICCVAM’s top priorities is the development and evaluation of non-animal approaches to identify potential skin sensitizers. The complexity of biological events necessary to produce skin sensitization suggests that no single alternative method will replace the currently accepted animal tests. ICCVAM is evaluating an integrated approach to testing and assessment based on the adverse outcome pathway for skin sensitization that uses machine learning approaches to predict human skin sensitization hazard. We combined data from three in chemico or in vitro assays—the direct peptide reactivity assay (DPRA), human cell line activation test (h-CLAT), and KeratinoSens™ assay—six physicochemical properties, and an in silico read-across prediction of skin sensitization hazard into 12 variable groups. The variable groups were evaluated using two machine learning approaches, logistic regression (LR) and support vector machine (SVM), to predict human skin sensitization hazard. Models were trained on 72 substances and tested on an external set of 24 substances. The six models (three LR and three SVM) with the highest accuracy (92%) used: (1) DPRA, h-CLAT, and read-across; (2) DPRA, h-CLAT, read-across, and KeratinoSens; or (3) DPRA, h-CLAT, read-across, KeratinoSens, and log P. The models performed better at predicting human skin sensitization hazard than the murine local lymph node assay (accuracy = 88%), any of the alternative methods alone (accuracy = 63–79%), or test batteries combining data from the individual methods (accuracy = 75%). These results suggest that computational methods are promising tools to effectively identify potential human skin sensitizers without animal testing. PMID:27480324

Prostate Cancer Information Available in Health-Care Provider Offices: An Analysis of Content, Readability, and Cultural Sensitivity.

PubMed

Choi, Seul Ki; Seel, Jessica S; Yelton, Brooks; Steck, Susan E; McCormick, Douglas P; Payne, Johnny; Minter, Anthony; Deutchki, Elizabeth K; Hébert, James R; Friedman, Daniela B

2018-07-01

Prostate cancer (PrCA) is the most common cancer affecting men in the United States, and African American men have the highest incidence among men in the United States. Little is known about the PrCA-related educational materials being provided to patients in health-care settings. Content, readability, and cultural sensitivity of materials available in providers' practices in South Carolina were examined. A total of 44 educational materials about PrCA and associated sexual dysfunction was collected from 16 general and specialty practices. The content of the materials was coded, and cultural sensitivity was assessed using the Cultural Sensitivity Assessment Tool. Flesch Reading Ease, Flesch-Kincaid Grade Level, and the Simple Measure of Gobbledygook were used to assess readability. Communication with health-care providers (52.3%), side effects of PrCA treatment (40.9%), sexual dysfunction and its treatment (38.6%), and treatment options (34.1%) were frequently presented. All materials had acceptable cultural sensitivity scores; however, 2.3% and 15.9% of materials demonstrated unacceptable cultural sensitivity regarding format and visual messages, respectively. Readability of the materials varied. More than half of the materials were written above a high-school reading level. PrCA-related materials available in health-care practices may not meet patients' needs regarding content, cultural sensitivity, and readability. A wide range of educational materials that address various aspects of PrCA, including treatment options and side effects, should be presented in plain language and be culturally sensitive.

Enhancing the detection of barcoded reads in high throughput DNA sequencing data by controlling the false discovery rate.

PubMed

Buschmann, Tilo; Zhang, Rong; Brash, Douglas E; Bystrykh, Leonid V

2014-08-07

DNA barcodes are short unique sequences used to label DNA or RNA-derived samples in multiplexed deep sequencing experiments. During the demultiplexing step, barcodes must be detected and their position identified. In some cases (e.g., with PacBio SMRT), the position of the barcode and DNA context is not well defined. Many reads start inside the genomic insert so that adjacent primers might be missed. The matter is further complicated by coincidental similarities between barcode sequences and reference DNA. Therefore, a robust strategy is required in order to detect barcoded reads and avoid a large number of false positives or negatives.For mass inference problems such as this one, false discovery rate (FDR) methods are powerful and balanced solutions. Since existing FDR methods cannot be applied to this particular problem, we present an adapted FDR method that is suitable for the detection of barcoded reads as well as suggest possible improvements. In our analysis, barcode sequences showed high rates of coincidental similarities with the Mus musculus reference DNA. This problem became more acute when the length of the barcode sequence decreased and the number of barcodes in the set increased. The method presented in this paper controls the tail area-based false discovery rate to distinguish between barcoded and unbarcoded reads. This method helps to establish the highest acceptable minimal distance between reads and barcode sequences. In a proof of concept experiment we correctly detected barcodes in 83% of the reads with a precision of 89%. Sensitivity improved to 99% at 99% precision when the adjacent primer sequence was incorporated in the analysis. The analysis was further improved using a paired end strategy. Following an analysis of the data for sequence variants induced in the Atp1a1 gene of C57BL/6 murine melanocytes by ultraviolet light and conferring resistance to ouabain, we found no evidence of cross-contamination of DNA material between samples. Our method offers a proper quantitative treatment of the problem of detecting barcoded reads in a noisy sequencing environment. It is based on the false discovery rate statistics that allows a proper trade-off between sensitivity and precision to be chosen.

msgbsR: An R package for analysing methylation-sensitive restriction enzyme sequencing data.

PubMed

Mayne, Benjamin T; Leemaqz, Shalem Y; Buckberry, Sam; Rodriguez Lopez, Carlos M; Roberts, Claire T; Bianco-Miotto, Tina; Breen, James

2018-02-01

Genotyping-by-sequencing (GBS) or restriction-site associated DNA marker sequencing (RAD-seq) is a practical and cost-effective method for analysing large genomes from high diversity species. This method of sequencing, coupled with methylation-sensitive enzymes (often referred to as methylation-sensitive restriction enzyme sequencing or MRE-seq), is an effective tool to study DNA methylation in parts of the genome that are inaccessible in other sequencing techniques or are not annotated in microarray technologies. Current software tools do not fulfil all methylation-sensitive restriction sequencing assays for determining differences in DNA methylation between samples. To fill this computational need, we present msgbsR, an R package that contains tools for the analysis of methylation-sensitive restriction enzyme sequencing experiments. msgbsR can be used to identify and quantify read counts at methylated sites directly from alignment files (BAM files) and enables verification of restriction enzyme cut sites with the correct recognition sequence of the individual enzyme. In addition, msgbsR assesses DNA methylation based on read coverage, similar to RNA sequencing experiments, rather than methylation proportion and is a useful tool in analysing differential methylation on large populations. The package is fully documented and available freely online as a Bioconductor package ( https://bioconductor.org/packages/release/bioc/html/msgbsR.html ).

CT colonography: investigation of the optimum reader paradigm by using computer-aided detection software.

PubMed

Taylor, Stuart A; Charman, Susan C; Lefere, Philippe; McFarland, Elizabeth G; Paulson, Erik K; Yee, Judy; Aslam, Rizwan; Barlow, John M; Gupta, Arun; Kim, David H; Miller, Chad M; Halligan, Steve

2008-02-01

To prospectively compare the diagnostic performance and time efficiency of both second and concurrent computer-aided detection (CAD) reading paradigms for retrospectively obtained computed tomographic (CT) colonography data sets by using consensus reading (three radiologists) of colonoscopic findings as a reference standard. Ethical permission, HIPAA compliance (for U.S. institutions), and patient consent were obtained from all institutions for use of CT colonography data sets in this study. Ten radiologists each read 25 CT colonography data sets (12 men, 13 women; mean age, 61 years) containing 69 polyps (28 were 1-5 mm, 41 were >or=6 mm) by using workstations integrated with CAD software. Reading was randomized to either "second read" CAD (applied only after initial unassisted assessment) or "concurrent read" CAD (applied at the start of assessment). Data sets were reread 6 weeks later by using the opposing paradigm. Polyp sensitivity and reading times were compared by using multilevel logistic and linear regression, respectively. Receiver operating characteristic (ROC) curves were generated. Compared with the unassisted read, odds of improved polyp (>or=6 mm) detection were 1.5 (95% confidence interval [CI]: 1.0, 2.2) and 1.3 (95% CI: 0.9, 1.9) by using CAD as second and concurrent reader, respectively. Detection odds by using CAD concurrently were 0.87 (95% CI: 0.59, 1.3) and 0.76 (95% CI: 0.57, 1.01) those of second read CAD, excluding and including polyps 1-5 mm, respectively. The concurrent read took 2.9 minutes (95% CI: -3.8, -1.9) less than did second read. The mean areas under the ROC curve (95% CI) for the unassisted read, second read CAD, and concurrent read CAD were 0.83 (95% CI: 0.78, 0.87), 0.86 (95% CI: 0.82, 0.90), and 0.88 (95% CI: 0.83, 0.92), respectively. CAD is more time efficient when used concurrently than when used as a second reader, with similar sensitivity for polyps 6 mm or larger. However, use of second read CAD maximizes sensitivity, particularly for smaller lesions. (c) RSNA, 2007.

The efficacy of using computer-aided detection (CAD) for detection of breast cancer in mammography screening: a systematic review.

PubMed

Henriksen, Emilie L; Carlsen, Jonathan F; Vejborg, Ilse Mm; Nielsen, Michael B; Lauridsen, Carsten A

2018-01-01

Background Early detection of breast cancer (BC) is crucial in lowering the mortality. Purpose To present an overview of studies concerning computer-aided detection (CAD) in screening mammography for early detection of BC and compare diagnostic accuracy and recall rates (RR) of single reading (SR) with SR + CAD and double reading (DR) with SR + CAD. Material and Methods PRISMA guidelines were used as a review protocol. Articles on clinical trials concerning CAD for detection of BC in a screening population were included. The literature search resulted in 1522 records. A total of 1491 records were excluded by abstract and 18 were excluded by full text reading. A total of 13 articles were included. Results All but two studies from the SR vs. SR + CAD group showed an increased sensitivity and/or cancer detection rate (CDR) when adding CAD. The DR vs. SR + CAD group showed no significant differences in sensitivity and CDR. Adding CAD to SR increased the RR and decreased the specificity in all but one study. For the DR vs. SR + CAD group only one study reported a significant difference in RR. Conclusion All but two studies showed an increase in RR, sensitivity and CDR when adding CAD to SR. Compared to DR no statistically significant differences in sensitivity or CDR were reported. Additional studies based on organized population-based screening programs, with longer follow-up time, high-volume readers, and digital mammography are needed to evaluate the efficacy of CAD.

Lowering the quantification limit of the QubitTM RNA HS assay using RNA spike-in.

PubMed

Li, Xin; Ben-Dov, Iddo Z; Mauro, Maurizio; Williams, Zev

2015-05-06

RNA quantification is often a prerequisite for most RNA analyses such as RNA sequencing. However, the relatively low sensitivity and large sample consumption of traditional RNA quantification methods such as UV spectrophotometry and even the much more sensitive fluorescence-based RNA quantification assays, such as the Qubit™ RNA HS Assay, are often inadequate for measuring minute levels of RNA isolated from limited cell and tissue samples and biofluids. Thus, there is a pressing need for a more sensitive method to reliably and robustly detect trace levels of RNA without interference from DNA. To improve the quantification limit of the Qubit™ RNA HS Assay, we spiked-in a known quantity of RNA to achieve the minimum reading required by the assay. Samples containing trace amounts of RNA were then added to the spike-in and measured as a reading increase over RNA spike-in baseline. We determined the accuracy and precision of reading increases between 1 and 20 pg/μL as well as RNA-specificity in this range, and compared to those of RiboGreen(®), another sensitive fluorescence-based RNA quantification assay. We then applied Qubit™ Assay with RNA spike-in to quantify plasma RNA samples. RNA spike-in improved the quantification limit of the Qubit™ RNA HS Assay 5-fold, from 25 pg/μL down to 5 pg/μL while maintaining high specificity to RNA. This enabled quantification of RNA with original concentration as low as 55.6 pg/μL compared to 250 pg/μL for the standard assay and decreased sample consumption from 5 to 1 ng. Plasma RNA samples that were not measurable by the Qubit™ RNA HS Assay were measurable by our modified method. The Qubit™ RNA HS Assay with RNA spike-in is able to quantify RNA with high specificity at 5-fold lower concentration and uses 5-fold less sample quantity than the standard Qubit™ Assay.

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

PubMed Central

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

2014-01-01

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

A Computer-Assisted Instruction Phonological Sensitivity Program for Preschool Children At-Risk for Reading Problems.

ERIC Educational Resources Information Center

Lonigan, Christopher J.; Driscoll, Kimberly; Phillips, Beth M.; Cantor, Brenlee G.; Anthony, Jason L.; Goldstein, Howard

2003-01-01

A study evaluated the use of computer-assisted instruction (CAI) to provide training in phonological sensitivity skills to 45 preschool children at-risk for reading problems. Children exposed to CAI made significantly greater gains on rhyming and elision skills compared to controls. Expressive vocabulary scores were predictive of pre- to posttest…

Contrast Sensitivity Function Scores, Choices of Illuminated Stand Magnifiers, and Reading

ERIC Educational Resources Information Center

Gerritsen, Bryan

2010-01-01

Far too often, professionals focus almost solely on individuals' needs for magnification level for reading. Visual acuities are measured and decisions are made for low vision devices largely on the basis of acuity levels. Contrast sensitivity function is often overlooked as a critical need for and predictor of the selection and preference for low…

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

PubMed

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

2018-01-22

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

Evaluation of three read-depth based CNV detection tools using whole-exome sequencing data.

PubMed

Yao, Ruen; Zhang, Cheng; Yu, Tingting; Li, Niu; Hu, Xuyun; Wang, Xiumin; Wang, Jian; Shen, Yiping

2017-01-01

Whole exome sequencing (WES) has been widely accepted as a robust and cost-effective approach for clinical genetic testing of small sequence variants. Detection of copy number variants (CNV) within WES data have become possible through the development of various algorithms and software programs that utilize read-depth as the main information. The aim of this study was to evaluate three commonly used, WES read-depth based CNV detection programs using high-resolution chromosomal microarray analysis (CMA) as a standard. Paired CMA and WES data were acquired for 45 samples. A total of 219 CNVs (size ranged from 2.3 kb - 35 mb) identified on three CMA platforms (Affymetrix, Agilent and Illumina) were used as standards. CNVs were called from WES data using XHMM, CoNIFER, and CNVnator with modified settings. All three software packages detected an elevated proportion of small variants (< 20 kb) compared to CMA. XHMM and CoNIFER had poor detection sensitivity (22.2 and 14.6%), which correlated with the number of capturing probes involved. CNVnator detected most variants and had better sensitivity (87.7%); however, suffered from an overwhelming detection of small CNVs below 20 kb, which required further confirmation. Size estimation of variants was exaggerated by CNVnator and understated by XHMM and CoNIFER. Low concordances of CNV, detected by three different read-depth based programs, indicate the immature status of WES-based CNV detection. Low sensitivity and uncertain specificity of WES-based CNV detection in comparison with CMA based CNV detection suggests that CMA will continue to play an important role in detecting clinical grade CNV in the NGS era, which is largely based on WES.

Prospective flutemetamol positron emission tomography and histopathology in normal pressure hydrocephalus.

PubMed

Rinne, Juha O; Frantzen, Janek; Leinonen, Ville; Lonnrot, Kimmo; Laakso, Aki; Virtanen, Kirsi A; Solin, Olof; Kotkansalo, Anna; Koivisto, Anne; Sajanti, Juha; Karppinen, Atte; Lehto, Hanna; Rummukainen, Jaana; Buckley, Chris; Smith, Adrian; Jones, Paul A; Sherwin, Paul; Farrar, Gill; McLain, Richard; Kailajarvi, Marita; Grachev, Igor D

2014-01-01

BACKGOUND/OBJECTIVE: To determine the level of association between uptake of the amyloid positron emission tomography (PET) imaging agent [(18)F]flutemetamol and the level of amyloid-β measured by immunohistochemical and histochemical staining in a frontal cortical region biopsy site. Seventeen patients with probable normal pressure hydrocephalus (NPH) underwent prospective [(18)F]flutemetamol PET and subsequent frontal cortical brain biopsy during ventriculoperitoneal shunting. Tissue amyloid-β was evaluated using the monoclonal antibody 4G8, thioflavin S and Bielschowsky silver stain. Four of the 17 patients (23.5%) had amyloid-β pathology based on the overall pathology read and also showed increased [(18)F]flutemetamol uptake. [(18)F]Flutemetamol standardized uptake values from the biopsy site were significantly associated with biopsy specimen amyloid-β levels (Pearson's r = 0.67; p = 0.006). There was also good correlation between the biopsy specimen amyloid-β level and uptake of [(18)F]flutemetamol in the region contralateral to the biopsy site (r = 0.67; p = 0.006), as well as with composite cortical [(18)F]flutemetamol uptake (r = 0.65; p = 0.008). The blinded visual read showed a high level of agreement between all readers (κ = 0.88). Two of 3 readers were in full agreement on all images; 1 reader disagreed on 1 of the 17 NPH cases. Blinded visual assessments of PET images by 1 reader were associated with 100% sensitivity to the overall pathology read, and assessments by the 2 others were associated with 75% sensitivity (overall sensitivity by majority read was 75%); specificity of all readers was 100%. [(18)F]Flutemetamol detects brain amyloid-β in vivo and shows promise as a valuable tool to study and possibly facilitate diagnosis of Alzheimer's disease both in patients with suspected NPH and among the wider population.

L2 Working Memory Capacity and L2 Reading Skill.

ERIC Educational Resources Information Center

Harrington, Mike; Sawyer, Mark

1992-01-01

Examines the sensitivity of second-language (L2) working memory (ability to store and process information simultaneously) to differences in reading skills among advanced L2 learners. Subjects with larger L2 working memory capacities scored higher on measures of L2 reading skills, but no correlation was found between reading and passive short-term…

Viewing Eye Movements During Reading through the Lens of Chaos Theory: How Reading Is Like the Weather

ERIC Educational Resources Information Center

Paulson, Eric J.

2005-01-01

This theoretical article examines reading processes using chaos theory as an analogy. Three principles of chaos theory are identified and discussed, then related to reading processes as revealed through eye movement research. Used as an analogy, the chaos theory principle of sensitive dependence contributes to understanding the difficulty in…

Stress Sensitivity and Reading Performance in Spanish: A Study with Children

ERIC Educational Resources Information Center

Gutierrez-Palma, Nicolas; Reyes, Alfonso Palma

2007-01-01

This paper investigates the relationship between ability to detect changes in prosody and reading performance in Spanish. Participants were children aged 7-8 years. Their tasks consisted of reading words, reading non-words, stressing non-words and reproducing sequences of two, three or four non-words by pressing the corresponding keys on the…

"Do You Understand What You Are Reading?"--Rhetoric, Ethics and Aesthetics in the Undergraduate Classroom

ERIC Educational Resources Information Center

Bowen, Deborah C

2016-01-01

Universities have a perhaps unique opportunity to provide training in the art of deep reading through attention to the interrelation of rhetoric, ethics, and aesthetics. While rhetorically sensitive reading will help students to become more sophisticated readers of voice and worldview, and ethically charitable reading will help them to become more…

Development of sensitivity versus specificity for print in the visual word form area.

PubMed

Centanni, Tracy M; King, Livia W; Eddy, Marianna D; Whitfield-Gabrieli, Susan; Gabrieli, John D E

2017-07-01

An area near the left lateral occipito-temporal sulcus that responds preferentially to print has been designated as the visual word form area (VWFA). Research suggests that specialization in this brain region increases as reading expertise is achieved. Here we aimed to characterize that development in terms of sensitivity (response to printed words relative to non-linguistic faces) versus specificity (response to printed words versus line drawings of nameable objects) in typically reading children ages 7-14 versus young adults as measured by functional magnetic resonance imaging (fMRI). Relative to adults, children displayed equivalent sensitivity but reduced specificity. These findings suggest that sensitivity for print relative to non-linguistic stimuli develops relatively early in the VWFA in the course of reading development, but that specificity for printed words in VWFA is still developing through at least age 14. Copyright © 2017 Elsevier Inc. All rights reserved.

Emotional effects of startling background music during reading news reports: The moderating influence of dispositional BIS and BAS sensitivities.

PubMed

Ravaja, Niklas; Kallinen, Kari

2004-07-01

We examined the moderating influence of dispositional behavioral inhibition system (BIS) and behavioral activation system (BAS) sensitivities on the relationship of startling background music with emotion-related subjective and physiological responses elicited during reading news reports, and with memory performance among 26 adult men and women. Physiological parameters measured were respiratory sinus arrhythmia (RSA), electrodermal activity (EDA), and facial electromyography (EMG). The results showed that, among high BAS individuals, news stories with startling background music were rated as more interesting and elicited higher zygomatic EMG activity and RSA than news stories with non-startling music. Among low BAS individuals, news stories with startling background music were rated as less pleasant and more arousing and prompted higher EDA. No BIS-related effects or effects on memory were found. Startling background music may have adverse (e.g., negative arousal) or beneficial effects (e.g., a positive emotional state and stronger positive engagement) depending on dispositional BAS sensitivity of an individual. Actual or potential applications of this research include the personalization of media presentations when using modern media and communications technologies.

COSMOS: accurate detection of somatic structural variations through asymmetric comparison between tumor and normal samples

PubMed Central

Yamagata, Koichi; Yamanishi, Ayako; Kokubu, Chikara; Takeda, Junji; Sese, Jun

2016-01-01

An important challenge in cancer genomics is precise detection of structural variations (SVs) by high-throughput short-read sequencing, which is hampered by the high false discovery rates of existing analysis tools. Here, we propose an accurate SV detection method named COSMOS, which compares the statistics of the mapped read pairs in tumor samples with isogenic normal control samples in a distinct asymmetric manner. COSMOS also prioritizes the candidate SVs using strand-specific read-depth information. Performance tests on modeled tumor genomes revealed that COSMOS outperformed existing methods in terms of F-measure. We also applied COSMOS to an experimental mouse cell-based model, in which SVs were induced by genome engineering and gamma-ray irradiation, followed by polymerase chain reaction-based confirmation. The precision of COSMOS was 84.5%, while the next best existing method was 70.4%. Moreover, the sensitivity of COSMOS was the highest, indicating that COSMOS has great potential for cancer genome analysis. PMID:26833260

A Planar Two-Dimensional Superconducting Bolometer Array for the Green Bank Telescope

NASA Technical Reports Server (NTRS)

Benford, Dominic; Staguhn, Johannes G.; Chervenak, James A.; Chen, Tina C.; Moseley, S. Harvey; Wollack, Edward J.; Devlin, Mark J.; Dicker, Simon R.; Supanich, Mark

2004-01-01

In order to provide high sensitivity rapid imaging at 3.3mm (90GHz) for the Green Bank Telescope - the world's largest steerable aperture - a camera is being built by the University of Pennsylvania, NASA/GSFC, and NRAO. The heart of this camera is an 8x8 close-packed, Nyquist-sampled detector array. We have designed and are fabricating a functional superconducting bolometer array system using a monolithic planar architecture. Read out by SQUID multiplexers, the superconducting transition edge sensors will provide fast, linear, sensitive response for high performance imaging. This will provide the first ever superconducting bolometer array on a facility instrument.

Breast cancer detection using double reading of unenhanced MRI including T1-weighted, T2-weighted STIR, and diffusion-weighted imaging: a proof of concept study.

PubMed

Trimboli, Rubina M; Verardi, Nicola; Cartia, Francesco; Carbonaro, Luca A; Sardanelli, Francesco

2014-09-01

The purpose of this study was to investigate the diagnostic performance of unenhanced MRI in detecting breast cancer and to assess the impact of double reading. A total of 116 breasts of 67 women who were 36-89 years old were studied at 1.5 T using an unenhanced protocol including axial T1-weighted gradient-echo, T2-weighted STIR, and echo-planar diffusion-weighted imaging (DWI). Two blinded readers (R1 and R2) independently evaluated unenhanced images using the BIRADS scale. A combination of pathology and negative follow-up served as the reference standard. McNemar and kappa statistics were used. Per-breast cancer prevalence was 37 of 116 (32%): 30 of 37 (81%) invasive ductal carcinoma, five of 37 (13%) ductal carcinoma in situ, and two of 37 (6%) invasive lobular carcinoma. Per-breast sensitivity of unenhanced MRI was 29 of 37 (78%) for R1, 28 of 37 (76%) for R2, and 29 of 37 (78%) for double reading. Specificity was 71 of 79 (90%) for both R1 and R2 and 69 of 79 (87%) for double reading. Double reading did not provide a significant increase in sensitivity. Interobserver agreement was almost perfect (Cohen κ = 0.873). An unenhanced breast MRI protocol composed of T1-weighted gradient echo, T2-weighted STIR, and echo-planar DWI enabled breast cancer detection with sensitivity of 76-78% and specificity of 90% without a gain in sensitivity from double reading.

Training on Movement Figure-Ground Discrimination Remediates Low-Level Visual Timing Deficits in the Dorsal Stream, Improving High-Level Cognitive Functioning, Including Attention, Reading Fluency, and Working Memory.

PubMed

Lawton, Teri; Shelley-Tremblay, John

2017-01-01

The purpose of this study was to determine whether neurotraining to discriminate a moving test pattern relative to a stationary background, figure-ground discrimination, improves vision and cognitive functioning in dyslexics, as well as typically-developing normal students. We predict that improving the speed and sensitivity of figure-ground movement discrimination ( PATH to Reading neurotraining) acts to remediate visual timing deficits in the dorsal stream, thereby improving processing speed, reading fluency, and the executive control functions of attention and working memory in both dyslexic and normal students who had PATH neurotraining more than in those students who had no neurotraining. This prediction was evaluated by measuring whether dyslexic and normal students improved on standardized tests of cognitive skills following neurotraining exercises, more than following computer-based guided reading ( Raz-Kids ( RK )). The neurotraining used in this study was visually-based training designed to improve magnocellular function at both low and high levels in the dorsal stream: the input to the executive control networks coding working memory and attention. This approach represents a paradigm shift from the phonologically-based treatment for dyslexia, which concentrates on high-level speech and reading areas. This randomized controlled-validation study was conducted by training the entire second and third grade classrooms (42 students) for 30 min twice a week before guided reading. Standardized tests were administered at the beginning and end of 12-weeks of intervention training to evaluate improvements in academic skills. Only movement-discrimination training remediated both low-level visual timing deficits and high-level cognitive functioning, including selective and sustained attention, reading fluency and working memory for both dyslexic and normal students. Remediating visual timing deficits in the dorsal stream revealed the causal role of visual movement discrimination training in improving high-level cognitive functions such as attention, reading acquisition and working memory. This study supports the hypothesis that faulty timing in synchronizing the activity of magnocellular with parvocellular visual pathways in the dorsal stream is a fundamental cause of dyslexia and being at-risk for reading problems in normal students, and argues against the assumption that reading deficiencies in dyslexia are caused by phonological or language deficits, requiring a paradigm shift from phonologically-based treatment of dyslexia to a visually-based treatment. This study shows that visual movement-discrimination can be used not only to diagnose dyslexia early, but also for its successful treatment, so that reading problems do not prevent children from readily learning.

Training on Movement Figure-Ground Discrimination Remediates Low-Level Visual Timing Deficits in the Dorsal Stream, Improving High-Level Cognitive Functioning, Including Attention, Reading Fluency, and Working Memory

PubMed Central

Lawton, Teri; Shelley-Tremblay, John

2017-01-01

The purpose of this study was to determine whether neurotraining to discriminate a moving test pattern relative to a stationary background, figure-ground discrimination, improves vision and cognitive functioning in dyslexics, as well as typically-developing normal students. We predict that improving the speed and sensitivity of figure-ground movement discrimination (PATH to Reading neurotraining) acts to remediate visual timing deficits in the dorsal stream, thereby improving processing speed, reading fluency, and the executive control functions of attention and working memory in both dyslexic and normal students who had PATH neurotraining more than in those students who had no neurotraining. This prediction was evaluated by measuring whether dyslexic and normal students improved on standardized tests of cognitive skills following neurotraining exercises, more than following computer-based guided reading (Raz-Kids (RK)). The neurotraining used in this study was visually-based training designed to improve magnocellular function at both low and high levels in the dorsal stream: the input to the executive control networks coding working memory and attention. This approach represents a paradigm shift from the phonologically-based treatment for dyslexia, which concentrates on high-level speech and reading areas. This randomized controlled-validation study was conducted by training the entire second and third grade classrooms (42 students) for 30 min twice a week before guided reading. Standardized tests were administered at the beginning and end of 12-weeks of intervention training to evaluate improvements in academic skills. Only movement-discrimination training remediated both low-level visual timing deficits and high-level cognitive functioning, including selective and sustained attention, reading fluency and working memory for both dyslexic and normal students. Remediating visual timing deficits in the dorsal stream revealed the causal role of visual movement discrimination training in improving high-level cognitive functions such as attention, reading acquisition and working memory. This study supports the hypothesis that faulty timing in synchronizing the activity of magnocellular with parvocellular visual pathways in the dorsal stream is a fundamental cause of dyslexia and being at-risk for reading problems in normal students, and argues against the assumption that reading deficiencies in dyslexia are caused by phonological or language deficits, requiring a paradigm shift from phonologically-based treatment of dyslexia to a visually-based treatment. This study shows that visual movement-discrimination can be used not only to diagnose dyslexia early, but also for its successful treatment, so that reading problems do not prevent children from readily learning. PMID:28555097

Reading impairment in schizophrenia: dysconnectivity within the visual system.

PubMed

Vinckier, Fabien; Cohen, Laurent; Oppenheim, Catherine; Salvador, Alexandre; Picard, Hernan; Amado, Isabelle; Krebs, Marie-Odile; Gaillard, Raphaël

2014-01-01

Patients with schizophrenia suffer from perceptual visual deficits. It remains unclear whether those deficits result from an isolated impairment of a localized brain process or from a more diffuse long-range dysconnectivity within the visual system. We aimed to explore, with a reading paradigm, the functioning of both ventral and dorsal visual pathways and their interaction in schizophrenia. Patients with schizophrenia and control subjects were studied using event-related functional MRI (fMRI) while reading words that were progressively degraded through word rotation or letter spacing. Reading intact or minimally degraded single words involves mainly the ventral visual pathway. Conversely, reading in non-optimal conditions involves both the ventral and the dorsal pathway. The reading paradigm thus allowed us to study the functioning of both pathways and their interaction. Behaviourally, patients with schizophrenia were selectively impaired at reading highly degraded words. While fMRI activation level was not different between patients and controls, functional connectivity between the ventral and dorsal visual pathways increased with word degradation in control subjects, but not in patients. Moreover, there was a negative correlation between the patients' behavioural sensitivity to stimulus degradation and dorso-ventral connectivity. This study suggests that perceptual visual deficits in schizophrenia could be related to dysconnectivity between dorsal and ventral visual pathways. © 2013 Published by Elsevier Ltd.

Diagnostic use of 3 techniques for identification of microsporidian spores among AIDS patients in Portugal.

PubMed

Matos, Olga; Lobo, Maria L; Gonçalves, Luzia; Antunes, Francisco

2002-01-01

The calcofluor stain (CF), the monoclonal antibody (MAb) 3B6 indirect immunofluorescence assay (IFA) and the modified trichrome blue stain (MT) were compared in terms of their reproducibility in a routine laboratory and in order to evaluate the percentage of cases of microsporidiosis in Portuguese HIV patients. A total of 166 faeces samples, 71 pulmonary specimens and 43 urine samples were studied using the 3 techniques. CF had a high sensitivity and a moderate specificity when applied to faeces samples. The sensitivity was lower with pulmonary specimens. The method is easy and quick to perform but readings take a long time to obtain. The MAb 3B6 IFA had a good to excellent sensitivity when applied to faeces and urine samples, but moderate sensitivity in pulmonary specimens. Readings were quick and easy to obtain, but the assay took longer to perform than the other 2 techniques. There was a greater correlation between the results obtained with the MT and MAb 3B6 IFA techniques than between those obtained with the MT and CF techniques. In conclusion, the MT performed better than the MAb 3B6 IFA and CF and continues to have an important place in a routine laboratory for the diagnosis of microsporidiosis. This work also confirms the existence of a relatively high proportion (30%) of cases of infection with Microsporidia, especially intestinal microsporidiosis, in HIV patients in Portugal.

Harnessing NGS and Big Data Optimally: Comparison of miRNA Prediction from Assembled versus Non-assembled Sequencing Data--The Case of the Grass Aegilops tauschii Complex Genome.

PubMed

Budak, Hikmet; Kantar, Melda

2015-07-01

MicroRNAs (miRNAs) are small, endogenous, non-coding RNA molecules that regulate gene expression at the post-transcriptional level. As high-throughput next generation sequencing (NGS) and Big Data rapidly accumulate for various species, efforts for in silico identification of miRNAs intensify. Surprisingly, the effect of the input genomics sequence on the robustness of miRNA prediction was not evaluated in detail to date. In the present study, we performed a homology-based miRNA and isomiRNA prediction of the 5D chromosome of bread wheat progenitor, Aegilops tauschii, using two distinct sequence data sets as input: (1) raw sequence reads obtained from 454-GS FLX Titanium sequencing platform and (2) an assembly constructed from these reads. We also compared this method with a number of available plant sequence datasets. We report here the identification of 62 and 22 miRNAs from raw reads and the assembly, respectively, of which 16 were predicted with high confidence from both datasets. While raw reads promoted sensitivity with the high number of miRNAs predicted, 55% (12 out of 22) of the assembly-based predictions were supported by previous observations, bringing specificity forward compared to the read-based predictions, of which only 37% were supported. Importantly, raw reads could identify several repeat-related miRNAs that could not be detected with the assembly. However, raw reads could not capture 6 miRNAs, for which the stem-loops could only be covered by the relatively longer sequences from the assembly. In summary, the comparison of miRNA datasets obtained by these two strategies revealed that utilization of raw reads, as well as assemblies for in silico prediction, have distinct advantages and disadvantages. Consideration of these important nuances can benefit future miRNA identification efforts in the current age of NGS and Big Data driven life sciences innovation.

Effects of Home Literacy, Parents' Beliefs, and Children's Task-Focused Behavior on Emergent Literacy and Word Reading Skills

ERIC Educational Resources Information Center

Stephenson, Kathy A.; Parrila, Rauno K.; Georgiou, George K.; Kirby, John R.

2008-01-01

We examined the effects of home literacy (shared book reading, teaching activities, and number of books), children's task-focused behavior, and parents' beliefs and expectations about their child's reading and academic ability on kindergarten children's (N = 61) phonological sensitivity and letter knowledge and on Grade 1 word reading. The results…

High sensitivity pressure transducer based on the phase characteristics of GMI magnetic sensors

NASA Astrophysics Data System (ADS)

Benavides, L. S.; Costa Silva, E.; Costa Monteiro, E.; Hall Barbosa, C. R.

2018-03-01

This paper presents a new configuration for a GMI pressure transducer based on the reading of the phase characteristics of GMI sensor, intended for biomedical applications. The development process of this new class of magnetic field transducers is discussed, beginning with the definition of the ideal conditioning of the GMI sensor elements (dc level and frequency of the excitation current and sample length) and continuing with computational simulations of the full electronic circuit performed using the experimental data obtained from measured GMI curves, and have shown that the improvement in the sensitivity of GMI magnetometers is larger when phase-based transducers are used instead of magnitude-based transducers. Parameters of interest of the developed prototype are thoroughly analyzed, such as: sensitivity, linearity and frequency response. Also, the spectral noise density of the developed pressure transducer is evaluated and its resolution in the passband is estimated. A low-cost GMI pressure transducer was developed, presenting high resolution, high sensitivity and a frequency bandwidth compatible to the desired biomedical applications.

De novo assembly of highly polymorphic metagenomic data using in situ generated reference sequences and a novel BLAST-based assembly pipeline.

PubMed

Lin, You-Yu; Hsieh, Chia-Hung; Chen, Jiun-Hong; Lu, Xuemei; Kao, Jia-Horng; Chen, Pei-Jer; Chen, Ding-Shinn; Wang, Hurng-Yi

2017-04-26

The accuracy of metagenomic assembly is usually compromised by high levels of polymorphism due to divergent reads from the same genomic region recognized as different loci when sequenced and assembled together. A viral quasispecies is a group of abundant and diversified genetically related viruses found in a single carrier. Current mainstream assembly methods, such as Velvet and SOAPdenovo, were not originally intended for the assembly of such metagenomics data, and therefore demands for new methods to provide accurate and informative assembly results for metagenomic data. In this study, we present a hybrid method for assembling highly polymorphic data combining the partial de novo-reference assembly (PDR) strategy and the BLAST-based assembly pipeline (BBAP). The PDR strategy generates in situ reference sequences through de novo assembly of a randomly extracted partial data set which is subsequently used for the reference assembly for the full data set. BBAP employs a greedy algorithm to assemble polymorphic reads. We used 12 hepatitis B virus quasispecies NGS data sets from a previous study to assess and compare the performance of both PDR and BBAP. Analyses suggest the high polymorphism of a full metagenomic data set leads to fragmentized de novo assembly results, whereas the biased or limited representation of external reference sequences included fewer reads into the assembly with lower assembly accuracy and variation sensitivity. In comparison, the PDR generated in situ reference sequence incorporated more reads into the final PDR assembly of the full metagenomics data set along with greater accuracy and higher variation sensitivity. BBAP assembly results also suggest higher assembly efficiency and accuracy compared to other assembly methods. Additionally, BBAP assembly recovered HBV structural variants that were not observed amongst assembly results of other methods. Together, PDR/BBAP assembly results were significantly better than other compared methods. Both PDR and BBAP independently increased the assembly efficiency and accuracy of highly polymorphic data, and assembly performances were further improved when used together. BBAP also provides nucleotide frequency information. Together, PDR and BBAP provide powerful tools for metagenomic data studies.

Evaluating approaches to find exon chains based on long reads.

PubMed

Kuosmanen, Anna; Norri, Tuukka; Mäkinen, Veli

2018-05-01

Transcript prediction can be modeled as a graph problem where exons are modeled as nodes and reads spanning two or more exons are modeled as exon chains. Pacific Biosciences third-generation sequencing technology produces significantly longer reads than earlier second-generation sequencing technologies, which gives valuable information about longer exon chains in a graph. However, with the high error rates of third-generation sequencing, aligning long reads correctly around the splice sites is a challenging task. Incorrect alignments lead to spurious nodes and arcs in the graph, which in turn lead to incorrect transcript predictions. We survey several approaches to find the exon chains corresponding to long reads in a splicing graph, and experimentally study the performance of these methods using simulated data to allow for sensitivity/precision analysis. Our experiments show that short reads from second-generation sequencing can be used to significantly improve exon chain correctness either by error-correcting the long reads before splicing graph creation, or by using them to create a splicing graph on which the long-read alignments are then projected. We also study the memory and time consumption of various modules, and show that accurate exon chains lead to significantly increased transcript prediction accuracy. The simulated data and in-house scripts used for this article are available at http://www.cs.helsinki.fi/group/gsa/exon-chains/exon-chains-bib.tar.bz2.

Genovo: De Novo Assembly for Metagenomes

NASA Astrophysics Data System (ADS)

Laserson, Jonathan; Jojic, Vladimir; Koller, Daphne

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

EXPERIMENTAL AND RESEARCH WORK IN NEUTRON DOSIMETRY. Final Summary Report for the Period May 15, 1959-June 15, 1960

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

Gorton, H.C.; Mengali, O.J.; Zacaroli, A.R.

A practical, prototype silicon p-n junction fast-neutron dosimeter, sensitive in the same range as human tissue, was developed, together with sn associated read-out circuit to facilitate the accurate measurement of accumulated dose. From both theoretical and experimental considerations, it was demonstrated that the dosimeter is essentially insensitive to the gamma and thermal components of a uranium fission spectrum. It was shown that accumulated damage effects appear to be environmentally stable up to an ambient temperature of 100 C. A rather raarked reversible temperature dependence of the read-out parameters requires either control of the read-out temperature or temperature compensation in themore » read-out device. A high degree of reproducibility of dosimeter characteristics from one device to another was not achieved. The lack of reproducibility was attributed to uncontrolled variables in the bulk silicon from which the devices are fabricated, and in the production procedure. (auth)« less

Phase Interrogation Used for a Wireless Passive Pressure Sensor in an 800 °C High-Temperature Environment

PubMed Central

Zhang, Huixin; Hong, Yingping; Liang, Ting; Zhang, Hairui; Tan, Qiulin; Xue, Chenyang; Liu, Jun; Zhang, Wendong; Xiong, Jijun

2015-01-01

A wireless passive pressure measurement system for an 800 °C high-temperature environment is proposed and the impedance variation caused by the mutual coupling between a read antenna and a LC resonant sensor is analyzed. The system consists of a ceramic-based LC resonant sensor, a readout device for impedance phase interrogation, heat insulating material, and a composite temperature-pressure test platform. Performances of the pressure sensor are measured by the measurement system sufficiently, including pressure sensitivity at room temperature, zero drift from room temperature to 800 °C, and the pressure sensitivity under the 800 °C high temperature environment. The results show that the linearity of sensor is 0.93%, the repeatability is 6.6%, the hysteretic error is 1.67%, and the sensor sensitivity is 374 KHz/bar. The proposed measurement system, with high engineering value, demonstrates good pressure sensing performance in a high temperature environment. PMID:25690546

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.

TH-AB-201-04: Clinical Protocol for Reuse of Optically Stimulated Luminescence Detectors

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

Graeper, G; Pillai, S

Purpose: OSLDs made of Al2O3:C have many useful dosimetric characteristics including their ability to be reused. The signal on an OSLD can be removed through heat or light. The objective of this study was to characterize the change in sensitivity associated with annealing OSLDs with light and in doing so define a range through which reuse is viable. Methods: Four groups of nanoDot OSLDs were repeatedly irradiated and bleached to create accumulated dose history. Each group’s repeated irradiation remained constant at either 50, 100, 200, or 500 cGy. Before both irradiation and bleaching the OSLDs were read out, giving themore » dose reading and ensuring that ample bleaching had occurred, respectively. New and used OSLDs were compared in several clinical situations to verify accuracy. One final test involved correcting the readout dose based on the loss of sensitivity seen in the accumulated dose data. Results: In the first 40 Gy of accumulated dose the sensitivity can be broken into two regions: a region of sensitivity change and a region of no sensitivity change. From 0 cGy to an average of 1080 cGy the sensitivity does not change. After 1080 cGy the sensitivity begins to decrease linearly with an average slope of 0.00456 cGy lost per cGy accumulated after the cutoff point. The slope and cutoff point were used to correct readings in the final test, reducing the error from 6.8% to 3.9%. Conclusion: In the region of no sensitivity change OSLDs can be reused without concern to the validity of their result. Readings must be corrected if OSLDs are to be used in the region of sensitivity change, above 1080 cGy. After 40 Gy OSLDs must be retired because the sensitivity change reverses, making linear correction no longer feasible.« less

Basic Processes in Reading: The Effect of Interletter Spacing

ERIC Educational Resources Information Center

Risko, Evan F.; Lanthier, Sophie N.; Besner, Derek

2011-01-01

Reading is acutely sensitive to the amount of space between letters within a string. In the present investigation, we explore the impairment caused by increasing interletter spacing when reading single words and nonwords aloud. Specifically, 2 hypotheses are tested: (a) whether increasing interletter spacing induces serial processing while reading…

Dynamic Visual Perception and Reading Development in Chinese School Children

ERIC Educational Resources Information Center

Meng, Xiangzhi; Cheng-Lai, Alice; Zeng, Biao; Stein, John F.; Zhou, Xiaolin

2011-01-01

The development of reading skills may depend to a certain extent on the development of basic visual perception. The magnocellular theory of developmental dyslexia assumes that deficits in the magnocellular pathway, indicated by less sensitivity in perceiving dynamic sensory stimuli, are responsible for a proportion of reading difficulties…

Visual versus semi-quantitative analysis of 18F-FDG-PET in amnestic MCI: an European Alzheimer's Disease Consortium (EADC) project.

PubMed

Morbelli, Silvia; Brugnolo, Andrea; Bossert, Irene; Buschiazzo, Ambra; Frisoni, Giovanni B; Galluzzi, Samantha; van Berckel, Bart N M; Ossenkoppele, Rik; Perneczky, Robert; Drzezga, Alexander; Didic, Mira; Guedj, Eric; Sambuceti, Gianmario; Bottoni, Gianluca; Arnaldi, Dario; Picco, Agnese; De Carli, Fabrizio; Pagani, Marco; Nobili, Flavio

2015-01-01

We aimed to investigate the accuracy of FDG-PET to detect the Alzheimer's disease (AD) brain glucose hypometabolic pattern in 142 patients with amnestic mild cognitive impairment (aMCI) and 109 healthy controls. aMCI patients were followed for at least two years or until conversion to dementia. Images were evaluated by means of visual read by either moderately-skilled or expert readers, and by means of a summary metric of AD-like hypometabolism (PALZ score). Seventy-seven patients converted to AD-dementia after 28.6 ± 19.3 months of follow-up. Expert reading was the most accurate tool to detect these MCI converters from healthy controls (sensitivity 89.6%, specificity 89.0%, accuracy 89.2%) while two moderately-skilled readers were less (p < 0.05) specific (sensitivity 85.7%, specificity 79.8%, accuracy 82.3%) and PALZ score was less (p < 0.001) sensitive (sensitivity 62.3%, specificity 91.7%, accuracy 79.6%). Among the remaining 67 aMCI patients, 50 were confirmed as aMCI after an average of 42.3 months, 12 developed other dementia, and 3 reverted to normalcy. In 30/50 persistent MCI patients, the expert recognized the AD hypometabolic pattern. In 13/50 aMCI, both the expert and PALZ score were negative while in 7/50, only the PALZ score was positive due to sparse hypometabolic clusters mainly in frontal lobes. Visual FDG-PET reads by an expert is the most accurate method but an automated, validated system may be particularly helpful to moderately-skilled readers because of high specificity, and should be mandatory when even a moderately-skilled reader is unavailable.

Graphene-based biosensors.

PubMed

Szunerits, Sabine; Boukherroub, Rabah

2018-06-06

Reliable data obtained from analysis of DNA, proteins, bacteria and other disease-related molecules or organisms in biological samples have become a fundamental and crucial part of human health diagnostics and therapy. The development of non-invasive tests that are rapid, sensitive, specific and simple would allow patient discomfort to be prevented, delays in diagnosis to be avoided and the status of a disease to be followed up. Bioanalysis is thus a progressive discipline for which the future holds many exciting opportunities. The use of biosensors for the early diagnosis of diseases has become widely accepted as a point-of-care diagnosis with appropriate specificity in a short time. To allow a reliable diagnosis of a disease at an early stage, highly sensitive biosensors are required as the corresponding biomarkers are generally expressed at very low concentrations. In the past 50 years, various biosensors have been researched and developed encompassing a wide range of applications. This contrasts the limited number of commercially available biosensors. When it comes to sensing of biomarkers with the required picomolar (pM) sensitivity for real-time sensing of biological samples, only a handful of sensing systems have been proposed, and these are often rather complex and costly. Lately, graphene-based materials have been considered as superior over other nanomaterials for the development of sensitive biosensors. The advantages of graphene-based sensor interfaces are numerous, including enhanced surface loading of the desired ligand due to the high surface-to-volume ratio, excellent conductivity and a small band gap that is beneficial for sensitive electrical and electrochemical read-outs, as well as tunable optical properties for optical read-outs such as fluorescence and plasmonics. In this paper, we review the advances made in recent years on graphene-based biosensors in the field of medical diagnosis.

Certain performance values arising from mammographic test set readings correlate well with clinical audit.

PubMed

Soh, BaoLin Pauline; Lee, Warwick Bruce; Mello-Thoms, Claudia; Tapia, Kriscia; Ryan, John; Hung, Wai Tak; Thompson, Graham; Heard, Rob; Brennan, Patrick

2015-08-01

Test sets have been increasingly utilised to augment clinical audit in breast screening programmes; however, their relationship has never been satisfactorily understood. This study examined the relationship between mammographic test set performance and clinical audit data. Clinical audit data over a 2-year period was generated for each of 20 radiologists. Sixty mammographic examinations, consisting of 40 normal and 20 cancer cases, formed the test set. Readers located any identifiable cancer, and levels of confidence were scored from 2 to 5, where a score of 3 and above is considered a recall rating. Jackknifing free response operating characteristic (JAFROC) figure-of-merit (FOM), location sensitivity and specificity were calculated for individual readers and then compared with clinical audit values using Spearman's rho. JAFROC FOM showed significant correlations to: recall rate at a first round of screening (r = 0.51; P = 0.02); rate of small invasive cancers per 10 000 reads (r = 0.5; P = 0.02); percentage of all cancers read that were not recalled (r = -0.51; P = 0.02); and sensitivity (r = 0.51; P = 0.02). Location sensitivity demonstrated significant correlations with: rate of small invasive cancers per 10 000 reads (r = 0.46; P = 0.04); rate of DCIS (ductal carcinoma in situ) per 10 000 reads (r = 0.44; P = 0.05); detection rate of all invasive cancers and DCIS per 10 000 reads (r = 0.54; P = 0.01); percentage of all cancers read that were not recalled (r = -0.57; P = 0.009); and sensitivity (r = 0.57; P = 0.009). No other significant relationships were noted. Performance indicators from test set demonstrate significant correlations with specific aspects of clinical performance, although caution needs to be exercised when generalising test set specificity to the clinical situation. © 2015 The Royal Australian and New Zealand College of Radiologists.

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.

High granularity tracker based on a Triple-GEM optically read by a CMOS-based camera

NASA Astrophysics Data System (ADS)

Marafini, M.; Patera, V.; Pinci, D.; Sarti, A.; Sciubba, A.; Spiriti, E.

2015-12-01

The detection of photons produced during the avalanche development in gas chambers has been the subject of detailed studies in the past. The great progresses achieved in last years in the performance of micro-pattern gas detectors on one side and of photo-sensors on the other provide the possibility of making high granularity and very sensitive particle trackers. In this paper, the results obtained with a triple-GEM structure read-out by a CMOS based sensor are described. The use of an He/CF4 (60/40) gas mixture and a detailed optimization of the electric fields made possible to obtain a very high GEM light yield. About 80 photons per primary electron were detected by the sensor resulting in a very good capability of tracking both muons from cosmic rays and electrons from natural radioactivity.

Pulse oximetry in the evaluation of peripheral vascular disease.

PubMed

Jawahar, D; Rachamalla, H R; Rafalowski, A; Ilkhani, R; Bharathan, T; Anandarao, N

1997-08-01

The role of pulse oximetry in the evaluation of peripheral vascular disease (PVD) was investigated. In addition, the value of elevating the limb to improve the sensitivity of detection of PVD by the pulse oximeter was also determined. Pulse oximetry reading in the toes were obtained in 40 young, healthy volunteers and in 40 randomly selected patients referred to the vascular investigation laboratory over a period of two months. All 40 healthy volunteers had normal pulse oximetry readings. Normal pulse oximetry reading in the toes was defined as > 95% O2 Sat and +/-2 of finger pulse oximetry reading. In all 40 patients, pulse oximetry readings were either normal or not detected at all. Since there was no gradation in decrease in the pulse oximetry reading with severity of disease or with elevation of the patient's lower extremity, an absent or no reading was considered as an abnormal result from the test. The frequency of abnormal pulse oximetry readings increased significantly in groups with abnormal ankle-brachial pressure index (ABPI) and also varied significantly with elevation of the patients' lower limbs. In patients with no PVD detected by Doppler (ABPI > 0.9), pulse oximetry readings were normal in all. However, in patients with moderate PVD (ABPI, 0.5-0.9), 84% of the patients' lower limbs had normal pulse oximetry readings and 16% had an abnormal reading at baseline level (flat). An additional 12% of the lower limbs in this group had an abnormal reading on elevation of the limb to 12 inches. In patients with severe PVD (ABPI < 0.5), 54% of the patients' lower limbs had an abnormal reading at baseline and an additional 23% had an abnormal reading at elevation of the limb to 12 inches. In conclusion, pulse oximetry was not a sensitive test for detecting early PVD.

Improved Detection of New MS Lesions during Follow-Up Using an Automated MR Coregistration-Fusion Method.

PubMed

Galletto Pregliasco, A; Collin, A; Guéguen, A; Metten, M A; Aboab, J; Deschamps, R; Gout, O; Duron, L; Sadik, J C; Savatovsky, J; Lecler, A

2018-06-07

MR imaging is the key examination in the follow-up of patients with MS, by identification of new high-signal T2 brain lesions. However, identifying new lesions when scrolling through 2 follow-up MR images can be difficult and time-consuming. Our aim was to compare an automated coregistration-fusion reading approach with the standard approach by identifying new high-signal T2 brain lesions in patients with multiple sclerosis during follow-up MR imaging. This prospective monocenter study included 94 patients (mean age, 38.9 years) treated for MS with dimethyl fumarate from January 2014 to August 2016. One senior neuroradiologist and 1 junior radiologist checked for new high-signal T2 brain lesions, independently analyzing blinded image datasets with automated coregistration-fusion or the standard scroll-through approach with a 3-week delay between the 2 readings. A consensus reading with a second senior neuroradiologist served as a criterion standard for analyses. A Poisson regression and logistic and γ regressions were used to compare the 2 methods. Intra- and interobserver agreement was assessed by the κ coefficient. There were significantly more new high-signal T2 lesions per patient detected with the coregistration-fusion method (7 versus 4, P < .001). The coregistration-fusion method detected significantly more patients with at least 1 new high-signal T2 lesion (59% versus 46%, P = .02) and was associated with significantly faster overall reading time (86 seconds faster, P < .001) and higher reader confidence (91% versus 40%, P < 1 × 10 -4 ). Inter- and intraobserver agreement was excellent for counting new high-signal T2 lesions. Our study showed that an automated coregistration-fusion method was more sensitive for detecting new high-signal T2 lesions in patients with MS and reducing reading time. This method could help to improve follow-up care. © 2018 by American Journal of Neuroradiology.

A Mismatch Between Patient Education Materials About Sickle Cell Disease and the Literacy Level of Their Intended Audience.

PubMed

McClure, Elizabeth; Ng, Jared; Vitzthum, Kelly; Rudd, Rima

2016-05-12

Despite the first goal of the 2010 National Action Plan to Improve Health Literacy, the literacy demands of much health information exceeds the reading skills of most US adults. The objective of this study was to assess the health literacy level of publicly available patient education materials for people with sickle cell disease (SCD). We used 5 validated tools to evaluate 9 print and 4 online patient education materials: the simple measure of gobbledygook (SMOG) to assess reading grade level, the Peter Mosenthal and Irwin Kirsch readability formula (PMOSE/IKIRSCH) to assess structure and density, the Patient Education Materials Assessment Tool (PEMAT) to assess actionability (how well readers will know what to do after reading the material) and understandability, the Centers for Disease Control and Prevention's (CDC's) Clear Communication Index (Index) to obtain a comprehensive literacy demand score, and the Printed Cancer Education Materials for African Americans Cultural Sensitivity Assessment Tool. Materials' scores reflected high reading levels ranging from 8th grade to 12th grade, appropriate (low) structural demand, and low actionability relative to understandability. CDC suggests that an appropriate Index score should fall in or above the 90th percentile. The scores yielded by materials evaluated in this assessment ranged from the 44th to the 76th percentiles. Eight of the 13 materials scored within the acceptable range for cultural sensitivity. Reading levels of available patient education materials exceed the documented average literacy level of the US adult population. Health literacy demands should be a key consideration in the revision and development of patient education materials for people with SCD.

Universal brain systems for recognizing word shapes and handwriting gestures during reading

PubMed Central

Nakamura, Kimihiro; Kuo, Wen-Jui; Pegado, Felipe; Cohen, Laurent; Tzeng, Ovid J. L.; Dehaene, Stanislas

2012-01-01

Do the neural circuits for reading vary across culture? Reading of visually complex writing systems such as Chinese has been proposed to rely on areas outside the classical left-hemisphere network for alphabetic reading. Here, however, we show that, once potential confounds in cross-cultural comparisons are controlled for by presenting handwritten stimuli to both Chinese and French readers, the underlying network for visual word recognition may be more universal than previously suspected. Using functional magnetic resonance imaging in a semantic task with words written in cursive font, we demonstrate that two universal circuits, a shape recognition system (reading by eye) and a gesture recognition system (reading by hand), are similarly activated and show identical patterns of activation and repetition priming in the two language groups. These activations cover most of the brain regions previously associated with culture-specific tuning. Our results point to an extended reading network that invariably comprises the occipitotemporal visual word-form system, which is sensitive to well-formed static letter strings, and a distinct left premotor region, Exner’s area, which is sensitive to the forward or backward direction with which cursive letters are dynamically presented. These findings suggest that cultural effects in reading merely modulate a fixed set of invariant macroscopic brain circuits, depending on surface features of orthographies. PMID:23184998

Identification of genomic indels and structural variations using split reads

PubMed Central

2011-01-01

Background Recent studies have demonstrated the genetic significance of insertions, deletions, and other more complex structural variants (SVs) in the human population. With the development of the next-generation sequencing technologies, high-throughput surveys of SVs on the whole-genome level have become possible. Here we present split-read identification, calibrated (SRiC), a sequence-based method for SV detection. Results We start by mapping each read to the reference genome in standard fashion using gapped alignment. Then to identify SVs, we score each of the many initial mappings with an assessment strategy designed to take into account both sequencing and alignment errors (e.g. scoring more highly events gapped in the center of a read). All current SV calling methods have multilevel biases in their identifications due to both experimental and computational limitations (e.g. calling more deletions than insertions). A key aspect of our approach is that we calibrate all our calls against synthetic data sets generated from simulations of high-throughput sequencing (with realistic error models). This allows us to calculate sensitivity and the positive predictive value under different parameter-value scenarios and for different classes of events (e.g. long deletions vs. short insertions). We run our calculations on representative data from the 1000 Genomes Project. Coupling the observed numbers of events on chromosome 1 with the calibrations gleaned from the simulations (for different length events) allows us to construct a relatively unbiased estimate for the total number of SVs in the human genome across a wide range of length scales. We estimate in particular that an individual genome contains ~670,000 indels/SVs. Conclusions Compared with the existing read-depth and read-pair approaches for SV identification, our method can pinpoint the exact breakpoints of SV events, reveal the actual sequence content of insertions, and cover the whole size spectrum for deletions. Moreover, with the advent of the third-generation sequencing technologies that produce longer reads, we expect our method to be even more useful. PMID:21787423

Dyslexia Limits the Ability to Categorize Talker Dialect

PubMed Central

Long, Gayle Beam; Jacewicz, Ewa

2016-01-01

Purpose The purpose of this study was to determine whether the underlying phonological impairment in dyslexia is associated with a deficit in categorizing regional dialects. Method Twenty adults with dyslexia, 20 school-age children with dyslexia, and 40 corresponding control listeners with average reading ability listened to sentences produced by multiple talkers (both sexes) representing two dialects: Midland dialect in Ohio (same as listeners' dialect) and Southern dialect in Western North Carolina. Participants' responses were analyzed using signal detection theory. Results Listeners with dyslexia were less sensitive to talker dialect than listeners with average reading ability. Children were less sensitive to dialect than adults. Under stimulus uncertainty, listeners with average reading ability were biased toward Ohio dialect, whereas listeners with dyslexia were unbiased in their responses. Talker sex interacted with sensitivity and bias differently for listeners with dyslexia than for listeners with average reading ability. The correlations between dialect sensitivity and phonological memory scores were strongest for adults with dyslexia. Conclusions The results imply that the phonological deficit in dyslexia arises from impaired access to intact phonological representations rather than from poorly specified representations. It can be presumed that the impeded access to implicit long-term memory representations for indexical (dialect) information is due to less efficient operations in working memory, including deficiencies in utilizing talker normalization processes. PMID:27575597

Scientific Structural Changes within Texts of Adapted Reading Materials

ERIC Educational Resources Information Center

Aziz, Anealka; Fook, Chan Yuen; Alsree, Zubaidah

2010-01-01

ESL instructors generally use ready-made reading materials in commercially published coursebooks. However, it would be more effective for learners if ESL instructors are involved in developing reading materials for them. This is because they are closer, more sensitive and responsive to the needs of their learners and they are also aware of the…

Neurological Processes and Reading Pathology: Knowing About Children and Reading Dysfunction.

ERIC Educational Resources Information Center

Roberts, David Harrill

For many years dyslexia has been incorrectly applied to those who have demonstrated difficulty in learning to read. Given the proper guidance and opportunities for becoming sensitive to demonstrations of the workings of language and engaging their minds in learning, many students will overcome their so-called learning disabilities. However, there…

Is There a Common Linkage among Reading Comprehension, Visual Attention, and Magnocellular Processing?

ERIC Educational Resources Information Center

Solan, Harold A.; Shelley-Tremblay, John F.; Hansen, Peter C.; Larson, Steven

2007-01-01

The authors examined the relationships between reading comprehension, visual attention, and magnocellular processing in 42 Grade 7 students. The goal was to quantify the sensitivity of visual attention and magnocellular visual processing as concomitants of poor reading comprehension in the absence of either vision therapy or cognitive…

Context-Sensitive Rules and Word Naming in Italian Children

ERIC Educational Resources Information Center

Barca, Laura; Ellis, Andrew W.; Burani, Cristina

2007-01-01

The present study examines the role of orthographic complexity on Italian children's word reading. Two experiments are reported in which elementary school children (3rd and 5th graders) read aloud words containing simple or contextual letter-sound conversion rules. In Experiment 1, both groups of participants read words containing contextual rules…

Multivariate models for prediction of human skin sensitization hazard.

PubMed

Strickland, Judy; Zang, Qingda; Paris, Michael; Lehmann, David M; Allen, David; Choksi, Neepa; Matheson, Joanna; Jacobs, Abigail; Casey, Warren; Kleinstreuer, Nicole

2017-03-01

One of the Interagency Coordinating Committee on the Validation of Alternative Method's (ICCVAM) top priorities is the development and evaluation of non-animal approaches to identify potential skin sensitizers. The complexity of biological events necessary to produce skin sensitization suggests that no single alternative method will replace the currently accepted animal tests. ICCVAM is evaluating an integrated approach to testing and assessment based on the adverse outcome pathway for skin sensitization that uses machine learning approaches to predict human skin sensitization hazard. We combined data from three in chemico or in vitro assays - the direct peptide reactivity assay (DPRA), human cell line activation test (h-CLAT) and KeratinoSens™ assay - six physicochemical properties and an in silico read-across prediction of skin sensitization hazard into 12 variable groups. The variable groups were evaluated using two machine learning approaches, logistic regression and support vector machine, to predict human skin sensitization hazard. Models were trained on 72 substances and tested on an external set of 24 substances. The six models (three logistic regression and three support vector machine) with the highest accuracy (92%) used: (1) DPRA, h-CLAT and read-across; (2) DPRA, h-CLAT, read-across and KeratinoSens; or (3) DPRA, h-CLAT, read-across, KeratinoSens and log P. The models performed better at predicting human skin sensitization hazard than the murine local lymph node assay (accuracy 88%), any of the alternative methods alone (accuracy 63-79%) or test batteries combining data from the individual methods (accuracy 75%). These results suggest that computational methods are promising tools to identify effectively the potential human skin sensitizers without animal testing. Published 2016. This article has been contributed to by US Government employees and their work is in the public domain in the USA. Published 2016. This article has been contributed to by US Government employees and their work is in the public domain in the USA.

Evaluation of a Kinematically-Driven Finite Element Footstrike Model.

PubMed

Hannah, Iain; Harland, Andy; Price, Dan; Schlarb, Heiko; Lucas, Tim

2016-06-01

A dynamic finite element model of a shod running footstrike was developed and driven with 6 degree of freedom foot segment kinematics determined from a motion capture running trial. Quadratic tetrahedral elements were used to mesh the footwear components with material models determined from appropriate mechanical tests. Model outputs were compared with experimental high-speed video (HSV) footage, vertical ground reaction force (GRF), and center of pressure (COP) excursion to determine whether such an approach is appropriate for the development of athletic footwear. Although unquantified, good visual agreement to the HSV footage was observed but significant discrepancies were found between the model and experimental GRF and COP readings (9% and 61% of model readings outside of the mean experimental reading ± 2 standard deviations, respectively). Model output was also found to be highly sensitive to input kinematics with a 120% increase in maximum GRF observed when translating the force platform 2 mm vertically. While representing an alternative approach to existing dynamic finite element footstrike models, loading highly representative of an experimental trial was not found to be achievable when employing exclusively kinematic boundary conditions. This significantly limits the usefulness of employing such an approach in the footwear development process.

The variation of radiologists' performance over the course of a reading session

NASA Astrophysics Data System (ADS)

Elze, Markus C.; Taylor-Phillips, Sian; Mello-Thoms, Claudia; Krupinski, Elizabeth A.; Gale, Alastair G.; Clarke, Aileen

2013-03-01

The radiologist's task of reviewing many cases successively is highly repetitive and requires a high level of concentration. Fatigue effects have, for example, been shown in studies comparing performance at different times of day. However, little is known about changes in performance during an individual reading session. During a session reading an enriched case set, performance may be affected by both fatigue (i.e. decreasing performance) and training (i.e. increasing performance) effects. In this paper, we reanalyze 3 datasets from 4 studies for changes in radiologist performance during a reading session. Studies feature 8-20 radiologists reading and assessing 27-60 cases in single, uninterrupted sessions. As the studies were not designed for this analysis, study setups range from bone fractures to mammograms and randomization varies between studies. Thus, they are analyzed separately using mixed-effects models. There is some indication that, as time goes on, specificity increases (shown with p<0.05 for 2 out of 3 datasets, no significant difference for the other) while sensitivity may also increase (p<0.05 for 1 out of 3 datasets). The difficulty of `normal' (healthy / non-malignant) and `abnormal' (unhealthy / malignant) cases differs (p<0.05 for 3 out of 3 datasets) and the reader's experience may also be relevant (p<0.05 for 1 out of 3 datasets). These results suggest that careful planning of breaks and session length may help optimize reader performance. Note that the overall results are still inconclusive and a targeted study to investigate fatigue and training effects within a reading session is recommended.

SU-E-T-315: The Change of Optically Stimulated Luminescent Dosimeters (OSLDs) Sensitivity by Accumulated Dose and High Dose

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

Han, S; Jung, H; Kim, M

2014-06-01

Purpose: The objective of this study is to evaluate radiation sensitivity of optical stimulated luminance dosimeters (OSLDs) by accumulated dose and high dose. Methods: This study was carried out in Co-60 unit (Theratron 780, AECL, and Canada) and used InLight MicroStar reader (Landauer, Inc., Glenwood, IL) for reading. We annealed for 30 min using optical annealing system which contained fluorescent lamps (Osram lumilux, 24 W, 280 ∼780 nm). To evaluate change of OSLDs sensitivity by repeated irradiation, the dosimeters were repeatedly irradiated with 1 Gy. And whenever a repeated irradiation, we evaluated OSLDs sensitivity. To evaluate OSLDs sensitivity after accumulatedmore » dose with 5 Gy, We irradiated dose accumulatively (from 1 Gy to 5 Gy) without annealing. And OSLDs was also irradiated with 15, 20, 30 Gy to certify change of OSLDs sensitivity after high dose irradiation. After annealing them, they were irradiated with 1Gy, repeatedly. Results: The OSLDs sensitivity increased up to 3% during irradiating seven times and decreased continuously above 8 times. That dropped by about 0.35 Gy per an irradiation. Finally, after 30 times irradiation, OSLDs sensitivity decreased by about 7%. For accumulated dose from 1 Gy to 5 Gy, OSLDs sensitivity about 1 Gy increased until 4.4% after second times accumulated dose compared with before that. OSLDs sensitivity about 1 Gy decreased by 1.6% in five times irradiation. When OSLDs were irradiated ten times with 1Gy after irradiating high dose (10, 15, 20 Gy), OSLDs sensitivity decreased until 6%, 9%, 12% compared with it before high dose irradiation, respectively. Conclusion: This study certified OSLDs sensitivity by accumulated dose and high dose. When irradiated with 1Gy, repeatedly, OSLDs sensitivity decreased linearly and the reduction rate of OSLDs sensitivity after high dose irradiation had dependence on irradiated dose.« less

Improving the range of UHF RFID transponders using solar energy harvesting under low light conditions

NASA Astrophysics Data System (ADS)

Ascher, A.; Lehner, M.; Eberhardt, M.; Biebl, E.

2015-11-01

The sensitivity of passive UHF RFID transponders (Radio Frequency Identification) is the key issue, which determines the maximum read range of an UHF RFID system. During this work the ability of improving the sensitivity using solar energy harvesting, especially for low light conditions, is shown. To use the additional energy harvested from the examined silicon and organic solar cells, the passive RFID system is changed into a semi-active one. This needs no changes on the reader hardware itself, only the used RFIC (Radio Frequency Integrated Circuit) of the transponder has to possess an additional input pin for an external supply voltage. The silicon and organic cells are evaluated and compared to each other regarding their low light performance. The different cells are examined in a shielded box, which is protected from the environmental lighting. Additionally, a demonstrator is shown, which makes the measurement of the extended read range with respect to the lighting conditions possible. If the cells are completely darkened, the sensitivity gain is ascertained using high capacity super caps. Due to the measurements an enhancement in range up to 70 % could be guaranteed even under low light conditions.

Evaluation of microRNA alignment techniques

PubMed Central

Kaspi, Antony; El-Osta, Assam

2016-01-01

Genomic alignment of small RNA (smRNA) sequences such as microRNAs poses considerable challenges due to their short length (∼21 nucleotides [nt]) as well as the large size and complexity of plant and animal genomes. While several tools have been developed for high-throughput mapping of longer mRNA-seq reads (>30 nt), there are few that are specifically designed for mapping of smRNA reads including microRNAs. The accuracy of these mappers has not been systematically determined in the case of smRNA-seq. In addition, it is unknown whether these aligners accurately map smRNA reads containing sequence errors and polymorphisms. By using simulated read sets, we determine the alignment sensitivity and accuracy of 16 short-read mappers and quantify their robustness to mismatches, indels, and nontemplated nucleotide additions. These were explored in the context of a plant genome (Oryza sativa, ∼500 Mbp) and a mammalian genome (Homo sapiens, ∼3.1 Gbp). Analysis of simulated and real smRNA-seq data demonstrates that mapper selection impacts differential expression results and interpretation. These results will inform on best practice for smRNA mapping and enable more accurate smRNA detection and quantification of expression and RNA editing. PMID:27284164

Too little, too late: reduced visual span and speed characterize pure alexia.

PubMed

Starrfelt, Randi; Habekost, Thomas; Leff, Alexander P

2009-12-01

Whether normal word reading includes a stage of visual processing selectively dedicated to word or letter recognition is highly debated. Characterizing pure alexia, a seemingly selective disorder of reading, has been central to this debate. Two main theories claim either that 1) Pure alexia is caused by damage to a reading specific brain region in the left fusiform gyrus or 2) Pure alexia results from a general visual impairment that may particularly affect simultaneous processing of multiple items. We tested these competing theories in 4 patients with pure alexia using sensitive psychophysical measures and mathematical modeling. Recognition of single letters and digits in the central visual field was impaired in all patients. Visual apprehension span was also reduced for both letters and digits in all patients. The only cortical region lesioned across all 4 patients was the left fusiform gyrus, indicating that this region subserves a function broader than letter or word identification. We suggest that a seemingly pure disorder of reading can arise due to a general reduction of visual speed and span, and explain why this has a disproportionate impact on word reading while recognition of other visual stimuli are less obviously affected.

Too Little, Too Late: Reduced Visual Span and Speed Characterize Pure Alexia

PubMed Central

Habekost, Thomas; Leff, Alexander P.

2009-01-01

Whether normal word reading includes a stage of visual processing selectively dedicated to word or letter recognition is highly debated. Characterizing pure alexia, a seemingly selective disorder of reading, has been central to this debate. Two main theories claim either that 1) Pure alexia is caused by damage to a reading specific brain region in the left fusiform gyrus or 2) Pure alexia results from a general visual impairment that may particularly affect simultaneous processing of multiple items. We tested these competing theories in 4 patients with pure alexia using sensitive psychophysical measures and mathematical modeling. Recognition of single letters and digits in the central visual field was impaired in all patients. Visual apprehension span was also reduced for both letters and digits in all patients. The only cortical region lesioned across all 4 patients was the left fusiform gyrus, indicating that this region subserves a function broader than letter or word identification. We suggest that a seemingly pure disorder of reading can arise due to a general reduction of visual speed and span, and explain why this has a disproportionate impact on word reading while recognition of other visual stimuli are less obviously affected. PMID:19366870

Print-specific multimodal brain activation in kindergarten improves prediction of reading skills in second grade.

PubMed

Bach, Silvia; Richardson, Ulla; Brandeis, Daniel; Martin, Ernst; Brem, Silvia

2013-11-15

Children who are poor readers usually experience troublesome school careers and consequently often suffer from secondary emotional and behavioural problems. Early identification and prediction of later reading problems thus are critical in order to start targeted interventions for those children with an elevated risk for emerging reading problems. In this study, behavioural precursors of reading were assessed in nineteen (aged 6.4 ± 0.3 years) non-reading kindergarteners before training letter-speech sound associations with a computerized game (Graphogame) for eight weeks. The training aimed to introduce the basic principles of letter-speech sound correspondences and to initialize the sensitization of specific brain areas to print. Event-related potentials (ERP) and functional magnetic resonance imaging (fMRI) data were recorded during an explicit word/symbol processing task after the training. Reading skills were assessed two years later in second grade. The focus of this study was on clarifying whether electrophysiological and fMRI data of kindergarten children significantly improve prediction of future reading skills in 2nd grade over behavioural data alone. Based on evidence from previous studies demonstrating the importance of initial print sensitivity in the left occipito-temporal visual word form system (VWFS) for learning to read, the first pronounced difference in processing words compared to symbols in the ERP, an occipito-temporal negativity (N1: 188-281 ms) along with the corresponding functional activation in the left occipito-temporal VWFS were defined as potential predictors. ERP and fMRI data in kindergarteners significantly improved the prediction of reading skills in 2nd grade over behavioural data alone. Together with the behavioural measures they explained up to 88% of the variance. An additional discriminant analysis revealed a remarkably high accuracy in classifying normal (n=11) and poor readers (n=6). Due to the key limitation of the study, i.e. the small group sizes, the results of our prediction analyses should be interpreted with caution and regarded as preliminary despite cross-validation. Nevertheless our results indicate the potential of combining neuroimaging and behavioural measures to improve prediction at an early stage, when literacy skills are acquired and interventions are most beneficial. Copyright © 2013 Elsevier Inc. All rights reserved.

Monolithic CMOS imaging x-ray spectrometers

NASA Astrophysics Data System (ADS)

Kenter, Almus; Kraft, Ralph; Gauron, Thomas; Murray, Stephen S.

2014-07-01

The Smithsonian Astrophysical Observatory (SAO) in collaboration with SRI/Sarnoff is developing monolithic CMOS detectors optimized for x-ray astronomy. The goal of this multi-year program is to produce CMOS x-ray imaging spectrometers that are Fano noise limited over the 0.1-10keV energy band while incorporating the many benefits of CMOS technology. These benefits include: low power consumption, radiation "hardness", high levels of integration, and very high read rates. Small format test devices from a previous wafer fabrication run (2011-2012) have recently been back-thinned and tested for response below 1keV. These devices perform as expected in regards to dark current, read noise, spectral response and Quantum Efficiency (QE). We demonstrate that running these devices at rates ~> 1Mpix/second eliminates the need for cooling as shot noise from any dark current is greatly mitigated. The test devices were fabricated on 15μm, high resistivity custom (~30kΩ-cm) epitaxial silicon and have a 16 by 192 pixel format. They incorporate 16μm pitch, 6 Transistor Pinned Photo Diode (6TPPD) pixels which have ~40μV/electron sensitivity and a highly parallel analog CDS signal chain. Newer, improved, lower noise detectors have just been fabricated (October 2013). These new detectors are fabricated on 9μm epitaxial silicon and have a 1k by 1k format. They incorporate similar 16μm pitch, 6TPPD pixels but have ~ 50% higher sensitivity and much (3×) lower read noise. These new detectors have undergone preliminary testing for functionality in Front Illuminated (FI) form and are presently being prepared for back thinning and packaging. Monolithic CMOS devices such as these, would be ideal candidate detectors for the focal planes of Solar, planetary and other space-borne x-ray astronomy missions. The high through-put, low noise and excellent low energy response, provide high dynamic range and good time resolution; bright, time varying x-ray features could be temporally and spectrally resolved without saturation. We present details of our camera design and device performance with particular emphasis on those aspects of interest to single photon counting x-ray astronomy. These features include read noise, x-ray spectral response and quantum efficiency. Funding for this work has been provided in large part by NASA Grant NNX09AE86G and a grant from the Betty and Gordon Moore Foundation.

Development of a Smartphone-based reading system for lateral flow immunoassay.

PubMed

Lee, Sangdae; Kim, Giyoung; Moon, Jihea

2014-11-01

This study was conducted to develop and evaluate the performance of the Smartphone-based reading system for the lateral flow immunoassay (LFIA). Smartphone-based reading system consists of a Samsung Galaxy S2 Smartphone, Smartphone application, and a LFIA reader. LFIA reader is composed of the close-up lens with a focal length up to 30 mm, white LED light, lithium polymer battery, and main body. The Smartphone application for image acquisition and data analysis was developed on the Android platform. The standard curve was obtained by plotting the measured P(T)/P(c) or A(T)/A(c) ratio versus Salmonella standard concentration. The mean, standard deviation (SD), recovery, and relative standard deviation (RSD) were also calculated using additional experimental results. These data were compared with that obtained from the benchtop LFIA reader. The LOD in both systems was observed with 10(6) CFU/mL. The results show high accuracy and good reproducibility with a RSD less than 10% in the range of 10(6) to 10(9) CFU/mL. Due to the simple structure, good sensitivity, and high accuracy of the Smartphone-based reading system, this system can be substituted for the benchtop LFIA reader for point-of-care medical diagnostics.

COSMOS: accurate detection of somatic structural variations through asymmetric comparison between tumor and normal samples.

PubMed

Yamagata, Koichi; Yamanishi, Ayako; Kokubu, Chikara; Takeda, Junji; Sese, Jun

2016-05-05

An important challenge in cancer genomics is precise detection of structural variations (SVs) by high-throughput short-read sequencing, which is hampered by the high false discovery rates of existing analysis tools. Here, we propose an accurate SV detection method named COSMOS, which compares the statistics of the mapped read pairs in tumor samples with isogenic normal control samples in a distinct asymmetric manner. COSMOS also prioritizes the candidate SVs using strand-specific read-depth information. Performance tests on modeled tumor genomes revealed that COSMOS outperformed existing methods in terms of F-measure. We also applied COSMOS to an experimental mouse cell-based model, in which SVs were induced by genome engineering and gamma-ray irradiation, followed by polymerase chain reaction-based confirmation. The precision of COSMOS was 84.5%, while the next best existing method was 70.4%. Moreover, the sensitivity of COSMOS was the highest, indicating that COSMOS has great potential for cancer genome analysis. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Verbal Processing Reaction Times in "Normal" and "Poor" Readers.

ERIC Educational Resources Information Center

Culbertson, Jack; And Others

After it had been determined that reaction time (RT) was a sensitive measure of hemispheric dominance in a verbal task performed by normal adult readers, the reaction times of three groups of subjects (20 normal reading college students, 12 normal reading third graders and 11 poor reading grade school students) were compared. Ss were exposed to…

The effects of context on processing words during sentence reading among adults varying in age and literacy skill.

PubMed

Steen-Baker, Allison A; Ng, Shukhan; Payne, Brennan R; Anderson, Carolyn J; Federmeier, Kara D; Stine-Morrow, Elizabeth A L

2017-08-01

The facilitation of word processing by sentence context reflects the interaction between the build-up of message-level semantics and lexical processing. Yet, little is known about how this effect varies through adulthood as a function of reading skill. In this study, Participants 18-64 years old with a range of literacy competence read simple sentences as their eye movements were monitored. We manipulated the predictability of a sentence-final target word, operationalized as cloze probability. First fixation durations showed an interaction between age and literacy skill, decreasing with age among more skilled readers but increasing among less skilled readers. This pattern suggests that age-related slowing may impact reading when not buffered by skill, but with continued practice, automatization of reading can continue to develop in adulthood. In absolute terms, readers were sensitive to predictability, regardless of age or literacy, in both early and later measures. Older readers showed differential contextual sensitivity in regression patterns, effects not moderated by literacy skill. Finally, comprehension performance increased with age and literacy skill, but performance among less skilled readers was especially reduced when predictability was low, suggesting that low-literacy adults (regardless of age) struggle when creating mental representations under weaker semantic constraints. Collectively, these findings suggest that aging readers (regardless of reading skill) are more sensitive to context for meaning-integration processes; that less skilled adult readers (regardless of age) depend more on a constrained semantic representation for comprehension; and that the capacity for literacy engagement enables continued development of efficient lexical processing in adult reading development. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Face and Word Recognition Can Be Selectively Affected by Brain Injury or Developmental Disorders.

PubMed

Robotham, Ro J; Starrfelt, Randi

2017-01-01

Face and word recognition have traditionally been thought to rely on highly specialised and relatively independent cognitive processes. Some of the strongest evidence for this has come from patients with seemingly category-specific visual perceptual deficits such as pure prosopagnosia, a selective face recognition deficit, and pure alexia, a selective word recognition deficit. Together, the patterns of impaired reading with preserved face recognition and impaired face recognition with preserved reading constitute a double dissociation. The existence of these selective deficits has been questioned over the past decade. It has been suggested that studies describing patients with these pure deficits have failed to measure the supposedly preserved functions using sensitive enough measures, and that if tested using sensitive measurements, all patients with deficits in one visual category would also have deficits in the other. The implications of this would be immense, with most textbooks in cognitive neuropsychology requiring drastic revisions. In order to evaluate the evidence for dissociations, we review studies that specifically investigate whether face or word recognition can be selectively affected by acquired brain injury or developmental disorders. We only include studies published since 2004, as comprehensive reviews of earlier studies are available. Most of the studies assess the supposedly preserved functions using sensitive measurements. We found convincing evidence that reading can be preserved in acquired and developmental prosopagnosia and also evidence (though weaker) that face recognition can be preserved in acquired or developmental dyslexia, suggesting that face and word recognition are at least in part supported by independent processes.

Reading Development in Young Children: Genetic and Environmental Influences

PubMed Central

Logan, Jessica A. R.; Hart, Sara A.; Cutting, Laurie; Deater-Deckard, Kirby; Schatschneider, Chris; Petrill, Stephen

2013-01-01

The development of reading skills in typical students is commonly described as a rapid growth across early grades of active reading education, with a slowing down of growth as active instruction tapers. This study examined the extent to which genetics and environments influence these growth rates. Participants were 371 twin pairs, aged approximately 6 through 12, from the Western Reserve Reading Project. Development of word-level reading, reading comprehension, and rapid naming was examined using genetically sensitive latent quadratic growth curve modeling. Results confirmed the developmental trajectory described in the phenotypic literature. Furthermore, the same shared environmental influences were related to early reading skills and subsequent growth, but genetic influences on these factors were unique. PMID:23574275

The Efficacy of Vigorous-Intensity Exercise as an Aid to Smoking Cessation in Adults With High Anxiety Sensitivity: A Randomized Controlled Trial.

PubMed

Smits, Jasper A J; Zvolensky, Michael J; Davis, Michelle L; Rosenfield, David; Marcus, Bess H; Church, Timothy S; Powers, Mark B; Frierson, Georita M; Otto, Michael W; Hopkins, Lindsey B; Brown, Richard A; Baird, Scarlett O

2016-04-01

High anxiety sensitivity predicts poor smoking cessation outcomes. Aerobic exercise reduces anxiety sensitivity and aspects of the risk conferred by anxiety sensitivity. In the current study, we examined whether exercise can aid smoking cessation in adults with high anxiety sensitivity. Participants were sedentary and low-activity adult daily smokers (n = 136) with elevated prescreen anxiety sensitivity. Participants received 15 weeks of standard smoking cessation treatment (ST; cognitive behavioral therapy plus nicotine replacement therapy). In addition, participants were simultaneously randomized to 15 weeks of either an exercise intervention (ST + EX; n = 72) or a wellness education control condition (ST + CTRL; n = 64). Self-reported smoking abstinence was assessed weekly during the intervention, at the end of treatment (10 weeks after the target quit date), and at 4 and 6 months after the target quit date. Abstinence was verified by expired carbon monoxide readings and saliva cotinine. Results indicated that point prevalence abstinence (PPA) and prolonged abstinence (PA) rates were significantly higher for ST + EX than for ST + CTRL at each of the major end points among persons with high anxiety sensitivity (PPA: b = -0.91, standard error [SE] = 0.393, t(1171) = -2.33, p = .020; PA: b = -0.98, SE = 0.346, t(132) = -2.84, p = .005), but not among those with low anxiety sensitivity (PPA: b = -0.23, SE = 0.218, t(1171) = -1.06, p = .29; PA: b = -0.31, SE = 0.306, t(132) = -1.01, p = .32). The present results suggest that exercise facilitates the odds of quit success for smokers with high levels of anxiety sensitivity and therefore may be a useful therapeutic tactic for this high-risk segment of the smoking population. ClinicalTrials.gov, NCT01065506.

The Efficacy of Vigorous-Intensity Exercise as an Aid to Smoking Cessation in Adults with High Anxiety Sensitivity: A Randomized Controlled Trial

PubMed Central

Smits, Jasper A. J.; Zvolensky, Michael J.; Davis, Michelle L.; Rosenfield, David; Marcus, Bess H.; Church, Timothy S.; Powers, Mark B.; Frierson, Georita M.; Otto, Michael W.; Hopkins, Lindsey B.; Brown, Richard A.; Baird, Scarlett O.

2015-01-01

Objective High anxiety sensitivity predicts poor smoking cessation outcomes. Aerobic exercise reduces anxiety sensitivity and aspects of the risk conferred by anxiety sensitivity. In the current study, we examined whether exercise can aid smoking cessation in adults with high anxiety sensitivity. Method Participants were sedentary and low activity adult daily smokers (N = 136) with elevated prescreen anxiety sensitivity. Participants received 15 weeks of standard smoking cessation treatment (ST: cognitive behavioral therapy plus nicotine replacement therapy). Additionally, participants were simultaneously randomized to 15 weeks of either an exercise intervention (ST+EX; n = 72) or a wellness education control condition (ST+CTRL; n = 64). Self-reported smoking abstinence was assessed weekly during the intervention, at the end of treatment (10 weeks following the target quit date), and at 4 and 6 months following the target quit date. Abstinence was verified by expired carbon monoxide readings and saliva cotinine. Results Results indicated that point prevalence abstinence (PPA) and prolonged abstinence (PA) rates were significantly higher for ST+EX than for ST+CTRL at each of the major end points among persons with high anxiety sensitivity (PPA: b=−.91, SE=.393, t(1171)=−2.33, p=.020; PA: b=−.98, SE=.346, t(132)=−2.84, p=.005), but not among those with low anxiety sensitivity (PPA: b=−.23, SE=.218, t(1171)=−1.06, p=..29; PA: b=−.31, SE=.306, t(132)=−1.01, p=.32) Conclusions The present results suggest that exercise faciliates the odds of quit success for smokers with high levels of anxiety sensitivity, and therefore, may be a useful therapeutic tactic for this high-risk segment of the smoking population. PMID:26513517

First images of a digital autoradiography system based on a Medipix2 hybrid silicon pixel detector.

PubMed

Mettivier, Giovanni; Montesi, Maria Cristina; Russo, Paolo

2003-06-21

We present the first images of beta autoradiography obtained with the high-resolution hybrid pixel detector consisting of the Medipix2 single photon counting read-out chip bump-bonded to a 300 microm thick silicon pixel detector. This room temperature system has 256 x 256 square pixels of 55 microm pitch (total sensitive area of 14 x 14 mm2), with a double threshold discriminator and a 13-bit counter in each pixel. It is read out via a dedicated electronic interface and control software, also developed in the framework of the European Medipix2 Collaboration. Digital beta autoradiograms of 14C microscale standard strips (containing separate bands of increasing specific activity in the range 0.0038-32.9 kBq g(-1)) indicate system linearity down to a total background noise of 1.8 x 10(-3) counts mm(-2) s(-1). The minimum detectable activity is estimated to be 0.012 Bq for 36,000 s exposure and 0.023 Bq for 10,800 s exposure. The measured minimum detection threshold is less than 1600 electrons (equivalent to about 6 keV Si). This real-time system for beta autoradiography offers lower pixel pitch and higher sensitive area than the previous Medipix1-based system. It has a 14C sensitivity better than that of micro channel plate based systems, which, however, shows higher spatial resolution and sensitive area.

Rydberg-atom based radio-frequency electrometry using frequency modulation spectroscopy in room temperature vapor cells.

PubMed

Kumar, Santosh; Fan, Haoquan; Kübler, Harald; Jahangiri, Akbar J; Shaffer, James P

2017-04-17

Rydberg atom-based electrometry enables traceable electric field measurements with high sensitivity over a large frequency range, from gigahertz to terahertz. Such measurements are particularly useful for the calibration of radio frequency and terahertz devices, as well as other applications like near field imaging of electric fields. We utilize frequency modulated spectroscopy with active control of residual amplitude modulation to improve the signal to noise ratio of the optical readout of Rydberg atom-based radio frequency electrometry. Matched filtering of the signal is also implemented. Although we have reached similarly, high sensitivity with other read-out methods, frequency modulated spectroscopy is advantageous because it is well-suited for building a compact, portable sensor. In the current experiment, ∼3 µV cm^-1 Hz^-1/2 sensitivity is achieved and is found to be photon shot noise limited.

Using Television Commercials to Develop Reading Comprehension.

ERIC Educational Resources Information Center

Bowman, James D.; Bowman, S. Ray

1991-01-01

Suggests that teachers can use reluctant readers' sensitivity to and sophistication with "musicomedy" to both assess and develop reading comprehension. Discusses several class activities using the musical and humorous expressions in television commercials for fulfilling this objective. (RS)

A structured reading algorithm improves telemetric detection of atrial fibrillation after acute ischemic stroke.

PubMed

Kallmünzer, Bernd; Breuer, Lorenz; Hering, Christiane; Raaz-Schrauder, Dorette; Kollmar, Rainer; Huttner, Hagen B; Schwab, Stefan; Köhrmann, Martin

2012-04-01

Anticoagulation is a highly effective secondary prevention in patients with cardioembolic stroke and atrial fibrillation/flutter (AF). However, the condition remains underdiagnosed, because paroxysmal AF may be missed by diagnostic tests in the acute phase. In this study, the sensitivity of AF detection was assessed for serial electrocardiographic recordings and continuous stroke unit telemetric monitoring with or without a structured algorithm to analyze telemetric data (SEA-AF). Three hundred forty-six consecutive patients with acute ischemic stroke were prospectively included and subjected to standard telemetric monitoring. In addition, telemetric data were separately analyzed following SEA-AF, consisting of a structured evaluation of episodes with high risk for AF and a chronological beat-to-beat screening of the full registration. Serial electrocardiograms were conducted in 24-hour intervals. Median effective telemetry monitoring time was 75.5 hours (interquartile range 64-86 hours). Overall, AF was diagnosed in 119 of 346 patients (34.4%). The structured reading algorithm was the most sensitive method to detected AF. Conventional telemetry and serial electrocardiographic assessments were less effective. However, only 35% of patients with previously documented paroxysmal AF and negative baseline electrocardiogram demonstrated AF episodes during monitoring. Continuous stroke unit telemetry using SEA-AF shows a significantly higher detection rate for AF compared with daily electrocardiographic assessments and standard telemetry without structured reading. The low overall probability to detect paroxysmal AF with either method during the first days after stroke demonstrates the urgent need for complementary diagnostic strategies such as long-term monitoring and frequent follow-up assessments. Clinical Trial Registration- URL: www.clinicaltrials.gov. Unique identifier: NCT01177748.

GAS PHOTOTUBE CIRCUIT

DOEpatents

Richardson, J.H.

1958-03-01

This patent pertains to electronic circuits for measuring the intensity of light and is especially concerned with measurement between preset light thresholds. Such a circuit has application in connection with devices for reading-out information stored on punch cards or tapes where the cards and tapes are translucent. By the novel arrangement of this invention thc sensitivity of a gas phototube is maintained at a low value when the light intensity is below a first threshold level. If the light level rises above the first threshold level, the tube is rendered highly sensitive and an output signal will vary in proportion to the light intensity change. When the light level decreases below a second threshold level, the gas phototube is automatically rendered highly insensitive. Each of these threshold points is adjustable.

High performance liquid level monitoring system based on polymer fiber Bragg gratings embedded in silicone rubber diaphragms

NASA Astrophysics Data System (ADS)

Marques, Carlos A. F.; Peng, Gang-Ding; Webb, David J.

2015-05-01

Liquid-level sensing technologies have attracted great prominence, because such measurements are essential to industrial applications, such as fuel storage, flood warning and in the biochemical industry. Traditional liquid level sensors are based on electromechanical techniques; however they suffer from intrinsic safety concerns in explosive environments. In recent years, given that optical fiber sensors have lots of well-established advantages such as high accuracy, costeffectiveness, compact size, and ease of multiplexing, several optical fiber liquid level sensors have been investigated which are based on different operating principles such as side-polishing the cladding and a portion of core, using a spiral side-emitting optical fiber or using silica fiber gratings. The present work proposes a novel and highly sensitive liquid level sensor making use of polymer optical fiber Bragg gratings (POFBGs). The key elements of the system are a set of POFBGs embedded in silicone rubber diaphragms. This is a new development building on the idea of determining liquid level by measuring the pressure at the bottom of a liquid container, however it has a number of critical advantages. The system features several FBG-based pressure sensors as described above placed at different depths. Any sensor above the surface of the liquid will read the same ambient pressure. Sensors below the surface of the liquid will read pressures that increase linearly with depth. The position of the liquid surface can therefore be approximately identified as lying between the first sensor to read an above-ambient pressure and the next higher sensor. This level of precision would not in general be sufficient for most liquid level monitoring applications; however a much more precise determination of liquid level can be made by linear regression to the pressure readings from the sub-surface sensors. There are numerous advantages to this multi-sensor approach. First, the use of linear regression using multiple sensors is inherently more accurate than using a single pressure reading to estimate depth. Second, common mode temperature induced wavelength shifts in the individual sensors are automatically compensated. Thirdly, temperature induced changes in the sensor pressure sensitivity are also compensated. Fourthly, the approach provides the possibility to detect and compensate for malfunctioning sensors. Finally, the system is immune to changes in the density of the monitored fluid and even to changes in the effective force of gravity, as might be obtained in an aerospace application. The performance of an individual sensor was characterized and displays a sensitivity (54 pm/cm), enhanced by more than a factor of 2 when compared to a sensor head configuration based on a silica FBG published in the literature, resulting from the much lower elastic modulus of POF. Furthermore, the temperature/humidity behavior and measurement resolution were also studied in detail. The proposed configuration also displays a highly linear response, high resolution and good repeatability. The results suggest the new configuration can be a useful tool in many different applications, such as aircraft fuel monitoring, and biochemical and environmental sensing, where accuracy and stability are fundamental.

BAUM: improving genome assembly by adaptive unique mapping and local overlap-layout-consensus approach.

PubMed

Wang, Anqi; Wang, Zhanyu; Li, Zheng; Li, Lei M

2018-06-15

It is highly desirable to assemble genomes of high continuity and consistency at low cost. The current bottleneck of draft genome continuity using the second generation sequencing (SGS) reads is primarily caused by uncertainty among repetitive sequences. Even though the single-molecule real-time sequencing technology is very promising to overcome the uncertainty issue, its relatively high cost and error rate add burden on budget or computation. Many long-read assemblers take the overlap-layout-consensus (OLC) paradigm, which is less sensitive to sequencing errors, heterozygosity and variability of coverage. However, current assemblers of SGS data do not sufficiently take advantage of the OLC approach. Aiming at minimizing uncertainty, the proposed method BAUM, breaks the whole genome into regions by adaptive unique mapping; then the local OLC is used to assemble each region in parallel. BAUM can (i) perform reference-assisted assembly based on the genome of a close species (ii) or improve the results of existing assemblies that are obtained based on short or long sequencing reads. The tests on two eukaryote genomes, a wild rice Oryza longistaminata and a parrot Melopsittacus undulatus, show that BAUM achieved substantial improvement on genome size and continuity. Besides, BAUM reconstructed a considerable amount of repetitive regions that failed to be assembled by existing short read assemblers. We also propose statistical approaches to control the uncertainty in different steps of BAUM. http://www.zhanyuwang.xin/wordpress/index.php/2017/07/21/baum. Supplementary data are available at Bioinformatics online.

CLAST: CUDA implemented large-scale alignment search tool.

PubMed

Yano, Masahiro; Mori, Hiroshi; Akiyama, Yutaka; Yamada, Takuji; Kurokawa, Ken

2014-12-11

Metagenomics is a powerful methodology to study microbial communities, but it is highly dependent on nucleotide sequence similarity searching against sequence databases. Metagenomic analyses with next-generation sequencing technologies produce enormous numbers of reads from microbial communities, and many reads are derived from microbes whose genomes have not yet been sequenced, limiting the usefulness of existing sequence similarity search tools. Therefore, there is a clear need for a sequence similarity search tool that can rapidly detect weak similarity in large datasets. We developed a tool, which we named CLAST (CUDA implemented large-scale alignment search tool), that enables analyses of millions of reads and thousands of reference genome sequences, and runs on NVIDIA Fermi architecture graphics processing units. CLAST has four main advantages over existing alignment tools. First, CLAST was capable of identifying sequence similarities ~80.8 times faster than BLAST and 9.6 times faster than BLAT. Second, CLAST executes global alignment as the default (local alignment is also an option), enabling CLAST to assign reads to taxonomic and functional groups based on evolutionarily distant nucleotide sequences with high accuracy. Third, CLAST does not need a preprocessed sequence database like Burrows-Wheeler Transform-based tools, and this enables CLAST to incorporate large, frequently updated sequence databases. Fourth, CLAST requires <2 GB of main memory, making it possible to run CLAST on a standard desktop computer or server node. CLAST achieved very high speed (similar to the Burrows-Wheeler Transform-based Bowtie 2 for long reads) and sensitivity (equal to BLAST, BLAT, and FR-HIT) without the need for extensive database preprocessing or a specialized computing platform. Our results demonstrate that CLAST has the potential to be one of the most powerful and realistic approaches to analyze the massive amount of sequence data from next-generation sequencing technologies.

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

PubMed Central

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

1978-01-01

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

An optimized protocol for generation and analysis of Ion Proton sequencing reads for RNA-Seq.

PubMed

Yuan, Yongxian; Xu, Huaiqian; Leung, Ross Ka-Kit

2016-05-26

Previous studies compared running cost, time and other performance measures of popular sequencing platforms. However, comprehensive assessment of library construction and analysis protocols for Proton sequencing platform remains unexplored. Unlike Illumina sequencing platforms, Proton reads are heterogeneous in length and quality. When sequencing data from different platforms are combined, this can result in reads with various read length. Whether the performance of the commonly used software for handling such kind of data is satisfactory is unknown. By using universal human reference RNA as the initial material, RNaseIII and chemical fragmentation methods in library construction showed similar result in gene and junction discovery number and expression level estimated accuracy. In contrast, sequencing quality, read length and the choice of software affected mapping rate to a much larger extent. Unspliced aligner TMAP attained the highest mapping rate (97.27 % to genome, 86.46 % to transcriptome), though 47.83 % of mapped reads were clipped. Long reads could paradoxically reduce mapping in junctions. With reference annotation guide, the mapping rate of TopHat2 significantly increased from 75.79 to 92.09 %, especially for long (>150 bp) reads. Sailfish, a k-mer based gene expression quantifier attained highly consistent results with that of TaqMan array and highest sensitivity. We provided for the first time, the reference statistics of library preparation methods, gene detection and quantification and junction discovery for RNA-Seq by the Ion Proton platform. Chemical fragmentation performed equally well with the enzyme-based one. The optimal Ion Proton sequencing options and analysis software have been evaluated.

Evaluation of Word Attack Skills.

ERIC Educational Resources Information Center

Follettie, Joseph F.

A framework for more apt and sensitive evaluation of generalized word attack skill--the heart of oral reading skill--is presented. The paper envisions the design and development of oral reading instruction as bounded by a fully-specified evaluation scheme. (Author)

Pathways of the inferior frontal occipital fasciculus in overt speech and reading.

PubMed

Rollans, Claire; Cheema, Kulpreet; Georgiou, George K; Cummine, Jacqueline

2017-11-19

In this study, we examined the relationship between tractography-based measures of white matter integrity (ex. fractional anisotropy [FA]) from diffusion tensor imaging (DTI) and five reading-related tasks, including rapid automatized naming (RAN) of letters, digits, and objects, and reading of real words and nonwords. Twenty university students with no reported history of reading difficulties were tested on all five tasks and their performance was correlated with diffusion measures extracted through DTI tractography. A secondary analysis using whole-brain Tract-Based Spatial Statistics (TBSS) was also used to find clusters showing significant negative correlations between reaction time and FA. Results showed a significant relationship between the left inferior fronto-occipital fasciculus FA and performance on the RAN of objects task, as well as a strong relationship to nonword reading, which suggests a role for this tract in slower, non-automatic and/or resource-demanding speech tasks. There were no significant relationships between FA and the faster, more automatic speech tasks (RAN of letters and digits, and real word reading). These findings provide evidence for the role of the inferior fronto-occipital fasciculus in tasks that are highly demanding of orthography-phonology translation (e.g., nonword reading) and semantic processing (e.g., RAN object). This demonstrates the importance of the inferior fronto-occipital fasciculus in basic naming and suggests that this tract may be a sensitive predictor of rapid naming performance within the typical population. We discuss the findings in the context of current models of reading and speech production to further characterize the white matter pathways associated with basic reading processes. Copyright © 2017 IBRO. Published by Elsevier Ltd. All rights reserved.

Improving the Reading of Bisyllabic Words That Involve Context-Sensitive Spelling Rules: Focus on Successes or on Failures?

ERIC Educational Resources Information Center

Steenbeek-Planting, Esther G.; van Bon, Wim H. J.; Schreuder, Robert

2013-01-01

The effect of two training procedures on the improvement of reading accuracy in poor readers was examined in relation to their initial reading level. A randomized controlled trial was conducted with 60 poor readers. Poor readers were assigned to a control group that received no training, or one of two training conditions. One training concentrated…

Ultra-high density optical data storage in common transparent plastics.

PubMed

Kallepalli, Deepak L N; Alshehri, Ali M; Marquez, Daniela T; Andrzejewski, Lukasz; Scaiano, Juan C; Bhardwaj, Ravi

2016-05-25

The ever-increasing demand for high data storage capacity has spurred research on development of innovative technologies and new storage materials. Conventional GByte optical discs (DVDs and Bluray) can be transformed into ultrahigh capacity storage media by encoding multi-level and multiplexed information within the three dimensional volume of a recording medium. However, in most cases the recording medium had to be photosensitive requiring doping with photochromic molecules or nanoparticles in a multilayer stack or in the bulk material. Here, we show high-density data storage in commonly available plastics without any special material preparation. A pulsed laser was used to record data in micron-sized modified regions. Upon excitation by the read laser, each modified region emits fluorescence whose intensity represents 32 grey levels corresponding to 5 bits. We demonstrate up to 20 layers of embedded data. Adjusting the read laser power and detector sensitivity storage capacities up to 0.2 TBytes can be achieved in a standard 120 mm disc.

Speed discrimination predicts word but not pseudo-word reading rate in adults and children

PubMed Central

Main, Keith L.; Pestilli, Franco; Mezer, Aviv; Yeatman, Jason; Martin, Ryan; Phipps, Stephanie; Wandell, Brian

2014-01-01

Word familiarity may affect magnocellular processes of word recognition. To explore this idea, we measured reading rate, speed-discrimination, and contrast detection thresholds in adults and children with a wide range of reading abilities. We found that speed-discrimination thresholds are higher in children than in adults and are correlated with age. Speed discrimination thresholds are also correlated with reading rate, but only for words, not for pseudo-words. Conversely, we found no correlation between contrast sensitivity and reading rate and no correlation between speed discrimination thresholds WASI subtest scores. These findings support the position that reading rate is influenced by magnocellular circuitry attuned to the recognition of familiar word-forms. PMID:25278418

Predicting memory benefits in the production effect: the use and misuse of self-generated distinctive cues when making judgments of learning.

PubMed

Castel, Alan D; Rhodes, Matthew G; Friedman, Michael C

2013-01-01

The production effect occurs when reading a word aloud leads to better memory for the item, relative to words that are read silently. In the present study, we assessed the degree to which judgments of learning (JOLs) are sensitive to the production effect, to determine whether people are aware of how distinctive cues can enhance memory. If the act of saying a word aloud is used as a cue for later memorability, then JOLs should be sensitive to production. Experiment 1 demonstrated that this was the case, as participants provided higher JOLs for produced items than for those read silently. This pattern of JOLs was also evident when participants silently mouthed words (Exp. 2). In Experiment 3, participants instead made a nonunique response as the production component (saying "yes" instead of the word itself). JOLs were still higher under production, although memory performance did not differ from that in a silent condition. The results suggest that the presence of both specific and nonspecific self-generated cues is used to make metacognitive judgments, likely due to the high accessibility of this information, but that participants are not precisely aware of how distinctiveness enhances encoding and retrieval. Such findings have implications for how distinctiveness is perceived by learners and for what cues would appropriately be incorporated when predicting future memory performance.

Nanophotonic lab-on-a-chip platforms including novel bimodal interferometers, microfluidics and grating couplers.

PubMed

Duval, Daphné; González-Guerrero, Ana Belén; Dante, Stefania; Osmond, Johann; Monge, Rosa; Fernández, Luis J; Zinoviev, Kirill E; Domínguez, Carlos; Lechuga, Laura M

2012-05-08

One of the main limitations for achieving truly lab-on-a-chip (LOC) devices for point-of-care diagnosis is the incorporation of the "on-chip" detection. Indeed, most of the state-of-the-art LOC devices usually require complex read-out instrumentation, losing the main advantages of portability and simplicity. In this context, we present our last advances towards the achievement of a portable and label-free LOC platform with highly sensitive "on-chip" detection by using nanophotonic biosensors. Bimodal waveguide interferometers fabricated by standard silicon processes have been integrated with sub-micronic grating couplers for efficient light in-coupling, showing a phase resolution of 6.6 × 10(-4)× 2π rad and a limit of detection of 3.3 × 10(-7) refractive index unit (RIU) in bulk. A 3D network of SU-8 polymer microfluidics monolithically assembled at the wafer-level was included, ensuring perfect sealing and compact packaging. To overcome some of the drawbacks inherent to interferometric read-outs, a novel all-optical wavelength modulation system has been implemented, providing a linear response and a direct read-out of the phase variation. Sensitivity, specificity and reproducibility of the wavelength modulated BiMW sensor has been demonstrated through the label-free immunodetection of the human hormone hTSH at picomolar level using a reliable biofunctionalization process.

A mix-and-read drop-based in vitro two-hybrid method for screening high-affinity peptide binders

PubMed Central

Cui, Naiwen; Zhang, Huidan; Schneider, Nils; Tao, Ye; Asahara, Haruichi; Sun, Zhiyi; Cai, Yamei; Koehler, Stephan A.; de Greef, Tom F. A.; Abbaspourrad, Alireza; Weitz, David A.; Chong, Shaorong

2016-01-01

Drop-based microfluidics have recently become a novel tool by providing a stable linkage between phenotype and genotype for high throughput screening. However, use of drop-based microfluidics for screening high-affinity peptide binders has not been demonstrated due to the lack of a sensitive functional assay that can detect single DNA molecules in drops. To address this sensitivity issue, we introduced in vitro two-hybrid system (IVT2H) into microfluidic drops and developed a streamlined mix-and-read drop-IVT2H method to screen a random DNA library. Drop-IVT2H was based on the correlation between the binding affinity of two interacting protein domains and transcriptional activation of a fluorescent reporter. A DNA library encoding potential peptide binders was encapsulated with IVT2H such that single DNA molecules were distributed in individual drops. We validated drop-IVT2H by screening a three-random-residue library derived from a high-affinity MDM2 inhibitor PMI. The current drop-IVT2H platform is ideally suited for affinity screening of small-to-medium-sized libraries (103–106). It can obtain hits within a single day while consuming minimal amounts of reagents. Drop-IVT2H simplifies and accelerates the drop-based microfluidics workflow for screening random DNA libraries, and represents a novel alternative method for protein engineering and in vitro directed protein evolution. PMID:26940078

cDNA Clones with Rare and Recurrent Mutations Found in Cancers | Office of Cancer Genomics

Cancer.gov

The CTD2 Center at UT- MD Anderson Cancer Center has developed High-Throughput Mutagenesis and Molecular Barcoding (HiTMMoB)1,2 pipeline to construct mutant alleles open reading frame expression clones that are either recurrent or rare in cancers. These barcoded genes can be used for context-specific functional validation, detection of novel biomarkers (pathway activation) and targets (drug sensitivity).

Acute Brain Imaging in Children: Can MRI Replace CT as a Screening Tool?

PubMed

Wagner, Matthias W; Kontzialis, Marinos; Seeburg, Daniel; Stern, Steven E; Oshmyansky, Alexander; Poretti, Andrea; Huisman, Thierry A G M

2016-01-01

To determine if axial T2-weighted imaging can serve as screening tool for pediatric brain imaging. We retrospectively evaluated consecutive brain magnetic resonance imaging (MRI) data of 161 children (74 girls) with a mean age of 7.44 ± 5.71 years. Standard of reference was the final report of neuroradiology attendings. Three readers with different levels of experience were blinded for clinical diagnoses and study indications. First, readers studied only the axial T2-weighted screening sequence. Second, they studied all available anatomical and functional MRI sequences as performed per standard protocol for each clinical indication. The readings were classified as normal or abnormal. Sensitivity and specificity were measured. Axial T2 screening yielded a sensitivity of 77-88% and a specificity of 92%. The full studies/data sets had a sensitivity of 89-95% and a specificity of 86-93%. Nineteen of 167 studies were acquired for acute and 148 of 167 studies for nonacute clinical indication. Twenty-five false-negative diagnoses paneled in three groups were made by all readers together. Readers misread four of 19 studies with acute and 21 of 148 studies with nonacute clinical indication. Four of 21 misread studies with nonacute indications harbored unexpected findings needing management. Axial T2 screening can detect pediatric brain abnormalities with high sensitivity and specificity and can possibly replace CT as screening tool if the reading physician is aware of possible limitations/pitfalls. The level of experience influences sensitivity and specificity. Adding diffusion-weighted imaging and susceptibility-weighted imaging to a 3-dimensional T2-weighted sequence would most likely further increase sensitivity and specificity. Copyright © 2015 by the American Society of Neuroimaging.

Comparison of the performance of Ion Torrent chips in noninvasive prenatal trisomy detection.

PubMed

Wang, Yanlin; Wen, Zujia; Shen, Jiawei; Cheng, Weiwei; Li, Jun; Qin, Xiaolan; Ma, Duan; Shi, Yongyong

2014-07-01

Semiconductor high-throughput sequencing, represented by Ion Torrent PGM/Proton, proves to be feasible in the noninvasive prenatal diagnosis of fetal aneuploidies. It is commendable that, with less data and relevant cost also, an accurate result can be achieved owing to the high sensitivity and specificity of such kind of technology. We conducted a comparative analysis of the performance of four different Ion chips in detecting fetal chromosomal aneuploidies. Eight maternal plasma DNA samples, including four pregnancies with normal fetuses and four with trisomy 21 fetuses, were sequenced on Ion Torrent 314/316/318/PI chips, respectively. Results such as read mapped ratio, correlation coefficient and phred quality score were calculated and parallelly compared. All samples were correctly classified even with low-throughput chip, and, among the four chips, the 316 chip had the highest read mapped ratio, correlation coefficient, mean read length and phred quality score. All chips were well consistent with each other. Our results showed that all Ion chips are applicable in noninvasive prenatal fetal aneuploidy diagnosis. We recommend researchers or clinicians to use the appropriate chip with barcoding technology on the basis of the sample number.

Evaluation of mobile smartphones app as a screening tool for environmental noise monitoring.

PubMed

Ibekwe, Titus S; Folorunsho, David O; Dahilo, Enoch A; Gbujie, Ibeneche O; Nwegbu, Maxwell M; Nwaorgu, Onyekwere G

2016-01-01

Noise is a global occupational and environmental health hazard with considerable social and physiological impact and, therefore, there is a need for regular measurements to boost monitoring and regulations of environmental noise levels in our communities. This necessitates a readily available, inexpensive, and easy to use noise measuring device. We aimed to test the sensitivity and validity of mobile "smart" phones for this purpose. This was a comparative analysis of a cross sectional study done between January 2014 and February 2015. Noise levels were measured simultaneously at different locations within Abuja Nigeria at day and night hours in real time environments. A sound level meter (SLM) (Extech407730 Digital Soundmeter, serial no.: 2310135, calibration no: 91037) and three smartphones (Samsung Galaxy note3, Nokia S, and Techno Phantom Z running on Android "Apps" Androidboy1) were used. Statistical calculations were done with Pearson correlation, T-test and Consistency within American National Standards Institute acceptable standard errors. Noise level readings for both daytime and night with the SLM and the mobile phones showed equivalent values. All noise level meters measured were <100dB. The daytime readings were nearly identical in six locations and the maximum difference in values between the SLM and Smartphone instruments was 3db, noted in two locations. Readings in dBA showed strong correlation (r = 0.9) within acceptable error limits for Type 2 SLM devices and no significant difference in the values (p = 0.12 & 0.58) for both day and night. Sensitivity of the instrument yielded 92.9%. The androidboy1 "app" performance in this study showed a good correlation and comparative high sensitivity to the Standard SLM (type 2 SLM device). However there is the need for further studies.

Improving digital breast tomosynthesis reading time: A pilot multi-reader, multi-case study using concurrent Computer-Aided Detection (CAD).

PubMed

Balleyguier, Corinne; Arfi-Rouche, Julia; Levy, Laurent; Toubiana, Patrick R; Cohen-Scali, Franck; Toledano, Alicia Y; Boyer, Bruno

2017-12-01

Evaluate concurrent Computer-Aided Detection (CAD) with Digital Breast Tomosynthesis (DBT) to determine impact on radiologist performance and reading time. The CAD system detects and extracts suspicious masses, architectural distortions and asymmetries from DBT planes that are blended into corresponding synthetic images to form CAD-enhanced synthetic images. Review of CAD-enhanced images and navigation to corresponding planes to confirm or dismiss potential lesions allows radiologists to more quickly review DBT planes. A retrospective, crossover study with and without CAD was conducted with six radiologists who read an enriched sample of 80 DBT cases including 23 malignant lesions in 21 women. Area Under the Receiver Operating Characteristic (ROC) Curve (AUC) compared the readings with and without CAD to determine the effect of CAD on overall interpretation performance. Sensitivity, specificity, recall rate and reading time were also assessed. Multi-reader, multi-case (MRMC) methods accounting for correlation and requiring correct lesion localization were used to analyze all endpoints. AUCs were based on a 0-100% probability of malignancy (POM) score. Sensitivity and specificity were based on BI-RADS scores, where 3 or higher was positive. Average AUC across readers without CAD was 0.854 (range: 0.785-0.891, 95% confidence interval (CI): 0.769,0.939) and 0.850 (range: 0.746-0.905, 95% CI: 0.751,0.949) with CAD (95% CI for difference: -0.046,0.039), demonstrating non-inferiority of AUC. Average reduction in reading time with CAD was 23.5% (95% CI: 7.0-37.0% improvement), from an average 48.2 (95% CI: 39.1,59.6) seconds without CAD to 39.1 (95% CI: 26.2,54.5) seconds with CAD. Per-patient sensitivity was the same with and without CAD (0.865; 95% CI for difference: -0.070,0.070), and there was a small 0.022 improvement (95% CI for difference: -0.046,0.089) in per-lesion sensitivity from 0.790 without CAD to 0.812 with CAD. A slight reduction in specificity with a -0.014 difference (95% CI for difference: -0.079,0.050) and a small 0.025 increase (95% CI for difference: -0.036,0.087) in recall rate in non-cancer cases were observed with CAD. Concurrent CAD resulted in faster reading time with non-inferiority of radiologist interpretation performance. Radiologist sensitivity, specificity and recall rate were similar with and without CAD. Copyright © 2017 Elsevier B.V. All rights reserved.

mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications.

PubMed

Hach, Faraz; Sarrafi, Iman; Hormozdiari, Farhad; Alkan, Can; Eichler, Evan E; Sahinalp, S Cenk

2014-07-01

High throughput sequencing (HTS) platforms generate unprecedented amounts of data that introduce challenges for processing and downstream analysis. While tools that report the 'best' mapping location of each read provide a fast way to process HTS data, they are not suitable for many types of downstream analysis such as structural variation detection, where it is important to report multiple mapping loci for each read. For this purpose we introduce mrsFAST-Ultra, a fast, cache oblivious, SNP-aware aligner that can handle the multi-mapping of HTS reads very efficiently. mrsFAST-Ultra improves mrsFAST, our first cache oblivious read aligner capable of handling multi-mapping reads, through new and compact index structures that reduce not only the overall memory usage but also the number of CPU operations per alignment. In fact the size of the index generated by mrsFAST-Ultra is 10 times smaller than that of mrsFAST. As importantly, mrsFAST-Ultra introduces new features such as being able to (i) obtain the best mapping loci for each read, and (ii) return all reads that have at most n mapping loci (within an error threshold), together with these loci, for any user specified n. Furthermore, mrsFAST-Ultra is SNP-aware, i.e. it can map reads to reference genome while discounting the mismatches that occur at common SNP locations provided by db-SNP; this significantly increases the number of reads that can be mapped to the reference genome. Notice that all of the above features are implemented within the index structure and are not simple post-processing steps and thus are performed highly efficiently. Finally, mrsFAST-Ultra utilizes multiple available cores and processors and can be tuned for various memory settings. Our results show that mrsFAST-Ultra is roughly five times faster than its predecessor mrsFAST. In comparison to newly enhanced popular tools such as Bowtie2, it is more sensitive (it can report 10 times or more mappings per read) and much faster (six times or more) in the multi-mapping mode. Furthermore, mrsFAST-Ultra has an index size of 2GB for the entire human reference genome, which is roughly half of that of Bowtie2. mrsFAST-Ultra is open source and it can be accessed at http://mrsfast.sourceforge.net. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Effects of reading goals on reading comprehension, reading rate, and allocation of working memory in children and adolescents with spina bifida meningomyelocele

PubMed Central

ENGLISH, LIANNE; BARNES, MARCIA A.; FLETCHER, JACK M.; DENNIS, MAUREEN; RAGHUBAR, KIMBERLY P.

2011-01-01

Spina bifida meningomyelocele (SBM) is a neurodevelopmental disorder associated with intact word decoding and deficient text and discourse comprehension. This study investigated the ability to adjust reading in accordance with specified reading goals in 79 children and adolescents with SBM (9–19 years of age) and 39 controls (8–17 years of age). Both groups demonstrated slower reading times and enhanced comprehension when reading to study or to come up with a title than when reading for specific information or for entertainment. For both groups, verbal working memory contributed to comprehension performance in those reading conditions hypothesized to require more cognitive effort. Despite their sensitivity to the goals of reading, the group with SBM answered fewer comprehension questions correctly across all reading goal conditions. The results are discussed in relation to the hypothesized cognitive underpinnings of comprehension deficits in SBM and to current models of text comprehension. PMID:20338082

A permanently installed guided wave system for pipe monitoring

NASA Astrophysics Data System (ADS)

Galvagni, Andrea; Cawley, Peter

2012-04-01

Ultrasonic guided waves are routinely used to inspect pipes. The advantage of this technique is that it enables a fullyvolumetric screening of several metres of pipe from a single transducer location, resulting in substantial time and cost savings. However, it suffers from limitations such as relatively low damage sensitivity and difficulties in dealing with intricate pipe networks; furthermore, for a pipe that is buried, submerged or high up in a plant, access to even a single point can be prohibitively expensive. The use of permanently attached sensors can overcome these limitations since access needs to be obtained only once during installation and they enable the use of baseline subtraction, so that any reading from a sensor can be compared to previous readings. This paper discusses the advantages of baseline subtraction and the challenge of compensating for signal changes due to effects other than the growth of damage. It is shown that the use of baseline subtraction allows significant damage sensitivity improvements, particularly in the vicinity of large reflectors. Data from four years of field experience is backed up by accelerated laboratory testing.

ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly.

PubMed

Yang, Rendong; Nelson, Andrew C; Henzler, Christine; Thyagarajan, Bharat; Silverstein, Kevin A T

2015-12-07

Comprehensive identification of insertions/deletions (indels) across the full size spectrum from second generation sequencing is challenging due to the relatively short read length inherent in the technology. Different indel calling methods exist but are limited in detection to specific sizes with varying accuracy and resolution. We present ScanIndel, an integrated framework for detecting indels with multiple heuristics including gapped alignment, split reads and de novo assembly. Using simulation data, we demonstrate ScanIndel's superior sensitivity and specificity relative to several state-of-the-art indel callers across various coverage levels and indel sizes. ScanIndel yields higher predictive accuracy with lower computational cost compared with existing tools for both targeted resequencing data from tumor specimens and high coverage whole-genome sequencing data from the human NIST standard NA12878. Thus, we anticipate ScanIndel will improve indel analysis in both clinical and research settings. ScanIndel is implemented in Python, and is freely available for academic use at https://github.com/cauyrd/ScanIndel.

Stigma Cues Increase Self-Conscious Emotions and Decrease Likelihood of Attention to Information about Preventing Stigmatized Health Issues

PubMed Central

Earl, Allison; Nisson, Christina A.; Albarracín, Dolores

2018-01-01

Health communications are only effective if target audiences actually receive the messages. One potential barrier to effective health communication is the potential stigma of attending to health information, particularly for stigmatizing health issues. The purpose of the present paper was to examine when participants report self-conscious emotions (e.g., shame, embarrassment) in response to health communications, as well as likelihood of reading health information associated with these emotions. Across three studies, participants read information about preventing diseases that are either highly stigmatized or non-stigmatized. Increased accessibility of stigma cues by (a) manipulating the perceived absence vs. presence of others, or (b) measuring lower vs. higher rejection sensitivity resulted in increased self-conscious emotions in response to information about stigmatized health issues. In addition, stigma cues decreased the likelihood of reading information about stigmatized (but not non-stigmatized) health information. Implications for health outcomes and intervention design are discussed. PMID:29809200

CNV-seq, a new method to detect copy number variation using high-throughput sequencing.

PubMed

Xie, Chao; Tammi, Martti T

2009-03-06

DNA copy number variation (CNV) has been recognized as an important source of genetic variation. Array comparative genomic hybridization (aCGH) is commonly used for CNV detection, but the microarray platform has a number of inherent limitations. Here, we describe a method to detect copy number variation using shotgun sequencing, CNV-seq. The method is based on a robust statistical model that describes the complete analysis procedure and allows the computation of essential confidence values for detection of CNV. Our results show that the number of reads, not the length of the reads is the key factor determining the resolution of detection. This favors the next-generation sequencing methods that rapidly produce large amount of short reads. Simulation of various sequencing methods with coverage between 0.1x to 8x show overall specificity between 91.7 - 99.9%, and sensitivity between 72.2 - 96.5%. We also show the results for assessment of CNV between two individual human genomes.

Development of 3He LPSDs and read-out system for the SANS spectrometer at CPHS

NASA Astrophysics Data System (ADS)

Huang, T. C.; Gong, H.; Shao, B. B.; Wang, X. W.; Zhang, Y.; Pang, B. B.

2014-01-01

The Compact Pulsed Hadron Source (CPHS) is a 13-MeV proton-linac-driven neutron source under construction in Tsinghua University. Time-of-flight (TOF) small-angle neutron scattering (SANS) spectrometer is one of the first instruments to be built. It is designed to use linear position-sensitive detectors (LPSDs) of 3He gas proportional counters to cover a 1 m×1 m area. Prototypical LPSDs (Φ = 12 mm, L=1 m) have been made and read-out system is developed based on charge division. This work describes the in-house fabrication of the prototypical LPSDs and design of the read-out system including front-end electronics and data acquisition (DAQ) system. Key factors of the front-end electronics are studied and optimized with PSPICE simulation. DAQ system is designed based on VME bus architecture and FPGA Mezzanine Card (FMC) standard with high flexibility and extendibility. Preliminary experiments are carried out and the results are present and discussed.

High Stakes Testing and Reading Assessment. National Reading Conference Policy Brief

ERIC Educational Resources Information Center

Afflerbach, Peter

2005-01-01

This National Reading Conference Policy Brief provides information related to high stakes reading tests and reading assessment. High stakes reading tests are those with highly consequential outcomes for students, teachers, and schools. These outcomes may include student promotion or retention, student placement in reading groups, school funding…

The Saccharomyces cerevisiae ETH1 Gene, an Inducible Homolog of Exonuclease III That Provides Resistance to DNA-Damaging Agents and Limits Spontaneous Mutagenesis

PubMed Central

Bennett, Richard A. O.

1999-01-01

The recently sequenced Saccharomyces cerevisiae genome was searched for a gene with homology to the gene encoding the major human AP endonuclease, a component of the highly conserved DNA base excision repair pathway. An open reading frame was found to encode a putative protein (34% identical to the Schizosaccharomyces pombe eth1+ [open reading frame SPBC3D6.10] gene product) with a 347-residue segment homologous to the exonuclease III family of AP endonucleases. Synthesis of mRNA from ETH1 in wild-type cells was induced sixfold relative to that in untreated cells after exposure to the alkylating agent methyl methanesulfonate (MMS). To investigate the function of ETH1, deletions of the open reading frame were made in a wild-type strain and a strain deficient in the known yeast AP endonuclease encoded by APN1. eth1 strains were not more sensitive to killing by MMS, hydrogen peroxide, or phleomycin D1, whereas apn1 strains were ∼3-fold more sensitive to MMS and ∼10-fold more sensitive to hydrogen peroxide than was the wild type. Double-mutant strains (apn1 eth1) were ∼15-fold more sensitive to MMS and ∼2- to 3-fold more sensitive to hydrogen peroxide and phleomycin D1 than were apn1 strains. Elimination of ETH1 in apn1 strains also increased spontaneous mutation rates 9- or 31-fold compared to the wild type as determined by reversion to adenine or lysine prototrophy, respectively. Transformation of apn1 eth1 cells with an expression vector containing ETH1 reversed the hypersensitivity to MMS and limited the rate of spontaneous mutagenesis. Expression of ETH1 in a dut-1 xthA3 Escherichia coli strain demonstrated that the gene product functionally complements the missing AP endonuclease activity. Thus, in apn1 cells where the major AP endonuclease activity is missing, ETH1 offers an alternate capacity for repair of spontaneous or induced damage to DNA that is normally repaired by Apn1 protein. PMID:10022867

Phonological Sensitivity: A Quasi-Parallel Progression of Word Structure Units and Cognitive Operations.

ERIC Educational Resources Information Center

Anthony, Jason L.; Lonigan, Christopher J.; Driscoll, Kimberly; Phillips, Beth M.; Burgess, Stephen R.

2003-01-01

Investigates the order of acquisition of phonological sensitivity skills among preschool and kindergarten children. Supports a developmental conceptualization of phonological sensitivity. Discusses findings in relation to their implications for improving assessment, early literacy instruction, and prevention of reading difficulties. (SG)

Quantitative digital image analysis of chromogenic assays for high throughput screening of alpha-amylase mutant libraries.

PubMed

Shankar, Manoharan; Priyadharshini, Ramachandran; Gunasekaran, Paramasamy

2009-08-01

An image analysis-based method for high throughput screening of an alpha-amylase mutant library using chromogenic assays was developed. Assays were performed in microplates and high resolution images of the assay plates were read using the Virtual Microplate Reader (VMR) script to quantify the concentration of the chromogen. This method is fast and sensitive in quantifying 0.025-0.3 mg starch/ml as well as 0.05-0.75 mg glucose/ml. It was also an effective screening method for improved alpha-amylase activity with a coefficient of variance of 18%.

A Feasibility Study of Real-Time Remote CT Reading for Suspected Acute Appendicitis Using an iPhone.

PubMed

Kim, Changsun; Kang, Bossng; Choi, Hyuk Joong; Park, Joon Bum

2015-08-01

We aimed to evaluate the feasibility of an iPhone-based remote control system as a real-time remote computed tomography (CT) reading tool for suspected appendicitis using a third-generation (3G) network under suboptimal illumination. One hundred twenty abdominal CT scans were selected; 60 had no signs of appendicitis, whereas the remaining 60 had signs of appendicitis. The 16 raters reviewed the images using the liquid crystal display (LCD) monitor of a picture archiving and communication system (PACS) workstation, as well as using an iPhone connected to the PACS workstation via a remote control system. We graded the probability of the presence of acute appendicitis for each examination using a five-point Likert scale. The overall sensitivity and specificity for the diagnosis of suspected appendicitis using the iPhone and the LCD monitor were high, and they were not significantly different (sensitivity P = 1.00, specificity P = 0.14). The average areas under the receiver operating characteristic curves for all CT readings with the iPhone and LCD monitor were 0.978 (confidence interval 0.965-0.991) and 0.974 (0.960-0.988), respectively, and the two devices did not have significantly different diagnostic performances (P = 0.55). The inter-rater agreement for both devices was very good; the kappa value for the iPhone was 0.809 (0.793-0.826), and that for the LCD monitor was 0.817 (0.801-0.834). Each rater had moderate-to-very good intra-observer agreement between the two devices. We verified the feasibility of an iPhone-based remote control system as a real-time remote CT reading tool for identifying suspected appendicitis using a 3G network and suboptimal illumination.

Evaluation of a LED-based flatbed document scanner for radiochromic film dosimetry in transmission mode.

PubMed

Lárraga-Gutiérrez, José Manuel; García-Garduño, Olivia Amanda; Treviño-Palacios, Carlos; Herrera-González, José Alfredo

2018-03-01

Flatbed scanners are the most frequently used reading instrument for radiochromic film dosimetry because its low cost, high spatial resolution, among other advantages. These scanners use a fluorescent lamp and a CCD array as light source and detector, respectively. Recently, manufacturers of flatbed scanners replaced the fluorescent lamp by light emission diodes (LED) as a light source. The goal of this work is to evaluate the performance of a commercial flatbed scanner with LED based source light for radiochromic film dosimetry. Film read out consistency, response uniformity, film-scanner sensitivity, long term stability and total dose uncertainty was evaluated. In overall, the performance of the LED flatbed scanner is comparable to that of a cold cathode fluorescent lamp (CCFL). There are important spectral differences between LED and CCFL lamps that results in a higher sensitivity of the LED scanner in the green channel. Total dose uncertainty, film response reproducibility and long-term stability of LED scanner are slightly better than those of the CCFL. However, the LED based scanner has a strong non-uniform response, up to 9%, that must be adequately corrected for radiotherapy dosimetry QA. The differences in light emission spectra between LED and CCFL lamps and its potential impact on film-scanner sensitivity suggest that the design of a dedicated flat-bed scanner with LEDs may improve sensitivity and dose uncertainty in radiochromic film dosimetry. Copyright © 2018 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Is Freedom Contagious? A Self-Regulatory Model of Reactance and Sensitivity to Deviant Peers.

PubMed

Leander, N Pontus; vanDellen, Michelle R; Rachl-Willberger, Judith; Shah, James Y; Fitzsimons, Gavan J; Chartrand, Tanya L

2016-12-01

Psychological reactance is typically assumed to motivate resistance to controlling peer influences and societal prohibitions. However, some peer influences encourage behaviors prohibited by society. We consider whether reactant individuals are sensitive to such opportunities to enhance their autonomy. We specifically propose a self-regulatory perspective on reactance, wherein freedom/autonomy is the superordinate goal, and thus highly reactant individuals will be sensitive to peer influences that could enhance their behavioral freedoms. In two studies, we find that reactant individuals can be cooperative in response to autonomy-supportive peer influences. Participants read a scenario in which a peer's intentions to engage in substance use were manipulated to imply freedom of choice or not. Results indicated that highly reactant participants were sensitive to deviant peers whose own behavior towards alcohol (Study 1, N = 160) or marijuana (Study 2, N = 124) appeared to be motivated by autonomy and thus afforded free choice. Altogether, the results support a self-regulatory model of reactance, wherein deviant peer influence can be a means to pursue autonomy.

Detection of breast cancer in automated 3D breast ultrasound

NASA Astrophysics Data System (ADS)

Tan, Tao; Platel, Bram; Mus, Roel; Karssemeijer, Nico

2012-03-01

Automated 3D breast ultrasound (ABUS) is a novel imaging modality, in which motorized scans of the breasts are made with a wide transducer through a membrane under modest compression. The technology has gained high interest and may become widely used in screening of dense breasts, where sensitivity of mammography is poor. ABUS has a high sensitivity for detecting solid breast lesions. However, reading ABUS images is time consuming, and subtle abnormalities may be missed. Therefore, we are developing a computer aided detection (CAD) system to help reduce reading time and errors. In the multi-stage system we propose, segmentations of the breast and nipple are performed, providing landmarks for the detection algorithm. Subsequently, voxel features characterizing coronal spiculation patterns, blobness, contrast, and locations with respect to landmarks are extracted. Using an ensemble of classifiers, a likelihood map indicating potential malignancies is computed. Local maxima in the likelihood map are determined using a local maxima detector and form a set of candidate lesions in each view. These candidates are further processed in a second detection stage, which includes region segmentation, feature extraction and a final classification. Region segmentation is performed using a 3D spiral-scanning dynamic programming method. Region features include descriptors of shape, acoustic behavior and texture. Performance was determined using a 78-patient dataset with 93 images, including 50 malignant lesions. We used 10-fold cross-validation. Using FROC analysis we found that the system obtains a lesion sensitivity of 60% and 70% at 2 and 4 false positives per image respectively.

A position- and time-sensitive photon-counting detector with delay- line read-out

NASA Astrophysics Data System (ADS)

Jagutzki, Ottmar; Dangendorf, Volker; Lauck, Ronald; Czasch, Achim; Milnes, James

2007-05-01

We have developed image intensifier tubes with delay-anode read-out for time- and position-sensitive photon counting. The timing precision is better than 1 ns with 1000x1000 pixels position resolution and up to one megacounts/s processing rate. Large format detectors of 40 and 75 mm active diameter with internal helical-wire delay-line anodes have been produced and specified. A different type of 40 and 25 mm tubes with semi-conducting screen for image charge read-out allow for an economic and robust tube design and for placing the read-out anodes outside the sealed housing. Two types of external delay-line anodes, i.e. pick-up electrodes for the image charge, have been tested. We present tests of the detector and anode performance. Due to the low background this technique is well suited for applications with very low light intensity and especially if a precise time tagging for each photon is required. As an example we present the application of scintillator read-out in time-of-flight (TOF) neutron radiography. Further applications so far are Fluorescence Life-time Microscopy (FLIM) and Astronomy.

Does sensitivity measured from screening test-sets predict clinical performance?

NASA Astrophysics Data System (ADS)

Soh, BaoLin P.; Lee, Warwick B.; Mello-Thoms, Claudia R.; Tapia, Kriscia A.; Ryan, John; Hung, Wai Tak; Thompson, Graham J.; Heard, Rob; Brennan, Patrick C.

2014-03-01

Aim: To examine the relationship between sensitivity measured from the BREAST test-set and clinical performance. Background: Although the UK and Australia national breast screening programs have regarded PERFORMS and BREAST test-set strategies as possible methods of estimating readers' clinical efficacy, the relationship between test-set and real life performance results has never been satisfactorily understood. Methods: Forty-one radiologists from BreastScreen New South Wales participated in this study. Each reader interpreted a BREAST test-set which comprised sixty de-identified mammographic examinations sourced from the BreastScreen Digital Imaging Library. Spearman's rank correlation coefficient was used to compare the sensitivity measured from the BREAST test-set with screen readers' clinical audit data. Results: Results shown statistically significant positive moderate correlations between test-set sensitivity and each of the following metrics: rate of invasive cancer per 10 000 reads (r=0.495; p < 0.01); rate of small invasive cancer per 10 000 reads (r=0.546; p < 0.001); detection rate of all invasive cancers and DCIS per 10 000 reads (r=0.444; p < 0.01). Conclusion: Comparison between sensitivity measured from the BREAST test-set and real life detection rate demonstrated statistically significant positive moderate correlations which validated that such test-set strategies can reflect readers' clinical performance and be used as a quality assurance tool. The strength of correlation demonstrated in this study was higher than previously found by others.

Effects of a small talking facial image on autonomic activity: the moderating influence of dispositional BIS and BAS sensitivities and emotions.

PubMed

Ravaja, Niklas

2004-01-01

We examined the moderating influence of dispositional behavioral inhibition system and behavioral activation system (BAS) sensitivities, Negative Affect, and Positive Affect on the relationship between a small moving vs. static facial image and autonomic responses when viewing/listening to news messages read by a newscaster among 36 young adults. Autonomic parameters measured were respiratory sinus arrhythmia (RSA), low-frequency (LF) component of heart rate variability (HRV), electrodermal activity, and pulse transit time (PTT). The results showed that dispositional BAS sensitivity, particularly BAS Fun Seeking, and Negative Affect interacted with facial image motion in predicting autonomic nervous system activity. A moving facial image was related to lower RSA and LF component of HRV and shorter PTTs as compared to a static facial image among high BAS individuals. Even a small talking facial image may contribute to sustained attentional engagement among high BAS individuals, given that the BAS directs attention toward the positive cue and a moving social stimulus may act as a positive incentive for high BAS individuals.

Validation of search filters for identifying pediatric studies in PubMed.

PubMed

Leclercq, Edith; Leeflang, Mariska M G; van Dalen, Elvira C; Kremer, Leontien C M

2013-03-01

To identify and validate PubMed search filters for retrieving studies including children and to develop a new pediatric search filter for PubMed. We developed 2 different datasets of studies to evaluate the performance of the identified pediatric search filters, expressed in terms of sensitivity, precision, specificity, accuracy, and number needed to read (NNR). An optimal search filter will have a high sensitivity and high precision with a low NNR. In addition to the PubMed Limits: All Child: 0-18 years filter (in May 2012 renamed to PubMed Filter Child: 0-18 years), 6 search filters for identifying studies including children were identified: 3 developed by Kastner et al, 1 developed by BestBets, one by the Child Health Field, and 1 by the Cochrane Childhood Cancer Group. Three search filters (Cochrane Childhood Cancer Group, Child Health Field, and BestBets) had the highest sensitivity (99.3%, 99.5%, and 99.3%, respectively) but a lower precision (64.5%, 68.4%, and 66.6% respectively) compared with the other search filters. Two Kastner search filters had a high precision (93.0% and 93.7%, respectively) but a low sensitivity (58.5% and 44.8%, respectively). They failed to identify many pediatric studies in our datasets. The search terms responsible for false-positive results in the reference dataset were determined. With these data, we developed a new search filter for identifying studies with children in PubMed with an optimal sensitivity (99.5%) and precision (69.0%). Search filters to identify studies including children either have a low sensitivity or a low precision with a high NNR. A new pediatric search filter with a high sensitivity and a low NNR has been developed. Copyright © 2013 Mosby, Inc. All rights reserved.

Effect of a change to mite-free bedding on children with mite-sensitive asthma: a controlled trial.

PubMed Central

Burr, M L; Neale, E; Dean, B V; Verrier-Jones, E R

1980-01-01

Twenty-one children with mite-sensitive asthma took part in a crossover randomised controlled trial of mite-free bedding. Each child was issued with a new sleeping bag and pillow for a month, and twice-daily peak flow readings were compared with those obtained during a month in the child's ordinary bedding. Seventeen of the children had higher mean peak flow readings during the period in the mite-free bedding (p < 0.01). The overall improvement was only modest, however, and some mites had appeared in most of the bedding by the end of the trial. New bedding may be helpful to patients with mite-sensitive asthma, but methods are needed to prevent colonisation by mites. PMID:7001668

Spelling in Adults: The Combined Influences of Language Skills and Reading Experience

ERIC Educational Resources Information Center

Burt, Jennifer S.

2006-01-01

One hundred and twelve university students completed 7 tests assessing word-reading accuracy, print exposure, phonological sensitivity, phonological coding and knowledge of English morphology as predictors of spelling accuracy. Together the tests accounted for 71% of the variance in spelling, with phonological skills and morphological knowledge…

Situational Context Affects Definiteness Preferences: Accommodation of Presuppositions

ERIC Educational Resources Information Center

Clifton, Charles, Jr.

2013-01-01

In 4 experiments, we used self-paced reading and eye tracking to demonstrate that readers are, under some conditions, sensitive to the presuppositions of definite versus indefinite determiner phrases (DPs). Reading was faster when the context stereotypically provided a single possible referent for a definite DP or multiple possible referents for…

Reflections of Life Through Books.

ERIC Educational Resources Information Center

Porter, Jane

The anthology by Jesse Perry, "Reading Ladders for Human Relations," constructed of a blend of best literary works, was compiled based on the conviction that reading selected books would increase the social sensitivity of young people and play a unique role in fostering better human relationships. Its main purposes are expressed in the section…

Improved Airborne Gravity Results Using New Relative Gravity Sensor Technology

NASA Astrophysics Data System (ADS)

Brady, N.

2013-12-01

Airborne gravity data has contributed greatly to our knowledge of subsurface geophysics particularly in rugged and otherwise inaccessible areas such as Antarctica. Reliable high quality GPS data has renewed interest in improving the accuracy of airborne gravity systems and recent improvements in the electronic control of the sensor have increased the accuracy and ability of the classic Lacoste and Romberg zero length spring gravity meters to operate in turbulent air conditions. Lacoste and Romberg type gravity meters provide increased sensitivity over other relative gravity meters by utilizing a mass attached to a horizontal beam which is balanced by a ';zero length spring'. This type of dynamic gravity sensor is capable of measuring gravity changes on the order of 0.05 milliGals in laboratory conditions but more commonly 0.7 to 1 milliGal in survey use. The sensor may have errors induced by the electronics used to read the beam position as well as noise induced by unwanted accelerations, commonly turbulence, which moves the beam away from its ideal balance position otherwise known as the reading line. The sensor relies on a measuring screw controlled by a computer which attempts to bring the beam back to the reading line position. The beam is also heavily damped so that it does not react to most unwanted high frequency accelerations. However this heavily damped system is slow to react, particularly in turns where there are very high Eotvos effects. New sensor technology utilizes magnetic damping of the beam coupled with an active feedback system which acts to effectively keep the beam locked at the reading line position. The feedback system operates over the entire range of the system so there is now no requirement for a measuring screw. The feedback system operates at very high speed so that even large turbulent events have minimal impact on data quality and very little, if any, survey line data is lost because of large beam displacement errors. Airborne testing along with results from ground based van testing and laboratory results have shown that the new sensor provides more consistent gravity data, as measured by repeated line surveys, as well as preserving the inherent sensitivity of the Lacoste and Romberg zero length spring design. The sensor also provides reliability during survey operation as there is no mechanical counter screw. Results will be presented which show the advantages of the new sensor system over the current technology in both data quality and survey productivity. Applications include high resolution geoid mapping, crustal structure investigations and resource mapping of minerals, oil and gas.

The Genetic and Environmental Foundation of the Simple View of Reading in Chinese

PubMed Central

Ho, Connie Suk-Han; Chow, Bonnie Wing-Yin; Wong, Simpson Wai-Lap; Waye, Mary M. Y.; Bishop, Dorothy V. M.

2012-01-01

The Simple View of Reading (SVR) in Chinese was examined in a genetically sensitive design. A total of 270 pairs of Chinese twins (190 pairs of monozygotic twins and 80 pairs of same-sex dizygotic twins) were tested on Chinese vocabulary and word reading at the mean age 7.8 years and reading comprehension of sentences and passages one year later. Results of behavior-genetic analyses showed that both vocabulary and word reading had significant independent genetic influences on reading comprehension, and the two factors together accounted for most but not all of the genetic influences on reading comprehension. In addition, sentence comprehension had a stronger genetic correlation with word reading while passage comprehension showed a trend of stronger genetic overlap with vocabulary. These findings suggest that the genetic foundation of the SVR in Chinese is largely supported in that language comprehension and decoding are two core skills for reading comprehension in nonalphabetic as well as alphabetic written languages. PMID:23112862

What Is in the Naming? A 5-Year Longitudinal Study of Early Rapid Naming and Phonological Sensitivity in Relation to Subsequent Reading Skills in Both Native Chinese and English as a Second Language

ERIC Educational Resources Information Center

Pan, Jinger; McBride-Chang, Catherine; Shu, Hua; Liu, Hongyun; Zhang, Yuping; Li, Hong

2011-01-01

Among 262 Chinese children, syllable awareness and rapid automatized naming (RAN) at age 5 years and invented spelling of Pinyin at age 6 years independently predicted subsequent Chinese character recognition and English word reading at ages 8 years and 10 years, even with initial Chinese character reading ability statistically controlled. In…

An accurate algorithm for the detection of DNA fragments from dilution pool sequencing experiments.

PubMed

Bansal, Vikas

2018-01-01

The short read lengths of current high-throughput sequencing technologies limit the ability to recover long-range haplotype information. Dilution pool methods for preparing DNA sequencing libraries from high molecular weight DNA fragments enable the recovery of long DNA fragments from short sequence reads. These approaches require computational methods for identifying the DNA fragments using aligned sequence reads and assembling the fragments into long haplotypes. Although a number of computational methods have been developed for haplotype assembly, the problem of identifying DNA fragments from dilution pool sequence data has not received much attention. We formulate the problem of detecting DNA fragments from dilution pool sequencing experiments as a genome segmentation problem and develop an algorithm that uses dynamic programming to optimize a likelihood function derived from a generative model for the sequence reads. This algorithm uses an iterative approach to automatically infer the mean background read depth and the number of fragments in each pool. Using simulated data, we demonstrate that our method, FragmentCut, has 25-30% greater sensitivity compared with an HMM based method for fragment detection and can also detect overlapping fragments. On a whole-genome human fosmid pool dataset, the haplotypes assembled using the fragments identified by FragmentCut had greater N50 length, 16.2% lower switch error rate and 35.8% lower mismatch error rate compared with two existing methods. We further demonstrate the greater accuracy of our method using two additional dilution pool datasets. FragmentCut is available from https://bansal-lab.github.io/software/FragmentCut. vibansal@ucsd.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Theoretical Noise Analysis on a Position-sensitive Metallic Magnetic Calorimeter

NASA Technical Reports Server (NTRS)

Smith, Stephen J.

2007-01-01

We report on the theoretical noise analysis for a position-sensitive Metallic Magnetic Calorimeter (MMC), consisting of MMC read-out at both ends of a large X-ray absorber. Such devices are under consideration as alternatives to other cryogenic technologies for future X-ray astronomy missions. We use a finite-element model (FEM) to numerically calculate the signal and noise response at the detector outputs and investigate the correlations between the noise measured at each MMC coupled by the absorber. We then calculate, using the optimal filter concept, the theoretical energy and position resolution across the detector and discuss the trade-offs involved in optimizing the detector design for energy resolution, position resolution and count rate. The results show, theoretically, the position-sensitive MMC concept offers impressive spectral and spatial resolving capabilities compared to pixel arrays and similar position-sensitive cryogenic technologies using Transition Edge Sensor (TES) read-out.

Crossmodal Semantic Priming by Naturalistic Sounds and Spoken Words Enhances Visual Sensitivity

ERIC Educational Resources Information Center

Chen, Yi-Chuan; Spence, Charles

2011-01-01

We propose a multisensory framework based on Glaser and Glaser's (1989) general reading-naming interference model to account for the semantic priming effect by naturalistic sounds and spoken words on visual picture sensitivity. Four experiments were designed to investigate two key issues: First, can auditory stimuli enhance visual sensitivity when…

Non-Instrumental Movement Inhibition (NIMI) Differentially Suppresses Head and Thigh Movements during Screenic Engagement: Dependence on Interaction

PubMed Central

Witchel, Harry J.; Santos, Carlos P.; Ackah, James K.; Westling, Carina E. I.; Chockalingam, Nachiappan

2016-01-01

Background: Estimating engagement levels from postural micromovements has been summarized by some researchers as: increased proximity to the screen is a marker for engagement, while increased postural movement is a signal for disengagement or negative affect. However, these findings are inconclusive: the movement hypothesis challenges other findings of dyadic interaction in humans, and experiments on the positional hypothesis diverge from it. Hypotheses: (1) Under controlled conditions, adding a relevant visual stimulus to an auditory stimulus will preferentially result in Non-Instrumental Movement Inhibition (NIMI) of the head. (2) When instrumental movements are eliminated and computer-interaction rate is held constant, for two identically-structured stimuli, cognitive engagement (i.e., interest) will result in measurable NIMI of the body generally. Methods: Twenty-seven healthy participants were seated in front of a computer monitor and speakers. Discrete 3-min stimuli were presented with interactions mediated via a handheld trackball without any keyboard, to minimize instrumental movements of the participant's body. Music videos and audio-only music were used to test hypothesis (1). Time-sensitive, highly interactive stimuli were used to test hypothesis (2). Subjective responses were assessed via visual analog scales. The computer users' movements were quantified using video motion tracking from the lateral aspect. Repeated measures ANOVAs with Tukey post hoc comparisons were performed. Results: For two equivalently-engaging music videos, eliminating the visual content elicited significantly increased non-instrumental movements of the head (while also decreasing subjective engagement); a highly engaging user-selected piece of favorite music led to further increased non-instrumental movement. For two comparable reading tasks, the more engaging reading significantly inhibited (42%) movement of the head and thigh; however, when a highly engaging video game was compared to the boring reading, even though the reading task and the game had similar levels of interaction (trackball clicks), only thigh movement was significantly inhibited, not head movement. Conclusions: NIMI can be elicited by adding a relevant visual accompaniment to an audio-only stimulus or by making a stimulus cognitively engaging. However, these results presume that all other factors are held constant, because total movement rates can be affected by cognitive engagement, instrumental movements, visual requirements, and the time-sensitivity of the stimulus. PMID:26941666

Non-Instrumental Movement Inhibition (NIMI) Differentially Suppresses Head and Thigh Movements during Screenic Engagement: Dependence on Interaction.

PubMed

Witchel, Harry J; Santos, Carlos P; Ackah, James K; Westling, Carina E I; Chockalingam, Nachiappan

2016-01-01

Estimating engagement levels from postural micromovements has been summarized by some researchers as: increased proximity to the screen is a marker for engagement, while increased postural movement is a signal for disengagement or negative affect. However, these findings are inconclusive: the movement hypothesis challenges other findings of dyadic interaction in humans, and experiments on the positional hypothesis diverge from it. (1) Under controlled conditions, adding a relevant visual stimulus to an auditory stimulus will preferentially result in Non-Instrumental Movement Inhibition (NIMI) of the head. (2) When instrumental movements are eliminated and computer-interaction rate is held constant, for two identically-structured stimuli, cognitive engagement (i.e., interest) will result in measurable NIMI of the body generally. Twenty-seven healthy participants were seated in front of a computer monitor and speakers. Discrete 3-min stimuli were presented with interactions mediated via a handheld trackball without any keyboard, to minimize instrumental movements of the participant's body. Music videos and audio-only music were used to test hypothesis (1). Time-sensitive, highly interactive stimuli were used to test hypothesis (2). Subjective responses were assessed via visual analog scales. The computer users' movements were quantified using video motion tracking from the lateral aspect. Repeated measures ANOVAs with Tukey post hoc comparisons were performed. For two equivalently-engaging music videos, eliminating the visual content elicited significantly increased non-instrumental movements of the head (while also decreasing subjective engagement); a highly engaging user-selected piece of favorite music led to further increased non-instrumental movement. For two comparable reading tasks, the more engaging reading significantly inhibited (42%) movement of the head and thigh; however, when a highly engaging video game was compared to the boring reading, even though the reading task and the game had similar levels of interaction (trackball clicks), only thigh movement was significantly inhibited, not head movement. NIMI can be elicited by adding a relevant visual accompaniment to an audio-only stimulus or by making a stimulus cognitively engaging. However, these results presume that all other factors are held constant, because total movement rates can be affected by cognitive engagement, instrumental movements, visual requirements, and the time-sensitivity of the stimulus.

The role of home literacy practices in preschool children's language and emergent literacy skills.

PubMed

Roberts, Joanne; Jurgens, Julia; Burchinal, Margaret

2005-04-01

This study examined how 4 specific measures of home literacy practices (i.e., shared book reading frequency, maternal book reading strategies, child's enjoyment of reading, and maternal sensitivity) and a global measure of the quality and responsiveness of the home environment during the preschool years predicted children's language and emergent literacy skills between the ages of 3 and 5 years. Study participants were 72 African American children and their mothers or primary guardians primarily from low-income families whose home literacy environment and development have been followed since infancy. Annually, between 18 months and 5 years of age, the children's mothers were interviewed about the frequency they read to their child and how much their child enjoyed being read to, and the overall quality and responsiveness of the home environment were observed. Mothers also were observed reading to their child once a year at 2, 3, and 4 years of age, and maternal sensitivity and types of maternal book reading strategies were coded. Children's receptive and expressive language and vocabulary were assessed annually between 3 years of age and kindergarten entry, and emergent literacy skills were assessed at 4 years and kindergarten entry. The specific home literacy practices showed moderate to large correlations with each other, and only a few significant associations with the language and literacy outcomes, after controlling for maternal education, maternal reading skills, and the child's gender. The global measure of overall responsiveness and support of the home environment was the strongest predictor of children's language and early literacy skills and contributed over and above the specific literacy practice measures in predicting children's early language and literacy development.

Influence of Second Language Proficiency and Syntactic Structure Similarities on the Sensitivity and Processing of English Passive Sentence in Late Chinese-English Bilinguists: An ERP Study

ERIC Educational Resources Information Center

Chang, Xin; Wang, Pei

2016-01-01

To investigate the influence of L2 proficiency and syntactic similarity on English passive sentence processing, the present ERP study asked 40 late Chinese-English bilinguals (27 females and 13 males, mean age = 23.88) with high or intermediate L2 proficiency to read the sentences carefully and to indicate for each sentence whether or not it was…

An IRT Analysis of the Reading the Mind in the Eyes Test.

PubMed

Black, Jessica E

2018-04-03

The Reading the Mind in the Eyes Test (RMET; Baron-Cohen, Wheelwright, Hill, Raste, & Plumb, 2001 ), originally designed for use in clinical populations, has been used with increasing frequency as a measure of advanced social cognition in nonclinical samples (e.g., Domes, Heinriches, Michel, Berger, & Herpertz, 2007 ; Kidd & Castano, 2013 ; Mar, Oatley, Hirsh, de la Paz, & Peterson, 2006 ). The purpose of this research was to use item response theory to assess the ability of the RMET to detect differences at the high levels of theory of mind to be expected in neurotypical adults. Results indicate that the RMET is an easy test that fails to discriminate between individuals exhibiting high ability. As such, it is unlikely that it could adequately or reliably capture the expected effects of manipulations designed to boost ability in samples of neurotypical populations. Reported effects and noneffects from such manipulations might reflect noise introduced by inaccurate measurement; a more sensitive instrument is needed to verify the effects of manipulations to enhance theory of mind.

Reading Angles in Maps

ERIC Educational Resources Information Center

Izard, Véronique; O'Donnell, Evan; Spelke, Elizabeth S.

2014-01-01

Preschool children can navigate by simple geometric maps of the environment, but the nature of the geometric relations they use in map reading remains unclear. Here, children were tested specifically on their sensitivity to angle. Forty-eight children (age 47:15-53:30 months) were presented with fragments of geometric maps, in which angle sections…

The Impact of Salient Advertisements on Reading and Attention on Web Pages

ERIC Educational Resources Information Center

Simola, Jaana; Kuisma, Jarmo; Oorni, Anssi; Uusitalo, Liisa; Hyona, Jukka

2011-01-01

Human vision is sensitive to salient features such as motion. Therefore, animation and onset of advertisements on Websites may attract visual attention and disrupt reading. We conducted three eye tracking experiments with authentic Web pages to assess whether (a) ads are efficiently ignored, (b) ads attract overt visual attention and disrupt…

Morphological Effects in Children Word Reading: A Priming Study in Fourth Graders

ERIC Educational Resources Information Center

Casalis, Severine; Dusautoir, Marion; Cole, Pascale; Ducrot, Stephanie

2009-01-01

A growing corpus of evidence suggests that morphology could play a role in reading acquisition, and that young readers could be sensitive to the morphemic structure of written words. In the present experiment, we examined whether and when morphological information is activated in word recognition. French fourth graders made visual lexical…

Population Invariance of Vertical Scaling Results

ERIC Educational Resources Information Center

Powers, Sonya; Turhan, Ahmet; Binici, Salih

2012-01-01

The population sensitivity of vertical scaling results was evaluated for a state reading assessment spanning grades 3-10 and a state mathematics test spanning grades 3-8. Subpopulations considered included males and females. The 3-parameter logistic model was used to calibrate math and reading items and a common item design was used to construct…

Native and Novel Language Prosodic Sensitivity in English-Speaking Children with and without Dyslexia

ERIC Educational Resources Information Center

Anderson, Alida; Lin, Candise Y.; Wang, Min

2013-01-01

Children with reading disability and normal reading development were compared in their ability to discriminate native (English) and novel language (Mandarin) from nonlinguistic sounds. Children's preference for native versus novel language sounds and for disyllables containing dominant trochaic versus non-dominant iambic stress patterns was also…

Semantic Preview Benefit in Eye Movements during Reading: A Parafoveal Fast-Priming Study

ERIC Educational Resources Information Center

Hohenstein, Sven; Laubrock, Jochen; Kliegl, Reinhold

2010-01-01

Eye movements in reading are sensitive to foveal and parafoveal word features. Whereas the influence of orthographic or phonological parafoveal information on gaze control is undisputed, there has been no reliable evidence for early parafoveal extraction of semantic information in alphabetic script. Using a novel combination of the gaze-contingent…

Development of Emergent Literacy and Early Reading Skills in Preschool Children: Evidence from a Latent-Variable Longitudinal Study.

ERIC Educational Resources Information Center

Lonigan, Christopher J.; Burgess, Stephen R.; Anthony, Jason L.

2000-01-01

Examined the joint and unique predictive significance of emergent literacy skills for later emergent literacy skills and reading in two samples of preschoolers. Structural equation modeling revealed significant developmental continuity of these skills, particularly for letter knowledge and phonological sensitivity from late preschool to early…

Energy dependence corrections to MOSFET dosimetric sensitivity.

PubMed

Cheung, T; Butson, M J; Yu, P K N

2009-03-01

Metal Oxide Semiconductor Field Effect Transistors (MOSFET's) are dosimeters which are now frequently utilized in radiotherapy treatment applications. An improved MOSFET, clinical semiconductor dosimetry system (CSDS) which utilizes improved packaging for the MOSFET device has been studied for energy dependence of sensitivity to x-ray radiation measurement. Energy dependence from 50 kVp to 10 MV x-rays has been studied and found to vary by up to a factor of 3.2 with 75 kVp producing the highest sensitivity response. The detectors average life span in high sensitivity mode is energy related and ranges from approximately 100 Gy for 75 kVp x-rays to approximately 300 Gy at 6 MV x-ray energy. The MOSFET detector has also been studied for sensitivity variations with integrated dose history. It was found to become less sensitive to radiation with age and the magnitude of this effect is dependant on radiation energy with lower energies producing a larger sensitivity reduction with integrated dose. The reduction in sensitivity is however approximated reproducibly by a slightly non linear, second order polynomial function allowing corrections to be made to readings to account for this effect to provide more accurate dose assessments both in phantom and in-vivo.

Pressure Sensitive Tape and Label Surface Coating Industry: New Source Performance Standards (NSPS)

EPA Pesticide Factsheets

Learn about the New Source Performance Standards (NSPS) for pressure sensitive tape and label surface coating. Read the rule summary and history, and find the code of federal regulations and federal register citations.

Accuracy of a real-time continuous glucose monitoring system in children with septic shock: A pilot study.

PubMed

Prabhudesai, Sumant; Kanjani, Amruta; Bhagat, Isha; Ravikumar, Karnam G; Ramachandran, Bala

2015-11-01

The aim of this prospective, observational study was to determine the accuracy of a real-time continuous glucose monitoring system (CGMS) in children with septic shock. Children aged 30 days to 18 years admitted to the Pediatric Intensive Care Unit with septic shock were included. A real-time CGMS sensor was used to obtain interstitial glucose readings. CGMS readings were compared statistically with simultaneous laboratory blood glucose (BG). Nineteen children were included, and 235 pairs of BG-CGMS readings were obtained. BG and CGMS had a correlation coefficient of 0.61 (P < 0.001) and a median relative absolute difference of 17.29%. On Clarke's error grid analysis, 222 (94.5%) readings were in the clinically acceptable zones (A and B). When BG was < 70, 70-180, and > 180 mg/dL, 44%, 100%, and 76.9% readings were in zones A and B, respectively (P < 0.001). The accuracy of CGMS was not affected by the presence of edema, acidosis, vasopressors, steroids, or renal replacement therapy. On receiver operating characteristics curve analysis, a CGMS reading <97 mg/dL predicted hypoglycemia (sensitivity 85.2%, specificity 75%, area under the curve [AUC] =0.85). A reading > 141 mg/dL predicted hyperglycemia (sensitivity 84.6%, specificity 89.6%, AUC = 0.87). CGMS provides a fairly, accurate estimate of BG in children with septic shock. It is unaffected by a variety of clinical variables. The accuracy over extremes of blood sugar may be a concern. We recommend larger studies to evaluate its use for the early detection of hypoglycemia and hyperglycemia.

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

PubMed

Dodell-Feder, David; Tamir, Diana I

2018-02-26

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

Mathematics is differentially related to reading comprehension and word decoding: Evidence from a genetically-sensitive design

PubMed Central

Harlaar, Nicole; Kovas, Yulia; Dale, Philip S.; Petrill, Stephen A.; Plomin, Robert

2013-01-01

Although evidence suggests that individual differences in reading and mathematics skills are correlated, this relationship has typically only been studied in relation to word decoding or global measures of reading. It is unclear whether mathematics is differentially related to word decoding and reading comprehension. The current study examined these relationships at both a phenotypic and etiological level in a population-based cohort of 5162 twin pairs at age 12. Multivariate genetic analyses of latent phenotypic factors of mathematics, word decoding and reading comprehension revealed substantial genetic and shared environmental correlations among all three domains. However, the phenotypic and genetic correlations between mathematics and reading comprehension were significantly greater than between mathematics and word decoding. Independent of mathematics, there was also evidence for genetic and nonshared environmental links between word decoding and reading comprehension. These findings indicate that word decoding and reading comprehension have partly distinct relationships with mathematics in the middle school years. PMID:24319294

Tackling the ‘dyslexia paradox’: reading brain and behavior for early markers of developmental dyslexia

PubMed Central

Ozernov-Palchik, Ola; Gaab, Nadine

2016-01-01

Developmental dyslexia is an unexplained inability to acquire accurate or fluent reading that affects approximately 5–17% of children. Dyslexia is associated with structural and functional alterations in various brain regions that support reading. Neuroimaging studies in infants and pre-reading children suggest that these alterations predate reading instruction and reading failure, supporting the hypothesis that variant function in dyslexia susceptibility genes lead to atypical neural migration and/or axonal growth during early, most likely in utero, brain development. Yet, dyslexia is typically not diagnosed until a child has failed to learn to read as expected (usually in second grade or later). There is emerging evidence that neuroimaging measures, when combined with key behavioral measures, can enhance the accuracy of identification of dyslexia risk in prereading children but its sensitivity, specificity, and cost-efficiency is still unclear. Early identification of dyslexia risk carries important implications for dyslexia remediation and the amelioration of the psychosocial consequences commonly associated with reading failure. PMID:26836227

Mathematics is differentially related to reading comprehension and word decoding: Evidence from a genetically-sensitive design.

PubMed

Harlaar, Nicole; Kovas, Yulia; Dale, Philip S; Petrill, Stephen A; Plomin, Robert

2012-08-01

Although evidence suggests that individual differences in reading and mathematics skills are correlated, this relationship has typically only been studied in relation to word decoding or global measures of reading. It is unclear whether mathematics is differentially related to word decoding and reading comprehension. The current study examined these relationships at both a phenotypic and etiological level in a population-based cohort of 5162 twin pairs at age 12. Multivariate genetic analyses of latent phenotypic factors of mathematics, word decoding and reading comprehension revealed substantial genetic and shared environmental correlations among all three domains. However, the phenotypic and genetic correlations between mathematics and reading comprehension were significantly greater than between mathematics and word decoding. Independent of mathematics, there was also evidence for genetic and nonshared environmental links between word decoding and reading comprehension. These findings indicate that word decoding and reading comprehension have partly distinct relationships with mathematics in the middle school years.

RIFM fragrance ingredient safety assessment, linalyl benzoate, CAS Registry Number 126-64-7.

PubMed

Api, A M; Belsito, D; Bhatia, S; Bruze, M; Calow, P; Dagli, M L; Dkant, W; Fryer, A D; Kromidas, L; La Cava, S; Lalko, J F; Lapczynski, A; Liebler, D C; Penning, T M; Politano, V T; Ritacco, G; Salvito, D; Schultz, T W; Shen, J; Sipes, I G; Wall, B; Wilcox, D K

2016-11-01

The use of this material under current conditions is supported by existing information. This material was evaluated for genotoxicity, repeated dose toxicity, developmental and reproductive toxicity, local respiratory toxicity, phototoxicity/photoallergenicity, skin sensitization, as well as environmental safety. Data show that this material is not genotoxic. Data from the suitable read across analog linalyl phenylacetate (CAS # 7143-69-3) show that this material does not have skin sensitization potential. The repeated dose toxicity endpoint was completed using linalyl cinnamate (CAS # 78-37-5) as a suitable read across analog, which provided a MOE > 100. The developmental and reproductive toxicity endpoint was completed using linalool (CAS # 78-70-6), dehydrolinalool (CAS # 29171-20-8), benzoic acid (CAS # 65-85-0) and sodium benzoate (CAS # 532-32-1) as suitable read across analogs, which provided a MOE > 100. The local respiratory toxicity endpoint was completed using linalool (CAS # 78-70-6) and benzoic acid (CAS # 65-85-0) as suitable read across analogs, which provided a MOE > 100. The phototoxicity/photoallergenicity endpoint was completed based on suitable UV spectra. The environmental endpoint was completed as described in the RIFM Framework along with data from the suitable read across analog linalyl cinnamate (CAS # 78-375). Copyright © 2016 Elsevier Ltd. All rights reserved.

Dissociation in Optokinetic Stimulation Sensitivity between Omission and Substitution Reading Errors in Neglect Dyslexia.

PubMed

Daini, Roberta; Albonico, Andrea; Malaspina, Manuela; Martelli, Marialuisa; Primativo, Silvia; Arduino, Lisa S

2013-01-01

Although omission and substitution errors in neglect dyslexia (ND) patients have always been considered as different manifestations of the same acquired reading disorder, recently, we proposed a new dual mechanism model. While omissions are related to the exploratory disorder which characterizes unilateral spatial neglect (USN), substitutions are due to a perceptual integration mechanism. A consequence of this hypothesis is that specific training for omission-type ND patients would aim at restoring the oculo-motor scanning and should not improve reading in substitution-type ND. With this aim we administered an optokinetic stimulation (OKS) to two brain-damaged patients with both USN and ND, MA and EP, who showed ND mainly characterized by omissions and substitutions, respectively. MA also showed an impairment in oculo-motor behavior with a non-reading task, while EP did not. The two patients presented a dissociation with respect to their sensitivity to OKS, so that, as expected, MA was positively affected, while EP was not. Our results confirm a dissociation between the two mechanisms underlying omission and substitution reading errors in ND patients. Moreover, they suggest that such a dissociation could possibly be extended to the effectiveness of rehabilitative procedures, and that patients who mainly omit contralesional-sided letters would benefit from OKS.

Screening for Dyslexia in French-Speaking University Students: An Evaluation of the Detection Accuracy of the Alouette Test.

PubMed

Cavalli, Eddy; Colé, Pascale; Leloup, Gilles; Poracchia-George, Florence; Sprenger-Charolles, Liliane; El Ahmadi, Abdessadek

Developmental dyslexia is a lifelong impairment affecting 5% to 10% of the population. In French-speaking countries, although a number of standardized tests for dyslexia in children are available, tools suitable to screen for dyslexia in adults are lacking. In this study, we administered the Alouette reading test to a normative sample of 164 French university students without dyslexia and a validation sample of 83 students with dyslexia. The Alouette reading test is designed to screen for dyslexia in children, since it taps skills that are typically deficient in dyslexia (i.e., phonological skills). However, the test's psychometric properties have not previously been available, and it is not standardized for adults. The results showed that, on the Alouette test, dyslexic readers were impaired on measures of accuracy, speed, and efficiency (accuracy/reading time). We also found significant correlations between the Alouette reading efficiency and phonological efficiency scores. Finally, in terms of the Alouette test, speed-accuracy trade-offs were found in both groups, and optimal cutoff scores were determined with receiver operator characteristic curves analysis, yielding excellent discriminatory power, with 83.1% sensitivity and 100% specificity for reading efficiency. Thus, this study supports the Alouette test as a sensitive and specific screening tool for adults with dyslexia.

Dissociation in Optokinetic Stimulation Sensitivity between Omission and Substitution Reading Errors in Neglect Dyslexia

PubMed Central

Daini, Roberta; Albonico, Andrea; Malaspina, Manuela; Martelli, Marialuisa; Primativo, Silvia; Arduino, Lisa S.

2013-01-01

Although omission and substitution errors in neglect dyslexia (ND) patients have always been considered as different manifestations of the same acquired reading disorder, recently, we proposed a new dual mechanism model. While omissions are related to the exploratory disorder which characterizes unilateral spatial neglect (USN), substitutions are due to a perceptual integration mechanism. A consequence of this hypothesis is that specific training for omission-type ND patients would aim at restoring the oculo-motor scanning and should not improve reading in substitution-type ND. With this aim we administered an optokinetic stimulation (OKS) to two brain-damaged patients with both USN and ND, MA and EP, who showed ND mainly characterized by omissions and substitutions, respectively. MA also showed an impairment in oculo-motor behavior with a non-reading task, while EP did not. The two patients presented a dissociation with respect to their sensitivity to OKS, so that, as expected, MA was positively affected, while EP was not. Our results confirm a dissociation between the two mechanisms underlying omission and substitution reading errors in ND patients. Moreover, they suggest that such a dissociation could possibly be extended to the effectiveness of rehabilitative procedures, and that patients who mainly omit contralesional-sided letters would benefit from OKS. PMID:24062678

Optical devices in highly myopic eyes with low vision: a prospective study.

PubMed

Scassa, C; Cupo, G; Bruno, M; Iervolino, R; Capozzi, S; Tempesta, C; Giusti, C

2012-01-01

To compare, in relation to the cause of visual impairment, the possibility of rehabilitation, the corrective systems already in use and the finally prescribed optical devices in highly myopic patients with low vision. Some considerations about the rehabilitation of these subjects, especially in relation to their different pathologies, have also been made. 25 highly myopic subjects were enrolled. We evaluated both visual acuity and retinal sensitivity by Scanning Laser Ophthalmoscope (SLO) microperimetry. 20 patients (80%) were rehabilitated by means of monocular optical devices while five patients (20%) were rehabilitated binocularly. We found a good correlation between visual acuity and retinal sensitivity only when the macular pathology did not induce large areas of chorioretinal atrophy that cause lack of stabilization of the preferential retinal locus. In fact, the best results in reading and performing daily visual tasks were obtained by maximizing the residual vision in patients with retinal sensitivity greater than 10 dB. A well circumscribed area of absolute scotoma with a defined new retinal fixation locus could be considered as a positive predictive factor for the final rehabilitation process. A more careful evaluation of visual acuity, retinal sensitivity and preferential fixation locus is necessary in order to prescribe the best optical devices to patients with low vision, thus reducing the impact of the disability on their daily life.

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.

MinION™ nanopore sequencing of environmental metagenomes: a synthetic approach

PubMed Central

Watson, Mick; Minot, Samuel S.; Rivera, Maria C.; Franklin, Rima B.

2017-01-01

Abstract Background: Environmental metagenomic analysis is typically accomplished by assigning taxonomy and/or function from whole genome sequencing or 16S amplicon sequences. Both of these approaches are limited, however, by read length, among other technical and biological factors. A nanopore-based sequencing platform, MinION™, produces reads that are ≥1 × 104 bp in length, potentially providing for more precise assignment, thereby alleviating some of the limitations inherent in determining metagenome composition from short reads. We tested the ability of sequence data produced by MinION (R7.3 flow cells) to correctly assign taxonomy in single bacterial species runs and in three types of low-complexity synthetic communities: a mixture of DNA using equal mass from four species, a community with one relatively rare (1%) and three abundant (33% each) components, and a mixture of genomic DNA from 20 bacterial strains of staggered representation. Taxonomic composition of the low-complexity communities was assessed by analyzing the MinION sequence data with three different bioinformatic approaches: Kraken, MG-RAST, and One Codex. Results: Long read sequences generated from libraries prepared from single strains using the version 5 kit and chemistry, run on the original MinION device, yielded as few as 224 to as many as 3497 bidirectional high-quality (2D) reads with an average overall study length of 6000 bp. For the single-strain analyses, assignment of reads to the correct genus by different methods ranged from 53.1% to 99.5%, assignment to the correct species ranged from 23.9% to 99.5%, and the majority of misassigned reads were to closely related organisms. A synthetic metagenome sequenced with the same setup yielded 714 high quality 2D reads of approximately 5500 bp that were up to 98% correctly assigned to the species level. Synthetic metagenome MinION libraries generated using version 6 kit and chemistry yielded from 899 to 3497 2D reads with lengths averaging 5700 bp with up to 98% assignment accuracy at the species level. The observed community proportions for “equal” and “rare” synthetic libraries were close to the known proportions, deviating from 0.1% to 10% across all tests. For a 20-species mock community with staggered contributions, a sequencing run detected all but 3 species (each included at <0.05% of DNA in the total mixture), 91% of reads were assigned to the correct species, 93% of reads were assigned to the correct genus, and >99% of reads were assigned to the correct family. Conclusions: At the current level of output and sequence quality (just under 4 × 103 2D reads for a synthetic metagenome), MinION sequencing followed by Kraken or One Codex analysis has the potential to provide rapid and accurate metagenomic analysis where the consortium is comprised of a limited number of taxa. Important considerations noted in this study included: high sensitivity of the MinION platform to the quality of input DNA, high variability of sequencing results across libraries and flow cells, and relatively small numbers of 2D reads per analysis limit. Together, these limited detection of very rare components of the microbial consortia, and would likely limit the utility of MinION for the sequencing of high-complexity metagenomic communities where thousands of taxa are expected. Furthermore, the limitations of the currently available data analysis tools suggest there is considerable room for improvement in the analytical approaches for the characterization of microbial communities using long reads. Nevertheless, the fact that the accurate taxonomic assignment of high-quality reads generated by MinION is approaching 99.5% and, in most cases, the inferred community structure mirrors the known proportions of a synthetic mixture warrants further exploration of practical application to environmental metagenomics as the platform continues to develop and improve. With further improvement in sequence throughput and error rate reduction, this platform shows great promise for precise real-time analysis of the composition and structure of more complex microbial communities. PMID:28327976

MinION™ nanopore sequencing of environmental metagenomes: a synthetic approach.

PubMed

Brown, Bonnie L; Watson, Mick; Minot, Samuel S; Rivera, Maria C; Franklin, Rima B

2017-03-01

Environmental metagenomic analysis is typically accomplished by assigning taxonomy and/or function from whole genome sequencing or 16S amplicon sequences. Both of these approaches are limited, however, by read length, among other technical and biological factors. A nanopore-based sequencing platform, MinION™, produces reads that are ≥1 × 104 bp in length, potentially providing for more precise assignment, thereby alleviating some of the limitations inherent in determining metagenome composition from short reads. We tested the ability of sequence data produced by MinION (R7.3 flow cells) to correctly assign taxonomy in single bacterial species runs and in three types of low-complexity synthetic communities: a mixture of DNA using equal mass from four species, a community with one relatively rare (1%) and three abundant (33% each) components, and a mixture of genomic DNA from 20 bacterial strains of staggered representation. Taxonomic composition of the low-complexity communities was assessed by analyzing the MinION sequence data with three different bioinformatic approaches: Kraken, MG-RAST, and One Codex. Results: Long read sequences generated from libraries prepared from single strains using the version 5 kit and chemistry, run on the original MinION device, yielded as few as 224 to as many as 3497 bidirectional high-quality (2D) reads with an average overall study length of 6000 bp. For the single-strain analyses, assignment of reads to the correct genus by different methods ranged from 53.1% to 99.5%, assignment to the correct species ranged from 23.9% to 99.5%, and the majority of misassigned reads were to closely related organisms. A synthetic metagenome sequenced with the same setup yielded 714 high quality 2D reads of approximately 5500 bp that were up to 98% correctly assigned to the species level. Synthetic metagenome MinION libraries generated using version 6 kit and chemistry yielded from 899 to 3497 2D reads with lengths averaging 5700 bp with up to 98% assignment accuracy at the species level. The observed community proportions for “equal” and “rare” synthetic libraries were close to the known proportions, deviating from 0.1% to 10% across all tests. For a 20-species mock community with staggered contributions, a sequencing run detected all but 3 species (each included at <0.05% of DNA in the total mixture), 91% of reads were assigned to the correct species, 93% of reads were assigned to the correct genus, and >99% of reads were assigned to the correct family. Conclusions: At the current level of output and sequence quality (just under 4 × 103 2D reads for a synthetic metagenome), MinION sequencing followed by Kraken or One Codex analysis has the potential to provide rapid and accurate metagenomic analysis where the consortium is comprised of a limited number of taxa. Important considerations noted in this study included: high sensitivity of the MinION platform to the quality of input DNA, high variability of sequencing results across libraries and flow cells, and relatively small numbers of 2D reads per analysis limit. Together, these limited detection of very rare components of the microbial consortia, and would likely limit the utility of MinION for the sequencing of high-complexity metagenomic communities where thousands of taxa are expected. Furthermore, the limitations of the currently available data analysis tools suggest there is considerable room for improvement in the analytical approaches for the characterization of microbial communities using long reads. Nevertheless, the fact that the accurate taxonomic assignment of high-quality reads generated by MinION is approaching 99.5% and, in most cases, the inferred community structure mirrors the known proportions of a synthetic mixture warrants further exploration of practical application to environmental metagenomics as the platform continues to develop and improve. With further improvement in sequence throughput and error rate reduction, this platform shows great promise for precise real-time analysis of the composition and structure of more complex microbial communities. © The Author 2017. Published by Oxford University Press.

Malaria diagnosis under field conditions in the Venezuelan Amazon.

PubMed

Metzger, W G; Vivas-Martínez, S; Rodriguez, I; Gonçalves, J; Bongard, E; Fanello, C I; Vivas, L; Magris, M

2008-01-01

To improve practical, accurate diagnosis of malaria in the Amazon rainforest of Venezuela, two rapid diagnostic tests (RDT) (OptiMAL-IT) and FalciVax) and a laboratory light microscope, used in the field with a battery-operated head lamp as an external light source, were evaluated against the standard laboratory microscope procedure for malaria detection. One hundred and thirty-six Yanomami patients were studied for the presence of malaria parasites. Thirty-three patients (24%) were positive for malaria (Plasmodium falciparum, P. vivax, P. malariae). Twenty-one (64%) of the positive patients had <100 parasites/microl. Both RDTs showed poor sensitivity (24.2% for OptiMAL-IT) and 36.4% for FalciVax) but good specificity (99% both for OptiMAL-IT) and FalciVax). Field and laboratory microscopy showed sensitivities of 94% and 91%, respectively. The kappa coefficient was 0.90, indicating a high agreement between field and laboratory microscopy. We conclude that (i) adequate slide reading cannot be substituted by either of the two RDTs in the Venezuelan Amazon and (ii) the use of a light source such as that described above makes slide reading more feasible than hitherto in remote areas without electricity.

Nanomechanical membrane-type surface stress sensor.

PubMed

Yoshikawa, Genki; Akiyama, Terunobu; Gautsch, Sebastian; Vettiger, Peter; Rohrer, Heinrich

2011-03-09

Nanomechanical cantilever sensors have been emerging as a key device for real-time and label-free detection of various analytes ranging from gaseous to biological molecules. The major sensing principle is based on the analyte-induced surface stress, which makes a cantilever bend. In this letter, we present a membrane-type surface stress sensor (MSS), which is based on the piezoresistive read-out integrated in the sensor chip. The MSS is not a simple "cantilever," rather it consists of an "adsorbate membrane" suspended by four piezoresistive "sensing beams," composing a full Wheatstone bridge. The whole analyte-induced isotropic surface stress on the membrane is efficiently transduced to the piezoresistive beams as an amplified uniaxial stress. Evaluation of a prototype MSS used in the present experiments demonstrates a high sensitivity which is comparable with that of optical methods and a factor of more than 20 higher than that obtained with a standard piezoresistive cantilever. The finite element analyses indicate that changing dimensions of the membrane and beams can substantially increase the sensitivity further. Given the various conveniences and advantages of the integrated piezoresistive read-out, this platform is expected to open a new era of surface stress-based sensing.

The role of line junctions in object recognition: The case of reading musical notation.

PubMed

Wong, Yetta Kwailing; Wong, Alan C-N

2018-04-30

Previous work has shown that line junctions are informative features for visual perception of objects, letters, and words. However, the sources of such sensitivity and their generalizability to other object categories are largely unclear. We addressed these questions by studying perceptual expertise in reading musical notation, a domain in which individuals with different levels of expertise are readily available. We observed that removing line junctions created by the contact between musical notes and staff lines selectively impaired recognition performance in experts and intermediate readers, but not in novices. The degree of performance impairment was predicted by individual fluency in reading musical notation. Our findings suggest that line junctions provide diagnostic information about object identity across various categories, including musical notation. However, human sensitivity to line junctions does not readily transfer from familiar to unfamiliar object categories, and has to be acquired through perceptual experience with the specific objects.

Random and Directed Walk-Based Top-k Queries in Wireless Sensor Networks

PubMed Central

Fu, Jun-Song; Liu, Yun

2015-01-01

In wireless sensor networks, filter-based top-k query approaches are the state-of-the-art solutions and have been extensively researched in the literature, however, they are very sensitive to the network parameters, including the size of the network, dynamics of the sensors’ readings and declines in the overall range of all the readings. In this work, a random walk-based top-k query approach called RWTQ and a directed walk-based top-k query approach called DWTQ are proposed. At the beginning of a top-k query, one or several tokens are sent to the specific node(s) in the network by the base station. Then, each token walks in the network independently to record and process the readings in a random or directed way. A strategy of choosing the “right” way in DWTQ is carefully designed for the token(s) to arrive at the high-value regions as soon as possible. When designing the walking strategy for DWTQ, the spatial correlations of the readings are also considered. Theoretical analysis and simulation results indicate that RWTQ and DWTQ both are very robust against these parameters discussed previously. In addition, DWTQ outperforms TAG, FILA and EXTOK in transmission cost, energy consumption and network lifetime. PMID:26016914

Study design requirements for RNA sequencing-based breast cancer diagnostics.

PubMed

Mer, Arvind Singh; Klevebring, Daniel; Grönberg, Henrik; Rantalainen, Mattias

2016-02-01

Sequencing-based molecular characterization of tumors provides information required for individualized cancer treatment. There are well-defined molecular subtypes of breast cancer that provide improved prognostication compared to routine biomarkers. However, molecular subtyping is not yet implemented in routine breast cancer care. Clinical translation is dependent on subtype prediction models providing high sensitivity and specificity. In this study we evaluate sample size and RNA-sequencing read requirements for breast cancer subtyping to facilitate rational design of translational studies. We applied subsampling to ascertain the effect of training sample size and the number of RNA sequencing reads on classification accuracy of molecular subtype and routine biomarker prediction models (unsupervised and supervised). Subtype classification accuracy improved with increasing sample size up to N = 750 (accuracy = 0.93), although with a modest improvement beyond N = 350 (accuracy = 0.92). Prediction of routine biomarkers achieved accuracy of 0.94 (ER) and 0.92 (Her2) at N = 200. Subtype classification improved with RNA-sequencing library size up to 5 million reads. Development of molecular subtyping models for cancer diagnostics requires well-designed studies. Sample size and the number of RNA sequencing reads directly influence accuracy of molecular subtyping. Results in this study provide key information for rational design of translational studies aiming to bring sequencing-based diagnostics to the clinic.

The Programming Optimization of Capacitorless 1T DRAM Based on the Dual-Gate TFET

NASA Astrophysics Data System (ADS)

Li, Wei; Liu, Hongxia; Wang, Shulong; Chen, Shupeng; Wang, Qianqiong

2017-09-01

The larger volume of capacitor and higher leakage current of transistor have become the inherent disadvantages for the traditional one transistor (1T)-one capacitor (1C) dynamic random access memory (DRAM). Recently, the tunneling FET (TFET) is applied in DRAM cell due to the low off-state current and high switching ratio. The dual-gate TFET (DG-TFET) DRAM cell with the capacitorless structure has the superior performance-higher retention time (RT) and weak temperature dependence. But the performance of TFET DRAM cell is sensitive to programming condition. In this paper, the guideline of programming optimization is discussed in detail by using simulation tool—Silvaco Atlas. Both the writing and reading operations of DG-TFET DRAM depend on the band-to-band tunneling (BTBT). During the writing operation, the holes coming from BTBT governed by Gate2 are stored in potential well under Gate2. A small negative voltage is applied at Gate2 to retain holes for a long time during holding "1". The BTBT governed by Gate1 mainly influences the reading current. Using the optimized programming condition, the DG-TFET DRAM obtains the higher current ratio of reading "1" to reading "0" (107) and RT of more than 2 s. The higher RT reduces the refresh rate and dynamic power consumption of DRAM.

Two Fiber Optical Fiber Thermometry

NASA Technical Reports Server (NTRS)

Jones, Mathew R.; Farmer, Jeffery T.; Breeding, Shawn P.

2000-01-01

An optical fiber thermometer consists of an optical fiber whose sensing tip is given a metallic coating. The sensing tip of the fiber is essentially an isothermal cavity, so the emission from this cavity will be approximately equal to the emission from a blackbody. Temperature readings are obtained by measuring the spectral radiative heat flux at the end of the fiber at two wavelengths. The ratio of these measurements and Planck's Law are used to infer the temperature at the sensing tip. Optical fiber thermometers have high accuracy, excellent long-term stability and are immune to electromagnetic interference. In addition, they can be operated for extended periods without requiring re-calibration. For these reasons. it is desirable to use optical fiber thermometers in environments such as the International Space Station. However, it has recently been shown that temperature readings are corrupted by emission from the fiber when extended portions of the probe are exposed to elevated temperatures. This paper will describe several ways in which the reading from a second fiber can be used to correct the corrupted temperature measurements. The accuracy and sensitivity to measurement uncertainty will be presented for each method.

High-speed high-sensitivity infrared spectroscopy using mid-infrared swept lasers (Conference Presentation)

NASA Astrophysics Data System (ADS)

Childs, David T. D.; Groom, Kristian M.; Hogg, Richard A.; Revin, Dmitry G.; Cockburn, John W.; Rehman, Ihtesham U.; Matcher, Stephen J.

2016-03-01

Infrared spectroscopy is a highly attractive read-out technology for compositional analysis of biomedical specimens because of its unique combination of high molecular sensitivity without the need for exogenous labels. Traditional techniques such as FTIR and Raman have suffered from comparatively low speed and sensitivity however recent innovations are challenging this situation. Direct mid-IR spectroscopy is being speeded up by innovations such as MEMS-based FTIR instruments with very high mirror speeds and supercontinuum sources producing very high sample irradiation levels. Here we explore another possible method - external cavity quantum cascade lasers (EC-QCL's) with high cavity tuning speeds (mid-IR swept lasers). Swept lasers have been heavily developed in the near-infrared where they are used for non-destructive low-coherence imaging (OCT). We adapt these concepts in two ways. Firstly by combining mid-IR quantum cascade gain chips with external cavity designs adapted from OCT we achieve spectral acquisition rates approaching 1 kHz and demonstrate potential to reach 100 kHz. Secondly we show that mid-IR swept lasers share a fundamental sensitivity advantage with near-IR OCT swept lasers. This makes them potentially able to achieve the same spectral SNR as an FTIR instrument in a time x N shorter (N being the number of spectral points) under otherwise matched conditions. This effect is demonstrated using measurements of a PDMS sample. The combination of potentially very high spectral acquisition rates, fundamental SNR advantage and the use of low-cost detector systems could make mid-IR swept lasers a powerful technology for high-throughput biomedical spectroscopy.

Operational implementation of LED fluorescence microscopy in screening tuberculosis suspects in an urban HIV clinic in Uganda.

PubMed

Albert, Heidi; Nakiyingi, Lydia; Sempa, Joseph; Mbabazi, Olive; Mukkada, Sheena; Nyesiga, Barnabas; Perkins, Mark D; Manabe, Yukari C

2013-01-01

Light emitting diode (LED) fluorescence microscopy (FM) is an affordable, technology targeted for use in resource-limited settings and recommended for widespread roll-out by the World Health Organization (WHO). We sought to compare the operational performance of three LED FM methods compared to light microscopy in a cohort of HIV-positive tuberculosis (TB) suspects at an urban clinic in a high TB burden country. Two spot specimens collected from TB suspects were included in the study. Smears were stained using auramine O method and read after blinding by three LED-based FM methods by trained laboratory technicians in the Infectious Diseases Institutelaboratory. Leftover portions of the refrigerated sputum specimens were transported to the FIND Tuberculosis Research Laboratory for Ziehl Neelsen (ZN) smear preparation and reading by experienced technologist as well as liquid and solid culture. 174 of 627 (27.8%) specimens collected yielded one or more positive mycobacterial cultures. 94.3% (164/174) were M. tuberculosis complex. LED FM was between 7.3-11.0% more sensitive compared to ZN microscopy. Of the 592 specimens examined by all microscopy methods, there was no significant difference in sensitivity between the three LED FM methods. The specificity of the LED FM methods was between 6.1% and 7.7% lower than ZN microscopy (P<0.001), although exclusion of the single poor reader resulted in over 98% specificity for all FM methods. Laboratory technicians in routine settings can be trained to use FM which is more sensitive than ZN microscopy. Despite rigorous proficiency testing, there were operator-dependent accuracy issues which highlight the critical need for intensive quality assurance procedures during LED FM implementation. The low sensitivity of FM for HIV-positive individuals particularly those with low CD4 T cell counts, will limit the number of additional patients found by LED FM in countries with high rates of HIV co-infection.

Operational Implementation of LED Fluorescence Microscopy in Screening Tuberculosis Suspects in an Urban HIV Clinic in Uganda

PubMed Central

Albert, Heidi; Nakiyingi, Lydia; Sempa, Joseph; Mbabazi, Olive; Mukkada, Sheena; Nyesiga, Barnabas; Perkins, Mark D.; Manabe, Yukari C.

2013-01-01

Background Light emitting diode (LED) fluorescence microscopy (FM) is an affordable, technology targeted for use in resource-limited settings and recommended for widespread roll-out by the World Health Organization (WHO). We sought to compare the operational performance of three LED FM methods compared to light microscopy in a cohort of HIV-positive tuberculosis (TB) suspects at an urban clinic in a high TB burden country. Methods Two spot specimens collected from TB suspects were included in the study. Smears were stained using auramine O method and read after blinding by three LED-based FM methods by trained laboratory technicians in the Infectious Diseases Institutelaboratory. Leftover portions of the refrigerated sputum specimens were transported to the FIND Tuberculosis Research Laboratory for Ziehl Neelsen (ZN) smear preparation and reading by experienced technologist as well as liquid and solid culture. Results 174 of 627 (27.8%) specimens collected yielded one or more positive mycobacterial cultures. 94.3% (164/174) were M. tuberculosis complex. LED FM was between 7.3–11.0% more sensitive compared to ZN microscopy. Of the 592 specimens examined by all microscopy methods, there was no significant difference in sensitivity between the three LED FM methods. The specificity of the LED FM methods was between 6.1% and 7.7% lower than ZN microscopy (P<0.001), although exclusion of the single poor reader resulted in over 98% specificity for all FM methods. Conclusions Laboratory technicians in routine settings can be trained to use FM which is more sensitive than ZN microscopy. Despite rigorous proficiency testing, there were operator-dependent accuracy issues which highlight the critical need for intensive quality assurance procedures during LED FM implementation. The low sensitivity of FM for HIV-positive individuals particularly those with low CD4 T cell counts, will limit the number of additional patients found by LED FM in countries with high rates of HIV co-infection. PMID:24039780

Do reading additions improve reading in pre-presbyopes with low vision?

PubMed

Alabdulkader, Balsam; Leat, Susan

2012-09-01

This study compared three different methods of determining a reading addition and the possible improvement on reading performance in children and young adults with low vision. Twenty-eight participants with low vision, aged 8 to 32 years, took part in the study. Reading additions were determined with (a) a modified Nott dynamic retinoscopy, (b) a subjective method, and (c) an age-based formula. Reading performance was assessed with MNREAD-style reading charts at 12.5 cm, with and without each reading addition in random order. Outcome measures were reading speed, critical print size, MNREAD threshold, and the area under the reading speed curve. For the whole group, there was no significant improvement in reading performance with any of the additions. When participants with normal accommodation at 12.5 cm were excluded, the area under the reading speed curve was significantly greater with all reading additions compared with no addition (p = 0.031, 0.028, and 0.028, respectively). Also, the reading acuity threshold was significantly better with all reading additions compared with no addition (p = 0.014, 0.030, and 0.036, respectively). Distance and near visual acuity, age, and contrast sensitivity did not predict improvement with a reading addition. All, but one, of the participants who showed a significant improvement in reading with an addition had reduced accommodation. A reading addition may improve reading performance for young people with low vision and should be considered as part of a low vision assessment, particularly when accommodation is reduced.

LAMP kit for diagnosis of non-falciparum malaria in Plasmodium ovale infected patients.

PubMed

Cuadros, Juan; Martin Ramírez, Alexandra; González, Iveth J; Ding, Xavier C; Perez Tanoira, Ramon; Rojo-Marcos, Gerardo; Gómez-Herruz, Peña; Rubio, Jose Miguel

2017-01-07

Microscopy and rapid diagnosis tests have a limited sensitivity in diagnosis of malaria by Plasmodium ovale. The LAMP kit (LoopAMP®) can be used in the field without special equipment and could have an important role in malaria control programmes in endemic areas and for malaria diagnosis in returned travellers. The performance of the Pan primer of the kit in detecting malaria by P. ovale was compared with the results of standard nPCR in samples of patients returning from P. ovale endemic areas. Plasmodium ovale positive samples (29, tested by PCR and/or microscopy) and malaria negative specimens (398, tested by microscopy and PCR) were collected in different hospitals of Europe from June 2014 to March 2016 and frozen at -20 °C. Boil and spin method was used to extract DNA from all samples and amplification was performed with LoopAMP® MALARIA kit (Eiken Chemical, Japan) in an automated turbidimeter (Eiken 500). The results of LAMP read by turbidimetry and with the naked eye were compared. The kit showed a sensitivity of 100% and a specificity of 97.24% with positive and negative predictive values of 72.5 and 100%, respectively. Naked eyed readings were in accordance with turbidimetry readings (sensitivity, 92.5%, specificity, 98.96% and positive and negative predictive values, respectively, 90.24 and 99.22%). The limit of detection of LAMP assay for P. ovale was between 0.8 and 2 parasites/µl. The Pan primer of the Malaria kit LoopAMP® can detect P. ovale at very low-levels and showed a predictive negative value of 100%. This tool can be useful in malaria control and elimination programmes and in returned travellers from P. ovale endemic areas. Naked eye readings are equivalent to automated turbidimeter readings in specimens obtained with EDTA.

A Rewritable, Random-Access DNA-Based Storage System.

PubMed

Yazdi, S M Hossein Tabatabaei; Yuan, Yongbo; Ma, Jian; Zhao, Huimin; Milenkovic, Olgica

2015-09-18

We describe the first DNA-based storage architecture that enables random access to data blocks and rewriting of information stored at arbitrary locations within the blocks. The newly developed architecture overcomes drawbacks of existing read-only methods that require decoding the whole file in order to read one data fragment. Our system is based on new constrained coding techniques and accompanying DNA editing methods that ensure data reliability, specificity and sensitivity of access, and at the same time provide exceptionally high data storage capacity. As a proof of concept, we encoded parts of the Wikipedia pages of six universities in the USA, and selected and edited parts of the text written in DNA corresponding to three of these schools. The results suggest that DNA is a versatile media suitable for both ultrahigh density archival and rewritable storage applications.

A Rewritable, Random-Access DNA-Based Storage System

NASA Astrophysics Data System (ADS)

Tabatabaei Yazdi, S. M. Hossein; Yuan, Yongbo; Ma, Jian; Zhao, Huimin; Milenkovic, Olgica

2015-09-01

We describe the first DNA-based storage architecture that enables random access to data blocks and rewriting of information stored at arbitrary locations within the blocks. The newly developed architecture overcomes drawbacks of existing read-only methods that require decoding the whole file in order to read one data fragment. Our system is based on new constrained coding techniques and accompanying DNA editing methods that ensure data reliability, specificity and sensitivity of access, and at the same time provide exceptionally high data storage capacity. As a proof of concept, we encoded parts of the Wikipedia pages of six universities in the USA, and selected and edited parts of the text written in DNA corresponding to three of these schools. The results suggest that DNA is a versatile media suitable for both ultrahigh density archival and rewritable storage applications.

Reading magnetic ink patterns with magnetoresistive sensors

NASA Astrophysics Data System (ADS)

Merazzo, K. J.; Costa, T.; Franco, F.; Ferreira, R.; Zander, M.; Türr, M.; Becker, T.; Freitas, P. P.; Cardoso, S.

2018-05-01

Information storage and monitoring relies on sensitive transducers with high robustness and reliability. This paper shows a methodology enabling the qualification of magnetic sensors for magnetic pattern readout, in applications different than hard disk magnetic recording. A magnetic tunnel junction MTJ sensor was incorporated in a reader setup for recognition of the magnetization of patterned arrays made of CoCrPt thin films and magnetic ink. The geometry of the sensor (in particular, the footprint and vertical distance to the media) was evaluated for two sensor configurations. The readout conditions were optimized to cope for variable media field intensity, resulting from CoCrPt film or magnetic ink thickness, with fixed reading distance and dimensions of the pattern. The calibration of the ink magnetic signal could be inferred from the analytical calculations carried out to validate the CoCrPt results.

The processing and comprehension of wh-questions among L2 German speakers

PubMed Central

Jackson, Carrie N.; Bobb, Susan C.

2009-01-01

Using the self-paced-reading paradigm, the present study examines whether highly proficient second language (L2) speakers of German (English L1) use case-marking information during the on-line comprehension of unambiguous wh-extractions, even when task demands do not draw explicit attention to this morphosyntactic feature in German. Results support previous findings, in that both the native and the L2 German speakers exhibited an immediate subject-preference in the matrix clause, suggesting they were sensitive to case-marking information. However, only among the native speakers did this subject-preference carry over to reading times in the complement clause. The results from the present study are discussed in light of current debates regarding the ability of L2 speakers to attain native-like processing strategies in their L2. PMID:20161006

Quality Assurance of Rapid Diagnostic Tests for Malaria in Routine Patient Care in Rural Tanzania

PubMed Central

McMorrow, Meredith L.; Masanja, M. Irene; Kahigwa, Elizeus; Abdulla, Salim M. K.; Kachur, S. Patrick

2010-01-01

Histidine-rich protein II (HRP2)-based malaria rapid diagnostic tests (RDTs) have shown high sensitivity and specificity for detecting Plasmodium falciparum malaria in a variety of study settings. However, RDTs are susceptible to heat and humidity and variation in individual performance, which may affect their use in field settings. We evaluated sensitivity and specificity of RDTs during routine use for malaria case management in peripheral health facilities. From December 2007 to October 2008, HRP2-based ParaHIT-f RDTs were introduced in 12 facilities without available microscopy in Rufiji District, Tanzania. Health workers received a single day of instruction on how to perform an RDT and thick blood smear. Job aids, Integrated Management of Childhood Illness guidelines, and national malaria treatment algorithms were reviewed. For quality assurance (QA), thick blood smears for reference microscopy were collected for 2 to 3 days per week from patients receiving RDTs; microscopy was not routinely performed at the health facilities. Slides were stained and read centrally within 72 hours of collection by a reference microscopist. When RDT and blood smear results were discordant, blood smears were read by additional reference microscopists blinded to earlier results. Facilities were supervised monthly by the district laboratory supervisor or a member of the study team. Ten thousand six hundred fifty (10,650) patients were tested with RDTs, and 51.5% (5,488/10,650) had a positive test result. Blood smear results were available for 3,914 patients, of whom 40.1% (1,577/3,914) were positive for P. falciparum malaria. Overall RDT sensitivity was 90.7% (range by facility 85.7–96.5%) and specificity was 73.5% (range 50.0–84.3%). Sensitivity increased with increasing parasite density. Successful implementation of RDTs was achieved in peripheral health facilities with adequate training and supervision. Quality assurance is essential to the adequate performance of any laboratory test. Centralized staining and reading of blood smears provided useful monitoring of RDT performance. However, this level of QA may not be sustainable nationwide. PMID:20065013

libgapmis: extending short-read alignments

PubMed Central

2013-01-01

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

A General Audiovisual Temporal Processing Deficit in Adult Readers with Dyslexia

ERIC Educational Resources Information Center

Francisco, Ana A.; Jesse, Alexandra; Groen, Margriet A.; McQueen, James M.

2017-01-01

Purpose: Because reading is an audiovisual process, reading impairment may reflect an audiovisual processing deficit. The aim of the present study was to test the existence and scope of such a deficit in adult readers with dyslexia. Method: We tested 39 typical readers and 51 adult readers with dyslexia on their sensitivity to the simultaneity of…

E-Reading Comprehension versus Conventional Reading Comprehension of Junior High Students

ERIC Educational Resources Information Center

Stevens, Brian

2014-01-01

Technology is an increasing part in the lives of junior high students, but little is known about how this technology affects their reading. Reading comprehension from e-books is compared to reading comprehension from conventional print books with junior high students. The problem is that students may be reading from a medium that is less than the…

Optomechanical terahertz detection with single meta-atom resonator.

PubMed

Belacel, Cherif; Todorov, Yanko; Barbieri, Stefano; Gacemi, Djamal; Favero, Ivan; Sirtori, Carlo

2017-11-17

Most of the common technologies for detecting terahertz photons (>1 THz) at room temperature rely on slow thermal devices. The realization of fast and sensitive detectors in this frequency range is indeed a notoriously difficult task. Here we propose a novel device consisting of a subwavelength terahertz meta-atom resonator, which integrates a nanomechanical element and allows energy exchange between the mechanical motion and the electromagnetic degrees of freedom. An incident terahertz wave thus produces a nanomechanical signal that can be read out optically with high precision. We exploit this concept to demonstrate a terahertz detector that operates at room temperature with high sensitivity and a much higher frequency response compared to standard detectors. Beyond the technological issue of terahertz detection, our architecture opens up new perspectives for fundamental science of light-matter interaction at terahertz frequencies, combining optomechanical approaches with semiconductor quantum heterostructures.

Uncooled infrared focal plane array imaging in China

NASA Astrophysics Data System (ADS)

Lei, Shuyu

2015-06-01

This article reviews the development of uncooled infrared focal plane array (UIFPA) imaging in China in the past decade. Sensors based on optical or electrical read-out mechanism were developed but the latter dominates the market. In resistive bolometers, VOx and amorphous silicon are still the two major thermal-sensing materials. The specifications of the IRFPA made by different manufactures were collected and compared. Currently more than five Chinese companies and institutions design and fabricate uncooled infrared focal plane array. Some devices have sensitivity as high as 30 mK; the largest array for commercial products is 640×512 and the smallest pixel size is 17 μm. Emphasis is given on the pixel MEMS design, ROIC design, fabrication, and packaging of the IRFPA manufactured by GWIC, especially on design for high sensitivities, low noise, better uniformity and linearity, better stabilization for whole working temperature range, full-digital design, etc.

Impact of Breast Reader Assessment Strategy on mammographic radiologists' test reading performance.

PubMed

Suleiman, Wasfi I; Rawashdeh, Mohammad A; Lewis, Sarah J; McEntee, Mark F; Lee, Warwick; Tapia, Kriscia; Brennan, Patrick C

2016-06-01

The detection of breast cancer is somewhat limited by human factors, and thus there is a need to improve reader performance. This study assesses whether radiologists who regularly undertake the education in the form of the Breast Reader Assessment Strategy (BREAST) demonstrate any changes in mammography interpretation performance over time. In 2011, 2012 and 2013, 14 radiologists independently assessed a year-specific BREAST mammographic test-set. Radiologists read a different single test-set once each year, with each comprising 60 digital mammogram cases. Radiologists marked the location of suspected lesions without computer-aided diagnosis (CAD) and assigned a confidence rating of 2 for benign and 3-5 for malignant lesions. The mean sensitivity, specificity, location sensitivity, JAFROC FOM and ROC AUC were calculated. A Kruskal-Wallis test was used to compare the readings for the 14 radiologists across the 3 years. Wilcoxon signed rank test was used to assess comparison between pairs of years. Relationships between changes in performance and radiologist characteristics were examined using a Spearman's test. Significant increases were noted in mean sensitivity (P = 0.01), specificity (P = 0.01), location sensitivity (P = 0.001) and JAFROC FOM (P = 0.001) between 2011 and 2012. Between 2012 and 2013, significant improvements were noted in mean sensitivity (P = 0.003), specificity (P = 0.002), location sensitivity (P = 0.02), JAFROC FOM (P = 0.005) and ROC AUC (P = 0.008). No statistically significant correlations were shown between the levels of improvement and radiologists' characteristics. Radiologists' who undertake the BREAST programme demonstrate significant improvements in test-set performance during a 3-year period, highlighting the value of ongoing education through the use of test-set. © 2016 The Royal Australian and New Zealand College of Radiologists.

Use of Ancillary Carbapenemase Tests To Improve Specificity of Phenotypic Definitions for Carbapenemase-Producing Enterobacteriaceae.

PubMed

Miller, Shelley A; Hindler, Janet A; Chengcuenca, Angelo; Humphries, Romney M

2017-06-01

Carbapenemase-producing Enterobacteriaceae (CPE) are a significant threat to public health. In 2015, CDC revised the surveillance definition for CPE to include all Enterobacteriaceae resistant to any carbapenem tested. However, this definition is associated with poor specificity. We evaluated the performance of this definition, compared to carbapenemase PCR, for a collection of 125 Enterobacteriaceae We also investigated the impact of ancillary testing for carbapenemase of isolates that met the CDC CPE surveillance definition. The two ancillary tests evaluated were the Xpert Carba-R assay, a molecular test, and the carbapenem inactivation method (CIM). Two variables were evaluated for the CIM: suspension of organisms in double-distilled water (ddH 2 O) versus tryptic soy broth (TSB) to incubate disks, and incubation of plates for 6 h versus 18 to 20 h. The sensitivity and specificity of the Carba-R assay were 100% compared to the results of in-house PCR. The sensitivities of the CIM performed with TSB were 94.6% when read at 6 h and 97.7% when read at 18 to 20 h; the sensitivities with ddH 2 O were 88.0% when read at 6 h and 93.0% when incubated for 18 to 20 h. The specificity was 100% for all variables tested. Without ancillary testing, the sensitivity of the CDC definition was 98.9% for CPE, and the specificity was 6.1%. Testing isolates that screened positive by the CDC definition with the Xpert Carba-R did not change the sensitivity, and it improved the specificity to 100%. Similarly, the use of the CIM (TSB and 18 to 20 h of incubation) to confirm screen-positive isolates resulted in a sensitivity of 95.6% and specificity of 100%. Copyright © 2017 American Society for Microbiology.

Characteristic of EBT-XD and EBT3 radiochromic film dosimetry for photon and proton beams

NASA Astrophysics Data System (ADS)

Khachonkham, Suphalak; Dreindl, Ralf; Heilemann, Gerd; Lechner, Wolfgang; Fuchs, Hermann; Palmans, Hugo; Georg, Dietmar; Kuess, Peter

2018-03-01

Recently, a new type of radiochromic film, the EBT-XD film, has been introduced for high dose radiotherapy. The EBT-XD film contains the same structure as the EBT3 film but has a slightly different composition and a thinner active layer. This study benchmarks the EBT-XD against EBT3 film for 6 MV and 10 MV photon beams, as well as for 97.4 MeV and 148.2 MeV proton beams and 15-100 kV x-rays. Dosimetric and film reading characteristics, such as post irradiation darkening, film orientation effect, lateral response artifact (LRA), film sensitivity, energy and beam quality dependency were investigated. Furthermore, quenching effects in the Bragg peak were investigated for a single proton beam energy for both film types, in addition measurements were performed in a spread-out Bragg peak. EBT-XD films showed the same characteristic on film darkening as EBT3. The effects between portrait and landscape orientation were reduced by 3.1% (in pixel value) for EBT-XD compared to EBT3 at a dose of 2000 cGy. The LRA is reduced for EBT-XD films for all investigated dose ranges. The sensitivity of EBT-XD films is superior to EBT3 for doses higher than 500 cGy. In addition, EBT-XD showed a similar dosimetric response for photon and proton irradiation with low energy and beam quality dependency. A quenching effect of 10% was found for both film types. The slight decrease in the thickness of the active layer and different composition configuration of EBT-XD resulted in a reduced film orientation effect and LRA, as well as a sensitivity increase in high-dose regions for both photon and proton beams. Overall, the EBT-XD film improved regarding film reading characteristics and showed advantages in the high-dose region for photon and proton beams.

Characteristic of EBT-XD and EBT3 radiochromic film dosimetry for photon and proton beams.

PubMed

Khachonkham, Suphalak; Dreindl, Ralf; Heilemann, Gerd; Lechner, Wolfgang; Fuchs, Hermann; Palmans, Hugo; Georg, Dietmar; Kuess, Peter

2018-03-15

Recently, a new type of radiochromic film, the EBT-XD film, has been introduced for high dose radiotherapy. The EBT-XD film contains the same structure as the EBT3 film but has a slightly different composition and a thinner active layer. This study benchmarks the EBT-XD against EBT3 film for 6 MV and 10 MV photon beams, as well as for 97.4 MeV and 148.2 MeV proton beams and 15-100 kV x-rays. Dosimetric and film reading characteristics, such as post irradiation darkening, film orientation effect, lateral response artifact (LRA), film sensitivity, energy and beam quality dependency were investigated. Furthermore, quenching effects in the Bragg peak were investigated for a single proton beam energy for both film types, in addition measurements were performed in a spread-out Bragg peak. EBT-XD films showed the same characteristic on film darkening as EBT3. The effects between portrait and landscape orientation were reduced by 3.1% (in pixel value) for EBT-XD compared to EBT3 at a dose of 2000 cGy. The LRA is reduced for EBT-XD films for all investigated dose ranges. The sensitivity of EBT-XD films is superior to EBT3 for doses higher than 500 cGy. In addition, EBT-XD showed a similar dosimetric response for photon and proton irradiation with low energy and beam quality dependency. A quenching effect of 10% was found for both film types. The slight decrease in the thickness of the active layer and different composition configuration of EBT-XD resulted in a reduced film orientation effect and LRA, as well as a sensitivity increase in high-dose regions for both photon and proton beams. Overall, the EBT-XD film improved regarding film reading characteristics and showed advantages in the high-dose region for photon and proton beams.

Asia-Pacific consensus statement on the optimal use of high-sensitivity troponin assays in acute coronary syndromes diagnosis: focus on hs-TnI

PubMed Central

Tan, Jack Wei Chieh; Lam, Carolyn S P; Kasim, Sazzli Shahlan; Aw, Tar Choon; Abanilla, Joel M; Chang, Wei-Ting; Dang, Van Phuoc; Iboleon-Dy, Maria; Mumpuni, Sari Sri; Phommintikul, Arintaya; Ta, Manh Cuong; Topipat, Punkiat; Yiu, Kai Hang; Cullen, Louise

2017-01-01

Objective High-sensitivity troponin (hs-Tn) assays need to be applied appropriately to improve diagnosis and patient outcomes in acute coronary syndromes (ACS). Methods Experts from Asia Pacific convened in 2015 to provide data-driven consensus-based, region-specific recommendations and develop an algorithm for the appropriate incorporation of this assay into the ACS assessment and treatment pathway. Results Nine recommendations were developed by the expert panel: (1) troponin is the preferred cardiac biomarker for diagnostic assessment of ACS and is indicated for patients with symptoms of possible ACS; (2) hs-Tn assays are recommended; (3) serial testing is required for all patients; (4) testing should be performed at presentation and 3 hours later; (5) gender-specific cut-off values should be used for hs-Tn I assays; (6) hs-Tn I level >10 times the upper limit of normal should be considered to ‘rule in’ a diagnosis of ACS; (7) dynamic change >50% in hs-Tn I level from presentation to 3-hour retest identifies patients at high risk for ACS; (8) where only point-of-care testing is available, patients with elevated readings should be considered at high risk, while patients with low/undetectable readings should be retested after 6 hours or sent for laboratory testing and (9) regular education on the appropriate use of troponin tests is essential. Conclusions We propose an algorithm that will potentially reduce delays in discharge by the accurate ‘rule out’ of non-ACS patients within 3 hours. Appropriate research should be undertaken to ensure the efficacy and safety of the algorithm in clinical practice, with the long-term goal of improvement of care of patients with ACS in Asia Pacific. PMID:28466882

Photovoltaic driven multiple quantum well optical modulator

NASA Technical Reports Server (NTRS)

Maserjian, Joseph (Inventor)

1990-01-01

Multiple quantum well (MQW) structures (12) are utilized to provide real-time, reliable, high-performance, optically-addressed spatial-light modulators (SLM) (10). The optically-addressed SLM comprises a vertical stack of quantum well layers (12a) within the penetration depth of an optical write signal 18, a plurality of space charge barriers (12b) having predetermined tunneling times by control of doping and thickness. The material comprising the quantum well layers has a lower bandgap than that of the space charge barrier layers. The write signal modulates a read signal (20). The modulation sensitivity of the device is high and no external voltage source is required. In a preferred embodiment, the SLM having interleaved doped semiconductor layers for driving the MQW photovoltaically is characterized by the use of a shift analogous to the Moss-Burnstein shift caused by the filling of two-dimensional states in the multiple quantum wells, thus allowing high modulation sensitivity in very narrow wells. Arrays (30) may be formed with a plurality of the modulators.

Indium antimonide large-format detector arrays

NASA Astrophysics Data System (ADS)

Davis, Mike; Greiner, Mark

2011-06-01

Large format infrared imaging sensors are required to achieve simultaneously high resolution and wide field of view image data. Infrared sensors are generally required to be cooled from room temperature to cryogenic temperatures in less than 10 min thousands of times during their lifetime. The challenge is to remove mechanical stress, which is due to different materials with different coefficients of expansion, over a very wide temperature range and at the same time, provide a high sensitivity and high resolution image data. These challenges are met by developing a hybrid where the indium antimonide detector elements (pixels) are unconnected islands that essentially float on a silicon substrate and form a near perfect match to the silicon read-out circuit. Since the pixels are unconnected and isolated from each other, the array is reticulated. This paper shows that the front side illuminated and reticulated element indium antimonide focal plane developed at L-3 Cincinnati Electronics are robust, approach background limited sensitivity limit, and provide the resolution expected of the reticulated pixel array.

Red Cloud Reading Test: American Indian Form of the Test of Individual Needs in Reading, a Competency Based Test of Reading Skills [and] Instructor's Manual.

ERIC Educational Resources Information Center

Gilliland, Hap

The oral Red Cloud Reading Test provides a complete analysis of reading level and skills for American Indian students in grades 1-7 or for high school and adult students reading at or below high school levels. The test determines the basic and recreational reading levels, identifies reading problems, determines reading speeds, and analyzes the…

PERFORMANCE OF OVID MEDLINE SEARCH FILTERS TO IDENTIFY HEALTH STATE UTILITY STUDIES.

PubMed

Arber, Mick; Garcia, Sonia; Veale, Thomas; Edwards, Mary; Shaw, Alison; Glanville, Julie M

2017-01-01

This study was designed to assess the sensitivity of three Ovid MEDLINE search filters developed to identify studies reporting health state utility values (HSUVs), to improve the performance of the best performing filter, and to validate resulting search filters. Three quasi-gold standard sets (QGS1, QGS2, QGS3) of relevant studies were harvested from reviews of studies reporting HSUVs. The performance of three initial filters was assessed by measuring their relative recall of studies in QGS1. The best performing filter was then developed further using QGS2. This resulted in three final search filters (FSF1, FSF2, and FSF3), which were validated using QGS3. FSF1 (sensitivity maximizing) retrieved 132/139 records (sensitivity: 95 percent) in the QGS3 validation set. FSF1 had a number needed to read (NNR) of 842. FSF2 (balancing sensitivity and precision) retrieved 128/139 records (sensitivity: 92 percent) with a NNR of 502. FSF3 (precision maximizing) retrieved 123/139 records (sensitivity: 88 percent) with a NNR of 383. We have developed and validated a search filter (FSF1) to identify studies reporting HSUVs with high sensitivity (95 percent) and two other search filters (FSF2 and FSF3) with reasonably high sensitivity (92 percent and 88 percent) but greater precision, resulting in a lower NNR. These seem to be the first validated filters available for HSUVs. The availability of filters with a range of sensitivity and precision options enables researchers to choose the filter which is most appropriate to the resources available for their specific research.

The Impact of Reading Success Academy on High School Reading Achievement

ERIC Educational Resources Information Center

Burlison, Kelly; Chave, Josh

2014-01-01

The study explores the effectiveness of the Reading Success Academy on the reading achievement of the selected group of ninth-grade students in a comprehensive high school. We examine in what ways the Reading Success Academy may improve the reading proficiency rates and amount of reading growth of ninth-grade students. The results indicate that…

ELL High School Students' Metacognitive Awareness of Reading Strategy Use and Reading Proficiency

ERIC Educational Resources Information Center

Hong-Nam, Kay

2014-01-01

This study investigated the metacognitive awareness and reading strategies use of high school-­aged English language learners (ELLs) and the relationship between ELL reading strategy use and reading proficiency as measured by a standardized reading test and self-­rated reading proficiency. Results reveal that participants reported moderate use of…

Highly Motivated Children's Perceptions of Reading

ERIC Educational Resources Information Center

Carney, Kelli Ann

2013-01-01

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

Exploring the Meaning of Reading among Highly Motivated Children

ERIC Educational Resources Information Center

Carney, Kelli Ann

2015-01-01

The purpose of this interpretive case study was to explore the reading perceptions and attitudes of children who exhibit high levels of motivation to read. In order to determine children who were highly motivated to read, the Motivation to Read Profile, from Gambrell, Palmer, Codling and Mazzoni (1996) was administered to 19 initial participants…

Monoscopic versus stereoscopic photography in screening for clinically significant macular edema.

PubMed

Welty, Christopher J; Agarwal, Anita; Merin, Lawrence M; Chomsky, Amy

2006-01-01

The purpose of the study was to determine whether monoscopic photography could serve as an accurate tool when used to screen for clinically significant macular edema. In a masked randomized fashion, two readers evaluated monoscopic and stereoscopic retinal photographs of 100 eyes. The photographs were evaluated first individually for probable clinically significant macular edema based on the Early Treatment Diabetic Retinopathy Study criteria and then as stereoscopic pairs. Graders were evaluated for sensitivity and specificity individually and in combination. Individually, reader one had a sensitivity of 0.93 and a specificity of 0.77, and reader two had a sensitivity of 0.88 and a specificity of 0.94. In combination, the readers had a sensitivity of 0.91 and a specificity of 0.86. They correlated on 0.76 of the stereoscopic readings and 0.92 of the monoscopic readings. These results indicate that the use of monoscopic retinal photography may be an accurate screening tool for clinically significant macular edema.

Concept for Mars Volcanic Emission Life Scout

NASA Technical Reports Server (NTRS)

2004-01-01

This artist's rendition depicts a concept for a Mars orbiter that would scrutinize the martian atmosphere for chemical traces of life or environments supportive of life that might be present anywhere on the planet.

The concept is named the Mars Volcanic Emission and Life Scout, or Marvel. It would equip a Mars orbiter with two types of instruments proven useful in studying Earth's atmosphere from Earth orbit. One, a solar occultation infrared spectrometer, would look sideways through Mars' atmosphere toward the setting or rising Sun for an extremely sensitive reading of what chemicals are in the air that sunlight passes through before hitting the instrument. The other, a submillimeter spectrometer would survey the atmosphere continuously, including during dust storms and polar night, to seek localized surface sources of the chemicals of interest. The infrared spectrometer has very high sensitivity for one chemical of great interest: methane, which is produced by many types of microbes, as well as by some volcanic sources. The submillimeter spectrometer has very high sensitivity for water vapor. Localized concentrations of water vapor in the atmosphere could identify places where subsurface water sources may be venting.

The Human Side of 18th-Century French History: Unique Readings for Secondary Students

ERIC Educational Resources Information Center

Roselle, Daniel, Ed.

1976-01-01

Nine short stories and excerpts are presented relating to 18th-Century French History. The purpose of the readings are to: 1) increase student sensitivity to conditions in 18th-Century France; 2) add to their appreciation of the variety of human experiences; and 3) strengthen student insight into the nature of human beings. (Author/JR)

Two-dimensional array of cold-electron bolometers for high-sensitivity polarization measurements

NASA Astrophysics Data System (ADS)

Kuzmin, L. S.

2012-01-01

A new concept of a two-dimensional array of cold-electron bolometers with distributed dipole antennas in the focal plane for high-sensitivity polarization measurements is proposed. The concept gives a unique combination of high polarization resolution due to a large uniforms array of cold-electron bolometers and optimal matching with junction field effect transistor (JFET) amplifiers because of flexibility in direct-current connections. The noise characteristics are improved due to arriving-signal power distribution among numerous cold-electron bolometers and an increase in their response. This should lead to a significant increase in the sensitivity and dynamic range compared with competing alternative bolometer technologies. The reliability of the twodimensional array significantly increases due to a series-parallel connection of a large number of cold-electron bolometers. High polarization resolution should be ensured due to uniform covering of a substrate by a two-dimensional array over a large area and the absence of the beam compression to small lumped elements. The fundamental sensitivity limit of the cold-electron bolometer array is smaller than photon noise which is considered to be the ultimate level restricted by the background radiation. Estimates of noise of bolometers with the JFET reading system show the possibility of realizing the ultimate sensitivity below the photon-noise level 5 ・10-17 W/Hz1/2 at a frequency of 350 GHz for an optical load with a power of 5 pW. These parameters correspond to the requirements to the receiving system of a BOOMERanG balloon telescope.

Detection of new-onset choroidal neovascularization using optical coherence tomography: the AMD DOC Study.

PubMed

Do, Diana V; Gower, Emily W; Cassard, Sandra D; Boyer, David; Bressler, Neil M; Bressler, Susan B; Heier, Jeffrey S; Jefferys, Joan L; Singerman, Lawrence J; Solomon, Sharon D

2012-04-01

To determine the sensitivity of time domain optical coherence tomography (OCT) in detecting conversion to neovascular age-related macular degeneration (AMD) in eyes at high risk for choroidal neovascularization (CNV), compared with detection using fluorescein angiography (FA) as the gold standard. Prospective, multicenter, observational study. Individuals aged ≥50 years with nonneovascular AMD at high risk of progressing to CNV in the study eye and evidence of neovascular AMD in the fellow eye. At study entry and every 3 months through 2 years, participants underwent best-corrected visual acuity, supervised Amsler grid testing, preferential hyperacuity perimetry (PHP) testing, stereoscopic digital fundus photographs with FA, and OCT imaging. A central Reading Center graded all images. The sensitivity of OCT in detecting conversion to neovascular AMD by 2 years, using FA as the reference standard. Secondary outcomes included comparison of sensitivity, specificity, positive predictive value, and negative predictive value of OCT, PHP, and supervised Amsler grid relative to FA for detecting incident CNV. A total of 98 participants were enrolled; 87 (89%) of these individuals either completed the 24-month visit or exited the study after developing CNV. Fifteen (17%) study eyes had incident CNV confirmed on FA by the Reading Center. The sensitivity of each modality for detecting CNV was: OCT 0.40 (95% confidence interval [CI], 0.16-0.68), supervised Amsler grid 0.42 (95% CI, 0.15-0.72), and PHP 0.50 (95% CI, 0.23-0.77). Treatment for incident CNV was recommended by the study investigator in 13 study eyes. Sensitivity of the testing modalities for detection of CNV in these 13 eyes was 0.69 (95% CI, 0.39-0.91) for OCT, 0.50 (95% CI, 0.19-0.81) for supervised Amsler grid, and 0.70 (95% CI, 0.35-0.93) for PHP. Specificity of the OCT was higher than that of the Amsler grid and PHP. Time-domain OCT, supervised Amsler grid, and PHP have low to moderate sensitivity for detection of new-onset CNV compared with FA. Optical coherence tomography has greater specificity than Amsler grid or PHP. Among fellow eyes of individuals with unilateral CNV, FA remains the best method to detect new-onset CNV. Copyright © 2012 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.

A novel helper phage enabling construction of genome-scale ORF-enriched phage display libraries.

PubMed

Gupta, Amita; Shrivastava, Nimisha; Grover, Payal; Singh, Ajay; Mathur, Kapil; Verma, Vaishali; Kaur, Charanpreet; Chaudhary, Vijay K

2013-01-01

Phagemid-based expression of cloned genes fused to the gIIIP coding sequence and rescue using helper phages, such as VCSM13, has been used extensively for constructing large antibody phage display libraries. However, for randomly primed cDNA and gene fragment libraries, this system encounters reading frame problems wherein only one of 18 phages display the translated foreign peptide/protein fused to phagemid-encoded gIIIP. The elimination of phages carrying out-of-frame inserts is vital in order to improve the quality of phage display libraries. In this study, we designed a novel helper phage, AGM13, which carries trypsin-sensitive sites within the linker regions of gIIIP. This renders the phage highly sensitive to trypsin digestion, which abolishes its infectivity. For open reading frame (ORF) selection, the phagemid-borne phages are rescued using AGM13, so that clones with in-frame inserts express fusion proteins with phagemid-encoded trypsin-resistant gIIIP, which becomes incorporated into the phages along with a few copies of AGM13-encoded trypsin-sensitive gIIIP. In contrast, clones with out-of-frame inserts produce phages carrying only AGM13-encoded trypsin-sensitive gIIIP. Trypsin treatment of the phage population renders the phages with out-of-frame inserts non-infectious, whereas phages carrying in-frame inserts remain fully infectious and can hence be enriched by infection. This strategy was applied efficiently at a genome scale to generate an ORF-enriched whole genome fragment library from Mycobacterium tuberculosis, in which nearly 100% of the clones carried in-frame inserts after selection. The ORF-enriched libraries were successfully used for identification of linear and conformational epitopes for monoclonal antibodies specific to mycobacterial proteins.

A Sensitive Microplate Assay for Lipase Activity Measurement Using Olive Oil Emulsion Substrate: Modification of the Copper Soap Colorimetric Method.

PubMed

Mustafa, Ahmad; Karmali, Amin; Abdelmoez, Wael

2016-01-01

The present work involves a sensitive high-throughput microtiter plate based colorimetric assay for estimating lipase activity using cupric acetate pyridine reagent (CAPR). In the first approach, three factors two levels factorial design methodology was used to evaluate the interactive effect of different parameters on the sensitivity of the assay method. The optimization study revealed that the optimum CAPR concentration was 7.5% w/v, the optimum solvent was heptane and the optimum CAPR pH was 6. In the second approach, the optimized colorimetric microplate assay was used to measure lipase activity based on enzymatic hydrolysis of olive oil emulsion substrate at 37°C and 150 rpm. The emulsion substrates were formulated by using olive oil, triton X-100 (10% v/v in pH 8) and sodium phosphate buffer of pH 8 in ratio of 1:1:1 in the case of Candida sp. lipase. While in the case of immobilized lipozyme RMIM, The emulsion substrates were formulated by using olive oil, triton X-100 (1% v/v in pH 8) and sodium phosphate buffer of pH 8 in ratio of 2:1:1. Absorbance was measured at 655 nm. The stability of this assay (in terms of colored heptane phase absorbance readings) retained more than 92.5% after 24 h at 4°C compared to the absorbance readings measured at zero time. In comparison with other lipase assay methods, beside the developed sensitivity, the reproducibility and the lower limit of detection (LOD) of the proposed method, it permits analyzing of 96 samples at one time in a 96-well microplate. Furthermore, it consumes small quantities of chemicals and unit operations.

A multiplexed TOF and DOI capable PET detector using a binary position sensitive network.

PubMed

Bieniosek, M F; Cates, J W; Levin, C S

2016-11-07

Time of flight (TOF) and depth of interaction (DOI) capabilities can significantly enhance the quality and uniformity of positron emission tomography (PET) images. Many proposed TOF/DOI PET detectors require complex readout systems using additional photosensors, active cooling, or waveform sampling. This work describes a high performance, low complexity, room temperature TOF/DOI PET module. The module uses multiplexed timing channels to significantly reduce the electronic readout complexity of the PET detector while maintaining excellent timing, energy, and position resolution. DOI was determined using a two layer light sharing scintillation crystal array with a novel binary position sensitive network. A 20 mm effective thickness LYSO crystal array with four 3 mm  ×  3 mm silicon photomultipliers (SiPM) read out by a single timing channel, one energy channel and two position channels achieved a full width half maximum (FWHM) coincidence time resolution of 180  ±  2 ps with 10 mm of DOI resolution and 11% energy resolution. With sixteen 3 mm  ×  3 mm SiPMs read out by a single timing channel, one energy channel and four position channels a coincidence time resolution 204  ±  1 ps was achieved with 10 mm of DOI resolution and 15% energy resolution. The methods presented here could significantly simplify the construction of high performance TOF/DOI PET detectors.

Digitized molecular diagnostics: reading disk-based bioassays with standard computer drives.

PubMed

Li, Yunchao; Ou, Lily M L; Yu, Hua-Zhong

2008-11-01

We report herein a digital signal readout protocol for screening disk-based bioassays with standard optical drives of ordinary desktop/notebook computers. Three different types of biochemical recognition reactions (biotin-streptavidin binding, DNA hybridization, and protein-protein interaction) were performed directly on a compact disk in a line array format with the help of microfluidic channel plates. Being well-correlated with the optical darkness of the binding sites (after signal enhancement by gold nanoparticle-promoted autometallography), the reading error levels of prerecorded audio files can serve as a quantitative measure of biochemical interaction. This novel readout protocol is about 1 order of magnitude more sensitive than fluorescence labeling/scanning and has the capability of examining multiplex microassays on the same disk. Because no modification to either hardware or software is needed, it promises a platform technology for rapid, low-cost, and high-throughput point-of-care biomedical diagnostics.

A Power-Efficient Capacitive Read-Out Circuit With Parasitic-Cancellation for MEMS Cochlea Sensors.

PubMed

Wang, Shiwei; Koickal, Thomas Jacob; Hamilton, Alister; Mastropaolo, Enrico; Cheung, Rebecca; Abel, Andrew; Smith, Leslie S; Wang, Lei

2016-02-01

This paper proposes a solution for signal read-out in the MEMS cochlea sensors that have very small sensing capacitance and do not have differential sensing structures. The key challenge in such sensors is the significant signal degradation caused by the parasitic capacitance at the MEMS-CMOS interface. Therefore, a novel capacitive read-out circuit with parasitic-cancellation mechanism is developed; the equivalent input capacitance of the circuit is negative and can be adjusted to cancel the parasitic capacitance. Chip results prove that the use of parasitic-cancellation is able to increase the sensor sensitivity by 35 dB without consuming any extra power. In general, the circuit follows a low-degradation low-amplification approach which is more power-efficient than the traditional high-degradation high-amplification approach; it employs parasitic-cancellation to reduce the signal degradation and therefore a lower gain is required in the amplification stage. Besides, the chopper-stabilization technique is employed to effectively reduce the low-frequency circuit noise and DC offsets. As a result of these design considerations, the prototype chip demonstrates the capability of converting a 7.5 fF capacitance change of a 1-Volt-biased 0.5 pF capacitive sensor pair into a 0.745 V signal-conditioned output at the cost of only 165.2 μW power consumption.

BusyBee Web: metagenomic data analysis by bootstrapped supervised binning and annotation

PubMed Central

Kiefer, Christina; Fehlmann, Tobias; Backes, Christina

2017-01-01

Abstract Metagenomics-based studies of mixed microbial communities are impacting biotechnology, life sciences and medicine. Computational binning of metagenomic data is a powerful approach for the culture-independent recovery of population-resolved genomic sequences, i.e. from individual or closely related, constituent microorganisms. Existing binning solutions often require a priori characterized reference genomes and/or dedicated compute resources. Extending currently available reference-independent binning tools, we developed the BusyBee Web server for the automated deconvolution of metagenomic data into population-level genomic bins using assembled contigs (Illumina) or long reads (Pacific Biosciences, Oxford Nanopore Technologies). A reversible compression step as well as bootstrapped supervised binning enable quick turnaround times. The binning results are represented in interactive 2D scatterplots. Moreover, bin quality estimates, taxonomic annotations and annotations of antibiotic resistance genes are computed and visualized. Ground truth-based benchmarks of BusyBee Web demonstrate comparably high performance to state-of-the-art binning solutions for assembled contigs and markedly improved performance for long reads (median F1 scores: 70.02–95.21%). Furthermore, the applicability to real-world metagenomic datasets is shown. In conclusion, our reference-independent approach automatically bins assembled contigs or long reads, exhibits high sensitivity and precision, enables intuitive inspection of the results, and only requires FASTA-formatted input. The web-based application is freely accessible at: https://ccb-microbe.cs.uni-saarland.de/busybee. PMID:28472498

AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework.

PubMed

Zheng, Qi; Grice, Elizabeth A

2016-10-01

Accurate mapping of next-generation sequencing (NGS) reads to reference genomes is crucial for almost all NGS applications and downstream analyses. Various repetitive elements in human and other higher eukaryotic genomes contribute in large part to ambiguously (non-uniquely) mapped reads. Most available NGS aligners attempt to address this by either removing all non-uniquely mapping reads, or reporting one random or "best" hit based on simple heuristics. Accurate estimation of the mapping quality of NGS reads is therefore critical albeit completely lacking at present. Here we developed a generalized software toolkit "AlignerBoost", which utilizes a Bayesian-based framework to accurately estimate mapping quality of ambiguously mapped NGS reads. We tested AlignerBoost with both simulated and real DNA-seq and RNA-seq datasets at various thresholds. In most cases, but especially for reads falling within repetitive regions, AlignerBoost dramatically increases the mapping precision of modern NGS aligners without significantly compromising the sensitivity even without mapping quality filters. When using higher mapping quality cutoffs, AlignerBoost achieves a much lower false mapping rate while exhibiting comparable or higher sensitivity compared to the aligner default modes, therefore significantly boosting the detection power of NGS aligners even using extreme thresholds. AlignerBoost is also SNP-aware, and higher quality alignments can be achieved if provided with known SNPs. AlignerBoost's algorithm is computationally efficient, and can process one million alignments within 30 seconds on a typical desktop computer. AlignerBoost is implemented as a uniform Java application and is freely available at https://github.com/Grice-Lab/AlignerBoost.

Laboratory Evaluation of a Smartphone-Based Electronic Reader of Rapid Dual Point-of-Care Tests for Antibodies to Human Immunodeficiency Virus and Treponema pallidum Infections.

PubMed

Herbst de Cortina, Sasha; Bristow, Claire C; Humphries, Romney; Vargas, Silver Keith; Konda, Kelika A; Caceres, Carlos F; Klausner, Jeffrey D

2017-07-01

Dual point-of-care tests for antibodies to human immunodeficiency virus (HIV) and Treponema pallidum allow for same-day testing and treatment and have been demonstrated to be cost-effective in preventing the adverse outcomes of HIV infection and syphilis. By recording and transmitting data as they are collected, electronic readers address challenges related to the decentralization of point-of-care testing. We evaluated a smartphone-based electronic reader using 201 sera tested with 2 dual rapid tests for detection of antibodies to HIV and T. pallidum in Los Angeles, USA, and Lima, Peru. Tests were read both visually and with the electronic reader. Enzyme immunoassay followed by Western blot and T. pallidum particle agglutination were the reference tests for HIV and T. pallidum, respectively. The sensitivities of the 2 rapid tests for detection of HIV were 94.1% and 97.0% for electronic readings. Both tests had a specificity of 100% for detection of HIV by electronic reading. The sensitivities of the 2 rapid tests for detection of T. pallidum were 86.5% and 92.4% for electronic readings. The specificities for detection of T. pallidum were 99.1% and 99.0% by electronic reading. There were no significant differences between the accuracies of visual and electronic readings, and the performance did not differ between the 2 study sites. Our results show the electronic reader to be a promising option for increasing the use of point-of-care testing programs.

A parallel and sensitive software tool for methylation analysis on multicore platforms.

PubMed

Tárraga, Joaquín; Pérez, Mariano; Orduña, Juan M; Duato, José; Medina, Ignacio; Dopazo, Joaquín

2015-10-01

DNA methylation analysis suffers from very long processing time, as the advent of Next-Generation Sequencers has shifted the bottleneck of genomic studies from the sequencers that obtain the DNA samples to the software that performs the analysis of these samples. The existing software for methylation analysis does not seem to scale efficiently neither with the size of the dataset nor with the length of the reads to be analyzed. As it is expected that the sequencers will provide longer and longer reads in the near future, efficient and scalable methylation software should be developed. We present a new software tool, called HPG-Methyl, which efficiently maps bisulphite sequencing reads on DNA, analyzing DNA methylation. The strategy used by this software consists of leveraging the speed of the Burrows-Wheeler Transform to map a large number of DNA fragments (reads) rapidly, as well as the accuracy of the Smith-Waterman algorithm, which is exclusively employed to deal with the most ambiguous and shortest reads. Experimental results on platforms with Intel multicore processors show that HPG-Methyl significantly outperforms in both execution time and sensitivity state-of-the-art software such as Bismark, BS-Seeker or BSMAP, particularly for long bisulphite reads. Software in the form of C libraries and functions, together with instructions to compile and execute this software. Available by sftp to anonymous@clariano.uv.es (password 'anonymous'). juan.orduna@uv.es or jdopazo@cipf.es. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Evaluation of attention training and metacognitive facilitation to improve reading comprehension in aphasia.

PubMed

Lee, Jaime B; Moore Sohlberg, McKay

2013-05-01

This pilot study investigated the impact of direct attention training combined with metacognitive facilitation on reading comprehension in individuals with aphasia. A single-subject, multiple baseline design was employed across 4 participants to evaluate potential changes in reading comprehension resulting from an 8-week intervention using Attention Process Training-3 (APT-3). The primary outcome measure was a maze reading task. Pre- and posttesting included attention and reading comprehension measures. Visual inspection of graphed performance data across conditions was used as the primary method of analysis. Treatment effect sizes were calculated for changes in reading comprehension probes from baseline to maintenance phases. Two of the study's 4 participants demonstrated improvements in maze reading, with corresponding effect sizes that were small in magnitude according to benchmarks for aphasia treatment research. All 4 participants made improvements on select standardized measures of attention. Interventions that include a metacognitive component with direct attention training may elicit improvements in participants' attention and allocation of resources. Maze passage reading is a repeated measure that appears sensitive to treatment-related changes in reading comprehension. Issues for future research related to measurement, candidacy, and clinical delivery are discussed.

Validity of a Protocol for Adult Self-Report of Dyslexia and Related Difficulties

PubMed Central

Snowling, Margaret; Dawes, Piers; Nash, Hannah; Hulme, Charles

2012-01-01

Background There is an increased prevalence of reading and related difficulties in children of dyslexic parents. In order to understand the causes of these difficulties, it is important to quantify the risk factors passed from parents to their offspring. Method 417 adults completed a protocol comprising a 15-item questionnaire rating reading and related skills and a scale assessing ADHD symptoms; 344 completed reading, nonword reading and spelling tests. Results A confirmatory factor analysis with four factors (Reading, Word Finding, Attention and Hyperactivity) provided a reasonable fit to the data. The Reading Factor showed robust correlations with measured literacy skills. Adults who reported as dyslexic, or rated their reading difficulties as more severe, gained lower scores on objective measures of literacy skills. Although the sensitivity of the new scale was acceptable, it tended to miss some cases of low literacy. Conclusions Self-report scales of reading and of attention difficulties are useful for identifying adults with reading and attention difficulties which may confer risks on their children of related problems. It is important for research following children at family risk of dyslexia to be aware of these effects. Copyright © 2012 John Wiley & Sons, Ltd. PMID:22271419

Validity of a protocol for adult self-report of dyslexia and related difficulties.

PubMed

Snowling, Margaret; Dawes, Piers; Nash, Hannah; Hulme, Charles

2012-02-01

There is an increased prevalence of reading and related difficulties in children of dyslexic parents. In order to understand the causes of these difficulties, it is important to quantify the risk factors passed from parents to their offspring. 417 adults completed a protocol comprising a 15-item questionnaire rating reading and related skills and a scale assessing ADHD symptoms; 344 completed reading, nonword reading and spelling tests. A confirmatory factor analysis with four factors (Reading, Word Finding, Attention and Hyperactivity) provided a reasonable fit to the data. The Reading Factor showed robust correlations with measured literacy skills. Adults who reported as dyslexic, or rated their reading difficulties as more severe, gained lower scores on objective measures of literacy skills. Although the sensitivity of the new scale was acceptable, it tended to miss some cases of low literacy. Self-report scales of reading and of attention difficulties are useful for identifying adults with reading and attention difficulties which may confer risks on their children of related problems. It is important for research following children at family risk of dyslexia to be aware of these effects. Copyright © 2011 John Wiley & Sons, Ltd.

The Sensitivity and Specificity of Loop-Mediated Isothermal Amplification (LAMP) Assay for Tuberculosis Diagnosis in Adults with Chronic Cough in Malawi.

PubMed

Nliwasa, Marriott; MacPherson, Peter; Chisala, Palesa; Kamdolozi, Mercy; Khundi, McEwen; Kaswaswa, Kruger; Mwapasa, Mphatso; Msefula, Chisomo; Sohn, Hojoon; Flach, Clare; Corbett, Elizabeth L

2016-01-01

Current tuberculosis diagnostics lack sensitivity, and are expensive. Highly accurate, rapid and cheaper diagnostic tests are required for point of care use in low resource settings with high HIV prevalence. To investigate the sensitivity and specificity, and cost of loop-mediated isothermal amplification (LAMP) assay for tuberculosis diagnosis in adults with chronic cough compared to Xpert® MTB/RIF, fluorescence smear microscopy. Between October 2013 and March 2014, consecutive adults at a primary care clinic were screened for cough, offered HIV testing and assessed for tuberculosis using LAMP, Xpert® MTB/RIF and fluorescence smear microscopy. Sensitivity and specificity (with culture as reference standard), and costs were estimated. Of 273 adults recruited, 44.3% (121/273) were HIV-positive and 19.4% (53/273) had bacteriogically confirmed tuberculosis. The sensitivity of LAMP compared to culture was 65.0% (95% CI: 48.3% to 79.4%) with 100% (95% CI: 98.0% to 100%) specificity. The sensitivity of Xpert® MTB/RIF (77.5%, 95% CI: 61.5% to 89.2%) was similar to that of LAMP, p = 0.132. The sensitivity of concentrated fluorescence smear microscopy with routine double reading (87.5%, 95% CI: 73.2% to 95.8%) was higher than that of LAMP, p = 0.020. All three tests had high specificity. The lowest cost per test of LAMP was at batch size of 14 samples (US$ 9.98); this was lower than Xpert® MTB/RIF (US$ 13.38) but higher than fluorescence smear microscopy (US$ 0.65). The sensitivity of LAMP was similar to Xpert® MTB/RIF but lower than fluorescence smear microscopy; all three tests had high specificity. These findings support the Malawi policy that recommends a combination of fluorescence smear microscopy and Xpert® MTB/RIF prioritised for people living with HIV, already found to be smear-negative, or being considered for retreatment of tuberculosis.

The Sensitivity and Specificity of Loop-Mediated Isothermal Amplification (LAMP) Assay for Tuberculosis Diagnosis in Adults with Chronic Cough in Malawi

PubMed Central

Nliwasa, Marriott; MacPherson, Peter; Chisala, Palesa; Kamdolozi, Mercy; Khundi, McEwen; Kaswaswa, Kruger; Mwapasa, Mphatso; Msefula, Chisomo; Sohn, Hojoon; Flach, Clare; Corbett, Elizabeth L.

2016-01-01

Background Current tuberculosis diagnostics lack sensitivity, and are expensive. Highly accurate, rapid and cheaper diagnostic tests are required for point of care use in low resource settings with high HIV prevalence. Objective To investigate the sensitivity and specificity, and cost of loop-mediated isothermal amplification (LAMP) assay for tuberculosis diagnosis in adults with chronic cough compared to Xpert® MTB/RIF, fluorescence smear microscopy. Methods Between October 2013 and March 2014, consecutive adults at a primary care clinic were screened for cough, offered HIV testing and assessed for tuberculosis using LAMP, Xpert® MTB/RIF and fluorescence smear microscopy. Sensitivity and specificity (with culture as reference standard), and costs were estimated. Results Of 273 adults recruited, 44.3% (121/273) were HIV-positive and 19.4% (53/273) had bacteriogically confirmed tuberculosis. The sensitivity of LAMP compared to culture was 65.0% (95% CI: 48.3% to 79.4%) with 100% (95% CI: 98.0% to 100%) specificity. The sensitivity of Xpert® MTB/RIF (77.5%, 95% CI: 61.5% to 89.2%) was similar to that of LAMP, p = 0.132. The sensitivity of concentrated fluorescence smear microscopy with routine double reading (87.5%, 95% CI: 73.2% to 95.8%) was higher than that of LAMP, p = 0.020. All three tests had high specificity. The lowest cost per test of LAMP was at batch size of 14 samples (US$ 9.98); this was lower than Xpert® MTB/RIF (US$ 13.38) but higher than fluorescence smear microscopy (US$ 0.65). Conclusion The sensitivity of LAMP was similar to Xpert® MTB/RIF but lower than fluorescence smear microscopy; all three tests had high specificity. These findings support the Malawi policy that recommends a combination of fluorescence smear microscopy and Xpert® MTB/RIF prioritised for people living with HIV, already found to be smear-negative, or being considered for retreatment of tuberculosis. PMID:27171380

Heritability of high reading ability and its interaction with parental education.

PubMed

Friend, Angela; DeFries, John C; Olson, Richard K; Pennington, Bruce; Harlaar, Nicole; Byrne, Brian; Samuelsson, Stefan; Willcutt, Erik G; Wadsworth, Sally J; Corley, Robin; Keenan, Janice M

2009-07-01

Moderation of the level of genetic influence on children's high reading ability by environmental influences associated with parental education was explored in two independent samples of identical and fraternal twins from the United States and Great Britain. For both samples, the heritability of high reading performance increased significantly with lower levels of parental education. Thus, resilience (high reading ability despite lower environmental support) is more strongly influenced by genotype than is high reading ability with higher environmental support. This result provides a coherent account when considered alongside results of previous research showing that heritability for low reading ability decreased with lower levels of parental education.

Reading Ability and Reading Engagement in Older Adults With Glaucoma

PubMed Central

Nguyen, Angeline M.; van Landingham, Suzanne W.; Massof, Robert W.; Rubin, Gary S.; Ramulu, Pradeep Y.

2014-01-01

Purpose. We evaluated the impact of glaucoma-related vision loss on reading ability and reading engagement in 10 reading activities. Methods. A total of 63 glaucoma patients and 59 glaucoma suspect controls self-rated their level of reading difficulty for 10 reading items, and responses were analyzed using Rasch analysis to determine reading ability. Reading engagement was assessed by asking subjects to report the number of days per week they engaged in each reading activity. Reading restriction was determined as a decrement in engagement. Results. Glaucoma subjects more often described greater reading difficulty than controls for all tasks except puzzles (P < 0.05). The most difficult reading tasks involved puzzles, books, and finances, while the least difficult reading tasks involved notes, bills, and mail. In multivariable weighted least squares regression models of Rasch-estimated person measures of reading ability, less reading ability was found for glaucoma patients compared to controls (β = −1.60 logits, P < 0.001). Among glaucoma patients, less reading ability was associated with more severe visual field (VF) loss (β = −0.68 logits per 5-dB decrement in better-eye VF mean deviation [MD], P < 0.001) and contrast sensitivity (β = −0.76 logits per 0.1-unit lower log CS, P < 0.001). Each 5-dB decrement in the better-eye VF MD was associated with book reading on 18% fewer days (P = 0.003) and newspaper reading on 10% fewer days (P = 0.008). No statistically significant reading restriction was observed for other reading activities (P > 0.05). Conclusions. Glaucoma patients have less reading ability and engage less in a variety of different reading activities, particularly those requiring sustained reading. Future work should evaluate the mechanisms underlying reading disability in glaucoma to determine how patients can maintain reading ability and engagement. PMID:25052992

An integrated general purpose SiPM based optical module with a high dynamic range

NASA Astrophysics Data System (ADS)

Bretz, T.; Engel, R.; Hebbeker, T.; Kemp, J.; Middendorf, L.; Peters, C.; Schumacher, J.; Šmída, R.; Veberič, D.

2018-06-01

Silicon photomultipliers (SiPMs) are semiconductor-based light-sensors offering a high gain, a mechanically and optically robust design and high photon detection efficiency. Due to these characteristics, they started to replace conventional photomultiplier tubes in many applications in recent years. This paper presents an optical module based on SiPMs designed for the application in scintillators as well as lab measurements. The module hosts the SiPM bias voltage supply and three pre-amplifiers with different gain levels to exploit the full dynamic range of the SiPMs. Two SiPMs, read-out in parallel, are equipped with light guides to increase the sensitive area. The light guides are optimized for the read-out of wavelength shifting fibers as used in many plastic scintillator detectors. The optical and electrical performance of the module is characterized in detail in laboratory measurements. Prototypes have been installed and tested in a modified version of the Scintillator Surface Detector developed for AugerPrime, the upgrade of the Pierre Auger Observatory. The SiPM module is operated in the Argentinian Pampas and first data proves its usability in such harsh environments.

Effects of Shuttle bay environment on UV sensitive photographic film - Instrumentation for Get-Away-Special

NASA Technical Reports Server (NTRS)

Kreplin, R. W.; Dohne, B.; Feldman, U.; Neupert, W. M.

1984-01-01

An account is given of a Get-Away-Special experiment flown on Space Shuttles 7 and 8 investigating the effect of the space environment on Shumann emulsions. Shumann emulsions, having low gelatin content and no protective gelatin overcoating, are useful detectors of ultraviolet radiation shorter than 2200 angstroms but are extremely sensitive to environmental conditions and handling. The instrument required no interface with the Shuttle. It was turned on by an aneroid switch at an altitude of 50,000 feet. After that, its operation was controlled completely by a CMOS digital controller. Each hour, two temperatures and one voltage were read and stored in a CMOS programmable read only memory. At intervals, valves were opened and closed to expose SO 652 film strips of three sensitivities to the cargo bay environment for various time periods. The design and operation of the instrument package is described.

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

The Programming Optimization of Capacitorless 1T DRAM Based on the Dual-Gate TFET.

PubMed

Li, Wei; Liu, Hongxia; Wang, Shulong; Chen, Shupeng; Wang, Qianqiong

2017-09-06

The larger volume of capacitor and higher leakage current of transistor have become the inherent disadvantages for the traditional one transistor (1T)-one capacitor (1C) dynamic random access memory (DRAM). Recently, the tunneling FET (TFET) is applied in DRAM cell due to the low off-state current and high switching ratio. The dual-gate TFET (DG-TFET) DRAM cell with the capacitorless structure has the superior performance-higher retention time (RT) and weak temperature dependence. But the performance of TFET DRAM cell is sensitive to programming condition. In this paper, the guideline of programming optimization is discussed in detail by using simulation tool-Silvaco Atlas. Both the writing and reading operations of DG-TFET DRAM depend on the band-to-band tunneling (BTBT). During the writing operation, the holes coming from BTBT governed by Gate2 are stored in potential well under Gate2. A small negative voltage is applied at Gate2 to retain holes for a long time during holding "1". The BTBT governed by Gate1 mainly influences the reading current. Using the optimized programming condition, the DG-TFET DRAM obtains the higher current ratio of reading "1" to reading "0" (10 7 ) and RT of more than 2 s. The higher RT reduces the refresh rate and dynamic power consumption of DRAM.

Situational Context Affects Definiteness Preferences: Accommodation of Presuppositions

PubMed Central

Clifton, Charles

2013-01-01

Four experiments used self-paced reading and eyetracking to demonstrate that readers are, under some conditions, sensitive to the presuppositions of definite vs. indefinite DPs (determiner phrases). Reading was faster when the context stereotypically provided a single possible referent for a definite DP or multiple possible referents for an indefinite DP than when context and DP definiteness were mismatched. This finding goes beyond previous evidence that definite DPs are processed more rapidly than indefinite DPs when there is a unique or familiar referent in the context, showing that readers are sensitive to the semantics and pragmatics of (in)definiteness. However, the finding was obtained only when readers had to perform a simple arithmetic task between reading a sentence and seeing a question about it. The intervening task may have encouraged them to process the sentence more deeply in order to form a representation that would persist while doing the arithmetic. The methodological implications of this observation are discussed. PMID:22732029

Tracking Irregular Morphophonological Dependencies in Natural Language: Evidence from the Acquisition of Subject-Verb Agreement in French

ERIC Educational Resources Information Center

Nazzi, Thierry; Barriere, Isabelle; Goyet, Louise; Kresh, Sarah; Legendre, Geraldine

2011-01-01

This study examines French-learning infants' sensitivity to grammatical non-adjacent dependencies involving subject-verb agreement (e.g., "le/les garcons lit/lisent" "the boy(s) read(s)") where number is audible on both the determiner of the subject DP and the agreeing verb, and the dependency is spanning across two syntactic phrases. A further…

Specificity control for read alignments using an artificial reference genome-guided false discovery rate.

PubMed

Giese, Sven H; Zickmann, Franziska; Renard, Bernhard Y

2014-01-01

Accurate estimation, comparison and evaluation of read mapping error rates is a crucial step in the processing of next-generation sequencing data, as further analysis steps and interpretation assume the correctness of the mapping results. Current approaches are either focused on sensitivity estimation and thereby disregard specificity or are based on read simulations. Although continuously improving, read simulations are still prone to introduce a bias into the mapping error quantitation and cannot capture all characteristics of an individual dataset. We introduce ARDEN (artificial reference driven estimation of false positives in next-generation sequencing data), a novel benchmark method that estimates error rates of read mappers based on real experimental reads, using an additionally generated artificial reference genome. It allows a dataset-specific computation of error rates and the construction of a receiver operating characteristic curve. Thereby, it can be used for optimization of parameters for read mappers, selection of read mappers for a specific problem or for filtering alignments based on quality estimation. The use of ARDEN is demonstrated in a general read mapper comparison, a parameter optimization for one read mapper and an application example in single-nucleotide polymorphism discovery with a significant reduction in the number of false positive identifications. The ARDEN source code is freely available at http://sourceforge.net/projects/arden/.

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

PubMed

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

2007-12-01

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

Noninvasive prenatal screening for fetal trisomies 21, 18, 13 and the common sex chromosome aneuploidies from maternal blood using massively parallel genomic sequencing of DNA.

PubMed

Porreco, Richard P; Garite, Thomas J; Maurel, Kimberly; Marusiak, Barbara; Ehrich, Mathias; van den Boom, Dirk; Deciu, Cosmin; Bombard, Allan

2014-10-01

The objective of this study was to validate the clinical performance of massively parallel genomic sequencing of cell-free deoxyribonucleic acid contained in specimens from pregnant women at high risk for fetal aneuploidy to test fetuses for trisomies 21, 18, and 13; fetal sex; and the common sex chromosome aneuploidies (45, X; 47, XXX; 47, XXY; 47, XYY). This was a prospective multicenter observational study of pregnant women at high risk for fetal aneuploidy who had made the decision to pursue invasive testing for prenatal diagnosis. Massively parallel single-read multiplexed sequencing of cell-free deoxyribonucleic acid was performed in maternal blood for aneuploidy detection. Data analysis was completed using sequence reads unique to the chromosomes of interest. A total of 3430 patients were analyzed for demographic characteristics and medical history. There were 137 fetuses with trisomy 21, 39 with trisomy 18, and 16 with trisomy 13 for a prevalence rate of the common autosomal trisomies of 5.8%. There were no false-negative results for trisomy 21, 3 for trisomy 18, and 2 for trisomy 13; all 3 false-positive results were for trisomy 21. The positive predictive values for trisomies 18 and 13 were 100% and 97.9% for trisomy 21. A total of 8.6% of the pregnancies were 21 weeks or beyond; there were no aneuploid fetuses in this group. All 15 of the common sex chromosome aneuploidies in this population were identified, although there were 11 false-positive results for 45,X. Taken together, the positive predictive value for the sex chromosome aneuploidies was 48.4% and the negative predictive value was 100%. Our prospective study demonstrates that noninvasive prenatal analysis of cell-free deoxyribonucleic acid from maternal plasma is an accurate advanced screening test with extremely high sensitivity and specificity for trisomy 21 (>99%) but with less sensitivity for trisomies 18 and 13. Despite high sensitivity, there was modest positive predictive value for the small number of common sex chromosome aneuploidies because of their very low prevalence rate. Copyright © 2014 Elsevier Inc. All rights reserved.

A Formative Study Investigating the Acquisition of Early Reading Skills among High School English Language Learners Beginning to Read English

ERIC Educational Resources Information Center

Bell, Athene Cooper

2012-01-01

A formative design experiment methodology was employed to investigate the acquisition of early reading skills for high school English language learners (ELLs) beginning to read English. A fundamental challenge facing high school ELLs entering schools in the United States for the first time is learning how to read. While there is considerable…

Comprehensive viral enrichment enables sensitive respiratory virus genomic identification and analysis by next generation sequencing.

PubMed

O'Flaherty, Brigid M; Li, Yan; Tao, Ying; Paden, Clinton R; Queen, Krista; Zhang, Jing; Dinwiddie, Darrell L; Gross, Stephen M; Schroth, Gary P; Tong, Suxiang

2018-06-01

Next generation sequencing (NGS) technologies have revolutionized the genomics field and are becoming more commonplace for identification of human infectious diseases. However, due to the low abundance of viral nucleic acids (NAs) in relation to host, viral identification using direct NGS technologies often lacks sufficient sensitivity. Here, we describe an approach based on two complementary enrichment strategies that significantly improves the sensitivity of NGS-based virus identification. To start, we developed two sets of DNA probes to enrich virus NAs associated with respiratory diseases. The first set of probes spans the genomes, allowing for identification of known viruses and full genome sequencing, while the second set targets regions conserved among viral families or genera, providing the ability to detect both known and potentially novel members of those virus groups. Efficiency of enrichment was assessed by NGS testing reference virus and clinical samples with known infection. We show significant improvement in viral identification using enriched NGS compared to unenriched NGS. Without enrichment, we observed an average of 0.3% targeted viral reads per sample. However, after enrichment, 50%-99% of the reads per sample were the targeted viral reads for both the reference isolates and clinical specimens using both probe sets. Importantly, dramatic improvements on genome coverage were also observed following virus-specific probe enrichment. The methods described here provide improved sensitivity for virus identification by NGS, allowing for a more comprehensive analysis of disease etiology. © 2018 O'Flaherty et al.; Published by Cold Spring Harbor Laboratory Press.

The relationship between children's sensitivity to dominant and non-dominant patterns of lexical stress and reading accuracy.

PubMed

Arciuli, Joanne

2017-05-01

This study reports on a new task for assessing children's sensitivity to lexical stress for words with different stress patterns and demonstrates that this task is useful in examining predictors of reading accuracy during the elementary years. In English, polysyllabic words beginning with a strong syllable exhibit the most common or dominant pattern of lexical stress (e.g., "coconut"), whereas polysyllabic words beginning with a weak syllable exhibit a less common non-dominant pattern (e.g., "banana"). The new Aliens Talking Underwater task assesses children's ability to match low-pass filtered recordings of words to pictures of objects. Via filtering, phonetic detail is removed but prosodic contour information relating to lexical stress is retained. In a series of two-alternative forced choice trials, participants see a picture and are asked to choose which of two filtered recordings matches the name of that picture; one recording exhibits the correct lexical stress of the target word, and the other recording reverses the pattern of stress over the initial two syllables of the target word rendering it incorrect. Target words exhibit either dominant stress or non-dominant stress. Analysis of data collected from 192 typically developing children aged 5 to 12years revealed that sensitivity to non dominant lexical stress was a significant predictor of reading accuracy even when age and phonological awareness were taken into account. A total of 76.3% of variance in children's reading accuracy was explained by these variables. Crown Copyright © 2016. Published by Elsevier Inc. All rights reserved.

Imaging performance of LabPET APD-based digital PET scanners for pre-clinical research

NASA Astrophysics Data System (ADS)

Bergeron, Mélanie; Cadorette, Jules; Tétrault, Marc-André; Beaudoin, Jean-François; Leroux, Jean-Daniel; Fontaine, Réjean; Lecomte, Roger

2014-02-01

The LabPET is an avalanche photodiode (APD) based digital PET scanner with quasi-individual detector read-out and highly parallel electronic architecture for high-performance in vivo molecular imaging of small animals. The scanner is based on LYSO and LGSO scintillation crystals (2×2×12/14 mm3), assembled side-by-side in phoswich pairs read out by an APD. High spatial resolution is achieved through the individual and independent read-out of an individual APD detector for recording impinging annihilation photons. The LabPET exists in three versions, LabPET4 (3.75 cm axial length), LabPET8 (7.5 cm axial length) and LabPET12 (11.4 cm axial length). This paper focuses on the systematic characterization of the three LabPET versions using two different energy window settings to implement a high-efficiency mode (250-650 keV) and a high-resolution mode (350-650 keV) in the most suitable operating conditions. Prior to measurements, a global timing alignment of the scanners and optimization of the APD operating bias have been carried out. Characteristics such as spatial resolution, absolute sensitivity, count rate performance and image quality have been thoroughly investigated following the NEMA NU 4-2008 protocol. Phantom and small animal images were acquired to assess the scanners' suitability for the most demanding imaging tasks in preclinical biomedical research. The three systems achieve the same radial FBP spatial resolution at 5 mm from the field-of-view center: 1.65/3.40 mm (FWHM/FWTM) for an energy threshold of 250 keV and 1.51/2.97 mm for an energy threshold of 350 keV. The absolute sensitivity for an energy window of 250-650 keV is 1.4%/2.6%/4.3% for LabPET4/8/12, respectively. The best count rate performance peaking at 362 kcps is achieved by the LabPET12 with an energy window of 250-650 keV and a mouse phantom (2.5 cm diameter) at an activity of 2.4 MBq ml-1. With the same phantom, the scatter fraction for all scanners is about 17% for an energy threshold of 250 keV and 10% for an energy threshold of 350 keV. The results obtained with two energy window settings confirm the relevance of high-efficiency and high-resolution operating modes to take full advantage of the imaging capabilities of the LabPET scanners for molecular imaging applications.

BreaKmer: detection of structural variation in targeted massively parallel sequencing data using kmers.

PubMed

Abo, Ryan P; Ducar, Matthew; Garcia, Elizabeth P; Thorner, Aaron R; Rojas-Rudilla, Vanesa; Lin, Ling; Sholl, Lynette M; Hahn, William C; Meyerson, Matthew; Lindeman, Neal I; Van Hummelen, Paul; MacConaill, Laura E

2015-02-18

Genomic structural variation (SV), a common hallmark of cancer, has important predictive and therapeutic implications. However, accurately detecting SV using high-throughput sequencing data remains challenging, especially for 'targeted' resequencing efforts. This is critically important in the clinical setting where targeted resequencing is frequently being applied to rapidly assess clinically actionable mutations in tumor biopsies in a cost-effective manner. We present BreaKmer, a novel approach that uses a 'kmer' strategy to assemble misaligned sequence reads for predicting insertions, deletions, inversions, tandem duplications and translocations at base-pair resolution in targeted resequencing data. Variants are predicted by realigning an assembled consensus sequence created from sequence reads that were abnormally aligned to the reference genome. Using targeted resequencing data from tumor specimens with orthogonally validated SV, non-tumor samples and whole-genome sequencing data, BreaKmer had a 97.4% overall sensitivity for known events and predicted 17 positively validated, novel variants. Relative to four publically available algorithms, BreaKmer detected SV with increased sensitivity and limited calls in non-tumor samples, key features for variant analysis of tumor specimens in both the clinical and research settings. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Pooled assembly of marine metagenomic datasets: enriching annotation through chimerism.

PubMed

Magasin, Jonathan D; Gerloff, Dietlind L

2015-02-01

Despite advances in high-throughput sequencing, marine metagenomic samples remain largely opaque. A typical sample contains billions of microbial organisms from thousands of genomes and quadrillions of DNA base pairs. Its derived metagenomic dataset underrepresents this complexity by orders of magnitude because of the sparseness and shortness of sequencing reads. Read shortness and sequencing errors pose a major challenge to accurate species and functional annotation. This includes distinguishing known from novel species. Often the majority of reads cannot be annotated and thus cannot help our interpretation of the sample. Here, we demonstrate quantitatively how careful assembly of marine metagenomic reads within, but also across, datasets can alleviate this problem. For 10 simulated datasets, each with species complexity modeled on a real counterpart, chimerism remained within the same species for most contigs (97%). For 42 real pyrosequencing ('454') datasets, assembly increased the proportion of annotated reads, and even more so when datasets were pooled, by on average 1.6% (max 6.6%) for species, 9.0% (max 28.7%) for Pfam protein domains and 9.4% (max 22.9%) for PANTHER gene families. Our results outline exciting prospects for data sharing in the metagenomics community. While chimeric sequences should be avoided in other areas of metagenomics (e.g. biodiversity analyses), conservative pooled assembly is advantageous for annotation specificity and sensitivity. Intriguingly, our experiment also found potential prospects for (low-cost) discovery of new species in 'old' data. dgerloff@ffame.org Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Investigation of Antarctic Marine Metazoan Biodiversity Through Metagenomic Analysis of Environmental DNA

NASA Astrophysics Data System (ADS)

Cowart, D. A.; Cheng, C. C.; Murphy, K.

2016-02-01

Environmental DNA (eDNA), or DNA extracted from environmental collections, is frequently used to gauge biodiversity and identify the presence of rare or invasive species within a habitat. Previous studies have demonstrated that compared to traditional surveying methods, high-throughput sequencing of eDNA can provide increased detection sensitivity of aquatic taxa, holding promise for various conservation applications. To determine the potential of eDNA for assessing biodiversity of Antarctic marine metazoan communities, we have extracted eDNA from seawater sampled from four regions near Palmer Station in West Antarctic Peninsula. Metagenomic sequencing of the eDNA was performed on Illumina HiSeq2500, and produced 325 million quality-processed reads. Preliminary read mapping for two regions, Gerlache Strait and Bismarck Strait, identified approximately 4% of reads mapping to eukaryotes for each region, with >50% of the those reads mapping to metazoan animals. Key groups investigated include the nototheniidae family of Antarctic fishes, to which 0.2 and 0.8 % of the metazoan reads were assigned for each region respectively. The presence of the recently invading lithodidae king crabs was also detected at both regions. Additionally, to estimate the persistence of eDNA in polar seawater, a rate of eDNA decay will be quantified from seawater samples collected over 20 days from Antarctic fish holding tanks and held at ambient Antarctic water temperatures. The ability to detect animal signatures from eDNA, as well as the quantification of eDNA decay over time, could provide another method for reliable monitoring of polar habitats at various spatial and temporal scales.

Radiographers supporting radiologists in the interpretation of screening mammography: a viable strategy to meet the shortage in the number of radiologists.

PubMed

Torres-Mejía, Gabriela; Smith, Robert A; Carranza-Flores, María de la Luz; Bogart, Andy; Martínez-Matsushita, Louis; Miglioretti, Diana L; Kerlikowske, Karla; Ortega-Olvera, Carolina; Montemayor-Varela, Ernesto; Angeles-Llerenas, Angélica; Bautista-Arredondo, Sergio; Sánchez-González, Gilberto; Martínez-Montañez, Olga G; Uscanga-Sánchez, Santos R; Lazcano-Ponce, Eduardo; Hernández-Ávila, Mauricio

2015-05-16

An alternative approach to the traditional model of radiologists interpreting screening mammography is necessary due to the shortage of radiologists to interpret screening mammograms in many countries. We evaluated the performance of 15 Mexican radiographers, also known as radiologic technologists, in the interpretation of screening mammography after a 6 months training period in a screening setting. Fifteen radiographers received 6 months standardized training with radiologists in the interpretation of screening mammography using the Breast Imaging Reporting and Data System (BI-RADS) system. A challenging test set of 110 cases developed by the Breast Cancer Surveillance Consortium was used to evaluate their performance. We estimated sensitivity, specificity, false positive rates, likelihood ratio of a positive test (LR+) and the area under the subject-specific Receiver Operating Characteristic (ROC) curve (AUC) for diagnostic accuracy. A mathematical model simulating the consequences in costs and performance of two hypothetical scenarios compared to the status quo in which a radiologist reads all screening mammograms was also performed. Radiographer's sensitivity was comparable to the sensitivity scores achieved by U.S. radiologists who took the test but their false-positive rate was higher. Median sensitivity was 73.3 % (Interquartile range, IQR: 46.7-86.7 %) and the median false positive rate was 49.5 % (IQR: 34.7-57.9 %). The median LR+ was 1.4 (IQR: 1.3-1.7 %) and the median AUC was 0.6 (IQR: 0.6-0.7). A scenario in which a radiographer reads all mammograms first, and a radiologist reads only those that were difficult for the radiographer, was more cost-effective than a scenario in which either the radiographer or radiologist reads all mammograms. Given the comparable sensitivity achieved by Mexican radiographers and U.S. radiologists on a test set, screening mammography interpretation by radiographers appears to be a possible adjunct to radiologists in countries with shortages of radiologists. Further studies are required to assess the effectiveness of different training programs in order to obtain acceptable screening accuracy, as well as the best approaches for the use of non-physician readers to interpret screening mammography.

Remote CT reading using an ultramobile PC and web-based remote viewing over a wireless network.

PubMed

Choi, Hyuk Joong; Lee, Jeong Hun; Kang, Bo Seung

2012-01-01

We developed a new type of mobile teleradiology system using an ultramobile PC (UMPC) for web-based remote viewing over a wireless network. We assessed the diagnostic performance of this system for abdominal CT interpretation. Performance was compared with an emergency department clinical monitor using a DICOM viewer. A total of 100 abdominal CT examinations were presented to four observers. There were 56 examinations showing appendicitis and 44 which were normal. The observers viewed the images using a UMPC display and an LCD monitor and rated each examination on a five-point scale. Receiver operating characteristics (ROC) analysis was used to test for differences. The sensitivity and specificities of all observers were similarly high. The average area under the ROC curve for readings performed on the UMPC and the LCD monitor was 0.959 and 0.976, respectively. There were no significant differences between the two display systems for interpreting abdominal CTs. The web-based mobile teleradiology system appears to be feasible for reading abdominal CTs for diagnosing appendicitis and may be valuable in emergency teleconsultation. Copyright © 2012 by the Royal Society of Medicine Press Ltd

Electroencephalographic coherences discriminate between children with different pedagogical evaluation.

PubMed

Marosi, E; Harmony, T; Becker, J; Reyes, A; Bernal, J; Fernández, T; Rodríguez, M; Silva, J; Guerrero, V

1995-02-01

The relationship of reading-writing ability and EEG coherences was studied in 84 subjects from two age groups 7.0-8.9 and 9-11.2 years old. All children were divided into three groups according to their performance on a pedagogical test: ped1, normal children; ped2, children with mild problems; ped3, children with reading-writing disability. The following results were obtained: in general, children showed higher coherences in groups with poor performance in the delta, theta and beta bands. In the alpha band, higher coherence values were related to better performance. The exceptions to this general pattern were rare. Group ped2 had higher coherences in delta, theta and alpha bands than ped1 and ped3, in left temporal leads. In older children the same tendency was observed, but group differences in the theta, alpha and beta bands were few. In this age range, the significant group differences were almost all interhemispheric coherences. The discriminant analysis that classified subjects by their coherence values gave very good results, fact that demonstrates, that EEG coherence is a highly sensitive measurement indicating not only the existence of a reading-writing problem, but also the degree of its severity.

The Effect of Speed Reading Instruction on Japanese High School Students' English Reading Comprehension and Vocabulary Development

ERIC Educational Resources Information Center

Underwood, Paul; Myskow, Gordon; Hattori, Takahiko

2012-01-01

This study investigated the effects of a six-month course in speed reading in three areas of reading proficiency development: 1) general reading comprehension, 2) knowledge of high-frequency vocabulary, and 3) reading-rate and accuracy. The participants (N = 105) were Japanese students studying English as a foreign language in Grade 10 at a…

Limitations and possibilities of low cell number ChIP-seq

PubMed Central

2012-01-01

Background Chromatin immunoprecipitation coupled with high-throughput DNA sequencing (ChIP-seq) offers high resolution, genome-wide analysis of DNA-protein interactions. However, current standard methods require abundant starting material in the range of 1–20 million cells per immunoprecipitation, and remain a bottleneck to the acquisition of biologically relevant epigenetic data. Using a ChIP-seq protocol optimised for low cell numbers (down to 100,000 cells / IP), we examined the performance of the ChIP-seq technique on a series of decreasing cell numbers. Results We present an enhanced native ChIP-seq method tailored to low cell numbers that represents a 200-fold reduction in input requirements over existing protocols. The protocol was tested over a range of starting cell numbers covering three orders of magnitude, enabling determination of the lower limit of the technique. At low input cell numbers, increased levels of unmapped and duplicate reads reduce the number of unique reads generated, and can drive up sequencing costs and affect sensitivity if ChIP is attempted from too few cells. Conclusions The optimised method presented here considerably reduces the input requirements for performing native ChIP-seq. It extends the applicability of the technique to isolated primary cells and rare cell populations (e.g. biobank samples, stem cells), and in many cases will alleviate the need for cell culture and any associated alteration of epigenetic marks. However, this study highlights a challenge inherent to ChIP-seq from low cell numbers: as cell input numbers fall, levels of unmapped sequence reads and PCR-generated duplicate reads rise. We discuss a number of solutions to overcome the effects of reducing cell number that may aid further improvements to ChIP performance. PMID:23171294

Home environmental influences on children's language and reading skills in a genetically sensitive design: Are socioeconomic status and home literacy environment environmental mediators and moderators?

PubMed

Chow, Bonnie Wing-Yin; Ho, Connie Suk-Han; Wong, Simpson W L; Waye, Mary M Y; Zheng, Mo

2017-12-01

This twin study examined how family socioeconomic status (SES) and home literacy environment (HLE) contributes to Chinese language and reading skills. It included 312 Chinese twin pairs aged 3 to 11. Children were individually administered tasks of Chinese word reading, receptive vocabulary and reading-related cognitive skills, and nonverbal reasoning ability. Information on home environment was collected through parent-reported questionnaires. Results showed that SES and HLE mediated shared environmental influences but did not moderate genetic influences on general language and reading abilities. Also, SES and HLE mediated shared environmental contributions to receptive vocabulary and syllable and rhyme awareness, but not orthographic skills. The findings of this study add to past twin studies that focused on alphabetic languages, suggesting that these links could be universal across languages. They also extend existing findings on SES and HLE's contributions to reading-related cognitive skills. © 2017 Scandinavian Psychological Associations and John Wiley & Sons Ltd.

Structural changes in white matter are uniquely related to children’s reading development

PubMed Central

Myers, Chelsea A.; Vandermosten, Maaike; Farris, Emily A.; Hancock, Roeland; Gimenez, Paul; Black, Jessica M.; Casto, Brandi; Drahos, Miroslav; Tumber, Mandeep; Hendren, Robert L.; Hulme, Charles; Hoeft, Fumiko

2014-01-01

This study examined whether variations in brain development between kindergarten and Grade 3 predicted individual differences in reading ability at the latter time point. Structural MRI measurements indicated that increases in volume of two left temporo-parietal white matter clusters are unique predictors of reading outcome at Grade 3. Using diffusion MRI, the larger of these two clusters was identified as a location where fibers of the long segment of arcuate fasciculus and superior corona radiata intersect, and the smaller cluster as the posterior arcuate fasciculus. Bias-free regression analyses using regions-of-interest from prior literature revealed white matter volume changes in temporo-parietal white matter, together with preliteracy measures, predicted 56% of the variance in reading outcomes. Our findings demonstrate the important contribution of developmental differences in areas of left dorsal white matter, often implicated in phonological processing, as a sensitive early biomarker for later reading abilities, and by extension, reading difficulties. PMID:25212581

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.

Comparison of Sofia Legionella FIA and BinaxNOW® Legionella urinary antigen card in two national reference centers.

PubMed

Beraud, L; Gervasoni, K; Freydiere, A M; Descours, G; Ranc, A G; Vandenesch, F; Lina, G; Gaia, V; Jarraud, S

2015-09-01

The Sofia Legionella Fluorescence Immunoassay (FIA; Quidel) is a recently introduced rapid immunochromatographic diagnostic test for Legionnaires' disease using immunofluorescence technology designed to enhance its sensitivity. The aim of this study was to evaluate its performance for the detection of urinary antigens for Legionella pneumophila serogroup 1 in two National Reference Centers for Legionella. The sensitivity and specificity of the Sofia Legionella FIA test were determined in concentrated and nonconcentrated urine samples, before and after boiling, in comparison with the BinaxNOW® Legionella Urinary Antigen Card (UAC; Alere). Compared with BinaxNOW® Legionella UAC, the sensitivity of the Sofia Legionella test was slightly higher in nonconcentrated urine samples and was identical in concentrated urine samples. The specificity of the Sofia Legionella FIA test was highly reduced by the concentration of urine samples. In nonconcentrated samples, a lack of specificity was observed in 2.3 % of samples, all of them resolved by heat treatment. The Sofia Legionella FIA is a sensitive test for detecting Legionella urinary antigens with no previous urine concentration. However, all positive samples have to be re-tested after boiling to reach a high specificity. The reading is automatized on the Sofia analyzer, which can be connected to laboratory information systems, facilitating accurate and rapid reporting of results.

Toward an Executive Origin for Acquired Phonological Dyslexia: A Case of Specific Deficit of Context-Sensitive Grapheme-to-Phoneme Conversion Rules

PubMed Central

Auclair-Ouellet, Noémie; Fossard, Marion; St-Pierre, Marie-Catherine; Macoir, Joël

2013-01-01

Phonological dyslexia is a written language disorder characterized by poor reading of nonwords when compared with relatively preserved ability in reading real words. In this study, we report the case of FG, a 74-year-old man with phonological dyslexia. The nature and origin of his reading impairment were assessed using tasks involving activation and explicit manipulation of phonological representations as well as reading of words and nonwords in which the nature and complexity of grapheme-to-phoneme conversion rules (GPC rules) were manipulated. FG also underwent an extensive neuropsychological assessment battery in which he showed impaired performance in tests exploring verbal working memory and executive functions. FG showed no phonological impairment, and his performance was also largely unimpaired for reading words, with no effect of concreteness, grammatical class, morphological complexity, length or nature and complexity of the GPC rules. However, he showed substantial difficulties when asked to read nonwords with contextual GPC rules. The contribution of FG’s executive deficits to his performance in reading is discussed. PMID:22713417

Does the Relation between Rapid Automatized Naming and Reading Depend on Age or on Reading Level? A Behavioral and ERP Study

PubMed Central

Cohen, Marjolaine; Mahé, G.; Laganaro, Marina; Zesiger, Pascal

2018-01-01

Reading predictors evolve through age: phonological awareness is the best predictor of reading abilities at the beginning of reading acquisition while Rapid Automatized Naming (RAN) becomes the best reading predictor in more experienced readers (around 9–10 years old). Those developmental changes in the relationship between RAN and reading have so far been explained in term of participants' age. However, it should be noted that in the previous experiments age always co-vary with participants reading level. It is thus not clear whether RAN-reading relationship is developmental in nature or related to the reading system itself. This study investigates whether the behavioral changes in the relationship between RAN and reading and their electrophysiological correlates are related to the chronological age or to the reading level of the participants. Thirty two French-speaking children aged 7–10 years took part to the experiment: they were divided into groups contrasted on age but with similar reading levels and the other way round. Participants performed two reading tasks and four RAN tasks. EEG/ERP was recorded during discrete letter and picture RAN. Behavioral results revealed that alphanumeric RAN is more sensitive to age variations than reading level differences. The inverse profile was revealed for picture RAN, which discriminate poor and good readers among typically developed children within the same age-group. ERPs of both letter and picture RAN differed across age groups whereas only for the picture RAN ERPs differed across reading levels. Taken together, these results suggest that picture RAN is a particularly good indicator of reading level variance independently of age. PMID:29520226

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

Bolotnikov, A. E., E-mail: bolotnik@bnl.gov; Camarda, G. S.; Cui, Y.

We investigated the feasibility of long-drift-time CdZnTe (CZT) gamma-ray detectors, fabricated from CZT material produced by Redlen Technologies. CZT crystals with cross-section areas of 5 × 5 mm{sup 2} and 6 × 6 mm{sup 2} and thicknesses of 20-, 30-, 40-, and 50-mm were configured as 3D position-sensitive drift detectors and were read out using a front-end ASIC. By correcting the electron charge losses caused by defects in the crystals, we demonstrated high performance for relatively thick detectors fabricated from unselected CZT material.

CMOS image sensor with organic photoconductive layer having narrow absorption band and proposal of stack type solid-state image sensors

NASA Astrophysics Data System (ADS)

Takada, Shunji; Ihama, Mikio; Inuiya, Masafumi

2006-02-01

Digital still cameras overtook film cameras in Japanese market in 2000 in terms of sales volume owing to their versatile functions. However, the image-capturing capabilities such as sensitivity and latitude of color films are still superior to those of digital image sensors. In this paper, we attribute the cause for the high performance of color films to their multi-layered structure, and propose the solid-state image sensors with stacked organic photoconductive layers having narrow absorption bands on CMOS read-out circuits.

Polarization stable plasmonic sensor based on tilted fiber Bragg grating

NASA Astrophysics Data System (ADS)

Tomyshev, Kirill A.; Chamorovskiy, Yuriy K.; Ustimchik, Vasily E.; Butov, Oleg V.

2017-04-01

This paper presents a solution to one of the major problems of plasmonic fiber Bragg grating sensors concerning their high sensitivity to changes in the polarization state of light propagating through optical fiber. For the first time these kind of sensors have been produced using polarization maintaining fibers, thereby stabilization has been achieved using mechanical action and bending the supplied fiber. Comparative experiments have demonstrated that the sensor readings stability is at least an order of magnitude higher relative to other sensors, which record in a standard fiber with an isotropic structure.

Behavioral and Molecular Genetics of Reading-Related AM and FM Detection Thresholds.

PubMed

Bruni, Matthew; Flax, Judy F; Buyske, Steven; Shindhelm, Amber D; Witton, Caroline; Brzustowicz, Linda M; Bartlett, Christopher W

2017-03-01

Auditory detection thresholds for certain frequencies of both amplitude modulated (AM) and frequency modulated (FM) dynamic auditory stimuli are associated with reading in typically developing and dyslexic readers. We present the first behavioral and molecular genetic characterization of these two auditory traits. Two extant extended family datasets were given reading tasks and psychoacoustic tasks to determine FM 2 Hz and AM 20 Hz sensitivity thresholds. Univariate heritabilities were significant for both AM (h 2  = 0.20) and FM (h 2  = 0.29). Bayesian posterior probability of linkage (PPL) analysis found loci for AM (12q, PPL = 81 %) and FM (10p, PPL = 32 %; 20q, PPL = 65 %). Bivariate heritability analyses revealed that FM is genetically correlated with reading, while AM was not. Bivariate PPL analysis indicates that FM loci (10p, 20q) are not also associated with reading.

Executive Function, Self-Regulated Learning, and Reading Comprehension: A Training Study.

PubMed

Cirino, Paul T; Miciak, Jeremy; Gerst, Elyssa; Barnes, Marcia A; Vaughn, Sharon; Child, Amanda; Huston-Warren, Emily

The goal of this study was to evaluate the extent to which training that emphasizes the process of executive function (EF) and self-regulated learning (SRL) would result in increased reading comprehension; we also evaluated interrelationships of EF, SRL, and reading. We report an experiment ( N = 75 fourth graders) that contrasted two researcher-implemented conditions (text-based reading [TB] and text-based reading plus executive function [TB+EF]) to a control. We also evaluated relationships among measures of SRL, EF, and reading. Both the TB and TB+EF groups outperformed the control group for proximal text comprehension (where the topic was similar to that covered in training) and background knowledge related to it, but the two researcher-led groups performed similarly. There were no significant differences for less proximal text, and again similar performance for both TB and TB+EF. Correlations among measures were weak in general, although the pattern was similar to that found in the extant literature. The findings speak to the difficulty in separating these components from those of strong instruction more generally. The relationships of these constructs to reading comprehension will likely be enhanced by more sensitive measurement of EF and reading comprehension, particularly where tied to active treatment components.

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

PubMed Central

Liao, Yang; Smyth, Gordon K.; Shi, Wei

2013-01-01

Read alignment is an ongoing challenge for the analysis of data from sequencing technologies. This article proposes an elegantly simple multi-seed strategy, called seed-and-vote, for mapping reads to a reference genome. The new strategy chooses the mapped genomic location for the read directly from the seeds. It uses a relatively large number of short seeds (called subreads) extracted from each read and allows all the seeds to vote on the optimal location. When the read length is <160 bp, overlapping subreads are used. More conventional alignment algorithms are then used to fill in detailed mismatch and indel information between the subreads that make up the winning voting block. The strategy is fast because the overall genomic location has already been chosen before the detailed alignment is done. It is sensitive because no individual subread is required to map exactly, nor are individual subreads constrained to map close by other subreads. It is accurate because the final location must be supported by several different subreads. The strategy extends easily to find exon junctions, by locating reads that contain sets of subreads mapping to different exons of the same gene. It scales up efficiently for longer reads. PMID:23558742

Increased Sensitivity of Diagnostic Mutation Detection by Re-analysis Incorporating Local Reassembly of Sequence Reads.

PubMed

Watson, Christopher M; Camm, Nick; Crinnion, Laura A; Clokie, Samuel; Robinson, Rachel L; Adlard, Julian; Charlton, Ruth; Markham, Alexander F; Carr, Ian M; Bonthron, David T

2017-12-01

Diagnostic genetic testing programmes based on next-generation DNA sequencing have resulted in the accrual of large datasets of targeted raw sequence data. Most diagnostic laboratories process these data through an automated variant-calling pipeline. Validation of the chosen analytical methods typically depends on confirming the detection of known sequence variants. Despite improvements in short-read alignment methods, current pipelines are known to be comparatively poor at detecting large insertion/deletion mutations. We performed clinical validation of a local reassembly tool, ABRA (assembly-based realigner), through retrospective reanalysis of a cohort of more than 2000 hereditary cancer cases. ABRA enabled detection of a 96-bp deletion, 4-bp insertion mutation in PMS2 that had been initially identified using a comparative read-depth approach. We applied an updated pipeline incorporating ABRA to the entire cohort of 2000 cases and identified one previously undetected pathogenic variant, a 23-bp duplication in PTEN. We demonstrate the effect of read length on the ability to detect insertion/deletion variants by comparing HiSeq2500 (2 × 101-bp) and NextSeq500 (2 × 151-bp) sequence data for a range of variants and thereby show that the limitations of shorter read lengths can be mitigated using appropriate informatics tools. This work highlights the need for ongoing development of diagnostic pipelines to maximize test sensitivity. We also draw attention to the large differences in computational infrastructure required to perform day-to-day versus large-scale reprocessing tasks.

Development of radiation tolerant monolithic active pixel sensors with fast column parallel read-out

NASA Astrophysics Data System (ADS)

Koziel, M.; Dorokhov, A.; Fontaine, J.-C.; De Masi, R.; Winter, M.

2010-12-01

Monolithic active pixel sensors (MAPS) [1] (Turchetta et al., 2001) are being developed at IPHC—Strasbourg to equip the EUDET telescope [2] (Haas, 2006) and vertex detectors for future high energy physics experiments, including the STAR upgrade at RHIC [3] (T.S. Collaboration, 2005) and the CBM experiment at FAIR/GSI [4] (Heuser, 2006). High granularity, low material budget and high read-out speed are systematically required for most applications, complemented, for some of them, with high radiation tolerance. A specific column-parallel architecture, implemented in the MIMOSA-22 sensor, was developed to achieve fast read-out MAPS. Previous studies of the front-end architecture integrated in this sensor, which includes in-pixel amplification, have shown that the fixed pattern noise increase consecutive to ionizing radiation can be controlled by means of a negative feedback [5] (Hu-Guo et al., 2008). However, an unexpected rise of the temporal noise was observed. A second version of this chip (MIMOSA-22bis) was produced in order to search for possible improvements of the radiation tolerance, regarding this type of noise. In this prototype, the feedback transistor was tuned in order to mitigate the sensitivity of the pixel to ionizing radiation. The performances of the pixels after irradiation were investigated for two types of feedback transistors: enclosed layout transistor (ELT) [6] (Snoeys et al., 2000) and "standard" transistor with either large or small transconductance. The noise performance of all test structures was studied in various conditions (expected in future experiments) regarding temperature, integration time and ionizing radiation dose. Test results are presented in this paper. Based on these observations, ideas for further improvement of the radiation tolerance of column parallel MAPS are derived.

Testing genotyping strategies for ultra-deep sequencing of a co-amplifying gene family: MHC class I in a passerine bird.

PubMed

Biedrzycka, Aleksandra; Sebastian, Alvaro; Migalska, Magdalena; Westerdahl, Helena; Radwan, Jacek

2017-07-01

Characterization of highly duplicated genes, such as genes of the major histocompatibility complex (MHC), where multiple loci often co-amplify, has until recently been hindered by insufficient read depths per amplicon. Here, we used ultra-deep Illumina sequencing to resolve genotypes at exon 3 of MHC class I genes in the sedge warbler (Acrocephalus schoenobaenus). We sequenced 24 individuals in two replicates and used this data, as well as a simulated data set, to test the effect of amplicon coverage (range: 500-20 000 reads per amplicon) on the repeatability of genotyping using four different genotyping approaches. A third replicate employed unique barcoding to assess the extent of tag jumping, that is swapping of individual tag identifiers, which may confound genotyping. The reliability of MHC genotyping increased with coverage and approached or exceeded 90% within-method repeatability of allele calling at coverages of >5000 reads per amplicon. We found generally high agreement between genotyping methods, especially at high coverages. High reliability of the tested genotyping approaches was further supported by our analysis of the simulated data set, although the genotyping approach relying primarily on replication of variants in independent amplicons proved sensitive to repeatable errors. According to the most repeatable genotyping method, the number of co-amplifying variants per individual ranged from 19 to 42. Tag jumping was detectable, but at such low frequencies that it did not affect the reliability of genotyping. We thus demonstrate that gene families with many co-amplifying genes can be reliably genotyped using HTS, provided that there is sufficient per amplicon coverage. © 2016 John Wiley & Sons Ltd.

Improve homology search sensitivity of PacBio data by correcting frameshifts.

PubMed

Du, Nan; Sun, Yanni

2016-09-01

Single-molecule, real-time sequencing (SMRT) developed by Pacific BioSciences produces longer reads than secondary generation sequencing technologies such as Illumina. The long read length enables PacBio sequencing to close gaps in genome assembly, reveal structural variations, and identify gene isoforms with higher accuracy in transcriptomic sequencing. However, PacBio data has high sequencing error rate and most of the errors are insertion or deletion errors. During alignment-based homology search, insertion or deletion errors in genes will cause frameshifts and may only lead to marginal alignment scores and short alignments. As a result, it is hard to distinguish true alignments from random alignments and the ambiguity will incur errors in structural and functional annotation. Existing frameshift correction tools are designed for data with much lower error rate and are not optimized for PacBio data. As an increasing number of groups are using SMRT, there is an urgent need for dedicated homology search tools for PacBio data. In this work, we introduce Frame-Pro, a profile homology search tool for PacBio reads. Our tool corrects sequencing errors and also outputs the profile alignments of the corrected sequences against characterized protein families. We applied our tool to both simulated and real PacBio data. The results showed that our method enables more sensitive homology search, especially for PacBio data sets of low sequencing coverage. In addition, we can correct more errors when comparing with a popular error correction tool that does not rely on hybrid sequencing. The source code is freely available at https://sourceforge.net/projects/frame-pro/ yannisun@msu.edu. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Diagnostic accuracy of an iPhone DICOM viewer for the interpretation of magnetic resonance imaging of the knee.

PubMed

De Maio, Peter; White, Lawrence M; Bleakney, Robert; Menezes, Ravi J; Theodoropoulos, John

2014-07-01

To evaluate the diagnostic performance of viewing magnetic resonance (MR) images on a handheld mobile device compared with a conventional radiology workstation for the diagnosis of intra-articular knee pathology. Prospective comparison study. Tertiary care center. Fifty consecutive subjects who had MR imaging of the knee followed by knee arthroscopy were prospectively evaluated. Two musculoskeletal radiologists independently reviewed each MR study using 2 different viewers: the OsiriX DICOM viewer software on an Apple iPhone 3GS device and eFilm Workstation software on a conventional picture archiving and communications system workstation. Sensitivity and specificity of the iPhone and workstation interpretations was performed using knee arthroscopy as the reference standard. Intraobserver concordance and agreement between the iPhone and workstation interpretations were determined. There was no statistically significant difference between the 2 devices for each paired comparison of diagnostic performance. For the iPhone interpretations, sensitivity ranged from 77% (13 of 17) for the lateral meniscus to 100% (17 of 17) for the anterior cruciate ligament. Specificity ranged from 74% (14 of 19) for cartilage to 100% (50 of 50) for the posterior cruciate ligament. There was a very high level of interobserver and intraobserver agreement between devices and readers. The iPhone reads took longer than the corresponding workstation reads, with a significant mean difference between the iPhone and workstation reads of 3.98 minutes (P < 0.001). The diagnostic performance of interpreting MR images on a handheld mobile device for the assessment of intra-articular knee pathology is similar to that of a conventional radiology workstation, however, requires a longer viewing time. Timely and accurate interpretation of complex medical images using mobile device solutions could result in new workflow efficiencies and ultimately improve patient care.

Content Area Reading: A Functional Approach.

ERIC Educational Resources Information Center

Plecki, Gerard D.

The implementation of a content reading program at Urbana High School, Urbana, Illinois, is discussed in this document. Reading staff hired with Title VII funds offered assistance to all teachers in the high school by working with classroom teachers in their classes for 60 minutes of class time per week. Free reading time devoted to high-interest…

Investigating a Reading Comprehension Intervention for High School Students with Autism Spectrum Disorder: A Pilot Study

ERIC Educational Resources Information Center

Reutebuch, Colleen K.; El Zein, Farah; Kyung Kim, Min; Weinberg, Aron N.; Vaughn, Sharon

2015-01-01

We adapted and piloted Collaborative Strategic Reading-High School, a reading comprehension intervention, with three high school students with autism spectrum disorder to investigate its effects on their reading comprehension. Using a nonconcurrent, multiple-baseline design, participants with autism spectrum disorder were paired with a…

Best Practices for Achieving High, Rapid Reading Gains

ERIC Educational Resources Information Center

Carbo, Marie

2008-01-01

The percentage of students who read at the proficient level on the National Assessment of Educational Progress (NAEP) has not improved, and is appallingly low. In order for students to achieve high reading gains and become life-long readers, reading comprehension and reading enjoyment must be the top two goals. This article presents several…

Beginning to Disentangle the Prosody-Literacy Relationship: A Multi-Component Measure of Prosodic Sensitivity

ERIC Educational Resources Information Center

Holliman, A. J.; Williams, G. J.; Mundy, I. R.; Wood, C.; Hart, L.; Waldron, S.

2014-01-01

A growing number of studies now suggest that sensitivity to the rhythmic patterning of speech (prosody) is implicated in successful reading acquisition. However, recent evidence suggests that prosody is not a unitary construct and that the different components of prosody (stress, intonation, and timing) operating at different linguistic levels…

In the Beginning Was the Rhyme? A Reflection on Hulme, Hatcher, Nation, Brown, Adams, and Stuart (2002).

ERIC Educational Resources Information Center

Goswami, Usha

2002-01-01

Describes phonological sensitivity at different grain sizes as a good predictor of reading acquisition in all languages. Presents information on development of phonological sensitivity for syllables, onsets, and rimes. Illustrates that phoneme-level skills develop fastest in children acquiring orthographically consistent languages with simple…

Reduced Sensitivity to Slow-Rate Dynamic Auditory Information in Children with Dyslexia

ERIC Educational Resources Information Center

Poelmans, Hanne; Luts, Heleen; Vandermosten, Maaike; Boets, Bart; Ghesquiere, Pol; Wouters, Jan

2011-01-01

The etiology of developmental dyslexia remains widely debated. An appealing theory postulates that the reading and spelling problems in individuals with dyslexia originate from reduced sensitivity to slow-rate dynamic auditory cues. This low-level auditory deficit is thought to provoke a cascade of effects, including inaccurate speech perception…

What Is the deficit in Phonological Processing Deficits: Auditory Sensitivity, Masking, or Category Formation?

ERIC Educational Resources Information Center

Nittrouer, Susan; Shune, Samantha; Lowenstein, Joanna H.

2011-01-01

Although children with language impairments, including those associated with reading, usually demonstrate deficits in phonological processing, there is minimal agreement as to the source of those deficits. This study examined two problems hypothesized to be possible sources: either poor auditory sensitivity to speech-relevant acoustic properties,…

Development and Refinement of Reading and Mathematics Tests for Grades 2 and 5. Beginning Teacher Evaluation Study. Technical Report Series. Technical Report III-1. Continuation of Phase III A.

ERIC Educational Resources Information Center

Filby, Nikola N.; Dishaw, Marilyn

Achievement tests that are maximally sensitive to effective instruction in reading and mathematics for grades 2 and 5 were developed and refined. Important considerations regarding the tests' validity were: its coverage of instructional content (opportunity to learn), and its reactivity to instruction. Student ability must be minimally related to…

RIFM fragrance ingredient safety assessment, 2-ethyl-1-butanol, CAS Registry Number 97-95-0.

PubMed

Api, A M; Belsito, D; Bhatia, S; Bruze, M; Calow, P; Dagli, M L; Dekant, W; Fryer, A D; Kromidas, L; La Cava, S; Lalko, J F; Lapczynski, A; Liebler, D C; Miyachi, Y; Politano, V T; Ritacco, G; Salvito, D; Schultz, T W; Shen, J; Sipes, I G; Wall, B; Wilcox, D K

2016-11-01

The use of this material under current conditions is supported by existing information. This material was evaluated for genotoxicity, repeated dose toxicity, developmental and reproductive toxicity, local respiratory toxicity, phototoxicity/photoallergenicity, skin sensitization, as well as environmental safety. Data from the suitable read across analog 2-ethylhexanol (CAS # 104-76-7) show that this material is not genotoxic. Data from the suitable read across analog isopropyl alcohol (CAS # 67-63-0) show that this material does not have skin sensitization potential. The local respiratory toxicity endpoint was completed using the TTC (Threshold of Toxicological Concern) for a Cramer Class I material (1.4 mg/day). The repeated dose toxicity endpoint was completed using 2-ethylhexanol (CAS # 104-76-7) and 1-heptanol, 2-propyl (CAS # 10042-59-8) as suitable read across analogs, which provided a MOE > 100. The developmental and reproductive toxicity endpoint was completed using 2-ethyl-hexanol (CAS # 104-76-7) and isobutyl alcohol (CAS # 78-83-1) as suitable read across analogs, which provided a MOE > 100. The phototoxicity/photoallergenicity endpoint was completed based on suitable UV spectra. The environmental endpoint was completed as described in the RIFM Framework. Copyright © 2016 Elsevier Ltd. All rights reserved.

Use of read-across and computer-based predictive analysis for the safety assessment of PEG cocamines.

PubMed

Skare, Julie A; Blackburn, Karen; Wu, Shengde; Re, Thomas A; Duche, Daniel; Ringeissen, Stephanie; Bjerke, Donald L; Srinivasan, Viny; Eisenmann, Carol

2015-04-01

In the European Union animal testing has been eliminated for cosmetic ingredients while the US Cosmetic Ingredient Review Expert Panel may request data from animal studies. The use of read-across and predictive toxicology provides a path for filling data gaps without additional animal testing. The PEG cocamines are tertiary amines with an alkyl group derived from coconut fatty acids and two PEG chains of varying length. Toxicology data gaps for the PEG cocamines can be addressed by read-across based on structure-activity relationship using the framework described by Wu et al. (2010) for identifying suitable structural analogs. Data for structural analogs supports the conclusion that the PEG cocamines are non-genotoxic and not expected to exhibit systemic or developmental/reproductive toxicity with use in cosmetics. Due to lack of reliable dermal sensitization data for suitable analogs, this endpoint was addressed using predictive software (TIMES SS) as a first step (Laboratory of Mathematical Chemistry). The prediction for PEG cocamines was the same as that for PEGs, which have been concluded to not present a significant concern for dermal sensitization. This evaluation for PEG cocamines demonstrates the utility of read-across and predictive toxicology tools to assess the safety of cosmetic ingredients. Copyright © 2015 Elsevier Inc. All rights reserved.

Screening for asymptomatic atrial fibrillation while monitoring the blood pressure at home: trial of regular versus irregular pulse for prevention of stroke (TRIPPS 2.0).

PubMed

Wiesel, Joseph; Abraham, Saji; Messineo, Frank C

2013-06-01

Asymptomatic atrial fibrillation (AF) is a common cause of strokes. Physician screening for AF has been recommended. Home screening for AF may increase the likelihood of detecting asymptomatic AF in patients at risk for stroke because of AF. The aim of this study was to assess the feasibility and accuracy of screening for AF when taking home blood pressure (BP) measurements using an automatic AF-detecting BP monitor. Subjects aged >64 years or those with hypertension, diabetes, congestive heart failure, or previous stroke were enrolled by their primary physicians and given the AF-BP monitor and an electrocardiographic event monitor to use at home for 30 days. The AF-BP monitor reading was compared with the electrocardiographic reading to calculate the sensitivity and specificity of the device for detecting AF. A total of 160 subjects were enrolled, with 10 withdrawing, 1 excluded, and 10 with no AF-BP monitor logs or electrocardiographic recordings. Of the 139 subjects included, 14 had known AF. There was a total of 3,316 days with AF-BP monitor readings and electrocardiographic readings. On the basis of the initial daily AF-BP monitor readings, the AF-BP monitor demonstrated sensitivity of 99.2% and specificity of 92.9% for detecting AF. Two subjects with no histories of AF had AF-BP monitor readings of AF that were confirmed by the electrocardiographic monitor. One of these subjects was started on warfarin. In conclusion, home screening for asymptomatic AF while taking BP measurements can be performed accurately. This can be used to detect new AF, allowing treatment with anticoagulation to reduce the future risk for stroke. Copyright © 2013 Elsevier Inc. All rights reserved.

AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework

PubMed Central

Zheng, Qi; Grice, Elizabeth A.

2016-01-01

Accurate mapping of next-generation sequencing (NGS) reads to reference genomes is crucial for almost all NGS applications and downstream analyses. Various repetitive elements in human and other higher eukaryotic genomes contribute in large part to ambiguously (non-uniquely) mapped reads. Most available NGS aligners attempt to address this by either removing all non-uniquely mapping reads, or reporting one random or "best" hit based on simple heuristics. Accurate estimation of the mapping quality of NGS reads is therefore critical albeit completely lacking at present. Here we developed a generalized software toolkit "AlignerBoost", which utilizes a Bayesian-based framework to accurately estimate mapping quality of ambiguously mapped NGS reads. We tested AlignerBoost with both simulated and real DNA-seq and RNA-seq datasets at various thresholds. In most cases, but especially for reads falling within repetitive regions, AlignerBoost dramatically increases the mapping precision of modern NGS aligners without significantly compromising the sensitivity even without mapping quality filters. When using higher mapping quality cutoffs, AlignerBoost achieves a much lower false mapping rate while exhibiting comparable or higher sensitivity compared to the aligner default modes, therefore significantly boosting the detection power of NGS aligners even using extreme thresholds. AlignerBoost is also SNP-aware, and higher quality alignments can be achieved if provided with known SNPs. AlignerBoost’s algorithm is computationally efficient, and can process one million alignments within 30 seconds on a typical desktop computer. AlignerBoost is implemented as a uniform Java application and is freely available at https://github.com/Grice-Lab/AlignerBoost. PMID:27706155

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

Debono, Josephine C, E-mail: josephine.debono@bci.org.au; Poulos, Ann E; Houssami, Nehmat

This study aimed to evaluate the accuracy of radiographers’ screen-reading mammograms. Currently, radiologist workforce shortages may be compromising the BreastScreen Australia screening program goal to detect early breast cancer. The solution to a similar problem in the United Kingdom has successfully encouraged radiographers to take on the role as one of two screen-readers. Prior to consideration of this strategy in Australia, educational and experiential differences between radiographers in the United Kingdom and Australia emphasise the need for an investigation of Australian radiographers’ screen-reading accuracy. Ten radiographers employed by the Westmead Breast Cancer Institute with a range of radiographic (median =more » 28 years), mammographic (median = 13 years) and BreastScreen (median = 8 years) experience were recruited to blindly and independently screen-read an image test set of 500 mammograms, without formal training. The radiographers indicated the presence of an abnormality using BI-RADS®. Accuracy was determined by comparison with the gold standard of known outcomes of pathology results, interval matching and client 6-year follow-up. Individual sensitivity and specificity levels ranged between 76.0% and 92.0%, and 74.8% and 96.2% respectively. Pooled screen-reader accuracy across the radiographers estimated sensitivity as 82.2% and specificity as 89.5%. Areas under the reading operating characteristic curve ranged between 0.842 and 0.923. This sample of radiographers in an Australian setting have adequate accuracy levels when screen-reading mammograms. It is expected that with formal screen-reading training, accuracy levels will improve, and with support, radiographers have the potential to be one of the two screen-readers in the BreastScreen Australia program, contributing to timeliness and improved program outcomes.« less

Repeatability of quantitative FDG-PET/CT and contrast-enhanced CT in recurrent ovarian carcinoma: test-retest measurements for tumor FDG uptake, diameter, and volume.

PubMed

Rockall, Andrea G; Avril, Norbert; Lam, Raymond; Iannone, Robert; Mozley, P David; Parkinson, Christine; Bergstrom, Donald; Sala, Evis; Sarker, Shah-Jalal; McNeish, Iain A; Brenton, James D

2014-05-15

Repeatability of baseline FDG-PET/CT measurements has not been tested in ovarian cancer. This dual-center, prospective study assessed variation in tumor 2[18F]fluoro-2-deoxy-D-glucose (FDG) uptake, tumor diameter, and tumor volume from sequential FDG-PET/CT and contrast-enhanced computed tomography (CECT) in patients with recurrent platinum-sensitive ovarian cancer. Patients underwent two pretreatment baseline FDG-PET/CT (n = 21) and CECT (n = 20) at two clinical sites with different PET/CT instruments. Patients were included if they had at least one target lesion in the abdomen with a standardized uptake value (SUV) maximum (SUVmax) of ≥ 2.5 and a long axis diameter of ≥ 15 mm. Two independent reading methods were used to evaluate repeatability of tumor diameter and SUV uptake: on site and at an imaging clinical research organization (CRO). Tumor volume reads were only performed by CRO. In each reading set, target lesions were independently measured on sequential imaging. Median time between FDG-PET/CT was two days (range 1-7). For site reads, concordance correlation coefficients (CCC) for SUVmean, SUVmax, and tumor diameter were 0.95, 0.94, and 0.99, respectively. Repeatability coefficients were 16.3%, 17.3%, and 8.8% for SUVmean, SUVmax, and tumor diameter, respectively. Similar results were observed for CRO reads. Tumor volume CCC was 0.99 with a repeatability coefficient of 28.1%. There was excellent test-retest repeatability for FDG-PET/CT quantitative measurements across two sites and two independent reading methods. Cutoff values for determining change in SUVmean, SUVmax, and tumor volume establish limits to determine metabolic and/or volumetric response to treatment in platinum-sensitive relapsed ovarian cancer. ©2014 American Association for Cancer Research.

Metacognition and Reading: Comparing Three Forms of Metacognition in Normally Developing Readers and Readers with Dyslexia.

PubMed

Furnes, Bjarte; Norman, Elisabeth

2015-08-01

Metacognition refers to 'cognition about cognition' and includes metacognitive knowledge, strategies and experiences (Efklides, 2008; Flavell, 1979). Research on reading has shown that better readers demonstrate more metacognitive knowledge than poor readers (Baker & Beall, 2009), and that reading ability improves through strategy instruction (Gersten, Fuchs, Williams, & Baker, 2001). The current study is the first to specifically compare the three forms of metacognition in dyslexic (N = 22) versus normally developing readers (N = 22). Participants read two factual texts, with learning outcome measured by a memory task. Metacognitive knowledge and skills were assessed by self-report. Metacognitive experiences were measured by predictions of performance and judgments of learning. Individuals with dyslexia showed insight into their reading problems, but less general knowledge of how to approach text reading. They more often reported lack of available reading strategies, but groups did not differ in the use of deep and surface strategies. Learning outcome and mean ratings of predictions of performance and judgments of learning were lower in dyslexic readers, but not the accuracy with which metacognitive experiences predicted learning. Overall, the results indicate that dyslexic reading and spelling problems are not generally associated with lower levels of metacognitive knowledge, metacognitive strategies or sensitivity to metacognitive experiences in reading situations. 2015 The Authors. Dyslexia Published by John Wiley & Sons Ltd.

A Proposal for a Diagnostic and Remedial Reading Center for the Educational Park Complex of the ESUHSD [East Side Union High School District, San Jose, California].

ERIC Educational Resources Information Center

Gillespie, Barbara

The emphases of the reading center proposed in this study are on the assessment of reading strengths, the isolation of reading deficiencies, and--in an instructor-learner environment--diagnosis and the prescription of action which will enable students to master the reading skills necessary for independent reading in their high school careers. This…

The PlusoptiX Photoscreener and the Retinomax Autorefractor as Community-based Screening Devices for Preschool Children.

PubMed

Kinori, Michael; Molina, Iliana; Hernandez, Eric O; Robbins, Shira L; Granet, David B; Coleman, Anne L; Brown, Stuart I

2018-05-01

To compare the performance of the PlusoptiX S12 mobile photoscreener and the Retinomax K+3 Autorefractor as screening devices in preschool children. Children ranging from 3 to 5 years of age from 11 San Diego County preschools underwent vision screening in their schools where ambient light could not always be controlled using both the Retinomax and the PlusoptiX. Cycloplegic refraction on the consented children was subsequently performed on the UCSD EyeMobile for children on-site at the school locations. A total of 321 children were screened with the PlusoptiX and Retinomax. The PlusoptiX referred 22% of children, of whom 70% of the referrals were read as "unable". The Retinomax referred 13% and there were no "unables". Similar results occurred in the cycloplegic-refracted 182 consented children-64% of the PlusoptiX referrals were read as "unable" . Only one third of these "unables" required glasses. Both devices referred the four children with amblyopia and one case of strabismus. However, PlusoptiX's 3 false negatives had amblyopia risk factors (ARFs) while the one Retinomax's false negative did not have ARFs. The Retinomax screening had 95% sensitivity and 94% specificity. The PlusoptiX screening had 86% sensitivity and 84% specificity. In this preschool population and environment, the PlusoptiX referred 63% more than the Retinomax in addition to a lower specificity and sensitivity. Adjusting PlusoptiX referral criteria might not substantially improve the specificity of the PlusoptiX due to the high numbers of "unables".

SU-E-T-675: Remote Dosimetry with a Novel PRESAGE Formulation

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

Mein, S; Juang, T; Malcolm, J

2015-06-15

Purpose: 3D-gel dosimetry provides high-resolution treatment validation; however, scanners aren’t widely available. In remote dosimetry, dosimeters are shipped out from a central base institution to a remote site for irradiation, then shipped back for scanning and analysis, affording a convenient service for treatment validation to institutions lacking the necessary equipment and resources. Previous works demonstrated the high-resolution performance and temporal stability of PRESAGE. Here the newest formulation is investigated for remote dosimetry use. Methods: A new formulation of PRESAGE was created with the aim of improved color stability post irradiation. Dose sensitivity was determined by irradiating cuvettes on a Varianmore » Linac (6MV) from 0–15Gy and measuring change in optical density at 633nm. Sensitivity readings were tracked over time in a temperature control study to determine long-term stability. A large volume study was performed to evaluate the accuracy for remote dosimetry. A 1kg dosimeter was pre-scanned, irradiated on-site with an 8Gy 4field box treatment, post-scanned and shipped to Princess Margaret Hospital for remote reading on an identical scanner. Results: Dose sensitivities ranged from 0.0194–0.0295 ΔOD/(Gy*cm)—similar to previous formulations. Post-irradiated cuvettes stored at 10°C retained 100% initial sensitivity over 5 days and 98.6% over 10 weeks while cuvettes stored at room temperature fell to 95.8% after 5 days and 37.4% after 10 weeks. The immediate and 5-day scans of the 4field box dosimeter data was reconstructed, registered to the corresponding eclipse dose-distribution, and compared with analytical tools in CERR. Immediate and 5-day scans looked visually similar. Line profiles revealed close agreement aside from a slight elevation in dose at the edge in the 5-day readout. Conclusion: The remote dosimetry formulation exhibits excellent temporal stability in small volumes. While immediate and 5-day readout scans of large volume dosimeters show promising agreement, further development is required to reduce an apparent time dependent edge elevation.« less

Supplementary Reading Instruction in Alternative High Schools: A Statewide Survey of Educator Reported Practices and Barriers

ERIC Educational Resources Information Center

Wilkerson, Kimber L.; Yan, Min-Chi; Perzigian, Aaron B.; Cakiroglu, Orhan

2016-01-01

Recent data suggest that a majority of secondary students read below the level considered proficient on state standardized tests of reading. Alternative high schools, in particular, serve a high proportion of struggling readers. This survey study investigated reading instruction provided to struggling readers in alternative schools in one state by…

The Relationships among Reported Strategy Use, Metacognitive Awareness, and Reading Achievement of High School Students

ERIC Educational Resources Information Center

Hong-Nam, Kay; Leavell, Alexandra G.; Maher, Sheila

2014-01-01

The metacognitive awareness and reading strategy use of high school students enrolled in two high schools were investigated. The correlations between reading scores and strategy use were examined as well as the variation in strategy use by self-rated reading proficiency and academic grades. The factor analysis revealed four factors on the…

Readability of Magazines of Interest to Reading-Deficit Students.

ERIC Educational Resources Information Center

Miller, Maurice; And Others

The reading abilities of low achieving high school students at two schools were compared to the readability levels of the magazines in which they showed interest. The median tested reading ability of these students was reported as third/fourth grade by their reading teachers. The reading specialist at one high school reported that boys had an…

Improving Reading Comprehension of At-Risk High-School Students: The ART of Reading Program

ERIC Educational Resources Information Center

McCallum, R. Steve; Krohn, Katherine R.; Skinner, Christopher H.; Hilton-Prillhart, Angela; Hopkins, Michael; Waller, Steven; Polite, Fritz

2011-01-01

Participants (115 low-socioeconomic-status [SES], inner-city, high-school students) were exposed to three reading conditions: (1) a control condition in which students silently read brief selected passages; (2) an experimental condition in which students were prompted to perform a three-part (Ask, Read, and Tell [ART]) comprehension enhancement…

Applying Learning Analytics to Explore the Effects of Motivation on Online Students' Reading Behavioral Patterns

ERIC Educational Resources Information Center

Sun, Jerry Chih-Yuan; Lin, Che-Tsun; Chou, Chien

2018-01-01

This study aims to apply a sequential analysis to explore the effect of learning motivation on online reading behavioral patterns. The study's participants consisted of 160 graduate students who were classified into three group types: low reading duration with low motivation, low reading duration with high motivation, and high reading duration…

Test set readings predict clinical performance to a limited extent: preliminary findings

NASA Astrophysics Data System (ADS)

Soh, BaoLin P.; Lee, Warwick M.; Kench, Peter L.; Reed, Warren M.; McEntee, Mark F.; Brennan, Patrick C.

2013-03-01

Aim: To investigate the level of agreement between test sets and actual clinical reading Background: The performance of screen readers in detecting breast cancer is being assessed in some countries by using mammographic test sets. However, previous studies have provided little evidence that performance assessed by test sets strongly correlate to performance in clinical reading. Methods: Five clinicians from BreastScreen New South Wales participated in this study. Each clinician was asked to read 200 de-identified mammographic examinations gathered from their own case history within the BreastScreen NSW Digital Imaging Library. All test sets were designed with specific proportions of true positive, true negative, false positive and false negative examinations from the previous actual clinical reads of each reader. A prior mammogram examination for comparison (when available) was also provided for each case. Results: Preliminary analyses have shown that there is a moderate level of agreement (Kappa 0.42-0.56, p < 0.001) between laboratory test sets and actual clinical reading. In addition, a mean increase of 38% in sensitivity in the laboratory test sets as compared to their actual clinical readings was demonstrated. Specificity is similar between the laboratory test sets and actual clinical reading. Conclusion: This study demonstrated a moderate level of agreement between actual clinical reading and test set reading, which suggests that test sets have a role in reflecting clinical performance.

Ultra-Low-Power Smart Electronic Nose System Based on Three-Dimensional Tin Oxide Nanotube Arrays.

PubMed

Chen, Jiaqi; Chen, Zhuo; Boussaid, Farid; Zhang, Daquan; Pan, Xiaofang; Zhao, Huijuan; Bermak, Amine; Tsui, Chi-Ying; Wang, Xinran; Fan, Zhiyong

2018-06-04

In this work, we present a high-performance smart electronic nose (E-nose) system consisting of a multiplexed tin oxide (SnO 2 ) nanotube sensor array, read-out circuit, wireless data transmission unit, mobile phone receiver, and data processing application (App). Using the designed nanotube sensor device structure in conjunction with multiple electrode materials, high-sensitivity gas detection and discrimination have been achieved at room temperature, enabling a 1000 times reduction of the sensor's power consumption as compared to a conventional device using thin film SnO 2 . The experimental results demonstrate that the developed E-nose can identify indoor target gases using a simple vector-matching gas recognition algorithm. In addition, the fabricated E-nose has achieved state-of-the-art sensitivity for H 2 and benzene detection at room temperature with metal oxide sensors. Such a smart E-nose system can address the imperative needs for distributed environmental monitoring in smart homes, smart buildings, and smart cities.

Large CMOS imager using hadamard transform based multiplexing

NASA Technical Reports Server (NTRS)

Karasik, Boris S.; Wadsworth, Mark V.

2005-01-01

We have developed a concept design for a large (10k x 10k) CMOS imaging array whose elements are grouped in small subarrays with N pixels in each. The subarrays are code-division multiplexed using the Hadamard Transform (HT) based encoding. The Hadamard code improves the signal-to-noise (SNR) ratio to the reference of the read-out amplifier by a factor of N^1/2. This way of grouping pixels reduces the number of hybridization bumps by N. A single chip layout has been designed and the architecture of the imager has been developed to accommodate the HT base multiplexing into the existing CMOS technology. The imager architecture allows for a trade-off between the speed and the sensitivity. The envisioned imager would operate at a speed >100 fps with the pixel noise < 20 e-. The power dissipation would be 100 pW/pixe1. The combination of the large format, high speed, high sensitivity and low power dissipation can be very attractive for space reconnaissance applications.

Transcutaneous measurement of hyperbilirubinaemia: comparison of the Minolta jaundice meter and the Ingram icterometer.

PubMed

Bilgen, H; Ince, Z; Ozek, E; Bekiroglu, N; Ors, R

1998-12-01

The effectiveness of two different non-invasive transcutaneous bilirubin measurement devices was compared with serum bilirubin levels in 96 healthy newborns. Transcutaneous measurements were obtained with the Minolta Air Shields jaundice meter and the Ingram icterometer and serum bilirubin levels were determined by a direct spectrophotometric method (Bilitron 444). A linear correlation existed between serum bilirubin values and the readings on both the Minolta jaundice meter (r = 0.83) and the Ingram icterometer (r = 0.78). The Kappa coefficient was 0.66. the sensitivity, specificity and positive and negative predictive values were 100%, 56%, 33% and 100% for the Minolta jaundice meter and 100%, 48%, 29% and 100% for the Ingram icterometer, respectively. The high sensitivity and negative predictive value of both devices render them suitable for screening neonatal hyperbilirubinaemia. However, because of its low cost, the Ingram icterometer is preferable to the more complex and expensive Minolta jaundice meter, especially in countries with a high birth rate, such as Turkey.

New application of superconductors: High sensitivity cryogenic light detectors

NASA Astrophysics Data System (ADS)

Cardani, L.; Bellini, F.; Casali, N.; Castellano, M. G.; Colantoni, I.; Coppolecchia, A.; Cosmelli, C.; Cruciani, A.; D'Addabbo, A.; Di Domizio, S.; Martinez, M.; Tomei, C.; Vignati, M.

2017-02-01

In this paper we describe the current status of the CALDER project, which is developing ultra-sensitive light detectors based on superconductors for cryogenic applications. When we apply an AC current to a superconductor, the Cooper pairs oscillate and acquire kinetic inductance, that can be measured by inserting the superconductor in a LC circuit with high merit factor. Interactions in the superconductor can break the Cooper pairs, causing sizable variations in the kinetic inductance and, thus, in the response of the LC circuit. The continuous monitoring of the amplitude and frequency modulation allows to reconstruct the incident energy with excellent sensitivity. This concept is at the basis of Kinetic Inductance Detectors (KIDs) that are characterized by natural aptitude to multiplexed read-out (several sensors can be tuned to different resonant frequencies and coupled to the same line), resolution of few eV, stable behavior over a wide temperature range, and ease in fabrication. We present the results obtained by the CALDER collaboration with 2×2 cm2 substrates sampled by 1 or 4 Aluminum KIDs. We show that the performances of the first prototypes are already competitive with those of other commonly used light detectors, and we discuss the strategies for a further improvement.

Concept for Mars Volcanic Emission Life Scout (3-D)

NASA Technical Reports Server (NTRS)

2004-01-01

This artist's rendition depicts a concept for a Mars orbiter that would scrutinize the martian atmosphere for chemical traces of life or environments supportive of life that might be present anywhere on the planet. The illustration is presented as a three-dimensional stereo view.

The concept is named the Mars Volcanic Emission and Life Scout, or Marvel. It would equip a Mars orbiter with two types of instruments proven useful in studying Earth's atmosphere from Earth orbit. One, a solar occultation infrared spectrometer, would look sideways through Mars' atmosphere toward the setting or rising Sun for an extremely sensitive reading of what chemicals are in the air that sunlight passes through before hitting the instrument. The other, a submillimeter spectrometer would survey the atmosphere continuously, including during dust storms and polar night, to seek localized surface sources of the chemicals of interest. The infrared spectrometer has very high sensitivity for one chemical of great interest: methane, which is produced by many types of microbes, as well as by some volcanic sources. The submillimeter spectrometer has very high sensitivity for water vapor. Localized concentrations of water vapor in the atmosphere could identify places where subsurface water sources may be venting.

A Wireless Fully Passive Neural Recording Device for Unobtrusive Neuropotential Monitoring.

PubMed

Kiourti, Asimina; Lee, Cedric W L; Chae, Junseok; Volakis, John L

2016-01-01

We propose a novel wireless fully passive neural recording device for unobtrusive neuropotential monitoring. Previous work demonstrated the feasibility of monitoring emulated brain signals in a wireless fully passive manner. In this paper, we propose a novel realistic recorder that is significantly smaller and much more sensitive. The proposed recorder utilizes a highly efficient microwave backscattering method and operates without any formal power supply or regulating elements. Also, no intracranial wires or cables are required. In-vitro testing is performed inside a four-layer head phantom (skin, bone, gray matter, and white matter). Compared to our former implementation, the neural recorder proposed in this study has the following improved features: 1) 59% smaller footprint, 2) up to 20-dB improvement in neuropotential detection sensitivity, and 3) encapsulation in biocompatible polymer. For the first time, temporal emulated neuropotentials as low as 63 μVpp can be detected in a wireless fully passive manner. Remarkably, the high-sensitivity achieved in this study implies reading of most neural signals generated by the human brain. The proposed recorder brings forward transformational possibilities in wireless fully passive neural detection for a very wide range of applications (e.g., epilepsy, Alzheimer's, mental disorders, etc.).

Surface plasmon resonance spectroscopy sensor and methods for using same

DOEpatents

Anderson, Brian Benjamin; Nave, Stanley Eugene

2002-01-01

A surface plasmon resonance ("SPR") probe with a detachable sensor head and system and methods for using the same in various applications is described. The SPR probe couples fiber optic cables directly to an SPR substrate that has a generally planar input surface and a generally curved reflecting surface, such as a substrate formed as a hemisphere. Forming the SPR probe in this manner allows the probe to be miniaturized and operate without the need for high precision, expensive and bulky collimating or focusing optics. Additionally, the curved reflecting surface of the substrate can be coated with one or multiple patches of sensing medium to allow the probe to detect for multiple analytes of interest or to provide multiple readings for comparison and higher precision. Specific applications for the probe are disclosed, including extremely high sensitive relative humidity and dewpoint detection for, e.g., moisture-sensitive environment such as volatile chemical reactions. The SPR probe disclosed operates with a large dynamic range and provides extremely high quality spectra despite being robust enough for field deployment and readily manufacturable.

Detection of pericardial effusion by chest roentgenography and electrocardiography versus echocardiography.

PubMed Central

Manyari, D. E.; Milliken, J. A.; Colwell, B. T.; Burggraf, G. W.

1978-01-01

To determine the sensitivity and specificity of chest roentgenography and electrocardiography in the detection of pericardial effusion, echocardiography was used as the diagnostic standard. Chest roentgenograms and electrocardiograms of 124 patients, 57 of whom had pericardial effusion, were read without knowledge of the echocardiographic interpretation. The sensitivity of roentgenographic diagnosis was low (20%), as was that of diagnosis from decreased voltage on the electrocardiogram (26%). The specificity of the chest roentgenogram was 89% and that of the low-voltage electrocardiogram 97%. The high specificity of the low-voltage electrocardiogram may have been due in part to the exclusion of obese and emphysematous subjects from the study. When cardiomegaly detected roentgenographically or a low-voltage electrocardiogram or both were considered as evidence of pericardial effusion, sensitivity improved to 82% but specificity declined to 29%. It is concluded the chest roentgenography and electrocardiography are unsatisfactory as screening investigations for the detection of pericardial effusion. Images FIG. 1 FIG. 2 FIG. 3 PMID:688146

Genotyping of 25 leukemia-associated genes in a single work flow by next-generation sequencing technology with low amounts of input template DNA.

PubMed

Rinke, Jenny; Schäfer, Vivien; Schmidt, Mathias; Ziermann, Janine; Kohlmann, Alexander; Hochhaus, Andreas; Ernst, Thomas

2013-08-01

We sought to establish a convenient, sensitive next-generation sequencing (NGS) method for genotyping the 26 most commonly mutated leukemia-associated genes in a single work flow and to optimize this method for low amounts of input template DNA. We designed 184 PCR amplicons that cover all of the candidate genes. NGS was performed with genomic DNA (gDNA) from a cohort of 10 individuals with chronic myelomonocytic leukemia. The results were compared with NGS data obtained from sequencing of DNA generated by whole-genome amplification (WGA) of 20 ng template gDNA. Differences between gDNA and WGA samples in variant frequencies were determined for 2 different WGA kits. For gDNA samples, 25 of 26 genes were successfully sequenced with a sensitivity of 5%, which was achieved by a median coverage of 492 reads (range, 308-636 reads) per amplicon. We identified 24 distinct mutations in 11 genes. With WGA samples, we reliably detected all mutations above 5% sensitivity with a median coverage of 506 reads (range, 256-653 reads) per amplicon. With all variants included in the analysis, WGA amplification by the 2 kits tested yielded differences in variant frequencies that ranged from -28.19% to +9.94% [mean (SD) difference, -0.2% (4.08%)] and from -35.03% to +18.67% [mean difference, -0.75% (5.12%)]. Our method permits simultaneous analysis of a wide range of leukemia-associated target genes in a single sequencing run. NGS can be performed after WGA of template DNA for reliable detection of variants without introducing appreciable bias.

Federal Programs in PUHSS: An Evaluation Report.

ERIC Educational Resources Information Center

Phoenix Union High School District, AZ.

The programs described in this report, including the South Mountain High School Reading Program, the Carl Hayden High School Reading Program, the Phoenix Union High School Reading Program, the South Mountain High School Saturation Guidance and Counseling Program (SGCP), the Work Incentive Program (WIN), the Phoenix Union High School Star Reach…

Efficient Detection of Copy Number Mutations in PMS2 Exons with a Close Homolog.

PubMed

Herman, Daniel S; Smith, Christina; Liu, Chang; Vaughn, Cecily P; Palaniappan, Selvi; Pritchard, Colin C; Shirts, Brian H

2018-07-01

Detection of 3' PMS2 copy-number mutations that cause Lynch syndrome is difficult because of highly homologous pseudogenes. To improve the accuracy and efficiency of clinical screening for these mutations, we developed a new method to analyze standard capture-based, next-generation sequencing data to identify deletions and duplications in PMS2 exons 9 to 15. The approach captures sequences using PMS2 targets, maps sequences randomly among regions with equal mapping quality, counts reads aligned to homologous exons and introns, and flags read count ratios outside of empirically derived reference ranges. The method was trained on 1352 samples, including 8 known positives, and tested on 719 samples, including 17 known positives. Clinical implementation of the first version of this method detected new mutations in the training (N = 7) and test (N = 2) sets that had not been identified by our initial clinical testing pipeline. The described final method showed complete sensitivity in both sample sets and false-positive rates of 5% (training) and 7% (test), dramatically decreasing the number of cases needing additional mutation evaluation. This approach leveraged the differences between gene and pseudogene to distinguish between PMS2 and PMS2CL copy-number mutations. These methods enable efficient and sensitive Lynch syndrome screening for 3' PMS2 copy-number mutations and may be applied similarly to other genomic regions with highly homologous pseudogenes. Copyright © 2018 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Reducing disk storage of full-3D seismic waveform tomography (F3DT) through lossy online compression

NASA Astrophysics Data System (ADS)

Lindstrom, Peter; Chen, Po; Lee, En-Jui

2016-08-01

Full-3D seismic waveform tomography (F3DT) is the latest seismic tomography technique that can assimilate broadband, multi-component seismic waveform observations into high-resolution 3D subsurface seismic structure models. The main drawback in the current F3DT implementation, in particular the scattering-integral implementation (F3DT-SI), is the high disk storage cost and the associated I/O overhead of archiving the 4D space-time wavefields of the receiver- or source-side strain tensors. The strain tensor fields are needed for computing the data sensitivity kernels, which are used for constructing the Jacobian matrix in the Gauss-Newton optimization algorithm. In this study, we have successfully integrated a lossy compression algorithm into our F3DT-SI workflow to significantly reduce the disk space for storing the strain tensor fields. The compressor supports a user-specified tolerance for bounding the error, and can be integrated into our finite-difference wave-propagation simulation code used for computing the strain fields. The decompressor can be integrated into the kernel calculation code that reads the strain fields from the disk and compute the data sensitivity kernels. During the wave-propagation simulations, we compress the strain fields before writing them to the disk. To compute the data sensitivity kernels, we read the compressed strain fields from the disk and decompress them before using them in kernel calculations. Experiments using a realistic dataset in our California statewide F3DT project have shown that we can reduce the strain-field disk storage by at least an order of magnitude with acceptable loss, and also improve the overall I/O performance of the entire F3DT-SI workflow significantly. The integration of the lossy online compressor may potentially open up the possibilities of the wide adoption of F3DT-SI in routine seismic tomography practices in the near future.

Reducing Disk Storage of Full-3D Seismic Waveform Tomography (F3DT) Through Lossy Online Compression

DOE PAGES

Lindstrom, Peter; Chen, Po; Lee, En-Jui

2016-05-05

Full-3D seismic waveform tomography (F3DT) is the latest seismic tomography technique that can assimilate broadband, multi-component seismic waveform observations into high-resolution 3D subsurface seismic structure models. The main drawback in the current F3DT implementation, in particular the scattering-integral implementation (F3DT-SI), is the high disk storage cost and the associated I/O overhead of archiving the 4D space-time wavefields of the receiver- or source-side strain tensors. The strain tensor fields are needed for computing the data sensitivity kernels, which are used for constructing the Jacobian matrix in the Gauss-Newton optimization algorithm. In this study, we have successfully integrated a lossy compression algorithmmore » into our F3DT SI workflow to significantly reduce the disk space for storing the strain tensor fields. The compressor supports a user-specified tolerance for bounding the error, and can be integrated into our finite-difference wave-propagation simulation code used for computing the strain fields. The decompressor can be integrated into the kernel calculation code that reads the strain fields from the disk and compute the data sensitivity kernels. During the wave-propagation simulations, we compress the strain fields before writing them to the disk. To compute the data sensitivity kernels, we read the compressed strain fields from the disk and decompress them before using them in kernel calculations. Experiments using a realistic dataset in our California statewide F3DT project have shown that we can reduce the strain-field disk storage by at least an order of magnitude with acceptable loss, and also improve the overall I/O performance of the entire F3DT-SI workflow significantly. The integration of the lossy online compressor may potentially open up the possibilities of the wide adoption of F3DT-SI in routine seismic tomography practices in the near future.« less

Comprehension of Health-related Written Materials by Older Adults

PubMed Central

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

2008-01-01

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

Development and Evaluation of Recombinant Nucleocapsid Protein Based Diagnostic ELISA for Detection of Nipah Virus Infection in Pigs.

PubMed

Kulkarni, Diwakar D; Venkatesh, Govindarajalu; Tosh, Chakradhar; Patel, Priyanka; Mashoria, Anita; Gupta, Vandana; Gupta, Sourabh; D, Senthilkumar

2016-01-01

The recombinant viral protein-based indirect enzyme-linked immunosorbent assay (ELISA) is a cost-effective, safe, specific, and rapid tool to diagnose the viral infection. Nipah virus nucleocapsid (NiV-N) protein was expressed in Escherichia coli and purified by histidine tag-based affinity chromatography. The N protein was selected based on its immuno dominance and conservation among different NiV strains. An indirect immunoglobulin G (IgG) enzyme-linked immunosorbent assay (ELISA) for swine sera was optimized using the recombinant NiV-N protein as an antigen along with negative and positive controls. The background reading was blocked using skim milk powder and chicken serum. A total number of 1709 swine serum samples from various states of India were tested with indirect ELISA and Western blot. The test was considered positive only when its total reactivity reading was higher than 0.2 cut-off value and the ratio of the total reactivity to the background reading was more than 2.0. Since specificity is high for Western blotting it was used as standard test for comparison of results of indirect ELISA. Sensitivity and specificity of indirect ELISA was 100% and 98.7%, respectively, in comparison with Western blotting. Recombinant N protein-based ELISA can be used in screening large number of serum samples for epidemiological investigations in developing countries where high containment laboratories are not available to handle this zoonotic virus.

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

PubMed

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

2014-07-01

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

The Effects of Repeated Readings on the Reading Fluency and Comprehension for High School Students with Specific Learning Disabilities

ERIC Educational Resources Information Center

Vandenberg, Amy C.; Boon, Richard T.; Fore, Cecil, III; Bender, William N.

2008-01-01

The purpose of this investigation was to examine the efficacy of repeated readings on the oral reading fluency rate and reading comprehension accuracy of high school students with specific learning disabilities. The participants included three tenth and eleventh grade students with specific learning disabilities in a study skills resource…

Reading Fluency as a Predictor of Reading Proficiency in Low-Performing, High-Poverty Schools

ERIC Educational Resources Information Center

Baker, Scott K.; Smolkowski, Keith; Katz, Rachell; Fien, Hank; Seeley, John R.; Kame'enui, Edward J.; Beck, Carrie Thomas

2008-01-01

The purpose of this study was to examine oral reading fluency (ORF) in the context of a large-scale federal reading initiative conducted in low performing, high poverty schools. The objectives were to (a) investigate the relation between ORF and comprehensive reading tests, (b) examine whether slope of performance over time on ORF predicted…

Reading depends on writing, in Chinese.

PubMed

Tan, Li Hai; Spinks, John A; Eden, Guinevere F; Perfetti, Charles A; Siok, Wai Ting

2005-06-14

Language development entails four fundamental and interactive abilities: listening, speaking, reading, and writing. Over the past four decades, a large body of evidence has indicated that reading acquisition is strongly associated with a child's listening skills, particularly the child's sensitivity to phonological structures of spoken language. Furthermore, it has been hypothesized that the close relationship between reading and listening is manifested universally across languages and that behavioral remediation using strategies addressing phonological awareness alleviates reading difficulties in dyslexics. The prevailing view of the central role of phonological awareness in reading development is largely based on studies using Western (alphabetic) languages, which are based on phonology. The Chinese language provides a unique medium for testing this notion, because logographic characters in Chinese are based on meaning rather than phonology. Here we show that the ability to read Chinese is strongly related to a child's writing skills and that the relationship between phonological awareness and Chinese reading is much weaker than that in reports regarding alphabetic languages. We propose that the role of logograph writing in reading development is mediated by two possibly interacting mechanisms. The first is orthographic awareness, which facilitates the development of coherent, effective links among visual symbols, phonology, and semantics; the second involves the establishment of motor programs that lead to the formation of long-term motor memories of Chinese characters. These findings yield a unique insight into how cognitive systems responsible for reading development and reading disability interact, and they challenge the prominent phonological awareness view.

Biologically sensitive field-effect transistors: from ISFETs to NanoFETs.

PubMed

Pachauri, Vivek; Ingebrandt, Sven

2016-06-30

Biologically sensitive field-effect transistors (BioFETs) are one of the most abundant classes of electronic sensors for biomolecular detection. Most of the time these sensors are realized as classical ion-sensitive field-effect transistors (ISFETs) having non-metallized gate dielectrics facing an electrolyte solution. In ISFETs, a semiconductor material is used as the active transducer element covered by a gate dielectric layer which is electronically sensitive to the (bio-)chemical changes that occur on its surface. This review will provide a brief overview of the history of ISFET biosensors with general operation concepts and sensing mechanisms. We also discuss silicon nanowire-based ISFETs (SiNW FETs) as the modern nanoscale version of classical ISFETs, as well as strategies to functionalize them with biologically sensitive layers. We include in our discussion other ISFET types based on nanomaterials such as carbon nanotubes, metal oxides and so on. The latest examples of highly sensitive label-free detection of deoxyribonucleic acid (DNA) molecules using SiNW FETs and single-cell recordings for drug screening and other applications of ISFETs will be highlighted. Finally, we suggest new device platforms and newly developed, miniaturized read-out tools with multichannel potentiometric and impedimetric measurement capabilities for future biomedical applications. © 2016 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Biologically sensitive field-effect transistors: from ISFETs to NanoFETs

PubMed Central

Pachauri, Vivek

2016-01-01

Biologically sensitive field-effect transistors (BioFETs) are one of the most abundant classes of electronic sensors for biomolecular detection. Most of the time these sensors are realized as classical ion-sensitive field-effect transistors (ISFETs) having non-metallized gate dielectrics facing an electrolyte solution. In ISFETs, a semiconductor material is used as the active transducer element covered by a gate dielectric layer which is electronically sensitive to the (bio-)chemical changes that occur on its surface. This review will provide a brief overview of the history of ISFET biosensors with general operation concepts and sensing mechanisms. We also discuss silicon nanowire-based ISFETs (SiNW FETs) as the modern nanoscale version of classical ISFETs, as well as strategies to functionalize them with biologically sensitive layers. We include in our discussion other ISFET types based on nanomaterials such as carbon nanotubes, metal oxides and so on. The latest examples of highly sensitive label-free detection of deoxyribonucleic acid (DNA) molecules using SiNW FETs and single-cell recordings for drug screening and other applications of ISFETs will be highlighted. Finally, we suggest new device platforms and newly developed, miniaturized read-out tools with multichannel potentiometric and impedimetric measurement capabilities for future biomedical applications. PMID:27365038

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

PubMed

Yamashita, Toshiya; Hayashi, Takashi

2012-01-01

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

The "Reading the Mind in the Voice" Test-Revised: A Study of Complex Emotion Recognition in Adults with and Without Autism Spectrum Conditions

ERIC Educational Resources Information Center

Golan, Ofer; Baron-Cohen, Simon; Hill, Jacqueline J.; Rutherford, M. D.

2007-01-01

This study reports a revised version of the "Reading the Mind in the Voice" (RMV) task. The original task (Rutherford et al., (2002), "Journal of Autism and Developmental Disorders, 32," 189-194) suffered from ceiling effects and limited sensitivity. To improve that, the task was shortened and two more foils were added to each of the remaining…

Evaluation of the Commercial, Off-the-Shelf (COTS) King-Devick Eye Tracking System

DTIC Science & Technology

duty decisions. The current literature suggests that the King Devick (KD) number reading test is a sensitive screener for concussion sustained during...sports activities. The KD test involves timing an individual reading aloud 120 single digit numbers, without error, printed on three standard cards...timing is performed with a stopwatch. The extensive literature commonly describes the KD test as revealing the disruption of eye movements that could be

Processing Tense/Aspect-Agreement Violations On-Line in the Second Language: A Self-Paced Reading Study with French and German L2 Learners of English

ERIC Educational Resources Information Center

Roberts, Leah; Liszka, Sarah Ann

2013-01-01

In this article, we report the results of a self-paced reading experiment designed to investigate the question of whether or not advanced French and German learners of English as a second language (L2) are sensitive to tense/aspect mismatches between a fronted temporal adverbial and the inflected verb that follows (e.g. *"Last week, James has…

On the Validity and Sensitivity of the Phonics Screening Check: Erratum and Further Analysis

ERIC Educational Resources Information Center

Gilchrist, James M.; Snowling, Margaret J.

2018-01-01

Duff, Mengoni, Bailey and Snowling ("Journal of Research in Reading," 38: 109-123; 2015) evaluated the sensitivity and specificity of the phonics screening check against two reference standards. This report aims to correct a minor data error in the original article and to present further analysis of the data. The methods used are…

Sensitivity to Lexical Stress in Dyslexia: A Case of Cognitive Not Perceptual Stress

ERIC Educational Resources Information Center

Barry, Johanna G.; Harbodt, Silke; Cantiani, Chiara; Sabisch, Beate; Zobay, Oliver

2012-01-01

Sensitivity to lexical stress in adult German-speaking students with reading difficulty was investigated using minimal pair prepositional verbs whose meaning and syntax depend on the location of the stressed syllable. Two tests of stress perception were used: (i) a stress location task, where listeners indicated the location of the perceptually…

Developing General Literacy Ability and Intercultural Sensitivity through English Literacy Instruction: Using Global Literature for Korean EFL Learners

ERIC Educational Resources Information Center

Bae, Jiyoung

2012-01-01

This study explored L2 literacy ability and intercultural sensitivity of Korean late elementary to early middle school students learning English as a foreign language. This study investigated the latent variable structure of L2 literacy abilities, including fluency, vocabulary, reading comprehension, and writing abilities, and intercultural…

Linguistic Gender Sensitivity Strategies in Current South African Intermediate Phase English Workbooks: Feminisation or Degenderisation?

ERIC Educational Resources Information Center

Sibanda, Jabulani; Sibanda, Lucy

2016-01-01

This study extends research on manifestations of gender insensitivity in learners' reading materials by shifting attention to the linguistic strategies that authors of current texts employ for the realisation of gender sensitivity. We analysed the content of 12 current (2014) English workbooks (Grade 4-6) used in South African government and…

Predicting Children's Reading and Mathematics Achievement from Early Quantitative Knowledge and Domain-General Cognitive Abilities

PubMed Central

Chu, Felicia W.; vanMarle, Kristy; Geary, David C.

2016-01-01

One hundred children (44 boys) participated in a 3-year longitudinal study of the development of basic quantitative competencies and the relation between these competencies and later mathematics and reading achievement. The children's preliteracy knowledge, intelligence, executive functions, and parental educational background were also assessed. The quantitative tasks assessed a broad range of symbolic and nonsymbolic knowledge and were administered four times across 2 years of preschool. Mathematics achievement was assessed at the end of each of 2 years of preschool, and mathematics and word reading achievement were assessed at the end of kindergarten. Our goals were to determine how domain-general abilities contribute to growth in children's quantitative knowledge and to determine how domain-general and domain-specific abilities contribute to children's preschool mathematics achievement and kindergarten mathematics and reading achievement. We first identified four core quantitative competencies (e.g., knowledge of the cardinal value of number words) that predict later mathematics achievement. The domain-general abilities were then used to predict growth in these competencies across 2 years of preschool, and the combination of domain-general abilities, preliteracy skills, and core quantitative competencies were used to predict mathematics achievement across preschool and mathematics and word reading achievement at the end of kindergarten. Both intelligence and executive functions predicted growth in the four quantitative competencies, especially across the first year of preschool. A combination of domain-general and domain-specific competencies predicted preschoolers' mathematics achievement, with a trend for domain-specific skills to be more strongly related to achievement at the beginning of preschool than at the end of preschool. Preschool preliteracy skills, sensitivity to the relative quantities of collections of objects, and cardinal knowledge predicted reading and mathematics achievement at the end of kindergarten. Preliteracy skills were more strongly related to word reading, whereas sensitivity to relative quantity was more strongly related to mathematics achievement. The overall results indicate that a combination of domain-general and domain-specific abilities contribute to development of children's early mathematics and reading achievement. PMID:27252675

Predicting Children's Reading and Mathematics Achievement from Early Quantitative Knowledge and Domain-General Cognitive Abilities.

PubMed

Chu, Felicia W; vanMarle, Kristy; Geary, David C

2016-01-01

One hundred children (44 boys) participated in a 3-year longitudinal study of the development of basic quantitative competencies and the relation between these competencies and later mathematics and reading achievement. The children's preliteracy knowledge, intelligence, executive functions, and parental educational background were also assessed. The quantitative tasks assessed a broad range of symbolic and nonsymbolic knowledge and were administered four times across 2 years of preschool. Mathematics achievement was assessed at the end of each of 2 years of preschool, and mathematics and word reading achievement were assessed at the end of kindergarten. Our goals were to determine how domain-general abilities contribute to growth in children's quantitative knowledge and to determine how domain-general and domain-specific abilities contribute to children's preschool mathematics achievement and kindergarten mathematics and reading achievement. We first identified four core quantitative competencies (e.g., knowledge of the cardinal value of number words) that predict later mathematics achievement. The domain-general abilities were then used to predict growth in these competencies across 2 years of preschool, and the combination of domain-general abilities, preliteracy skills, and core quantitative competencies were used to predict mathematics achievement across preschool and mathematics and word reading achievement at the end of kindergarten. Both intelligence and executive functions predicted growth in the four quantitative competencies, especially across the first year of preschool. A combination of domain-general and domain-specific competencies predicted preschoolers' mathematics achievement, with a trend for domain-specific skills to be more strongly related to achievement at the beginning of preschool than at the end of preschool. Preschool preliteracy skills, sensitivity to the relative quantities of collections of objects, and cardinal knowledge predicted reading and mathematics achievement at the end of kindergarten. Preliteracy skills were more strongly related to word reading, whereas sensitivity to relative quantity was more strongly related to mathematics achievement. The overall results indicate that a combination of domain-general and domain-specific abilities contribute to development of children's early mathematics and reading achievement.

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

Spectral performance of DEPFET and gateable DEPFET macropixel devices

NASA Astrophysics Data System (ADS)

Bähr, A.; Aschauer, S.; Bergbauer, B.; Hermenau, K.; Lauf, T.; Lechner, P.; Lutz, G.; Majewski, P.; Meidinger, N.; Miessner, D.; Porro, M.; Richter, R.; Schaller, G.; Schopper, F.; Stefanescu, A.; Strüder, L.; Treis, J.

2014-03-01

Future x-ray observatories, such as the proposed ATHENA+ mission, will investigate bright and rapidly evolving radiation sources. To reach the scientific goals, high speed, spatial resolving sensors with excellent spectroscopic performance are mandatory. Well suited for this task are matrices of Depleted P-channel Field Effect Transistors (DEPFETs). DEPFETs provide intrinsic signal amplification, 100 percent fill factor, charge storage capability and a low read noise. Previous studies of DEPFET matrices of 256 × 256 pixels demonstrated an excellent energy resolution of 126 eV FWHM at 5.9 keV (compared to the theoretical Fano limit 120 eV). Usually these matrices are read out on demand, using e.g. the ASTEROID ASIC. Because the DEPFET is always sensitive, charge collected during the readout, causes so called misfits, which increase the background. For low frame rates this can be neglected. However, for fast timings, as suggested for ATHENA+, this effect reduces the spectral performance. We will present measurements on DEPFET macropixel structures, read out using a semi-Gaussian shaper, which demonstrate the excellent spectroscopic performance of these devices. Furthermore we will investigate the effect of misfits on the spectral background of DEPFET devices read out on demand. These measurements show the necessity to suppress misfits when the devices are operated for fast timing modes. As will be shown this can be done using so called gateable DEPFETs. The general advantage of gateable DEPFETs at fast timings, in terms of peak-to-background ratio will be demonstrated.

Linguistic Feature Development Across Grades and Genre in Elementary Writing.

PubMed

Hall-Mills, Shannon; Apel, Kenn

2015-07-01

As children develop skills in writing across academic contexts, clinicians and educators need to have a fundamental understanding of typical writing development as well as valid and reliable assessment methods. The purpose of this study was to examine the progression of linguistic elements in school-age children's narrative and expository writing development. Narrative and expository writing samples produced by 89 children in Grades 2 through 4 were analyzed at the microstructure and macrostructure levels. Measures of receptive vocabulary, word-level reading, and reading comprehension were obtained. Exploratory factor analyses revealed 4 microstructure factors (e.g., productivity, grammatical complexity, grammatical accuracy, and lexical density) and 1 macrostructure factor (e.g., a combination of organization, text structure, and cohesion). Multivariate analyses of covariance with reading comprehension as a covariate showed that productivity and macrostructure were sensitive to grade-level and genre differences and that expository grammatical complexity was sensitive to grade-level differences. Findings are discussed in light of grade-level standards for narrative and expository writing and current practices in writing assessment. Multiple suggestions are offered for clinical and educational implications, and specific directions are provided for future research.

RIFM fragrance ingredient safety assessment, 2-methylundecanol, CAS Registry Number 10522-26-6.

PubMed

Api, A M; Belsito, D; Bhatia, S; Bruze, M; Calow, P; Dagli, M L; Dekant, W; Fryer, A D; Kromidas, L; La Cava, S; Lalko, J F; Lapczynski, A; Liebler, D C; Penning, T M; Politano, V T; Ritacco, G; Salvito, D; Schultz, T W; Shen, J; Sipes, I G; Wall, B; Wilcox, D K

2016-11-01

This material was evaluated for genotoxicity, repeated dose toxicity, reproductive toxicity, local respiratory toxicity, phototoxicity/photoallergenicity, skin sensitization, as well as environmental safety. Data from the suitable read across analogs 2-butyloctan-1-ol (CAS # 3913-02-8) and 2-ethyl-1-hexanol (CAS # 104-76-7) show that this material is not genotoxic nor does it have skin sensitization potential. The reproductive and local respiratory toxicity endpoints were completed using the TTC (Threshold of Toxicological Concern) for a Cramer Class I material (0.03 and 1.4 mg/day, respectively). The repeated dose toxicity endpoint was completed using 2-ethyl-1-hexanol (CAS # 104-76-7) and 1-heptanol, 2-propyl (CAS # 10042-59-8) as suitable read across analogs, which provided a MOE > 100. The developmental toxicity endpoint was completed using 2-ethyl-1-hexanol (CAS # 104-76-7) as a suitable read across analog, which provided a MOE > 100 The phototoxicity/photoallergenicity endpoint was completed based on suitable UV spectra. The environmental endpoint was completed as described in the RIFM Framework. Copyright © 2016 Elsevier Ltd. All rights reserved.

Non-localization and localization ROC analyses using clinically based scoring

NASA Astrophysics Data System (ADS)

Paquerault, Sophie; Samuelson, Frank W.; Myers, Kyle J.; Smith, Robert C.

2009-02-01

We are investigating the potential for differences in study conclusions when assessing the estimated impact of a computer-aided detection (CAD) system on readers' performance. The data utilized in this investigation were derived from a multi-reader multi-case observer study involving one hundred mammographic background images to which fixed-size and fixed-intensity Gaussian signals were added, generating a low- and high-intensity signal sets. The study setting allowed CAD assessment in two situations: when CAD sensitivity was 1) superior or 2) lower than the average reader. Seven readers were asked to review each set in the unaided and CAD-aided reading modes, mark and rate their findings. Using this data, we studied the effect on study conclusion of three clinically-based receiver operating characteristic (ROC) scoring definitions. These scoring definitions included both location-specific and non-location-specific rules. The results showed agreement in the estimated impact of CAD on the overall reader performance. In the study setting where CAD sensitivity is superior to the average reader, the mean difference in AUC between the CAD-aided read and unaided read was 0.049 (95%CIs: -0.027; 0.130) for the image scoring definition that is based on non-location-specific rules, and 0.104 (95%CIs: 0.036; 0.174) and 0.090 (95%CIs: 0.031; 0.155) for image scoring definitions that are based on location-specific rules. The increases in AUC were statistically significant for the location-specific scoring definitions. It was further observed that the variance on these estimates was reduced when using the location-specific scoring definitions compared to that using a non-location-specific scoring definition. In the study setting where CAD sensitivity is equivalent or lower than the average reader, the mean differences in AUC are slightly above 0.01 for all image scoring definitions. These increases in AUC were not statistical significant for any of the image scoring definitions. The results on the variance analysis differed from those observed in the other study setting. This investigation furthers our understanding of the relationships between non-localization-specific and localization-specific ROC assessment methodologies and their relevance to clinical practice.

Sensitive and specific detection of EML4-ALK rearrangements in non-small cell lung cancer (NSCLC) specimens by multiplex amplicon RNA massive parallel sequencing.

PubMed

Moskalev, Evgeny A; Frohnauer, Judith; Merkelbach-Bruse, Sabine; Schildhaus, Hans-Ulrich; Dimmler, Arno; Schubert, Thomas; Boltze, Carsten; König, Helmut; Fuchs, Florian; Sirbu, Horia; Rieker, Ralf J; Agaimy, Abbas; Hartmann, Arndt; Haller, Florian

2014-06-01

Recurrent gene fusions of anaplastic lymphoma receptor tyrosine kinase (ALK) and echinoderm microtubule-associated protein-like 4 (EML4) have been recently identified in ∼5% of non-small cell lung cancers (NSCLCs) and are targets for selective tyrosine kinase inhibitors. While fluorescent in situ hybridization (FISH) is the current gold standard for detection of EML4-ALK rearrangements, several limitations exist including high costs, time-consuming evaluation and somewhat equivocal interpretation of results. In contrast, targeted massive parallel sequencing has been introduced as a powerful method for simultaneous and sensitive detection of multiple somatic mutations even in limited biopsies, and is currently evolving as the method of choice for molecular diagnostic work-up of NSCLCs. We developed a novel approach for indirect detection of EML4-ALK rearrangements based on 454 massive parallel sequencing after reverse transcription and subsequent multiplex amplification (multiplex ALK RNA-seq) which takes advantage of unbalanced expression of the 5' and 3' ALK mRNA regions. Two lung cancer cell lines and a selected series of 32 NSCLC samples including 11 cases with EML4-ALK rearrangement were analyzed with this novel approach in comparison to ALK FISH, ALK qRT-PCR and EML4-ALK RT-PCR. The H2228 cell line with known EML4-ALK rearrangement showed 171 and 729 reads for 5' and 3' ALK regions, respectively, demonstrating a clearly unbalanced expression pattern. In contrast, the H1299 cell line with ALK wildtype status displayed no reads for both ALK regions. Considering a threshold of 100 reads for 3' ALK region as indirect indicator of EML4-ALK rearrangement, there was 100% concordance between the novel multiplex ALK RNA-seq approach and ALK FISH among all 32 NSCLC samples. Multiplex ALK RNA-seq is a sensitive and specific method for indirect detection of EML4-ALK rearrangements, and can be easily implemented in panel based molecular diagnostic work-up of NSCLCs by massive parallel sequencing. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

A new automatic blood pressure kit auscultates for accurate reading with a smartphone: A diagnostic accuracy study.

PubMed

Wu, Hongjun; Wang, Bingjian; Zhu, Xinpu; Chu, Guang; Zhang, Zhi

2016-08-01

The widely used oscillometric automated blood pressure (BP) monitor was continuously questioned on its accuracy. A novel BP kit named Accutension which adopted Korotkoff auscultation method was then devised. Accutension worked with a miniature microphone, a pressure sensor, and a smartphone. The BP values were automatically displayed on the smartphone screen through the installed App. Data recorded in the phone could be played back and reconfirmed after measurement. They could also be uploaded and saved to the iCloud. The accuracy and consistency of this novel electronic auscultatory sphygmomanometer was preliminarily verified here. Thirty-two subjects were included and 82 qualified readings were obtained. The mean differences ± SD for systolic and diastolic BP readings between Accutension and mercury sphygmomanometer were 0.87 ± 2.86 and -0.94 ± 2.93 mm Hg. Agreements between Accutension and mercury sphygmomanometer were highly significant for systolic (ICC = 0.993, 95% confidence interval (CI): 0.989-0.995) and diastolic (ICC = 0.987, 95% CI: 0.979-0.991). In conclusion, Accutension worked accurately based on our pilot study data. The difference was acceptable. ICC and Bland-Altman plot charts showed good agreements with manual measurements. Systolic readings of Accutension were slightly higher than those of manual measurement, while diastolic readings were slightly lower. One possible reason was that Accutension captured the first and the last korotkoff sound more sensitively than human ear during manual measurement and avoided sound missing, so that it might be more accurate than traditional mercury sphygmomanometer. By documenting and analyzing of variant tendency of BP values, Accutension helps management of hypertension and therefore contributes to the mobile heath service.

QuickView video preview software of colon capsule endoscopy: reliability in presenting colorectal polyps as compared to normal mode reading.

PubMed

Farnbacher, Michael J; Krause, Horst H; Hagel, Alexander F; Raithel, Martin; Neurath, Markus F; Schneider, Thomas

2014-03-01

OBJECTIVE. Colon capsule endoscopy (CCE) proved to be highly sensitive in detection of colorectal polyps (CP). Major limitation is the time-consuming video reading. The aim of this prospective, double-center study was to assess the theoretical time-saving potential and its possible impact on the reliability of "QuickView" (QV), in the presentation of CP as compared to normal mode (NM). METHODS. During NM reading of 65 CCE videos (mean patient´s age 56 years), all frames showing CPs were collected and compared to the number of frames presented by QV at increasing QV settings (10, 20, ... 80%). Reliability of QV in presenting polyps <6 mm and ≥6 mm (significant polyp), and identifying patients for subsequent therapeutic colonoscopy, capsule egestion rate, cleansing level, and estimated time-saving potential were assessed. RESULTS. At a 30% QV setting, the QV video presented 89% of the significant polyps and 86% of any polyps with ≥1 frame (per-polyp analysis) identified in NM before. At a 10% QV setting, 98% of the 52 patients with significant polyps could be identified (per-patient analysis) by QV video analysis. Capsule excretion rate was 74% and colon cleanliness was adequate in 85%. QV´s presentation rate correlates to the QV setting, the polyp size, and the number of frames per finding. CONCLUSIONS. Depending on its setting, the reliability of QV in presenting CP as compared to NM reading is notable. However, if no significant polyp is presented by QV, NM reading must be performed afterwards. The reduction of frames to be analyzed in QV might speed up identification of candidates for therapeutic colonoscopy.

A new automatic blood pressure kit auscultates for accurate reading with a smartphone

PubMed Central

Wu, Hongjun; Wang, Bingjian; Zhu, Xinpu; Chu, Guang; Zhang, Zhi

2016-01-01

Abstract The widely used oscillometric automated blood pressure (BP) monitor was continuously questioned on its accuracy. A novel BP kit named Accutension which adopted Korotkoff auscultation method was then devised. Accutension worked with a miniature microphone, a pressure sensor, and a smartphone. The BP values were automatically displayed on the smartphone screen through the installed App. Data recorded in the phone could be played back and reconfirmed after measurement. They could also be uploaded and saved to the iCloud. The accuracy and consistency of this novel electronic auscultatory sphygmomanometer was preliminarily verified here. Thirty-two subjects were included and 82 qualified readings were obtained. The mean differences ± SD for systolic and diastolic BP readings between Accutension and mercury sphygmomanometer were 0.87 ± 2.86 and −0.94 ± 2.93 mm Hg. Agreements between Accutension and mercury sphygmomanometer were highly significant for systolic (ICC = 0.993, 95% confidence interval (CI): 0.989–0.995) and diastolic (ICC = 0.987, 95% CI: 0.979–0.991). In conclusion, Accutension worked accurately based on our pilot study data. The difference was acceptable. ICC and Bland–Altman plot charts showed good agreements with manual measurements. Systolic readings of Accutension were slightly higher than those of manual measurement, while diastolic readings were slightly lower. One possible reason was that Accutension captured the first and the last korotkoff sound more sensitively than human ear during manual measurement and avoided sound missing, so that it might be more accurate than traditional mercury sphygmomanometer. By documenting and analyzing of variant tendency of BP values, Accutension helps management of hypertension and therefore contributes to the mobile heath service. PMID:27512876

Imaging-based molecular barcoding with pixelated dielectric metasurfaces

NASA Astrophysics Data System (ADS)

Tittl, Andreas; Leitis, Aleksandrs; Liu, Mingkai; Yesilkoy, Filiz; Choi, Duk-Yong; Neshev, Dragomir N.; Kivshar, Yuri S.; Altug, Hatice

2018-06-01

Metasurfaces provide opportunities for wavefront control, flat optics, and subwavelength light focusing. We developed an imaging-based nanophotonic method for detecting mid-infrared molecular fingerprints and implemented it for the chemical identification and compositional analysis of surface-bound analytes. Our technique features a two-dimensional pixelated dielectric metasurface with a range of ultrasharp resonances, each tuned to a discrete frequency; this enables molecular absorption signatures to be read out at multiple spectral points, and the resulting information is then translated into a barcode-like spatial absorption map for imaging. The signatures of biological, polymer, and pesticide molecules can be detected with high sensitivity, covering applications such as biosensing and environmental monitoring. Our chemically specific technique can resolve absorption fingerprints without the need for spectrometry, frequency scanning, or moving mechanical parts, thereby paving the way toward sensitive and versatile miniaturized mid-infrared spectroscopy devices.

Evaluation of sensitivity and selectivity of piezoresistive cantilever-array sensors

NASA Astrophysics Data System (ADS)

Yoshikawa, Genki; Lang, Hans-Peter; Staufer, Urs; Vettiger, Peter; Sakurai, Toshio; Gerber, Christoph

2008-03-01

Microfabricated cantilever-array sensors have attracted much attention in recent years due to their real-time detection of low concentration of molecules. Since the piezoresistive cantilever-array sensors do not require a bulky and expensive optical read-out system, they possess many advantages compared with optical read-out cantilever-array sensors. They can be miniaturized and integrated into a match-box sized device. In this study, we present the piezoresistive cantilever-array sensor system and evaluate its sensitivity and selectivity using various vapors of molecules, including alkane molecules with different chain length from 5 (n-pentane) to 12 (n-dodecane). Piezoresistive cantilevers were coated with different polymers (PVP, PAAM, PEI, and PVA) using an inkjet spotter. Each cantilever has a reference cantilever, constituting a Wheatstone-bridge. Each vapor was mixed with a constant nitrogen gas flow and introduced into the measurement chamber. According to the principle component analysis of data obtained, each molecule can be clearly distinguished from others. We also confirmed that this piezoresistive cantilever-array sensor system has sub-ppm sensitivity.

Online Sentence Reading in People With Aphasia: Evidence From Eye Tracking

PubMed Central

Knilans, Jessica

2015-01-01

Purpose There is a lot of evidence that people with aphasia have more difficulty understanding structurally complex sentences (e.g., object clefts) than simpler sentences (subject clefts). However, subject clefts also occur more frequently in English than object clefts. Thus, it is possible that both structural complexity and frequency affect how people with aphasia understand these structures. Method Nine people with aphasia and 8 age-matched controls participated in the study. The stimuli consisted of 24 object cleft and 24 subject cleft sentences. The task was eye tracking during reading, which permits a more fine-grained analysis of reading performance than measures such as self-paced reading. Results As expected, controls had longer reading times for critical regions in object cleft sentences compared with subject cleft sentences. People with aphasia showed the predicted effects of structural frequency. Effects of structural complexity in people with aphasia did not emerge on their first pass through the sentence but were observed when they were rereading critical regions of complex sentences. Conclusions People with aphasia are sensitive to both structural complexity and structural frequency when reading. However, people with aphasia may use different reading strategies than controls when confronted with relatively infrequent and complex sentence structures. PMID:26383779

Online Sentence Reading in People With Aphasia: Evidence From Eye Tracking.

PubMed

Knilans, Jessica; DeDe, Gayle

2015-11-01

There is a lot of evidence that people with aphasia have more difficulty understanding structurally complex sentences (e.g., object clefts) than simpler sentences (subject clefts). However, subject clefts also occur more frequently in English than object clefts. Thus, it is possible that both structural complexity and frequency affect how people with aphasia understand these structures. Nine people with aphasia and 8 age-matched controls participated in the study. The stimuli consisted of 24 object cleft and 24 subject cleft sentences. The task was eye tracking during reading, which permits a more fine-grained analysis of reading performance than measures such as self-paced reading. As expected, controls had longer reading times for critical regions in object cleft sentences compared with subject cleft sentences. People with aphasia showed the predicted effects of structural frequency. Effects of structural complexity in people with aphasia did not emerge on their first pass through the sentence but were observed when they were rereading critical regions of complex sentences. People with aphasia are sensitive to both structural complexity and structural frequency when reading. However, people with aphasia may use different reading strategies than controls when confronted with relatively infrequent and complex sentence structures.

A new approach for detecting adventitious viruses shows Sf-rhabdovirus-negative Sf-RVN cells are suitable for safe biologicals production.

PubMed

Geisler, Christoph

2018-02-07

Adventitious viral contamination in cell substrates used for biologicals production is a major safety concern. A powerful new approach that can be used to identify adventitious viruses is a combination of bioinformatics tools with massively parallel sequencing technology. Typically, this involves mapping or BLASTN searching individual reads against viral nucleotide databases. Although extremely sensitive for known viruses, this approach can easily miss viruses that are too dissimilar to viruses in the database. Moreover, it is computationally intensive and requires reference cell genome databases. To avoid these drawbacks, we set out to develop an alternative approach. We reasoned that searching genome and transcriptome assemblies for adventitious viral contaminants using TBLASTN with a compact viral protein database covering extant viral diversity as the query could be fast and sensitive without a requirement for high performance computing hardware. We tested our approach on Spodoptera frugiperda Sf-RVN, a recently isolated insect cell line, to determine if it was contaminated with one or more adventitious viruses. We used Illumina reads to assemble the Sf-RVN genome and transcriptome and searched them for adventitious viral contaminants using TBLASTN with our viral protein database. We found no evidence of viral contamination, which was substantiated by the fact that our searches otherwise identified diverse sequences encoding virus-like proteins. These sequences included Maverick, R1 LINE, and errantivirus transposons, all of which are common in insect genomes. We also identified previously described as well as novel endogenous viral elements similar to ORFs encoded by diverse insect viruses. Our results demonstrate TBLASTN searching massively parallel sequencing (MPS) assemblies with a compact, manually curated viral protein database is more sensitive for adventitious virus detection than BLASTN, as we identified various sequences that encoded virus-like proteins, but had no similarity to viral sequences at the nucleotide level. Moreover, searches were fast without requiring high performance computing hardware. Our study also documents the enhanced biosafety profile of Sf-RVN as compared to other Sf cell lines, and supports the notion that Sf-RVN is highly suitable for the production of safe biologicals.

The Problem of Reading and Reading Culture Improvement of Students-Bachelors of Elementary Education in Modern High Institution

ERIC Educational Resources Information Center

Kamalova, Lera A.; Koletvinova, Natal'ya D.

2016-01-01

This article is aimed to study the problems of reading and improve reading culture of students-bachelors of elementary education in modern high institutions and development of the most effective methods and techniques for improving of reading culture of students in the study of Humanities disciplines. The leading method to the study of this…

The Effectiveness of a Reading Curriculum on High School Students' Achievement, Confidence in Reading and Teachers' Perceptions

ERIC Educational Resources Information Center

Moody, Kristie

2017-01-01

The purpose of this study was to examine the effectiveness of a reading curriculum on high school students' achievement, confidence in reading and teachers' perceptions. A paired samples t test was used to compare students' pretest and posttest scores on the reading curriculum. Two independent samples t tests were run to compare the control and…

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

Executive Function, Self-Regulated Learning, and Reading Comprehension: A Training Study

PubMed Central

Cirino, Paul T.; Miciak, Jeremy; Gerst, Elyssa; Barnes, Marcia A.; Vaughn, Sharon; Child, Amanda; Huston-Warren, Emily

2016-01-01

The goal of this study was to evaluate the extent to which training that emphasizes the process of executive function (EF) and self-regulated learning (SRL) would result in increased reading comprehension; we also evaluated interrelationships of EF, SRL, and reading. We report an experiment (N = 75 fourth graders) that contrasted two researcher-implemented conditions (text-based reading [TB] and text-based reading plus executive function [TB+EF]) to a control. We also evaluated relationships among measures of SRL, EF, and reading. Both the TB and TB+EF groups outperformed the control group for proximal text comprehension (where the topic was similar to that covered in training) and background knowledge related to it, but the two researcher-led groups performed similarly. There were no significant differences for less proximal text, and again similar performance for both TB and TB+EF. Correlations among measures were weak in general, although the pattern was similar to that found in the extant literature. The findings speak to the difficulty in separating these components from those of strong instruction more generally. The relationships of these constructs to reading comprehension will likely be enhanced by more sensitive measurement of EF and reading comprehension, particularly where tied to active treatment components. PMID:26746314

Optical elements design of optical pick-up with characteristics of read-out spot for high density optical storage

NASA Astrophysics Data System (ADS)

Li, Lihua; Ma, Jianshe; Liu, Lin; Pan, Longfa; Zhang, Jianyong; Lu, Junhui

2005-09-01

It is well known that the optical pick-up (OPU) plays a very important role in optical storage system. And the quality of OPU can be measured by the characteristics of OPU read-out spot for high density optical storage. Therefore this paper mainly designs an OPU model for high density optical storage to study the characteristics of OPU read-out spot. Firstly it analyses the optical read-out principle in OPU and contrives an optical read-out system based on the hereinbefore theory. In this step it chiefly designs the grating, splitter, collimator lens and objective lens. Secondly based on the aberrations analysis and theory involved by the splitter, the collimator lens and the optical lens, the paper uses the software CODE V to calculate the aberrations and to optimize the optical read-out system. Then the author can receive an ideal OPU read-out spot for high density optical storage and obtain the characteristics of the ideal OPU read-out spot. At the same time this paper analyses some influence factors which can directly affect the characteristics of the OPU read-out spot. Thirdly according to the up data the author practically manufactures a real optical pick-up to validate the hereinbefore designed optical read-out system. And it uses the Optical Spot Analyzer to get the image of the read-out spot. Comparing the ideal image to the actual image of the designed optical read-out system, the author finds out that the upwards analyses and design is suitable for high density storage and can be used in the actual production. And the author also receives the conclusion that the mostly influences on characteristics of OPU read-out spot for high density optical storage factors is not only the process of designing the grating, splitter, collimator lens and objective lens, but also the assembling work precision

Transcriptomic Changes of Drought-Tolerant and Sensitive Banana Cultivars Exposed to Drought Stress

PubMed Central

Muthusamy, Muthusamy; Uma, Subbaraya; Backiyarani, Suthanthiram; Saraswathi, Marimuthu Somasundaram; Chandrasekar, Arumugam

2016-01-01

In banana, drought responsive gene expression profiles of drought-tolerant and sensitive genotypes remain largely unexplored. In this research, the transcriptome of drought-tolerant banana cultivar (Saba, ABB genome) and sensitive cultivar (Grand Naine, AAA genome) was monitored using mRNA-Seq under control and drought stress condition. A total of 162.36 million reads from tolerant and 126.58 million reads from sensitive libraries were produced and mapped onto the Musa acuminata genome sequence and assembled into 23,096 and 23,079 unigenes. Differential gene expression between two conditions (control and drought) showed that at least 2268 and 2963 statistically significant, functionally known, non-redundant differentially expressed genes (DEGs) from tolerant and sensitive libraries. Drought has up-regulated 991 and 1378 DEGs and down-regulated 1104 and 1585 DEGs respectively in tolerant and sensitive libraries. Among DEGs, 15.9% are coding for transcription factors (TFs) comprising 46 families and 9.5% of DEGs are constituted by protein kinases from 82 families. Most enriched DEGs are mainly involved in protein modifications, lipid metabolism, alkaloid biosynthesis, carbohydrate degradation, glycan metabolism, and biosynthesis of amino acid, cofactor, nucleotide-sugar, hormone, terpenoids and other secondary metabolites. Several, specific genotype-dependent gene expression pattern was observed for drought stress in both cultivars. A subset of 9 DEGs was confirmed using quantitative reverse transcription-PCR. These results will provide necessary information for developing drought-resilient banana plants. PMID:27867388

Reading and listening comprehension and their relation to inattention and hyperactivity.

PubMed

Cain, Kate; Bignell, Simon

2014-03-01

Children with diagnoses of attention-deficit/hyperactivity disorder (ADHD) frequently have reading problems. To date, it is not clear whether poor reading is associated with both inattention and hyperactivity and also whether poor reading comprehension is the result of poor word reading skills or more general language comprehension weaknesses. We report two studies to examine how reading and listening comprehension skills are related to inattention and hyperactivity/impulsivity. Separate groups of 7- to 11-year-olds participated in each study. In both studies, we used teacher ratings of inattention and hyperactivity/impulsivity to identify three groups at risk of ADHD: poor attention, high hyperactivity, poor attention and high hyperactivity, and also same-age controls. In Study 1, we explored how inattention and hyperactivity predicted reading after controlling for non-verbal IQ and vocabulary. In Study 2, we compared listening and reading comprehension in these groups. Poor attention was related to poor reading comprehension, although the relation was partially mediated by word reading skill (Study 1). Groups with high hyperactivity had weak listening comprehension relative to reading comprehension (Study 2). These results indicate that the reading comprehension problems of children with attention difficulties are related to poor word reading and that listening comprehension is particularly vulnerable in children at risk of ADHD. © 2013 The British Psychological Society.

Advancing the technology of monolithic CMOS detectors for use as x-ray imaging spectrometers

NASA Astrophysics Data System (ADS)

Kenter, Almus; Kraft, Ralph; Gauron, Thomas; Amato, Stephen

2017-08-01

The Smithsonian Astrophysical Observatory (SAO) in collaboration with SRI/Sarnoff has been engaged in a multi year effort to advance the technology of monolithic back-thinned CMOS detectors for use as X-ray imaging spectrometers. The long term goal of this campaign is to produce X-ray Active Pixel Sensor (APS) detectors with Fano limited performance over the 0.1-10keV band while incorporating the many benefits of CMOS technology. These benefits include: low power consumption, radiation "hardness", high levels of integration, and very high read rates. Such devices would be ideal for candidate post 2020 decadal missions such as LYNX and for smaller more immediate applications such as CubeX. Devices from a recent fabrication have been back-thinned, packaged and tested for soft X-ray response. These devices have 16μm pitch, 6 Transistor Pinned Photo Diode (6TPPD) pixels with ˜135μV/electron sensitivity and a highly parallel signal chain. These new detectors are fabricated on 10μm epitaxial silicon and have a 1k by 1k format. We present details of our camera design and device performance with particular emphasis on those aspects of interest to single photon counting X-ray astronomy. These features include read noise, X-ray spectral response and quantum efficiency.

Comparison of LED and Conventional Fluorescence Microscopy for Detection of Acid Fast Bacilli in a Low-Incidence Setting

PubMed Central

Minion, Jessica; Pai, Madhukar; Ramsay, Andrew; Menzies, Dick; Greenaway, Christina

2011-01-01

Introduction Light emitting diode fluorescence microscopes have many practical advantages over conventional mercury vapour fluorescence microscopes, which would make them the preferred choice for laboratories in both low- and high-resource settings, provided performance is equivalent. Methods In a nested case-control study, we compared diagnostic accuracy and time required to read slides with the Zeiss PrimoStar iLED, LW Scientific Lumin, and a conventional fluorescence microscope (Leica DMLS). Mycobacterial culture was used as the reference standard, and subgroup analysis by specimen source and organism isolated were performed. Results There was no difference in sensitivity or specificity between the three microscopes, and agreement was high for all comparisons and subgroups. The Lumin and the conventional fluorescence microscope were equivalent with respect to time required to read smears, but the Zeiss iLED was significantly time saving compared to both. Conclusions Light emitting diode microscopy should be considered by all tuberculosis diagnostic laboratories, including those in high income countries, as a replacement for conventional fluorescence microscopes. Our findings provide support to the recent World Health Organization policy recommending that conventional fluorescence microscopy be replaced by light emitting diode microscopy using auramine staining in all settings where fluorescence microscopy is currently used. PMID:21811622

An Examination of the LVA Approach to Teaching Reading

ERIC Educational Resources Information Center

Murphy, Jean C.

2004-01-01

The Language Vocabulary Acquisition (LVA) Approach is a revolutionary method of reading instruction for emergent and developing readers. It is an intense reading program with high levels of student participation, engagement, and interaction with print text, that yields high outcomes in phonological awareness, reading and writing fluency, and…

Paragraph-reading comprehension ability in Mandarin-speaking children with cochlear implants.

PubMed

Wu, Che-Ming; Lee, Li-Ang; Chao, Wei-Chieh; Tsou, Yung-Ting; Chen, Yen-An

2015-06-01

1) To investigate different aspects of paragraph reading in Mandarin-speaking students with cochlear implants (CIs) and the factors associated with unfavorable outcomes, and 2) to understand the replaceability of a paragraph-reading test with a sentence-reading test. Cross-sectional, case-controlled study. Fifty-three students with CIs (aged 11.0 ± 1.4 years) and 53 grade- and gender-matched children with normal hearing (NH) participated in the study. A paragraph-reading comprehension test was conducted. Sentence and word reading, speech perception, language skills, and child/family characteristics were examined. An unfavorable paragraph-reading outcome was defined as a score lower than one standard deviation below the NH mean. The CI subjects had significantly worse paragraph-reading comprehension than did the NH controls (P = 0.017, d = 0.54). Their performance in grades 5 to 6 was not significantly higher than of those with NH in grades 2 to 4. The CI children's abilities to understand semantics (P = 0.012) and syntax (P = 0.020) significantly fell behind the NH controls in grades 2 to 4, and the lag continued in grades 5 to 6 (P = 0.039, P = 0.002, respectively). Grade and sentence reading were independently associated with unfavorable paragraph-reading outcomes (R(2)  = 0.453). The optimal sensitivity and specificity of the sentence-reading test in identifying unfavorable paragraph-reading outcomes were 90.9% and 90.0%, respectively (area under the curve = 0.923). Specialists should pay attention to CI students' development of different reading skills. Paragraph-reading tests enable a multidimensional evaluation of reading competence. Use of sentence-reading tests is suggested only as a tool for preliminary screening for basic reading capacities. 3b. © 2014 The American Laryngological, Rhinological and Otological Society, Inc.

ISRNA: an integrative online toolkit for short reads from high-throughput sequencing data.

PubMed

Luo, Guan-Zheng; Yang, Wei; Ma, Ying-Ke; Wang, Xiu-Jie

2014-02-01

Integrative Short Reads NAvigator (ISRNA) is an online toolkit for analyzing high-throughput small RNA sequencing data. Besides the high-speed genome mapping function, ISRNA provides statistics for genomic location, length distribution and nucleotide composition bias analysis of sequence reads. Number of reads mapped to known microRNAs and other classes of short non-coding RNAs, coverage of short reads on genes, expression abundance of sequence reads as well as some other analysis functions are also supported. The versatile search functions enable users to select sequence reads according to their sub-sequences, expression abundance, genomic location, relationship to genes, etc. A specialized genome browser is integrated to visualize the genomic distribution of short reads. ISRNA also supports management and comparison among multiple datasets. ISRNA is implemented in Java/C++/Perl/MySQL and can be freely accessed at http://omicslab.genetics.ac.cn/ISRNA/.

RIFM fragrance ingredient safety assessment, p-Isopropylbenzyl acetate, CAS Registry Number 59230-57-8.

PubMed

Api, A M; Belsito, D; Bhatia, S; Bruze, M; Calow, P; Dagli, M L; Dekant, W; Fryer, A D; Kromidas, L; La Cava, S; Lalko, J F; Lapczynski, A; Liebler, D C; Politano, V T; Ritacco, G; Salvito, D; Schultz, T W; Shen, J; Sipes, I G; Wall, B; Wilcox, D K

2016-11-01

The use of this material under current use conditions is supported by the existing information. This material was evaluated for genotoxicity, repeated dose toxicity, developmental toxicity, reproductive toxicity, local respiratory toxicity, phototoxicity, skin sensitization, as well as environmental safety. Data from the suitable read across analog, benzyl acetate (CAS # 140-11-4), show that this material is not genotoxic nor does it have skin sensitization potential. The repeated dose, developmental and reproductive, and local respiratory toxicity endpoints were completed using benzyl acetate (CAS # 140-11-4) as a suitable read across analog, which provided a MOE > 100. The phototoxicity/photoallergenicity endpoint was completed based on suitable UV spectra. The environmental endpoint was completed as described in the RIFM Framework. Copyright © 2016 Elsevier Ltd. All rights reserved.

A Cu2+-selective fluorescent chemosensor based on BODIPY with two pyridine ligands and logic gate

NASA Astrophysics Data System (ADS)

Huang, Liuqian; Zhang, Jing; Yu, Xiaoxiu; Ma, Yifan; Huang, Tianjiao; Shen, Xi; Qiu, Huayu; He, Xingxing; Yin, Shouchun

2015-06-01

A novel near-infrared fluorescent chemosensor based on BODIPY (Py-1) has been synthesized and characterized. Py-1 displays high selectivity and sensitivity for sensing Cu2+ over other metal ions in acetonitrile. Upon addition of Cu2+ ions, the maximum absorption band of Py-1 in CH3CN displays a red shift from 603 to 608 nm, which results in a visual color change from pink to blue. When Py-1 is excited at 600 nm in the presence of Cu2+, the fluorescent emission intensity of Py-1 at 617 nm is quenched over 86%. Notably, the complex of Py-1-Cu2+ can be restored with the introduction of EDTA or S2-. Consequently, an IMPLICATION logic gate at molecular level operating in fluorescence mode with Cu2+ and S2- as chemical inputs can be constructed. Finally, based on the reversible and reproducible system, a nanoscale sequential memory unit displaying "Writing-Reading-Erasing-Reading" functions can be integrated.

Gene expression profiling of human breast tissue samples using SAGE-Seq.

PubMed

Wu, Zhenhua Jeremy; Meyer, Clifford A; Choudhury, Sibgat; Shipitsin, Michail; Maruyama, Reo; Bessarabova, Marina; Nikolskaya, Tatiana; Sukumar, Saraswati; Schwartzman, Armin; Liu, Jun S; Polyak, Kornelia; Liu, X Shirley

2010-12-01

We present a powerful application of ultra high-throughput sequencing, SAGE-Seq, for the accurate quantification of normal and neoplastic mammary epithelial cell transcriptomes. We develop data analysis pipelines that allow the mapping of sense and antisense strands of mitochondrial and RefSeq genes, the normalization between libraries, and the identification of differentially expressed genes. We find that the diversity of cancer transcriptomes is significantly higher than that of normal cells. Our analysis indicates that transcript discovery plateaus at 10 million reads/sample, and suggests a minimum desired sequencing depth around five million reads. Comparison of SAGE-Seq and traditional SAGE on normal and cancerous breast tissues reveals higher sensitivity of SAGE-Seq to detect less-abundant genes, including those encoding for known breast cancer-related transcription factors and G protein-coupled receptors (GPCRs). SAGE-Seq is able to identify genes and pathways abnormally activated in breast cancer that traditional SAGE failed to call. SAGE-Seq is a powerful method for the identification of biomarkers and therapeutic targets in human disease.

Oral Reading Fluency in Second Language Reading

ERIC Educational Resources Information Center

Jeon, Eun Hee

2012-01-01

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

Mass-tag enhanced immuno-laser desorption/ionization mass spectrometry for sensitive detection of intact protein antigens.

PubMed

Lorey, Martina; Adler, Belinda; Yan, Hong; Soliymani, Rabah; Ekström, Simon; Yli-Kauhaluoma, Jari; Laurell, Thomas; Baumann, Marc

2015-05-19

A new read-out method for antibody arrays using laser desorption/ionization-mass spectrometry (LDI-MS) is presented. Small, photocleavable reporter molecules with a defined mass called "mass-tags" are used for detection of immunocaptured proteins from human plasma. Using prostate specific antigen (PSA), a biomarker for prostate cancer, as a model antigen, a high sensitivity generic detection methodology based immunocapture with a primary antibody and with a biotin labeled secondary antibody coupled to mass-tagged avidin is demonstrated. As each secondary antibody can bind several avidin molecules, each having a large number of mass-tags, signal amplification can be achieved. The developed PSA sandwich mass-tag analysis method provided a limit of detection below 200 pg/mL (6 pM) for a 10 μL plasma sample, well below the clinically relevant cutoff value of 3-4 ng/mL. This brings the limit of detection (LOD) for detection of intact antigens with matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) down to levels comparable to capture by anti-peptide antibodies selected reaction monitoring (SISCAPA SRM) and enzyme linked immunosorbent assay (ELISA), as 6 pM corresponds to a maximal amount of 60 amol PSA captured on-spot. We propose the potential use of LDI (laser desorption/ionization) with mass-tag read-out implemented in a sandwich assay format for low abundant and/or early disease biomarker detection.

Crowdsourcing for identification of polyp-free segments in virtual colonoscopy videos

NASA Astrophysics Data System (ADS)

Park, Ji Hwan; Mirhosseini, Seyedkoosha; Nadeem, Saad; Marino, Joseph; Kaufman, Arie; Baker, Kevin; Barish, Matthew

2017-03-01

Virtual colonoscopy (VC) allows a physician to virtually navigate within a reconstructed 3D colon model searching for colorectal polyps. Though VC is widely recognized as a highly sensitive and specific test for identifying polyps, one limitation is the reading time, which can take over 30 minutes per patient. Large amounts of the colon are often devoid of polyps, and a way of identifying these polyp-free segments could be of valuable use in reducing the required reading time for the interrogating radiologist. To this end, we have tested the ability of the collective crowd intelligence of non-expert workers to identify polyp candidates and polyp-free regions. We presented twenty short videos flying through a segment of a virtual colon to each worker, and the crowd was asked to determine whether or not a possible polyp was observed within that video segment. We evaluated our framework on Amazon Mechanical Turk and found that the crowd was able to achieve a sensitivity of 80.0% and specificity of 86.5% in identifying video segments which contained a clinically proven polyp. Since each polyp appeared in multiple consecutive segments, all polyps were in fact identified. Using the crowd results as a first pass, 80% of the video segments could in theory be skipped by the radiologist, equating to a significant time savings and enabling more VC examinations to be performed.

Toward a real-time in vivo dosimetry system using plastic scintillation detectors

PubMed Central

Archambault, Louis; Briere, Tina M.; Pönisch, Falk; Beaulieu, Luc; Kuban, Deborah A.; Lee, Andrew; Beddar, Sam

2010-01-01

Purpose In this work, we present and validate a plastic scintillation detector (PSD) system designed for real-time multi-probe in vivo measurements. Methods and Materials The PSDs were built with a dose-sensitive volume of 0.4 mm3. PSDs were assembled into modular detector patches, each containing 5 closely packed PSDs. Continuous dose readings were performed every 150 ms, with a gap between consecutive readings of less than 0.3 ms. We first studied the effect of electron multiplication. We then assessed system performance in acrylic and anthropomorphic pelvic phantoms. Results The PSDs are compatible with clinical rectal balloons and are easily inserted into the anthropomorphic phantom. With an electron multiplication average gain factor of 40, a twofold increase in the signal-to-noise ratio was observed, making near real-time dosimetry feasible. Under calibration conditions, the PSDs agreed with ion chamber measurements to 0.08%. Precision, evaluated as a function of the total dose delivered, ranged from 2.3% at 2 cGy to 0.4% at 200 cGy. Conclusion Real-time PSD measurements are highly accurate and precise. These PSDs can be mounted onto rectal balloons, transforming these clinical devices into in vivo dose detectors without modifying current clinical practice. Real-time monitoring of the dose delivered near the rectum during prostate radiation therapy should help radiation oncologists protect this sensitive normal structure. PMID:20231074

BAW sensor readout circuit based on Pierce oscillator architecture

NASA Astrophysics Data System (ADS)

Gao, Yang; Yin, Xi-Yang; Han, Bin; Wang, Yu-Hang

2017-10-01

Bulk Acoustic Wave Resonators (BAWRs) have been well developed both as filters and as high sensitivity sensors in recent years. In contrast to traditional megahertz quartz resonators, BAWRs offer significant increases in resonant frequency, typically operating in gigahertz regimes. This translates into a potential sensitivity increase of more than three orders of magnitude over traditional QCM (Quartz Crystal Microbalance) devices. Given the micrometer-scale size of BAW sensor-head, read-out circuitry can monolithic integrated with this GHz transducer is urgently needed to produce small, robust, and inexpensive sensor systems. A BAW sensor read-out circuit prototype based on Pierce oscillator architecture is fulfilled in this paper. Based on the differential measurement scheme, two uniform BAWRs are used to constitute two BAW oscillators as a reference and a measurement branch respectively. The resonant frequency shift caused by the measurand is obtained by mixing and filtering the two oscillator signals. Then, the intermediate signal is amplified, shaped and converted to a digital one. And a FPGA is used for frequency detection. Taking 2 GHz BAW mass sensor as a case study, deign procedure are given in details. Simulation and experimental results reveal a 0-99 MHz frequency shift measurement range. Main factors affecting phase noise of the BAW oscillator (i.e. mainly frequency stability of the BAW sensor readout circuit) are also discussed for further optimizations.

Assessment of Sentinel Node Biopsies With Full-Field Optical Coherence Tomography.

PubMed

Grieve, Kate; Mouslim, Karima; Assayag, Osnath; Dalimier, Eugénie; Harms, Fabrice; Bruhat, Alexis; Boccara, Claude; Antoine, Martine

2016-04-01

Current techniques for the intraoperative analysis of sentinel lymph nodes during breast cancer surgery present drawbacks such as time and tissue consumption. Full-field optical coherence tomography is a novel noninvasive, high-resolution, fast imaging technique. This study investigated the use of full-field optical coherence tomography as an alternative technique for the intraoperative analysis of sentinel lymph nodes. Seventy-one axillary lymph nodes from 38 patients at Tenon Hospital were imaged minutes after excision with full-field optical coherence tomography in the pathology laboratory, before being handled for histological analysis. A pathologist performed a blind diagnosis (benign/malignant), based on the full-field optical coherence tomography images alone, which resulted in a sensitivity of 92% and a specificity of 83% (n = 65 samples). Regular feedback was given during the blind diagnosis, with thorough analysis of the images, such that features of normal and suspect nodes were identified in the images and compared with histology. A nonmedically trained imaging expert also performed a blind diagnosis aided by the reading criteria defined by the pathologist, which resulted in 85% sensitivity and 90% specificity (n = 71 samples). The number of false positives of the pathologist was reduced by 3 in a second blind reading a few months later. These results indicate that following adequate training, full-field optical coherence tomography can be an effective noninvasive diagnostic tool for extemporaneous sentinel node biopsy qualification. © The Author(s) 2015.

The Effects of Teacher Read-Alouds and Student Silent Reading on Predominantly Bilingual High School Seniors' Learning and Retention of Social Studies Content

ERIC Educational Resources Information Center

Reed, Deborah K.; Swanson, Elizabeth; Petscher, Yaacov; Vaughn, Sharon

2014-01-01

Teacher read-alouds (TRA) are common in middle and high school content area classes. Because the practice of reading the textbook out loud to students is often used out of concern about students' ability to understand and learn from text when reading silently (SR), this randomized controlled trial was designed to experimentally manipulate text…

Reading skills of students with speech sound disorders at three stages of literacy development.

PubMed

Skebo, Crysten M; Lewis, Barbara A; Freebairn, Lisa A; Tag, Jessica; Avrich Ciesla, Allison; Stein, Catherine M

2013-10-01

The relationship between phonological awareness, overall language, vocabulary, and nonlinguistic cognitive skills to decoding and reading comprehension was examined for students at 3 stages of literacy development (i.e., early elementary school, middle school, and high school). Students with histories of speech sound disorders (SSD) with and without language impairment (LI) were compared to students without histories of SSD or LI (typical language; TL). In a cross-sectional design, students ages 7;0 (years;months) to 17;9 completed tests that measured reading, language, and nonlinguistic cognitive skills. For the TL group, phonological awareness predicted decoding at early elementary school, and overall language predicted reading comprehension at early elementary school and both decoding and reading comprehension at middle school and high school. For the SSD-only group, vocabulary predicted both decoding and reading comprehension at early elementary school, and overall language predicted both decoding and reading comprehension at middle school and decoding at high school. For the SSD and LI group, overall language predicted decoding at all 3 literacy stages and reading comprehension at early elementary school and middle school, and vocabulary predicted reading comprehension at high school. Although similar skills contribute to reading across the age span, the relative importance of these skills changes with children's literacy stages.

Reading Skills of Students With Speech Sound Disorders at Three Stages of Literacy Development

PubMed Central

Skebo, Crysten M.; Lewis, Barbara A.; Freebairn, Lisa A.; Tag, Jessica; Ciesla, Allison Avrich; Stein, Catherine M.

2015-01-01

Purpose The relationship between phonological awareness, overall language, vocabulary, and nonlinguistic cognitive skills to decoding and reading comprehension was examined for students at 3 stages of literacy development (i.e., early elementary school, middle school, and high school). Students with histories of speech sound disorders (SSD) with and without language impairment (LI) were compared to students without histories of SSD or LI (typical language; TL). Method In a cross-sectional design, students ages 7;0 (years; months) to 17;9 completed tests that measured reading, language, and nonlinguistic cognitive skills. Results For the TL group, phonological awareness predicted decoding at early elementary school, and overall language predicted reading comprehension at early elementary school and both decoding and reading comprehension at middle school and high school. For the SSD-only group, vocabulary predicted both decoding and reading comprehension at early elementary school, and overall language predicted both decoding and reading comprehension at middle school and decoding at high school. For the SSD and LI group, overall language predicted decoding at all 3 literacy stages and reading comprehension at early elementary school and middle school, and vocabulary predicted reading comprehension at high school. Conclusion Although similar skills contribute to reading across the age span, the relative importance of these skills changes with children’s literacy stages. PMID:23833280

Basic processes in reading aloud and colour naming: towards a better understanding of the role of spatial attention.

PubMed

Robidoux, Serje; Rauwerda, Derek; Besner, Derek

2014-05-01

Whether or not lexical access from print requires spatial attention has been debated intensively for the last 30 years. Studies involving colour naming generally find evidence that "unattended" words are processed. In contrast, reading-based experiments do not find evidence of distractor processing. One theory ascribes the discrepancy to weaker attentional demands for colour identification. If colour naming does not capture all of a subject's attention, the remaining attentional resources can be deployed to process the distractor word. The present study combined exogenous spatial cueing with colour naming and reading aloud separately and found that colour naming is less sensitive to the validity of a spatial cue than is reading words aloud. Based on these results, we argue that colour naming studies do not effectively control attention so that no conclusions about unattended distractor processing can be drawn from them. Thus we reiterate the consistent conclusion drawn from reading aloud and lexical decision studies: There is no word identification without (spatial) attention.

Skill dependent audiovisual integration in the fusiform induces repetition suppression.

PubMed

McNorgan, Chris; Booth, James R

2015-02-01

Learning to read entails mapping existing phonological representations to novel orthographic representations and is thus an ideal context for investigating experience driven audiovisual integration. Because two dominant brain-based theories of reading development hinge on the sensitivity of the visual-object processing stream to phonological information, we were interested in how reading skill relates to audiovisual integration in this area. Thirty-two children between 8 and 13 years of age spanning a range of reading skill participated in a functional magnetic resonance imaging experiment. Participants completed a rhyme judgment task to word pairs presented unimodally (auditory- or visual-only) and cross-modally (auditory followed by visual). Skill-dependent sub-additive audiovisual modulation was found in left fusiform gyrus, extending into the putative visual word form area, and was correlated with behavioral orthographic priming. These results suggest learning to read promotes facilitatory audiovisual integration in the ventral visual-object processing stream and may optimize this region for orthographic processing. Copyright © 2014 Elsevier Inc. All rights reserved.

Skill Dependent Audiovisual Integration in the Fusiform Induces Repetition Suppression

PubMed Central

McNorgan, Chris; Booth, James R.

2015-01-01

Learning to read entails mapping existing phonological representations to novel orthographic representations and is thus an ideal context for investigating experience driven audiovisual integration. Because two dominant brain-based theories of reading development hinge on the sensitivity of the visual-object processing stream to phonological information, we were interested in how reading skill relates to audiovisual integration in this area. Thirty-two children between 8 and 13 years of age spanning a range of reading skill participated in a functional magnetic resonance imaging experiment. Participants completed a rhyme judgment task to word pairs presented unimodally (auditory- or visual-only) and cross-modally (auditory followed by visual). Skill-dependent sub-additive audiovisual modulation was found in left fusiform gyrus, extending into the putative visual word form area, and was correlated with behavioral orthographic priming. These results suggest learning to read promotes facilitatory audiovisual integration in the ventral visual-object processing stream and may optimize this region for orthographic processing. PMID:25585276

The utility of modeling word identification from visual input within models of eye movements in reading

PubMed Central

Bicknell, Klinton; Levy, Roger

2012-01-01

Decades of empirical work have shown that a range of eye movement phenomena in reading are sensitive to the details of the process of word identification. Despite this, major models of eye movement control in reading do not explicitly model word identification from visual input. This paper presents a argument for developing models of eye movements that do include detailed models of word identification. Specifically, we argue that insights into eye movement behavior can be gained by understanding which phenomena naturally arise from an account in which the eyes move for efficient word identification, and that one important use of such models is to test which eye movement phenomena can be understood this way. As an extended case study, we present evidence from an extension of a previous model of eye movement control in reading that does explicitly model word identification from visual input, Mr. Chips (Legge, Klitz, & Tjan, 1997), to test two proposals for the effect of using linguistic context on reading efficiency. PMID:23074362

An association between auditory-visual synchrony processing and reading comprehension: Behavioral and electrophysiological evidence

PubMed Central

Mossbridge, Julia; Zweig, Jacob; Grabowecky, Marcia; Suzuki, Satoru

2016-01-01

The perceptual system integrates synchronized auditory-visual signals in part to promote individuation of objects in cluttered environments. The processing of auditory-visual synchrony may more generally contribute to cognition by synchronizing internally generated multimodal signals. Reading is a prime example because the ability to synchronize internal phonological and/or lexical processing with visual orthographic processing may facilitate encoding of words and meanings. Consistent with this possibility, developmental and clinical research has suggested a link between reading performance and the ability to compare visual spatial/temporal patterns with auditory temporal patterns. Here, we provide converging behavioral and electrophysiological evidence suggesting that greater behavioral ability to judge auditory-visual synchrony (Experiment 1) and greater sensitivity of an electrophysiological marker of auditory-visual synchrony processing (Experiment 2) both predict superior reading comprehension performance, accounting for 16% and 25% of the variance, respectively. These results support the idea that the mechanisms that detect auditory-visual synchrony contribute to reading comprehension. PMID:28129060

An Association between Auditory-Visual Synchrony Processing and Reading Comprehension: Behavioral and Electrophysiological Evidence.

PubMed

Mossbridge, Julia; Zweig, Jacob; Grabowecky, Marcia; Suzuki, Satoru

2017-03-01

The perceptual system integrates synchronized auditory-visual signals in part to promote individuation of objects in cluttered environments. The processing of auditory-visual synchrony may more generally contribute to cognition by synchronizing internally generated multimodal signals. Reading is a prime example because the ability to synchronize internal phonological and/or lexical processing with visual orthographic processing may facilitate encoding of words and meanings. Consistent with this possibility, developmental and clinical research has suggested a link between reading performance and the ability to compare visual spatial/temporal patterns with auditory temporal patterns. Here, we provide converging behavioral and electrophysiological evidence suggesting that greater behavioral ability to judge auditory-visual synchrony (Experiment 1) and greater sensitivity of an electrophysiological marker of auditory-visual synchrony processing (Experiment 2) both predict superior reading comprehension performance, accounting for 16% and 25% of the variance, respectively. These results support the idea that the mechanisms that detect auditory-visual synchrony contribute to reading comprehension.

Characterization of optically stimulated luminescent dosimeters, OSLDs, for clinical dosimetric measurements.

PubMed

Jursinic, Paul A

2007-12-01

Optically stimulated luminescent dosimeters, OSLDs, are plastic disks infused with aluminum oxide doped with carbon (Al2O3 : C). These disks are encased in a light-tight plastic holder. Crystals of Al2O3 : C when exposed to ionizing radiation store energy that is released as luminescence (420 nm) when the OSLD is illuminated with stimulation light (540 nm). The intensity of the luminescence depends on the dose absorbed by the OSLD and the intensity of the stimulation light. OSLDs used in this work were InLight/OSL Dot dosimeters, which were read with a MicroStar reader (Landauer, Inc., Glenwood, IL). The following are dosimetric properties of the OSLD that were determined: After a single irradiation, repeated readings cause the signal to decrease by 0.05% per reading; the signal could be discharged by greater than 98% by illuminating them for more than 45 s with a 150 W tungsten-halogen light; after irradiation there was a transient signal that decayed with a 0.8 min halftime; after the transient signal decay the signal was stable for days; repeated irradiations and readings of an individual OSLD gave a signal with a coefficient of variation of 0.6%; the dose sensitivity of OSLDs from a batch of detectors has a coefficient of variation of 0.9%, response was linear with absorbed dose over a test range of 1-300 cGy; above 300 cGy a small supra-linear behavior occurs; there was no dose-per-pulse dependence over a 388-fold range; there was no dependence on radiation energy or mode for 6 and 15 MV x rays and 6-20 MeV electrons; for Ir-192 gamma rays OSLD had 6% higher sensitivity; the dose sensitivity was unchanged up to an accumulated dose of 20 Gy and thereafter decreased by 4% per 10 Gy of additional accumulated dose; dose sensitivity was not dependent on the angle of incidence of radiation; the OSLD in its light-tight case has an intrinsic buildup of 0.04 g/cm2; dose sensitivity of the OSLD was not dependent on temperature at the time of irradiation in the range of 10-40 degrees C. The clinical use of OSLDs for in vivo dosimetric measurements is shown to be feasible.

Characterization of optically stimulated luminescent dosimeters, OSLDs, for clinical dosimetric measurements

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

Jursinic, Paul A.

2007-12-15

Optically stimulated luminescent dosimeters, OSLDs, are plastic disks infused with aluminum oxide doped with carbon (Al{sub 2}O{sub 3}:C). These disks are encased in a light-tight plastic holder. Crystals of Al{sub 2}O{sub 3}:C when exposed to ionizing radiation store energy that is released as luminescence (420 nm) when the OSLD is illuminated with stimulation light (540 nm). The intensity of the luminescence depends on the dose absorbed by the OSLD and the intensity of the stimulation light. OSLDs used in this work were InLight/OSL Dot dosimeters, which were read with a MicroStar reader (Landauer, Inc., Glenwood, IL). The following are dosimetricmore » properties of the OSLD that were determined: After a single irradiation, repeated readings cause the signal to decrease by 0.05% per reading; the signal could be discharged by greater than 98% by illuminating them for more than 45 s with a 150 W tungsten-halogen light; after irradiation there was a transient signal that decayed with a 0.8 min halftime; after the transient signal decay the signal was stable for days; repeated irradiations and readings of an individual OSLD gave a signal with a coefficient of variation of 0.6%; the dose sensitivity of OSLDs from a batch of detectors has a coefficient of variation of 0.9%, response was linear with absorbed dose over a test range of 1-300 cGy; above 300 cGy a small supra-linear behavior occurs; there was no dose-per-pulse dependence over a 388-fold range; there was no dependence on radiation energy or mode for 6 and 15 MV x rays and 6-20 MeV electrons; for Ir-192 gamma rays OSLD had 6% higher sensitivity; the dose sensitivity was unchanged up to an accumulated dose of 20 Gy and thereafter decreased by 4% per 10 Gy of additional accumulated dose; dose sensitivity was not dependent on the angle of incidence of radiation; the OSLD in its light-tight case has an intrinsic buildup of 0.04 g/cm{sup 2}; dose sensitivity of the OSLD was not dependent on temperature at the time of irradiation in the range of 10-40 deg. C. The clinical use of OSLDs for in vivo dosimetric measurements is shown to be feasible.« less

The influence of reading expertise in mirror-letter perception: Evidence from beginning and expert readers

PubMed Central

Duñabeitia, Jon Andoni; Dimitropoulou, María; Estévez, Adelina; Carreiras, Manuel

2013-01-01

The visual word recognition system recruits neuronal systems originally developed for object perception which are characterized by orientation insensitivity to mirror reversals. It has been proposed that during reading acquisition beginning readers have to “unlearn” this natural tolerance to mirror reversals in order to efficiently discriminate letters and words. Therefore, it is supposed that this unlearning process takes place in a gradual way and that reading expertise modulates mirror-letter discrimination. However, to date no supporting evidence for this has been obtained. We present data from an eye-movement study that investigated the degree of sensitivity to mirror-letters in a group of beginning readers and a group of expert readers. Participants had to decide which of the two strings presented on a screen corresponded to an auditorily presented word. Visual displays always included the correct target word and one distractor word. Results showed that those distractors that were the same as the target word except for the mirror lateralization of two internal letters attracted participants’ attention more than distractors created by replacement of two internal letters. Interestingly, the time course of the effects was found to be different for the two groups, with beginning readers showing a greater tolerance (decreased sensitivity) to mirror-letters than expert readers. Implications of these findings are discussed within the framework of preceding evidence showing how reading expertise modulates letter identification. PMID:24273596

Portable high precision pressure transducer system

DOEpatents

Piper, Thomas C.; Morgan, John P.; Marchant, Norman J.; Bolton, Steven M.

1994-01-01

A high precision pressure transducer system for checking the reliability of a second pressure transducer system used to monitor the level of a fluid confined in a holding tank. Since the response of the pressure transducer is temperature sensitive, it is continually housed in an battery powered oven which is configured to provide a temperature stable environment at specified temperature for an extended period of time. Further, a high precision temperature stabilized oscillator and counter are coupled to a single board computer to accurately determine the pressure transducer oscillation frequency and convert it to an applied pressure. All of the components are powered by the batteries which during periods of availability of line power are charged by an on board battery charger. The pressure readings outputs are transmitted to a line printer and a vacuum florescent display.

The Role of Left Occipitotemporal Cortex in Reading: Reconciling Stimulus, Task, and Lexicality Effects

PubMed Central

Humphries, Colin; Desai, Rutvik H.; Seidenberg, Mark S.; Osmon, David C.; Stengel, Ben C.; Binder, Jeffrey R.

2013-01-01

Although the left posterior occipitotemporal sulcus (pOTS) has been called a visual word form area, debate persists over the selectivity of this region for reading relative to general nonorthographic visual object processing. We used high-resolution functional magnetic resonance imaging to study left pOTS responses to combinatorial orthographic and object shape information. Participants performed naming and visual discrimination tasks designed to encourage or suppress phonological encoding. During the naming task, all participants showed subregions within left pOTS that were more sensitive to combinatorial orthographic information than to object information. This difference disappeared, however, when phonological processing demands were removed. Responses were stronger to pseudowords than to words, but this effect also disappeared when phonological processing demands were removed. Subregions within the left pOTS are preferentially activated when visual input must be mapped to a phonological representation (i.e., a name) and particularly when component parts of the visual input must be mapped to corresponding phonological elements (consonant or vowel phonemes). Results indicate a specialized role for subregions within the left pOTS in the isomorphic mapping of familiar combinatorial visual patterns to phonological forms. This process distinguishes reading from picture naming and accounts for a wide range of previously reported stimulus and task effects in left pOTS. PMID:22505661

RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets.

PubMed

Scheuch, Matthias; Höper, Dirk; Beer, Martin

2015-03-03

Fuelled by the advent and subsequent development of next generation sequencing technologies, metagenomics became a powerful tool for the analysis of microbial communities both scientifically and diagnostically. The biggest challenge is the extraction of relevant information from the huge sequence datasets generated for metagenomics studies. Although a plethora of tools are available, data analysis is still a bottleneck. To overcome the bottleneck of data analysis, we developed an automated computational workflow called RIEMS - Reliable Information Extraction from Metagenomic Sequence datasets. RIEMS assigns every individual read sequence within a dataset taxonomically by cascading different sequence analyses with decreasing stringency of the assignments using various software applications. After completion of the analyses, the results are summarised in a clearly structured result protocol organised taxonomically. The high accuracy and performance of RIEMS analyses were proven in comparison with other tools for metagenomics data analysis using simulated sequencing read datasets. RIEMS has the potential to fill the gap that still exists with regard to data analysis for metagenomics studies. The usefulness and power of RIEMS for the analysis of genuine sequencing datasets was demonstrated with an early version of RIEMS in 2011 when it was used to detect the orthobunyavirus sequences leading to the discovery of Schmallenberg virus.

Challenges in Routine Implementation and Quality Control of Rapid Diagnostic Tests for Malaria–Rufiji District, Tanzania

PubMed Central

McMorrow, Meredith L.; Masanja, M. Irene; Abdulla, Salim M. K.; Kahigwa, Elizeus; Kachur, S. Patrick

2018-01-01

Rapid diagnostic tests (RDTs) represent an alternative to microscopy for malaria diagnosis and have shown high sensitivity and specificity in a variety of study settings. Current World Health Organization (WHO) guidelines for quality control of RDTs provide detailed instructions on pre-field testing, but offer little guidance for quality assurance once RDTs are deployed in health facilities. From September 2006 to April 2007, we introduced a histidine-rich protein II (HRP2)-based RDT (Paracheck) for suspected malaria cases five years of age and older in nine health facilities in Rufiji District, Tanzania, to assess sensitivity and specificity of RDTs in routine use at rural health facilities. Thick blood smears were collected for all patients tested with RDTs and stained and read by laboratory personnel in each facility. Thick smears were subsequently reviewed by a reference microscopist to determine RDT sensitivity and specificity. In all nine health facilities, there were significant problems with the quality of staining and microscopy. Sensitivity and specificity of RDTs were difficult to assess given the poor quality of routine blood smear staining. Mean operational sensitivity of RDTs based on reference microscopy was 64.8%, but varied greatly by health facility, range 18.8–85.9%. Sensitivity of RDTs increased with increasing parasite density. Specificity remained high at 87.8% despite relatively poor slide quality. Institution of quality control of RDTs based on poor quality blood smear staining may impede reliable measurement of sensitivity and specificity and undermine confidence in the new diagnostic. There is an urgent need for the development of alternative quality control procedures for rapid diagnostic tests that can be performed at the facility level. PMID:18784230

Practical Considerations for Optimizing Position Sensitivity in Arrays of Position-sensitive TES's

NASA Technical Reports Server (NTRS)

Smith, Stephen J.; Bandler, Simon R.; Figueroa-Feliciano, Encetali; Iyomoto, Naoko; Kelley, Richard L.; Kilbourne, Caroline A.; Porder, Frederick S.; Sadleir, John E.

2007-01-01

We are developing Position-Sensitive Transitions-Edge Sensors (PoST's) for future X-ray astronomy missions such as NASA's Constellation-X. The PoST consists of one or more Transitions Edge Sensors (TES's) thermally connected to a large X-ray absorber, which through heat diffusion, gives rise to position dependence. The development of PoST's is motivated by the desire to achieve the largest the focal-plan coverage with the fewest number of readout channels. In order to develop a practical array, consisting of an inner pixellated core with an outer array of large absorber PoST's, we must be able to simultaneously read out all (-1800) channels in the array. This is achievable using time division multiplexing (TDM), but does set stringent slew rate requirements on the array. Typically, we must damp the pulses to reduce the slew rate of the input signal to the TDM. This is achieved by applying a low-pass analog filter with large inductance to the signal. This attenuates the high frequency components of the signal, essential for position discrimination in PoST's, relative to the white noise of the readout chain and degrades the position sensitivity. Using numerically simulated data, we investigate the position sensing ability of typical PoST designs under such high inductance conditions. We investigate signal-processing techniques for optimal determination of the event position and discuss the practical considerations for real-time implementation.

Simple, multiplexed, PCR-based barcoding of DNA enables sensitive mutation detection in liquid biopsies using sequencing.

PubMed

Ståhlberg, Anders; Krzyzanowski, Paul M; Jackson, Jennifer B; Egyud, Matthew; Stein, Lincoln; Godfrey, Tony E

2016-06-20

Detection of cell-free DNA in liquid biopsies offers great potential for use in non-invasive prenatal testing and as a cancer biomarker. Fetal and tumor DNA fractions however can be extremely low in these samples and ultra-sensitive methods are required for their detection. Here, we report an extremely simple and fast method for introduction of barcodes into DNA libraries made from 5 ng of DNA. Barcoded adapter primers are designed with an oligonucleotide hairpin structure to protect the molecular barcodes during the first rounds of polymerase chain reaction (PCR) and prevent them from participating in mis-priming events. Our approach enables high-level multiplexing and next-generation sequencing library construction with flexible library content. We show that uniform libraries of 1-, 5-, 13- and 31-plex can be generated. Utilizing the barcodes to generate consensus reads for each original DNA molecule reduces background sequencing noise and allows detection of variant alleles below 0.1% frequency in clonal cell line DNA and in cell-free plasma DNA. Thus, our approach bridges the gap between the highly sensitive but specific capabilities of digital PCR, which only allows a limited number of variants to be analyzed, with the broad target capability of next-generation sequencing which traditionally lacks the sensitivity to detect rare variants. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Haplotype estimation using sequencing reads.

PubMed

Delaneau, Olivier; Howie, Bryan; Cox, Anthony J; Zagury, Jean-François; Marchini, Jonathan

2013-10-03

High-throughput sequencing technologies produce short sequence reads that can contain phase information if they span two or more heterozygote genotypes. This information is not routinely used by current methods that infer haplotypes from genotype data. We have extended the SHAPEIT2 method to use phase-informative sequencing reads to improve phasing accuracy. Our model incorporates the read information in a probabilistic model through base quality scores within each read. The method is primarily designed for high-coverage sequence data or data sets that already have genotypes called. One important application is phasing of single samples sequenced at high coverage for use in medical sequencing and studies of rare diseases. Our method can also use existing panels of reference haplotypes. We tested the method by using a mother-father-child trio sequenced at high-coverage by Illumina together with the low-coverage sequence data from the 1000 Genomes Project (1000GP). We found that use of phase-informative reads increases the mean distance between switch errors by 22% from 274.4 kb to 328.6 kb. We also used male chromosome X haplotypes from the 1000GP samples to simulate sequencing reads with varying insert size, read length, and base error rate. When using short 100 bp paired-end reads, we found that using mixtures of insert sizes produced the best results. When using longer reads with high error rates (5-20 kb read with 4%-15% error per base), phasing performance was substantially improved. Copyright © 2013 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Design and performance of a high spatial resolution, time-of-flight PET detector

PubMed Central

Krishnamoorthy, Srilalan; LeGeyt, Benjamin; Werner, Matthew E.; Kaul, Madhuri; Newcomer, F. M.; Karp, Joel S.; Surti, Suleman

2014-01-01

This paper describes the design and performance of a high spatial resolution PET detector with time-of-flight capabilities. With an emphasis on high spatial resolution and sensitivity, we initially evaluated the performance of several 1.5 × 1.5 and 2.0 × 2.0 mm2 and 12–15 mm long LYSO crystals read out by several appropriately sized PMTs. Experiments to evaluate the impact of reflector on detector performance were performed and the final detector consisted of a 32 × 32 array of 1.5 × 1.5 × 15 mm3 LYSO crystals packed with a diffuse reflector and read out by a single Hamamatsu 64 channel multi-anode PMT. Such a design made it compact, modular and offered a cost-effective solution to obtaining excellent energy and timing resolution. To minimize the number of readout signals, a compact front-end readout electronics that summed anode signals along each of the orthogonal directions was also developed. Experimental evaluation of detector performance demonstrates clear discrimination of the crystals within the detector. An average energy resolution (FWHM) of 12.7 ± 2.6% and average coincidence timing resolution (FWHM) of 348 ps was measured, demonstrating suitability for use in the development of a high spatial resolution time-of-flight scanner for dedicated breast PET imaging. PMID:25246711

A Model Critical Reading Lesson for Secondary High-Risk Students.

ERIC Educational Resources Information Center

Haney, Gail; Thistlethwaite, Linda

1991-01-01

This article defines critical reading, discusses associated frameworks, and lists considerations for choosing topics and reading materials. A sample critical reading lesson using a "mapping" approach with a reading on euthanasia demonstrates guiding secondary learning-disabled students in critical reading. (DB)

A Biologically Realistic Cortical Model of Eye Movement Control in Reading

ERIC Educational Resources Information Center

Heinzle, Jakob; Hepp, Klaus; Martin, Kevan A. C.

2010-01-01

Reading is a highly complex task involving a precise integration of vision, attention, saccadic eye movements, and high-level language processing. Although there is a long history of psychological research in reading, it is only recently that imaging studies have identified some neural correlates of reading. Thus, the underlying neural mechanisms…

The Collaboration Model and Reading Improvement of High School Students with Learning Disabilities

ERIC Educational Resources Information Center

Sacchetto, Jorge A.

2014-01-01

In the field of reading research, studies that focus on improving the reading achievement of high school students with learning disabilities are lacking. Although collaborative interventions for elementary age students have been shown to be effective, a gap exists in the current research regarding effective collaborative reading interventions for…

Reading Motivation and Engagement at a Rural Georgia High School

ERIC Educational Resources Information Center

Winfree, Linda

2013-01-01

As college and workplace success becomes increasingly dependent on reading, parents and educators have become more interested in how to engage students in reading. Teachers at a rural Georgia high school have reported that students are reluctant to engage in academic reading. Guided by previous research on the factors that promote or discourage…

Free Reading Is UTOPIA

ERIC Educational Resources Information Center

LeCrone, Nancy

2010-01-01

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

African American English and Spelling: How Do Second Graders Spell Dialect-Sensitive Features of Words?

ERIC Educational Resources Information Center

Patton-Terry, Nicole; Connor, Carol

2010-01-01

This study explored the spelling skills of African American second graders who produced African American English (AAE) features in speech. The children (N = 92), who varied in spoken AAE use and word reading skills, were asked to spell words that contained phonological and morphological dialect-sensitive (DS) features that can vary between AAE and…

Thermal Profiling of Residential Energy Use

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

Albert, A; Rajagopal, R

This work describes a methodology for informing targeted demand-response (DR) and marketing programs that focus on the temperature-sensitive part of residential electricity demand. Our methodology uses data that is becoming readily available at utility companies-hourly energy consumption readings collected from "smart" electricity meters, as well as hourly temperature readings. To decompose individual consumption into a thermal-sensitive part and a base load (non-thermally-sensitive), we propose a model of temperature response that is based on thermal regimes, i.e., unobserved decisions of consumers to use their heating or cooling appliances. We use this model to extract useful benchmarks that compose thermal profiles ofmore » individual users, i.e., terse characterizations of the statistics of these users' temperature-sensitive consumption. We present example profiles generated using our model on real consumers, and show its performance on a large sample of residential users. This knowledge may, in turn, inform the DR program by allowing scarce operational and marketing budgets to be spent on the right users-those whose influencing will yield highest energy reductions-at the right time. We show that such segmentation and targeting of users may offer savings exceeding 100% of a random strategy.« less

Positron emission mammography (PEM): Effect of activity concentration, object size, and object contrast on phantom lesion detection

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

MacDonald, Lawrence R.; Wang, Carolyn L.; Eissa, Marna

2012-10-15

Purpose: To characterize the relationship between lesion detection sensitivity and injected activity as a function of lesion size and contrast on the PEM (positron emission mammography) Flex Solo II scanner using phantom experiments. Methods: Phantom lesions (spheres 4, 8, 12, 16, and 20 mm diameter) were randomly located in uniform background. Sphere activity concentrations were 3 to 21 times the background activity concentration (BGc). BGc was a surrogate for injected activity; BGc ranged from 0.44-4.1 kBq/mL, corresponding to 46-400 MBq injections. Seven radiologists read 108 images containing zero, one, or two spheres. Readers used a 5-point confidence scale to scoremore » the presence of spheres. Results: Sensitivity was 100% for lesions {>=}12 mm under all conditions except for one 12 mm sphere with the lowest contrast and lowest BGc (60% sensitivity). Sensitivity was 100% for 8 mm spheres when either contrast or BGc was high, and 100% for 4 mm spheres only when both contrast and BGc were highest. Sphere contrast recovery coefficients (CRC) were 49%, 34%, 26%, 14%, and 2.8% for the largest to smallest spheres. Cumulative specificity was 98%. Conclusions: Phantom lesion detection sensitivity depends more on sphere size and contrast than on BGc. Detection sensitivity remained {>=}90% for injected activities as low as 100 MBq, for lesions {>=}8 mm. Low CRC in 4 mm objects results in moderate detection sensitivity even for 400 MBq injected activity, making it impractical to optimize injected activity for such lesions. Low CRC indicates that when lesions <8 mm are observed on PEM images they are highly tracer avid with greater potential of clinical significance. High specificity (98%) suggests that image statistical noise does not lead to false positive findings. These results apply to the 85 mm thick object used to obtain them; lesion detectability should be better (worse) for thinner (thicker) objects based on the reduced (increased) influence of photon attenuation.« less

Development of visual expertise for reading: rapid emergence of visual familiarity for an artificial script

PubMed Central

Maurer, Urs; Blau, Vera C.; Yoncheva, Yuliya N.; McCandliss, Bruce D.

2010-01-01

Adults produce left-lateralized N170 responses to visual words relative to control stimuli, even within tasks that do not require active reading. This specialization begins in preschoolers as a right-lateralized N170 effect. We investigated whether this developmental shift reflects an early learning phenomenon, such as attaining visual familiarity with a script, by training adults in an artificial script and measuring N170 responses before and afterward. Training enhanced the N170 response, especially over the right hemisphere. This suggests N170 sensitivity to visual familiarity with a script before reading becomes sufficiently automatic to drive left-lateralized effects in a shallow encoding task. PMID:20614357

Assessing spelling in kindergarten: further comparison of scoring metrics and their relation to reading skills.

PubMed

Clemens, Nathan H; Oslund, Eric L; Simmons, Leslie E; Simmons, Deborah

2014-02-01

Early reading and spelling development share foundational skills, yet spelling assessment is underutilized in evaluating early reading. This study extended research comparing the degree to which methods for scoring spelling skills at the end of kindergarten were associated with reading skills measured at the same time as well as at the end of first grade. Five strategies for scoring spelling responses were compared: totaling the number of words spelled correctly, totaling the number of correct letter sounds, totaling the number of correct letter sequences, using a rubric for scoring invented spellings, and calculating the Spelling Sensitivity Score (Masterson & Apel, 2010b). Students (N=287) who were identified at kindergarten entry as at risk for reading difficulty and who had received supplemental reading intervention were administered a standardized spelling assessment in the spring of kindergarten, and measures of phonological awareness, decoding, word recognition, and reading fluency were administered concurrently and at the end of first grade. The five spelling scoring metrics were similar in their strong relations with factors summarizing reading subskills (phonological awareness, decoding, and word reading) on a concurrent basis. Furthermore, when predicting first-grade reading skills based on spring-of-kindergarten performance, spelling scores from all five metrics explained unique variance over the autoregressive effects of kindergarten word identification. The practical advantages of using a brief spelling assessment for early reading evaluation and the relative tradeoffs of each scoring metric are discussed. Copyright © 2013 Society for the Study of School Psychology. Published by Elsevier Ltd. All rights reserved.

Do eye movements reveal differences between monolingual and bilingual children's first-language and second-language reading? A focus on word frequency effects.

PubMed

Whitford, Veronica; Joanisse, Marc F

2018-09-01

An extensive body of research has examined reading acquisition and performance in monolingual children. Surprisingly, however, much less is known about reading in bilingual children, who outnumber monolingual children globally. Here, we address this important imbalance in the literature by employing eye movement recordings to examine both global (i.e., text-level) and local (i.e., word-level) aspects of monolingual and bilingual children's reading performance across their first-language (L1) and second-language (L2). We also had a specific focus on lexical accessibility, indexed by word frequency effects. We had three main findings. First, bilingual children displayed reduced global and local L1 reading performance relative to monolingual children, including larger L1 word frequency effects. Second, bilingual children displayed reduced global and local L2 versus L1 reading performance, including larger L2 word frequency effects. Third, both groups of children displayed reduced global and local reading performance relative to adult comparison groups (across their known languages), including larger word frequency effects. Notably, our first finding was not captured by traditional offline measures of reading, such as standardized tests, suggesting that these measures may lack the sensitivity to detect such nuanced between-group differences in reading performance. Taken together, our findings demonstrate that bilingual children's simultaneous exposure to two reading systems leads to eye movement reading behavior that differs from that of monolingual children and has important consequences for how lexical information is accessed and integrated in both languages. Copyright © 2018 Elsevier Inc. All rights reserved.

The Effect of Guided Reading Instruction on Reading Achievement

ERIC Educational Resources Information Center

Underwood, Vanda Lea

2010-01-01

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

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

PubMed

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

2015-01-01

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

Selected Factors in Reading Comprehension for Deaf and Hearing Adults: Phonological Skills and Metacognition.

PubMed

Wang, Ye; Silvestri, Julia A; Jahromi, Laudan B

2018-01-01

The purpose of the study was to identify factors related to reading comprehension, and to compare similarities and differences in the reading processes of deaf and hearing adults. The sample included four groups, each consisting of 15 adults. The groups were identified as (a) deaf high-achieving readers, (b) deaf low-achieving readers, (c) hearing high-achieving readers, and (d) hearing low-achieving readers. Measurement instruments included a demographic form along with assessments of reading comprehension, phonological skills, and metacognition, the latter of which contained both a making-inferences measure and a think-aloud discussion with a reading strategies checklist. Results indicated that deaf high-achieving readers performed similarly to hearing high-achieving readers, except for phonological skills, and that for all participants, phonological skills and metacognition were related to reading comprehension skills.

The Influence of Self-Efficacy on Reading Achievement of General Educational Development (GED) and High School Graduates Enrolled in Developmental Reading Skills Courses in an Urban Community College System

ERIC Educational Resources Information Center

Barnes, Martha J.

2010-01-01

This study was undertaken to investigate the effects of self-efficacy on the performance of General Educational Development (GED) and high school graduates enrolled in developmental reading skills courses. The sample for the study consisted of 100 high school and 31 GED graduates enrolled in developmental reading courses in a midwestern community…

Molecular Diagnosis of Orthopedic-Device-Related Infection Directly from Sonication Fluid by Metagenomic Sequencing

PubMed Central

Sanderson, Nicholas D.; Atkins, Bridget L.; Brent, Andrew J.; Cole, Kevin; Foster, Dona; McNally, Martin A.; Oakley, Sarah; Peto, Leon; Taylor, Adrian; Peto, Tim E. A.; Crook, Derrick W.; Eyre, David W.

2017-01-01

ABSTRACT Culture of multiple periprosthetic tissue samples is the current gold standard for microbiological diagnosis of prosthetic joint infections (PJI). Additional diagnostic information may be obtained through culture of sonication fluid from explants. However, current techniques can have relatively low sensitivity, with prior antimicrobial therapy and infection by fastidious organisms influencing results. We assessed if metagenomic sequencing of total DNA extracts obtained direct from sonication fluid can provide an alternative rapid and sensitive tool for diagnosis of PJI. We compared metagenomic sequencing with standard aerobic and anaerobic culture in 97 sonication fluid samples from prosthetic joint and other orthopedic device infections. Reads from Illumina MiSeq sequencing were taxonomically classified using Kraken. Using 50 derivation samples, we determined optimal thresholds for the number and proportion of bacterial reads required to identify an infection and confirmed our findings in 47 independent validation samples. Compared to results from sonication fluid culture, the species-level sensitivity of metagenomic sequencing was 61/69 (88%; 95% confidence interval [CI], 77 to 94%; for derivation samples 35/38 [92%; 95% CI, 79 to 98%]; for validation samples, 26/31 [84%; 95% CI, 66 to 95%]), and genus-level sensitivity was 64/69 (93%; 95% CI, 84 to 98%). Species-level specificity, adjusting for plausible fastidious causes of infection, species found in concurrently obtained tissue samples, and prior antibiotics, was 85/97 (88%; 95% CI, 79 to 93%; for derivation samples, 43/50 [86%; 95% CI, 73 to 94%]; for validation samples, 42/47 [89%; 95% CI, 77 to 96%]). High levels of human DNA contamination were seen despite the use of laboratory methods to remove it. Rigorous laboratory good practice was required to minimize bacterial DNA contamination. We demonstrate that metagenomic sequencing can provide accurate diagnostic information in PJI. Our findings, combined with the increasing availability of portable, random-access sequencing technology, offer the potential to translate metagenomic sequencing into a rapid diagnostic tool in PJI. PMID:28490492

Wireless implantable passive strain sensor: design, fabrication and characterization

NASA Astrophysics Data System (ADS)

Umbrecht, F.; Wägli, P.; Dechand, S.; Gattiker, F.; Neuenschwander, J.; Sennhauser, U.; Hierold, Ch

2010-08-01

This work presents a new passive sensor concept for monitoring the deformation of orthopedic implants. The novel sensing principle of the WIPSS (wireless implantable passive strain sensor) is based on a hydro-mechanical amplification effect. The WIPSS is entirely made from biocompatible PMMA and consists of a microchannel attached to a reservoir, which is filled with an incompressible fluid. As the reservoir is exposed to strain, its volume changes and consequently the fill level inside the microchannel varies. The wireless detection of the microchannel's strain-dependent fill level is based on ultrasound. The WIPSS' sensing principle is proved by finite-element simulations and the reservoir's design is optimized toward maximum volume change, in order to achieve high sensitivity. A fabrication process for WIPSS sensor devices entirely made from PMMA is presented. The obtained measurement results confirmed the sensor's functionality and showed very good agreement with the obtained results of the conducted FE simulations regarding the sensor's sensitivity. A strain resolution of 1.7 ± 0.2 × 10-5 was achieved. Further, the determination of the cross-sensitivity to temperature and strains applied out of the sensing direction is presented. The response to dynamic inputs (0.1-5 Hz) has been measured and showed decreasing sensor output with increasing frequency. Test structures of the sensor device allow the application of a signal bandwidth up to 1 Hz. Therefore, the proposed sensor concept of the WIPSS presents a promising new sensor system for static in vivo strain monitoring of orthopedic implants. In combination with the developed ultrasound-based read-out method, this new sensor system offers the potential of wireless sensor read-out with medical ultrasound scanners, which are commercially available.

Pilot study analyzing automated ECG screening of hypertrophic cardiomyopathy.

PubMed

Campbell, Matthew J; Zhou, Xuefu; Han, Chia; Abrishami, Hedayat; Webster, Gregory; Miyake, Christina Y; Sower, Christopher T; Anderson, Jeffrey B; Knilans, Timothy K; Czosek, Richard J

2017-06-01

Hypertrophic cardiomyopathy (HCM) is one of the leading causes of sudden cardiac death in athletes. However, preparticipation ECG screening has often been criticized for failing to meet cost-effectiveness thresholds, in part because of high false-positive rates and the cost of ECG screening itself. The purpose of this study was to assess the testing characteristics of an automated ECG algorithm designed to screen for HCM in a multi-institutional pediatric cohort. ECGs from patients with HCM aged 12 to 20 years from 3 pediatric institutions were screened for ECG criteria for HCM using a previously described automated computer algorithm developed specifically for HCM ECG screening. The results were compared to a known healthy pediatric cohort. The studies then were read by trained electrophysiologists using standard ECG criteria and compared to the results of automated screening. One hundred twenty-eight ECGs from unique patients with phenotypic HCM were obtained and compared with 256 studies from healthy control patients matched in 2:1 fashion. When presented with the ECGs, the non-voltage-based algorithm resulted in 81.2% sensitivity and 90.7% specificity. A trained electrophysiologist read the same data according to the Seattle Criteria, with 71% sensitivity with 95.7% specificity. The sensitivity of screening as well as the components of the ECG screening itself varied by institution. This pilot study demonstrates a potential for automated ECG screening algorithms to detect HCM with testing characteristics similar to that of a trained electrophysiologist. In addition, there appear to be differences in ECG characteristics between patient populations, which may account for the difficulties in universal screening. Copyright © 2017 Heart Rhythm Society. Published by Elsevier Inc. All rights reserved.

[Relationship between clinical symptoms and Hiragana reading ability in children with difficulties in reading and writing:usefulness of a clinical-symptoms-checklist].

PubMed

Kita, Yosuke; Kobayashi, Tomoka; Koike, Toshihide; Koeda, Tatsuya; Wakamiya, Eiji; Hosokawa, Torn; Kaga, Makiko; Inagaki, Masumi

2010-11-01

We investigated the clinical symptoms of children with developmental dyslexia (DD) and evaluated the relationship between these symptoms and their Hiragana reading abilities. In order to detect the clinical symptoms of DD, we newly developed a clinical-symptoms-checklist (CL), which consisted of a total of 30 yes/no questions regarding symptoms linked to reading (15 questions) and writing (15 questions). Subjects were 98 Japanese school grade (1 to 9) children, aged 6 to 15 years old, with normal intelligence confirmed by the Wechsler Intelligence Test for Children (WISC-Ill) and they were divided into 2 groups according to their diagnosis. Twenty four children diagnosed as developmental dyslexia consisted the DD group, and the remaining 74 children were grouped in the non-DD group. CL showed significant construct validity (p<0.05) and inner consistency (reading: a =0.82, writing: a =0.72) after deleting two questions from the originals. The number of questions checked in the CL reading subcategory significantly correlated with the Hiragana reading ability of articulation time in all Hiragana reading tasks (p<0.001). More severe clinical symptoms and lower reading ability were observed in the DD group compared to the non-DD group. Receiver Operating Characteristics (ROC) analysis indicated that these two groups could be discriminated by the CL and the results of the reading task, and both sensitivity and specificity rate were approximately 80%. It was suggested that 7 or more positive checks in the CL and 2 or more abnormal scores in the reading tasks might discriminate DD from other conditions which cause difficulties in reading and writing in Japanese children.

Added value of double reading in diagnostic radiology,a systematic review.

PubMed

Geijer, Håkan; Geijer, Mats

2018-06-01

Double reading in diagnostic radiology can find discrepancies in the original report, but a systematic program of double reading is resource consuming. There are conflicting opinions on the value of double reading. The purpose of the current study was to perform a systematic review on the value of double reading. A systematic review was performed to find studies calculating the rate of misses and overcalls with the aim of establishing the added value of double reading by human observers. The literature search resulted in 1610 hits. After abstract and full-text reading, 46 articles were selected for analysis. The rate of discrepancy varied from 0.4 to 22% depending on study setting. Double reading by a sub-specialist, in general, led to high rates of changed reports. The systematic review found rather low discrepancy rates. The benefit of double reading must be balanced by the considerable number of working hours a systematic double-reading scheme requires. A more profitable scheme might be to use systematic double reading for selected, high-risk examination types. A second conclusion is that there seems to be a value of sub-specialisation for increased report quality. A consequent implementation of this would have far-reaching organisational effects. • In double reading, two or more radiologists read the same images. • A systematic literature review was performed. • The discrepancy rates varied from 0.4 to 22% in various studies. • Double reading by sub-specialists found high discrepancy rates.

RIF + USSR = R.E.A.D.

ERIC Educational Resources Information Center

Ball, Diane A.

A junior high school reading program entitled Reading for Enjoyment and Development (READ) that combines the Reading is Fundamental (RIF) inexpensive book distribution program and the practice of entire school participation in uninterrupted sustained silent reading (USSR) is described in this paper. The development of the project and practical…

Reading Comprehension Profiles of High-Functioning Students on the Autism Spectrum: A Grounded Theory

ERIC Educational Resources Information Center

Williamson, Pamela; Carnahan, Christina R.; Jacobs, Jennifer A.

2012-01-01

Using a constructivist grounded theory approach, this study sought to understand what influences reading comprehension and how meaning is made from text among high-functioning individuals with autism spectrum disorder (ASD). Using a think-aloud procedure, 13 individuals ages 7-13 with ASD read 16 passages at their instructional reading level.…

Reading Aloud in High Schools: Students and Teachers across the Curriculum

ERIC Educational Resources Information Center

Warner, Lionel; Crolla, Caroline; Goodwyn, Andy; Hyder, Eileen; Richards, Brian

2016-01-01

Reading aloud is apparently an indispensible part of teaching. Nevertheless, little is known about reading aloud across the curriculum by students and teachers in high schools. Nor do we understand teachers' attitudes towards issues such as error correction, rehearsal time, and selecting students to read. A survey of 360 teachers in England shows…

High School Students and "Read Across America"?

ERIC Educational Resources Information Center

Fisher, Julieta Dias; Hill, Ann

2004-01-01

Although more commonly associated with elementary school rather than high school students, "Read Across America" celebrations can cater to any age group and generate enthusiasm for reading long after the festivities have ended. In this article, the authors, library media specialists at Washington Township High School in Sewell, New Jersey, share …

Klinefelter Syndrome

MedlinePlus

... Enlarged breast tissue (gynecomastia) Weak bones Low energy levels Tendency to be shy and sensitive Difficulty expressing thoughts and feelings or socializing Problems with reading, writing, spelling or math Men Low sperm count or no sperm Small ...

What if Reading is Easy but Unimportant? How Students’ Patterns of Affirming and Undermining Motivation for Reading Information Texts Predict Different Reading Outcomes

PubMed Central

Rosenzweig, Emily Q.; Wigfield, Allan

2016-01-01

Many affirming and undermining motivational constructs affect students as they read information texts, but few researchers have explored how these motivations are patterned within students. In this study we used cluster analysis to classify middle school students (n = 1,134) based on their patterns of self-efficacy, perceived difficulty, value, and devalue for reading school information texts. We then compared how the patterns predicted students’ language arts grades, science information text comprehension, and dedication to reading school information texts. We found and validated a four-cluster solution. One cluster included a pattern of high affirming and low undermining motivations, and another included low affirming and high undermining motivations. Students with these patterns earned the highest and lowest scores, respectively, on all outcomes. A third pattern showed high self-efficacy/low difficulty with low value/high devalue, and a fourth showed moderate levels of all four motivational constructs. Students with the high efficacy and devalue pattern showed high information text comprehension but relatively low dedication. Students with the moderate pattern showed high dedication but low initial information text comprehension. Students with these two patterns earned similar grades. We discuss the implications of our findings for motivation theories and for school instruction that involves information text reading. PMID:28496289

What if Reading is Easy but Unimportant? How Students' Patterns of Affirming and Undermining Motivation for Reading Information Texts Predict Different Reading Outcomes.

PubMed

Rosenzweig, Emily Q; Wigfield, Allan

2017-01-01

Many affirming and undermining motivational constructs affect students as they read information texts, but few researchers have explored how these motivations are patterned within students. In this study we used cluster analysis to classify middle school students (n = 1,134) based on their patterns of self-efficacy, perceived difficulty, value, and devalue for reading school information texts. We then compared how the patterns predicted students' language arts grades, science information text comprehension, and dedication to reading school information texts. We found and validated a four-cluster solution. One cluster included a pattern of high affirming and low undermining motivations, and another included low affirming and high undermining motivations. Students with these patterns earned the highest and lowest scores, respectively, on all outcomes. A third pattern showed high self-efficacy/low difficulty with low value/high devalue, and a fourth showed moderate levels of all four motivational constructs. Students with the high efficacy and devalue pattern showed high information text comprehension but relatively low dedication. Students with the moderate pattern showed high dedication but low initial information text comprehension. Students with these two patterns earned similar grades. We discuss the implications of our findings for motivation theories and for school instruction that involves information text reading.

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

PubMed Central

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

2014-01-01

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

Selected High School History Teachers' Suggestions for Teaching Reading and Study Skills Needed in High School History Classes.

ERIC Educational Resources Information Center

Davis, E. Dale

A summary of recommendations from the recent literature dealing with reading and study skills in high school history and social studies and data from interviews with high school history teachers are presented. The literature search revealed that little teaching of reading and study skills is done in high schools but that history and social studies…