Research-Driven Reading Assessment: Drilling to the Core

ERIC Educational Resources Information Center

Hempenstall, Kerry

2009-01-01

There is considerable interest and controversy in the community concerning how our students are faring in the task of mastering reading. Broad scale assessment, formerly at a State level and now at a National level (NAPLAN), is potentially valuable in helping answer this question in a broad sense. However, there are limitations to the value of…

Selected Readings in Genetic Engineering

ERIC Educational Resources Information Center

Mertens, Thomas R.; Robinson, Sandra K.

1973-01-01

Describes different sources of readings for understanding issues and concepts of genetic engineering. Broad categories of reading materials are: concerns about genetic engineering; its background; procedures; and social, ethical and legal issues. References are listed. (PS)

MetaCAA: A clustering-aided methodology for efficient assembly of metagenomic datasets.

PubMed

Reddy, Rachamalla Maheedhar; Mohammed, Monzoorul Haque; Mande, Sharmila S

2014-01-01

A key challenge in analyzing metagenomics data pertains to assembly of sequenced DNA fragments (i.e. reads) originating from various microbes in a given environmental sample. Several existing methodologies can assemble reads originating from a single genome. However, these methodologies cannot be applied for efficient assembly of metagenomic sequence datasets. In this study, we present MetaCAA - a clustering-aided methodology which helps in improving the quality of metagenomic sequence assembly. MetaCAA initially groups sequences constituting a given metagenome into smaller clusters. Subsequently, sequences in each cluster are independently assembled using CAP3, an existing single genome assembly program. Contigs formed in each of the clusters along with the unassembled reads are then subjected to another round of assembly for generating the final set of contigs. Validation using simulated and real-world metagenomic datasets indicates that MetaCAA aids in improving the overall quality of assembly. A software implementation of MetaCAA is available at https://metagenomics.atc.tcs.com/MetaCAA. Copyright © 2014 Elsevier Inc. All rights reserved.

Looking Ahead with Hope: Reviving the Reading Maturity Construct as Social Science for Adolescent and Adult Readers

ERIC Educational Resources Information Center

Thomas, Matt

2013-01-01

"Reading maturity" is a construct that looks broadly at reading development encompassing not only basic reading skills but reading habits, attitudes, and dispositions. It has a rich history and this article calls for a need to make reading maturity a necessary part of the literacy curriculum. It offers a working description and reviews…

Broad spectrum antibiotic compounds and use thereof

DOEpatents

Koglin, Alexander; Strieker, Matthias

2016-07-05

The discovery of a non-ribosomal peptide synthetase (NRPS) gene cluster in the genome of Clostridium thermocellum that produces a secondary metabolite that is assembled outside of the host membrane is described. Also described is the identification of homologous NRPS gene clusters from several additional microorganisms. The secondary metabolites produced by the NRPS gene clusters exhibit broad spectrum antibiotic activity. Thus, antibiotic compounds produced by the NRPS gene clusters, and analogs thereof, their use for inhibiting bacterial growth, and methods of making the antibiotic compounds are described.

Genetic and Biochemical Map for the Biosynthesis of Occidiofungin, an Antifungal Produced by Burkholderia contaminans Strain MS14 ▿†

PubMed Central

Gu, Ganyu; Smith, Leif; Liu, Aixin; Lu, Shi-En

2011-01-01

A striking feature of Burkholderia contaminans strain MS14 is the production of a glycolipopeptide named occidiofungin. Occidiofungin has a broad range of antifungal activities against plant and animal pathogens. In this study, a complete covalent structure characterization and identification of the whole genomic DNA region for the occidiofungin gene (ocf) cluster are described. Discovery of the presence of 2,4-diaminobutyric acid and 3-chloro-β-hydroxytyrosine and elucidation of the structure of a novel C18 fatty amino acid residue have been achieved. In addition, seven additional putative open reading frames (the genes from ocfI to ocfN [ocfI-N] and ORF16) were identified. Transcription of all the putative genes ocfI-N identified in the region except ORF16 was regulated by both ambR1 and ambR2. Elucidation of the structure and the ocf gene cluster provides insight into the biosynthesis of occidiofungin and promotes future aims at understanding the biosynthetic machinery. This work provides new avenues for optimizing the production and synthesis of structural analogs of occidiofungin. PMID:21742901

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.

Can You Read Me Now? Disciplinary Literacy Reading Strategies in the 7th Grade Science Classroom

ERIC Educational Resources Information Center

McQuaid, Kelly Kathleen

2017-01-01

Adolescent readers require a broad range of reading skills to deal with the challenges of reading complex text. Some researchers argue for a discipline-specific focus to address the low reading proficiency rates among secondary students. Disciplinary literacy attends to the different ways disciplines, such as science, generate and communicate…

Action Research and Differentiating Reading Instruction in Mississippi: Fourth-Grade Students' Reading Success

ERIC Educational Resources Information Center

Mims, Wyn, M.; Lockley, Jeannie

2017-01-01

A fourth-grade teacher utilized action research in order to make data-driven decisions about reading interventions with her students. The teacher decided on a broad intervention, which was differentiating reading instruction, implemented differentiated instruction, collected data and continuously adjusted interventions based on monitoring data.…

Self-government of complex reading and writing brains informed by cingulo-opercular network for adaptive control and working memory components for language learning.

PubMed

Richards, Todd L; Abbott, Robert D; Yagle, Kevin; Peterson, Dan; Raskind, Wendy; Berninger, Virginia W

2017-01-01

To understand mental self-government of the developing reading and writing brain, correlations of clustering coefficients on fMRI reading or writing tasks with BASC 2 Adaptivity ratings (time 1 only) or working memory components (time 1 before and time 2 after instruction previously shown to improve achievement and change magnitude of fMRI connectivity) were investigated in 39 students in grades 4 to 9 who varied along a continuum of reading and writing skills. A Philips 3T scanner measured connectivity during six leveled fMRI reading tasks (subword-letters and sounds, word-word-specific spellings or affixed words, syntax comprehension-with and without homonym foils or with and without affix foils, and text comprehension) and three fMRI writing tasks-writing next letter in alphabet, adding missing letter in word spelling, and planning for composing. The Brain Connectivity Toolbox generated clustering coefficients based on the cingulo-opercular (CO) network; after controlling for multiple comparisons and movement, significant fMRI connectivity clustering coefficients for CO were identified in 8 brain regions bilaterally (cingulate gyrus, superior frontal gyrus, middle frontal gyrus, inferior frontal gyrus, superior temporal gyrus, insula, cingulum-cingulate gyrus, and cingulum-hippocampus). BASC2 Parent Ratings for Adaptivity were correlated with CO clustering coefficients on three reading tasks (letter-sound, word affix judgments and sentence comprehension) and one writing task (writing next letter in alphabet). Before instruction, each behavioral working memory measure (phonology, orthography, morphology, and syntax coding, phonological and orthographic loops for integrating internal language and output codes, and supervisory focused and switching attention) correlated significantly with at least one CO clustering coefficient. After instruction, the patterning of correlations changed with new correlations emerging. Results show that the reading and writing brain's mental government, supported by both CO Adaptive Control and multiple working memory components, had changed in response to instruction during middle childhood/early adolescence.

A Multisite Cluster Randomized Field Trial of Open Court Reading

ERIC Educational Resources Information Center

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

2008-01-01

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

Genotyping in the cloud with Crossbow.

PubMed

Gurtowski, James; Schatz, Michael C; Langmead, Ben

2012-09-01

Crossbow is a scalable, portable, and automatic cloud computing tool for identifying SNPs from high-coverage, short-read resequencing data. It is built on Apache Hadoop, an implementation of the MapReduce software framework. Hadoop allows Crossbow to distribute read alignment and SNP calling subtasks over a cluster of commodity computers. Two robust tools, Bowtie and SOAPsnp, implement the fundamental alignment and variant calling operations respectively, and have demonstrated capabilities within Crossbow of analyzing approximately one billion short reads per hour on a commodity Hadoop cluster with 320 cores. Through protocol examples, this unit will demonstrate the use of Crossbow for identifying variations in three different operating modes: on a Hadoop cluster, on a single computer, and on the Amazon Elastic MapReduce cloud computing service.

Reading in the Writing Classroom.

ERIC Educational Resources Information Center

Fagan, Edward R.

Reading in the writing classroom can be defined as a cluster of arbitrary categories, each with its own effect on the reading/writing process. Given this definition, it can be said that (1) perceptions significantly affect both reading and writing, (2) attitudes are factors in reading and writing, (3) rhetorical triangles are useful in teaching…

Reading Fluency Instruction for Students at Risk for Reading Failure

ERIC Educational Resources Information Center

Ring, Jeremiah J.; Barefoot, Lexie C.; Avrit, Karen J.; Brown, Sasha A.; Black, Jeffrey L.

2013-01-01

The important role of reading fluency in the comprehension and motivation of readers is well documented. Two reading rate intervention programs were compared in a cluster-randomized clinical trial of students who were considered at-risk for reading failure. One program focused instruction at the word level; the second program focused instruction…

Changing Conceptions of Reading: Literacy Learning Instruction. Seventh Yearbook of the American Reading Forum.

ERIC Educational Resources Information Center

Lumpkin, Donavon, Ed.; And Others

Articles in this yearbook contribute to a broad perspective of changing concepts of reading, each focusing attention on an area of major factors exercising current impact on reading and on the education of reading teachers. The articles and their authors are as follows: "Learning from Text" (T. Estes); "Untying the Gordian Knot" (W. Blanton and G.…

Revisiting the Relations between the WJ-IV Measures of Cattell-Horn-Carroll (CHC) Cognitive Abilities and Reading Achievement during the School-Age Years

ERIC Educational Resources Information Center

Cormier, Damien C.; McGrew, Kevin S.; Bulut, Okan; Funamoto, Allyson

2017-01-01

This study examined associations between broad cognitive abilities (Fluid Reasoning [Gf], Short-Term Working Memory [Gwm], Long-Term Storage and Retrieval [Glr], Processing Speed [Gs], Comprehension-Knowledge [Gc], Visual Processing [Gv], and Auditory Processing [Ga]) and reading achievement (Basic Reading Skills, Reading Rate, Reading Fluency,…

Common Core, Commonplaces, and Community in Teaching Reading

ERIC Educational Resources Information Center

Roskos, Kathleen; Neuman, Susan B.

2013-01-01

Joseph Schwab, a curriculum theorist, described four commonplaces, or universals, of teaching: content, students, milieu and teachers. This article considers how the Reading Standards of the ELA-CCSS are shaping these commonplaces in the teaching of reading. The organization of the Reading Standards, for example, focuses on two broad grade bands,…

Storytelling: Learning to Read as Social and Cultural Processes

ERIC Educational Resources Information Center

Bloome, David; Kim, Minjeong

2016-01-01

The argument here is that learning to read for young people in school is not a monolithic process but, rather, consists of multiple and differentiated pathways involving the acquisition of diverse reading practices and cultural ideologies embedded in a broad range of social and cultural contexts. Such a view of learning to read entails…

Applying Piaget's Theory to Reading Instruction.

ERIC Educational Resources Information Center

Heatherly, Anna L.

This paper discusses beginning reading instruction in the light of Piaget's theory, which demands that we think more broadly about the term "where the child is" in terms of his level of thinking, not simply his reading level or reading skill level. Using Piaget's four major developmental stages as the basis, the task of instruction in…

Clustering of reads with alignment-free measures and quality values.

PubMed

Comin, Matteo; Leoni, Andrea; Schimd, Michele

2015-01-01

The data volume generated by Next-Generation Sequencing (NGS) technologies is growing at a pace that is now challenging the storage and data processing capacities of modern computer systems. In this context an important aspect is the reduction of data complexity by collapsing redundant reads in a single cluster to improve the run time, memory requirements, and quality of post-processing steps like assembly and error correction. Several alignment-free measures, based on k-mers counts, have been used to cluster reads. Quality scores produced by NGS platforms are fundamental for various analysis of NGS data like reads mapping and error detection. Moreover future-generation sequencing platforms will produce long reads but with a large number of erroneous bases (up to 15 %). In this scenario it will be fundamental to exploit quality value information within the alignment-free framework. To the best of our knowledge this is the first study that incorporates quality value information and k-mers counts, in the context of alignment-free measures, for the comparison of reads data. Based on this principles, in this paper we present a family of alignment-free measures called D (q) -type. A set of experiments on simulated and real reads data confirms that the new measures are superior to other classical alignment-free statistics, especially when erroneous reads are considered. Also results on de novo assembly and metagenomic reads classification show that the introduction of quality values improves over standard alignment-free measures. These statistics are implemented in a software called QCluster (http://www.dei.unipd.it/~ciompin/main/qcluster.html).

Spinning Gland Transcriptomics from Two Main Clades of Spiders (Order: Araneae) - Insights on Their Molecular, Anatomical and Behavioral Evolution

PubMed Central

Prosdocimi, Francisco; Bittencourt, Daniela; da Silva, Felipe Rodrigues; Kirst, Matias; Motta, Paulo C.; Rech, Elibio L.

2011-01-01

Characterized by distinctive evolutionary adaptations, spiders provide a comprehensive system for evolutionary and developmental studies of anatomical organs, including silk and venom production. Here we performed cDNA sequencing using massively parallel sequencers (454 GS-FLX Titanium) to generate ∼80,000 reads from the spinning gland of Actinopus spp. (infraorder: Mygalomorphae) and Gasteracantha cancriformis (infraorder: Araneomorphae, Orbiculariae clade). Actinopus spp. retains primitive characteristics on web usage and presents a single undifferentiated spinning gland while the orbiculariae spiders have seven differentiated spinning glands and complex patterns of web usage. MIRA, Celera Assembler and CAP3 software were used to cluster NGS reads for each spider. CAP3 unigenes passed through a pipeline for automatic annotation, classification by biological function, and comparative transcriptomics. Genes related to spider silks were manually curated and analyzed. Although a single spidroin gene family was found in Actinopus spp., a vast repertoire of specialized spider silk proteins was encountered in orbiculariae. Astacin-like metalloproteases (meprin subfamily) were shown to be some of the most sampled unigenes and duplicated gene families in G. cancriformis since its evolutionary split from mygalomorphs. Our results confirm that the evolution of the molecular repertoire of silk proteins was accompanied by the (i) anatomical differentiation of spinning glands and (ii) behavioral complexification in the web usage. Finally, a phylogenetic tree was constructed to cluster most of the known spidroins in gene clades. This is the first large-scale, multi-organism transcriptome for spider spinning glands and a first step into a broad understanding of spider web systems biology and evolution. PMID:21738742

Bridging Theory and Practice: Developing Lower-Level Skills in L2 Reading

ERIC Educational Resources Information Center

Kato, Shigeo

2012-01-01

Studies on L2 reading have provided extensive evidence for the significant contribution of lower-level processing skills in learning to read and the critical impact on the overall development of L2 reading of more accurate and fluent connections between three sub-lexical components: phonology, orthography and semantics. The broad consensus among…

Photometry Using Kepler "Superstamps" of Open Clusters NGC 6791 & NGC 6819

NASA Astrophysics Data System (ADS)

Kuehn, Charles A.; Drury, Jason A.; Bellamy, Beau R.; Stello, Dennis; Bedding, Timothy R.; Reed, Mike; Quick, Breanna

2015-09-01

The Kepler space telescope has proven to be a gold mine for the study of variable stars. Usually, Kepler only reads out a handful of pixels around each pre-selected target star, omitting a large number of stars in the Kepler field. Fortunately, for the open clusters NGC 6791 and NGC 6819, Kepler also read out larger "superstamps" which contained complete images of the central region of each cluster. These cluster images can be used to study additional stars in the open clusters that were not originally on Kepler's target list. We discuss our work on using two photometric techniques to analyze these superstamps and present sample results from this project to demonstrate the value of this technique for a wide variety of variable stars.

How To Read Faster. Power of the Printed Word.

ERIC Educational Resources Information Center

Cosby, Bill

Three practical ways to get the meaning from printed words quickly and efficiently are: (1) previewing; (2) skimming; and (3) clustering. Previewing and skimming are ways of getting through a lot of reading material without reading every word. Previewing is especially helpful for heavy reading like long articles, business reports, and nonfiction…

Comparison of Taiwanese and Canadian Students' Metacognitive Awareness of Science Reading, Text, and Strategies

ERIC Educational Resources Information Center

Wang, Jing-Ru; Chen, Shin-Feng; Fang, I.; Chou, Ching-Ting

2014-01-01

This study used a Chinese-language version of the Index of Science Reading Awareness to explore the science reading metacognition and comprehension of Taiwanese students. Structural equation modelling results confirmed the underlying model comprised three clusters of metacognitive knowledge: beliefs and confidence in science reading, knowledge of…

A longitudinal cluster-randomized controlled study on the accumulating effects of individualized literacy instruction on students' reading from first through third grade.

PubMed

Connor, Carol McDonald; Morrison, Frederick J; Fishman, Barry; Crowe, Elizabeth C; Al Otaiba, Stephanie; Schatschneider, Christopher

2013-08-01

Using a longitudinal cluster-randomized controlled design, we examined whether students' reading outcomes differed when they received 1, 2, or 3 years of individualized reading instruction from first through third grade, compared with a treated control group. More than 45% of students came from families living in poverty. Following students, we randomly assigned their teachers each year to deliver individualized reading instruction or a treated control condition intervention focused on mathematics. Students who received individualized reading instruction in all three grades showed the strongest reading skills by the end of third grade compared with those who received fewer years of such instruction. There was inconsistent evidence supporting a sustained first-grade treatment effect: Individualized instruction in first grade was necessary but not sufficient for stronger third-grade reading outcomes. These effects were achieved by regular classroom teachers who received professional development, which indicates that policies that support the use of evidence-based reading instruction and teacher training can yield increased student achievement.

Inference of Markovian properties of molecular sequences from NGS data and applications to comparative genomics.

PubMed

Ren, Jie; Song, Kai; Deng, Minghua; Reinert, Gesine; Cannon, Charles H; Sun, Fengzhu

2016-04-01

Next-generation sequencing (NGS) technologies generate large amounts of short read data for many different organisms. The fact that NGS reads are generally short makes it challenging to assemble the reads and reconstruct the original genome sequence. For clustering genomes using such NGS data, word-count based alignment-free sequence comparison is a promising approach, but for this approach, the underlying expected word counts are essential.A plausible model for this underlying distribution of word counts is given through modeling the DNA sequence as a Markov chain (MC). For single long sequences, efficient statistics are available to estimate the order of MCs and the transition probability matrix for the sequences. As NGS data do not provide a single long sequence, inference methods on Markovian properties of sequences based on single long sequences cannot be directly used for NGS short read data. Here we derive a normal approximation for such word counts. We also show that the traditional Chi-square statistic has an approximate gamma distribution ,: using the Lander-Waterman model for physical mapping. We propose several methods to estimate the order of the MC based on NGS reads and evaluate those using simulations. We illustrate the applications of our results by clustering genomic sequences of several vertebrate and tree species based on NGS reads using alignment-free sequence dissimilarity measures. We find that the estimated order of the MC has a considerable effect on the clustering results ,: and that the clustering results that use a N: MC of the estimated order give a plausible clustering of the species. Our implementation of the statistics developed here is available as R package 'NGS.MC' at http://www-rcf.usc.edu/∼fsun/Programs/NGS-MC/NGS-MC.html fsun@usc.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Predicting writing development in dual language instructional contexts: exploring cross-linguistic relationships.

PubMed

Savage, Robert; Kozakewich, Meagan; Genesee, Fred; Erdos, Caroline; Haigh, Corinne

2017-01-01

This study examined whether decoding and linguistic comprehension abilities, broadly defined by the Simple View of Reading, in grade 1 each uniquely predicted the grade 6 writing performance of English-speaking children (n = 76) who were educated bilingually in both English their first language and French, a second language. Prediction was made from (1) English to English; (2) French to French; and (3) English to French. Results showed that both decoding and linguistic comprehension scores predicted writing accuracy but rarely predicted persuasive writing. Within the linguistic comprehension cluster of tests, Formulating Sentences was a strong consistent within- and between-language predictor of writing accuracy. In practical terms, the present results indicate that early screening for later writing ability using measures of sentence formulation early in students' schooling, in their L1 or L2, can provide greatest predictive power and allow teachers to differentiate instruction in the primary grades. Theoretically, the present results argue that there are correlations between reading-related abilities and writing abilities not only within the same language but also across languages, adding to the growing body of evidence for facilitative cross-linguistic relationships between bilinguals' developing languages. © 2016 John Wiley & Sons Ltd.

Computer Applications in Reading. Third Edition.

ERIC Educational Resources Information Center

Blanchard, Jay S.; And Others

Intended as a reference for researchers, teachers, and administrators, this book chronicles research, programs, and uses of computers in reading. Chapter 1 provides a broad view of computer applications in education, while Chapter 2 provides annotated references for computer based reading and language arts programs for children and adults in…

Deriving physical parameters of unresolved star clusters. V. M 31 PHAT star clusters

NASA Astrophysics Data System (ADS)

de Meulenaer, P.; Stonkutė, R.; Vansevičius, V.

2017-06-01

Context. This study is the fifth of a series that investigates the degeneracy and stochasticity problems present in the determination of physical parameters such as age, mass, extinction, and metallicity of partially resolved or unresolved star cluster populations in external galaxies when using HST broad-band photometry. Aims: In this work we aim to derive parameters of star clusters using models with fixed and free metallicity based on the HST WFC3+ACS photometric system. The method is applied to derive parameters of a subsample of 1363 star clusters in the Andromeda galaxy observed with the HST. Methods: Following Paper III, we derive the star cluster parameters using a large grid of stochastic models that are compared to the six observed integrated broad-band WFC3+ACS magnitudes of star clusters. Results: We show that the age, mass, and extinction of the M 31 star clusters, derived assuming fixed solar metallicity, are in agreement with previous studies. We also demonstrate the ability of the WFC3+ACS photometric system to derive metallicity of star clusters older than 1 Gyr. We show that the metallicity derived using broad-band photometry of 36 massive M 31 star clusters is in good agreement with the metallicity derived using spectroscopy. Table 1 is only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/602/A112

Longitudinal Metagenomic Analysis of Hospital Air Identifies Clinically Relevant Microbes.

PubMed

King, Paula; Pham, Long K; Waltz, Shannon; Sphar, Dan; Yamamoto, Robert T; Conrad, Douglas; Taplitz, Randy; Torriani, Francesca; Forsyth, R Allyn

2016-01-01

We describe the sampling of sixty-three uncultured hospital air samples collected over a six-month period and analysis using shotgun metagenomic sequencing. Our primary goals were to determine the longitudinal metagenomic variability of this environment, identify and characterize genomes of potential pathogens and determine whether they are atypical to the hospital airborne metagenome. Air samples were collected from eight locations which included patient wards, the main lobby and outside. The resulting DNA libraries produced 972 million sequences representing 51 gigabases. Hierarchical clustering of samples by the most abundant 50 microbial orders generated three major nodes which primarily clustered by type of location. Because the indoor locations were longitudinally consistent, episodic relative increases in microbial genomic signatures related to the opportunistic pathogens Aspergillus, Penicillium and Stenotrophomonas were identified as outliers at specific locations. Further analysis of microbial reads specific for Stenotrophomonas maltophilia indicated homology to a sequenced multi-drug resistant clinical strain and we observed broad sequence coverage of resistance genes. We demonstrate that a shotgun metagenomic sequencing approach can be used to characterize the resistance determinants of pathogen genomes that are uncharacteristic for an otherwise consistent hospital air microbial metagenomic profile.

Metagenome assembly through clustering of next-generation sequencing data using protein sequences.

PubMed

Sim, Mikang; Kim, Jaebum

2015-02-01

The study of environmental microbial communities, called metagenomics, has gained a lot of attention because of the recent advances in next-generation sequencing (NGS) technologies. Microbes play a critical role in changing their environments, and the mode of their effect can be solved by investigating metagenomes. However, the difficulty of metagenomes, such as the combination of multiple microbes and different species abundance, makes metagenome assembly tasks more challenging. In this paper, we developed a new metagenome assembly method by utilizing protein sequences, in addition to the NGS read sequences. Our method (i) builds read clusters by using mapping information against available protein sequences, and (ii) creates contig sequences by finding consensus sequences through probabilistic choices from the read clusters. By using simulated NGS read sequences from real microbial genome sequences, we evaluated our method in comparison with four existing assembly programs. We found that our method could generate relatively long and accurate metagenome assemblies, indicating that the idea of using protein sequences, as a guide for the assembly, is promising. Copyright © 2015 Elsevier B.V. All rights reserved.

Toward the Tailoring of Sexual Health Education Messages for Young Women: A Focus on Tourist Experiences.

PubMed

Berdychevsky, Liza

2017-01-01

Perceived anonymity and decreased influence of sexual double standards in tourism provide female travelers with opportunities for sexual experimentation and risk taking. The purpose of this study was (a) to identify the clusters of risk takers among young women based on their perceptions of and motivations for sexual risk taking in tourism and (b) to profile the clusters with respect to the psychological, sexual, demographic, and tourist characteristics. The data were collected through an online survey of 853 women (age in years: M = 23.5, SD = 6.67). Five clusters of sexual risk takers emerged based on their factor-analyzed risk perceptions and motivations. These clusters were interpreted as (a) diversely motivated broad risk perceivers; (b) fun-seeking broad risk perceivers; (c) diversely motivated physical risk perceivers; (d) anonymity- and empowerment-seeking risk disregarders; and (e) unmotivated broad risk perceivers. Women in these clusters differed in their intentions to engage in sexual risk taking in tourism, sensation-seeking propensities, perceptions of tourist characteristics, levels of sexual experience, and demographic backgrounds. Results suggest tailoring sexual health promotion messages based on cluster affiliation, leveraging cluster-specific risk perceptions, motivations, and personal characteristics. This study provides recommendations for individually tailored, context-specific, age-appropriate, and gender-sensitive sexual health education programs.

Exploring the IMF of star clusters: a joint SLUG and LEGUS effort

NASA Astrophysics Data System (ADS)

Ashworth, G.; Fumagalli, M.; Krumholz, M. R.; Adamo, A.; Calzetti, D.; Chandar, R.; Cignoni, M.; Dale, D.; Elmegreen, B. G.; Gallagher, J. S., III; Gouliermis, D. A.; Grasha, K.; Grebel, E. K.; Johnson, K. E.; Lee, J.; Tosi, M.; Wofford, A.

2017-08-01

We present the implementation of a Bayesian formalism within the Stochastically Lighting Up Galaxies (slug) stellar population synthesis code, which is designed to investigate variations in the initial mass function (IMF) of star clusters. By comparing observed cluster photometry to large libraries of clusters simulated with a continuously varying IMF, our formalism yields the posterior probability distribution function (PDF) of the cluster mass, age and extinction, jointly with the parameters describing the IMF. We apply this formalism to a sample of star clusters from the nearby galaxy NGC 628, for which broad-band photometry in five filters is available as part of the Legacy ExtraGalactic UV Survey (LEGUS). After allowing the upper-end slope of the IMF (α3) to vary, we recover PDFs for the mass, age and extinction that are broadly consistent with what is found when assuming an invariant Kroupa IMF. However, the posterior PDF for α3 is very broad due to a strong degeneracy with the cluster mass, and it is found to be sensitive to the choice of priors, particularly on the cluster mass. We find only a modest improvement in the constraining power of α3 when adding Hα photometry from the companion Hα-LEGUS survey. Conversely, Hα photometry significantly improves the age determination, reducing the frequency of multi-modal PDFs. With the aid of mock clusters, we quantify the degeneracy between physical parameters, showing how constraints on the cluster mass that are independent of photometry can be used to pin down the IMF properties of star clusters.

Growth in Early Reading Skills from Kindergarten to Third Grade

ERIC Educational Resources Information Center

Speece, Deborah L.; Ritchey, Kristen D.; Cooper, David H.; Roth, Froma P.; Schatschneider, Christopher

2004-01-01

We examined models of individual change and correlates of change in the growth of reading skills in a sample of 40 children from kindergarten through third grade. A broad range of correlates was examined and included family literacy, oral language, emergent reading, intelligence, spelling, and demographic variables. Individual growth curve…

The Reading-Writing Connection: An Overview and Annotated Bibliography.

ERIC Educational Resources Information Center

Malinowski, Patricia A.

Addressing the need for developmental or remedial reading and writing courses at the college level, this paper provides a broad perspective on the strengthening of such programs for students deficient in these skills. The paper first enumerates various reasons for developing reading-writing courses for pre-college students, then provides evidence…

Global, broad, or specific cognitive differences? Using a MIMIC model to examine differences in CHC abilities in children with learning disabilities.

PubMed

Niileksela, Christopher R; Reynolds, Matthew R

2014-01-01

This study was designed to better understand the relations between learning disabilities and different levels of latent cognitive abilities, including general intelligence (g), broad cognitive abilities, and specific abilities based on the Cattell-Horn-Carroll theory of intelligence (CHC theory). Data from the Differential Ability Scales-Second Edition (DAS-II) were used to create a multiple-indicator multiple cause model to examine the latent mean differences in cognitive abilities between children with and without learning disabilities in reading (LD reading), math (LD math), and reading and writing(LD reading and writing). Statistically significant differences were found in the g factor between the norm group and the LD groups. After controlling for differences in g, the LD reading and LD reading and writing groups showed relatively lower latent processing speed, and the LD math group showed relatively higher latent comprehension-knowledge. There were also some differences in some specific cognitive abilities, including lower scores in spatial relations and numerical facility for the LD math group, and lower scores in visual memory for the LD reading and writing group. These specific mean differences were above and beyond any differences in the latent cognitive factor means.

Positive Reading Attitudes of Low-Income Bilingual Latinos

ERIC Educational Resources Information Center

Bussert-webb, Kathy M.; Zhang, Zhidong

2018-01-01

Many assume low-income, emergent bilingual Latinos have poor reading attitudes. To investigate this issue, we surveyed 1,503 Texas public high school students through stratified cluster sampling to determine their reading attitudes. Most represented Latinos and mixed-race Latinos/Whites who heard Spanish at home and whose mother tongue was…

ALLPATHS: Assembling Large Genomes with Short Illumina Reads

ScienceCinema

Gnerre, Sante

2018-02-06

Sante Gnerre from the Broad Institute speaks on the challenge of developing high quality assemblies of large genomes using short reads at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

Elevation, west portal. Sign on portal reads Watson Mill Bridge, ...

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

Elevation, west portal. Sign on portal reads Watson Mill Bridge, est. 1885. - Watson Mill Bridge, Spanning South Fork Broad River, Watson Mill Road, Watson Mill Bridge State Park, Comer, Madison County, GA

cluster trials v. 1.0

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

Mitchell, John; Castillo, Andrew

2016-09-21

This software contains a set of python modules – input, search, cluster, analysis; these modules read input files containing spatial coordinates and associated attributes which can be used to perform nearest neighbor search (spatial indexing via kdtree), cluster analysis/identification, and calculation of spatial statistics for analysis.

CMOS: Efficient Clustered Data Monitoring in Sensor Networks

PubMed Central

2013-01-01

Tiny and smart sensors enable applications that access a network of hundreds or thousands of sensors. Thus, recently, many researchers have paid attention to wireless sensor networks (WSNs). The limitation of energy is critical since most sensors are battery-powered and it is very difficult to replace batteries in cases that sensor networks are utilized outdoors. Data transmission between sensor nodes needs more energy than computation in a sensor node. In order to reduce the energy consumption of sensors, we present an approximate data gathering technique, called CMOS, based on the Kalman filter. The goal of CMOS is to efficiently obtain the sensor readings within a certain error bound. In our approach, spatially close sensors are grouped as a cluster. Since a cluster header generates approximate readings of member nodes, a user query can be answered efficiently using the cluster headers. In addition, we suggest an energy efficient clustering method to distribute the energy consumption of cluster headers. Our simulation results with synthetic data demonstrate the efficiency and accuracy of our proposed technique. PMID:24459444

CMOS: efficient clustered data monitoring in sensor networks.

PubMed

Min, Jun-Ki

2013-01-01

Tiny and smart sensors enable applications that access a network of hundreds or thousands of sensors. Thus, recently, many researchers have paid attention to wireless sensor networks (WSNs). The limitation of energy is critical since most sensors are battery-powered and it is very difficult to replace batteries in cases that sensor networks are utilized outdoors. Data transmission between sensor nodes needs more energy than computation in a sensor node. In order to reduce the energy consumption of sensors, we present an approximate data gathering technique, called CMOS, based on the Kalman filter. The goal of CMOS is to efficiently obtain the sensor readings within a certain error bound. In our approach, spatially close sensors are grouped as a cluster. Since a cluster header generates approximate readings of member nodes, a user query can be answered efficiently using the cluster headers. In addition, we suggest an energy efficient clustering method to distribute the energy consumption of cluster headers. Our simulation results with synthetic data demonstrate the efficiency and accuracy of our proposed technique.

Cluster formation by allelomimesis in real-world complex adaptive systems

NASA Astrophysics Data System (ADS)

Juanico, Dranreb Earl; Monterola, Christopher; Saloma, Caesar

2005-04-01

Animal and human clusters are complex adaptive systems and many organize in cluster sizes s that obey the frequency distribution D(s)∝s-τ . The exponent τ describes the relative abundance of the cluster sizes in a given system. Data analyses reveal that real-world clusters exhibit a broad spectrum of τ values, 0.7 (tuna fish schools) ⩽τ⩽4.61 (T4 bacteriophage gene family sizes). Allelomimesis is proposed as an underlying mechanism for adaptation that explains the observed broad τ spectrum. Allelomimesis is the tendency of an individual to imitate the actions of others and two cluster systems have different τ values when their component agents display unequal degrees of allelomimetic tendencies. Cluster formation by allelomimesis is shown to be of three general types: namely, blind copying, information-use copying, and noncopying. Allelomimetic adaptation also reveals that the most stable cluster size is formed by three strongly allelomimetic individuals. Our finding is consistent with available field data taken from killer whales and marmots.

76 FR 35379 - Archers Creek, Ribbon Creek, and Broad River; U.S. Marine Corps Recruit Depot, Parris Island, SC...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-17

..., Ribbon Creek, and Broad River; U.S. Marine Corps Recruit Depot, Parris Island, SC; Danger Zone AGENCY... use these portions of Archers Creek, Ribbon Creek, and the Broad River when the rifle and pistol.... 334.480 to read as follows: Sec. 334.480 Archers Creek, Ribbon Creek, and Broad River; U.S. Marine...

"More Than Lessons in How To Read": Burke, Freud, and the Resources of Symbolic Transformation.

ERIC Educational Resources Information Center

Quandahl, Ellen

2001-01-01

Argues that Kenneth Burke used "The Interpretation of Dreams," as well as other works by Sigmund Freud, as a lesson on reading, taking over the central tropes of dreamwork and making them broadly dialectical rather than strictly psychoanalytic terms. Suggests that Freud's "tropology" of dreaming is crucial for reading Burke.…

"Este Libro Es Mi Historia": Mother-Child Interactions during Storybook Reading in a Mexican-American Household.

ERIC Educational Resources Information Center

Manyak, Patrick

A study explored the storybook reading experiences between Ms. Garza and her children. A broad conception of the zone of proximal development, involving use, adaptation, and transformation of culturally shaped tools in the process of shared activity, provides the framework for examining this particular Mexican-American family's reading behavior.…

Notes and Talk: An Examination of a Long-Term English Learner Reading-to-Learn in a High School Biology Classroom

ERIC Educational Resources Information Center

Brooks, Maneka Deanna

2016-01-01

Long-term English learners (LTELs) are frequently characterized as struggling with academic reading in English. This paper moves beyond broad generalizations about this population's English-reading practices to a situated analysis of one "LTEL"--Lizbeth Sanchez's--making meaning in her sophomore biology classroom. This analysis of…

Emergent Writing in Preschoolers: Preliminary Evidence for a Theoretical Framework

ERIC Educational Resources Information Center

Puranik, Cynthia S.; Lonigan, Christopher J.

2014-01-01

Researchers and educators use the term "emergent literacy" to refer to a broad set of skills and attitudes that serve as foundational skills for acquiring success in later reading and writing; however, models of emergent literacy have generally focused on reading and reading-related behaviors. Hence, the primary aim of this study was to…

The transcriptome of the novel dinoflagellate Oxyrrhis marina (Alveolata: Dinophyceae): response to salinity examined by 454 sequencing

PubMed Central

2011-01-01

Background The heterotrophic dinoflagellate Oxyrrhis marina is increasingly studied in experimental, ecological and evolutionary contexts. Its basal phylogenetic position within the dinoflagellates make O. marina useful for understanding the origin of numerous unusual features of the dinoflagellate lineage; its broad distribution has lent O. marina to the study of protist biogeography; and nutritive flexibility and eurytopy have made it a common lab rat for the investigation of physiological responses of marine heterotrophic flagellates. Nevertheless, genome-scale resources for O. marina are scarce. Here we present a 454-based transcriptome survey for this organism. In addition, we assess sequence read abundance, as a proxy for gene expression, in response to salinity, an environmental factor potentially important in determining O. marina spatial distributions. Results Sequencing generated ~57 Mbp of data which assembled into 7, 398 contigs. Approximately 24% of contigs were nominally identified by BLAST. A further clustering of contigs (at ≥ 90% identity) revealed 164 transcript variant clusters, the largest of which (Phosphoribosylaminoimidazole-succinocarboxamide synthase) was composed of 28 variants displaying predominately synonymous variation. In a genomic context, a sample of 5 different genes were demonstrated to occur as tandem repeats, separated by short (~200-340 bp) inter-genic regions. For HSP90 several intergenic variants were detected suggesting a potentially complex genomic arrangement. In response to salinity, analysis of 454 read abundance highlighted 9 and 20 genes over or under expressed at 50 PSU, respectively. However, 454 read abundance and subsequent qPCR validation did not correlate well - suggesting that measures of gene expression via ad hoc analysis of sequence read abundance require careful interpretation. Conclusion Here we indicate that tandem gene arrangements and the occurrence of multiple transcribed gene variants are common and indicate potentially complex genomic arrangements in O. marina. Comparison of the reported data set with existing O. marina and other dinoflagellates ESTs indicates little sequence overlap likely as a result of the relatively limited extent of genome scale sequence data currently available for the dinoflagellates. This is one of the first 454-based transcriptome surveys of an ancestral dinoflagellate taxon and will undoubtedly prove useful for future comparative studies aimed at reconstructing the origin of novel features of the dinoflagellates. PMID:22014029

Mining Student Behavior Patterns in Reading Comprehension Tasks

ERIC Educational Resources Information Center

Peckham, Terry; McCalla, Gord

2012-01-01

Reading comprehension is critical in life-long learning as well as in the workplace. In this paper, we describe how multidimensional k-means clustering combined with Bloom's Taxonomy can be used to determine positive and negative cognitive skill sets with respect to reading comprehension tasks. This information could be used to inform environments…

Reading Profiles for Adults with Low-Literacy: Cluster Analysis with Power and Speeded Measures

ERIC Educational Resources Information Center

Mellard, Daryl F.; Fall, Emily; Mark, Caroline

2009-01-01

The United States' National Institute for Literacy's (NIFL) review of adult literacy instruction research recommended adult education (AE) programs assess underlying reading abilities in order to plan appropriate instruction for low-literacy learners. This study developed adult reading ability groups using measures from power tests and speeded…

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

PubMed

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

2016-06-15

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

Workload Characterization of a Leadership Class Storage Cluster

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

Kim, Youngjae; Gunasekaran, Raghul; Shipman, Galen M

2010-01-01

Understanding workload characteristics is critical for optimizing and improving the performance of current systems and software, and architecting new storage systems based on observed workload patterns. In this paper, we characterize the scientific workloads of the world s fastest HPC (High Performance Computing) storage cluster, Spider, at the Oak Ridge Leadership Computing Facility (OLCF). Spider provides an aggregate bandwidth of over 240 GB/s with over 10 petabytes of RAID 6 formatted capacity. OLCFs flagship petascale simulation platform, Jaguar, and other large HPC clusters, in total over 250 thousands compute cores, depend on Spider for their I/O needs. We characterize themore » system utilization, the demands of reads and writes, idle time, and the distribution of read requests to write requests for the storage system observed over a period of 6 months. From this study we develop synthesized workloads and we show that the read and write I/O bandwidth usage as well as the inter-arrival time of requests can be modeled as a Pareto distribution.« less

Naturally selected hepatitis C virus polymorphisms confer broad neutralizing antibody resistance.

PubMed

Bailey, Justin R; Wasilewski, Lisa N; Snider, Anna E; El-Diwany, Ramy; Osburn, William O; Keck, Zhenyong; Foung, Steven K H; Ray, Stuart C

2015-01-01

For hepatitis C virus (HCV) and other highly variable viruses, broadly neutralizing mAbs are an important guide for vaccine development. The development of resistance to anti-HCV mAbs is poorly understood, in part due to a lack of neutralization testing against diverse, representative panels of HCV variants. Here, we developed a neutralization panel expressing diverse, naturally occurring HCV envelopes (E1E2s) and used this panel to characterize neutralizing breadth and resistance mechanisms of 18 previously described broadly neutralizing anti-HCV human mAbs. The observed mAb resistance could not be attributed to polymorphisms in E1E2 at known mAb-binding residues. Additionally, hierarchical clustering analysis of neutralization resistance patterns revealed relationships between mAbs that were not predicted by prior epitope mapping, identifying 3 distinct neutralization clusters. Using this clustering analysis and envelope sequence data, we identified polymorphisms in E2 that confer resistance to multiple broadly neutralizing mAbs. These polymorphisms, which are not at mAb contact residues, also conferred resistance to neutralization by plasma from HCV-infected subjects. Together, our method of neutralization clustering with sequence analysis reveals that polymorphisms at noncontact residues may be a major immune evasion mechanism for HCV, facilitating viral persistence and presenting a challenge for HCV vaccine development.

CLUSTOM-CLOUD: In-Memory Data Grid-Based Software for Clustering 16S rRNA Sequence Data in the Cloud Environment.

PubMed

Oh, Jeongsu; Choi, Chi-Hwan; Park, Min-Kyu; Kim, Byung Kwon; Hwang, Kyuin; Lee, Sang-Heon; Hong, Soon Gyu; Nasir, Arshan; Cho, Wan-Sup; Kim, Kyung Mo

2016-01-01

High-throughput sequencing can produce hundreds of thousands of 16S rRNA sequence reads corresponding to different organisms present in the environmental samples. Typically, analysis of microbial diversity in bioinformatics starts from pre-processing followed by clustering 16S rRNA reads into relatively fewer operational taxonomic units (OTUs). The OTUs are reliable indicators of microbial diversity and greatly accelerate the downstream analysis time. However, existing hierarchical clustering algorithms that are generally more accurate than greedy heuristic algorithms struggle with large sequence datasets. To keep pace with the rapid rise in sequencing data, we present CLUSTOM-CLOUD, which is the first distributed sequence clustering program based on In-Memory Data Grid (IMDG) technology-a distributed data structure to store all data in the main memory of multiple computing nodes. The IMDG technology helps CLUSTOM-CLOUD to enhance both its capability of handling larger datasets and its computational scalability better than its ancestor, CLUSTOM, while maintaining high accuracy. Clustering speed of CLUSTOM-CLOUD was evaluated on published 16S rRNA human microbiome sequence datasets using the small laboratory cluster (10 nodes) and under the Amazon EC2 cloud-computing environments. Under the laboratory environment, it required only ~3 hours to process dataset of size 200 K reads regardless of the complexity of the human microbiome data. In turn, one million reads were processed in approximately 20, 14, and 11 hours when utilizing 20, 30, and 40 nodes on the Amazon EC2 cloud-computing environment. The running time evaluation indicates that CLUSTOM-CLOUD can handle much larger sequence datasets than CLUSTOM and is also a scalable distributed processing system. The comparative accuracy test using 16S rRNA pyrosequences of a mock community shows that CLUSTOM-CLOUD achieves higher accuracy than DOTUR, mothur, ESPRIT-Tree, UCLUST and Swarm. CLUSTOM-CLOUD is written in JAVA and is freely available at http://clustomcloud.kopri.re.kr.

CLUSTOM-CLOUD: In-Memory Data Grid-Based Software for Clustering 16S rRNA Sequence Data in the Cloud Environment

PubMed Central

Park, Min-Kyu; Kim, Byung Kwon; Hwang, Kyuin; Lee, Sang-Heon; Hong, Soon Gyu; Nasir, Arshan; Cho, Wan-Sup; Kim, Kyung Mo

2016-01-01

High-throughput sequencing can produce hundreds of thousands of 16S rRNA sequence reads corresponding to different organisms present in the environmental samples. Typically, analysis of microbial diversity in bioinformatics starts from pre-processing followed by clustering 16S rRNA reads into relatively fewer operational taxonomic units (OTUs). The OTUs are reliable indicators of microbial diversity and greatly accelerate the downstream analysis time. However, existing hierarchical clustering algorithms that are generally more accurate than greedy heuristic algorithms struggle with large sequence datasets. To keep pace with the rapid rise in sequencing data, we present CLUSTOM-CLOUD, which is the first distributed sequence clustering program based on In-Memory Data Grid (IMDG) technology–a distributed data structure to store all data in the main memory of multiple computing nodes. The IMDG technology helps CLUSTOM-CLOUD to enhance both its capability of handling larger datasets and its computational scalability better than its ancestor, CLUSTOM, while maintaining high accuracy. Clustering speed of CLUSTOM-CLOUD was evaluated on published 16S rRNA human microbiome sequence datasets using the small laboratory cluster (10 nodes) and under the Amazon EC2 cloud-computing environments. Under the laboratory environment, it required only ~3 hours to process dataset of size 200 K reads regardless of the complexity of the human microbiome data. In turn, one million reads were processed in approximately 20, 14, and 11 hours when utilizing 20, 30, and 40 nodes on the Amazon EC2 cloud-computing environment. The running time evaluation indicates that CLUSTOM-CLOUD can handle much larger sequence datasets than CLUSTOM and is also a scalable distributed processing system. The comparative accuracy test using 16S rRNA pyrosequences of a mock community shows that CLUSTOM-CLOUD achieves higher accuracy than DOTUR, mothur, ESPRIT-Tree, UCLUST and Swarm. CLUSTOM-CLOUD is written in JAVA and is freely available at http://clustomcloud.kopri.re.kr. PMID:26954507

Can cognitive models explain brain activation during word and pseudoword reading? A meta-analysis of 36 neuroimaging studies.

PubMed

Taylor, J S H; Rastle, Kathleen; Davis, Matthew H

2013-07-01

Reading in many alphabetic writing systems depends on both item-specific knowledge used to read irregular words (sew, yacht) and generative spelling-sound knowledge used to read pseudowords (tew, yash). Research into the neural basis of these abilities has been directed largely by cognitive accounts proposed by the dual-route cascaded and triangle models of reading. We develop a framework that enables predictions for neural activity to be derived from cognitive models of reading using 2 principles: (a) the extent to which a model component or brain region is engaged by a stimulus and (b) how much effort is exerted in processing that stimulus. To evaluate the derived predictions, we conducted a meta-analysis of 36 neuroimaging studies of reading using the quantitative activation likelihood estimation technique. Reliable clusters of activity are localized during word versus pseudoword and irregular versus regular word reading and demonstrate a great deal of convergence between the functional organization of the reading system put forward by cognitive models and the neural systems activated during reading tasks. Specifically, left-hemisphere activation clusters are revealed reflecting orthographic analysis (occipitotemporal cortex), lexical and/or semantic processing (anterior fusiform, middle temporal gyrus), spelling-sound conversion (inferior parietal cortex), and phonological output resolution (inferior frontal gyrus). Our framework and results establish that cognitive models of reading are relevant for interpreting neuroimaging studies and that neuroscientific studies can provide data relevant for advancing cognitive models. This article thus provides a firm empirical foundation from which to improve integration between cognitive and neural accounts of the reading process. 2013 APA, all rights reserved

Introduction to Vocations Comprehensive Middle School Program: Mathematics Activities.

ERIC Educational Resources Information Center

Gartner, Karen; And Others

Junior high or middle school student activities in mathematics are provided for three entry level occupations in each of fifteen career clusters. The fifteen cluster titles including one of the three occupations for each cluster with an example of a student activity follow: (1) Agri-business and Natural Resources (cropdusting pilot, reading an…

Cluster Analysis of the Luria-Nebraska Neuropsychological Battery with Learning Disabled Adults.

ERIC Educational Resources Information Center

McCue, Michael; And Others

The study reports a cluster analysis of Luria-Nebraska Neuropsychological Battery sources of 25 learning disabled adults. The cluster analysis suggested the presence of three subgroups within this sample, one having high elevations on the Rhythm, Writing, Reading, and Arithmetic Rhythm scales, the second having an extremely high evelation on the…

A Comparison of Seventh Grade Thai Students' Reading Comprehension and Motivation to Read English through Applied Instruction Based on the Genre-Based Approach and the Teacher's Manual

ERIC Educational Resources Information Center

Sawangsamutchai, Yutthasak; Rattanavich, Saowalak

2016-01-01

The objective of this research is to compare the English reading comprehension and motivation to read of seventh grade Thai students taught with applied instruction through the genre-based approach and teachers' manual. A randomized pre-test post-test control group design was used through the cluster random sampling technique. The data were…

Openness to Experience and Night-Sky Watching Interest as Predictors of Reading for Pleasure: Path Analysis of a Mediation Model

ERIC Educational Resources Information Center

Kelly, William E.

2010-01-01

The relation between reading for pleasure, night-sky watching interest, and openness to experience were examined in a sample of 129 college students. Results of a path analysis examining a mediation model indicated that the influence of night-sky interest on reading for pleasure was not mediated by the broad personality domain openness to…

Using Concept Mapping in the Development of a School of Public Health.

PubMed

Hsu, Laura J; Pacheco, Misty Y; Crabtree, Christopher; Maddock, Jay E

2015-07-01

Schools of Public Health have a wide variety of essential stakeholders. Broad input in program planning should assist in ensuring well-developed plans and strong community buy-in. The planning of a school can better address the needs of multiple stakeholders from systematic broad-based input from these constituents using concept mapping. In this study, we used concept mapping to prioritize a set of recommendations from diverse stakeholders to assist in the process of planning a school. A set of statements was generated on essential elements for the proposed school from a broad group of stakeholders. The statements were then distilled into unique themes, which were then rated on importance and feasibility. Cluster maps and pattern matches were used to analyze the ratings. Unique themes (N = 147) were identified and grouped into 12 clusters. Cluster themes included leadership, faculty, culture, school, and curriculum. Pattern matches revealed a significant, modest correlation between importance and feasibility (r = 0.27). A broad range of perspectives was used to identify relevant areas to address in the development of a school.

Clustering: An Interactive Technique to Enhance Learning in Biology.

ERIC Educational Resources Information Center

Ambron, Joanna

1988-01-01

Explains an interdisciplinary approach to biology and writing which increases students' mastery of vocabulary, scientific concepts, creativity, and expression. Describes modifications of the clustering technique used to summarize lectures, integrate reading and understand textbook material. (RT)

A novel polyomavirus from the nasal cavity of a giant panda (Ailuropoda melanoleuca).

PubMed

Qi, Dunwu; Shan, Tongling; Liu, Zhijian; Deng, Xutao; Zhang, Zhihe; Bi, Wenlei; Owens, Jacob Robert; Feng, Feifei; Zheng, Lisong; Huang, Feng; Delwart, Eric; Hou, Rong; Zhang, Wen

2017-10-27

Polyomaviruses infect a wide variety of mammalian and avian hosts with a broad spectrum of outcomes including asymptomatic infection, acute systemic disease, and tumor induction. Viral metagenomics and general PCR methods were used to detected viral nucleic acid in the samples from a diseased and healthy giant pandas. A novel polyomavirus, the giant panda polyomavirus 1 (GPPyV1) from the nasal cavity of a dead giant panda (Ailuropoda melanoleuca) was characterized. The GPPyV1 genome is 5144 bp in size and reveals five putative open-reading frames coding for the classic small and large T antigens in the early region, and the VP1, VP2 and VP3 capsid proteins in the late region. Phylogenetic analyses of the large T antigen of the GPPyV1 indicated GPPyV1 belonged to a putative new species within genus Deltapolyomavirus, clustering with four human polyomavirus species. The GPPyV1 VP1 and VP2 clustered with genus Alphapolyomavirus. Our epidemiologic study indicated that this novel polyomavirus was also detected in nasal swabs and fecal samples collected from captive healthy giant pandas. A novel polyomavirus was detected in giant pandas and its complete genome was characterized, which may cause latency infection in giant pandas.

A Study to Determine the Existence and Characteristics of Distinctively Different Subpopulations Subsumed within the Reading Disabled Population.

ERIC Educational Resources Information Center

Steinberg, Laurie S.

Forty-five third-grade and fourth-grade boys identified by their schools as being both normal in intelligence and severely disabled in reading were given a battery of tests of language, visual perception, silent reading comprehension, and finger agnosia. Three consistent groups of subjects emerged from cluster analyses of the results. One group…

Reading Culture: Best Practice Needed for the Survival of Nigerian Tertiary Institutions

ERIC Educational Resources Information Center

Okecha, Rita Ebele

2012-01-01

This paper examined the importance of reading culture, the role of parents, teachers and government in ensuring that reading culture is imbibed early in life. A sample of eighty (80) students from Ambrose Alli University in their clusters was used for the study. The questionnaire was used to obtain the data which were analysed using frequencies,…

Short-Term Effects of Grade Retention on the Growth Rate of Woodcock-Johnson III Broad Math and Reading Scores

PubMed Central

Wu, Wei; West, Stephen G.; Hughes, Jan N.

2008-01-01

We investigated the effects of grade retention in first grade on the growth of the Woodcock-Johnson broad mathematics and reading scores over three years using linear growth curve modeling on an academically at-risk sample. A large sample (n = 784) of first grade children who were at risk for retention were initially identified based on low literacy scores. Scores representing propensity for retention were constructed based on 72 variables collected in comprehensive baseline testing in first grade. We closely matched 97 pairs of retained and promoted children based on their propensity scores using optimal matching procedures. This procedure adjusted for baseline differences between the retained and promoted children. We found that grade retention decreased the growth rate of mathematical skills but had no significant effect on reading skills. In addition, several potential moderators of the effect of retention on growth of mathematical and reading skills were identified including limited English language proficiency and children's conduct problems. PMID:19083352

Short-term effects of grade retention on the growth rate of Woodcock-Johnson III broad math and reading scores.

PubMed

Wu, Wei; West, Stephen G; Hughes, Jan N

2008-02-01

We investigated the effects of grade retention in first grade on the growth of the Woodcock-Johnson broad mathematics and reading scores over three years using linear growth curve modeling on an academically at-risk sample. A large sample (n=784) of first grade children who were at risk for retention was initially identified based on low literacy scores. Scores representing propensity for retention were constructed based on 72 variables collected in comprehensive baseline testing in first grade. We closely matched 97 pairs of retained and promoted children based on their propensity scores using optimal matching procedures. This procedure adjusted for baseline differences between the retained and promoted children. We found that grade retention decreased the growth rate of mathematical skills but had no significant effect on reading skills. In addition, several potential moderators of the effect of retention on growth of mathematical and reading skills were identified including limited English language proficiency and children's conduct problems.

The Little Mermaid: an icon of woman's condition in patriarchy, and the human condition of castration.

PubMed

Tseëlon, E

1995-10-01

Hans Christian Andersen's story 'The Little Mermaid' is read as a creation myth and a metaphor for woman's condition in patriarchy, broadly conceptualised within a Lacanian framework. In the first part, the psychoanalytic concept of castration (broadly conceptualised as containing any existential severance which forms the basis for sexual difference and subjectivity) is utilised to argue that the myth is about a construction of (mostly female) subjectivity through a series of separations or splits: (1) birth, (2) growing up, (3) desire and (4) death. Birth and death are read as representing real separations. Growing up is read as structured around a symbolic castration of tongue and voice, while desire is read as structured around lack. In the second part the ideological implications of Disney's adaptation of the original for its symbolic status are explored. It is argued that by simplifying and externalising internal complex conflicts in the Andersen story, Disney's version reduces the myth to a fairy tale, and reproduces the ideology of romantic love.

Module Cluster: RTE-001.00 (GSC) Advanced Teaching of Reading.

ERIC Educational Resources Information Center

Brown, Estelle

Several module clusters were developed at Glassboro State College as the result of involvement in the Camden Teacher Corps project. The clusters are the primary mode of instruction in this competency-based teacher education program. Many of these modules are based on a list of teacher competencies developed by members of the Elementary Education…

Subtyping of Children with Developmental Dyslexia via Bootstrap Aggregated Clustering and the Gap Statistic: Comparison with the Double-Deficit Hypothesis

ERIC Educational Resources Information Center

King, Wayne M.; Giess, Sally A.; Lombardino, Linda J.

2007-01-01

Background: The marked degree of heterogeneity in persons with developmental dyslexia has motivated the investigation of possible subtypes. Attempts have proceeded both from theoretical models of reading and the application of unsupervised learning (clustering) methods. Previous cluster analyses of data obtained from persons with reading…

Working Memory, Short-Term Memory, and Reading Disabilities: A Selective Meta-Analysis of the Literature

ERIC Educational Resources Information Center

Swanson, H. Lee; Zheng, Xinhua; Jerman, Olga

2009-01-01

The purpose of the present study was to synthesize research that compares children with and without reading disabilities (RD) on measures of short-term memory (STM) and working memory (WM). Across a broad age, reading, and IQ range, 578 effect sizes (ESs) were computed, yielding a mean ES across studies of -0.89 (SD = 1.03). A total of 257 ESs…

Impacts after One Year of "Healing Classroom" on Children's Reading and Math Skills in DRC: Results from a Cluster Randomized Trial

ERIC Educational Resources Information Center

Aber, J. Lawrence; Torrente, Catalina; Starkey, Leighann; Johnston, Brian; Seidman, Edward; Halpin, Peter; Shivshanker, Anjuli; Weisenhorn, Nina; Annan, Jeannie; Wolf, Sharon

2017-01-01

This article examines the effects of one year of exposure to "Learning to Read in a Healing Classroom" (LRHC) on the reading and math skills of second- to fourth-grade children in the low-income and conflict-affected Democratic Republic of the Congo. LRHC consists of two primary components: teacher resource materials that infuse…

Clandestine Readers: Boys and Girls Going "Undercover" in School Spaces

ERIC Educational Resources Information Center

Scholes, Laura

2015-01-01

Exploring the diverse nature of students' interpretations of their reading experiences, this study moves beyond broad generalizations about boys and girls to consider complexities inherent in the social processes that influence students' engagement in reading. While the study aimed to develop understandings about the ways notions of masculinity…

Anxiety and Response to Reading Intervention among First Grade Students

ERIC Educational Resources Information Center

Grills, Amie E.; Fletcher, Jack M.; Vaughn, Sharon; Barth, Amy; Denton, Carolyn A.; Stuebing, Karla K.

2014-01-01

Background: For school-aged children with reading difficulties, an emerging and important area of investigation concerns determining predictors of intervention response. Previous studies have focused exclusively on cognitive and broadly defined behavioral variables. What has been missing, however, are studies examining anxiety, which is among the…

Lernen Wir Deutsch! Part 10, German: 7535.02.

ERIC Educational Resources Information Center

Dade County Public Schools, Miami, FL.

This course in German prescribes broad goals and performance objectives for the development of cultural awareness, student attitudes, and listening, speaking, writing, and reading skills. The content of the course, based on Units 21 and 22 of "A-LM German: Level 2" and "Reading for Meaning," requires mastery of selected…

Learning from Longitudinal Research in Criminology and the Health Sciences

ERIC Educational Resources Information Center

Vanderstaay, Steven L.

2006-01-01

This article reviews longitudinal research within criminology and the health sciences on the relationship between reading and criminal, delinquent, or antisocial behavior. Longitudinal research in criminology, medicine, and psychology examines the role of reading within a broad set of interactive processes, connecting literacy to public health via…

Is the orthographic/phonological onset a single unit in reading aloud?

PubMed

Mousikou, Petroula; Coltheart, Max; Saunders, Steven; Yen, Lisa

2010-02-01

Two main theories of visual word recognition have been developed regarding the way orthographic units in printed words map onto phonological units in spoken words. One theory suggests that a string of single letters or letter clusters corresponds to a string of phonemes (Coltheart, 1978; Venezky, 1970), while the other suggests that a string of single letters or letter clusters corresponds to coarser phonological units, for example, onsets and rimes (Treiman & Chafetz, 1987). These theoretical assumptions were critical for the development of coding schemes in prominent computational models of word recognition and reading aloud. In a reading-aloud study, we tested whether the human reading system represents the orthographic/phonological onset of printed words and nonwords as single units or as separate letters/phonemes. Our results, which favored a letter and not an onset-coding scheme, were successfully simulated by the dual-route cascaded (DRC) model (Coltheart, Rastle, Perry, Langdon, & Ziegler, 2001). A separate experiment was carried out to further adjudicate between 2 versions of the DRC model.

Partial bisulfite conversion for unique template sequencing

PubMed Central

Kumar, Vijay; Rosenbaum, Julie; Wang, Zihua; Forcier, Talitha; Ronemus, Michael; Wigler, Michael

2018-01-01

Abstract We introduce a new protocol, mutational sequencing or muSeq, which uses sodium bisulfite to randomly deaminate unmethylated cytosines at a fixed and tunable rate. The muSeq protocol marks each initial template molecule with a unique mutation signature that is present in every copy of the template, and in every fragmented copy of a copy. In the sequenced read data, this signature is observed as a unique pattern of C-to-T or G-to-A nucleotide conversions. Clustering reads with the same conversion pattern enables accurate count and long-range assembly of initial template molecules from short-read sequence data. We explore count and low-error sequencing by profiling 135 000 restriction fragments in a PstI representation, demonstrating that muSeq improves copy number inference and significantly reduces sporadic sequencer error. We explore long-range assembly in the context of cDNA, generating contiguous transcript clusters greater than 3,000 bp in length. The muSeq assemblies reveal transcriptional diversity not observable from short-read data alone. PMID:29161423

75 FR 41523 - Delphi Corporation, a Subsidiary of Delphi Holdings, LLC, Including On-Site Leased Workers From...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-16

... workers are engaged in the production of fuel modules, instrument clusters, and air meters. The review... production of instrument clusters, separated from employment on or after March 30, 2006 through May 15, 2009... date established for TA-W-70,988 to read May 16, 2009 for workers producing instrument clusters and...

Using Early Literacy Profiles of Hispanic English Language Learners to Predict Later Reading Achievement

ERIC Educational Resources Information Center

Huang, Francis; Ford, Karen; Invernizzi, Marcia

2011-01-01

Following a cohort of students from fall of kindergarten to spring of first grade, the authors investigated whether the general cluster profiles identified in Burrow et al.'s (2010) study remained consistent over time. If cluster profiles in the fall of kindergarten held, their goal was to investigate the differences between clusters in terms of…

Longitudinal Prediction of 1st and 2nd Grade English Oral Reading Fluency in English Language Learners: Which Early Reading and Language Skills Are Better Predictors?

ERIC Educational Resources Information Center

Solari, Emily J.; Aceves, Terese C.; Higareda, Ignacio; Richards-Tutor, Cara; Filippini, Alexis L.; Gerber, Michael M.; Leafstedt, Jill

2014-01-01

This study investigates the relation between Spanish and English early literacy skills in kindergarten and first grade, and English oral reading fluency at the end of first and second grade in a sample of 150 Spanish-speaking English language learners. Students were assessed in kindergarten, first, and second grades on a broad bilingual academic…

Attributes of quality programs in universities in developing countries: Case studies of two private universities in Ecuador and beyond

NASA Astrophysics Data System (ADS)

Uriguen, Monica I.

This study sought to identify the key attributes of high-quality programs with an eye toward helping developing countries such as Ecuador advance program quality. The dissertation is divided into five chapters: (1) introduction to high-quality programs; (2) literature review of attributes of high-quality programs; (3) grounded theory method (including interviews with 60 individuals) used to identify program attributes that enhance student learning; (4) findings; and (5) conclusions and recommendations. Following are the five clusters and thirteen attributes of high-quality programs that I identified: Cluster One: Highly Qualified Participants: (1) Highly Qualified Faculty, and (2) Highly Qualified Students; Cluster Two: Learning-Centered Cultures: (3) Shared Program Direction Focused on Learning, (4) Real-World Learning Experiences, (5) Reading-Centered Culture, and (6) Supportive and Risk-Taking Environment; Cluster Three: Interactive Teaching and Learning: (7) Integrative learning: Theory with Practice, Self with Subject, and (8) Exclusive Tutoring and Mentoring; Cluster Four: Connected Program Requirements: (9) Planned Breadth and Depth Course Work, and (10) Tangible Products; and Cluster Five: Adequate Resources: (11) Support for Students, (12) Support for Faculty, and (13) Support for Campus Infrastructure. The study was guided by Haworth and Conrad's (1997) "Engagement Theory of High-Quality Programs." Eleven of the attributes of high-quality programs are closely connected to Haworth and Conrad's theory and the other two attributes---real-world learning experiences and a reading-centered culture---make the signature theoretical contributions of the study. Real-world learning experiences encourage the active involvement of stakeholders in designing curricula with real-world learning experiences. The second attribute---a reading-centered culture---has never before been identified in the literature. There are four key differences between Haworth and Conrad's theory and the theory developed in this study. This study identified four attributes that are highly important in Ecuador and, possibly, other developing countries: highly-qualified faculty, highly-qualified students, reading-centered cultures, and real-world learning experiences. If Latin American universities implement the recommendations proposed in the study, particularly Ecuadorian universities, there is a foundation for envisioning a better future for Ecuadorian universities.

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

PubMed

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

2016-04-09

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

Assessment Data-Informed Guidance to Individualize Kindergarten Reading Instruction: Findings from a Cluster-Randomized Control Field Trial

PubMed Central

Al Otaiba, Stephanie; Connor, Carol M; Folsom, Jessica Sidler; Greulich, Luana; Meadows, Jane; Li, Zhi

2010-01-01

The purpose of this cluster-randomized control field trial was to was to examine the extent to which kindergarten teachers could learn a promising instructional strategy, wherein kindergarten reading instruction was differentiated based upon students’ ongoing assessments of language and literacy skills and documented child characteristic by instruction (CXI) interactions; and to test the efficacy of this differentiated reading instruction on the reading outcomes of students from culturally diverse backgrounds. The study involved 14 schools and included 23 treatment (n = 305 students) and 21 contrast teacher (n = 251 students). Teachers in the contrast condition received only a baseline professional development that included a researcher-delivered summer day-long workshop on individualized instruction. Data sources included parent surveys, individually administered child assessments of language, cognitive, and reading skills and videotapes of classroom instruction. Using Hierarchical Multivariate Linear Modeling (HMLM), we found students in treatment classrooms outperformed students in the contrast classrooms on a latent measure of reading skills, comprised of letter-word reading, decoding, alphabetic knowledge, and phonological awareness (ES = .52). Teachers in both conditions provided small group instruction, but teachers in the treatment condition provided significantly more individualized instruction. Our findings extend research on the efficacy of teachers using Individualized Student Instruction to individualize instruction based upon students’ language and literacy skills in first through third grade. Findings are discussed regarding the value of professional development related to differentiating core reading instruction and the challenges of using Response to Intervention approaches to address students’ needs in the areas of reading in general education contexts. PMID:21818158

Curriculum Guide Construction Cluster.

ERIC Educational Resources Information Center

Kline, Ken

As part of a model construction cluster curriculum development project, this guide was developed and implemented in the Beaverton (Oregon) School District. The curriculum guide contains 16 units covering the following topics: introduction to construction jobs; safety and first aid; blueprint readings; basic mathematics; site work; framing; roofing…

Structure-based design of broadly protective group a streptococcal M protein-based vaccines.

PubMed

Dale, James B; Smeesters, Pierre R; Courtney, Harry S; Penfound, Thomas A; Hohn, Claudia M; Smith, Jeremy C; Baudry, Jerome Y

2017-01-03

A major obstacle to the development of broadly protective M protein-based group A streptococcal (GAS) vaccines is the variability within the N-terminal epitopes that evoke potent bactericidal antibodies. The concept of M type-specific protective immune responses has recently been challenged based on the observation that multivalent M protein vaccines elicited cross-reactive bactericidal antibodies against a number of non-vaccine M types of GAS. Additionally, a new "cluster-based" typing system of 175M proteins identified a limited number of clusters containing closely related M proteins. In the current study, we used the emm cluster typing system, in combination with computational structure-based peptide modeling, as a novel approach to the design of potentially broadly protective M protein-based vaccines. M protein sequences (AA 16-50) from the E4 cluster containing 17 emm types of GAS were analyzed using de novo 3-D structure prediction tools and the resulting structures subjected to chemical diversity analysis to identify sequences that were the most representative of the 3-D physicochemical properties of the M peptides in the cluster. Five peptides that spanned the range of physicochemical attributes of all 17 peptides were used to formulate synthetic and recombinant vaccines. Rabbit antisera were assayed for antibodies that cross-reacted with E4 peptides and whole bacteria by ELISA and for bactericidal activity against all E4GAS. The synthetic vaccine rabbit antisera reacted with all 17 E4M peptides and demonstrated bactericidal activity against 15/17 E4GAS. A recombinant hybrid vaccine containing the same E4 peptides also elicited antibodies that cross-reacted with all E4M peptides. Comprehensive studies using structure-based design may result in a broadly protective M peptide vaccine that will elicit cluster-specific and emm type-specific antibody responses against the majority of clinically relevant emm types of GAS. Copyright © 2016 Elsevier Ltd. All rights reserved.

Measuring Standards in Primary English: The Validity of PIRLS--A Response to Mary Hilton

ERIC Educational Resources Information Center

Whetton, Chris; Twist, Liz; Sainsbury, Marian

2007-01-01

Hilton (2006) criticises the PIRLS (Progress in International Reading Literacy Study) tests and the survey conduct, raising questions about the validity of international surveys of reading. Her criticisms fall into four broad areas: cultural validity, methodological issues, construct validity and the survey in England. However, her criticisms are…

Messages Are Everywhere: Reading Perceptions, Habits, and Preferences of Undergraduates

ERIC Educational Resources Information Center

Nadelson, Louis S.; Villagómez, Amanda; Konkol, Danielle; Haskell, Chris; McCulley, Meleah; Campbell, Denise

2013-01-01

As society continues to evolve, so do the methods that are used for text-based communication. Electronic books, mobile phone text messaging, and an array of internet-based texts are now combined with traditional print forms of text, broadly expanding text-based communication. However, student perceptions of reading may still be limited to…

Differential Ability Scales-II Prediction of Reading Performance: Global Scores Are Not Enough

ERIC Educational Resources Information Center

Elliott, Colin D.; Hale, James B.; Fiorello, Catherine A.; Dorvil, Cledicianne; Moldovan, Jaime

2010-01-01

This study investigated the effects of broad cognitive abilities derived from the Cattell-Horn-Carroll (CHC) taxonomy, together with the effect of the general factor ("g"), on Wechsler Individual Achievement Test, Second Edition (WIAT-II) reading achievement. Structural equation modeling (SEM) and commonality analyses were applied to the…

Museum Literacies in Mexico City: Formations of Power, Texts, and Identities

ERIC Educational Resources Information Center

Eakle, A. Jonathan; Chavez-Eakle, Rosa Aurora

2013-01-01

Background/Context: Drawing from critical theory and new literacies studies, the article examines the design and production of museum literacies--broadly conceived to comprise reading spaces and objects, including language texts--and how these practices can be read in terms of political, social, historical, and economic relations. Because museums…

Reading Probe Will Continue on Capitol Hill

ERIC Educational Resources Information Center

Manzo, Kathleen Kennedy

2007-01-01

The recent wrap-up of an intensive, two-year examination of the federal Reading First initiative is not expected to halt debate over the program. Given the broad agreement in seven federal reports that serious problems occurred in the oversight of the program's implementation, the findings have sparked interest on Capitol Hill, as lawmakers…

Reading Minds: Using Literary Resources in Family Therapy.

ERIC Educational Resources Information Center

Burns, Liz

A qualitative enquiry explored, with a range of family therapists and systemic practitioners, the influence they perceive to have been made on their personal and professional lives by the literary texts they have read. Noting that "literary" is broadly interpreted to include poetry, prose, drama/film, song lyrics, etc., the study's aims…

Identity Literacy: Reading and Teaching Texts as Resources for Identity Formation

ERIC Educational Resources Information Center

Schachter, Elli P.; Galili-Schachter, Inbar

2012-01-01

Background/Context: Literacy has been traditionally posited as a primary educational goal. The concept is now understood in the literature as extending way beyond the mere technicalities of proficiency in reading and writing, encompassing a broad range of skills and practices related to comprehension, communication, and the ability to use texts in…

Reading vocabulary in children with and without hearing loss: the roles of task and word type.

PubMed

Coppens, Karien M; Tellings, Agnes; Verhoeven, Ludo; Schreuder, Robert

2013-04-01

To address the problem of low reading comprehension scores among children with hearing impairment, it is necessary to have a better understanding of their reading vocabulary. In this study, the authors investigated whether task and word type differentiate the reading vocabulary knowledge of children with and without severe hearing loss. Seventy-two children with hearing loss and 72 children with normal hearing performed a lexical and a use decision task. Both tasks contained the same 180 words divided over 7 clusters, each cluster containing words with a similar pattern of scores on 8 word properties (word class, frequency, morphological family size, length, age of acquisition, mode of acquisition, imageability, and familiarity). Whereas the children with normal hearing scored better on the 2 tasks than the children with hearing loss, the size of the difference varied depending on the type of task and word. Performance differences between the 2 groups increased as words and tasks became more complex. Despite delays, children with hearing loss showed a similar pattern of vocabulary acquisition as their peers with normal hearing. For the most precise assessment of reading vocabulary possible, a range of tasks and word types should be used.

Adult Developmental Dyslexia in a Shallow Orthography: Are There Subgroups?

ERIC Educational Resources Information Center

Laasonen, Marja; Service, Elisabet; Lipsanen, Jari; Virsu, Veijo

2012-01-01

The existence and stability of subgroups among adult dyslexic readers of a shallow orthography was explored by comparing three different cluster analyses based on previously suggested combinations of two variables. These were oral reading speed versus accuracy, word versus pseudoword reading speed, and phonological awareness versus rapid naming.…

REMOVING COOL CORES AND CENTRAL METALLICITY PEAKS IN GALAXY CLUSTERS WITH POWERFUL ACTIVE GALACTIC NUCLEUS OUTBURSTS

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

Guo Fulai; Mathews, William G., E-mail: fulai@ucolick.or

2010-07-10

Recent X-ray observations of galaxy clusters suggest that cluster populations are bimodally distributed according to central gas entropy and are separated into two distinct classes: cool core (CC) and non-cool core (NCC) clusters. While it is widely accepted that active galactic nucleus (AGN) feedback plays a key role in offsetting radiative losses and maintaining many clusters in the CC state, the origin of NCC clusters is much less clear. At the same time, a handful of extremely powerful AGN outbursts have recently been detected in clusters, with a total energy {approx}10{sup 61}-10{sup 62} erg. Using two-dimensional hydrodynamic simulations, we showmore » that if a large fraction of this energy is deposited near the centers of CC clusters, which is likely common due to dense cores, these AGN outbursts can completely remove CCs, transforming them to NCC clusters. Our model also has interesting implications for cluster abundance profiles, which usually show a central peak in CC systems. Our calculations indicate that during the CC to NCC transformation, AGN outbursts efficiently mix metals in cluster central regions and may even remove central abundance peaks if they are not broad enough. For CC clusters with broad central abundance peaks, AGN outbursts decrease peak abundances, but cannot effectively destroy the peaks. Our model may simultaneously explain the contradictory (possibly bimodal) results of abundance profiles in NCC clusters, some of which are nearly flat, while others have strong central peaks similar to those in CC clusters. A statistical analysis of the sizes of central abundance peaks and their redshift evolution may shed interesting insights on the origin of both types of NCC clusters and the evolution history of thermodynamics and AGN activity in clusters.« less

Transcriptome resources for the frogs Lithobates clamitans and Pseudacris regilla, emphasizing antimicrobial peptides and conserved loci for phylogenetics

USGS Publications Warehouse

Robertson, Laura S.; Cornman, Robert S.

2014-01-01

We developed genetic resources for two North American frogs, Lithobates clamitans and Pseudacris regilla, widespread native amphibians that are potential indicator species of environmental health. For both species, mRNA from multiple tissues was sequenced using 454 technology. De novo assemblies with Mira3 resulted in 50 238 contigs (N50 = 687 bp) and 48 213 contigs (N50 = 686 bp) for L. clamitans and P. regilla, respectively, after clustering with CD-Hit-EST and purging contigs below 200 bp. We performed BLASTX similarity searches against the Xenopus tropicalis proteome and, for predicted ORFs, HMMER similarity searches against the Pfam-A database. Because there is broad interest in amphibian immune factors, we manually annotated putative antimicrobial peptides. To identify conserved regions suitable for amplicon resequencing across a broad taxonomic range, we performed an additional assembly of public short-read transcriptome data derived from two species of the genus Rana and identified reciprocal best TBLASTX matches among all assemblies. Although P. regilla, a hylid frog, is substantially more diverged from the ranid species, we identified 56 genes that were sufficiently conserved to allow nondegenerate primer design with Primer3. In addition to providing a foundation for comparative genomics and quantitative gene expression analysis, our results enable quick development of nuclear sequence-based markers for phylogenetics or population genetics.

The hot interstellar medium in NGC 1399

NASA Technical Reports Server (NTRS)

Loewenstein, Michael; Serlemitsos, Peter J.

1993-01-01

The first two high signal-to-noise, broad bandpass x-ray spectra of elliptical galaxies were obtained with the Broad Band X-ray Telescope (BBXRT) as part of the December 1990 Astro mission. These observations provided unprecedented information on the thermal and metallicity structure of the hot interstellar media in two ellipticals: NGC 1399, the central galaxy in the Fornax cluster, and NGC 4472, the brightest galaxy in the Virgo cluster. The finalized analysis and interpretation of the approximately 4000 sec of BBXRT data on NGC 1399 is reported.

Leveraging long sequencing reads to investigate R-gene clustering and variation in sugar beet

USDA-ARS?s Scientific Manuscript database

Host-pathogen interactions are of prime importance to modern agriculture. Plants utilize various types of resistance genes to mitigate pathogen damage. Identification of the specific gene responsible for a specific resistance can be difficult due to duplication and clustering within R-gene families....

Resolving misassembled cattle immune gene clusters with hierarchical, long read sequencing

USDA-ARS?s Scientific Manuscript database

Animal health is a critical component of productivity; however, current genomic selection genotyping tools have a paucity of genetic markers within key immune gene clusters (IGC) involved in the cattle innate and adaptive immune systems. With diseases such as Bovine Tuberculosis and Johne’s disease ...

50 Years of "Reading Research Quarterly" (1965-2014): Looking Back, Moving Forward

ERIC Educational Resources Information Center

Reutzel, D. Ray; Mohr, Kathleen A. J.

2015-01-01

This issue of "Reading Research Quarterly" ("RRQ") marks the journal's golden (50th) anniversary and 200th published issue. Given this historic milestone, an understanding of the journal's content and impact might inform its readership about the field of literacy broadly and the contribution of "RRQ" in…

Enhancing Emergent Literacy Skills in Inclusive Preschools for Young Children with Visual Impairments

ERIC Educational Resources Information Center

Day, Janice Neibaur; McDonnell, Andrea P.; Heathfield, Lora Tuesday

2005-01-01

Emergent literacy can be viewed as skills that are precursors to later reading and writing (Sulzby & Teale, 1991) or can be more broadly conceptualized as literacy acquisition that occurs along a developmental continuum. Because children with disabilities, such as visual impairments, can be at risk for later reading difficulties, it is critical…

Panda-Monium at the Library: 1995 Arizona Reading Program.

ERIC Educational Resources Information Center

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

Panda bears are the theme of this guide which includes many reading-related activities, crafts, and programs on a broad range of topics, and which can be expanded to other theme approaches such as endangered species, bears in general, and the concept of black and white. The program begins with a general definition and discussion of goals,…

When Tests Dare to Be Progressive: Contradictions in the Classroom.

ERIC Educational Resources Information Center

Willinsky, John; Bobie, Allen

Statewide competency testing as a high school graduation requirement represents a threat to those who encourage broad notions of reading and writing, even when a number of testing innovations in reading and writing mean a step forward in education. In Alberta, Canada, the English exam comes in a non-academic and an academic version, and…

Substance Abuse in the Workingplace: Readings in the Labor-Management Issues.

ERIC Educational Resources Information Center

Hogler, Raymond L., Ed.

This document contains a collection of readings offering a broad overview of the subject of drug and alcohol abuse in the workplace. Included are: (1) "'Miller Time' in Antebellum America: An Historical Appraisal of the Drinking Habits of the Working Class" (John C. McWilliams); (2) "The Impact of Substance Abuse at the…

A Place on the Shelf

ERIC Educational Resources Information Center

Thomas, Devon

2007-01-01

If we read to discover new worlds, we also read to find ourselves. For gays and lesbians, this act of discovery can be problematic: literature has so often excluded them. In the last decades, as gays and lesbians have grown increasingly vocal in the effort to secure their rightful place in society, a broad range of fiction has emerged that…

Reduction of CMOS Image Sensor Read Noise to Enable Photon Counting

PubMed Central

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

2016-01-01

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

A Research Trilogy: American and Mexican Vision Studies.

ERIC Educational Resources Information Center

Hinds, Lillian R.

1983-01-01

Describes three studies relating to visual functioning. Finds that reading retardation is the result of a clustering of factors, of multiple causation. Discusses the need to determine whether or not a student has the necessary lateral and other functional vision skills to maintain sufficient body energy for the demands of the reading task. (MG)

College Textbook Reading Assignments and Class Time Activity

ERIC Educational Resources Information Center

Aagaard, Lola; Conner, Timothy W., II.; Skidmore, Ronald L.

2014-01-01

A convenient cluster sample of 105 undergraduate students at a regional university in the midsouth completed a survey regarding their use of college textbooks, what strategies might increase the likelihood of their reading textbook assignments, and their preference for how class time was used. Descriptive analysis was conducted on the results and…

Partial bisulfite conversion for unique template sequencing.

PubMed

Kumar, Vijay; Rosenbaum, Julie; Wang, Zihua; Forcier, Talitha; Ronemus, Michael; Wigler, Michael; Levy, Dan

2018-01-25

We introduce a new protocol, mutational sequencing or muSeq, which uses sodium bisulfite to randomly deaminate unmethylated cytosines at a fixed and tunable rate. The muSeq protocol marks each initial template molecule with a unique mutation signature that is present in every copy of the template, and in every fragmented copy of a copy. In the sequenced read data, this signature is observed as a unique pattern of C-to-T or G-to-A nucleotide conversions. Clustering reads with the same conversion pattern enables accurate count and long-range assembly of initial template molecules from short-read sequence data. We explore count and low-error sequencing by profiling 135 000 restriction fragments in a PstI representation, demonstrating that muSeq improves copy number inference and significantly reduces sporadic sequencer error. We explore long-range assembly in the context of cDNA, generating contiguous transcript clusters greater than 3,000 bp in length. The muSeq assemblies reveal transcriptional diversity not observable from short-read data alone. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

DistMap: a toolkit for distributed short read mapping on a Hadoop cluster.

PubMed

Pandey, Ram Vinay; Schlötterer, Christian

2013-01-01

With the rapid and steady increase of next generation sequencing data output, the mapping of short reads has become a major data analysis bottleneck. On a single computer, it can take several days to map the vast quantity of reads produced from a single Illumina HiSeq lane. In an attempt to ameliorate this bottleneck we present a new tool, DistMap - a modular, scalable and integrated workflow to map reads in the Hadoop distributed computing framework. DistMap is easy to use, currently supports nine different short read mapping tools and can be run on all Unix-based operating systems. It accepts reads in FASTQ format as input and provides mapped reads in a SAM/BAM format. DistMap supports both paired-end and single-end reads thereby allowing the mapping of read data produced by different sequencing platforms. DistMap is available from http://code.google.com/p/distmap/

DistMap: A Toolkit for Distributed Short Read Mapping on a Hadoop Cluster

PubMed Central

Pandey, Ram Vinay; Schlötterer, Christian

2013-01-01

With the rapid and steady increase of next generation sequencing data output, the mapping of short reads has become a major data analysis bottleneck. On a single computer, it can take several days to map the vast quantity of reads produced from a single Illumina HiSeq lane. In an attempt to ameliorate this bottleneck we present a new tool, DistMap - a modular, scalable and integrated workflow to map reads in the Hadoop distributed computing framework. DistMap is easy to use, currently supports nine different short read mapping tools and can be run on all Unix-based operating systems. It accepts reads in FASTQ format as input and provides mapped reads in a SAM/BAM format. DistMap supports both paired-end and single-end reads thereby allowing the mapping of read data produced by different sequencing platforms. DistMap is available from http://code.google.com/p/distmap/ PMID:24009693

Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics.

PubMed

Weber, Marc; Teeling, Hanno; Huang, Sixing; Waldmann, Jost; Kassabgy, Mariette; Fuchs, Bernhard M; Klindworth, Anna; Klockow, Christine; Wichels, Antje; Gerdts, Gunnar; Amann, Rudolf; Glöckner, Frank Oliver

2011-05-01

Next-generation sequencing (NGS) technologies have enabled the application of broad-scale sequencing in microbial biodiversity and metagenome studies. Biodiversity is usually targeted by classifying 16S ribosomal RNA genes, while metagenomic approaches target metabolic genes. However, both approaches remain isolated, as long as the taxonomic and functional information cannot be interrelated. Techniques like self-organizing maps (SOMs) have been applied to cluster metagenomes into taxon-specific bins in order to link biodiversity with functions, but have not been applied to broad-scale NGS-based metagenomics yet. Here, we provide a novel implementation, demonstrate its potential and practicability, and provide a web-based service for public usage. Evaluation with published data sets mimicking varyingly complex habitats resulted into classification specificities and sensitivities of close to 100% to above 90% from phylum to genus level for assemblies exceeding 8 kb for low and medium complexity data. When applied to five real-world metagenomes of medium complexity from direct pyrosequencing of marine subsurface waters, classifications of assemblies above 2.5 kb were in good agreement with fluorescence in situ hybridizations, indicating that biodiversity was mostly retained within the metagenomes, and confirming high classification specificities. This was validated by two protein-based classifications (PBCs) methods. SOMs were able to retrieve the relevant taxa down to the genus level, while surpassing PBCs in resolution. In order to make the approach accessible to a broad audience, we implemented a feature-rich web-based SOM application named TaxSOM, which is freely available at http://www.megx.net/toolbox/taxsom. TaxSOM can classify reads or assemblies exceeding 2.5 kb with high accuracy and thus assists in linking biodiversity and functions in metagenome studies, which is a precondition to study microbial ecology in a holistic fashion.

First Hard X-Ray Detection of the Non-Thermal Emission Around the Arches Cluster: Morphology and Spectral Studies With NuSTAR

NASA Technical Reports Server (NTRS)

Krivonos, Roman A.; Tomsick, John A.; Bauer, Franz E.; Baganoff, Frederick K.; Barriere, Nicolas M.; Bodaghee, Arash; Boggs, Steven E.; Christensen, Finn E.; Craig, William W.; Grefenstette, Brian W.;

A Chandra Survey of high-redshift (0.7 < z < 0.8) clusters selected in the 100 deg^2 SPT-Pol Deep Field

NASA Astrophysics Data System (ADS)

Garmire, Gordon

2016-09-01

We propose to observe a complete sample of 10 galaxy clusters at 1e14 < M500 < 5e14 and 0.7 < z < 0.8. These systems were selected from the 100 deg^2 deep field of the SPT-Pol SZ survey. This survey are has significant complementary data, including uniform depth ATCA, Herschel, Spitzer, and DES imaging, enabling a wide variety of astrophysical and cosmological studies. This sample complements the successful SPT-XVP survey, which has a broad redshift range and a narrow mass range, by including clusters over a narrow redshift range and broad mass range. These systems are such low mass and high redshift that they will not be detected in the eRosita all-sky survey.

Artful Reading, Spontaneous Design: Integrating Philosophy, English, and Art in a Creativity Cluster

ERIC Educational Resources Information Center

Albrecht, Vera; Comins, Barbara

2014-01-01

This article informs about a multidisciplinary learning community targeting first year students from diverse cultural backgrounds at an urban community college. The combination of English, art, and philosophy of art in a "Creativity Cluster" offers an excellent opportunity for great teaching and learning experiences. Yet, how can faculty…

Construction Cluster Volume I [Wood Structural Framing].

ERIC Educational Resources Information Center

Pennsylvania State Dept. of Justice, Harrisburg. Bureau of Correction.

The document is the first of a series, to be integrated with a G.E.D. program, containing instructional materials at the basic skills level for the construction cluster. It focuses on wood structural framing and contains 20 units: (1) occupational information; (2) blueprint reading; (3) using leveling instruments and laying out building lines; (4)…

Biochemistry in an undergraduate writing-intensive first-year program: Seminar courses in drugs and bioethics.

PubMed

Mills, Kenneth V

2015-01-01

The College of the Holy Cross offers a universal first-year program called Montserrat, in which first-year students participate in a living-learning experience anchored by a yearlong seminar course. The seminar courses are part of a thematic cluster of four to eight courses; students in the cluster live together in a common dormitory and participate in shared co-curricular events designed to engage the entire cluster in intellectual discourse related to the theme. A two-semester seminar within the "Natural World" cluster was offered using biochemical principles as the underlying content. In the first semester, students were introduced to drug design, activity and abuse via student presentations and guided readings on ethnobotany, drug laws, drug use in religion, and prescription drug costs. In the second semester, students discussed primary readings in ethics followed by case study analyses of assisted reproduction technologies, informed consent, genetic privacy, performance enhancing drugs and genetically modified organisms. Student learning outcomes were evaluated via rubrics and a College-facilitated survey. © 2015 The International Union of Biochemistry and Molecular Biology.

Reading in Multilingual Learners of Urdu (L1), English (L2) and Arabic (L3)

ERIC Educational Resources Information Center

Mirza, Amna; Gottardo, Alexandra; Chen, Xi

2017-01-01

The present study examined the language and literacy skills and their relations to each other in multilingual children, who have a broad range of oral and written language proficiency in each language that they "know". Reading and vocabulary skills were tested in 50 Canadian children (ages 6-10 years) who were Urdu-English speakers,…

Current Readings on the Iran-Iraq Conflict and Its Effects on U.S. Foreign Relations and Policy.

ERIC Educational Resources Information Center

El-Sherbini, Magda

1989-01-01

Provides background on the Iran-Iraq conflict and suggests readings dating from 1980 to 1988 in both English and Arabic which are classified under seven broad categories: the roots of the conflict; Iran-United States relations; the American hostage crisis; the Iran-Contra affair; periodicals and indexes; online databases; and bibliographies. (105…

Effectiveness of Structured Teacher Adaptations to an Evidence-Based Summer Literacy Program

ERIC Educational Resources Information Center

Kim, James S.; Burkhauser, Mary A.; Quinn, David M.; Guryan, Jonathan; Kingston, Helen Chen; Aleman, Kirsten

2017-01-01

The authors conducted a cluster-randomized trial to examine the effectiveness of structured teacher adaptations to the implementation of an evidence-based summer literacy program that provided students with (a) books matched to their reading level and interests and (b) teacher scaffolding for summer reading in the form of end-of-year comprehension…

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

ERIC Educational Resources Information Center

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

2018-01-01

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

HUGO: Hierarchical mUlti-reference Genome cOmpression for aligned reads

PubMed Central

Li, Pinghao; Jiang, Xiaoqian; Wang, Shuang; Kim, Jihoon; Xiong, Hongkai; Ohno-Machado, Lucila

2014-01-01

Background and objective Short-read sequencing is becoming the standard of practice for the study of structural variants associated with disease. However, with the growth of sequence data largely surpassing reasonable storage capability, the biomedical community is challenged with the management, transfer, archiving, and storage of sequence data. Methods We developed Hierarchical mUlti-reference Genome cOmpression (HUGO), a novel compression algorithm for aligned reads in the sorted Sequence Alignment/Map (SAM) format. We first aligned short reads against a reference genome and stored exactly mapped reads for compression. For the inexact mapped or unmapped reads, we realigned them against different reference genomes using an adaptive scheme by gradually shortening the read length. Regarding the base quality value, we offer lossy and lossless compression mechanisms. The lossy compression mechanism for the base quality values uses k-means clustering, where a user can adjust the balance between decompression quality and compression rate. The lossless compression can be produced by setting k (the number of clusters) to the number of different quality values. Results The proposed method produced a compression ratio in the range 0.5–0.65, which corresponds to 35–50% storage savings based on experimental datasets. The proposed approach achieved 15% more storage savings over CRAM and comparable compression ratio with Samcomp (CRAM and Samcomp are two of the state-of-the-art genome compression algorithms). The software is freely available at https://sourceforge.net/projects/hierachicaldnac/with a General Public License (GPL) license. Limitation Our method requires having different reference genomes and prolongs the execution time for additional alignments. Conclusions The proposed multi-reference-based compression algorithm for aligned reads outperforms existing single-reference based algorithms. PMID:24368726

Relations between the Woodcock-Johnson III Clinical Clusters and Measures of Executive Functions from the Delis-Kaplan Executive Function System

ERIC Educational Resources Information Center

Floyd, Randy G.; McCormack, Allison C.; Ingram, Elizabeth L.; Davis, Amy E.; Bergeron, Renee; Hamilton, Gloria

2006-01-01

This study examined the convergent relations between scores from four clinical clusters from the Woodcock-Johnson III Tests of Cognitive Abilities (WJ III) and measures of executive functions using a sample of school-aged children and a sample of adults. The WJ III clinical clusters included the Working Memory, Cognitive Fluency, Broad Attention,…

Speaker Clustering for a Mixture of Singing and Reading (Preprint)

DTIC Science & Technology

2012-03-01

diarization [2, 3] which answers the ques- tion of ”who spoke when?” is a combination of speaker segmentation and clustering. Although it is possible to...focuses on speaker clustering, the techniques developed here can be applied to speaker diarization . For the remainder of this paper, the term ”speech...and retrieval,” Proceedings of the IEEE, vol. 88, 2000. [2] S. Tranter and D. Reynolds, “An overview of automatic speaker diarization systems,” IEEE

Concerted Changes in Gene Expression and Cell Physiology of the Cyanobacterium Synechocystis sp. Strain PCC 6803 during Transitions between Nitrogen and Light-Limited Growth1[W][OA

PubMed Central

Aguirre von Wobeser, Eneas; Ibelings, Bas W.; Bok, Jasper; Krasikov, Vladimir; Huisman, Jef; Matthijs, Hans C.P.

2011-01-01

Physiological adaptation and genome-wide expression profiles of the cyanobacterium Synechocystis sp. strain PCC 6803 in response to gradual transitions between nitrogen-limited and light-limited growth conditions were measured in continuous cultures. Transitions induced changes in pigment composition, light absorption coefficient, photosynthetic electron transport, and specific growth rate. Physiological changes were accompanied by reproducible changes in the expression of several hundred open reading frames, genes with functions in photosynthesis and respiration, carbon and nitrogen assimilation, protein synthesis, phosphorus metabolism, and overall regulation of cell function and proliferation. Cluster analysis of the nearly 1,600 regulated open reading frames identified eight clusters, each showing a different temporal response during the transitions. Two large clusters mirrored each other. One cluster included genes involved in photosynthesis, which were up-regulated during light-limited growth but down-regulated during nitrogen-limited growth. Conversely, genes in the other cluster were down-regulated during light-limited growth but up-regulated during nitrogen-limited growth; this cluster included several genes involved in nitrogen uptake and assimilation. These results demonstrate complementary regulation of gene expression for two major metabolic activities of cyanobacteria. Comparison with batch-culture experiments revealed interesting differences in gene expression between batch and continuous culture and illustrates that continuous-culture experiments can pick up subtle changes in cell physiology and gene expression. PMID:21205618

Using Fuzzy Clustering for Real-time Space Flight Safety

NASA Technical Reports Server (NTRS)

Lee, Charles; Haskell, Richard E.; Hanna, Darrin; Alena, Richard L.

2004-01-01

To ensure space flight safety, it is necessary to monitor myriad sensor readings on the ground and in flight. Since a space shuttle has many sensors, monitoring data and drawing conclusions from information contained within the data in real time is challenging. The nature of the information can be critical to the success of the mission and safety of the crew and therefore, must be processed with minimal data-processing time. Data analysis algorithms could be used to synthesize sensor readings and compare data associated with normal operation with the data obtained that contain fault patterns to draw conclusions. Detecting abnormal operation during early stages in the transition from safe to unsafe operation requires a large amount of historical data that can be categorized into different classes (non-risk, risk). Even though the 40 years of shuttle flight program has accumulated volumes of historical data, these data don t comprehensively represent all possible fault patterns since fault patterns are usually unknown before the fault occurs. This paper presents a method that uses a similarity measure between fuzzy clusters to detect possible faults in real time. A clustering technique based on a fuzzy equivalence relation is used to characterize temporal data. Data collected during an initial time period are separated into clusters. These clusters are characterized by their centroids. Clusters formed during subsequent time periods are either merged with an existing cluster or added to the cluster list. The resulting list of cluster centroids, called a cluster group, characterizes the behavior of a particular set of temporal data. The degree to which new clusters formed in a subsequent time period are similar to the cluster group is characterized by a similarity measure, q. This method is applied to downlink data from Columbia flights. The results show that this technique can detect an unexpected fault that has not been present in the training data set.

General and Specific Effects on Cattell-Horn-Carroll Broad Ability Composites: Analysis of the Woodcock-Johnson III Normative Update Cattell-Horn-Carroll Factor Clusters across Development

ERIC Educational Resources Information Center

Floyd, Randy G.; McGrew, Kevin S.; Barry, Amberly; Rafael, Fawziya; Rogers, Joshua

2009-01-01

Many school psychologists focus their interpretation on composite scores from intelligence test batteries designed to measure the broad abilities from the Cattell-Horn-Carroll theory. The purpose of this study was to investigate the general factor loadings and specificity of the broad ability composite scores from one such intelligence test…

Allele Identification for Transcriptome-Based Population Genomics in the Invasive Plant Centaurea solstitialis

PubMed Central

Dlugosch, Katrina M.; Lai, Zhao; Bonin, Aurélie; Hierro, José; Rieseberg, Loren H.

2013-01-01

Transcriptome sequences are becoming more broadly available for multiple individuals of the same species, providing opportunities to derive population genomic information from these datasets. Using the 454 Life Science Genome Sequencer FLX and FLX-Titanium next-generation platforms, we generated 11−430 Mbp of sequence for normalized cDNA for 40 wild genotypes of the invasive plant Centaurea solstitialis, yellow starthistle, from across its worldwide distribution. We examined the impact of sequencing effort on transcriptome recovery and overlap among individuals. To do this, we developed two novel publicly available software pipelines: SnoWhite for read cleaning before assembly, and AllelePipe for clustering of loci and allele identification in assembled datasets with or without a reference genome. AllelePipe is designed specifically for cases in which read depth information is not appropriate or available to assist with disentangling closely related paralogs from allelic variation, as in transcriptome or previously assembled libraries. We find that modest applications of sequencing effort recover most of the novel sequences present in the transcriptome of this species, including single-copy loci and a representative distribution of functional groups. In contrast, the coverage of variable sites, observation of heterozygosity, and overlap among different libraries are all highly dependent on sequencing effort. Nevertheless, the information gained from overlapping regions was informative regarding coarse population structure and variation across our small number of population samples, providing the first genetic evidence in support of hypothesized invasion scenarios. PMID:23390612

Module Cluster: TTP-001.00 (GSC) Reinforcement Principles for Classroom Use.

ERIC Educational Resources Information Center

Brent, George

The purpose of this module cluster is to enable students to define the basic operant terms, to state the basic operant principles, to read operant measurement charts, and to use operant principles in elementary classrooms with both social and academic behaviors. It is intended for use by teacher education students with the cooperation of an…

Genome Sequence of JangDynasty, a Newly Isolated Mycobacteriophage

PubMed Central

Jang, Casey; Kalaj, Nancy; Hwang, Brian; Hughes, Lorelei; Yang, Connie; Pak, Thomas; Kim, John; Han, Dong Yoon; Tedjakusnadi, Jason; Fernandez, Nicholas; Dean, Natasha; Muthiah, Arun; Sutter, Nathaniel B.

2018-01-01

ABSTRACT JangDynasty is a bacteriophage that infects Mycobacterium smegmatis mc2155. It has a genome length of 70,883 bp, with 124 predicted open reading frames (ORFs), 42 of which have known functions. JangDynasty belongs to cluster O, and like other cluster O phages, it is a siphovirus with a prolate capsid. PMID:29798914

A Chandra Survey of low-mass clusters at 0.8 < z < 0.9 selected in the 100 deg^2 SPT-Pol Deep Field

NASA Astrophysics Data System (ADS)

Kraft, Ralph

2016-09-01

We propose to observe a complete sample of 4 galaxy clusters at 1e14 < M500 < 3e14 and 0.8 < z < 0.9. These systems were selected from the 100 deg^2 deep field of the SPT-Pol SZ survey. This survey are has significant complementary data, including uniform depth ATCA, Herschel, Spitzer, and DES imaging, enabling a wide variety of astrophysical and cosmological studies. This sample complements the successful SPT-XVP survey, which has a broad redshift range and a narrow mass range, by including clusters over a narrow redshift range and broad mass range. These systems are such low mass and high redshift that they will not be detected in the eRosita all-sky survey.

A Chandra Survey of low-mass clusters at 0.7 < z < 0.8 selected in the 100 deg^2 SPT-Pol Deep Field

NASA Astrophysics Data System (ADS)

Kraft, Ralph

2016-09-01

We propose to observe a complete sample of 4 galaxy clusters at 1e14 < M500 < 3e14 and 0.7 < z < 0.8. These systems were selected from the 100 deg^2 deep field of the SPT-Pol SZ survey. This survey are has significant complementary data, including uniform depth ATCA, Herschel, Spitzer, and DES imaging, enabling a wide variety of astrophysical and cosmological studies. This sample complements the successful SPT-XVP survey, which has a broad redshift range and a narrow mass range, by including clusters over a narrow redshift range and broad mass range. These systems are such low mass and high redshift that they will not be detected in the eRosita all-sky survey.

Full genome analysis of bovine astrovirus from fecal samples of cattle in Japan: identification of possible interspecies transmission of bovine astrovirus.

PubMed

Nagai, Makoto; Omatsu, Tsutomu; Aoki, Hiroshi; Otomaru, Konosuke; Uto, Takehiko; Koizumi, Motoya; Minami-Fukuda, Fujiko; Takai, Hikaru; Murakami, Toshiaki; Masuda, Tsuneyuki; Yamasato, Hiroshi; Shiokawa, Mai; Tsuchiaka, Shinobu; Naoi, Yuki; Sano, Kaori; Okazaki, Sachiko; Katayama, Yukie; Oba, Mami; Furuya, Tetsuya; Shirai, Junsuke; Mizutani, Tetsuya

2015-10-01

A viral metagenomics approach was used to investigate fecal samples of Japanese calves with and without diarrhea. Of the different viral pathogens detected, read counts gave nearly complete astrovirus-related RNA sequences in 15 of the 146 fecal samples collected in three distinct areas (Hokkaido, Ishikawa, and Kagoshima Prefectures) between 2009 and 2015. Due to the lack of genetic information about bovine astroviruses (BoAstVs) in Japan, these sequences were analyzed in this study. Nine of the 15 Japanese BoAstVs were closely related to Chinese BoAstVs and clustered into a lineage (tentatively named lineage 1) in all phylogenetic trees. Three of 15 strains were phylogenetically separate from lineage 1, showing low sequence identities, and clustered instead with an American strain isolated from cattle with respiratory disease (tentatively named lineage 2). Interestingly, two of 15 strains clustered with lineage 1 in the open reading frame (ORF)1a and ORF1b regions, while they clustered with lineage 2 in the ORF2 region. Remarkably, one of 15 strains exhibited low amino acid sequence similarity to other BoAstVs and was clustered separately with porcine astrovirus type 5 in all trees, and ovine astrovirus in the ORF2 region, suggesting past interspecies transmission.

Measurement of lengths and angles by means of a photoelectric direct reading-off microscope

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

Priver, L.S.

1995-11-01

We consider the measurement of lengths and angles over a broad range with error amounting to fractions of a micrometer or angular second using a newly designed mockup of a photoelectric direct reading-off microscope. The microscope implements a pulse-position method of transforming information through application of a scanner in the form of a rotating polyhedral mirror.

Instructional Practices for Students with Behavioral Disorders: Strategies for Reading, Writing, and Math. What Works for Special-Needs Learners

ERIC Educational Resources Information Center

Nelson, J. Ron; Benner, Gregory J.; Mooney, Paul

2008-01-01

Presenting a broad range of instructional programs and practices that are proven effective for students with behavioral disorders, this is the first resource of its kind for K-3 teachers and special educators. Described are clear-cut strategies for promoting mastery and fluency in early reading, writing, and math, while tailoring instruction to…

Four-year-old outcomes of a universal infant-toddler shared reading intervention: the let's read trial.

PubMed

Goldfeld, Sharon; Quach, Jon; Nicholls, Ruth; Reilly, Sheena; Ukoumunne, Obioha C; Wake, Melissa

2012-11-01

To determine the emergent literacy and language effects of a low-intensity literacy promotion program (Let's Read) provided via universal well-child services to parents during the first 4 years of their child's life. Population-based, cluster randomized controlled trial performed between March 1, 2006, and December 10, 2010. Maternal and child health centers (clusters) in 5 relatively disadvantaged local government areas in Melbourne, Australia. All parents attending their 4-week well-child appointments in participating centers were invited to take part in the study. The Let's Read program was delivered at 4, 12, 18, and 42 months during universal well-child care visits. Child emergent literacy skills (intrasyllabic, phonemic, and sound/letter knowledge) and language (core, receptive, and expressive), measured at 4 years of age. A total of 630 parents participated, with 365 children in 32 intervention clusters and 265 children in 33 control clusters; 563 children (89.4%) were retained in the study to 4 years of age. The adjusted mean differences (intervention minus control) for emergent literacy was 0.2 (95% CI, -0.2 to 0.6; P = .29) for intrasyllabic units, 0.05 (95% CI, -0.4 to 0.5; P = .85) for phonemic awareness, and 0.1 (95% CI, -1.5 to 1.6; P = .92) for letter knowledge. For language, the differences were 1.6 (95% CI, -1.1 to 4.3; P = .25) for core, 0.8 (95% CI, -2.0 to 3.7; P = .56) for receptive, and 1.4 (95% CI, -1.4 to 4.2; P = .32) for expressive scores. This population-wide primary care literacy promotion and book distribution program provided neither the anticipated benefits to literacy and language nor enhanced uptake of literacy activities at 4 years of age, even when targeted to relatively disadvantaged areas. isrctn.org Identifier: ISRCTN04602902.

Reading comprehension in Parkinson's disease.

PubMed

Murray, Laura L; Rutledge, Stefanie

2014-05-01

Although individuals with Parkinson's disease (PD) self-report reading problems and experience difficulties in cognitive-linguistic functions that support discourse-level reading, prior research has primarily focused on sentence-level processing and auditory comprehension. Accordingly, the authors investigated the presence and nature of reading comprehension in PD, hypothesizing that (a) individuals with PD would display impaired accuracy and/or speed on reading comprehension tests and (b) reading performances would be correlated with cognitive test results. Eleven adults with PD and 9 age- and education-matched control participants completed tests that evaluated reading comprehension; general language and cognitive abilities; and aspects of attention, memory, and executive functioning. The PD group obtained significantly lower scores on several, but not all, reading comprehension, language, and cognitive measures. Memory, language, and disease severity were significantly correlated with reading comprehension for the PD group. Individuals in the early stages of PD without dementia or broad cognitive deficits can display reading comprehension difficulties, particularly for high- versus basic-level reading tasks. These reading difficulties are most closely related to memory, high-level language, and PD symptom severity status. The findings warrant additional research to delineate further the types and nature of reading comprehension impairments experienced by individuals with PD.

Examining the Efficacy of a Multitiered Intervention for At-Risk Readers in Grade 1

ERIC Educational Resources Information Center

Smith, Jean Louise M.; Nelson, Nancy J.; Fien, Hank; Smolkowski, Keith; Kosty, Derek; Baker, Scott K.

2016-01-01

This study reports the results of a cluster RCT evaluating the impact of Enhanced Core Reading Instruction on reading achievement of grade 1 at-risk readers. Forty-four elementary schools, blocked by district, were randomly assigned to condition. In both conditions, at-risk readers received 90 minutes of whole-group instruction (Tier 1) plus an…

Phonological Awareness Errors Mirror Underlying Phonological Representations: Evidence from Hebrew L1-English L2 Adults

ERIC Educational Resources Information Center

Russak, Susie; Saiegh-Haddad, Elinor

2017-01-01

This article examines the effect of phonological context (singleton vs. clustered consonants) on full phoneme segmentation in Hebrew first language (L1) and in English second language (L2) among typically reading adults (TR) and adults with reading disability (RD) (n = 30 per group), using quantitative analysis and a fine-grained analysis of…

T & I--Drafting, Reading the Architect's Scale. Kit No. 16. Instructor's Manual [and] Student Learning Activity Guide.

ERIC Educational Resources Information Center

Jones, Philip

An instructor's manual and student activity guide on reading the architect's scale and the metric scale are provided in this set of prevocational education materials which focuses on the vocational area of trade and industry (drafting). (This set of materials is one of ninety-two prevocational education sets arranged around a cluster of seven…

Speech reading and learning to read: a comparison of 8-year-old profoundly deaf children with good and poor reading ability.

PubMed

Harris, Margaret; Moreno, Constanza

2006-01-01

Nine children with severe-profound prelingual hearing loss and single-word reading scores not more than 10 months behind chronological age (Good Readers) were matched with 9 children whose reading lag was at least 15 months (Poor Readers). Good Readers had significantly higher spelling and reading comprehension scores. They produced significantly more phonetic errors (indicating the use of phonological coding) and more often correctly represented the number of syllables in spelling than Poor Readers. They also scored more highly on orthographic awareness and were better at speech reading. Speech intelligibility was the same in the two groups. Cluster analysis revealed that only three Good Readers showed strong evidence of phonetic coding in spelling although seven had good representation of syllables; only four had high orthographic awareness scores. However, all 9 children were good speech readers, suggesting that a phonological code derived through speech reading may underpin reading success for deaf children.

A New Measure of Reading Habit: Going Beyond Behavioral Frequency

PubMed Central

Schmidt, Fabian T. C.; Retelsdorf, Jan

2016-01-01

Reading habit is considered an important construct in reading research as it serves as a significant predictor of reading achievement. However, there is still no consensus on how to best measure reading habit. In recent research, it has mostly been measured as behavioral frequency; this approach neglects the fact that repeated behavior does not cover the broad content of habitual behavior—such as automaticity and the expression of one’s identity. In this study, we aimed to adapt a 10-item scale on the basis of the Self-Report Habit Index by Verplanken and Orbell (2003) that is comprehensive but still economical for measuring reading habit. It was tested by drawing on a sample of N = 1,418 upper secondary school students. The scale showed good psychometric properties and the internal and external validity was supported. Moreover, the scale predicted reading achievement and decoding speed over and above reading frequency. The implications of an elaborated but still economical way of measuring reading habit are discussed giving new impetus on research on reading habit, challenging conventional approaches of traditional measures. PMID:27660619

Reading literary fiction improves theory of mind.

PubMed

Kidd, David Comer; Castano, Emanuele

2013-10-18

Understanding others' mental states is a crucial skill that enables the complex social relationships that characterize human societies. Yet little research has investigated what fosters this skill, which is known as Theory of Mind (ToM), in adults. We present five experiments showing that reading literary fiction led to better performance on tests of affective ToM (experiments 1 to 5) and cognitive ToM (experiments 4 and 5) compared with reading nonfiction (experiments 1), popular fiction (experiments 2 to 5), or nothing at all (experiments 2 and 5). Specifically, these results show that reading literary fiction temporarily enhances ToM. More broadly, they suggest that ToM may be influenced by engagement with works of art.

Parental Education Moderates Genetic Influences on Reading Disability

PubMed Central

Friend, Angela; DeFries, John C.; Olson, Richard K.

2008-01-01

Environmental moderation of the level of genetic influence on children's reading disabilities (RD) was explored in a sample of 545 identical and fraternal twins (mean age = 11.5 years). Parents' years of education, which are correlated with a broad range of environmental factors related to reading development, were significantly related to the level of genetic influence on reading disability (t = 3.23, Prep = .99). Genetic influence was higher and environmental influence was lower among children with higher compared to children with lower parent education. We discuss the implications of these results for behavior- and molecular-genetic research, for the diagnosis and remediation of RD, and for policy in public education. PMID:19076484

Business Education: The Creative Approaches of Three Small High Schools.

ERIC Educational Resources Information Center

Rawers, Lois J.

1983-01-01

To encourage the schools to train students in broad and flexible occupational competencies rather than specific job skills, the Oregon Department of Education has promoted the cluster concept of vocational education. Of the 14 occupational clusters identified as being economically significant in Oregon, business competencies in the accounting,…

Next Generation Distributed Computing for Cancer Research

PubMed Central

Agarwal, Pankaj; Owzar, Kouros

2014-01-01

Advances in next generation sequencing (NGS) and mass spectrometry (MS) technologies have provided many new opportunities and angles for extending the scope of translational cancer research while creating tremendous challenges in data management and analysis. The resulting informatics challenge is invariably not amenable to the use of traditional computing models. Recent advances in scalable computing and associated infrastructure, particularly distributed computing for Big Data, can provide solutions for addressing these challenges. In this review, the next generation of distributed computing technologies that can address these informatics problems is described from the perspective of three key components of a computational platform, namely computing, data storage and management, and networking. A broad overview of scalable computing is provided to set the context for a detailed description of Hadoop, a technology that is being rapidly adopted for large-scale distributed computing. A proof-of-concept Hadoop cluster, set up for performance benchmarking of NGS read alignment, is described as an example of how to work with Hadoop. Finally, Hadoop is compared with a number of other current technologies for distributed computing. PMID:25983539

Next generation distributed computing for cancer research.

PubMed

Agarwal, Pankaj; Owzar, Kouros

2014-01-01

Advances in next generation sequencing (NGS) and mass spectrometry (MS) technologies have provided many new opportunities and angles for extending the scope of translational cancer research while creating tremendous challenges in data management and analysis. The resulting informatics challenge is invariably not amenable to the use of traditional computing models. Recent advances in scalable computing and associated infrastructure, particularly distributed computing for Big Data, can provide solutions for addressing these challenges. In this review, the next generation of distributed computing technologies that can address these informatics problems is described from the perspective of three key components of a computational platform, namely computing, data storage and management, and networking. A broad overview of scalable computing is provided to set the context for a detailed description of Hadoop, a technology that is being rapidly adopted for large-scale distributed computing. A proof-of-concept Hadoop cluster, set up for performance benchmarking of NGS read alignment, is described as an example of how to work with Hadoop. Finally, Hadoop is compared with a number of other current technologies for distributed computing.

QSdpR: Viral quasispecies reconstruction via correlation clustering.

PubMed

Barik, Somsubhra; Das, Shreepriya; Vikalo, Haris

2017-12-19

RNA viruses are characterized by high mutation rates that give rise to populations of closely related genomes, known as viral quasispecies. Underlying heterogeneity enables the quasispecies to adapt to changing conditions and proliferate over the course of an infection. Determining genetic diversity of a virus (i.e., inferring haplotypes and their proportions in the population) is essential for understanding its mutation patterns, and for effective drug developments. Here, we present QSdpR, a method and software for the reconstruction of quasispecies from short sequencing reads. The reconstruction is achieved by solving a correlation clustering problem on a read-similarity graph and the results of the clustering are used to estimate frequencies of sub-species; the number of sub-species is determined using pseudo F index. Extensive tests on both synthetic datasets and experimental HIV-1 and Zika virus data demonstrate that QSdpR compares favorably to existing methods in terms of various performance metrics. Copyright © 2018 Elsevier Inc. All rights reserved.

Reading to deaf children who sign: a response to Williams (2012) and suggestions for future research.

PubMed

Andrews, Jean F

2012-01-01

A commentary on Williams's (2012) invited article on the use of adapted vocabulary learning interventions focuses on three areas: (a) Vocabulary interventions with storybook reading originally designed for hearing children can be adapted for deaf children. (b) Teachers are invited to reflect on how the read-aloud process in English differs from the read-aloud process in sign. (b) Teachers are asked to consider adding drawing and writing activities to reading lessons to show young deaf readers how reading and writing are reciprocal processes. The emergent literacy theory is used, as it informs and drives instructional vocabulary teaching practices for deaf children in preschool, kindergarten, and first grade. The emergent literacy theory broadly captures cognitive, social, perceptual, and linguistic understandings of how young signing deaf children acquire both English word recognition abilities and vocabulary knowledge, among other important prereading concepts.

Juvenile Psychopathic Personality Traits are Associated with Poor Reading Achievement

PubMed Central

DeLisi, Matt; Beaver, Kevin M.; Wexler, Jade; Barth, Amy; Fletcher, Jack

2011-01-01

The current study sought to further the understanding of the linkage between maladaptive behavior and cognitive problems by examining the relations between psychopathic personality traits and reading comprehension performance. Data were derived from a study of 432 predominately African-American and Hispanic middle-school students. Dependent variables consisted of three measures of reading comprehension. Psychopathy measures included the Inventory of Callous-Unemotional traits (ICU—teacher rated) and the self-reported Youth Psychopathic traits Inventory (YPI). Findings from regression models indicated that self-report and teacher ratings of psychopathy were statistically significant inverse predictors of reading performance. Specifically, affective facets of psychopathy were potent predictors of reading comprehension over and above ADHD, IQ, and an impulsivity component of psychopathy. Study results extend the utility of psychopathy construct generally and affective traits specifically to reading achievement, which has broad implications. Findings are discussed with respect to future research and prevention. PMID:20957434

Genome Sequence of JangDynasty, a Newly Isolated Mycobacteriophage.

PubMed

Jang, Casey; Kalaj, Nancy; Hwang, Brian; Hughes, Lorelei; Yang, Connie; Pak, Thomas; Kim, John; Han, Dong Yoon; Tedjakusnadi, Jason; Fernandez, Nicholas; Dean, Natasha; Muthiah, Arun; Sutter, Nathaniel B; Diaz, Arturo

2018-05-24

JangDynasty is a bacteriophage that infects Mycobacterium smegmatis mc 2 155. It has a genome length of 70,883 bp, with 124 predicted open reading frames (ORFs), 42 of which have known functions. JangDynasty belongs to cluster O, and like other cluster O phages, it is a siphovirus with a prolate capsid. Copyright © 2018 Jang et al.

Capable Reader Program: Language Arts. Career Education Resource Worksheets for Units A1 through B4. Bulletin No. 336.

ERIC Educational Resources Information Center

Long, Sandra; And Others

Part of a curriculum series for academically gifted elementary students in the area of reading, the guide presents worksheets for a combined career education and critical reading curriculum for the sixth grade. Among the five career education objectives are the exploration of 15 career clusters and knowledge of the nine elements of career…

Investigation of correlation classification techniques

NASA Technical Reports Server (NTRS)

Haskell, R. E.

1975-01-01

A two-step classification algorithm for processing multispectral scanner data was developed and tested. The first step is a single pass clustering algorithm that assigns each pixel, based on its spectral signature, to a particular cluster. The output of that step is a cluster tape in which a single integer is associated with each pixel. The cluster tape is used as the input to the second step, where ground truth information is used to classify each cluster using an iterative method of potentials. Once the clusters have been assigned to classes the cluster tape is read pixel-by-pixel and an output tape is produced in which each pixel is assigned to its proper class. In addition to the digital classification programs, a method of using correlation clustering to process multispectral scanner data in real time by means of an interactive color video display is also described.

Educational Policy and the Drug Problem--A Redistributive Politics Issue

ERIC Educational Resources Information Center

Caliguri, Joseph P.

1975-01-01

The drug problem exists as a cluster of problems affecting broad interests or groups. The issues are redistributive in that everything relates to everything else. It seems apparent that a cluster of policies and programs need development as well as genuine citizen participation in the formulation of these policies. (Author)

What’s the Story? The Tale of Reading Fluency Told at Speed

PubMed Central

Benjamin, Christopher F. A.; Gaab, Nadine

2012-01-01

Fluent readers process written text rapidly and accurately, and comprehend what they read. Historically, reading fluency has been modeled as the product of discrete skills such as single word decoding. More recent conceptualizations emphasize that fluent reading is the product of competency in, and the coordination of, multiple cognitive sub-skills (a multi-componential view). In this study, we examined how the pattern of activation in core reading regions changes as the ability to read fluently is manipulated through reading speed. We evaluated 13 right-handed adults with a novel fMRI task assessing fluent sentence reading and lower-order letter reading at each participant’s normal fluent reading speed, as well as constrained (slowed) and accelerated reading speeds. Comparing fluent reading conditions with rest revealed regions including bilateral occipito-fusiform, left middle temporal, and inferior frontal gyral clusters across reading speeds. The selectivity of these regions’ responses to fluent sentence reading was shown by comparison with the letter reading task. Region of interest analyses showed that at constrained and accelerated speeds these regions responded significantly more to fluent sentence reading. Critically, as reading speed increased, activation increased in a single reading-related region: occipital/fusiform cortex (left > right). These results demonstrate that while brain regions engaged in reading respond selectively during fluent reading, these regions respond differently as the ability to read fluently is manipulated. Implications for our understanding of reading fluency, reading development, and reading disorders are discussed. PMID:21954000

Reading Disorders: Pro-Eating Disorder Rhetoric and Anorexia Life-Writing.

PubMed

Seaber, Emma

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

Reading Disorders:

PubMed Central

Seaber, Emma

2016-01-01

This article explores the relationship between eating disorders and reading behaviors, arguing that there is a meaningful difference in a minority of readers' approach to and understanding of anorexia life-writing, and of literary texts more broadly. To illuminate this distinction, this article begins by considering the reported deleterious influence of Marya Hornbacher’s anorexia memoir, Wasted, elaborating the ways Hornbacher offers a positive presentation of anorexia nervosa that may, intentionally or not, induce certain readers to “try it” themselves. This is followed by an exploration of how Hornbacher’s own reading praxis is implicated in a discursive feedback loop around anorexia narratives. It concludes with a discussion of disordered reading attitudes in relation to the emergence of the “pro-anorexia” phenomenon. PMID:28569728

Spiral waves characterization: Implications for an automated cardiodynamic tissue characterization.

PubMed

Alagoz, Celal; Cohen, Andrew R; Frisch, Daniel R; Tunç, Birkan; Phatharodom, Saran; Guez, Allon

2018-07-01

Spiral waves are phenomena observed in cardiac tissue especially during fibrillatory activities. Spiral waves are revealed through in-vivo and in-vitro studies using high density mapping that requires special experimental setup. Also, in-silico spiral wave analysis and classification is performed using membrane potentials from entire tissue. In this study, we report a characterization approach that identifies spiral wave behaviors using intracardiac electrogram (EGM) readings obtained with commonly used multipolar diagnostic catheters that perform localized but high-resolution readings. Specifically, the algorithm is designed to distinguish between stationary, meandering, and break-up rotors. The clustering and classification algorithms are tested on simulated data produced using a phenomenological 2D model of cardiac propagation. For EGM measurements, unipolar-bipolar EGM readings from various locations on tissue using two catheter types are modeled. The distance measure between spiral behaviors are assessed using normalized compression distance (NCD), an information theoretical distance. NCD is a universal metric in the sense it is solely based on compressibility of dataset and not requiring feature extraction. We also introduce normalized FFT distance (NFFTD) where compressibility is replaced with a FFT parameter. Overall, outstanding clustering performance was achieved across varying EGM reading configurations. We found that effectiveness in distinguishing was superior in case of NCD than NFFTD. We demonstrated that distinct spiral activity identification on a behaviorally heterogeneous tissue is also possible. This report demonstrates a theoretical validation of clustering and classification approaches that provide an automated mapping from EGM signals to assessment of spiral wave behaviors and hence offers a potential mapping and analysis framework for cardiac tissue wavefront propagation patterns. Copyright © 2018 Elsevier B.V. All rights reserved.

Luminance level of a monitor: influence on detectability and detection rate of breast cancer in 2D mammography

NASA Astrophysics Data System (ADS)

Bemelmans, Frédéric; Rashidnasab, Alaleh; Chesterman, Frédérique; Kimpe, Tom; Bosmans, Hilde

2016-03-01

Purpose: To evaluate lesion detectability and reading time as a function of luminance level of the monitor. Material and Methods: 3D mass models and microcalcification clusters were simulated into ROIs of for processing mammograms. Randomly selected ROIs were subdivided in three groups according to their background glandularity: high (>30%), medium (15-30%) and low (<15%). 6 non-spiculated masses (9 - 11mm), 6 spiculated masses (5 - 7mm) and 6 microcalcification clusters (2 - 4mm) were scaled in 3D to create a range of sizes. The linear attenuation coefficient (AC) of the masses was adjusted from 100% glandular tissue to 90%, 80%, 70%, to create different contrasts. Six physicists read the full database on Barco's Coronis Uniti monitor for four different luminance levels (300, 800, 1000 and 1200 Cd/m2), using a 4-AFC tool. Percentage correct (PC) and time were computed for all different conditions. A paired t-test was performed to evaluate the effect of luminance on PC and time. A multi-factorial analysis was performed using MANOVA.. Results: Paired t-test indicated a statistically significant difference for the average time per session between 300 and 1200; 800 and 1200; 1000 and 1200 Cd/m2, for all participants combined. There was no effect on PC. MANOVA denoted significantly lower reading times for high glandularity images at 1200 Cd/m2. Both types of masses were significantly faster detected at 1200 Cd/m2, for the contrast study. In the size study, microcalcification clusters and spiculated masses had a significantly higher detection rate at 1200 Cd/m2. Conclusion: These results demonstrate a significant decrease in reading time, while detectability remained constant.

A cluster analytic study of the Wechsler Intelligence Test for Children-IV in children referred for psychoeducational assessment due to persistent academic difficulties.

PubMed

Hale, Corinne R; Casey, Joseph E; Ricciardi, Philip W R

2014-02-01

Wechsler Intelligence Test for Children-IV core subtest scores of 472 children were cluster analyzed to determine if reliable and valid subgroups would emerge. Three subgroups were identified. Clusters were reliable across different stages of the analysis as well as across algorithms and samples. With respect to external validity, the Globally Low cluster differed from the other two clusters on Wechsler Individual Achievement Test-II Word Reading, Numerical Operations, and Spelling subtests, whereas the latter two clusters did not differ from one another. The clusters derived have been identified in studies using previous WISC editions. Clusters characterized by poor performance on subtests historically associated with the VIQ (i.e., VCI + WMI) and PIQ (i.e., POI + PSI) did not emerge, nor did a cluster characterized by low scores on PRI subtests. Picture Concepts represented the highest subtest score in every cluster, failing to vary in a predictable manner with the other PRI subtests.

The relationship of global form and motion detection to reading fluency.

PubMed

Englund, Julia A; Palomares, Melanie

2012-08-15

Visual motion processing in typical and atypical readers has suggested aspects of reading and motion processing share a common cortical network rooted in dorsal visual areas. Few studies have examined the relationship between reading performance and visual form processing, which is mediated by ventral cortical areas. We investigated whether reading fluency correlates with coherent motion detection thresholds in typically developing children using random dot kinematograms. As a comparison, we also evaluated the correlation between reading fluency and static form detection thresholds. Results show that both dorsal and ventral visual functions correlated with components of reading fluency, but that they have different developmental characteristics. Motion coherence thresholds correlated with reading rate and accuracy, which both improved with chronological age. Interestingly, when controlling for non-verbal abilities and age, reading accuracy significantly correlated with thresholds for coherent form detection but not coherent motion detection in typically developing children. Dorsal visual functions that mediate motion coherence seem to be related maturation of broad cognitive functions including non-verbal abilities and reading fluency. However, ventral visual functions that mediate form coherence seem to be specifically related to accurate reading in typically developing children. Copyright © 2012 Elsevier Ltd. All rights reserved.

Identifying Subgroups of Tinnitus Using Novel Resting State fMRI Biomarkers and Cluster Analysis

DTIC Science & Technology

2016-10-01

AWARD NUMBER: W81XWH-15-2-0032 TITLE: Identifying Subgroups of Tinnitus Using Novel Resting State fMRI Biomarkers and Cluster Analysis PRINCIPAL...4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Identifying Subgroups of Tinnitus Using Novel Resting State fMRI Biomarkers and Cluster Analysis 5b...Public Release; Distribution Unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT The subject of the project is FY14 PRMRP Topic Area – Tinnitus . The broad

Special issue on cluster algebras in mathematical physics

NASA Astrophysics Data System (ADS)

Di Francesco, Philippe; Gekhtman, Michael; Kuniba, Atsuo; Yamazaki, Masahito

2014-02-01

This is a call for contributions to a special issue of Journal of Physics A: Mathematical and Theoretical dedicated to cluster algebras in mathematical physics. Over the ten years since their introduction by Fomin and Zelevinsky, the theory of cluster algebras has witnessed a spectacular growth, first and foremost due to the many links that have been discovered with a wide range of subjects in mathematics and, increasingly, theoretical and mathematical physics. The main motivation of this special issue is to gather together reviews, recent developments and open problems, mainly from a mathematical physics viewpoint, into a single comprehensive issue. We expect that such a special issue will become a valuable reference for the broad scientific community working in mathematical and theoretical physics. The issue will consist of invited review articles and contributed papers containing new results on the interplays of cluster algebras with mathematical physics. Editorial policy The Guest Editors for this issue are Philippe Di Francesco, Michael Gekhtman, Atsuo Kuniba and Masahito Yamazaki. The areas and topics for this issue include, but are not limited to: discrete integrable systems arising from cluster mutations cluster structure on Poisson varieties cluster algebras and soliton interactions cluster positivity conjecture Y-systems in the thermodynamic Bethe ansatz and Zamolodchikov's periodicity conjecture T-system of transfer matrices of integrable lattice models dilogarithm identities in conformal field theory wall crossing in 4d N = 2 supersymmetric gauge theories 4d N = 1 quiver gauge theories described by networks scattering amplitudes of 4d N = 4 theories 3d N = 2 gauge theories described by flat connections on 3-manifolds integrability of dimer/Ising models on graphs. All contributions will be refereed and processed according to the usual procedure of the journal. Guidelines for preparation of contributions The deadline for contributed papers is 31 March 2014. This deadline will allow the special issue to appear at the end of 2014. There is no strict regulation on article size, but as a guide the preferable size is 15-30 pages for contributed papers and 40-60 pages for reviews. Further advice on publishing your work in Journal of Physics A may be found at iopscience.iop.org/jphysa. Contributions to the special issue should be submitted by web upload via ScholarOne Manuscripts, quoting 'JPhysA special issue on cluster algebras in mathematical physics'. Submissions should ideally be in standard LaTeX form. Please see the website for further information on electronic submissions. All contributions should be accompanied by a read-me file or covering letter giving the postal and e-mail addresses for correspondence. The Publishing Office should be notified of any subsequent change of address. The special issue will be published in the print and online versions of the journal.

Special issue on cluster algebras in mathematical physics

NASA Astrophysics Data System (ADS)

Di Francesco, Philippe; Gekhtman, Michael; Kuniba, Atsuo; Yamazaki, Masahito

2013-12-01

This is a call for contributions to a special issue of Journal of Physics A: Mathematical and Theoretical dedicated to cluster algebras in mathematical physics. Over the ten years since their introduction by Fomin and Zelevinsky, the theory of cluster algebras has witnessed a spectacular growth, first and foremost due to the many links that have been discovered with a wide range of subjects in mathematics and, increasingly, theoretical and mathematical physics. The main motivation of this special issue is to gather together reviews, recent developments and open problems, mainly from a mathematical physics viewpoint, into a single comprehensive issue. We expect that such a special issue will become a valuable reference for the broad scientific community working in mathematical and theoretical physics. The issue will consist of invited review articles and contributed papers containing new results on the interplays of cluster algebras with mathematical physics. Editorial policy The Guest Editors for this issue are Philippe Di Francesco, Michael Gekhtman, Atsuo Kuniba and Masahito Yamazaki. The areas and topics for this issue include, but are not limited to: discrete integrable systems arising from cluster mutations cluster structure on Poisson varieties cluster algebras and soliton interactions cluster positivity conjecture Y-systems in the thermodynamic Bethe ansatz and Zamolodchikov's periodicity conjecture T-system of transfer matrices of integrable lattice models dilogarithm identities in conformal field theory wall crossing in 4d N = 2 supersymmetric gauge theories 4d N = 1 quiver gauge theories described by networks scattering amplitudes of 4d N = 4 theories 3d N = 2 gauge theories described by flat connections on 3-manifolds integrability of dimer/Ising models on graphs. All contributions will be refereed and processed according to the usual procedure of the journal. Guidelines for preparation of contributions The deadline for contributed papers is 31 March 2014. This deadline will allow the special issue to appear at the end of 2014. There is no strict regulation on article size, but as a guide the preferable size is 15-30 pages for contributed papers and 40-60 pages for reviews. Further advice on publishing your work in Journal of Physics A may be found at iopscience.iop.org/jphysa. Contributions to the special issue should be submitted by web upload via ScholarOne Manuscripts, quoting 'JPhysA special issue on cluster algebras in mathematical physics'. Submissions should ideally be in standard LaTeX form. Please see the website for further information on electronic submissions. All contributions should be accompanied by a read-me file or covering letter giving the postal and e-mail addresses for correspondence. The Publishing Office should be notified of any subsequent change of address. The special issue will be published in the print and online versions of the journal.

Special issue on cluster algebras in mathematical physics

NASA Astrophysics Data System (ADS)

Di Francesco, Philippe; Gekhtman, Michael; Kuniba, Atsuo; Yamazaki, Masahito

2013-11-01

This is a call for contributions to a special issue of Journal of Physics A: Mathematical and Theoretical dedicated to cluster algebras in mathematical physics. Over the ten years since their introduction by Fomin and Zelevinsky, the theory of cluster algebras has witnessed a spectacular growth, first and foremost due to the many links that have been discovered with a wide range of subjects in mathematics and, increasingly, theoretical and mathematical physics. The main motivation of this special issue is to gather together reviews, recent developments and open problems, mainly from a mathematical physics viewpoint, into a single comprehensive issue. We expect that such a special issue will become a valuable reference for the broad scientific community working in mathematical and theoretical physics. The issue will consist of invited review articles and contributed papers containing new results on the interplays of cluster algebras with mathematical physics. Editorial policy The Guest Editors for this issue are Philippe Di Francesco, Michael Gekhtman, Atsuo Kuniba and Masahito Yamazaki. The areas and topics for this issue include, but are not limited to: discrete integrable systems arising from cluster mutations cluster structure on Poisson varieties cluster algebras and soliton interactions cluster positivity conjecture Y-systems in the thermodynamic Bethe ansatz and Zamolodchikov's periodicity conjecture T-system of transfer matrices of integrable lattice models dilogarithm identities in conformal field theory wall crossing in 4d N = 2 supersymmetric gauge theories 4d N = 1 quiver gauge theories described by networks scattering amplitudes of 4d N = 4 theories 3d N = 2 gauge theories described by flat connections on 3-manifolds integrability of dimer/Ising models on graphs. All contributions will be refereed and processed according to the usual procedure of the journal. Guidelines for preparation of contributions The deadline for contributed papers is 31 March 2014. This deadline will allow the special issue to appear at the end of 2014. There is no strict regulation on article size, but as a guide the preferable size is 15-30 pages for contributed papers and 40-60 pages for reviews. Further advice on publishing your work in Journal of Physics A may be found at iopscience.iop.org/jphysa. Contributions to the special issue should be submitted by web upload via ScholarOne Manuscripts, quoting 'JPhysA special issue on cluster algebras in mathematical physics'. Submissions should ideally be in standard LaTeX form. Please see the website for further information on electronic submissions. All contributions should be accompanied by a read-me file or covering letter giving the postal and e-mail addresses for correspondence. The Publishing Office should be notified of any subsequent change of address. The special issue will be published in the print and online versions of the journal.

Effectiveness of Music Education for the Improvement of Reading Skills and Academic Achievement in Young Poor Readers: A Pragmatic Cluster-Randomized, Controlled Clinical Trial

PubMed Central

Cogo-Moreira, Hugo; de Ávila, Clara Regina Brandão; Ploubidis, George B.; Mari, Jair de Jesus

2013-01-01

Introduction Difficulties in word-level reading skills are prevalent in Brazilian schools and may deter children from gaining the knowledge obtained through reading and academic achievement. Music education has emerged as a potential method to improve reading skills because due to a common neurobiological substratum. Objective To evaluate the effectiveness of music education for the improvement of reading skills and academic achievement among children (eight to 10 years of age) with reading difficulties. Method 235 children with reading difficulties in 10 schools participated in a five-month, randomized clinical trial in cluster (RCT) in an impoverished zone within the city of São Paulo to test the effects of music education intervention while assessing reading skills and academic achievement during the school year. Five schools were chosen randomly to incorporate music classes (n = 114), and five served as controls (n = 121). Two different methods of analysis were used to evaluate the effectiveness of the intervention: The standard method was intention-to-treat (ITT), and the other was the Complier Average Causal Effect (CACE) estimation method, which took compliance status into account. Results The ITT analyses were not very promising; only one marginal effect existed for the rate of correct real words read per minute. Indeed, considering ITT, improvements were observed in the secondary outcomes (slope of Portuguese = 0.21 [p<0.001] and slope of math = 0.25 [p<0.001]). As for CACE estimation (i.e., complier children versus non-complier children), more promising effects were observed in terms of the rate of correct words read per minute [β = 13.98, p<0.001] and phonological awareness [β = 19.72, p<0.001] as well as secondary outcomes (academic achievement in Portuguese [β = 0.77, p<0.0001] and math [β = 0.49, p<0.001] throughout the school year). Conclusion The results may be seen as promising, but they are not, in themselves, enough to make music lessons as public policy. PMID:23544117

Effectiveness of music education for the improvement of reading skills and academic achievement in young poor readers: a pragmatic cluster-randomized, controlled clinical trial.

PubMed

Cogo-Moreira, Hugo; Brandão de Ávila, Clara Regina; Ploubidis, George B; Mari, Jair de Jesus

2013-01-01

Difficulties in word-level reading skills are prevalent in Brazilian schools and may deter children from gaining the knowledge obtained through reading and academic achievement. Music education has emerged as a potential method to improve reading skills because due to a common neurobiological substratum. To evaluate the effectiveness of music education for the improvement of reading skills and academic achievement among children (eight to 10 years of age) with reading difficulties. 235 children with reading difficulties in 10 schools participated in a five-month, randomized clinical trial in cluster (RCT) in an impoverished zone within the city of São Paulo to test the effects of music education intervention while assessing reading skills and academic achievement during the school year. Five schools were chosen randomly to incorporate music classes (n = 114), and five served as controls (n = 121). Two different methods of analysis were used to evaluate the effectiveness of the intervention: The standard method was intention-to-treat (ITT), and the other was the Complier Average Causal Effect (CACE) estimation method, which took compliance status into account. The ITT analyses were not very promising; only one marginal effect existed for the rate of correct real words read per minute. Indeed, considering ITT, improvements were observed in the secondary outcomes (slope of Portuguese = 0.21 [p<0.001] and slope of math = 0.25 [p<0.001]). As for CACE estimation (i.e., complier children versus non-complier children), more promising effects were observed in terms of the rate of correct words read per minute [β = 13.98, p<0.001] and phonological awareness [β = 19.72, p<0.001] as well as secondary outcomes (academic achievement in Portuguese [β = 0.77, p<0.0001] and math [β = 0.49, p<0.001] throughout the school year). The results may be seen as promising, but they are not, in themselves, enough to make music lessons as public policy.

Improving Congolese Children's Early Math and Reading Ability: Preliminary Results from a Cluster Randomized Trial in the Democratic Republic of the Congo

ERIC Educational Resources Information Center

Starkey, Leighann; Aber, J. Lawrence; Johnston, Brian M.

2014-01-01

Mastering basic numeracy and literacy skills is one of the most fundamental goals of education. However, it is estimated that 250 million primary-school-age children lack basic reading, writing and math skills (UN, 2013). Children living in war and poverty stricken countries are among the least likely to attain those basic goals. The United States…

Origin of Broad Visible Emission from Branched Polysilane and Polygermane Chains

NASA Astrophysics Data System (ADS)

Watanabe, Akira; Sato, Takaaki; Matsuda, Minoru

2001-11-01

The emission properties of branched polysilane and polygermane are studied using time-resolved emission spectroscopy. As branched polymers, the organosilicon cluster (OSI) and organogermanium cluster (OGE) are investigated, which are prepared from tetrachlorosilane and tetrachlorogermane, respectively, and have a hyperbranched structure. The broad visible emissions of OSI and OGE are explained by the energy diagram based on a configuration coordinate model, and the excited states are attributed to a localized state around the branching point. The molecular orbital (MO) calculation suggested the formation of a localized state by the distortion around the branching point in the excited state. The potential barrier for the nonradiative relaxation process was determined from the temperature dependence of the emission lifetime.

Understanding I/O workload characteristics of a Peta-scale storage system

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

Kim, Youngjae; Gunasekaran, Raghul

2015-01-01

Understanding workload characteristics is critical for optimizing and improving the performance of current systems and software, and architecting new storage systems based on observed workload patterns. In this paper, we characterize the I/O workloads of scientific applications of one of the world s fastest high performance computing (HPC) storage cluster, Spider, at the Oak Ridge Leadership Computing Facility (OLCF). OLCF flagship petascale simulation platform, Titan, and other large HPC clusters, in total over 250 thousands compute cores, depend on Spider for their I/O needs. We characterize the system utilization, the demands of reads and writes, idle time, storage space utilization,more » and the distribution of read requests to write requests for the Peta-scale Storage Systems. From this study, we develop synthesized workloads, and we show that the read and write I/O bandwidth usage as well as the inter-arrival time of requests can be modeled as a Pareto distribution. We also study the I/O load imbalance problems using I/O performance data collected from the Spider storage system.« less

The COMT Val/Met polymorphism is associated with reading-related skills and consistent patterns of functional neural activation.

PubMed

Landi, Nicole; Frost, Stephen J; Mencl, W Einar; Preston, Jonathan L; Jacobsen, Leslie K; Lee, Maria; Yrigollen, Carolyn; Pugh, Kenneth R; Grigorenko, Elena L

2013-01-01

In both children and adults there is large variability in reading skill, with approximately 5-10% of individuals characterized as having reading disability; these individuals struggle to learn to read despite adequate intelligence and opportunity. Although it is well established that a substantial portion of this variability is attributed to the genetic differences between individuals, specifics of the connections between reading and the genome are not understood. This article presents data that suggest that variation in the COMT gene, which has previously been associated with variation in higher-order cognition, is associated with reading and reading-related skills, at the level of both brain and behavior. In particular, we found that the COMT Val/Met polymorphism at rs4680, which results in the substitution of the ancestral Valine (Val) by Methionine (Met), was associated with better performance on a number of critical reading measures and with patterns of functional neural activation that have been linked to better readers. We argue that this polymorphism, known for its broad effects on cognition, may modulate (likely through frontal lobe function) reading skill. © 2012 Blackwell Publishing Ltd.

The COMT Val/Met polymorphism is associated with reading related skills and consistent patterns of functional neural activation

PubMed Central

Landi, Nicole; Frost, Stephen J.; Mencl, W. Einar; Preston, Jonathan L.; Jacobsen, Leslie K.; Lee, Maria; Yrigollen, Carolyn; Pugh, Kenneth R.; Grigorenko, Elena L.

2013-01-01

In both children and adults there is large variability in reading skill, with approximately 5–10% of individuals characterized as having reading disability; these individuals struggle to learn to read despite adequate intelligence and opportunity. Although it is well established that a substantial portion of this variability is attributed to the genetic differences between individuals, specifics of the connections between reading and the genome are not understood. This article presents data that suggest that variation in the COMT gene, which has previously been associated with variation in higher-order cognition, is associated with reading and reading-related skills, both at the level of brain and behavior. In particular, we found that the COMT Val/Met polymorphism at rs4680, which results in the substitution of the ancestral Valine (Val) by Methionine (Met), was associated with better performance on a number of critical reading measures and with patterns of functional neural activation that have been linked to better readers. We argue that this polymorphism, known for its broad effects on cognition, may modulate (likely through frontal lobe function) reading skill. PMID:23278923

HISTORY OF EMPLOYMENT AND MANPOWER POLICY IN THE UNITED STATES. PARTS I AND II, DEPRESSION EXPERIENCE, PROPOSALS, AND PROGRAMS. SELECTED READINGS IN EMPLOYMENT AND MANPOWER, VOLUME 5.

ERIC Educational Resources Information Center

Congress of the U.S., Washington, DC. Senate Committee on Labor and Public Welfare.

THE SELECTED READINGS WERE COMPILED TO PROVIDE SUBCOMMITTEE MEMBERS WITH A BROAD BACKGROUND OF DEVELOPMENTS LEADING TO THE EMPLOYMENT ACT OF 1946 AND WITH APPRAISALS OF ITS ADEQUACY AND EFFECTIVENESS. MATERIAL IN THIS VOLUME SPANS THE LATE 1920'S AND THE GREAT DEPRESSION. PARTS III AND IV (VT 004 820) CONTINUE THE HISTORICAL BACKGROUND AND REVIEW.…

Isolation and Characterization of Canthaxanthin Biosynthesis Genes from the Photosynthetic Bacterium Bradyrhizobium sp. Strain ORS278

PubMed Central

Hannibal, Laure; Lorquin, Jean; D'Ortoli, Nicolas Angles; Garcia, Nelly; Chaintreuil, Clemence; Masson-Boivin, Catherine; Dreyfus, Bernard; Giraud, Eric

2000-01-01

A carotenoid biosynthesis gene cluster involved in canthaxanthin production was isolated from the photosynthetic Bradyrhizobium sp. strain ORS278. This cluster includes five genes identified as crtE, crtY, crtI, crtB, and crtW that are organized in at least two operons. The functional assignment of each open reading frame was confirmed by complementation studies. PMID:10851005

Attention Dysfunction Subtypes of Developmental Dyslexia

PubMed Central

Lewandowska, Monika; Milner, Rafał; Ganc, Małgorzata; Włodarczyk, Elżbieta; Skarżyński, Henryk

2014-01-01

Background Previous studies indicate that many different aspects of attention are impaired in children diagnosed with developmental dyslexia (DD). The objective of the present study was to identify cognitive profiles of DD on the basis of attentional test performance. Material/Methods 78 children with DD (30 girls, 48 boys, mean age of 12 years ±8 months) and 32 age- and sex-matched non-dyslexic children (14 girls, 18 boys) were examined using a battery of standardized tests of reading, phonological and attentional processes (alertness, covert shift of attention, divided attention, inhibition, flexibility, vigilance, and visual search). Cluster analysis was used to identify subtypes of DD. Results Dyslexic children showed deficits in alertness, covert shift of attention, divided attention, flexibility, and visual search. Three different subtypes of DD were identified, each characterized by poorer performance on the reading, phonological awareness, and visual search tasks. Additionally, children in cluster no. 1 displayed deficits in flexibility and divided attention. In contrast to non-dyslexic children, cluster no. 2 performed poorer in tasks involving alertness, covert shift of attention, divided attention, and vigilance. Cluster no. 3 showed impaired covert shift of attention. Conclusions These results indicate different patterns of attentional impairments in dyslexic children. Remediation programs should address the individual child’s deficit profile. PMID:25387479

ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition.

PubMed

Koslicki, David; Chatterjee, Saikat; Shahrivar, Damon; Walker, Alan W; Francis, Suzanna C; Fraser, Louise J; Vehkaperä, Mikko; Lan, Yueheng; Corander, Jukka

2015-01-01

Estimation of bacterial community composition from high-throughput sequenced 16S rRNA gene amplicons is a key task in microbial ecology. Since the sequence data from each sample typically consist of a large number of reads and are adversely impacted by different levels of biological and technical noise, accurate analysis of such large datasets is challenging. There has been a recent surge of interest in using compressed sensing inspired and convex-optimization based methods to solve the estimation problem for bacterial community composition. These methods typically rely on summarizing the sequence data by frequencies of low-order k-mers and matching this information statistically with a taxonomically structured database. Here we show that the accuracy of the resulting community composition estimates can be substantially improved by aggregating the reads from a sample with an unsupervised machine learning approach prior to the estimation phase. The aggregation of reads is a pre-processing approach where we use a standard K-means clustering algorithm that partitions a large set of reads into subsets with reasonable computational cost to provide several vectors of first order statistics instead of only single statistical summarization in terms of k-mer frequencies. The output of the clustering is then processed further to obtain the final estimate for each sample. The resulting method is called Aggregation of Reads by K-means (ARK), and it is based on a statistical argument via mixture density formulation. ARK is found to improve the fidelity and robustness of several recently introduced methods, with only a modest increase in computational complexity. An open source, platform-independent implementation of the method in the Julia programming language is freely available at https://github.com/dkoslicki/ARK. A Matlab implementation is available at http://www.ee.kth.se/ctsoftware.

A Randomised Controlled Trial of the Use of a Piece of Commercial Software for the Acquisition of Reading Skills

ERIC Educational Resources Information Center

Khan, Muhammad Ahmad; Gorard, Stephen

2012-01-01

We report here the overall results of a cluster randomised controlled trial of the use of computer-aided instruction with 672 Year 7 pupils in 23 secondary school classes in the north of England. A new piece of commercial software, claimed on the basis of publisher testing to be effective in improving reading after just six weeks of use in the…

Evaluation of Seeds of Science/Roots of Reading: Effective Tools for Developing Literacy through Science in the Early Grades-Light Energy Unit. CRESST Report 781

ERIC Educational Resources Information Center

Goldschmidt, Pete; Jung, Hyekyung

2011-01-01

This evaluation focuses on the Seeds of Science/Roots of Reading: Effective Tools for Developing Literacy through Science in the Early Grades ("Seeds/Roots") model of science-literacy integration. The evaluation is based on a cluster randomized design of 100 teachers, half of which were in the treatment group. Multi-level models are employed to…

Resting state functional connectivity of the anterior striatum and prefrontal cortex predicts reading performance in school-age children.

PubMed

Alcauter, Sarael; García-Mondragón, Liliana; Gracia-Tabuenca, Zeus; Moreno, Martha B; Ortiz, Juan J; Barrios, Fernando A

2017-11-01

The current study investigated the neural basis of reading performance in 60 school-age Spanish-speaking children, aged 6 to 9years. By using a data-driven approach and an automated matching procedure, we identified a left-lateralized resting state network that included typical language regions (Wernicke's and Broca's regions), prefrontal cortex, pre- and post-central gyri, superior and middle temporal gyri, cerebellum, and subcortical regions, and explored its relevance for reading performance (accuracy, comprehension and speed). Functional connectivity of the left frontal and temporal cortices and subcortical regions predicted reading speed. These results extend previous findings on the relationship between functional connectivity and reading competence in children, providing new evidence about such relationships in previously unexplored regions in the resting brain, including the left caudate, putamen and thalamus. This work highlights the relevance of a broad network, functionally synchronized in the resting state, for the acquisition and perfecting of reading abilities in young children. Copyright © 2017 Elsevier Inc. All rights reserved.

Neural organization of ventral white matter tracts parallels the initial steps of reading development: A DTI tractography study.

PubMed

Vanderauwera, Jolijn; De Vos, Astrid; Forkel, Stephanie J; Catani, Marco; Wouters, Jan; Vandermosten, Maaike; Ghesquière, Pol

2018-05-18

Insight in the developmental trajectory of the neuroanatomical reading correlates is important to understand related cognitive processes and disorders. In adults, a dual pathway model has been suggested encompassing a dorsal phonological and a ventral orthographic white matter system. This dichotomy seems not present in pre-readers, and the specific role of ventral white matter in reading remains unclear. Therefore, the present longitudinal study investigated the relation between ventral white matter and cognitive processes underlying reading in children with a broad range of reading skills (n = 61). Ventral pathways of the reading network were manually traced using diffusion tractography: the inferior fronto-occipital fasciculus (IFOF), inferior longitudinal fasciculus (ILF) and uncinate fasciculus (UF). Pathways were examined pre-reading (5-6 years) and after two years of reading acquisition (7-8 years). Dimension reduction for the cognitive measures resulted in one component for pre-reading cognitive measures and a separate phonological and orthographic component for the early reading measures. Regression analyses revealed a relation between the pre-reading cognitive component and bilateral IFOF and left ILF. Interestingly, exclusively the left IFOF was related to the orthographic component, whereas none of the pathways was related to the phonological component. Hence, the left IFOF seems to serve as the lexical reading route, already in the earliest reading stages. Copyright © 2018 Elsevier Inc. All rights reserved.

75 FR 71642 - Group E Post Office Box Service

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-24

...: PART 111--[AMENDED] 1. The authority citation for 39 CFR part 111 continues to read as follows... box units, apartment style receptacles, mailrooms, or clusters of roadside receptacles. 3. Locations...

Atropos: specific, sensitive, and speedy trimming of sequencing reads.

PubMed

Didion, John P; Martin, Marcel; Collins, Francis S

2017-01-01

A key step in the transformation of raw sequencing reads into biological insights is the trimming of adapter sequences and low-quality bases. Read trimming has been shown to increase the quality and reliability while decreasing the computational requirements of downstream analyses. Many read trimming software tools are available; however, no tool simultaneously provides the accuracy, computational efficiency, and feature set required to handle the types and volumes of data generated in modern sequencing-based experiments. Here we introduce Atropos and show that it trims reads with high sensitivity and specificity while maintaining leading-edge speed. Compared to other state-of-the-art read trimming tools, Atropos achieves significant increases in trimming accuracy while remaining competitive in execution times. Furthermore, Atropos maintains high accuracy even when trimming data with elevated rates of sequencing errors. The accuracy, high performance, and broad feature set offered by Atropos makes it an appropriate choice for the pre-processing of Illumina, ABI SOLiD, and other current-generation short-read sequencing datasets. Atropos is open source and free software written in Python (3.3+) and available at https://github.com/jdidion/atropos.

Atropos: specific, sensitive, and speedy trimming of sequencing reads

PubMed Central

Collins, Francis S.

2017-01-01

A key step in the transformation of raw sequencing reads into biological insights is the trimming of adapter sequences and low-quality bases. Read trimming has been shown to increase the quality and reliability while decreasing the computational requirements of downstream analyses. Many read trimming software tools are available; however, no tool simultaneously provides the accuracy, computational efficiency, and feature set required to handle the types and volumes of data generated in modern sequencing-based experiments. Here we introduce Atropos and show that it trims reads with high sensitivity and specificity while maintaining leading-edge speed. Compared to other state-of-the-art read trimming tools, Atropos achieves significant increases in trimming accuracy while remaining competitive in execution times. Furthermore, Atropos maintains high accuracy even when trimming data with elevated rates of sequencing errors. The accuracy, high performance, and broad feature set offered by Atropos makes it an appropriate choice for the pre-processing of Illumina, ABI SOLiD, and other current-generation short-read sequencing datasets. Atropos is open source and free software written in Python (3.3+) and available at https://github.com/jdidion/atropos. PMID:28875074

White Dwarf Stars

NASA Image and Video Library

1999-12-01

Peering deep inside a cluster of several hundred thousand stars, NASA Hubble Space Telescope has uncovered the oldest burned-out stars in our Milky Way Galaxy, giving astronomers a fresh reading on the age of the universe.

Special Session 2: Cosmic Evolution of Groups and Clusters

NASA Astrophysics Data System (ADS)

Vrtilek, J. M.; David, L. P.

2015-03-01

During the past decade observations across the electromagnetic spectrum have led to broad progress in the understanding of galaxy clusters and their far more abundant smaller siblings, groups. From the X-rays, where Chandra and XMM have illuminated old phenomena such as cooling cores and discovered new ones such as shocks, cold fronts, bubbles and cavities, through rich collections of optical data (including vast and growing arrays of redshifts), to the imaging of AGN outbursts of various ages through radio observations, our access to cluster and group measurements has leaped forward, while parallel advances in theory and modeling have kept pace. This Special Session offered a survey of progress to this point, an assessment of outstanding problems, and a multiwavelength overview of the uses of the next generation of observatories. Holding the symposium in conjuction with the XXVIIIth General Assembly provided the significant advantage of involving not only a specialist audience, but also interacting with a broad cross-section of the world astronomical community.

Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics

PubMed Central

Weber, Marc; Teeling, Hanno; Huang, Sixing; Waldmann, Jost; Kassabgy, Mariette; Fuchs, Bernhard M; Klindworth, Anna; Klockow, Christine; Wichels, Antje; Gerdts, Gunnar; Amann, Rudolf; Glöckner, Frank Oliver

2011-01-01

Next-generation sequencing (NGS) technologies have enabled the application of broad-scale sequencing in microbial biodiversity and metagenome studies. Biodiversity is usually targeted by classifying 16S ribosomal RNA genes, while metagenomic approaches target metabolic genes. However, both approaches remain isolated, as long as the taxonomic and functional information cannot be interrelated. Techniques like self-organizing maps (SOMs) have been applied to cluster metagenomes into taxon-specific bins in order to link biodiversity with functions, but have not been applied to broad-scale NGS-based metagenomics yet. Here, we provide a novel implementation, demonstrate its potential and practicability, and provide a web-based service for public usage. Evaluation with published data sets mimicking varyingly complex habitats resulted into classification specificities and sensitivities of close to 100% to above 90% from phylum to genus level for assemblies exceeding 8 kb for low and medium complexity data. When applied to five real-world metagenomes of medium complexity from direct pyrosequencing of marine subsurface waters, classifications of assemblies above 2.5 kb were in good agreement with fluorescence in situ hybridizations, indicating that biodiversity was mostly retained within the metagenomes, and confirming high classification specificities. This was validated by two protein-based classifications (PBCs) methods. SOMs were able to retrieve the relevant taxa down to the genus level, while surpassing PBCs in resolution. In order to make the approach accessible to a broad audience, we implemented a feature-rich web-based SOM application named TaxSOM, which is freely available at http://www.megx.net/toolbox/taxsom. TaxSOM can classify reads or assemblies exceeding 2.5 kb with high accuracy and thus assists in linking biodiversity and functions in metagenome studies, which is a precondition to study microbial ecology in a holistic fashion. PMID:21160538

A functional gene cluster for toxoflavin biosynthesis in the genome of the soil bacterium Pseudomonas protegens Pf-5

USDA-ARS?s Scientific Manuscript database

Toxoflavin is a broad-spectrum toxin best known for its role in virulence of Burkholderia glumae, which causes panicle blight of rice. A gene cluster containing homologs of toxoflavin biosynthesis genes (toxA-E) of B. glumae is present in the genome of Pseudomonas protegens Pf-5, a biological contr...

A search for quasars in the Virgo cluster region

NASA Technical Reports Server (NTRS)

He, X.-T.; Cannon, R. D.; Peacock, J. A.; Smith, M. G.; Oke, J. B.

1984-01-01

Using objective-prism plates taken with the 44-arcmin objective prism mounted on the UK Schmidt telescope, 53 emission-line quasar candidates and 29 ultraviolet-excess objects (possible low-redshift quasars) have been found in a 5 x 5-degree field centered on 12 h 27 m, + 13 deg 30 min (1950) in the Virgo cluster of galaxies. Eighteen of these 82 candidates were observed using the double spectrograph on the Palomar 5-meter telescope; 13 of the observed objects proved to be quasars. The broad-absorption-line QSO Q1232 + 134 is the first example of the class to show broad low-ionization absorption lines (such as Mg II 2798 A) in addition to the usual high-excitation lines such as Nv 1240 A. Although no conclusive evidence for quasar-galaxy associations is found in this field, there do exist nonuniformities in the distribution of the quasar candidates which may merit further investigation. These objects will provide a useful network of probes for absorbing material in the Virgo cluster. The lines-of-sight to two of the confirmed quasars pass very close to NGC galaxies; the respective projected QSO-galaxy separations are only 4 and 11 kpc at the assumed distance of the Virgo cluster.

Occidiofungin is an important component responsible for the antifungal activity of Burkholderia pyrrocinia strain Lyc2.

PubMed

Wang, X Q; Liu, A X; Guerrero, A; Liu, J; Yu, X Q; Deng, P; Ma, L; Baird, S M; Smith, L; Li, X D; Lu, S E

2016-03-01

To identify the taxonomy of tobacco rhizosphere-isolated strain Lyc2 and investigate the mechanisms of the antifungal activities, focusing on antimicrobials gene clusters identification and function analysis. Multilocus sequence typing and 16S rRNA analyses indicated that strain Lyc2 belongs to Burkholderia pyrrocinia. Bioassay results indicated strain Lyc2 showed significant antifungal activities against a broad range of plant and animal fungal pathogens and control efficacy on seedling damping off disease of cotton. A 55·2-kb gene cluster which was homologous to ocf gene clusters in Burkholderia contaminans MS14 was confirmed to be responsible for antifungal activities by random mutagenesis; HPLC was used to verify the production of antifungal compounds. Multiple antibiotic and secondary metabolized biosynthesis gene clusters predicated by antiSMASH revealed the broad spectrum of antimicrobials activities of the strain. Our results revealed the mechanisms of antifungal activities of strain Lyc2 and expand our knowledge about production of occidiofungin in the bacteria Burkholderia. Understanding the mechanisms of antifungal activities of strain Lyc2 has contributed to discovery of new antibiotics and expand our knowledge of production of occidiofungin in the bacteria Burkholderia. © 2015 The Society for Applied Microbiology.

Rewards of reading: Toward the development of possible selves and identities

PubMed Central

Richardson, Paul W.; Eccles, Jacquelynne S.

2013-01-01

Children’s voluntary reading positively correlates with school grades, vocabulary growth, reading comprehension, verbal fluency, general information, and attitudes towards reading. Drawing on qualitative interviews collected alongside six waves of longitudinal survey data in an urban setting in eastern USA, We argue that voluntary reading by adolescents also provides learning opportunities that scaffold identity formation, afford ‘spaces’ where youth rehearse and relationally enact gender roles, ethnic/racial identification, and fashion educational aspirations. The interviews with African American and European American youth were conducted in five visits and spanned 3 years through senior high school and 1 year post-high school. Methods of inductive and narrative analysis identified patterns of benefits and potential drawbacks of voluntary reading. Amount of voluntary reading was affected by school, family, and social and work commitment pressures, and fulfilled a number of broad roles. What and how youth were reading was as important as the amount. Significantly, reading allowed adolescents to explore possible selves—an interest in historical figures helped one African American male to develop values resisting stereotypes of male or African American, just as an African American female came to resist conforming to gender and racial stereotypes in dress and occupational ambitions. Relationships between voluntary reading habits, family context and educational aspirations were identifiable for a number of the interviewees. PMID:24659853

Central hardwood forest types

Treesearch

Ivan L. Sander; Burnell C. Fischer

1989-01-01

Each of the four broad forest types, often called associations, that you will read about in these Notes is a complex, highly variable mixture of trees, shrubs, and herbs. This Note describes the species you will generally find in each type.

Language, reading, and math learning profiles in an epidemiological sample of school age children.

PubMed

Archibald, Lisa M D; Oram Cardy, Janis; Joanisse, Marc F; Ansari, Daniel

2013-01-01

Dyscalculia, dyslexia, and specific language impairment (SLI) are relatively specific developmental learning disabilities in math, reading, and oral language, respectively, that occur in the context of average intellectual capacity and adequate environmental opportunities. Past research has been dominated by studies focused on single impairments despite the widespread recognition that overlapping and comorbid deficits are common. The present study took an epidemiological approach to study the learning profiles of a large school age sample in language, reading, and math. Both general learning profiles reflecting good or poor performance across measures and specific learning profiles involving either weak language, weak reading, weak math, or weak math and reading were observed. These latter four profiles characterized 70% of children with some evidence of a learning disability. Low scores in phonological short-term memory characterized clusters with a language-based weakness whereas low or variable phonological awareness was associated with the reading (but not language-based) weaknesses. The low math only group did not show these phonological deficits. These findings may suggest different etiologies for language-based deficits in language, reading, and math, reading-related impairments in reading and math, and isolated math disabilities.

Language, Reading, and Math Learning Profiles in an Epidemiological Sample of School Age Children

PubMed Central

Archibald, Lisa M. D.; Oram Cardy, Janis; Joanisse, Marc F.; Ansari, Daniel

2013-01-01

Dyscalculia, dyslexia, and specific language impairment (SLI) are relatively specific developmental learning disabilities in math, reading, and oral language, respectively, that occur in the context of average intellectual capacity and adequate environmental opportunities. Past research has been dominated by studies focused on single impairments despite the widespread recognition that overlapping and comorbid deficits are common. The present study took an epidemiological approach to study the learning profiles of a large school age sample in language, reading, and math. Both general learning profiles reflecting good or poor performance across measures and specific learning profiles involving either weak language, weak reading, weak math, or weak math and reading were observed. These latter four profiles characterized 70% of children with some evidence of a learning disability. Low scores in phonological short-term memory characterized clusters with a language-based weakness whereas low or variable phonological awareness was associated with the reading (but not language-based) weaknesses. The low math only group did not show these phonological deficits. These findings may suggest different etiologies for language-based deficits in language, reading, and math, reading-related impairments in reading and math, and isolated math disabilities. PMID:24155959

Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses.

PubMed

Hurwitz, Bonnie L; Westveld, Anton H; Brum, Jennifer R; Sullivan, Matthew B

2014-07-22

Long-standing questions in marine viral ecology are centered on understanding how viral assemblages change along gradients in space and time. However, investigating these fundamental ecological questions has been challenging due to incomplete representation of naturally occurring viral diversity in single gene- or morphology-based studies and an inability to identify up to 90% of reads in viral metagenomes (viromes). Although protein clustering techniques provide a significant advance by helping organize this unknown metagenomic sequence space, they typically use only ∼75% of the data and rely on assembly methods not yet tuned for naturally occurring sequence variation. Here, we introduce an annotation- and assembly-free strategy for comparative metagenomics that combines shared k-mer and social network analyses (regression modeling). This robust statistical framework enables visualization of complex sample networks and determination of ecological factors driving community structure. Application to 32 viromes from the Pacific Ocean Virome dataset identified clusters of samples broadly delineated by photic zone and revealed that geographic region, depth, and proximity to shore were significant predictors of community structure. Within subsets of this dataset, depth, season, and oxygen concentration were significant drivers of viral community structure at a single open ocean station, whereas variability along onshore-offshore transects was driven by oxygen concentration in an area with an oxygen minimum zone and not depth or proximity to shore, as might be expected. Together these results demonstrate that this highly scalable approach using complete metagenomic network-based comparisons can both test and generate hypotheses for ecological investigation of viral and microbial communities in nature.

Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses

PubMed Central

Hurwitz, Bonnie L.; Westveld, Anton H.; Brum, Jennifer R.; Sullivan, Matthew B.

2014-01-01

Long-standing questions in marine viral ecology are centered on understanding how viral assemblages change along gradients in space and time. However, investigating these fundamental ecological questions has been challenging due to incomplete representation of naturally occurring viral diversity in single gene- or morphology-based studies and an inability to identify up to 90% of reads in viral metagenomes (viromes). Although protein clustering techniques provide a significant advance by helping organize this unknown metagenomic sequence space, they typically use only ∼75% of the data and rely on assembly methods not yet tuned for naturally occurring sequence variation. Here, we introduce an annotation- and assembly-free strategy for comparative metagenomics that combines shared k-mer and social network analyses (regression modeling). This robust statistical framework enables visualization of complex sample networks and determination of ecological factors driving community structure. Application to 32 viromes from the Pacific Ocean Virome dataset identified clusters of samples broadly delineated by photic zone and revealed that geographic region, depth, and proximity to shore were significant predictors of community structure. Within subsets of this dataset, depth, season, and oxygen concentration were significant drivers of viral community structure at a single open ocean station, whereas variability along onshore–offshore transects was driven by oxygen concentration in an area with an oxygen minimum zone and not depth or proximity to shore, as might be expected. Together these results demonstrate that this highly scalable approach using complete metagenomic network-based comparisons can both test and generate hypotheses for ecological investigation of viral and microbial communities in nature. PMID:25002514

HISTORY OF EMPLOYMENT AND MANPOWER POLICY IN THE UNITED STATES. PARTS III AND IV, LOOKING AHEAD TO THE POSTWAR ECONOMY AND THE CONCEPT OF FULL EMPLOYMENT IN CONGRESS. SELECTED READINGS IN EMPLOYMENT AND MANPOWER, VOLUME 6.

ERIC Educational Resources Information Center

Congress of the U.S., Washington, DC. Senate Committee on Labor and Public Welfare.

THE SELECTED READINGS WERE COMPILED TO PROVIDE SUBCOMMITTEE MEMBERS WITH A BROAD BACKGROUND OF DEVELOPMENTS LEADING TO THE EMPLOYMENT ACT OF 1946 AND ARE CONCERNED WITH THE FORMULATION OF U.S. EMPLOYMENT POLICIES FOLLOWING WORLD WAR II. PARTS I AND II (VT 004 819) PROVIDE THE HISTORICAL BACKGROUND FROM THE LATE 1920'S THROUGH THE GREAT DEPRESSION.…

Strategies Used by Cantonese Speakers in Pronouncing English Initial Consonant Clusters: Insights into the Interlanguage Phonology of Cantonese ESL Learners in Hong Kong

ERIC Educational Resources Information Center

Chan, Alice Y. W.

2006-01-01

This article discusses the strategies used by Cantonese ESL learners to cope with their problems in pronouncing English initial consonant clusters. A small-scale research study was carried out with six secondary and six university students in Hong Kong, who were asked to perform four speech tasks: the reading of a word list, the description of a…

Swarm v2: highly-scalable and high-resolution amplicon clustering.

PubMed

Mahé, Frédéric; Rognes, Torbjørn; Quince, Christopher; de Vargas, Colomban; Dunthorn, Micah

2015-01-01

Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs), free of arbitrary global clustering thresholds and input-order dependency. Swarm v1 worked with an initial phase that used iterative single-linkage with a local clustering threshold (d), followed by a phase that used the internal abundance structures of clusters to break chained OTUs. Here we present Swarm v2, which has two important novel features: (1) a new algorithm for d = 1 that allows the computation time of the program to scale linearly with increasing amounts of data; and (2) the new fastidious option that reduces under-grouping by grafting low abundant OTUs (e.g., singletons and doubletons) onto larger ones. Swarm v2 also directly integrates the clustering and breaking phases, dereplicates sequencing reads with d = 0, outputs OTU representatives in fasta format, and plots individual OTUs as two-dimensional networks.

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

PubMed

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

2013-12-01

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

Hot and solid gallium clusters: too small to melt.

PubMed

Breaux, Gary A; Benirschke, Robert C; Sugai, Toshiki; Kinnear, Brian S; Jarrold, Martin F

2003-11-21

A novel multicollision induced dissociation scheme is employed to determine the energy content for mass-selected gallium cluster ions as a function of their temperature. Measurements were performed for Ga(+)(n) (n=17 39, and 40) over a 90-720 K temperature range. For Ga+39 and Ga+40 a broad maximum in the heat capacity-a signature of a melting transition for a small cluster-occurs at around 550 K. Thus small gallium clusters melt at substantially above the 302.9 K melting point of bulk gallium, in conflict with expectations that they will remain liquid to below 150 K. No melting transition is observed for Ga+17.

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

PubMed

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

2013-01-01

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

Crystal structure of the 3C protease from Southern African Territories type 2 foot-and-mouth disease virus

PubMed Central

Yang, Jingjie; Leen, Eoin N.; Maree, Francois F.

2016-01-01

The replication of foot-and-mouth disease virus (FMDV) is dependent on the virus-encoded 3C protease (3Cpro). As in other picornaviruses, 3Cpro performs most of the proteolytic processing of the polyprotein expressed from the large open reading frame in the RNA genome of the virus. Previous work revealed that the 3Cpro from serotype A—one of the seven serotypes of FMDV—adopts a trypsin-like fold. On the basis of capsid sequence comparisons the FMDV serotypes are grouped into two phylogenetic clusters, with O, A, C, and Asia 1 in one, and the three Southern African Territories serotypes, (SAT-1, SAT-2 and SAT-3) in another, a grouping pattern that is broadly, but not rigidly, reflected in 3Cpro amino acid sequences. We report here the cloning, expression and purification of 3C proteases from four SAT serotype viruses (SAT2/GHA/8/91, SAT1/NIG/5/81, SAT1/UGA/1/97, and SAT2/ZIM/7/83) and the crystal structure at 3.2 Å resolution of 3Cpro from SAT2/GHA/8/91. PMID:27168976

Chirally directed formation of nanometer-scale proline clusters.

PubMed

Myung, Sunnie; Fioroni, Marco; Julian, Ryan R; Koeniger, Stormy L; Baik, Mu-Hyun; Clemmer, David E

2006-08-23

Ion mobility measurements, combined with molecular mechanics simulations, are used to study enantiopure and racemic proline clusters formed by electrospray ionization. Broad distributions of cluster sizes and charge states are observed, ranging from clusters containing only a few proline units to clusters that contain more than 100 proline units (i.e., protonated clusters of the form [xPro + nH](n+) with x = 1 to >100 and n = 1-7). As the sizes of clusters increase, there is direct evidence for nanometer scale, chirally induced organization into specific structures. For n = 4 and 5, enantiopure clusters of approximately 50 to 100 prolines assemble into structures that are more elongated than the most compact structure that is observed from the racemic proline clusters. A molecular analogue, cis-4-hydroxy-proline, displays significantly different behavior, indicating that in addition to the rigidity of the side chain ring, intermolecular interactions are important in the formation of chirally directed clusters. This is the first case in which assemblies of chirally selective elongated structures are observed in this size range of amino acid clusters. Relationships between enantiopurity, cluster shape, and overall energetics are discussed.

Self-aggregation in scaled principal component space

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

Ding, Chris H.Q.; He, Xiaofeng; Zha, Hongyuan

2001-10-05

Automatic grouping of voluminous data into meaningful structures is a challenging task frequently encountered in broad areas of science, engineering and information processing. These data clustering tasks are frequently performed in Euclidean space or a subspace chosen from principal component analysis (PCA). Here we describe a space obtained by a nonlinear scaling of PCA in which data objects self-aggregate automatically into clusters. Projection into this space gives sharp distinctions among clusters. Gene expression profiles of cancer tissue subtypes, Web hyperlink structure and Internet newsgroups are analyzed to illustrate interesting properties of the space.

Predicting radiologists' true and false positive decisions in reading mammograms by using gaze parameters and image-based features

NASA Astrophysics Data System (ADS)

Gandomkar, Ziba; Tay, Kevin; Ryder, Will; Brennan, Patrick C.; Mello-Thoms, Claudia

2016-03-01

Radiologists' gaze-related parameters combined with image-based features were utilized to classify suspicious mammographic areas ultimately scored as True Positives (TP) and False Positives (FP). Eight breast radiologists read 120 two-view digital mammograms of which 59 had biopsy proven cancer. Eye tracking data was collected and nearby fixations were clustered together. Suspicious areas on mammograms were independently identified based on thresholding an intensity saliency map followed by automatic segmentation and pruning steps. For each radiologist reported area, radiologist's fixation clusters in the area, as well as neighboring suspicious areas within 2.5° of the center of fixation, were found. A 45-dimensional feature vector containing gaze parameters of the corresponding cluster along with image-based characteristics was constructed. Gaze parameters included total number of fixations in the cluster, dwell time, time to hit the cluster for the first time, maximum number of consecutive fixations, and saccade magnitude of the first fixation in the cluster. Image-based features consisted of intensity, shape, and texture descriptors extracted from the region around the suspicious area, its surrounding tissue, and the entire breast. For each radiologist, a userspecific Support Vector Machine (SVM) model was built to classify the reported areas as TPs or FPs. Leave-one-out cross validation was utilized to avoid over-fitting. A feature selection step was embedded in the SVM training procedure by allowing radial basis function kernels to have 45 scaling factors. The proposed method was compared with the radiologists' performance using the jackknife alternative free-response receiver operating characteristic (JAFROC). The JAFROC figure of merit increased significantly for six radiologists.

Separating the influences of prereading skills on early word and nonword reading.

PubMed

Shapiro, Laura R; Carroll, Julia M; Solity, Jonathan E

2013-10-01

The essential first step for a beginning reader is to learn to match printed forms to phonological representations. For a new word, this is an effortful process where each grapheme must be translated individually (serial decoding). The role of phonological awareness in developing a decoding strategy is well known. We examined whether beginning readers recruit different skills depending on the nature of the words being read (familiar words vs. nonwords). Print knowledge, phoneme and rhyme awareness, rapid automatized naming (RAN), phonological short-term memory (STM), nonverbal reasoning, vocabulary, auditory skills, and visual attention were measured in 392 prereaders 4 and 5 years of age. Word and nonword reading were measured 9 months later. We used structural equation modeling to examine the skills-reading relationship and modeled correlations between our two reading outcomes and among all prereading skills. We found that a broad range of skills were associated with reading outcomes: early print knowledge, phonological STM, phoneme awareness and RAN. Whereas all of these skills were directly predictive of nonword reading, early print knowledge was the only direct predictor of word reading. Our findings suggest that beginning readers draw most heavily on their existing print knowledge to read familiar words. Copyright © 2013 Elsevier Inc. All rights reserved.

Very Broad [O III] λλ4959, 5007 Emission from the NGC 4472 Globular Cluster RZ 2109 and Implications for the Mass of Its Black Hole X-Ray Source

NASA Astrophysics Data System (ADS)

Zepf, Stephen E.; Stern, Daniel; Maccarone, Thomas J.; Kundu, Arunav; Kamionkowski, Marc; Rhode, Katherine L.; Salzer, John J.; Ciardullo, Robin; Gronwall, Caryl

2008-08-01

We present Keck LRIS spectroscopy of the black hole-hosting globular cluster RZ 2109 in the Virgo elliptical galaxy NGC 4472. We find that this object has extraordinarily broad [O III] λ5007 and [O III] λ4959 emission lines, with velocity widths of approximately 2000 km s-1. This result has significant implications for the nature of this accreting black hole system and the mass of the globular cluster black hole. We show that the broad [O III] λ5007 emission must arise from material driven at high velocity from the black hole system. This is because the volume available near the black hole is too small by many orders of magnitude to have enough [O III]-emitting atoms to account for the observed L([O III] λ5007) at high velocities, even if this volume is filled with oxygen at the critical density for [O III] λ5007. The Balmer emission is also weak, indicating the observed [O III] is not due to shocks. We therefore conclude that the [O III] λλ4959, 5007 is produced by photoionization of material driven across the cluster. The only known way to drive significant material at high velocity is for a system accreting mass near or above its Eddington limit, which indicates a stellar-mass black hole. Since it is dynamically implausible to form an accreting stellar-mass black hole system in a globular cluster with an intermediate-mass black hole (IMBH), it appears this massive globular cluster does not have an IMBH. We discuss further tests of this conclusion, and its implications for the MBH - Mstellar and MBH - σ relations. Based on observations made at the W. M. Keck Observatory, which is operated as a scientific partnership among the California Institute of Technology, the University of California, and the National Aeronautics and Space Administration. The Observatory was made possible by the generous financial support of the W. M. Keck Foundation.

Network Analysis Tools: from biological networks to clusters and pathways.

PubMed

Brohée, Sylvain; Faust, Karoline; Lima-Mendez, Gipsi; Vanderstocken, Gilles; van Helden, Jacques

2008-01-01

Network Analysis Tools (NeAT) is a suite of computer tools that integrate various algorithms for the analysis of biological networks: comparison between graphs, between clusters, or between graphs and clusters; network randomization; analysis of degree distribution; network-based clustering and path finding. The tools are interconnected to enable a stepwise analysis of the network through a complete analytical workflow. In this protocol, we present a typical case of utilization, where the tasks above are combined to decipher a protein-protein interaction network retrieved from the STRING database. The results returned by NeAT are typically subnetworks, networks enriched with additional information (i.e., clusters or paths) or tables displaying statistics. Typical networks comprising several thousands of nodes and arcs can be analyzed within a few minutes. The complete protocol can be read and executed in approximately 1 h.

Robust continuous clustering

PubMed Central

Shah, Sohil Atul

2017-01-01

Clustering is a fundamental procedure in the analysis of scientific data. It is used ubiquitously across the sciences. Despite decades of research, existing clustering algorithms have limited effectiveness in high dimensions and often require tuning parameters for different domains and datasets. We present a clustering algorithm that achieves high accuracy across multiple domains and scales efficiently to high dimensions and large datasets. The presented algorithm optimizes a smooth continuous objective, which is based on robust statistics and allows heavily mixed clusters to be untangled. The continuous nature of the objective also allows clustering to be integrated as a module in end-to-end feature learning pipelines. We demonstrate this by extending the algorithm to perform joint clustering and dimensionality reduction by efficiently optimizing a continuous global objective. The presented approach is evaluated on large datasets of faces, hand-written digits, objects, newswire articles, sensor readings from the Space Shuttle, and protein expression levels. Our method achieves high accuracy across all datasets, outperforming the best prior algorithm by a factor of 3 in average rank. PMID:28851838

Can You Read Me Now? Disciplinary Literacy Reading Strategies in the 7th Grade Science Classroom

NASA Astrophysics Data System (ADS)

McQuaid, Kelly Kathleen

Adolescent readers require a broad range of reading skills to deal with the challenges of reading complex text. Some researchers argue for a discipline-specific focus to address the low reading proficiency rates among secondary students. Disciplinary literacy attends to the different ways disciplines, such as science, generate and communicate knowledge. The purpose of this quasi-experimental study was to examine if and to what degree disciplinary literacy reading strategies impact student learning outcomes in reading comprehension and science content knowledge for 132 7th grade science students in five Southern Arizona charter schools and whether reading ability moderates that impact. The theoretical foundation for this study rested on expert-novice theory and Halliday's theory of critical moments of language development. It is not known if and to what degree disciplinary literacy reading strategies impact student learning outcomes in reading comprehension and science content knowledge for 7th grade science students and whether or not reading ability has a moderating effect on those student learning outcomes. The results for MANCOVA did not produce statistically significant results nor did the moderation analysis for the influence of reading ability on reading comprehension in the disciplinary literacy group. However, the moderation analysis for the influence of reading ability on science content knowledge resulted in conditional significant results for low (p < .01) and average readers (p <. 05). Low to average readers in the disciplinary literacy group appeared to benefit the most from reading comprehension instruction focused on learning science content in the science classroom.

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

Special issue on cluster algebras in mathematical physics

NASA Astrophysics Data System (ADS)

Di Francesco, Philippe; Gekhtman, Michael; Kuniba, Atsuo; Yamazaki, Masahito

2013-10-01

This is a call for contributions to a special issue of Journal of Physics A: Mathematical and Theoretical dedicated to cluster algebras in mathematical physics. Over the ten years since their introduction by Fomin and Zelevinsky, the theory of cluster algebras has witnessed a spectacular growth, first and foremost due to the many links that have been discovered with a wide range of subjects in mathematics and, increasingly, theoretical and mathematical physics. The main motivation of this special issue is to gather together reviews, recent developments and open problems, mainly from a mathematical physics viewpoint, into a single comprehensive issue. We expect that such a special issue will become a valuable reference for the broad scientific community working in mathematical and theoretical physics. The issue will consist of invited review articles and contributed papers containing new results on the interplays of cluster algebras with mathematical physics. Editorial policy The Guest Editors for this issue are Philippe Di Francesco, Michael Gekhtman, Atsuo Kuniba and Masahito Yamazaki. The areas and topics for this issue include, but are not limited to: discrete integrable systems arising from cluster mutations cluster structure on Poisson varieties cluster algebras and soliton interactions cluster positivity conjecture Y-systems in the thermodynamic Bethe ansatz and Zamolodchikov's periodicity conjecture T-system of transfer matrices of integrable lattice models dilogarithm identities in conformal field theory wall crossing in 4d N = 2 supersymmetric gauge theories 4d N = 1 quiver gauge theories described by networks scattering amplitudes of 4d N = 4 theories 3d N = 2 gauge theories described by flat connections on 3-manifolds integrability of dimer/Ising models on graphs. All contributions will be refereed and processed according to the usual procedure of the journal. Guidelines for preparation of contributions The deadline for contributed papers is 31 March 2014. This deadline will allow the special issue to appear at the end of 2014. There is no strict regulation on article size, but as a guide the preferable size is 15-30 pages for contributed papers and 40-60 pages for reviews. Further advice on publishing your work in Journal of Physics A may be found at iopscience.iop.org/jphysa. Contributions to the special issue should be submitted by web upload via authors.iop.org/, or by email to jphysa@iop.org, quoting 'JPhysA special issue on cluster algebras in mathematical physics'. Submissions should ideally be in standard LaTeX form. Please see the website for further information on electronic submissions. All contributions should be accompanied by a read-me file or covering letter giving the postal and e-mail addresses for correspondence. The Publishing Office should be notified of any subsequent change of address. The special issue will be published in the print and online versions of the journal.

clustep: Initial conditions for galaxy cluster halo simulations

NASA Astrophysics Data System (ADS)

Ruggiero, Rafael

2017-11-01

clustep generates a snapshot in GADGET-2 (ascl:0003.001) format containing a galaxy cluster halo in equilibrium; this snapshot can also be read in RAMSES (ascl:1011.007) using the DICE patch. The halo is made of a dark matter component and a gas component, with the latter representing the ICM. Each of these components follows a Dehnen density profile, with gamma=0 or gamma=1. If gamma=1, then the profile corresponds to a Hernquist profile.

Theoretical Prediction of Si 2–Si 33 Absorption Spectra

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

Zhao, Li -Zhen; Lu, Wen -Cai; Qin, Wei

Here, the optical absorption spectra of Si 2–Si 33 clusters were systematically studied by a time-dependent density functional theory approach. The calculations revealed that the absorption spectrum becomes significantly broad with increasing cluster size, stretching from ultraviolet to the infrared region. The absorption spectra are closely related to the structural motifs. With increasing cluster size, the absorption intensity of cage structures gradually increases, but the absorption curves of the prolate and the Y-shaped structures are very sensitive to cluster size. If the transition energy reaches ~12 eV, it is noted that all the clusters have remarkable absorption in deep ultravioletmore » region of 100–200 nm, and the maximum absorption intensity is ~100 times that in the visible region. Further, the optical responses to doping in the Si clusters were studied.« less

Theoretical Prediction of Si 2–Si 33 Absorption Spectra

DOE PAGES

Zhao, Li -Zhen; Lu, Wen -Cai; Qin, Wei; ...

2017-07-07

Here, the optical absorption spectra of Si 2–Si 33 clusters were systematically studied by a time-dependent density functional theory approach. The calculations revealed that the absorption spectrum becomes significantly broad with increasing cluster size, stretching from ultraviolet to the infrared region. The absorption spectra are closely related to the structural motifs. With increasing cluster size, the absorption intensity of cage structures gradually increases, but the absorption curves of the prolate and the Y-shaped structures are very sensitive to cluster size. If the transition energy reaches ~12 eV, it is noted that all the clusters have remarkable absorption in deep ultravioletmore » region of 100–200 nm, and the maximum absorption intensity is ~100 times that in the visible region. Further, the optical responses to doping in the Si clusters were studied.« less

Academic reading format preferences and behaviors among university students worldwide: A comparative survey analysis

PubMed Central

Kurbanoglu, Serap; Boustany, Joumana

2018-01-01

This study reports the descriptive and inferential statistical findings of a survey of academic reading format preferences and behaviors of 10,293 tertiary students worldwide. The study hypothesized that country-based differences in schooling systems, socioeconomic development, culture or other factors might have an influence on preferred formats, print or electronic, for academic reading, as well as the learning engagement behaviors of students. The main findings are that country of origin has little to no relationship with or effect on reading format preferences of university students, and that the broad majority of students worldwide prefer to read academic course materials in print. The majority of participants report better focus and retention of information presented in print formats, and more frequently prefer print for longer texts. Additional demographic and post-hoc analysis suggests that format preference has a small relationship with academic rank. The relationship between task demands, format preferences and reading comprehension are discussed. Additional outcomes and implications for the fields of education, psychology, computer science, information science and human-computer interaction are considered. PMID:29847560

Preparing beginning reading teachers: An experimental comparison of initial early literacy field experiences.

PubMed

Al Otaiba, Stephanie; Lake, Vickie E; Greulich, Luana; Folsom, Jessica S; Guidry, Lisa

2012-01-01

This randomized-control trial examined the learning of preservice teachers taking an initial Early Literacy course in an early childhood education program and of the kindergarten or first grade students they tutored in their field experience. Preservice teachers were randomly assigned to one of two tutoring programs: Book Buddies and Tutor Assisted Intensive Learning Strategies (TAILS), which provided identical meaning-focused instruction (shared book reading), but differed in the presentation of code-focused skills. TAILS used explicit, scripted lessons, and the Book Buddies required that code-focused instruction take place during shared book reading. Our research goal was to understand which tutoring program would be most effective in improving knowledge about reading, lead to broad and deep language and preparedness of the novice preservice teachers, and yield the most successful student reading outcomes. Findings indicate that all pre-service teachers demonstrated similar gains in knowledge, but preservice teachers in the TAILS program demonstrated broader and deeper application of knowledge and higher self-ratings of preparedness to teach reading. Students in both conditions made similar comprehension gains, but students tutored with TAILS showed significantly stronger decoding gains.

Delivering phonological and phonics training within whole-class teaching.

PubMed

Shapiro, Laura R; Solity, Jonathan

2008-12-01

Early, intensive phonological awareness and phonics training is widely held to be beneficial for children with poor phonological awareness. However, most studies have delivered this training separately from children's normal whole-class reading lessons. We examined whether integrating this training into whole class, mixed-ability reading lessons could impact on children with poor phonological awareness, whilst also benefiting normally developing readers. Teachers delivered the training within a broad reading programme to whole classes of children from Reception to the end of Year 1 (N=251). A comparison group of children received standard teaching methods (N=213). Children's literacy was assessed at the beginning of Reception, and then at the end of each year until 1 year post-intervention. The strategy significantly impacted on reading performance for normally developing readers and those with poor phonological awareness, vastly reducing the incidence of reading difficulties from 20% in comparison schools to 5% in intervention schools. Phonological and phonics training is highly effective for children with poor phonological awareness, even when incorporated into whole-class teaching.

LoRTE: Detecting transposon-induced genomic variants using low coverage PacBio long read sequences.

PubMed

Disdero, Eric; Filée, Jonathan

2017-01-01

Population genomic analysis of transposable elements has greatly benefited from recent advances of sequencing technologies. However, the short size of the reads and the propensity of transposable elements to nest in highly repeated regions of genomes limits the efficiency of bioinformatic tools when Illumina or 454 technologies are used. Fortunately, long read sequencing technologies generating read length that may span the entire length of full transposons are now available. However, existing TE population genomic softwares were not designed to handle long reads and the development of new dedicated tools is needed. LoRTE is the first tool able to use PacBio long read sequences to identify transposon deletions and insertions between a reference genome and genomes of different strains or populations. Tested against simulated and genuine Drosophila melanogaster PacBio datasets, LoRTE appears to be a reliable and broadly applicable tool to study the dynamic and evolutionary impact of transposable elements using low coverage, long read sequences. LoRTE is an efficient and accurate tool to identify structural genomic variants caused by TE insertion or deletion. LoRTE is available for download at http://www.egce.cnrs-gif.fr/?p=6422.

[Level of reading skills as a measure of cognitive reserve in elderly adults].

PubMed

Soto-Añari, Marcio; Flores-Valdivia, Gilda; Fernández-Guinea, Sara

2013-01-16

Cognitive reserve modulates between neurodegenerative processes and the clinical manifestations of cognitive impairment and dementia. This construct is associated with the capacity to optimise the execution of tasks by recruiting neuronal networks and with the use of alternative cognitive strategies that would be mediated by formal educational processes. To analyse the level of reading skills as a measure of cognitive reserve and as a reliable predictor of performance in tests for evaluating different cognitive domains. The sample consisted of 87 healthy subjects who were asked to complete the Word Naming test as an indicator of the level of reading skills; this allowed us to divide the sample into subjects with a low and a high level of reading ability. A broad neuropsychological battery was then applied. The subjects with a low level of reading skills displayed lower general cognitive performance, reduced processing speed and cognitive deficits. Furthermore, the level of reading skills is a better predictor of performance in executive functions and general cognitive performance than the variables age, years of schooling and education. The level of reading skills has shown itself to be a good measure of cognitive reserve and a reliable predictor of executive and cognitive functioning in ageing.

Soil and Culture

USDA-ARS?s Scientific Manuscript database

Editors Ed Landa and Christian Feller have assembled an international ensemble cast of writers, artists, historians, philosophers, and scientists of broad perspective to create a book of truly fascinating reading for any soils enthusiast. When so little we see in print is truly new or original, Soil...

Amazing Space: Explanations, Investigations, & 3D Visualizations

NASA Astrophysics Data System (ADS)

Summers, Frank

2011-05-01

The Amazing Space website is STScI's online resource for communicating Hubble discoveries and other astronomical wonders to students and teachers everywhere. Our team has developed a broad suite of materials, readings, activities, and visuals that are not only engaging and exciting, but also standards-based and fully supported so that they can be easily used within state and national curricula. These products include stunning imagery, grade-level readings, trading card games, online interactives, and scientific visualizations. We are currently exploring the potential use of stereo 3D in astronomy education.

The zoom lens of attention: Simulating shuffled versus normal text reading using the SWIFT model

PubMed Central

Schad, Daniel J.; Engbert, Ralf

2012-01-01

Assumptions on the allocation of attention during reading are crucial for theoretical models of eye guidance. The zoom lens model of attention postulates that attentional deployment can vary from a sharp focus to a broad window. The model is closely related to the foveal load hypothesis, i.e., the assumption that the perceptual span is modulated by the difficulty of the fixated word. However, these important theoretical concepts for cognitive research have not been tested quantitatively in eye movement models. Here we show that the zoom lens model, implemented in the SWIFT model of saccade generation, captures many important patterns of eye movements. We compared the model's performance to experimental data from normal and shuffled text reading. Our results demonstrate that the zoom lens of attention might be an important concept for eye movement control in reading. PMID:22754295

Dynamic microscopy of nanoscale cluster growth at the solid-liquid interface.

PubMed

Williamson, M J; Tromp, R M; Vereecken, P M; Hull, R; Ross, F M

2003-08-01

Dynamic processes at the solid-liquid interface are of key importance across broad areas of science and technology. Electrochemical deposition of copper, for example, is used for metallization in integrated circuits, and a detailed understanding of nucleation, growth and coalescence is essential in optimizing the final microstructure. Our understanding of processes at the solid-vapour interface has advanced tremendously over the past decade due to the routine availability of real-time, high-resolution imaging techniques yielding data that can be compared quantitatively with theory. However, the difficulty of studying the solid-liquid interface leaves our understanding of processes there less complete. Here we analyse dynamic observations--recorded in situ using a novel transmission electron microscopy technique--of the nucleation and growth of nanoscale copper clusters during electrodeposition. We follow in real time the evolution of individual clusters, and compare their development with simulations incorporating the basic physics of electrodeposition during the early stages of growth. The experimental technique developed here is applicable to a broad range of dynamic phenomena at the solid-liquid interface.

Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples.

PubMed

Lin, Jake; Kramna, Lenka; Autio, Reija; Hyöty, Heikki; Nykter, Matti; Cinek, Ondrej

2017-05-15

Next generation sequencing (NGS) technology allows laboratories to investigate virome composition in clinical and environmental samples in a culture-independent way. There is a need for bioinformatic tools capable of parallel processing of virome sequencing data by exactly identical methods: this is especially important in studies of multifactorial diseases, or in parallel comparison of laboratory protocols. We have developed a web-based application allowing direct upload of sequences from multiple virome samples using custom parameters. The samples are then processed in parallel using an identical protocol, and can be easily reanalyzed. The pipeline performs de-novo assembly, taxonomic classification of viruses as well as sample analyses based on user-defined grouping categories. Tables of virus abundance are produced from cross-validation by remapping the sequencing reads to a union of all observed reference viruses. In addition, read sets and reports are created after processing unmapped reads against known human and bacterial ribosome references. Secured interactive results are dynamically plotted with population and diversity charts, clustered heatmaps and a sortable and searchable abundance table. The Vipie web application is a unique tool for multi-sample metagenomic analysis of viral data, producing searchable hits tables, interactive population maps, alpha diversity measures and clustered heatmaps that are grouped in applicable custom sample categories. Known references such as human genome and bacterial ribosomal genes are optionally removed from unmapped ('dark matter') reads. Secured results are accessible and shareable on modern browsers. Vipie is a freely available web-based tool whose code is open source.

Master-equation approach to the study of phase-change processes in data storage media

NASA Astrophysics Data System (ADS)

Blyuss, K. B.; Ashwin, P.; Bassom, A. P.; Wright, C. D.

2005-07-01

We study the dynamics of crystallization in phase-change materials using a master-equation approach in which the state of the crystallizing material is described by a cluster size distribution function. A model is developed using the thermodynamics of the processes involved and representing the clusters of size two and greater as a continuum but clusters of size one (monomers) as a separate equation. We present some partial analytical results for the isothermal case and for large cluster sizes, but principally we use numerical simulations to investigate the model. We obtain results that are in good agreement with experimental data and the model appears to be useful for the fast simulation of reading and writing processes in phase-change optical and electrical memories.

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

Thermodynamic properties of small aggregates of rare-gas atoms

NASA Technical Reports Server (NTRS)

Etters, R. D.; Kaelberer, J.

1975-01-01

The present work reports on the equilibrium thermodynamic properties of small clusters of xenon, krypton, and argon atoms, determined from a biased random-walk Monte Carlo procedure. Cluster sizes ranged from 3 to 13 atoms. Each cluster was found to have an abrupt liquid-gas phase transition at a temperature much less than for the bulk material. An abrupt solid-liquid transition is observed for thirteen- and eleven-particle clusters. For cluster sizes smaller than 11, a gradual transition from solid to liquid occurred over a fairly broad range of temperatures. Distribution of number of bond lengths as a function of bond length was calculated for several systems at various temperatures. The effects of box boundary conditions are discussed. Results show the importance of a correct description of boundary conditions. A surprising result is the slow rate at which system properties approach bulk behavior as cluster size is increased.

Clustering of health-related behaviors, health outcomes and demographics in Dutch adolescents: a cross-sectional study.

PubMed

Busch, Vincent; Van Stel, Henk F; Schrijvers, Augustinus J P; de Leeuw, Johannes R J

2013-12-04

Recent studies show several health-related behaviors to cluster in adolescents. This has important implications for public health. Interrelated behaviors have been shown to be most effectively targeted by multimodal interventions addressing wider-ranging improvements in lifestyle instead of via separate interventions targeting individual behaviors. However, few previous studies have taken into account a broad, multi-disciplinary range of health-related behaviors and connected these behavioral patterns to health-related outcomes. This paper presents an analysis of the clustering of a broad range of health-related behaviors with relevant demographic factors and several health-related outcomes in adolescents. Self-report questionnaire data were collected from a sample of 2,690 Dutch high school adolescents. Behavioral patterns were deducted via Principal Components Analysis. Subsequently a Two-Step Cluster Analysis was used to identify groups of adolescents with similar behavioral patterns and health-related outcomes. Four distinct behavioral patterns describe the analyzed individual behaviors: 1- risk-prone behavior, 2- bully behavior, 3- problematic screen time use, and 4- sedentary behavior. Subsequent cluster analysis identified four clusters of adolescents. Multi-problem behavior was associated with problematic physical and psychosocial health outcomes, as opposed to those exerting relatively few unhealthy behaviors. These associations were relatively independent of demographics such as ethnicity, gender and socio-economic status. The results show that health-related behaviors tend to cluster, indicating that specific behavioral patterns underlie individual health behaviors. In addition, specific patterns of health-related behaviors were associated with specific health outcomes and demographic factors. In general, unhealthy behavior on account of multiple health-related behaviors was associated with both poor psychosocial and physical health. These findings have significant meaning for future public health programs, which should be more tailored with use of such knowledge on behavioral clustering via e.g. Transfer Learning.

Clustering of health-related behaviors, health outcomes and demographics in Dutch adolescents: a cross-sectional study

PubMed Central

2013-01-01

Background Recent studies show several health-related behaviors to cluster in adolescents. This has important implications for public health. Interrelated behaviors have been shown to be most effectively targeted by multimodal interventions addressing wider-ranging improvements in lifestyle instead of via separate interventions targeting individual behaviors. However, few previous studies have taken into account a broad, multi-disciplinary range of health-related behaviors and connected these behavioral patterns to health-related outcomes. This paper presents an analysis of the clustering of a broad range of health-related behaviors with relevant demographic factors and several health-related outcomes in adolescents. Methods Self-report questionnaire data were collected from a sample of 2,690 Dutch high school adolescents. Behavioral patterns were deducted via Principal Components Analysis. Subsequently a Two-Step Cluster Analysis was used to identify groups of adolescents with similar behavioral patterns and health-related outcomes. Results Four distinct behavioral patterns describe the analyzed individual behaviors: 1- risk-prone behavior, 2- bully behavior, 3- problematic screen time use, and 4- sedentary behavior. Subsequent cluster analysis identified four clusters of adolescents. Multi-problem behavior was associated with problematic physical and psychosocial health outcomes, as opposed to those exerting relatively few unhealthy behaviors. These associations were relatively independent of demographics such as ethnicity, gender and socio-economic status. Conclusions The results show that health-related behaviors tend to cluster, indicating that specific behavioral patterns underlie individual health behaviors. In addition, specific patterns of health-related behaviors were associated with specific health outcomes and demographic factors. In general, unhealthy behavior on account of multiple health-related behaviors was associated with both poor psychosocial and physical health. These findings have significant meaning for future public health programs, which should be more tailored with use of such knowledge on behavioral clustering via e.g. Transfer Learning. PMID:24305509

Swarm v2: highly-scalable and high-resolution amplicon clustering

PubMed Central

Quince, Christopher; de Vargas, Colomban; Dunthorn, Micah

2015-01-01

Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs), free of arbitrary global clustering thresholds and input-order dependency. Swarm v1 worked with an initial phase that used iterative single-linkage with a local clustering threshold (d), followed by a phase that used the internal abundance structures of clusters to break chained OTUs. Here we present Swarm v2, which has two important novel features: (1) a new algorithm for d = 1 that allows the computation time of the program to scale linearly with increasing amounts of data; and (2) the new fastidious option that reduces under-grouping by grafting low abundant OTUs (e.g., singletons and doubletons) onto larger ones. Swarm v2 also directly integrates the clustering and breaking phases, dereplicates sequencing reads with d = 0, outputs OTU representatives in fasta format, and plots individual OTUs as two-dimensional networks. PMID:26713226

APPLICATIONS OF RESEARCH TO THE PROBLEM OF INSTRUCTIONAL FLEXIBILITY.

ERIC Educational Resources Information Center

SARTAIN, HARRY W.

SELECTED RESEARCH ON THE PROBLEM OF INSTRUCTIONAL FLEXIBILITY IS SURVEYED AND DISCUSSED. BROAD TOPICS OF DISCUSSION ARE DEPARTMENTALIZATION, HOMOGENEOUS SECTIONING, INTERCLASS ABILITY SECTIONING, THE EXTENT OF VARIABILITY IN READING DEVELOPMENT, AND PRACTICES THAT MAY INCREASE FLEXIBILITY. AMONG THOSE PRACTICES TO INCREASE FLEXIBILITY ARE TEAM…

How Generalization Inferences Are Constructed in Expository Text Comprehension

ERIC Educational Resources Information Center

Ritchey, Kristin A.

2011-01-01

Three questions regarding adult readers' processing of generalization inferences (conceptually broad statements that subsume several specific statements) are investigated. College students (N=193) read expository texts containing target statements that were consistent, inconsistent, or off-topic in relation to a generalization implied by one…

Profiles of Discourse Recognition

ERIC Educational Resources Information Center

Singer, Murray

2013-01-01

A discourse recognition theory derived from more general memory formulations would be broad in its psychological implications. This study compared discourse recognition with some established profiles of item recognition. Participants read 10 stories either once or twice each. They then rated their confidence in recognizing explicit, paraphrased,…

Broad phonetic class definition driven by phone confusions

NASA Astrophysics Data System (ADS)

Lopes, Carla; Perdigão, Fernando

2012-12-01

Intermediate representations between the speech signal and phones may be used to improve discrimination among phones that are often confused. These representations are usually found according to broad phonetic classes, which are defined by a phonetician. This article proposes an alternative data-driven method to generate these classes. Phone confusion information from the analysis of the output of a phone recognition system is used to find clusters at high risk of mutual confusion. A metric is defined to compute the distance between phones. The results, using TIMIT data, show that the proposed confusion-driven phone clustering method is an attractive alternative to the approaches based on human knowledge. A hierarchical classification structure to improve phone recognition is also proposed using a discriminative weight training method. Experiments show improvements in phone recognition on the TIMIT database compared to a baseline system.

Mass spectrometric identification of intermediates in the O2-driven [4Fe-4S] to [2Fe-2S] cluster conversion in FNR

PubMed Central

Crack, Jason C.; Thomson, Andrew J.

2017-01-01

The iron-sulfur cluster containing protein Fumarate and Nitrate Reduction (FNR) is the master regulator for the switch between anaerobic and aerobic respiration in Escherichia coli and many other bacteria. The [4Fe-4S] cluster functions as the sensory module, undergoing reaction with O2 that leads to conversion to a [2Fe-2S] form with loss of high-affinity DNA binding. Here, we report studies of the FNR cluster conversion reaction using time-resolved electrospray ionization mass spectrometry. The data provide insight into the reaction, permitting the detection of cluster conversion intermediates and products, including a [3Fe-3S] cluster and persulfide-coordinated [2Fe-2S] clusters [[2Fe-2S](S)n, where n = 1 or 2]. Analysis of kinetic data revealed a branched mechanism in which cluster sulfide oxidation occurs in parallel with cluster conversion and not as a subsequent, secondary reaction to generate [2Fe-2S](S)n species. This methodology shows great potential for broad application to studies of protein cofactor–small molecule interactions. PMID:28373574

Individual Differences in Adult Reading Are Associated with Left Temporo-parietal to Dorsal Striatal Functional Connectivity

PubMed Central

Achal, Sanjay; Hoeft, Fumiko; Bray, Signe

2016-01-01

Reading skills vary widely in both children and adults, with a number of factors contributing to this variability. The most prominent factor may be related to efficiency of storage, representation, or retrieval of speech sounds. This phonological hypothesis is supported by findings of reduced activation in poor readers in left hemisphere ventro-lateral prefrontal and temporo-parietal phonological processing regions. Less well explained by phonological theories are reported hyperactivation in prefrontal, striatal, and insular regions. This study investigated functional connectivity of a core phonological processing region, the temporo-parietal junction (TPJ), in relation to reading skill in an adult community sample. We hypothesized that connectivity between TPJ and regions implicated in meta-analyses of reading disorder would correlate with individual differences in reading. Forty-four adults aged 30–54, ranging in reading ability, underwent resting fMRI scans. Data-driven connectivity clustering was used to identify TPJ subregions for seed-based connectivity analyses. Correlations were assessed between TPJ connectivity and timed-pseudoword reading (decoding) ability. We found a significant correlation wherein greater left supramarginal gyrus to anterior caudate connectivity was associated with weaker decoding. This suggests that hyperactivation of the dorsal striatum, reported in poor readers during reading tasks, may reflect compensatory or inefficient overintegration into attention networks. PMID:26400921

Effect of functionalization of boron nitride flakes by main group metal clusters on their optoelectronic properties

NASA Astrophysics Data System (ADS)

Chakraborty, Debdutta; Chattaraj, Pratim Kumar

2017-10-01

The possibility of functionalizing boron nitride flakes (BNFs) with some selected main group metal clusters, viz. OLi4, NLi5, CLi6, BLI7 and Al12Be, has been analyzed with the aid of density functional theory (DFT) based computations. Thermochemical as well as energetic considerations suggest that all the metal clusters interact with the BNF moiety in a favorable fashion. As a result of functionalization, the static (first) hyperpolarizability (β ) values of the metal cluster supported BNF moieties increase quite significantly as compared to that in the case of pristine BNF. Time dependent DFT analysis reveals that the metal clusters can lower the transition energies associated with the dominant electronic transitions quite significantly thereby enabling the metal cluster supported BNF moieties to exhibit significant non-linear optical activity. Moreover, the studied systems demonstrate broad band absorption capability spanning the UV-visible as well as infra-red domains. Energy decomposition analysis reveals that the electrostatic interactions principally stabilize the metal cluster supported BNF moieties.

Effect of functionalization of boron nitride flakes by main group metal clusters on their optoelectronic properties.

PubMed

Chakraborty, Debdutta; Chattaraj, Pratim Kumar

2017-10-25

The possibility of functionalizing boron nitride flakes (BNFs) with some selected main group metal clusters, viz. OLi 4 , NLi 5 , CLi 6 , BLI 7 and Al 12 Be, has been analyzed with the aid of density functional theory (DFT) based computations. Thermochemical as well as energetic considerations suggest that all the metal clusters interact with the BNF moiety in a favorable fashion. As a result of functionalization, the static (first) hyperpolarizability ([Formula: see text]) values of the metal cluster supported BNF moieties increase quite significantly as compared to that in the case of pristine BNF. Time dependent DFT analysis reveals that the metal clusters can lower the transition energies associated with the dominant electronic transitions quite significantly thereby enabling the metal cluster supported BNF moieties to exhibit significant non-linear optical activity. Moreover, the studied systems demonstrate broad band absorption capability spanning the UV-visible as well as infra-red domains. Energy decomposition analysis reveals that the electrostatic interactions principally stabilize the metal cluster supported BNF moieties.

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

Sehgal, Ray M.; Maroudas, Dimitrios, E-mail: maroudas@ecs.umass.edu, E-mail: ford@ecs.umass.edu; Ford, David M., E-mail: maroudas@ecs.umass.edu, E-mail: ford@ecs.umass.edu

We have developed a coarse-grained description of the phase behavior of the isolated 38-atom Lennard-Jones cluster (LJ{sub 38}). The model captures both the solid-solid polymorphic transitions at low temperatures and the complex cluster breakup and melting transitions at higher temperatures. For this coarse model development, we employ the manifold learning technique of diffusion mapping. The outcome of the diffusion mapping analysis over a broad temperature range indicates that two order parameters are sufficient to describe the cluster's phase behavior; we have chosen two such appropriate order parameters that are metrics of condensation and overall crystallinity. In this well-justified coarse-variable space,more » we calculate the cluster's free energy landscape (FEL) as a function of temperature, employing Monte Carlo umbrella sampling. These FELs are used to quantify the phase behavior and onsets of phase transitions of the LJ{sub 38} cluster.« less

Hartree-Fock calculation of the differential photoionization cross sections of small Li clusters

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

Galitskiy, S. A.; Artemyev, A. N.; Jänkälä, K.

2015-01-21

Cross sections and angular distribution parameters for the single-photon ionization of all electron orbitals of Li{sub 2−8} are systematically computed in a broad interval of the photoelectron kinetic energies for the energetically most stable geometry of each cluster. Calculations of the partial photoelectron continuum waves in clusters are carried out by the single center method within the Hartree-Fock approximation. We study photoionization cross sections per one electron and analyze in some details general trends in the photoionization of inner and outer shells with respect to the size and geometry of a cluster. The present differential cross sections computed for Li{submore » 2} are in a good agreement with the available theoretical data, whereas those computed for Li{sub 3−8} clusters can be considered as theoretical predictions.« less

Locality-Aware CTA Clustering For Modern GPUs

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

Li, Ang; Song, Shuaiwen; Liu, Weifeng

2017-04-08

In this paper, we proposed a novel clustering technique for tapping into the performance potential of a largely ignored type of locality: inter-CTA locality. We first demonstrated the capability of the existing GPU hardware to exploit such locality, both spatially and temporally, on L1 or L1/Tex unified cache. To verify the potential of this locality, we quantified its existence in a broad spectrum of applications and discussed its sources of origin. Based on these insights, we proposed the concept of CTA-Clustering and its associated software techniques. Finally, We evaluated these techniques on all modern generations of NVIDIA GPU architectures. Themore » experimental results showed that our proposed clustering techniques could significantly improve on-chip cache performance.« less

Rome Foundation-Asian working team report: Asian functional gastrointestinal disorder symptom clusters.

PubMed

Siah, Kewin Tien Ho; Gong, Xiaorong; Yang, Xi Jessie; Whitehead, William E; Chen, Minhu; Hou, Xiaohua; Pratap, Nitesh; Ghoshal, Uday C; Syam, Ari F; Abdullah, Murdani; Choi, Myung-Gyu; Bak, Young-Tae; Lu, Ching-Liang; Gonlachanvit, Sutep; Boon, Chua Seng; Fang, Fan; Cheong, Pui Kuan; Wu, Justin C Y; Gwee, Kok-Ann

2018-06-01

Functional gastrointestinal disorders (FGIDs) are diagnosed by the presence of a characteristic set of symptoms. However, the current criteria-based diagnostic approach is to some extent subjective and largely derived from observations in English-speaking Western patients. We aimed to identify latent symptom clusters in Asian patients with FGID. 1805 consecutive unselected patients with FGID who presented for primary or secondary care to 11 centres across Asia completed a cultural and linguistic adaptation of the Rome III Diagnostic Questionnaire that was translated to the local languages. Principal components factor analysis with varimax rotation was used to identify symptom clusters. Nine symptom clusters were identified, consisting of two oesophageal factors (F6: globus, odynophagia and dysphagia; F9: chest pain and heartburn), two gastroduodenal factors (F5: bloating, fullness, belching and flatulence; F8 regurgitation, nausea and vomiting), three bowel factors (F2: abdominal pain and diarrhoea; F3: meal-related bowel symptoms; F7: upper abdominal pain and constipation) and two anorectal factors (F1: anorectal pain and constipation; F4: diarrhoea, urgency and incontinence). We found that the broad categorisation used both in clinical practice and in the Rome system, that is, broad anatomical divisions, and certain diagnoses with long historical records, that is, IBS with diarrhoea, and chronic constipation, are still valid in our Asian societies. In addition, we found a bowel symptom cluster with meal trigger and a gas cluster that suggests a different emphasis in our populations. Future studies to compare a non-Asian cohort and to match to putative pathophysiology will help to verify our findings. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

REACH. Residential Electrical Wiring Units.

ERIC Educational Resources Information Center

Ansley, Jimmy; Ennis, Mike

As a part of the REACH (Refrigeration, Electro-Mechanical, Air-Conditioning, Heating) electromechanical cluster, this student manual contains individualized instructional units in the area of residential electrical wiring. The instructional units focus on grounded outlets, service entrance, and blueprint reading. Each unit follows a typical format…

Restoring Fun to Game Theory

ERIC Educational Resources Information Center

Dixit, Avinash

2005-01-01

The author suggests methods for teaching game theory at an introductory level, using interactive games to be played in the classroom or in computer clusters, clips from movies to be screened and discussed, and excerpts from novels and historical books to be read and discussed.

Toward Multicuturalism: A Reader in Multicultural Education.

ERIC Educational Resources Information Center

Wurzel, Jaime S., Ed.

This book of readings lays the foundation for the introduction of a broad multicultural perspective in education. "Multiculturalism and Multicultural Education" (J. S. Wurzel) outlines the multicultural process. Part 1, "Human Condition Themes," comprises the following sections: (1) "Ethnocentrism," including "Eating Christmas in the Kalahari" (R.…

Communicate in Russian--Part 2: 7543.04.

ERIC Educational Resources Information Center

Dade County Public Schools, Miami, FL.

This second volume of a three-part series intended to follow the Quinmester course "Survive a Russian Party" prescribes broad goals and performance objectives for the development of listening, reading, speaking, and writing skills. Cultural objectives and desirable student attitudes are suggested. Students take an imaginary flight to…

Community composition and cellulase activity of cellulolytic bacteria from forest soils planted with broad-leaved deciduous and evergreen trees.

PubMed

Yang, Jiang-Ke; Zhang, Jing-Jing; Yu, Heng-Yu; Cheng, Jian-Wen; Miao, Li-Hong

2014-02-01

Cellulolytic bacteria in forest soil provide carbon sources to improve the soil fertility and sustain the nutrient balance of the forest ecological system through the decomposition of cellulosic remains. These bacteria can also be utilized for the biological conversion of biomass into renewable biofuels. In this study, the community compositions and activities of cellulolytic bacteria in the soils of forests planted with broad-leaved deciduous (Chang Qing Garden, CQG) and broad-leaved evergreen (Forest Park, FP) trees in Wuhan, China were resolved through restriction fragment length polymorphism (RFLP) and sequencing analysis of the 16S rRNA gene. All of the isolates exhibited 35 RFLP fingerprint patterns and were clustered into six groups at a similarity level of 50 %. The phylogeny analysis based on the 16S rRNA gene sequence revealed that these RFLP groups could be clustered into three phylogenetic groups and further divided into six subgroups at a higher resolution. Group I consists of isolates from Bacillus cereus, Bacillus subtilis complex (I-A) and from Paenibacillus amylolyticus-related complex (I-B) and exhibited the highest cellulase activity among all of the cellulolytic bacteria isolates. Cluster II consists of isolates belonging to Microbacterium testaceum (II-A), Chryseobacterium indoltheticum (II-B), and Flavobacterium pectinovorum and the related complex (II-C). Cluster III consists of isolates belonging to Pseudomonas putida-related species. The community shift with respect to the plant species and the soil properties was evidenced by the phylogenetic composition of the communities. Groups I-A and I-B, which account for 36.0 % of the cellulolytic communities in the CQG site, are the dominant groups (88.4 %) in the FP site. Alternatively, the ratio of the bacteria belonging to group III (P. putida-related isolates) shifted from 28.0 % in CQG to 4.0 % in FP. The soil nutrient analysis revealed that the CQG site planted with deciduous broad-leaved trees has a richer organic nutrient (total organic carbon and total nitrogen) than the FP site planted with evergreen broad-leaved trees. Against this background, the population density and the diversity of cellulolytic bacteria in the CQG site are clearly higher than those in the FP site, and the latter was dominated with high-cellulase-activity Bacillus- and Paenibacillus-related bacteria. The canonical correspondence analysis further indicated that the distribution of these groups is correlated with the FP site, whereas groups II and III are correlated with the organic nutrient-rich CQG site.

COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge.

PubMed

Lu, Yang Young; Chen, Ting; Fuhrman, Jed A; Sun, Fengzhu

2017-03-15

The advent of next-generation sequencing technologies enables researchers to sequence complex microbial communities directly from the environment. Because assembly typically produces only genome fragments, also known as contigs, instead of an entire genome, it is crucial to group them into operational taxonomic units (OTUs) for further taxonomic profiling and down-streaming functional analysis. OTU clustering is also referred to as binning. We present COCACOLA, a general framework automatically bin contigs into OTUs based on sequence composition and coverage across multiple samples. The effectiveness of COCACOLA is demonstrated in both simulated and real datasets in comparison with state-of-art binning approaches such as CONCOCT, GroopM, MaxBin and MetaBAT. The superior performance of COCACOLA relies on two aspects. One is using L 1 distance instead of Euclidean distance for better taxonomic identification during initialization. More importantly, COCACOLA takes advantage of both hard clustering and soft clustering by sparsity regularization. In addition, the COCACOLA framework seamlessly embraces customized knowledge to facilitate binning accuracy. In our study, we have investigated two types of additional knowledge, the co-alignment to reference genomes and linkage of contigs provided by paired-end reads, as well as the ensemble of both. We find that both co-alignment and linkage information further improve binning in the majority of cases. COCACOLA is scalable and faster than CONCOCT, GroopM, MaxBin and MetaBAT. The software is available at https://github.com/younglululu/COCACOLA . fsun@usc.edu. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Older versus newer media and the well-being of United States youth: results from a national longitudinal panel.

PubMed

Romer, Daniel; Bagdasarov, Zhanna; More, Eian

2013-05-01

To determine the effects of both older and newer media use on academic, social, and mental health outcomes in adolescents and young adults. We interviewed a nationally representative panel of youth ages 14-24 years (N = 719) twice 1 year apart to determine time spent with television, the Internet, videogames, and book reading, as well as the purpose of those uses. A cluster analysis identified major combinations of media use. Regression models tested hypotheses regarding changes in self-reported school grades, participation in clubs and sports, and symptoms of depression, as predicted by recent media use and differences in cluster membership. Use of older media was related to grades, with television inversely and book reading positively related to performance. Moderate use of the Internet was positively related to participation in both sports and clubs. Although heavy use of the Internet and videogames was associated with an increase in depression, increased depression also predicted greater use of these media as well as withdrawal from sports and clubs. Clusters that used media in moderation with an emphasis on information gathering were most associated with healthy outcomes. Despite concerns that excessive use of new media is harmful to adolescent development, the findings reinforce previous conclusions that television detracts from academic performance and book reading supports it. Heavy use of the Internet and video gaming may be more a symptom of mental health problems than a cause. Moderate use of the Internet, especially for acquiring information, is most supportive of healthy development. Copyright © 2013 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

An RNA-Seq Transcriptome Analysis of Orthophosphate-Deficient White Lupin Reveals Novel Insights into Phosphorus Acclimation in Plants1[W][OA

PubMed Central

O’Rourke, Jamie A.; Yang, S. Samuel; Miller, Susan S.; Bucciarelli, Bruna; Liu, Junqi; Rydeen, Ariel; Bozsoki, Zoltan; Uhde-Stone, Claudia; Tu, Zheng Jin; Allan, Deborah; Gronwald, John W.; Vance, Carroll P.

2013-01-01

Phosphorus, in its orthophosphate form (Pi), is one of the most limiting macronutrients in soils for plant growth and development. However, the whole-genome molecular mechanisms contributing to plant acclimation to Pi deficiency remain largely unknown. White lupin (Lupinus albus) has evolved unique adaptations for growth in Pi-deficient soils, including the development of cluster roots to increase root surface area. In this study, we utilized RNA-Seq technology to assess global gene expression in white lupin cluster roots, normal roots, and leaves in response to Pi supply. We de novo assembled 277,224,180 Illumina reads from 12 complementary DNA libraries to build what is to our knowledge the first white lupin gene index (LAGI 1.0). This index contains 125,821 unique sequences with an average length of 1,155 bp. Of these sequences, 50,734 were transcriptionally active (reads per kilobase per million reads ≥ 3), representing approximately 7.8% of the white lupin genome, using the predicted genome size of Lupinus angustifolius as a reference. We identified a total of 2,128 sequences differentially expressed in response to Pi deficiency with a 2-fold or greater change and P ≤ 0.05. Twelve sequences were consistently differentially expressed due to Pi deficiency stress in three species, Arabidopsis (Arabidopsis thaliana), potato (Solanum tuberosum), and white lupin, making them ideal candidates to monitor the Pi status of plants. Additionally, classic physiological experiments were coupled with RNA-Seq data to examine the role of cytokinin and gibberellic acid in Pi deficiency-induced cluster root development. This global gene expression analysis provides new insights into the biochemical and molecular mechanisms involved in the acclimation to Pi deficiency. PMID:23197803

An RNA-Seq transcriptome analysis of orthophosphate-deficient white lupin reveals novel insights into phosphorus acclimation in plants.

PubMed

O'Rourke, Jamie A; Yang, S Samuel; Miller, Susan S; Bucciarelli, Bruna; Liu, Junqi; Rydeen, Ariel; Bozsoki, Zoltan; Uhde-Stone, Claudia; Tu, Zheng Jin; Allan, Deborah; Gronwald, John W; Vance, Carroll P

2013-02-01

Phosphorus, in its orthophosphate form (P(i)), is one of the most limiting macronutrients in soils for plant growth and development. However, the whole-genome molecular mechanisms contributing to plant acclimation to P(i) deficiency remain largely unknown. White lupin (Lupinus albus) has evolved unique adaptations for growth in P(i)-deficient soils, including the development of cluster roots to increase root surface area. In this study, we utilized RNA-Seq technology to assess global gene expression in white lupin cluster roots, normal roots, and leaves in response to P(i) supply. We de novo assembled 277,224,180 Illumina reads from 12 complementary DNA libraries to build what is to our knowledge the first white lupin gene index (LAGI 1.0). This index contains 125,821 unique sequences with an average length of 1,155 bp. Of these sequences, 50,734 were transcriptionally active (reads per kilobase per million reads ≥ 3), representing approximately 7.8% of the white lupin genome, using the predicted genome size of Lupinus angustifolius as a reference. We identified a total of 2,128 sequences differentially expressed in response to P(i) deficiency with a 2-fold or greater change and P ≤ 0.05. Twelve sequences were consistently differentially expressed due to P(i) deficiency stress in three species, Arabidopsis (Arabidopsis thaliana), potato (Solanum tuberosum), and white lupin, making them ideal candidates to monitor the P(i) status of plants. Additionally, classic physiological experiments were coupled with RNA-Seq data to examine the role of cytokinin and gibberellic acid in P(i) deficiency-induced cluster root development. This global gene expression analysis provides new insights into the biochemical and molecular mechanisms involved in the acclimation to P(i) deficiency.

t4 report*: Toward Good Read-Across Practice (GRAP) Guidance

PubMed Central

Ball, Nicholas; Cronin, Mark T. D.; Shen, Jie; Blackburn, Karen; Booth, Ewan D.; Bouhifd, Mounir; Donley, Elizabeth; Egnash, Laura; Hastings, Charles; Juberg, Daland R.; Kleensang, Andre; Kleinstreuer, Nicole; Kroese, E. Dinant; Lee, Adam C.; Luechtefeld, Thomas; Maertens, Alexandra; Marty, Sue; Naciff, Jorge M.; Palmer, Jessica; Pamies, David; Penman, Mike; Richarz, Andrea-Nicole; Russo, Daniel P.; Stuard, Sharon B.; Patlewicz, Grace; van Ravenzwaay, Bennard; Wu, Shengde; Zhu, Hao; Hartung, Thomas

2017-01-01

Summary Grouping of substances and utilizing read-across of data within those groups represents an important data gap filling technique for chemical safety assessments. Categories/analogue groups are typically developed based on structural similarity and, increasingly often, also on mechanistic (biological) similarity. While read-across can play a key role in complying with legislation such as the European REACH regulation, the lack of consensus regarding the extent and type of evidence necessary to support it often hampers its successful application and acceptance by regulatory authorities. Despite a potentially broad user community, expertise is still concentrated across a handful of organizations and individuals. In order to facilitate the effective use of read-across, this document presents the state of the art, summarizes insights learned from reviewing ECHA published decisions regarding the relative successes/pitfalls surrounding read-across under REACH, and compiles the relevant activities and guidance documents. Special emphasis is given to the available existing tools and approaches, an analysis of ECHA's published final decisions associated with all levels of compliance checks and testing proposals, the consideration and expression of uncertainty, the use of biological support data, and the impact of the ECHA Read-Across Assessment Framework (RAAF) published in 2015. PMID:26863606

CAAT Altex workshop paper entitled "Towards Good Read ...

EPA Pesticide Factsheets

Grouping of substances and utilizing read-across within those groups represents an important data gap filling technique for chemical safety assessments. Categories/analogue groups are typically developed based on structural similarity, and increasingly often, also on mechanistic similarity. While read-across can play a key role in complying with legislations such as the European REACH legislation, the lack of consensus regarding the extent and type of evidence necessary to support it often hampers it’s successful application and acceptance by regulatory authorities. Despite a potentially broad user community, expertise is still concentrated across a handful of organizations and individuals. In order to facilitate the effective use of read-across, this document aims to summarize the state-of-the-art, summarise insights learned from reviewing ECHA published decisions as far as the relative successes/pitfalls surrounding read-across under the REACH and compile the relevant activities and guidance documents. Special emphasis is given to the available existing tools and approaches, the consideration and expression of uncertainty, the use of biological support data and the potential impact of the ECHA Read-Across Assessment Framework (RAAF) which was published in 2015. This is a paper that summarises different activities and research needs for read-across for regulatory purposes that has been compiled as a result of a CAAT initiative led by Thomas Hartung.

Reading in Autism Spectrum Disorders: A Literature Review.

PubMed

Fernandes, Fernanda Dreux Miranda; de La Higuera Amato, Cibelle Albuquerque; Cardoso, Carla; Navas, Ana Luiza Gomes Pinto; Molini-Avejonas, Daniela Regina

2015-01-01

To review what the literature says about reading abilities of children on the autism spectrum (autism spectrum disorders, ASD) as well as to assess the results of intervention proposals. The broad ASD diagnosis used in the last decades and the resulting changes in the prevalence of these disorders have led to a relevant increase in the number of children diagnosed with ASD in the school system. The purpose of this review is to identify the different profiles of reading abilities shown by children with ASD described in the recent literature and the results of reported intervention methods. A review of the literature was conducted in the Web of Sciences and PubMed databases with the keywords 'autism' AND 'read*' and the filter 2010-2015. All articles published in the last 5 years focusing on description of and intervention for reading abilities in individuals with ASD were included. Review articles were excluded. The selected 58 articles were divided into those that described reading abilities in individuals with ASD (n = 27) and those that reported intervention procedures for reading development (n = 31). Direct comparisons and associations were prevented due to different inclusion criteria and lack of detailed information about intervention processes. We propose tentative conclusions that should be confirmed by further studies. © 2016 S. Karger AG, Basel.

[Dust absorption capacities of eight evergreen broad-leaved plants in Beijing, China.

PubMed

Fan, Shu Xin; Cai, Yu; Dong, Li

2017-02-01

Aiming at selecting the evergreen broad-leaved plants with excellent dust capturing capacity that can be applied in Beijing area for improving the urban vegetation dust removal, this study selected 8 evergreen (including semi-evergreen) broad-leaved plants used in urban green-space in Beijing area to measure the dust absorption per unit leaf area by the elution-mass method during winter and early spring in 2014. The dust deposition per leaf and per plant of each species was further calculated for tested species. Based on the dust capturing capacity measured in different units, cluster analysis on the comprehensive dust absorption capacities of different plants was carried out from the corresponding aspect. Results showed that the dust absorption ability differed significantly among the 8 evergreen broad-leaved (including semi-evergreen) species including Buxus sinica, Euonymus japonicus, Ligustrum quihoui, L. vicaryi, E. kiautschovicus, Indocalamus tessellatus, Phyllostachys violascens and Ph. aureosulcata. E. japonicus was best in dust absorption per unit leaf area and per plant, with 1.36 g·m -2 and 59.63 g·plant -1 . I. tessellates (with 1.62 mg·leaf -1 ) had the strongest dust absorption ability per leaf. With different measurement units selected, the ranking changed. The cluster analysis based on the multi index comprehensive dust absorption capacities could roughly divided the 8 evergreen broad-leaved species into 4 categories representing different dust absorption capacity levels. E. japonicus and Ph. sviolascens had the outstanding comprehensive dust capturing capacity, while B. sinica, L. vicaryi and Ph. aureosulcata showed the weak performance.

A paralogue of the phosphomutase-like gene family in Candida glabrata, CgPmu2, gained broad-range phosphatase activity due to a small number of clustered substitutions.

PubMed

Orlando, Kelly A; Iosue, Christine L; Leone, Sarah G; Davies, Danielle L; Wykoff, Dennis D

2015-10-15

Inorganic phosphate is required for a range of cellular processes, such as DNA/RNA synthesis and intracellular signalling. The phosphate starvation-inducible phosphatase activity of Candida glabrata is encoded by the gene CgPMU2 (C. glabrata phosphomutase-like protein). CgPMU2 is part of a three-gene family (∼75% identical) created through gene duplication in the C. glabrata clade; only CgPmu2 is a PHO-regulated broad range acid phosphatase. We identified amino acids that confer broad range phosphatase activity on CgPmu2 by creating fusions of sections of CgPMU2 with CgPMU1, a paralogue with little broad range phosphatase activity. We used site-directed mutagenesis on various fusions to sequentially convert CgPmu1 to CgPmu2. Based on molecular modelling of the Pmu proteins on to a histidine phosphatase crystal structure, clusters of amino acids were found in two distinct regions that were able to confer phosphatase activity. Substitutions in these two regions together conferred broad phosphatase activity on CgPmu1. Interestingly, one change is a histidine adjacent to the active site histidine of CgPmu2 and it exhibits a novel ability to partially replace the conserved active site histidine in CgPmu2. Additionally, a second amino acid change was able to confer nt phosphatase activity to CgPmu1, suggesting single amino acid changes neofunctionalize CgPmu2. © 2015 Authors; published by Portland Press Limited.

Elevated levels of ferrimagnetic metals in foodchains supporting the Guam cluster of neurodegeneration: do metal nucleated crystal contaminants [corrected] evoke magnetic fields that initiate the progressive pathogenesis of neurodegeneration?

PubMed

Purdey, Mark

2004-01-01

Elevated levels of aluminium (Al), strontium (Sr), barium (Ba), iron (Fe), manganese (Mn) cations - combined with deficiencies of magnesium (Mg)/calcium (Ca) - have been observed in the foodchains that traditionally support the Chamorro populations affected by high incidence clusters of Alzheimer (AD), Parkinson-like (PD), motor neurone diseases and multiple sclerosis on the island of Guam. Soils drawn from the cluster region demonstrated an excessive fivefold increase in 'magnetic susceptibility' readings in relation to soils from disease free adjoining regions. A multifactorial aetiological hypothesis is proposed that pivots upon the combined exposure to high levels of natural/industrial sources of ferrimagnetic/ferroelectric compounds incorporating Al, Fe, Mn, Sr, Ba (e.g., via yam/seafood consumption or exposure to world war 2 (WW2) munitions) and to low levels of Mg/Ca in all S. Pacific locations where these clusters of neurodegenerative disease have simultaneously erupted. Once gut/blood brain barrier permeability is impaired, the increased uptake of Al, Fe, Sr, Ba, or Mn into the Mg/Ca depleted brain leads to rogue metal substitutions at the Mg/Ca vacated binding domains on various enzyme/proteoglycan groups, causing a broad ranging disruption in Mg/Ca dependent systems - such as the glutamine synthetase which prevents the accumulation of neurotoxic glutamate. The rogue metals chelate sulphate, disrupting sulphated-proteoglycan mediated inhibition of crystal proliferation, as well as its regulation of the Fibroblast growth factor receptor complex which disturbs the molecular conformation of those receptors and their regulation of transphosphorylation between intracellular kinase domains; ultimately collapsing proteoglycan mediated cell-cell signalling pathways which maintain the growth and structural integrity of the neuronal networks. The depression of Mg/Ca dependent systems in conjunction with the progressive ferrimagnetisation of the CNS due to an overload of rogue ferroelectric/ferrimagnetic metal contaminants, enables 'seeding' of metal-protein crystalline arrays that can proliferate in the proteoglycan depleted brain. The resulting magnetic field emissions initiate a free radical mediated progressive pathogenesis of neurodegeneration. The co-clustering of these various types of disease in select geographical pockets around the world suggests that all of these conditions share a common early life exposure to ferromagnetic metal nucleating agents in their multifactorial aetiology. Factors such as individual genetics, the species of metal involved, etc., dictate which specific class of disease will emerge as a delayed neurotoxic response to these environmental insults.

Custom-made foot orthoses: an analysis of prescription characteristics from an Australian commercial orthotic laboratory.

PubMed

Menz, Hylton B; Allan, Jamie J; Bonanno, Daniel R; Landorf, Karl B; Murley, George S

2017-01-01

Foot orthoses are widely used in the prevention and treatment of foot disorders. The aim of this study was to describe characteristics of custom-made foot orthosis prescriptions from a Australian podiatric orthotic laboratory. One thousand consecutive foot orthosis prescription forms were obtained from a commercial prescription foot orthosis laboratory located in Melbourne, Victoria, Australia (Footwork Podiatric Laboratory). Each item from the prescription form was documented in relation to orthosis type, cast correction, arch fill technique, cast modifications, shell material, shell modifications and cover material. Cluster analysis and discriminant function analysis were applied to identify patterns in the prescription data. Prescriptions were obtained from 178 clinical practices across Australia and Hong Kong, with patients ranging in age from 5 to 92 years. Three broad categories ('clusters') were observed that were indicative of increasing 'control' of rearfoot pronation. A combination of five variables (rearfoot cast correction, cover shape, orthosis type, forefoot cast correction and plantar fascial accommodation) was able to identify these clusters with an accuracy of 70%. Significant differences between clusters were observed in relation to age and sex of the patient and the geographic location of the prescribing clinician. Foot orthosis prescriptions are complex, but can be broadly classified into three categories. Selection of these prescription subtypes appears to be influenced by both patient factors (age and sex) and clinician factors (clinic location).

Biosynthesis of the acetyl‐CoA carboxylase‐inhibiting antibiotic, andrimid in Serratia is regulated by Hfq and the LysR‐type transcriptional regulator, AdmX

PubMed Central

Nogellova, Veronika; Morel, Bertrand; Krell, Tino

2016-01-01

Summary Infections due to multidrug‐resistant bacteria represent a major global health challenge. To combat this problem, new antibiotics are urgently needed and some plant‐associated bacteria are a promising source. The rhizobacterium Serratia plymuthica A153 produces several bioactive secondary metabolites, including the anti‐oomycete and antifungal haterumalide, oocydin A and the broad spectrum polyamine antibiotic, zeamine. In this study, we show that A153 produces a second broad spectrum antibiotic, andrimid. Using genome sequencing, comparative genomics and mutagenesis, we defined new genes involved in andrimid (adm) biosynthesis. Both the expression of the adm gene cluster and regulation of andrimid synthesis were investigated. The biosynthetic cluster is operonic and its expression is modulated by various environmental cues, including temperature and carbon source. Analysis of the genome context of the adm operon revealed a gene encoding a predicted LysR‐type regulator, AdmX, apparently unique to Serratia strains. Mutagenesis and gene expression assays demonstrated that AdmX is a transcriptional activator of the adm gene cluster. At the post‐transcriptional level, the expression of the adm cluster is positively regulated by the RNA chaperone, Hfq, in an RpoS‐independent manner. Our results highlight the complexity of andrimid biosynthesis – an antibiotic with potential clinical and agricultural utility. PMID:26914969

Coherent clusters of inertial particles in homogeneous turbulence

NASA Astrophysics Data System (ADS)

Baker, Lucia; Frankel, Ari; Mani, Ali; Coletti, Filippo

2016-11-01

Clustering of heavy particles in turbulent flows manifests itself in a broad spectrum of physical phenomena, including sediment transport, cloud formation, and spray combustion. However, a clear topological definition of particle cluster has been lacking, limiting our ability to describe their features and dynamics. Here we introduce a definition of coherent cluster based on self-similarity, and apply it to the distribution of heavy particles in direct numerical simulations of homogeneous isotropic turbulence. We consider a range of particle Stokes numbers, with and without the effect of gravity. Clusters show self-similarity at length scales larger than twice the Kolmogorov length, with a specific fractal dimension. In the absence of gravity, clusters demonstrate a tendency to sample regions of the flow where strain is dominant over vorticity, and to align themselves with the local vorticity vector; when gravity is present, the clusters tend to align themselves with gravity, and their fall speed is different from the average settling velocity. This approach yields observations which are consistent with findings obtained from previous studies while opening new avenues for analysis of the topology and evolution of particle clusters in a wealth of applications.

Distinct differences in striatal dysmorphology between attention deficit hyperactivity disorder boys with and without a comorbid reading disability.

PubMed

Goradia, Dhruman D; Vogel, Sherry; Mohl, Brianne; Khatib, Dalal; Zajac-Benitez, Caroline; Rajan, Usha; Robin, Arthur; Rosenberg, David R; Stanley, Jeffrey A

2016-12-30

There is evidence of greater cognitive deficits in attention deficit hyperactivity disorder with a comorbid reading disability (ADHD/+RD) compared to ADHD alone (ADHD/-RD). Additionally, the striatum has been consistently implicated in ADHD. However, the extent of morphological alterations in the striatum of ADHD/+RD is poorly understood, which is the main purpose of this study. Based on structural MRI images, the surface deformation of the caudate and putamen was assessed in 59 boys matching in age and IQ [19 ADHD/-RD, 15 ADHD/+RD and 25 typically developing controls (TDC)]. A vertex based analysis with multiple comparison correction was conducted to compare ADHD/-RD and ADHD/+RD to TDC. Compared to TDC, ADHD/+RD showed multiple bilateral significant clusters of surface compression. In contrast, ADHD/-RD showed fewer significant clusters of surface compression and restricted to the left side. Regarding the putamen, only ADHD/-RD showed significant clusters of surface compression. Results demonstrate for the first time a greater extent of morphological alterations in the caudate of ADHD/+RD than ADHD/-RD compared to TDC, which may suggest greater implicated cortical areas projecting to the caudate that are associated with the greater neuropsychological impairments observed in ADHD/+RD. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Map reading tools for map libraries.

USGS Publications Warehouse

Greenberg, G.L.

1982-01-01

Engineers, navigators and military strategists employ a broad array of mechanical devices to facilitate map use. A larger number of map users such as educators, students, tourists, journalists, historians, politicians, economists and librarians are unaware of the available variety of tools which can be used with maps to increase the speed and efficiency of their application and interpretation. This paper identifies map reading tools such as coordinate readers, protractors, dividers, planimeters, and symbol-templets according to a functional classification. Particularly, arrays of tools are suggested for use in determining position, direction, distance, area and form (perimeter-shape-pattern-relief). -from Author

A cluster randomized control field trial of the ABRACADABRA web-based reading technology: replication and extension of basic findings

PubMed Central

Piquette, Noella A.; Savage, Robert S.; Abrami, Philip C.

2014-01-01

The present paper reports a cluster randomized control trial evaluation of teaching using ABRACADABRA (ABRA), an evidence-based and web-based literacy intervention (http://abralite.concordia.ca) with 107 kindergarten and 96 grade 1 children in 24 classes (12 intervention 12 control classes) from all 12 elementary schools in one school district in Canada. Children in the intervention condition received 10–12 h of whole class instruction using ABRA between pre- and post-test. Hierarchical linear modeling of post-test results showed significant gains in letter-sound knowledge for intervention classrooms over control classrooms. In addition, medium effect sizes were evident for three of five outcome measures favoring the intervention: letter-sound knowledge (d= +0.66), phonological blending (d = +0.52), and word reading (d = +0.52), over effect sizes for regular teaching. It is concluded that regular teaching with ABRA technology adds significantly to literacy in the early elementary years. PMID:25538663

Cascades on a class of clustered random networks

NASA Astrophysics Data System (ADS)

Hackett, Adam; Melnik, Sergey; Gleeson, James P.

2011-05-01

We present an analytical approach to determining the expected cascade size in a broad range of dynamical models on the class of random networks with arbitrary degree distribution and nonzero clustering introduced previously in [M. E. J. Newman, Phys. Rev. Lett. PRLTAO0031-900710.1103/PhysRevLett.103.058701103, 058701 (2009)]. A condition for the existence of global cascades is derived as well as a general criterion that determines whether increasing the level of clustering will increase, or decrease, the expected cascade size. Applications, examples of which are provided, include site percolation, bond percolation, and Watts’ threshold model; in all cases analytical results give excellent agreement with numerical simulations.

Stages of Drama: Classical to Contemporary Theater. Third Edition.

ERIC Educational Resources Information Center

Klaus, Carl H.; And Others

Organized along broadly historical lines, this comprehensive collection of outstanding plays includes 41 works from the classical Greek period to the contemporary. As an introduction to the theater, the collection is unmatched for its theatrical variety and cultural diversity. It provides: (1) a general introduction on reading and witnessing a…

Einstein as a Missionary of Science

ERIC Educational Resources Information Center

Renn, Jürgen

2013-01-01

The paper reviews Einstein's engagement as a mediator and popularizer of science. It discusses the formative role of popular scientific literature for the young Einstein, showing that not only his broad scientific outlook but also his internationalist political views were shaped by these readings. Then, on the basis of recent detailed…

Promising Practices for Providing Alternative Media to Postsecondary Students with Print Disabilities

ERIC Educational Resources Information Center

Wolfe, Gerri L.; Lee, Christopher

2007-01-01

For postsecondary students with disabilities influencing reading performance, printed class materials pose a substantial barrier and have a negative impact on academic achievement. Digital technologies offer alternative ways of accessing print materials for students with print-related disabilities. Alternative media is a broad term that…

Motivating Literacy Learners in Today's World

ERIC Educational Resources Information Center

Fletcher, J., Ed.; Parkhill, F., Ed.; Gillon, G., Ed.

2010-01-01

"Motivating Literacy Learners in Today's World" provides insights into a broad spectrum of children's literacy learning. Motivation is the key theme and the authors show how this can be achieved through reading for pleasure; in writing activities at a number of levels; and through oral language development. Chapters include: (1)…

Language and Literacy Development of Children with Williams Syndrome

ERIC Educational Resources Information Center

Mervis, Carolyn B.

2009-01-01

Williams syndrome is a rare neurodevelopmental disorder caused by deletion of approximately 25 genes on chromosome 7q11.23. Children with the syndrome evidence large individual differences in both broad language and reading abilities. Nevertheless, as a group, children with this syndrome show a consistent pattern characterized by relative…

A New Kind of Currency: Informational Text Literacy in Elementary School

ERIC Educational Resources Information Center

Rowe, Sarah Stebbe

2012-01-01

In the current global economy, skills in the informational text genres are increasingly important for communicating ideas among professionals. The Reading Framework for the 2009 National Assessment of Educational Progress described informational text broadly as a major type of text that includes exposition, argumentation or persuasive text, and…

Literacy and Schooling.

ERIC Educational Resources Information Center

Bloome, David, Ed.

This book offers a broad range of perspectives on the study of literacy in which reading and writing is examined as it occurs in classrooms, businesses, communities, and families, among other settings. The book contains the following chapters: (1) "In Search of Meaning" (Judith Green); (2) "The Development of Literacy: Access, Acquisition and…

Learning by Experience in a Standardized Testing Culture: Investigation of a Middle School Experiential Learning Program

ERIC Educational Resources Information Center

Scogin, Stephen C.; Kruger, Christopher J.; Jekkals, Regan E.; Steinfeldt, Chelsea

2017-01-01

Standardized testing pressure sometimes discourages schools from broadly implementing experiential learning opportunities. However, some K-12 schools are challenging the trend with greater commitment to learning by experience. STREAM (science, technology, reading, engineering, arts, mathematics) school is a project-based program providing students…

Transformation of Patriarchal Regimes, Literacy, and Schooling

ERIC Educational Resources Information Center

Miller, Pavla

2003-01-01

Literacy has been among the most publicly contested domains in gender struggles; the way that history of literacy is gendered and interpreted makes a difference to the way reading and writing is thought of today. Broadly understood, gender signals a wide range of concerns with subjectivities, social relations, and historical dynamics. Literacy…

Le Francais Moderne, (Modern French) Part II.

ERIC Educational Resources Information Center

Dade County Public Schools, Miami, FL.

Performance objectives and broad goals for listening, speaking, reading, and writing skills in French instruction are presented in this text. Cultural awareness and student attitude are also considered. Vocabulary and structure of the course are presented through three situations: shopping, meeting a train, and making vacation plans. Short films…

Neither Broad nor Bold

ERIC Educational Resources Information Center

Peterson, Paul E.

2012-01-01

Children raised in families with higher incomes score higher on math and reading tests. But is parental income the "cause" of a child's success? Or is the connection between income and achievement largely a symptom of something else: genetic heritage, parental skill, or a supportive educational setting? The Broader, Bolder Approach to Education, a…

Using Technology to Support STEM Reading

ERIC Educational Resources Information Center

Schneps, Matthew H.; O'Keeffe, Jamie K.; Heffner-Wong, Amanda; Sonnert, Gerhard

2010-01-01

Tasks in science, technology, engineering, and mathematics (STEM) are unusually varied because they target phenomena occurring in diverse domains and call upon a wide range of abilities to perform them. The fact that STEM tasks cover such a broad spectrum of abilities makes these fields uncharacteristically inclusive: Individuals with disabilities…

Designing and Delivering Cross-Cultural Instruction.

ERIC Educational Resources Information Center

Ben-Yoseph, Miriam

A course on management in a cross-cultural environment was designed to address dilemmas and opportunities that individuals might encounter in work or study. The course attracted students with a broad variety of backgrounds. A main textbook was supplemented with readings, guest lectures, and a variety of class activities including case studies,…

Title VI-B Evaluation Report 1976-77. New York State Education for the Handicapped Act.

ERIC Educational Resources Information Center

Cronk, George A., Jr.

The report summarizes pupil behavioral change data from 176 instructional projects involving handicapped children in New York state. Data are presented for reading achievement, mathematics achievement, and a broad category that encompassed language arts, corrective speech, psychomotor, auditory and visual perceptions, personal hygiene, societal…

Teaching Interdisciplinary Thematic Units in Language Arts. ERIC Digest.

ERIC Educational Resources Information Center

Ritter, Naomi

This Digest discusses teaching interdisciplinary thematic units in language arts, noting that such units typically integrate broad areas of knowledge, such as social studies, mathematics, or ecology with the teaching of the four major language skills: reading, writing, listening, and speaking. The Digest presents a definition and rationale for…

Inferred vs Realized Patterns of Gene Flow: An Analysis of Population Structure in the Andros Island Rock Iguana

PubMed Central

Colosimo, Giuliano; Knapp, Charles R.; Wallace, Lisa E.; Welch, Mark E.

2014-01-01

Ecological data, the primary source of information on patterns and rates of migration, can be integrated with genetic data to more accurately describe the realized connectivity between geographically isolated demes. In this paper we implement this approach and discuss its implications for managing populations of the endangered Andros Island Rock Iguana, Cyclura cychlura cychlura. This iguana is endemic to Andros, a highly fragmented landmass of large islands and smaller cays. Field observations suggest that geographically isolated demes were panmictic due to high, inferred rates of gene flow. We expand on these observations using 16 polymorphic microsatellites to investigate the genetic structure and rates of gene flow from 188 Andros Iguanas collected across 23 island sites. Bayesian clustering of specimens assigned individuals to three distinct genotypic clusters. An analysis of molecular variance (AMOVA) indicates that allele frequency differences are responsible for a significant portion of the genetic variance across the three defined clusters (Fst =  0.117, p0.01). These clusters are associated with larger islands and satellite cays isolated by broad water channels with strong currents. These findings imply that broad water channels present greater obstacles to gene flow than was inferred from field observation alone. Additionally, rates of gene flow were indirectly estimated using BAYESASS 3.0. The proportion of individuals originating from within each identified cluster varied from 94.5 to 98.7%, providing further support for local isolation. Our assessment reveals a major disparity between inferred and realized gene flow. We discuss our results in a conservation perspective for species inhabiting highly fragmented landscapes. PMID:25229344

Molecular Cloning and Characterization of a P-Glycoprotein from the Diamondback Moth, Plutella xylostella (Lepidoptera: Plutellidae)

PubMed Central

Tian, Lixia; Yang, Jiaqiang; Hou, Wenjie; Xu, Baoyun; Xie, Wen; Wang, Shaoli; Zhang, Youjun; Zhou, Xuguo; Wu, Qingjun

2013-01-01

Macrocyclic lactones such as abamectin and ivermectin constitute an important class of broad-spectrum insecticides. Widespread resistance to synthetic insecticides, including abamectin and ivermectin, poses a serious threat to the management of diamondback moth, Plutella xylostella (L.) (Lepidoptera: Plutellidae), a major pest of cruciferous plants worldwide. P-glycoprotein (Pgp), a member of the ABC transporter superfamily, plays a crucial role in the removal of amphiphilic xenobiotics, suggesting a mechanism for drug resistance in target organisms. In this study, PxPgp1, a putative Pgp gene from P. xylostella, was cloned and characterized. The open reading frame (ORF) of PxPgp1 consists of 3774 nucleotides, which encodes a 1257-amino acid peptide. The deduced PxPgp1 protein possesses structural characteristics of a typical Pgp, and clusters within the insect ABCB1. PxPgp1 was expressed throughout all developmental stages, and showed the highest expression level in adult males. PxPgp1 was highly expressed in midgut, malpighian tubules and testes. Elevated expression of PxPgp1 was observed in P. xylostella strains after they were exposed to the abamectin treatment. In addition, the constitutive expressions of PxPgp1 were significantly higher in laboratory-selected and field-collected resistant strains in comparison to their susceptible counterpart. PMID:24264038

Intensive Reading Remediation in Grade 2 or 3: Are There Effects a Decade Later?

PubMed Central

Blachman, Benita A.; Schatschneider, Christopher; Fletcher, Jack M.; Murray, Maria S.; Munger, Kristen A.; Vaughn, Michael G.

2014-01-01

Despite data supporting the benefits of early reading interventions, there has been little evaluation of the long-term educational impact of these interventions, with most follow-up studies lasting less than two years (Suggate, 2010). This study evaluated reading outcomes more than a decade after the completion of an 8-month reading intervention using a randomized design with second and third graders selected on the basis of poor word-level skills (Blachman et al., 2004). Fifty-eight (84%) of the original 69 participants took part in the study. The treatment group demonstrated a moderate to small effect size advantage on reading and spelling measures over the comparison group. There were statistically significant differences with moderate effect sizes between treatment and comparison groups on standardized measures of word recognition (i.e., Woodcock Basic Skills Cluster, d = 0.53; Woodcock Word Identification, d = 0.62), the primary, but not exclusive, focus of the intervention. Statistical tests on other reading and spelling measures did not reach thresholds for statistical significance. Patterns in the data related to other educational outcomes, such as high school completion, favored the treatment participants, although differences were not significant. PMID:24578581

Distinguishing Fear Versus Distress Symptomatology in Pediatric OCD.

PubMed

Rozenman, Michelle; Peris, Tara; Bergman, R Lindsey; Chang, Susanna; O'Neill, Joseph; McCracken, James T; Piacentini, John

2017-02-01

Prior research has identified OCD subtypes or "clusters" of symptoms that differentially relate to clinical features of the disorder. Given the high comorbidity between OCD and anxiety, OCD symptom clusters may more broadly associate with fear and/or distress internalizing constructs. This study examines fear and distress dimensions, including physical concerns (fear), separation anxiety (fear), perfectionism (distress), and anxious coping (distress), as predictors of previously empirically-derived OCD symptom clusters in a sample of 215 youth diagnosed with primary OCD (ages 7-17, mean age = 12.25). Self-reported separation fears predicted membership in Cluster 1 (aggressive, sexual, religious, somatic obsessions, and checking compulsions) while somatic/autonomic fears predicted membership in Cluster 2 (symmetry obsessions and ordering, counting, repeating compulsions). Results highlight the diversity of pediatric OCD symptoms and their differential association with fear, suggesting the need to carefully assess both OCD and global fear constructs that might be directly targeted in treatment.

Near-Infrared Spectroscopy of Small Protonated Water Clusters

NASA Astrophysics Data System (ADS)

Wagner, J. Philipp; McDonald, David C., II; McCoy, Anne B.; Duncan, Michael A.

2017-06-01

Small protonated water clusters and their argon tagged analogues of the general formula H^{+}(H_{2}O)_{n}Ar_{m} have been generated in a pulsed electric discharge source. Clusters containing n=1-8 water molecules were mass-selected and their absorptions in the near-infrared were probed with a tunable Nd/colonYAG pumped OPA/OPA laser system in the region from 4850-7350 cm^{-1}. A doublet corresponding to overtones of the free O-H stretches of the external waters was observed around 7200 cm^{-1} that was continuously decreasing in intensity with increasing cluster size. Broad, mostly featureless absorptions were found around 5300 cm^{-1} associated with stretch/bend combinations and with the hydrogen bonded waters in the core of the clusters. Vibrational assignments were substantiated by comparison to anharmonic frequency computations via second-order vibrational perturbation theory (VPT2) at the MP2/aug-cc-pVTZ level of theory.

A taxonomy of accountable care organizations for policy and practice.

PubMed

Shortell, Stephen M; Wu, Frances M; Lewis, Valerie A; Colla, Carrie H; Fisher, Elliott S

2014-12-01

To develop an exploratory taxonomy of Accountable Care Organizations (ACOs) to describe and understand early ACO development and to provide a basis for technical assistance and future evaluation of performance. Data from the National Survey of Accountable Care Organizations, fielded between October 2012 and May 2013, of 173 Medicare, Medicaid, and commercial payer ACOs. Drawing on resource dependence and institutional theory, we develop measures of eight attributes of ACOs such as size, scope of services offered, and the use of performance accountability mechanisms. Data are analyzed using a two-step cluster analysis approach that accounts for both continuous and categorical data. We identified a reliable and internally valid three-cluster solution: larger, integrated systems that offer a broad scope of services and frequently include one or more postacute facilities; smaller, physician-led practices, centered in primary care, and that possess a relatively high degree of physician performance management; and moderately sized, joint hospital-physician and coalition-led groups that offer a moderately broad scope of services with some involvement of postacute facilities. ACOs can be characterized into three distinct clusters. The taxonomy provides a framework for assessing performance, for targeting technical assistance, and for diagnosing potential antitrust violations. © Health Research and Educational Trust.

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

PubMed

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

2010-06-01

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

Rotational velocities of newly discovered, low-mass members of the Alpha Persei cluster

NASA Technical Reports Server (NTRS)

Stauffer, John R.; Hartmann, Lee W.; Jones, Burton F.

1989-01-01

About 30 new, low-mass members of the young open cluster Alpha Persei are identified via a proper-motion study and subsequent photometric and spectroscopic observations. Membership in the cluster is confirmed for a number of the fainter proper-motion candidates from Heckman, Dieckvoss, and Kox (1956). Coordinates, finding charts, BVRI photometry, and rotational velocities are provided for most of the stars. At least two of the stars show peculiar H-alpha emission profiles, with weak but very broad emission wings, and relatively narrow absorption reversals. The rotational velocity distribution for low-mass stars in the Alpha Per cluster are compared with recently derived rotational velocity distributions for T Tauri stars, placing strong constraints on the mechanisms for angular momentum loss during pre-main-sequence evolution.

Human Services. Georgia Core Standards for Occupational Clusters.

ERIC Educational Resources Information Center

Georgia Univ., Athens. Dept. of Occupational Studies.

This document lists core standards and occupational knowledge and skills that have been identified and validated by industry as necessary to all Georgia students in secondary-level human services occupations programs. First, foundation skills are grouped as follows: basic skills (reading, writing, arithmetic/mathematics, listening, speaking);…

Technical/Engineering. Georgia Core Standards for Occupational Clusters.

ERIC Educational Resources Information Center

Georgia Univ., Athens. Dept. of Occupational Studies.

This document lists core standards and occupational knowledge and skills that have been identified and validated by industry as necessary to all Georgia students in secondary-level technical/engineering programs. First, foundation skills are grouped as follows: basic skills (reading, writing, arithmetic/mathematics, listening, speaking); thinking…

Health Care. Georgia Core Standards for Occupational Clusters.

ERIC Educational Resources Information Center

Georgia Univ., Athens. Dept. of Occupational Studies.

This document lists core standards and occupational knowledge and skills that have been identified/validated by industry as necessary to all Georgia students in secondary-level health care occupations programs. First, foundation skills are grouped as follows: basic skills (reading, writing, arithmetic/mathematics, listening, speaking); thinking…

Softly, Softly

ERIC Educational Resources Information Center

Diamond, Abigail

2008-01-01

The term "soft skills" encompasses a cluster of personality traits, language abilities, personal habits and, ultimately, values and attitudes. Soft skills complement "harder", more technical, skills, such as being able to read or type a letter, but they also have a significant impact on the ability of people to do their jobs…

Publisher Correction: Cluster richness-mass calibration with cosmic microwave background lensing

NASA Astrophysics Data System (ADS)

Geach, James E.; Peacock, John A.

2018-03-01

Owing to a technical error, the `Additional information' section of the originally published PDF version of this Letter incorrectly gave J.A.P. as the corresponding author; it should have read J.E.G. This has now been corrected. The HTML version is correct.

Recovery in a letter-by-letter reader: more efficiency at the expense of normal reading strategy.

PubMed

Ablinger, Irene; Huber, Walter; Schattka, Kerstin I; Radach, Ralph

2013-01-01

Although changes in reading performance of recovering letter-by-letter readers have been described in some detail, no prior research has provided an in-depth analysis of the underlying adaptive word processing strategies. Our work examined the reading performance of a letter-by-letter reader, FH, over a period of 15 months, using eye movement methodology to delineate the recovery process at two different time points (T1, T2). A central question is whether recovery is characterized either by moving back towards normal word processing or by refinement and possibly automatization of an existing pathological strategy that was developed in response to the impairment. More specifically, we hypothesized that letter-by-letter reading may be executed with at least four different strategies and our work sought to distinguish between these alternatives. During recovery significant improvements in reading performance were achieved. A shift of fixation positions from the far left to the extreme right of target words was combined with many small and very few longer regressive saccades. Apparently, 'letter-by-letter reading' took the form of local clustering, most likely corresponding to the formation of sublexical units of analysis. This pattern was more pronounced at T2, suggesting that improvements in reading efficiency may come at the expense of making it harder to eventually return to normal reading.

Reading in the brain of children and adults: a meta-analysis of 40 functional magnetic resonance imaging studies.

PubMed

Martin, Anna; Schurz, Matthias; Kronbichler, Martin; Richlan, Fabio

2015-05-01

We used quantitative, coordinate-based meta-analysis to objectively synthesize age-related commonalities and differences in brain activation patterns reported in 40 functional magnetic resonance imaging (fMRI) studies of reading in children and adults. Twenty fMRI studies with adults (age means: 23-34 years) were matched to 20 studies with children (age means: 7-12 years). The separate meta-analyses of these two sets showed a pattern of reading-related brain activation common to children and adults in left ventral occipito-temporal (OT), inferior frontal, and posterior parietal regions. The direct statistical comparison between the two meta-analytic maps of children and adults revealed higher convergence in studies with children in left superior temporal and bilateral supplementary motor regions. In contrast, higher convergence in studies with adults was identified in bilateral posterior OT/cerebellar and left dorsal precentral regions. The results are discussed in relation to current neuroanatomical models of reading and tentative functional interpretations of reading-related activation clusters in children and adults are provided. © 2015 Wiley Periodicals, Inc.

Molecular Subtyping to Detect Human Listeriosis Clusters

PubMed Central

Sauders, Brian D.; Fortes, Esther D.; Morse, Dale L.; Dumas, Nellie; Kiehlbauch, Julia A.; Schukken, Ynte; Hibbs, Jonathan R.

2003-01-01

We analyzed the diversity (Simpson’s Index, D) and distribution of Listeria monocytogenes in human listeriosis cases in New York State (excluding New York City) from November 1996 to June 2000 by using automated ribotyping and pulsed-field gel electrophoresis (PFGE). We applied a scan statistic (p<0.05) to detect listeriosis clusters caused by a specific Listeria monocytogenes subtype. Of 131 human isolates, 34 (D=0.923) ribotypes and 74 (D=0.975) PFGE types were found. Nine (31% of cases) clusters were identified by ribotype or PFGE; five (18% of cases) clusters were identified by using both methods. Two of the nine clusters (13% of cases) identified corresponded with investigated multistate listeriosis outbreaks. While most human listeriosis cases are considered sporadic, highly discriminatory molecular subtyping approaches thus indicated that 13% to 31% of cases reported in New York State may represent single-source clusters. Listeriosis control and reduction efforts should include broad-based subtyping of human isolates and consider that a large number of cases may represent outbreaks. PMID:12781006

Transcriptome deep-sequencing and clustering of expressed isoforms from Favia corals

PubMed Central

2013-01-01

Background Genomic and transcriptomic sequence data are essential tools for tackling ecological problems. Using an approach that combines next-generation sequencing, de novo transcriptome assembly, gene annotation and synthetic gene construction, we identify and cluster the protein families from Favia corals from the northern Red Sea. Results We obtained 80 million 75 bp paired-end cDNA reads from two Favia adult samples collected at 65 m (Fav1, Fav2) on the Illumina GA platform, and generated two de novo assemblies using ABySS and CAP3. After removing redundancy and filtering out low quality reads, our transcriptome datasets contained 58,268 (Fav1) and 62,469 (Fav2) contigs longer than 100 bp, with N50 values of 1,665 bp and 1,439 bp, respectively. Using the proteome of the sea anemone Nematostella vectensis as a reference, we were able to annotate almost 20% of each dataset using reciprocal homology searches. Homologous clustering of these annotated transcripts allowed us to divide them into 7,186 (Fav1) and 6,862 (Fav2) homologous transcript clusters (E-value ≤ 2e-30). Functional annotation categories were assigned to homologous clusters using the functional annotation of Nematostella vectensis. General annotation of the assembled transcripts was improved 1-3% using the Acropora digitifera proteome. In addition, we screened these transcript isoform clusters for fluorescent proteins (FPs) homologs and identified seven potential FP homologs in Fav1, and four in Fav2. These transcripts were validated as bona fide FP transcripts via robust fluorescence heterologous expression. Annotation of the assembled contigs revealed that 1.34% and 1.61% (in Fav1 and Fav2, respectively) of the total assembled contigs likely originated from the corals’ algal symbiont, Symbiodinium spp. Conclusions Here we present a study to identify the homologous transcript isoform clusters from the transcriptome of Favia corals using a far-related reference proteome. Furthermore, the symbiont-derived transcripts were isolated from the datasets and their contribution quantified. This is the first annotated transcriptome of the genus Favia, a major increase in genomics resources available in this important family of corals. PMID:23937070

Segmentation of overweight Americans and opportunities for social marketing

PubMed Central

Kolodinsky, Jane; Reynolds, Travis

2009-01-01

Background The food industry uses market segmentation to target products toward specific groups of consumers with similar attitudinal, demographic, or lifestyle characteristics. Our aims were to identify distinguishable segments within the US overweight population to be targeted with messages and media aimed at moving Americans toward more healthy weights. Methods Cluster analysis was used to identify segments of consumers based on both food and lifestyle behaviors related to unhealthy weights. Drawing from Social Learning Theory, the Health Belief Model, and existing market segmentation literature, the study identified five distinct, recognizable market segments based on knowledge and behavioral and environmental factors. Implications for social marketing campaigns designed to move Americans toward more healthy weights were explored. Results The five clusters identified were: Highest Risk (19%); At Risk (22%); Right Behavior/Wrong Results (33%); Getting Best Results (13%); and Doing OK (12%). Ninety-nine percent of those in the Highest Risk cluster were overweight; members watched the most television and exercised the least. Fifty-five percent of those in the At Risk cluster were overweight; members logged the most computer time and almost half rarely or never read food labels. Sixty-six percent of those in the Right Behavior/Wrong Results cluster were overweight; however, 95% of them were familiar with the food pyramid. Members reported eating a low percentage of fast food meals (8%) compared to other groups but a higher percentage of other restaurant meals (15%). Less than six percent of those in the Getting Best Results cluster were overweight; every member read food labels and 75% of members' meals were "made from scratch." Eighteen percent of those in the Doing OK cluster were overweight; members watched the least television and reported eating 78% of their meals "made from scratch." Conclusion This study demonstrated that five distinct market segments can be identified for social marketing efforts aimed at addressing the obesity epidemic. Through the identification of these five segments, social marketing campaigns can utilize selected channels and messages that communicate the most relevant and important information. The results of this study offer insight into how segmentation strategies and social marketing messages may improve public health. PMID:19267936

Segmentation of overweight Americans and opportunities for social marketing.

PubMed

Kolodinsky, Jane; Reynolds, Travis

2009-03-08

The food industry uses market segmentation to target products toward specific groups of consumers with similar attitudinal, demographic, or lifestyle characteristics. Our aims were to identify distinguishable segments within the US overweight population to be targeted with messages and media aimed at moving Americans toward more healthy weights. Cluster analysis was used to identify segments of consumers based on both food and lifestyle behaviors related to unhealthy weights. Drawing from Social Learning Theory, the Health Belief Model, and existing market segmentation literature, the study identified five distinct, recognizable market segments based on knowledge and behavioral and environmental factors. Implications for social marketing campaigns designed to move Americans toward more healthy weights were explored. The five clusters identified were: Highest Risk (19%); At Risk (22%); Right Behavior/Wrong Results (33%); Getting Best Results (13%); and Doing OK (12%). Ninety-nine percent of those in the Highest Risk cluster were overweight; members watched the most television and exercised the least. Fifty-five percent of those in the At Risk cluster were overweight; members logged the most computer time and almost half rarely or never read food labels. Sixty-six percent of those in the Right Behavior/Wrong Results cluster were overweight; however, 95% of them were familiar with the food pyramid. Members reported eating a low percentage of fast food meals (8%) compared to other groups but a higher percentage of other restaurant meals (15%). Less than six percent of those in the Getting Best Results cluster were overweight; every member read food labels and 75% of members' meals were "made from scratch." Eighteen percent of those in the Doing OK cluster were overweight; members watched the least television and reported eating 78% of their meals "made from scratch." This study demonstrated that five distinct market segments can be identified for social marketing efforts aimed at addressing the obesity epidemic. Through the identification of these five segments, social marketing campaigns can utilize selected channels and messages that communicate the most relevant and important information. The results of this study offer insight into how segmentation strategies and social marketing messages may improve public health.

Identifying Subgroups of Tinnitus Using Novel Resting State fMRI Biomarkers and Cluster Analysis

DTIC Science & Technology

2017-10-13

AWARD NUMBER: W81XWH-15-2-0032 TITLE: Identifying Subgroups of Tinnitus Using Novel Resting State fMRI Biomarkers and Cluster Analysis...TITLE AND SUBTITLE 5a. CONTRACT NUMBER W81XWH-15-2-0032 5b. GRANT NUMBER Identifying Subgroups of Tinnitus Using Novel Resting State fMRI...Release; Distribution Unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT The subject of the project is FY14 PRMRP Topic Area – Tinnitus . The broad goal is

Visualization of Unsteady Computational Fluid Dynamics

NASA Technical Reports Server (NTRS)

Haimes, Robert

1997-01-01

The current compute environment that most researchers are using for the calculation of 3D unsteady Computational Fluid Dynamic (CFD) results is a super-computer class machine. The Massively Parallel Processors (MPP's) such as the 160 node IBM SP2 at NAS and clusters of workstations acting as a single MPP (like NAS's SGI Power-Challenge array and the J90 cluster) provide the required computation bandwidth for CFD calculations of transient problems. If we follow the traditional computational analysis steps for CFD (and we wish to construct an interactive visualizer) we need to be aware of the following: (1) Disk space requirements. A single snap-shot must contain at least the values (primitive variables) stored at the appropriate locations within the mesh. For most simple 3D Euler solvers that means 5 floating point words. Navier-Stokes solutions with turbulence models may contain 7 state-variables. (2) Disk speed vs. Computational speeds. The time required to read the complete solution of a saved time frame from disk is now longer than the compute time for a set number of iterations from an explicit solver. Depending, on the hardware and solver an iteration of an implicit code may also take less time than reading the solution from disk. If one examines the performance improvements in the last decade or two, it is easy to see that depending on disk performance (vs. CPU improvement) may not be the best method for enhancing interactivity. (3) Cluster and Parallel Machine I/O problems. Disk access time is much worse within current parallel machines and cluster of workstations that are acting in concert to solve a single problem. In this case we are not trying to read the volume of data, but are running the solver and the solver outputs the solution. These traditional network interfaces must be used for the file system. (4) Numerics of particle traces. Most visualization tools can work upon a single snap shot of the data but some visualization tools for transient problems require dealing with time.

Identification of the Coumermycin A1 Biosynthetic Gene Cluster of Streptomyces rishiriensis DSM 40489

PubMed Central

Wang, Zhao-Xin; Li, Shu-Ming; Heide, Lutz

2000-01-01

The biosynthetic gene cluster of the aminocoumarin antibiotic coumermycin A1 was cloned by screening of a cosmid library of Streptomyces rishiriensis DSM 40489 with heterologous probes from a dTDP-glucose 4,6-dehydratase gene, involved in deoxysugar biosynthesis, and from the aminocoumarin resistance gyrase gene gyrBr. Sequence analysis of a 30.8-kb region upstream of gyrBr revealed the presence of 28 complete open reading frames (ORFs). Fifteen of the identified ORFs showed, on average, 84% identity to corresponding ORFs in the biosynthetic gene cluster of novobiocin, another aminocoumarin antibiotic. Possible functions of 17 ORFs in the biosynthesis of coumermycin A1 could be assigned by comparison with sequences in GenBank. Experimental proof for the function of the identified gene cluster was provided by an insertional gene inactivation experiment, which resulted in an abolishment of coumermycin A1 production. PMID:11036020

SPAX - PAX with Super-Pages

NASA Astrophysics Data System (ADS)

Bößwetter, Daniel

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

Redox Biochemistry | Bioenergy | NREL

Science.gov Websites

binuclear cofactors of the hydrogenase catalytic sites. (A) shows the NiFe cluster of [NiFe(Se font) are labeled. Ni, nickel; Se, selenium; Fe, iron. [FeFe]- and [NiFe]-hydrogenase diversity [NiFe]-hydrogenase diversity, mechanism, and maturation. Read more Previous Story Next Story Featured

Environmental and Agricultural Sciences. Georgia Core Standards for Occupational Clusters.

ERIC Educational Resources Information Center

Georgia Univ., Athens. Dept. of Occupational Studies.

This document lists core standards and occupational knowledge amd skills that have been identified/validated by industry as necessary to all Georgia students in secondary-level environmental and agricultural sciences programs. First, foundation skills are grouped as follows: basic skills (reading, writing, arithmetic/mathematics, listening,…

Business, Marketing, and Information Management. Georgia Core Standards for Occupational Clusters.

ERIC Educational Resources Information Center

Georgia Univ., Athens. Dept. of Occupational Studies.

This document lists core standards and occupational knowledge and skills that have been identified and validated by industry as necessary to all Georgia students in business, marketing, and information management programs. First, foundation skills are grouped as follows: basic skills (reading, writing, arithmetic/mathematics, listening, speaking);…

Critical Perspectives on the National Policy on Education 2016

ERIC Educational Resources Information Center

Bhattacharya, Somdatta; Deb, Swarupa; Nair, Hari; Shukla, Tanu; Yadav, Anupam

2017-01-01

This article brings together critical perspectives on a broad range of issues that emerge from a reading of the National Policy on Education 2016. The issues vary from accountability to transdisciplinarity and from the marginalization of transgender people to value education. Such a complex task of critiquing this policy document cannot be…

Schools and Society: A Sociological Approach to Education, Third Edition

ERIC Educational Resources Information Center

Ballantine, Jeanne H., Ed.; Spade, Joan Z., Ed.

2007-01-01

This third edition, now published by Pine Forge Press, features original readings and article excerpts by leaders in the area of Sociology of Education. With a wide array of theoretical perspectives, a broad range of respected sources, and inclusion of both classic and contemporary studies, this comprehensive, integrated text addresses key issues…

Estimating the Reliability of Dichotomous or Trichotomous Scores

ERIC Educational Resources Information Center

Feldt, Leonard S.

2005-01-01

To meet the requirements of the No Child Left Behind Act, school districts and states must compile summary reports of the levels of student achievement in reading and mathematics. The levels are to be described in broad categories: "basic and below," "proficient," or "advanced." Educational units are given considerable latitude in defining the…

Democracy and Bildung/Erziehung--Towards a Universal Theory of Education

ERIC Educational Resources Information Center

Bellmann, Johannes; Su, Hanno

2017-01-01

Dewey's "Democracy and Education" is re-read as an attempt to develop a universal theory of education that, on the one hand, gives the broadest, most general view on education and, on the other hand, contextualizes every observation by binding it to the assumed perspective. Dewey's broad concept of education encompasses two dimensions…

On the Irrelevance of Intelligence in Predicting Responsiveness to Reading Instruction

ERIC Educational Resources Information Center

Fuchs, Douglas; Young, Caresa L.

2006-01-01

There is increasingly negative sentiment against IQ-achievement discrepancy as a method to identify children with learning disabilities (LD) and, more broadly, intelligence as an explanation of poor academic performance. The evidence for this latter view was examined by reviewing 13 studies involving 1,542 children who were at risk or reading…

English Linguistics, An Introductory Reader.

ERIC Educational Resources Information Center

Hungerford, Harold, Ed.; And Others

The readings in this volume have been selected for college level and graduate students in English who need an introduction to English linguistics which is neither too advanced or specialized, but has a broad range of interests. The editors (Harold Hungerford, Jay Robinson, and James Sledd) have prepared this anthology to use in their own teaching,…

Methods of Identification of Students with Learning Disabilities in Reading: Perceptions of Administrators in Illinois and Implications for School Psychologists

ERIC Educational Resources Information Center

Hopper, Christy L.

2014-01-01

School psychologists' training provides a variety of skills from which its practitioners may draw, including consultation, intervention, counseling, staff development, and assessment. Despite these broad skills, school psychologists' primary roles involve assessment and assessment-related tasks, generally as related to eligibility determination…

Broad & Balanced Accountability

ERIC Educational Resources Information Center

Rothstein, Richard; Jacobsen, Rebecca

2009-01-01

From the time of the Founding Fathers to the late 20th century, U.S. citizens have expected their schools to teach math and reading--and also social studies, history, science, the arts and music, character development, citizenship education, work skills, and emotional and physical health and fitness. Yet because No Child Left Behind (NCLB) and its…

Physical Education: Essential Issues

ERIC Educational Resources Information Center

Green, Ken, Ed.; Hardman, Ken, Ed.

2005-01-01

This book is aimed primarily at under and postgraduate students pursuing entire programmes or discrete courses and modules in the broad area of physical education and sport in schools. It consists of a collection of what is considered to be essential readings in the sense that they are contributions from eminent authors on a breadth of salient…

Literary Ideas and Scripts for Young Playwrights

ERIC Educational Resources Information Center

Kaniut Cobb, Lisa

2006-01-01

This collection presents techniques for tapping a broad range of literary sources to inspire young writers. Drawing upon poetry, folk tales, story jokes, and more, Literary Ideas walks students in grades 3-8 through the process of creating new stories and developing them as scripts for choral readings, readers theatre, and classroom plays. The…

The Development of a Broad Spectrum Treatment for Patients with Alcohol Dependence in Early Recovery

ERIC Educational Resources Information Center

Gulliver, Suzy Bird; Longabaugh, Richard; Davidson, Dena; Swift, Robert

2005-01-01

Estimates of the prevalence of alcohol dependence among Americans approach 14% (Read, Kahler, & Stevenson, 2001). Alcohol dependence was once considered among the most recalcitrant of problem behaviors, with only 20% to 30% attaining sustained abstinence (Hunt Barnett & Branch 1971). Although current definitions of treatment success now consider…

Caring for young forests

Treesearch

W. Keith Moser

2012-01-01

Sustaining Young Forest Communities is a good compilation of knowledge about an important forest ecosystem and belongs on the bookshelf of every natural resource practitioner tasked with managing this important resource. One of the principal benefits for anyone who reads this book is that it provides both a broad overview and a reference source for the various...

Fiction-reading for good or ill: eating disorders, interpretation and the case for creative bibliotherapy research.

PubMed

Troscianko, Emily T

2018-04-21

Compared with self-help bibliotherapy, little is known about the efficacy of creative bibliotherapy or the mechanisms of its possible efficacy for eating disorders or any other mental health condition. It is clear, however, that fiction is widely used informally as a therapeutic or antitherapeutic tool and that it has considerable potential in both directions, with a possibly significant distinction between the effects of reading fiction about eating disorders (which may-contrary to theoretical predictions-be broadly negative in effect) or one's preferred genre of other fiction (which may be broadly positive). Research on creative bibliotherapy, especially systematic experimental research, is lacking and requires a medical humanities approach, drawing on knowledge and methods from psychology and cognitive literary studies as well as clinical disciplines to expand our understanding of how the dynamic processes of interpretation mediate between textual structures and characteristics of mental health and illness. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Mothers' reading skills and child survival in Nigeria: examining the relevance of mothers' decision-making power.

PubMed

Smith-Greenaway, Emily

2013-11-01

Mothers' literacy skills are emerging as a key determinant of children's health and survival in low-income contexts, with emphasis on the cognitive and psychological agency that literacy skills provide. This work has clearly established a strong association between mothers' reading skills--a key subcomponent of broader literacy and language skills--and child mortality. However, this relatively nascent literature has not yet considered how broader social structures condition the process. In Nigeria and in sub-Saharan Africa more broadly, gender-based social inequality constrains many mothers' decision-making power over children's health matters; this structural feature may condition the association between mothers' reading skills and child mortality. This paper uses data from the 2003 Nigerian Demographic and Health Survey (N = 12,076) to test the conditionality of the relationship between mothers' reading skills and child survival on mothers' decision-making power, highlighting how structural realities should factor more heavily into this individual-action-oriented literature. Among Nigerian children whose mothers have decision-making power, mothers' reading skills convey a 27 percent lower risk of child mortality; however, for children whose mothers lack decision-making power, mothers' reading skills do not yield a significant survival advantage. Overall, these findings support the need for future work to further analyze how broader social structures condition the benefits of mothers' reading skills for children's health. Copyright © 2013 Elsevier Ltd. All rights reserved.

Mothers’ Reading Skills and Child Survival in Nigeria: Examining the Relevance of Mothers’ Decision-Making Power

PubMed Central

Smith-Greenaway, Emily

2013-01-01

Mothers’ literacy skills are emerging as a key determinant of children’s health and survival in low-income contexts, with emphasis on the cognitive and psychological agency that literacy skills provide. This work has clearly established a strong association between mothers’ reading skills—a key subcomponent of broader literacy and language skills—and child mortality. However, this relatively nascent literature has not yet considered how broader social structures condition the process. In Nigeria and in sub-Saharan Africa more broadly, gender-based social inequality constrains many mothers’ decision-making power over children’s health matters; this structural feature may condition the association between mothers’ reading skills and child mortality. This paper uses data from the 2003 Nigerian Demographic and Health Survey (N = 12,076) to test the conditionality of the relationship between mothers’ reading skills and child survival on mothers’ decision-making power, highlighting how structural realities should factor more heavily into this individual-action-oriented literature. Among Nigerian children whose mothers have decision-making power, mothers’ reading skills convey a 27 percent lower risk of child mortality; however, for children whose mothers lack decision-making power, mothers’ reading skills do not yield a significant survival advantage. Overall, these findings support the need for future work to further analyze how broader social structures condition the benefits of mothers’ reading skills for children’s health. PMID:24161100

Differences in the effects of school meals on children's cognitive performance according to gender, household education and baseline reading skills.

PubMed

Sørensen, L B; Damsgaard, C T; Petersen, R A; Dalskov, S-M; Hjorth, M F; Dyssegaard, C B; Egelund, N; Tetens, I; Astrup, A; Lauritzen, L; Michaelsen, K F

2016-10-01

We previously found that the OPUS School Meal Study improved reading and increased errors related to inattention and impulsivity. This study explored whether the cognitive effects differed according to gender, household education and reading proficiency at baseline. This is a cluster-randomised cross-over trial comparing Nordic school meals with packed lunch from home (control) for 3 months each among 834 children aged 8 to 11 years. At baseline and at the end of each dietary period, we assessed children's performance in reading, mathematics and the d2-test of attention. Interactions were evaluated using mixed models. Analyses included 739 children. At baseline, boys and children from households without academic education were poorer readers and had a higher d2-error%. Effects on dietary intake were similar in subgroups. However, the effect of the intervention on test outcomes was stronger in boys, in children from households with academic education and in children with normal/good baseline reading proficiency. Overall, this resulted in increased socioeconomic inequality in reading performance and reduced inequality in impulsivity. Contrary to this, the gender difference decreased in reading and increased in impulsivity. Finally, the gap between poor and normal/good readers was increased in reading and decreased for d2-error%. The effects of healthy school meals on reading, impulsivity and inattention were modified by gender, household education and baseline reading proficiency. The differential effects might be related to environmental aspects of the intervention and deserves to be investigated further in future school meal trials.

Advanced Reading Comprehension Expectations in Secondary School: Considerations for Students with Emotional or Behavior Disorders

PubMed Central

Ciullo, Stephen; Ortiz, Miriam B.; Al Otaiba, Stephanie; Lane, Kathleen Lynne

2015-01-01

The debate around recent implementation of the Common Core Standards (CCSS) has perplexed many policy makers, practitioners, and researchers; yet there remains broad agreement for the need to improve reading outcomes and college and career readiness for all students, including students with disabilities. One of the most vulnerable populations with disabilities in terms of college and career readiness is students with emotional disorders (ED). A considerable percentage of students with ED encounter unfavorable academic and long-term outcomes, often due to reading difficulties and behavioral variables that impede learning. To date, the impact of rising expectations in reading on the education of students with ED has been absent from this conversation about CCSS. In this article, we consider the implications of new reading expectations in the critical period of Grades 6-12 for students with ED. First, we summarize grade level expectations of the standards. Then, we describe the characteristics and underachievement of students with ED. Next, we evaluate challenges in meeting the expectations based on extant research, and provide recommendations for practice based on the intervention literature. We conclude by prioritizing a research and policy agenda that advocates for increasing the likelihood of success in reading for students with ED in middle school and high school. PMID:27403040

Rate- and accuracy-disabled subtype profiles among adults with dyslexia in the Hebrew orthography.

PubMed

Shany, Michal; Breznitz, Zvia

2011-01-01

This study examined a subtyping scheme rooted in the dissociation between reading rate and accuracy in an exceptionally large sample of adult readers with dyslexia using a wide variety of behavioral and event-related potential (ERP) measures. Stage 1 was a behavioral study, in which basic reading skill, reading comprehension, linguistic and cognitive tasks were administered to 661 learning-disabled university students (n = 382) and their non-learning-disabled peers (n = 279). Based on a word reading measure, accuracy-disabled and rate-disabled subgroups were identified, as was a subgroup with deficits in both rate and accuracy. The results support the persistence of a rate versus accuracy dissociation into adulthood. Accuracy disability was related to a broad range of deficits affecting phonological, orthographic, and morphological processing, verbal memory, attention, and reading comprehension. Rate disability appeared to be associated with slower processing of printed material, alongside largely intact functioning resembling those of skilled readers. In stage 2, electroencephalogram (EEG)-ERP measurements were obtained from 140 participants recruited from the larger sample. Activation in visual association cortex, indicated by the N170 amplitude, was found to be lower for accuracy-disabled than skilled readers, and comparable between rate-disabled and skilled readers. The lowest amplitude was found in the double-deficit subgroup. The findings support the existence of distinctive reading disability profiles, based on selective deficits in reading rate versus accuracy and associated with different basic reading, linguistic, and cognitive skills as well as electrophysiological responses.

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

PubMed

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

2018-05-01

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

The impact of radiation feedback on the assembly of star clusters in a galactic context

NASA Astrophysics Data System (ADS)

Guillard, Nicolas; Emsellem, Eric; Renaud, Florent

2018-07-01

Massive star clusters are observed in galaxies spanning a broad range of luminosities and types, and are assumed to form in dense gas-rich environments. Using a parsec-resolution hydrodynamical simulation of an isolated gas-rich low-mass galaxy, we discuss here the non-linear effects of stellar feedback on the properties of star clusters with a focus on the progenitors of nuclear clusters. Our simulation shows two categories of star clusters: those for which feedback expels gas leftovers associated with their formation sites, and those, in a denser environment, around which feedback fails to totally clear the gas. We confirm that radiation feedback (photoionization and radiative pressure) plays a more important role than Type II supernovae in destroying dense gas structures, and in altering or quenching the subsequent cluster formation. Radiation feedback also disturbs the cluster mass growth, by increasing the internal energy of the gas component to the point at which radiation pressure overcomes the cluster gravity. We discuss how these effects may depend on the local properties of the interstellar medium, and also on the details of the subgrid recipes, which can affect the available cluster gas reservoirs, the evolution of potential nuclear cluster progenitors, and the overall galaxy morphology.

Locating qualitative studies in dementia on MEDLINE, EMBASE, CINAHL, and PsycINFO: A comparison of search strategies.

PubMed

Rogers, Morwenna; Bethel, Alison; Abbott, Rebecca

2017-10-28

Qualitative research in dementia improves understanding of the experience of people affected by dementia. Searching databases for qualitative studies is problematic. Qualitative-specific search strategies might help with locating studies. To examine the effectiveness (sensitivity and precision) of 5 qualitative strategies on locating qualitative research studies in dementia in 4 major databases (MEDLINE, EMBASE, PsycINFO, and CINAHL). Qualitative dementia studies were checked for inclusion on MEDLINE, EMBASE, PsycINFO, and CINAHL. Five qualitative search strategies (subject headings, simple free-text terms, complex free-text terms, and 2 broad-based strategies) were tested for study retrieval. Specificity, precision and number needed to read were calculated. Two hundred fourteen qualitative studies in dementia were included. PsycINFO and CINAHL held the most qualitative studies out the 4 databases studied (N = 171 and 166, respectively) and both held unique records (N = 14 and 7, respectively). The controlled vocabulary strategy in CINAHL returned 96% (N = 192) of studies held; by contrast, controlled vocabulary in PsycINFO returned 7% (N = 13) of studies held. The broad-based strategies returned more studies (93-99%) than the other free-text strategies (22-82%). Precision ranged from 0.061 to 0.004 resulting in a number needed to read to obtain 1 relevant study ranging from 16 (simple free-text search in CINAHL) to 239 (broad-based search in EMBASE). Qualitative search strategies using 3 broad terms were more sensitive than long complex searches. The controlled vocabulary for qualitative research in CINAHL was particularly effective. Furthermore, results indicate that MEDLINE and EMBASE offer little benefit for locating qualitative dementia research if CINAHL and PSYCINFO are also searched. Copyright © 2017 John Wiley & Sons, Ltd.

Study on the coloration response of a radiochromic film to MeV cluster ion beams

NASA Astrophysics Data System (ADS)

Yuri, Yosuke; Narumi, Kazumasa; Chiba, Atsuya; Hirano, Yoshimi; Saitoh, Yuichi

2017-11-01

A radiochromic film, Gafchromic HD-V2, is applied to a possible method of measuring a two-dimensional (2D) spatial profile of MeV cluster ion beams. The coloration responses of the HD-V2 film to MeV carbon and gold cluster ion beams are experimentally investigated since some cluster effect may appear. The degree of the film coloration is quantified as a change in optical density (OD) by reading the films with an image scanner for high-resolution measurement of the 2D beam profile. The OD response of HD-V2 is characterized as a function of the ion and atom fluence for comparison. The dependences of the OD response on the cluster size, kinetic energy, and ion species are discussed. It is found that the sensitivity of the OD change is reduced when the cluster size is large. The beam profile of MeV cluster ion beams delivered from the tandem accelerator in TIARA is characterized from the measurement result using HD-V2 films. The present results show that the use of the Gafchromic HD-V2 film is suitable for the detail beam profile measurement of MeV cluster ions, especially C60 ions, whose available intensity is rather low in comparison with that of monatomic ion beams.

The miR-290-295 cluster as multi-faceted players in mouse embryonic stem cells.

PubMed

Yuan, Kai; Ai, Wen-Bing; Wan, Lin-Yan; Tan, Xiao; Wu, Jiang-Feng

2017-01-01

Increasing evidence indicates that embryonic stem cell specific microRNAs (miRNAs) play an essential role in the early development of embryo. Among them, the miR-290-295 cluster is the most highly expressed in the mouse embryonic stem cells and involved in various biological processes. In this paper, we reviewed the research progress of the function of the miR-290-295 cluster in embryonic stem cells. The miR-290-295 cluster is involved in regulating embryonic stem cell pluripotency maintenance, self-renewal, and reprogramming somatic cells to an embryonic stem cell-like state. Moreover, the miR-290-295 cluster has a latent pro-survival function in embryonic stem cells and involved in tumourigenesis and senescence with a great significance. Elucidating the interaction between the miR-290-295 cluster and other modes of gene regulation will provide us new ideas on the biology of pluripotent stem cells. In the near future, the broad prospects of the miRNA cluster will be shown in the stem cell field, such as altering cell identities with high efficiency through the transient introduction of tissue-specific miRNA cluster.

Plasma flow around and charge distribution of a dust cluster in a rf discharge

NASA Astrophysics Data System (ADS)

Schleede, J.; Lewerentz, L.; Bronold, F. X.; Schneider, R.; Fehske, H.

2018-04-01

We employ a particle-in-cell Monte Carlo collision/particle-particle particle-mesh simulation to study the plasma flow around and the charge distribution of a three-dimensional dust cluster in the sheath of a low-pressure rf argon discharge. The geometry of the cluster and its position in the sheath are fixed to the experimental values, prohibiting a mechanical response of the cluster. Electrically, however, the cluster and the plasma environment, mimicking also the experimental situation, are coupled self-consistently. We find a broad distribution of the charges collected by the grains. The ion flux shows on the scale of the Debye length strong focusing and shadowing inside and outside the cluster due to the attraction of the ions to the negatively charged grains, whereas the electron flux is characterized on this scale only by a weak spatial modulation of its magnitude depending on the rf phase. On the scale of the individual dust potentials, however, the electron flux deviates in the vicinity of the cluster strongly from the laminar flow associated with the plasma sheath. It develops convection patterns to compensate for the depletion of electrons inside the dust cluster.

Hitomi Constraints on the 3.5 keV Line in the Perseus Galaxy Cluster

DOE PAGES

Aharonian, F. A.; Akamatsu, H.; Akimoto, F.; ...

2017-03-03

High-resolution X-ray spectroscopy with Hitomi was expected to resolve the origin of the faint unidentifiedmore » $$E\\approx 3.5\\,\\mathrm{keV}$$ emission line reported in several low-resolution studies of various massive systems, such as galaxies and clusters, including the Perseus cluster. We have analyzed the Hitomi first-light observation of the Perseus cluster. The emission line expected for Perseus based on the XMM-Newton signal from the large cluster sample under the dark matter decay scenario is too faint to be detectable in the Hitomi data. However, the previously reported 3.5 keV flux from Perseus was anomalously high compared to the sample-based prediction. We find no unidentified line at the reported high flux level. Taking into account the XMM measurement uncertainties for this region, the inconsistency with Hitomi is at a 99% significance for a broad dark matter line and at 99.7% for a narrow line from the gas. We do not find anomalously high fluxes of the nearby faint K line or the Ar satellite line that were proposed as explanations for the earlier 3.5 keV detections. We do find a hint of a broad excess near the energies of high-n transitions of S xvi ($$E\\simeq 3.44\\,\\mathrm{keV}$$ rest-frame)—a possible signature of charge exchange in the molecular nebula and another proposed explanation for the unidentified line. While its energy is consistent with XMM pn detections, it is unlikely to explain the MOS signal. In conclusion, a confirmation of this interesting feature has to wait for a more sensitive observation with a future calorimeter experiment.« less

Emission of terahertz waves in the interaction of a laser pulse with clusters

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

Frolov, A. A., E-mail: frolov@ihed.ras.ru

2016-07-15

A theory of generation of terahertz radiation in the interaction of a femtosecond laser pulse with a spherical cluster is developed for the case in which the density of free electrons in the cluster plasma exceeds the critical value. The spectral, angular, and energy characteristics of the emitted terahertz radiation are investigated, as well as its spatiotemporal structure. It is shown that the directional pattern of radiation has a quadrupole structure and that the emission spectrum has a broad maximum at a frequency nearly equal to the reciprocal of the laser pulse duration. It is found that the total radiatedmore » energy depends strongly on the cluster size. Analysis of the spatiotemporal profile of the terahertz signal shows that it has a femtosecond duration and contains only two oscillation cycles.« less

Draft Genome Sequencing and Comparative Analysis of Aspergillus sojae NBRC4239

PubMed Central

Sato, Atsushi; Oshima, Kenshiro; Noguchi, Hideki; Ogawa, Masahiro; Takahashi, Tadashi; Oguma, Tetsuya; Koyama, Yasuji; Itoh, Takehiko; Hattori, Masahira; Hanya, Yoshiki

2011-01-01

We conducted genome sequencing of the filamentous fungus Aspergillus sojae NBRC4239 isolated from the koji used to prepare Japanese soy sauce. We used the 454 pyrosequencing technology and investigated the genome with respect to enzymes and secondary metabolites in comparison with other Aspergilli sequenced. Assembly of 454 reads generated a non-redundant sequence of 39.5-Mb possessing 13 033 putative genes and 65 scaffolds composed of 557 contigs. Of the 2847 open reading frames with Pfam domain scores of >150 found in A. sojae NBRC4239, 81.7% had a high degree of similarity with the genes of A. oryzae. Comparative analysis identified serine carboxypeptidase and aspartic protease genes unique to A. sojae NBRC4239. While A. oryzae possessed three copies of α-amyalse gene, A. sojae NBRC4239 possessed only a single copy. Comparison of 56 gene clusters for secondary metabolites between A. sojae NBRC4239 and A. oryzae revealed that 24 clusters were conserved, whereas 32 clusters differed between them that included a deletion of 18 508 bp containing mfs1, mao1, dmaT, and pks-nrps for the cyclopiazonic acid (CPA) biosynthesis, explaining the no productivity of CPA in A. sojae. The A. sojae NBRC4239 genome data will be useful to characterize functional features of the koji moulds used in Japanese industries. PMID:21659486

New Statistical Methodology for Determining Cancer Clusters

Cancer.gov

The development of an innovative statistical technique that shows that women living in a broad stretch of the metropolitan northeastern United States, which includes Long Island, are slightly more likely to die from breast cancer than women in other parts of the Northeast.

Molecular comparison of the structural proteins encoding gene clusters of two related Lactobacillus delbrueckii bacteriophages.

PubMed Central

Vasala, A; Dupont, L; Baumann, M; Ritzenthaler, P; Alatossava, T

1993-01-01

Virulent phage LL-H and temperate phage mv4 are two related bacteriophages of Lactobacillus delbrueckii. The gene clusters encoding structural proteins of these two phages have been sequenced and further analyzed. Six open reading frames (ORF-1 to ORF-6) were detected. Protein sequencing and Western immunoblotting experiments confirmed that ORF-3 (g34) encoded the main capsid protein Gp34. The presence of a putative late promoter in front of the phage LL-H g34 gene was suggested by primer extension experiments. Comparative sequence analysis between phage LL-H and phage mv4 revealed striking similarities in the structure and organization of this gene cluster, suggesting that the genes encoding phage structural proteins belong to a highly conservative module. Images PMID:8497043

A broad survey reveals substitution tolerance of residues ligating FeS clusters in [NiFe] hydrogenase

PubMed Central

2014-01-01

Background In order to understand the effects of FeS cluster attachment in [NiFe] hydrogenase, we undertook a study to substitute all 12 amino acid positions normally ligating the three FeS clusters in the hydrogenase small subunit. Using the hydrogenase from Alteromonas macleodii “deep ecotype” as a model, we substituted one of four amino acids (Asp, His, Asn, Gln) at each of the 12 ligating positions because these amino acids are alternative coordinating residues in otherwise conserved-cysteine positions found in a broad survey of NiFe hydrogenase sequences. We also hoped to discover an enzyme with elevated hydrogen evolution activity relative to a previously reported “G1” (H230C/P285C) improved enzyme in which the medial FeS cluster Pro and the distal FeS cluster His were each substituted for Cys. Results Among all the substitutions screened, aspartic acid substitutions were generally well-tolerated, and examination suggests that the observed deficiency in enzyme activity may be largely due to misprocessing of the small subunit of the enzyme. Alignment of hydrogenase sequences from sequence databases revealed many rare substitutions; the five substitutions present in databases that we tested all exhibited measurable hydrogen evolution activity. Select substitutions were purified and tested, supporting the results of the screening assay. Analysis of these results confirms the importance of small subunit processing. Normalizing activity to quantity of mature small subunit, indicative of total enzyme maturation, weakly suggests an improvement over the “G1” enzyme. Conclusions We have comprehensively screened 48 amino acid substitutions of the hydrogenase from A. macleodii “deep ecotype”, to understand non-canonical ligations of amino acids to FeS clusters and to improve hydrogen evolution activity of this class of hydrogenase. Our studies show that non-canonical ligations can be functional and also suggests a new limiting factor in the production of active enzyme. PMID:24934472

Broad DNA methylation changes of spermatogenesis, inflammation and immune response-related genes in a subgroup of sperm samples for assisted reproduction.

PubMed

Schütte, B; El Hajj, N; Kuhtz, J; Nanda, I; Gromoll, J; Hahn, T; Dittrich, M; Schorsch, M; Müller, T; Haaf, T

2013-11-01

Aberrant sperm DNA methylation patterns, mainly in imprinted genes, have been associated with male subfertility and oligospermia. Here, we performed a genome-wide methylation analysis in sperm samples representing a wide range of semen parameters. Sperm DNA samples of 38 males attending a fertility centre were analysed with Illumina HumanMethylation27 BeadChips, which quantify methylation of >27 000 CpG sites in cis-regulatory regions of almost 15 000 genes. In an unsupervised analysis of methylation of all analysed sites, the patient samples clustered into a major and a minor group. The major group clustered with samples from normozoospermic healthy volunteers and, thus, may more closely resemble the normal situation. When correlating the clusters with semen and clinical parameters, the sperm counts were significantly different between groups with the minor group exhibiting sperm counts in the low normal range. A linear model identified almost 3000 CpGs with significant methylation differences between groups. Functional analysis revealed a broad gain of methylation in spermatogenesis-related genes and a loss of methylation in inflammation- and immune response-related genes. Quantitative bisulfite pyrosequencing validated differential methylation in three of five significant candidate genes on the array. Collectively, we identified a subgroup of sperm samples for assisted reproduction with sperm counts in the low normal range and broad methylation changes (affecting approximately 10% of analysed CpG sites) in specific pathways, most importantly spermatogenesis-related genes. We propose that epigenetic analysis can supplement traditional semen parameters and has the potential to provide new insights into the aetiology of male subfertility. © 2013 American Society of Andrology and European Academy of Andrology.

Localization and orientation of heavy-atom cluster compounds in protein crystals using molecular replacement

PubMed Central

Dahms, Sven O.; Kuester, Miriam; Streb, Carsten; Roth, Christian; Sträter, Norbert; Than, Manuel E.

2013-01-01

Heavy-atom clusters (HA clusters) containing a large number of specifically arranged electron-dense scatterers are especially useful for experimental phase determination of large complex structures, weakly diffracting crystals or structures with large unit cells. Often, the determination of the exact orientation of the HA cluster and hence of the individual heavy-atom positions proves to be the critical step in successful phasing and subsequent structure solution. Here, it is demonstrated that molecular replacement (MR) with either anomalous or isomorphous differences is a useful strategy for the correct placement of HA cluster compounds. The polyoxometallate cluster hexasodium α-metatungstate (HMT) was applied in phasing the structure of death receptor 6. Even though the HA cluster is bound in alternate partially occupied orientations and is located at a special position, its correct localization and orientation could be determined at resolutions as low as 4.9 Å. The broad applicability of this approach was demonstrated for five different derivative crystals that included the compounds tantalum tetradeca­bromide and trisodium phosphotungstate in addition to HMT. The correct placement of the HA cluster depends on the length of the intramolecular vectors chosen for MR, such that both a larger cluster size and the optimal choice of the wavelength used for anomalous data collection strongly affect the outcome. PMID:23385464

A synthesis of research on color, typography and graphics as they relate to readability

NASA Astrophysics Data System (ADS)

Lamoreaux, M. E.

1985-09-01

A foundation for future research on the use of color, typography, and graphics to improve readability is provided. Articles from the broad fields of education and psychology, as well as from the fields of journalism and printing, have been reviewed for research relating color, typography, and graphics to reading ease, speed, or comprehension. The most relevant articles reviewed are presented in an annoated bibliography; the remaining articles are also presented in bibliographic format. This literature review indicates that recognition and recall of printed material may be improved through the use of headings, underlining, color, and, especially, illustrations. Current research suggests that individuals can remember pictures far longer than past research indicates. However, researchers are divided on the usefulness of illustrations to improve reading comprehension. On the other hand, reading comprehension can be improved through the use of statistical graphs and tables if the reader is properly trained in the use of these devices.

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

ERIC Educational Resources Information Center

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

2012-01-01

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

Taoscore Teacher's Guides: Phase 3.

ERIC Educational Resources Information Center

Taos Municipal Schools, NM.

The teacher's guide to elementary level career education is comprised of 11 units of learning activities, two each for grades 1-6. Each unit is a simulation of a career cluster; through active participation in the simulation, the students develop career awareness as well as curriculum-related concepts in math, language, reading, social studies,…

The Relationship between Speech Impairment, Phonological Awareness and Early Literacy Development

ERIC Educational Resources Information Center

Harris, Judy; Botting, Nicola; Myers, Lucy; Dodd, Barbara

2011-01-01

Although children with speech impairment are at increased risk for impaired literacy, many learn to read and spell without difficulty. Around half the children with speech impairment have delayed acquisition, making errors typical of a normally developing younger child (e.g. reducing consonant clusters so that "spoon" is pronounced as…

On Sources of the Word Length Effect in Young Readers

ERIC Educational Resources Information Center

Gagl, Benjamin; Hawelka, Stefan; Wimmer, Heinz

2015-01-01

We investigated how letter length, phoneme length, and consonant clusters contribute to the word length effect in 2nd- and 4th-grade children. They read words from three different conditions: In one condition, letter length increased but phoneme length did not due to multiletter graphemes (H"aus"-B"auch"-S"chach"). In…

Issues in Education: Language Building Blocks for Climbing the Learning Tree

ERIC Educational Resources Information Center

Pandey, Anita

2012-01-01

Language is the essence of humanity and the backbone of early childhood education. Academic content clusters on it. Math, science, and social studies, for instance, are best taught through "content area language." Critical thinking and other key math, listening, and reading comprehension skills are mirrored in language. Not surprisingly, spoken…

Efficacy of Rich Vocabulary Instruction in Fourth- and Fifth-Grade Classrooms

ERIC Educational Resources Information Center

Vadasy, Patricia F.; Sanders, Elizabeth A.; Logan Herrera, Becky

2015-01-01

A multi-cohort cluster randomized trial was conducted to estimate effects of rich vocabulary classroom instruction on vocabulary and reading comprehension. A total of 1,232 fourth- and fifth-grade students from 61 classrooms in 24 schools completed the study. Students received instruction in 140 Tier Two vocabulary words featured in two…

Assessment in English 3 to 11

ERIC Educational Resources Information Center

Richmond, John

2017-01-01

This article critiques the current arrangements for the assessment and testing of English in early-years settings and primary schools in England. It is broadly supportive of the Early Years Foundation Stage Profile. It is highly critical of the Year 1 phonics check, and of the tests of reading and of grammar, punctuation and spelling at the end of…

Dynamic Indicators of Basic Early Literacy Skills: An Effective Tool to Assess Adult Literacy Students?

ERIC Educational Resources Information Center

Binder, Katherine S.; Snyder, Melissa A.; Ardoin, Scott P.; Morris, Robin K.

2011-01-01

This study examined the reliability and validity of administering Dynamic Indicators of Basic Early Literacy Skills (DIBELS) to adult basic education (ABE) students. Ninety ABE participants were administered DIBELS measures, the Woodcock-Johnson III Broad Reading (WJ III BR) measures, and four orthographic ability tests. Since ABE students are a…

Creative Process and Experiences Leading to Creative Achievement in the Case of Accomplished Architects

ERIC Educational Resources Information Center

Lee, Seon-Young; Lee, Ghang

2017-01-01

This study has identified factors stimulating creative ideas, transforming creative ideas to products, and continuing creative performance in the field of architecture based on interviews with 10 creative and successful architects. Having a penchant for liberal arts and reading books on a broad range of topics on arts, humanities, social sciences,…

Directed Activities Related to Text: Text Analysis and Text Reconstruction.

ERIC Educational Resources Information Center

Davies, Florence; Greene, Terry

This paper describes Directed Activities Related to Text (DART), procedures that were developed and are used in the Reading for Learning Project at the University of Nottingham (England) to enhance learning from texts and that fall into two broad categories: (1) text analysis procedures, which require students to engage in some form of analysis of…

Assessing a Faculty Development Program for the Adoption of Brain-Based Learning Strategies

ERIC Educational Resources Information Center

Lavis, Catherine C.; Williams, Kimberly A.; Fallin, Jana; Barnes, Pamela K.; Fishback, Sarah J.; Thien, Stephen

2016-01-01

Kansas State University designed a 20-month faculty development program with the goal of fostering broad, institution-wide adoption of teaching practices that focus on brain-based learning. Components of the program included annual teaching and learning workshops, reading and discussion groups based on content of a book about how the brain learns…

Defense Threat Reduction Agency > Research > DTRIAC > Media Collection

Science.gov Websites

*Cover a broad scope of both the pre- and post-test activities of a test series or operation *Detonations FOIA Electronic Reading Room Privacy Impact Assessment DTRA No Fear Act Reporting Nuclear Test Personnel Review NTPR Fact Sheets NTPR Radiation Dose Assessment Documents US Atmospheric Nuclear Test

Predicting Writing Development in Dual Language Instructional Contexts: Exploring Cross-Linguistic Relationships

ERIC Educational Resources Information Center

Savage, Robert; Kozakewich, Meagan; Genesee, Fred; Erdos, Caroline; Haigh, Corinne

2017-01-01

This study examined whether decoding and linguistic comprehension abilities, broadly defined by the Simple View of Reading, in grade 1 each uniquely predicted the grade 6 writing performance of English-speaking children (n = 76) who were educated bilingually in both English their first language and French, a second language. Prediction was made…

"A Feminist Just Like Us?" Teaching Mariama Ba's "So Long a Letter."

ERIC Educational Resources Information Center

Champagne, John

1996-01-01

Investigates a broad question in light of the author's own background: what is it that educators think they are doing while teaching postcolonial literature? Investigates an analogy between postcolonial and gay and lesbian studies by looking at the author's reading and teaching approach to Mariama Ba's novel "So Long a Letter." (TB)

Books for Adult New Readers. Second Revised Edition.

ERIC Educational Resources Information Center

O'Brien, Roberta Luther, Comp.

This document is an annotated bibliography of recommended print materials for English-speaking adults reading at the seventh-grade level or below. (Sixty percent of the titles are at fifth-grade level or below.) More than 95 percent of the titles are paperbacks. The titles were selected for their broad appeal to the average adult new reader.…

"The Reality of It All": History Students Read the Movies

ERIC Educational Resources Information Center

Marcus, Alan S.; Paxton, Richard J.; Meyerson, Peter

2006-01-01

What and how do students learn about history from motion pictures? How does this knowledge interact with the history they learn in school? This is a complex problem space that has seen little empirical research. To lay the groundwork for addressing these questions, we describe two exploratory studies. The first study takes a broad view, using…

Morphological Awareness and Learning to Read: A Cross-Language Perspective

ERIC Educational Resources Information Center

Kuo, Li-jen; Anderson, Richard C.

2006-01-01

In the past decade, there has been a surge of interest in morphological awareness, which refers to the ability to reflect on and manipulate morphemes and word formation rules in a language. This review provides a critical synthesis of empirical studies on this topic from a broad cross-linguistic perspective. Research with children speaking several…

Serogroup-level resolution of the “Super-7” Shiga toxin-producing Escherichia coli using nanopore single-molecule DNA sequencing

USDA-ARS?s Scientific Manuscript database

DNA sequencing and other DNA-based methods, such as PCR, are now broadly used for detection and identification of bacterial foodborne pathogens. For the identification of foodborne bacterial pathogens, it is important to make taxonomic assignments to the species, or even subspecies level. Long-read ...

Transition to College: Nonacademic Factors That Influence Persistence for Underprepared Community College Students

ERIC Educational Resources Information Center

Paulson, Ann

2012-01-01

Community colleges provide access to higher education for a broad range of students. The majority require "remedial" coursework in reading, writing and, especially, math. Most students who begin with this remedial coursework do not go on to earn a certificate or degree. Low levels of college graduation have high direct cost, adversely…

A Taxonomy of Accountable Care Organizations for Policy and Practice

PubMed Central

Shortell, Stephen M; Wu, Frances M; Lewis, Valerie A; Colla, Carrie H; Fisher, Elliott S

2014-01-01

Objective To develop an exploratory taxonomy of Accountable Care Organizations (ACOs) to describe and understand early ACO development and to provide a basis for technical assistance and future evaluation of performance. Data Sources/Study Setting Data from the National Survey of Accountable Care Organizations, fielded between October 2012 and May 2013, of 173 Medicare, Medicaid, and commercial payer ACOs. Study Design Drawing on resource dependence and institutional theory, we develop measures of eight attributes of ACOs such as size, scope of services offered, and the use of performance accountability mechanisms. Data are analyzed using a two-step cluster analysis approach that accounts for both continuous and categorical data. Principal Findings We identified a reliable and internally valid three-cluster solution: larger, integrated systems that offer a broad scope of services and frequently include one or more postacute facilities; smaller, physician-led practices, centered in primary care, and that possess a relatively high degree of physician performance management; and moderately sized, joint hospital–physician and coalition-led groups that offer a moderately broad scope of services with some involvement of postacute facilities. Conclusions ACOs can be characterized into three distinct clusters. The taxonomy provides a framework for assessing performance, for targeting technical assistance, and for diagnosing potential antitrust violations. PMID:25251146

Study of BenW (n = 1-12) clusters: An electron collision perspective

NASA Astrophysics Data System (ADS)

Modak, Paresh; Kaur, Jaspreet; Antony, Bobby

2017-08-01

This article explores electron scattering cross sections by Beryllium-Tungsten clusters (BenW). Beryllium and tungsten are important elements for plasma facing wall components, especially for the deuterium/tritium phase of ITER and in the recently installed JET. The present study focuses on different electron impact interactions in terms of elastic cross section (Qel), inelastic cross section (Qinel), ionization cross section (Qion), and momentum transfer cross section (Qmtcs) for the first twelve clusters belonging to the BenW family. It also predicts the evolution of the cross section with the size of the cluster. These cross sections are used as an input to model processes in plasma. The ionization cross section presented here is compared with the available reported data. This is the first comprehensive report on cross section data for all the above-mentioned scattering channels, to the best of our knowledge. Such broad analysis of cross section data gives vital insight into the study of local chemistry of electron interactions with BenW (n = 1-12) clusters in plasma.

Influence of the electron density on the characteristics of terahertz waves generated under laser–cluster interaction

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

Frolov, A. A., E-mail: frolov@ihed.ras.ru

2016-12-15

A theory of generation of terahertz radiation under laser–cluster interaction, developed earlier for an overdense cluster plasma [A. A. Frolov, Plasma Phys. Rep. 42. 637 (2016)], is generalized for the case of arbitrary electron density. The spectral composition of radiation is shown to substantially depend on the density of free electrons in the cluster. For an underdense cluster plasma, there is a sharp peak in the terahertz spectrum at the frequency of the quadrupole mode of a plasma sphere. As the electron density increases to supercritical values, this spectral line vanishes and a broad maximum at the frequency comparable withmore » the reciprocal of the laser pulse duration appears in the spectrum. The dependence of the total energy of terahertz radiation on the density of free electrons is analyzed. The radiation yield is shown to increase significantly under resonance conditions, when the laser frequency is close to the eigenfrequency of the dipole or quadrupole mode of a plasma sphere.« less

Using Serial and Discrete Digit Naming to Unravel Word Reading Processes

PubMed Central

Altani, Angeliki; Protopapas, Athanassios; Georgiou, George K.

2018-01-01

During reading acquisition, word recognition is assumed to undergo a developmental shift from slow serial/sublexical processing of letter strings to fast parallel processing of whole word forms. This shift has been proposed to be detected by examining the size of the relationship between serial- and discrete-trial versions of word reading and rapid naming tasks. Specifically, a strong association between serial naming of symbols and single word reading suggests that words are processed serially, whereas a strong association between discrete naming of symbols and single word reading suggests that words are processed in parallel as wholes. In this study, 429 Grade 1, 3, and 5 English-speaking Canadian children were tested on serial and discrete digit naming and word reading. Across grades, single word reading was more strongly associated with discrete naming than with serial naming of digits, indicating that short high-frequency words are processed as whole units early in the development of reading ability in English. In contrast, serial naming was not a unique predictor of single word reading across grades, suggesting that within-word sequential processing was not required for the successful recognition for this set of words. Factor mixture analysis revealed that our participants could be clustered into two classes, namely beginning and more advanced readers. Serial naming uniquely predicted single word reading only among the first class of readers, indicating that novice readers rely on a serial strategy to decode words. Yet, a considerable proportion of Grade 1 students were assigned to the second class, evidently being able to process short high-frequency words as unitized symbols. We consider these findings together with those from previous studies to challenge the hypothesis of a binary distinction between serial/sublexical and parallel/lexical processing in word reading. We argue instead that sequential processing in word reading operates on a continuum, depending on the level of reading proficiency, the degree of orthographic transparency, and word-specific characteristics. PMID:29706918

Using Serial and Discrete Digit Naming to Unravel Word Reading Processes.

PubMed

Altani, Angeliki; Protopapas, Athanassios; Georgiou, George K

2018-01-01

During reading acquisition, word recognition is assumed to undergo a developmental shift from slow serial/sublexical processing of letter strings to fast parallel processing of whole word forms. This shift has been proposed to be detected by examining the size of the relationship between serial- and discrete-trial versions of word reading and rapid naming tasks. Specifically, a strong association between serial naming of symbols and single word reading suggests that words are processed serially, whereas a strong association between discrete naming of symbols and single word reading suggests that words are processed in parallel as wholes. In this study, 429 Grade 1, 3, and 5 English-speaking Canadian children were tested on serial and discrete digit naming and word reading. Across grades, single word reading was more strongly associated with discrete naming than with serial naming of digits, indicating that short high-frequency words are processed as whole units early in the development of reading ability in English. In contrast, serial naming was not a unique predictor of single word reading across grades, suggesting that within-word sequential processing was not required for the successful recognition for this set of words. Factor mixture analysis revealed that our participants could be clustered into two classes, namely beginning and more advanced readers. Serial naming uniquely predicted single word reading only among the first class of readers, indicating that novice readers rely on a serial strategy to decode words. Yet, a considerable proportion of Grade 1 students were assigned to the second class, evidently being able to process short high-frequency words as unitized symbols. We consider these findings together with those from previous studies to challenge the hypothesis of a binary distinction between serial/sublexical and parallel/lexical processing in word reading. We argue instead that sequential processing in word reading operates on a continuum, depending on the level of reading proficiency, the degree of orthographic transparency, and word-specific characteristics.

Newspaper Reporting on a Cluster of Suicides in the UK.

PubMed

John, Ann; Hawton, Keith; Gunnell, David; Lloyd, Keith; Scourfield, Jonathan; Jones, Phillip A; Luce, Ann; Marchant, Amanda; Platt, Steve; Price, Sian; Dennis, Michael S

2017-01-01

Media reporting may influence suicide clusters through imitation or contagion. In 2008 there was extensive national and international newspaper coverage of a cluster of suicides in young people in the Bridgend area of South Wales, UK. To explore the quantity and quality of newspaper reporting during the identified cluster. Searches were conducted for articles on suicide in Bridgend for 6 months before and after the defined cluster (June 26, 2007, to September 16, 2008). Frequency, quality (using the PRINTQUAL instrument), and sensationalism were examined. In all, 577 newspaper articles were identified. One in seven articles included the suicide method in the headline, 47.3% referred to earlier suicides, and 44% used phrases that guidelines suggest should be avoided. Only 13% included sources of information or advice. A high level of poor-quality and sensationalist reporting was found during an ongoing suicide cluster at the very time when good-quality reporting could be considered important. A broad awareness of media guidelines and expansion and adherence to press codes of practice are required by journalists to ensure ethical reporting.

The quantum structure of anionic hydrogen clusters

NASA Astrophysics Data System (ADS)

Calvo, F.; Yurtsever, E.

2018-03-01

A flexible and polarizable interatomic potential has been developed to model hydrogen clusters interacting with one hydrogen anion, (H2)nH-, in a broad range of sizes n = 1-54 and parametrized against coupled cluster quantum chemical calculations. Using path-integral molecular dynamics simulations at 1 K initiated from the putative classical global minima, the equilibrium structures are found to generally rely on icosahedral shells with the hydrogen molecules pointing toward the anion, producing geometric magic numbers at sizes n = 12, 32, and 44 that are in agreement with recent mass spectrometry measurements. The energetic stability of the clusters is also connected with the extent of vibrational delocalization, measured here by the fluctuations among inherent structures hidden in the vibrational wave function. As the clusters grow, the outer molecules become increasingly free to rotate, and strong finite size effects are also found between magic numbers, associated with more prominent vibrational delocalization. The effective icosahedral structure of the 44-molecule cluster is found to originate from quantum nuclear effects as well, the classical structure showing no particular symmetry.

Comparative analysis of prophages in Streptococcus mutans genomes

PubMed Central

Fu, Tiwei; Fan, Xiangyu; Long, Quanxin; Deng, Wanyan; Song, Jinlin

2017-01-01

Prophages have been considered genetic units that have an intimate association with novel phenotypic properties of bacterial hosts, such as pathogenicity and genomic variation. Little is known about the genetic information of prophages in the genome of Streptococcus mutans, a major pathogen of human dental caries. In this study, we identified 35 prophage-like elements in S. mutans genomes and performed a comparative genomic analysis. Comparative genomic and phylogenetic analyses of prophage sequences revealed that the prophages could be classified into three main large clusters: Cluster A, Cluster B, and Cluster C. The S. mutans prophages in each cluster were compared. The genomic sequences of phismuN66-1, phismuNLML9-1, and phismu24-1 all shared similarities with the previously reported S. mutans phages M102, M102AD, and ϕAPCM01. The genomes were organized into seven major gene clusters according to the putative functions of the predicted open reading frames: packaging and structural modules, integrase, host lysis modules, DNA replication/recombination modules, transcriptional regulatory modules, other protein modules, and hypothetical protein modules. Moreover, an integrase gene was only identified in phismuNLML9-1 prophages. PMID:29158986

Application of Classification Methods for Forecasting Mid-Term Power Load Patterns

NASA Astrophysics Data System (ADS)

Piao, Minghao; Lee, Heon Gyu; Park, Jin Hyoung; Ryu, Keun Ho

Currently an automated methodology based on data mining techniques is presented for the prediction of customer load patterns in long duration load profiles. The proposed approach in this paper consists of three stages: (i) data preprocessing: noise or outlier is removed and the continuous attribute-valued features are transformed to discrete values, (ii) cluster analysis: k-means clustering is used to create load pattern classes and the representative load profiles for each class and (iii) classification: we evaluated several supervised learning methods in order to select a suitable prediction method. According to the proposed methodology, power load measured from AMR (automatic meter reading) system, as well as customer indexes, were used as inputs for clustering. The output of clustering was the classification of representative load profiles (or classes). In order to evaluate the result of forecasting load patterns, the several classification methods were applied on a set of high voltage customers of the Korea power system and derived class labels from clustering and other features are used as input to produce classifiers. Lastly, the result of our experiments was presented.

Service-Aware Clustering: An Energy-Efficient Model for the Internet-of-Things

PubMed Central

Bagula, Antoine; Abidoye, Ademola Philip; Zodi, Guy-Alain Lusilao

2015-01-01

Current generation wireless sensor routing algorithms and protocols have been designed based on a myopic routing approach, where the motes are assumed to have the same sensing and communication capabilities. Myopic routing is not a natural fit for the IoT, as it may lead to energy imbalance and subsequent short-lived sensor networks, routing the sensor readings over the most service-intensive sensor nodes, while leaving the least active nodes idle. This paper revisits the issue of energy efficiency in sensor networks to propose a clustering model where sensor devices’ service delivery is mapped into an energy awareness model, used to design a clustering algorithm that finds service-aware clustering (SAC) configurations in IoT settings. The performance evaluation reveals the relative energy efficiency of the proposed SAC algorithm compared to related routing algorithms in terms of energy consumption, the sensor nodes’ life span and its traffic engineering efficiency in terms of throughput and delay. These include the well-known low energy adaptive clustering hierarchy (LEACH) and LEACH-centralized (LEACH-C) algorithms, as well as the most recent algorithms, such as DECSA and MOCRN. PMID:26703619

Service-Aware Clustering: An Energy-Efficient Model for the Internet-of-Things.

PubMed

Bagula, Antoine; Abidoye, Ademola Philip; Zodi, Guy-Alain Lusilao

2015-12-23

Current generation wireless sensor routing algorithms and protocols have been designed based on a myopic routing approach, where the motes are assumed to have the same sensing and communication capabilities. Myopic routing is not a natural fit for the IoT, as it may lead to energy imbalance and subsequent short-lived sensor networks, routing the sensor readings over the most service-intensive sensor nodes, while leaving the least active nodes idle. This paper revisits the issue of energy efficiency in sensor networks to propose a clustering model where sensor devices' service delivery is mapped into an energy awareness model, used to design a clustering algorithm that finds service-aware clustering (SAC) configurations in IoT settings. The performance evaluation reveals the relative energy efficiency of the proposed SAC algorithm compared to related routing algorithms in terms of energy consumption, the sensor nodes' life span and its traffic engineering efficiency in terms of throughput and delay. These include the well-known low energy adaptive clustering hierarchy (LEACH) and LEACH-centralized (LEACH-C) algorithms, as well as the most recent algorithms, such as DECSA and MOCRN.

Read-across of ready biodegradability based on the substrate specificity of N-alkyl polypropylene polyamine-degrading microorganisms.

PubMed

Geerts, R; van Ginkel, C G; Plugge, C M

2017-04-01

The biodegradation of N-alkyl polypropylene polyamines (NAPPs) was studied using pure and mixed cultures to enable read-across of ready biodegradability test results. Two Pseudomonas spp. were isolated from activated sludge with N-oleyl alkyl propylene diamine and N-coco alkyl dipropylene triamine, respectively. Both strains utilized all NAPPs tested as the sole source of carbon, nitrogen and energy for growth. Mineralization of NAPPs was independent of the alkyl chain length and the size of the polyamine moiety. NAPPs degraded in closed bottle tests (CBTs) using both river water and activated sludge. However, ready biodegradability of NAPPs with alkyl chain lengths of 16-18 carbon atoms and polyamine moieties with three and four nitrogen atoms could not be demonstrated. Biodegradation in the CBT was hampered by their limited bioavailability, making assessment of the true ready biodegradability of these highly adsorptive surfactants impossible. All NAPPs are therefore classified as readily biodegradable through read-across. Read-across is justified by the broad substrate specificity of NAPP-degrading microorganisms, their omnipresence and the mineralization of NAPPs.

Attentional focus affects how events are segmented and updated in narrative reading.

PubMed

Bailey, Heather R; Kurby, Christopher A; Sargent, Jesse Q; Zacks, Jeffrey M

2017-08-01

Readers generate situation models representing described events, but the nature of these representations may differ depending on the reading goals. We assessed whether instructions to pay attention to different situational dimensions affect how individuals structure their situation models (Exp. 1) and how they update these models when situations change (Exp. 2). In Experiment 1, participants read and segmented narrative texts into events. Some readers were oriented to pay specific attention to characters or space. Sentences containing character or spatial-location changes were perceived as event boundaries-particularly if the reader was oriented to characters or space, respectively. In Experiment 2, participants read narratives and responded to recognition probes throughout the texts. Readers who were oriented to the spatial dimension were more likely to update their situation models at spatial changes; all readers tracked the character dimension. The results from both experiments indicated that attention to individual situational dimensions influences how readers segment and update their situation models. More broadly, the results provide evidence for a global situation model updating mechanism that serves to set up new models at important narrative changes.

Post-genome research on the biosynthesis of ergot alkaloids.

PubMed

Li, Shu-Ming; Unsöld, Inge A

2006-10-01

Genome sequencing provides new opportunities and challenges for identifying genes for the biosynthesis of secondary metabolites. A putative biosynthetic gene cluster of fumigaclavine C, an ergot alkaloid of the clavine type, was identified in the genome sequence of ASPERGILLUS FUMIGATUS by a bioinformatic approach. This cluster spans 22 kb of genomic DNA and comprises at least 11 open reading frames (ORFs). Seven of them are orthologous to genes from the biosynthetic gene cluster of ergot alkaloids in CLAVICEPS PURPUREA. Experimental evidence of the identified cluster was provided by heterologous expression and biochemical characterization of two ORFs, FgaPT1 and FgaPT2, in the cluster of A. FUMIGATUS, which show remarkable similarities to dimethylallyltryptophan synthase from C. PURPUREA and function as prenyltransferases. FgaPT2 converts L-tryptophan to dimethylallyltryptophan and thereby catalyzes the first step of ergot alkaloid biosynthesis, whilst FgaPT1 catalyzes the last step of the fumigaclavine C biosynthesis, i. e., the prenylation of fumigaclavine A at C-2 position of the indole nucleus. In addition to information obtained from the gene cluster of ergot alkaloids from C. PURPUREA, the identification of the biosynthetic gene cluster of fumigaclavine C in A. FUMIGATUS opens an alternative way to study the biosynthesis of ergot alkaloids in fungi.

The Problem of “Just for Fun”: Patterns of Use Situations among Active Club Drug Users

PubMed Central

Starks, Tyrel J.; Golub, Sarit; Kelly, Brian C.; Parsons, Jeffrey T.

2010-01-01

Existing research has demonstrated the significance of situational antecedents to substance use. The current study used a cluster analytic approach to identify groups of club drug users who report using substances in similar situations (assessed by the Inventory of Drug Taking Situations) with longitudinal data from 400 active drug users. A three-cluster solution emerged in baseline data and was replicated in 12-month follow-up data. Groups were identified as Situationally Restricted, Pleasure Driven, and Situationally Broad users. Group differences were observed on measures of mental health, attitudes towards substance use, amount of substance use, and rates of substance dependence. Cluster membership predicted substance dependence after controlling for past dependence, current use, and current depression/anxiety. PMID:20696530

IR wireless cluster synapses of HYDRA very large neural networks

NASA Astrophysics Data System (ADS)

Jannson, Tomasz; Forrester, Thomas

2008-04-01

RF/IR wireless (virtual) synapses are critical components of HYDRA (Hyper-Distributed Robotic Autonomy) neural networks, already discussed in two earlier papers. The HYDRA network has the potential to be very large, up to 10 11-neurons and 10 18-synapses, based on already established technologies (cellular RF telephony and IR-wireless LANs). It is organized into almost fully connected IR-wireless clusters. The HYDRA neurons and synapses are very flexible, simple, and low-cost. They can be modified into a broad variety of biologically-inspired brain-like computing capabilities. In this third paper, we focus on neural hardware in general, and on IR-wireless synapses in particular. Such synapses, based on LED/LD-connections, dominate the HYDRA neural cluster.

Tribute to A. W. Castleman, Jr.

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

Knappenberger, Jr., Kenneth L.; Johnson, Grant E.; El-Sayed, Mostafa A.

It is with great pleasure that we join our many colleagues who contributed to this special issue of The Journal of Physical Chemistry A in dedicating it in honor of Professor A. W. “Will” Castleman, Jr. Will is a pioneer in the field of cluster science, and the far-reaching impact of his career is demonstrated by the broad range of topics covered in this issue. This diversity validates Will’s teaching that “fundamental research in cluster science allows you to explore any problem you want”. This ability to extend to other research areas comes because, as Will has shown both rigorouslymore » and elegantly, clusters are an intermediate state of matter that bridge the gap between molecular and bulk levels.« less

Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale

PubMed Central

Schmidt, Thomas S. B.; Matias Rodrigues, João F.; von Mering, Christian

2014-01-01

Operational Taxonomic Units (OTUs), usually defined as clusters of similar 16S/18S rRNA sequences, are the most widely used basic diversity units in large-scale characterizations of microbial communities. However, it remains unclear how well the various proposed OTU clustering algorithms approximate ‘true’ microbial taxa. Here, we explore the ecological consistency of OTUs – based on the assumption that, like true microbial taxa, they should show measurable habitat preferences (niche conservatism). In a global and comprehensive survey of available microbial sequence data, we systematically parse sequence annotations to obtain broad ecological descriptions of sampling sites. Based on these, we observe that sequence-based microbial OTUs generally show high levels of ecological consistency. However, different OTU clustering methods result in marked differences in the strength of this signal. Assuming that ecological consistency can serve as an objective external benchmark for cluster quality, we conclude that hierarchical complete linkage clustering, which provided the most ecologically consistent partitions, should be the default choice for OTU clustering. To our knowledge, this is the first approach to assess cluster quality using an external, biologically meaningful parameter as a benchmark, on a global scale. PMID:24763141

ODE, RDE and SDE models of cell cycle dynamics and clustering in yeast.

PubMed

Boczko, Erik M; Gedeon, Tomas; Stowers, Chris C; Young, Todd R

2010-07-01

Biologists have long observed periodic-like oxygen consumption oscillations in yeast populations under certain conditions, and several unsatisfactory explanations for this phenomenon have been proposed. These ‘autonomous oscillations’ have often appeared with periods that are nearly integer divisors of the calculated doubling time of the culture. We hypothesize that these oscillations could be caused by a form of cell cycle synchronization that we call clustering. We develop some novel ordinary differential equation models of the cell cycle. For these models, and for random and stochastic perturbations, we give both rigorous proofs and simulations showing that both positive and negative growth rate feedback within the cell cycle are possible agents that can cause clustering of populations within the cell cycle. It occurs for a variety of models and for a broad selection of parameter values. These results suggest that the clustering phenomenon is robust and is likely to be observed in nature. Since there are necessarily an integer number of clusters, clustering would lead to periodic-like behaviour with periods that are nearly integer divisors of the period of the cell cycle. Related experiments have shown conclusively that cell cycle clustering occurs in some oscillating yeast cultures.

MC 2 : galaxy imaging and redshift analysis of the merging cluster Ciza J2242.8+5301

DOE PAGES

Dawson, William A.; Jee, M. James; Stroe, Andra; ...

2015-05-28

X-ray and radio observations of CIZA J2242.8+5301 suggest that it is a major cluster merger. Despite being well studied in the X-ray, and radio, little has been presented on the cluster structure and dynamics inferred from its galaxy population. We carried out a deep (i < 25) broad band imaging survey of the system with Subaru SuprimeCam (g & i bands) and the Canada France Hawaii Telescope (r band) as well as a comprehensive spectroscopic survey of the cluster area (505 redshifts) using Keck DEIMOS. We use this data to perform a comprehensive galaxy/redshift analysis of the system, which ismore » the first step to a proper understanding the geometry and dynamics of the merger, as well as using the merger to constrain self-interacting dark matter.« less

Distinguishing fear versus distress symptomatology in pediatric OCD

PubMed Central

Rozenman, Michelle; Peris, Tara; Bergman, R. Lindsey; Chang, Susanna; O’Neill, Joseph; McCracken, James T.; Piacentini, John

2018-01-01

Prior research has identified OCD subtypes or “clusters” of symptoms that differentially relate to clinical features of the disorder. Given the high comorbidity between OCD and anxiety, OCD symptom clusters may more broadly associate with fear and/or distress internalizing constructs. This study examines fear and distress dimensions, including physical concerns (fear), separation anxiety (fear), perfectionism (distress), and anxious coping (distress), as predictors of previously empirically-derived OCD symptom clusters in a sample of 215 youth diagnosed with primary OCD (ages 7 to 17, mean age = 12.25). Self-reported separation fears predicted membership in Cluster 1 (aggressive, sexual, religious, somatic obsessions, and checking compulsions) while somatic/autonomic fears predicted membership in Cluster 2 (symmetry obsessions and ordering, counting, repeating compulsions). Results highlight the diversity of pediatric OCD symptoms and their differential association with fear, suggesting the need to carefully assess both OCD and global fear constructs that might be directly targeted in treatment. PMID:27225633

Clustering of 770,000 genomes reveals post-colonial population structure of North America

NASA Astrophysics Data System (ADS)

Han, Eunjung; Carbonetto, Peter; Curtis, Ross E.; Wang, Yong; Granka, Julie M.; Byrnes, Jake; Noto, Keith; Kermany, Amir R.; Myres, Natalie M.; Barber, Mathew J.; Rand, Kristin A.; Song, Shiya; Roman, Theodore; Battat, Erin; Elyashiv, Eyal; Guturu, Harendra; Hong, Eurie L.; Chahine, Kenneth G.; Ball, Catherine A.

2017-02-01

Despite strides in characterizing human history from genetic polymorphism data, progress in identifying genetic signatures of recent demography has been limited. Here we identify very recent fine-scale population structure in North America from a network of over 500 million genetic (identity-by-descent, IBD) connections among 770,000 genotyped individuals of US origin. We detect densely connected clusters within the network and annotate these clusters using a database of over 20 million genealogical records. Recent population patterns captured by IBD clustering include immigrants such as Scandinavians and French Canadians; groups with continental admixture such as Puerto Ricans; settlers such as the Amish and Appalachians who experienced geographic or cultural isolation; and broad historical trends, including reduced north-south gene flow. Our results yield a detailed historical portrait of North America after European settlement and support substantial genetic heterogeneity in the United States beyond that uncovered by previous studies.

Clustering of 770,000 genomes reveals post-colonial population structure of North America

PubMed Central

Han, Eunjung; Carbonetto, Peter; Curtis, Ross E.; Wang, Yong; Granka, Julie M.; Byrnes, Jake; Noto, Keith; Kermany, Amir R.; Myres, Natalie M.; Barber, Mathew J.; Rand, Kristin A.; Song, Shiya; Roman, Theodore; Battat, Erin; Elyashiv, Eyal; Guturu, Harendra; Hong, Eurie L.; Chahine, Kenneth G.; Ball, Catherine A.

2017-01-01

Despite strides in characterizing human history from genetic polymorphism data, progress in identifying genetic signatures of recent demography has been limited. Here we identify very recent fine-scale population structure in North America from a network of over 500 million genetic (identity-by-descent, IBD) connections among 770,000 genotyped individuals of US origin. We detect densely connected clusters within the network and annotate these clusters using a database of over 20 million genealogical records. Recent population patterns captured by IBD clustering include immigrants such as Scandinavians and French Canadians; groups with continental admixture such as Puerto Ricans; settlers such as the Amish and Appalachians who experienced geographic or cultural isolation; and broad historical trends, including reduced north-south gene flow. Our results yield a detailed historical portrait of North America after European settlement and support substantial genetic heterogeneity in the United States beyond that uncovered by previous studies. PMID:28169989

Mg II Spectral Atlas and Flux Catalog for Late-Type Stars in the Hyades Cluster

NASA Technical Reports Server (NTRS)

Simon, Theodore

2001-01-01

In the course of a long-running IUE Guest Observer program, UV spectral images were obtained for more than 60 late-type members of the Hyades Cluster in order to investigate their chromospheric emissions. The emission line fluxes extracted from those observations were used to study the dependence of stellar dynamo activity upon age and rotation (IUE Observations of Rapidly Rotating Low-Mass Stars in Young Clusters: The Relation between Chromospheric Activity and Rotation). However, the details of those measurements, including a tabulation of the line fluxes, were never published. The purpose of the investigation summarized here was to extract all of the existing Hyades long-wavelength Mg II spectra in the IUE public archives in order to survey UV chromospheric emission in the cluster, thereby providing a consistent dataset for statistical and correlative studies of the relationship between stellar dynamo activity, rotation, and age over a broad range in mass.

Clustering of 770,000 genomes reveals post-colonial population structure of North America.

PubMed

Han, Eunjung; Carbonetto, Peter; Curtis, Ross E; Wang, Yong; Granka, Julie M; Byrnes, Jake; Noto, Keith; Kermany, Amir R; Myres, Natalie M; Barber, Mathew J; Rand, Kristin A; Song, Shiya; Roman, Theodore; Battat, Erin; Elyashiv, Eyal; Guturu, Harendra; Hong, Eurie L; Chahine, Kenneth G; Ball, Catherine A

2017-02-07

Despite strides in characterizing human history from genetic polymorphism data, progress in identifying genetic signatures of recent demography has been limited. Here we identify very recent fine-scale population structure in North America from a network of over 500 million genetic (identity-by-descent, IBD) connections among 770,000 genotyped individuals of US origin. We detect densely connected clusters within the network and annotate these clusters using a database of over 20 million genealogical records. Recent population patterns captured by IBD clustering include immigrants such as Scandinavians and French Canadians; groups with continental admixture such as Puerto Ricans; settlers such as the Amish and Appalachians who experienced geographic or cultural isolation; and broad historical trends, including reduced north-south gene flow. Our results yield a detailed historical portrait of North America after European settlement and support substantial genetic heterogeneity in the United States beyond that uncovered by previous studies.

Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets.

PubMed

Samadian, Soroush; Bruce, Jeff P; Pugh, Trevor J

2018-03-01

Somatic copy number variations (CNVs) play a crucial role in development of many human cancers. The broad availability of next-generation sequencing data has enabled the development of algorithms to computationally infer CNV profiles from a variety of data types including exome and targeted sequence data; currently the most prevalent types of cancer genomics data. However, systemic evaluation and comparison of these tools remains challenging due to a lack of ground truth reference sets. To address this need, we have developed Bamgineer, a tool written in Python to introduce user-defined haplotype-phased allele-specific copy number events into an existing Binary Alignment Mapping (BAM) file, with a focus on targeted and exome sequencing experiments. As input, this tool requires a read alignment file (BAM format), lists of non-overlapping genome coordinates for introduction of gains and losses (bed file), and an optional file defining known haplotypes (vcf format). To improve runtime performance, Bamgineer introduces the desired CNVs in parallel using queuing and parallel processing on a local machine or on a high-performance computing cluster. As proof-of-principle, we applied Bamgineer to a single high-coverage (mean: 220X) exome sequence file from a blood sample to simulate copy number profiles of 3 exemplar tumors from each of 10 tumor types at 5 tumor cellularity levels (20-100%, 150 BAM files in total). To demonstrate feasibility beyond exome data, we introduced read alignments to a targeted 5-gene cell-free DNA sequencing library to simulate EGFR amplifications at frequencies consistent with circulating tumor DNA (10, 1, 0.1 and 0.01%) while retaining the multimodal insert size distribution of the original data. We expect Bamgineer to be of use for development and systematic benchmarking of CNV calling algorithms by users using locally-generated data for a variety of applications. The source code is freely available at http://github.com/pughlab/bamgineer.

Integral field spectroscopy with GEMINI: Extragalactic star cluster in NGC1275

NASA Astrophysics Data System (ADS)

Trancho, Gelys; Miller, Bryan; García-Lorenzo, Begoña; Sánchez, Sebastián F.

2006-01-01

Studies of globular cluster systems play a critical role in our understanding of galaxy formation. Imaging with the Hubble Space Telescope has revealed that young star clusters are formed copiously in galaxy mergers, strengthening theories in which giant elliptical galaxies are formed by the merger of spirals [e.g. Whitmore, B.C., Schweizer, F., Leitherer, C., Borne, K., Robert, C., 1993. Astronomical Journal. 106, 1354; Miller, B.W., Whitmore, B.C., Schweizer, F., Fall, S.M., 1997. Astronomical Journal. 114, 2381; Zepf, S.E., Ashman, K.M., English, J., Freeman, K.C., Sharples, R.M., 1999. Astronomical Journal. 118, 752; Ashman, K.M., Zepf, S.E., 1992. Astrophysical Journal. 384, 50]. However, the formation and evolution of globular cluster systems is still not well understood. Ages and metallicities of the clusters are uncertain either because of degeneracy in the broad-band colors or due to variable reddening. Also, the luminosity function of the young clusters, which depends critically on the metallicities and ages of the clusters, appears to be single power-laws while the luminosity function of old clusters has a well-defined break. Either there is significant dynamical evolution of the cluster systems or metallicity affects the mass function of forming clusters. Spectroscopy of these clusters are needed to improve the metallicity and age measurements and to study the kinematics of young cluster systems. Therefore, we have obtained GMOS IFU data of 4 clusters in NGC1275. We will present preliminary results like metallicities, ages, and velocities of the star clusters from IFU spectroscopy.

Research Messages 2010

ERIC Educational Resources Information Center

National Centre for Vocational Education Research (NCVER), 2011

2011-01-01

Research messages 2010 is a collection of summaries of research projects published by the National Centre for Vocational Education Research (NCVER). The summaries are clustered under five broad themes used by NCVER to organise its research and analysis: Industry and employers; Students and individuals; Teaching and learning: VET system; and VET in…

Career Education: The Marine Science Occupations Cluster.

ERIC Educational Resources Information Center

Farning, Maxwell

This paper discusses career opportunities in eight broad groups of marine science occupations: (1) harbor construction and maintenance, (2) ship construction, (3) merchant marine activities, (4) towboating, (5) longshoring, (6) fishing and fish farming, (7) petroleum and natural gas exploration and extraction, and (8) research activities. The…

Two horizontally transferred xenobiotic resistance gene clusters associated with detoxification of benzoxazolinones by Fusarium species

USDA-ARS?s Scientific Manuscript database

Microbes encounter a broad spectrum of chemical compounds in their diverse environments. These xenobiotics may negatively impact growth or cause death. To counter such adverse effects, many microbes possess metabolic strategies to detoxify and biotransform xenobiotics. Fusarium verticillioides is a ...

Blended Instruction: Integrating the Curriculum through Projects and Curriculum Alignment.

ERIC Educational Resources Information Center

Maryland State Dept. of Education, Baltimore. Div. of Career Technology and Adult Learning.

"Blended instruction" is an approach to integrating high school curriculum around broad career clusters or areas of student interest and study. Blended instruction is intended to engage students in more challenging assignments, increase attendance, and increase student academic and technical achievement. This Maryland guide contains…

Modeling to optimize operational practices to limit shallow dose and dose to the lens at the Weldon Spring Site Remedial Action Project.

PubMed

Hillman, D J; Green, S W

1994-10-01

The Weldon Spring Site Remedial Action Project (WSSRAP) began remediation of its chemical plant buildings in June 1992. The chemical plant was used by the Atomic Energy Commission in the 1950's and 1960's to process uranium ore and natural thorium. Many remaining equipment surfaces were highly contaminated with uranium and thorium product residues, which are relatively weak gamma emitters, but are strong beta emitters that deposit the majority of their energy within the first centimeter of tissue. An essential part of the remediation, therefore, is to control the dose to the skin, extremities, and the lens of the eye from the broad range of betas emitted by uranium and thorium decay series radionuclides. The WSSRAP planned to quantitatively record the dose to the skin, extremities, and the lens of the eye, when warranted, through selection and use of appropriate passive dosimeters. That would not, however, constitute control. A direct-reading instrument was needed that could be used by field technicians to anticipate and prevent work methods and situations that would otherwise result in the unnecessary commitment of dose. However, the interpretation of real-time instrument readings produced by a broad spectrum of beta energies is typically challenging at best, particularly when the shallow dose rate and the lens dose rate are both of interest. The purpose of this effort was, therefore, to (1) select a direct-reading instrument for use in the buildings that could be used to provide rule-of-thumb action levels for field technicians, which, if exceeded, would warrant worker protective measures; (2) determine the approximate conversions between the instrument readings and the shallow (including extremity) dose rate and lens of the eye dose rate; and (3) specify protective measures and dosimetry for the lens of the eye, if warranted. Methods described in the literature are used to estimate action levels for direct instrument readings and to demonstrate that lens dosimetry and special protective measures for the lens of the eye are not necessary at the WSSRAP.

The Open Connectome Project Data Cluster: Scalable Analysis and Vision for High-Throughput Neuroscience.

PubMed

Burns, Randal; Roncal, William Gray; Kleissas, Dean; Lillaney, Kunal; Manavalan, Priya; Perlman, Eric; Berger, Daniel R; Bock, Davi D; Chung, Kwanghun; Grosenick, Logan; Kasthuri, Narayanan; Weiler, Nicholas C; Deisseroth, Karl; Kazhdan, Michael; Lichtman, Jeff; Reid, R Clay; Smith, Stephen J; Szalay, Alexander S; Vogelstein, Joshua T; Vogelstein, R Jacob

2013-01-01

We describe a scalable database cluster for the spatial analysis and annotation of high-throughput brain imaging data, initially for 3-d electron microscopy image stacks, but for time-series and multi-channel data as well. The system was designed primarily for workloads that build connectomes - neural connectivity maps of the brain-using the parallel execution of computer vision algorithms on high-performance compute clusters. These services and open-science data sets are publicly available at openconnecto.me. The system design inherits much from NoSQL scale-out and data-intensive computing architectures. We distribute data to cluster nodes by partitioning a spatial index. We direct I/O to different systems-reads to parallel disk arrays and writes to solid-state storage-to avoid I/O interference and maximize throughput. All programming interfaces are RESTful Web services, which are simple and stateless, improving scalability and usability. We include a performance evaluation of the production system, highlighting the effec-tiveness of spatial data organization.

ORGANIZATION OF THE nif GENES OF THE NONHETEROCYSTOUS CYANOBACTERIUM TRICHODESMIUM SP. IMS101.

PubMed

Dominic, Benny; Zani, Sabino; Chen, Yi-Bu; Mellon, Mark T; Zehr, Jonathan P

2000-08-26

An approximately 16-kb fragment of the Trichodesmium sp. IMS101 (a nonheterocystous filamentous cyanobacterium) "conventional"nif gene cluster was cloned and sequenced. The gene organization of the Trichodesmium and Anabaena variabilis vegetative (nif 2) nitrogenase gene clusters spanning the region from nif B to nif W are similar except for the absence of two open reading frames (ORF3 and ORF1) in Trichodesmium. The Trichodesmium nif EN genes encode a fused Nif EN polypeptide that does not appear to be processed into individual Nif E and Nif N polypeptides. Fused nif EN genes were previously found in the A. variabilis nif 2 genes, but we have found that fused nif EN genes are widespread in the nonheterocystous cyanobacteria. Although the gene organization of the nonheterocystous filamentous Trichodesmium nif gene cluster is very similar to that of the A. variabilis vegetative nif 2 gene cluster, phylogenetic analysis of nif sequences do not support close relatedness of Trichodesmium and A. variabilis vegetative (nif 2) nitrogenase genes.

The Open Connectome Project Data Cluster: Scalable Analysis and Vision for High-Throughput Neuroscience

PubMed Central

Burns, Randal; Roncal, William Gray; Kleissas, Dean; Lillaney, Kunal; Manavalan, Priya; Perlman, Eric; Berger, Daniel R.; Bock, Davi D.; Chung, Kwanghun; Grosenick, Logan; Kasthuri, Narayanan; Weiler, Nicholas C.; Deisseroth, Karl; Kazhdan, Michael; Lichtman, Jeff; Reid, R. Clay; Smith, Stephen J.; Szalay, Alexander S.; Vogelstein, Joshua T.; Vogelstein, R. Jacob

2013-01-01

We describe a scalable database cluster for the spatial analysis and annotation of high-throughput brain imaging data, initially for 3-d electron microscopy image stacks, but for time-series and multi-channel data as well. The system was designed primarily for workloads that build connectomes— neural connectivity maps of the brain—using the parallel execution of computer vision algorithms on high-performance compute clusters. These services and open-science data sets are publicly available at openconnecto.me. The system design inherits much from NoSQL scale-out and data-intensive computing architectures. We distribute data to cluster nodes by partitioning a spatial index. We direct I/O to different systems—reads to parallel disk arrays and writes to solid-state storage—to avoid I/O interference and maximize throughput. All programming interfaces are RESTful Web services, which are simple and stateless, improving scalability and usability. We include a performance evaluation of the production system, highlighting the effec-tiveness of spatial data organization. PMID:24401992

Distribution and Genetic Diversity of Bacteriocin Gene Clusters in Rumen Microbial Genomes.

PubMed

Azevedo, Analice C; Bento, Cláudia B P; Ruiz, Jeronimo C; Queiroz, Marisa V; Mantovani, Hilário C

2015-10-01

Some species of ruminal bacteria are known to produce antimicrobial peptides, but the screening procedures have mostly been based on in vitro assays using standardized methods. Recent sequencing efforts have made available the genome sequences of hundreds of ruminal microorganisms. In this work, we performed genome mining of the complete and partial genome sequences of 224 ruminal bacteria and 5 ruminal archaea to determine the distribution and diversity of bacteriocin gene clusters. A total of 46 bacteriocin gene clusters were identified in 33 strains of ruminal bacteria. Twenty gene clusters were related to lanthipeptide biosynthesis, while 11 gene clusters were associated with sactipeptide production, 7 gene clusters were associated with class II bacteriocin production, and 8 gene clusters were associated with class III bacteriocin production. The frequency of strains whose genomes encode putative antimicrobial peptide precursors was 14.4%. Clusters related to the production of sactipeptides were identified for the first time among ruminal bacteria. BLAST analysis indicated that the majority of the gene clusters (88%) encoding putative lanthipeptides contained all the essential genes required for lanthipeptide biosynthesis. Most strains of Streptococcus (66.6%) harbored complete lanthipeptide gene clusters, in addition to an open reading frame encoding a putative class II bacteriocin. Albusin B-like proteins were found in 100% of the Ruminococcus albus strains screened in this study. The in silico analysis provided evidence of novel biosynthetic gene clusters in bacterial species not previously related to bacteriocin production, suggesting that the rumen microbiota represents an underexplored source of antimicrobial peptides. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Quantum cluster algebras and quantum nilpotent algebras.

PubMed

Goodearl, Kenneth R; Yakimov, Milen T

2014-07-08

A major direction in the theory of cluster algebras is to construct (quantum) cluster algebra structures on the (quantized) coordinate rings of various families of varieties arising in Lie theory. We prove that all algebras in a very large axiomatically defined class of noncommutative algebras possess canonical quantum cluster algebra structures. Furthermore, they coincide with the corresponding upper quantum cluster algebras. We also establish analogs of these results for a large class of Poisson nilpotent algebras. Many important families of coordinate rings are subsumed in the class we are covering, which leads to a broad range of applications of the general results to the above-mentioned types of problems. As a consequence, we prove the Berenstein-Zelevinsky conjecture [Berenstein A, Zelevinsky A (2005) Adv Math 195:405-455] for the quantized coordinate rings of double Bruhat cells and construct quantum cluster algebra structures on all quantum unipotent groups, extending the theorem of Geiß et al. [Geiß C, et al. (2013) Selecta Math 19:337-397] for the case of symmetric Kac-Moody groups. Moreover, we prove that the upper cluster algebras of Berenstein et al. [Berenstein A, et al. (2005) Duke Math J 126:1-52] associated with double Bruhat cells coincide with the corresponding cluster algebras.

The role of nickel in radiation damage of ferritic alloys

DOE PAGES

Osetsky, Y.; Anento, Napoleon; Serra, Anna; ...

2014-11-26

According to modern theory, damage evolution under neutron irradiation depends on the fraction of self-interstitial atoms (SIAs) produced in the form of one-dimensional glissile clusters. These clusters, having a low interaction cross-section with other defects, are absorbed mainly by grain boundaries and dislocations, creating the so-called production bias. It is known empirically that the addition of certain alloying elements influences many radiation effects, including swelling; however, the mechanisms are unknown in many cases. In this study, we report the results of an extensive multi-technique atomistic level modeling study of SIA clusters mobility in body-centered cubic Fe–Ni alloys. We have foundmore » that Ni interacts strongly with the periphery of clusters, affecting their mobility. The total effect is defined by the number of Ni atoms interacting with the cluster at the same time and can be significant, even in low-Ni alloys. Thus a 1 nm (37SIAs) cluster is practically immobile at T < 500 K in the Fe–0.8 at.% Ni alloy. Increasing cluster size and Ni content enhances cluster immobilization. Finally, this effect should have quite broad consequences in void swelling, matrix damage accumulation and radiation induced hardening and the results obtained help to better understand and predict the effects of radiation in Fe–Ni ferritic alloys.« less

Quantum cluster algebras and quantum nilpotent algebras

PubMed Central

Goodearl, Kenneth R.; Yakimov, Milen T.

2014-01-01

A major direction in the theory of cluster algebras is to construct (quantum) cluster algebra structures on the (quantized) coordinate rings of various families of varieties arising in Lie theory. We prove that all algebras in a very large axiomatically defined class of noncommutative algebras possess canonical quantum cluster algebra structures. Furthermore, they coincide with the corresponding upper quantum cluster algebras. We also establish analogs of these results for a large class of Poisson nilpotent algebras. Many important families of coordinate rings are subsumed in the class we are covering, which leads to a broad range of applications of the general results to the above-mentioned types of problems. As a consequence, we prove the Berenstein–Zelevinsky conjecture [Berenstein A, Zelevinsky A (2005) Adv Math 195:405–455] for the quantized coordinate rings of double Bruhat cells and construct quantum cluster algebra structures on all quantum unipotent groups, extending the theorem of Geiß et al. [Geiß C, et al. (2013) Selecta Math 19:337–397] for the case of symmetric Kac–Moody groups. Moreover, we prove that the upper cluster algebras of Berenstein et al. [Berenstein A, et al. (2005) Duke Math J 126:1–52] associated with double Bruhat cells coincide with the corresponding cluster algebras. PMID:24982197

The virulence gene cluster of Listeria monocytogenes is also present in Listeria ivanovii, an animal pathogen, and Listeria seeligeri, a nonpathogenic species.

PubMed Central

Gouin, E; Mengaud, J; Cossart, P

1994-01-01

Most known Listeria monocytogenes virulence genes cluster within a 9.6-kb chromosomal region. This region is flanked on one end by two uncharacterized open reading frames (ORF A and ORF B) and ldh, an ORF presumably encoding the L. monocytogenes lactate dehydrogenase (J.-A. Vazquez-Boland, C. Kocks, S. Dramsi, H. Ohayon, C. Geoffroy, J. Mengaud, and P. Cossart, Infect. Immun. 60:219-230, 1992). We report here that the other end is flanked by prs, and ORF homologous to phosphoribosyl PPi synthetase genes. ORF B and prs were detected in all Listeria species and thus delimit the virulence region. This virulence gene cluster was detected exclusively in hemolytic Listeria species, Listeria ivanovii, an animal pathogen, and Listeria seeligeri, a nonpathogenic species. Images PMID:8039927

Impact of Sampling Density on the Extent of HIV Clustering

PubMed Central

Novitsky, Vlad; Moyo, Sikhulile; Lei, Quanhong; DeGruttola, Victor

2014-01-01

Abstract Identifying and monitoring HIV clusters could be useful in tracking the leading edge of HIV transmission in epidemics. Currently, greater specificity in the definition of HIV clusters is needed to reduce confusion in the interpretation of HIV clustering results. We address sampling density as one of the key aspects of HIV cluster analysis. The proportion of viral sequences in clusters was estimated at sampling densities from 1.0% to 70%. A set of 1,248 HIV-1C env gp120 V1C5 sequences from a single community in Botswana was utilized in simulation studies. Matching numbers of HIV-1C V1C5 sequences from the LANL HIV Database were used as comparators. HIV clusters were identified by phylogenetic inference under bootstrapped maximum likelihood and pairwise distance cut-offs. Sampling density below 10% was associated with stochastic HIV clustering with broad confidence intervals. HIV clustering increased linearly at sampling density >10%, and was accompanied by narrowing confidence intervals. Patterns of HIV clustering were similar at bootstrap thresholds 0.7 to 1.0, but the extent of HIV clustering decreased with higher bootstrap thresholds. The origin of sampling (local concentrated vs. scattered global) had a substantial impact on HIV clustering at sampling densities ≥10%. Pairwise distances at 10% were estimated as a threshold for cluster analysis of HIV-1 V1C5 sequences. The node bootstrap support distribution provided additional evidence for 10% sampling density as the threshold for HIV cluster analysis. The detectability of HIV clusters is substantially affected by sampling density. A minimal genotyping density of 10% and sampling density of 50–70% are suggested for HIV-1 V1C5 cluster analysis. PMID:25275430

Brain basis of cognitive resilience: Prefrontal cortex predicts better reading comprehension in relation to decoding

PubMed Central

Patael, Smadar Z.; Farris, Emily A.; Black, Jessica M.; Hancock, Roeland; Gabrieli, John D. E.; Cutting, Laurie E.; Hoeft, Fumiko

2018-01-01

Objective The ultimate goal of reading is to understand written text. To accomplish this, children must first master decoding, the ability to translate printed words into sounds. Although decoding and reading comprehension are highly interdependent, some children struggle to decode but comprehend well, whereas others with good decoding skills fail to comprehend. The neural basis underlying individual differences in this discrepancy between decoding and comprehension abilities is virtually unknown. Methods We investigated the neural basis underlying reading discrepancy, defined as the difference between reading comprehension and decoding skills, in a three-part study: 1) The neuroanatomical basis of reading discrepancy in a cross-sectional sample of school-age children with a wide range of reading abilities (Experiment-1; n = 55); 2) Whether a discrepancy-related neural signature is present in beginning readers and predictive of future discrepancy (Experiment-2; n = 43); and 3) Whether discrepancy-related regions are part of a domain-general or a language specialized network, utilizing the 1000 Functional Connectome data and large-scale reverse inference from Neurosynth.org (Experiment-3). Results Results converged onto the left dorsolateral prefrontal cortex (DLPFC), as related to having discrepantly higher reading comprehension relative to decoding ability. Increased gray matter volume (GMV) was associated with greater discrepancy (Experiment-1). Region-of-interest (ROI) analyses based on the left DLPFC cluster identified in Experiment-1 revealed that regional GMV within this ROI in beginning readers predicted discrepancy three years later (Experiment-2). This region was associated with the fronto-parietal network that is considered fundamental for working memory and cognitive control (Experiment-3). Interpretation Processes related to the prefrontal cortex might be linked to reading discrepancy. The findings may be important for understanding cognitive resilience, which we operationalize as those individuals with greater higher-order reading skills such as reading comprehension compared to lower-order reading skills such as decoding skills. Our study provides insights into reading development, existing theories of reading, and cognitive processes that are potentially significant to a wide range of reading disorders. PMID:29902208

Is the Orthographic/Phonological Onset a Single Unit in Reading Aloud?

ERIC Educational Resources Information Center

Mousikou, Petroula; Coltheart, Max; Saunders, Steven; Yen, Lisa

2010-01-01

Two main theories of visual word recognition have been developed regarding the way orthographic units in printed words map onto phonological units in spoken words. One theory suggests that a string of single letters or letter clusters corresponds to a string of phonemes (Coltheart, 1978; Venezky, 1970), while the other suggests that a string of…

78 FR 13755 - Notice of Receipt of Petition for Decision That Nonconforming 2003 Jeep Wrangler Multi-Purpose...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-28

... System, 114 Theft Protection, 116 Motor Vehicle Brake Fluids, 118 Power-Operated Window, Partition, and...: Replacement of the instrument cluster with a U.S.-model component with inscription of the word ``brake'' on the brake failure warning light as well as reading speed in mph. Standard No. 108 Lamps, Reflective...

The Effect of Content-Focused Coaching on the Quality of Classroom Text Discussions

ERIC Educational Resources Information Center

Matsumura, Lindsay Clare; Garnier, Helen E.; Spybrook, Jessaca

2012-01-01

This study examines the effect of a comprehensive literacy-coaching program focused on enacting a discussion-based approach to reading comprehension instruction (content-focused coaching [CFC]) on the quality of classroom text discussions over 2 years. The study used a cluster-randomized trial in which schools were assigned to either CFC or…

Strategies Used by Saudi EFL Students to Determine the Meaning of English Words

ERIC Educational Resources Information Center

Baniabdelrahman, Abdallah Ahmad; Al-shumaimeri, Yousif

2014-01-01

This study investigated the strategies which first-year Saudi university EFL students used to derive the meaning of unfamiliar words while reading English texts. Using cluster sampling method, participants chosen to be included in the study consisted of six male and six female classes (120 male and 120 female students) of the preparatory year…

Academic Competencies: Their Interrelatedness and Gender Differences at Their High End

ERIC Educational Resources Information Center

Bergold, Sebastian; Wendt, Heike; Kasper, Daniel; Steinmayr, Ricarda

2017-01-01

The present study investigated (a) how a latent profile analysis based on representative data of N = 74,868 4th graders from 17 European countries would cluster the students on the basis of their reading, mathematics, and science achievement test scores; (b) whether there would be gender differences at various competency levels, especially among…

Food Choice and Nutrition: A Social Psychological Perspective.

PubMed

Hardcastle, Sarah J; Thøgersen-Ntoumani, Cecilie; Chatzisarantis, Nikos L D

2015-10-01

In this Special Issue, entitled "Food choice and Nutrition: A Social Psychological Perspective", three broad themes have been identified: (1) social and environmental influences on food choice; (2) psychological influences on eating behaviour; and (3) eating behaviour profiling.The studies that addressed the social and environmental influences indicated that further research would do well to promote positive food choices rather than reduce negative food choices; promote the reading and interpretation of food labels and find ways to effectively market healthy food choices through accessibility, availability and presentation. The studies on psychological influences found that intentions, perceived behavioural control, and confidence were predictors of healthy eating. Given the importance of psychological factors, such as perceived behavioural control and self-efficacy, healthy eating interventions should reduce barriers to healthy eating and foster perceptions of confidence to consume a healthy diet. The final theme focused on the clustering of individuals according to eating behaviour. Some "types" of individuals reported more frequent consumption of fast foods, ready meals or convenience meals or greater levels of disinhibitiona nd less control over food cravings. Intervention designs which make use of multi-level strategies as advocated by the Ecological Model of Behaviour change that proposes multi-level (combining psychological, social and environmental) strategies are likely to be more effective in reaching and engaging individuals susceptible to unhealthy eating habits than interventions operating on a single level.

MetaABC--an integrated metagenomics platform for data adjustment, binning and clustering.

PubMed

Su, Chien-Hao; Hsu, Ming-Tsung; Wang, Tse-Yi; Chiang, Sufeng; Cheng, Jen-Hao; Weng, Francis C; Kao, Cheng-Yan; Wang, Daryi; Tsai, Huai-Kuang

2011-08-15

MetaABC is a metagenomic platform that integrates several binning tools coupled with methods for removing artifacts, analyzing unassigned reads and controlling sampling biases. It allows users to arrive at a better interpretation via series of distinct combinations of analysis tools. After execution, MetaABC provides outputs in various visual formats such as tables, pie and bar charts as well as clustering result diagrams. MetaABC source code and documentation are available at http://bits2.iis.sinica.edu.tw/MetaABC/ CONTACT: dywang@gate.sinica.edu.tw; hktsai@iis.sinica.edu.tw Supplementary data are available at Bioinformatics online.

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

NASA Astrophysics Data System (ADS)

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

2017-07-01

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

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

ERIC Educational Resources Information Center

Van Hoewyk, Doug

2012-01-01

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

Non-Nuclear Alternatives to Monitoring Moisture-Density Response in Soils

DTIC Science & Technology

2013-03-01

devices can be done pretest or posttest , as they all provide a means to correct the raw field data readings. Moisture Density Indicator (M+DI) The...obtained from the soil nuclear density gauge. The devices and techniques that were tested are grouped into four broad families: nuclear, electrical...43  Details of device rejection based on errors .............................................................................. 43  Accuracy of

Diagnostic Assessment of Reading and Listening in a Second or Foreign Language: Elaborating on Diagnostic Principles

ERIC Educational Resources Information Center

Harding, Luke; Alderson, J. Charles; Brunfaut, Tineke

2015-01-01

Alderson, Brunfaut and Harding (2014) recently investigated how diagnosis is practised across a range of professions in order to develop a tentative framework for a theory of diagnosis in second or foreign language (SFL) assessment. In articulating this framework, a set of five broad principles were proposed, encompassing the entire enterprise of…

Becoming Ryan: Lines of Flight from Majoritarian Understandings of Masculinity through a High School Reading and Mentoring Program. A Story of Possibility

ERIC Educational Resources Information Center

Rogers, Mandy; Rowan, Leonie; Walker, Rachel

2014-01-01

Within literature relating to the broad field of boys' education attention is regularly drawn to the significant difference between essentialist and anti-essentialist accounts of "the boy problem" and the limitations of gender-based educational reforms which rely upon deterministic notions of what boys are "really" like and, by…

A Partial Agenda for Modern European Educational History

ERIC Educational Resources Information Center

Albisetti, James C.

2013-01-01

Attempting to establish an agenda for one's own research is often challenging; trying to do so for a broad swath of one's field is even more so. James Albisetti accepted the invitation to propose one in the hope that graduate students and younger colleagues, especially those willing to put in the work to obtain at least reading fluency in foreign…

Redefining Literacy: The Realities of Digital Literacy for Students with Disabilities in K-12

ERIC Educational Resources Information Center

Alsalem, Majed A.

2016-01-01

Technology has shaped the definition of literacy from the traditional meaning of having the ability to read and write to being a social practice that enables individuals to learn and interact with the world. With this notion of literacy, technology has become a tool to motivate and engage all learners through broad practices and platforms that…

A Polio Immunization Pamphlet with Increased Appeal and Simplified Language Does Not Improve Comprehension to an Acceptable Level.

ERIC Educational Resources Information Center

Davis, Terry C.; Fredrickson, Doren D.; Arnold, Connie; Murphy, Peggy W.; Herbst, Melissa; Bocchini, Joseph A.

1998-01-01

Two polio-vaccine pamphlets written on a sixth-grade level were compared for readability, comprehension, and preference among a broad range of parents. The easy-to-read version was widely preferred, and comprehension was significantly higher. However, the use of instructional graphics was required to achieve an acceptable level of comprehension.…

Reconsidering SES and Gender Divides in Literacy Achievement: Are the Gaps across Social Class and Gender Necessary?

ERIC Educational Resources Information Center

Raag, Tarja; Kusiak, Karen; Tumilty, Meredith; Kelemen, Anna; Bernheimer, Hilana; Bond, Jessica

2011-01-01

This study evaluated factors within families that enhance kindergarten reading readiness of children and are also linked to maternal education (a common proxy for SES). We were interested in identifying factors that would be more accessible to families and school administrators as sources of potential change than broad and un-malleable reflections…

Super Star Clusters and H II Regions in Nuclear Rings

NASA Astrophysics Data System (ADS)

Filippenko, Alex

1996-07-01

We propose to obtain WFPC2 optical broad-band {F547M and F814W} and narrow-band Halpha+ionN2 {F658N} images of nuclear starburst rings in four nearby galaxies for which we already have ultraviolet {F220W} FOC data. Nuclear rings {or ``hot- spot'' regions} in barred spirals are some of the nearest and least obscured starburst regions, and HST images of nuclear rings in several galaxies show that the rings contain large populations of super star clusters similar to those recently discovered in other types of starburst systems. These compact clusters, many having luminosities exceeding that of the R136 cluster in 30 Doradus, represent a violent mode of star formation distinct from that seen in ordinary disk ionH2 regions, and the nuclear rings present us with an opportunity to study large numbers of these extreme clusters in relatively unobscured starburst environments. It has been suggested that super star clusters are present-day versions of young globular clusters. To evaluate this hypothesis, it is important to understand the physical properties and stellar contents of the clusters, but previous HST studies of nuclear ring galaxies have only used single-filter observations. Together with our UV data, new WFPC2 images will enable us to determine the H II region and cluster luminosity functions within nuclear rings, measure cluster radii, derive age and mass estimates for the clusters by comparison with evolutionary synthesis models, and study the structure and evolution of nuclear rings.

High-throughput platform for the discovery of elicitors of silent bacterial gene clusters.

PubMed

Seyedsayamdost, Mohammad R

2014-05-20

Over the past decade, bacterial genome sequences have revealed an immense reservoir of biosynthetic gene clusters, sets of contiguous genes that have the potential to produce drugs or drug-like molecules. However, the majority of these gene clusters appear to be inactive for unknown reasons prompting terms such as "cryptic" or "silent" to describe them. Because natural products have been a major source of therapeutic molecules, methods that rationally activate these silent clusters would have a profound impact on drug discovery. Herein, a new strategy is outlined for awakening silent gene clusters using small molecule elicitors. In this method, a genetic reporter construct affords a facile read-out for activation of the silent cluster of interest, while high-throughput screening of small molecule libraries provides potential inducers. This approach was applied to two cryptic gene clusters in the pathogenic model Burkholderia thailandensis. The results not only demonstrate a prominent activation of these two clusters, but also reveal that the majority of elicitors are themselves antibiotics, most in common clinical use. Antibiotics, which kill B. thailandensis at high concentrations, act as inducers of secondary metabolism at low concentrations. One of these antibiotics, trimethoprim, served as a global activator of secondary metabolism by inducing at least five biosynthetic pathways. Further application of this strategy promises to uncover the regulatory networks that activate silent gene clusters while at the same time providing access to the vast array of cryptic molecules found in bacteria.

Cool Core Bias in Sunyaev-Zel’dovich Galaxy Cluster Surveys

DOE PAGES

Lin, Henry W.; McDonald, Michael; Benson, Bradford; ...

2015-03-18

Sunyaev-Zeldovich (SZ) surveys find massive clusters of galaxies by measuring the inverse Compton scattering of cosmic microwave background off of intra-cluster gas. The cluster selection function from such surveys is expected to be nearly independent of redshift and cluster astrophysics. In this work, we estimate the effect on the observed SZ signal of centrally-peaked gas density profiles (cool cores) and radio emission from the brightest cluster galaxy (BCG) by creating mock observations of a sample of clusters that span the observed range of classical cooling rates and radio luminosities. For each cluster, we make simulated SZ observations by the Southmore » Pole Telescope and characterize the cluster selection function, but note that our results are broadly applicable to other SZ surveys. We find that the inclusion of a cool core can cause a change in the measured SPT significance of a cluster between 0.01%–10% at z > 0.3, increasing with cuspiness of the cool core and angular size on the sky of the cluster (i.e., decreasing redshift, increasing mass). We provide quantitative estimates of the bias in the SZ signal as a function of a gas density cuspiness parameter, redshift, mass, and the 1.4 GHz radio luminosity of the central AGN. Based on this work, we estimate that, for the Phoenix cluster (one of the strongest cool cores known), the presence of a cool core is biasing the SZ significance high by ~6%. The ubiquity of radio galaxies at the centers of cool core clusters will offset the cool core bias to varying degrees« less

Nuclear Rings in the IR: Hidden Super Star Clusters

NASA Astrophysics Data System (ADS)

Maoz, Dan

1997-07-01

We propose NICMOS broad-band {F160W, F187W} and Paschen Alpha {F187N} imaging of nuclear starburst rings in two nearby galaxies. We already have UV {F220W} FOC data, and are scheduled to obtain WFPC2 images in U, V, I, and Halpha+[NII] of these rings. The rings contain large populations of super star clusters similar to those recently discovered in other types of starburst systems. Nuclear rings contain large numbers of these clusters in relatively unobscured starburst environments. Measurement of the age, size, and stellar contents of the clusters can test the hypothesis that super star clusters are young globular clusters. Together with our UV and optical data, NICMOS images will provide the SED of numerous super star clusters over a decade in wavelength. Our already-approved observations will allow us to estimate, by comparison with evolutionary synthesis models, the masses and ages of the clusters. The proposed IR data will be sensitive to the number of supergiants {1.6 micron} and O-stars {Paschen Alpha} in each of the clusters. The observations will provide an independent determination of the reddening, mass, and age of each cluster. We expect to see in the IR numerous clusters that are obscured in the UV and optical. These clusters may be the younger ones, which are still embedded in their molecular clouds. By measuring the mass, age, and size of a large number of clusters, we can actually obtain an evolutionary picture of these objects at different stages in their lives.

Story time turbocharger? Child engagement during shared reading and cerebellar activation and connectivity in preschool-age children listening to stories.

PubMed

Hutton, John S; Phelan, Kieran; Horowitz-Kraus, Tzipi; Dudley, Jonathan; Altaye, Mekibib; DeWitt, Thomas; Holland, Scott K

2017-01-01

Expanding behavioral and neurobiological evidence affirms benefits of shared (especially parent-child) reading on cognitive development during early childhood. However, the majority of this evidence involves factors under caregiver control, the influence of those intrinsic to the child, such as interest or engagement in reading, largely indirect or unclear. The cerebellum is increasingly recognized as playing a "smoothing" role in higher-level cognitive processing and learning, via feedback loops with language, limbic and association cortices. We utilized functional MRI to explore the relationship between child engagement during a mother-child reading observation and neural activation and connectivity during a story listening task, in a sample of 4-year old girls. Children exhibiting greater interest and engagement in the narrative showed increased activation in right-sided cerebellar association areas during the task, and greater functional connectivity between this activation cluster and language and executive function areas. Our findings suggest a potential cerebellar "boost" mechanism responsive to child engagement level that may contribute to emergent literacy development during early childhood, and synergy between caregiver and child factors during story sharing.

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.

Basic number processing in children with specific learning disorders: Comorbidity of reading and mathematics disorders.

PubMed

Moll, Kristina; Göbel, Silke M; Snowling, Margaret J

2015-01-01

As well as being the hallmark of mathematics disorders, deficits in number processing have also been reported for individuals with reading disorders. The aim of the present study was to investigate separately the components of numerical processing affected in reading and mathematical disorders within the framework of the Triple Code Model. Children with reading disorders (RD), mathematics disorders (MD), comorbid deficits (RD + MD), and typically developing children (TD) were tested on verbal, visual-verbal, and nonverbal number tasks. As expected, children with MD were impaired across a broad range of numerical tasks. In contrast, children with RD were impaired in (visual-)verbal number tasks but showed age-appropriate performance in nonverbal number skills, suggesting their impairments were domain specific and related to their reading difficulties. The comorbid group showed an additive profile of the impairments of the two single-deficit groups. Performance in speeded verbal number tasks was related to rapid automatized naming, a measure of visual-verbal access in the RD but not in the MD group. The results indicate that deficits in number skills are due to different underlying cognitive deficits in children with RD compared to children with MD: a phonological deficit in RD and a deficit in processing numerosities in MD.

Poor anchoring limits dyslexics' perceptual, memory, and reading skills.

PubMed

Oganian, Yulia; Ahissar, Merav

2012-07-01

The basic deficits underlying the severe and persistent reading difficulties in dyslexia are still highly debated. One of the major topics of debate is whether these deficits are language specific, or affect both verbal and non-verbal stimuli. Recently, Ahissar and colleagues proposed the "anchoring-deficit hypothesis" (Ahissar, Lubin, Putter-Katz, & Banai, 2006), which suggests that dyslexics have a general difficulty in automatic extraction of stimulus regularities from auditory inputs. This hypothesis explained a broad range of dyslexics' verbal and non-verbal difficulties. However, it was not directly tested in the context of reading and verbal memory, which poses the main stumbling blocks to dyslexics. Here we assessed the abilities of adult dyslexics to efficiently benefit from ("anchor to") regularities embedded in repeated tones, orally presented syllables, and written words. We also compared dyslexics' performance to that of individuals with attention disorder (ADHD), but no reading disability. We found an anchoring effect in all groups: all gained from stimulus repetition. However, in line with the anchoring-deficit hypothesis, controls and ADHD participants showed a significantly larger anchoring effect in all tasks. This study is the first that directly shows that the same domain-general deficit, poor anchoring, characterizes dyslexics' performance in perceptual, working memory and reading tasks. Copyright © 2012 Elsevier Ltd. All rights reserved.

Complete Genome Sequence of the Broad-Host-Range Vibriophage KVP40: Comparative Genomics of a T4-Related Bacteriophage

PubMed Central

Miller, Eric S.; Heidelberg, John F.; Eisen, Jonathan A.; Nelson, William C.; Durkin, A. Scott; Ciecko, Ann; Feldblyum, Tamara V.; White, Owen; Paulsen, Ian T.; Nierman, William C.; Lee, Jong; Szczypinski, Bridget; Fraser, Claire M.

2003-01-01

The complete genome sequence of the T4-like, broad-host-range vibriophage KVP40 has been determined. The genome sequence is 244,835 bp, with an overall G+C content of 42.6%. It encodes 386 putative protein-encoding open reading frames (CDSs), 30 tRNAs, 33 T4-like late promoters, and 57 potential rho-independent terminators. Overall, 92.1% of the KVP40 genome is coding, with an average CDS size of 587 bp. While 65% of the CDSs were unique to KVP40 and had no known function, the genome sequence and organization show specific regions of extensive conservation with phage T4. At least 99 KVP40 CDSs have homologs in the T4 genome (Blast alignments of 45 to 68% amino acid similarity). The shared CDSs represent 36% of all T4 CDSs but only 26% of those from KVP40. There is extensive representation of the DNA replication, recombination, and repair enzymes as well as the viral capsid and tail structural genes. KVP40 lacks several T4 enzymes involved in host DNA degradation, appears not to synthesize the modified cytosine (hydroxymethyl glucose) present in T-even phages, and lacks group I introns. KVP40 likely utilizes the T4-type sigma-55 late transcription apparatus, but features of early- or middle-mode transcription were not identified. There are 26 CDSs that have no viral homolog, and many did not necessarily originate from Vibrio spp., suggesting an even broader host range for KVP40. From these latter CDSs, an NAD salvage pathway was inferred that appears to be unique among bacteriophages. Features of the KVP40 genome that distinguish it from T4 are presented, as well as those, such as the replication and virion gene clusters, that are substantially conserved. PMID:12923095

A Comprehensive Horticulture Curriculum Guide for New Jersey Schools.

ERIC Educational Resources Information Center

Rutgers, The State Univ., New Brunswick, NJ. Cook Coll.

A horticultural core curriculum and draft copies of three horticultural cluster curricula are provided. Materials related to the curriculum development project appear first. The core curriculum is designed to provide broad initial instruction in horticulture for students in the first year of a secondary-level vocational horticulture program. The…

Visualizing the Structure of Medical Informatics Using Term Co-Occurrence Analysis.

ERIC Educational Resources Information Center

Morris, Theodore Allan

2000-01-01

Examines the structure of medical informatics and the relationship between biomedicine and information science and information technology. Uses co-occurrence analysis of subject headings assigned to items indexed for MEDLINE as well as multidimensional scaling to show seven to eight broad multidisciplinary subject clusters. (Contains 28…

Missouri Introduction to Energy and Power Technology Guide.

ERIC Educational Resources Information Center

Missouri Univ., Columbia. Instructional Materials Lab.

This guide provides materials for the first high school specialization course beyond the broad-based foundation provided by the Introduction to Industrial Technology and Exploration of Technology courses. Section I is the Instructor's Guide, which contains suggestions about how the energy and power technology cluster might be taught as a course…

Application of an Adaptive Clustering Network to Flight Control of a Fighter Aircraft. Phase 1

DTIC Science & Technology

1991-12-19

whether the underlying neurodynamics are appropriate to the dynamics of the controlled element as well as the broad objectives of the control process...Dept. of Brain & Cognitive Sciences ........................ 1 Massachusetts Institute of Technology Cambridge, MA 02139 Attn: Dr. M. Jordan Dept. of

Massive Stars in Interactive Binaries

NASA Astrophysics Data System (ADS)

St.-Louis, Nicole; Moffat, Anthony F. J.

Massive stars start their lives above a mass of ~8 time solar, finally exploding after a few million years as core-collapse or pair-production supernovae. Above ~15 solar masses, they also spend most of their lives driving especially strong, hot winds due to their extreme luminosities. All of these aspects dominate the ecology of the Universe, from element enrichment to stirring up and ionizing the interstellar medium. But when they occur in close pairs or groups separated by less than a parsec, the interaction of massive stars can lead to various exotic phenomena which would not be seen if there were no binaries. These depend on the actual separation, and going from wie to close including colliding winds (with non-thermal radio emission and Wolf-Rayet dust spirals), cluster dynamics, X-ray binaries, Roche-lobe overflow (with inverse mass-ratios and rapid spin up), collisions, merging, rejuventation and massive blue stragglers, black-hole formation, runaways and gamma-ray bursts. Also, one wonders whether the fact that a massive star is in a binary affects its parameters compared to its isolated equivalent. These proceedings deal with all of these phenomena, plus binary statistics and determination of general physical properties of massive stars, that would not be possible with their single cousins. The 77 articles published in these proceedings, all based on oral talks, vary from broad revies to the lates developments in the field. About a third of the time was spent in open discussion of all participants, both for ~5 minutes after each talk and 8 half-hour long general dialogues, all audio-recorded, transcribed and only moderately edited to yield a real flavour of the meeting. The candid information in these discussions is sometimes more revealing than the article(s) that preceded them and also provide entertaining reading. The book is suitable for researchers and graduate students interested in stellar astrophysics and in various physical processes involved when stars occur in bound pairs, groups or tight clusters.

Ground state structure of random magnets

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

Bastea, S.; Duxbury, P.M.

1998-10-01

Using exact optimization methods, we find all of the ground states of ({plus_minus}h) random-field Ising magnets (RFIM) and of dilute antiferromagnets in a field (DAFF). The degenerate ground states are usually composed of isolated clusters (two-level systems) embedded in a frozen background. We calculate the paramagnetic response (sublattice response) and the ground state entropy for the RFIM (DAFF) due to these clusters. In both two and three dimensions there is a broad regime in which these quantities are strictly positive, even at irrational values of h/J (J is the exchange constant). {copyright} {ital 1998} {ital The American Physical Society}

On the Scatter of the Present-day Stellar Metallicity–Mass Relation of Cluster Dwarf Galaxies

NASA Astrophysics Data System (ADS)

Engler, Christoph; Lisker, Thorsten; Pillepich, Annalisa

2018-04-01

We examine the scatter of the relation between stellar mass and stellar metallicity for cluster dwarf galaxies in the cosmological simulation Illustris. The mass-metallicity relation exhibits the smallest intrinsic scatter at the galaxies' times of peak stellar mass, suggesting stellar mass stripping to be the primary effect responsible for the rather broad relation at present. However, for about 40% of galaxies in the high-metallicity tail of the relation, we find mass stripping to coincide with an increased enrichment of stellar metallicity, possibly caused by the stripping of low-metallicity stars in the galaxy outskirts.

Baseline MNREAD Measures for Normally Sighted Subjects From Childhood to Old Age

PubMed Central

Calabrèse, Aurélie; Cheong, Allen M. Y.; Cheung, Sing-Hang; He, Yingchen; Kwon, MiYoung; Mansfield, J. Stephen; Subramanian, Ahalya; Yu, Deyue; Legge, Gordon E.

2016-01-01

Purpose The continuous-text reading-acuity test MNREAD is designed to measure the reading performance of people with normal and low vision. This test is used to estimate maximum reading speed (MRS), critical print size (CPS), reading acuity (RA), and the reading accessibility index (ACC). Here we report the age dependence of these measures for normally sighted individuals, providing baseline data for MNREAD testing. Methods We analyzed MNREAD data from 645 normally sighted participants ranging in age from 8 to 81 years. The data were collected in several studies conducted by different testers and at different sites in our research program, enabling evaluation of robustness of the test. Results Maximum reading speed and reading accessibility index showed a trilinear dependence on age: first increasing from 8 to 16 years (MRS: 140–200 words per minute [wpm]; ACC: 0.7–1.0); then stabilizing in the range of 16 to 40 years (MRS: 200 ± 25 wpm; ACC: 1.0 ± 0.14); and decreasing to 175 wpm and 0.88 by 81 years. Critical print size was constant from 8 to 23 years (0.08 logMAR), increased slowly until 68 years (0.21 logMAR), and then more rapidly until 81 years (0.34 logMAR). logMAR reading acuity improved from −0.1 at 8 years to −0.18 at 16 years, then gradually worsened to −0.05 at 81 years. Conclusions We found a weak dependence of the MNREAD parameters on age in normal vision. In broad terms, MNREAD performance exhibits differences between three age groups: children 8 to 16 years, young adults 16 to 40 years, and middle-aged to older adults >40 years. PMID:27442222

Reading Comprehension in Boys with ADHD: The Mediating Roles of Working Memory and Orthographic Conversion.

PubMed

Friedman, Lauren M; Rapport, Mark D; Raiker, Joseph S; Orban, Sarah A; Eckrich, Samuel J

2017-02-01

Reading comprehension difficulties in children with ADHD are well established; however, limited information exists concerning the cognitive mechanisms that contribute to these difficulties and the extent to which they interact with one another. The current study examines two broad cognitive processes known to be involved in children's reading comprehension abilities-(a) working memory (i.e., central executive processes [CE], phonological short-term memory [PH STM], and visuospatial short-term memory [VS STM]) and (b) orthographic conversion (i.e., conversion of visually presented text to a phonological code)-to elucidate their unique and interactive contribution to ADHD-related reading comprehension differences. Thirty-one boys with ADHD-combined type and 30 typically developing (TD) boys aged 8 to 12 years (M = 9.64, SD = 1.22) were administered multiple counterbalanced tasks assessing WM and orthographic conversion processes. Relative to TD boys, boys with ADHD exhibited significant deficits in PH STM (d = -0.70), VS STM (d = -0.92), CE (d = -1.58), and orthographic conversion (d = -0.93). Bias-corrected, bootstrapped mediation analyses revealed that CE and orthographic conversion processes modeled separately mediated ADHD-related reading comprehension differences partially, whereas PH STM and VS STM did not. CE and orthographic conversion modeled jointly mediated ADHD-related reading comprehension differences fully wherein orthographic conversion's large magnitude influence on reading comprehension occurred indirectly through CE's impact on the orthographic system. The findings suggest that adaptive cognitive interventions designed to improve reading-related outcomes in children with ADHD may benefit by including modules that train CE and orthographic conversion processes independently and interactively.

Testing for X-Ray–SZ Differences and Redshift Evolution in the X-Ray Morphology of Galaxy Clusters

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

Nurgaliev, D.; McDonald, M.; Benson, B. A.

We present a quantitative study of the X-ray morphology of galaxy clusters, as a function of their detection method and redshift. We analyze two separate samples of galaxy clusters: a sample of 36 clusters atmore » $$0.35\\lt z\\lt 0.9$$ selected in the X-ray with the ROSAT PSPC 400 deg(2) survey, and a sample of 90 clusters at $$0.25\\lt z\\lt 1.2$$ selected via the Sunyaev–Zel’dovich (SZ) effect with the South Pole Telescope. Clusters from both samples have similar-quality Chandra observations, which allow us to quantify their X-ray morphologies via two distinct methods: centroid shifts (w) and photon asymmetry ($${A}_{\\mathrm{phot}}$$). The latter technique provides nearly unbiased morphology estimates for clusters spanning a broad range of redshift and data quality. We further compare the X-ray morphologies of X-ray- and SZ-selected clusters with those of simulated clusters. We do not find a statistically significant difference in the measured X-ray morphology of X-ray and SZ-selected clusters over the redshift range probed by these samples, suggesting that the two are probing similar populations of clusters. We find that the X-ray morphologies of simulated clusters are statistically indistinguishable from those of X-ray- or SZ-selected clusters, implying that the most important physics for dictating the large-scale gas morphology (outside of the core) is well-approximated in these simulations. Finally, we find no statistically significant redshift evolution in the X-ray morphology (both for observed and simulated clusters), over the range of $$z\\sim 0.3$$ to $$z\\sim 1$$, seemingly in contradiction with the redshift-dependent halo merger rate predicted by simulations.« less

Observing Stellar Clusters in the Computer

NASA Astrophysics Data System (ADS)

Borch, A.; Spurzem, R.; Hurley, J.

2006-08-01

We present a new approach to combine direct N-body simulations to stellar population synthesis modeling in order to model the dynamical evolution and color evolution of globular clusters at the same time. This allows us to model the spectrum, colors and luminosities of each star in the simulated cluster. For this purpose the NBODY6++ code (Spurzem 1999) is used, which is a parallel version of the NBODY code. J. Hurley implemented simple recipes to follow the changes of stellar masses, radii, and luminosities due to stellar evolution into the NBODY6++ code (Hurley et al. 2001), in the sense that each simulation particle represents one star. These prescriptions cover all evolutionary phases and solar to globular cluster metallicities. We used the stellar parameters obtained by this stellar evolution routine and coupled them to the stellar library BaSeL 2.0 (Lejeune et al. 1997). As a first application we investigated the integrated broad band colors of simulated clusters. We modeled tidally disrupted globular clusters and compared the results with isolated globular clusters. Due to energy equipartition we expected a relative blueing of tidally disrupted clusters, because of the higher escape probability of red, low-mass stars. This behaviour we actually observe for concentrated globular clusters. The mass-to-light ratio of isolated clusters follows exactly a color-M/L correlation, similar as described in Bell and de Jong (2001) in the case of spiral galaxies. At variance to this correlation, in tidally disrupted clusters the M/L ratio becomes significantly lower at the time of cluster dissolution. Hence, for isolated clusters the behavior of the stellar population is not influenced by dynamical evolution, whereas the stellar population of tidally disrupted clusters is strongly influenced by dynamical effects.

Testing for X-Ray–SZ Differences and Redshift Evolution in the X-Ray Morphology of Galaxy Clusters

DOE PAGES

Nurgaliev, D.; McDonald, M.; Benson, B. A.; ...

2017-05-16

We present a quantitative study of the X-ray morphology of galaxy clusters, as a function of their detection method and redshift. We analyze two separate samples of galaxy clusters: a sample of 36 clusters atmore » $$0.35\\lt z\\lt 0.9$$ selected in the X-ray with the ROSAT PSPC 400 deg(2) survey, and a sample of 90 clusters at $$0.25\\lt z\\lt 1.2$$ selected via the Sunyaev–Zel’dovich (SZ) effect with the South Pole Telescope. Clusters from both samples have similar-quality Chandra observations, which allow us to quantify their X-ray morphologies via two distinct methods: centroid shifts (w) and photon asymmetry ($${A}_{\\mathrm{phot}}$$). The latter technique provides nearly unbiased morphology estimates for clusters spanning a broad range of redshift and data quality. We further compare the X-ray morphologies of X-ray- and SZ-selected clusters with those of simulated clusters. We do not find a statistically significant difference in the measured X-ray morphology of X-ray and SZ-selected clusters over the redshift range probed by these samples, suggesting that the two are probing similar populations of clusters. We find that the X-ray morphologies of simulated clusters are statistically indistinguishable from those of X-ray- or SZ-selected clusters, implying that the most important physics for dictating the large-scale gas morphology (outside of the core) is well-approximated in these simulations. Finally, we find no statistically significant redshift evolution in the X-ray morphology (both for observed and simulated clusters), over the range of $$z\\sim 0.3$$ to $$z\\sim 1$$, seemingly in contradiction with the redshift-dependent halo merger rate predicted by simulations.« less

De novo assembly of the transcriptome of the non-model plant Streptocarpus rexii employing a novel heuristic to recover locus-specific transcript clusters.

PubMed

Chiara, Matteo; Horner, David S; Spada, Alberto

2013-01-01

De novo transcriptome characterization from Next Generation Sequencing data has become an important approach in the study of non-model plants. Despite notable advances in the assembly of short reads, the clustering of transcripts into unigene-like (locus-specific) clusters remains a somewhat neglected subject. Indeed, closely related paralogous transcripts are often merged into single clusters by current approaches. Here, a novel heuristic method for locus-specific clustering is compared to that implemented in the de novo assembler Oases, using the same initial transcript collections, derived from Arabidopsis thaliana and the developmental model Streptocarpus rexii. We show that the proposed approach improves cluster specificity in the A. thaliana dataset for which the reference genome is available. Furthermore, for the S. rexii data our filtered transcript collection matches a larger number of distinct annotated loci in reference genomes than the Oases set, while containing a reduced overall number of loci. A detailed discussion of advantages and limitations of our approach in processing de novo transcriptome reconstructions is presented. The proposed method should be widely applicable to other organisms, irrespective of the transcript assembly method employed. The S. rexii transcriptome is available as a sophisticated and augmented publicly available online database.

Comparative Investigation of Shared Filesystems for the LHCb Online Cluster

NASA Astrophysics Data System (ADS)

Vijay Kartik, S.; Neufeld, Niko

2012-12-01

This paper describes the investigative study undertaken to evaluate shared filesystem performance and suitability in the LHCb Online environment. Particular focus is given to the measurements and field tests designed and performed on an in-house OpenAFS setup; related comparisons with NFSv4 and GPFS (a clustered filesystem from IBM) are presented. The motivation for the investigation and the test setup arises from the need to serve common user-space like home directories, experiment software and control areas, and clustered log areas. Since the operational requirements on such user-space are stringent in terms of read-write operations (in frequency and access speed) and unobtrusive data relocation, test results are presented with emphasis on file-level performance, stability and “high-availability” of the shared filesystems. Use cases specific to the experiment operation in LHCb, including the specific handling of shared filesystems served to a cluster of 1500 diskless nodes, are described. Issues of prematurely expiring authenticated sessions are explicitly addressed, keeping in mind long-running analysis jobs on the Online cluster. In addition, quantitative test results are also presented with alternatives including NFSv4. Comparative measurements of filesystem performance benchmarks are presented, which are seen to be used as reference for decisions on potential migration of the current storage solution deployed in the LHCb online cluster.

Web Program for Development of GUIs for Cluster Computers

NASA Technical Reports Server (NTRS)

Czikmantory, Akos; Cwik, Thomas; Klimeck, Gerhard; Hua, Hook; Oyafuso, Fabiano; Vinyard, Edward

2003-01-01

WIGLAF (a Web Interface Generator and Legacy Application Facade) is a computer program that provides a Web-based, distributed, graphical-user-interface (GUI) framework that can be adapted to any of a broad range of application programs, written in any programming language, that are executed remotely on any cluster computer system. WIGLAF enables the rapid development of a GUI for controlling and monitoring a specific application program running on the cluster and for transferring data to and from the application program. The only prerequisite for the execution of WIGLAF is a Web-browser program on a user's personal computer connected with the cluster via the Internet. WIGLAF has a client/server architecture: The server component is executed on the cluster system, where it controls the application program and serves data to the client component. The client component is an applet that runs in the Web browser. WIGLAF utilizes the Extensible Markup Language to hold all data associated with the application software, Java to enable platform-independent execution on the cluster system and the display of a GUI generator through the browser, and the Java Remote Method Invocation software package to provide simple, effective client/server networking.

Cluster size resolving analysis of CH3F-(ortho-H2)n in solid para-hydrogen using FTIR absorption spectroscopy at 3 μm region.

PubMed

Miyamoto, Yuki; Momose, Takamasa; Kanamori, Hideto

2012-11-21

Infrared absorption spectra of methyl fluoride with ortho-hydrogen (ortho-H(2)) clusters in a solid para-hydrogen (para-H(2)) crystal at 3.6 K were studied in the C-H stretching fundamental region (~3000 cm(-1)) using an FTIR spectrometer. As shown previously, the ν(3) C-F stretching fundamental band of CH(3)F-(ortho-H(2))(n) (n = 0, 1, 2, ...) clusters at 1040 cm(-1) shows a series of n discrete absorption lines, which correspond to different-sized clusters. We observed three unresolved broad peaks in the C-H stretching region and applied this cluster model to them assuming the same intensity distribution function as the ν(3) band. A fitting analysis successfully gave us the linewidth and lineshift of the components in each vibrational band. It was found that the separately determined linewidth, matrix shift of the band origin, and cluster shift are dependent on the vibrational mode. From the transition intensities of the monomer component derived from the fitting analysis, we discuss the mixing ratio of the vibrational modes due to Fermi resonance.

Weak lensing measurement of the mass–richness relation of SDSS redMaPPer clusters

DOE PAGES

Simet, Melanie; McClintock, Tom; Mandelbaum, Rachel; ...

2016-12-15

Here, we perform a measurement of the mass–richness relation of the redMaPPer galaxy cluster catalogue using weak lensing data from the Sloan Digital Sky Survey. We carefully characterized a broad range of systematic uncertainties, including shear calibration errors, photo-zz biases, dilution by member galaxies, source obscuration, magnification bias, incorrect assumptions about cluster mass profiles, cluster centering, halo triaxiality, and projection effects. We then compare measurements of the lensing signal from two independently-produced shear and photometric redshift catalogues to characterize systematic errors in the lensing signal itself. Using a sample of 5,570 clusters from 0.1 ≤ zz ≤ 0.33, the normalization of our power-law mass vs. λ relation is log 10[M 200m/h -1 M ⊙] = 14.344 ± 0.021 (statistical) ±0.023 (systematic) at a richness λ = 40, a 7 per cent calibration uncertainty, with a power-law index of 1.33+0.09-0.101.33more » $$+0.09\\atop{-0.10}$$ (1σ). Finally, the detailed systematics characterization in this work renders it the definitive weak lensing mass calibration for SDSS redMaPPer clusters at this time.« less

MALINA: a web service for visual analytics of human gut microbiota whole-genome metagenomic reads.

PubMed

Tyakht, Alexander V; Popenko, Anna S; Belenikin, Maxim S; Altukhov, Ilya A; Pavlenko, Alexander V; Kostryukova, Elena S; Selezneva, Oksana V; Larin, Andrei K; Karpova, Irina Y; Alexeev, Dmitry G

2012-12-07

MALINA is a web service for bioinformatic analysis of whole-genome metagenomic data obtained from human gut microbiota sequencing. As input data, it accepts metagenomic reads of various sequencing technologies, including long reads (such as Sanger and 454 sequencing) and next-generation (including SOLiD and Illumina). It is the first metagenomic web service that is capable of processing SOLiD color-space reads, to authors' knowledge. The web service allows phylogenetic and functional profiling of metagenomic samples using coverage depth resulting from the alignment of the reads to the catalogue of reference sequences which are built into the pipeline and contain prevalent microbial genomes and genes of human gut microbiota. The obtained metagenomic composition vectors are processed by the statistical analysis and visualization module containing methods for clustering, dimension reduction and group comparison. Additionally, the MALINA database includes vectors of bacterial and functional composition for human gut microbiota samples from a large number of existing studies allowing their comparative analysis together with user samples, namely datasets from Russian Metagenome project, MetaHIT and Human Microbiome Project (downloaded from http://hmpdacc.org). MALINA is made freely available on the web at http://malina.metagenome.ru. The website is implemented in JavaScript (using Ext JS), Microsoft .NET Framework, MS SQL, Python, with all major browsers supported.

The Hubble Space Telescope UV Legacy Survey of Galactic Globular Clusters. XV. The Dynamical Clock: Reading Cluster Dynamical Evolution from the Segregation Level of Blue Straggler Stars

NASA Astrophysics Data System (ADS)

Ferraro, F. R.; Lanzoni, B.; Raso, S.; Nardiello, D.; Dalessandro, E.; Vesperini, E.; Piotto, G.; Pallanca, C.; Beccari, G.; Bellini, A.; Libralato, M.; Anderson, J.; Aparicio, A.; Bedin, L. R.; Cassisi, S.; Milone, A. P.; Ortolani, S.; Renzini, A.; Salaris, M.; van der Marel, R. P.

2018-06-01

The parameter A +, defined as the area enclosed between the cumulative radial distribution of blue straggler stars (BSSs) and that of a reference population, is a powerful indicator of the level of BSS central segregation. As part of the Hubble Space Telescope UV Legacy Survey of Galactic globular clusters (GCs), here we present the BSS population and the determination of A + in 27 GCs observed out to about one half-mass radius. In combination with 21 additional clusters discussed in a previous paper, this provides us with a global sample of 48 systems (corresponding to ∼32% of the Milky Way GC population), for which we find a strong correlation between A + and the ratio of cluster age to the current central relaxation time. Tight relations have also been found with the core radius and the central luminosity density, which are expected to change with the long-term cluster dynamical evolution. An interesting relation is emerging between A + and the ratio of the BSS velocity dispersion relative to that of main sequence turn-off stars, which measures the degree of energy equipartition experienced by BSSs in the cluster. These results provide further confirmation that BSSs are invaluable probes of GC internal dynamics and that A + is a powerful dynamical clock.

Generalized Self-Organizing Maps for Automatic Determination of the Number of Clusters and Their Multiprototypes in Cluster Analysis.

PubMed

Gorzalczany, Marian B; Rudzinski, Filip

2017-06-07

This paper presents a generalization of self-organizing maps with 1-D neighborhoods (neuron chains) that can be effectively applied to complex cluster analysis problems. The essence of the generalization consists in introducing mechanisms that allow the neuron chain--during learning--to disconnect into subchains, to reconnect some of the subchains again, and to dynamically regulate the overall number of neurons in the system. These features enable the network--working in a fully unsupervised way (i.e., using unlabeled data without a predefined number of clusters)--to automatically generate collections of multiprototypes that are able to represent a broad range of clusters in data sets. First, the operation of the proposed approach is illustrated on some synthetic data sets. Then, this technique is tested using several real-life, complex, and multidimensional benchmark data sets available from the University of California at Irvine (UCI) Machine Learning repository and the Knowledge Extraction based on Evolutionary Learning data set repository. A sensitivity analysis of our approach to changes in control parameters and a comparative analysis with an alternative approach are also performed.

Ghostly Glow Reveals a Hidden Class of Long-Wavelength Radio Emitters

NASA Astrophysics Data System (ADS)

2008-10-01

(Washington, DC. 08)- A team of scientists, including astronomers from the Naval Research Laboratory (NRL), have detected long wavelength radio emission from a colliding, massive galaxy cluster which, surprisingly, is not detected at the shorter wavelengths typically seen in these objects. The discovery implies that existing radio telescopes have missed a large population of these colliding objects. It also provides an important confirmation of the theoretical prediction that colliding galaxy clusters accelerate electrons and other particles to very high energies through the process of turbulent waves. The team revealed their findings in the October 16, 2008 edition of Nature. This new population of objects is most easily detected at long wavelengths. Professor Greg Taylor of the University of New Mexico and scientific director of the Long Wavelength Array (LWA) points out, "This result is just the tip of the iceberg. When an emerging suite of much more powerful low frequency telescopes, including the LWA in New Mexico, turn their views to the cosmos, the sky will 'light up' with hundreds or even thousands of colliding galaxy clusters." NRL has played a key role in promoting the development of this generation of new instruments and is currently involved with the development of the LWA. NRL radio astronomer and LWA Project Scientist Namir Kassim says "Our discovery of a previously hidden class of low frequency cluster-radio sources is particularly important since the study of galaxy clusters was a primary motivation for development of the LWA." The discovery of the emission in the galaxy cluster Abell 521 (or A521 for short) was made using the Giant Metrewave Radiotelescope (GMRT) in India, and its long wavelength nature was confirmed by the National Science Foundation's (NRAO) Very Large Array (VLA) radio telescope in New Mexico. The attached image shows the radio emission at a wavelength of 125cm in red superimposed on a blue image made from data taken by the Chandra X-ray Observatory. X-ray Chandra X-ray Image The X-ray emission comes from hot thermal gas, a well-known sign-post of massive galaxy clusters. Furthermore, its elongated shape indicates that the cluster has undergone a recent violent collision or "merger event" in which another group or cluster of galaxies was swallowed up by the gravitational potential of the main cluster. Interferometrics Inc. and NRL scientist Tracy Clarke, who is also the LWA System Scientist, notes "In addition to teaching us about the nature of Dark Matter, merging clusters are also important in studies of the mysterious nature of Dark Energy. Understanding these two strange components of the Universe will help us understand its ultimate destiny." In the radio image there is a strong, oblong source of emission located on the lower left periphery of the X-ray gas detected by Chandra; this is a separate source. In the center of the cluster, within the region indicated by a dashed circle, there is radio emission which changes significantly with wavelength. At the longest wavelength (125 cm, shown) it is clearly detected, but at a wavelength of 49 cm it is much fainter, and it is almost entirely gone at 21 cm wavelength. This multi-wavelength picture of the diffuse emission is in good agreement with theoretical predictions for particle acceleration by turbulent waves generated by a violent collision. People Who Read This Also Read... Black Holes Have Simple Feeding Habits NASA’s Swift Satellite Catches First Supernova in The Act of Exploding Oldest Known Objects Are Surprisingly Immature Chandra Data Reveal Rapidly Whirling Black Holes In a broader astrophysical context, galaxy clusters are the largest gravitationally bound systems in the Universe and their collisions are the most energetic events since the Big Bang. Says team leader Gianfranco Brunetti (Instituto di Radioastronomia, Bologna, Italy), "The A521 system provides evidence that turbulence acts as a source of particle acceleration in an environment that is unique in the Universe due to its large spatial and temporal scales, and due to the low density and high temperature of the gas." The team included scientists from Instituto di Radioastronomia, the University of Bologna, the Smithsonian Astrophysical Observatory, the National Radio Astronomy Observatory, and the Naval Research Laboratory. Basic research in radio astronomy at the Naval Research Laboratory is supported by 6.1 base funding. The NRAO is a facility of the National Science Foundation operated under cooperative agreement by Associated Universities, Inc. The GMRT is run by the National Centre for Radio Astrophysics of the Tata Institute of Fundamental Research. The LWA, funding for which is provided by the Office of Naval Research, is led by the University of New Mexico, and includes NRL, The Applied Research Laboratory at the University of Texas at Austin, Virginia Tech, the Los Alamos National Laboratory, and the University of Iowa, with contributions and cooperation from NRAO. The Long Wavelength Array (LWA) website is http://lwa.unm.edu The Naval Research Laboratory is the Department of the Navy's corporate laboratory. NRL conducts a broad program of scientific research, technology, and advanced development. The Laboratory, with a total complement of nearly 2,500 personnel, is located in southwest Washington, DC, with other major sites at the Stennis Space Center, MS; and Monterey, CA.

Defining the transcriptome assembly and its use for genome dynamics and transcriptome profiling studies in pigeonpea (Cajanus cajan L.)

USDA-ARS?s Scientific Manuscript database

This study reports generation of large-scale genomic resources for pigeonpea, a so-called ‘orphan crop species’ of the semi-arid tropic regions. Roche FLX/454 sequencing was carried out on a normalized cDNA pool prepared from 31 tissues produced 494,353 short transcript reads (STRs). Cluster analysi...

Effectiveness of Supplemental Kindergarten Vocabulary Instruction for English Learners: A Randomized Study of Immediate and Longer-Term Effects of Two Approaches

ERIC Educational Resources Information Center

Vadasy, Patricia F.; Sanders, Elizabeth A.; Nelson, J. Ron

2015-01-01

A two-cohort cluster randomized trial was conducted to estimate effects of small-group supplemental vocabulary instruction for at-risk kindergarten English learners (ELs). "Connections" students received explicit instruction in high-frequency decodable root words, and interactive book reading (IBR) students were taught the same words in…

Neural Correlates of Lexicon and Grammar: Evidence from the Production, Reading, and Judgment of Inflection in Aphasia

ERIC Educational Resources Information Center

Ullman, M.T.; Pancheva, R.; Love, T.; Yee, E.; Swinney, D.; Hickok, G.

2005-01-01

Are the linguistic forms that are memorized in the mental lexicon and those that are specified by the rules of grammar subserved by distinct neurocognitive systems or by a single computational system with relatively broad anatomic distribution? On a dual-system view, the productive -ed-suffixation of English regular past tense forms (e.g.,…

The role of sphingolipids in neuronal plasticity of the brain.

PubMed

Sonnino, Sandro; Prinetti, Alessandro

2016-05-01

This Editorial highlights a study by Müller et al. in which the authors suggest a new sphingolipid-dependent mechanism for behavioral extinction. Their study should be considered in the broad perspective of sphingolipid metabolic pathways and traffic (depicted in the graphic). Read the highlighted article 'A sphingolipid mechanism for behavioral extinction' on page 589. © 2016 International Society for Neurochemistry.

Video Games vs. Reading and School/Cognitive Performances: A Study on 27000 Middle School Teenagers

ERIC Educational Resources Information Center

Lieury, Alain; Lorant, Sonia; Trosseille, Bruno; Champault, Françoise; Vourc'h, Ronan

2016-01-01

Video games are a very common leisure activity among teenagers and the aim of this study is to analyse their relations with cognitive and school performances. This study is part of a broad survey, conducted on 27,000 French teenagers (14.5 years old) in middle school (9th grade). The survey contained both a questionnaire on leisure activities…

Minimal spanning trees at the percolation threshold: a numerical calculation

NASA Astrophysics Data System (ADS)

Sweeney, Sean; Middleton, A. Alan

2013-03-01

Through computer simulations on a hypercubic lattice, we grow minimal spanning trees (MSTs) in up to five dimensions and examine their fractal dimensions. Understanding MSTs is imporant for studying systems with quenched disorder such as spin glasses. We implement a combination of Prim's and Kruskal's algorithms for finding MSTs in order to reduce memory usage and allow for simulation of larger systems than would otherwise be possible. These fractal objects are analyzed in an attempt to numerically verify predictions of the perturbation expansion developed by T. S. Jackson and N. Read for the pathlength fractal dimension ds of MSTs on percolation clusters at criticality [T. S. Jackson and N. Read, Phys. Rev. E 81, 021131 (2010)]. Examining these trees also sparked the development of an analysis technique for dealing with correlated data that could be easily generalized to other systems and should be a robust method for analyzing a wide array of randomly generated fractal structures. This work was made possible in part by NSF Grant No. DMR-1006731 and by the Syracuse University Gravitation and Relativity computing cluster, which is supported in part by NSF Grant No. PHY-0600953.

Lexical frequency and voice assimilation in complex words in Dutch

NASA Astrophysics Data System (ADS)

Ernestus, Mirjam; Lahey, Mybeth; Verhees, Femke; Baayen, Harald

2004-05-01

Words with higher token frequencies tend to have more reduced acoustic realizations than lower frequency words (e.g., Hay, 2000; Bybee, 2001; Jurafsky et al., 2001). This study documents frequency effects for regressive voice assimilation (obstruents are voiced before voiced plosives) in Dutch morphologically complex words in the subcorpus of read-aloud novels in the corpus of spoken Dutch (Oostdijk et al., 2002). As expected, the initial obstruent of the cluster tends to be absent more often as lexical frequency increases. More importantly, as frequency increases, the duration of vocal-fold vibration in the cluster decreases, and the duration of the bursts in the cluster increases, after partialing out cluster duration. This suggests that there is less voicing for higher-frequency words. In fact, phonetic transcriptions show regressive voice assimilation for only half of the words and progressive voice assimilation for one third. Interestingly, the progressive voice assimilation observed for higher-frequency complex words renders these complex words more similar to monomorphemic words: Dutch monomorphemic words typically contain voiceless obstruent clusters (Zonneveld, 1983). Such high-frequency complex words may therefore be less easily parsed into their constituent morphemes (cf. Hay, 2000), favoring whole word lexical access (Bertram et al., 2000).

Egocentric daily activity recognition via multitask clustering.

PubMed

Yan, Yan; Ricci, Elisa; Liu, Gaowen; Sebe, Nicu

2015-10-01

Recognizing human activities from videos is a fundamental research problem in computer vision. Recently, there has been a growing interest in analyzing human behavior from data collected with wearable cameras. First-person cameras continuously record several hours of their wearers' life. To cope with this vast amount of unlabeled and heterogeneous data, novel algorithmic solutions are required. In this paper, we propose a multitask clustering framework for activity of daily living analysis from visual data gathered from wearable cameras. Our intuition is that, even if the data are not annotated, it is possible to exploit the fact that the tasks of recognizing everyday activities of multiple individuals are related, since typically people perform the same actions in similar environments, e.g., people working in an office often read and write documents). In our framework, rather than clustering data from different users separately, we propose to look for clustering partitions which are coherent among related tasks. In particular, two novel multitask clustering algorithms, derived from a common optimization problem, are introduced. Our experimental evaluation, conducted both on synthetic data and on publicly available first-person vision data sets, shows that the proposed approach outperforms several single-task and multitask learning methods.

Electrical probing of field-driven cascading quantized transitions of skyrmion cluster states in MnSi nanowires

NASA Astrophysics Data System (ADS)

Du, Haifeng; Liang, Dong; Jin, Chiming; Kong, Lingyao; Stolt, Matthew J.; Ning, Wei; Yang, Jiyong; Xing, Ying; Wang, Jian; Che, Renchao; Zang, Jiadong; Jin, Song; Zhang, Yuheng; Tian, Mingliang

2015-07-01

Magnetic skyrmions are topologically stable whirlpool-like spin textures that offer great promise as information carriers for future spintronic devices. To enable such applications, particular attention has been focused on the properties of skyrmions in highly confined geometries such as one-dimensional nanowires. Hitherto, it is still experimentally unclear what happens when the width of the nanowire is comparable to that of a single skyrmion. Here, we achieve this by measuring the magnetoresistance in ultra-narrow MnSi nanowires. We observe quantized jumps in magnetoresistance versus magnetic field curves. By tracking the size dependence of the jump number, we infer that skyrmions are assembled into cluster states with a tunable number of skyrmions, in agreement with the Monte Carlo simulations. Our results enable an electric reading of the number of skyrmions in the cluster states, thus laying a solid foundation to realize skyrmion-based memory devices.

Clustering microcalcifications techniques in digital mammograms

NASA Astrophysics Data System (ADS)

Díaz, Claudia. C.; Bosco, Paolo; Cerello, Piergiorgio

2008-11-01

Breast cancer has become a serious public health problem around the world. However, this pathology can be treated if it is detected in early stages. This task is achieved by a radiologist, who should read a large amount of mammograms per day, either for a screening or diagnostic purpose in mammography. However human factors could affect the diagnosis. Computer Aided Detection is an automatic system, which can help to specialists in the detection of possible signs of malignancy in mammograms. Microcalcifications play an important role in early detection, so we focused on their study. The two mammographic features that indicate the microcalcifications could be probably malignant are small size and clustered distribution. We worked with density techniques for automatic clustering, and we applied them on a mammography CAD prototype developed at INFN-Turin, Italy. An improvement of performance is achieved analyzing images from a Perugia-Assisi Hospital, in Italy.

Timing the impact of literacy on visual processing

PubMed Central

Pegado, Felipe; Comerlato, Enio; Ventura, Fabricio; Jobert, Antoinette; Nakamura, Kimihiro; Buiatti, Marco; Ventura, Paulo; Dehaene-Lambertz, Ghislaine; Kolinsky, Régine; Morais, José; Braga, Lucia W.; Cohen, Laurent; Dehaene, Stanislas

2014-01-01

Learning to read requires the acquisition of an efficient visual procedure for quickly recognizing fine print. Thus, reading practice could induce a perceptual learning effect in early vision. Using functional magnetic resonance imaging (fMRI) in literate and illiterate adults, we previously demonstrated an impact of reading acquisition on both high- and low-level occipitotemporal visual areas, but could not resolve the time course of these effects. To clarify whether literacy affects early vs. late stages of visual processing, we measured event-related potentials to various categories of visual stimuli in healthy adults with variable levels of literacy, including completely illiterate subjects, early-schooled literate subjects, and subjects who learned to read in adulthood (ex-illiterates). The stimuli included written letter strings forming pseudowords, on which literacy is expected to have a major impact, as well as faces, houses, tools, checkerboards, and false fonts. To evaluate the precision with which these stimuli were encoded, we studied repetition effects by presenting the stimuli in pairs composed of repeated, mirrored, or unrelated pictures from the same category. The results indicate that reading ability is correlated with a broad enhancement of early visual processing, including increased repetition suppression, suggesting better exemplar discrimination, and increased mirror discrimination, as early as ∼100–150 ms in the left occipitotemporal region. These effects were found with letter strings and false fonts, but also were partially generalized to other visual categories. Thus, learning to read affects the magnitude, precision, and invariance of early visual processing. PMID:25422460

Timing the impact of literacy on visual processing.

PubMed

Pegado, Felipe; Comerlato, Enio; Ventura, Fabricio; Jobert, Antoinette; Nakamura, Kimihiro; Buiatti, Marco; Ventura, Paulo; Dehaene-Lambertz, Ghislaine; Kolinsky, Régine; Morais, José; Braga, Lucia W; Cohen, Laurent; Dehaene, Stanislas

2014-12-09

Learning to read requires the acquisition of an efficient visual procedure for quickly recognizing fine print. Thus, reading practice could induce a perceptual learning effect in early vision. Using functional magnetic resonance imaging (fMRI) in literate and illiterate adults, we previously demonstrated an impact of reading acquisition on both high- and low-level occipitotemporal visual areas, but could not resolve the time course of these effects. To clarify whether literacy affects early vs. late stages of visual processing, we measured event-related potentials to various categories of visual stimuli in healthy adults with variable levels of literacy, including completely illiterate subjects, early-schooled literate subjects, and subjects who learned to read in adulthood (ex-illiterates). The stimuli included written letter strings forming pseudowords, on which literacy is expected to have a major impact, as well as faces, houses, tools, checkerboards, and false fonts. To evaluate the precision with which these stimuli were encoded, we studied repetition effects by presenting the stimuli in pairs composed of repeated, mirrored, or unrelated pictures from the same category. The results indicate that reading ability is correlated with a broad enhancement of early visual processing, including increased repetition suppression, suggesting better exemplar discrimination, and increased mirror discrimination, as early as ∼ 100-150 ms in the left occipitotemporal region. These effects were found with letter strings and false fonts, but also were partially generalized to other visual categories. Thus, learning to read affects the magnitude, precision, and invariance of early visual processing.

Glaucoma and disability: which tasks are affected, and at what stage of disease?

PubMed

Ramulu, Pradeep

2009-03-01

To summarize recent work from clinical and epidemiological studies that describe how, and at what stage, glaucoma affects the performance of important vision-related activities. Difficulties with the extremes of lighting are the most frequent complaint in glaucoma. Individuals with bilateral glaucoma also self-report difficulty with a broad array of tasks, including reading, walking, and driving. Bilateral glaucoma is associated with driving cessation and limitation, bumping into objects, slower walking, and falls. Some, but not all, studies also demonstrate higher accident rates in glaucoma. Measurable effects on reading speed have only been observed with field damage severe enough to affect binocular central acuity. Glaucoma with bilateral visual field loss is associated with increased symptoms and a measurable decline in mobility and driving. Further work is necessary to establish whether unilateral glaucoma has a significant impact on patients, to determine whether reading difficulty is common in patients with bilateral glaucoma, and to establish the effects of lighting conditions on task performance in glaucoma.

Chrominance watermark for mobile applications

NASA Astrophysics Data System (ADS)

Reed, Alastair; Rogers, Eliot; James, Dan

2010-01-01

Creating an imperceptible watermark which can be read by a broad range of cell phone cameras is a difficult problem. The problems are caused by the inherently low resolution and noise levels of typical cell phone cameras. The quality limitations of these devices compared to a typical digital camera are caused by the small size of the cell phone and cost trade-offs made by the manufacturer. In order to achieve this, a low resolution watermark is required which can be resolved by a typical cell phone camera. The visibility of a traditional luminance watermark was too great at this lower resolution, so a chrominance watermark was developed. The chrominance watermark takes advantage of the relatively low sensitivity of the human visual system to chrominance changes. This enables a chrominance watermark to be inserted into an image which is imperceptible to the human eye but can be read using a typical cell phone camera. Sample images will be presented showing images with a very low visibility which can be easily read by a typical cell phone camera.

Emergent Writing in Preschoolers: Preliminary Evidence for a Theoretical Framework

PubMed Central

Puranik, Cynthia S.; Lonigan, Christopher J.

2014-01-01

Researchers and educators use the term emergent literacy to refer to a broad set of skills and attitudes that serve as foundational skills for acquiring success in later reading and writing; however, models of emergent literacy have generally focused on reading and reading-related behaviors. Hence, the primary aim of this study was to articulate and evaluate a theoretical model of the components of emergent writing. Alternative models of the structure of individual and developmental differences of emergent writing and writing-related skills were examined in 372 preschool children who ranged in age from 3- to 5-years using confirmatory factor analysis. Results from a confirmatory factor analysis provide evidence that these emergent writing skills are best described by three correlated but distinct factors, (a) Conceptual Knowledge, (b) Procedural Knowledge, and (c) Generative Knowledge. Evidence that these three emergent writing factors show different patterns of relations to emergent literacy constructs is presented. Implications for understanding the development of writing and assessment of early writing skills are discussed. PMID:25316955

Analysis of NFU-1 metallocofactor binding-site substitutions-impacts on iron-sulfur cluster coordination and protein structure and function.

PubMed

Wesley, Nathaniel A; Wachnowsky, Christine; Fidai, Insiya; Cowan, J A

2017-11-01

Iron-sulfur (Fe/S) clusters are ancient prosthetic groups found in numerous metalloproteins and are conserved across all kingdoms of life due to their diverse, yet essential functional roles. Genetic mutations to a specific subset of mitochondrial Fe/S cluster delivery proteins are broadly categorized as disease-related under multiple mitochondrial dysfunction syndrome (MMDS), with symptoms indicative of a general failure of the metabolic system. Multiple mitochondrial dysfunction syndrome 1 (MMDS1) arises as a result of the missense mutation in NFU1, an Fe/S cluster scaffold protein, which substitutes a glycine near the Fe/S cluster-binding pocket to a cysteine (p.Gly208Cys). This substitution has been shown to promote protein dimerization such that cluster delivery to NFU1 is blocked, preventing downstream cluster trafficking. However, the possibility of this additional cysteine, located adjacent to the cluster-binding site, serving as an Fe/S cluster ligand has not yet been explored. To fully understand the consequences of this Gly208Cys replacement, complementary substitutions at the Fe/S cluster-binding pocket for native and Gly208Cys NFU1 were made, along with six other variants. Herein, we report the results of an investigation on the effect of these substitutions on both cluster coordination and NFU1 structure and function. The data suggest that the G208C substitution does not contribute to cluster binding. Rather, replacement of the glycine at position 208 changes the oligomerization state as a result of global structural alterations that result in the downstream effects manifest as MMDS1, but does not perturb the coordination chemistry of the Fe-S cluster. © 2017 Federation of European Biochemical Societies.

Spatial and kinematic distributions of transition populations in intermediate redshift galaxy clusters

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

Crawford, Steven M.; Wirth, Gregory D.; Bershady, Matthew A., E-mail: crawford@saao.ac.za, E-mail: wirth@keck.hawaii.edu, E-mail: mab@astro.wisc.edu

2014-05-01

We analyze the spatial and velocity distributions of confirmed members in five massive clusters of galaxies at intermediate redshift (0.5 < z < 0.9) to investigate the physical processes driving galaxy evolution. Based on spectral classifications derived from broad- and narrow-band photometry, we define four distinct galaxy populations representing different evolutionary stages: red sequence (RS) galaxies, blue cloud (BC) galaxies, green valley (GV) galaxies, and luminous compact blue galaxies (LCBGs). For each galaxy class, we derive the projected spatial and velocity distribution and characterize the degree of subclustering. We find that RS, BC, and GV galaxies in these clusters havemore » similar velocity distributions, but that BC and GV galaxies tend to avoid the core of the two z ≈ 0.55 clusters. GV galaxies exhibit subclustering properties similar to RS galaxies, but their radial velocity distribution is significantly platykurtic compared to the RS galaxies. The absence of GV galaxies in the cluster cores may explain their somewhat prolonged star-formation history. The LCBGs appear to have recently fallen into the cluster based on their larger velocity dispersion, absence from the cores of the clusters, and different radial velocity distribution than the RS galaxies. Both LCBG and BC galaxies show a high degree of subclustering on the smallest scales, leading us to conclude that star formation is likely triggered by galaxy-galaxy interactions during infall into the cluster.« less

Application of a Self-Similar Pressure Profile to Sunyaev-Zeldovich Effect Data from Galaxy Clusters

NASA Technical Reports Server (NTRS)

Mroczkowski, Tony; Bonamente, Max; Carlstrom, John E.; Culverhouse, Thomas L.; Greer, Christopher; Hawkins, David; Hennessy, Ryan; Joy, Marshall; Lamb, James W.; Leitch, Erik M.;

Working memory, short-term memory, and reading disabilities: a selective meta-analysis of the literature.

PubMed

Swanson, H Lee; Xinhua Zheng; Jerman, Olga

2009-01-01

The purpose of the present study was to synthesize research that compares children with and without reading disabilities (RD) on measures of short-term memory (STM) and working memory (WM). Across a broad age, reading, and IQ range, 578 effect sizes (ESs) were computed, yielding a mean ES across studies of -.89 (SD = 1.03). A total of 257 ESs were in the moderate range for STM measures (M = -.61, 95% confidence range of -.65 to -.58), and 320 ESs were in the moderate range for WM measures (M = -.67, 95% confidence range of -.68 to -.64). The results indicated that children with RD were distinctively disadvantaged compared with average readers on (a) STM measures requiring the recall of phonemes and digit sequences and (b) WM measures requiring the simultaneous processing and storage of digits within sentence sequences and final words from unrelated sentences. No significant moderating effects emerged for age, IQ, or reading level on memory ESs. The findings indicated that domain-specific STM and WM differences between ability groups persisted across age, suggesting that a verbal deficit model that fails to efficiently draw resources from both a phonological and executive system underlies RD.

Effect of pH on the Electrophoretic Mobility of Spores of Bacillus anthracis and Its Surrogates in Aqueous Solutions

EPA Science Inventory

Electrophoretic mobility (EPM) of endospores of Bacillus anthracis and surrogates were measured in aqueous solution across a broad pH range and several ionic strengths. EPM values trended around phylogenetic clustering based on the 16S rRNA gene. Measurements reported here prov...

Assumptions of Asian American Similarity: The Case of Filipino and Chinese American Students

ERIC Educational Resources Information Center

Agbayani-Siewert, Pauline

2004-01-01

The conventional research model of clustering ethnic groups into four broad categories risks perpetuating a pedagogy of stereotypes in social work policies and practice methods. Using an elaborated research model, this study tested the assumption of cultural similarity of Filipino and Chinese American college students by examining attitudes,…

Australian Vocational Education and Training: Research Messages, 2008

ERIC Educational Resources Information Center

National Centre for Vocational Education Research (NCVER), 2009

2009-01-01

"Research Messages 2008" is a collection of summaries of research projects published by the National Centre for Vocational Education Research in 2008, including conference papers and occasional papers. It also has an overview of the research highlights for the year. The summaries are clustered under five broad themes used by NCVER to…

Looking Backward: James Madison University's General Education Reform.

ERIC Educational Resources Information Center

Reynolds, Charles W.; Allain, Violet Anselmini; Erwin, T. Dary; Halpern, Linda Cabe; McNallie, Robin; Ross, Martha K.

1998-01-01

Describes the new general education program at James Madison University (Virginia) and the process by which it was developed. Indicates that the program is organized by five broad areas of knowledge that are defined by interdisciplinary clusters of learning objectives, which in turn were developed using input from every academic department on…

The effects of Nordic school meals on concentration and school performance in 8- to 11-year-old children in the OPUS School Meal Study: a cluster-randomised, controlled, cross-over trial.

PubMed

Sørensen, Louise B; Dyssegaard, Camilla B; Damsgaard, Camilla T; Petersen, Rikke A; Dalskov, Stine-Mathilde; Hjorth, Mads F; Andersen, Rikke; Tetens, Inge; Ritz, Christian; Astrup, Arne; Lauritzen, Lotte; Michaelsen, Kim F; Egelund, Niels

2015-04-28

It is widely assumed that nutrition can improve school performance in children; however, evidence remains limited and inconclusive. In the present study, we investigated whether serving healthy school meals influenced concentration and school performance of 8- to 11-year-old Danish children. The OPUS (Optimal well-being, development and health for Danish children through a healthy New Nordic Diet) School Meal Study was a cluster-randomised, controlled, cross-over trial comparing a healthy school meal programme with the usual packed lunch from home (control) each for 3 months (NCT 01457794). The d2 test of attention, the Learning Rating Scale (LRS) and standard tests on reading and mathematics proficiency were administered at baseline and at the end of each study period. Intervention effects were evaluated using hierarchical mixed models. The school meal intervention did not influence concentration performance (CP; primary outcome, n 693) or processing speed; however, the decrease in error percentage was 0·18 points smaller (P<0·001) in the intervention period than in the control period (medians: baseline 2·03%; intervention 1·46%; control 1·37%). In contrast, the intervention increased reading speed (0·7 sentence, P=0·009) and the number of correct sentences (1·8 sentences, P<0·001), which corresponded to 11 and 25%, respectively, of the effect of one school year. The percentage of correct sentences also improved (P<0·001), indicating that the number correct improved relatively more than reading speed. There was no effect on overall math performance or outcomes from the LRS. In conclusion, school meals did not affect CP, but improved reading performance, which is a complex cognitive activity that involves inference, and increased errors related to impulsivity and inattention. These findings are worth examining in future trials.

Biosynthetic Investigations of Lactonamycin and Lactonamycin Z: Cloning of the Biosynthetic Gene Clusters and Discovery of an Unusual Starter Unit▿ †

PubMed Central

Zhang, Xiujun; Alemany, Lawrence B.; Fiedler, Hans-Peter; Goodfellow, Michael; Parry, Ronald J.

2008-01-01

The antibiotics lactonamycin and lactonamycin Z provide attractive leads for antibacterial drug development. Both antibiotics contain a novel aglycone core called lactonamycinone. To gain insight into lactonamycinone biosynthesis, cloning and precursor incorporation experiments were undertaken. The lactonamycin gene cluster was initially cloned from Streptomyces rishiriensis. Sequencing of ca. 61 kb of S. rishiriensis DNA revealed the presence of 57 open reading frames. These included genes coding for the biosynthesis of l-rhodinose, the sugar found in lactonamycin, and genes similar to those in the tetracenomycin biosynthetic gene cluster. Since lactonamycin production by S. rishiriensis could not be sustained, additional proof for the identity of the S. rishiriensis cluster was obtained by cloning the lactonamycin Z gene cluster from Streptomyces sanglieri. Partial sequencing of the S. sanglieri cluster revealed 15 genes that exhibited a very high degree of similarity to genes within the lactonamycin cluster, as well as an identical organization. Double-crossover disruption of one gene in the S. sanglieri cluster abolished lactonamycin Z production, and production was restored by complementation. These results confirm the identity of the genetic locus cloned from S. sanglieri and indicate that the highly similar locus in S. rishiriensis encodes lactonamycin biosynthetic genes. Precursor incorporation experiments with S. sanglieri revealed that lactonamycinone is biosynthesized in an unusual manner whereby glycine or a glycine derivative serves as a starter unit that is extended by nine acetate units. Analysis of the gene clusters and of the precursor incorporation data suggested a hypothetical scheme for lactonamycinone biosynthesis. PMID:18070976

Role and Regulation of the Flp/Tad Pilus in the Virulence of Pectobacterium atrosepticum SCRI1043 and Pectobacterium wasabiae SCC3193

PubMed Central

Nykyri, Johanna; Mattinen, Laura; Niemi, Outi; Adhikari, Satish; Kõiv, Viia; Somervuo, Panu; Fang, Xin; Auvinen, Petri; Mäe, Andres; Palva, E. Tapio; Pirhonen, Minna

2013-01-01

In this study, we characterized a putative Flp/Tad pilus-encoding gene cluster, and we examined its regulation at the transcriptional level and its role in the virulence of potato pathogenic enterobacteria of the genus Pectobacterium. The Flp/Tad pilus-encoding gene clusters in Pectobacterium atrosepticum, Pectobacterium wasabiae and Pectobacterium aroidearum were compared to previously characterized flp/tad gene clusters, including that of the well-studied Flp/Tad pilus model organism Aggregatibacter actinomycetemcomitans, in which this pilus is a major virulence determinant. Comparative analyses revealed substantial protein sequence similarity and open reading frame synteny between the previously characterized flp/tad gene clusters and the cluster in Pectobacterium, suggesting that the predicted flp/tad gene cluster in Pectobacterium encodes a Flp/Tad pilus-like structure. We detected genes for a novel two-component system adjacent to the flp/tad gene cluster in Pectobacterium, and mutant analysis demonstrated that this system has a positive effect on the transcription of selected Flp/Tad pilus biogenesis genes, suggesting that this response regulator regulate the flp/tad gene cluster. Mutagenesis of either the predicted regulator gene or selected Flp/Tad pilus biogenesis genes had a significant impact on the maceration ability of the bacterial strains in potato tubers, indicating that the Flp/Tad pilus-encoding gene cluster represents a novel virulence determinant in Pectobacterium. Soft-rot enterobacteria in the genera Pectobacterium and Dickeya are of great agricultural importance, and an investigation of the virulence of these pathogens could facilitate improvements in agricultural practices, thus benefiting farmers, the potato industry and consumers. PMID:24040039

Role and regulation of the Flp/Tad pilus in the virulence of Pectobacterium atrosepticum SCRI1043 and Pectobacterium wasabiae SCC3193.

PubMed

Nykyri, Johanna; Mattinen, Laura; Niemi, Outi; Adhikari, Satish; Kõiv, Viia; Somervuo, Panu; Fang, Xin; Auvinen, Petri; Mäe, Andres; Palva, E Tapio; Pirhonen, Minna

2013-01-01

In this study, we characterized a putative Flp/Tad pilus-encoding gene cluster, and we examined its regulation at the transcriptional level and its role in the virulence of potato pathogenic enterobacteria of the genus Pectobacterium. The Flp/Tad pilus-encoding gene clusters in Pectobacterium atrosepticum, Pectobacterium wasabiae and Pectobacterium aroidearum were compared to previously characterized flp/tad gene clusters, including that of the well-studied Flp/Tad pilus model organism Aggregatibacter actinomycetemcomitans, in which this pilus is a major virulence determinant. Comparative analyses revealed substantial protein sequence similarity and open reading frame synteny between the previously characterized flp/tad gene clusters and the cluster in Pectobacterium, suggesting that the predicted flp/tad gene cluster in Pectobacterium encodes a Flp/Tad pilus-like structure. We detected genes for a novel two-component system adjacent to the flp/tad gene cluster in Pectobacterium, and mutant analysis demonstrated that this system has a positive effect on the transcription of selected Flp/Tad pilus biogenesis genes, suggesting that this response regulator regulate the flp/tad gene cluster. Mutagenesis of either the predicted regulator gene or selected Flp/Tad pilus biogenesis genes had a significant impact on the maceration ability of the bacterial strains in potato tubers, indicating that the Flp/Tad pilus-encoding gene cluster represents a novel virulence determinant in Pectobacterium. Soft-rot enterobacteria in the genera Pectobacterium and Dickeya are of great agricultural importance, and an investigation of the virulence of these pathogens could facilitate improvements in agricultural practices, thus benefiting farmers, the potato industry and consumers.

An Artificial Functional Family Filter in Homolog Searching in Next-generation Sequencing Metagenomics

PubMed Central

Du, Ruofei; Mercante, Donald; Fang, Zhide

2013-01-01

In functional metagenomics, BLAST homology search is a common method to classify metagenomic reads into protein/domain sequence families such as Clusters of Orthologous Groups of proteins (COGs) in order to quantify the abundance of each COG in the community. The resulting functional profile of the community is then used in downstream analysis to correlate the change in abundance to environmental perturbation, clinical variation, and so on. However, the short read length coupled with next-generation sequencing technologies poses a barrier in this approach, essentially because similarity significance cannot be discerned by searching with short reads. Consequently, artificial functional families are produced, in which those with a large number of reads assigned decreases the accuracy of functional profile dramatically. There is no method available to address this problem. We intended to fill this gap in this paper. We revealed that BLAST similarity scores of homologues for short reads from COG protein members coding sequences are distributed differently from the scores of those derived elsewhere. We showed that, by choosing an appropriate score cut-off, we are able to filter out most artificial families and simultaneously to preserve sufficient information in order to build the functional profile. We also showed that, by incorporated application of BLAST and RPS-BLAST, some artificial families with large read counts can be further identified after the score cutoff filtration. Evaluated on three experimental metagenomic datasets with different coverages, we found that the proposed method is robust against read coverage and consistently outperforms the other E-value cutoff methods currently used in literatures. PMID:23516532

Nucleotide sequence of a cluster of early and late genes in a conserved segment of the vaccinia virus genome.

PubMed Central

Plucienniczak, A; Schroeder, E; Zettlmeissl, G; Streeck, R E

1985-01-01

The nucleotide sequence of a 7.6 kb vaccinia DNA segment from a genomic region conserved among different orthopox virus has been determined. This segment contains a tight cluster of 12 partly overlapping open reading frames most of which can be correlated with previously identified early and late proteins and mRNAs. Regulatory signals used by vaccinia virus have been studied. Presumptive promoter regions are rich in A, T and carry the consensus sequences TATA and AATAA spaced at 20-24 base pairs. Tandem repeats of a CTATTC consensus sequence are proposed to be involved in the termination of early transcription. PMID:2987815