Sample records for alignments code english

  1. Syntactic Alignment and Shared Word Order in Code-Switched Sentence Production: Evidence from Bilingual Monologue and Dialogue

    ERIC Educational Resources Information Center

    Kootstra, Gerrit Jan; van Hell, Janet G.; Dijkstra, Ton

    2010-01-01

    In four experiments, we investigated the role of shared word order and alignment with a dialogue partner in the production of code-switched sentences. In Experiments 1 and 2, Dutch-English bilinguals code-switched in describing pictures while being cued with word orders that are either shared or not shared between Dutch and English. In Experiments…

  2. Aligning Greek-English parallel texts

    NASA Astrophysics Data System (ADS)

    Galiotou, Eleni; Koronakis, George; Lazari, Vassiliki

    2015-02-01

    In this paper, we discuss issues concerning the alignment of parallel texts written in languages with different alphabets based on an experiment of aligning texts from the proceedings of the European Parliament in Greek and English. First, we describe our implementation of the k-vec algorithm and its application to the bilingual corpus. Then the output of the algorithm is used as a starting point for an alignment procedure at a sentence level which also takes into account mark-ups of meta-information. The results of the implementation are compared to those of the application of the Church and Gale alignment algorithm on the Europarl corpus. The conclusions of this comparison can give useful insights as for the efficiency of alignment algorithms when applied to the particular bilingual corpus.

  3. Aligning English Language Testing with Curriculum

    ERIC Educational Resources Information Center

    Palacio, Marcela; Gaviria, Sandra; Brown, James Dean

    2016-01-01

    Frustrations with traditional testing led a group of teachers at the English for adults program at Universidad EAFIT (Colombia) to design tests aligned with the institutional teaching philosophy and classroom practices. This article reports on a study of an item-by-item evaluation of a series of English exams for validity and reliability in an…

  4. Analysis of the Length of Braille Texts in English Braille American Edition, the Nemeth Code, and Computer Braille Code versus the Unified English Braille Code

    ERIC Educational Resources Information Center

    Knowlton, Marie; Wetzel, Robin

    2006-01-01

    This study compared the length of text in English Braille American Edition, the Nemeth code, and the computer braille code with the Unified English Braille Code (UEBC)--also known as Unified English Braille (UEB). The findings indicate that differences in the length of text are dependent on the type of material that is transcribed and the grade…

  5. CombAlign: a code for generating a one-to-many sequence alignment from a set of pairwise structure-based sequence alignments.

    PubMed

    Zhou, Carol L Ecale

    2015-01-01

    In order to better define regions of similarity among related protein structures, it is useful to identify the residue-residue correspondences among proteins. Few codes exist for constructing a one-to-many multiple sequence alignment derived from a set of structure or sequence alignments, and a need was evident for creating such a tool for combining pairwise structure alignments that would allow for insertion of gaps in the reference structure. This report describes a new Python code, CombAlign, which takes as input a set of pairwise sequence alignments (which may be structure based) and generates a one-to-many, gapped, multiple structure- or sequence-based sequence alignment (MSSA). The use and utility of CombAlign was demonstrated by generating gapped MSSAs using sets of pairwise structure-based sequence alignments between structure models of the matrix protein (VP40) and pre-small/secreted glycoprotein (sGP) of Reston Ebolavirus and the corresponding proteins of several other filoviruses. The gapped MSSAs revealed structure-based residue-residue correspondences, which enabled identification of structurally similar versus differing regions in the Reston proteins compared to each of the other corresponding proteins. CombAlign is a new Python code that generates a one-to-many, gapped, multiple structure- or sequence-based sequence alignment (MSSA) given a set of pairwise sequence alignments (which may be structure based). CombAlign has utility in assisting the user in distinguishing structurally conserved versus divergent regions on a reference protein structure relative to other closely related proteins. CombAlign was developed in Python 2.6, and the source code is available for download from the GitHub code repository.

  6. Adverb Code-Switching among Miami's Haitian Creole-English Second Generation

    ERIC Educational Resources Information Center

    Hebblethwaite, Benjamin

    2010-01-01

    The findings for adverbs and adverbial phrases in a naturalistic corpus of Miami Haitian Creole-English code-switching show that one language, Haitian Creole, asymmetrically supplies the grammatical frame while the other language, English, asymmetrically supplies mixed lexical categories like adverbs. Traces of code-switching with an English frame…

  7. Transferring Standard English Braille Skills to the Unified English Braille Code: A Pilot Study

    ERIC Educational Resources Information Center

    Steinman, Bernard A.; Kimbrough, B. T.; Johnson, Franklin; LeJeune, B. J.

    2004-01-01

    The enormously complex and sometimes controversial project to unify the traditional literary Braille code used in English-speaking countries with the technical and mathematical codes authorized by the Braille Authority of North America (BANA) and the Braille Authority of the United Kingdom (BAUK) proposes to change English Grade Two Braille on a…

  8. Code-Switching in English and Science Classrooms: More than Translation

    ERIC Educational Resources Information Center

    Then, David Chen-On; Ting, Su-Hie

    2011-01-01

    The study examined the use of code-switching by English and science teachers in secondary schools in Malaysia. It focuses on the functions of code-switching in multilingual classrooms where English is the language of instruction, examining in particular the reiterative function of code-switching and its association with translation. Thirty six…

  9. Congruence and Welsh-English Code-Switching

    ERIC Educational Resources Information Center

    Deuchar, Margaret

    2005-01-01

    This paper aims to contribute to elucidating the notion of congruence in code-switching with particular reference to Welsh-English data. It has been suggested that a sufficient degree of congruence or equivalence between the constituents of one language and another is necessary in order for code-switching to take place. We shall distinguish…

  10. Creating a medical English-Swedish dictionary using interactive word alignment.

    PubMed

    Nyström, Mikael; Merkel, Magnus; Ahrenberg, Lars; Zweigenbaum, Pierre; Petersson, Håkan; Ahlfeldt, Hans

    2006-10-12

    This paper reports on a parallel collection of rubrics from the medical terminology systems ICD-10, ICF, MeSH, NCSP and KSH97-P and its use for semi-automatic creation of an English-Swedish dictionary of medical terminology. The methods presented are relevant for many other West European language pairs than English-Swedish. The medical terminology systems were collected in electronic format in both English and Swedish and the rubrics were extracted in parallel language pairs. Initially, interactive word alignment was used to create training data from a sample. Then the training data were utilised in automatic word alignment in order to generate candidate term pairs. The last step was manual verification of the term pair candidates. A dictionary of 31,000 verified entries has been created in less than three man weeks, thus with considerably less time and effort needed compared to a manual approach, and without compromising quality. As a side effect of our work we found 40 different translation problems in the terminology systems and these results indicate the power of the method for finding inconsistencies in terminology translations. We also report on some factors that may contribute to making the process of dictionary creation with similar tools even more expedient. Finally, the contribution is discussed in relation to other ongoing efforts in constructing medical lexicons for non-English languages. In three man weeks we were able to produce a medical English-Swedish dictionary consisting of 31,000 entries and also found hidden translation errors in the utilized medical terminology systems.

  11. Creating a medical English-Swedish dictionary using interactive word alignment

    PubMed Central

    Nyström, Mikael; Merkel, Magnus; Ahrenberg, Lars; Zweigenbaum, Pierre; Petersson, Håkan; Åhlfeldt, Hans

    2006-01-01

    Background This paper reports on a parallel collection of rubrics from the medical terminology systems ICD-10, ICF, MeSH, NCSP and KSH97-P and its use for semi-automatic creation of an English-Swedish dictionary of medical terminology. The methods presented are relevant for many other West European language pairs than English-Swedish. Methods The medical terminology systems were collected in electronic format in both English and Swedish and the rubrics were extracted in parallel language pairs. Initially, interactive word alignment was used to create training data from a sample. Then the training data were utilised in automatic word alignment in order to generate candidate term pairs. The last step was manual verification of the term pair candidates. Results A dictionary of 31,000 verified entries has been created in less than three man weeks, thus with considerably less time and effort needed compared to a manual approach, and without compromising quality. As a side effect of our work we found 40 different translation problems in the terminology systems and these results indicate the power of the method for finding inconsistencies in terminology translations. We also report on some factors that may contribute to making the process of dictionary creation with similar tools even more expedient. Finally, the contribution is discussed in relation to other ongoing efforts in constructing medical lexicons for non-English languages. Conclusion In three man weeks we were able to produce a medical English-Swedish dictionary consisting of 31,000 entries and also found hidden translation errors in the utilized medical terminology systems. PMID:17034649

  12. Alignment-based and alignment-free methods converge with experimental data on amino acids coded by stop codons at split between nuclear and mitochondrial genetic codes.

    PubMed

    Seligmann, Hervé

    2018-05-01

    Genetic codes mainly evolve by reassigning punctuation codons, starts and stops. Previous analyses assuming that undefined amino acids translate stops showed greater divergence between nuclear and mitochondrial genetic codes. Here, three independent methods converge on which amino acids translated stops at split between nuclear and mitochondrial genetic codes: (a) alignment-free genetic code comparisons inserting different amino acids at stops; (b) alignment-based blast analyses of hypothetical peptides translated from non-coding mitochondrial sequences, inserting different amino acids at stops; (c) biases in amino acid insertions at stops in proteomic data. Hence short-term protein evolution models reconstruct long-term genetic code evolution. Mitochondria reassign stops to amino acids otherwise inserted at stops by codon-anticodon mismatches (near-cognate tRNAs). Hence dual function (translation termination and translation by codon-anticodon mismatch) precedes mitochondrial reassignments of stops to amino acids. Stop ambiguity increases coded information, compensates endocellular mitogenome reduction. Mitochondrial codon reassignments might prevent viral infections. Copyright © 2018 Elsevier B.V. All rights reserved.

  13. Bilingual processing of ASL-English code-blends: The consequences of accessing two lexical representations simultaneously

    PubMed Central

    Emmorey, Karen; Petrich, Jennifer; Gollan, Tamar H.

    2012-01-01

    Bilinguals who are fluent in American Sign Language (ASL) and English often produce code-blends - simultaneously articulating a sign and a word while conversing with other ASL-English bilinguals. To investigate the cognitive mechanisms underlying code-blend processing, we compared picture-naming times (Experiment 1) and semantic categorization times (Experiment 2) for code-blends versus ASL signs and English words produced alone. In production, code-blending did not slow lexical retrieval for ASL and actually facilitated access to low-frequency signs. However, code-blending delayed speech production because bimodal bilinguals synchronized English and ASL lexical onsets. In comprehension, code-blending speeded access to both languages. Bimodal bilinguals’ ability to produce code-blends without any cost to ASL implies that the language system either has (or can develop) a mechanism for switching off competition to allow simultaneous production of close competitors. Code-blend facilitation effects during comprehension likely reflect cross-linguistic (and cross-modal) integration at the phonological and/or semantic levels. The absence of any consistent processing costs for code-blending illustrates a surprising limitation on dual-task costs and may explain why bimodal bilinguals code-blend more often than they code-switch. PMID:22773886

  14. English-Afrikaans Intrasentential Code Switching: Testing a Feature Checking Account

    ERIC Educational Resources Information Center

    van Dulm, Ondene

    2009-01-01

    The work presented here aims to account for the structure of intrasentential code switching between English and Afrikaans within the framework of feature checking theory, a theory associated with minimalist syntax. Six constructions in which verb position differs between English and Afrikaans were analysed in terms of differences in the strength…

  15. Code-Switching in English as a Foreign Language Classroom: Teachers' Attitudes

    ERIC Educational Resources Information Center

    Ibrahim, Engku Haliza Engku; Shah, Mohamed Ismail Ahamad; Armia, Najwa Tgk.

    2013-01-01

    Code-switching has always been an intriguing phenomenon to sociolinguists. While the general attitude to it seems negative, people seem to code-switch quite frequently. Teachers of English as a foreign language too frequently claim that they do not like to code-switch in the language classroom for various reasons--many are of the opinion that only…

  16. Bilingual Processing of ASL-English Code-Blends: The Consequences of Accessing Two Lexical Representations Simultaneously

    ERIC Educational Resources Information Center

    Emmorey, Karen; Petrich, Jennifer A. F.; Gollan, Tamar H.

    2012-01-01

    Bilinguals who are fluent in American Sign Language (ASL) and English often produce "code-blends"--simultaneously articulating a sign and a word while conversing with other ASL-English bilinguals. To investigate the cognitive mechanisms underlying code-blend processing, we compared picture-naming times (Experiment 1) and semantic categorization…

  17. The Wildcat Corpus of Native- and Foreign-Accented English: Communicative Efficiency across Conversational Dyads with Varying Language Alignment Profiles

    PubMed Central

    Van Engen, Kristin J.; Baese-Berk, Melissa; Baker, Rachel E.; Choi, Arim; Kim, Midam; Bradlow, Ann R.

    2012-01-01

    This paper describes the development of the Wildcat Corpus of native- and foreign-accented English, a corpus containing scripted and spontaneous speech recordings from 24 native speakers of American English and 52 non-native speakers of English. The core element of this corpus is a set of spontaneous speech recordings, for which a new method of eliciting dialogue-based, laboratory-quality speech recordings was developed (the Diapix task). Dialogues between two native speakers of English, between two non-native speakers of English (with either shared or different L1s), and between one native and one non-native speaker of English are included and analyzed in terms of general measures of communicative efficiency. The overall finding was that pairs of native talkers were most efficient, followed by mixed native/non-native pairs and non-native pairs with shared L1. Non-native pairs with different L1s were least efficient. These results support the hypothesis that successful speech communication depends both on the alignment of talkers to the target language and on the alignment of talkers to one another in terms of native language background. PMID:21313992

  18. Focus Group Research on the Implications of Adopting the Unified English Braille Code

    ERIC Educational Resources Information Center

    Wetzel, Robin; Knowlton, Marie

    2006-01-01

    Five focus groups explored concerns about adopting the Unified English Braille Code. The consensus was that while the proposed changes to the literary braille code would be minor, those to the mathematics braille code would be much more extensive. The participants emphasized that "any code that reduces the number of individuals who can access…

  19. Simultaneous perception of a spoken and a signed language: The brain basis of ASL-English code-blends

    PubMed Central

    Weisberg, Jill; McCullough, Stephen; Emmorey, Karen

    2018-01-01

    Code-blends (simultaneous words and signs) are a unique characteristic of bimodal bilingual communication. Using fMRI, we investigated code-blend comprehension in hearing native ASL-English bilinguals who made a semantic decision (edible?) about signs, audiovisual words, and semantically equivalent code-blends. English and ASL recruited a similar fronto-temporal network with expected modality differences: stronger activation for English in auditory regions of bilateral superior temporal cortex, and stronger activation for ASL in bilateral occipitotemporal visual regions and left parietal cortex. Code-blend comprehension elicited activity in a combination of these regions, and no cognitive control regions were additionally recruited. Furthermore, code-blends elicited reduced activation relative to ASL presented alone in bilateral prefrontal and visual extrastriate cortices, and relative to English alone in auditory association cortex. Consistent with behavioral facilitation observed during semantic decisions, the findings suggest that redundant semantic content induces more efficient neural processing in language and sensory regions during bimodal language integration. PMID:26177161

  20. Bilingual term alignment from comparable corpora in English discharge summary and Chinese discharge summary.

    PubMed

    Xu, Yan; Chen, Luoxin; Wei, Junsheng; Ananiadou, Sophia; Fan, Yubo; Qian, Yi; Chang, Eric I-Chao; Tsujii, Junichi

    2015-05-09

    Electronic medical record (EMR) systems have become widely used throughout the world to improve the quality of healthcare and the efficiency of hospital services. A bilingual medical lexicon of Chinese and English is needed to meet the demand for the multi-lingual and multi-national treatment. We make efforts to extract a bilingual lexicon from English and Chinese discharge summaries with a small seed lexicon. The lexical terms can be classified into two categories: single-word terms (SWTs) and multi-word terms (MWTs). For SWTs, we use a label propagation (LP; context-based) method to extract candidates of translation pairs. For MWTs, which are pervasive in the medical domain, we propose a term alignment method, which firstly obtains translation candidates for each component word of a Chinese MWT, and then generates their combinations, from which the system selects a set of plausible translation candidates. We compare our LP method with a baseline method based on simple context-similarity. The LP based method outperforms the baseline with the accuracies: 4.44% Acc1, 24.44% Acc10, and 62.22% Acc100, where AccN means the top N accuracy. The accuracy of the LP method drops to 5.41% Acc10 and 8.11% Acc20 for MWTs. Our experiments show that the method based on term alignment improves the performance for MWTs to 16.22% Acc10 and 27.03% Acc20. We constructed a framework for building an English-Chinese term dictionary from discharge summaries in the two languages. Our experiments have shown that the LP-based method augmented with the term alignment method will contribute to reduction of manual work required to compile a bilingual sydictionary of clinical terms.

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

    PubMed Central

    Wright, Imogen A.; Travers, Simon A.

    2014-01-01

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

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

    PubMed

    Wright, Imogen A; Travers, Simon A

    2014-07-01

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

  3. 3D Radiative Transfer Code for Polarized Scattered Light with Aligned Grains

    NASA Astrophysics Data System (ADS)

    Pelkonen, V. M.; Penttilä, A.; Juvela, M.; Muinonen, K.

    2017-12-01

    Polarized scattered light has been observed in cometary comae and in circumstellar disks. It carries information about the grains from which the light scattered. However, modelling polarized scattered light is a complicated problem. We are working on a 3D Monte Carlo radiative transfer code which incorporates hierarchical grid structure (octree) and the full Stokes vector for both the incoming radiation and the radiation scattered by dust grains. In octree grid format an upper level cell can be divided into 8 subcells by halving the cell in each of the three axis. Levels of further refinement of the grid may be added, until the desired resolution is reached. The radiation field is calculated with Monte Carlo methods. The path of the model ray is traced in the cloud: absorbed intensity is counted in each cell, and from time to time, the model ray is scattered towards a new direction as determined by the dust model. Due to the non-spherical grains and the polarization, the scattering problem will be the main issue for the code and most time consuming. The scattering parameters will be taken from the models for individual grains. We can introduce populations of different grain shapes into the dust model, and randomly select, based on their amounts, from which shape the model ray scatters. Similarly, we can include aligned and non-aligned subpopulations of these grains, based on the grain alignment calculations, to see which grains should be oriented with the magnetic field, or, in the absence of a magnetic field close to the comet nucleus, with another axis of alignment (e.g., the radiation direction). The 3D nature of the grid allows us to assign these values, as well as density, for each computational cell, to model phenomena like e.g., cometary jets. The code will record polarized scattered light towards one or more observer directions within a single simulation run. These results can then be compared with the observations of comets at different phase angles, or

  4. A System for English Vocabulary Acquisition Based on Code-Switching

    ERIC Educational Resources Information Center

    Mazur, Michal; Karolczak, Krzysztof; Rzepka, Rafal; Araki, Kenji

    2016-01-01

    Vocabulary plays an important part in second language learning and there are many existing techniques to facilitate word acquisition. One of these methods is code-switching, or mixing the vocabulary of two languages in one sentence. In this paper the authors propose an experimental system for computer-assisted English vocabulary learning in…

  5. A Learning Environment for English Vocabulary Using Quick Response Codes

    ERIC Educational Resources Information Center

    Arikan, Yuksel Deniz; Ozen, Sevil Orhan

    2015-01-01

    This study focuses on the process of developing a learning environment that uses tablets and Quick Response (QR) codes to enhance participants' English language vocabulary knowledge. The author employed the concurrent triangulation strategy, a mixed research design. The study was conducted at a private school in Izmir, Turkey during the 2012-2013…

  6. "Do They Even Know That They Do It?": Exploring Awareness of Spanish-English Code-Switching in a Sixth-Grade English Language Arts Classroom

    ERIC Educational Resources Information Center

    Martínez, Ramón Antonio

    2014-01-01

    This article draws on scholarship in educational and linguistic anthropology to explore awareness of Spanish-English code-switching among bilingual Chicana/o and Latina/o students in a sixth-grade English Language Arts classroom. Analysis of qualitative data gathered via participant observation, video/audio recording, and semistructured interviews…

  7. Dynamic Alignment Models for Neural Coding

    PubMed Central

    Kollmorgen, Sepp; Hahnloser, Richard H. R.

    2014-01-01

    Recently, there have been remarkable advances in modeling the relationships between the sensory environment, neuronal responses, and behavior. However, most models cannot encompass variable stimulus-response relationships such as varying response latencies and state or context dependence of the neural code. Here, we consider response modeling as a dynamic alignment problem and model stimulus and response jointly by a mixed pair hidden Markov model (MPH). In MPHs, multiple stimulus-response relationships (e.g., receptive fields) are represented by different states or groups of states in a Markov chain. Each stimulus-response relationship features temporal flexibility, allowing modeling of variable response latencies, including noisy ones. We derive algorithms for learning of MPH parameters and for inference of spike response probabilities. We show that some linear-nonlinear Poisson cascade (LNP) models are a special case of MPHs. We demonstrate the efficiency and usefulness of MPHs in simulations of both jittered and switching spike responses to white noise and natural stimuli. Furthermore, we apply MPHs to extracellular single and multi-unit data recorded in cortical brain areas of singing birds to showcase a novel method for estimating response lag distributions. MPHs allow simultaneous estimation of receptive fields, latency statistics, and hidden state dynamics and so can help to uncover complex stimulus response relationships that are subject to variable timing and involve diverse neural codes. PMID:24625448

  8. Grammar Coding in the "Oxford Advanced Learner's Dictionary of Current English."

    ERIC Educational Resources Information Center

    Wekker, Herman

    1992-01-01

    Focuses on the revised system of grammar coding for verbs in the fourth edition of the "Oxford Advanced Learner's Dictionary of Current English" (OALD4), comparing it with two other similar dictionaries. It is shown that the OALD4 is found to be more favorable on many criteria than the other comparable dictionaries. (16 references) (VWL)

  9. The Effects of Using Bloom's Taxonomy to Align Reading Instruction with the Virginia Standards of Learning Framework for English

    ERIC Educational Resources Information Center

    Crews, Charla Faulkner

    2010-01-01

    This study examined the effects of aligning the "Virginia Standards of Learning (SOL)" English Framework with Bloom's Taxonomy on student achievement. Changes prompted by "No Child Left Behind" legislation increased accountability for student success, as well as mandated testing to determine annual academic growth of all…

  10. Non-Insertional Code-Switching in English-Japanese Bilingual Children: Alternation and Congruent Lexicalisation

    ERIC Educational Resources Information Center

    Namba, Kazuhiko

    2012-01-01

    This article investigates English-Japanese children's code-switching (CS) from the structural point of view. Muysken categorises it into three types, that is, insertion, alternation and congruent lexicalisation. Regarding insertion, using Myers-Scotton's matrix language frame (MLF) model, for example, the matrix language (ML) of a bilingual clause…

  11. The Unified English Braille Code: Examination by Science, Mathematics, and Computer Science Technical Expert Braille Readers

    ERIC Educational Resources Information Center

    Holbrook, M. Cay; MacCuspie, P. Ann

    2010-01-01

    Braille-reading mathematicians, scientists, and computer scientists were asked to examine the usability of the Unified English Braille Code (UEB) for technical materials. They had little knowledge of the code prior to the study. The research included two reading tasks, a short tutorial about UEB, and a focus group. The results indicated that the…

  12. English Code Switching in Indonesian Language

    ERIC Educational Resources Information Center

    Setiawan, Dedy

    2016-01-01

    There is a growing phenomenon, worldwide, of inserting English words, phrases or expressions, into the local language: this is part of the acceptance of English as current world language. Indonesia is experiencing the use of this mixture of language when using either their own Indonesian or local language; English words, phrases and expressions…

  13. Studies of Braille Reading Rates and Implications for the Unified English Braille Code

    ERIC Educational Resources Information Center

    Wetzel, Robin; Knowlton, Marie

    2006-01-01

    Reading rate data was collected from both print and braille readers in the areas of mathematics and literary braille. Literary braille data was collected for contracted and uncontracted braille text with dropped whole-word contractions and part-word contractions as they would appear in the Unified English Braille Code. No significant differences…

  14. Code Switching in English Language Teaching (ELT) Teaching Practice in Turkey: Student Teacher Practices, Beliefs and Identity

    ERIC Educational Resources Information Center

    Bilgin, Sezen Seymen

    2016-01-01

    Code switching involves the interplay of two languages and as well as serving linguistic functions, it has social and psychological implications. In the context of English language teaching, these psychological implications reveal themselves as teachers' thought processes. While the nature of code switching in language classrooms has been widely…

  15. Cantonese-English Code-Switching Research in Hong Kong: A Y2K Review.

    ERIC Educational Resources Information Center

    Li, David C. S.

    2000-01-01

    Reviews the major works on code switching in Hong Kong to date. Four context-specific motivations commonly found in the Hong Kong Chinese Press--euphemism, specificity, bilingual punning, and principle of economy--are adduced to show that English is one of the important linguistic resources used by Chinese Hongkongers to fulfill a variety of…

  16. Functions of Arabic-English Code-Switching: Sociolinguistic Insights from a Study Abroad Program

    ERIC Educational Resources Information Center

    Al Masaeed, Khaled

    2013-01-01

    This sociolinguistic study examines the functions and motivations of code-switching, which is used here to mean the use of more than one language in the same conversation. The conversations studied here take place in a very particular context: one-on-one speaking sessions in a study abroad program in Morocco where English is the L1 and Arabic the…

  17. Phonetic Change in Newfoundland English

    ERIC Educational Resources Information Center

    Clarke, Sandra

    2012-01-01

    Newfoundland English has long been considered autonomous within the North American context. Sociolinguistic studies conducted over the past three decades, however, typically suggest cross-generational change in phonetic feature use, motivated by greater alignment with mainland Canadian English norms. The present study uses data spanning the past…

  18. Comparison of Virginia's 2010 English Standards of Learning with the Common Core State Standards for English and Literacy

    ERIC Educational Resources Information Center

    Virginia Department of Education, 2010

    2010-01-01

    The "Comparison of Virginia's 2010 English Standards of Learning (SOL) with the Common Core State Standards (CCSS) for English Language Arts and Literacy (ELAL)" provides a side-by-side overview demonstrating how the 2010 English SOL are aligned to the CCSS for ELAL. The comparison was made using Virginia's complete standards program for…

  19. "Only When I Am Not Ashamed of Myself Can I Teach Others": Preservice English-Language Teachers in Vietnam and Code-Switching Practices

    ERIC Educational Resources Information Center

    Vu, Hai Ha

    2017-01-01

    As the younger generation in Vietnam increasingly switches between the English and the Vietnamese languages, numerous linguistic and sociocultural strictures arise. Foregrounding the preservice English-language teachers of this generation, this article locates them in a dilemma between the discourse of globalization and their code-switching…

  20. Vamos a Traducir los MRV (let's translate the VRM): linguistic and cultural inferences drawn from translating a verbal coding system from English into Spanish.

    PubMed

    Caro, I; Stiles, W B

    1997-01-01

    Translating a verbal coding system from one language to another can yield unexpected insights into the process of communication in different cultures. This paper describes the problems and understandings we encountered as we translated a verbal response modes (VRM) taxonomy from English into Spanish. Standard translations of text (e.g., psychotherapeutic dialogue) systematically change the form of certain expressions, so supposedly equivalent expressions had different VRM codings in the two languages. Prominent examples of English forms whose translation had different codes in Spanish included tags, question forms, and "let's" expressions. Insofar as participants use such forms to convey nuances of their relationship, standard translations of counseling or psychotherapy sessions or other conversations may systematically misrepresent the relationship between the participants. The differences revealed in translating the VRM system point to subtle but important differences in the degrees of verbal directiveness and inclusion in English versus Spanish, which converge with other observations of differences in individualism and collectivism between Anglo and Hispanic cultures.

  1. Automatic Construction of English/Chinese Parallel Corpora.

    ERIC Educational Resources Information Center

    Yang, Christopher C.; Li, Kar Wing

    2003-01-01

    Discussion of multilingual corpora and cross-lingual information retrieval focuses on research that constructed English/Chinese parallel corpus automatically from the World Wide Web. Presents an alignment method which is based on dynamic programming to identify one-to-one Chinese and English title pairs and discusses results of experiments…

  2. Contribution to terminology internationalization by word alignment in parallel corpora.

    PubMed

    Deléger, Louise; Merkel, Magnus; Zweigenbaum, Pierre

    2006-01-01

    Creating a complete translation of a large vocabulary is a time-consuming task, which requires skilled and knowledgeable medical translators. Our goal is to examine to which extent such a task can be alleviated by a specific natural language processing technique, word alignment in parallel corpora. We experiment with translation from English to French. Build a large corpus of parallel, English-French documents, and automatically align it at the document, sentence and word levels using state-of-the-art alignment methods and tools. Then project English terms from existing controlled vocabularies to the aligned word pairs, and examine the number and quality of the putative French translations obtained thereby. We considered three American vocabularies present in the UMLS with three different translation statuses: the MeSH, SNOMED CT, and the MedlinePlus Health Topics. We obtained several thousand new translations of our input terms, this number being closely linked to the number of terms in the input vocabularies. Our study shows that alignment methods can extract a number of new term translations from large bodies of text with a moderate human reviewing effort, and thus contribute to help a human translator obtain better translation coverage of an input vocabulary. Short-term perspectives include their application to a corpus 20 times larger than that used here, together with more focused methods for term extraction.

  3. Contribution to Terminology Internationalization by Word Alignment in Parallel Corpora

    PubMed Central

    Deléger, Louise; Merkel, Magnus; Zweigenbaum, Pierre

    2006-01-01

    Background and objectives Creating a complete translation of a large vocabulary is a time-consuming task, which requires skilled and knowledgeable medical translators. Our goal is to examine to which extent such a task can be alleviated by a specific natural language processing technique, word alignment in parallel corpora. We experiment with translation from English to French. Methods Build a large corpus of parallel, English-French documents, and automatically align it at the document, sentence and word levels using state-of-the-art alignment methods and tools. Then project English terms from existing controlled vocabularies to the aligned word pairs, and examine the number and quality of the putative French translations obtained thereby. We considered three American vocabularies present in the UMLS with three different translation statuses: the MeSH, SNOMED CT, and the MedlinePlus Health Topics. Results We obtained several thousand new translations of our input terms, this number being closely linked to the number of terms in the input vocabularies. Conclusion Our study shows that alignment methods can extract a number of new term translations from large bodies of text with a moderate human reviewing effort, and thus contribute to help a human translator obtain better translation coverage of an input vocabulary. Short-term perspectives include their application to a corpus 20 times larger than that used here, together with more focused methods for term extraction. PMID:17238328

  4. Effect of Alignment on L2 Written Production

    ERIC Educational Resources Information Center

    Wang, Chuming; Wang, Min

    2015-01-01

    This article aims to uncover how L2 writing is affected by alignment, a socio-cognitive process involving dynamic coordination and adaptation. For this, two studies were conducted. Study 1 required two groups of 24 learners of English as a foreign language (EFL) to continue in English two stories with their endings removed, both of which had a…

  5. Linguistically Directed Attention to the Temporal Aspect of Action Events in Monolingual English Speakers and Chinese-English Bilingual Speakers with Varying English Proficiency

    ERIC Educational Resources Information Center

    Chen, Jenn-Yeu; Su, Jui-Ju; Lee, Chao-Yang; O'Seaghdha, Padraig G.

    2012-01-01

    Chinese and English speakers seem to hold different conceptions of time which may be related to the different codings of time in the two languages. Employing a sentence-picture matching task, we have investigated this linguistic relativity in Chinese-English bilinguals varying in English proficiency and found that those with high proficiency…

  6. Understanding Mixed Code and Classroom Code-Switching: Myths and Realities

    ERIC Educational Resources Information Center

    Li, David C. S.

    2008-01-01

    Background: Cantonese-English mixed code is ubiquitous in Hong Kong society, and yet using mixed code is widely perceived as improper. This paper presents evidence of mixed code being socially constructed as bad language behavior. In the education domain, an EDB guideline bans mixed code in the classroom. Teachers are encouraged to stick to…

  7. The Ecology of Global English

    ERIC Educational Resources Information Center

    Canagarajah, A. Suresh

    2007-01-01

    Global English is under contestation. Although some consider lingua franca English (LFE) as a neutral medium or code that does not belong to any specific culture or nationality, others see the deceptive nature of this linguistic globalization. Along with Spring (2007/this issue), they see global English as embodying partisan interests and values.…

  8. Alignment-Annotator web server: rendering and annotating sequence alignments

    PubMed Central

    Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

    2014-01-01

    Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. Availability: http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. PMID:24813445

  9. Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV)

    PubMed Central

    Martin, Andrew C. R.

    2014-01-01

    The JavaScript Sequence Alignment Viewer (JSAV) is designed as a simple-to-use JavaScript component for displaying sequence alignments on web pages. The display of sequences is highly configurable with options to allow alternative coloring schemes, sorting of sequences and ’dotifying’ repeated amino acids. An option is also available to submit selected sequences to another web site, or to other JavaScript code. JSAV is implemented purely in JavaScript making use of the JQuery and JQuery-UI libraries. It does not use any HTML5-specific options to help with browser compatibility. The code is documented using JSDOC and is available from http://www.bioinf.org.uk/software/jsav/. PMID:25653836

  10. Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV).

    PubMed

    Martin, Andrew C R

    2014-01-01

    The JavaScript Sequence Alignment Viewer (JSAV) is designed as a simple-to-use JavaScript component for displaying sequence alignments on web pages. The display of sequences is highly configurable with options to allow alternative coloring schemes, sorting of sequences and 'dotifying' repeated amino acids. An option is also available to submit selected sequences to another web site, or to other JavaScript code. JSAV is implemented purely in JavaScript making use of the JQuery and JQuery-UI libraries. It does not use any HTML5-specific options to help with browser compatibility. The code is documented using JSDOC and is available from http://www.bioinf.org.uk/software/jsav/.

  11. Alignment-Annotator web server: rendering and annotating sequence alignments.

    PubMed

    Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

    2014-07-01

    Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. Using automatic alignment to analyze endangered language data: Testing the viability of untrained alignment

    PubMed Central

    DiCanio, Christian; Nam, Hosung; Whalen, Douglas H.; Timothy Bunnell, H.; Amith, Jonathan D.; García, Rey Castillo

    2013-01-01

    While efforts to document endangered languages have steadily increased, the phonetic analysis of endangered language data remains a challenge. The transcription of large documentation corpora is, by itself, a tremendous feat. Yet, the process of segmentation remains a bottleneck for research with data of this kind. This paper examines whether a speech processing tool, forced alignment, can facilitate the segmentation task for small data sets, even when the target language differs from the training language. The authors also examined whether a phone set with contextualization outperforms a more general one. The accuracy of two forced aligners trained on English (hmalign and p2fa) was assessed using corpus data from Yoloxóchitl Mixtec. Overall, agreement performance was relatively good, with accuracy at 70.9% within 30 ms for hmalign and 65.7% within 30 ms for p2fa. Segmental and tonal categories influenced accuracy as well. For instance, additional stop allophones in hmalign's phone set aided alignment accuracy. Agreement differences between aligners also corresponded closely with the types of data on which the aligners were trained. Overall, using existing alignment systems was found to have potential for making phonetic analysis of small corpora more efficient, with more allophonic phone sets providing better agreement than general ones. PMID:23967953

  13. Using automatic alignment to analyze endangered language data: testing the viability of untrained alignment.

    PubMed

    DiCanio, Christian; Nam, Hosung; Whalen, Douglas H; Bunnell, H Timothy; Amith, Jonathan D; García, Rey Castillo

    2013-09-01

    While efforts to document endangered languages have steadily increased, the phonetic analysis of endangered language data remains a challenge. The transcription of large documentation corpora is, by itself, a tremendous feat. Yet, the process of segmentation remains a bottleneck for research with data of this kind. This paper examines whether a speech processing tool, forced alignment, can facilitate the segmentation task for small data sets, even when the target language differs from the training language. The authors also examined whether a phone set with contextualization outperforms a more general one. The accuracy of two forced aligners trained on English (hmalign and p2fa) was assessed using corpus data from Yoloxóchitl Mixtec. Overall, agreement performance was relatively good, with accuracy at 70.9% within 30 ms for hmalign and 65.7% within 30 ms for p2fa. Segmental and tonal categories influenced accuracy as well. For instance, additional stop allophones in hmalign's phone set aided alignment accuracy. Agreement differences between aligners also corresponded closely with the types of data on which the aligners were trained. Overall, using existing alignment systems was found to have potential for making phonetic analysis of small corpora more efficient, with more allophonic phone sets providing better agreement than general ones.

  14. 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

  15. National Evaluation of Title III Implementation Supplemental Report: Exploring Approaches to Setting English Language Proficiency Performance Criteria and Monitoring English Learner Progress. Draft

    ERIC Educational Resources Information Center

    Cook, Gary; Linquanti, Robert; Chinen, Marjorie; Jung, Hyekyung

    2012-01-01

    The Elementary and Secondary Education Act (ESEA), as amended by the No Child Left Behind Act of 2001 inaugurated important changes in assessment and accountability for English Learner (EL) students. Specifically, Title III of the law required states to develop or adopt English-language proficiency (ELP) standards aligned with language demands of…

  16. GATA: A graphic alignment tool for comparative sequenceanalysis

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

    Nix, David A.; Eisen, Michael B.

    2005-01-01

    Several problems exist with current methods used to align DNA sequences for comparative sequence analysis. Most dynamic programming algorithms assume that conserved sequence elements are collinear. This assumption appears valid when comparing orthologous protein coding sequences. Functional constraints on proteins provide strong selective pressure against sequence inversions, and minimize sequence duplications and feature shuffling. For non-coding sequences this collinearity assumption is often invalid. For example, enhancers contain clusters of transcription factor binding sites that change in number, orientation, and spacing during evolution yet the enhancer retains its activity. Dotplot analysis is often used to estimate non-coding sequence relatedness. Yet dotmore » plots do not actually align sequences and thus cannot account well for base insertions or deletions. Moreover, they lack an adequate statistical framework for comparing sequence relatedness and are limited to pairwise comparisons. Lastly, dot plots and dynamic programming text outputs fail to provide an intuitive means for visualizing DNA alignments.« less

  17. Transcript mapping for handwritten English documents

    NASA Astrophysics Data System (ADS)

    Jose, Damien; Bharadwaj, Anurag; Govindaraju, Venu

    2008-01-01

    Transcript mapping or text alignment with handwritten documents is the automatic alignment of words in a text file with word images in a handwritten document. Such a mapping has several applications in fields ranging from machine learning where large quantities of truth data are required for evaluating handwriting recognition algorithms, to data mining where word image indexes are used in ranked retrieval of scanned documents in a digital library. The alignment also aids "writer identity" verification algorithms. Interfaces which display scanned handwritten documents may use this alignment to highlight manuscript tokens when a person examines the corresponding transcript word. We propose an adaptation of the True DTW dynamic programming algorithm for English handwritten documents. The integration of the dissimilarity scores from a word-model word recognizer and Levenshtein distance between the recognized word and lexicon word, as a cost metric in the DTW algorithm leading to a fast and accurate alignment, is our primary contribution. Results provided, confirm the effectiveness of our approach.

  18. Chinese-English Machine Translation System.

    ERIC Educational Resources Information Center

    Wang, William S-Y; And Others

    The report documents results of a two-year R&D effort directed at the completion of a prototype system for Chinese-English machine translation of S&T literature. The system, designated QUINCE, accepts Chinese input exactly as printed, with no pre-editing of any kind, and produces English output on experimental basis. Coding of Chinese text via…

  19. Creating a medical dictionary using word alignment: the influence of sources and resources.

    PubMed

    Nyström, Mikael; Merkel, Magnus; Petersson, Håkan; Ahlfeldt, Hans

    2007-11-23

    Automatic word alignment of parallel texts with the same content in different languages is among other things used to generate dictionaries for new translations. The quality of the generated word alignment depends on the quality of the input resources. In this paper we report on automatic word alignment of the English and Swedish versions of the medical terminology systems ICD-10, ICF, NCSP, KSH97-P and parts of MeSH and how the terminology systems and type of resources influence the quality. We automatically word aligned the terminology systems using static resources, like dictionaries, statistical resources, like statistically derived dictionaries, and training resources, which were generated from manual word alignment. We varied which part of the terminology systems that we used to generate the resources, which parts that we word aligned and which types of resources we used in the alignment process to explore the influence the different terminology systems and resources have on the recall and precision. After the analysis, we used the best configuration of the automatic word alignment for generation of candidate term pairs. We then manually verified the candidate term pairs and included the correct pairs in an English-Swedish dictionary. The results indicate that more resources and resource types give better results but the size of the parts used to generate the resources only partly affects the quality. The most generally useful resources were generated from ICD-10 and resources generated from MeSH were not as general as other resources. Systematic inter-language differences in the structure of the terminology system rubrics make the rubrics harder to align. Manually created training resources give nearly as good results as a union of static resources, statistical resources and training resources and noticeably better results than a union of static resources and statistical resources. The verified English-Swedish dictionary contains 24,000 term pairs in base

  20. Creating a medical dictionary using word alignment: The influence of sources and resources

    PubMed Central

    Nyström, Mikael; Merkel, Magnus; Petersson, Håkan; Åhlfeldt, Hans

    2007-01-01

    Background Automatic word alignment of parallel texts with the same content in different languages is among other things used to generate dictionaries for new translations. The quality of the generated word alignment depends on the quality of the input resources. In this paper we report on automatic word alignment of the English and Swedish versions of the medical terminology systems ICD-10, ICF, NCSP, KSH97-P and parts of MeSH and how the terminology systems and type of resources influence the quality. Methods We automatically word aligned the terminology systems using static resources, like dictionaries, statistical resources, like statistically derived dictionaries, and training resources, which were generated from manual word alignment. We varied which part of the terminology systems that we used to generate the resources, which parts that we word aligned and which types of resources we used in the alignment process to explore the influence the different terminology systems and resources have on the recall and precision. After the analysis, we used the best configuration of the automatic word alignment for generation of candidate term pairs. We then manually verified the candidate term pairs and included the correct pairs in an English-Swedish dictionary. Results The results indicate that more resources and resource types give better results but the size of the parts used to generate the resources only partly affects the quality. The most generally useful resources were generated from ICD-10 and resources generated from MeSH were not as general as other resources. Systematic inter-language differences in the structure of the terminology system rubrics make the rubrics harder to align. Manually created training resources give nearly as good results as a union of static resources, statistical resources and training resources and noticeably better results than a union of static resources and statistical resources. The verified English-Swedish dictionary contains

  1. Unraveling High School English Literature Pedagogic Practices: A Legitimation Code Theory Analysis

    ERIC Educational Resources Information Center

    Jackson, Fiona

    2016-01-01

    Mapping the knowledge formations of language teachers within their pedagogic practices is underresearched, particularly for subject English, a multi-faceted, elusively defined discipline. Deeper knowledge of the pedagogy of subject English teachers is critical, especially within South African education, given the socio-economic power of English in…

  2. MICA: Multiple interval-based curve alignment

    NASA Astrophysics Data System (ADS)

    Mann, Martin; Kahle, Hans-Peter; Beck, Matthias; Bender, Bela Johannes; Spiecker, Heinrich; Backofen, Rolf

    2018-01-01

    MICA enables the automatic synchronization of discrete data curves. To this end, characteristic points of the curves' shapes are identified. These landmarks are used within a heuristic curve registration approach to align profile pairs by mapping similar characteristics onto each other. In combination with a progressive alignment scheme, this enables the computation of multiple curve alignments. Multiple curve alignments are needed to derive meaningful representative consensus data of measured time or data series. MICA was already successfully applied to generate representative profiles of tree growth data based on intra-annual wood density profiles or cell formation data. The MICA package provides a command-line and graphical user interface. The R interface enables the direct embedding of multiple curve alignment computation into larger analyses pipelines. Source code, binaries and documentation are freely available at https://github.com/BackofenLab/MICA

  3. Coding and English Language Teaching

    ERIC Educational Resources Information Center

    Stevens, Vance; Verschoor, Jennifer

    2017-01-01

    According to Dudeney, Hockly, and Pegrum (2013) coding is a deeper skill subsumed under the four main digital literacies of language, connections, information, and (re)design. Coders or programmers are people who write the programmes behind everything we see and do on a computer. Most students spend several hours playing online games, but few know…

  4. Multiple network alignment via multiMAGNA+.

    PubMed

    Vijayan, Vipin; Milenkovic, Tijana

    2017-08-21

    Network alignment (NA) aims to find a node mapping that identifies topologically or functionally similar network regions between molecular networks of different species. Analogous to genomic sequence alignment, NA can be used to transfer biological knowledge from well- to poorly-studied species between aligned network regions. Pairwise NA (PNA) finds similar regions between two networks while multiple NA (MNA) can align more than two networks. We focus on MNA. Existing MNA methods aim to maximize total similarity over all aligned nodes (node conservation). Then, they evaluate alignment quality by measuring the amount of conserved edges, but only after the alignment is constructed. Directly optimizing edge conservation during alignment construction in addition to node conservation may result in superior alignments. Thus, we present a novel MNA method called multiMAGNA++ that can achieve this. Indeed, multiMAGNA++ outperforms or is on par with existing MNA methods, while often completing faster than existing methods. That is, multiMAGNA++ scales well to larger network data and can be parallelized effectively. During method evaluation, we also introduce new MNA quality measures to allow for more fair MNA method comparison compared to the existing alignment quality measures. MultiMAGNA++ code is available on the method's web page at http://nd.edu/~cone/multiMAGNA++/.

  5. STELLAR: fast and exact local alignments

    PubMed Central

    2011-01-01

    Background Large-scale comparison of genomic sequences requires reliable tools for the search of local alignments. Practical local aligners are in general fast, but heuristic, and hence sometimes miss significant matches. Results We present here the local pairwise aligner STELLAR that has full sensitivity for ε-alignments, i.e. guarantees to report all local alignments of a given minimal length and maximal error rate. The aligner is composed of two steps, filtering and verification. We apply the SWIFT algorithm for lossless filtering, and have developed a new verification strategy that we prove to be exact. Our results on simulated and real genomic data confirm and quantify the conjecture that heuristic tools like BLAST or BLAT miss a large percentage of significant local alignments. Conclusions STELLAR is very practical and fast on very long sequences which makes it a suitable new tool for finding local alignments between genomic sequences under the edit distance model. Binaries are freely available for Linux, Windows, and Mac OS X at http://www.seqan.de/projects/stellar. The source code is freely distributed with the SeqAn C++ library version 1.3 and later at http://www.seqan.de. PMID:22151882

  6. Kinematic alignment is a possible alternative to mechanical alignment in total knee arthroplasty.

    PubMed

    Lee, Yong Seuk; Howell, Stephen M; Won, Ye-Yeon; Lee, O-Sung; Lee, Seung Hoon; Vahedi, Hamed; Teo, Seow Hui

    2017-11-01

    A systematic review was conducted to answer the following questions: (1) Does kinematically aligned (KA) total knee arthroplasty (TKA) achieve clinical outcomes comparable to those of mechanically aligned (MA) TKA? (2) How do the limb, knee, and component alignments differ between KA and MA TKA? (3) How is joint line orientation angle (JLOA) changed from the native knee in KA TKA compared to that in MA TKA? Nine full-text articles in English that reported the clinical and radiological outcomes of KA TKA were included. Five studies had a control group of patients who underwent MA TKA. Data on patient demographics, clinical scores, and radiological results were extracted. There were two level I, one level II, three level III, and three level IV studies. Six of the nine studies used patient-specific instrumentation, one study used computer navigation, and two studies used manual instrumentation. The clinical outcomes of KA TKA were comparable or superior to those of MA TKA with a minimum 2-year follow-up. Limb and knee alignment in KA TKA was similar to those in MA TKA, and component alignment showed slightly more varus in the tibial component and slightly more valgus in the femoral component. The JLOA in KA TKA was relatively parallel to the floor compared to that in the native knee and not oblique (medial side up and lateral side down) compared to that in MA TKA. The implant survivorship and complication rate of the KA TKA were similar to those of the MA TKA. Similar or better clinical outcomes were produced by using a KA TKA at early-term follow-up and the component alignment differed from that of MA TKA. KA TKA seemed to restore function without catastrophic failure regardless of the alignment category up to midterm follow-up. The JLOA in KA TKA was relatively parallel to the floor similar to the native knee compared to that in MA TKA. The present review of nine published studies suggests that relatively new kinematic alignment is an acceptable and alternative

  7. Pidgin and English in Melanesia: Is There a Continuum?

    ERIC Educational Resources Information Center

    Siegel, Jeff

    1997-01-01

    Examines the linguistic features of Tok Pisin (the Papua New Guinea variety of Melanesian Pidgin) resulting from decreolization and the linguistic features of Papua New Guinea English. Discusses code-switching and transference between Tok Pisin and English and concludes that an English-to-pidgin continuum does not exist in Papua New Guinea or in…

  8. "¿Cómo Estas?" "I'm Good." Conversational Code-Switching Is Related to Profiles of Expressive and Receptive Proficiency in Spanish-English Bilingual Toddlers

    ERIC Educational Resources Information Center

    Ribot, Krystal M.; Hoff, Erika

    2014-01-01

    Relations between bilingual children's patterns of conversational code-switching (responding to one language with another), the balance of their dual language input, and their expressive and receptive proficiency in two languages were examined in 115 2½-year-old simultaneous Spanish-English bilinguals in the U.S. Children were more likely to…

  9. Researching English in the Philippines: Bibliographical Resources

    ERIC Educational Resources Information Center

    Bautista, Ma. Lourdes S.

    2004-01-01

    The academic literature on issues related to the Philippine English language and literature is substantial. This bibliography surveys relevant work on such related fields as the sociology of language and language planning, Bilingualism, bilingual education, and languages in education, language attitudes, code-switching and code-mixing, Philippine…

  10. XGC developments for a more efficient XGC-GENE code coupling

    NASA Astrophysics Data System (ADS)

    Dominski, Julien; Hager, Robert; Ku, Seung-Hoe; Chang, Cs

    2017-10-01

    In the Exascale Computing Program, the High-Fidelity Whole Device Modeling project initially aims at delivering a tightly-coupled simulation of plasma neoclassical and turbulence dynamics from the core to the edge of the tokamak. To permit such simulations, the gyrokinetic codes GENE and XGC will be coupled together. Numerical efforts are made to improve the numerical schemes agreement in the coupling region. One of the difficulties of coupling those codes together is the incompatibility of their grids. GENE is a continuum grid-based code and XGC is a Particle-In-Cell code using unstructured triangular mesh. A field-aligned filter is thus implemented in XGC. Even if XGC originally had an approximately field-following mesh, this field-aligned filter permits to have a perturbation discretization closer to the one solved in the field-aligned code GENE. Additionally, new XGC gyro-averaging matrices are implemented on a velocity grid adapted to the plasma properties, thus ensuring same accuracy from the core to the edge regions.

  11. Codeswitching Techniques: Evidence-Based Instructional Practices for the ASL/English Bilingual Classroom

    ERIC Educational Resources Information Center

    Andrews, Jean F.; Rusher, Melissa

    2010-01-01

    The authors present a perspective on emerging bilingual deaf students who are exposed to, learning, and developing two languages--American Sign Language (ASL) and English (spoken English, manually coded English, and English reading and writing). The authors suggest that though deaf children may lack proficiency or fluency in either language during…

  12. Alignment of Motivational Strategies: The Perceptions of Teachers and Students

    ERIC Educational Resources Information Center

    Wong, Ruth; Wong, Renee

    2017-01-01

    In order to enhance ESL students' motivation to learn learning English, teachers around the world have been employing various motivational strategies in classrooms. However, there is scarce research focusing on both alignments and misalignments of secondary students' evaluation of the effectiveness of motivational strategies (MS) and teachers' use…

  13. Code-switched English Pronunciation Modeling for Swahili Spoken Term Detection (Pub Version, Open Access)

    DTIC Science & Technology

    2016-05-03

    using additional English resources. 2. Background The Babel program1 is an international collaborative effort sponsored by the US Intelligence Advanced...phenomenon is not as well studied for English / African language pairs, but some results are available8,9. 3. Experimental Setup The Swahili analysis...word pronunciations. From the analysis it was concluded that in most cases English words were pronounced using standard English letter-to-sound rules

  14. How to secure your servers, code and data

    ScienceCinema

    Lopienski, Sebastian

    2018-04-30

    Oral presentation in English, slides in English. Advice and best practices regarding the security of your servers, code and data will be presented. We will also describe how the Computer Security Team can help you reduce the risks.

  15. DNAAlignEditor: DNA alignment editor tool

    PubMed Central

    Sanchez-Villeda, Hector; Schroeder, Steven; Flint-Garcia, Sherry; Guill, Katherine E; Yamasaki, Masanori; McMullen, Michael D

    2008-01-01

    Background With advances in DNA re-sequencing methods and Next-Generation parallel sequencing approaches, there has been a large increase in genomic efforts to define and analyze the sequence variability present among individuals within a species. For very polymorphic species such as maize, this has lead to a need for intuitive, user-friendly software that aids the biologist, often with naïve programming capability, in tracking, editing, displaying, and exporting multiple individual sequence alignments. To fill this need we have developed a novel DNA alignment editor. Results We have generated a nucleotide sequence alignment editor (DNAAlignEditor) that provides an intuitive, user-friendly interface for manual editing of multiple sequence alignments with functions for input, editing, and output of sequence alignments. The color-coding of nucleotide identity and the display of associated quality score aids in the manual alignment editing process. DNAAlignEditor works as a client/server tool having two main components: a relational database that collects the processed alignments and a user interface connected to database through universal data access connectivity drivers. DNAAlignEditor can be used either as a stand-alone application or as a network application with multiple users concurrently connected. Conclusion We anticipate that this software will be of general interest to biologists and population genetics in editing DNA sequence alignments and analyzing natural sequence variation regardless of species, and will be particularly useful for manual alignment editing of sequences in species with high levels of polymorphism. PMID:18366684

  16. ARYANA: Aligning Reads by Yet Another Approach

    PubMed Central

    2014-01-01

    Motivation Although there are many different algorithms and software tools for aligning sequencing reads, fast gapped sequence search is far from solved. Strong interest in fast alignment is best reflected in the $106 prize for the Innocentive competition on aligning a collection of reads to a given database of reference genomes. In addition, de novo assembly of next-generation sequencing long reads requires fast overlap-layout-concensus algorithms which depend on fast and accurate alignment. Contribution We introduce ARYANA, a fast gapped read aligner, developed on the base of BWA indexing infrastructure with a completely new alignment engine that makes it significantly faster than three other aligners: Bowtie2, BWA and SeqAlto, with comparable generality and accuracy. Instead of the time-consuming backtracking procedures for handling mismatches, ARYANA comes with the seed-and-extend algorithmic framework and a significantly improved efficiency by integrating novel algorithmic techniques including dynamic seed selection, bidirectional seed extension, reset-free hash tables, and gap-filling dynamic programming. As the read length increases ARYANA's superiority in terms of speed and alignment rate becomes more evident. This is in perfect harmony with the read length trend as the sequencing technologies evolve. The algorithmic platform of ARYANA makes it easy to develop mission-specific aligners for other applications using ARYANA engine. Availability ARYANA with complete source code can be obtained from http://github.com/aryana-aligner PMID:25252881

  17. ARYANA: Aligning Reads by Yet Another Approach.

    PubMed

    Gholami, Milad; Arbabi, Aryan; Sharifi-Zarchi, Ali; Chitsaz, Hamidreza; Sadeghi, Mehdi

    2014-01-01

    Although there are many different algorithms and software tools for aligning sequencing reads, fast gapped sequence search is far from solved. Strong interest in fast alignment is best reflected in the $10(6) prize for the Innocentive competition on aligning a collection of reads to a given database of reference genomes. In addition, de novo assembly of next-generation sequencing long reads requires fast overlap-layout-concensus algorithms which depend on fast and accurate alignment. We introduce ARYANA, a fast gapped read aligner, developed on the base of BWA indexing infrastructure with a completely new alignment engine that makes it significantly faster than three other aligners: Bowtie2, BWA and SeqAlto, with comparable generality and accuracy. Instead of the time-consuming backtracking procedures for handling mismatches, ARYANA comes with the seed-and-extend algorithmic framework and a significantly improved efficiency by integrating novel algorithmic techniques including dynamic seed selection, bidirectional seed extension, reset-free hash tables, and gap-filling dynamic programming. As the read length increases ARYANA's superiority in terms of speed and alignment rate becomes more evident. This is in perfect harmony with the read length trend as the sequencing technologies evolve. The algorithmic platform of ARYANA makes it easy to develop mission-specific aligners for other applications using ARYANA engine. ARYANA with complete source code can be obtained from http://github.com/aryana-aligner.

  18. Disadvantages of publishing biomedical research articles in English for non-native speakers of English

    PubMed Central

    Rezaeian, Mohsen

    2015-01-01

    OBJECTIVES: English has become the most frequently used language for scientific communication in the biomedical field. Therefore, scholars from all over the world try to publish their findings in English. This trend has a number of advantages, along with several disadvantages. METHODS: In the current article, the most important disadvantages of publishing biomedical research articles in English for non-native speakers of English are reviewed. RESULTS: The most important disadvantages of publishing biomedical research articles in English for non-native speakers may include: Overlooking, either unintentionally or even deliberately, the most important local health problems; failure to carry out groundbreaking research due to limited medical research budgets; violating generally accepted codes of publication ethics and committing research misconduct and publications in open-access scam/predatory journals rather than prestigious journals. CONCLUSIONS: The above mentioned disadvantages could eventually result in academic establishments becoming irresponsible or, even worse, corrupt. In order to avoid this, scientists, scientific organizations, academic institutions, and scientific associations all over the world should design and implement a wider range of collaborative and comprehensive plans. PMID:25968115

  19. Disadvantages of publishing biomedical research articles in English for non-native speakers of English.

    PubMed

    Rezaeian, Mohsen

    2015-01-01

    English has become the most frequently used language for scientific communication in the biomedical field. Therefore, scholars from all over the world try to publish their findings in English. This trend has a number of advantages, along with several disadvantages. In the current article, the most important disadvantages of publishing biomedical research articles in English for non-native speakers of English are reviewed. The most important disadvantages of publishing biomedical research articles in English for non-native speakers may include: Overlooking, either unintentionally or even deliberately, the most important local health problems; failure to carry out groundbreaking research due to limited medical research budgets; violating generally accepted codes of publication ethics and committing research misconduct and publications in open-access scam/predatory journals rather than prestigious journals. The above mentioned disadvantages could eventually result in academic establishments becoming irresponsible or, even worse, corrupt. In order to avoid this, scientists, scientific organizations, academic institutions, and scientific associations all over the world should design and implement a wider range of collaborative and comprehensive plans.

  20. Bilingual Dual Coding in Japanese Returnee Students.

    ERIC Educational Resources Information Center

    Taura, Hideyuki

    1998-01-01

    Investigates effects of second-language acquisition age, length of exposure to the second language, and Japanese language specificity on the bilingual dual coding hypothesis proposed by Paivio and Desrochers (1980). Balanced Japanese-English bilingual returnee (having resided in an English-speaking country) subjects were presented with pictures to…

  1. Spanish and English Early Literacy Profiles of Preschool Latino English Language Learner Children

    ERIC Educational Resources Information Center

    Gonzalez, Jorge; Pollard-Durodola, Sharolyn; Saenz, Laura; Soares, Denise; Davis, Heather; Resendez, Nora; Zhu, Leina

    2016-01-01

    Research Findings: The purpose of this study was to examine within-group individual differences in the code-related and oral language abilities of an economically stressed Spanish-speaking English language learner (ELL) preschool sample and to evaluate the predictive relationship of these differences to later listening comprehension. Latent class…

  2. English Medieval Churches, 'Festival Orientation' and William Wordsworth

    NASA Astrophysics Data System (ADS)

    Hoare, Peter G.; Ketel, Hans

    2015-05-01

    A church that is shown to be aligned with sunrise or sunset on the feast day of the saint to whom the building was dedicated is said to display 'festival orientation'. The earliest work to touch upon this practice in English dates from c. 1678. William Wordsworth gave impetus to the subject in two poems published in 1827; he also played a part in the design of St Mary's chapel (1823-4), Rydal, Cumbria in the English Lake District. The 14th-century St Catherine's chapel at Houghton St Giles, Norfolk, was constructed for the use of pilgrims on their way to nearby Walsingham. Careful measurement of the orientation and eastern horizon of these two buildings has shown that St Mary's is aligned with sunrise on the Marian festival of The Visitation (2 July), and St Catherine's is directed towards the rising Sun on the feast of St Catherine of Alexandria (25 November). It is only by taking into account the character of the horizon that meaningful tests for festival orientation may be carried out.

  3. Sentence alignment using feed forward neural network.

    PubMed

    Fattah, Mohamed Abdel; Ren, Fuji; Kuroiwa, Shingo

    2006-12-01

    Parallel corpora have become an essential resource for work in multi lingual natural language processing. However, sentence aligned parallel corpora are more efficient than non-aligned parallel corpora for cross language information retrieval and machine translation applications. In this paper, we present a new approach to align sentences in bilingual parallel corpora based on feed forward neural network classifier. A feature parameter vector is extracted from the text pair under consideration. This vector contains text features such as length, punctuate score, and cognate score values. A set of manually prepared training data has been assigned to train the feed forward neural network. Another set of data was used for testing. Using this new approach, we could achieve an error reduction of 60% over length based approach when applied on English-Arabic parallel documents. Moreover this new approach is valid for any language pair and it is quite flexible approach since the feature parameter vector may contain more/less or different features than that we used in our system such as lexical match feature.

  4. DNA Multiple Sequence Alignment Guided by Protein Domains: The MSA-PAD 2.0 Method.

    PubMed

    Balech, Bachir; Monaco, Alfonso; Perniola, Michele; Santamaria, Monica; Donvito, Giacinto; Vicario, Saverio; Maggi, Giorgio; Pesole, Graziano

    2018-01-01

    Multiple sequence alignment (MSA) is a fundamental component in many DNA sequence analyses including metagenomics studies and phylogeny inference. When guided by protein profiles, DNA multiple alignments assume a higher precision and robustness. Here we present details of the use of the upgraded version of MSA-PAD (2.0), which is a DNA multiple sequence alignment framework able to align DNA sequences coding for single/multiple protein domains guided by PFAM or user-defined annotations. MSA-PAD has two alignment strategies, called "Gene" and "Genome," accounting for coding domains order and genomic rearrangements, respectively. Novel options were added to the present version, where the MSA can be guided by protein profiles provided by the user. This allows MSA-PAD 2.0 to run faster and to add custom protein profiles sometimes not present in PFAM database according to the user's interest. MSA-PAD 2.0 is currently freely available as a Web application at https://recasgateway.cloud.ba.infn.it/ .

  5. Net2Align: An Algorithm For Pairwise Global Alignment of Biological Networks

    PubMed Central

    Wadhwab, Gulshan; Upadhyayaa, K. C.

    2016-01-01

    The amount of data on molecular interactions is growing at an enormous pace, whereas the progress of methods for analysing this data is still lacking behind. Particularly, in the area of comparative analysis of biological networks, where one wishes to explore the similarity between two biological networks, this holds a potential problem. In consideration that the functionality primarily runs at the network level, it advocates the need for robust comparison methods. In this paper, we describe Net2Align, an algorithm for pairwise global alignment that can perform node-to-node correspondences as well as edge-to-edge correspondences into consideration. The uniqueness of our algorithm is in the fact that it is also able to detect the type of interaction, which is essential in case of directed graphs. The existing algorithm is only able to identify the common nodes but not the common edges. Another striking feature of the algorithm is that it is able to remove duplicate entries in case of variable datasets being aligned. This is achieved through creation of a local database which helps exclude duplicate links. In a pervasive computational study on gene regulatory network, we establish that our algorithm surpasses its counterparts in its results. Net2Align has been implemented in Java 7 and the source code is available as supplementary files. PMID:28356678

  6. Spanish-English Speech Perception in Children and Adults: Developmental Trends

    ERIC Educational Resources Information Center

    Brice, Alejandro E.; Gorman, Brenda K.; Leung, Cynthia B.

    2013-01-01

    This study explored the developmental trends and phonetic category formation in bilingual children and adults. Participants included 30 fluent Spanish-English bilingual children, aged 8-11, and bilingual adults, aged 18-40. All completed gating tasks that incorporated code-mixed Spanish-English stimuli. There were significant differences in…

  7. English Studies as Creole Scholarship: Reconfiguring the Discipline for Postcolonial Conditions

    ERIC Educational Resources Information Center

    Canagarajah, Suresh

    2011-01-01

    The shifts underway in contemporary social conditions call for a new alignment between the specializations constituting English Studies: namely, literature, applied linguistics, and rhetoric and composition. Postcolonial social movements have generated new language, textual, and literary practices. These developments bring to the fore practices…

  8. Characteristics of clinical trials that require participants to be fluent in English

    PubMed Central

    Egleston, Brian L; Pedraza, Omar; Wong, Yu-Ning; Dunbrack, Roland L; Griffin, Candace L; Ross, Eric A; Beck, J Robert

    2015-01-01

    Background/Aims Diverse samples in clinical trials can make findings more generalizable. We sought to characterize the prevalence of clinical trials in the United States that required English fluency for participants to enroll in the trial. Methods We randomly chose over 10,000 clinical trial protocols registered with ClinicalTrials.gov and examined the inclusion and exclusion criteria of the trials. We compared the relationship of clinical trial characteristics with English fluency inclusion requirements. We merged the ClinicalTrials.gov data with U.S. Census and American Community Survey data to investigate the association of English language restrictions with ZIP-code level demographic characteristics of participating institutions. We used Chi-squared tests, t-tests, and logistic regression models for analyses. Results English fluency requirements have been increasing over time, from 1.7% of trials having such requirements before 2000 to 9.0% after 2010 (p<0.001 from Chi-squared test). Industry sponsored trials had low rates of English fluency requirements (1.8%) while behavioral trials had high rates (28.4%). Trials opening in the Northeast of the U.S. had the highest regional English requirement rates (10.7%) while trials opening in more than one region had the lowest (3.3%, p<0.001). Since 1995, trials opening in ZIP-codes with larger Hispanic populations were less likely to have English fluency requirements (OR=0.92 for each 10 percent increase in proportion of Hispanics, 95% CI 0.86–0.98, p=0.013). Trials opening in ZIP-codes with more residents self-identifying as Black/African American (OR=1.87, 95% CI 1.36–2.58, p<0.001 for restricted cubic spline term) or Asian (OR=1.16 for linear term, 95% CI 1.07–1.25, p<0.001) were more likely to have English fluency requirements. ZIP-codes with higher poverty rates had trials with more English language restrictions (OR=1.06 for a 10 percent poverty rate increase, 95% CI 1.001–1.11, p=0.045). There was a

  9. Characteristics of clinical trials that require participants to be fluent in English.

    PubMed

    Egleston, Brian L; Pedraza, Omar; Wong, Yu-Ning; Dunbrack, Roland L; Griffin, Candace L; Ross, Eric A; Beck, J Robert

    2015-12-01

    Diverse samples in clinical trials can make findings more generalizable. We sought to characterize the prevalence of clinical trials in the United States that required English fluency for participants to enroll in the trial. We randomly chose over 10,000 clinical trial protocols registered with ClinicalTrials.gov and examined the inclusion and exclusion criteria of the trials. We compared the relationship of clinical trial characteristics with English fluency inclusion requirements. We merged the ClinicalTrials.gov data with US Census and American Community Survey data to investigate the association of English-language restrictions with ZIP-code-level demographic characteristics of participating institutions. We used Chi-squared tests, t-tests, and logistic regression models for analyses. English fluency requirements have been increasing over time, from 1.7% of trials having such requirements before 2000 to 9.0% after 2010 (p < 0.001 from Chi-squared test). Industry-sponsored trials had low rates of English fluency requirements (1.8%), while behavioral trials had high rates (28.4%). Trials opening in the Northeast of the United States had the highest regional English requirement rates (10.7%), while trials opening in more than one region had the lowest (3.3%, p<0.001). Since 1995, trials opening in ZIP codes with larger Hispanic populations were less likely to have English fluency requirements (odds ratio=0.92 for each 10% increase in proportion of Hispanics, 95% confidence interval=0.86-0.98, p=0.013). Trials opening in ZIP codes with more residents self-identifying as Black/African American (odds ratio=1.87, 95% confidence interval=1.36-2.58, p<0.001 for restricted cubic spline term) or Asian (odds ratio=1.16 for linear term, 95% confidence interval=1.07-1.25, p<0.001) were more likely to have English fluency requirements. ZIP codes with higher poverty rates had trials with more English-language restrictions (odds ratio=1.06 for a 10% poverty rate increase

  10. Tonal Targets in Early Child English, Spanish, and Catalan

    ERIC Educational Resources Information Center

    Astruc, Lluisa; Payne, Elinor; Post, Brechtje; Vanrell, Maria del Mar; Prieto, Pilar

    2013-01-01

    This study analyses the scaling and alignment of low and high intonational targets in the speech of 27 children--nine English-speaking, nine Catalan-speaking and nine Spanish-speaking--between the ages of two and six years. We compared the intonational patterns of words controlled for number of syllables and stress position in the child speech to…

  11. Strategies and tools for whole genome alignments

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

    Couronne, Olivier; Poliakov, Alexander; Bray, Nicolas

    2002-11-25

    The availability of the assembled mouse genome makespossible, for the first time, an alignment and comparison of two largevertebrate genomes. We have investigated different strategies ofalignment for the subsequent analysis of conservation of genomes that areeffective for different quality assemblies. These strategies were appliedto the comparison of the working draft of the human genome with the MouseGenome Sequencing Consortium assembly, as well as other intermediatemouse assemblies. Our methods are fast and the resulting alignmentsexhibit a high degree of sensitivity, covering more than 90 percent ofknown coding exons in the human genome. We have obtained such coveragewhile preserving specificity. With amore » view towards the end user, we havedeveloped a suite of tools and websites for automatically aligning, andsubsequently browsing and working with whole genome comparisons. Wedescribe the use of these tools to identify conserved non-coding regionsbetween the human and mouse genomes, some of which have not beenidentified by other methods.« less

  12. English-Thai Code-Switching of Teachers in ESP Classes

    ERIC Educational Resources Information Center

    Promnath, Korawan; Tayjasanant, Chamaipak

    2016-01-01

    The term code-switching (CS) that occurs in everyday situations, or naturalistic code-switching, has been a controversial strategy regarding whether it benefits or impedes language learning. The aim of this study was to investigate CS in conversations between teachers and students of ESP classes in order to explore the types and functions of CS…

  13. A Correlational Study: Code of Ethics in Testing and EFL Instructors' Professional Behavior

    ERIC Educational Resources Information Center

    Ashraf, Hamid; Kafi, Zahra; Saeedan, Azaam

    2018-01-01

    The present study has aimed at delving the code of ethics in testing in English language institutions to see how far adhering to these ethical codes will result in EFL teachers' professional behavior. Therefore, 300 EFL instructors teaching at English language schools in Khorasan Razavi Province, Zabansara Language School, as well as Khorasan…

  14. Aligning HST Images to Gaia: A Faster Mosaicking Workflow

    NASA Astrophysics Data System (ADS)

    Bajaj, V.

    2017-11-01

    We present a fully programmatic workflow for aligning HST images using the high-quality astrometry provided by Gaia Data Release 1. Code provided in a Jupyter Notebook works through this procedure, including parsing the data to determine the query area parameters, querying Gaia for the coordinate catalog, and using the catalog with TweakReg as reference catalog. This workflow greatly simplifies the normally time-consuming process of aligning HST images, especially those taken as part of mosaics.

  15. CAMPways: constrained alignment framework for the comparative analysis of a pair of metabolic pathways.

    PubMed

    Abaka, Gamze; Bıyıkoğlu, Türker; Erten, Cesim

    2013-07-01

    Given a pair of metabolic pathways, an alignment of the pathways corresponds to a mapping between similar substructures of the pair. Successful alignments may provide useful applications in phylogenetic tree reconstruction, drug design and overall may enhance our understanding of cellular metabolism. We consider the problem of providing one-to-many alignments of reactions in a pair of metabolic pathways. We first provide a constrained alignment framework applicable to the problem. We show that the constrained alignment problem even in a primitive setting is computationally intractable, which justifies efforts for designing efficient heuristics. We present our Constrained Alignment of Metabolic Pathways (CAMPways) algorithm designed for this purpose. Through extensive experiments involving a large pathway database, we demonstrate that when compared with a state-of-the-art alternative, the CAMPways algorithm provides better alignment results on metabolic networks as far as measures based on same-pathway inclusion and biochemical significance are concerned. The execution speed of our algorithm constitutes yet another important improvement over alternative algorithms. Open source codes, executable binary, useful scripts, all the experimental data and the results are freely available as part of the Supplementary Material at http://code.google.com/p/campways/. Supplementary data are available at Bioinformatics online.

  16. Linguistic Alternants and Code Selection in Baba Malay.

    ERIC Educational Resources Information Center

    Pakir, Anne

    1989-01-01

    Provides a brief account and explanation of the phenomenon of language use among the Baba community, which uses Hokkien, Malay, and English in the process of code selection and code mixing/switching. Data are drawn from recordings of conversation of the Babas and Nyonyas. (Author/OD)

  17. Edge equilibrium code for tokamaks

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

    Li, Xujing; Zakharov, Leonid E.; Drozdov, Vladimir V.

    2014-01-15

    The edge equilibrium code (EEC) described in this paper is developed for simulations of the near edge plasma using the finite element method. It solves the Grad-Shafranov equation in toroidal coordinate and uses adaptive grids aligned with magnetic field lines. Hermite finite elements are chosen for the numerical scheme. A fast Newton scheme which is the same as implemented in the equilibrium and stability code (ESC) is applied here to adjust the grids.

  18. Toward a Probabilistic Automata Model of Some Aspects of Code-Switching.

    ERIC Educational Resources Information Center

    Dearholt, D. W.; Valdes-Fallis, G.

    1978-01-01

    The purpose of the model is to select either Spanish or English as the language to be used; its goals at this stage of development include modeling code-switching for lexical need, apparently random code-switching, dependency of code-switching upon sociolinguistic context, and code-switching within syntactic constraints. (EJS)

  19. Code-Mixing as a Bilingual Instructional Strategy

    ERIC Educational Resources Information Center

    Jiang, Yih-Lin Belinda; García, Georgia Earnest; Willis, Arlette Ingram

    2014-01-01

    This study investigated code-mixing practices, specifically the use of L2 (English) in an L1 (Chinese) class in a U.S. bilingual program. Our findings indicate that the code-mixing practices made and prompted by the teacher served five pedagogical functions: (a) to enhance students' bilingualism and bilingual learning, (b) to review and…

  20. BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC

    PubMed Central

    Satija, Rahul; Novák, Ádám; Miklós, István; Lyngsø, Rune; Hein, Jotun

    2009-01-01

    Background We have previously combined statistical alignment and phylogenetic footprinting to detect conserved functional elements without assuming a fixed alignment. Considering a probability-weighted distribution of alignments removes sensitivity to alignment errors, properly accommodates regions of alignment uncertainty, and increases the accuracy of functional element prediction. Our method utilized standard dynamic programming hidden markov model algorithms to analyze up to four sequences. Results We present a novel approach, implemented in the software package BigFoot, for performing phylogenetic footprinting on greater numbers of sequences. We have developed a Markov chain Monte Carlo (MCMC) approach which samples both sequence alignments and locations of slowly evolving regions. We implement our method as an extension of the existing StatAlign software package and test it on well-annotated regions controlling the expression of the even-skipped gene in Drosophila and the α-globin gene in vertebrates. The results exhibit how adding additional sequences to the analysis has the potential to improve the accuracy of functional predictions, and demonstrate how BigFoot outperforms existing alignment-based phylogenetic footprinting techniques. Conclusion BigFoot extends a combined alignment and phylogenetic footprinting approach to analyze larger amounts of sequence data using MCMC. Our approach is robust to alignment error and uncertainty and can be applied to a variety of biological datasets. The source code and documentation are publicly available for download from PMID:19715598

  1. BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC.

    PubMed

    Satija, Rahul; Novák, Adám; Miklós, István; Lyngsø, Rune; Hein, Jotun

    2009-08-28

    We have previously combined statistical alignment and phylogenetic footprinting to detect conserved functional elements without assuming a fixed alignment. Considering a probability-weighted distribution of alignments removes sensitivity to alignment errors, properly accommodates regions of alignment uncertainty, and increases the accuracy of functional element prediction. Our method utilized standard dynamic programming hidden markov model algorithms to analyze up to four sequences. We present a novel approach, implemented in the software package BigFoot, for performing phylogenetic footprinting on greater numbers of sequences. We have developed a Markov chain Monte Carlo (MCMC) approach which samples both sequence alignments and locations of slowly evolving regions. We implement our method as an extension of the existing StatAlign software package and test it on well-annotated regions controlling the expression of the even-skipped gene in Drosophila and the alpha-globin gene in vertebrates. The results exhibit how adding additional sequences to the analysis has the potential to improve the accuracy of functional predictions, and demonstrate how BigFoot outperforms existing alignment-based phylogenetic footprinting techniques. BigFoot extends a combined alignment and phylogenetic footprinting approach to analyze larger amounts of sequence data using MCMC. Our approach is robust to alignment error and uncertainty and can be applied to a variety of biological datasets. The source code and documentation are publicly available for download from http://www.stats.ox.ac.uk/~satija/BigFoot/

  2. A Plain English Map of the Human Glycolysis Enzymes.

    ERIC Educational Resources Information Center

    Offner, Susan

    1999-01-01

    Presents a plain English map of the gene coding for the glycolysis enzymes in humans to be used as a teaching tool. The map can be used to illustrate that every reaction in a cell requires an enzyme, and that every enzyme is a protein coded for by a gene somewhere on the chromosomes. (WRM)

  3. Pitch contour matching and interactional alignment across turns: an acoustic investigation.

    PubMed

    Gorisch, Jan; Wells, Bill; Brown, Guy J

    2012-03-01

    In order to explore the influence of context on the phonetic design of talk-in-interaction, we investigated the pitch characteristics of short turns (insertions) that are produced by one speaker between turns from another speaker. We investigated the hypothesis that the speaker of the insertion designs her turn as a pitch match to the prior turn in order to align with the previous speaker's agenda, whereas non-matching displays that the speaker of the insertion is non-aligning, for example to initiate a new action. Data were taken from the AMI meeting corpus, focusing on the spontaneous talk of first-language English participants. Using sequential analysis, 177 insertions were classified as either aligning or non-aligning in accordance with definitions of these terms in the Conversation Analysis literature. The degree of similarity between the pitch contour of the insertion and that of the prior speaker's turn was measured, using a new technique that integrates normalized F0 and intensity information. The results showed that aligning insertions were significantly more similar to the immediately preceding turn, in terms of pitch contour, than were non-aligning insertions. This supports the view that choice of pitch contour is managed locally, rather than by reference to an intonational lexicon.

  4. Note: A simple sample transfer alignment for ultra-high vacuum systems.

    PubMed

    Tamtögl, A; Carter, E A; Ward, D J; Avidor, N; Kole, P R; Jardine, A P; Allison, W

    2016-06-01

    The alignment of ultra-high-vacuum sample transfer systems can be problematic when there is no direct line of sight to assist the user. We present the design of a simple and cheap system which greatly simplifies the alignment of sample transfer devices. Our method is based on the adaptation of a commercial digital camera which provides live views from within the vacuum chamber. The images of the camera are further processed using an image recognition and processing code which determines any misalignments and reports them to the user. Installation has proven to be extremely useful in order to align the sample with respect to the transfer mechanism. Furthermore, the alignment software can be easily adapted for other systems.

  5. Research on the Language of the English Classroom: A Disconnected Dream.

    ERIC Educational Resources Information Center

    Kluwin, Thomas N.

    Methods used in studies of the classroom language of the English teacher are described in this paper and some results of the research are reported. The paper first describes three methods traditionally employed in the description of the language of the English classroom--live observation systems, coding systems based on transcripts, and…

  6. A Professional Learning Community Approach to Improving English/Language Arts Instructional Planning

    ERIC Educational Resources Information Center

    Kotsko, Adrienne

    2017-01-01

    Simply defined, effective English Language Arts (ELA) instruction is cohesive, integrated, and requires students to think deeply. Creating such instruction is difficult, however, because of insufficient training in instructional planning and the numerous types of curricula teachers must navigate that may not align well. Therefore, new secondary…

  7. Overcoming Common Misunderstandings about Students with Disabilities Who Are English Language Learners

    ERIC Educational Resources Information Center

    Cheatham, Gregory A.; Hart Barnett, Juliet E.

    2017-01-01

    Special education programs are increasingly serving students with disabilities who are English language learners and their families. Facilitating bilingualism is an effective practice and aligns with culturally responsive special education service provision. It is critical for special educators and service providers to learn about bilingualism,…

  8. Reviewing the Challenges and Opportunities Presented by Code Switching and Mixing in Bangla

    ERIC Educational Resources Information Center

    Hasan, Md. Kamrul; Akhand, Mohd. Moniruzzaman

    2015-01-01

    This paper investigates the issues related to code-switching/code-mixing in an ESL context. Some preliminary data on Bangla-English code-switching/code-mixing has been analyzed in order to determine which structural pattern of code-switching/code-mixing is predominant in different social strata. This study also explores the relationship of…

  9. Reviewing the Challenges and Opportunities Presented by Code Switching and Mixing in Bangla

    ERIC Educational Resources Information Center

    Hasan, Md. Kamrul; Akhand, Mohd. Moniruzzaman

    2014-01-01

    This paper investigates the issues related to code-switching/code-mixing in an ESL context. Some preliminary data on Bangla-English code-switching/code-mixing has been analyzed in order to determine which structural pattern of code-switching/code-mixing is predominant in different social strata. This study also explores the relationship of…

  10. Code-Switching in Persian-English and Telugu-English Conversations: With a Focus on Light Verb Constructions

    ERIC Educational Resources Information Center

    Moradi, Hamzeh

    2014-01-01

    Depending on the demands of a particular communicative situation, bilingual or multilingual speakers ("bilingualism-multilingualism") will switch between language varieties. Code-switching is the practice of moving between variations of languages in different contexts. In an educational context, code-switching is defined as the practice…

  11. ChromA: signal-based retention time alignment for chromatography-mass spectrometry data.

    PubMed

    Hoffmann, Nils; Stoye, Jens

    2009-08-15

    We describe ChromA, a web-based alignment tool for chromatography-mass spectrometry data from the metabolomics and proteomics domains. Users can supply their data in open and standardized file formats for retention time alignment using dynamic time warping with different configurable local distance and similarity functions. Additionally, user-defined anchors can be used to constrain and speedup the alignment. A neighborhood around each anchor can be added to increase the flexibility of the constrained alignment. ChromA offers different visualizations of the alignment for easier qualitative interpretation and comparison of the data. For the multiple alignment of more than two data files, the center-star approximation is applied to select a reference among input files to align to. ChromA is available at http://bibiserv.techfak.uni-bielefeld.de/chroma. Executables and source code under the L-GPL v3 license are provided for download at the same location.

  12. libgapmis: extending short-read alignments

    PubMed Central

    2013-01-01

    pairwise short-read alignments. We show that libgapmis is better-suited and more efficient than existing algorithms for this task. The importance of our contribution is underlined by the fact that the provided functions may be seamlessly integrated into any short-read alignment pipeline. The open-source code of libgapmis is available at http://www.exelixis-lab.org/gapmis. PMID:24564250

  13. Quantum image coding with a reference-frame-independent scheme

    NASA Astrophysics Data System (ADS)

    Chapeau-Blondeau, François; Belin, Etienne

    2016-07-01

    For binary images, or bit planes of non-binary images, we investigate the possibility of a quantum coding decodable by a receiver in the absence of reference frames shared with the emitter. Direct image coding with one qubit per pixel and non-aligned frames leads to decoding errors equivalent to a quantum bit-flip noise increasing with the misalignment. We show the feasibility of frame-invariant coding by using for each pixel a qubit pair prepared in one of two controlled entangled states. With just one common axis shared between the emitter and receiver, exact decoding for each pixel can be obtained by means of two two-outcome projective measurements operating separately on each qubit of the pair. With strictly no alignment information between the emitter and receiver, exact decoding can be obtained by means of a two-outcome projective measurement operating jointly on the qubit pair. In addition, the frame-invariant coding is shown much more resistant to quantum bit-flip noise compared to the direct non-invariant coding. For a cost per pixel of two (entangled) qubits instead of one, complete frame-invariant image coding and enhanced noise resistance are thus obtained.

  14. Early Learning Foundations. Indiana's Early Learning Development Framework Aligned to the Indiana Academic Standards, 2014

    ERIC Educational Resources Information Center

    Indiana Department of Education, 2015

    2015-01-01

    The "Foundations" (English/language arts, mathematics, social emotional skills, approaches to play and learning, science, social studies, creative arts, and physical health and growth) are Indiana's early learning development framework and are aligned to the 2014 Indiana Academic Standards. This framework provides core elements that…

  15. NetCoffee: a fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks.

    PubMed

    Hu, Jialu; Kehr, Birte; Reinert, Knut

    2014-02-15

    Owing to recent advancements in high-throughput technologies, protein-protein interaction networks of more and more species become available in public databases. The question of how to identify functionally conserved proteins across species attracts a lot of attention in computational biology. Network alignments provide a systematic way to solve this problem. However, most existing alignment tools encounter limitations in tackling this problem. Therefore, the demand for faster and more efficient alignment tools is growing. We present a fast and accurate algorithm, NetCoffee, which allows to find a global alignment of multiple protein-protein interaction networks. NetCoffee searches for a global alignment by maximizing a target function using simulated annealing on a set of weighted bipartite graphs that are constructed using a triplet approach similar to T-Coffee. To assess its performance, NetCoffee was applied to four real datasets. Our results suggest that NetCoffee remedies several limitations of previous algorithms, outperforms all existing alignment tools in terms of speed and nevertheless identifies biologically meaningful alignments. The source code and data are freely available for download under the GNU GPL v3 license at https://code.google.com/p/netcoffee/.

  16. Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization.

    PubMed

    Bauer, Markus; Klau, Gunnar W; Reinert, Knut

    2007-07-27

    The discovery of functional non-coding RNA sequences has led to an increasing interest in algorithms related to RNA analysis. Traditional sequence alignment algorithms, however, fail at computing reliable alignments of low-homology RNA sequences. The spatial conformation of RNA sequences largely determines their function, and therefore RNA alignment algorithms have to take structural information into account. We present a graph-based representation for sequence-structure alignments, which we model as an integer linear program (ILP). We sketch how we compute an optimal or near-optimal solution to the ILP using methods from combinatorial optimization, and present results on a recently published benchmark set for RNA alignments. The implementation of our algorithm yields better alignments in terms of two published scores than the other programs that we tested: This is especially the case with an increasing number of input sequences. Our program LARA is freely available for academic purposes from http://www.planet-lisa.net.

  17. Predicting Foreign Language Usage from English-Only Social Media Posts

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

    Volkova, Svitlana; Ranshous, Stephen M.; Phillips, Lawrence A.

    Social media is known for its multicultural and multilingual interactions, a natural product of which is code-mixing. Multilingual speakers mix languages they tweet to address a different audience, express certain feelings, or attract attention. This paper presents a large-scale analysis of 6 million tweets produced by 23 thousand multilingual users speaking 11 other languages besides English. We rely on this multilingual corpus to build predictive models for a novel task – inferring non- English languages that users speak exclusively from their English tweets. We contrast the predictive power of different linguistic signals and report that lexical content and syntactic structuremore » of English tweets are the most predictive of non-English languages that users speak on Twitter. By analyzing cross-lingual transfer – the influence of non-English languages on various levels of linguistic performance in English, we present novel findings on stylistic and syntactic variations across speakers of 11 languages.« less

  18. Edge Equilibrium Code (EEC) For Tokamaks

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

    Li, Xujling

    2014-02-24

    The edge equilibrium code (EEC) described in this paper is developed for simulations of the near edge plasma using the finite element method. It solves the Grad-Shafranov equation in toroidal coordinate and uses adaptive grids aligned with magnetic field lines. Hermite finite elements are chosen for the numerical scheme. A fast Newton scheme which is the same as implemented in the equilibrium and stability code (ESC) is applied here to adjust the grids

  19. English, French, Spanish, Italian, Portuguese? Code Choice and Austrian Export

    ERIC Educational Resources Information Center

    Lavric, Eva; Back, Bernhard

    2009-01-01

    This article deals with how "export oriented Austrian companies effect code choice in their business relationships with customers from Romance language speaking countries". The focus lies on the most widespread Romance languages, therefore on French, Spanish, Italian and Portuguese speaking customers.The question of code choice in export…

  20. From technical jargon to plain English for application.

    PubMed Central

    Lindsley, O R

    1991-01-01

    These examples of translating technical jargon into plain English application words, acronyms, letter codes, and simple tests were necessary as we developed Precision Teaching. I hope our experience is useful to others facing the problems of applying technology in practical settings. At the least, our experience should give you an idea of the work and time involved in making your own translations. Above all, be patient. Accurate plain English translations do not come easily. They cannot be made at your desk. A search often takes years to produce one new accurate plain English translation. Rapid publication pressures, journal editorial policies, and investments in materials, books, and computer programs all combine to hamper these translations. It's possible that you will find some of our plain English equivalents useful in your own applied behavior analysis applications. PMID:1752836

  1. Statistical inference of protein structural alignments using information and compression.

    PubMed

    Collier, James H; Allison, Lloyd; Lesk, Arthur M; Stuckey, Peter J; Garcia de la Banda, Maria; Konagurthu, Arun S

    2017-04-01

    Structural molecular biology depends crucially on computational techniques that compare protein three-dimensional structures and generate structural alignments (the assignment of one-to-one correspondences between subsets of amino acids based on atomic coordinates). Despite its importance, the structural alignment problem has not been formulated, much less solved, in a consistent and reliable way. To overcome these difficulties, we present here a statistical framework for the precise inference of structural alignments, built on the Bayesian and information-theoretic principle of Minimum Message Length (MML). The quality of any alignment is measured by its explanatory power-the amount of lossless compression achieved to explain the protein coordinates using that alignment. We have implemented this approach in MMLigner , the first program able to infer statistically significant structural alignments. We also demonstrate the reliability of MMLigner 's alignment results when compared with the state of the art. Importantly, MMLigner can also discover different structural alignments of comparable quality, a challenging problem for oligomers and protein complexes. Source code, binaries and an interactive web version are available at http://lcb.infotech.monash.edu.au/mmligner . arun.konagurthu@monash.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  2. Overcoming low-alignment signal contrast induced alignment failure by alignment signal enhancement

    NASA Astrophysics Data System (ADS)

    Lee, Byeong Soo; Kim, Young Ha; Hwang, Hyunwoo; Lee, Jeongjin; Kong, Jeong Heung; Kang, Young Seog; Paarhuis, Bart; Kok, Haico; de Graaf, Roelof; Weichselbaum, Stefan; Droste, Richard; Mason, Christopher; Aarts, Igor; de Boeij, Wim P.

    2016-03-01

    Overlay is one of the key factors which enables optical lithography extension to 1X node DRAM manufacturing. It is natural that accurate wafer alignment is a prerequisite for good device overlay. However, alignment failures or misalignments are commonly observed in a fab. There are many factors which could induce alignment problems. Low alignment signal contrast is one of the main issues. Alignment signal contrast can be degraded by opaque stack materials or by alignment mark degradation due to processes like CMP. This issue can be compounded by mark sub-segmentation from design rules in combination with double or quadruple spacer process. Alignment signal contrast can be improved by applying new material or process optimization, which sometimes lead to the addition of another process-step with higher costs. If we can amplify the signal components containing the position information and reduce other unwanted signal and background contributions then we can improve alignment performance without process change. In this paper we use ASML's new alignment sensor (as was introduced and released on the NXT:1980Di) and sample wafers with special stacks which can induce poor alignment signal to demonstrate alignment and overlay improvement.

  3. DNA Translator and Aligner: HyperCard utilities to aid phylogenetic analysis of molecules.

    PubMed

    Eernisse, D J

    1992-04-01

    DNA Translator and Aligner are molecular phylogenetics HyperCard stacks for Macintosh computers. They manipulate sequence data to provide graphical gene mapping, conversions, translations and manual multiple-sequence alignment editing. DNA Translator is able to convert documented GenBank or EMBL documented sequences into linearized, rescalable gene maps whose gene sequences are extractable by clicking on the corresponding map button or by selection from a scrolling list. Provided gene maps, complete with extractable sequences, consist of nine metazoan, one yeast, and one ciliate mitochondrial DNAs and three green plant chloroplast DNAs. Single or multiple sequences can be manipulated to aid in phylogenetic analysis. Sequences can be translated between nucleic acids and proteins in either direction with flexible support of alternate genetic codes and ambiguous nucleotide symbols. Multiple aligned sequence output from diverse sources can be converted to Nexus, Hennig86 or PHYLIP format for subsequent phylogenetic analysis. Input or output alignments can be examined with Aligner, a convenient accessory stack included in the DNA Translator package. Aligner is an editor for the manual alignment of up to 100 sequences that toggles between display of matched characters and normal unmatched sequences. DNA Translator also generates graphic displays of amino acid coding and codon usage frequency relative to all other, or only synonymous, codons for approximately 70 select organism-organelle combinations. Codon usage data is compatible with spreadsheet or UWGCG formats for incorporation of additional molecules of interest. The complete package is available via anonymous ftp and is free for non-commercial uses.

  4. Code-Switching in Iranian Elementary EFL Classrooms: An Exploratory Investigation

    ERIC Educational Resources Information Center

    Rezvani, Ehsan; Street, Hezar Jerib; Rasekh, Abbass Eslami

    2011-01-01

    This paper presents the results of a small-scale exploratory investigation of code-switching (CS) between English and Farsi by 4 Iranian English foreign language (EFL) teachers in elementary level EFL classrooms in a language school in Isfahan, Iran. Specifically, the present study aimed at exploring the syntactical identification of switches and…

  5. Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification.

    PubMed

    Borozan, Ivan; Watt, Stuart; Ferretti, Vincent

    2015-05-01

    Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed in many bacterial and viral genomes. Here, we propose a classification model that exploits the complementary nature of alignment-based and alignment-free similarity measures with the aim to improve the accuracy with which DNA and protein sequences are characterized. Our model classifies sequences using a combined sequence similarity score calculated by adaptively weighting the contribution of different sequence similarity measures. Weights are determined independently for each sequence in the test set and reflect the discriminatory ability of individual similarity measures in the training set. Because the similarity between some sequences is determined more accurately with one type of measure rather than another, our classifier allows different sets of weights to be associated with different sequences. Using five different similarity measures, we show that our model significantly improves the classification accuracy over the current composition- and alignment-based models, when predicting the taxonomic lineage for both short viral sequence fragments and complete viral sequences. We also show that our model can be used effectively for the classification of reads from a real metagenome dataset as well as protein sequences. All the datasets and the code used in this study are freely available at https://collaborators.oicr.on.ca/vferretti/borozan_csss/csss.html. ivan.borozan@gmail.com Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

  6. Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification

    PubMed Central

    Borozan, Ivan; Watt, Stuart; Ferretti, Vincent

    2015-01-01

    Motivation: Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed in many bacterial and viral genomes. Here, we propose a classification model that exploits the complementary nature of alignment-based and alignment-free similarity measures with the aim to improve the accuracy with which DNA and protein sequences are characterized. Results: Our model classifies sequences using a combined sequence similarity score calculated by adaptively weighting the contribution of different sequence similarity measures. Weights are determined independently for each sequence in the test set and reflect the discriminatory ability of individual similarity measures in the training set. Because the similarity between some sequences is determined more accurately with one type of measure rather than another, our classifier allows different sets of weights to be associated with different sequences. Using five different similarity measures, we show that our model significantly improves the classification accuracy over the current composition- and alignment-based models, when predicting the taxonomic lineage for both short viral sequence fragments and complete viral sequences. We also show that our model can be used effectively for the classification of reads from a real metagenome dataset as well as protein sequences. Availability and implementation: All the datasets and the code used in this study are freely available at https://collaborators.oicr.on.ca/vferretti/borozan_csss/csss.html. Contact: ivan.borozan@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25573913

  7. Two-Stream Transformer Networks for Video-based Face Alignment.

    PubMed

    Liu, Hao; Lu, Jiwen; Feng, Jianjiang; Zhou, Jie

    2017-08-01

    In this paper, we propose a two-stream transformer networks (TSTN) approach for video-based face alignment. Unlike conventional image-based face alignment approaches which cannot explicitly model the temporal dependency in videos and motivated by the fact that consistent movements of facial landmarks usually occur across consecutive frames, our TSTN aims to capture the complementary information of both the spatial appearance on still frames and the temporal consistency information across frames. To achieve this, we develop a two-stream architecture, which decomposes the video-based face alignment into spatial and temporal streams accordingly. Specifically, the spatial stream aims to transform the facial image to the landmark positions by preserving the holistic facial shape structure. Accordingly, the temporal stream encodes the video input as active appearance codes, where the temporal consistency information across frames is captured to help shape refinements. Experimental results on the benchmarking video-based face alignment datasets show very competitive performance of our method in comparisons to the state-of-the-arts.

  8. Objective speech quality assessment and the RPE-LTP coding algorithm in different noise and language conditions.

    PubMed

    Hansen, J H; Nandkumar, S

    1995-01-01

    The formulation of reliable signal processing algorithms for speech coding and synthesis require the selection of a prior criterion of performance. Though coding efficiency (bits/second) or computational requirements can be used, a final performance measure must always include speech quality. In this paper, three objective speech quality measures are considered with respect to quality assessment for American English, noisy American English, and noise-free versions of seven languages. The purpose is to determine whether objective quality measures can be used to quantify changes in quality for a given voice coding method, with a known subjective performance level, as background noise or language conditions are changed. The speech coding algorithm chosen is regular-pulse excitation with long-term prediction (RPE-LTP), which has been chosen as the standard voice compression algorithm for the European Digital Mobile Radio system. Three areas are considered for objective quality assessment which include: (i) vocoder performance for American English in a noise-free environment, (ii) speech quality variation for three additive background noise sources, and (iii) noise-free performance for seven languages which include English, Japanese, Finnish, German, Hindi, Spanish, and French. It is suggested that although existing objective quality measures will never replace subjective testing, they can be a useful means of assessing changes in performance, identifying areas for improvement in algorithm design, and augmenting subjective quality tests for voice coding/compression algorithms in noise-free, noisy, and/or non-English applications.

  9. Collaborative online projects for English language learners in science

    NASA Astrophysics Data System (ADS)

    Terrazas-Arellanes, Fatima E.; Knox, Carolyn; Rivas, Carmen

    2013-12-01

    This paper summarizes how collaborative online projects (COPs) are used to facilitate science content-area learning for English Learners of Hispanic origin. This is a Mexico-USA partnership project funded by the National Science Foundation. A COP is a 10-week thematic science unit, completely online, and bilingual (Spanish and English) designed to provide collaborative learning experiences with culturally and linguistically relevant science instruction in an interactive and multimodal learning environment. Units are integrated with explicit instructional lessons that include: (a) hands-on and laboratory activities, (b) interactive materials and interactive games with immediate feedback, (c) animated video tutorials, (d) discussion forums where students exchange scientific learning across classrooms in the USA and in Mexico, and (e) summative and formative assessments. Thematic units have been aligned to U.S. National Science Education Standards and are under current revisions for alignment to the Common Core State Standards. Training materials for the teachers have been integrated into the project website to facilitate self-paced and independent learning. Preliminary findings of our pre-experimental study with a sample of 53 students (81 % ELs), distributed across three different groups, resulted in a 21 % statistically significant points increase from pretest to posttest assessments of science content learning, t( 52) = 11.07, p = .000.

  10. Intonational Rises and Dialog Acts in the Australian English Map Task.

    ERIC Educational Resources Information Center

    Fletcher, Janet; Stirling, Lesley; Mushin, Ilana; Wales, Roger

    2002-01-01

    Eight map task dialogs representative of general Australian English were coded for speaker turn and for dialog acts using a version of SWBD-DAMSL, a dialog act annotation scheme. High, low, simple, and complex rising tunes, and any corresponding dialog act codes were then compared. The Australian statement high rise (usually realized as a L…

  11. Acquisition of stress and pitch accent in English-Spanish bilingual children

    NASA Astrophysics Data System (ADS)

    Kim, Sahyang; Andruski, Jean; Nathan, Geoffrey S.; Casielles, Eugenia; Work, Richard

    2005-09-01

    Although understanding of prosodic development is considered crucial for understanding of language acquisition in general, few studies have focused on how children develop native-like prosody in their speech production. This study will examine the acquisition of lexical stress and postlexical pitch accent in two English-Spanish bilingual children. Prosodic characteristics of English and Spanish are different in terms of frequent stress patterns (trochaic versus penultimate), phonetic realization of stress (reduced unstressed vowel versus full unstressed vowel), and frequent pitch accent types (H* versus L*+H), among others. Thus, English-Spanish bilingual children's prosodic development may provide evidence of their awareness of language differences relatively early during language development, and illustrate the influence of markedness or input frequency in prosodic acquisition. For this study, recordings from the children's one-word stage are used. Durations of stressed and unstressed syllables and F0 peak alignment are measured, and pitch accent types in different accentual positions (nuclear versus prenuclear) are transcribed using American English ToBI and Spanish ToBI. Prosodic development is compared across ages within each language and across languages at each age. Furthermore, the bilingual children's productions are compared with monolingual English and Spanish parents' productions.

  12. The Wildcat Corpus of Native- and Foreign-Accented English: Communicative Efficiency across Conversational Dyads with Varying Language Alignment Profiles

    ERIC Educational Resources Information Center

    Van Engen, Kristin J.; Baese-Berk, Melissa; Baker, Rachel E.; Choi, Arim; Kim, Midam; Bradlow, Ann R.

    2010-01-01

    This paper describes the development of the Wildcat Corpus of native- and foreign-accented English, a corpus containing scripted and spontaneous speech recordings from 24 native speakers of American English and 52 non-native speakers of English. The core element of this corpus is a set of spontaneous speech recordings, for which a new method of…

  13. FRAGS: estimation of coding sequence substitution rates from fragmentary data

    PubMed Central

    Swart, Estienne C; Hide, Winston A; Seoighe, Cathal

    2004-01-01

    Background Rates of substitution in protein-coding sequences can provide important insights into evolutionary processes that are of biomedical and theoretical interest. Increased availability of coding sequence data has enabled researchers to estimate more accurately the coding sequence divergence of pairs of organisms. However the use of different data sources, alignment protocols and methods to estimate substitution rates leads to widely varying estimates of key parameters that define the coding sequence divergence of orthologous genes. Although complete genome sequence data are not available for all organisms, fragmentary sequence data can provide accurate estimates of substitution rates provided that an appropriate and consistent methodology is used and that differences in the estimates obtainable from different data sources are taken into account. Results We have developed FRAGS, an application framework that uses existing, freely available software components to construct in-frame alignments and estimate coding substitution rates from fragmentary sequence data. Coding sequence substitution estimates for human and chimpanzee sequences, generated by FRAGS, reveal that methodological differences can give rise to significantly different estimates of important substitution parameters. The estimated substitution rates were also used to infer upper-bounds on the amount of sequencing error in the datasets that we have analysed. Conclusion We have developed a system that performs robust estimation of substitution rates for orthologous sequences from a pair of organisms. Our system can be used when fragmentary genomic or transcript data is available from one of the organisms and the other is a completely sequenced genome within the Ensembl database. As well as estimating substitution statistics our system enables the user to manage and query alignment and substitution data. PMID:15005802

  14. MUSCLE: multiple sequence alignment with high accuracy and high throughput.

    PubMed

    Edgar, Robert C

    2004-01-01

    We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.

  15. ChromA: signal-based retention time alignment for chromatography–mass spectrometry data

    PubMed Central

    Hoffmann, Nils; Stoye, Jens

    2009-01-01

    Summary: We describe ChromA, a web-based alignment tool for chromatography–mass spectrometry data from the metabolomics and proteomics domains. Users can supply their data in open and standardized file formats for retention time alignment using dynamic time warping with different configurable local distance and similarity functions. Additionally, user-defined anchors can be used to constrain and speedup the alignment. A neighborhood around each anchor can be added to increase the flexibility of the constrained alignment. ChromA offers different visualizations of the alignment for easier qualitative interpretation and comparison of the data. For the multiple alignment of more than two data files, the center-star approximation is applied to select a reference among input files to align to. Availability: ChromA is available at http://bibiserv.techfak.uni-bielefeld.de/chroma. Executables and source code under the L-GPL v3 license are provided for download at the same location. Contact: stoye@techfak.uni-bielefeld.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19505941

  16. A New Phenomenon in Saudi Females' Code-Switching: A Morphemic Analysis

    ERIC Educational Resources Information Center

    Turjoman, Mona O.

    2016-01-01

    This sociolinguistics study investigates a new phenomenon that has recently surfaced in the field of code-switching among Saudi females residing in the Western region of Saudi Arabia. This phenomenon basically combines bound Arabic pronouns, tense markers or definite article to English free morphemes or the combination of bound English affixes to…

  17. Running Records and First Grade English Learners: An Analysis of Language Related Errors

    ERIC Educational Resources Information Center

    Briceño, Allison; Klein, Adria F.

    2018-01-01

    The purpose of this study was to determine if first-grade English Learners made patterns of language related errors when reading, and if so, to identify those patterns and how teachers coded language related errors when analyzing English Learners' running records. Using research from the fields of both literacy and Second Language Acquisition, we…

  18. Codeswitching techniques: evidence-based instructional practices for the ASL/English bilingual classroom.

    PubMed

    Andrews, Jean F; Rusher, Melissa

    2010-01-01

    The authors present a perspective on emerging bilingual deaf students who are exposed to, learning, and developing two languages--American Sign Language (ASL) and English (spoken English, manually coded English, and English reading and writing). The authors suggest that though deaf children may lack proficiency or fluency in either language during early language-learning development, they still engage in codeswitching activities, in which they go back and forth between signing and English to communicate. The authors then provide a second meaning of codeswitching--as a purpose-driven instructional technique in which the teacher strategically changes from ASL to English print for purposes of vocabulary and reading comprehension. The results of four studies are examined that suggest that certain codeswitching strategies support English vocabulary learning and reading comprehension. These instructional strategies are couched in a five-pronged approach to furthering the development of bilingual education for deaf students.

  19. Aligning the unalignable: bacteriophage whole genome alignments.

    PubMed

    Bérard, Sèverine; Chateau, Annie; Pompidor, Nicolas; Guertin, Paul; Bergeron, Anne; Swenson, Krister M

    2016-01-13

    In recent years, many studies focused on the description and comparison of large sets of related bacteriophage genomes. Due to the peculiar mosaic structure of these genomes, few informative approaches for comparing whole genomes exist: dot plots diagrams give a mostly qualitative assessment of the similarity/dissimilarity between two or more genomes, and clustering techniques are used to classify genomes. Multiple alignments are conspicuously absent from this scene. Indeed, whole genome aligners interpret lack of similarity between sequences as an indication of rearrangements, insertions, or losses. This behavior makes them ill-prepared to align bacteriophage genomes, where even closely related strains can accomplish the same biological function with highly dissimilar sequences. In this paper, we propose a multiple alignment strategy that exploits functional collinearity shared by related strains of bacteriophages, and uses partial orders to capture mosaicism of sets of genomes. As classical alignments do, the computed alignments can be used to predict that genes have the same biological function, even in the absence of detectable similarity. The Alpha aligner implements these ideas in visual interactive displays, and is used to compute several examples of alignments of Staphylococcus aureus and Mycobacterium bacteriophages, involving up to 29 genomes. Using these datasets, we prove that Alpha alignments are at least as good as those computed by standard aligners. Comparison with the progressive Mauve aligner - which implements a partial order strategy, but whose alignments are linearized - shows a greatly improved interactive graphic display, while avoiding misalignments. Multiple alignments of whole bacteriophage genomes work, and will become an important conceptual and visual tool in comparative genomics of sets of related strains. A python implementation of Alpha, along with installation instructions for Ubuntu and OSX, is available on bitbucket (https://bitbucket.org/thekswenson/alpha).

  20. CRITICA: coding region identification tool invoking comparative analysis

    NASA Technical Reports Server (NTRS)

    Badger, J. H.; Olsen, G. J.; Woese, C. R. (Principal Investigator)

    1999-01-01

    Gene recognition is essential to understanding existing and future DNA sequence data. CRITICA (Coding Region Identification Tool Invoking Comparative Analysis) is a suite of programs for identifying likely protein-coding sequences in DNA by combining comparative analysis of DNA sequences with more common noncomparative methods. In the comparative component of the analysis, regions of DNA are aligned with related sequences from the DNA databases; if the translation of the aligned sequences has greater amino acid identity than expected for the observed percentage nucleotide identity, this is interpreted as evidence for coding. CRITICA also incorporates noncomparative information derived from the relative frequencies of hexanucleotides in coding frames versus other contexts (i.e., dicodon bias). The dicodon usage information is derived by iterative analysis of the data, such that CRITICA is not dependent on the existence or accuracy of coding sequence annotations in the databases. This independence makes the method particularly well suited for the analysis of novel genomes. CRITICA was tested by analyzing the available Salmonella typhimurium DNA sequences. Its predictions were compared with the DNA sequence annotations and with the predictions of GenMark. CRITICA proved to be more accurate than GenMark, and moreover, many of its predictions that would seem to be errors instead reflect problems in the sequence databases. The source code of CRITICA is freely available by anonymous FTP (rdp.life.uiuc.edu in/pub/critica) and on the World Wide Web (http:/(/)rdpwww.life.uiuc.edu).

  1. L-GRAAL: Lagrangian graphlet-based network aligner.

    PubMed

    Malod-Dognin, Noël; Pržulj, Nataša

    2015-07-01

    Discovering and understanding patterns in networks of protein-protein interactions (PPIs) is a central problem in systems biology. Alignments between these networks aid functional understanding as they uncover important information, such as evolutionary conserved pathways, protein complexes and functional orthologs. A few methods have been proposed for global PPI network alignments, but because of NP-completeness of underlying sub-graph isomorphism problem, producing topologically and biologically accurate alignments remains a challenge. We introduce a novel global network alignment tool, Lagrangian GRAphlet-based ALigner (L-GRAAL), which directly optimizes both the protein and the interaction functional conservations, using a novel alignment search heuristic based on integer programming and Lagrangian relaxation. We compare L-GRAAL with the state-of-the-art network aligners on the largest available PPI networks from BioGRID and observe that L-GRAAL uncovers the largest common sub-graphs between the networks, as measured by edge-correctness and symmetric sub-structures scores, which allow transferring more functional information across networks. We assess the biological quality of the protein mappings using the semantic similarity of their Gene Ontology annotations and observe that L-GRAAL best uncovers functionally conserved proteins. Furthermore, we introduce for the first time a measure of the semantic similarity of the mapped interactions and show that L-GRAAL also uncovers best functionally conserved interactions. In addition, we illustrate on the PPI networks of baker's yeast and human the ability of L-GRAAL to predict new PPIs. Finally, L-GRAAL's results are the first to show that topological information is more important than sequence information for uncovering functionally conserved interactions. L-GRAAL is coded in C++. Software is available at: http://bio-nets.doc.ic.ac.uk/L-GRAAL/. n.malod-dognin@imperial.ac.uk Supplementary data are available at

  2. PARTS: Probabilistic Alignment for RNA joinT Secondary structure prediction

    PubMed Central

    Harmanci, Arif Ozgun; Sharma, Gaurav; Mathews, David H.

    2008-01-01

    A novel method is presented for joint prediction of alignment and common secondary structures of two RNA sequences. The joint consideration of common secondary structures and alignment is accomplished by structural alignment over a search space defined by the newly introduced motif called matched helical regions. The matched helical region formulation generalizes previously employed constraints for structural alignment and thereby better accommodates the structural variability within RNA families. A probabilistic model based on pseudo free energies obtained from precomputed base pairing and alignment probabilities is utilized for scoring structural alignments. Maximum a posteriori (MAP) common secondary structures, sequence alignment and joint posterior probabilities of base pairing are obtained from the model via a dynamic programming algorithm called PARTS. The advantage of the more general structural alignment of PARTS is seen in secondary structure predictions for the RNase P family. For this family, the PARTS MAP predictions of secondary structures and alignment perform significantly better than prior methods that utilize a more restrictive structural alignment model. For the tRNA and 5S rRNA families, the richer structural alignment model of PARTS does not offer a benefit and the method therefore performs comparably with existing alternatives. For all RNA families studied, the posterior probability estimates obtained from PARTS offer an improvement over posterior probability estimates from a single sequence prediction. When considering the base pairings predicted over a threshold value of confidence, the combination of sensitivity and positive predictive value is superior for PARTS than for the single sequence prediction. PARTS source code is available for download under the GNU public license at http://rna.urmc.rochester.edu. PMID:18304945

  3. The Effectiveness of the Continuation Task on Second Language Learning of English Articles

    ERIC Educational Resources Information Center

    Jiang, Lin

    2015-01-01

    This article aims to uncover how alignment in the continuation task affects second language (L2) learning of English articles. Two classes of 47 Chinese students participated in the study which employed a pretest-treatment-posttest research design and lasted for a period of 20 weeks. One class received the continuation task treatment, during which…

  4. Aligning Game Activity with Educational Goals: Following a Constrained Design Approach to Instructional Computer Games

    ERIC Educational Resources Information Center

    Shelton, Brett E.; Scoresby, Jon

    2011-01-01

    We discuss the design, creation and implementation of an instructional game for use in a high school poetry class following a commitment to an educational game design principle of "alignment". We studied groups of instructional designers and an interactive fiction computer game they built. The game was implemented in a 9th grade English classroom…

  5. MaxAlign: maximizing usable data in an alignment.

    PubMed

    Gouveia-Oliveira, Rodrigo; Sackett, Peter W; Pedersen, Anders G

    2007-08-28

    The presence of gaps in an alignment of nucleotide or protein sequences is often an inconvenience for bioinformatical studies. In phylogenetic and other analyses, for instance, gapped columns are often discarded entirely from the alignment. MaxAlign is a program that optimizes the alignment prior to such analyses. Specifically, it maximizes the number of nucleotide (or amino acid) symbols that are present in gap-free columns - the alignment area - by selecting the optimal subset of sequences to exclude from the alignment. MaxAlign can be used prior to phylogenetic and bioinformatical analyses as well as in other situations where this form of alignment improvement is useful. In this work we test MaxAlign's performance in these tasks and compare the accuracy of phylogenetic estimates including and excluding gapped columns from the analysis, with and without processing with MaxAlign. In this paper we also introduce a new simple measure of tree similarity, Normalized Symmetric Similarity (NSS) that we consider useful for comparing tree topologies. We demonstrate how MaxAlign is helpful in detecting misaligned or defective sequences without requiring manual inspection. We also show that it is not advisable to exclude gapped columns from phylogenetic analyses unless MaxAlign is used first. Finally, we find that the sequences removed by MaxAlign from an alignment tend to be those that would otherwise be associated with low phylogenetic accuracy, and that the presence of gaps in any given sequence does not seem to disturb the phylogenetic estimates of other sequences. The MaxAlign web-server is freely available online at http://www.cbs.dtu.dk/services/MaxAlign where supplementary information can also be found. The program is also freely available as a Perl stand-alone package.

  6. China English and ELT for English Majors

    ERIC Educational Resources Information Center

    Zhang, Mingjuan

    2008-01-01

    This paper is a general study of one of varieties of English--China English and its influence on English Language Teaching (ELT) for English majors. The status of English as an International language breaks the situation in which British English or American English is the sole standard. English becomes World Englishes, taking on a plural form,…

  7. Switching Codes in the Plurilingual Classroom

    ERIC Educational Resources Information Center

    Corcoll López, Cristina; González-Davies, Maria

    2016-01-01

    The English as a foreign language classroom is a plurilingual setting par excellence since it involves at least two languages. However, plurilingual practices such as code-switching and translation have been consistently discouraged in formal learning contexts, based on the belief that keeping languages compartmentalized helps learning, and…

  8. ProfileGrids: a sequence alignment visualization paradigm that avoids the limitations of Sequence Logos.

    PubMed

    Roca, Alberto I

    2014-01-01

    The 2013 BioVis Contest provided an opportunity to evaluate different paradigms for visualizing protein multiple sequence alignments. Such data sets are becoming extremely large and thus taxing current visualization paradigms. Sequence Logos represent consensus sequences but have limitations for protein alignments. As an alternative, ProfileGrids are a new protein sequence alignment visualization paradigm that represents an alignment as a color-coded matrix of the residue frequency occurring at every homologous position in the aligned protein family. The JProfileGrid software program was used to analyze the BioVis contest data sets to generate figures for comparison with the Sequence Logo reference images. The ProfileGrid representation allows for the clear and effective analysis of protein multiple sequence alignments. This includes both a general overview of the conservation and diversity sequence patterns as well as the interactive ability to query the details of the protein residue distributions in the alignment. The JProfileGrid software is free and available from http://www.ProfileGrid.org.

  9. Mentor Texts and the Coding of Academic Writing Structures: A Functional Approach

    ERIC Educational Resources Information Center

    Escobar Alméciga, Wilder Yesid; Evans, Reid

    2014-01-01

    The purpose of the present pedagogical experience was to address the English language writing needs of university-level students pursuing a degree in bilingual education with an emphasis in the teaching of English. Using mentor texts and coding academic writing structures, an instructional design was developed to directly address the shortcomings…

  10. English in Political Discourse of Post-Suharto Indonesia.

    ERIC Educational Resources Information Center

    Bernsten, Suzanne

    This paper illustrates increases in the use of English in political speeches in post-Suharto Indonesia by analyzing the phonological, morphological, and syntactic assimilation of loanwords (linguistic borrowing), as well as hybridization and code switching, and phenomena such as doubling and loan translations. The paper also examines the mixed…

  11. Chemical education experiences from the English language learner perspective

    NASA Astrophysics Data System (ADS)

    Flores, Annette

    2011-12-01

    The Rio Grande Valley (RGV) is a region populated by Spanish-speaking immigrants and their descendants producing a large English Language Learner (ELL) student population. ELLs have historically had low literacy rates and achievement levels when compared to their counterparts. In order to address this achievement gap, previous research efforts and curriculum interventions have focused on language acquisition as being the determining factor in ELL education, with little attention given to academic content acquisition. More current research efforts have transitioned into English language acquisition through academic content instruction; this present research study specifically focuses on ELL experiences in chemistry. Participants were high school chemistry students who identified as ELL or had recently exited out of ELL status. Students were interviewed to identify factors that attributed to their experiences in chemistry. Findings indicate code-switching as a key to learning chemistry in English but also the deterrent in English language acquisition.

  12. Signal Processing Expert Code (SPEC)

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

    Ames, H.S.

    1985-12-01

    The purpose of this paper is to describe a prototype expert system called SPEC which was developed to demonstrate the utility of providing an intelligent interface for users of SIG, a general purpose signal processing code. The expert system is written in NIL, runs on a VAX 11/750 and consists of a backward chaining inference engine and an English-like parser. The inference engine uses knowledge encoded as rules about the formats of SIG commands and about how to perform frequency analyses using SIG. The system demonstrated that expert system can be used to control existing codes.

  13. Experience with code-switching modulates the use of grammatical gender during sentence processing

    PubMed Central

    Valdés Kroff, Jorge R.; Dussias, Paola E.; Gerfen, Chip; Perrotti, Lauren; Bajo, M. Teresa

    2016-01-01

    Using code-switching as a tool to illustrate how language experience modulates comprehension, the visual world paradigm was employed to examine the extent to which gender-marked Spanish determiners facilitate upcoming target nouns in a group of Spanish-English bilingual code-switchers. The first experiment tested target Spanish nouns embedded in a carrier phrase (Experiment 1b) and included a control Spanish monolingual group (Experiment 1a). The second set of experiments included critical trials in which participants heard code-switches from Spanish determiners into English nouns (e.g., la house) either in a fixed carrier phrase (Experiment 2a) or in variable and complex sentences (Experiment 2b). Across the experiments, bilinguals revealed an asymmetric gender effect in processing, showing facilitation only for feminine target items. These results reflect the asymmetric use of gender in the production of code-switched speech. The extension of the asymmetric effect into Spanish (Experiment 1b) underscores the permeability between language modes in bilingual code-switchers. PMID:28663771

  14. The Role of Language Learning Progressions in Improved Instruction and Assessment of English Language Learners

    ERIC Educational Resources Information Center

    Bailey, Alison L.; Heritage, Margaret

    2014-01-01

    This article addresses theoretical and empirical issues relevant for the development and evaluation of language learning progressions. The authors explore how learning progressions aligned with new content standards can form a central basis of efforts to describe the English language needed in school contexts for learning, instruction, and…

  15. Noch Einmal:American English - British English (Once More: American English -- British English).

    ERIC Educational Resources Information Center

    Botts, M.

    1980-01-01

    Replies critically to the article by D. K. Stevenson and R. J. Brunt, "Living English: Seeing the Forest in Spite of the Trees -- On Differences between American English and British English," in this journal, issue 1979/2. A reply by Stevenson and Brunt continues the controversy. (IFS/WGA)

  16. An MHD simulation of By-dependent magnetospheric convection and field-aligned currents during northward IMF

    NASA Technical Reports Server (NTRS)

    Ogino, T.; Walker, R. J.; Ashour-Abdalla, M.; Dawson, J. M.

    1985-01-01

    A three-dimensional MHD simulation code is used to model the magnetospheric configuration when the IMF has both a northward B(z) component and a B(y) component in the east-west direction. Projections of the plasma pressure, the field-aligned velocity, the field-aligned vorticity, and the field-aligned current along the magnetic field lines into the northern ionosphere are shown and discussed. Cross-sectional patterns of these parameters are shown. The results demonstrate that the B(y) component of the IMF strongly influences the plasma sheet configuration and the magnetospheric convection pattern.

  17. An Investigation of English Language Teachers and Students' Views on Ethical Principles towards Students

    ERIC Educational Resources Information Center

    Cephe, Pasa Tevfik; Keles, Yener

    2015-01-01

    The purpose of this study is to raise the quality of teaching English language and to contribute to the improvement of ELT Teachers profession by investigating the extent to which English teachers at Mugla Sitki Koçman University apply the ethical code towards students during their teaching process. The study was conducted in Preparatory School of…

  18. Ancient DNA sequence revealed by error-correcting codes.

    PubMed

    Brandão, Marcelo M; Spoladore, Larissa; Faria, Luzinete C B; Rocha, Andréa S L; Silva-Filho, Marcio C; Palazzo, Reginaldo

    2015-07-10

    A previously described DNA sequence generator algorithm (DNA-SGA) using error-correcting codes has been employed as a computational tool to address the evolutionary pathway of the genetic code. The code-generated sequence alignment demonstrated that a residue mutation revealed by the code can be found in the same position in sequences of distantly related taxa. Furthermore, the code-generated sequences do not promote amino acid changes in the deviant genomes through codon reassignment. A Bayesian evolutionary analysis of both code-generated and homologous sequences of the Arabidopsis thaliana malate dehydrogenase gene indicates an approximately 1 MYA divergence time from the MDH code-generated sequence node to its paralogous sequences. The DNA-SGA helps to determine the plesiomorphic state of DNA sequences because a single nucleotide alteration often occurs in distantly related taxa and can be found in the alternative codon patterns of noncanonical genetic codes. As a consequence, the algorithm may reveal an earlier stage of the evolution of the standard code.

  19. Ancient DNA sequence revealed by error-correcting codes

    PubMed Central

    Brandão, Marcelo M.; Spoladore, Larissa; Faria, Luzinete C. B.; Rocha, Andréa S. L.; Silva-Filho, Marcio C.; Palazzo, Reginaldo

    2015-01-01

    A previously described DNA sequence generator algorithm (DNA-SGA) using error-correcting codes has been employed as a computational tool to address the evolutionary pathway of the genetic code. The code-generated sequence alignment demonstrated that a residue mutation revealed by the code can be found in the same position in sequences of distantly related taxa. Furthermore, the code-generated sequences do not promote amino acid changes in the deviant genomes through codon reassignment. A Bayesian evolutionary analysis of both code-generated and homologous sequences of the Arabidopsis thaliana malate dehydrogenase gene indicates an approximately 1 MYA divergence time from the MDH code-generated sequence node to its paralogous sequences. The DNA-SGA helps to determine the plesiomorphic state of DNA sequences because a single nucleotide alteration often occurs in distantly related taxa and can be found in the alternative codon patterns of noncanonical genetic codes. As a consequence, the algorithm may reveal an earlier stage of the evolution of the standard code. PMID:26159228

  20. Code-Switching in Vietnamese University EFL Teachers' Classroom Instruction: A Pedagogical Focus

    ERIC Educational Resources Information Center

    Grant, Lynn E.; Nguyen, Thi Hang

    2017-01-01

    This study examines the under-explored phenomenon in Vietnamese tertiary settings of code-switching practised by EFL (English as a foreign language) teachers in classroom instruction, as well as their awareness of this practice. Among the foreign languages taught and learned in Vietnamese universities, English is the most popular. The research…

  1. AlignMe—a membrane protein sequence alignment web server

    PubMed Central

    Stamm, Marcus; Staritzbichler, René; Khafizov, Kamil; Forrest, Lucy R.

    2014-01-01

    We present a web server for pair-wise alignment of membrane protein sequences, using the program AlignMe. The server makes available two operational modes of AlignMe: (i) sequence to sequence alignment, taking two sequences in fasta format as input, combining information about each sequence from multiple sources and producing a pair-wise alignment (PW mode); and (ii) alignment of two multiple sequence alignments to create family-averaged hydropathy profile alignments (HP mode). For the PW sequence alignment mode, four different optimized parameter sets are provided, each suited to pairs of sequences with a specific similarity level. These settings utilize different types of inputs: (position-specific) substitution matrices, secondary structure predictions and transmembrane propensities from transmembrane predictions or hydrophobicity scales. In the second (HP) mode, each input multiple sequence alignment is converted into a hydrophobicity profile averaged over the provided set of sequence homologs; the two profiles are then aligned. The HP mode enables qualitative comparison of transmembrane topologies (and therefore potentially of 3D folds) of two membrane proteins, which can be useful if the proteins have low sequence similarity. In summary, the AlignMe web server provides user-friendly access to a set of tools for analysis and comparison of membrane protein sequences. Access is available at http://www.bioinfo.mpg.de/AlignMe PMID:24753425

  2. ProfileGrids: a sequence alignment visualization paradigm that avoids the limitations of Sequence Logos

    PubMed Central

    2014-01-01

    Background The 2013 BioVis Contest provided an opportunity to evaluate different paradigms for visualizing protein multiple sequence alignments. Such data sets are becoming extremely large and thus taxing current visualization paradigms. Sequence Logos represent consensus sequences but have limitations for protein alignments. As an alternative, ProfileGrids are a new protein sequence alignment visualization paradigm that represents an alignment as a color-coded matrix of the residue frequency occurring at every homologous position in the aligned protein family. Results The JProfileGrid software program was used to analyze the BioVis contest data sets to generate figures for comparison with the Sequence Logo reference images. Conclusions The ProfileGrid representation allows for the clear and effective analysis of protein multiple sequence alignments. This includes both a general overview of the conservation and diversity sequence patterns as well as the interactive ability to query the details of the protein residue distributions in the alignment. The JProfileGrid software is free and available from http://www.ProfileGrid.org. PMID:25237393

  3. MSAViewer: interactive JavaScript visualization of multiple sequence alignments

    PubMed Central

    Yachdav, Guy; Wilzbach, Sebastian; Rauscher, Benedikt; Sheridan, Robert; Sillitoe, Ian; Procter, James; Lewis, Suzanna E.; Rost, Burkhard; Goldberg, Tatyana

    2016-01-01

    Summary: The MSAViewer is a quick and easy visualization and analysis JavaScript component for Multiple Sequence Alignment data of any size. Core features include interactive navigation through the alignment, application of popular color schemes, sorting, selecting and filtering. The MSAViewer is ‘web ready’: written entirely in JavaScript, compatible with modern web browsers and does not require any specialized software. The MSAViewer is part of the BioJS collection of components. Availability and Implementation: The MSAViewer is released as open source software under the Boost Software License 1.0. Documentation, source code and the viewer are available at http://msa.biojs.net/. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: msa@bio.sh PMID:27412096

  4. NAEYC Code of Ethical Conduct. Revised = Codigo de Conducta Etica. Revisada

    ERIC Educational Resources Information Center

    National Association of Elementary School Principals (NAESP), 2005

    2005-01-01

    This document presents a code of ethics for early childhood educators that offers guidelines for responsible behavior and sets forth a common basis for resolving ethical dilemmas encountered in early education. It represents the English and Spanish versions of the revised code. Its contents were approved by the NAEYC Governing Board in April 2005…

  5. Pre-calculated protein structure alignments at the RCSB PDB website.

    PubMed

    Prlic, Andreas; Bliven, Spencer; Rose, Peter W; Bluhm, Wolfgang F; Bizon, Chris; Godzik, Adam; Bourne, Philip E

    2010-12-01

    With the continuous growth of the RCSB Protein Data Bank (PDB), providing an up-to-date systematic structure comparison of all protein structures poses an ever growing challenge. Here, we present a comparison tool for calculating both 1D protein sequence and 3D protein structure alignments. This tool supports various applications at the RCSB PDB website. First, a structure alignment web service calculates pairwise alignments. Second, a stand-alone application runs alignments locally and visualizes the results. Third, pre-calculated 3D structure comparisons for the whole PDB are provided and updated on a weekly basis. These three applications allow users to discover novel relationships between proteins available either at the RCSB PDB or provided by the user. A web user interface is available at http://www.rcsb.org/pdb/workbench/workbench.do. The source code is available under the LGPL license from http://www.biojava.org. A source bundle, prepared for local execution, is available from http://source.rcsb.org andreas@sdsc.edu; pbourne@ucsd.edu.

  6. Two Influential Primate Classifications Logically Aligned

    PubMed Central

    Franz, Nico M.; Pier, Naomi M.; Reeder, Deeann M.; Chen, Mingmin; Yu, Shizhuo; Kianmajd, Parisa; Bowers, Shawn; Ludäscher, Bertram

    2016-01-01

    Classifications and phylogenies of perceived natural entities change in the light of new evidence. Taxonomic changes, translated into Code-compliant names, frequently lead to name:meaning dissociations across succeeding treatments. Classification standards such as the Mammal Species of the World (MSW) may experience significant levels of taxonomic change from one edition to the next, with potential costs to long-term, large-scale information integration. This circumstance challenges the biodiversity and phylogenetic data communities to express taxonomic congruence and incongruence in ways that both humans and machines can process, that is, to logically represent taxonomic alignments across multiple classifications. We demonstrate that such alignments are feasible for two classifications of primates corresponding to the second and third MSW editions. Our approach has three main components: (i) use of taxonomic concept labels, that is name sec. author (where sec. means according to), to assemble each concept hierarchy separately via parent/child relationships; (ii) articulation of select concepts across the two hierarchies with user-provided Region Connection Calculus (RCC-5) relationships; and (iii) the use of an Answer Set Programming toolkit to infer and visualize logically consistent alignments of these input constraints. Our use case entails the Primates sec. Groves (1993; MSW2–317 taxonomic concepts; 233 at the species level) and Primates sec. Groves (2005; MSW3–483 taxonomic concepts; 376 at the species level). Using 402 RCC-5 input articulations, the reasoning process yields a single, consistent alignment and 153,111 Maximally Informative Relations that constitute a comprehensive meaning resolution map for every concept pair in the Primates sec. MSW2/MSW3. The complete alignment, and various partitions thereof, facilitate quantitative analyses of name:meaning dissociation, revealing that nearly one in three taxonomic names are not reliable across

  7. A Study of Sociolinguistic Characteristics of Taiwan Children's Peer-Talk in a Mandarin-English-Speaking Preschool

    ERIC Educational Resources Information Center

    Wang, Li-Chen; Hyun, Eunsook

    2009-01-01

    This qualitative study presents sociolinguistic characteristics of peer-talk of 44 children in a Mandarin-English-speaking preschool in Taiwan where English was taught as a foreign language (EFL). Key findings: teacher-dominated talk influences children's peer-talk; EFL and code-switching emerge in spontaneous peer-talk; children actively engage…

  8. Narratives in Two Languages: Storytelling of Bilingual Cantonese-English Preschoolers.

    PubMed

    Rezzonico, Stefano; Goldberg, Ahuva; Mak, Katy Ka-Yan; Yap, Stephanie; Milburn, Trelani; Belletti, Adriana; Girolametto, Luigi

    2016-06-01

    The aim of this study was to compare narratives generated by 4-year-old and 5-year-old children who were bilingual in English and Cantonese. The sample included 47 children (23 who were 4 years old and 24 who were 5 years old) living in Toronto, Ontario, Canada, who spoke both Cantonese and English. The participants spoke and heard predominantly Cantonese in the home. Participants generated a story in English and Cantonese by using a wordless picture book; language order was counterbalanced. Data were transcribed and coded for story grammar, morphosyntactic quality, mean length of utterance in words, and the number of different words. Repeated measures analysis of variance revealed higher story grammar scores in English than in Cantonese, but no other significant main effects of language were observed. Analyses also revealed that older children had higher story grammar, mean length of utterance in words, and morphosyntactic quality scores than younger children in both languages. Hierarchical regressions indicated that Cantonese story grammar predicted English story grammar and Cantonese microstructure predicted English microstructure. However, no correlation was observed between Cantonese and English morphosyntactic quality. The results of this study have implications for speech-language pathologists who collect narratives in Cantonese and English from bilingual preschoolers. The results suggest that there is a possible transfer in narrative abilities between the two languages.

  9. The spatial alignment of time: Differences in alignment of deictic and sequence time along the sagittal and lateral axes.

    PubMed

    Walker, Esther J; Bergen, Benjamin K; Núñez, Rafael

    2017-04-01

    People use space in a variety of ways to structure their thoughts about time. The present report focuses on the different ways that space is employed when reasoning about deictic (past/future relationships) and sequence (earlier/later relationships) time. In the first study, we show that deictic and sequence time are aligned along the lateral axis in a manner consistent with previous work, with past and earlier events associated with left space and future and later events associated with right space. However, the alignment of time with space is different along the sagittal axis. Participants associated future events and earlier events-not later events-with the space in front of their body and past and later events with the space behind, consistent with the sagittal spatial terms (e.g., ahead, in front of) that we use to talk about deictic and sequence time. In the second study, we show that these associations between sequence time and sagittal space are sensitive to person-perspective. This suggests that the particular space-time associations observed in English speakers are influenced by a variety of different spatial properties, including spatial location and perspective. Copyright © 2016. Published by Elsevier B.V.

  10. The Effects of Single and Dual Coded Multimedia Instructional Methods on Chinese Character Learning

    ERIC Educational Resources Information Center

    Wang, Ling

    2013-01-01

    Learning Chinese characters is a difficult task for adult English native speakers due to the significant differences between the Chinese and English writing system. The visuospatial properties of Chinese characters have inspired the development of instructional methods using both verbal and visual information based on the Dual Coding Theory. This…

  11. Categories of Code-Switching in Hispanic Communities: Untangling the Terminology. Sociolinguistic Working Paper Number 76.

    ERIC Educational Resources Information Center

    Baker, Opal Ruth

    Research on Spanish/English code switching is reviewed and the definitions and categories set up by the investigators are examined. Their methods of locating, limiting, and classifying true code switches, and the terms used and results obtained, are compared. It is found that in these studies, conversational (intra-discourse) code switching is…

  12. Biclustering as a method for RNA local multiple sequence alignment.

    PubMed

    Wang, Shu; Gutell, Robin R; Miranker, Daniel P

    2007-12-15

    Biclustering is a clustering method that simultaneously clusters both the domain and range of a relation. A challenge in multiple sequence alignment (MSA) is that the alignment of sequences is often intended to reveal groups of conserved functional subsequences. Simultaneously, the grouping of the sequences can impact the alignment; precisely the kind of dual situation biclustering is intended to address. We define a representation of the MSA problem enabling the application of biclustering algorithms. We develop a computer program for local MSA, BlockMSA, that combines biclustering with divide-and-conquer. BlockMSA simultaneously finds groups of similar sequences and locally aligns subsequences within them. Further alignment is accomplished by dividing both the set of sequences and their contents. The net result is both a multiple sequence alignment and a hierarchical clustering of the sequences. BlockMSA was tested on the subsets of the BRAliBase 2.1 benchmark suite that display high variability and on an extension to that suite to larger problem sizes. Also, alignments were evaluated of two large datasets of current biological interest, T box sequences and Group IC1 Introns. The results were compared with alignments computed by ClustalW, MAFFT, MUCLE and PROBCONS alignment programs using Sum of Pairs (SPS) and Consensus Count. Results for the benchmark suite are sensitive to problem size. On problems of 15 or greater sequences, BlockMSA is consistently the best. On none of the problems in the test suite are there appreciable differences in scores among BlockMSA, MAFFT and PROBCONS. On the T box sequences, BlockMSA does the most faithful job of reproducing known annotations. MAFFT and PROBCONS do not. On the Intron sequences, BlockMSA, MAFFT and MUSCLE are comparable at identifying conserved regions. BlockMSA is implemented in Java. Source code and supplementary datasets are available at http://aug.csres.utexas.edu/msa/

  13. High-speed all-optical DNA local sequence alignment based on a three-dimensional artificial neural network.

    PubMed

    Maleki, Ehsan; Babashah, Hossein; Koohi, Somayyeh; Kavehvash, Zahra

    2017-07-01

    This paper presents an optical processing approach for exploring a large number of genome sequences. Specifically, we propose an optical correlator for global alignment and an extended moiré matching technique for local analysis of spatially coded DNA, whose output is fed to a novel three-dimensional artificial neural network for local DNA alignment. All-optical implementation of the proposed 3D artificial neural network is developed and its accuracy is verified in Zemax. Thanks to its parallel processing capability, the proposed structure performs local alignment of 4 million sequences of 150 base pairs in a few seconds, which is much faster than its electrical counterparts, such as the basic local alignment search tool.

  14. RNAcode: Robust discrimination of coding and noncoding regions in comparative sequence data

    PubMed Central

    Washietl, Stefan; Findeiß, Sven; Müller, Stephan A.; Kalkhof, Stefan; von Bergen, Martin; Hofacker, Ivo L.; Stadler, Peter F.; Goldman, Nick

    2011-01-01

    With the availability of genome-wide transcription data and massive comparative sequencing, the discrimination of coding from noncoding RNAs and the assessment of coding potential in evolutionarily conserved regions arose as a core analysis task. Here we present RNAcode, a program to detect coding regions in multiple sequence alignments that is optimized for emerging applications not covered by current protein gene-finding software. Our algorithm combines information from nucleotide substitution and gap patterns in a unified framework and also deals with real-life issues such as alignment and sequencing errors. It uses an explicit statistical model with no machine learning component and can therefore be applied “out of the box,” without any training, to data from all domains of life. We describe the RNAcode method and apply it in combination with mass spectrometry experiments to predict and confirm seven novel short peptides in Escherichia coli and to analyze the coding potential of RNAs previously annotated as “noncoding.” RNAcode is open source software and available for all major platforms at http://wash.github.com/rnacode. PMID:21357752

  15. RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.

    PubMed

    Washietl, Stefan; Findeiss, Sven; Müller, Stephan A; Kalkhof, Stefan; von Bergen, Martin; Hofacker, Ivo L; Stadler, Peter F; Goldman, Nick

    2011-04-01

    With the availability of genome-wide transcription data and massive comparative sequencing, the discrimination of coding from noncoding RNAs and the assessment of coding potential in evolutionarily conserved regions arose as a core analysis task. Here we present RNAcode, a program to detect coding regions in multiple sequence alignments that is optimized for emerging applications not covered by current protein gene-finding software. Our algorithm combines information from nucleotide substitution and gap patterns in a unified framework and also deals with real-life issues such as alignment and sequencing errors. It uses an explicit statistical model with no machine learning component and can therefore be applied "out of the box," without any training, to data from all domains of life. We describe the RNAcode method and apply it in combination with mass spectrometry experiments to predict and confirm seven novel short peptides in Escherichia coli and to analyze the coding potential of RNAs previously annotated as "noncoding." RNAcode is open source software and available for all major platforms at http://wash.github.com/rnacode.

  16. Components and context: exploring sources of reading difficulties for language minority learners and native English speakers in urban schools.

    PubMed

    Kieffer, Michael J; Vukovic, Rose K

    2012-01-01

    Drawing on the cognitive and ecological domains within the componential model of reading, this longitudinal study explores heterogeneity in the sources of reading difficulties for language minority learners and native English speakers in urban schools. Students (N = 150) were followed from first through third grade and assessed annually on standardized English language and reading measures. Structural equation modeling was used to investigate the relative contributions of code-related and linguistic comprehension skills in first and second grade to third grade reading comprehension. Linguistic comprehension and the interaction between linguistic comprehension and code-related skills each explained substantial variation in reading comprehension. Among students with low reading comprehension, more than 80% demonstrated weaknesses in linguistic comprehension alone, whereas approximately 15% demonstrated weaknesses in both linguistic comprehension and code-related skills. Results were remarkably similar for the language minority learners and native English speakers, suggesting the importance of their shared socioeconomic backgrounds and schooling contexts.

  17. MSAViewer: interactive JavaScript visualization of multiple sequence alignments.

    PubMed

    Yachdav, Guy; Wilzbach, Sebastian; Rauscher, Benedikt; Sheridan, Robert; Sillitoe, Ian; Procter, James; Lewis, Suzanna E; Rost, Burkhard; Goldberg, Tatyana

    2016-11-15

    The MSAViewer is a quick and easy visualization and analysis JavaScript component for Multiple Sequence Alignment data of any size. Core features include interactive navigation through the alignment, application of popular color schemes, sorting, selecting and filtering. The MSAViewer is 'web ready': written entirely in JavaScript, compatible with modern web browsers and does not require any specialized software. The MSAViewer is part of the BioJS collection of components. The MSAViewer is released as open source software under the Boost Software License 1.0. Documentation, source code and the viewer are available at http://msa.biojs.net/Supplementary information: Supplementary data are available at Bioinformatics online. msa@bio.sh. © The Author 2016. Published by Oxford University Press.

  18. Exploring Intercultural and Ethical Understanding through "Ethical Intelligence" and Drama in Asian Texts for the "Australian Curriculum: English"

    ERIC Educational Resources Information Center

    Jetnikoff, Anita

    2013-01-01

    This paper focuses on Australian texts with Asian representations, which will be discussed in terms of Ethical Intelligence (Weinstein, 2011) explored through drama. This approach aligns with the architecture of the "Australian Curriculum: English" (AC:E, v5, 2013), in particular the general capabilities of "ethical…

  19. An MHD Code for the Study of Magnetic Structures in the Solar Wind

    NASA Technical Reports Server (NTRS)

    Allred, J. C.; MacNeice, P. J.

    2015-01-01

    We have developed a 2.5D MHD code designed to study how the solar wind influences the evolution of transient events in the solar corona and inner heliosphere. The code includes thermal conduction, coronal heating and radiative cooling. Thermal conduction is assumed to be magnetic field-aligned in the inner corona and transitions to a collisionless formulation in the outer corona. We have developed a stable method to handle field-aligned conduction around magnetic null points. The inner boundary is placed in the upper transition region, and the mass flux across the boundary is determined from 1D field-aligned characteristics and a 'radiative energy balance' condition. The 2.5D nature of this code makes it ideal for parameter studies not yet possible with 3D codes. We have made this code publicly available as a tool for the community. To this end we have developed a graphical interface to aid in the selection of appropriate options and a graphical interface that can process and visualize the data produced by the simulation. As an example, we show a simulation of a dipole field stretched into a helmet streamer by the solar wind. Plasmoids periodically erupt from the streamer, and we perform a parameter study of how the frequency and location of these eruptions changed in response to different levels of coronal heating. As a further example, we show the solar wind stretching a compact multi-polar flux system. This flux system will be used to study breakout coronal mass ejections in the presence of the solar wind.

  20. ADOMA: A Command Line Tool to Modify ClustalW Multiple Alignment Output.

    PubMed

    Zaal, Dionne; Nota, Benjamin

    2016-01-01

    We present ADOMA, a command line tool that produces alternative outputs from ClustalW multiple alignments of nucleotide or protein sequences. ADOMA can simplify the output of alignments by showing only the different residues between sequences, which is often desirable when only small differences such as single nucleotide polymorphisms are present (e.g., between different alleles). Another feature of ADOMA is that it can enhance the ClustalW output by coloring the residues in the alignment. This tool is easily integrated into automated Linux pipelines for next-generation sequencing data analysis, and may be useful for researchers in a broad range of scientific disciplines including evolutionary biology and biomedical sciences. The source code is freely available at https://sourceforge. net/projects/adoma/. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. IUS prerelease alignment

    NASA Technical Reports Server (NTRS)

    Evans, F. A.

    1978-01-01

    Space shuttle orbiter/IUS alignment transfer was evaluated. Although the orbiter alignment accuracy was originally believed to be the major contributor to the overall alignment transfer error, it was shown that orbiter alignment accuracy is not a factor affecting IUS alignment accuracy, if certain procedures are followed. Results are reported of alignment transfer accuracy analysis.

  2. American PARCC and SBAC and Their Implications on the Construction of English Assessment System in China

    ERIC Educational Resources Information Center

    Zhang, Haiyan; Kang, Kai

    2017-01-01

    The Partnership for Assessment of Readiness for College and Careers (PARCC) and Smarter Balanced Assessment Systems (SBAC) started in the 2014-2015 academic year and has been regarded by many in the field as a radical effort to improve the American English Language Art (ELA) educational standards. These two consortia, being aligned with Common…

  3. Design and realization of the optical and electron beam alignment system for the HUST-FEL oscillator

    NASA Astrophysics Data System (ADS)

    Fu, Q.; Tan, P.; Liu, K. F.; Qin, B.; Liu, X.

    2018-06-01

    A Free Electron Laser(FEL) oscillator with radiation wavelength at 30-100 μ m is under commissioning at Huazhong University of Science and Technology (HUST). This work presents the schematic design and realization procedures for the optical and beam alignment system in the HUST FEL facility. The optical cavity misalignment effects are analyzed with the code OPC + Genesis 1.3, and the tolerance of misalignment is proposed with the simulation result. Depending on undulator mechanical benchmarks, a laser indicating system has been built up as reference datum. The alignment of both optical axis and beam trajectory were achieved by this alignment system.

  4. Understanding and Evaluating English Learners' Oral Reading with Miscue Analysis

    ERIC Educational Resources Information Center

    Latham Keh, Melissa

    2017-01-01

    Miscue analysis provides a unique opportunity to explore English learners' (ELs') oral reading from an asset-based perspective. This article focuses on insights about eight adolescent ELs' oral reading patterns that were gained through miscue analysis. The participants' miscues were coded with the Reading Miscue Inventory, and participants were…

  5. Towards Automatically Aligning German Compounds with English Word Groups in an Example-Based Translation System.

    ERIC Educational Resources Information Center

    Jones, Daniel; Alexa, Melina

    As part of the development of a completely sub-symbolic machine translation system, a method for automatically identifying German compounds was developed. Given a parallel bilingual corpus, German compounds are identified along with their English word groupings by statistical processing alone. The underlying principles and the design process are…

  6. Kinematically aligned TKA can align knee joint line to horizontal.

    PubMed

    Ji, Hyung-Min; Han, Jun; Jin, Dong San; Seo, Hyunseok; Won, Ye-Yeon

    2016-08-01

    The joint line of the native knee is horizontal to the floor and perpendicular to the vertical weight-bearing axis of the patient in a bipedal stance. The purposes of this study were as follows: (1) to find out the distribution of the native joint line in a population of normal patients with normal knees; (2) to compare the native joint line orientation between patients receiving conventional mechanically aligned total knee arthroplasty (TKA), navigated mechanically aligned TKA, and kinematically aligned TKA; and (3) to determine which of the three TKA methods aligns the postoperative knee joint perpendicular to the weight-bearing axis of the limb in bipedal stance. To determine the joint line orientation of a native knee, 50 full-length standing hip-to-ankle digital radiographs were obtained in 50 young, healthy individuals. The angle between knee joint line and the line parallel to the floor was measured and defined as joint line orientation angle (JLOA). JLOA was also measured prior to and after conventional mechanically aligned TKA (65 knees), mechanically aligned TKA using imageless navigation (65 knees), and kinematically aligned TKA (65 knees). The proportion of the knees similar to the native joint line was calculated for each group. The mean JLOA in healthy individuals was parallel to the floor (0.2° ± 1.1°). The pre-operative JLOA of all treatment groups slanted down to the lateral side. Postoperative JLOA slanted down to the lateral side in conventional mechanically aligned TKA (-3.3° ± 2.2°) and in navigation mechanically aligned TKA (-2.6° ± 1.8°), while it was horizontal to the floor in kinematically aligned TKA (0.6° ± 1.7°). Only 6.9 % of the conventional mechanically aligned TKA and 16.9 % of the navigation mechanically aligned TKA were within one SD of the mean JLOA of the native knee, while the proportion was significantly higher (50.8 %) in kinematically aligned TKA. The portion was statistically greater in mechanically

  7. The Impact of Codes of Conduct on Stakeholders

    ERIC Educational Resources Information Center

    Newman, Wayne R.

    2015-01-01

    The purpose of this study was to determine how an urban school district's code of conduct aligned with actual school/class behaviors, and how stakeholders perceived the ability of this document to achieve its number one goal: safe and productive learning environments. Twenty participants including students, teachers, parents, and administrators…

  8. Two Influential Primate Classifications Logically Aligned.

    PubMed

    Franz, Nico M; Pier, Naomi M; Reeder, Deeann M; Chen, Mingmin; Yu, Shizhuo; Kianmajd, Parisa; Bowers, Shawn; Ludäscher, Bertram

    2016-07-01

    Classifications and phylogenies of perceived natural entities change in the light of new evidence. Taxonomic changes, translated into Code-compliant names, frequently lead to name:meaning dissociations across succeeding treatments. Classification standards such as the Mammal Species of the World (MSW) may experience significant levels of taxonomic change from one edition to the next, with potential costs to long-term, large-scale information integration. This circumstance challenges the biodiversity and phylogenetic data communities to express taxonomic congruence and incongruence in ways that both humans and machines can process, that is, to logically represent taxonomic alignments across multiple classifications. We demonstrate that such alignments are feasible for two classifications of primates corresponding to the second and third MSW editions. Our approach has three main components: (i) use of taxonomic concept labels, that is name sec. author (where sec. means according to), to assemble each concept hierarchy separately via parent/child relationships; (ii) articulation of select concepts across the two hierarchies with user-provided Region Connection Calculus (RCC-5) relationships; and (iii) the use of an Answer Set Programming toolkit to infer and visualize logically consistent alignments of these input constraints. Our use case entails the Primates sec. Groves (1993; MSW2-317 taxonomic concepts; 233 at the species level) and Primates sec. Groves (2005; MSW3-483 taxonomic concepts; 376 at the species level). Using 402 RCC-5 input articulations, the reasoning process yields a single, consistent alignment and 153,111 Maximally Informative Relations that constitute a comprehensive meaning resolution map for every concept pair in the Primates sec. MSW2/MSW3. The complete alignment, and various partitions thereof, facilitate quantitative analyses of name:meaning dissociation, revealing that nearly one in three taxonomic names are not reliable across treatments

  9. Image correlation method for DNA sequence alignment.

    PubMed

    Curilem Saldías, Millaray; Villarroel Sassarini, Felipe; Muñoz Poblete, Carlos; Vargas Vásquez, Asticio; Maureira Butler, Iván

    2012-01-01

    The complexity of searches and the volume of genomic data make sequence alignment one of bioinformatics most active research areas. New alignment approaches have incorporated digital signal processing techniques. Among these, correlation methods are highly sensitive. This paper proposes a novel sequence alignment method based on 2-dimensional images, where each nucleic acid base is represented as a fixed gray intensity pixel. Query and known database sequences are coded to their pixel representation and sequence alignment is handled as object recognition in a scene problem. Query and database become object and scene, respectively. An image correlation process is carried out in order to search for the best match between them. Given that this procedure can be implemented in an optical correlator, the correlation could eventually be accomplished at light speed. This paper shows an initial research stage where results were "digitally" obtained by simulating an optical correlation of DNA sequences represented as images. A total of 303 queries (variable lengths from 50 to 4500 base pairs) and 100 scenes represented by 100 x 100 images each (in total, one million base pair database) were considered for the image correlation analysis. The results showed that correlations reached very high sensitivity (99.01%), specificity (98.99%) and outperformed BLAST when mutation numbers increased. However, digital correlation processes were hundred times slower than BLAST. We are currently starting an initiative to evaluate the correlation speed process of a real experimental optical correlator. By doing this, we expect to fully exploit optical correlation light properties. As the optical correlator works jointly with the computer, digital algorithms should also be optimized. The results presented in this paper are encouraging and support the study of image correlation methods on sequence alignment.

  10. English Verb Accuracy of Bilingual Cantonese-English Preschoolers.

    PubMed

    Rezzonico, Stefano; Goldberg, Ahuva; Milburn, Trelani; Belletti, Adriana; Girolametto, Luigi

    2017-07-26

    Knowledge of verb development in typically developing bilingual preschoolers may inform clinicians about verb accuracy rates during the 1st 2 years of English instruction. This study aimed to investigate tensed verb accuracy in 2 assessment contexts in 4- and 5-year-old Cantonese-English bilingual preschoolers. The sample included 47 Cantonese-English bilinguals enrolled in English preschools. Half of the children were in their 1st 4 months of English language exposure, and half had completed 1 year and 4 months of exposure to English. Data were obtained from the Test of Early Grammatical Impairment (Rice & Wexler, 2001) and from a narrative generated in English. By the 2nd year of formal exposure to English, children in the present study approximated 33% accuracy of tensed verbs in a formal testing context versus 61% in a narrative context. The use of the English verb BE approximated mastery. Predictors of English third-person singular verb accuracy were task, grade, English expressive vocabulary, and lemma frequency. Verb tense accuracy was low across both groups, but a precocious mastery of BE was observed. The results of the present study suggest that speech-language pathologists may consider, in addition to an elicitation task, evaluating the use of verbs during narratives in bilingual Cantonese-English bilingual children.

  11. Unified English Braille in the United Kingdom: Part 1--Examination by Technical Expert Braille Users

    ERIC Educational Resources Information Center

    Cryer, Heather; Home, Sarah; Morley Wilkins, Sarah

    2013-01-01

    The Unified English Braille (UEB) code has already been adopted by various countries. To inform the decision about UK adoption, a suite of research was carried out with UK braille readers and other stakeholders. Previous research indicates that readers of technical braille codes may be most affected by a move to UEB. In this study, six technical…

  12. World Englishes and English-Using Communities.

    ERIC Educational Resources Information Center

    Kachru, Braj B.

    1997-01-01

    A review of literature since 1990 on world English focuses on theoretical, conceptual, descriptive, ideological, and power-related issues, including: types of diaspora; English-using communities; dynamics of those communities; monolingual paradigms and heteroglossic English forms; transcultural literary creativity; codification and authentication…

  13. Shared Book Reading and English Learners' Narrative Production and Comprehension

    ERIC Educational Resources Information Center

    Gámez, Perla B.; González, Dahlia; Urbin, LaNette M.

    2017-01-01

    This study examined the relation between exposure to shared book reading and Spanish-speaking English learners' (ELs'; n = 102) narrative production and comprehension skills in kindergarten (mean age = 6.12 years). Audio- and videotaped book-reading sessions in Spanish were coded in terms of teachers' extratextual talk and gestures. Using a silent…

  14. Web-Beagle: a web server for the alignment of RNA secondary structures.

    PubMed

    Mattei, Eugenio; Pietrosanto, Marco; Ferrè, Fabrizio; Helmer-Citterich, Manuela

    2015-07-01

    Web-Beagle (http://beagle.bio.uniroma2.it) is a web server for the pairwise global or local alignment of RNA secondary structures. The server exploits a new encoding for RNA secondary structure and a substitution matrix of RNA structural elements to perform RNA structural alignments. The web server allows the user to compute up to 10 000 alignments in a single run, taking as input sets of RNA sequences and structures or primary sequences alone. In the latter case, the server computes the secondary structure prediction for the RNAs on-the-fly using RNAfold (free energy minimization). The user can also compare a set of input RNAs to one of five pre-compiled RNA datasets including lncRNAs and 3' UTRs. All types of comparison produce in output the pairwise alignments along with structural similarity and statistical significance measures for each resulting alignment. A graphical color-coded representation of the alignments allows the user to easily identify structural similarities between RNAs. Web-Beagle can be used for finding structurally related regions in two or more RNAs, for the identification of homologous regions or for functional annotation. Benchmark tests show that Web-Beagle has lower computational complexity, running time and better performances than other available methods. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. Revisiting Code-Switching Practice in TESOL: A Critical Perspective

    ERIC Educational Resources Information Center

    Wang, Hao; Mansouri, Behzad

    2017-01-01

    In academic circles, the "English Only" view and "Balanced view" have established their grounds after volumes of work on the topic of code-switching in TESOL. With recent development in Critical Applied Linguistics, poststructural theory, postmodern theory, and the emergence of multilingualism, scholars have begun to view ELT…

  16. Triangular Alignment (TAME). A Tensor-based Approach for Higher-order Network Alignment

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

    Mohammadi, Shahin; Gleich, David F.; Kolda, Tamara G.

    2015-11-01

    Network alignment is an important tool with extensive applications in comparative interactomics. Traditional approaches aim to simultaneously maximize the number of conserved edges and the underlying similarity of aligned entities. We propose a novel formulation of the network alignment problem that extends topological similarity to higher-order structures and provide a new objective function that maximizes the number of aligned substructures. This objective function corresponds to an integer programming problem, which is NP-hard. Consequently, we approximate this objective function as a surrogate function whose maximization results in a tensor eigenvalue problem. Based on this formulation, we present an algorithm called Triangularmore » AlignMEnt (TAME), which attempts to maximize the number of aligned triangles across networks. We focus on alignment of triangles because of their enrichment in complex networks; however, our formulation and resulting algorithms can be applied to general motifs. Using a case study on the NAPABench dataset, we show that TAME is capable of producing alignments with up to 99% accuracy in terms of aligned nodes. We further evaluate our method by aligning yeast and human interactomes. Our results indicate that TAME outperforms the state-of-art alignment methods both in terms of biological and topological quality of the alignments.« less

  17. Ligand Binding Site Detection by Local Structure Alignment and Its Performance Complementarity

    PubMed Central

    Lee, Hui Sun; Im, Wonpil

    2013-01-01

    Accurate determination of potential ligand binding sites (BS) is a key step for protein function characterization and structure-based drug design. Despite promising results of template-based BS prediction methods using global structure alignment (GSA), there is a room to improve the performance by properly incorporating local structure alignment (LSA) because BS are local structures and often similar for proteins with dissimilar global folds. We present a template-based ligand BS prediction method using G-LoSA, our LSA tool. A large benchmark set validation shows that G-LoSA predicts drug-like ligands’ positions in single-chain protein targets more precisely than TM-align, a GSA-based method, while the overall success rate of TM-align is better. G-LoSA is particularly efficient for accurate detection of local structures conserved across proteins with diverse global topologies. Recognizing the performance complementarity of G-LoSA to TM-align and a non-template geometry-based method, fpocket, a robust consensus scoring method, CMCS-BSP (Complementary Methods and Consensus Scoring for ligand Binding Site Prediction), is developed and shows improvement on prediction accuracy. The G-LoSA source code is freely available at http://im.bioinformatics.ku.edu/GLoSA. PMID:23957286

  18. Multiple Marking of English Compositions: An Account of an Experiment.

    ERIC Educational Resources Information Center

    Britton, J. N.; And Others

    An experiment was conducted to find a better method of marking English composition than that which is in general use. The method tested was one in which each composition was assessed independently by three markers who judged the general impression of the writing, and by a fourth marker who applied a code of penalties for mechanical errors. Brief…

  19. Reconciliation of international administrative coding systems for comparison of colorectal surgery outcome.

    PubMed

    Munasinghe, A; Chang, D; Mamidanna, R; Middleton, S; Joy, M; Penninckx, F; Darzi, A; Livingston, E; Faiz, O

    2014-07-01

    Significant variation in colorectal surgery outcomes exists between different countries. Better understanding of the sources of variable outcomes using administrative data requires alignment of differing clinical coding systems. We aimed to map similar diagnoses and procedures across administrative coding systems used in different countries. Administrative data were collected in a central database as part of the Global Comparators (GC) Project. In order to unify these data, a systematic translation of diagnostic and procedural codes was undertaken. Codes for colorectal diagnoses, resections, operative complications and reoperative interventions were mapped across the respective national healthcare administrative coding systems. Discharge data from January 2006 to June 2011 for patients who had undergone colorectal surgical resections were analysed to generate risk-adjusted models for mortality, length of stay, readmissions and reoperations. In all, 52 544 case records were collated from 31 institutions in five countries. Mapping of all the coding systems was achieved so that diagnosis and procedures from the participant countries could be compared. Using the aligned coding systems to develop risk-adjusted models, the 30-day mortality rate for colorectal surgery was 3.95% (95% CI 0.86-7.54), the 30-day readmission rate was 11.05% (5.67-17.61), the 28-day reoperation rate was 6.13% (3.68-9.66) and the mean length of stay was 14 (7.65-46.76) days. The linkage of international hospital administrative data that we developed enabled comparison of documented surgical outcomes between countries. This methodology may facilitate international benchmarking. Colorectal Disease © 2014 The Association of Coloproctology of Great Britain and Ireland.

  20. Reconsidering English Grammar Teaching for Improving Non-English Majors' English Writing Ability

    ERIC Educational Resources Information Center

    Shen, Yuru

    2012-01-01

    With the globalization of world economy, English learners' writing ability has been attached less and less importance. As a result, many college students in China, especially the non-English majors, cannot express themselves effectively in written English. They make various kinds of mistakes, mostly grammar mistakes, such as writing sentence…

  1. Basic English Writers' Japanese-English Wordbook.

    ERIC Educational Resources Information Center

    Daniels, F. J.

    The author of this Japanese-English wordbook suggests that it may be used by Japanese writers of English, by those translating from Japanese into English, and by learners of Japanese, in addition to its main intended uses as an aid to the preparation of teaching material and as a work of reference for teachers. A translator will need to supplement…

  2. Stepwise detection of recombination breakpoints in sequence alignments.

    PubMed

    Graham, Jinko; McNeney, Brad; Seillier-Moiseiwitsch, Françoise

    2005-03-01

    We propose a stepwise approach to identify recombination breakpoints in a sequence alignment. The approach can be applied to any recombination detection method that uses a permutation test and provides estimates of breakpoints. We illustrate the approach by analyses of a simulated dataset and alignments of real data from HIV-1 and human chromosome 7. The presented simulation results compare the statistical properties of one-step and two-step procedures. More breakpoints are found with a two-step procedure than with a single application of a given method, particularly for higher recombination rates. At higher recombination rates, the additional breakpoints were located at the cost of only a slight increase in the number of falsely declared breakpoints. However, a large proportion of breakpoints still go undetected. A makefile and C source code for phylogenetic profiling and the maximum chi2 method, tested with the gcc compiler on Linux and WindowsXP, are available at http://stat-db.stat.sfu.ca/stepwise/ jgraham@stat.sfu.ca.

  3. Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments

    DOE PAGES

    Daily, Jeffrey A.

    2016-02-10

    Sequence alignment algorithms are a key component of many bioinformatics applications. Though various fast Smith-Waterman local sequence alignment implementations have been developed for x86 CPUs, most are embedded into larger database search tools. In addition, fast implementations of Needleman-Wunsch global sequence alignment and its semi-global variants are not as widespread. This article presents the first software library for local, global, and semi-global pairwise intra-sequence alignments and improves the performance of previous intra-sequence implementations. As a result, a faster intra-sequence pairwise alignment implementation is described and benchmarked. Using a 375 residue query sequence a speed of 136 billion cell updates permore » second (GCUPS) was achieved on a dual Intel Xeon E5-2670 12-core processor system, the highest reported for an implementation based on Farrar’s ’striped’ approach. When using only a single thread, parasail was 1.7 times faster than Rognes’s SWIPE. For many score matrices, parasail is faster than BLAST. The software library is designed for 64 bit Linux, OS X, or Windows on processors with SSE2, SSE41, or AVX2. Source code is available from https://github.com/jeffdaily/parasail under the Battelle BSD-style license. In conclusion, applications that require optimal alignment scores could benefit from the improved performance. For the first time, SIMD global, semi-global, and local alignments are available in a stand-alone C library.« less

  4. Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments

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

    Daily, Jeffrey A.

    Sequence alignment algorithms are a key component of many bioinformatics applications. Though various fast Smith-Waterman local sequence alignment implementations have been developed for x86 CPUs, most are embedded into larger database search tools. In addition, fast implementations of Needleman-Wunsch global sequence alignment and its semi-global variants are not as widespread. This article presents the first software library for local, global, and semi-global pairwise intra-sequence alignments and improves the performance of previous intra-sequence implementations. As a result, a faster intra-sequence pairwise alignment implementation is described and benchmarked. Using a 375 residue query sequence a speed of 136 billion cell updates permore » second (GCUPS) was achieved on a dual Intel Xeon E5-2670 12-core processor system, the highest reported for an implementation based on Farrar’s ’striped’ approach. When using only a single thread, parasail was 1.7 times faster than Rognes’s SWIPE. For many score matrices, parasail is faster than BLAST. The software library is designed for 64 bit Linux, OS X, or Windows on processors with SSE2, SSE41, or AVX2. Source code is available from https://github.com/jeffdaily/parasail under the Battelle BSD-style license. In conclusion, applications that require optimal alignment scores could benefit from the improved performance. For the first time, SIMD global, semi-global, and local alignments are available in a stand-alone C library.« less

  5. Teachers' Perceptions of the Implementation of the Literacy Common Core State Standards for English Language Learners and Students with Disabilities

    ERIC Educational Resources Information Center

    Murphy, Audrey Figueroa; Haller, Elizabeth

    2015-01-01

    This qualitative study explored the experiences of U.S. teachers of English language learners (ELLs) and students with disabilities (SWDs) as they sought to align the new Common Core State Standards (CCSS) with previously used standards and instructional approaches during the first year of CCSS implementation. Open-ended interviews were conducted…

  6. Effects of a Treatment Package to Facilitate English/Language Arts Learning for Middle School Students with Moderate to Severe Disabilities

    ERIC Educational Resources Information Center

    Mims, Pamela J.; Lee, Angel; Browder, Diane M.; Zakas, Tracie-Lynn; Flynn, Susan

    2012-01-01

    This pilot study sought to develop and evaluate the use of a treatment package that included systematic and direct instruction on acquisition of literacy skills aligned with middle school English/Language Arts standards for students with moderate to severe disabilities, including autism. Participants included five teachers and 15 middle school…

  7. Code Switching among Bilingual and Limited English Proficient Students: Possible Indicators of Giftedness

    ERIC Educational Resources Information Center

    Hughes, Claire E.; Shaunessy, Elizabeth S.; Brice, Alejandro R.; Ratliff, Mary Anne; McHatton, Patricia Alvarez

    2006-01-01

    Code switching includes the use of complete sentences, phrases, and borrowed words from another language (Brice & Brice, 2000). It is a common linguistic phenomenon noted among bilingual populations. In order to code switch effectively, students must possess a high level of understanding of the 2 cultures, as well as a deep understanding of the…

  8. The dependence of frequency distributions on multiple meanings of words, codes and signs

    NASA Astrophysics Data System (ADS)

    Yan, Xiaoyong; Minnhagen, Petter

    2018-01-01

    The dependence of the frequency distributions due to multiple meanings of words in a text is investigated by deleting letters. By coding the words with fewer letters the number of meanings per coded word increases. This increase is measured and used as an input in a predictive theory. For a text written in English, the word-frequency distribution is broad and fat-tailed, whereas if the words are only represented by their first letter the distribution becomes exponential. Both distribution are well predicted by the theory, as is the whole sequence obtained by consecutively representing the words by the first L = 6 , 5 , 4 , 3 , 2 , 1 letters. Comparisons of texts written by Chinese characters and the same texts written by letter-codes are made and the similarity of the corresponding frequency-distributions are interpreted as a consequence of the multiple meanings of Chinese characters. This further implies that the difference of the shape for word-frequencies for an English text written by letters and a Chinese text written by Chinese characters is due to the coding and not to the language per se.

  9. Teaching English through English: Proficiency, Pedagogy and Performance

    ERIC Educational Resources Information Center

    Richards, Jack C.

    2017-01-01

    Most of the world's English language teachers speak English as a second or third language rather than as their first language. For many, their level of proficiency in English may not reach benchmarks established by their employers, raising the issue that is the focus of this article, namely, what kind of proficiency in English is necessary to be…

  10. Orientation to Language Code and Actions in Group Work

    ERIC Educational Resources Information Center

    Aline, David; Hosoda, Yuri

    2009-01-01

    This conversation analytic study reveals how learners themselves, as speakers and listeners, demonstrate their own orientation to language code and actions on a moment by moment basis during collaborative tasks in English as a foreign language classrooms. The excerpts presented in this article were drawn from 23 hours of audio- and video-recorded…

  11. Pre-service teachers' experiences teaching secondary mathematics in English-medium schools in Tanzania

    NASA Astrophysics Data System (ADS)

    Kasmer, Lisa

    2013-09-01

    In order to promote mathematical understanding among English Language Learners (ELLs), it is necessary to modify instructional strategies to effectively communicate mathematical content. This paper discusses the instructional strategies used by four pre-service teachers to teach mathematics to secondary students in English-medium schools in Arusha, Tanzania as a result of the tensions they faced and reflections on their teaching. Strategies such as code switching, attending to sentence structure, non-linguistic representations, and placing the content within a familiar context proved to be beneficial strategies for conveying mathematical ideas.

  12. All-optical OFDM network coding scheme for all-optical virtual private communication in PON

    NASA Astrophysics Data System (ADS)

    Li, Lijun; Gu, Rentao; Ji, Yuefeng; Bai, Lin; Huang, Zhitong

    2014-03-01

    A novel optical orthogonal frequency division multiplexing (OFDM) network coding scheme is proposed over passive optical network (PON) system. The proposed scheme for all-optical virtual private network (VPN) does not only improve transmission efficiency, but also realize full-duplex communication mode in a single fiber. Compared with the traditional all-optical VPN architectures, the all-optical OFDM network coding scheme can support higher speed, more flexible bandwidth allocation, and higher spectrum efficiency. In order to reduce the difficulty of alignment for encoding operation between inter-communication traffic, the width of OFDM subcarrier pulse is stretched in our proposed scheme. The feasibility of all-optical OFDM network coding scheme for VPN is verified, and the relevant simulation results show that the full-duplex inter-communication traffic stream can be transmitted successfully. Furthermore, the tolerance of misalignment existing in inter-ONUs traffic is investigated and analyzed for all-optical encoding operation, and the difficulty of pulse alignment is proved to be lower.

  13. Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign

    PubMed Central

    2007-01-01

    Background Joint alignment and secondary structure prediction of two RNA sequences can significantly improve the accuracy of the structural predictions. Methods addressing this problem, however, are forced to employ constraints that reduce computation by restricting the alignments and/or structures (i.e. folds) that are permissible. In this paper, a new methodology is presented for the purpose of establishing alignment constraints based on nucleotide alignment and insertion posterior probabilities. Using a hidden Markov model, posterior probabilities of alignment and insertion are computed for all possible pairings of nucleotide positions from the two sequences. These alignment and insertion posterior probabilities are additively combined to obtain probabilities of co-incidence for nucleotide position pairs. A suitable alignment constraint is obtained by thresholding the co-incidence probabilities. The constraint is integrated with Dynalign, a free energy minimization algorithm for joint alignment and secondary structure prediction. The resulting method is benchmarked against the previous version of Dynalign and against other programs for pairwise RNA structure prediction. Results The proposed technique eliminates manual parameter selection in Dynalign and provides significant computational time savings in comparison to prior constraints in Dynalign while simultaneously providing a small improvement in the structural prediction accuracy. Savings are also realized in memory. In experiments over a 5S RNA dataset with average sequence length of approximately 120 nucleotides, the method reduces computation by a factor of 2. The method performs favorably in comparison to other programs for pairwise RNA structure prediction: yielding better accuracy, on average, and requiring significantly lesser computational resources. Conclusion Probabilistic analysis can be utilized in order to automate the determination of alignment constraints for pairwise RNA structure prediction

  14. PIPI: PTM-Invariant Peptide Identification Using Coding Method.

    PubMed

    Yu, Fengchao; Li, Ning; Yu, Weichuan

    2016-12-02

    In computational proteomics, the identification of peptides with an unlimited number of post-translational modification (PTM) types is a challenging task. The computational cost associated with database search increases exponentially with respect to the number of modified amino acids and linearly with respect to the number of potential PTM types at each amino acid. The problem becomes intractable very quickly if we want to enumerate all possible PTM patterns. To address this issue, one group of methods named restricted tools (including Mascot, Comet, and MS-GF+) only allow a small number of PTM types in database search process. Alternatively, the other group of methods named unrestricted tools (including MS-Alignment, ProteinProspector, and MODa) avoids enumerating PTM patterns with an alignment-based approach to localizing and characterizing modified amino acids. However, because of the large search space and PTM localization issue, the sensitivity of these unrestricted tools is low. This paper proposes a novel method named PIPI to achieve PTM-invariant peptide identification. PIPI belongs to the category of unrestricted tools. It first codes peptide sequences into Boolean vectors and codes experimental spectra into real-valued vectors. For each coded spectrum, it then searches the coded sequence database to find the top scored peptide sequences as candidates. After that, PIPI uses dynamic programming to localize and characterize modified amino acids in each candidate. We used simulation experiments and real data experiments to evaluate the performance in comparison with restricted tools (i.e., Mascot, Comet, and MS-GF+) and unrestricted tools (i.e., Mascot with error tolerant search, MS-Alignment, ProteinProspector, and MODa). Comparison with restricted tools shows that PIPI has a close sensitivity and running speed. Comparison with unrestricted tools shows that PIPI has the highest sensitivity except for Mascot with error tolerant search and Protein

  15. Cross-language Activation and the Phonetics of Code-switching

    NASA Astrophysics Data System (ADS)

    Piccinini, Page Elizabeth

    It is now well established that bilinguals have both languages activated to some degree at all times. This cross-language activation has been documented in several research paradigms, including picture naming, reading, and electrophysiological studies. What is less well understood is how the degree a language is activated can vary in different language environments or contexts. Furthermore, when investigating effects of order of acquisition and language dominance, past research has been mixed, as the two variables are often conflated. In this dissertation, I test how degree of cross-language activation can vary according to context by examining phonetic productions in code-switching speech. Both spontaneous speech and scripted speech are analyzed. Follow-up perception experiments are conducted to see if listeners are able to anticipate language switches, potentially due to the phonetic cues in the signal. Additionally, by focusing on early bilinguals who are L1 Spanish but English dominant, I am able to see what plays a greater role in cross-language activation, order of acquisition or language dominance. I find that speakers do have intermediate phonetic productions in code-switching contexts relative to monolingual contexts. Effects are larger and more consistent in English than Spanish. Similar effects are found in speech perception. Listeners are able to anticipate language switches from English to Spanish but not Spanish to English. Together these results suggest that language dominance is a more important factor than order of acquisition in cross-language activation for early bilinguals. Future models on bilingual language organization and access should take into account both context and language dominance when modeling degrees of cross-language activation.

  16. SeqLib: a C ++ API for rapid BAM manipulation, sequence alignment and sequence assembly

    PubMed Central

    Wala, Jeremiah; Beroukhim, Rameen

    2017-01-01

    Abstract We present SeqLib, a C ++ API and command line tool that provides a rapid and user-friendly interface to BAM/SAM/CRAM files, global sequence alignment operations and sequence assembly. Four C libraries perform core operations in SeqLib: HTSlib for BAM access, BWA-MEM and BLAT for sequence alignment and Fermi for error correction and sequence assembly. Benchmarking indicates that SeqLib has lower CPU and memory requirements than leading C ++ sequence analysis APIs. We demonstrate an example of how minimal SeqLib code can extract, error-correct and assemble reads from a CRAM file and then align with BWA-MEM. SeqLib also provides additional capabilities, including chromosome-aware interval queries and read plotting. Command line tools are available for performing integrated error correction, micro-assemblies and alignment. Availability and Implementation: SeqLib is available on Linux and OSX for the C ++98 standard and later at github.com/walaj/SeqLib. SeqLib is released under the Apache2 license. Additional capabilities for BLAT alignment are available under the BLAT license. Contact: jwala@broadinstitue.org; rameen@broadinstitute.org PMID:28011768

  17. CHROMA: consensus-based colouring of multiple alignments for publication.

    PubMed

    Goodstadt, L; Ponting, C P

    2001-09-01

    CHROMA annotates multiple protein sequence alignments by consensus to produce formatted and coloured text suitable for incorporation into other documents for publication. The package is designed to be flexible and reliable, and has a simple-to-use graphical user interface running under Microsoft Windows. Both the executables and source code for CHROMA running under Windows and Linux (portable command-line only) are freely available at http://www.lg.ndirect.co.uk/chroma. Software enquiries should be directed to CHROMA@lg.ndirect.co.uk.

  18. Using Quasi-Horizontal Alignment in the absence of the actual alignment.

    PubMed

    Banihashemi, Mohamadreza

    2016-10-01

    Horizontal alignment is a major roadway characteristic used in safety and operational evaluations of many facility types. The Highway Safety Manual (HSM) uses this characteristic in crash prediction models for rural two-lane highways, freeway segments, and freeway ramps/C-D roads. Traffic simulation models use this characteristic in their processes on almost all types of facilities. However, a good portion of roadway databases do not include horizontal alignment data; instead, many contain point coordinate data along the roadways. SHRP 2 Roadway Information Database (RID) is a good example of this type of data. Only about 5% of this geodatabase contains alignment information and for the rest, point data can easily be produced. Even though the point data can be used to extract actual horizontal alignment data but, extracting horizontal alignment is a cumbersome and costly process, especially for a database of miles and miles of highways. This research introduces a so called "Quasi-Horizontal Alignment" that can be produced easily and automatically from point coordinate data and can be used in the safety and operational evaluations of highways. SHRP 2 RID for rural two-lane highways in Washington State is used in this study. This paper presents a process through which Quasi-Horizontal Alignments are produced from point coordinates along highways by using spreadsheet software such as MS EXCEL. It is shown that the safety and operational evaluations of the highways with Quasi-Horizontal Alignments are almost identical to the ones with the actual alignments. In the absence of actual alignment the Quasi-Horizontal Alignment can easily be produced from any type of databases that contain highway coordinates such geodatabases and digital maps. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. pyPaSWAS: Python-based multi-core CPU and GPU sequence alignment.

    PubMed

    Warris, Sven; Timal, N Roshan N; Kempenaar, Marcel; Poortinga, Arne M; van de Geest, Henri; Varbanescu, Ana L; Nap, Jan-Peter

    2018-01-01

    Our previously published CUDA-only application PaSWAS for Smith-Waterman (SW) sequence alignment of any type of sequence on NVIDIA-based GPUs is platform-specific and therefore adopted less than could be. The OpenCL language is supported more widely and allows use on a variety of hardware platforms. Moreover, there is a need to promote the adoption of parallel computing in bioinformatics by making its use and extension more simple through more and better application of high-level languages commonly used in bioinformatics, such as Python. The novel application pyPaSWAS presents the parallel SW sequence alignment code fully packed in Python. It is a generic SW implementation running on several hardware platforms with multi-core systems and/or GPUs that provides accurate sequence alignments that also can be inspected for alignment details. Additionally, pyPaSWAS support the affine gap penalty. Python libraries are used for automated system configuration, I/O and logging. This way, the Python environment will stimulate further extension and use of pyPaSWAS. pyPaSWAS presents an easy Python-based environment for accurate and retrievable parallel SW sequence alignments on GPUs and multi-core systems. The strategy of integrating Python with high-performance parallel compute languages to create a developer- and user-friendly environment should be considered for other computationally intensive bioinformatics algorithms.

  20. English Vocabulary Instruction in Six Early Childhood Classrooms in Hong Kong

    ERIC Educational Resources Information Center

    Lau, Carrie; Rao, Nirmala

    2013-01-01

    Vocabulary instruction during English language learning was observed for one week in six classrooms (three K2 classes for four-year olds and three K3 classes for five-year olds) from three kindergartens in two districts of Hong Kong. From 23 sessions of observations and 535 minutes of data, field notes were coded to identify instances of…

  1. The best bits in an iris code.

    PubMed

    Hollingsworth, Karen P; Bowyer, Kevin W; Flynn, Patrick J

    2009-06-01

    Iris biometric systems apply filters to iris images to extract information about iris texture. Daugman's approach maps the filter output to a binary iris code. The fractional Hamming distance between two iris codes is computed and decisions about the identity of a person are based on the computed distance. The fractional Hamming distance weights all bits in an iris code equally. However, not all the bits in an iris code are equally useful. Our research is the first to present experiments documenting that some bits are more consistent than others. Different regions of the iris are compared to evaluate their relative consistency, and contrary to some previous research, we find that the middle bands of the iris are more consistent than the inner bands. The inconsistent-bit phenomenon is evident across genders and different filter types. Possible causes of inconsistencies, such as segmentation, alignment issues, and different filters are investigated. The inconsistencies are largely due to the coarse quantization of the phase response. Masking iris code bits corresponding to complex filter responses near the axes of the complex plane improves the separation between the match and nonmatch Hamming distance distributions.

  2. Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments.

    PubMed

    Daily, Jeff

    2016-02-10

    Sequence alignment algorithms are a key component of many bioinformatics applications. Though various fast Smith-Waterman local sequence alignment implementations have been developed for x86 CPUs, most are embedded into larger database search tools. In addition, fast implementations of Needleman-Wunsch global sequence alignment and its semi-global variants are not as widespread. This article presents the first software library for local, global, and semi-global pairwise intra-sequence alignments and improves the performance of previous intra-sequence implementations. A faster intra-sequence local pairwise alignment implementation is described and benchmarked, including new global and semi-global variants. Using a 375 residue query sequence a speed of 136 billion cell updates per second (GCUPS) was achieved on a dual Intel Xeon E5-2670 24-core processor system, the highest reported for an implementation based on Farrar's 'striped' approach. Rognes's SWIPE optimal database search application is still generally the fastest available at 1.2 to at best 2.4 times faster than Parasail for sequences shorter than 500 amino acids. However, Parasail was faster for longer sequences. For global alignments, Parasail's prefix scan implementation is generally the fastest, faster even than Farrar's 'striped' approach, however the opal library is faster for single-threaded applications. The software library is designed for 64 bit Linux, OS X, or Windows on processors with SSE2, SSE41, or AVX2. Source code is available from https://github.com/jeffdaily/parasail under the Battelle BSD-style license. Applications that require optimal alignment scores could benefit from the improved performance. For the first time, SIMD global, semi-global, and local alignments are available in a stand-alone C library.

  3. Improving the coding and classification of ambulance data through the application of International Classification of Disease 10th revision.

    PubMed

    Cantwell, Kate; Morgans, Amee; Smith, Karen; Livingston, Michael; Dietze, Paul

    2014-02-01

    This paper aims to examine whether an adaptation of the International Classification of Disease (ICD) coding system can be applied retrospectively to final paramedic assessment data in an ambulance dataset with a view to developing more fine-grained, clinically relevant case definitions than are available through point-of-call data. Over 1.2 million case records were extracted from the Ambulance Victoria data warehouse. Data fields included dispatch code, cause (CN) and final primary assessment (FPA). Each FPA was converted to an ICD-10-AM code using word matching or best fit. ICD-10-AM codes were then converted into Major Diagnostic Categories (MDC). CN was aligned with the ICD-10-AM codes for external cause of morbidity and mortality. The most accurate results were obtained when ICD-10-AM codes were assigned using information from both FPA and CN. Comparison of cases coded as unconscious at point-of-call with the associated paramedic assessment highlighted the extra clinical detail obtained when paramedic assessment data are used. Ambulance paramedic assessment data can be aligned with ICD-10-AM and MDC with relative ease, allowing retrospective coding of large datasets. Coding of ambulance data using ICD-10-AM allows for comparison of not only ambulance service users but also with other population groups. WHAT IS KNOWN ABOUT THE TOPIC? There is no reliable and standard coding and categorising system for paramedic assessment data contained in ambulance service databases. WHAT DOES THIS PAPER ADD? This study demonstrates that ambulance paramedic assessment data can be aligned with ICD-10-AM and MDC with relative ease, allowing retrospective coding of large datasets. Representation of ambulance case types using ICD-10-AM-coded information obtained after paramedic assessment is more fine grained and clinically relevant than point-of-call data, which uses caller information before ambulance attendance. WHAT ARE THE IMPLICATIONS FOR PRACTITIONERS? This paper describes

  4. English Learners: Reaching the Highest Level of English Literacy.

    ERIC Educational Resources Information Center

    Garcia, Gilbert C., Ed.

    This collection of papers examines the critical literacy development of English learners, focusing on English reading instruction in an immersion setting, English language development, and cultural issues pertaining to English learners in and out of the classroom. The 16 papers include the following: (1) "Reading and the Bilingual Student: Fact…

  5. Increased alignment sensitivity improves the usage of genome alignments for comparative gene annotation.

    PubMed

    Sharma, Virag; Hiller, Michael

    2017-08-21

    Genome alignments provide a powerful basis to transfer gene annotations from a well-annotated reference genome to many other aligned genomes. The completeness of these annotations crucially depends on the sensitivity of the underlying genome alignment. Here, we investigated the impact of the genome alignment parameters and found that parameters with a higher sensitivity allow the detection of thousands of novel alignments between orthologous exons that have been missed before. In particular, comparisons between species separated by an evolutionary distance of >0.75 substitutions per neutral site, like human and other non-placental vertebrates, benefit from increased sensitivity. To systematically test if increased sensitivity improves comparative gene annotations, we built a multiple alignment of 144 vertebrate genomes and used this alignment to map human genes to the other 143 vertebrates with CESAR. We found that higher alignment sensitivity substantially improves the completeness of comparative gene annotations by adding on average 2382 and 7440 novel exons and 117 and 317 novel genes for mammalian and non-mammalian species, respectively. Our results suggest a more sensitive alignment strategy that should generally be used for genome alignments between distantly-related species. Our 144-vertebrate genome alignment and the comparative gene annotations (https://bds.mpi-cbg.de/hillerlab/144VertebrateAlignment_CESAR/) are a valuable resource for comparative genomics. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. English(es) in Urban Contexts: Politics, Pluralism, and Possibilities

    ERIC Educational Resources Information Center

    Kirkland, David E.

    2010-01-01

    English as taught in city schools does not always reflect the Englishes city students travel with. Their urban English landscape is enriched by a procession of many voices that march in various directions in, around, and through the monuments of the city. These languages--Englishes, in this case--which have been traded on through various public…

  7. Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer.

    PubMed

    Bromberg, Raquel; Grishin, Nick V; Otwinowski, Zbyszek

    2016-06-01

    Advances in sequencing have generated a large number of complete genomes. Traditionally, phylogenetic analysis relies on alignments of orthologs, but defining orthologs and separating them from paralogs is a complex task that may not always be suited to the large datasets of the future. An alternative to traditional, alignment-based approaches are whole-genome, alignment-free methods. These methods are scalable and require minimal manual intervention. We developed SlopeTree, a new alignment-free method that estimates evolutionary distances by measuring the decay of exact substring matches as a function of match length. SlopeTree corrects for horizontal gene transfer, for composition variation and low complexity sequences, and for branch-length nonlinearity caused by multiple mutations at the same site. We tested SlopeTree on 495 bacteria, 73 archaea, and 72 strains of Escherichia coli and Shigella. We compared our trees to the NCBI taxonomy, to trees based on concatenated alignments, and to trees produced by other alignment-free methods. The results were consistent with current knowledge about prokaryotic evolution. We assessed differences in tree topology over different methods and settings and found that the majority of bacteria and archaea have a core set of proteins that evolves by descent. In trees built from complete genomes rather than sets of core genes, we observed some grouping by phenotype rather than phylogeny, for instance with a cluster of sulfur-reducing thermophilic bacteria coming together irrespective of their phyla. The source-code for SlopeTree is available at: http://prodata.swmed.edu/download/pub/slopetree_v1/slopetree.tar.gz.

  8. Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer

    PubMed Central

    Grishin, Nick V.; Otwinowski, Zbyszek

    2016-01-01

    Advances in sequencing have generated a large number of complete genomes. Traditionally, phylogenetic analysis relies on alignments of orthologs, but defining orthologs and separating them from paralogs is a complex task that may not always be suited to the large datasets of the future. An alternative to traditional, alignment-based approaches are whole-genome, alignment-free methods. These methods are scalable and require minimal manual intervention. We developed SlopeTree, a new alignment-free method that estimates evolutionary distances by measuring the decay of exact substring matches as a function of match length. SlopeTree corrects for horizontal gene transfer, for composition variation and low complexity sequences, and for branch-length nonlinearity caused by multiple mutations at the same site. We tested SlopeTree on 495 bacteria, 73 archaea, and 72 strains of Escherichia coli and Shigella. We compared our trees to the NCBI taxonomy, to trees based on concatenated alignments, and to trees produced by other alignment-free methods. The results were consistent with current knowledge about prokaryotic evolution. We assessed differences in tree topology over different methods and settings and found that the majority of bacteria and archaea have a core set of proteins that evolves by descent. In trees built from complete genomes rather than sets of core genes, we observed some grouping by phenotype rather than phylogeny, for instance with a cluster of sulfur-reducing thermophilic bacteria coming together irrespective of their phyla. The source-code for SlopeTree is available at: http://prodata.swmed.edu/download/pub/slopetree_v1/slopetree.tar.gz. PMID:27336403

  9. Arabic Natural Language Processing System Code Library

    DTIC Science & Technology

    2014-06-01

    Code Compilation 2 4. Training Instructions 2 5. Applying the System to New Examples 2 6. License 3 7. History 3 8. Important Note 4 9. Papers to...a slightly different English dependency scheme and contained a variety of improvements. However, the PropBank-style SRL module was not maintained...than those in the http://sourceforge.net/projects/miacp/ release.) 8. Important Note This release contains a variety of bug fixes and other generally

  10. Discourse Matrix in Filipino-English Code-Switching: Students' Attitudes and Feelings

    ERIC Educational Resources Information Center

    dela Rosa, Rona

    2016-01-01

    Undeniably, one language may be considered more valuable than other languages. Hence, most bilingual communities suffer from language imbalances. The present study attempts to identify the factors of code-switching during classroom presentations. Its functions were identified through analysing conversational contexts in which it occurs. Through…

  11. How Teachers of English in South African Schools Recognise Their Change Agency

    ERIC Educational Resources Information Center

    Pillay, Ansurie

    2017-01-01

    The South African Council for Educators' Code of Professional Ethics requires teachers to help learners develop values consistent with the fundamental rights contained in the Constitution of South Africa. To engage with such rights, teachers need to have the agency to develop such values, and this article explores how teachers of English in South…

  12. Development of Code-Switching: A Case Study on a Turkish/English/Arabic Multilingual Child

    ERIC Educational Resources Information Center

    Tunaz, Mehmet

    2016-01-01

    The purpose of this research was to investigate the early code switching patterns of a simultaneous multilingual subject (Aris) in accordance with Muysken's (2000) code switching typology: insertion and alternation. Firstly, the records of naturalistic spontaneous conversations were obtained from the parents via e-mail, phone calls and…

  13. Semantic Integration and Age of Acquisition Effects in Code-Blend Comprehension

    ERIC Educational Resources Information Center

    Giezen, Marcel R.; Emmorey, Karen

    2016-01-01

    Semantic and lexical decision tasks were used to investigate the mechanisms underlying code-blend facilitation: the finding that hearing bimodal bilinguals comprehend signs in American Sign Language (ASL) and spoken English words more quickly when they are presented together simultaneously than when each is presented alone. More robust…

  14. Aligning for Innovation - Alignment Strategy to Drive Innovation

    NASA Technical Reports Server (NTRS)

    Johnson, Hurel; Teltschik, David; Bussey, Horace, Jr.; Moy, James

    2010-01-01

    With the sudden need for innovation that will help the country achieve its long-term space exploration objectives, the question of whether NASA is aligned effectively to drive the innovation that it so desperately needs to take space exploration to the next level should be entertained. Authors such as Robert Kaplan and David North have noted that companies that use a formal system for implementing strategy consistently outperform their peers. They have outlined a six-stage management systems model for implementing strategy, which includes the aligning of the organization towards its objectives. This involves the alignment of the organization from the top down. This presentation will explore the impacts of existing U.S. industrial policy on technological innovation; assess the current NASA organizational alignment and its impacts on driving technological innovation; and finally suggest an alternative approach that may drive the innovation needed to take the world to the next level of space exploration, with NASA truly leading the way.

  15. Learning Strategies in Alleviating English Writing Anxiety for English Language Learners (ELLs) with Limited English Proficiency (LEP)

    ERIC Educational Resources Information Center

    Wu, Chia-Pei; Lin, Huey-Ju

    2016-01-01

    This study utilized the Oxford Strategy Inventory for Language Learning (SILL) and an English writing anxiety scale to examine the relationship between learning strategies and English writing anxiety in 102 university-level English language learners (ELLs) with Limited English Proficiency (LEP) in a university in Taiwan. Kruskal Wallis Test…

  16. English in the Workplace: McDonald's Executive English.

    ERIC Educational Resources Information Center

    Pagurek, Joyce; Fitzgerald, Brigid

    The McDonald's Executive English Course was developed by Carleton University's Centre for Applied Language Studies in response to a francophone supervisor's request. As a basis for course development, information was gathered on English language use on the job, the level of English proficiency needed, and the personalities, backgrounds, and goals…

  17. SeqLib: a C ++ API for rapid BAM manipulation, sequence alignment and sequence assembly.

    PubMed

    Wala, Jeremiah; Beroukhim, Rameen

    2017-03-01

    We present SeqLib, a C ++ API and command line tool that provides a rapid and user-friendly interface to BAM/SAM/CRAM files, global sequence alignment operations and sequence assembly. Four C libraries perform core operations in SeqLib: HTSlib for BAM access, BWA-MEM and BLAT for sequence alignment and Fermi for error correction and sequence assembly. Benchmarking indicates that SeqLib has lower CPU and memory requirements than leading C ++ sequence analysis APIs. We demonstrate an example of how minimal SeqLib code can extract, error-correct and assemble reads from a CRAM file and then align with BWA-MEM. SeqLib also provides additional capabilities, including chromosome-aware interval queries and read plotting. Command line tools are available for performing integrated error correction, micro-assemblies and alignment. SeqLib is available on Linux and OSX for the C ++98 standard and later at github.com/walaj/SeqLib. SeqLib is released under the Apache2 license. Additional capabilities for BLAT alignment are available under the BLAT license. jwala@broadinstitue.org ; rameen@broadinstitute.org. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  18. Code-Switching and Vernacular Support: An Early Middle English Case Study

    ERIC Educational Resources Information Center

    Skaffari, Janne

    2016-01-01

    In the multilingual history of England, the period following the Norman Conquest in 1066 is a particularly intriguing phase, but its code-switching patterns have so far received little attention. The present article describes and analyses the multilingual practices evinced in London, British Library, MS Stowe 34, containing one instructional prose…

  19. Bahasa Gado-Gado in Indonesian Popular Texts: Expanding Indonesian Identities through Code-Switching with English

    ERIC Educational Resources Information Center

    Martin, Nelly

    2017-01-01

    This study explores the relationship between language selection and identity construction in contemporary Indonesia through an examination of the function of English, a language that still receives stigma from many Indonesians and the government, particularly in Indonesian popular texts published after 1998. Utilizing hybrid critical approaches…

  20. ENGLISH FOR TODAY. BOOK SIX, LITERATURE IN ENGLISH.

    ERIC Educational Resources Information Center

    SLAGER, WILLIAM R.; AND OTHERS

    THE SIXTH AND LAST VOLUME IN THE "ENGLISH FOR TODAY" SERIES, "LITERATURE IN ENGLISH" PRESENTS A WIDE RANGE OF WELL-KNOWN CONTEMPORARY WRITERS FROM THE ENGLISH-SPEAKING WORLD--ENGLAND, THE UNITED STATES, AUSTRALIA, CANADA, INDIA, IRELAND, AND SCOTLAND. THE SELECTIONS INCLUDE--(I) SHORT STORIES BY SAKI, CALLAGHAN, O'CONNOR, HEMINGWAY, JOYCE,…

  1. Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic.

    PubMed

    Brown, Peter; Pullan, Wayne; Yang, Yuedong; Zhou, Yaoqi

    2016-02-01

    The three dimensional tertiary structure of a protein at near atomic level resolution provides insight alluding to its function and evolution. As protein structure decides its functionality, similarity in structure usually implies similarity in function. As such, structure alignment techniques are often useful in the classifications of protein function. Given the rapidly growing rate of new, experimentally determined structures being made available from repositories such as the Protein Data Bank, fast and accurate computational structure comparison tools are required. This paper presents SPalignNS, a non-sequential protein structure alignment tool using a novel asymmetrical greedy search technique. The performance of SPalignNS was evaluated against existing sequential and non-sequential structure alignment methods by performing trials with commonly used datasets. These benchmark datasets used to gauge alignment accuracy include (i) 9538 pairwise alignments implied by the HOMSTRAD database of homologous proteins; (ii) a subset of 64 difficult alignments from set (i) that have low structure similarity; (iii) 199 pairwise alignments of proteins with similar structure but different topology; and (iv) a subset of 20 pairwise alignments from the RIPC set. SPalignNS is shown to achieve greater alignment accuracy (lower or comparable root-mean squared distance with increased structure overlap coverage) for all datasets, and the highest agreement with reference alignments from the challenging dataset (iv) above, when compared with both sequentially constrained alignments and other non-sequential alignments. SPalignNS was implemented in C++. The source code, binary executable, and a web server version is freely available at: http://sparks-lab.org yaoqi.zhou@griffith.edu.au. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  2. StructAlign, a Program for Alignment of Structures of DNA-Protein Complexes.

    PubMed

    Popov, Ya V; Galitsyna, A A; Alexeevski, A V; Karyagina, A S; Spirin, S A

    2015-11-01

    Comparative analysis of structures of complexes of homologous proteins with DNA is important in the analysis of DNA-protein recognition. Alignment is a necessary stage of the analysis. An alignment is a matching of amino acid residues and nucleotides of one complex to residues and nucleotides of the other. Currently, there are no programs available for aligning structures of DNA-protein complexes. We present the program StructAlign, which should fill this gap. The program inputs a pair of complexes of DNA double helix with proteins and outputs an alignment of DNA chains corresponding to the best spatial fit of the protein chains.

  3. Training alignment parameters for arbitrary sequencers with LAST-TRAIN.

    PubMed

    Hamada, Michiaki; Ono, Yukiteru; Asai, Kiyoshi; Frith, Martin C

    2017-03-15

    LAST-TRAIN improves sequence alignment accuracy by inferring substitution and gap scores that fit the frequencies of substitutions, insertions, and deletions in a given dataset. We have applied it to mapping DNA reads from IonTorrent and PacBio RS, and we show that it reduces reference bias for Oxford Nanopore reads. the source code is freely available at http://last.cbrc.jp/. mhamada@waseda.jp or mcfrith@edu.k.u-tokyo.ac.jp. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  4. HAL: a hierarchical format for storing and analyzing multiple genome alignments.

    PubMed

    Hickey, Glenn; Paten, Benedict; Earl, Dent; Zerbino, Daniel; Haussler, David

    2013-05-15

    Large multiple genome alignments and inferred ancestral genomes are ideal resources for comparative studies of molecular evolution, and advances in sequencing and computing technology are making them increasingly obtainable. These structures can provide a rich understanding of the genetic relationships between all subsets of species they contain. Current formats for storing genomic alignments, such as XMFA and MAF, are all indexed or ordered using a single reference genome, however, which limits the information that can be queried with respect to other species and clades. This loss of information grows with the number of species under comparison, as well as their phylogenetic distance. We present HAL, a compressed, graph-based hierarchical alignment format for storing multiple genome alignments and ancestral reconstructions. HAL graphs are indexed on all genomes they contain. Furthermore, they are organized phylogenetically, which allows for modular and parallel access to arbitrary subclades without fragmentation because of rearrangements that have occurred in other lineages. HAL graphs can be created or read with a comprehensive C++ API. A set of tools is also provided to perform basic operations, such as importing and exporting data, identifying mutations and coordinate mapping (liftover). All documentation and source code for the HAL API and tools are freely available at http://github.com/glennhickey/hal. hickey@soe.ucsc.edu or haussler@soe.ucsc.edu Supplementary data are available at Bioinformatics online.

  5. CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area.

    PubMed

    Terashi, Genki; Takeda-Shitaka, Mayuko

    2015-01-01

    Proteins are flexible, and this flexibility has an essential functional role. Flexibility can be observed in loop regions, rearrangements between secondary structure elements, and conformational changes between entire domains. However, most protein structure alignment methods treat protein structures as rigid bodies. Thus, these methods fail to identify the equivalences of residue pairs in regions with flexibility. In this study, we considered that the evolutionary relationship between proteins corresponds directly to the residue-residue physical contacts rather than the three-dimensional (3D) coordinates of proteins. Thus, we developed a new protein structure alignment method, contact area-based alignment (CAB-align), which uses the residue-residue contact area to identify regions of similarity. The main purpose of CAB-align is to identify homologous relationships at the residue level between related protein structures. The CAB-align procedure comprises two main steps: First, a rigid-body alignment method based on local and global 3D structure superposition is employed to generate a sufficient number of initial alignments. Then, iterative dynamic programming is executed to find the optimal alignment. We evaluated the performance and advantages of CAB-align based on four main points: (1) agreement with the gold standard alignment, (2) alignment quality based on an evolutionary relationship without 3D coordinate superposition, (3) consistency of the multiple alignments, and (4) classification agreement with the gold standard classification. Comparisons of CAB-align with other state-of-the-art protein structure alignment methods (TM-align, FATCAT, and DaliLite) using our benchmark dataset showed that CAB-align performed robustly in obtaining high-quality alignments and generating consistent multiple alignments with high coverage and accuracy rates, and it performed extremely well when discriminating between homologous and nonhomologous pairs of proteins in both

  6. Engaging the Demons. Report on a Collaboration between English Faculty of Baldwin High School and Georgia College & State University, Milledgeville, Georgia: 2001-02.

    ERIC Educational Resources Information Center

    Carriere, Peter M.; Smith, Melissa

    A collaborative project between Georgia College and State University (GC&SU) and Baldwin High School (BHS) in Milledgeville, Georgia, had as its initial goals: to provide an opportunity for two-way mentoring between the GC&SU's Arts and Sciences faculty and BHS's English faculty; to improve curriculum alignment; to establish realistic…

  7. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

    PubMed Central

    Margulies, Elliott H.; Cooper, Gregory M.; Asimenos, George; Thomas, Daryl J.; Dewey, Colin N.; Siepel, Adam; Birney, Ewan; Keefe, Damian; Schwartz, Ariel S.; Hou, Minmei; Taylor, James; Nikolaev, Sergey; Montoya-Burgos, Juan I.; Löytynoja, Ari; Whelan, Simon; Pardi, Fabio; Massingham, Tim; Brown, James B.; Bickel, Peter; Holmes, Ian; Mullikin, James C.; Ureta-Vidal, Abel; Paten, Benedict; Stone, Eric A.; Rosenbloom, Kate R.; Kent, W. James; Bouffard, Gerard G.; Guan, Xiaobin; Hansen, Nancy F.; Idol, Jacquelyn R.; Maduro, Valerie V.B.; Maskeri, Baishali; McDowell, Jennifer C.; Park, Morgan; Thomas, Pamela J.; Young, Alice C.; Blakesley, Robert W.; Muzny, Donna M.; Sodergren, Erica; Wheeler, David A.; Worley, Kim C.; Jiang, Huaiyang; Weinstock, George M.; Gibbs, Richard A.; Graves, Tina; Fulton, Robert; Mardis, Elaine R.; Wilson, Richard K.; Clamp, Michele; Cuff, James; Gnerre, Sante; Jaffe, David B.; Chang, Jean L.; Lindblad-Toh, Kerstin; Lander, Eric S.; Hinrichs, Angie; Trumbower, Heather; Clawson, Hiram; Zweig, Ann; Kuhn, Robert M.; Barber, Galt; Harte, Rachel; Karolchik, Donna; Field, Matthew A.; Moore, Richard A.; Matthewson, Carrie A.; Schein, Jacqueline E.; Marra, Marco A.; Antonarakis, Stylianos E.; Batzoglou, Serafim; Goldman, Nick; Hardison, Ross; Haussler, David; Miller, Webb; Pachter, Lior; Green, Eric D.; Sidow, Arend

    2007-01-01

    A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation, alignment, and evolutionary constraint analyses of 23 mammalian species for all ENCODE targets. Alignments were generated using four different methods; comparisons of these methods reveal large-scale consistency but substantial differences in terms of small genomic rearrangements, sensitivity (sequence coverage), and specificity (alignment accuracy). We describe the quantitative and qualitative trade-offs concomitant with alignment method choice and the levels of technical error that need to be accounted for in applications that require multisequence alignments. Using the generated alignments, we identified constrained regions using three different methods. While the different constraint-detecting methods are in general agreement, there are important discrepancies relating to both the underlying alignments and the specific algorithms. However, by integrating the results across the alignments and constraint-detecting methods, we produced constraint annotations that were found to be robust based on multiple independent measures. Analyses of these annotations illustrate that most classes of experimentally annotated functional elements are enriched for constrained sequences; however, large portions of each class (with the exception of protein-coding sequences) do not overlap constrained regions. The latter elements might not be under primary sequence constraint, might not be constrained across all mammals, or might have expendable molecular functions. Conversely, 40% of the constrained sequences do not overlap any of the functional elements that have been experimentally identified. Together, these findings demonstrate and quantify how many genomic functional elements await basic molecular characterization. PMID:17567995

  8. A survey and evaluations of histogram-based statistics in alignment-free sequence comparison.

    PubMed

    Luczak, Brian B; James, Benjamin T; Girgis, Hani Z

    2017-12-06

    Since the dawn of the bioinformatics field, sequence alignment scores have been the main method for comparing sequences. However, alignment algorithms are quadratic, requiring long execution time. As alternatives, scientists have developed tens of alignment-free statistics for measuring the similarity between two sequences. We surveyed tens of alignment-free k-mer statistics. Additionally, we evaluated 33 statistics and multiplicative combinations between the statistics and/or their squares. These statistics are calculated on two k-mer histograms representing two sequences. Our evaluations using global alignment scores revealed that the majority of the statistics are sensitive and capable of finding similar sequences to a query sequence. Therefore, any of these statistics can filter out dissimilar sequences quickly. Further, we observed that multiplicative combinations of the statistics are highly correlated with the identity score. Furthermore, combinations involving sequence length difference or Earth Mover's distance, which takes the length difference into account, are always among the highest correlated paired statistics with identity scores. Similarly, paired statistics including length difference or Earth Mover's distance are among the best performers in finding the K-closest sequences. Interestingly, similar performance can be obtained using histograms of shorter words, resulting in reducing the memory requirement and increasing the speed remarkably. Moreover, we found that simple single statistics are sufficient for processing next-generation sequencing reads and for applications relying on local alignment. Finally, we measured the time requirement of each statistic. The survey and the evaluations will help scientists with identifying efficient alternatives to the costly alignment algorithm, saving thousands of computational hours. The source code of the benchmarking tool is available as Supplementary Materials. © The Author 2017. Published by Oxford

  9. 7 CFR 247.13 - Provisions for non-English or limited-English speakers.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 4 2010-01-01 2010-01-01 false Provisions for non-English or limited-English speakers... § 247.13 Provisions for non-English or limited-English speakers. (a) What must State and local agencies do to ensure that non-English or limited-English speaking persons are aware of their rights and...

  10. Multi-profile Bayesian alignment model for LC-MS data analysis with integration of internal standards

    PubMed Central

    Tsai, Tsung-Heng; Tadesse, Mahlet G.; Di Poto, Cristina; Pannell, Lewis K.; Mechref, Yehia; Wang, Yue; Ressom, Habtom W.

    2013-01-01

    Motivation: Liquid chromatography-mass spectrometry (LC-MS) has been widely used for profiling expression levels of biomolecules in various ‘-omic’ studies including proteomics, metabolomics and glycomics. Appropriate LC-MS data preprocessing steps are needed to detect true differences between biological groups. Retention time (RT) alignment, which is required to ensure that ion intensity measurements among multiple LC-MS runs are comparable, is one of the most important yet challenging preprocessing steps. Current alignment approaches estimate RT variability using either single chromatograms or detected peaks, but do not simultaneously take into account the complementary information embedded in the entire LC-MS data. Results: We propose a Bayesian alignment model for LC-MS data analysis. The alignment model provides estimates of the RT variability along with uncertainty measures. The model enables integration of multiple sources of information including internal standards and clustered chromatograms in a mathematically rigorous framework. We apply the model to LC-MS metabolomic, proteomic and glycomic data. The performance of the model is evaluated based on ground-truth data, by measuring correlation of variation, RT difference across runs and peak-matching performance. We demonstrate that Bayesian alignment model improves significantly the RT alignment performance through appropriate integration of relevant information. Availability and implementation: MATLAB code, raw and preprocessed LC-MS data are available at http://omics.georgetown.edu/alignLCMS.html Contact: hwr@georgetown.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24013927

  11. New primary renal diagnosis codes for the ERA-EDTA

    PubMed Central

    Venkat-Raman, Gopalakrishnan; Tomson, Charles R.V.; Gao, Yongsheng; Cornet, Ronald; Stengel, Benedicte; Gronhagen-Riska, Carola; Reid, Chris; Jacquelinet, Christian; Schaeffner, Elke; Boeschoten, Els; Casino, Francesco; Collart, Frederic; De Meester, Johan; Zurriaga, Oscar; Kramar, Reinhard; Jager, Kitty J.; Simpson, Keith

    2012-01-01

    The European Renal Association-European Dialysis and Transplant Association (ERA-EDTA) Registry has produced a new set of primary renal diagnosis (PRD) codes that are intended for use by affiliated registries. It is designed specifically for use in renal centres and registries but is aligned with international coding standards supported by the WHO (International Classification of Diseases) and the International Health Terminology Standards Development Organization (SNOMED Clinical Terms). It is available as supplementary material to this paper and free on the internet for non-commercial, clinical, quality improvement and research use, and by agreement with the ERA-EDTA Registry for use by commercial organizations. Conversion between the old and the new PRD codes is possible. The new codes are very flexible and will be actively managed to keep them up-to-date and to ensure that renal medicine can remain at the forefront of the electronic revolution in medicine, epidemiology research and the use of decision support systems to improve the care of patients. PMID:23175621

  12. Japanese Learners' Self Revisions and Peer Revisions of Their Written Compositions in English

    ERIC Educational Resources Information Center

    Suzuki, Manami

    2008-01-01

    The current study examined 24 Japanese university students' processes of negotiation in conditions of self revision and of peer revision about their English as a foreign language (EFL) writing. Analyzing their negotiation episodes and text changes, I categorized within a common coding scheme the types of negotiation from (a) think-aloud protocols…

  13. AMAS: a fast tool for alignment manipulation and computing of summary statistics.

    PubMed

    Borowiec, Marek L

    2016-01-01

    The amount of data used in phylogenetics has grown explosively in the recent years and many phylogenies are inferred with hundreds or even thousands of loci and many taxa. These modern phylogenomic studies often entail separate analyses of each of the loci in addition to multiple analyses of subsets of genes or concatenated sequences. Computationally efficient tools for handling and computing properties of thousands of single-locus or large concatenated alignments are needed. Here I present AMAS (Alignment Manipulation And Summary), a tool that can be used either as a stand-alone command-line utility or as a Python package. AMAS works on amino acid and nucleotide alignments and combines capabilities of sequence manipulation with a function that calculates basic statistics. The manipulation functions include conversions among popular formats, concatenation, extracting sites and splitting according to a pre-defined partitioning scheme, creation of replicate data sets, and removal of taxa. The statistics calculated include the number of taxa, alignment length, total count of matrix cells, overall number of undetermined characters, percent of missing data, AT and GC contents (for DNA alignments), count and proportion of variable sites, count and proportion of parsimony informative sites, and counts of all characters relevant for a nucleotide or amino acid alphabet. AMAS is particularly suitable for very large alignments with hundreds of taxa and thousands of loci. It is computationally efficient, utilizes parallel processing, and performs better at concatenation than other popular tools. AMAS is a Python 3 program that relies solely on Python's core modules and needs no additional dependencies. AMAS source code and manual can be downloaded from http://github.com/marekborowiec/AMAS/ under GNU General Public License.

  14. Effects of a Technology-Assisted Reading Comprehension Intervention for English Learners with Learning Disabilities

    ERIC Educational Resources Information Center

    Jozwik, Sara L.; Douglas, Karen H.

    2017-01-01

    This study integrated technology tools into a reading comprehension intervention that used explicit instruction to teach strategies (i.e., asking questions, making connections, and coding the text to monitor for meaning) to mixed-ability small groups, which included four English Learners with learning disabilities in a fourth-grade general…

  15. Learner Views on English and English Language Teaching in China

    ERIC Educational Resources Information Center

    Liu, Na; Lin, Chih-Kai; Wiley, Terrence G.

    2016-01-01

    Since the 1980s, China has represented one of the major growth areas in the world for English language education, and studying English has been a priority among its foreign language educational policies. As English has gained more popularity in China, some have noted the potential value of English as a means to greater educational access and…

  16. The Examination of Alignment between National Assessment and English Curriculum Objectives Using Revised Bloom's Taxonomy

    ERIC Educational Resources Information Center

    Kozikoglu, Ishak

    2018-01-01

    Bloom's taxonomy for the classification of the objectives in cognitive domain was developed in mid 1950s and this taxonomy was revised by a group with Anderson and Krathwohl by making some changes and revisions. The purpose of this research was to evaluate the objectives of 8th grade English curriculum and TEOG exam questions (national assessment…

  17. Earphone English.

    ERIC Educational Resources Information Center

    Goldsmith, Francisca

    2002-01-01

    Describes Earphone English, a student club sponsored through a partnership between Berkeley High School and the Berkeley Public Library that offers students whose primary language is not English to practice their spoken and aural English skills. Discusses the audiobooks used in the program and the importance of multicultural content and age…

  18. Application of Quaternion in improving the quality of global sequence alignment scores for an ambiguous sequence target in Streptococcus pneumoniae DNA

    NASA Astrophysics Data System (ADS)

    Lestari, D.; Bustamam, A.; Novianti, T.; Ardaneswari, G.

    2017-07-01

    DNA sequence can be defined as a succession of letters, representing the order of nucleotides within DNA, using a permutation of four DNA base codes including adenine (A), guanine (G), cytosine (C), and thymine (T). The precise code of the sequences is determined using DNA sequencing methods and technologies, which have been developed since the 1970s and currently become highly developed, advanced and highly throughput sequencing technologies. So far, DNA sequencing has greatly accelerated biological and medical research and discovery. However, in some cases DNA sequencing could produce any ambiguous and not clear enough sequencing results that make them quite difficult to be determined whether these codes are A, T, G, or C. To solve these problems, in this study we can introduce other representation of DNA codes namely Quaternion Q = (PA, PT, PG, PC), where PA, PT, PG, PC are the probability of A, T, G, C bases that could appear in Q and PA + PT + PG + PC = 1. Furthermore, using Quaternion representations we are able to construct the improved scoring matrix for global sequence alignment processes, by applying a dot product method. Moreover, this scoring matrix produces better and higher quality of the match and mismatch score between two DNA base codes. In implementation, we applied the Needleman-Wunsch global sequence alignment algorithm using Octave, to analyze our target sequence which contains some ambiguous sequence data. The subject sequences are the DNA sequences of Streptococcus pneumoniae families obtained from the Genebank, meanwhile the target DNA sequence are received from our collaborator database. As the results we found the Quaternion representations improve the quality of the sequence alignment score and we can conclude that DNA sequence target has maximum similarity with Streptococcus pneumoniae.

  19. Constructing English as a Ugandan Language through an English Textbook

    ERIC Educational Resources Information Center

    Stranger-Johannessen, Espen

    2015-01-01

    English is a national language in Uganda and is widely used in elite areas such as politics and business, but most Ugandans master English to only a limited degree. In this situation, English can be seen as either a foreign language or a second language--influencing how English is taught. One goal of language teaching espoused in this article is…

  20. Practices That Promote English Reading for English Learners (Els)

    ERIC Educational Resources Information Center

    Martínez, Rebecca S.; Harris, Bryn; McClain, Maryellen Brunson

    2014-01-01

    Schools are becoming increasingly diversified; however, training and professional development related to working with English language learners (ELs), especially in the area of English reading, is limited. In this article, we identify three "Big Ideas" of effective and collaborative practices that promote English reading achievement for…

  1. Edge-relevant plasma simulations with the continuum code COGENT

    NASA Astrophysics Data System (ADS)

    Dorf, M.; Dorr, M.; Ghosh, D.; Hittinger, J.; Rognlien, T.; Cohen, R.; Lee, W.; Schwartz, P.

    2016-10-01

    We describe recent advances in cross-separatrix and other edge-relevant plasma simulations with COGENT, a continuum gyro-kinetic code being developed by the Edge Simulation Laboratory (ESL) collaboration. The distinguishing feature of the COGENT code is its high-order finite-volume discretization methods, which employ arbitrary mapped multiblock grid technology (nearly field-aligned on blocks) to handle the complexity of tokamak divertor geometry with high accuracy. This paper discusses the 4D (axisymmetric) electrostatic version of the code, and the presented topics include: (a) initial simulations with kinetic electrons and development of reduced fluid models; (b) development and application of implicit-explicit (IMEX) time integration schemes; and (c) conservative modeling of drift-waves and the universal instability. Work performed for USDOE, at LLNL under contract DE-AC52-07NA27344 and at LBNL under contract DE-AC02-05CH11231.

  2. The New English.

    ERIC Educational Resources Information Center

    O'Donnell, John F.

    1968-01-01

    Traditional English curriculums are giving way to new English programs built on the foundations of research and scholarship. The "new" English, being developed by the Project English Centers throughout the country, attempts to utilize the characteristic structure of the subject to plan sequential and spiral curriculums replacing outdated…

  3. Perception of English palatal codas by Korean speakers of English

    NASA Astrophysics Data System (ADS)

    Yeon, Sang-Hee

    2003-04-01

    This study aimed at looking at perception of English palatal codas by Korean speakers of English to determine if perception problems are the source of production problems. In particular, first, this study looked at the possible first language effect on the perception of English palatal codas. Second, a possible perceptual source of vowel epenthesis after English palatal codas was investigated. In addition, individual factors, such as length of residence, TOEFL score, gender and academic status, were compared to determine if those affected the varying degree of the perception accuracy. Eleven adult Korean speakers of English as well as three native speakers of English participated in the study. Three sets of a perception test including identification of minimally different English pseudo- or real words were carried out. The results showed that, first, the Korean speakers perceived the English codas significantly worse than the Americans. Second, the study supported the idea that Koreans perceived an extra /i/ after the final affricates due to final release. Finally, none of the individual factors explained the varying degree of the perceptional accuracy. In particular, TOEFL scores and the perception test scores did not have any statistically significant association.

  4. Teaching English.

    ERIC Educational Resources Information Center

    Nemanich, Donald, Ed.

    1975-01-01

    Articles in this volume of the "Illinois English Bulletin" include "Competencies in Teaching English" by Alan C. Purves, which sets forth a tentative model for planning competency-based instruction and certification based on concepts, teaching acts, skills, and strategies; "Passing the Buck Versus the Teaching of English" by Dennis Q. McInerny,…

  5. "There are too many, but never enough": qualitative case study investigating routine coding of clinical information in depression.

    PubMed

    Cresswell, Kathrin; Morrison, Zoe; Kalra, Dipak; Sheikh, Aziz

    2012-01-01

    We sought to understand how clinical information relating to the management of depression is routinely coded in different clinical settings and the perspectives of and implications for different stakeholders with a view to understanding how these may be aligned. Qualitative investigation exploring the views of a purposefully selected range of healthcare professionals, managers, and clinical coders spanning primary and secondary care. Our dataset comprised 28 semi-structured interviews, a focus group, documents relating to clinical coding standards and participant observation of clinical coding activities. We identified a range of approaches to coding clinical information including templates and order entry systems. The challenges inherent in clearly establishing a diagnosis, identifying appropriate clinical codes and possible implications of diagnoses for patients were particularly prominent in primary care. Although a range of managerial and research benefits were identified, there were no direct benefits from coded clinical data for patients or professionals. Secondary care staff emphasized the role of clinical coders in ensuring data quality, which was at odds with the policy drive to increase real-time clinical coding. There was overall no evidence of clear-cut direct patient care benefits to inform immediate care decisions, even in primary care where data on patients with depression were more extensively coded. A number of important secondary uses were recognized by healthcare staff, but the coding of clinical data to serve these ends was often poorly aligned with clinical practice and patient-centered considerations. The current international drive to encourage clinical coding by healthcare professionals during the clinical encounter may need to be critically examined.

  6. Phylogenetic inference under varying proportions of indel-induced alignment gaps

    PubMed Central

    Dwivedi, Bhakti; Gadagkar, Sudhindra R

    2009-01-01

    Background The effect of alignment gaps on phylogenetic accuracy has been the subject of numerous studies. In this study, we investigated the relationship between the total number of gapped sites and phylogenetic accuracy, when the gaps were introduced (by means of computer simulation) to reflect indel (insertion/deletion) events during the evolution of DNA sequences. The resulting (true) alignments were subjected to commonly used gap treatment and phylogenetic inference methods. Results (1) In general, there was a strong – almost deterministic – relationship between the amount of gap in the data and the level of phylogenetic accuracy when the alignments were very "gappy", (2) gaps resulting from deletions (as opposed to insertions) contributed more to the inaccuracy of phylogenetic inference, (3) the probabilistic methods (Bayesian, PhyML & "MLε, " a method implemented in DNAML in PHYLIP) performed better at most levels of gap percentage when compared to parsimony (MP) and distance (NJ) methods, with Bayesian analysis being clearly the best, (4) methods that treat gapped sites as missing data yielded less accurate trees when compared to those that attribute phylogenetic signal to the gapped sites (by coding them as binary character data – presence/absence, or as in the MLε method), and (5) in general, the accuracy of phylogenetic inference depended upon the amount of available data when the gaps resulted from mainly deletion events, and the amount of missing data when insertion events were equally likely to have caused the alignment gaps. Conclusion When gaps in an alignment are a consequence of indel events in the evolution of the sequences, the accuracy of phylogenetic analysis is likely to improve if: (1) alignment gaps are categorized as arising from insertion events or deletion events and then treated separately in the analysis, (2) the evolutionary signal provided by indels is harnessed in the phylogenetic analysis, and (3) methods that utilize the

  7. Reducing beam shaper alignment complexity: diagnostic techniques for alignment and tuning

    NASA Astrophysics Data System (ADS)

    Lizotte, Todd E.

    2011-10-01

    Safe and efficient optical alignment is a critical requirement for industrial laser systems used in a high volume manufacturing environment. Of specific interest is the development of techniques to align beam shaping optics within a beam line; having the ability to instantly verify by a qualitative means that each element is in its proper position as the beam shaper module is being aligned. There is a need to reduce these types of alignment techniques down to a level where even a newbie to optical alignment will be able to complete the task. Couple this alignment need with the fact that most laser system manufacturers ship their products worldwide and the introduction of a new set of variables including cultural and language barriers, makes this a top priority for manufacturers. Tools and methodologies for alignment of complex optical systems need to be able to cross these barriers to ensure the highest degree of up time and reduce the cost of maintenance on the production floor. Customers worldwide, who purchase production laser equipment, understand that the majority of costs to a manufacturing facility is spent on system maintenance and is typically the largest single controllable expenditure in a production plant. This desire to reduce costs is driving the trend these days towards predictive and proactive, not reactive maintenance of laser based optical beam delivery systems [10]. With proper diagnostic tools, laser system developers can develop proactive approaches to reduce system down time, safe guard operational performance and reduce premature or catastrophic optics failures. Obviously analytical data will provide quantifiable performance standards which are more precise than qualitative standards, but each have a role in determining overall optical system performance [10]. This paper will discuss the use of film and fluorescent mirror devices as diagnostic tools for beam shaper module alignment off line or in-situ. The paper will also provide an overview

  8. To Teach Standard English or World Englishes? A Balanced Approach to Instruction

    ERIC Educational Resources Information Center

    Farrell, Thomas S. C.; Martin, Sonia

    2009-01-01

    This article suggests that English language teachers should consider all varieties of English, not just British Standard English or American Standard English. In order to better prepare students for the global world, and to show them that their own English is valued, teachers can implement a balanced approach that incorporates the teaching and…

  9. HubAlign: an accurate and efficient method for global alignment of protein-protein interaction networks.

    PubMed

    Hashemifar, Somaye; Xu, Jinbo

    2014-09-01

    High-throughput experimental techniques have produced a large amount of protein-protein interaction (PPI) data. The study of PPI networks, such as comparative analysis, shall benefit the understanding of life process and diseases at the molecular level. One way of comparative analysis is to align PPI networks to identify conserved or species-specific subnetwork motifs. A few methods have been developed for global PPI network alignment, but it still remains challenging in terms of both accuracy and efficiency. This paper presents a novel global network alignment algorithm, denoted as HubAlign, that makes use of both network topology and sequence homology information, based upon the observation that topologically important proteins in a PPI network usually are much more conserved and thus, more likely to be aligned. HubAlign uses a minimum-degree heuristic algorithm to estimate the topological and functional importance of a protein from the global network topology information. Then HubAlign aligns topologically important proteins first and gradually extends the alignment to the whole network. Extensive tests indicate that HubAlign greatly outperforms several popular methods in terms of both accuracy and efficiency, especially in detecting functionally similar proteins. HubAlign is available freely for non-commercial purposes at http://ttic.uchicago.edu/∼hashemifar/software/HubAlign.zip. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

  10. Wisconsin Model Early Learning Standards Alignment with Wisconsin Common Core State Standards for English Language Arts and Mathematics

    ERIC Educational Resources Information Center

    Wisconsin Department of Public Instruction, 2011

    2011-01-01

    Wisconsin's adoption of the Common Core State Standards provides an excellent opportunity for Wisconsin school districts and communities to define expectations from birth through preparation for college and work. By aligning the existing Wisconsin Model Early Learning Standards with the Wisconsin Common Core State Standards, expectations can be…

  11. LIGSIFT: an open-source tool for ligand structural alignment and virtual screening.

    PubMed

    Roy, Ambrish; Skolnick, Jeffrey

    2015-02-15

    Shape-based alignment of small molecules is a widely used approach in computer-aided drug discovery. Most shape-based ligand structure alignment applications, both commercial and freely available ones, use the Tanimoto coefficient or similar functions for evaluating molecular similarity. Major drawbacks of using such functions are the size dependence of the score and the fact that the statistical significance of the molecular match using such metrics is not reported. We describe a new open-source ligand structure alignment and virtual screening (VS) algorithm, LIGSIFT, that uses Gaussian molecular shape overlay for fast small molecule alignment and a size-independent scoring function for efficient VS based on the statistical significance of the score. LIGSIFT was tested against the compounds for 40 protein targets available in the Directory of Useful Decoys and the performance was evaluated using the area under the ROC curve (AUC), the Enrichment Factor (EF) and Hit Rate (HR). LIGSIFT-based VS shows an average AUC of 0.79, average EF values of 20.8 and a HR of 59% in the top 1% of the screened library. LIGSIFT software, including the source code, is freely available to academic users at http://cssb.biology.gatech.edu/LIGSIFT. Supplementary data are available at Bioinformatics online. skolnick@gatech.edu. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  12. English speech sound development in preschool-aged children from bilingual English-Spanish environments.

    PubMed

    Gildersleeve-Neumann, Christina E; Kester, Ellen S; Davis, Barbara L; Peña, Elizabeth D

    2008-07-01

    English speech acquisition by typically developing 3- to 4-year-old children with monolingual English was compared to English speech acquisition by typically developing 3- to 4-year-old children with bilingual English-Spanish backgrounds. We predicted that exposure to Spanish would not affect the English phonetic inventory but would increase error frequency and type in bilingual children. Single-word speech samples were collected from 33 children. Phonetically transcribed samples for the 3 groups (monolingual English children, English-Spanish bilingual children who were predominantly exposed to English, and English-Spanish bilingual children with relatively equal exposure to English and Spanish) were compared at 2 time points and for change over time for phonetic inventory, phoneme accuracy, and error pattern frequencies. Children demonstrated similar phonetic inventories. Some bilingual children produced Spanish phonemes in their English and produced few consonant cluster sequences. Bilingual children with relatively equal exposure to English and Spanish averaged more errors than did bilingual children who were predominantly exposed to English. Both bilingual groups showed higher error rates than English-only children overall, particularly for syllable-level error patterns. All language groups decreased in some error patterns, although the ones that decreased were not always the same across language groups. Some group differences of error patterns and accuracy were significant. Vowel error rates did not differ by language group. Exposure to English and Spanish may result in a higher English error rate in typically developing bilinguals, including the application of Spanish phonological properties to English. Slightly higher error rates are likely typical for bilingual preschool-aged children. Change over time at these time points for all 3 groups was similar, suggesting that all will reach an adult-like system in English with exposure and practice.

  13. Whose English Counts? Native Speakers as English Language Learners

    ERIC Educational Resources Information Center

    Grill, Jennifer

    2010-01-01

    The author, a teacher educator, explains that because of a lack of training in language studies, many teachers do not view language as linguists do. She identifies three misconceptions (and the implications they have for English language learners) that still persist in education: Standard English is the best and most correct form of English,…

  14. The English of Business Is the Business of English.

    ERIC Educational Resources Information Center

    Versluis, Edward B.

    Three arguments lead to the conclusion that the English of business is the business of English. First, reluctance to fully appreciate the English of Business stems in part from a serious misunderstanding about the development of written language in the Western tradition. While studying folktales and the origins of myths has made an awareness of…

  15. The Development of Bilingual Narrative Retelling Among Spanish-English Dual Language Learners Over Two Years.

    PubMed

    Lucero, Audrey

    2018-05-25

    This exploratory study investigates the development of oral narrative retell proficiency among Spanish-English emergent bilingual children longitudinally from kindergarten to second grade in Spanish and English as they learned literacy in the 2 languages concurrently. Oral narrative retell assessments were conducted with children who spoke Spanish at home and were enrolled in a dual language immersion program (N = 12) in the spring of kindergarten and second grade. Retells were transcribed and coded for vocabulary and grammar at the microlevel (Miller, 2012) and story structure at the macrolevel (Heilmann, Miller, Nockerts, & Dunaway, 2010). In microstructure paired-sample t tests, children showed significant improvements in vocabulary in both languages (Spanish total number of words η2 = .43, Spanish number of different words η2 = .44, English total number of words η2 = .61, English number of different words η2 = .62) but not grammar by second grade. At the macrostructure level, children showed significantly higher performance in English only (English narrative scoring scheme η2 = .47). The finding that children significantly improved in vocabulary in both languages but in overall story structure only in English suggests that discourse skills were being facilitated in English whereas Spanish discourse development may have stagnated even within a dual language immersion program. Results contribute to what is currently known about bilingual oral narrative development among young Spanish speakers enrolled in such programs and can inform assessment and instructional decisions.

  16. English Voices in "Text-to-Speech Tools": Representation of English Users and Their Varieties from a World Englishes Perspective

    ERIC Educational Resources Information Center

    Karakas, Ali

    2017-01-01

    English has experienced grave transformations recently in terms of socio-demographic and geographical characteristics. While such transformations have resulted in diverse types of English uses and various English users, the existing ELT materials still fail to represent the global varieties and dynamic uses and users of English. Moving from a…

  17. Quantum Communication without Alignment using Multiple-Qubit Single-Photon States

    NASA Astrophysics Data System (ADS)

    Aolita, L.; Walborn, S. P.

    2007-03-01

    We propose a scheme for encoding logical qubits in a subspace protected against collective rotations around the propagation axis using the polarization and transverse spatial degrees of freedom of single photons. This encoding allows for quantum key distribution without the need of a shared reference frame. We present methods to generate entangled states of two logical qubits using present day down-conversion sources and linear optics, and show that the application of these entangled logical states to quantum information schemes allows for alignment-free tests of Bell’s inequalities, quantum dense coding, and quantum teleportation.

  18. Tidal alignment of galaxies

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

    Blazek, Jonathan; Vlah, Zvonimir; Seljak, Uroš

    We develop an analytic model for galaxy intrinsic alignments (IA) based on the theory of tidal alignment. We calculate all relevant nonlinear corrections at one-loop order, including effects from nonlinear density evolution, galaxy biasing, and source density weighting. Contributions from density weighting are found to be particularly important and lead to bias dependence of the IA amplitude, even on large scales. This effect may be responsible for much of the luminosity dependence in IA observations. The increase in IA amplitude for more highly biased galaxies reflects their locations in regions with large tidal fields. We also consider the impact ofmore » smoothing the tidal field on halo scales. We compare the performance of this consistent nonlinear model in describing the observed alignment of luminous red galaxies with the linear model as well as the frequently used "nonlinear alignment model," finding a significant improvement on small and intermediate scales. We also show that the cross-correlation between density and IA (the "GI" term) can be effectively separated into source alignment and source clustering, and we accurately model the observed alignment down to the one-halo regime using the tidal field from the fully nonlinear halo-matter cross correlation. Inside the one-halo regime, the average alignment of galaxies with density tracers no longer follows the tidal alignment prediction, likely reflecting nonlinear processes that must be considered when modeling IA on these scales. Finally, we discuss tidal alignment in the context of cosmic shear measurements.« less

  19. Tidal alignment of galaxies

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

    Blazek, Jonathan; Vlah, Zvonimir; Seljak, Uroš, E-mail: blazek@berkeley.edu, E-mail: zvlah@stanford.edu, E-mail: useljak@berkeley.edu

    We develop an analytic model for galaxy intrinsic alignments (IA) based on the theory of tidal alignment. We calculate all relevant nonlinear corrections at one-loop order, including effects from nonlinear density evolution, galaxy biasing, and source density weighting. Contributions from density weighting are found to be particularly important and lead to bias dependence of the IA amplitude, even on large scales. This effect may be responsible for much of the luminosity dependence in IA observations. The increase in IA amplitude for more highly biased galaxies reflects their locations in regions with large tidal fields. We also consider the impact ofmore » smoothing the tidal field on halo scales. We compare the performance of this consistent nonlinear model in describing the observed alignment of luminous red galaxies with the linear model as well as the frequently used 'nonlinear alignment model,' finding a significant improvement on small and intermediate scales. We also show that the cross-correlation between density and IA (the 'GI' term) can be effectively separated into source alignment and source clustering, and we accurately model the observed alignment down to the one-halo regime using the tidal field from the fully nonlinear halo-matter cross correlation. Inside the one-halo regime, the average alignment of galaxies with density tracers no longer follows the tidal alignment prediction, likely reflecting nonlinear processes that must be considered when modeling IA on these scales. Finally, we discuss tidal alignment in the context of cosmic shear measurements.« less

  20. Homeotropic alignment of multiple bent-core liquid crystal phases using a polydimethylsiloxane alignment layer

    NASA Astrophysics Data System (ADS)

    Carlson, Eric D.; Foley, Lee M.; Guzman, Edward; Korblova, Eva D.; Visvanathan, Rayshan; Ryu, SeongHo; Gim, Min-Jun; Tuchband, Michael R.; Yoon, Dong Ki; Clark, Noel A.; Walba, David M.

    2017-08-01

    The control of the molecular orientation of liquid crystals (LCs) is important in both understanding phase properties and the continuing development of new LC technologies including displays, organic transistors, and electro-optic devices. Many techniques have been developed for successfully inducing alignment of calamitic LCs, though these techniques typically do not translate to the alignment of bent-core liquid crystals (BCLCs). Some techniques have been utilized to align various phases of BCLCs, but these techniques are often unsuccessful for general alignment of multiple materials and/or multiple phases. Here, we demonstrate that glass cells treated with polydimethylsiloxane (PDMS) thin films induce high quality homeotropic alignment of multiple mesophases of four BCLCs. On cooling to the lowest temperature phase the homeotropic alignment is lost, and spherulitic growth is seen in crystal and crystal-like phases including the dark conglomerate (DC) and helical nanofilament (HNF) phases. Evidence of homeotropic alignment is observed using polarized optical microscopy. We speculate that the methyl groups on the surface of the PDMS films strongly interact with the aliphatic tails of each mesogens, resulting in homeotropic alignment.

  1. A Structural History of English.

    ERIC Educational Resources Information Center

    Nist, John

    This book combines a traditional history-of-the-language approach with modern linguistic analysis to discuss the history of English from Old English through Middle English, Early Modern English, Authoritarian English, Mature Modern English, to American English. The book begins with a discussion of the present status and structure of English. Each…

  2. Functions of Code-Switching among Iranian Advanced and Elementary Teachers and Students

    ERIC Educational Resources Information Center

    Momenian, Mohammad; Samar, Reza Ghafar

    2011-01-01

    This paper reports on the findings of a study carried out on the advanced and elementary teachers' and students' functions and patterns of code-switching in Iranian English classrooms. This concept has not been adequately examined in L2 (second language) classroom contexts than in outdoor natural contexts. Therefore, besides reporting on the…

  3. Other People's Students Elaborated Codes and Dialect in Basic Writing

    ERIC Educational Resources Information Center

    Evans, Jason Cory

    2012-01-01

    English teachers, especially those in the field of basic writing, have long debated how to teach writing to students whose home language differs from the perceived norm. This thesis intervenes in that stalemated debate by re-examining "elaborated codes" and by arguing for a type of correctness in writing that includes being correct…

  4. Linguistic measures of the referential process in psychodynamic treatment: the English and Italian versions.

    PubMed

    Mariani, Rachele; Maskit, Bernard; Bucci, Wilma; De Coro, Alessandra

    2013-01-01

    The referential process is defined in the context of Bucci's multiple code theory as the process by which nonverbal experience is connected to language. The English computerized measures of the referential process, which have been applied in psychotherapy research, include the Weighted Referential Activity Dictionary (WRAD), and measures of Reflection, Affect and Disfluency. This paper presents the development of the Italian version of the IWRAD by modeling Italian texts scored by judges, and shows the application of the IWRAD and other Italian measures in three psychodynamic treatments evaluated for personality change using the Shedler-Westen Assessment Procedure (SWAP-200). Clinical predictions based on applications of the English measures were supported.

  5. Alcohol marketing in televised English professional football: a frequency analysis.

    PubMed

    Graham, Andrew; Adams, Jean

    2014-01-01

    The aim of the study was to explore the frequency of alcohol marketing (both formal commercials and otherwise) in televised top-class English professional football matches. A purposive sample of six broadcasts (total = 1101 min) of televised top-class English club football matches were identified and recorded in full. A customized coding framework was used to identify and categorize all verbal and visual alcohol references in non-commercial broadcasting. The number and the duration of all formal alcohol commercials were also noted. A mean of 111 visual references and 2 verbal references to alcohol per hour of broadcast were identified. Nearly all visual references were to beer products and were primarily simple logos or branding. The majority of verbal alcohol references were related to title-sponsorship of competitions. A total of 17 formal alcohol commercials were identified, accounting for <1% of total broadcast time. Visual alcohol references in televised top-class English football matches are common with an average of nearly two per minute. Verbal references are rare and formal alcohol commercials account for <1% of broadcast time. Restriction of all alcohol sports sponsorship, as seen for tobacco, may be justified.

  6. Nuclear reactor alignment plate configuration

    DOEpatents

    Altman, David A; Forsyth, David R; Smith, Richard E; Singleton, Norman R

    2014-01-28

    An alignment plate that is attached to a core barrel of a pressurized water reactor and fits within slots within a top plate of a lower core shroud and upper core plate to maintain lateral alignment of the reactor internals. The alignment plate is connected to the core barrel through two vertically-spaced dowel pins that extend from the outside surface of the core barrel through a reinforcement pad and into corresponding holes in the alignment plate. Additionally, threaded fasteners are inserted around the perimeter of the reinforcement pad and into the alignment plate to further secure the alignment plate to the core barrel. A fillet weld also is deposited around the perimeter of the reinforcement pad. To accomodate thermal growth between the alignment plate and the core barrel, a gap is left above, below and at both sides of one of the dowel pins in the alignment plate holes through with the dowel pins pass.

  7. Energy level alignment at molecule-metal interfaces from an optimally tuned range-separated hybrid functional

    DOE PAGES

    Liu, Zhen-Fei; Egger, David A.; Refaely-Abramson, Sivan; ...

    2017-02-21

    The alignment of the frontier orbital energies of an adsorbed molecule with the substrate Fermi level at metal-organic interfaces is a fundamental observable of significant practical importance in nanoscience and beyond. Typical density functional theory calculations, especially those using local and semi-local functionals, often underestimate level alignment leading to inaccurate electronic structure and charge transport properties. Here, we develop a new fully self-consistent predictive scheme to accurately compute level alignment at certain classes of complex heterogeneous molecule-metal interfaces based on optimally tuned range-separated hybrid functionals. Starting from a highly accurate description of the gas-phase electronic structure, our method by constructionmore » captures important nonlocal surface polarization effects via tuning of the long-range screened exchange in a range-separated hybrid in a non-empirical and system-specific manner. We implement this functional in a plane-wave code and apply it to several physisorbed and chemisorbed molecule-metal interface systems. Our results are in quantitative agreement with experiments, the both the level alignment and work function changes. This approach constitutes a new practical scheme for accurate and efficient calculations of the electronic structure of molecule-metal interfaces.« less

  8. Energy level alignment at molecule-metal interfaces from an optimally tuned range-separated hybrid functional

    NASA Astrophysics Data System (ADS)

    Liu, Zhen-Fei; Egger, David A.; Refaely-Abramson, Sivan; Kronik, Leeor; Neaton, Jeffrey B.

    2017-03-01

    The alignment of the frontier orbital energies of an adsorbed molecule with the substrate Fermi level at metal-organic interfaces is a fundamental observable of significant practical importance in nanoscience and beyond. Typical density functional theory calculations, especially those using local and semi-local functionals, often underestimate level alignment leading to inaccurate electronic structure and charge transport properties. In this work, we develop a new fully self-consistent predictive scheme to accurately compute level alignment at certain classes of complex heterogeneous molecule-metal interfaces based on optimally tuned range-separated hybrid functionals. Starting from a highly accurate description of the gas-phase electronic structure, our method by construction captures important nonlocal surface polarization effects via tuning of the long-range screened exchange in a range-separated hybrid in a non-empirical and system-specific manner. We implement this functional in a plane-wave code and apply it to several physisorbed and chemisorbed molecule-metal interface systems. Our results are in quantitative agreement with experiments, the both the level alignment and work function changes. Our approach constitutes a new practical scheme for accurate and efficient calculations of the electronic structure of molecule-metal interfaces.

  9. LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening.

    PubMed

    Hu, Jun; Liu, Zi; Yu, Dong-Jun; Zhang, Yang

    2018-02-15

    Sequence-order independent structural comparison, also called structural alignment, of small ligand molecules is often needed for computer-aided virtual drug screening. Although many ligand structure alignment programs are proposed, most of them build the alignments based on rigid-body shape comparison which cannot provide atom-specific alignment information nor allow structural variation; both abilities are critical to efficient high-throughput virtual screening. We propose a novel ligand comparison algorithm, LS-align, to generate fast and accurate atom-level structural alignments of ligand molecules, through an iterative heuristic search of the target function that combines inter-atom distance with mass and chemical bond comparisons. LS-align contains two modules of Rigid-LS-align and Flexi-LS-align, designed for rigid-body and flexible alignments, respectively, where a ligand-size independent, statistics-based scoring function is developed to evaluate the similarity of ligand molecules relative to random ligand pairs. Large-scale benchmark tests are performed on prioritizing chemical ligands of 102 protein targets involving 1,415,871 candidate compounds from the DUD-E (Database of Useful Decoys: Enhanced) database, where LS-align achieves an average enrichment factor (EF) of 22.0 at the 1% cutoff and the AUC score of 0.75, which are significantly higher than other state-of-the-art methods. Detailed data analyses show that the advanced performance is mainly attributed to the design of the target function that combines structural and chemical information to enhance the sensitivity of recognizing subtle difference of ligand molecules and the introduces of structural flexibility that help capture the conformational changes induced by the ligand-receptor binding interactions. These data demonstrate a new avenue to improve the virtual screening efficiency through the development of sensitive ligand structural alignments. http://zhanglab.ccmb.med.umich.edu/LS-align

  10. BCM-2.0 - The new version of computer code ;Basic Channeling with Mathematica©;

    NASA Astrophysics Data System (ADS)

    Abdrashitov, S. V.; Bogdanov, O. V.; Korotchenko, K. B.; Pivovarov, Yu. L.; Rozhkova, E. I.; Tukhfatullin, T. A.; Eikhorn, Yu. L.

    2017-07-01

    The new symbolic-numerical code devoted to investigation of the channeling phenomena in periodic potential of a crystal has been developed. The code has been written in Wolfram Language taking advantage of analytical programming method. Newly developed different packages were successfully applied to simulate scattering, radiation, electron-positron pair production and other effects connected with channeling of relativistic particles in aligned crystal. The result of the simulation has been validated against data from channeling experiments carried out at SAGA LS.

  11. English Speech Sound Development in Preschool-Aged Children from Bilingual English-Spanish Environments

    ERIC Educational Resources Information Center

    Gildersleeve-Neumann, Christina E.; Kester, Ellen S.; Davis, Barbara L.; Pena, Elizabeth D.

    2008-01-01

    Purpose: English speech acquisition by typically developing 3- to 4-year-old children with monolingual English was compared to English speech acquisition by typically developing 3- to 4-year-old children with bilingual English-Spanish backgrounds. We predicted that exposure to Spanish would not affect the English phonetic inventory but would…

  12. The Processing of English Derived Words by Chinese-English Bilinguals

    ERIC Educational Resources Information Center

    Li, Junmin; Taft, Marcus; Xu, Joe

    2017-01-01

    This study examined the sensitivity of Chinese-English bilinguals to derivational word structure in English. In the first experiment, English monolinguals showed masked priming effects for prime-target pairs related both transparently (e.g., "hunter-HUNT") and opaquely (e.g., "corner-CORN") but not for those related purely in…

  13. English Teaching Profile: Iraq.

    ERIC Educational Resources Information Center

    British Council, London (England). English Language and Literature Div.

    A description of the role and status of the English language in Iraq begins with an overview of the distribution of English speakers and the most common uses of English. Subsequent sections outline: (1) the use and status of English within the educational system at all levels, including teacher education; (2) the availability of English language…

  14. Reframing the Principle of Specialisation in Legitimation Code Theory: A Blended Learning Perspective

    ERIC Educational Resources Information Center

    Owusu-Agyeman, Yaw; Larbi-Siaw, Otu

    2017-01-01

    This study argues that in developing a robust framework for students in a blended learning environment, Structural Alignment (SA) becomes the third principle of specialisation in addition to Epistemic Relation (ER) and Social Relation (SR). We provide an extended code: (ER+/-, SR+/-, SA+/-) that present strong classification and framing to the…

  15. "English for the Global": Discourses in/of English-Language Voluntourism

    ERIC Educational Resources Information Center

    Jakubiak, Cori

    2012-01-01

    Drawing upon the notion of hyperglobalism and critical perspectives on English as an international language, this study examines the ways in which English language teaching via volunteer tourism (i.e. English-language voluntourism) is represented and legitimated as an altruistic practice among organizational sponsors and in the talk of current and…

  16. A generalized global alignment algorithm.

    PubMed

    Huang, Xiaoqiu; Chao, Kun-Mao

    2003-01-22

    Homologous sequences are sometimes similar over some regions but different over other regions. Homologous sequences have a much lower global similarity if the different regions are much longer than the similar regions. We present a generalized global alignment algorithm for comparing sequences with intermittent similarities, an ordered list of similar regions separated by different regions. A generalized global alignment model is defined to handle sequences with intermittent similarities. A dynamic programming algorithm is designed to compute an optimal general alignment in time proportional to the product of sequence lengths and in space proportional to the sum of sequence lengths. The algorithm is implemented as a computer program named GAP3 (Global Alignment Program Version 3). The generalized global alignment model is validated by experimental results produced with GAP3 on both DNA and protein sequences. The GAP3 program extends the ability of standard global alignment programs to recognize homologous sequences of lower similarity. The GAP3 program is freely available for academic use at http://bioinformatics.iastate.edu/aat/align/align.html.

  17. Onorbit IMU alignment error budget

    NASA Technical Reports Server (NTRS)

    Corson, R. W.

    1980-01-01

    The Star Tracker, Crew Optical Alignment Sight (COAS), and Inertial Measurement Unit (IMU) from a complex navigation system with a multitude of error sources were combined. A complete list of the system errors is presented. The errors were combined in a rational way to yield an estimate of the IMU alignment accuracy for STS-1. The expected standard deviation in the IMU alignment error for STS-1 type alignments was determined to be 72 arc seconds per axis for star tracker alignments and 188 arc seconds per axis for COAS alignments. These estimates are based on current knowledge of the star tracker, COAS, IMU, and navigation base error specifications, and were partially verified by preliminary Monte Carlo analysis.

  18. Precision alignment and mounting apparatus

    NASA Technical Reports Server (NTRS)

    Preston, Dennis R. (Inventor)

    1993-01-01

    An alignment and mounting apparatus for mounting two modules (10,12) includes a first portion having a cylindrical alignment pin (16) projecting normal to a module surface, a second portion having a three-stage alignment guide (18) including a shoehorn flange (34), a Y-slot (42) and a V-block (22) which sequentially guide the alignment pin (16) with successively finer precision and a third portion in the form of a spring-loaded captive fastener (20) for connecting the two modules after alignment is achieved.

  19. Examining the relationship between comprehension and production processes in code-switched language.

    PubMed

    Guzzardo Tamargo, Rosa E; Valdés Kroff, Jorge R; Dussias, Paola E

    2016-08-01

    We employ code-switching (the alternation of two languages in bilingual communication) to test the hypothesis, derived from experience-based models of processing (e.g., Boland, Tanenhaus, Carlson, & Garnsey, 1989; Gennari & MacDonald, 2009), that bilinguals are sensitive to the combinatorial distributional patterns derived from production and that they use this information to guide processing during the comprehension of code-switched sentences. An analysis of spontaneous bilingual speech confirmed the existence of production asymmetries involving two auxiliary + participle phrases in Spanish-English code-switches. A subsequent eye-tracking study with two groups of bilingual code-switchers examined the consequences of the differences in distributional patterns found in the corpus study for comprehension. Participants' comprehension costs mirrored the production patterns found in the corpus study. Findings are discussed in terms of the constraints that may be responsible for the distributional patterns in code-switching production and are situated within recent proposals of the links between production and comprehension.

  20. Examining the relationship between comprehension and production processes in code-switched language

    PubMed Central

    Guzzardo Tamargo, Rosa E.; Valdés Kroff, Jorge R.; Dussias, Paola E.

    2016-01-01

    We employ code-switching (the alternation of two languages in bilingual communication) to test the hypothesis, derived from experience-based models of processing (e.g., Boland, Tanenhaus, Carlson, & Garnsey, 1989; Gennari & MacDonald, 2009), that bilinguals are sensitive to the combinatorial distributional patterns derived from production and that they use this information to guide processing during the comprehension of code-switched sentences. An analysis of spontaneous bilingual speech confirmed the existence of production asymmetries involving two auxiliary + participle phrases in Spanish–English code-switches. A subsequent eye-tracking study with two groups of bilingual code-switchers examined the consequences of the differences in distributional patterns found in the corpus study for comprehension. Participants’ comprehension costs mirrored the production patterns found in the corpus study. Findings are discussed in terms of the constraints that may be responsible for the distributional patterns in code-switching production and are situated within recent proposals of the links between production and comprehension. PMID:28670049

  1. A new method for species identification via protein-coding and non-coding DNA barcodes by combining machine learning with bioinformatic methods.

    PubMed

    Zhang, Ai-bing; Feng, Jie; Ward, Robert D; Wan, Ping; Gao, Qiang; Wu, Jun; Zhao, Wei-zhong

    2012-01-01

    Species identification via DNA barcodes is contributing greatly to current bioinventory efforts. The initial, and widely accepted, proposal was to use the protein-coding cytochrome c oxidase subunit I (COI) region as the standard barcode for animals, but recently non-coding internal transcribed spacer (ITS) genes have been proposed as candidate barcodes for both animals and plants. However, achieving a robust alignment for non-coding regions can be problematic. Here we propose two new methods (DV-RBF and FJ-RBF) to address this issue for species assignment by both coding and non-coding sequences that take advantage of the power of machine learning and bioinformatics. We demonstrate the value of the new methods with four empirical datasets, two representing typical protein-coding COI barcode datasets (neotropical bats and marine fish) and two representing non-coding ITS barcodes (rust fungi and brown algae). Using two random sub-sampling approaches, we demonstrate that the new methods significantly outperformed existing Neighbor-joining (NJ) and Maximum likelihood (ML) methods for both coding and non-coding barcodes when there was complete species coverage in the reference dataset. The new methods also out-performed NJ and ML methods for non-coding sequences in circumstances of potentially incomplete species coverage, although then the NJ and ML methods performed slightly better than the new methods for protein-coding barcodes. A 100% success rate of species identification was achieved with the two new methods for 4,122 bat queries and 5,134 fish queries using COI barcodes, with 95% confidence intervals (CI) of 99.75-100%. The new methods also obtained a 96.29% success rate (95%CI: 91.62-98.40%) for 484 rust fungi queries and a 98.50% success rate (95%CI: 96.60-99.37%) for 1094 brown algae queries, both using ITS barcodes.

  2. A UNIFIED MODEL OF GRAIN ALIGNMENT: RADIATIVE ALIGNMENT OF INTERSTELLAR GRAINS WITH MAGNETIC INCLUSIONS

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

    Hoang, Thiem; Lazarian, A.

    The radiative torque (RAT) alignment of interstellar grains with ordinary paramagnetic susceptibilities has been supported by earlier studies. The alignment of such grains depends on the so-called RAT parameter q {sup max}, which is determined by the grain shape. In this paper, we elaborate on our model of RAT alignment for grains with enhanced magnetic susceptibility due to iron inclusions, such that RAT alignment is magnetically enhanced, which we term the MRAT mechanism. Such grains can be aligned with high angular momentum at the so-called high- J attractor points, achieving a high degree of alignment. Using our analytical model ofmore » RATs, we derive the critical value of the magnetic relaxation parameter δ {sub m} to produce high- J attractor points as functions of q {sup max} and the anisotropic radiation angle relative to the magnetic field ψ . We find that if about 10% of the total iron abundance present in silicate grains is forming iron clusters, this is sufficient to produce high- J attractor points for all reasonable values of q {sup max}. To calculate the degree of grain alignment, we carry out numerical simulations of MRAT alignment by including stochastic excitations from gas collisions and magnetic fluctuations. We show that large grains can achieve perfect alignment when the high- J attractor point is present, regardless of the values of q {sup max}. Our obtained results pave the way for the physical modeling of polarized thermal dust emission as well as magnetic dipole emission. We also find that millimeter-sized grains in accretion disks may be aligned with the magnetic field if they are incorporated with iron nanoparticles.« less

  3. Remapping Englishness--the Impact of Globalization on College English Instruction in Taiwan

    ERIC Educational Resources Information Center

    Lee, Jade Tsui-yu

    2008-01-01

    The purpose of this paper is to examine the impact of globalization upon the college-level instruction of English/American literature in Taiwan. The examination will be centered upon the subject of Englishness as demonstrated in the courses of English/American Literature taught in Taiwan. By focusing on the term "Englishness," the paper…

  4. Why Do Primary School English Teachers Decide to Teach English?

    ERIC Educational Resources Information Center

    Amengual-Pizarro, Marian; Garcia Laborda, Jesus

    2015-01-01

    This study is an attempt to explore the nature of L2 teachers' motivation towards English language learning and their decision to become English teachers. A total of 45 third-year prospective Primary school English teachers at the University of the Balearic Islands completed a small-scale survey adapted from Gardner's Attitude/Motivation Test…

  5. The Trouble Is English: Reframing English Studies in Secondary Schools

    ERIC Educational Resources Information Center

    Brauer, Lydia; Clark, Caroline T.

    2008-01-01

    Sybil Wilson is a composite representation of an English teacher that typifies much of what most preservice English teachers have seen and experienced in U.S. classrooms. The authors' aim is to articulate textual frameworks often competing and unnamed in English curriculum (and evident in Sybil's classroom) and to argue for a particular reframing…

  6. World Englishes, English as an International Language and Applied Linguistics

    ERIC Educational Resources Information Center

    Kilickaya, Ferit

    2009-01-01

    The paper discusses World Englishes (WEs) in relation to English as an International Language (EIL) and Applied Linguistics. Taking into account Kachru's interesting but at the same time controversial debate about the status of English in its varieties, which are commonly called WEs and the opposing ideas presented by Quirk, it is aimed to present…

  7. Comparing Bilingual to Monolingual Learners on English Spelling: A Meta-analytic Review.

    PubMed

    Zhao, Jing; Quiroz, Blanca; Dixon, L Quentin; Joshi, R Malatesha

    2016-08-01

    This study reports on a meta-analysis to examine how bilingual learners compare with English monolingual learners on two English spelling outcomes: real-word spelling and pseudo-word spelling. Eighteen studies published in peer-reviewed journals between 1990 and 2014 were retrieved. The study-level variables and characteristics (e.g. sample size, study design and research instruments) were coded, and 29 independent effect sizes across the 18 retrieved studies were analysed. We found that bilinguals outperformed monolinguals on real-word spelling overall and more so in early grades, but monolinguals outperformed bilinguals on pseudo-word spelling. Further, bilinguals at risk for reading difficulties did better on real-word spelling than monolinguals at risk for reading difficulties. Having investigated systematic sources of variability in effect sizes, we conclude that in comparison with their monolingual peers, bilingual learners, especially those from alphabetic L1 backgrounds, are able to master constrained skills, such as English spelling, in the current instructional context. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  8. English Clubs: Introducing English to Young Learners

    ERIC Educational Resources Information Center

    Afia, Jawida Ben

    2006-01-01

    This article introduces an approach taken in Tunisia to introduce English as a foreign language to children in primary school classrooms. The author states that in Tunisia, children in primary schools are first taught Arabic and then French. The government does not want to overburden the students with English learning. Then, the author describes…

  9. English in Fiji.

    ERIC Educational Resources Information Center

    Siegel, Jeff

    1989-01-01

    Traces the history of English in Fiji, especially in relation to education. The role of English in interethnic communication and as a language of wider communication with the outside world is discussed, and features of Fiji English, a local language variety, are described. (Author/CB)

  10. Reasoning over taxonomic change: exploring alignments for the Perelleschus use case.

    PubMed

    Franz, Nico M; Chen, Mingmin; Yu, Shizhuo; Kianmajd, Parisa; Bowers, Shawn; Ludäscher, Bertram

    2015-01-01

    Classifications and phylogenetic inferences of organismal groups change in light of new insights. Over time these changes can result in an imperfect tracking of taxonomic perspectives through the re-/use of Code-compliant or informal names. To mitigate these limitations, we introduce a novel approach for aligning taxonomies through the interaction of human experts and logic reasoners. We explore the performance of this approach with the Perelleschus use case of Franz & Cardona-Duque (2013). The use case includes six taxonomies published from 1936 to 2013, 54 taxonomic concepts (i.e., circumscriptions of names individuated according to their respective source publications), and 75 expert-asserted Region Connection Calculus articulations (e.g., congruence, proper inclusion, overlap, or exclusion). An Open Source reasoning toolkit is used to analyze 13 paired Perelleschus taxonomy alignments under heterogeneous constraints and interpretations. The reasoning workflow optimizes the logical consistency and expressiveness of the input and infers the set of maximally informative relations among the entailed taxonomic concepts. The latter are then used to produce merge visualizations that represent all congruent and non-congruent taxonomic elements among the aligned input trees. In this small use case with 6-53 input concepts per alignment, the information gained through the reasoning process is on average one order of magnitude greater than in the input. The approach offers scalable solutions for tracking provenance among succeeding taxonomic perspectives that may have differential biases in naming conventions, phylogenetic resolution, ingroup and outgroup sampling, or ostensive (member-referencing) versus intensional (property-referencing) concepts and articulations.

  11. Reasoning over Taxonomic Change: Exploring Alignments for the Perelleschus Use Case

    PubMed Central

    Franz, Nico M.; Chen, Mingmin; Yu, Shizhuo; Kianmajd, Parisa; Bowers, Shawn; Ludäscher, Bertram

    2015-01-01

    Classifications and phylogenetic inferences of organismal groups change in light of new insights. Over time these changes can result in an imperfect tracking of taxonomic perspectives through the re-/use of Code-compliant or informal names. To mitigate these limitations, we introduce a novel approach for aligning taxonomies through the interaction of human experts and logic reasoners. We explore the performance of this approach with the Perelleschus use case of Franz & Cardona-Duque (2013). The use case includes six taxonomies published from 1936 to 2013, 54 taxonomic concepts (i.e., circumscriptions of names individuated according to their respective source publications), and 75 expert-asserted Region Connection Calculus articulations (e.g., congruence, proper inclusion, overlap, or exclusion). An Open Source reasoning toolkit is used to analyze 13 paired Perelleschus taxonomy alignments under heterogeneous constraints and interpretations. The reasoning workflow optimizes the logical consistency and expressiveness of the input and infers the set of maximally informative relations among the entailed taxonomic concepts. The latter are then used to produce merge visualizations that represent all congruent and non-congruent taxonomic elements among the aligned input trees. In this small use case with 6-53 input concepts per alignment, the information gained through the reasoning process is on average one order of magnitude greater than in the input. The approach offers scalable solutions for tracking provenance among succeeding taxonomic perspectives that may have differential biases in naming conventions, phylogenetic resolution, ingroup and outgroup sampling, or ostensive (member-referencing) versus intensional (property-referencing) concepts and articulations. PMID:25700173

  12. Base-By-Base: single nucleotide-level analysis of whole viral genome alignments.

    PubMed

    Brodie, Ryan; Smith, Alex J; Roper, Rachel L; Tcherepanov, Vasily; Upton, Chris

    2004-07-14

    With ever increasing numbers of closely related virus genomes being sequenced, it has become desirable to be able to compare two genomes at a level more detailed than gene content because two strains of an organism may share the same set of predicted genes but still differ in their pathogenicity profiles. For example, detailed comparison of multiple isolates of the smallpox virus genome (each approximately 200 kb, with 200 genes) is not feasible without new bioinformatics tools. A software package, Base-By-Base, has been developed that provides visualization tools to enable researchers to 1) rapidly identify and correct alignment errors in large, multiple genome alignments; and 2) generate tabular and graphical output of differences between the genomes at the nucleotide level. Base-By-Base uses detailed annotation information about the aligned genomes and can list each predicted gene with nucleotide differences, display whether variations occur within promoter regions or coding regions and whether these changes result in amino acid substitutions. Base-By-Base can connect to our mySQL database (Virus Orthologous Clusters; VOCs) to retrieve detailed annotation information about the aligned genomes or use information from text files. Base-By-Base enables users to quickly and easily compare large viral genomes; it highlights small differences that may be responsible for important phenotypic differences such as virulence. It is available via the Internet using Java Web Start and runs on Macintosh, PC and Linux operating systems with the Java 1.4 virtual machine.

  13. Nuclear reactor internals alignment configuration

    DOEpatents

    Gilmore, Charles B [Greensburg, PA; Singleton, Norman R [Murrysville, PA

    2009-11-10

    An alignment system that employs jacking block assemblies and alignment posts around the periphery of the top plate of a nuclear reactor lower internals core shroud to align an upper core plate with the lower internals and the core shroud with the core barrel. The distal ends of the alignment posts are chamfered and are closely received within notches machined in the upper core plate at spaced locations around the outer circumference of the upper core plate. The jacking block assemblies are used to center the core shroud in the core barrel and the alignment posts assure the proper orientation of the upper core plate. The alignment posts may alternately be formed in the upper core plate and the notches may be formed in top plate.

  14. ENGLISH FOR TODAY. BOOK FIVE, LIFE IN ENGLISH-SPEAKING COUNTRIES.

    ERIC Educational Resources Information Center

    SLAGER, WILLIAM R.; AND OTHERS

    ON AN UPPER-INTERMEDIATE TO ADVANCED LEVEL OF ENGLISH AS A FOREIGN LANGUAGE FOR SECONDARY STUDENTS, "LIFE IN ENGLISH-SPEAKING COUNTRIES" IS THE FIFTH VOLUME IN THE "ENGLISH FOR TODAY" SERIES. THE MAIN EMPHASIS IN THIS VOLUME IS THE TRANSITION FROM READING TO COMPOSITION. EACH OF THE 14 READINGS IS FOLLOWED BY INTENSIVE COMPREHENSION QUESTIONS,…

  15. BAYESIAN PROTEIN STRUCTURE ALIGNMENT.

    PubMed

    Rodriguez, Abel; Schmidler, Scott C

    The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over evolutionary timescales. A key challenge is the identification and evaluation of structural similarity between proteins; such analysis can aid in understanding the role of newly discovered proteins and help elucidate evolutionary relationships between organisms. Computational biologists have developed many clever algorithmic techniques for comparing protein structures, however, all are based on heuristic optimization criteria, making statistical interpretation somewhat difficult. Here we present a fully probabilistic framework for pairwise structural alignment of proteins. Our approach has several advantages, including the ability to capture alignment uncertainty and to estimate key "gap" parameters which critically affect the quality of the alignment. We show that several existing alignment methods arise as maximum a posteriori estimates under specific choices of prior distributions and error models. Our probabilistic framework is also easily extended to incorporate additional information, which we demonstrate by including primary sequence information to generate simultaneous sequence-structure alignments that can resolve ambiguities obtained using structure alone. This combined model also provides a natural approach for the difficult task of estimating evolutionary distance based on structural alignments. The model is illustrated by comparison with well-established methods on several challenging protein alignment examples.

  16. Shifting to the World Englishes Paradigm by Way of the Translingual Approach: Code-Meshing as a Necessary Means of Transforming Composition Pedagogy

    ERIC Educational Resources Information Center

    Lee, Melissa E.

    2014-01-01

    "English" classrooms in U.S. institutions of higher education are not linguistically homogeneous. It is not logical, ethical, or realistic to designate "standard" English as the only discourse acceptable for the writing classroom. This praxis-oriented article chronicles a U.S. composition instructor's process of…

  17. “There Are Too Many, but Never Enough": Qualitative Case Study Investigating Routine Coding of Clinical Information in Depression

    PubMed Central

    Cresswell, Kathrin; Morrison, Zoe; Sheikh, Aziz; Kalra, Dipak

    2012-01-01

    Background We sought to understand how clinical information relating to the management of depression is routinely coded in different clinical settings and the perspectives of and implications for different stakeholders with a view to understanding how these may be aligned. Materials and Methods Qualitative investigation exploring the views of a purposefully selected range of healthcare professionals, managers, and clinical coders spanning primary and secondary care. Results Our dataset comprised 28 semi-structured interviews, a focus group, documents relating to clinical coding standards and participant observation of clinical coding activities. We identified a range of approaches to coding clinical information including templates and order entry systems. The challenges inherent in clearly establishing a diagnosis, identifying appropriate clinical codes and possible implications of diagnoses for patients were particularly prominent in primary care. Although a range of managerial and research benefits were identified, there were no direct benefits from coded clinical data for patients or professionals. Secondary care staff emphasized the role of clinical coders in ensuring data quality, which was at odds with the policy drive to increase real-time clinical coding. Conclusions There was overall no evidence of clear-cut direct patient care benefits to inform immediate care decisions, even in primary care where data on patients with depression were more extensively coded. A number of important secondary uses were recognized by healthcare staff, but the coding of clinical data to serve these ends was often poorly aligned with clinical practice and patient-centered considerations. The current international drive to encourage clinical coding by healthcare professionals during the clinical encounter may need to be critically examined. PMID:22937106

  18. Galaxy Alignments: Theory, Modelling & Simulations

    NASA Astrophysics Data System (ADS)

    Kiessling, Alina; Cacciato, Marcello; Joachimi, Benjamin; Kirk, Donnacha; Kitching, Thomas D.; Leonard, Adrienne; Mandelbaum, Rachel; Schäfer, Björn Malte; Sifón, Cristóbal; Brown, Michael L.; Rassat, Anais

    2015-11-01

    The shapes of galaxies are not randomly oriented on the sky. During the galaxy formation and evolution process, environment has a strong influence, as tidal gravitational fields in the large-scale structure tend to align nearby galaxies. Additionally, events such as galaxy mergers affect the relative alignments of both the shapes and angular momenta of galaxies throughout their history. These "intrinsic galaxy alignments" are known to exist, but are still poorly understood. This review will offer a pedagogical introduction to the current theories that describe intrinsic galaxy alignments, including the apparent difference in intrinsic alignment between early- and late-type galaxies and the latest efforts to model them analytically. It will then describe the ongoing efforts to simulate intrinsic alignments using both N-body and hydrodynamic simulations. Due to the relative youth of this field, there is still much to be done to understand intrinsic galaxy alignments and this review summarises the current state of the field, providing a solid basis for future work.

  19. Implied alignment: a synapomorphy-based multiple-sequence alignment method and its use in cladogram search

    NASA Technical Reports Server (NTRS)

    Wheeler, Ward C.

    2003-01-01

    A method to align sequence data based on parsimonious synapomorphy schemes generated by direct optimization (DO; earlier termed optimization alignment) is proposed. DO directly diagnoses sequence data on cladograms without an intervening multiple-alignment step, thereby creating topology-specific, dynamic homology statements. Hence, no multiple-alignment is required to generate cladograms. Unlike general and globally optimal multiple-alignment procedures, the method described here, implied alignment (IA), takes these dynamic homologies and traces them back through a single cladogram, linking the unaligned sequence positions in the terminal taxa via DO transformation series. These "lines of correspondence" link ancestor-descendent states and, when displayed as linearly arrayed columns without hypothetical ancestors, are largely indistinguishable from standard multiple alignment. Since this method is based on synapomorphy, the treatment of certain classes of insertion-deletion (indel) events may be different from that of other alignment procedures. As with all alignment methods, results are dependent on parameter assumptions such as indel cost and transversion:transition ratios. Such an IA could be used as a basis for phylogenetic search, but this would be questionable since the homologies derived from the implied alignment depend on its natal cladogram and any variance, between DO and IA + Search, due to heuristic approach. The utility of this procedure in heuristic cladogram searches using DO and the improvement of heuristic cladogram cost calculations are discussed. c2003 The Willi Hennig Society. Published by Elsevier Science (USA). All rights reserved.

  20. Relation between film character and wafer alignment: critical alignment issues on HV device for VLSI manufacturing

    NASA Astrophysics Data System (ADS)

    Lo, Yi-Chuan; Lee, Chih-Hsiung; Lin, Hsun-Peng; Peng, Chiou-Shian

    1998-06-01

    Several continuous splits for wafer alignment target topography conditions to improve epitaxy film alignment were applied. The alignment evaluation among former layer pad oxide thickness (250 angstrom - 500 angstrom), drive oxide thickness (6000 angstrom - 10000 angstrom), nitride film thickness (600 angstrom - 1500 angstrom), initial oxide etch (fully wet etch, fully dry etch and dry plus wet etch) will be split to this experiment. Also various epitaxy deposition recipe such as: epitaxy source (SiHCl2 or SiCHCl3) and growth rate (1.3 micrometer/min approximately 2.0 micrometer/min) will be used to optimize the process window for alignment issue. All the reflectance signal and cross section photography of alignment target during NIKON stepper alignment process will be examined. Experimental results show epitaxy recipe plays an important role to wafer alignment. Low growth rate with good performance conformity epitaxy lead to alignment target avoid washout, pattern shift and distortion. All the results (signal monitor and film character) combined with NIKON's stepper standard laser scanning alignment system will be discussed in this paper.

  1. An algebraic hypothesis about the primeval genetic code architecture.

    PubMed

    Sánchez, Robersy; Grau, Ricardo

    2009-09-01

    A plausible architecture of an ancient genetic code is derived from an extended base triplet vector space over the Galois field of the extended base alphabet {D,A,C,G,U}, where symbol D represents one or more hypothetical bases with unspecific pairings. We hypothesized that the high degeneration of a primeval genetic code with five bases and the gradual origin and improvement of a primeval DNA repair system could make possible the transition from ancient to modern genetic codes. Our results suggest that the Watson-Crick base pairing G identical with C and A=U and the non-specific base pairing of the hypothetical ancestral base D used to define the sum and product operations are enough features to determine the coding constraints of the primeval and the modern genetic code, as well as, the transition from the former to the latter. Geometrical and algebraic properties of this vector space reveal that the present codon assignment of the standard genetic code could be induced from a primeval codon assignment. Besides, the Fourier spectrum of the extended DNA genome sequences derived from the multiple sequence alignment suggests that the called period-3 property of the present coding DNA sequences could also exist in the ancient coding DNA sequences. The phylogenetic analyses achieved with metrics defined in the N-dimensional vector space (B(3))(N) of DNA sequences and with the new evolutionary model presented here also suggest that an ancient DNA coding sequence with five or more bases does not contradict the expected evolutionary history.

  2. BigBWA: approaching the Burrows-Wheeler aligner to Big Data technologies.

    PubMed

    Abuín, José M; Pichel, Juan C; Pena, Tomás F; Amigo, Jorge

    2015-12-15

    BigBWA is a new tool that uses the Big Data technology Hadoop to boost the performance of the Burrows-Wheeler aligner (BWA). Important reductions in the execution times were observed when using this tool. In addition, BigBWA is fault tolerant and it does not require any modification of the original BWA source code. BigBWA is available at the project GitHub repository: https://github.com/citiususc/BigBWA. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  3. Importance of Phonological and Orthographic Skills for English Reading and Spelling: A Comparison of English Monolingual and Mandarin-English Bilingual Children

    ERIC Educational Resources Information Center

    Yeong, Stephanie H. M.; Fletcher, Janet; Bayliss, Donna M.

    2014-01-01

    This cross-sectional study examines the importance of English phonological and orthographic processing skills to English word reading and spelling in 3 groups of younger (8-9 years) and older (11-12 years) children from different language backgrounds: English monolingual, English first language (L1)-Mandarin second language (L2), and Mandarin…

  4. Pairwise Sequence Alignment Library

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

    Jeff Daily, PNNL

    2015-05-20

    Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, amore » novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.« less

  5. Alignment-free protein interaction network comparison

    PubMed Central

    Ali, Waqar; Rito, Tiago; Reinert, Gesine; Sun, Fengzhu; Deane, Charlotte M.

    2014-01-01

    Motivation: Biological network comparison software largely relies on the concept of alignment where close matches between the nodes of two or more networks are sought. These node matches are based on sequence similarity and/or interaction patterns. However, because of the incomplete and error-prone datasets currently available, such methods have had limited success. Moreover, the results of network alignment are in general not amenable for distance-based evolutionary analysis of sets of networks. In this article, we describe Netdis, a topology-based distance measure between networks, which offers the possibility of network phylogeny reconstruction. Results: We first demonstrate that Netdis is able to correctly separate different random graph model types independent of network size and density. The biological applicability of the method is then shown by its ability to build the correct phylogenetic tree of species based solely on the topology of current protein interaction networks. Our results provide new evidence that the topology of protein interaction networks contains information about evolutionary processes, despite the lack of conservation of individual interactions. As Netdis is applicable to all networks because of its speed and simplicity, we apply it to a large collection of biological and non-biological networks where it clusters diverse networks by type. Availability and implementation: The source code of the program is freely available at http://www.stats.ox.ac.uk/research/proteins/resources. Contact: w.ali@stats.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25161230

  6. Antares alignment gimbal positioner

    NASA Astrophysics Data System (ADS)

    Day, R. D.; Viswanathan, V. K.; Saxman, A. C.; Lujan, R. E.; Woodfin, W. C.; Sweatt, W. C.

    Antares is a 24-beam 40-TW carbon dioxide (CO2) laser fusion system currently under construction at the Los Alamos National Laboratory. The Antares alignment gimbal positioner (AGP) is an optomechanical instrument that will be used for target alignment and alignment of the 24 laser beams, as well as beam quality assessments. The AGP will be capable of providing pointing, focusing, an wavefront optical path difference, as well as aberration information at both helium neon (He-Ne) and CO2 wavelengths. It is designed to allow the laser beams to be aligned to any position within a 1 cm cube to a tolerance of 10 micrometers.

  7. Antares Alignment Gimbal Positioner

    NASA Astrophysics Data System (ADS)

    Day, R. D.; Viswanathan, V. K.; Saxman, A. C.; Lujan, R. E.; Woodfin, G. L.; Sweatt, W. C.

    1981-12-01

    Antares is a 24-beam 40-TW carbon-dioxide (CO2) laser fusion system currently under construction at the Los Alamos National Laboratory. The Antares alignment gimbal positioner (AGP) is an optomechanical instrument that will be used for target alignment and alignment of the 24 laser beams, as well as beam quality assessments. The AGP will be capable of providing pointing, focusing, and wavefront optical path difference, as well as aberration information at both helium-neon (He-Ne) and CO2 wavelengths. It is designed to allow the laser beams to be aligned to any position within a 1-cm cube to a tolerance of 10 μm.

  8. A method of alignment masking for refining the phylogenetic signal of multiple sequence alignments.

    PubMed

    Rajan, Vaibhav

    2013-03-01

    Inaccurate inference of positional homologies in multiple sequence alignments and systematic errors introduced by alignment heuristics obfuscate phylogenetic inference. Alignment masking, the elimination of phylogenetically uninformative or misleading sites from an alignment before phylogenetic analysis, is a common practice in phylogenetic analysis. Although masking is often done manually, automated methods are necessary to handle the much larger data sets being prepared today. In this study, we introduce the concept of subsplits and demonstrate their use in extracting phylogenetic signal from alignments. We design a clustering approach for alignment masking where each cluster contains similar columns-similarity being defined on the basis of compatible subsplits; our approach then identifies noisy clusters and eliminates them. Trees inferred from the columns in the retained clusters are found to be topologically closer to the reference trees. We test our method on numerous standard benchmarks (both synthetic and biological data sets) and compare its performance with other methods of alignment masking. We find that our method can eliminate sites more accurately than other methods, particularly on divergent data, and can improve the topologies of the inferred trees in likelihood-based analyses. Software available upon request from the author.

  9. English Teaching Profile: Korea.

    ERIC Educational Resources Information Center

    British Council, London (England). English Language and Literature Div.

    The role and status of English instruction in Korea is outlined. The role of English in Korea as a whole, English instruction within the educational system, language teacher training, textbook use, educational administration, educational development and planning, English instruction outside of the educational system, British and American support…

  10. Japanese Media in English.

    ERIC Educational Resources Information Center

    Tanaka, Sachiko Oda

    1995-01-01

    Describes the use of English in the media in Japan, focusing on the role and history of English-language newspapers, radio, and television programs, as well as the proliferation of English-language films shown in Japanese cinemas. Discusses the implications of English in the Japanese media. (20 references) (MDM)

  11. English as "Tyrannosaurus Rex."

    ERIC Educational Resources Information Center

    Swales, John M.

    1997-01-01

    The increasing domination of English as the world's leading medium of international professional communication has begun to impact English for Academic Purposes (EAP) programs, specifically the question of whether English is becoming too successful. The article argues that resistance to the "triumphalism" of English is a responsibility of EAP…

  12. icoshift: A versatile tool for the rapid alignment of 1D NMR spectra

    NASA Astrophysics Data System (ADS)

    Savorani, F.; Tomasi, G.; Engelsen, S. B.

    2010-02-01

    The increasing scientific and industrial interest towards metabonomics takes advantage from the high qualitative and quantitative information level of nuclear magnetic resonance (NMR) spectroscopy. However, several chemical and physical factors can affect the absolute and the relative position of an NMR signal and it is not always possible or desirable to eliminate these effects a priori. To remove misalignment of NMR signals a posteriori, several algorithms have been proposed in the literature. The icoshift program presented here is an open source and highly efficient program designed for solving signal alignment problems in metabonomic NMR data analysis. The icoshift algorithm is based on correlation shifting of spectral intervals and employs an FFT engine that aligns all spectra simultaneously. The algorithm is demonstrated to be faster than similar methods found in the literature making full-resolution alignment of large datasets feasible and thus avoiding down-sampling steps such as binning. The algorithm uses missing values as a filling alternative in order to avoid spectral artifacts at the segment boundaries. The algorithm is made open source and the Matlab code including documentation can be downloaded from www.models.life.ku.dk.

  13. cljam: a library for handling DNA sequence alignment/map (SAM) with parallel processing.

    PubMed

    Takeuchi, Toshiki; Yamada, Atsuo; Aoki, Takashi; Nishimura, Kunihiro

    2016-01-01

    Next-generation sequencing can determine DNA bases and the results of sequence alignments are generally stored in files in the Sequence Alignment/Map (SAM) format and the compressed binary version (BAM) of it. SAMtools is a typical tool for dealing with files in the SAM/BAM format. SAMtools has various functions, including detection of variants, visualization of alignments, indexing, extraction of parts of the data and loci, and conversion of file formats. It is written in C and can execute fast. However, SAMtools requires an additional implementation to be used in parallel with, for example, OpenMP (Open Multi-Processing) libraries. For the accumulation of next-generation sequencing data, a simple parallelization program, which can support cloud and PC cluster environments, is required. We have developed cljam using the Clojure programming language, which simplifies parallel programming, to handle SAM/BAM data. Cljam can run in a Java runtime environment (e.g., Windows, Linux, Mac OS X) with Clojure. Cljam can process and analyze SAM/BAM files in parallel and at high speed. The execution time with cljam is almost the same as with SAMtools. The cljam code is written in Clojure and has fewer lines than other similar tools.

  14. Iterative non-sequential protein structural alignment.

    PubMed

    Salem, Saeed; Zaki, Mohammed J; Bystroff, Christopher

    2009-06-01

    Structural similarity between proteins gives us insights into their evolutionary relationships when there is low sequence similarity. In this paper, we present a novel approach called SNAP for non-sequential pair-wise structural alignment. Starting from an initial alignment, our approach iterates over a two-step process consisting of a superposition step and an alignment step, until convergence. We propose a novel greedy algorithm to construct both sequential and non-sequential alignments. The quality of SNAP alignments were assessed by comparing against the manually curated reference alignments in the challenging SISY and RIPC datasets. Moreover, when applied to a dataset of 4410 protein pairs selected from the CATH database, SNAP produced longer alignments with lower rmsd than several state-of-the-art alignment methods. Classification of folds using SNAP alignments was both highly sensitive and highly selective. The SNAP software along with the datasets are available online at http://www.cs.rpi.edu/~zaki/software/SNAP.

  15. Do the symptoms of language disorder align with treatment goals? An exploratory study of primary-grade students' IEPs.

    PubMed

    Schmitt, Mary Beth; Justice, Laura M; Logan, Jessica A R; Schatschneider, Christopher; Bartlett, Christopher W

    2014-01-01

    Individual Education Plans (IEPs) are legal documents that guide the treatment of students with language disorder (LD). This exploratory study investigated the extent to which students' symptoms of LD align with goals on their IEPs. A total of 99 kindergarten and first-grade students receiving treatment for LD in the public schools participated. IEPs were collected and coded for each student and norm-referenced measures were used to assess students' grammar, vocabulary, listening comprehension, and literacy skills in the fall of the academic year. Results showed there to be alignment between students' symptoms and IEP goals only in the area of vocabulary, such that students who had an IEP goal for vocabulary had lower scores on a vocabulary assessment than those without a goal. In general, there is limited alignment between observed symptoms of LD and treated symptoms as identified on students' IEPs. The limited alignment found in this study suggests more investigation is needed to understand the extent to which IEP goals, as potential indicators of treatment foci, should map on to students' symptoms. Readers will be able to: (1) explain the theoretical and practical relevance of treatment goals aligning to symptoms for children with language impairment; (2) identify three analytic methods used to investigate alignment between treatment goals and symptoms; and (3) describe the extent to which IEP goals align to children's symptoms in a sample of children receiving services in the public schools. Copyright © 2014 Elsevier Inc. All rights reserved.

  16. Fingerspelled and Printed Words Are Recoded into a Speech-based Code in Short-term Memory.

    PubMed

    Sehyr, Zed Sevcikova; Petrich, Jennifer; Emmorey, Karen

    2017-01-01

    We conducted three immediate serial recall experiments that manipulated type of stimulus presentation (printed or fingerspelled words) and word similarity (speech-based or manual). Matched deaf American Sign Language signers and hearing non-signers participated (mean reading age = 14-15 years). Speech-based similarity effects were found for both stimulus types indicating that deaf signers recoded both printed and fingerspelled words into a speech-based phonological code. A manual similarity effect was not observed for printed words indicating that print was not recoded into fingerspelling (FS). A manual similarity effect was observed for fingerspelled words when similarity was based on joint angles rather than on handshape compactness. However, a follow-up experiment suggested that the manual similarity effect was due to perceptual confusion at encoding. Overall, these findings suggest that FS is strongly linked to English phonology for deaf adult signers who are relatively skilled readers. This link between fingerspelled words and English phonology allows for the use of a more efficient speech-based code for retaining fingerspelled words in short-term memory and may strengthen the representation of English vocabulary. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  17. Simulation of neoclassical transport with the continuum gyrokinetic code COGENT

    DOE PAGES

    Dorf, M. A.; Cohen, R. H.; Dorr, M.; ...

    2013-01-25

    The development of the continuum gyrokinetic code COGENT for edge plasma simulations is reported. The present version of the code models a nonlinear axisymmetric 4D (R, v∥, μ) gyrokinetic equation coupled to the long-wavelength limit of the gyro-Poisson equation. Here, R is the particle gyrocenter coordinate in the poloidal plane, and v∥ and μ are the guiding center velocity parallel to the magnetic field and the magnetic moment, respectively. The COGENT code utilizes a fourth-order finite-volume (conservative) discretization combined with arbitrary mapped multiblock grid technology (nearly field-aligned on blocks) to handle the complexity of tokamak divertor geometry with high accuracy.more » Furthermore, topics presented are the implementation of increasingly detailed model collision operators, and the results of neoclassical transport simulations including the effects of a strong radial electric field characteristic of a tokamak pedestal under H-mode conditions.« less

  18. On Observing World English.

    ERIC Educational Resources Information Center

    Urdang, Lawrence

    1990-01-01

    Reviews the current state of World English. Subjects addressed include standard accents and dialects, prejudicial attitudes toward nonstandard "local" usages, the use of English as the language of diplomacy, American influences on the language, and the fracturing of English in non-English-speaking countries around the world. (17 references) (JL)

  19. Chinese College Students' Views on Native English and Non-Native English in EFL Classrooms

    ERIC Educational Resources Information Center

    Qian, Yang; Jingxia, Liu

    2016-01-01

    With the development of globalization, English is clearly spoken by many more non-native than native speakers, which raises the discussion of English varieties and the debate regarding the conformity to Standard English. Although a large number of studies have shown scholars' attitudes towards native English and non-native English, little research…

  20. A Language without Borders: English Slang and Bulgarian Learners of English

    ERIC Educational Resources Information Center

    Charkova, Krassimira D.

    2007-01-01

    This study investigated the acquisition of English slang in a foreign language context. The participants were 101 Bulgarian learners of English, 58 high school students, and 43 university students. The instrument included knowledge tests of English slang terms and questions about attitudes, sources, reasons, and methods employed in learning…

  1. Study on Correlation of English Pronunciation Self-Concept to English Learning

    ERIC Educational Resources Information Center

    Tang, Xin; Zhang, Shengqi; Li, Yucong; Zhao, Miqiang

    2013-01-01

    English pronunciation self-concept is formed in the process of pronunciation learning, which refers to the learners' self-conception and assessment of one's English pronunciation proficiency and pronunciation (Gimson, A. C. 1980). This paper reports an investigation on 237 non-English major college students into the relationship between English…

  2. Can bilingual two-year-olds code-switch?

    PubMed

    Lanza, E

    1992-10-01

    Sociolinguists have investigated language mixing as code-switching in the speech of bilingual children three years old and older. Language mixing by bilingual two-year-olds, however, has generally been interpreted in the child language literature as a sign of the child's lack of language differentiation. The present study applies perspectives from sociolinguistics to investigate the language mixing of a bilingual two-year-old acquiring Norwegian and English simultaneously in Norway. Monthly recordings of the child's spontaneous speech in interactions with her parents were made from the age of 2;0 to 2;7. An investigation into the formal aspects of the child's mixing and the context of the mixing reveals that she does differentiate her language use in contextually sensitive ways, hence that she can code-switch. This investigation stresses the need to examine more carefully the roles of dominance and context in the language mixing of young bilingual children.

  3. Orbit Alignment in Triple Stars

    NASA Astrophysics Data System (ADS)

    Tokovinin, Andrei

    2017-08-01

    The statistics of the angle Φ between orbital angular momenta in hierarchical triple systems with known inner visual or astrometric orbits are studied. A correlation between apparent revolution directions proves the partial orbit alignment known from earlier works. The alignment is strong in triples with outer projected separation less than ˜50 au, where the average Φ is about 20^\\circ . In contrast, outer orbits wider than 1000 au are not aligned with the inner orbits. It is established that the orbit alignment decreases with the increasing mass of the primary component. The average eccentricity of inner orbits in well-aligned triples is smaller than in randomly aligned ones. These findings highlight the role of dissipative interactions with gas in defining the orbital architecture of low-mass triple systems. On the other hand, chaotic dynamics apparently played a role in shaping more massive hierarchies. The analysis of projected configurations and triples with known inner and outer orbits indicates that the distribution of Φ is likely bimodal, where 80% of triples have {{Φ }}< 70^\\circ and the remaining ones are randomly aligned.

  4. English Teaching in Argentina.

    ERIC Educational Resources Information Center

    Arazi, Blanca

    2002-01-01

    Examines the teaching of English in Argentina, a country that has had a myriad of English language teaching activities at all levels for many decades--mostly in British English. Looks at English in binational centers, in schools, and at the university level; methodological approach; language assessment; teacher training; and the current economic…

  5. Functional Alignment of Metabolic Networks.

    PubMed

    Mazza, Arnon; Wagner, Allon; Ruppin, Eytan; Sharan, Roded

    2016-05-01

    Network alignment has become a standard tool in comparative biology, allowing the inference of protein function, interaction, and orthology. However, current alignment techniques are based on topological properties of networks and do not take into account their functional implications. Here we propose, for the first time, an algorithm to align two metabolic networks by taking advantage of their coupled metabolic models. These models allow us to assess the functional implications of genes or reactions, captured by the metabolic fluxes that are altered following their deletion from the network. Such implications may spread far beyond the region of the network where the gene or reaction lies. We apply our algorithm to align metabolic networks from various organisms, ranging from bacteria to humans, showing that our alignment can reveal functional orthology relations that are missed by conventional topological alignments.

  6. Comparative profiling of microRNAs in the winged and wingless English grain aphid, Sitobion avenae (F.) (Homoptera: Aphididae)

    USDA-ARS?s Scientific Manuscript database

    English green aphid, Sitobion avenae (F.), show a classic polyphenic wing dimorphism among isogenic adults that is an intriguing model for the study of morphological plasticity in response to the environment. Short non-coding microRNA (miRNA) molecules regulate gene expression by post-transcriptiona...

  7. R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures.

    PubMed

    Rahrig, Ryan R; Petrov, Anton I; Leontis, Neocles B; Zirbel, Craig L

    2013-07-01

    The R3D Align web server provides online access to 'RNA 3D Align' (R3D Align), a method for producing accurate nucleotide-level structural alignments of RNA 3D structures. The web server provides a streamlined and intuitive interface, input data validation and output that is more extensive and easier to read and interpret than related servers. The R3D Align web server offers a unique Gallery of Featured Alignments, providing immediate access to pre-computed alignments of large RNA 3D structures, including all ribosomal RNAs, as well as guidance on effective use of the server and interpretation of the output. By accessing the non-redundant lists of RNA 3D structures provided by the Bowling Green State University RNA group, R3D Align connects users to structure files in the same equivalence class and the best-modeled representative structure from each group. The R3D Align web server is freely accessible at http://rna.bgsu.edu/r3dalign/.

  8. Aligned Layers of Silver Nano-Fibers.

    PubMed

    Golovin, Andrii B; Stromer, Jeremy; Kreminska, Liubov

    2012-02-01

    We describe a new dichroic polarizers made by ordering silver nano-fibers to aligned layers. The aligned layers consist of nano-fibers and self-assembled molecular aggregates of lyotropic liquid crystals. Unidirectional alignment of the layers is achieved by means of mechanical shearing. Aligned layers of silver nano-fibers are partially transparent to a linearly polarized electromagnetic radiation. The unidirectional alignment and density of the silver nano-fibers determine degree of polarization of transmitted light. The aligned layers of silver nano-fibers might be used in optics, microwave applications, and organic electronics.

  9. Online English-English Learner Dictionaries Boost Word Learning

    ERIC Educational Resources Information Center

    Nurmukhamedov, Ulugbek

    2012-01-01

    Learners of English might be familiar with several online monolingual dictionaries that are not necessarily the best choices for the English as Second/Foreign Language (ESL/EFL) context. Although these monolingual online dictionaries contain definitions, pronunciation guides, and other elements normally found in general-use dictionaries, they are…

  10. High-throughput flow alignment of barcoded hydrogel microparticles†

    PubMed Central

    Chapin, Stephen C.; Pregibon, Daniel C.

    2010-01-01

    Suspension (particle-based) arrays offer several advantages over conventional planar arrays in the detection and quantification of biomolecules, including the use of smaller sample volumes, more favorable probe-target binding kinetics, and rapid probe-set modification. We present a microfluidic system for the rapid alignment of multifunctional hydrogel microparticles designed to bear one or several biomolecule probe regions, as well as a graphical code to identify the embedded probes. Using high-speed imaging, we have developed and optimized a flow-through system that (1) allows for a high particle throughput, (2) ensures proper particle alignment for decoding and target quantification, and (3) can be reliably operated continuously without clogging. A tapered channel flanked by side focusing streams is used to orient the flexible, tablet-shaped particles into a well-ordered flow in the center of the channel. The effects of channel geometry, particle geometry, particle composition, particle loading density, and barcode design are explored to determine the best combination for eventual use in biological assays. Particles in the optimized system move at velocities of ~50 cm s−1 and with throughputs of ~40 particles s−1. Simple physical models and CFD simulations have been used to investigate flow behavior in the device. PMID:19823726

  11. Conversational English Program, 2.

    ERIC Educational Resources Information Center

    Instituto de Idiomas Yazigi, Sao Paulo (Brazil). Centro de Linguistica Aplicada.

    This second book of a conversational English program for adults contains an introductory section in Portuguese and exercises in English. The text centers around an English-speaking family from the United States that goes to live in Brazil. It contains color photographs with captions followed by exercises. The exercises are in English and involve…

  12. Conversational English Program, 1.

    ERIC Educational Resources Information Center

    Instituto de Idiomas Yazigi, Sao Paulo (Brazil). Centro de Linguistica Aplicada.

    This first book of a conversational English program for adults contains an introductory section in Portuguese and exercises in English. The text centers around an English-speaking family from the United States that goes to live in Brazil. It contains color photographs with captions followed by exercises. The exercises are in English and involve…

  13. Secondary Science Homework and Instructional Methodologies: An Investigation of the Alignment of Homework Assignments and Teachers' Self-Professed Instructional Methodology

    ERIC Educational Resources Information Center

    Lucas, Paul M.

    2009-01-01

    This study utilized a mixed-method design in order to investigate the alignment of secondary science teachers' instructional methodologies and their homework designs. Surveys were distributed to educators from a Center for Ocean Sciences Excellence Education (COSEE) database. Coding rubrics were developed to categorize the participants' responses…

  14. A Comparison of English Language Acquisition Patterns in English Monolingual and Bilingual Children.

    ERIC Educational Resources Information Center

    Glad, Diana; And Others

    English monolingual and Spanish/English bilingual children in kindergarten and first grade in 11 states were administered two tests from the EL CIRCO (CIRCUS) battery. The purpose of the study was to determine comparative acquisition of English grammar for kindergarteners and first graders and for bilingual and English monolingual children. Data…

  15. Antares alignment gimbal positioner

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

    Day, R.D.; Viswanathan, V.K.; Saxman, A.C.

    1981-01-01

    Antares is a 24-beam 40-TW carbon-dioxide (CO/sub 2/) laser fusion system currently under construction at the Los Alamos National Laboratory. The Antares alignment gimbal positioner (AGP) is an optomechanical instrument that will be used for target alignment and alignment of the 24 laser beams, as well as beam quality assessments. The AGP will be capable of providing pointing, focusing, and wavefront optical path difference, as well as aberration information at both helium-neon (He-Ne) and CO/sub 2/ wavelengths. It is designed to allow the laser beams to be aligned to any position within a 1-cm cube to a tolerance of 10more » ..mu..m.« less

  16. Eye Movements when Reading Spaced and Unspaced Thai and English: A Comparison of Thai-English Bilinguals and English Monolinguals

    ERIC Educational Resources Information Center

    Winskel, Heather; Radach, Ralph; Luksaneeyanawin, Sudaporn

    2009-01-01

    The study investigated the eye movements of Thai-English bilinguals when reading both Thai and English with and without interword spaces, in comparison with English monolinguals. Thai is an alphabetic orthography without interword spaces. Participants read sentences with high and low frequency target words embedded in same sentence frames with and…

  17. Precision alignment device

    DOEpatents

    Jones, Nelson E.

    1990-01-01

    Apparatus for providing automatic alignment of beam devices having an associated structure for directing, collimating, focusing, reflecting, or otherwise modifying the main beam. A reference laser is attached to the structure enclosing the main beam producing apparatus and produces a reference beam substantially parallel to the main beam. Detector modules containing optical switching devices and optical detectors are positioned in the path of the reference beam and are effective to produce an electrical output indicative of the alignment of the main beam. This electrical output drives servomotor operated adjustment screws to adjust the position of elements of the structure associated with the main beam to maintain alignment of the main beam.

  18. Free Energy Gap and Statistical Thermodynamic Fidelity of DNA Codes

    DTIC Science & Technology

    2007-10-01

    reverse-complement unless otherwise stated. For strand x, let Nx denote its complement. A (perfect) Watson - Crick duplex is the joining of complement...is possible for complementary sequences to form a non-perfectly aligned duplex, we will call any x W Nx duplex a Watson - Crick (WC) duplex. Two...DATES COVERED (From - To) 4. TITLE AND SUBTITLE FREE ENERGY GAP AND STATISTICAL THERMODYNAMIC FIDELITY OF DNA CODES 5a. CONTRACT NUMBER FA8750-07

  19. Non-Native English Speakers and Nonstandard English: An In-Depth Investigation

    ERIC Educational Resources Information Center

    Polat, Brittany

    2012-01-01

    Given the rising prominence of nonstandard varieties of English around the world (Jenkins 2007), learners of English as a second language are increasingly called on to communicate with speakers of both native and non-native nonstandard English varieties. In many classrooms around the world, however, learners continue to be exposed only to…

  20. Non-Native English Varieties: Thainess in English Narratives

    ERIC Educational Resources Information Center

    Singhasak, Piyahathai; Methitham, Phongsakorn

    2016-01-01

    This study aims at examining Thainess as a writing strategy used in non-literary texts written by non-professional bilingual writers. These writers are advanced language learners who are pursuing their Master's degree in English. Seven English narratives of their language learning experiences were analyzed based on Kachruvian's framework of…

  1. Physician-Hospital Alignment in Orthopedic Surgery.

    PubMed

    Bushnell, Brandon D

    2015-09-01

    The concept of "alignment" between physicians and hospitals is a popular buzzword in the age of health care reform. Despite their often tumultuous histories, physicians and hospitals find themselves under increasing pressures to work together toward common goals. However, effective alignment is more than just simple cooperation between parties. The process of achieving alignment does not have simple, universal steps. Alignment will differ based on individual situational factors and the type of specialty involved. Ultimately, however, there are principles that underlie the concept of alignment and should be a part of any physician-hospital alignment efforts. In orthopedic surgery, alignment involves the clinical, administrative, financial, and even personal aspects of a surgeon's practice. It must be based on the principles of financial interest, clinical authority, administrative participation, transparency, focus on the patient, and mutual necessity. Alignment can take on various forms as well, with popular models consisting of shared governance and comanagement, gainsharing, bundled payments, accountable care organizations, and other methods. As regulatory and financial pressures continue to motivate physicians and hospitals to develop alignment relationships, new and innovative methods of alignment will also appear. Existing models will mature and evolve, with individual variability based on local factors. However, certain trends seem to be appearing as time progresses and alignment relationships deepen, including regional and national collaboration, population management, and changes in the legal system. This article explores the history, principles, and specific methods of physician-hospital alignment and its critical importance for the future of health care delivery. Copyright 2015, SLACK Incorporated.

  2. English Medium Instruction and Idiomaticity in English as a Lingua Franca

    ERIC Educational Resources Information Center

    Briggs, Jessica G.; Smith, Sarah Ashley

    2017-01-01

    This paper critically considers the implications of the growth of English-medium instruction (EMI) globally for idiomaticity in English as a Lingua Franca (ELF). We first make the case for idiomaticity in English in terms of its contribution to language processing and use and regarding the challenges and affordances it presents to users of English…

  3. Lexical alignment in triadic communication

    PubMed Central

    Foltz, Anouschka; Gaspers, Judith; Thiele, Kristina; Stenneken, Prisca; Cimiano, Philipp

    2015-01-01

    Lexical alignment refers to the adoption of one’s interlocutor’s lexical items. Accounts of the mechanisms underlying such lexical alignment differ (among other aspects) in the role assigned to addressee-centered behavior. In this study, we used a triadic communicative situation to test which factors may modulate the extent to which participants’ lexical alignment reflects addressee-centered behavior. Pairs of naïve participants played a picture matching game and received information about the order in which pictures were to be matched from a voice over headphones. On critical trials, participants did or did not hear a name for the picture to be matched next over headphones. Importantly, when the voice over headphones provided a name, it did not match the name that the interlocutor had previously used to describe the object. Participants overwhelmingly used the word that the voice over headphones provided. This result points to non-addressee-centered behavior and is discussed in terms of disrupting alignment with the interlocutor as well as in terms of establishing alignment with the voice over headphones. In addition, the type of picture (line drawing vs. tangram shape) independently modulated lexical alignment, such that participants showed more lexical alignment to their interlocutor for (more ambiguous) tangram shapes compared to line drawings. Overall, the results point to a rather large role for non-addressee-centered behavior during lexical alignment. PMID:25762955

  4. Orientations towards English among English-Medium Instruction Students

    ERIC Educational Resources Information Center

    Karakas, Ali

    2015-01-01

    Based on the empirical data of my PhD research, this paper analyses the perceptions of 351 undergraduate students enrolled at English-medium universities towards English in terms of the language ideology framework. The students were purposively sampled from three programs at three Turkish universities. The data were drawn from student opinion…

  5. Teaching College English and English Education: Reflective Stories.

    ERIC Educational Resources Information Center

    McCracken, H. Thomas, Ed.; Larson, Richard L., Ed.; Entes, Judith, Ed.

    In this collection of 32 narrative essays, scholars and teachers of English and English education share their excitement as they reflect on their professional growth over the last 30 years. The firsthand stories in the collection represent "a study of theory and applied theory, grounded in personal experience and academic study over many…

  6. Perception of "English" and Motivation in Learning English

    ERIC Educational Resources Information Center

    Sahin, Mehmet; Seçer, Sule Y. E.; Erisen, Yavuz

    2016-01-01

    This study aims to present high school students' perception of "English" through the impressions and images and the effect of these perceptions on their motivation in learning English. This qualitative study is based on the data about students' metaphors and the focus group interview to determine their effect on the students' motivation.…

  7. English Verb Accuracy of Bilingual Cantonese-English Preschoolers

    ERIC Educational Resources Information Center

    Rezzonico, Stefano; Goldberg, Ahuva; Milburn, Trelani; Belletti, Adriana; Girolametto, Luigi

    2017-01-01

    Purpose: Knowledge of verb development in typically developing bilingual preschoolers may inform clinicians about verb accuracy rates during the 1st 2 years of English instruction. This study aimed to investigate tensed verb accuracy in 2 assessment contexts in 4- and 5-year-old Cantonese-English bilingual preschoolers. Method: The sample included…

  8. The Cambridge History of the English Language. Volume VI: English in North America.

    ERIC Educational Resources Information Center

    Algeo, John, Ed.

    This book is one volume in a series that examines the history of English. It traces the history of English in North America during the past 400 years, from its British background to its present position among the varieties of English used worldwide. Influences that have formed American English include political, social, and cultural changes in…

  9. Aligning Plasma-Arc Welding Oscillations

    NASA Technical Reports Server (NTRS)

    Norris, Jeff; Fairley, Mike

    1989-01-01

    Tool aids in alignment of oscillator probe on variable-polarity plasma-arc welding torch. Probe magnetically pulls arc from side to side as it moves along joint. Tensile strength of joint depends on alignment of weld bead and on alignment of probe. Operator installs new tool on front of torch body, levels it with built-in bubble glass, inserts probe in slot on tool, and locks probe in place. Procedure faster and easier and resulting alignment more accurate and repeatable.

  10. Thanking Responders in Cameroon English

    ERIC Educational Resources Information Center

    Ouafeu, Yves Talla Sando

    2009-01-01

    An analysis of authentic or genuine interactions among Cameroon English speakers reveals that conversational routines in this variety of English differ a good deal from those obtained in other varieties of English, non-native varieties of English inclusive, and more specifically in native varieties of English. This paper looks at "thanking…

  11. Teaching Speaking Skills in English Language Using Classroom Activities in Secondary School Level in Eldoret Municipality, Kenya

    ERIC Educational Resources Information Center

    Gudu, Benter Oseno

    2015-01-01

    There is a general public concern in Kenya that majority of Form Four school leavers lack communicative and linguistic competence and thus cannot sustain conversation in English language without occasionally code switching to "Sheng" or Kiswahili. This study sought to find out the classroom activities used by teachers to promote…

  12. Understanding Disorder Within Variation: Production of English Grammatical Forms by English Language Learners.

    PubMed

    Bedore, Lisa M; Peña, Elizabeth D; Anaya, Jissel B; Nieto, Ricardo; Lugo-Neris, Mirza J; Baron, Alisa

    2018-04-05

    This study examines English performance on a set of 11 grammatical forms in Spanish-English bilingual, school-age children in order to understand how item difficulty of grammatical constructions helps correctly classify language impairment (LI) from expected variability in second language acquisition when taking into account linguistic experience and exposure. Three hundred seventy-eight children's scores on the Bilingual English-Spanish Assessment-Middle Extension (Peña, Bedore, Gutiérrez-Clellen, Iglesias, & Goldstein, 2008) morphosyntax cloze task were analyzed by bilingual experience groups (high Spanish experience, balanced English-Spanish experience, high English experience, ability (typically developing [TD] vs. LI), and grammatical form. Classification accuracy was calculated for the forms that best differentiated TD and LI groups. Children with LI scored lower than TD children across all bilingual experience groups. There were differences by grammatical form across bilingual experience and ability groups. Children from high English experience and balanced English-Spanish experience groups could be accurately classified on the basis of all the English grammatical forms tested except for prepositions. For bilinguals with high Spanish experience, it was possible to rule out LI on the basis of grammatical production but not rule in LI. It is possible to accurately identify LI in English language learners once they use English 40% of the time or more. However, for children with high Spanish experience, more information about development and patterns of impairment is needed to positively identify LI.

  13. Representation of Gravity-Aligned Scene Structure in Ventral Pathway Visual Cortex.

    PubMed

    Vaziri, Siavash; Connor, Charles E

    2016-03-21

    The ventral visual pathway in humans and non-human primates is known to represent object information, including shape and identity [1]. Here, we show the ventral pathway also represents scene structure aligned with the gravitational reference frame in which objects move and interact. We analyzed shape tuning of recently described macaque monkey ventral pathway neurons that prefer scene-like stimuli to objects [2]. Individual neurons did not respond to a single shape class, but to a variety of scene elements that are typically aligned with gravity: large planes in the orientation range of ground surfaces under natural viewing conditions, planes in the orientation range of ceilings, and extended convex and concave edges in the orientation range of wall/floor/ceiling junctions. For a given neuron, these elements tended to share a common alignment in eye-centered coordinates. Thus, each neuron integrated information about multiple gravity-aligned structures as they would be seen from a specific eye and head orientation. This eclectic coding strategy provides only ambiguous information about individual structures but explicit information about the environmental reference frame and the orientation of gravity in egocentric coordinates. In the ventral pathway, this could support perceiving and/or predicting physical events involving objects subject to gravity, recognizing object attributes like animacy based on movement not caused by gravity, and/or stabilizing perception of the world against changes in head orientation [3-5]. Our results, like the recent discovery of object weight representation [6], imply that the ventral pathway is involved not just in recognition, but also in physical understanding of objects and scenes. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. Alignment as a Teacher Variable

    ERIC Educational Resources Information Center

    Porter, Andrew C.; Smithson, John; Blank, Rolf; Zeidner, Timothy

    2007-01-01

    With the exception of the procedures developed by Porter and colleagues (Porter, 2002), other methods of defining and measuring alignment are essentially limited to alignment between tests and standards. Porter's procedures have been generalized to investigating the alignment between content standards, tests, textbooks, and even classroom…

  15. Comparison of Online Dementia Information in Chinese and in English Languages

    PubMed Central

    Tsiang, John T

    2017-01-01

    Introduction There is a deficit of avenues for obtaining dementia information in the Asian American community. This study aims to compare the content and quality differences between websites providing information on dementia as found by a Google search conducted both in simplified Chinese characters and in English. Methods A Google search was performed for the phrase “dementia” in simplified Chinese characters and in English. The resultant websites were categorized by whether they were commercial in nature, the type of website, and whether the website provided an explanation of dementia signs and symptoms. The quality of the websites was assessed via readability and the Health on the Net Code of Conduct (HONcode). Chi-squared analyses were performed to establish differences between the English and simplified Chinese results. Results The simplified Chinese search websites were more likely to be commercial (p=0.045) and were more likely to not meet HONcode standards (p=0.008). No statistical significance was observed between the types of websites (p=0.127), the prevalence of signs and symptom explanations (p=0.073), and the readability of the website (p=0.151). Conclusion The quality of websites obtained from the simplified Chinese character Google search was lower than those obtained from searches using the English language. Given the limited sources of language and culturally appropriate information on dementia, improvement of Internet resources may help to improve health outcomes of dementia patients in the Asian American population. PMID:29308336

  16. The emotional symbolism of two English e-sounds: /i/ as in "cheap" is pleasant and /I/ as in "chip" active.

    PubMed

    Whissell, Cynthia

    2003-02-01

    This article aligns the symbolism of the long (/i/) and short (/I/) e sounds in English with the two dimensions of emotional space-Pleasantness and Activation. On the basis of this alignment, the four quadrants of emotional space are labelled Cheerful (high /i/, high /I/), Cheerless (low /i/, low /I/), Tough (low /i/, high /I/), and Tender (high /i/, low /I/). In four phases, data from over 50 samples (mainly, poetry, song lyrics, and names) were plotted and compared in terms of their use of the two e sounds. Significant and meaningful differences among samples were discovered in all phases. The placement of samples in quadrants was additionally informative. Data samples including many long e sounds (/i/) tended to be more Pleasant and those including many short e sounds (/I/) tended to be more Active.

  17. The Configuration of Liberia's Englishes.

    ERIC Educational Resources Information Center

    Singler, John Victor

    1997-01-01

    Discusses the varieties of Liberian English spoken in Liberia: Kru Pidgin English, spoken by Kru mariners and migrant workers; Settler English, spoken by descendants of 19th-century African American immigrants to Liberia; and Vernacular Liberian English (VLE), spoken by the rest of Liberia's English-speaking population. Focuses on tense aspect in…

  18. Unified Alignment of Protein-Protein Interaction Networks.

    PubMed

    Malod-Dognin, Noël; Ban, Kristina; Pržulj, Nataša

    2017-04-19

    Paralleling the increasing availability of protein-protein interaction (PPI) network data, several network alignment methods have been proposed. Network alignments have been used to uncover functionally conserved network parts and to transfer annotations. However, due to the computational intractability of the network alignment problem, aligners are heuristics providing divergent solutions and no consensus exists on a gold standard, or which scoring scheme should be used to evaluate them. We comprehensively evaluate the alignment scoring schemes and global network aligners on large scale PPI data and observe that three methods, HUBALIGN, L-GRAAL and NATALIE, regularly produce the most topologically and biologically coherent alignments. We study the collective behaviour of network aligners and observe that PPI networks are almost entirely aligned with a handful of aligners that we unify into a new tool, Ulign. Ulign enables complete alignment of two networks, which traditional global and local aligners fail to do. Also, multiple mappings of Ulign define biologically relevant soft clusterings of proteins in PPI networks, which may be used for refining the transfer of annotations across networks. Hence, PPI networks are already well investigated by current aligners, so to gain additional biological insights, a paradigm shift is needed. We propose such a shift come from aligning all available data types collectively rather than any particular data type in isolation from others.

  19. Some aspects of SR beamline alignment

    NASA Astrophysics Data System (ADS)

    Gaponov, Yu. A.; Cerenius, Y.; Nygaard, J.; Ursby, T.; Larsson, K.

    2011-09-01

    Based on the Synchrotron Radiation (SR) beamline optical element-by-element alignment with analysis of the alignment results an optimized beamline alignment algorithm has been designed and developed. The alignment procedures have been designed and developed for the MAX-lab I911-4 fixed energy beamline. It has been shown that the intermediate information received during the monochromator alignment stage can be used for the correction of both monochromator and mirror without the next stages of alignment of mirror, slits, sample holder, etc. Such an optimization of the beamline alignment procedures decreases the time necessary for the alignment and becomes useful and helpful in the case of any instability of the beamline optical elements, storage ring electron orbit or the wiggler insertion device, which could result in the instability of angular and positional parameters of the SR beam. A general purpose software package for manual, semi-automatic and automatic SR beamline alignment has been designed and developed using the developed algorithm. The TANGO control system is used as the middle-ware between the stand-alone beamline control applications BLTools, BPMonitor and the beamline equipment.

  20. Precision alignment device

    DOEpatents

    Jones, N.E.

    1988-03-10

    Apparatus for providing automatic alignment of beam devices having an associated structure for directing, collimating, focusing, reflecting, or otherwise modifying the main beam. A reference laser is attached to the structure enclosing the main beam producing apparatus and produces a reference beam substantially parallel to the main beam. Detector modules containing optical switching devices and optical detectors are positioned in the path of the reference beam and are effective to produce an electrical output indicative of the alignment of the main beam. This electrical output drives servomotor operated adjustment screws to adjust the position of elements of the structure associated with the main beam to maintain alignment of the main beam. 5 figs.

  1. Analyzing the Curriculum Alignment of Teachers

    ERIC Educational Resources Information Center

    Turan-Özpolat, Esen; Bay, Erdal

    2017-01-01

    The purpose of this research was to analyze the curriculum alignment of teachers in secondary education 5th grade Science course. Alignment levels of teachers in dimensions of acquisition, content, teaching methods and techniques, activity, material and measurement - assessment, and the reasons for their alignment/non-alignment to the curriculum…

  2. English Language Learners and English-Only Learners' Response to Direct Vocabulary Instruction

    ERIC Educational Resources Information Center

    Crevecoeur, Yvel C.; Coyne, Michael D.; McCoach, D. Betsy

    2014-01-01

    We examined data from an 18-week kindergarten vocabulary intervention study to determine whether treatment outcomes had differential effects that favored English language learners (ELLs) or English-only learners (EOLs) and whether the relationship between initial English general receptive vocabulary knowledge and response to vocabulary…

  3. The Irony of Ethics: (De)coding the Lived Experience of Women and Minority Faculty

    ERIC Educational Resources Information Center

    Reybold, L. Earle

    2014-01-01

    What does it mean to "be" an ethical faculty member? A number of scholars point to legal and moral issues, aligning ethics with professional codes and regulated by institutional policy. From this perspective, being ethical is a matter of knowing and following the professional rules--the goal is to avoid certain actions. On the other…

  4. English Language Education in Cuba.

    ERIC Educational Resources Information Center

    Irizar, Tony

    2001-01-01

    Provides an overview of English language education in Cuba. Discusses the historical role of English in Cuba, the introduction of English for specific purposes, and the current status of English instruction. (Author/VWL)

  5. Alignment of dynamic networks

    PubMed Central

    Vijayan, V.; Critchlow, D.; Milenković, T.

    2017-01-01

    Abstract Motivation: Network alignment (NA) aims to find a node mapping that conserves similar regions between compared networks. NA is applicable to many fields, including computational biology, where NA can guide the transfer of biological knowledge from well- to poorly-studied species across aligned network regions. Existing NA methods can only align static networks. However, most complex real-world systems evolve over time and should thus be modeled as dynamic networks. We hypothesize that aligning dynamic network representations of evolving systems will produce superior alignments compared to aligning the systems’ static network representations, as is currently done. Results: For this purpose, we introduce the first ever dynamic NA method, DynaMAGNA ++. This proof-of-concept dynamic NA method is an extension of a state-of-the-art static NA method, MAGNA++. Even though both MAGNA++ and DynaMAGNA++ optimize edge as well as node conservation across the aligned networks, MAGNA++ conserves static edges and similarity between static node neighborhoods, while DynaMAGNA++ conserves dynamic edges (events) and similarity between evolving node neighborhoods. For this purpose, we introduce the first ever measure of dynamic edge conservation and rely on our recent measure of dynamic node conservation. Importantly, the two dynamic conservation measures can be optimized with any state-of-the-art NA method and not just MAGNA++. We confirm our hypothesis that dynamic NA is superior to static NA, on synthetic and real-world networks, in computational biology and social domains. DynaMAGNA++ is parallelized and has a user-friendly graphical interface. Availability and implementation: http://nd.edu/∼cone/DynaMAGNA++/. Contact: tmilenko@nd.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28881980

  6. Alignment method for solar collector arrays

    DOEpatents

    Driver, Jr., Richard B

    2012-10-23

    The present invention is directed to an improved method for establishing camera fixture location for aligning mirrors on a solar collector array (SCA) comprising multiple mirror modules. The method aligns the mirrors on a module by comparing the location of the receiver image in photographs with the predicted theoretical receiver image location. To accurately align an entire SCA, a common reference is used for all of the individual module images within the SCA. The improved method can use relative pixel location information in digital photographs along with alignment fixture inclinometer data to calculate relative locations of the fixture between modules. The absolute locations are determined by minimizing alignment asymmetry for the SCA. The method inherently aligns all of the mirrors in an SCA to the receiver, even with receiver position and module-to-module alignment errors.

  7. English Speech Acquisition in 3- to 5-Year-Old Children Learning Russian and English

    ERIC Educational Resources Information Center

    Gildersleeve-Neumann, Christina E.; Wright, Kira L.

    2010-01-01

    Purpose: English speech acquisition in Russian-English (RE) bilingual children was investigated, exploring the effects of Russian phonetic and phonological properties on English single-word productions. Russian has more complex consonants and clusters and a smaller vowel inventory than English. Method: One hundred thirty-seven single-word samples…

  8. Psychological Factor Affecting English Speaking Performance for the English Learners in Indonesia

    ERIC Educational Resources Information Center

    Haidara, Youssouf

    2016-01-01

    In every learning situation or environment, human psychology plays a significant role. English speaking is a language skill that is highly affected by human psychology. This research aimed at describing the psychological factor that affects negatively the English speaking performance for the English learners in Indonesia. A descriptive qualitative…

  9. Position Paper: English Language Curriculum Guidelines for Elementary School English Language Learners

    ERIC Educational Resources Information Center

    Miele, Anthony

    2007-01-01

    English Language Development (ELD) and Academic English Development (AED) curricula in most public schools lack a communicative method and consist mostly of dry, meaningless grammar lessons devoid of relevance and authentic context. The purpose of this project is to develop guidelines to teach English language to elementary school children…

  10. DR-TAMAS: Diffeomorphic Registration for Tensor Accurate alignMent of Anatomical Structures

    PubMed Central

    Irfanoglu, M. Okan; Nayak, Amritha; Jenkins, Jeffrey; Hutchinson, Elizabeth B.; Sadeghi, Neda; Thomas, Cibu P.; Pierpaoli, Carlo

    2016-01-01

    In this work, we propose DR-TAMAS (Diffeomorphic Registration for Tensor Accurate alignMent of Anatomical Structures), a novel framework for intersubject registration of Diffusion Tensor Imaging (DTI) data sets. This framework is optimized for brain data and its main goal is to achieve an accurate alignment of all brain structures, including white matter (WM), gray matter (GM), and spaces containing cerebrospinal fluid (CSF). Currently most DTI-based spatial normalization algorithms emphasize alignment of anisotropic structures. While some diffusion-derived metrics, such as diffusion anisotropy and tensor eigenvector orientation, are highly informative for proper alignment of WM, other tensor metrics such as the trace or mean diffusivity (MD) are fundamental for a proper alignment of GM and CSF boundaries. Moreover, it is desirable to include information from structural MRI data, e.g., T1-weighted or T2-weighted images, which are usually available together with the diffusion data. The fundamental property of DR-TAMAS is to achieve global anatomical accuracy by incorporating in its cost function the most informative metrics locally. Another important feature of DR-TAMAS is a symmetric time-varying velocity-based transformation model, which enables it to account for potentially large anatomical variability in healthy subjects and patients. The performance of DR-TAMAS is evaluated with several data sets and compared with other widely-used diffeomorphic image registration techniques employing both full tensor information and/or DTI-derived scalar maps. Our results show that the proposed method has excellent overall performance in the entire brain, while being equivalent to the best existing methods in WM. PMID:26931817

  11. Coded continuous wave meteor radar

    NASA Astrophysics Data System (ADS)

    Chau, J. L.; Vierinen, J.; Pfeffer, N.; Clahsen, M.; Stober, G.

    2016-12-01

    The concept of a coded continuous wave specular meteor radar (SMR) is described. The radar uses a continuously transmitted pseudorandom phase-modulated waveform, which has several advantages compared to conventional pulsed SMRs. The coding avoids range and Doppler aliasing, which are in some cases problematic with pulsed radars. Continuous transmissions maximize pulse compression gain, allowing operation at lower peak power than a pulsed system. With continuous coding, the temporal and spectral resolution are not dependent on the transmit waveform and they can be fairly flexibly changed after performing a measurement. The low signal-to-noise ratio before pulse compression, combined with independent pseudorandom transmit waveforms, allows multiple geographically separated transmitters to be used in the same frequency band simultaneously without significantly interfering with each other. Because the same frequency band can be used by multiple transmitters, the same interferometric receiver antennas can be used to receive multiple transmitters at the same time. The principles of the signal processing are discussed, in addition to discussion of several practical ways to increase computation speed, and how to optimally detect meteor echoes. Measurements from a campaign performed with a coded continuous wave SMR are shown and compared with two standard pulsed SMR measurements. The type of meteor radar described in this paper would be suited for use in a large-scale multi-static network of meteor radar transmitters and receivers. Such a system would be useful for increasing the number of meteor detections to obtain improved meteor radar data products, such as wind fields. This type of a radar would also be useful for over-the-horizon radar, ionosondes, and observations of field-aligned-irregularities.

  12. Integrating Science and English Proficiency for English Language Learners

    ERIC Educational Resources Information Center

    Lee, Okhee; Buxton, Cory A.

    2013-01-01

    Despite the expectation that all students should achieve high academic standards, content area instruction and English for speakers of other languages instruction for English language learners (ELLs) have traditionally been conceptualized as separate domains, resulting in educational inequities for ELLs. This is because effective instruction to…

  13. AlignNemo: a local network alignment method to integrate homology and topology.

    PubMed

    Ciriello, Giovanni; Mina, Marco; Guzzi, Pietro H; Cannataro, Mario; Guerra, Concettina

    2012-01-01

    Local network alignment is an important component of the analysis of protein-protein interaction networks that may lead to the identification of evolutionary related complexes. We present AlignNemo, a new algorithm that, given the networks of two organisms, uncovers subnetworks of proteins that relate in biological function and topology of interactions. The discovered conserved subnetworks have a general topology and need not to correspond to specific interaction patterns, so that they more closely fit the models of functional complexes proposed in the literature. The algorithm is able to handle sparse interaction data with an expansion process that at each step explores the local topology of the networks beyond the proteins directly interacting with the current solution. To assess the performance of AlignNemo, we ran a series of benchmarks using statistical measures as well as biological knowledge. Based on reference datasets of protein complexes, AlignNemo shows better performance than other methods in terms of both precision and recall. We show our solutions to be biologically sound using the concept of semantic similarity applied to Gene Ontology vocabularies. The binaries of AlignNemo and supplementary details about the algorithms and the experiments are available at: sourceforge.net/p/alignnemo.

  14. mTM-align: a server for fast protein structure database search and multiple protein structure alignment.

    PubMed

    Dong, Runze; Pan, Shuo; Peng, Zhenling; Zhang, Yang; Yang, Jianyi

    2018-05-21

    With the rapid increase of the number of protein structures in the Protein Data Bank, it becomes urgent to develop algorithms for efficient protein structure comparisons. In this article, we present the mTM-align server, which consists of two closely related modules: one for structure database search and the other for multiple structure alignment. The database search is speeded up based on a heuristic algorithm and a hierarchical organization of the structures in the database. The multiple structure alignment is performed using the recently developed algorithm mTM-align. Benchmark tests demonstrate that our algorithms outperform other peering methods for both modules, in terms of speed and accuracy. One of the unique features for the server is the interplay between database search and multiple structure alignment. The server provides service not only for performing fast database search, but also for making accurate multiple structure alignment with the structures found by the search. For the database search, it takes about 2-5 min for a structure of a medium size (∼300 residues). For the multiple structure alignment, it takes a few seconds for ∼10 structures of medium sizes. The server is freely available at: http://yanglab.nankai.edu.cn/mTM-align/.

  15. Process for Considering Special Exit Criteria from Bilingual/English as a Second Language (ESL) Services under 19 TAC §89.1225(k). School Year: 2013-2014, Grades 1-12

    ERIC Educational Resources Information Center

    Texas Education Agency, 2014

    2014-01-01

    Under Texas Administrative Code (TAC) §89.1225(h), districts are required to use the exit criteria represented in the chart titled "2013-2014 English Proficiency Exit Criteria Chart" found at (http://www.tea.state.tx.us/index2.aspx?id=4098) to exit English language learners (ELLs) from bilingual/ESL programs. The exit criteria under TAC…

  16. Alignment method for parabolic trough solar concentrators

    DOEpatents

    Diver, Richard B [Albuquerque, NM

    2010-02-23

    A Theoretical Overlay Photographic (TOP) alignment method uses the overlay of a theoretical projected image of a perfectly aligned concentrator on a photographic image of the concentrator to align the mirror facets of a parabolic trough solar concentrator. The alignment method is practical and straightforward, and inherently aligns the mirror facets to the receiver. When integrated with clinometer measurements for which gravity and mechanical drag effects have been accounted for and which are made in a manner and location consistent with the alignment method, all of the mirrors on a common drive can be aligned and optimized for any concentrator orientation.

  17. Homework Practices of English and Non-English-Speaking Parents

    ERIC Educational Resources Information Center

    Thelamour, Barbara; Jacobs, D'Andrea L.

    2014-01-01

    This study compared the homework practices of English-speaking and non-English-speaking parents. Using a national data set of 7,992 students across ages and ethnicities, the frequency and type of homework practices were investigated. Statistical analysis revealed significant (though small) differences between the overall homework practices between…

  18. An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data.

    PubMed

    Vu, Trung N; Valkenborg, Dirk; Smets, Koen; Verwaest, Kim A; Dommisse, Roger; Lemière, Filip; Verschoren, Alain; Goethals, Bart; Laukens, Kris

    2011-10-20

    -to-earth quantitative analysis works well for the CluPA-aligned spectra. The whole workflow is embedded into a modular and statistically sound framework that is implemented as an R package called "speaq" ("spectrum alignment and quantitation"), which is freely available from http://code.google.com/p/speaq/.

  19. Alignment of dynamic networks.

    PubMed

    Vijayan, V; Critchlow, D; Milenkovic, T

    2017-07-15

    Network alignment (NA) aims to find a node mapping that conserves similar regions between compared networks. NA is applicable to many fields, including computational biology, where NA can guide the transfer of biological knowledge from well- to poorly-studied species across aligned network regions. Existing NA methods can only align static networks. However, most complex real-world systems evolve over time and should thus be modeled as dynamic networks. We hypothesize that aligning dynamic network representations of evolving systems will produce superior alignments compared to aligning the systems' static network representations, as is currently done. For this purpose, we introduce the first ever dynamic NA method, DynaMAGNA ++. This proof-of-concept dynamic NA method is an extension of a state-of-the-art static NA method, MAGNA++. Even though both MAGNA++ and DynaMAGNA++ optimize edge as well as node conservation across the aligned networks, MAGNA++ conserves static edges and similarity between static node neighborhoods, while DynaMAGNA++ conserves dynamic edges (events) and similarity between evolving node neighborhoods. For this purpose, we introduce the first ever measure of dynamic edge conservation and rely on our recent measure of dynamic node conservation. Importantly, the two dynamic conservation measures can be optimized with any state-of-the-art NA method and not just MAGNA++. We confirm our hypothesis that dynamic NA is superior to static NA, on synthetic and real-world networks, in computational biology and social domains. DynaMAGNA++ is parallelized and has a user-friendly graphical interface. http://nd.edu/∼cone/DynaMAGNA++/ . tmilenko@nd.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  20. English and Tok Pisin (New Guinea Pidgin English) in Papua New Guinea.

    ERIC Educational Resources Information Center

    Romaine, Suzanne

    1989-01-01

    Tok Pisin, New Guinea Pidgin English, is becoming increasingly important as a "lingua franca" in Papua New Guinea, even though English is the country's official language. Urban versus rural and spoken versus written varieties of the pidgin are examined, and the influence of English on Tok Pisin is investigated. 73 references. (Author/CB)

  1. Is Overall Oral English Ability Related to Young Latinos' English Reading Growth?

    ERIC Educational Resources Information Center

    Fitzgerald, Jill; Amendum, Steven J.; Relyea, Jackie Eunjung; Garcia, Sandra G.

    2015-01-01

    The present study investigated whether young Latino dual-language learners' 2-year English reading growth varied over time according to their initial overall oral English ability. We followed 41 Latino children for 2 years. We tested overall oral English at the beginning of the study and administered multiple curriculum-based reading assessments…

  2. War of Ontology Worlds: Mathematics, Computer Code, or Esperanto?

    PubMed Central

    Rzhetsky, Andrey; Evans, James A.

    2011-01-01

    The use of structured knowledge representations—ontologies and terminologies—has become standard in biomedicine. Definitions of ontologies vary widely, as do the values and philosophies that underlie them. In seeking to make these views explicit, we conducted and summarized interviews with a dozen leading ontologists. Their views clustered into three broad perspectives that we summarize as mathematics, computer code, and Esperanto. Ontology as mathematics puts the ultimate premium on rigor and logic, symmetry and consistency of representation across scientific subfields, and the inclusion of only established, non-contradictory knowledge. Ontology as computer code focuses on utility and cultivates diversity, fitting ontologies to their purpose. Like computer languages C++, Prolog, and HTML, the code perspective holds that diverse applications warrant custom designed ontologies. Ontology as Esperanto focuses on facilitating cross-disciplinary communication, knowledge cross-referencing, and computation across datasets from diverse communities. We show how these views align with classical divides in science and suggest how a synthesis of their concerns could strengthen the next generation of biomedical ontologies. PMID:21980276

  3. War of ontology worlds: mathematics, computer code, or Esperanto?

    PubMed

    Rzhetsky, Andrey; Evans, James A

    2011-09-01

    The use of structured knowledge representations-ontologies and terminologies-has become standard in biomedicine. Definitions of ontologies vary widely, as do the values and philosophies that underlie them. In seeking to make these views explicit, we conducted and summarized interviews with a dozen leading ontologists. Their views clustered into three broad perspectives that we summarize as mathematics, computer code, and Esperanto. Ontology as mathematics puts the ultimate premium on rigor and logic, symmetry and consistency of representation across scientific subfields, and the inclusion of only established, non-contradictory knowledge. Ontology as computer code focuses on utility and cultivates diversity, fitting ontologies to their purpose. Like computer languages C++, Prolog, and HTML, the code perspective holds that diverse applications warrant custom designed ontologies. Ontology as Esperanto focuses on facilitating cross-disciplinary communication, knowledge cross-referencing, and computation across datasets from diverse communities. We show how these views align with classical divides in science and suggest how a synthesis of their concerns could strengthen the next generation of biomedical ontologies.

  4. Probabilistic biological network alignment.

    PubMed

    Todor, Andrei; Dobra, Alin; Kahveci, Tamer

    2013-01-01

    Interactions between molecules are probabilistic events. An interaction may or may not happen with some probability, depending on a variety of factors such as the size, abundance, or proximity of the interacting molecules. In this paper, we consider the problem of aligning two biological networks. Unlike existing methods, we allow one of the two networks to contain probabilistic interactions. Allowing interaction probabilities makes the alignment more biologically relevant at the expense of explosive growth in the number of alternative topologies that may arise from different subsets of interactions that take place. We develop a novel method that efficiently and precisely characterizes this massive search space. We represent the topological similarity between pairs of aligned molecules (i.e., proteins) with the help of random variables and compute their expected values. We validate our method showing that, without sacrificing the running time performance, it can produce novel alignments. Our results also demonstrate that our method identifies biologically meaningful mappings under a comprehensive set of criteria used in the literature as well as the statistical coherence measure that we developed to analyze the statistical significance of the similarity of the functions of the aligned protein pairs.

  5. Alignment telescope for Antares

    NASA Astrophysics Data System (ADS)

    Appert, Q. D.; Swann, T. A.; Ward, J. H.; Hardesty, C.; Wright, L.

    The Antares Automatic Alignment System employs a specially designed telescope for alignment of its laser beamlines. There are two telescopes in the system, and since each telescope is a primary alignment reference, stringent boresight accuracy and stability over the focus range were required. Optical and mechanical designs, which meet this requirements as well as that of image quality over a wide wavelength band, are described. Special test techniques for initial assembly and alignment of the telescope are also presented. The telescope, which has a 180-mm aperture FK51-KZF2 type glass doublet objective, requires a boresight accuracy of 2.8 (SIGMA)rad at two focal lengths, and object distances between 11 meters and infinity. Travel of a smaller secondary doublet provides focus from 11 m to infinity with approximately 7.8 m effective focal length. By flipping in a third doublet, the effective focal length is reduced to 2.5 m. Telescope alignment was accomplished by using a rotary air bearing to establish an axis in front of the system and placing the focus of a Laser Unequal Path Interferometer (LUPI) at the image plane.

  6. Alignment Telescope For Antares

    NASA Astrophysics Data System (ADS)

    Appert, Q. D.; Swann, T. A.; Ward, J. H.; Hardesty, C.; Wrignt, L.

    1983-11-01

    The Antares Automatic Alignment System employs a specially designed telescope for alignment of its laser beamlines. There are two telescopes in the system, and since eacn telescope is a primary alignment reference, stringent boresight accuracy and stability over the focus range were required. Optical and mechanical designs, which meet this requirement as well as that of image quality over a wide wavelength band, are described. Special test techniques for initial assembly and alignment of the telescope are also presented. The telescope, which has a 180-mm aperture FK51-KZF2 type glass doublet objective, requires a boresight accuracy of 2.8 prad at two focal lengths, and object distances between 11 meters and infinity. Travel of a smaller secondary doublet provides focus from 11 m to infinity with approximately 7.8 m effective focal length. By flipping in a third doublet, the effective focal length is reduced to 2.5 m. Telescope alignment was accomplished by using a rotary air bearing to establish an axis in front of the system and placing the focus of a Laser Unequal Path Interferometer (LUPI) at the image plane.

  7. Align-and-shine photolithography

    NASA Astrophysics Data System (ADS)

    Petrusis, Audrius; Rector, Jan H.; Smith, Kristen; de Man, Sven; Iannuzzi, Davide

    2009-10-01

    At the beginning of 2009, our group has introduced a new technique that allows fabrication of photolithographic patterns on the cleaved end of an optical fibre: the align-and-shine photolithography technique (see A. Petrušis et al., "The align-and-shine technique for series production of photolithography patterns on optical fibres", J. Micromech. Microeng. 19, 047001, 2009). Align-and-shine photolithography combines standard optical lithography with imagebased active fibre alignment processes. The technique adapts well to series production, opening the way to batch fabrication of fibre-top devices (D. Iannuzzi et al., "Monolithic fibre-top cantilever for critical environments and standard applications", Appl. Phys. Lett. 88, 053501, 2006) and all other devices that rely on suitable machining of engineered parts on the tip of a fibre. In this paper we review our results and briefly discuss its potential applications.

  8. Spatio-temporal alignment of multiple sensors

    NASA Astrophysics Data System (ADS)

    Zhang, Tinghua; Ni, Guoqiang; Fan, Guihua; Sun, Huayan; Yang, Biao

    2018-01-01

    Aiming to achieve the spatio-temporal alignment of multi sensor on the same platform for space target observation, a joint spatio-temporal alignment method is proposed. To calibrate the parameters and measure the attitude of cameras, an astronomical calibration method is proposed based on star chart simulation and collinear invariant features of quadrilateral diagonal between the observed star chart. In order to satisfy a temporal correspondence and spatial alignment similarity simultaneously, the method based on the astronomical calibration and attitude measurement in this paper formulates the video alignment to fold the spatial and temporal alignment into a joint alignment framework. The advantage of this method is reinforced by exploiting the similarities and prior knowledge of velocity vector field between adjacent frames, which is calculated by the SIFT Flow algorithm. The proposed method provides the highest spatio-temporal alignment accuracy compared to the state-of-the-art methods on sequences recorded from multi sensor at different times.

  9. Projected power iteration for network alignment

    NASA Astrophysics Data System (ADS)

    Onaran, Efe; Villar, Soledad

    2017-08-01

    The network alignment problem asks for the best correspondence between two given graphs, so that the largest possible number of edges are matched. This problem appears in many scientific problems (like the study of protein-protein interactions) and it is very closely related to the quadratic assignment problem which has graph isomorphism, traveling salesman and minimum bisection problems as particular cases. The graph matching problem is NP-hard in general. However, under some restrictive models for the graphs, algorithms can approximate the alignment efficiently. In that spirit the recent work by Feizi and collaborators introduce EigenAlign, a fast spectral method with convergence guarantees for Erd-s-Renyí graphs. In this work we propose the algorithm Projected Power Alignment, which is a projected power iteration version of EigenAlign. We numerically show it improves the recovery rates of EigenAlign and we describe the theory that may be used to provide performance guarantees for Projected Power Alignment.

  10. English Teachers, Angels & Poverty: Writing on English Curriculum and Pedagogy (Reflections on Editing "English in Australia").

    ERIC Educational Resources Information Center

    Doecke, Brenton

    2002-01-01

    Explores the cultural politics of writing about English curriculum and pedagogy, focusing on the author's role as the editor of this journal. Describes his role as editor as one of providing a discursive space in which English teachers and literacy educators can begin to write about their work. (SG)

  11. Free Energy Gap and Statistical Thermodynamic Fidelity of DNA Codes (Postprint)

    DTIC Science & Technology

    2007-01-01

    reverse-complement unless otherwise stated. For strand x, let Nx denote its complement. A (perfect) Watson - Crick duplex is the joining of complement...is possible for complementary sequences to form a non-perfectly aligned duplex, we will call any x W Nx duplex a Watson - Crick (WC) duplex. Two...DATES COVERED (From - To) 4. TITLE AND SUBTITLE FREE ENERGY GAP AND STATISTICAL THERMODYNAMIC FIDELITY OF DNA CODES 5a. CONTRACT NUMBER FA8750-07

  12. Unified English Braille in the United Kingdom: Part 2--Examination by Literary Braille Users, Braille Teachers, and Transcribers

    ERIC Educational Resources Information Center

    Cryer, Heather; Home, Sarah; Morley Wilkins, Sarah

    2013-01-01

    To inform decision-making around the adoption of the Unified English Braille (UEB) code in the United Kingdom, a suite of research was carried out. This study involved a variety of braille stakeholders--student braille readers (in full time education), adult braille readers, braille teachers, and braille transcribers. Participants were sent…

  13. Hybrid vehicle motor alignment

    DOEpatents

    Levin, Michael Benjamin

    2001-07-03

    A rotor of an electric motor for a motor vehicle is aligned to an axis of rotation for a crankshaft of an internal combustion engine having an internal combustion engine and an electric motor. A locator is provided on the crankshaft, a piloting tool is located radially by the first locator to the crankshaft. A stator of the electric motor is aligned to a second locator provided on the piloting tool. The stator is secured to the engine block. The rotor is aligned to the crankshaft and secured thereto.

  14. Persistent Use of Mixed Code: An Exploration of Its Functions in Hong Kong Schools

    ERIC Educational Resources Information Center

    Low, Winnie W. M.; Lu, Dan

    2006-01-01

    Codemixing of Cantonese Chinese and English is a common speech behaviour used by bilingual people in Hong Kong. Though codemixing is repeatedly criticised as a cause of the decline of students' language competence, there is little hard evidence to indicate its detrimental effects. This study examines the use of mixed code in the context of the…

  15. Online English Learning Using Internet for English-as-a-Foreign-Language Students.

    ERIC Educational Resources Information Center

    Wang, Lih-Ching Chen; Dalton, David W.

    Learning to communicate in English is an essential tool to access many resources via worldwide networks in the global society. Like students from many other countries, students in Taiwan study English for years, but lack opportunities to practice. For English-as-a-Second-Language students, the World Wide Web provides a learning environment in…

  16. Attitudes toward Spanish and Code-Switching in Belize: Stigmatization and Innovation in the Spanish Classroom

    ERIC Educational Resources Information Center

    Balam, Osmer; de Prada Pérez, Ana

    2017-01-01

    Through the analysis of survey and interview data, we investigated the attitudes and perceptions of 32 multilingual teachers of Spanish in Belize, a code-switching (CS) context where Spanish is in intense contact with English and Belizean Kriol. More specifically, we examined teachers' and students' attitudes toward Spanish and CS and teachers'…

  17. World Englishes, English as a Lingua Franca, and Intelligibility

    ERIC Educational Resources Information Center

    Berns, Margie

    2008-01-01

    This paper tests claims concerning the English as Lingua Franca (ELF) movement's position within the world Englishes paradigm. To do so, it considers the writings of Jennifer Jenkins, a leader in this movement, on what she calls "phonological intelligibility", and the writings of Larry Smith, an established scholar on intelligibility in…

  18. Standards and Dialects in English.

    ERIC Educational Resources Information Center

    Shopen, Timothy; Williams, Joseph M.

    A collection of essays on linguistic variation in English that distinguishes communities and social groups from one another includes: "Standard English: Biography of a Symbol" (Shirley Brice Heath); "The Rise of Standard English" (Margaret Shaklee); "English Orthography" (Wayne O'Neil); "How Pablo Says 'Love' and…

  19. Forced Alignment for Understudied Language Varieties: Testing Prosodylab-Aligner with Tongan Data

    ERIC Educational Resources Information Center

    Johnson, Lisa M.; Di Paolo, Marianna; Bell, Adrian

    2018-01-01

    Automated alignment of transcriptions to audio files expedites the process of preparing data for acoustic analysis. Unfortunately, the benefits of auto-alignment have generally been available only to researchers studying majority languages, for which large corpora exist and for which acoustic models have been created by large-scale research…

  20. Jig Aligns Shadow Mask On CCD

    NASA Technical Reports Server (NTRS)

    Matus, Carlos V.

    1989-01-01

    Alignment viewed through microscope. Alignment jig positions shadow mask on charge-coupled device (CCD) so metal film deposited on it precisely. Allows CCD package to be inserted and removed without disturbing alignment of mask. Holds CCD packages securely and isolates it electrostatically while providing electrical contact to each of its pins. When alignment jig assembled with CCD, used to move mask under micrometer control.

  1. Multi-stained whole slide image alignment in digital pathology

    NASA Astrophysics Data System (ADS)

    Déniz, Oscar; Toomey, David; Conway, Catherine; Bueno, Gloria

    2015-03-01

    In Digital Pathology, one of the most simple and yet most useful feature is the ability to view serial sections of tissue simultaneously on a computer monitor. This enables the pathologist to evaluate the histology and expression of multiple markers for a patient in a single review. However, the rate limiting step in this process is the time taken for the pathologist to open each individual image, align the sections within the viewer, with a maximum of four slides at a time, and then manually move around the section. In addition, due to tissue processing and pre-analytical steps, sections with different stains have non-linear variations between the two acquisitions, that is, they will stretch and change shape from section to section. To date, no solution has come close to a workable solution to automatically align the serial sections into one composite image. This research work address this problem to obtain an automated serial section alignment tool enabling the pathologists to simply scroll through the various sections in a single viewer. To this aim a multi-resolution intensity-based registration method using mutual information as a similarity metric, an optimizer based on an evolutionary process and a bilinear transformation has been used. To characterize the performance of the algorithm 40 cases x 5 different serial sections stained with hematoxiline-eosine (HE), estrogen receptor (ER), progesterone receptor (PR), Ki67 and human epidermal growth factor receptor 2 (Her2), have been considered. The qualitative results obtained are promising, with average computation time of 26.4s for up to 14660x5799 images running interpreted code.

  2. English Language Teaching Profile: Saudi Arabia.

    ERIC Educational Resources Information Center

    British Council, London (England). English Language and Literature Div.

    The role and status of English in Saudi Arabia are examined, with attention directed to: (1) English within the education system; (2) teachers of English; (3) English outside the education system; (4) materials support; (5) British support for the teaching of English; and (6) English syllabi at intermediate, secondary, and higher education levels.…

  3. Modified alignment CGHs for aspheric surface test

    NASA Astrophysics Data System (ADS)

    Song, Jae-Bong; Yang, Ho-Soon; Rhee, Hyug-Gyo; Lee, Yun-Woo

    2009-08-01

    Computer Generated Holograms (CGH) for optical test are commonly consisted of one main pattern for testing aspheric surface and some alignment patterns for aligning the interferometer, CGH, and the test optics. To align the CGH plate and the test optics, we designed the alignment CGHs modified from the cat's eye alignment method, which are consisted of a couple of CGH patterns. The incident beam passed through the one part of the alignment CGH pattern is focused onto the one radius position of the test aspheric surface, and is reflected to the other part, and vice versa. This method has several merits compared to the conventional cat's eye alignment method. First, this method can be used in testing optics with a center hole, and the center part of CGH plate can be assigned to the alignment pattern. Second, the alignment pattern becomes a concentric circular arc pattern. The whole CGH patterns including the main pattern and alignment patterns are consisted of only concentric circular fringes. This concentric circular pattern can be easily made by the polar coordinated writer with circular scanning. The required diffraction angle becomes relatively small, so the 1st order diffraction beams instead of the 3rd order diffraction beam can be used as alignment beams, and the visibility can be improved. This alignment method also is more sensitive to the tilt and the lateral shift of the test aspheric surface. Using this alignment pattern, a 200 mm diameter F/0.5 aspheric mirror and a 600 mm diameter F/0.9 mirror were tested.

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

    PubMed Central

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

    2011-01-01

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

  5. INTERNATIONAL ENGLISH MANUAL

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

    AMADOR, MABLE; KELLER, YVONNE KELLER

    This document presents a set of guidelines for authors who wish to express themselves more clearly to foreign readers, or readers whose first language is not American English. Topics include idioms, technical terms, jargon, word meaning, acronyms, and international conventions of measurement. The guidelines will help writers of technical documents present their ideas more effectively to audiences that may include individuals whose first language is not American English, including audiences with individuals from other English-speaking countries.

  6. Roles of Non-Coding RNA in Sugarcane-Microbe Interaction.

    PubMed

    Thiebaut, Flávia; Rojas, Cristian A; Grativol, Clícia; Calixto, Edmundo P da R; Motta, Mariana R; Ballesteros, Helkin G F; Peixoto, Barbara; de Lima, Berenice N S; Vieira, Lucas M; Walter, Maria Emilia; de Armas, Elvismary M; Entenza, Júlio O P; Lifschitz, Sergio; Farinelli, Laurent; Hemerly, Adriana S; Ferreira, Paulo C G

    2017-12-20

    Studies have highlighted the importance of non-coding RNA regulation in plant-microbe interaction. However, the roles of sugarcane microRNAs (miRNAs) in the regulation of disease responses have not been investigated. Firstly, we screened the sRNA transcriptome of sugarcane infected with Acidovorax avenae . Conserved and novel miRNAs were identified. Additionally, small interfering RNAs (siRNAs) were aligned to differentially expressed sequences from the sugarcane transcriptome. Interestingly, many siRNAs aligned to a transcript encoding a copper-transporter gene whose expression was induced in the presence of A. avenae , while the siRNAs were repressed in the presence of A. avenae . Moreover, a long intergenic non-coding RNA was identified as a potential target or decoy of miR408. To extend the bioinformatics analysis, we carried out independent inoculations and the expression patterns of six miRNAs were validated by quantitative reverse transcription-PCR (qRT-PCR). Among these miRNAs, miR408-a copper-microRNA-was downregulated. The cleavage of a putative miR408 target, a laccase, was confirmed by a modified 5'RACE (rapid amplification of cDNA ends) assay. MiR408 was also downregulated in samples infected with other pathogens, but it was upregulated in the presence of a beneficial diazotrophic bacteria. Our results suggest that regulation by miR408 is important in sugarcane sensing whether microorganisms are either pathogenic or beneficial, triggering specific miRNA-mediated regulatory mechanisms accordingly.

  7. Roles of Non-Coding RNA in Sugarcane-Microbe Interaction

    PubMed Central

    Grativol, Clícia; Motta, Mariana R.; Ballesteros, Helkin G. F.; Peixoto, Barbara; Vieira, Lucas M.; Walter, Maria Emilia; de Armas, Elvismary M.; Entenza, Júlio O. P.; Lifschitz, Sergio; Farinelli, Laurent; Hemerly, Adriana S.

    2017-01-01

    Studies have highlighted the importance of non-coding RNA regulation in plant-microbe interaction. However, the roles of sugarcane microRNAs (miRNAs) in the regulation of disease responses have not been investigated. Firstly, we screened the sRNA transcriptome of sugarcane infected with Acidovorax avenae. Conserved and novel miRNAs were identified. Additionally, small interfering RNAs (siRNAs) were aligned to differentially expressed sequences from the sugarcane transcriptome. Interestingly, many siRNAs aligned to a transcript encoding a copper-transporter gene whose expression was induced in the presence of A. avenae, while the siRNAs were repressed in the presence of A. avenae. Moreover, a long intergenic non-coding RNA was identified as a potential target or decoy of miR408. To extend the bioinformatics analysis, we carried out independent inoculations and the expression patterns of six miRNAs were validated by quantitative reverse transcription-PCR (qRT-PCR). Among these miRNAs, miR408—a copper-microRNA—was downregulated. The cleavage of a putative miR408 target, a laccase, was confirmed by a modified 5′RACE (rapid amplification of cDNA ends) assay. MiR408 was also downregulated in samples infected with other pathogens, but it was upregulated in the presence of a beneficial diazotrophic bacteria. Our results suggest that regulation by miR408 is important in sugarcane sensing whether microorganisms are either pathogenic or beneficial, triggering specific miRNA-mediated regulatory mechanisms accordingly. PMID:29657296

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

    PubMed

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

    2017-02-01

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

  9. JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures.

    PubMed

    Muth, Thilo; García-Martín, Juan A; Rausell, Antonio; Juan, David; Valencia, Alfonso; Pazos, Florencio

    2012-02-15

    We have implemented in a single package all the features required for extracting, visualizing and manipulating fully conserved positions as well as those with a family-dependent conservation pattern in multiple sequence alignments. The program allows, among other things, to run different methods for extracting these positions, combine the results and visualize them in protein 3D structures and sequence spaces. JDet is a multiplatform application written in Java. It is freely available, including the source code, at http://csbg.cnb.csic.es/JDet. The package includes two of our recently developed programs for detecting functional positions in protein alignments (Xdet and S3Det), and support for other methods can be added as plug-ins. A help file and a guided tutorial for JDet are also available.

  10. CAFE: A New Relativistic MHD Code

    NASA Astrophysics Data System (ADS)

    Lora-Clavijo, F. D.; Cruz-Osorio, A.; Guzmán, F. S.

    2015-06-01

    We introduce CAFE, a new independent code designed to solve the equations of relativistic ideal magnetohydrodynamics (RMHD) in three dimensions. We present the standard tests for an RMHD code and for the relativistic hydrodynamics regime because we have not reported them before. The tests include the one-dimensional Riemann problems related to blast waves, head-on collisions of streams, and states with transverse velocities, with and without magnetic field, which is aligned or transverse, constant or discontinuous across the initial discontinuity. Among the two-dimensional (2D) and 3D tests without magnetic field, we include the 2D Riemann problem, a one-dimensional shock tube along a diagonal, the high-speed Emery wind tunnel, the Kelvin-Helmholtz (KH) instability, a set of jets, and a 3D spherical blast wave, whereas in the presence of a magnetic field we show the magnetic rotor, the cylindrical explosion, a case of Kelvin-Helmholtz instability, and a 3D magnetic field advection loop. The code uses high-resolution shock-capturing methods, and we present the error analysis for a combination that uses the Harten, Lax, van Leer, and Einfeldt (HLLE) flux formula combined with a linear, piecewise parabolic method and fifth-order weighted essentially nonoscillatory reconstructors. We use the flux-constrained transport and the divergence cleaning methods to control the divergence-free magnetic field constraint.

  11. Language Growth in English Monolingual and Spanish-English Bilingual Children from 2.5 to 5 Years.

    PubMed

    Hoff, Erika; Ribot, Krystal M

    2017-11-01

    To describe the trajectories of English and Spanish language growth in typically developing children from bilingual homes and compare those with the trajectories of English growth in children from monolingual homes, to assess effects of dual language exposure on language growth in typically developing children. Expressive vocabularies were assessed at 6-month intervals from age 30 to 60 months, in English for monolinguals and English and Spanish for bilinguals. Use of English and Spanish in the home was assessed via parental report. Multilevel modeling, including parent education as a covariate, revealed that children from bilingual homes lagged 6 months to 1 year behind monolingual children in English vocabulary growth. The size of the lag was related to the relative amount of English use in the home, but the relation was not linear. Increments in English use conferred the greatest benefit most among homes with already high levels of English use. These homes also were likely to have 1 parent who was a native English speaker. Bilingual children showed stronger growth in English than in Spanish. Bilingual children can lag 6 months to 1 year behind monolingual children in normal English language development. Such lags may not necessarily signify clinically relevant delay if parents report that children also have skills in the home language. Shorter lags are associated with 2 correlated factors: more English exposure and more exposure from native English speakers. Early exposure to Spanish in the home does not guarantee acquisition of Spanish. Copyright © 2017 Elsevier Inc. All rights reserved.

  12. Laser beam alignment apparatus and method

    DOEpatents

    Gruhn, C.R.; Hammond, R.B.

    The disclosure related to an apparatus and method for laser beam alignment. Thermoelectric properties of a disc in a laser beam path are used to provide an indication of beam alignment and/or automatic laser alignment.

  13. Laser beam alignment apparatus and method

    DOEpatents

    Gruhn, Charles R.; Hammond, Robert B.

    1981-01-01

    The disclosure relates to an apparatus and method for laser beam alignment. Thermoelectric properties of a disc in a laser beam path are used to provide an indication of beam alignment and/or automatic laser alignment.

  14. ChromAlign: A two-step algorithmic procedure for time alignment of three-dimensional LC-MS chromatographic surfaces.

    PubMed

    Sadygov, Rovshan G; Maroto, Fernando Martin; Hühmer, Andreas F R

    2006-12-15

    We present an algorithmic approach to align three-dimensional chromatographic surfaces of LC-MS data of complex mixture samples. The approach consists of two steps. In the first step, we prealign chromatographic profiles: two-dimensional projections of chromatographic surfaces. This is accomplished by correlation analysis using fast Fourier transforms. In this step, a temporal offset that maximizes the overlap and dot product between two chromatographic profiles is determined. In the second step, the algorithm generates correlation matrix elements between full mass scans of the reference and sample chromatographic surfaces. The temporal offset from the first step indicates a range of the mass scans that are possibly correlated, then the correlation matrix is calculated only for these mass scans. The correlation matrix carries information on highly correlated scans, but it does not itself determine the scan or time alignment. Alignment is determined as a path in the correlation matrix that maximizes the sum of the correlation matrix elements. The computational complexity of the optimal path generation problem is reduced by the use of dynamic programming. The program produces time-aligned surfaces. The use of the temporal offset from the first step in the second step reduces the computation time for generating the correlation matrix and speeds up the process. The algorithm has been implemented in a program, ChromAlign, developed in C++ language for the .NET2 environment in WINDOWS XP. In this work, we demonstrate the applications of ChromAlign to alignment of LC-MS surfaces of several datasets: a mixture of known proteins, samples from digests of surface proteins of T-cells, and samples prepared from digests of cerebrospinal fluid. ChromAlign accurately aligns the LC-MS surfaces we studied. In these examples, we discuss various aspects of the alignment by ChromAlign, such as constant time axis shifts and warping of chromatographic surfaces.

  15. Text-image alignment for historical handwritten documents

    NASA Astrophysics Data System (ADS)

    Zinger, S.; Nerbonne, J.; Schomaker, L.

    2009-01-01

    We describe our work on text-image alignment in context of building a historical document retrieval system. We aim at aligning images of words in handwritten lines with their text transcriptions. The images of handwritten lines are automatically segmented from the scanned pages of historical documents and then manually transcribed. To train automatic routines to detect words in an image of handwritten text, we need a training set - images of words with their transcriptions. We present our results on aligning words from the images of handwritten lines and their corresponding text transcriptions. Alignment based on the longest spaces between portions of handwriting is a baseline. We then show that relative lengths, i.e. proportions of words in their lines, can be used to improve the alignment results considerably. To take into account the relative word length, we define the expressions for the cost function that has to be minimized for aligning text words with their images. We apply right to left alignment as well as alignment based on exhaustive search. The quality assessment of these alignments shows correct results for 69% of words from 100 lines, or 90% of partially correct and correct alignments combined.

  16. Sentential Negation in English

    ERIC Educational Resources Information Center

    Mowarin, Macaulay

    2009-01-01

    This paper undertakes a detailed analysis of sentential negation in the English language with Chomsky's Government-Binding theory of Transformational Grammar as theoretical model. It distinguishes between constituent and sentential negation in English. The essay identifies the exact position of Negation phrase in an English clause structure. It…

  17. Axiological Role of English Adjectives in English Language Teaching

    ERIC Educational Resources Information Center

    Zerkina, Natalya N.; Kostina, Nataliia N.; Urazayeva, Nailya R.; Lomakina, Yekaterina A.; Emets, Tatiana V.; Gallyamova, Maria S.; Melnikova, Elena P.; Trutnev, Alexey Yu.; Lukina, Oksana A.

    2016-01-01

    The article focuses on peculiarities of English adjective teaching as one of main and important lexicological basis. As the English language nowadays is important and universal as a native language of worldwide society, exactly that's why process of learning must include wide range of techniques not only as a process of learning theories but also…

  18. Method for alignment of microwires

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

    Beardslee, Joseph A.; Lewis, Nathan S.; Sadtler, Bryce

    2017-01-24

    A method of aligning microwires includes modifying the microwires so they are more responsive to a magnetic field. The method also includes using a magnetic field so as to magnetically align the microwires. The method can further include capturing the microwires in a solid support structure that retains the longitudinal alignment of the microwires when the magnetic field is not applied to the microwires.

  19. The Ideological Construction of English: A Critical Review on the Discourse of English in East Asia

    ERIC Educational Resources Information Center

    Lin, Han-Yi

    2014-01-01

    This research investigates the ideological character of the English language in East Asia. It focuses on the prevailing beliefs, values and propositions relating to English as a global language and the spread of English in the non-English East Asian countries, namely China, Japan, South Korea and Taiwan. By analyzing how English is presented in…

  20. Algorithms for Automatic Alignment of Arrays

    NASA Technical Reports Server (NTRS)

    Chatterjee, Siddhartha; Gilbert, John R.; Oliker, Leonid; Schreiber, Robert; Sheffler, Thomas J.

    1996-01-01

    Aggregate data objects (such as arrays) are distributed across the processor memories when compiling a data-parallel language for a distributed-memory machine. The mapping determines the amount of communication needed to bring operands of parallel operations into alignment with each other. A common approach is to break the mapping into two stages: an alignment that maps all the objects to an abstract template, followed by a distribution that maps the template to the processors. This paper describes algorithms for solving the various facets of the alignment problem: axis and stride alignment, static and mobile offset alignment, and replication labeling. We show that optimal axis and stride alignment is NP-complete for general program graphs, and give a heuristic method that can explore the space of possible solutions in a number of ways. We show that some of these strategies can give better solutions than a simple greedy approach proposed earlier. We also show how local graph contractions can reduce the size of the problem significantly without changing the best solution. This allows more complex and effective heuristics to be used. We show how to model the static offset alignment problem using linear programming, and we show that loop-dependent mobile offset alignment is sometimes necessary for optimum performance. We describe an algorithm with for determining mobile alignments for objects within do loops. We also identify situations in which replicated alignment is either required by the program itself or can be used to improve performance. We describe an algorithm based on network flow that replicates objects so as to minimize the total amount of broadcast communication in replication.

  1. MEMS Integrated Submount Alignment for Optoelectronics

    NASA Astrophysics Data System (ADS)

    Shakespeare, W. Jeffrey; Pearson, Raymond A.; Grenestedt, Joachim L.; Hutapea, Parsaoran; Gupta, Vikas

    2005-02-01

    One of the most expensive and time-consuming production processes for single-mode fiber-optic components is the alignment of the photonic chip or waveguide to the fiber. The alignment equipment is capital intensive and usually requires trained technicians to achieve desired results. Current technology requires active alignment since tolerances are only ~0.2 μ m or less for a typical laser diode. This is accomplished using piezoelectric actuated stages and active optical feedback. Joining technologies such as soldering, epoxy bonding, or laser welding may contribute significant postbond shift, and final coupling efficiencies are often less than 80%. This paper presents a method of adaptive optical alignment to freeze in place directly on an optical submount using a microelectromechanical system (MEMS) shape memory alloy (SMA) actuation technology. Postbond shift is eliminated since the phase change is the alignment actuation. This technology is not limited to optical alignment but can be applied to a variety of MEMS actuations, including nano-actuation and nano-alignment for biomedical applications. Experimental proof-of-concept results are discussed, and a simple analytical model is proposed to predict the stress strain behavior of the optical submount. Optical coupling efficiencies and alignment times are compared with traditional processes. The feasibility of this technique in high-volume production is discussed.

  2. A Study of the Use of a Monolingual Pedagogical Dictionary by Learners of English Engaged in Writing.

    ERIC Educational Resources Information Center

    Harvey, Keith; Yuill, Deborah

    1997-01-01

    Presents an account of a study of the role played by a dictionary in the completion of written (encoding) tasks by students of English as a foreign language. The study uses an introspective methodology based on the completion of flowcharts. Results indicate the importance of information on spelling and meanings and the neglect of coded syntactic…

  3. Semantic processing in native and second language: evidence from hemispheric differences in fine and coarse semantic coding.

    PubMed

    Faust, Miriam; Ben-Artzi, Elisheva; Vardi, Nili

    2012-12-01

    Previous studies suggest that whereas the left hemisphere (LH) is involved in fine semantic processing, the right hemisphere (RH) is uniquely engaged in coarse semantic coding including the comprehension of distinct types of language such as figurative language, lexical ambiguity and verbal humor (e.g., Chiarello, 2003; Faust, 2012). The present study examined the patterns of hemispheric involvement in fine/coarse semantic processing in native and non-native languages using a split visual field priming paradigm. Thirty native Hebrew speaking students made lexical decision judgments of Hebrew and English target words preceded by strongly, weakly, or unrelated primes. Results indicated that whereas for Hebrew pairs, priming effect for the weakly-related word pairs was obtained only for RH presented target words, for English pairs, no priming effect for the weakly-related pairs emerged for either LH or RH presented targets, suggesting that coarse semantic coding is much weaker for a non-native than native language. Copyright © 2012 Elsevier Inc. All rights reserved.

  4. English as Cultural Action.

    ERIC Educational Resources Information Center

    Prodromou, Luke

    1988-01-01

    Discusses teaching and learning English as a foreign language in its cultural context, and the culture of the native speaker of English and its relation to the culture of the learner. Native-speaking teachers should recognize the international status of English and work from local varieties of the language. (Author/LMO)

  5. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

    PubMed Central

    Haas, Brian J; Salzberg, Steven L; Zhu, Wei; Pertea, Mihaela; Allen, Jonathan E; Orvis, Joshua; White, Owen; Buell, C Robin; Wortman, Jennifer R

    2008-01-01

    EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation. PMID:18190707

  6. Alignment system for SGII-Up laser facility

    NASA Astrophysics Data System (ADS)

    Gao, Yanqi; Cui, Yong; Li, Hong; Gong, Lei; Lin, Qiang; Liu, Daizhong; Zhu, Baoqiang; Ma, Weixin; Zhu, Jian; Lin, Zunqi

    2018-03-01

    The SGII-Up laser facility in Shanghai is one of the most important high-power laser facilities in China. It is designed to obtain 24 kJ (3ω) of energy with a square pulse of 3 ns using eight laser beams (two bundles). To satisfy the requirements for the safety, efficiency, and quality, an alignment system is developed for this facility. This alignment system can perform automatic alignment of the preamplifier system, main amplifier system, and harmonic conversion system within 30 min before every shot during the routine operation of the facility. In this article, an overview of the alignment system is first presented. Then, its alignment characteristics are discussed, along with the alignment process. Finally, experimental results, including the alignment results and the facility performance, are reported. The results show that the far-field beam pointing alignment accuracy is better than 3 μrad, and the alignment error of the near-field beam centering is no larger than 1 mm. These satisfy the design requirements very well.

  7. English Teaching Profile: Sabah--Malaysia.

    ERIC Educational Resources Information Center

    British Council, London (England). English Language and Literature Div.

    This review of the status of English language instruction in Sabah, Malaysia, provides an overview of the role of English in the society in general and outlines the status of English use and instruction in both the Chinese and government educational systems at all levels. Topics covered are: the characteristics and training of English language…

  8. An Introduction to Liberian English.

    ERIC Educational Resources Information Center

    Singler, John Victor; And Others

    The aim of this text is to introduce Liberian English, which includes the many varieties of English spoken by Liberians, to Peace Corps volunteers. The text is divided into two sections. The first part talks about Liberian English, while the second part uses Liberian English to describe aspects of contemporary Liberian culture. Part one contains…

  9. English Teaching Profile: Colombia.

    ERIC Educational Resources Information Center

    British Council, London (England). English Language and Literature Div.

    A review of the status of English language instruction in Colombia provides an overview of the role of English in the society in general and outlines the status of English use and instruction in the educational system at all levels (elementary, secondary, postsecondary, and teacher education). The following topics are covered: the characteristics…

  10. English Teaching in Mexico.

    ERIC Educational Resources Information Center

    Salazar, Denise

    2002-01-01

    Discusses teaching English in Mexico, a country with important social, cultural, and economic ties to the United States. Looks at the various English teaching situations as well as teacher education for teachers in Mexico. Concludes that the English teaching situation in Mexico reflects great diversity and growth, and that the knowledge of English…

  11. Moodling English Language Education

    ERIC Educational Resources Information Center

    Coskun, Abdullah; Arslan, Abdullah

    2014-01-01

    This paper aims to emphasize the importance of using Moodle in foreign language learning and teaching by reviewing relevant literature and introducing a Moodle-based environment aiming to help English learners to practice their English by themselves. Firstly, the use of Moodle in education and more specifically in English Language Teaching is…

  12. Simultaneous phylogeny reconstruction and multiple sequence alignment

    PubMed Central

    Yue, Feng; Shi, Jian; Tang, Jijun

    2009-01-01

    Background A phylogeny is the evolutionary history of a group of organisms. To date, sequence data is still the most used data type for phylogenetic reconstruction. Before any sequences can be used for phylogeny reconstruction, they must be aligned, and the quality of the multiple sequence alignment has been shown to affect the quality of the inferred phylogeny. At the same time, all the current multiple sequence alignment programs use a guide tree to produce the alignment and experiments showed that good guide trees can significantly improve the multiple alignment quality. Results We devise a new algorithm to simultaneously align multiple sequences and search for the phylogenetic tree that leads to the best alignment. We also implemented the algorithm as a C program package, which can handle both DNA and protein data and can take simple cost model as well as complex substitution matrices, such as PAM250 or BLOSUM62. The performance of the new method are compared with those from other popular multiple sequence alignment tools, including the widely used programs such as ClustalW and T-Coffee. Experimental results suggest that this method has good performance in terms of both phylogeny accuracy and alignment quality. Conclusion We present an algorithm to align multiple sequences and reconstruct the phylogenies that minimize the alignment score, which is based on an efficient algorithm to solve the median problems for three sequences. Our extensive experiments suggest that this method is very promising and can produce high quality phylogenies and alignments. PMID:19208110

  13. Whole-genome alignment.

    PubMed

    Dewey, Colin N

    2012-01-01

    Whole-genome alignment (WGA) is the prediction of evolutionary relationships at the nucleotide level between two or more genomes. It combines aspects of both colinear sequence alignment and gene orthology prediction, and is typically more challenging to address than either of these tasks due to the size and complexity of whole genomes. Despite the difficulty of this problem, numerous methods have been developed for its solution because WGAs are valuable for genome-wide analyses, such as phylogenetic inference, genome annotation, and function prediction. In this chapter, we discuss the meaning and significance of WGA and present an overview of the methods that address it. We also examine the problem of evaluating whole-genome aligners and offer a set of methodological challenges that need to be tackled in order to make the most effective use of our rapidly growing databases of whole genomes.

  14. Effective instruction for English learners.

    PubMed

    Calderón, Margarita; Slavin, Robert; Sánchez, Marta

    2011-01-01

    The fastest-growing student population in U.S. schools today is children of immigrants, half of whom do not speak English fluently and are thus labeled English learners. Although the federal government requires school districts to provide services to English learners, it offers states no policies to follow in identifying, assessing, placing, or instructing them. Margarita Calderón, Robert Slavin, and Marta Sánchez identify the elements of effective instruction and review a variety of successful program models. During 2007-08, more than 5.3 million English learners made up 10.6 percent of the nation's K-12 public school enrollment. Wide and persistent achievement disparities between these English learners and English-proficient students show clearly, say the authors, that schools must address the language, literacy, and academic needs of English learners more effectively. Researchers have fiercely debated the merits of bilingual and English-only reading instruction. In elementary schools, English learners commonly receive thirty minutes of English as a Second Language (ESL) instruction but attend general education classes for the rest of the day, usually with teachers who are unprepared to teach them. Though English learners have strikingly diverse levels of skills, in high school they are typically lumped together, with one teacher to address their widely varying needs. These in-school factors contribute to the achievement disparities. Based on the studies presented here, Calderón, Slavin, and Sánchez assert that the quality of instruction is what matters most in educating English learners. They highlight comprehensive reform models, as well as individual components of these models: school structures and leadership; language and literacy instruction; integration of language, literacy, and content instruction in secondary schools; cooperative learning; professional development; parent and family support teams; tutoring; and monitoring implementation and outcomes

  15. Navajo-English Dictionary.

    ERIC Educational Resources Information Center

    Wall, Leon; Morgan, William

    A brief summary of the sound system of the Navajo language introduces this Navajo-English dictionary. Diacritical markings and an English definition are given for each Navajo word. Words are listed alphabetically by Navajo sound. (VM)

  16. English Language Teaching Profile: Sweden.

    ERIC Educational Resources Information Center

    British Council, London (England). English-Teaching Information Centre.

    This profile in outline form of the English language teaching situation in Sweden discusses the role of English within Swedish society and within the Swedish educational system. The status of English as the principal foreign language since 1945 for use in business, the media and tourism is pointed out. The system of English instruction in the…

  17. My Hesitation to Speak English

    ERIC Educational Resources Information Center

    Oda, Naruha

    2015-01-01

    Even though English was the author's favorite subject, she was not good at speaking in English, and always tried to avoid it. However, it did not matter because she did not have to speak to demonstrate her English ability. After entering university, her lack of confidence in speaking English became a major issue, and other students face the same…

  18. History of the English Language.

    ERIC Educational Resources Information Center

    Regional Curriculum Project, Atlanta, GA.

    This curriculum guide, developed for pre-kindergartners through grade 12 as part of the total English curriculum, is concerned with the English language as it is now known and as it evolved from its Indo-European roots. Materials include (1) an overview of the origin and development of the English language from Old English through middle English…

  19. Heuristics for multiobjective multiple sequence alignment.

    PubMed

    Abbasi, Maryam; Paquete, Luís; Pereira, Francisco B

    2016-07-15

    Aligning multiple sequences arises in many tasks in Bioinformatics. However, the alignments produced by the current software packages are highly dependent on the parameters setting, such as the relative importance of opening gaps with respect to the increase of similarity. Choosing only one parameter setting may provide an undesirable bias in further steps of the analysis and give too simplistic interpretations. In this work, we reformulate multiple sequence alignment from a multiobjective point of view. The goal is to generate several sequence alignments that represent a trade-off between maximizing the substitution score and minimizing the number of indels/gaps in the sum-of-pairs score function. This trade-off gives to the practitioner further information about the similarity of the sequences, from which she could analyse and choose the most plausible alignment. We introduce several heuristic approaches, based on local search procedures, that compute a set of sequence alignments, which are representative of the trade-off between the two objectives (substitution score and indels). Several algorithm design options are discussed and analysed, with particular emphasis on the influence of the starting alignment and neighborhood search definitions on the overall performance. A perturbation technique is proposed to improve the local search, which provides a wide range of high-quality alignments. The proposed approach is tested experimentally on a wide range of instances. We performed several experiments with sequences obtained from the benchmark database BAliBASE 3.0. To evaluate the quality of the results, we calculate the hypervolume indicator of the set of score vectors returned by the algorithms. The results obtained allow us to identify reasonably good choices of parameters for our approach. Further, we compared our method in terms of correctly aligned pairs ratio and columns correctly aligned ratio with respect to reference alignments. Experimental results show

  20. Design and optimization of a portable LQCD Monte Carlo code using OpenACC

    NASA Astrophysics Data System (ADS)

    Bonati, Claudio; Coscetti, Simone; D'Elia, Massimo; Mesiti, Michele; Negro, Francesco; Calore, Enrico; Schifano, Sebastiano Fabio; Silvi, Giorgio; Tripiccione, Raffaele

    The present panorama of HPC architectures is extremely heterogeneous, ranging from traditional multi-core CPU processors, supporting a wide class of applications but delivering moderate computing performance, to many-core Graphics Processor Units (GPUs), exploiting aggressive data-parallelism and delivering higher performances for streaming computing applications. In this scenario, code portability (and performance portability) become necessary for easy maintainability of applications; this is very relevant in scientific computing where code changes are very frequent, making it tedious and prone to error to keep different code versions aligned. In this work, we present the design and optimization of a state-of-the-art production-level LQCD Monte Carlo application, using the directive-based OpenACC programming model. OpenACC abstracts parallel programming to a descriptive level, relieving programmers from specifying how codes should be mapped onto the target architecture. We describe the implementation of a code fully written in OpenAcc, and show that we are able to target several different architectures, including state-of-the-art traditional CPUs and GPUs, with the same code. We also measure performance, evaluating the computing efficiency of our OpenACC code on several architectures, comparing with GPU-specific implementations and showing that a good level of performance-portability can be reached.

  1. English Teaching Profile: Malaysia.

    ERIC Educational Resources Information Center

    British Council, London (England). English Language and Literature Div.

    The status of the use and instruction of English in Malaysia, where it is a commonly-used second language, is described. The following topics are discussed: (1) the general status and role of English in Malaysian society in recent years; (2) English within the educational system (preschool, elementary, secondary, higher, adult, military, prison,…

  2. SU-E-J-33: Comparison Between Soft Tissue Alignment and Bony Alignment for Pancreatic Cancer Radiotherapy

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

    Suh, Y; Crane, C; Krishnan, S

    Purpose An IGRT modality for pancreatic cancer treatment with dose escalation at our institution is in-room daily CT imaging. The purpose of this study is to assess the difference between soft tissue alignment and bony alignment for pancreatic tumor localization. Methods Eighteen patients with pancreatic tumors who underwent IMRT treatment with an inspiration breath-hold technique between July 2012 and February 2015 are included in this study. Prior to each treatment, a CT scan was acquired. The CT image guidance started with auto-alignment to either the bony anatomy (vertebral bodies) or fiducials (for the six patients with the stent in/near themore » tumor) and then, when necessary, manual adjustments were made based on soft tissue alignment using clinical software (CT-Assisted Targeting system). The difference between soft tissue alignment and bony/fiducial alignment was evaluated. Results Of all 380 treatments, manual adjustment was made in 225 treatments, ranging from 11% (3 treatments out of 28) to 96% (27 treatments out of 28) per patient. The mean of the difference between soft tissue alignment and bony/fiducial alignment per patient ranged from −3.6 to 0.3 mm, −1.5 to 2.8 mm, and −3.3 to 3.4 mm in the AP, SI, and RL directions, respectively. The maximum difference over all treatments was −9.5, −14.6, and −14.6 mm in the AP, SI, and RL directions, respectively. Conclusion About 60% of the time, manual adjustment based on soft tissue alignment was required. The extent of manual adjustment was usually small but varied significantly from patient to patient. The ultimate goal of the IGRT modality using daily CT imaging is not to fully cover the target but to spare organs-at-risk as much as possible to avoid them moving into higher dose gradients than accepted in the treatment plan. To this end, manual adjustment based on soft tissue alignment is critically important.« less

  3. Developmental and communicative factors affecting VOT production in English and Arabic bilingual and monolingual speakers

    NASA Astrophysics Data System (ADS)

    Khattab, Ghada

    2004-05-01

    VOT patterns were investigated in the production of three Lebanese-English bilinguals' aged 5, 7, and 10, six aged-matched monolingual controls from the bilinguals' immediate communities, and the parents of bilinguals and monolinguals. The aim was to examine the extent to which children exposed to two languages acquire separate VOT patterns for each language and to determine the factors that affect such acquisition. Results showed that VOT patterns for each bilingual child differed significantly across the two languages. But while the contrast in English resembled a monolingual-like model, that for Arabic exhibited persisting developmental features; explanations were offered in terms of the relationship between input and complexity of voicing lead production. Evidence was used from developmental changes that were noted for two of the bilingual subjects over a period of 18 months. English code-switches produced by the bilinguals during Arabic sessions exhibited different VOT patterns from those produced during English sessions, which underlined the importance of taking the language context into consideration. Finally, results from monolinguals and bilinguals showed that the short lag categories for the two languages were different despite a degree of overlap. Such findings require finer divisions of the three universal VOT categories to account for language-specific patterns.

  4. SIM Lite: Ground Alignment of the Instrument

    NASA Technical Reports Server (NTRS)

    Dekens, Frank G.; Goullioud, Renaud; Nicaise, Fabien; Kuan, Gary; Morales, Mauricio

    2010-01-01

    We present the start of the ground alignment plan for the SIM Lite Instrument. We outline the integration and alignment of the individual benches on which all the optics are mounted, and then the alignment of the benches to form the Science and Guide interferometers. The Instrument has a guide interferometer with only a 40 arc-seconds field of regard, and 200 arc-seconds of alignment adjustability. This requires each sides of the interferometer to be aligned to a fraction of that, while at the same time be orthogonal to the baseline defined by the External Metrology Truss. The baselines of the Science and Guide interferometers must also be aligned to be parallel. The start of these alignment plans is captured in a SysML Instrument System model, in the form of activity diagrams. These activity diagrams are then related to the hardware design and requirements. We finish with future plans for the alignment and integration activities and requirements.

  5. SIM Lite: ground alignment of the instrument

    NASA Astrophysics Data System (ADS)

    Dekens, Frank G.; Goullioud, Renaud; Nicaise, Fabien; Kuan, Gary; Morales, Mauricio

    2010-07-01

    We present the start of the ground alignment plan for the SIM Lite Instrument. We outline the integration and alignment of the individual benches on which all the optics are mounted, and then the alignment of the benches to form the Science and Guide interferometers. The Instrument has a guide interferometer with only a 40 arc-seconds field of regard, and 200 arc-seconds of alignment adjustability. This requires each sides of the interferometer to be aligned to a fraction of that, while at the same time be orthogonal to the baseline defined by the External Metrology Truss. The baselines of the Science and Guide interferometers must also be aligned to be parallel. The start of these alignment plans is captured in a SysML Instrument System model, in the form of activity diagrams. These activity diagrams are then related to the hardware design and requirements. We finish with future plans for the alignment and integration activities and requirements.

  6. Image alignment

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

    Dowell, Larry Jonathan

    Disclosed is a method and device for aligning at least two digital images. An embodiment may use frequency-domain transforms of small tiles created from each image to identify substantially similar, "distinguishing" features within each of the images, and then align the images together based on the location of the distinguishing features. To accomplish this, an embodiment may create equal sized tile sub-images for each image. A "key" for each tile may be created by performing a frequency-domain transform calculation on each tile. A information-distance difference between each possible pair of tiles on each image may be calculated to identify distinguishingmore » features. From analysis of the information-distance differences of the pairs of tiles, a subset of tiles with high discrimination metrics in relation to other tiles may be located for each image. The subset of distinguishing tiles for each image may then be compared to locate tiles with substantially similar keys and/or information-distance metrics to other tiles of other images. Once similar tiles are located for each image, the images may be aligned in relation to the identified similar tiles.« less

  7. BASiNET-BiologicAl Sequences NETwork: a case study on coding and non-coding RNAs identification.

    PubMed

    Ito, Eric Augusto; Katahira, Isaque; Vicente, Fábio Fernandes da Rocha; Pereira, Luiz Filipe Protasio; Lopes, Fabrício Martins

    2018-06-05

    With the emergence of Next Generation Sequencing (NGS) technologies, a large volume of sequence data in particular de novo sequencing was rapidly produced at relatively low costs. In this context, computational tools are increasingly important to assist in the identification of relevant information to understand the functioning of organisms. This work introduces BASiNET, an alignment-free tool for classifying biological sequences based on the feature extraction from complex network measurements. The method initially transform the sequences and represents them as complex networks. Then it extracts topological measures and constructs a feature vector that is used to classify the sequences. The method was evaluated in the classification of coding and non-coding RNAs of 13 species and compared to the CNCI, PLEK and CPC2 methods. BASiNET outperformed all compared methods in all adopted organisms and datasets. BASiNET have classified sequences in all organisms with high accuracy and low standard deviation, showing that the method is robust and non-biased by the organism. The proposed methodology is implemented in open source in R language and freely available for download at https://cran.r-project.org/package=BASiNET.

  8. Attitudes toward English & English Learning at an Iranian Military University: A Preliminary Survey

    ERIC Educational Resources Information Center

    Mahdavi Zafarghandi, Amir; Jodai, Hojat

    2012-01-01

    This study intends to represent attitudes toward English and English learning at an Iranian military university. Iranian military staff is required to study English in a social environment where there is little immediate need or opportunity to use the language for real communicative purposes.The subjects included 34 Iranian military personnel who…

  9. MUSE optical alignment procedure

    NASA Astrophysics Data System (ADS)

    Laurent, Florence; Renault, Edgard; Loupias, Magali; Kosmalski, Johan; Anwand, Heiko; Bacon, Roland; Boudon, Didier; Caillier, Patrick; Daguisé, Eric; Dubois, Jean-Pierre; Dupuy, Christophe; Kelz, Andreas; Lizon, Jean-Louis; Nicklas, Harald; Parès, Laurent; Remillieux, Alban; Seifert, Walter; Valentin, Hervé; Xu, Wenli

    2012-09-01

    MUSE (Multi Unit Spectroscopic Explorer) is a second generation VLT integral field spectrograph (1x1arcmin² Field of View) developed for the European Southern Observatory (ESO), operating in the visible wavelength range (0.465-0.93 μm). A consortium of seven institutes is currently assembling and testing MUSE in the Integration Hall of the Observatoire de Lyon for the Preliminary Acceptance in Europe, scheduled for 2013. MUSE is composed of several subsystems which are under the responsibility of each institute. The Fore Optics derotates and anamorphoses the image at the focal plane. A Splitting and Relay Optics feed the 24 identical Integral Field Units (IFU), that are mounted within a large monolithic instrument mechanical structure. Each IFU incorporates an image slicer, a fully refractive spectrograph with VPH-grating and a detector system connected to a global vacuum and cryogenic system. During 2011, all MUSE subsystems were integrated, aligned and tested independently in each institute. After validations, the systems were shipped to the P.I. institute at Lyon and were assembled in the Integration Hall This paper describes the end-to-end optical alignment procedure of the MUSE instrument. The design strategy, mixing an optical alignment by manufacturing (plug and play approach) and few adjustments on key components, is presented. We depict the alignment method for identifying the optical axis using several references located in pupil and image planes. All tools required to perform the global alignment between each subsystem are described. The success of this alignment approach is demonstrated by the good results for the MUSE image quality. MUSE commissioning at the VLT (Very Large Telescope) is planned for 2013.

  10. Alignment methods: strategies, challenges, benchmarking, and comparative overview.

    PubMed

    Löytynoja, Ari

    2012-01-01

    Comparative evolutionary analyses of molecular sequences are solely based on the identities and differences detected between homologous characters. Errors in this homology statement, that is errors in the alignment of the sequences, are likely to lead to errors in the downstream analyses. Sequence alignment and phylogenetic inference are tightly connected and many popular alignment programs use the phylogeny to divide the alignment problem into smaller tasks. They then neglect the phylogenetic tree, however, and produce alignments that are not evolutionarily meaningful. The use of phylogeny-aware methods reduces the error but the resulting alignments, with evolutionarily correct representation of homology, can challenge the existing practices and methods for viewing and visualising the sequences. The inter-dependency of alignment and phylogeny can be resolved by joint estimation of the two; methods based on statistical models allow for inferring the alignment parameters from the data and correctly take into account the uncertainty of the solution but remain computationally challenging. Widely used alignment methods are based on heuristic algorithms and unlikely to find globally optimal solutions. The whole concept of one correct alignment for the sequences is questionable, however, as there typically exist vast numbers of alternative, roughly equally good alignments that should also be considered. This uncertainty is hidden by many popular alignment programs and is rarely correctly taken into account in the downstream analyses. The quest for finding and improving the alignment solution is complicated by the lack of suitable measures of alignment goodness. The difficulty of comparing alternative solutions also affects benchmarks of alignment methods and the results strongly depend on the measure used. As the effects of alignment error cannot be predicted, comparing the alignments' performance in downstream analyses is recommended.

  11. English Language Proficiency and Content Assessment Performance: A Comparison of English Learners and Native English Speakers Achievement

    ERIC Educational Resources Information Center

    Miley, Suzi Keller; Farmer, Aarek

    2017-01-01

    As a result of the accountability requirements established in Title III of the Elementary and Secondary Educational Act (ESEA) legislation, English Learners (ELs) are expected to make progress in both content area academic achievement and English Language Proficiency (ELP). In Tennessee ELs progress is measured by administering WIDA-Access to…

  12. English Teaching Profile: Brazil.

    ERIC Educational Resources Information Center

    British Council, London (England). English Language and Literature Div.

    This review of the status of English language instruction in Brazil provides an overview of the Brazilian geographic, historical, and political context and the role of English in the society in general and in the educational system. The following topics are covered: an outline of the status of English use and instruction in the educational system…

  13. English Teaching Profile: Algeria.

    ERIC Educational Resources Information Center

    British Council, London (England). English Language and Literature Div.

    A survey of the status and use of the English language in Algeria is presented. The following topics are outlined: (1) the role of English as a third language, (2) its place within the educational system at all levels and in each graduate institution, (3) the status of British expatriates teaching English in Algeria and of Algerian teachers of…

  14. System alignment using the Talbot effect

    NASA Astrophysics Data System (ADS)

    Chevallier, Raymond; Le Falher, Eric; Heggarty, Kevin

    1990-08-01

    The Talbot effect is utilized to correct an alignment problem related to a neural network used for image recognition, which required the alignment of a spatial light modulator (SLM) with the input module. A mathematical model which employs the Fresnel diffraction theory is presented to describe the method. The calculation of the diffracted amplitude describes the wavefront sphericity and the original object transmittance function in order to qualify the lateral shift of the Talbot image. Another explanation is set forth in terms of plane-wave illumination in the neural network. Using a Fourier series and by describing planes where all the harmonics are in phase, the reconstruction of Talbot images is explained. The alignment is effective when the lenslet array is aligned on the even Talbot images of the SLM pixels and the incident wave is a plane wave. The alignment is evaluated in terms of source and periodicity errors, tilt of the incident plane waves, and finite object dimensions. The effects of the error sources are concluded to be negligible, the lenslet array is shown to be successfully aligned with the SLM, and other alignment applications are shown to be possible.

  15. The twilight zone of cis element alignments.

    PubMed

    Sebastian, Alvaro; Contreras-Moreira, Bruno

    2013-02-01

    Sequence alignment of proteins and nucleic acids is a routine task in bioinformatics. Although the comparison of complete peptides, genes or genomes can be undertaken with a great variety of tools, the alignment of short DNA sequences and motifs entails pitfalls that have not been fully addressed yet. Here we confront the structural superposition of transcription factors with the sequence alignment of their recognized cis elements. Our goals are (i) to test TFcompare (http://floresta.eead.csic.es/tfcompare), a structural alignment method for protein-DNA complexes; (ii) to benchmark the pairwise alignment of regulatory elements; (iii) to define the confidence limits and the twilight zone of such alignments and (iv) to evaluate the relevance of these thresholds with elements obtained experimentally. We find that the structure of cis elements and protein-DNA interfaces is significantly more conserved than their sequence and measures how this correlates with alignment errors when only sequence information is considered. Our results confirm that DNA motifs in the form of matrices produce better alignments than individual sequences. Finally, we report that empirical and theoretically derived twilight thresholds are useful for estimating the natural plasticity of regulatory sequences, and hence for filtering out unreliable alignments.

  16. English-language competency of self-declared English-speaking Hispanic patients using written tests of health literacy.

    PubMed Central

    Zun, Leslie S.; Sadoun, Tania; Downey, LaVonne

    2006-01-01

    INTRODUCTION: Hispanic patients comprise the largest minority population in the United States. The federal government mandates that healthcare providers be able to communicate with those patients who have limited English ability. The primary purpose of this study was to assess the English-language proficiency of self-declared English-speaking Hispanic patients in the emergency department (ED). The secondary purpose was to determine concordance between patients' tested English proficiency and perceived proficiency by nurses and physicians. We hypothesized that many patients who state that they are able to speak English do not in fact possess sufficient ability to communicate in English. METHODS: A convenience study was conducted in an urban level-1 pediatrics and adult trauma center with 45,000 annual visits. Participants included adult patients and parents of pediatric patients, all of which spoke Spanish as their first language. Since there were no verbal tests of English-language ability used in medicine, two written tests were used as surrogates-the Rapid Estimate of Adult Literacy in Medicine (REALM) and the Short Test of Functional Health Literacy in Adults (STOFHLA). Research assistants administered these tests to patients with Hispanic surnames to assess the English comprehension of patients who stated that they spoke English. Score of seventh grade or better on the REALM and > or = 23 on the STOFHLA was considered a level of English competency. Data was entered into SPSS and analyzed for correlations. This study was approved by the institutional review board as exempt. RESULTS: Three-hundred-fifty-four patients with Hispanic names were approached and asked if they spoke English, Spanish or both. One-hundred-five patients, all self-proclaimed English speakers, were enrolled in the study. Patients ranged from 18-89 years of age, with 37.1% (39/105) male and 62.9% (66/105) and female; 49% (50/102) patients had only completed grade school. Sixty-five of 98 (66

  17. System and method for 2D workpiece alignment

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

    Weaver, William T.; Carlson, Charles T.; Smith, Scott A.

    2015-07-14

    A carrier capable of holding one or more workpieces is disclosed. The carrier includes movable projections located along the sides of each cell in the carrier. This carrier, in conjunction with a separate alignment apparatus, aligns each workpiece within its respective cell against several alignment pins, using a multiple step alignment process to guarantee proper positioning of the workpiece in the cell. First, the workpieces are moved toward one side of the cell. Once the workpieces have been aligned against this side, the workpieces are then moved toward an adjacent orthogonal side such that the workpieces are aligned to twomore » sides of the cell. Once aligned, the workpiece is held in place by the projections located along each side of each cell. In addition, the alignment pins are also used to align the associated mask, thereby guaranteeing that the mask is properly aligned to the workpiece.« less

  18. A novel specimen-specific methodology to optimise the alignment of long bones for experimental testing.

    PubMed

    Cheong, Vee San; Bull, Anthony M J

    2015-12-16

    The choice of coordinate system and alignment of bone will affect the quantification of mechanical properties obtained during in-vitro biomechanical testing. Where these are used in predictive models, such as finite element analysis, the fidelic description of these properties is paramount. Currently in bending and torsional tests, bones are aligned on a pre-defined fixed span based on the reference system marked out. However, large inter-specimen differences have been reported. This suggests a need for the development of a specimen-specific alignment system for use in experimental work. Eleven ovine tibiae were used in this study and three-dimensional surface meshes were constructed from micro-Computed Tomography scan images. A novel, semi-automated algorithm was developed and applied to the surface meshes to align the whole bone based on its calculated principal directions. Thereafter, the code isolates the optimised location and length of each bone for experimental testing. This resulted in a lowering of the second moment of area about the chosen bending axis in the central region. More importantly, the optimisation method decreases the irregularity of the shape of the cross-sectional slices as the unbiased estimate of the population coefficient of variation of the second moment of area decreased from a range of (0.210-0.435) to (0.145-0.317) in the longitudinal direction, indicating a minimisation of the product moment, which causes eccentric loading. Thus, this methodology serves as an important pre-step to align the bone for mechanical tests or simulation work, is optimised for each specimen, ensures repeatability, and is general enough to be applied to any long bone. Copyright © 2015 Elsevier Ltd. All rights reserved.

  19. LZW-Kernel: fast kernel utilizing variable length code blocks from LZW compressors for protein sequence classification.

    PubMed

    Filatov, Gleb; Bauwens, Bruno; Kertész-Farkas, Attila

    2018-05-07

    Bioinformatics studies often rely on similarity measures between sequence pairs, which often pose a bottleneck in large-scale sequence analysis. Here, we present a new convolutional kernel function for protein sequences called the LZW-Kernel. It is based on code words identified with the Lempel-Ziv-Welch (LZW) universal text compressor. The LZW-Kernel is an alignment-free method, it is always symmetric, is positive, always provides 1.0 for self-similarity and it can directly be used with Support Vector Machines (SVMs) in classification problems, contrary to normalized compression distance (NCD), which often violates the distance metric properties in practice and requires further techniques to be used with SVMs. The LZW-Kernel is a one-pass algorithm, which makes it particularly plausible for big data applications. Our experimental studies on remote protein homology detection and protein classification tasks reveal that the LZW-Kernel closely approaches the performance of the Local Alignment Kernel (LAK) and the SVM-pairwise method combined with Smith-Waterman (SW) scoring at a fraction of the time. Moreover, the LZW-Kernel outperforms the SVM-pairwise method when combined with BLAST scores, which indicates that the LZW code words might be a better basis for similarity measures than local alignment approximations found with BLAST. In addition, the LZW-Kernel outperforms n-gram based mismatch kernels, hidden Markov model based SAM and Fisher kernel, and protein family based PSI-BLAST, among others. Further advantages include the LZW-Kernel's reliance on a simple idea, its ease of implementation, and its high speed, three times faster than BLAST and several magnitudes faster than SW or LAK in our tests. LZW-Kernel is implemented as a standalone C code and is a free open-source program distributed under GPLv3 license and can be downloaded from https://github.com/kfattila/LZW-Kernel. akerteszfarkas@hse.ru. Supplementary data are available at Bioinformatics Online.

  20. Does Adding Mathematics to English Language Learners' Timetables Improve Their Acquisition of English?

    ERIC Educational Resources Information Center

    Stacey, Jenny

    2016-01-01

    This enquiry based project set out to find out if adult English language learners, known as ESOL (English for Speakers of Other Languages) learners in the UK, might benefit, in terms of their acquisition of English, from studying maths. This research has been conducted at a medium sized FE college in the East Midlands where I teach. I evaluate…

  1. Teaching English or Producing Docility? Foucauldian Analysis of Pakistani State-Mandated English Textbooks

    ERIC Educational Resources Information Center

    Channa, Liaquat Ali; Gilhooly, Daniel; Channa, Abdul Razaque; Manan, Syed Abdul

    2017-01-01

    The scholarship of language education, particularly with reference to learning and use of English, is marked by varieties of English. One may note two broad models: (1) ENL, ESL, and EFL; (2) EIL, ELF, and WEs. Although the scholarship is replete with debates, the debates seem to only construct and maintain that learning English and its use are…

  2. RF Jitter Modulation Alignment Sensing

    NASA Astrophysics Data System (ADS)

    Ortega, L. F.; Fulda, P.; Diaz-Ortiz, M.; Perez Sanchez, G.; Ciani, G.; Voss, D.; Mueller, G.; Tanner, D. B.

    2017-01-01

    We will present the numerical and experimental results of a new alignment sensing scheme which can reduce the complexity of alignment sensing systems currently used, while maintaining the same shot noise limited sensitivity. This scheme relies on the ability of electro-optic beam deflectors to create angular modulation sidebands in radio frequency, and needs only a single-element photodiode and IQ demodulation to generate error signals for tilt and translation degrees of freedom in one dimension. It distances itself from current techniques by eliminating the need for beam centering servo systems, quadrant photodetectors and Gouy phase telescopes. RF Jitter alignment sensing can be used to reduce the complexity in the alignment systems of many laser optical experiments, including LIGO and the ALPS experiment.

  3. Fixture for aligning motor assembly

    DOEpatents

    Shervington, Roger M.; Vaghani, Vallabh V.; Vanek, Laurence D.; Christensen, Scott A.

    2009-12-08

    An alignment fixture includes a rotor fixture, a stator fixture and a sensor system which measures a rotational displacement therebetween. The fixture precisely measures rotation of a generator stator assembly away from a NULL position referenced by a unique reference spline on the rotor shaft. By providing an adjustable location of the stator assembly within the housing, the magnetic axes within each generator shall be aligned to a predetermined and controlled tolerance between the generator interface mounting pin and the reference spline on the rotor shaft. Once magnetically aligned, each generator is essentially a line replaceable unit which may be readily mounted to any input of a multi-generator gearbox assembly with the assurance that the magnetic alignment will be within a predetermined tolerance.

  4. Vane segment support and alignment device

    DOEpatents

    McLaurin, Leroy Dixon; Sizemore, John Derek

    1999-01-01

    A support and alignment assembly for supporting and aligning a vane segment is provided. The support and alignment assembly comprises a torque plate which defines an opening for receiving an eccentric pin and a locking end member for receiving a lock socket member. An eccentric pin adjustably supported by the torque plate opening for supporting and aligning a vane segment is provided. A lock socket member adapted to securely receive the eccentric pin and rotated therewith, and adjustably engage the torque plate locking end is provided. The lock socket member receives the eccentric pin, such that when the eccentric pin is adjusted to align the vane segment, the lock socket member engages the torque plate locking end to secure the vane segment in the desired position.

  5. From Pixels to Response Maps: Discriminative Image Filtering for Face Alignment in the Wild.

    PubMed

    Asthana, Akshay; Zafeiriou, Stefanos; Tzimiropoulos, Georgios; Cheng, Shiyang; Pantic, Maja

    2015-06-01

    We propose a face alignment framework that relies on the texture model generated by the responses of discriminatively trained part-based filters. Unlike standard texture models built from pixel intensities or responses generated by generic filters (e.g. Gabor), our framework has two important advantages. First, by virtue of discriminative training, invariance to external variations (like identity, pose, illumination and expression) is achieved. Second, we show that the responses generated by discriminatively trained filters (or patch-experts) are sparse and can be modeled using a very small number of parameters. As a result, the optimization methods based on the proposed texture model can better cope with unseen variations. We illustrate this point by formulating both part-based and holistic approaches for generic face alignment and show that our framework outperforms the state-of-the-art on multiple "wild" databases. The code and dataset annotations are available for research purposes from http://ibug.doc.ic.ac.uk/resources.

  6. English speech acquisition in 3- to 5-year-old children learning Russian and English.

    PubMed

    Gildersleeve-Neumann, Christina E; Wright, Kira L

    2010-10-01

    English speech acquisition in Russian-English (RE) bilingual children was investigated, exploring the effects of Russian phonetic and phonological properties on English single-word productions. Russian has more complex consonants and clusters and a smaller vowel inventory than English. One hundred thirty-seven single-word samples were phonetically transcribed from 14 RE and 28 English-only (E) children, ages 3;3 (years;months) to 5;7. Language and age differences were compared descriptively for phonetic inventories. Multivariate analyses compared phoneme accuracy and error rates between the two language groups. RE children produced Russian-influenced phones in English, including palatalized consonants and trills, and demonstrated significantly higher rates of trill substitution, final devoicing, and vowel errors than E children, suggesting Russian language effects on English. RE and E children did not differ in their overall production complexity, with similar final consonant deletion and cluster reduction error rates, similar phonetic inventories by age, and similar levels of phonetic complexity. Both older language groups were more accurate than the younger language groups. We observed effects of Russian on English speech acquisition; however, there were similarities between the RE and E children that have not been reported in previous studies of speech acquisition in bilingual children. These findings underscore the importance of knowing the phonological properties of both languages of a bilingual child in assessment.

  7. Flavivirus and Filovirus EvoPrinters: New alignment tools for the comparative analysis of viral evolution.

    PubMed

    Brody, Thomas; Yavatkar, Amarendra S; Park, Dong Sun; Kuzin, Alexander; Ross, Jermaine; Odenwald, Ward F

    2017-06-01

    Flavivirus and Filovirus infections are serious epidemic threats to human populations. Multi-genome comparative analysis of these evolving pathogens affords a view of their essential, conserved sequence elements as well as progressive evolutionary changes. While phylogenetic analysis has yielded important insights, the growing number of available genomic sequences makes comparisons between hundreds of viral strains challenging. We report here a new approach for the comparative analysis of these hemorrhagic fever viruses that can superimpose an unlimited number of one-on-one alignments to identify important features within genomes of interest. We have adapted EvoPrinter alignment algorithms for the rapid comparative analysis of Flavivirus or Filovirus sequences including Zika and Ebola strains. The user can input a full genome or partial viral sequence and then view either individual comparisons or generate color-coded readouts that superimpose hundreds of one-on-one alignments to identify unique or shared identity SNPs that reveal ancestral relationships between strains. The user can also opt to select a database genome in order to access a library of pre-aligned genomes of either 1,094 Flaviviruses or 460 Filoviruses for rapid comparative analysis with all database entries or a select subset. Using EvoPrinter search and alignment programs, we show the following: 1) superimposing alignment data from many related strains identifies lineage identity SNPs, which enable the assessment of sublineage complexity within viral outbreaks; 2) whole-genome SNP profile screens uncover novel Dengue2 and Zika recombinant strains and their parental lineages; 3) differential SNP profiling identifies host cell A-to-I hyper-editing within Ebola and Marburg viruses, and 4) hundreds of superimposed one-on-one Ebola genome alignments highlight ultra-conserved regulatory sequences, invariant amino acid codons and evolutionarily variable protein-encoding domains within a single genome

  8. Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets.

    PubMed

    Hoffmann, Nils; Keck, Matthias; Neuweger, Heiko; Wilhelm, Mathias; Högy, Petra; Niehaus, Karsten; Stoye, Jens

    2012-08-27

    Modern analytical methods in biology and chemistry use separation techniques coupled to sensitive detectors, such as gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS). These hyphenated methods provide high-dimensional data. Comparing such data manually to find corresponding signals is a laborious task, as each experiment usually consists of thousands of individual scans, each containing hundreds or even thousands of distinct signals. In order to allow for successful identification of metabolites or proteins within such data, especially in the context of metabolomics and proteomics, an accurate alignment and matching of corresponding features between two or more experiments is required. Such a matching algorithm should capture fluctuations in the chromatographic system which lead to non-linear distortions on the time axis, as well as systematic changes in recorded intensities. Many different algorithms for the retention time alignment of GC-MS and LC-MS data have been proposed and published, but all of them focus either on aligning previously extracted peak features or on aligning and comparing the complete raw data containing all available features. In this paper we introduce two algorithms for retention time alignment of multiple GC-MS datasets: multiple alignment by bidirectional best hits peak assignment and cluster extension (BIPACE) and center-star multiple alignment by pairwise partitioned dynamic time warping (CeMAPP-DTW). We show how the similarity-based peak group matching method BIPACE may be used for multiple alignment calculation individually and how it can be used as a preprocessing step for the pairwise alignments performed by CeMAPP-DTW. We evaluate the algorithms individually and in combination on a previously published small GC-MS dataset studying the Leishmania parasite and on a larger GC-MS dataset studying grains of wheat (Triticum aestivum). We have shown that BIPACE achieves very high precision

  9. Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets

    PubMed Central

    2012-01-01

    Background Modern analytical methods in biology and chemistry use separation techniques coupled to sensitive detectors, such as gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS). These hyphenated methods provide high-dimensional data. Comparing such data manually to find corresponding signals is a laborious task, as each experiment usually consists of thousands of individual scans, each containing hundreds or even thousands of distinct signals. In order to allow for successful identification of metabolites or proteins within such data, especially in the context of metabolomics and proteomics, an accurate alignment and matching of corresponding features between two or more experiments is required. Such a matching algorithm should capture fluctuations in the chromatographic system which lead to non-linear distortions on the time axis, as well as systematic changes in recorded intensities. Many different algorithms for the retention time alignment of GC-MS and LC-MS data have been proposed and published, but all of them focus either on aligning previously extracted peak features or on aligning and comparing the complete raw data containing all available features. Results In this paper we introduce two algorithms for retention time alignment of multiple GC-MS datasets: multiple alignment by bidirectional best hits peak assignment and cluster extension (BIPACE) and center-star multiple alignment by pairwise partitioned dynamic time warping (CeMAPP-DTW). We show how the similarity-based peak group matching method BIPACE may be used for multiple alignment calculation individually and how it can be used as a preprocessing step for the pairwise alignments performed by CeMAPP-DTW. We evaluate the algorithms individually and in combination on a previously published small GC-MS dataset studying the Leishmania parasite and on a larger GC-MS dataset studying grains of wheat (Triticum aestivum). Conclusions We have shown that BIPACE

  10. MACSIMS : multiple alignment of complete sequences information management system

    PubMed Central

    Thompson, Julie D; Muller, Arnaud; Waterhouse, Andrew; Procter, Jim; Barton, Geoffrey J; Plewniak, Frédéric; Poch, Olivier

    2006-01-01

    Background In the post-genomic era, systems-level studies are being performed that seek to explain complex biological systems by integrating diverse resources from fields such as genomics, proteomics or transcriptomics. New information management systems are now needed for the collection, validation and analysis of the vast amount of heterogeneous data available. Multiple alignments of complete sequences provide an ideal environment for the integration of this information in the context of the protein family. Results MACSIMS is a multiple alignment-based information management program that combines the advantages of both knowledge-based and ab initio sequence analysis methods. Structural and functional information is retrieved automatically from the public databases. In the multiple alignment, homologous regions are identified and the retrieved data is evaluated and propagated from known to unknown sequences with these reliable regions. In a large-scale evaluation, the specificity of the propagated sequence features is estimated to be >99%, i.e. very few false positive predictions are made. MACSIMS is then used to characterise mutations in a test set of 100 proteins that are known to be involved in human genetic diseases. The number of sequence features associated with these proteins was increased by 60%, compared to the features available in the public databases. An XML format output file allows automatic parsing of the MACSIM results, while a graphical display using the JalView program allows manual analysis. Conclusion MACSIMS is a new information management system that incorporates detailed analyses of protein families at the structural, functional and evolutionary levels. MACSIMS thus provides a unique environment that facilitates knowledge extraction and the presentation of the most pertinent information to the biologist. A web server and the source code are available at . PMID:16792820

  11. The twilight zone of cis element alignments

    PubMed Central

    Sebastian, Alvaro; Contreras-Moreira, Bruno

    2013-01-01

    Sequence alignment of proteins and nucleic acids is a routine task in bioinformatics. Although the comparison of complete peptides, genes or genomes can be undertaken with a great variety of tools, the alignment of short DNA sequences and motifs entails pitfalls that have not been fully addressed yet. Here we confront the structural superposition of transcription factors with the sequence alignment of their recognized cis elements. Our goals are (i) to test TFcompare (http://floresta.eead.csic.es/tfcompare), a structural alignment method for protein–DNA complexes; (ii) to benchmark the pairwise alignment of regulatory elements; (iii) to define the confidence limits and the twilight zone of such alignments and (iv) to evaluate the relevance of these thresholds with elements obtained experimentally. We find that the structure of cis elements and protein–DNA interfaces is significantly more conserved than their sequence and measures how this correlates with alignment errors when only sequence information is considered. Our results confirm that DNA motifs in the form of matrices produce better alignments than individual sequences. Finally, we report that empirical and theoretically derived twilight thresholds are useful for estimating the natural plasticity of regulatory sequences, and hence for filtering out unreliable alignments. PMID:23268451

  12. Sparse alignment for robust tensor learning.

    PubMed

    Lai, Zhihui; Wong, Wai Keung; Xu, Yong; Zhao, Cairong; Sun, Mingming

    2014-10-01

    Multilinear/tensor extensions of manifold learning based algorithms have been widely used in computer vision and pattern recognition. This paper first provides a systematic analysis of the multilinear extensions for the most popular methods by using alignment techniques, thereby obtaining a general tensor alignment framework. From this framework, it is easy to show that the manifold learning based tensor learning methods are intrinsically different from the alignment techniques. Based on the alignment framework, a robust tensor learning method called sparse tensor alignment (STA) is then proposed for unsupervised tensor feature extraction. Different from the existing tensor learning methods, L1- and L2-norms are introduced to enhance the robustness in the alignment step of the STA. The advantage of the proposed technique is that the difficulty in selecting the size of the local neighborhood can be avoided in the manifold learning based tensor feature extraction algorithms. Although STA is an unsupervised learning method, the sparsity encodes the discriminative information in the alignment step and provides the robustness of STA. Extensive experiments on the well-known image databases as well as action and hand gesture databases by encoding object images as tensors demonstrate that the proposed STA algorithm gives the most competitive performance when compared with the tensor-based unsupervised learning methods.

  13. ALIGNING JIG

    DOEpatents

    Culver, J.S.; Tunnell, W.C.

    1958-08-01

    A jig or device is described for setting or aligning an opening in one member relative to another member or structure, with a predetermined offset, or it may be used for measuring the amount of offset with which the parts have previously been sct. This jig comprises two blocks rabbeted to each other, with means for securing thc upper block to the lower block. The upper block has fingers for contacting one of the members to be a1igmed, the lower block is designed to ride in grooves within the reference member, and calibration marks are provided to determine the amount of offset. This jig is specially designed to align the collimating slits of a mass spectrometer.

  14. The Story of an Arts Integration School on English-Language-Learner Development: A Qualitative Study of Collaboration, Integrity, and Confidence

    ERIC Educational Resources Information Center

    Ingraham, Nissa; Nuttall, Susanne

    2016-01-01

    This qualitative case study of a southwest regional elementary school used interviews, focus groups, and document collection to better understand how this arts-integrated school is meeting the needs of English-language learner (ELL) students, discerning increased test performance on state standardized tests. Data were analyzed using open coding.…

  15. Characteristics of an Effective English Language Teacher as Perceived by Iranian Teachers and Learners of English

    ERIC Educational Resources Information Center

    Shishavan, Homa Babai; Sadeghi, Karim

    2009-01-01

    This study attempted to characterize qualities of an effective English language teacher (EELT) as perceived by Iranian English language teachers and learners. For this purpose, a tailor-made questionnaire was administered to 59 English language teachers and 215 learners of English at universities, high schools and language institutes in Iran. The…

  16. Borrowing Legitimacy as English Learner (EL) Leaders: Indiana's 14-Year History with English Language Proficiency Standards

    ERIC Educational Resources Information Center

    Morita-Mullaney, Trish

    2017-01-01

    English language proficiency or English language development (ELP/D) standards guide how content-specific instruction and assessment is practiced by teachers and how English learners (ELs) at varying levels of English proficiency can perform grade-level-specific academic standards in K-12 US schools. With the transition from the state-developed…

  17. Vane segment support and alignment device

    DOEpatents

    McLaurin, L.D.; Sizemore, J.D.

    1999-07-13

    A support and alignment assembly for supporting and aligning a vane segment is provided. The support and alignment assembly comprises a torque plate which defines an opening for receiving an eccentric pin and a locking end member for receiving a lock socket member. An eccentric pin adjustably supported by the torque plate opening for supporting and aligning a vane segment is provided. A lock socket member adapted to securely receive the eccentric pin and rotated therewith, and adjustably engage the torque plate locking end is provided. The lock socket member receives the eccentric pin, such that when the eccentric pin is adjusted to align the vane segment, the lock socket member engages the torque plate locking end to secure the vane segment in the desired position. 5 figs.

  18. Vane segment support and alignment device

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

    McLaurin, L.D.; Sizemore, J.D.

    1999-07-13

    A support and alignment assembly for supporting and aligning a vane segment is provided. The support and alignment assembly comprises a torque plate which defines an opening for receiving an eccentric pin and a locking end member for receiving a lock socket member. An eccentric pin adjustably supported by the torque plate opening for supporting and aligning a vane segment is provided. A lock socket member adapted to securely receive the eccentric pin and rotated therewith, and adjustably engage the torque plate locking end is provided. The lock socket member receives the eccentric pin, such that when the eccentric pinmore » is adjusted to align the vane segment, the lock socket member engages the torque plate locking end to secure the vane segment in the desired position. 5 figs.« less

  19. The Yale Kamusi Project: A Swahili-English, English-Swahili Dictionary.

    ERIC Educational Resources Information Center

    Hinnebusch, Thomas

    2001-01-01

    Evaluates the strengths and weaknesses of the Yale Online Kamusi project, an electronic Web-based Swahili-English and English-Swahili dictionary. The dictionary is described and checked for comprehensiveness, the adequacy and quality of the glosses and definitions are tested, and a number of recommendations are made to help make it a better and…

  20. Docking alignment system

    NASA Technical Reports Server (NTRS)

    Monford, Leo G. (Inventor)

    1990-01-01

    Improved techniques are provided for alignment of two objects. The present invention is particularly suited for three-dimensional translation and three-dimensional rotational alignment of objects in outer space. A camera 18 is fixedly mounted to one object, such as a remote manipulator arm 10 of the spacecraft, while the planar reflective surface 30 is fixed to the other object, such as a grapple fixture 20. A monitor 50 displays in real-time images from the camera, such that the monitor displays both the reflected image of the camera and visible markings on the planar reflective surface when the objects are in proper alignment. The monitor may thus be viewed by the operator and the arm 10 manipulated so that the reflective surface is perpendicular to the optical axis of the camera, the roll of the reflective surface is at a selected angle with respect to the camera, and the camera is spaced a pre-selected distance from the reflective surface.