bluuebunny/crossref_metadata_2025_split huggingface dataset:
Translation of tree-processing programs into stream-processing programs based on ordered linear type
Authors: KODAMA KOICHI , SUENAGA KOHEI , KOBAYASHI NAOKI 
Published: January 2008

AbstractThere are two ways to write a program for manipulating tree-structured data such as XML documents: One is to write a tree-processing program focusing on the logical structure of the data and the other is to write a stream-processing program focusing on the physical structure. While tree-processing programs are easier to write than stream-processing programs, tree-processing programs are less efficient in memory usage since they use trees as intermediate data. Our aim is to establish a method for automatically translating a tree-processing program to a stream-processing one in order to take the best of both worlds. We first define a programming language for processing binary trees and a type system based on ordered linear type, and show that every well-typed program can be translated to an equivalent stream-processing program. We then extend the language and the type system to deal with XML documents. We have implemented an XML stream processor generator based on our algorithm, and obtained promising experimental results.
Language testing and technology: problems of transition to a new era
Authors: Dooey Patricia 
Published: January 2008

AbstractTechnological advances have revolutionised methods of both teaching and testing in languages, and practitioners have eagerly embraced the opportunity to provide more innovative ways of doing this. The unique features offered by technology make it increasingly possible to test for a wide range of language skills required for a specific purpose. With the increasing need to test for English language proficiency and the importance placed on this facility, technology is being utilised to address issues of practicality, speed and efficiency. However, such advantages should not be embraced without due consideration for the essential qualities of any test; validity and reliability. With the inevitable shift towards computer-based testing, certain areas need special consideration. While computer-based tests can provide constructive diagnostic information to complement the language learning process, they should be used more selectively in other contexts, for example in high-stakes tests, examples of which are International English Language Testing System (IELTS) and Test of English as a Foreign Language (TOEFL). These tests provide an assessment of English language proficiency, a key component of university admissions criteria. This paper examines a number of issues related to the design and application of computer-based tests, with particular reference to construct validity, computer familiarity and practicality. It is recommended that in the short term at least, test-takers be offered the choice of test medium in the interests of fairness and equity.
Wikis: a collective approach to language production
Authors: Lund Andreas 
Published: January 2008

AbstractWikis represent a particular type of collaborative learning environment where collaboration can result in aggregated, collective products. This study makes the claim that such potential challenges language production practices in school where the individual learner's output is often the focus of attention. The argument is put forth by juxtaposing theory, literature review, and videotaped wiki activities. Wikis are examined in a sociocultural perspective, in particular the notions of collective zones of proximal development and sociogenesis – that we come to knowledge by taking part in activities where individuals relate to a greater collective that evolves over time and where language and material artifacts function as structural resources. A review of some recent research in CALL and Second Language Acquisition (SLA) seeks to form a backdrop for this study of collective language production. Empirically the argument is illustrated and supported by selected videotape transcripts of learner interactions involving the use of a wiki in an English as a Foreign Language (EFL) classroom. The study shows that learners work in and across activity types that create tensions between individual and collective, institutional and novel practices, but that the wiki also holds the potential for collective knowledge advancement and language development.
Comparing the outcomes of online listening versus online text-based tasks in university level Italian L2 study
Authors: Absalom Matthew , Rizzi Andrea 
Published: January 2008

AbstractIn this paper, we describe an initial exploratory study designed to compare the outcomes of online listening and online text-based tasks in the context of the study of Italian at The University of Melbourne. Our findings allow us to characterise online listening and online reading as a qualitative difference between deep and surface approaches to learning. Online listening seems to promote an integrative orientation and heighten students' desire to deconstruct and understand texts. There also appears to be higher vocabulary acquisition and knowledge retention with online listening tasks.
Blogs for specific purposes: Expressivist or socio-cognitivist
approach?
Authors: Murray Liam , Hourigan Tríona 
Published: January 2008

AbstractThis paper represents an earnest attempt to identify specific pedagogical roles
for blogs in language learning. After briefly describing various types of blogs
and defining their purposes (Herring et al.,
2005) we attempt to accommodate their position and application within language
teaching (Thorne & Scott Payne, 2005), relating evidence from
teachers' blogs (Edublog.org) and also within Second Language Acquisition (SLA) theories.
In particular, we shall be concentrating on the process and post-process writing
approaches (Matsuda, 2003), with particular emphasis on current cognitivist
(Atkinson, 2003; Ferris & Hodgcock, 1998) and expressivist (Berlin,
1988) theories. These approaches will be discussed in terms of their
effectiveness when establishing specific blog writing tasks. Whilst some
researchers have advocated for a ‘lead blog’ or template
for other students to follow (Stone, 2004), we have been seeking an eclectic
approach based on the three approaches mentioned above. We shall describe our
own blended task methodology (Abermann, 2004; Thorne, 2003) wherein language
students at a Third Level Institution were set a blog writing task initially
over a complete semester (12 weeks). The blog exercise employed both an early
expressivist approach and later a (socio-) cognitivist one. Our findings, with
examples from students' blogs (and also from students who continued
their blogs over a 6 month period), will be presented as well as our
recommendations for the integration of blogs into L2 virtual writing
environments.
RECOVERING “COVERING END”: WHAT QUEER THEORY CAN DO FORTHE TURN OF THE SCREW
Authors: Soltysik Agnieszka M. 
Published: January 2008

The Turn of the Screwwas published in five authorized forms during Henry James's life: as a serial inCollier's Weeklyearly in 1898, as one of two tales in a “duplex” edition published simultaneously in America and England in October 1898, as the second of four works in a volume of the New York Edition in 1908, and as the first volume ofThe Uniform Tales of Henry James, edited by Martin Secker in 1915. The first version, in addition to the frame narrative and twenty-four chapters, was divided into twelve installments and five “Parts.” The version published in the duplex edition under the titleThe Two Magicswas altered to suppress these “Parts,” delete the ending of one chapter, raise Flora's age, and place “more focus. . . on the governess,” among other minor alterations (James,The Turn of the Screw87). The New York Edition underwent even more substantial alterations.
Guarded hybrid knowledge bases
Authors: HEYMANS STIJN , DE BRUIJN JOS , PREDOIU LIVIA , FEIER CRISTINA , VAN NIEWENBORGH DAVY 
Published: January 2008

AbstractRecently, there has been a lot of interest in the integration of Description Logics (DL) and rules on the Semantic Web. We defineguarded hybrid knowledge bases(org-hybrid knowledge bases) as knowledge bases that consist of a Description Logic knowledge base and aguardedlogic program, similar to the$\mathcal{DL}$+logknowledge bases from Rosati (In Proceedings of the 10th International Conference on Principles of Knowledge Representation and Reasoning, AAAI Press, Menlo Park, CA, 2006, pp. 68–78.). g-Hybrid knowledge bases enable an integration of Description Logics and Logic Programming where, unlike in other approaches, variables in the rules of a guarded program do not need to appear in positive non-DL atoms of the body, i.e., DL atoms can act asguardsas well. Decidability of satisfiability checking of g-hybrid knowledge bases is shown for the particular DL$\mathcal{DLRO}^{\-{le}}$, which is close to OWL DL, by a reduction to guarded programs under the open answer set semantics. Moreover, we show 2-Exptime-completeness for satisfiability checking of such g-hybrid knowledge bases. Finally, we discuss advantages and disadvantages of our approach compared with$\mathcal{DL}$+logknowledge bases.
New map of Antarctica
Authors: Showstack Randy 
Published: January 2008

A new map of Antarctica that provides the most geographically accurate, true‐color, high‐resolution views of the continent to date was unveiled on 27 November. The Landsat Image Mosaic of Antarctica—completed by researchers from NASA, the U.S. Geological Survey, the U.S. National Science Foundation, and the British Antarctic Survey—is a realistic, nearly cloudless satellite view of the continent, piecing together 1100 Landsat images.The map “will open new windows of opportunity for scientific research as well as enable the public to become much more familiar with Antarctica and how scientists use imagery in their research. This innovation is like watching high‐definition TV in living color versus watching the picture on a grainy black‐and‐white television,” said Robert Bindschadler, chief scientist of the Hydrospheric and Biospheric Sciences Laboratory at NASA Goddard Space Flight Center in Greenbelt, Md. For more details, visit http://lima.usgs.gov, http://www.nasa.gov/vision/earth/lookingatearth/lima_press_conf.html, and http://lima.nasa.gov.
Synchrotron radiation needs for molecular environmental science
Authors: Reeder Richard J. , Bargar John , Kemner Kenneth , Lanzirotti Antonio , Shuh David K. 
Published: January 2008

Synchrotron facilities provide exceptionally high brightness, tunable X‐ray sources that make possible a range of novel techniques allowing molecular‐scale and sometimes time‐resolved characterization of diverse types of materials. Focusing the X‐ray beam to nanometer to micrometer sizes enables spectroscopic and scattering measurements at high spatial resolution, thereby allowing study of complex, heterogeneous environmental samples in which elements of interest are commonly dilute. Such molecular‐scale characterization provides the basis for understanding fundamental reaction mechanisms, chemical speciation of trace and major elements, contaminant mobility/bioavailability, and element cycling in the hydrosphere.It is no surprise therefore that synchrotron radiation techniques, such as X‐ray absorption spectroscopy and scattering, have become core techniques in the fields of molecular environmental science (MES) and low‐temperature geochemistry (LTG). The synchrotron user group EnviroSync organized a workshop in Rockville, Md., to assess current capabilities at U.S. synchrotron facilities and future needs for these communities. Sponsorship was provided by the U.S. Department of Energy's Office of Basic Energy Sciences and Office of Biological and Environmental Remediation and by the U.S. National Science Foundation's Earth Sciences Directorate. The 50+ participants included academic and national laboratory researchers, beam line scientists, instrument designers, and facility directors and representatives. Program managers from funding agencies provided perspectives from Washington.
Monitoring Earth Surface Dynamics With Optical Imagery
Authors: Leprince Sébastien , Berthier Etienne , Ayoub François , Delacourt Christophe , Avouac Jean‐Philippe 
Published: January 2008

The increasing availability of high‐quality optical satellite images should allow, in principle, continuous monitoring of Earth's surface changes due to geologic processes, climate change, or anthropic activity. For instance, sequential optical images have been used to measure displacements at Earth's surface due to coseismic ground deformation [e.g., Van Puymbroeck et al., 2000], ice flow [Scambos et al., 1992; Berthier et al., 2005], sand dune migration [Crippen, 1992], and landslides [Kääb, 2002; Delacourt et al., 2004].Surface changes related to agriculture, deforestation, urbanization, and erosion—which do not involve ground displacement—might also be monitored, provided that the images can be registered with sufficient accuracy. Although the approach is simple in principle, its use is still limited, mainly because of geometric distortion of the images induced by the imaging system, biased correlation techniques, and implementation difficulties.
A novel zinc-dependent D-serine dehydratase from Saccharomyces cerevisiae
Authors: Ito Tomokazu , Hemmi Hisashi , Kataoka Kunishige , Mukai Yukio , Yoshimura Tohru 
Published: January 2008

YGL196W of Saccharomyces cerevisiae encodes a putative protein that is unidentified but is predicted to have a motif similar to that of the N-terminal domain of the bacterial alanine racemase. In the present study we found that YGL196W encodes a novel D-serine dehydratase, which belongs to a different protein family from that of the known bacterial enzyme. The yeast D-serine dehydratase purified from recombinant Escherichia coli cells depends on pyridoxal 5′-phosphate and zinc, and catalyses the conversion of D-serine into pyruvate and ammonia with the Km and kcat values of 0.39 mM and 13.1 s−1 respectively. D-Threonine and β-Cl-D-alanine also serve as substrates with catalytic efficiencies which are approx. 3 and 2% of D-serine respectively. L-Serine, L-threonine and β-Cl-L-alanine are inert as substrates. Atomic absorption analysis revealed that the enzyme contains one zinc atom per enzyme monomer. The enzyme activities toward D-serine and D-threonine were decreased by EDTA treatment and recovered by the addition of Zn2+. Little recovery was observed with Mg2+, Mn2+, Ca2+, Ni2+, Cu2+, K+ or Na+. In contrast, the activity towards β-Cl-D-alanine was retained after EDTA treatment. These results suggest that zinc is involved in the elimination of the hydroxy group of D-serine and D-threonine. D-Serine dehydratase of S. cerevisiae is probably the first example of a eukaryotic D-serine dehydratase and that of a specifically zinc-dependent pyridoxal enzyme as well.
Uses and interpretations of non‐word repetition tasks in children with and without specific language impairments (SLI)
Authors: Coady Jeffry A. , Evans Julia L. 
Published: January 2008

Background: The non‐word repetition task (NRT) has gained wide acceptance in describing language acquisition in both children with normal language development (NL) and children with specific language impairments (SLI). This task has gained wide acceptance because it so closely matches the phonological component of word learning, and correlates with measures of phonological working memory, a deficit in which is hypothesized to underlie SLI.Aims/Methods & Procedures: Recent uses of the NRT seem to accept it as a measure of phonological working memory capacity in spite of the fact that researchers have consistently acknowledged that the task taps many language processes, including speech perception, phonological encoding, phonological memory, phonological assembly and articulation. This paper reviews the literature on the use of the non‐word repetition task (NRT) in children with NL and children with SLI, emphasizing the component skills necessary for successful repetition.Main Contribution: For children with NL, discussion has focused on (1) the relationship between non‐word repetition ability and vocabulary, and (2) lexical and sublexical influences on repetition accuracy. For children with SLI, discussion has focused on these factors as well, but has also considered other component skills that support non‐word repetition. Researchers have examined speech perception and discrimination, phonological encoding, phonological memory, phonological assembly, motor planning, and articulation, and have found evidence that children with SLI exhibit impairments in each of these supporting skills.Conclusions: Because repetition accuracy depends on lexical and sublexical properties, the NRT can be used to examine the structural properties of the lexicon in both children with NL and with SLI. Further, because the task taps so many underlying skills, it is a powerful tool that can be used to identify children with language impairments.
Reliability of speech diadochokinetic test measurement
Authors: Gadesmann Miriam , Miller Nick 
Published: January 2008

Background: Measures of articulatory diadochokinesis (DDK) are widely used in the assessment of motor speech disorders and they play a role in detecting abnormality, monitoring speech performance changes and classifying syndromes. Although in clinical practice DDK is generally measured perceptually, without support from instrumental methods that display the acoustic waveform, no standard measurement procedures are employed and studies on inter‐ and intra‐rater reliability are lacking.Aims: To investigate the inter‐ and intra‐rater reliability of perceptual DDK measurement and the possible impact of experience on rating performance.Methods & Procedures: Ten speech and language therapists and ten untrained controls rated 12 DDK speech samples, including two pairs of identical samples, of speakers with different neurological speech disorders. We compared timing for repetitions as close as possible to 5 s, for 5 s exactly, and for as long as the speaker could manage; as well as four qualitative features (rhythm, distinctness, loudness and overall impression). Counts by time were compared with objective outcomes from sound spectrograms.Outcomes & Results: Inter‐ and intra‐rater reliability was lower than should be acceptable for clinical diagnostic and outcome assessment. The most accurate and repeatable procedure (compared with objective measurement) was counting the syllables within the first 5 s. There was no unequivocal influence of clinical experience on accuracy.Conclusions: The findings suggest caution in employing and interpreting clinical DDK measures as diagnostic and outcome measures. More research is necessary to settle the influence of experience on time and count accuracy and what modifications to timing might bring increased agreement that permits DDK to realize its full potential in assessment.
Automated programming for bioinformatics algorithm deployment
Authors: Alterovitz Gil , Jiwaji Adnaan , Ramoni Marco F. 
Published: January 2008

Abstract
Summary: Many bioinformatics solutions suffer from the lack of usable interface/platform from which results can be analyzed and visualized. Overcoming this hurdle would allow for more widespread dissemination of bioinformatics algorithms within the biological and medical communities. The algorithms should be accessible without extensive technical support or programming knowledge. Here, we propose a dynamic wizard platform that provides users with a Graphical User Interface (GUI) for most Java bioinformatics library toolkits. The application interface is generated in real-time based on the original source code. This platform lets developers focus on designing algorithms and biologists/physicians on testing hypotheses and analyzing results.
Availability: The open source code can be downloaded from: http://bcl.med.harvard.edu/proteomics/proj/APBA/
Contact: gil@mit.edu
Prediction of protein functional residues from sequence by probability density estimation
Authors: Fischer J. D. , Mayer C. E. , Söding J. 
Published: January 2008

AbstractMotivation: The prediction of ligand-binding residues or catalytically active residues of a protein may give important hints that can guide further genetic or biochemical studies. Existing sequence-based prediction methods mostly rank residue positions by evolutionary conservation calculated from a multiple sequence alignment of homologs. A problem hampering more wide-spread application of these methods is the low per-residue precision, which at 20% sensitivity is around 35% for ligand-binding residues and 20% for catalytic residues.Results: We combine information from the conservation at each site, its amino acid distribution, as well as its predicted secondary structure (ss) and relative solvent accessibility (rsa). First, we measure conservation by how much the amino acid distribution at each site differs from the distribution expected for the predicted ss and rsa states. Second, we include the conservation of neighboring residues in a weighted linear score by analytically optimizing the signal-to-noise ratio of the total score. Third, we use conditional probability density estimation to calculate the probability of each site to be functional given its conservation, the observed amino acid distribution, and the predicted ss and rsa states.We have constructed two large data sets, one based on the Catalytic Site Atlas and the other on PDB SITE records, to benchmark methods for predicting functional residues. The new method FRcons predicts ligand-binding and catalytic residues with higher precision than alternative methods over the entire sensitivity range, reaching 50% and 40% precision at 20% sensitivity, respectively.Availability: Server: http://frpred.tuebingen.mpg.de. Data sets: ftp://ftp.tuebingen.mpg.de/pub/protevo/FRpred/Contact: soeding@lmb.uni-muenchen.deSupplementary information: Supplementary data are available at Bioinformatics Online.
Beyond the ‘best’ match: machine learning annotation of protein sequences by integration of different sources of information
Authors: Tetko Igor V. , Rodchenkov Igor V. , Walter Mathias C. , Rattei Thomas , Mewes Hans-Werner 
Published: January 2008

Abstract
Motivation: Accurate automatic assignment of protein functions remains a challenge for genome annotation. We have developed and compared the automatic annotation of four bacterial genomes employing a 5-fold cross-validation procedure and several machine learning methods.
Results: The analyzed genomes were manually annotated with FunCat categories in MIPS providing a gold standard. Features describing a pair of sequences rather than each sequence alone were used. The descriptors were derived from sequence alignment scores, InterPro domains, synteny information, sequence length and calculated protein properties. Following training we scored all pairs from the validation sets, selected a pair with the highest predicted score and annotated the target protein with functional categories of the prototype protein. The data integration using machine-learning methods provided significantly higher annotation accuracy compared to the use of individual descriptors alone. The neural network approach showed the best performance. The descriptors derived from the InterPro domains and sequence similarity provided the highest contribution to the method performance. The predicted annotation scores allow differentiation of reliable versus non-reliable annotations. The developed approach was applied to annotate the protein sequences from 180 complete bacterial genomes.
Availability: The FUNcat Annotation Tool (FUNAT) is available on-line as Web Services at http://mips.gsf.de/proj/funat
Contact: i.tetko@gsf.de
Supplementary information: Supplementary data are available at Bioinformatics online.