CiteULike: Author Hyland

Academic clusters: text patterning in published and postgraduate writing

Ken Hyland — 2008-08-09T01:50:58-00:00

International Journal of Applied Linguistics, Vol. 18, No. 1. (2008), pp. 41-62.

An important component of fluent linguistic production is control of the multi-word expressions referred to as "clusters", "chunks" or "bundles". These are extended collocations which appear more frequently than expected by chance, helping to shape meanings and contributing to our sense of coherence in a text. Clusters seem to present considerable challenges to student writers struggling to make their texts both fluent and assured to readers in their new communities. This paper explores the forms, structures and functions of 4-word clusters in a corpus of research articles, doctoral dissertations and master's theses of 3.5 million words to show not only that clusters are central to academic discourse but that they offer an important means of differentiating genres, with implications for more evidence-based instructional practices in advanced writing contexts. Componente essenziale di una produzione linguistica scorrevole è la padronanza di espressioni multilessicali comunemente denominate clusters, chunks o bundles. Tali espressioni si presentano come collocazioni estese che ricorrono con frequenza superiore alla casualità, contribuendo alla formazione del significato e alla nostra percezione della coerenza testuale. I clusters appaiono un'area particolarmente problematica per chi, nel processo di acquisizione di una specifica scrittura disciplinare, necessita di rivolgersi alla nuova comunità scientifica con testi a un tempo scorrevoli e sicuri. Questo articolo esplora forma, struttura e funzioni dei clusters di quattro parole in un corpus di articoli di ricerca, tesi di dottorato e tesi di master (3.5 milioni di parole) e si propone di mostrare che i clusters non solo sono un elemento centrale nel discorso accademico, ma offrono un importante strumento di differenziazione dei generi, con una ricaduta verso pratiche di formazione alla scrittura avanzata sempre più basate su dati autentici.1

Focusing on form: student engagement with teacher feedback

Fiona Hyland — 2008-07-31T11:39:42-00:00

System, Vol. 31, No. 2. (June 2003), pp. 217-230.

This paper explores the relationship between teacher feedback and student revision in two academic writing classes. The study adopts a case study approach and looks at all the feedback given to six students over a complete course. Using data from teacher think aloud protocols, teacher and student interviews and student texts, it examines the extent to which teachers focused on formal language concerns when they gave feedback and the use that students made of this feedback in their revisions. Findings suggest that despite the teachers' beliefs and teaching approaches, language accuracy was a very important focus for their feedback. While most of the students engaged with this feedback when revising their drafts, the extent to which they used it varied among the case study subjects. Two case studies who made consistent and sustained use of form-focused feedback are discussed in greater detail to examine student engagement with form-focused feedback over a complete course.

Firing modes of midbrain dopamine cells in the freely moving rat

BI Hyland — 2008-06-27T05:34:19-00:00

Neuroscience, Vol. 114, No. 2. (1 October 2002), pp. 475-492.

There is a large body of data on the firing properties of dopamine cells in anaesthetised rats or rat brain slices. However, the extent to which these data relate to more natural conditions is uncertain, as there is little quantitative information available on the firing properties of these cells in freely moving rats. We examined this by recording from the midbrain dopamine cell fields using chronically implanted microwire electrodes. (1) In most cases, slowly firing cells with broad action potentials were profoundly inhibited by the dopamine agonist apomorphine, consistent with previously accepted criteria. However, a small group of cells was found that were difficult to classify because of ambiguous combinations of properties. (2) Presumed dopamine cells could be divided into low and high bursting (>40% of their spikes in bursts) groups, with the majority having low bursting rates. The distribution of burst incidence was similar to that previously reported with chloral hydrate anaesthesia, but the average intraburst frequency was higher in the conscious animal at rest and was higher again in bursts triggered by salient stimuli. (3) There was no evidence for spike frequency adaptation within bursts on average, consistent with the hypothesis that afterhyperpolarisation currents may be disabled during behaviourally induced bursting. (4) Presumed dopamine cells responded to reward-related stimuli with increased bursting rates and significantly higher intraburst frequencies compared to bursts emitted outside task context, indicating that modulation of afferent activity might not only trigger bursting, but may also regulate burst intensity. (5) In addition to the irregular single spike and bursting modes we found that extremely regular (clock-like) firing, previously only described for dopamine cells in reduced preparations, can also be expressed in the freely moving animal. (6) Cross-correlation analysis of activity recorded from simultaneously recorded neurones revealed coordinated activity in a quarter of dopamine cell pairs consistent with at least [`]functional' connectivity. On the other hand, most dopamine cell pairs showed no correlation, leaving open the possibility of functional sub-groupings within the dopamine cell fields. Taken together, the data suggest that the basic firing modes described for dopamine cells in reduced or anaesthetised preparations do reflect natural patterns of activity for these neurones, but also that the details of this activity are dependent upon modulation of afferent inputs by behavioural stimuli.

A low noise remotely controllable wireless telemetry system for single-unit recording in rats navigating in a vertical maze

Hsin-Yung Chen — 2008-06-23T11:19:07-00:00

Medical and Biological Engineering and Computing

Abstract The use of cables for recording neural activity limits the scope of behavioral tests used in conscious free-moving animals. Particularly, cable attachments make it impossible to record in three-dimensional (3D) mazes where levels are vertically stacked or in enclosed spaces. Such environments are of particular interest in investigations of hippocampal place cells, in which neural activity is correlated with spatial position in the environment. We developed a flexible miniaturized Bluetooth-based wireless data acquisition system. The wireless module included an 8-channel analogue front end, digital controller, and Bluetooth transceiver mounted on a backpack. Our bidirectional wireless design allowed all data channels to be previewed at 1 kHz sample rate, and one channel, selected by remote control, to be sampled at 10 kHz. Extracellular recordings of neuronal activity are highly susceptible to ambient electrical noise due to the high electrode impedance. Through careful design of appropriate shielding and hardware configuration to avoid ground loops, mains power and Bluetooth hopping frequency noise were reduced sufficiently to yield signal quality comparable to those recorded by wired systems. With this system we were able to obtain single-unit recordings of hippocampal place cells in rats running an enclosed vertical maze, over a range of 5 m.

Stance and engagement: a model of interaction in academic discourse

Ken Hyland — 2008-05-29T03:18:33-00:00

Discourse Studies, Vol. 7, No. 2. (1 May 2005), pp. 173-192.

A great deal of research has now established that written texts embody interactions between writers and readers. A range of linguistic features have been identified as contributing to the writer's projection of a stance to the material referenced by the text, and, to a lesser extent, the strategies employed to presuppose the active role of an addressee. As yet, however, there is no overall typology of the resources writers employ to express their positions and connect with readers. Based on an analysis of 240 published research articles from eight disciplines and insider informant interviews, I attempt to address this gap and consolidate much of my earlier work to offer a framework for analysing the linguistic resources of intersubjective positioning. Attending to both stance and engagement, the model provides a comprehensive and integrated way of examining the means by which interaction is achieved in academic argument and how the discoursal preferences of disciplinary communities construct both writers and readers. 10.1177/1461445605050365

DRUG-DRUG INTERACTIONS FOR UDP-GLUCURONOSYLTRANSFERASE SUBSTRATES: A PHARMACOKINETIC EXPLANATION FOR TYPICALLY OBSERVED LOW EXPOSURE (AUCI/AUC) RATIOS

Andrew Williams — 2008-04-29T15:25:03-00:00

Drug Metab Dispos, Vol. 32, No. 11. (1 November 2004), pp. 1201-1208.

Glucuronidation is a listed clearance mechanism for 1 in 10 of the top 200 prescribed drugs. The objective of this article is to encourage those studying ligand interactions with UDP-glucuronosyltransferases (UGTs) to adequately consider the potential consequences of in vitro UGT inhibition in humans. Spurred on by interest in developing potent and selective inhibitors for improved confidence around UGT reaction phenotyping, and the increased availability of recombinant forms of human UGTs, several recent studies have reported in vitro inhibition of UGT enzymes. In some cases, the observed potency of UGT inhibitors in vitro has been interpreted as having potential relevance in humans via pharmacokinetic drug-drug interactions. Although there are reported examples of clinically relevant drug-drug interactions for UGT substrates, exposure increases of the aglycone are rarely greater than 100% in the presence of an inhibitor relative to its absence (i.e., AUCi/AUC [≤]2). This small magnitude in change is in contrast to drugs primarily cleared by cytochrome P450 enzymes, where exposures have been reported to increase as much as 35-fold on coadministration with an inhibitor (e.g., ketoconazole inhibition of CYP3A4-catalyzed terfenadine metabolism). In this article the evidence for purported clinical relevance of potent in vitro inhibition of UGT enzymes will be assessed, taking the following into account: in vitro data on the enzymology of glucuronide formation from aglycone, pharmacokinetic principles based on empirical data for inhibition of metabolism, and clinical data on the pharmacokinetic drug-drug interactions of drugs primarily cleared by glucuronidation. 10.1124/dmd.104.000794

metaSHARK: a WWW platform for interactive exploration of metabolic networks.

C Hyland — 2008-04-29T10:06:49-00:00

Nucleic acids research, Vol. 34, No. Web Server issue. (1 July 2006)

The metaSHARK (metabolic search and reconstruction kit) web server offers users an intuitive, fully interactive way to explore the KEGG metabolic network via a WWW browser. Metabolic reconstruction information for specific organisms, produced by our automated SHARKhunt tool or from other programs or genome annotations, may be uploaded to the website and overlaid on the generic network. Additional data from gene expression experiments can also be incorporated, allowing the visualization of differential gene expression in the context of the predicted metabolic network. metaSHARK is available at http://bioinformatics.leeds.ac.uk/shark/.

Feedback in Second Language Writing: Contexts and Issues (Cambridge Applied Linguistics)

Ken Hyland — 2008-04-27T03:04:40-00:00

(14 August 2006)

How to provide appropriate feedback to students on their writing has long been an area of central significance to teachers and educators. Feedback in Second Language Writing: Context and Issues provides scholarly articles on the topic by leading researchers, who explore topics such as the socio-cultural assumptions that participants bring to the writing class; feedback delivery and negotiation systems; and the role of student and teacher identity in negotiating feedback and expectations. This text provides empirical data and an up-to-date analysis of the complex issues involved in offering appropriate feedback during the writing process.

Directives: Argument and Engagement in Academic Writing

Ken Hyland — 2008-04-21T04:18:35-00:00

Applied Linguistics, Vol. 23, No. 2. (1 June 2002), pp. 215-239.

Successful academic writing involved both clear exposition and appropriate audience relationships, but the use of directives potentially undermines the harmony of such relationships. Because they instruct the reader to perform an action or to see things in a way determined by the writer, directives are potentially risky devices which are often regarded as bald-on-record threats to face (Brown and Levinson 1987). The widespread use of this feature in academic writing however suggests a more complex rhetorical picture. In this paper I explore the use of directives through an analysis of a 2.5 million word corpus of published articles, textbooks, and L2 student essays, and through interviews with insider informants on their perceptions and practices. The study reveals that directives are used for very different strategic purposes and indicates considerable variations in the ways they are employed across genres and disciplines. The weight of imposition carried by directives crucially depends on these purposes and participants' perceptions of rhetorical context. 10.1093/applin/23.2.215

Pi-Calculus, Dialogue Games and PCF

JME Hyland — 2008-04-20T20:05:09-00:00

Game semantics is an unusual denotational semantics in that it captures the intensional (or algorithmic) and dynamical aspects of the computation. This makes it an ideal semantical framework in which to seek to unify analyses of both the qualitative (correctness) as well as the quantitative (efficiency) properties of programming languages. This paper reports work arising from a recent construction of an order (or inequationally) fully abstract model for Scott's functional programming language...

Validation of the performance of a comprehensive genotyping assay panel of single nucleotide polymorphisms in drug metabolism enzyme genes.

Robert A Welch — 2008-03-29T03:08:30-00:00

Hum Mutat (7 March 2008)

A class of genes, known as drug metabolism enzymes (DMEs) are responsible for the metabolism and transport of drugs and other xenobiotics. Variation in DME genes most likely accounts for a proportion of the variability in drug response in humans, and may contribute to complex diseases such as cancer (Nebert DW, Dieter MZ. Pharmacology 2000;61:124-135). To date, assessing the extent of this variation has proven difficult, especially because of sequence paralogy issues that cause difficulty when attempting to genotype polymorphisms in very closely-related gene families (Murphy MP. Pharmacogenomics 2000;1:115-123; Ingelman-Sundberg M. Drug Metab Rev 1999;31:449-459). We have developed and genotyped a panel of N=2,325 individual TaqMan((R)) genotyping assays for polymorphisms in >200 DME genes; many of the variants in the panel are single nucleotide polymorphisms (SNPs) that are of known or putative function (e.g., missense, nonsense or frameshift). Using these assays, we have examined genetic variation among several groups of populations, including: 1) the two SNP500 Cancer population panels (http://snp500cancer.nci.nih.gov; last accessed: 11 December 2007); and 2) the panel used in the International HapMap Project panel (www.hapmap.org; last accessed: 11 December 2007). We have developed a comprehensive validation strategy to ensure reproducibility and accuracy of the assays and estimated minor allele frequencies. Here, we present the results of these analyses, which strongly suggest that this panel of DME assays are of extremely high quality and produce robust, accurate, and reproducible results. Hum Mutat 0,1-7, 2008. Published 2008, Wiley-Liss, Inc.

The Category Theoretic Understanding of Universal Algebra: Lawvere Theories and Monads

Martin Hyland — 2007-08-04T09:26:15-00:00

Electron. Notes Theor. Comput. Sci., Vol. 172 (2007), pp. 437-458.

As can be seen: Lexical bundles and disciplinary variation

Ken Hyland — 2008-02-19T07:32:58-00:00

English for Specific Purposes, Vol. 27, No. 1. (2008), pp. 4-21.

An important component of fluent linguistic production is control of the multi-word expressions referred to as clusters, chunks or bundles. These are extended collocations which appear more frequently than expected by chance, helping to shape meanings in specific contexts and contributing to our sense of coherence in a text. Bundles have begun to attract considerable attention in corpus studies in EAP, although the extent to which they differ by discipline remains an open question. This paper explores the forms, structures and functions of 4-word bundles in a 3.5 million word corpus of research articles, doctoral dissertations and Master's theses in four disciplines to learn something of disciplinary variations in their frequencies and preferred uses. The analysis shows that bundles are not only central to the creation of academic discourse, but that they offer an important means of differentiating written texts by discipline.

Is There an "Academic Vocabulary"?

Hyland — 2007-07-29T12:39:49-00:00

TESOL Quarterly, Vol. 41, No. 2. (June 2007), pp. 235-253.

Are smokers adequately informed about the health risks of smoking and medicinal nicotine?

KM Cummings — 2008-01-23T22:53:08-00:00

Nicotine Tob Res, Vol. 6 Suppl 3 (December 2004)

The present study assessed smokers' beliefs about the health risks of smoking and the benefits of smoking filtered and low-tar cigarettes, and their awareness of and interest in trying so-called reduced-risk tobacco products. Results were based on a nationally representative random-digit-dialed telephone survey of 1,046 adult (aged 18 years or older) current cigarette smokers. Data were gathered on demographic characteristics, tobacco use behaviors, awareness and use of nicotine medications, beliefs about the health risks of smoking, content of smoke and design features of cigarettes, and the safety and efficacy of nicotine medications. In addition, respondents were asked about their interest in and perceived ability to stop smoking and about their desire for more information about the health risks of smoking. Smokers were least knowledgeable about low-tar and filter cigarettes (65% of responses were incorrect or "don't know") and most knowledgeable about the health risks of smoking (39% of responses were incorrect or "don't know"). The smokers' characteristics most commonly associated with misinformation when all six indices were combined into a summary index were as follows: those aged 45 years or older, smokers of ultralight cigarettes, smokers who believe they will stop smoking before they experience a serious health problem caused by smoking, smokers who have never used a stop-smoking medication, and smokers with a lower education level. Those who believed they would stop smoking in the next year were more knowledgeable about smoking. Some 77% of respondents reported a desire for additional information from tobacco companies on the health dangers of smoking. The present findings demonstrate that smokers are misinformed about many aspects of the cigarettes they smoke and stop-smoking medications and that they want more information about ways to reduce their health risks.

Authority and invisibility: authorial identity in academic writing

Ken Hyland — 2008-01-22T11:35:59-00:00

Journal of Pragmatics, Vol. 34, No. 8. (August 2002), pp. 1091-1112.

Academic writing is not just about conveying an ideational `content', it is also about the representation of self. Recent research has suggested that academic prose is not completely impersonal, but that writers gain credibility by projecting an identity invested with individual authority, displaying confidence in their evaluations and commitment to their ideas. Perhaps the most visible manifestation of such an authorial identity is the use of first person pronouns and their corresponding determiners. But while the use of these forms are a powerful rhetorical strategy for emphasising a contribution, many second language writers feel uncomfortable using them because of their connotations of authority. In this paper I explore the notion of identity in L2 writing by examining the use of personal pronouns in 64 Hong Kong undergraduate theses, comparisons with a large corpus of research articles, and interviews with students and their supervisors. The study shows significant underuse of authorial reference by students and clear preferences for avoiding these forms in contexts which involved making arguments or claims. I conclude that the individualistic identity implied in the use of I may be problematic for many L2 writers.

Changes in hospitality workers' exposure to secondhand smoke following the implementation of New York's smoke-free law

MC Farrelly — 2008-01-16T19:42:14-00:00

Tob Control, Vol. 14, No. 4. (1 August 2005), pp. 236-241.

Objective: To assess the impact on hospitality workers' exposure to secondhand smoke of New York's smoke-free law that prohibits smoking in all places of employment, including restaurants, bars, and bowling facilities. Design: Pre-post longitudinal follow up design. Settings: Restaurants, bars, and bowling facilities in New York State. Subjects: At baseline, 104 non-smoking workers in restaurants, bars, and bowling facilities were recruited with newspaper ads, flyers, and radio announcements. Of these, 68 completed a telephone survey and provided at least one saliva cotinine specimen at baseline. At three, six, and 12 month follow up studies, 47, 38, and 32 workers from the baseline sample of 68 completed a telephone survey and provided at least one saliva cotinine specimen. Intervention: The smoke-free law went into effect 24 July 2003. Main outcome measures: Self reported sensory and respiratory symptoms and exposure to secondhand smoke; self administered saliva cotinine specimens. Analyses were limited to subjects in all four study periods who completed a telephone survey and provided at least one saliva cotinine specimen. Results: All analyses were limited to participants who completed both an interview and a saliva specimen for all waves of data collection (n = 30) and who had cotinine concentrations [<=] 15 ng/ml (n = 24). Hours of exposure to secondhand smoke in hospitality jobs decreased from 12.1 hours (95% confidence interval (CI) 8.0 to 16.3 hours) to 0.2 hours (95% CI -0.1 to 0.5 hours) (p < 0.01) and saliva cotinine concentration decreased from 3.6 ng/ml (95% CI 2.6 to 4.7 ng/ml) to 0.8 ng/ml (95% CI 0.4 to 1.2 ng/ml) (p < 0.01) from baseline to the 12 month follow up. The prevalence of workers reporting sensory symptoms declined from 88% (95% CI 66% to 96%) to 38% (95% CI 20% to 59%) (p < 0.01); there was no change in the overall prevalence of upper respiratory symptoms (p < 0.16). Conclusion: New York's smoke-free law had its intended effect of protecting hospitality workers from exposure to secondhand smoke within three months of implementation. One year after implementation, the results suggest continued compliance with the law. 10.1136/tc.2004.008839

Persuasion and context: The pragmatics of academic metadiscourse

Ken Hyland — 2008-01-15T15:35:52-00:00

Journal of Pragmatics, Vol. 30, No. 4. (October 1998), pp. 437-455.

Metadiscourse refers to aspects of a text which explicitly organise the discourse, engage the audience and signal the writer's attitude. Its use by writers to guide readers and display an appropriate professional persona is an important aspect of persuasive writing. Its role in establishing and maintaining contact between the writer and the reader and between the writer and the message also makes it a central pragmatic concept. Based on a textual analysis of 28 research articles in four academic disciplines, this paper seeks to show how the appropriate use of metadiscourse crucially depends on rhetorical context. The study identifies a taxonomy of metadiscourse functions and suggests that metadiscourse reflects one way in which context and linguistic meaning are integrated to allow readers to derive intended interpretations. It is argued that metadiscourse provides writers with a means of constructing appropriate contexts and alluding to shared disciplinary assumptions. The study of academic metadiscourse can therefore offer insights into our understanding of this concept and illuminate an important dimension of rhetorical variation among disciplinary communities.

Metabolic reconstruction and analysis for parasite genomes.

JW Pinney — 2008-01-09T18:03:43-00:00

Trends Parasitol, Vol. 23, No. 11. (November 2007), pp. 548-554.

With the completion of sequencing projects for several parasite genomes, efforts are ongoing to make sense of this mass of information in terms of the gene products encoded and their interactions in the growth, development and survival of parasites. The emerging science of systems biology aims to explain the complex relationship between genotype and phenotype by using network models. One area in which this approach has been particularly successful is in the modeling of metabolism. With an accurate picture of the set of metabolic reactions encoded in a genome, it is now possible to identify enzymes or transporters that might be viable targets for new drugs. Because these predictions greatly depend on the quality and completeness of the genome annotation, there are substantial efforts in the scientific community to increase the numbers of metabolic enzymes identified. In this review, we discuss the opportunities for using metabolic reconstruction and analysis tools in parasitology research, and their applications to protozoan parasites.

A cellular mechanism of reward-related learning.

JN Reynolds — 2005-02-08T05:10:43-00:00

Nature, Vol. 413, No. 6851. (6 September 2001), pp. 67-70.

Positive reinforcement helps to control the acquisition of learned behaviours. Here we report a cellular mechanism in the brain that may underlie the behavioural effects of positive reinforcement. We used intracranial self-stimulation (ICSS) as a model of reinforcement learning, in which each rat learns to press a lever that applies reinforcing electrical stimulation to its own substantia nigra. The outputs from neurons of the substantia nigra terminate on neurons in the striatum in close proximity to inputs from the cerebral cortex on the same striatal neurons. We measured the effect of substantia nigra stimulation on these inputs from the cortex to striatal neurons and also on how quickly the rats learned to press the lever. We found that stimulation of the substantia nigra (with the optimal parameters for lever-pressing behaviour) induced potentiation of synapses between the cortex and the striatum, which required activation of dopamine receptors. The degree of potentiation within ten minutes of the ICSS trains was correlated with the time taken by the rats to learn ICSS behaviour. We propose that stimulation of the substantia nigra when the lever is pressed induces a similar potentiation of cortical inputs to the striatum, positively reinforcing the learning of the behaviour by the rats.

Dopamine cells respond to predicted events during classical conditioning: evidence for eligibility traces in the reward-learning network.

WX Pan — 2005-07-21T15:04:16-00:00

J Neurosci, Vol. 25, No. 26. (29 June 2005), pp. 6235-6242.

Behavioral conditioning of cue-reward pairing results in a shift of midbrain dopamine (DA) cell activity from responding to the reward to responding to the predictive cue. However, the precise time course and mechanism underlying this shift remain unclear. Here, we report a combined single-unit recording and temporal difference (TD) modeling approach to this question. The data from recordings in conscious rats showed that DA cells retain responses to predicted reward after responses to conditioned cues have developed, at least early in training. This contrasts with previous TD models that predict a gradual stepwise shift in latency with responses to rewards lost before responses develop to the conditioned cue. By exploring the TD parameter space, we demonstrate that the persistent reward responses of DA cells during conditioning are only accurately replicated by a TD model with long-lasting eligibility traces (nonzero values for the parameter lambda) and low learning rate (alpha). These physiological constraints for TD parameters suggest that eligibility traces and low per-trial rates of plastic modification may be essential features of neural circuits for reward learning in the brain. Such properties enable rapid but stable initiation of learning when the number of stimulus-reward pairings is limited, conferring significant adaptive advantages in real-world environments.

A miniaturized interdigital microstrip bandpass filter

Kao-Cheng Huang — 2007-11-26T20:31:03-00:00

Applied Superconductivity, IEEE Transactions on, Vol. 9, No. 2. (1999), pp. 3889-3892.

A 2.4 GHz three-stage microstrip bandpass filter was designed using a miniaturized interdigital capacitor structure to reduce the configuration in size. The filter was simulated by a finite element method software and then fabricated using TBCCO superconducting films on 20 mm×20 mm×0.5 mm MgO substrates. It was generated by photolithographic and wet etching process and packaged in a brass box. The bandwidth is 4% and the passband insertion loss of the filter was measured to be -0.4 dB at 77 K. The return loss is better than -8 dB. In particular, this filter has a sharper performance at its edge of fundamental pass band

Genre pedagogy: Language, literacy and L2 writing instruction

Ken Hyland — 2007-11-18T09:58:54-00:00

Journal of Second Language Writing, Vol. 16, No. 3. (September 2007), pp. 148-164.

For teacher educators, genre-based pedagogies offer a valuable resource for assisting both pre- and in-service writing instructors to assist their students to produce effective and relevant texts. Instead of focusing on the process of composition, the content of texts, or the abstract prescriptions of disembodied grammars, genre pedagogies enable teachers to ground their courses in the texts that students will have to write in their target contexts, thereby supporting learners to participate effectively in the world outside the ESL classroom. Genre theory and research thus give teacher educators a more central role in preparing individuals to teach second language writing and to confidently advise them on the development of curriculum materials and activities for writing classes. In this paper, I will briefly introduce the principles of genre-based language instruction and sketch some broad classroom models, looking at ESP and SFL approaches. I then explore what it means to implement genre teaching in more practical terms, setting out some key ways in which teachers can plan, sequence, support, and assess learning.

The method of hypersequents in the proof theory of propositional non-classical logics

Arnon Avron — 2007-10-08T23:43:17-00:00

(1996), pp. 1-32.

This paper is devoted to a description, with many examples, of one particular framework of this sort: that of hypersequents. We shall show that this framework is indeed stronger than that of ordinary sequents, but still has properties (1)-(6) above. In addition, the following two points concerning it should be noted:

Large scale real-time PCR validation on gene expression measurements from two commercial long-oligonucleotide microarrays.

Y Wang — 2007-08-03T21:55:32-00:00

BMC Genomics, Vol. 7 (2006)

BACKGROUND: DNA microarrays are rapidly becoming a fundamental tool in discovery-based genomic and biomedical research. However, the reliability of the microarray results is being challenged due to the existence of different technologies and non-standard methods of data analysis and interpretation. In the absence of a "gold standard"/"reference method" for the gene expression measurements, studies evaluating and comparing the performance of various microarray platforms have often yielded subjective and conflicting conclusions. To address this issue we have conducted a large scale TaqMan Gene Expression Assay based real-time PCR experiment and used this data set as the reference to evaluate the performance of two representative commercial microarray platforms. RESULTS: In this study, we analyzed the gene expression profiles of three human tissues: brain, lung, liver and one universal human reference sample (UHR) using two representative commercial long-oligonucleotide microarray platforms: (1) Applied Biosystems Human Genome Survey Microarrays (based on single-color detection); (2) Agilent Whole Human Genome Oligo Microarrays (based on two-color detection). 1,375 genes represented by both microarray platforms and spanning a wide dynamic range in gene expression levels, were selected for TaqMan Gene Expression Assay based real-time PCR validation. For each platform, four technical replicates were performed on the same total RNA samples according to each manufacturer's standard protocols. For Agilent arrays, comparative hybridization was performed using incorporation of Cy5 for brain/lung/liver RNA and Cy3 for UHR RNA (common reference). Using the TaqMan Gene Expression Assay based real-time PCR data set as the reference set, the performance of the two microarray platforms was evaluated focusing on the following criteria: (1) Sensitivity and accuracy in detection of expression; (2) Fold change correlation with real-time PCR data in pair-wise tissues as well as in gene expression profiles determined across all tissues; (3) Sensitivity and accuracy in detection of differential expression. CONCLUSION: Our study provides one of the largest "reference" data set of gene expression measurements using TaqMan Gene Expression Assay based real-time PCR technology. This data set allowed us to use an alternative gene expression technology to evaluate the performance of different microarray platforms. We conclude that microarrays are indeed invaluable discovery tools with acceptable reliability for genome-wide gene expression screening, though validation of putative changes in gene expression remains advisable. Our study also characterizes the limitations of microarrays; understanding these limitations will enable researchers to more effectively evaluate microarray results in a more cautious and appropriate manner.

Combining Effects: Sum and Tensor

Martin Hyland — 2005-10-05T18:09:00-00:00

We seek a unified account of modularity for computational effects. We begin by reformulating Moggi's monadic paradigm for modelling computational effects using the notion of enriched Lawvere theory, together with its relationship with strong monads; this emphasises the importance of the operations that produce the effects. Effects qua theories are then combined by appropriate bifunctors on the category of theories. We give a theory for the sum of computational effects, which in particular...

MET Amplification Leads to Gefitinib Resistance in Lung Cancer by Activating ERBB3 Signaling.

Jeffrey A Engelman — 2007-05-08T20:02:16-00:00

Science (26 April 2007)

The epidermal growth factor receptor (EGFR) kinase inhibitors gefitinib and erlotinib are used clinically for the treatment of lung cancers with EGFR activating mutations, but the tumors invariably develop drug resistance. To investigate resistance mechanisms, we isolated gefitinib-resistant clones from an EGFR mutant lung cancer cell line. The resistant cells displayed amplification of the MET oncogene and maintained activation of ERBB3/PI3K/Akt signaling in the presence of gefitinib. Inhibition of MET signaling in these cells restored their sensitivity to gefitinib. MET amplification was detected in 4 out of 18 (22%) lung cancer specimens that had become resistant to gefitinib or erlotinib. Because amplified MET activates the ERBB3/PI3K pathway in other tumor cell lines, our results raise the possibility that MET amplification promotes drug resistance in other ERBB-driven cancers.

SIX1 mutations cause branchio-oto-renal syndrome by disruption of EYA1-SIX1-DNA complexes.

RG Ruf — 2007-04-26T10:48:46-00:00

Proc Natl Acad Sci U S A, Vol. 101, No. 21. (25 May 2004), pp. 8090-8095.

Urinary tract malformations constitute the most frequent cause of chronic renal failure in the first two decades of life. Branchio-otic (BO) syndrome is an autosomal dominant developmental disorder characterized by hearing loss. In branchio-oto-renal (BOR) syndrome, malformations of the kidney or urinary tract are associated. Haploinsufficiency for the human gene EYA1, a homologue of the Drosophila gene eyes absent (eya), causes BOR and BO syndromes. We recently mapped a locus for BOR/BO syndrome (BOS3) to human chromosome 14q23.1. Within the 33-megabase critical genetic interval, we located the SIX1, SIX4, and SIX6 genes, which act within a genetic network of EYA and PAX genes to regulate organogenesis. These genes, therefore, represented excellent candidate genes for BOS3. By direct sequencing of exons, we identified three different SIX1 mutations in four BOR/BO kindreds, thus identifying SIX1 as a gene causing BOR and BO syndromes. To elucidate how these mutations cause disease, we analyzed the functional role of these SIX1 mutations with respect to protein-protein and protein-DNA interactions. We demonstrate that all three mutations are crucial for Eya1-Six1 interaction, and the two mutations within the homeodomain region are essential for specific Six1-DNA binding. Identification of SIX1 mutations as causing BOR/BO offers insights into the molecular basis of otic and renal developmental diseases in humans.

Combining Continuations with Other Effects

Martin Hyland — 2007-04-06T22:06:30-00:00

A fundamental question, in modelling computational effects, is how to give a unified semantic account of modularity, i.e., a mathematical theory that supports the various combinations one naturally makes of computational effects such as exceptions, side-effects, interactive input/output, nondeterminism, and, particularly for this workshop, continuations [2, 3, 5]. We have begun to give such an account over recent years for all of these effects other than continuations [8], describing the sum...

Combining computational effects: Commutativity and sum

M Hyland — 2007-04-06T21:21:09-00:00

(2002)

We begin to develop a unified account of modularity for computational effects. We use the notion of enriched Lawvere theory, together with its relationship with strong monads, to reformulate Moggi's paradigm for modelling computational efects; we emphasise the importance here of the operations that induce computational effects. Effects qua theories are then combined by appropriate bifunctors (on the category of theories). We give a theory of the commutative combination of effects, which in...

Molecular detection of prostate cells in ejaculate and urethral washings in men with suspected prostate cancer.

JA Clements — 2007-04-02T12:40:43-00:00

J Urol, Vol. 161, No. 4. (April 1999), pp. 1337-1343.

PURPOSE: To determine whether prostatic cells were normally present in ejaculate and if the sensitivity and specificity of the detection of malignant prostate cells in ejaculate and urethral washings from men with suspected prostate cancer could be improved using the more sensitive molecular technique of reverse transcriptase-polymerase chain reaction (RT-PCR). MATERIALS AND METHODS: RT-PCR for prostate-specific antigen (PSA), prostate-specific membrane antigen (PSM) and Apoliprotein D (3 putative prostate-specific and/or cancer-specific markers) was performed on RNA extracts of ejaculate (80) and urethral washings (52) from 77 men with suspected prostate cancer and 12 young controls (<30 years of age) and urines from 5 men who had radical prostatectomies and 10 women. RESULTS: PSA, PSM and Apolipoprotein D expression was detected in ejaculates and urethral washings from both patient and control groups. No differences were observed in the results obtained for 58 men with suspected or 19 men with confirmed prostate cancer or the 18 vasectomized men within the patient group. Urines from the 5 men who had radical prostatectomies and 10 women were all negative for PSA, but PSM was detected in 2 female urines and in 3 radical prostatectomy samples. As few as 10 LNCaP prostate tumor cells could be detected by PSA RT-PCR when added to female urine. CONCLUSION: We have established a sensitive method of detecting prostatic cells in ejaculate and urethral washings and shown that PSA RT-PCR is a reliable indicator of prostate cells in these samples. However, RT-PCR for PSA, PSM and Apoliprotein D were not useful for discriminating malignant from non-malignant prostate cells.

The influence of the vibration signal on worker interactions with the nest and nest mates in established and newly founded colonies of the honey bee, Apis mellifera

TT Cao — 2007-03-21T09:31:21-00:00

Insectes Sociaux

Clinton's World: Remaking American Foreign Policy

William Hyland — 2007-03-01T17:31:16-00:00

(30 March 1999)

No modern U.S. president inherited a stronger, safer international position than Bill Clinton. In 1992, the Cold War was over, and the nation was at peace and focused on domestic issues. Despite this temporary tranquility, Clinton would soon be faced with a barrage of crises, including flare-ups of unrest in the Middle East, ethnic conflict in Yugoslavia, uneasy relations with Japan and China, persistent trouble in the Persian Gulf, the dissolution of the USSR, and disastrous situations in Somalia and Haiti. In this comprehensive and balanced examination of Clinton's foreign policy--the first such book to cover all the global focal points of his administration to date--William G. Hyland brilliantly shows the effects of combining this confusion with Clinton's unique personality characteristics. His first term was marked, in the author's analysis, by murky policy, unrealistic goals, and the mishandling of several crises. By the end of that term he learned some hard lessons, was able to alter his pattern of response, and reversed himself on some major aspects of foreign policy--all to benefit, in the author's view, the country and the world as a whole.

Modulation of an afterhyperpolarization by the substantia nigra induces pauses in the tonic firing of striatal cholinergic interneurons.

JN Reynolds — 2005-10-14T16:48:44-00:00

J Neurosci, Vol. 24, No. 44. (3 November 2004), pp. 9870-9877.

Striatal cholinergic interneurons, also known as tonically active neurons (TANs), acquire a pause in firing during learning of stimulus-reward associations. This pause response to a sensory stimulus emerges after repeated pairing with a reward. The conditioned pause is dependent on dopamine from the substantia nigra, but its underlying cellular mechanism is unknown. Using in vivo intracellular recording, we found that both subthreshold and suprathreshold depolarizations in cholinergic interneurons induced a prolonged after-hyperpolarization (AHP) associated with a pause in their tonic firing. The AHP duration was dependent on the level of depolarization, whether elicited by intracellular current injection or by activation of excitatory inputs from the cortex. High-frequency stimulation of the substantia nigra induced potentiation of the cortically evoked excitation and increased the prolonged AHP after the stimulus. These findings from anesthetized animals suggest that a substantia nigra-induced AHP produces stimulus-associated firing pauses in cholinergic interneurons. This mechanism may underlie the acquisition of the pause response in TANs recorded from behaving animals during learning.

Disciplinary Discourses : Social Interactions in Academic Writing

Ken Hyland — 2005-05-18T15:50:13-00:00

(22 July 2004)

Crossing the boundaries of genre studies: Commentaries by experts

Ann Johns — 2006-12-10T15:26:32-00:00

Journal of Second Language Writing, Vol. 15, No. 3. (December 2006), pp. 234-249.

Glueing and orthogonality for models of linear logic

Martin Hyland — 2006-12-02T17:47:15-00:00

Theoretical Computer Science, Vol. 294, No. 1-2. (15 February 2003), pp. 183-231.

We present the general theory of the method of glueing and associated technique of orthogonality for constructing categorical models of all the structure of linear logic: in particular we treat the exponentials in detail. We indicate simple applications of the methods and show that they cover familiar examples.

Combining Computational Effects: commutativity & sum

Martin Hyland — 2006-09-28T09:37:58-00:00

(2002), pp. 474-484.

Reductions in tobacco smoke pollution and increases in support for smoke-free public places following the implementation of comprehensive smoke-free workplace legislation in the Republic of Ireland: findings from the ITC Ireland/UK Survey.

GT Fong — 2006-08-22T20:59:00-00:00

Tob Control, Vol. 15 Suppl 3 (June 2006)

OBJECTIVE: To evaluate the psychosocial and behavioural impact of the first ever national level comprehensive workplace smoke-free law, implemented in Ireland in March 2004. DESIGN: Quasi-experimental prospective cohort survey: parallel cohort telephone surveys of national representative samples of adult smokers in Ireland (n = 769) and the UK (n = 416), surveyed before the law (December 2003 to January 2004) and 8-9 months after the law (December 2004 to January 2005). MAIN OUTCOME MEASURES: Respondents' reports of smoking in key public venues, support for total bans in those key venues, and behavioural changes due to the law. RESULTS: The Irish law led to dramatic declines in reported smoking in all venues, including workplaces (62% to 14%), restaurants (85% to 3%), and bars/pubs (98% to 5%). Support for total bans among Irish smokers increased in all venues, including workplaces (43% to 67%), restaurants (45% to 77%), and bars/pubs (13% to 46%). Overall, 83% of Irish smokers reported that the smoke-free law was a "good" or "very good" thing. The proportion of Irish homes with smoking bans also increased. Approximately 46% of Irish smokers reported that the law had made them more likely to quit. Among Irish smokers who had quit at post-legislation, 80% reported that the law had helped them quit and 88% reported that the law helped them stay quit. CONCLUSION: The Ireland smoke-free law stands as a positive example of how a population-level policy intervention can achieve its public health goals while achieving a high level of acceptance among smokers. These findings support initiatives in many countries toward implementing smoke-free legislation, particularly those who have ratified the Framework Convention on Tobacco Control, which calls for legislation to reduce tobacco smoke pollution.

Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags.

SJ Hubbard — 2006-07-22T13:17:41-00:00

Genome Res, Vol. 15, No. 1. (January 2005), pp. 174-183.

We present an analysis of the chicken (Gallus gallus) transcriptome based on the full insert sequences for 19,626 cDNAs, combined with 485,337 EST sequences. The cDNA data set has been functionally annotated and describes a minimum of 11,929 chicken coding genes, including the sequence for 2260 full-length cDNAs together with a collection of noncoding (nc) cDNAs that have been stringently filtered to remove untranslated regions of coding mRNAs. The combined collection of cDNAs and ESTs describe 62,546 clustered transcripts and provide transcriptional evidence for a total of 18,989 chicken genes, including 88% of the annotated Ensembl gene set. Analysis of the ncRNAs reveals a set that is highly conserved in chickens and mammals, including sequences for 14 pri-miRNAs encoding 23 different miRNAs. The data sets described here provide a transcriptome toolkit linked to physical clones for bioinformaticians and experimental biologists who wish to use chicken systems as a low-cost, accessible alternative to mammals for the analysis of vertebrate development, immunology, and cell biology.

FILOCHAT: handwritten notes provide access to recorded conversations

Steve Whittaker — 2006-04-10T22:02:28-00:00

(1994), pp. 271-277.

Altered CD45 isoform expression affects lymphocyte function in CD45 Tg mice.

EZ Tchilian — 2006-03-17T09:34:57-00:00

Int Immunol, Vol. 16, No. 9. (September 2004), pp. 1323-1332.

Transgenic mice have been constructed expressing high (CD45RABC) and low (CD45R0) molecular weight CD45 isoforms on a CD45-/- background. Phenotypic analysis and in vivo challenge of these mice with influenza and lymphocytic choriomeningitis viruses shows that T cell differentiation and peripheral T cell function are related to the level of CD45 expression but not to which CD45 isoform is expressed. In contrast, B cell differentiation is not restored, irrespective of the level of expression of a single isoform. All CD45 trangenic mice have T cells with an activated phenotype and increased T cell turnover. These effects are more prominent in CD8 than CD4 cells. The transgenic mice share several properties with humans expressing variant CD45 alleles and provide a model to understand immune function in variant individuals.

Beyond Keywords: Accurate Retrieval from Full Text Documents

Richard Sutcliffe — 2006-02-22T20:52:14-00:00

this article we first describe and justify 1

Glueing and orthogonality for models of linear logic

M Hyland — 2005-12-27T21:45:41-00:00

We present the general theory of the method of glueing and associated technique of orthogonality for constructing categorical models of all the structure of linear logic: in particular we treat the exponentials in detail. We indicate simple applications of the methods and show that they cover familiar examples. 1

Linear lambda-calculus and categorical models revisited

N Benton — 2005-11-19T16:44:45-00:00

(1993), pp. 61-84.

this paper we shall consider multiplicative exponential linear logic (MELL), i.e. the fragment which has multiplicative conjunction or tensor,Ω , linear implication, Γffi, and the logical operator "exponential", !. We recall the rules for MELL in a sequent calculus system in Fig. 1. We use capital Greek letters Γ; Δ for sequences of formulae and A; B for single formulae. The Exchange rule simply allows the permutation of assumptions. The `! rules' have been given names by...

A Term Calculus for Intuitionistic Linear Logic

Nick Benton — 2005-11-19T16:40:45-00:00

Vol. 664 (1993), pp. 75-90.

. In this paper we consider the problem of deriving a term assignment system for Girard's Intuitionistic Linear Logic for both the sequent calculus and natural deduction proof systems. Our system differs from previous calculi (e.g. that of Abramsky [1]) and has two important properties which they lack. These are the substitution property (the set of valid deductions is closed under substitution) and subject reduction (reduction on terms is well-typed). We also consider term reduction arising...

Writing: Texts, Processes & Practices

Cristopher Candlin — 2005-05-18T15:48:38-00:00

(30 November 1999)

Genre-based pedagogies: A social response to process

Ken Hyland — 2005-06-30T15:51:26-00:00

Journal of Second Language Writing, Vol. 12, No. 1. (February 2003), pp. 17-29.

Process theories have been extremely influential in the evolution of L2 writing instruction. Responding to purely formal views of writing, proponents borrowed the techniques and theories of cognitive psychology and L1 composition to refine the ways we understand and teach writing. While remaining the dominant pedagogical orthodoxy for over 30 years, however, process models have for some time found themselves under siege from more socially-oriented views of writing which reject their inherent liberal individualism. Instead, genre approaches see ways of writing as purposeful, socially situated responses to particular contexts and communities. In this paper, I discuss the importance of genre approaches to teaching L2 writing and how they complement process views by emphasising the role of language in written communication.

Pedunculopontine tegmental nucleus controls conditioned responses of midbrain dopamine neurons in behaving rats.

WX Pan — 2005-06-29T22:22:19-00:00

J Neurosci, Vol. 25, No. 19. (11 May 2005), pp. 4725-4732.

Midbrain dopamine (DA) neurons respond to sensory cues that predict reward. We tested the hypothesis that projections from the pedunculopontine tegmental nucleus (PPTg) are involved in driving this DA cell activity. First, the activity of PPTg and DA neurons was compared in a cued-reward associative learning paradigm. The majority of PPTg neurons showed phasic responses to the onset of sensory cues, at significantly shorter latency than DA cells, consistent with a PPTg-to-DA transmission of information. However, unlike DA cells, PPTg responses were almost entirely independent of whether signals were associated with rewards. Second, DA neuron responses to the cues were recorded in free-moving rats during reversible inactivation of the PPTg by microinfusion of local anesthetic. The results showed clear suppression of conditioned sensory responses of DA neurons after PPTg inactivation that was not seen after saline infusion or in non-DA cells. We propose that the PPTg relays information about the precise timing of attended sensory events, which is integrated with information about reward context by DA neurons.