Whole-proteome phylogeny of large dsDNA viruses and parvoviruses through a composition vector method related to dynamical language model

Background The vast sequence divergence among different virus groups has presented a great challenge to alignment-based analysis of virus phylogeny. Due to the problems caused by the uncertainty in alignment, existing tools for phylogenetic analysis based on multiple alignment could not be directly applied to the whole-genome comparison and phylogenomic studies of viruses. There has been a growing interest in alignment-free methods for phylogenetic analysis using complete genome data. Among the alignment-free methods, a dynamical language (DL) method proposed by our group has successfully been applied to the phylogenetic analysis of bacteria and chloroplast genomes. Results In this paper, the DL method is used to analyze the whole-proteome phylogeny of 124 large dsDNA viruses and 30 parvoviruses, two data sets with large difference in genome size. The trees from our analyses are in good agreement to the latest classification of large dsDNA viruses and parvoviruses by the International Committee on Taxonomy of Viruses (ICTV). Conclusions The present method provides a new way for recovering the phylogeny of large dsDNA viruses and parvoviruses, and also some insights on the affiliation of a number of unclassified viruses. In comparison, some alignment-free methods such as the CV Tree method can be used for recovering the phylogeny of large dsDNA viruses, but they are not suitable for resolving the phylogeny of parvoviruses with a much smaller genome size.

Here’s a story : using student podcasts to raise awareness of language

Thirty-five years ago, a landmark article entitled 'What The "Good Language Learner" Can Teach Us' suggested that if more was known about what 'successful learners' did, then those strategies could be taught to poorer learners to enhance learning (Rubin, 1975, p. 42). Since publication of Rubin's article, language instruction has begun to encompass technological applications (Chinnery, 2006) through mobile-assisted language learning (MALL or m-learning) like podcasts. Podcasting extends the classroom, offers convenience for diverse learners, and provides authentic listening opportunities. Although the effects of podcasting in higher education have yet to be investigated (Educause, 2007), this article describes how action research lead to the creation of a student learning strategy webpage featuring peer podcasts and successful language learning strategies in higher education.

Assessment policy change in relation to English language teaching and learning in China : a study of perspectives from two universities

In response to concerns about the quality of English Language Learning (ELL) education at tertiary level, the Chinese Ministry of Education (CMoE) launched the College English Reform Program (CERP) in 2004. By means of a press release (CMoE, 2005) and a guideline document titled College English Curriculum Requirements (CECR) (CMoE, 2007), the CERP proposed two major changes to the College English assessment policy, which were: (1) the shift to optional status for the compulsory external test, the College English Test Band 4 (CET4); and (2) the incorporation of formative assessment into the existing summative assessment framework. This study investigated the interactions between the College English assessment policy change, the theoretical underpinnings, and the assessment practices within two Chinese universities (one Key University and one Non-Key University). It adopted a sociocultural theoretical perspective to examine the implementation process as experienced by local actors of institutional and classroom levels. Systematic data analysis using a constant comparative method (Merriam, 1998) revealed that contextual factors and implementation issues did not lead to significant differences in the two cases. Lack of training in assessment and the sociocultural factors such as the traditional emphasis on the product of learning and hierarchical teacher/students relationship are decisive and responsible for the limited effect of the reform.

An effective approach to verbose queries using a limited dependencies language model

Intuitively, any ‘bag of words’ approach in IR should benefit from taking term dependencies into account. Unfortunately, for years the results of exploiting such dependencies have been mixed or inconclusive. To improve the situation, this paper shows how the natural language properties of the target documents can be used to transform and enrich the term dependencies to more useful statistics. This is done in three steps. The term co-occurrence statistics of queries and documents are each represented by a Markov chain. The paper proves that such a chain is ergodic, and therefore its asymptotic behavior is unique, stationary, and independent of the initial state. Next, the stationary distribution is taken to model queries and documents, rather than their initial distributions. Finally, ranking is achieved following the customary language modeling paradigm. The main contribution of this paper is to argue why the asymptotic behavior of the document model is a better representation then just the document’s initial distribution. A secondary contribution is to investigate the practical application of this representation in case the queries become increasingly verbose. In the experiments (based on Lemur’s search engine substrate) the default query model was replaced by the stable distribution of the query. Just modeling the query this way already resulted in significant improvements over a standard language model baseline. The results were on a par or better than more sophisticated algorithms that use fine-tuned parameters or extensive training. Moreover, the more verbose the query, the more effective the approach seems to become.

Are alphabetic language-derived models of L2 reading relevant to L1 logographic background readers?

In this paper, we argue that second language (L2) reading research, which has been informed by studies involving first language (L1) alphabetic English reading, may be less relevant to L2 readers with non-alphabetic reading backgrounds, such as Chinese readers with an L1 logographic (Chinese character) learning history. We provide both neuroanatomical and behavioural evidence from Chinese language reading studies to support our claims. The paper concludes with an argument outlining the need for a universal L2 reading model which can adequately account for readers with diverse L1 orthographic language learning histories.

A unified description language for human to automated services

Through the rise of cloud computing, on-demand applications, and business networks, services are increasingly being exposed and delivered on the Internet and through mobile communications. So far, services have mainly been described through technical interface descriptions. The description of business details, such as pricing, service-level, or licensing, has been neglected and is therefore hard to automatically process by service consumers. Also, third-party intermediaries, such as brokers, cloud providers, or channel partners, are interested in the business details in order to extend services and their delivery and, thus, further monetize services. In this paper, the constructivist design of the UnifiedServiceDescriptionLanguage (USDL), aimed at describing services across the human-to-automation continuum, is presented. The proposal of USDL follows well-defined requirements which are expressed against a common service discourse and synthesized from currently available servicedescription efforts. USDL's concepts and modules are evaluated for their support of the different requirements and use cases.

Instructing foreign language learners how to listen through metacognitive strategies : an empirical study

This study uses a mixed method approach to investigate the impact of metacognitive strategies instruction on listening comprehension. An experimental group (N = 30) of university students are guided through a process-approach pedagogy over one semester (10 weeks) in Iran. IELTS listening tests are used to track development of listening comprehension in participants who are then asked to complete a Metacognitive Awareness Listening Questionnaire (MALQ). The questionnaire examines students’ employment of metacognitive strategies in listening comprehension. Finally, interviews are used to explore students’ use of strategies in listening. Results indicate that participants develop listening comprehension, but no metacognitive awareness in listening. Students reported in the interviews that they use multiple strategies (cognitive and metacognitive) to approach listening comprehension.

Responding to national curriculum goals for English language learners : enhancing reading strategies in high school content areas

The official need for content teachers to teach the language features of their fields has never been greater in Australia than now. In 2012, the recently formed national curriculum board announced that all teachers are responsible for the English language development of students whose first language or dialect is not Standard Australian English (SAE). This formal endorsement is an important juncture regarding the way expertise might be developed, perceived and exchanged between content and language teachers through collaboration, in order for the goals of English language learners in content areas to be realised. To that end, we conducted an action research project to explore and extend the reading strategies pedagogy of one English language teacher who teaches English language learners in a parallel junior high school Geography program. Such pedagogy will be valuable for all teachers as they seek to contribute to English language development goals as outlined in national curricula.

Soundage : a practice-led approach to Gertrude Stein, sound, and generative language

In this practice-led research project I work to show how a re-reading and a particular form of listening to the sound-riddled nature of Gertrude Stein's work, Two: Gertrude Stein and her Brother, presents us with a contemporary theory of sound in language. This theory, though in its infancy, is a particular enjambment of sounded language that presents itself as an event, engaged with meaning, with its own inherent voice. It displays a propensity through engagement with the 'other' to erupt into love. In this thesis these qualities are reverberated further through the work of Seth Kim-Cohen's notion of the non-cochlear, Simon Jarvis's notion of musical thinking, Jean-Jacques Lecercle's notion of délire or nonsense, Luce Irigaray's notion of jouissant love and the Bracha Ettinger's notion of the generative matrixial border space. This reading then is simultaneously paired with my own work of scoring and creating a digital opera from Stein's work, thereby testing and performing Stein's theory. In this I show how a re-reading and relistening to Stein's work can be significant to feminist ethical language frames, contemporary philosophy, sonic art theory and digital language frames. Further significance of this study is that when the reverberation of Stein's engagements with language through sound can be listened to, a pattern emerges, one that encouragingly problematizes subjectivity and interweaves genres/methods and means, creating a new frame for sound in language, one with its own voice that I call soundage.

Educational paradox : the hidden obstacles to the integration of mobile phones in the language classroom

This paper reports on the findings of an international telecollaboration study using Facebook, in which teachers studying in M. Ed programs in Australia and Greece, discussed the use of mobile phones in language classrooms. Results suggest that invisible barriers exist in the use of mobile phones in the classroom, including bans on use in schools, lack of familiarity with educational uses for mobile phones, and negative perceptions about mobile phones specifically in terms of classroom management.

Towards a potential model to enhance language learner autonomy in the Vietnamese higher education context

This constructivist theory-led case study explored how the term language learner autonomy (LLA) is interpreted and the appropriate pedagogy to foster LLA in the Vietnamese higher education context. Evidence through the exploration of the government policies and the cases of three EFL classes confirms the interpretation that learner autonomy and language acquisition are mutually supported. The study has proposed project work as a potential model while demonstrating the role of the teacher and the use of target language as mediators to enhance LLA in the local context. Findings of the study contribute a theoretical and pedagogical justification for encouraging LLA in Vietnam and other similar contexts.

Orientations to Critical Literacy for English as an Additional Language or Dialect (EAL/D) learners: A case study of four teachers of senior English

Recently, the debate around critical literacy has dissipated as literacy education agendas and attendant policies shift to embrace more hybrid approaches to the teaching of senior English. This paper reports on orientations towards critical literacy as expressed by four teachers of senior English who teach culturally and linguistically diverse learners. Teachers’ understandings of critical literacy are important given the emphasis on Critical and Creative Thinking as well as Literacy as General Capabilities underpinning the Australian Curriculum. Using critical discourse analysis and Janks' (2010) Synthesis Model of Critical Literacy, interview and classroom data from four teachers of English as an Additional Language or Dialect (EAL/D) learners in two high schools were analysed for the ways these teachers constructed critical literacy in their talk and practice. While all four teachers indicated significant commitment to critical literacy as an approach to English language teaching, their understandings varied. These ranged from providing access to powerful genres, to rationalist approaches to interrogating text, with less emphasis on multimodal design and drawing on learner diversity. This has significant implications for what kind of learning is being offered to EAL/D learners in the name of English teaching, for syllabus design, and for teacher professional development.