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.

The role of vegetation in enhancing radon concentration and ion production in the atmosphere

The role of ions in the production of atmospheric particles has gained wide interest due to their profound impact on climate. Away from anthropogenic sources, molecules are ionized by alpha radiation from radon exhaled from the ground and cosmic gamma radiation from space. These molecular ions quickly form into ‘cluster ions’, typically smaller than about 1.5 nm. Using our measurements and the published literature, we present evidence to show that cluster ion concentrations in forest areas are consistently higher than outside. Since alpha radiation cannot penetrate more than a few centimetres of soil, radon present deep in the ground cannot directly contribute to the measured cluster ion concentrations. We propose an additional mechanism whereby radon, which is water soluble, is brought up by trees and plants through the uptake of groundwater and released into the atmosphere by transpiration. We estimate that, in a forest comprising eucalyptus trees spaced 4m apart, approximately 28% of the radon in the air may be released by transpiration. Considering that 24% of the earth’s land area is still covered in forests; these findings have potentially important implications for atmospheric aerosol formation and climate.

Hypercapitalism : a political economy of informational idealism

In this this paper I identify specific historical trajectories that are directly contingent upon the deployment and use of new media, but which are actually hidden by a focus on the purely technological. They are: the increasingly abstract and alienated nature of economic value; the subsumption of all labour - material and intellectual - under systemic capital; and the convergence of formerly distinct spheres of analysis –the spheres of production, circulation, and consumption. This paper examines the implications of the knowledge economy from an historical materialist perspective. I synthesise the systemic views of Marx (1846/1972, 1875/1972 1970 1973 1976 1978 1981), Adorno (1951/1974 1964/1973 1991; Horkheimer and Adorno 1944/1998; Jarvis 1998), and Bourdieu (1991 1998) to argue for a language-focused approach to new media research and suggest aspects of Marxist thought which might be useful in researching emergent socio-technical domains. I also identify specific categories in the Marxist tradition which may no longer be analytically useful for researching the effects of new media.

Photocatalytic hydrogen production with iron oxide under solar irradiation

As solar hydrogen is a sustainable and environmental friendly energy carrier, it is considered to take the place of fossil fuels in the near future. Solar hydrogen can be generated by splitting of water under solar light illumination. In this study, the use of nanostructured hematite thin-film electrodes in photocatalytic water splitting was investigated. Hematite (á-Fe2O3) has a narrow band-gap of 2.2 eV, which is able to utilise approximately 40% of solar radiation. However, poor photoelectrochemical performance is observed for hematite due to low electrical conductivity and a high rate of electron-hole recombination. An extensive review of useful measures taken to overcoming the disadvantages of hematite so as to enhance its performance was presented including thin-film structure, nanostructuring, doping, etc. Since semiconductoring materials which exhibit an inverse opal structure are expected to have a high surface-volume ratio, unique optical characteristics and a shorter distance for photogenerated holes to travel to the electrode/electrolyte interface, inverse opals of hematite thin films deposited on FTO glass substrate were successfully prepared by doctor blading using PMMA as a template. However, due to the poor adhesion of the films, an acidic medium (i.e., 2 M HCl) was employed to significantly enhance the adhesion of the films, which completely destroyed the inverse opal structure. Therefore, undoped, Ti and Zn-doped hematite thin films deposied on FTO glass substrate without an inverse opal structure were prepared by doctor blading and spray pyrolysis and characterised using SEM, EDX, XRD, TGA, UV-Vis spectroscopy and photoelectrochemical measurements. Regarding the doped hematite thin films prepared by doctor blading, the photoelectrochemical activity of the hematite photoelectrodes was improved by incorporation of Ti, most likely owing to the increased electrical conductivity of the films, the stabilisation of oxygen vacancies by Ti4+ ions and the increased electric field of the space charge layer. A highest photoresponse was recorded in case of 2.5 at.% Ti which seemed to be an optimal concentration. The effect of doping content, thickness, and calcination temperature on the performance of the Ti-doped photoelectrodes was investigated. Also, the photoactivity of the 2.5 at.% Ti-doped samples was examined in two different types of electrochemical cells. Zn doping did not enhance the photoactivity of the hematite thin films though Zn seemed to enhance the hole transport due to the slow hole mobility of hematite which could not be overcome by the enhancement. The poor performance was also obtained for the Ti-doped samples prepared by spray pyrolysis, which appeared to be a result of introduction of impurities from the metallic parts of the spray gun in an acidic medium. Further characterisation of the thin-film electrodes is required to explain the mechanism by which enhanced performance was obtained for Ti-doped electrodes (doctor blading) and poor photoactivity for Zn and Ti-doped samples which were synthesised by doctor blading and spray pyrolysis, respectively. Ti-doped hematite thin films will be synthesised in another way, such as dip coating so as to maintain an inverse opal structure as well as well adhesion. Also, a comparative study of the films will be carried out.

Autopoiesis, language, literacy and the brain

When we attempt to speak about the relationship between language, literacy, and the brain, we find ourselves ill equipped to deal with these conceptually and qualitatively different phenomena. Immediately we must straddle different academic traditions that treat each of these as separate “things”. Broadly speaking, the study of language firstly belongs to the domain of biology, then to anthropology, sociology, and linguistics. At its most functional, a study of literacy education is a study of a particular technology, its diffusion techniques, and the abilities and motivations of people to adopt, or adapt themselves to, this technology. The brain is most commonly studied in the field of neurology, which is also a sub-discipline of biology, biochemistry, and medicine.

Reflections, successes and pitfalls of coordinating online discussion forums in a foreign language

The advent of e-learning has seen the adaptation and use of a plethora of educational techniques. Of these, online discussion forums have met with success and been used widely in both undergraduate and postgraduate education. The authors of this paper, having previously used online discussion forums in the postgraduate arena with success, adopted this approach for the design and subsequent delivery of a learning and teaching subject. This learning and teaching subject, however, was part of an international collaboration and designed for nurse academics in another country – Vietnam. With the nursing curriculum in Vietnam currently moving to adopt a competency based approach, two learning and teaching subjects were designed by an Australian university for Vietnamese nurse academics. Subject materials constituted a DVD which arrived by post and access to an online platform. Assessment for the subject included (but was not limited to) mandatory participation in online discussion with the other nurse academics enrolled in the subject. The purpose behind the online discussion was to generate discourse between the Vietnamese nurse academics located across Vietnam. Consequently the online discussions occurred in both Vietnamese and English; the Australian academic moderating the discussion did so in Australia with a Vietnamese translator. For the Australian University delivering this subject the difference between this and past online discussions were twofold: delivery was in a foreign language; and the teaching experience of the Vietnamese nurse teachers was mixed and frequently very limited. This paper will provide a discussion addressing the design of an online learning environment for foreign correspondents, the resources and translation required to maximise the success of the online discussion, the lessons learnt and consequent changes made, as well as the rationale of delivering complex content in a foreign language. While specifically addressing the first iteration of the first learning module designed, this paper will also address subsequent changes made for the second iteration of the first module and comment on their success. While a translator is clearly a key component of success, the elements of simplicity and clarity in hand with supportive online moderation must not be overlooked.

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.

The cultural production sector in Manchester

A quantitative and qualitative review of the cultural industries in Manchester at the end of the 1990s

Summary : Cultural Production in Manchester

Summary of the larger report of the same name

Ceremony and cybrary : Digital libraries and the dialectic of place and space

This article examines social, cultural and technological change in the systems and economies of educational information management. Since the Sumerians first collected, organized and supervised administrative and religious records some six millennia ago, libraries have been key physical depositories and cultural signifiers in the production and mediation of social capital and power through education. To date, the textual, archival and discursive practices perpetuating libraries have remained exempt from inquiry. My aim here is to remedy this hiatus by making the library itself the terrain and object of critical analysis and investigation. The paper argues that in the three dominant communications eras—namely, oral, print and digital cultures—society’s centres of knowledge and learning have resided in the ceremony, the library and the cybrary respectively. In a broad-brush historical grid, each of these key educational institutions—the ceremony in oral culture, the library in print culture and the cybrary in digital culture—are mapped against social, cultural and technological orders pertaining to their era. Following a description of these shifts in society’s collective cultural memory, the paper then examines the question of what the development of global information systems and economies mean for schools and libraries of today, and for teachers and learners as knowledge consumers and producers?