Open and networked initiatives and the digital transformation of academic publishing in China

Many aspects of China's academic publishing system differ from the systems found in liberal market based economies of the United States, Western Europe and Australia. A high level of government intervention in both the publishing industry and academia and the challenges associated with attempting to make a transition from a centrally controlled towards a more market based publishing industry are two notable differences; however, as in other countries, academic communities and publishers are being transformed by digital technologies. This research explores the complex yet dynamic digital transformation of academic publishing in China, with a specific focus of the open and networked initiatives inspired by Web 2.0 and social media. The thesis draws on two case studies: Science Paper Online, a government-operated online preprint platform and open access mandate; and New Science, a social reference management website operated by a group of young PhD students. Its analysis of the innovations, business models, operating strategies, influences, and difficulties faced by these two initiatives highlights important characteristics and trends in digital publishing experiments in China. The central argument of this thesis is that the open and collaborative possibilities of Web 2.0 inspired initiatives are emerging outside the established journal and monograph publishing system in China, introducing innovative and somewhat disruptive approaches to the certification, communication and commercial exploitation of knowledge. Moreover, emerging publishing models are enabling and encouraging a new system of practising and communicating science in China, putting into practice some elements of the Open Science ethos. There is evidence of both disruptive change to old publishing structures and the adaptive modification of emergent replacements in the Chinese practice. As such, the transformation from traditional to digital and interactive modes of publishing, involves both competition and convergence between new and old publishers, as well as dynamics of co-evolution involving new technologies, business models, social norms, and government reform agendas. One key concern driving this work is whether there are new opportunities and new models for academic publishing in the Web 2.0 age and social media environment, which might allow the basic functions of communication and certification to be achieved more effectively. This thesis enriches existing knowledge of open and networked transformations of scholarly publishing by adding a Chinese story. Although the development of open and networked publishing platforms in China remains in its infancy, the lessons provided by this research are relevant to practitioners and stakeholders interested in understanding the transformative dynamics of networked technologies for publishing and advocating open access in practice, not only in China, but also internationally.

Segmentation of cone-beam CT using a hidden Markov random field with informative priors

Cone-beam computed tomography (CBCT) has enormous potential to improve the accuracy of treatment delivery in image-guided radiotherapy (IGRT). To assist radiotherapists in interpreting these images, we use a Bayesian statistical model to label each voxel according to its tissue type. The rich sources of prior information in IGRT are incorporated into a hidden Markov random field model of the 3D image lattice. Tissue densities in the reference CT scan are estimated using inverse regression and then rescaled to approximate the corresponding CBCT intensity values. The treatment planning contours are combined with published studies of physiological variability to produce a spatial prior distribution for changes in the size, shape and position of the tumour volume and organs at risk. The voxel labels are estimated using iterated conditional modes. The accuracy of the method has been evaluated using 27 CBCT scans of an electron density phantom. The mean voxel-wise misclassification rate was 6.2\%, with Dice similarity coefficient of 0.73 for liver, muscle, breast and adipose tissue. By incorporating prior information, we are able to successfully segment CBCT images. This could be a viable approach for automated, online image analysis in radiotherapy.

A novel representation of bioacoustic events for content-based search in field audio data

Bioacoustic data can provide an important base for environmental monitoring. To explore a large amount of field recordings collected, an automated similarity search algorithm is presented in this paper. A region of an audio defined by frequency and time bounds is provided by a user; the content of the region is used to construct a query. In the retrieving process, our algorithm will automatically scan through recordings to search for similar regions. In detail, we present a feature extraction approach based on the visual content of vocalisations – in this case ridges, and develop a generic regional representation of vocalisations for indexing. Our feature extraction method works best for bird vocalisations showing ridge characteristics. The regional representation method allows the content of an arbitrary region of a continuous recording to be described in a compressed format.

User-centred study on quality of mobile video services

Mobile video, as an emerging market and a promising research field, has attracted much attention from both industry and researchers. Considering the quality of user-experience as the crux of mobile video services, this chapter aims to provide a guide to user-centered studies of mobile video quality. This will benefit future research in better understanding user needs and experiences, designing effective research, and providing solid solutions to improve the quality of mobile video. This chapter is organized in three main parts: (1) a review of recent user studies from the perspectives of research focuses, user study methods, and data analysis methods; (2) an example of conducting a user study of mobile video research, together with the discussion on a series of relative issues, such as participants, materials and devices, study procedure, and analysis results, and; (3) a conclusion with an open discussion about challenges and opportunities in mobile video related research, and associated potential future improvements.

Dependence of residual amplitude noise in electro-optic phase modulators on the intensity distribution of the incident field

Our results demonstrate that photorefractive residual amplitude modulation (RAM) noise in electro-optic modulators (EOMs) can be reduced by modifying the incident beam intensity distribution. Here we report an order of magnitude reduction in RAM when beams with uniform intensity (flat-top) profiles, generated with an LCOS-SLM, are used instead of the usual fundamental Gaussian mode (TEM00). RAM arises from the photorefractive amplified scatter noise off the defects and impurities within the crystal. A reduction in RAM is observed with increasing intensity uniformity (flatness), which is attributed to a reduction in space charge field on the beam axis. The level of RAM reduction that can be achieved is physically limited by clipping at EOM apertures, with the observed results agreeing well with a simple model. These results are particularly important in applications where the reduction of residual amplitude modulation to 10^-6 is essential.

Incorporating spatial correlations into multispecies mean-field models

In biology, we frequently observe different species existing within the same environment. For example, there are many cell types in a tumour, or different animal species may occupy a given habitat. In modelling interactions between such species, we often make use of the mean field approximation, whereby spatial correlations between the locations of individuals are neglected. Whilst this approximation holds in certain situations, this is not always the case, and care must be taken to ensure the mean field approximation is only used in appropriate settings. In circumstances where the mean field approximation is unsuitable we need to include information on the spatial distributions of individuals, which is not a simple task. In this paper we provide a method that overcomes many of the failures of the mean field approximation for an on-lattice volume-excluding birth-death-movement process with multiple species. We explicitly take into account spatial information on the distribution of individuals by including partial differential equation descriptions of lattice site occupancy correlations. We demonstrate how to derive these equations for the multi-species case, and show results specific to a two-species problem. We compare averaged discrete results to both the mean field approximation and our improved method which incorporates spatial correlations. We note that the mean field approximation fails dramatically in some cases, predicting very different behaviour from that seen upon averaging multiple realisations of the discrete system. In contrast, our improved method provides excellent agreement with the averaged discrete behaviour in all cases, thus providing a more reliable modelling framework. Furthermore, our method is tractable as the resulting partial differential equations can be solved efficiently using standard numerical techniques.

Library Research Support in developing, testing and promoting an open cyberinfrastructure

QUT Library continues to rethink research support with eResearch as a primary driver. The support to the development of the Lens, an open global cyberinfrastructure, has been especially important in the light of technology transfer promotion, and partly in the response to researchers’ needs in following the innovation landscapes not only within the scientific but also patent literature. The Lens http://www.lens.org/lens/ project makes innovation more efficient, fair, transparent and inclusive. It is a joint effort between Cambia http://www.cambia.org.au and Queensland University of Technology (QUT). The Lens serves more than 84 million patent documents in the world as open, annotatable digital public goods that are integrated with scholarly and technical literature along with regulatory and business data. Users can link from search results to visualization and document clusters; from a patent document description to its full-text; from there, if applicable, the sequence data can also be found. Figure 1 shows a BLAST Alignment (DNA) using the Lens. A unique feature of the Lens is the ability to embed search and BLAST results into blogs and websites, and provide real-time updates to them. PatSeq Explorer http://www.lens.org/lens/bio/patseqexplorer allows users to navigate patent sequences that map onto the human genome and in the future, many other genomes. PatSeq Explorer offers three level views for the sequence information and links each group of sequences at the chromosomal level to their corresponding patent documents in the Lens. By integrating sequence and patent search and document clustering capabilities, users can now understand the big and small details on the true extent and scope of genetic sequence patents. QUT Library supported Cambia in developing, testing and promoting the Lens. This poster demonstrates QUT Library’s provision of best practice and holistic research support to a research group and how QUT Librarians have acquired new capabilities to meet the needs of the researchers beyond traditional research support practices.

Candidate gene association studies : a comprehensive guide to useful in silico tools

The candidate gene approach has been a pioneer in the field of genetic epidemiology, identifying risk alleles and their association with clinical traits. With the advent of rapidly changing technology, there has been an explosion of in silico tools available to researchers, giving them fast, efficient resources and reliable strategies important to find casual gene variants for candidate or genome wide association studies (GWAS). In this review, following a description of candidate gene prioritisation, we summarise the approaches to single nucleotide polymorphism (SNP) prioritisation and discuss the tools available to assess functional relevance of the risk variant with consideration to its genomic location. The strategy and the tools discussed are applicable to any study investigating genetic risk factors associated with a particular disease. Some of the tools are also applicable for the functional validation of variants relevant to the era of GWAS and next generation sequencing (NGS).

Enabling open access to and re-use of publicly funded research data in Malaysian public universities : a legal and policy analysis

Numerous statements and declarations have been made over recent decades in support of open access to research data. The growing recognition of the importance of open access to research data has been accompanied by calls on public research funding agencies and universities to facilitate better access to publicly funded research data so that it can be re-used and redistributed as public goods. International and inter-governmental bodies such as the ICSU/CODATA, the OECD and the European Union are strong supporters of open access to and re-use of publicly funded research data. This thesis focuses on the research data created by university researchers in Malaysian public universities whose research activities are funded by the Federal Government of Malaysia. Malaysia, like many countries, has not yet formulated a policy on open access to and re-use of publicly funded research data. Therefore, the aim of this thesis is to develop a policy to support the objective of enabling open access to and re-use of publicly funded research data in Malaysian public universities. Policy development is very important if the objective of enabling open access to and re-use of publicly funded research data is to be successfully achieved. In developing the policy, this thesis identifies a myriad of legal impediments arising from intellectual property rights, confidentiality, privacy and national security laws, novelty requirements in patent law and lack of a legal duty to ensure data quality. Legal impediments such as these have the effect of restricting, obstructing, hindering or slowing down the objective of enabling open access to and re-use of publicly funded research data. A key focus in the formulation of the policy was the need to resolve the various legal impediments that have been identified. This thesis analyses the existing policies and guidelines of Malaysian public universities to ascertain to what extent the legal impediments have been resolved. An international perspective is adopted by making a comparative analysis of the policies of public research funding agencies and universities in the United Kingdom, the United States and Australia to understand how they have dealt with the identified legal impediments. These countries have led the way in introducing policies which support open access to and re-use of publicly funded research data. As well as proposing a policy supporting open access to and re-use of publicly funded research data in Malaysian public universities, this thesis provides procedures for the implementation of the policy and guidelines for addressing the legal impediments to open access and re-use.

Acute hamstring strain injury in track and field athletes : a 3-year observational study at the Penn Relay Carnival

Purpose To observe the incidence rates of hamstring strain injuries (HSIs) across different competition levels and ages during the Penn Relays Carnival. Methods Over a 3-year period all injuries treated by the medical staff were recorded. The type of injury, anatomic location, event in which the injury occurred, competition level and demographic data were documented. Absolute and relative HSI (per 1000 participants) were determined and odds ratios (OR) were calculated between genders, competition levels and events. Results Throughout the study period 48,473 athletes registered to participate in the Penn Relays Carnival, with 118 HSIs treated by the medical team. High school females displayed lesser risk of HSI than high school males (OR = 0.55, p = 0.021), and masters athletes were more likely than high school (OR = 4.26, p < 0.001) and college (OR = 3.55, p = 0.001) level athletes to suffer a HSI. The 4x400m relay displayed a greater likelihood of HSI compared to the 4x100m relay (OR = 1.77, p = 0.008). Conclusions High school males and masters levels athletes are most likely to suffer HSI, and there is higher risk in 400m events compared to 100m events.

Peripheral refraction patterns out to large field angles

Purpose To investigate hyperopic shifts and the oblique (or 45-degree/135-degree) component of astigmatism at large angles in the horizontal visual field using the Hartmann-Shack technique. Methods The adult participants consisted of 6 hypermetropes, 13 emmetropes and 11 myopes. Measurements were made with a modified COAS-HD Hartmann-Shack aberrometer across T60 degrees along the horizontal visual field in 5-degree steps. Eyes were dilated with 1% cyclopentolate. Peripheral refraction was estimated as mean spherical (or spherical equivalent) refraction, with/against the rule of astigmatism and oblique astigmatism components, and as horizontal and vertical refraction components based on 3-mm major diameter elliptical pupils. Results Thirty percent of eyes showed a pattern that was a combination of type IV and type I patterns of Rempt et al. (Rempt F, Hoogerheide J, Hoogenboom WP. Peripheral retinoscopy and the skiagram. Ophthalmologica 1971;162:1Y10), which shows the characteristics of type IV (relative hypermetropia along the vertical meridian and relative myopia along the horizontal meridian) out to an angle of between 40 and 50 degrees before behaving like type I (both meridians show relative hypermetropia). We classified this pattern as type IV/I. Seven of 13 emmetropes had this pattern. As a group, there was no significant variation of the oblique component of astigmatism with angle, but about one-half of the eyes showed significant positive slopes (more positive or less negative values in the nasal field than in the temporal field) and one-fourth showed significant negative slopes. Conclusions It is often considered that a pattern of relative peripheral hypermetropia predisposes to the development of myopia. In this context, the finding of a considerable portion of emmetropes with the IV/I pattern suggests that it is unlikely that refraction at visual field angles beyond 40 degrees from fixation contributes to myopia development.

Students' cultural capital : a study of assessment for learning as a field of exchange

This study was conducted within the context of a flexible education institution where conventional educational assessment practices and tests fail to recognise and assess the creativity and cultural capital of a cohort of marginalised young people. A new assessment model which included an electronic-portfolio-social-networking system (EPS) was developed and trialled to identify and exhibit evidence of students' learning. The study aimed to discern unique forms of cultural capital (Bourdieu, 1986) possessed by students who attend the Edmund Rice Education Australia Flexible Learning Centre Network (EREAFLCN). The EPS was trialled at the case study schools in an intervention and developed a space where students could make evident culturally specific forms of capital and funds of knowledge (Gonzalez, Moll, & Amanti, 2005). These resources were evaluated, modified and developed through dialogic processes utilising assessment for learning approaches (Qualifications and Curriculum Development Agency, 2009) in online and classroom settings. Students, peers and staff engaged in the recognition, judgement, revision and evaluation of students' cultural capital in a subfield of exchange (Bourdieu, 1990). The study developed the theory of assessment for learning as a field of exchange incorporating an online system as a teaching and assessment model. The term efield has been coined to describe this particular capital exchange model. A quasi-ethnographic approach was used to develop a collective case study (Stake, 1995). This case study involved an in-depth exploration of five students' forms of cultural capital and the ways in which this capital could be assessed and exchanged using the efield model. A comparative analysis of the five cases was conducted to identify the emergent issues of students' recognisable cultural capital resources and the processes of exchange that can be facilitated to acquire legitimate credentials for these students in the Australian field of education. The participants in the study were young people at two EREAFLC schools aged between 12 and 18 years. Data was collected through interviews, observations and examination of documents made available by the EREAFLCN. The data was coded and analysed using a theoretical framework based on Bourdieu's analytical tools and a sociocultural psychology theoretical perspective. Findings suggest that processes based on dialogic relationships can identify and recognise students' forms of cultural capital that are frequently misrecognised in mainstream school environments. The theory of assessment for learning as a field of exchange was developed into praxis and integrated in an intervention. The efield model was found to be an effective sociocultural tool in converting and exchanging students' capital resources for legitimated cultural and symbolic capital in the field of education.

Exploring the experiences of embedding Indigenous knowledge and perspectives on teaching practicum through interpretive phenomenology

In this paper, we discuss interpretive/hermeneutic phenomenology as a theoretical approach to explore the experiences of three stakeholder groups in embedding Indigenous knowledge and perspectives on teaching practicum, a project sponsored by ALTC. We begin by asking the phenomenological question ‘what is your experience of practice teaching?’ An open, explorative, phenomenological framework seeks the meanings of experiences, not truths, from the participants’ words themselves. Interpretive phenomenology is particularly suitable to explore educational experiences (Grumet, 1992; M. van Manen, 1990), as it provides rich ground for listening to the stakeholders’ lived experience and documenting it for interpretation. In an interpretive process, perspectives on lifeworlds, worldview and lenses get highlighted (Cunningham & Stanley, 2003). We establish how through various project stages, interpretive phenomenology gets to the essence of practice teaching experience creating a pedagogical ‘understanding’ of the essential nature of shared experience as lived by the participants (M van Manen, 2002). Thereby, it foregrounds voices of agency, dissent, acceptance and resistance. We consider how our research study focuses on the pedagogic voice of Indigenous pre-service teachers and the recognition of complex pedagogic fields in Indigenous education. We explain how this study seeks insights into their evaluation of pedagogic relations with two other education stakeholders – their practicum supervising teachers at schools and university staff involved practicum experience. As such, our study aims to support and develop long term, future-oriented opportunities for Indigenous pre-service teachers to embed Indigenous knowledge in the curricula. We conclude with some projections into the discourse on how Indigenous knowledge (IK) and perspectives might be diversely exemplified in pre-service teachers’ professional works (particularly E-portfolios). We speculate how this change could in turn maximise opportunities for Indigenous pre-service teachers, their supervising teachers and university staff to demonstrate leadership in their field through the creation of future tangible products such as units of work, resources, assessment and reflection tools. The processes contextualising the cultural interface of competing knowledge systems (Nakata, 2007) provide important analytical tools for understanding issues affecting student-teacher-mentor relationships occurring on practicum.

Hemi-field and full-field form-deprivation induce timing changes in multifocal ERG responses in chick

Purpose: In animal models hemi-field deprivation results in localised, graded vitreous chamber elongation and presumably deprivation induced localised changes in retinal processing. The aim of this research was to determine if there are variations in ERG responses across the retina in normal chick eyes and to examine the effect of hemi-field and full-field deprivation on ERG responses across the retina and at earlier times than have previously been examined electrophysiologically. Methods: Chicks were either untreated, wore monocular full-diffusers or half-diffusers (depriving nasal retina) (n = 6-8 each group) from day 8. mfERG responses were measured using the VERIS mfERG system across the central 18.2º× 16.7º (H × V) field. The stimulus consisted of 61 unscaled hexagons with each hexagon modulated between black and white according to a pseudorandom binary m-sequence. The mfERG was measured on day 12 in untreated chicks, following 4 days of hemi-field diffuser wear, and 2, 48 and 96 h after application of full-field diffusers. Results: The ERG response of untreated chick eyes did not vary across the measured field; there was no effect of retinal location on the N1-P1 amplitude (p = 0.108) or on P1 implicit time (p > 0.05). This finding is consistent with retinal ganglion cell density of the chick varying by only a factor of two across the entire retina. Half-diffusers produced a ramped retina and a graded effect of negative lens correction (p < 0.0001); changes in retinal processing were localized. The untreated retina showed increasing complexity of the ERG waveform with development; form-deprivation prevented the increasing complexity of the response at the 2, 48 and 96 h measurement times and produced alterations in response timing. Conclusions: Form-deprivation and its concomitant loss of image contrast and high spatial frequency images prevented development of the ERG responses, consistent with a disruption of development of retinal feedback systems. The characterisation of ERG responses in normal and deprived chick eyes across the retina allows the assessment of concurrent visual and retinal manipulations in this model. (Ophthalmic & Physiological Optics © 2013 The College of Optometrists.)

Cetuximab plus chemotherapy in patients with advanced non-small-cell lung cancer (FLEX) : an open-label randomised phase III trial

Background: Use of cetuximab, a monoclonal antibody targeting the epidermal growth factor receptor (EGFR), has the potential to increase survival in patients with advanced non-small-cell lung cancer. We therefore compared chemotherapy plus cetuximab with chemotherapy alone in patients with advanced EGFR-positive non-small-cell lung cancer. Methods: In a multinational, multicentre, open-label, phase III trial, chemotherapy-naive patients (≥18 years) with advanced EGFR-expressing histologically or cytologically proven stage wet IIIB or stage IV non-small-cell lung cancer were randomly assigned in a 1:1 ratio to chemotherapy plus cetuximab or just chemotherapy. Chemotherapy was cisplatin 80 mg/m 2 intravenous infusion on day 1, and vinorelbine 25 mg/m 2 intravenous infusion on days 1 and 8 of every 3-week cycle) for up to six cycles. Cetuximab-at a starting dose of 400 mg/m 2 intravenous infusion over 2 h on day 1, and from day 8 onwards at 250 mg/m 2 over 1 h per week-was continued after the end of chemotherapy until disease progression or unacceptable toxicity had occurred. The primary endpoint was overall survival. Analysis was by intention to treat. This study is registered with ClinicalTrials.gov, number NCT00148798. Findings: Between October, 2004, and January, 2006, 1125 patients were randomly assigned to chemotherapy plus cetuximab (n=557) or chemotherapy alone (n=568). Patients given chemotherapy plus cetuximab survived longer than those in the chemotherapy-alone group (median 11·3 months vs 10·1 months; hazard ratio for death 0·871 [95% CI 0·762-0·996]; p=0·044). The main cetuximab-related adverse event was acne-like rash (57 [10%] of 548, grade 3). Interpretation: Addition of cetuximab to platinum-based chemotherapy represents a new treatment option for patients with advanced non-small-cell lung cancer. Funding: Merck KGaA. © 2009 Elsevier Ltd. All rights reserved.