Advanced mass spectrometry-based multi-omics technologies for exploring the pathogenesis of hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is one of the primary hepatic malignancies and is the third most common cause of cancer related death worldwide. Although a wealth of knowledge has been gained concerning the initiation and progression of HCC over the last half century, efforts to improve our understanding of its pathogenesis at a molecular level are still greatly needed, to enable clinicians to enhance the standards of the current diagnosis and treatment of HCC. In the post-genome era, advanced mass spectrometry driven multi-omics technologies (e.g., profiling of DNA damage adducts, RNA modification profiling, proteomics, and metabolomics) stand at the interface between chemistry and biology, and have yielded valuable outcomes from the study of a diversity of complicated diseases. Particularly, these technologies are being broadly used to dissect various biological aspects of HCC with the purpose of biomarker discovery, interrogating pathogenesis as well as for therapeutic discovery. This proof of knowledge-based critical review aims at exploring the selected applications of those defined omics technologies in the HCC niche with an emphasis on translational applications driven by advanced mass spectrometry, toward the specific clinical use for HCC patients. This approach will enable the biomedical community, through both basic research and the clinical sciences, to enhance the applicability of mass spectrometry-based omics technologies in dissecting the pathogenesis of HCC and could lead to novel therapeutic discoveries for HCC.

A public perspective on the adoption of microgeneration technologies in New Zealand: A multivariate probit approach

The growing demand for electricity in New Zealand has led to the construction of new hydro-dams or power stations that have had environmental, social and cultural effects. These effects may drive increases in electricity prices, as such prices reflect the cost of running existing power stations as well as building new ones. This study uses Canterbury and Central Otago as case studies because both regions face similar issues in building new hydro-dams and ever-increasing electricity prices that will eventually prompt households to buy power at higher prices. One way for households to respond to these price changes is to generate their own electricity through microgeneration technologies (MGT). The objective of this study is to investigate public perception and preferences regarding MGT and to analyze the factors that influence people's decision to adopt such new technologies in New Zealand. The study uses a multivariate probit approach to examine households' willingness to adopt any one MGT system or a combination of the MGT systems. Our findings provide valuable information for policy makers and marketers who wish to promote effective microgeneration technologies.

The complete genome sequence of Escherichia coli EC958: a high quality reference sequence for the globally disseminated multidrug resistant E. coli O25b:H4-ST131 clone

Escherichia coli ST131 is now recognised as a leading contributor to urinary tract and bloodstream infections in both community and clinical settings. Here we present the complete, annotated genome of E. coli EC958, which was isolated from the urine of a patient presenting with a urinary tract infection in the Northwest region of England and represents the most well characterised ST131 strain. Sequencing was carried out using the Pacific Biosciences platform, which provided sufficient depth and read-length to produce a complete genome without the need for other technologies. The discovery of spurious contigs within the assembly that correspond to site-specific inversions in the tail fibre regions of prophages demonstrates the potential for this technology to reveal dynamic evolutionary mechanisms. E. coli EC958 belongs to the major subgroup of ST131 strains that produce the CTX-M-15 extended spectrum β-lactamase, are fluoroquinolone resistant and encode the fimH30 type 1 fimbrial adhesin. This subgroup includes the Indian strain NA114 and the North American strain JJ1886. A comparison of the genomes of EC958, JJ1886 and NA114 revealed that differences in the arrangement of genomic islands, prophages and other repetitive elements in the NA114 genome are not biologically relevant and are due to misassembly. The availability of a high quality uropathogenic E. coli ST131 genome provides a reference for understanding this multidrug resistant pathogen and will facilitate novel functional, comparative and clinical studies of the E. coli ST131 clonal lineage.

Locality-sensitive hashing for protein classification

Determination of sequence similarity is a central issue in computational biology, a problem addressed primarily through BLAST, an alignment based heuristic which has underpinned much of the analysis and annotation of the genomic era. Despite their success, alignment-based approaches scale poorly with increasing data set size, and are not robust under structural sequence rearrangements. Successive waves of innovation in sequencing technologies – so-called Next Generation Sequencing (NGS) approaches – have led to an explosion in data availability, challenging existing methods and motivating novel approaches to sequence representation and similarity scoring, including adaptation of existing methods from other domains such as information retrieval. In this work, we investigate locality-sensitive hashing of sequences through binary document signatures, applying the method to a bacterial protein classification task. Here, the goal is to predict the gene family to which a given query protein belongs. Experiments carried out on a pair of small but biologically realistic datasets (the full protein repertoires of families of Chlamydia and Staphylococcus aureus genomes respectively) show that a measure of similarity obtained by locality sensitive hashing gives highly accurate results while offering a number of avenues which will lead to substantial performance improvements over BLAST..

Migrants, refugees and mobility : how useful are information communication technologies in the first phase of resettlement?

The rate at which people move and resettle around the world is unprecedented. Mobility and resettlement is now greatly assisted by the use of inexpensive internet communication technologies (ICTs) for a wide variety of functions: to communicate locally and across territories, for localised information seeking, geo – locational mapping and for forging new social connections in host countries and cities. This article is based on a qualitative study of newly arrived migrants and mobile people from non English speaking backgrounds (NESB) to the city of Brisbane, Australia and investigates how the internet is used to assist the initial period of settling into the city. As increasing amounts of essential information is placed online, the study asks how people from NESB communities manage to negotiate the types of information they require during the early stages of resettlement, given varying levels of access to ICTs, digital and language literacy. The study finds that the internet is widely used for specific location information seeking (such as accommodation and job-seeking), but this is often supplemented with other non-mediated sources of information. The study identified implications for social policy in regard to the resourcing and access of information. While findings are specific to the study location, it is feasible that the patterns of internet use for resettlement have relevance in a broader context.

Information and communication technologies transform the practice of medicine

Information and Communication Technologies are dramatically transforming Allopathic medicine. Technological developments including Tele-medicine, Electronic health records, Standards to ensure computer systems inter-operate, Data mining, Simulation, Decision Support and easy access to medical information each contribute to empowering patients in new ways and change the practice of medicine. To date, informatics has had little impact on Ayurvedic medicine. This tutorial provides an introduction to key informatics initiatives in Allopothic medicine using real examples and suggests how applications can be applied to Ayurvedic medicine.

SHM through flexible vibration sensing technologies and robust safety evaluation paradigm

This research has successfully developed a novel synthetic structural health monitoring system model that is cost-effective and flexible in sensing and data acquisition; and robust in the structural safety evaluation aspect for the purpose of long-term and frequent monitoring of large-scale civil infrastructure during their service lives. Not only did it establish a real-world structural monitoring test-bed right at the heart of QUT Gardens Point Campus but it can also facilitate reliable and prompt protection for any built infrastructure system as well as the user community involved.

Siteworks : ecologies and technologies [Abstract]

SITEWORKS is an interdisciplinary research and practice project that invites artists, scientists and scholars to respond to the Bundanon property through the lens of their specific discipline. Over four years this has led to a series of interactive projects, many utilising electronic technologies. The inaugural investigations focussed on the geomorphology of the site and palaeoenvironmental research, specifically in the area of sea level rise and climate change [1]. In subsequent years the focus has been on water and the river; land management; Indigenous cultural heritage, and food security.

Going live : building academic capacity in blended learning using web-conferencing technologies

This paper reports on a current initiative at Queensland University of Technology to provide timely, flexible and sustainable training and support to academic staff in blended learning and associated techno-pedagogies via a web-conferencing classroom and collaboration tool, Elluminate Live!. This technology was first introduced to QUT in 2008 as part of the university‘s ongoing commitment to meeting the learning needs of diverse student cohorts. The centralised Learning Design team, in collaboration with the university‘s department of eLearning Services, was given the task of providing training and support to academic staff in the effective use of the technology for teaching and learning, as part of the team‘s ongoing brief to support and enhance the provision of blended learning throughout the university. The resulting program, ―Learning Design Live‖ (LDL) is informed by Rogers‘ theory of innovation and diffusion (2003) and structured according to Wilson‘s framework for faculty development (2007). This paper discusses the program‘s design and structure, considers the program‘s impact on academic capacity in blended learning within the institution, and reflects on future directions for the program and emerging insights into blended learning and participant engagement for both staff and students.

Differential effects of tissue culture coating substrates on prostate cancer cell adherence, morphology and behavior

Weak cell-surface adhesion of cell lines to tissue culture surfaces is a common problem and presents technical limitations to the design of experiments. To overcome this problem, various surface coating protocols have been developed. However, a comparative and precise real-time measurement of their impact on cell behavior has not been conducted. The prostate cancer cell line LNCaP, derived from a patient lymph node metastasis, is a commonly used model system in prostate cancer research. However, the cells’ characteristically weak attachment to the surface of tissue culture vessels and cover slips has impeded their manipulation and analysis and use in high throughput screening. To improve the adherence of LNCaP cells to the culture surface, we compared different coating reagents (poly-L-lysine, poly-L-ornithine, collagen type IV, fibronectin, and laminin) and culturing conditions and analyzed their impact on cell proliferation, adhesion, morphology, mobility and gene expression using real-time technologies. The results showed that fibronectin, poly-L-lysine and poly-L-ornithine improved LNCaP cells adherence and provoked cell morphology alterations, such as increase of nuclear and cellular area. These coating reagents also induced a higher expression of F-actin and reduced cell mobility. In contrast, laminin and collagen type IV did not improve adherence but promoted cell aggregation and affected cell morphology. Cells cultured in the presence of laminin displayed higher mobility than control cells. All the coating conditions significantly affected cell viability; however, they did not affect the expression of androgen receptor-regulated genes. Our comparative findings provide important insight for the selection of the ideal coating reagent and culture conditions for the cancer cell lines with respect to their effect on proliferation rate, attachment, morphology, migration, transcriptional response and cellular cytoskeleton arrangement.

Tissue-engineered 3D tumor angiogenesis models : potential technologies for anti-cancer drug discovery

Angiogenesis is indispensable for solid tumor expansion, and thus it has become a major target of cancer research and anti-cancer therapies. Deciphering the arcane actions of various cell populations during tumor angiogenesis requires sophisticated research models, which could capture the dynamics and complexity of the process. There is a continuous need for improvement of existing research models, which engages interdisciplinary approaches of tissue engineering with life sciences. Tireless efforts to develop a new model to study tumor angiogenesis result in innovative solutions, which bring us one step closer to decipher the dubious nature of cancer. This review aims to overview the recent developments, current limitations and future challenges in three-dimensional tissue-engineered models for the study of tumor angiogenesis and for the purpose of elucidating novel targets aimed at anti-cancer drug discovery.

Enabling a positive first year experience in higher education through social media and mobile technologies

The first year experience for students within Higher Education institutions has become increasingly important as these institutions strive to improve student retention rates. With many universities also focusing on transforming teaching and learning in an effort to attract and retain students, there is a growing demand to understand and respond to individual student requirements, such as the need to feel a sense of belonging. The literature identifies a sense of belonging as being paramount to a students satisfaction with the institution and it is within this context that this paper reports on a three year study of how first year pre-service education students use social media and mobile technologies in their personal lives and their formal education. More specifically, the study identifies trends in the use of these technologies and the growing need for students to use digital media sharing tools to connect and engage with their peers. The paper contrasts the differences in use between these groups as it seeks to identify the role these technologies can play in their teaching and learning, as well as in promoting an overall positive first year experience.

The use of multimodal technologies to enhance reflective writing in teacher education

For preservice teachers new to the teaching profession, reflective practice can be a difficult process. Yet reflective writing, once mastered, has the capacity to support preservice teachers to make connections between teaching theory and professional practice, and to start to take control of their own professional learning journey. The reflective practice described in this chapter was scaffolded through a framework for writing, the use of annotated work samples and explicit teaching. This approach was enhanced through multimodal resources including written peer assessment, audio teacher feedback and a video recording of the class presentation. The video footage assisted the preservice teachers to reconcile the feedback that they received from multiple sources. This chapter describes and analyses the implementation of the PRT Pattern (Prompting Reflection using Technology). Results of this practice revealed that the multiple forms of feedback assisted the preservice teachers to analyse their performance in terms of their developing professional identity and practice.

Emerging water treatment technologies for decentralised systems : an overview of selected systems suited for application in towns and settlements in remote and very remote regions of Australia and vulnerable and lagging rural regions in Sri Lanka

The primary purpose of this paper is to overview a selection of advanced water treatment technology systems that are suited for application in towns and settlements in remote and very remote regions of Australia and vulnerable and lagging rural regions in Sri Lanka. This recognises that sanitation and water treatment are inextricably linked and both are needed to reduce risks to environment and population health from contaminated water sources. For both Australia and Sri Lanka only a small fraction of the settlements in rural and remote regions are connected to water treatment facilities and town water supplies. In Australia’s remote/very remote regions raw water is drawn from underground sources and rainwater capture. Most settlements in rural Sri Lanka rely on rivers, reservoirs, wells, springs or carted water. Furthermore, Sri Lanka has more than 25,000 hand pumped tube wells which saved the communities during recent droughts. Decentralised water supply systems offer the opportunity to provide safe drinking water to these remote/very remote and rural regions where centralised systems are not feasible due to socio-cultural, economic, political, technological reasons. These systems reduce health risks from contaminated water supplies. In remote areas centralized systems fail due to low population density and less affordability. Globally, a new generation of advanced water treatment technologies are positioned to make a major impact on the provision of safe potable water in remote/very remote regions in Australia and rural regions in Sri Lanka. Some of these systems were developed for higher income countries. However, with careful selection and further research they can be tailored to match local socio-economic conditions and technical capacity. As such, they can equally be used to provide decentralised water supply in communities in developed and developing countries such as Australia and Sri Lanka.