RNASeqBrowser: A genome browser for simultaneous visualization of raw strand specific RNAseq reads and UCSC genome browser custom tracks

Background Strand specific RNAseq data is now more common in RNAseq projects. Visualizing RNAseq data has become an important matter in Analysis of sequencing data. The most widely used visualization tool is the UCSC genome browser that introduced the custom track concept that enabled researchers to simultaneously visualize gene expression at a particular locus from multiple experiments. Our objective of the software tool is to provide friendly interface for visualization of RNAseq datasets. Results This paper introduces a visualization tool (RNASeqBrowser) that incorporates and extends the functionality of the UCSC genome browser. For example, RNASeqBrowser simultaneously displays read coverage, SNPs, InDels and raw read tracks with other BED and wiggle tracks -- all being dynamically built from the BAM file. Paired reads are also connected in the browser to enable easier identification of novel exon/intron borders and chimaeric transcripts. Strand specific RNAseq data is also supported by RNASeqBrowser that displays reads above (positive strand transcript) or below (negative strand transcripts) a central line. Finally, RNASeqBrowser was designed for ease of use for users with few bioinformatic skills, and incorporates the features of many genome browsers into one platform. Conclusions The features of RNASeqBrowser: (1) RNASeqBrowser integrates UCSC genome browser and NGS visualization tools such as IGV. It extends the functionality of the UCSC genome browser by adding several new types of tracks to show NGS data such as individual raw reads, SNPs and InDels. (2) RNASeqBrowser can dynamically generate RNA secondary structure. It is useful for identifying non-coding RNA such as miRNA. (3) Overlaying NGS wiggle data is helpful in displaying differential expression and is simple to implement in RNASeqBrowser. (4) NGS data accumulates a lot of raw reads. Thus, RNASeqBrowser collapses exact duplicate reads to reduce visualization space. Normal PC’s can show many windows of NGS individual raw reads without much delay. (5) Multiple popup windows of individual raw reads provide users with more viewing space. This avoids existing approaches (such as IGV) which squeeze all raw reads into one window. This will be helpful for visualizing multiple datasets simultaneously. RNASeqBrowser and its manual are freely available at http://www.australianprostatecentre.org/research/software/rnaseqbrowser webcite or http://sourceforge.net/projects/rnaseqbrowser/ webcite

Tracking the defining moments of crisis process and practice

Crisis holds the potential for profound change in organizations and industries. The past 50 years of crisis management highlight key shifts in crisis practice, creating opportunities for multiple theories and research tracks. Defining crises such as Tylenol, Exxon Valdez, and September 11 terrorist attacks have influenced or challenged the principles of best practice of crisis communication in public relations. This study traces the development of crisis process and practice by identifying shifts in crisis research and models and mapping these against key management theories and practices. The findings define three crisis domains: crisis planning, building and testing predictive models, and mapping and measuring external environmental influences. These crisis domains mirror but lag the evolution of management theory, suggesting challenges for researchers to reshape the research agenda to close the gap and lead the next stage of development in the field of crisis communication for effective organizational outcomes.

The SEA-CALIPSO volcano imaging experiment at Montserrat : plans, campaigns at sea and on land, scientific results, and lessons learned

Since 1995 the eruption of the andesitic Soufrière Hills Volcano (SHV), Montserrat, has been studied in substantial detail. As an important contribution to this effort, the Seismic Experiment with Airgunsource-Caribbean Andesitic Lava Island Precision Seismo-geodetic Observatory (SEA-CALIPSO) experiment was devised to image the arc crust underlying Montserrat, and, if possible, the magma system at SHV using tomography and reflection seismology. Field operations were carried out in October–December 2007, with deployment of 238 seismometers on land supplementing seven volcano observatory stations, and with an array of 10 ocean-bottom seismometers deployed offshore. The RRS James Cook on NERC cruise JC19 towed a tuned airgun array plus a digital 48-channel streamer on encircling and radial tracks for 77 h about Montserrat during December 2007, firing 4414 airgun shots and yielding about 47 Gb of data. The main objecctives of the experiment were achieved. Preliminary analyses of these data published in 2010 generated images of heterogeneous high-velocity bodies representing the cores of volcanoes and subjacent intrusions, and shallow areas of low velocity on the flanks of the island that reflect volcaniclastic deposits and hydrothermal alteration. The resolution of this preliminary work did not extend beyond 5 km depth. An improved three-dimensional (3D) seismic velocity model was then obtained by inversion of 181 665 first-arrival travel times from a more-complete sampling of the dataset, yielding clear images to 7.5 km depth of a low-velocity volume that was interpreted as the magma chamber which feeds the current eruption, with an estimated volume 13 km3. Coupled thermal and seismic modelling revealed properties of the partly crystallized magma. Seismic reflection analyses aimed at imaging structures under southern Montserrat had limited success, and suggest subhorizontal layering interpreted as sills at a depth of between 6 and 19 km. Seismic reflection profiles collected offshore reveal deep fans of volcaniclastic debris and fault offsets, leading to new tectonic interpretations. This chapter presents the project goals and planning concepts, describes in detail the campaigns at sea and on land, summarizes the major results, and identifies the key lessons learned.

Vibration based baseline updating method to localize crack formation and propagation in reinforced concrete members

Structural Health Monitoring (SHM) schemes are useful for proper management of the performance of structures and for preventing their catastrophic failures. Vibration based SHM schemes has gained popularity during the past two decades resulting in significant research. It is hence evitable that future SHM schemes will include robust and automated vibration based damage assessment techniques (VBDAT) to detect, localize and quantify damage. In this context, the Damage Index (DI) method which is classified as non-model or output based VBDAT, has the ability to automate the damage assessment process without using a computer or numerical model along with actual measurements. Although damage assessment using DI methods have been able to achieve reasonable success for structures made of homogeneous materials such as steel, the same success level has not been reported with respect to Reinforced Concrete (RC) structures. The complexity of flexural cracks is claimed to be the main reason to hinder the applicability of existing DI methods in RC structures. Past research also indicates that use of a constant baseline throughout the damage assessment process undermines the potential of the Modal Strain Energy based Damage Index (MSEDI). To address this situation, this paper presents a novel method that has been developed as part of a comprehensive research project carried out at Queensland University of Technology, Brisbane, Australia. This novel process, referred to as the baseline updating method, continuously updates the baseline and systematically tracks both crack formation and propagation with the ability to automate the damage assessment process using output only data. The proposed method is illustrated through examples and the results demonstrate the capability of the method to achieve the desired outcomes.

Numerical modelling and design of unlined cold-formed steel wall frames

Cold-formed steel wall frame systems using lipped or unlipped C-sections and gypsum plasterboard lining are commonly utilised in the construction of both the load bearing and non-load bearing walls in the residential, commercial and industrial buildings. However, the structural behaviour of unlined and lined stud wall frames is not well understood and adequate design rules are not available. A detailed research program was therefore undertaken to investigate the behaviour of stud wall frame systems. As the first step in this research, the problem relating to the degree of end fixity of stud was investigated. The studs are usually connected to the top and bottom tracks and the degree of end fixity provided by these tracks is not adequately addressed by the design codes. A finite element model of unlined frames was therefore developed, and validated using full scale experimental results. It was then used in a detailed parametric study to develop appropriate design rules for unlined wall frames. This study has shown that by using appropriate effective length factors, the ultimate load and failure modes of the unlined studs can be accurately predicted using the provisions of Australian or American cold-formed steel structures design codes. This paper presents the details of the finite element analyses, the results and recommended design rules for unlined wall frames.

Zeolite from alkali modified kaolin increases NH4+ retention by sandy soil : column experiments

Sandy soils have low water and nutrient retention capabilities so that zeolite soil amendments are used for high value land uses including turf and horticulture to reduce leaching losses of NH4+ fertilisers. MesoLite is a zeolitic material made by caustic treatment of kaolin at 80-95oC. It has a moderately low surface area (9-12m2/g) and very high cation exchange capacity (494 cmol(+)/kg). Laboratory column experiments showed that an addition of 0.4% MesoLite to a sandy soil greatly (90%) reduced leaching of added NH4+ compared to an unamended soil and MesoLite is 11 times more efficient in retaining NH4+ than natural zeolite. Furthermore, NH4+-MesoLite slowly releases NH4+ to soil solution and is likely to be an effective slow release fertiliser.

Increasing NH4+ retention efficiency of sandy soils by adding a modified kaolin material: Mesolite

Water and ammonium retention by sandy soils may be low and result in leaching of applied fertiliser. To increase water and nutrient retention, zeolite is sometimes applied as a soil ameliorant for high value land uses including turf and horticulture. We have used a new modified kaolin material (MesoLite) as a soil amendment to test the efficiency of NH4+ retention and compared the results with natural zeolite. MesoLite is made by caustic reaction of kaolin at temperature between 80-95°C; although it has a moderate surface area, its cation exchange capacity is very high;(SA=13m2/g,CEC=500meq/100g). A 13cm tall sand column filled with ~450g of sandy soil homogeneously mixed with 1, 2, 4, and 8g of MesoLite or natural zeolite per 1kg of soil was prepared. After saturation with local bore water, concentrated ammonium sulfate solution was injected at the base. Then, bore water was passed from bottom to top through the column at amounts up to 6 pore volumes and at a constant flow rate of 10ml/min using a peristaltic pump. Concentrations of leached NH4+ were determined using an AutoAnalyser. The concentration of NH4+ leached from the column with 0.4% MesoLite was greatly (90%) reduced relative to unamended soil. Under these conditions NH4+ retention by the soil-MesoLite mixture was 11.5 times more efficient than the equivalent soil-natural zeolite mixture. Glasshouse experiments conducted in a separate study show that NH4+ adsorbed by MesoLite is available to plants.

Detecting anomalous events at railway level crossings

Collisions between pedestrians and vehicles continue to be a major problem throughout the world. Pedestrians trying to cross roads and railway tracks without any caution are often highly susceptible to collisions with vehicles and trains. Continuous financial, human and other losses have prompted transport related organizations to come up with various solutions addressing this issue. However, the quest for new and significant improvements in this area is still ongoing. This work addresses this issue by building a general framework using computer vision techniques to automatically monitor pedestrian movements in such high-risk areas to enable better analysis of activity, and the creation of future alerting strategies. As a result of rapid development in the electronics and semi-conductor industry there is extensive deployment of CCTV cameras in public places to capture video footage. This footage can then be used to analyse crowd activities in those particular places. This work seeks to identify the abnormal behaviour of individuals in video footage. In this work we propose using a Semi-2D Hidden Markov Model (HMM), Full-2D HMM and Spatial HMM to model the normal activities of people. The outliers of the model (i.e. those observations with insufficient likelihood) are identified as abnormal activities. Location features, flow features and optical flow textures are used as the features for the model. The proposed approaches are evaluated using the publicly available UCSD datasets, and we demonstrate improved performance using a Semi-2D Hidden Markov Model compared to other state of the art methods. Further we illustrate how our proposed methods can be applied to detect anomalous events at rail level crossings.

State-of-the-art : track degradation at bridge transitions

Transition zones between bridge decks and rail tracks suffer early failure due to poor interaction between rail vehicles and sudden changes of stiffness. This has been an ongoing problem to rail industry and yet still no systematic studies appear to have been taken to maintain a gradually smoothening transmission of forces between the bridge and its approach. Differential settlement between the bridge deck and rail track in the transition zone is the fundamental issue, which negatively impacts the rail industry by causing passenger discomfort, early damage to infrastructure and vehicle components, speed reduction, and frequent maintenance cycles. Identification of mechanism of the track degradation and factors affecting is imperative to design any mitigation method for reducing track degradation rate at the bridge transition zone. Unfortunately this issue is still not well understood, after conducting a numbers of reviews to evaluate the key causes, and introducing a wide range of mitigation techniques. In this study, a comprehensive analysis of the available literature has been carried out to develop either a novel design framework or a mitigation technique for the bridge transition zone. This paper addresses three critical questions in relation to the track degradation at transition zone: (1) what are the causes of bridge transition track degradation?; (2) what are the available mitigation techniques in reducing the track degradation rate?; (3) what are the factors affecting on poor performance of the existing mitigation techniques?. It is found that the absence of soil-water response, dynamic loading response, and behaviour of geotechnical characteristics under long-term conditions in existing track transition design frameworks critically influence on the failures of existing mitigation techniques. This paper also evaluates some of the existing design frameworks to identify how each design framework addresses the track degradation at the bridge transition zone.

Twelve : the best Of IMP's 100 Songs Project 2011

12 Original recordings curated by leading national industry figures. It’s a 12 track album full of remixed, rerecorded and rejigged tracks from the project that were shortlisted by our friends at MGM Distribution, Music Sales, and EMI Music Australia. The TWELVE album is already receiving critical acclaim from Australia's music industry.

Eleven : best of 100 Songs Project 2012

Eleven original recordings curated by leading industry figures. This is a compilation album from QUT's 2012 100 Songs project. It's called Eleven: Best of 100 Songs Project 2012 and was released in May 2013. It’s an 11 track album with a bonus track, full of remixed, rerecorded and rejigged tracks from the project that were shortlisted by our friends at MGM Distribution, Mushroom Music, Island Records and Music Sales Australia. The Eleven album is already receiving critical acclaim from Australia's music industry.

The Situated Cases

In this chapter, we meet the eight children whose documented lives are the heart of this book. The children are spread across 6 continents, so we have some textual traveling to do. We find each child in a local school. There they venture into literacy along official paths negotiated with their teachers and, also, along unofficial paths tied to their desire for peer companionship and social belonging (Corsaro, 2011; Nelson, 2007). We are most interested in their literate productions—their composing, be it with stick and dirt, pencil, crayons, and paper, tablet computer, or chalk and slate. Each child is a unique story, and each story is told by an author with particular interests in the goings-on in school, that is, with a particular angle of vision. All the authors, though, take us into a child’s educational circumstance; they give us a sense of the school’s physical site and its official curricular guidelines. Most importantly, they collectively allow us a global view of children as symbol users and social participants in the official and the unofficial worlds of school. No matter where young children go to school, they are expected to learn to “write” (although writing, as the cases illustrate, does not always mean “composing”)...

Dirt Circus League : power and belonging in posthuman young adult fiction

This creative practice-led thesis consists of a creative work titled Dirt Circus League, which tells of a female teenaged medical intuitive who follows an enigmatic cult leader to his isolated home in Cape York, and an exegesis. The exegesis explores the representations and complexities of neuroscience and posthumanism in contemporary young adult fiction. The exegesis also discusses how the mechanics of storytelling changed the novel's original focus from one of neuroscience in relation to impacts and effects on teenage brains to the broader social concerns of posthumanism.

Apples, oranges and fruit salad : a Delphi study of the IMC educational mix

Once, we thought that comparing advertising and public relations was a bit like comparing apples and oranges. But with integration the new flavour, many academics are trying to cut and combine and create a fruit salad that will entice their customers and satisfy their stakeholders. While this has produced some culinary triumphs, it has also produced heartburn in equal quantity. This paper seeks the perfect recipe for integrated marketing communication (IMC) education by asking a Delphi panel of IMC champions questions relating to the place of IMC in the university setting; the teaching, research and curriculum development issues and the future for IMC education. The panel draws a chaotic picture of IMC education and identifies some important obstacles to curriculum development. It also predicts a number of key challenges for the future, including turf wars; the lack of faculty experience and enthusiasm to embrace IMC and the desperate need to grow the IMC brand. But perhaps the greatest challenge is how to create a generalist education in a culture of pecialisation that exists both in the university and in the workplace.

Revisiting the conceptualization and measurement of service quality

Since the 1980s, industries and researchers have sought to better understand the quality of services due to the rise in their importance (Brogowicz, Delene and Lyth 1990). More recent developments with online services, coupled with growing recognition of service quality (SQ) as a key contributor to national economies and as an increasingly important competitive differentiator, amplify the need to revisit our understanding of SQ and its measurement. Although ‘SQ’ can be broadly defined as “a global overarching judgment or attitude relating to the overall excellence or superiority of a service” (Parasuraman, Berry and Zeithaml 1988), the term has many interpretations. There has been considerable progress on how to measure SQ perceptions, but little consensus has been achieved on what should be measured. There is agreement that SQ is multi-dimensional, but little agreement as to the nature or content of these dimensions (Brady and Cronin 2001). For example, within the banking sector, there exist multiple SQ models, each consisting of varying dimensions. The existence of multiple conceptions and the lack of a unifying theory bring the credibility of existing conceptions into question, and beg the question of whether it is possible at some higher level to define SQ broadly such that it spans all service types and industries. This research aims to explore the viability of a universal conception of SQ, primarily through a careful re-visitation of the services and SQ literature. The study analyses the strengths and weaknesses of the highly regarded and widely used global SQ model (SERVQUAL) which reflects a single-level approach to SQ measurement. The SERVQUAL model states that customers evaluate SQ (of each service encounter) based on five dimensions namely reliability, assurance, tangibles, empathy and responsibility. SERVQUAL, however, failed to address what needs to be reliable, assured, tangible, empathetic and responsible. This research also addresses a more recent global SQ model from Brady and Cronin (2001); the B&C (2001) model, that has potential to be the successor of SERVQUAL in that it encompasses other global SQ models and addresses the ‘what’ questions that SERVQUAL didn’t. The B&C (2001) model conceives SQ as being multidimensional and multi-level; this hierarchical approach to SQ measurement better reflecting human perceptions. In-line with the initial intention of SERVQUAL, which was developed to be generalizable across industries and service types, this research aims to develop a conceptual understanding of SQ, via literature and reflection, that encompasses the content/nature of factors related to SQ; and addresses the benefits and weaknesses of various SQ measurement approaches (i.e. disconfirmation versus perceptions-only). Such understanding of SQ seeks to transcend industries and service types with the intention of extending our knowledge of SQ and assisting practitioners in understanding and evaluating SQ. The candidate’s research has been conducted within, and seeks to contribute to, the ‘IS-Impact’ research track of the IT Professional Services (ITPS) Research Program at QUT. The vision of the track is “to develop the most widely employed model for benchmarking Information Systems in organizations for the joint benefit of research and practice.” The ‘IS-Impact’ research track has developed an Information Systems (IS) success measurement model, the IS-Impact Model (Gable, Sedera and Chan 2008), which seeks to fulfill the track’s vision. Results of this study will help future researchers in the ‘IS-Impact’ research track address questions such as: • Is SQ an antecedent or consequence of the IS-Impact model or both? • Has SQ already been addressed by existing measures of the IS-Impact model? • Is SQ a separate, new dimension of the IS-Impact model? • Is SQ an alternative conception of the IS? Results from the candidate’s research suggest that SQ dimensions can be classified at a higher level which is encompassed by the B&C (2001) model’s 3 primary dimensions (interaction, physical environment and outcome). The candidate also notes that it might be viable to re-word the ‘physical environment quality’ primary dimension to ‘environment quality’ so as to better encompass both physical and virtual scenarios (E.g: web sites). The candidate does not rule out the global feasibility of the B&C (2001) model’s nine sub-dimensions, however, acknowledges that more work has to be done to better define the sub-dimensions. The candidate observes that the ‘expertise’, ‘design’ and ‘valence’ sub-dimensions are supportive representations of the ‘interaction’, physical environment’ and ‘outcome’ primary dimensions respectively. The latter statement suggests that customers evaluate each primary dimension (or each higher level of SQ classification) namely ‘interaction’, physical environment’ and ‘outcome’ based on the ‘expertise’, ‘design’ and ‘valence’ sub-dimensions respectively. The ability to classify SQ dimensions at a higher level coupled with support for the measures that make up this higher level, leads the candidate to propose the B&C (2001) model as a unifying theory that acts as a starting point to measuring SQ and the SQ of IS. The candidate also notes, in parallel with the continuing validation and generalization of the IS-Impact model, that there is value in alternatively conceptualizing the IS as a ‘service’ and ultimately triangulating measures of IS SQ with the IS-Impact model. These further efforts are beyond the scope of the candidate’s study. Results from the candidate’s research also suggest that both the disconfirmation and perceptions-only approaches have their merits and the choice of approach would depend on the objective(s) of the study. Should the objective(s) be an overall evaluation of SQ, the perceptions-only approached is more appropriate as this approach is more straightforward and reduces administrative overheads in the process. However, should the objective(s) be to identify SQ gaps (shortfalls), the (measured) disconfirmation approach is more appropriate as this approach has the ability to identify areas that need improvement.