miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data

miRDeep and its varieties are widely used to quantify known and novel micro RNA (miRNA) from small RNA sequencing (RNAseq). This article describes miRDeep*, our integrated miRNA identification tool, which is modeled off miRDeep, but the precision of detecting novel miRNAs is improved by introducing new strategies to identify precursor miRNAs. miRDeep* has a user-friendly graphic interface and accepts raw data in FastQ and Sequence Alignment Map (SAM) or the binary equivalent (BAM) format. Known and novel miRNA expression levels, as measured by the number of reads, are displayed in an interface, which shows each RNAseq read relative to the pre-miRNA hairpin. The secondary pre-miRNA structure and read locations for each predicted miRNA are shown and kept in a separate figure file. Moreover, the target genes of known and novel miRNAs are predicted using the TargetScan algorithm, and the targets are ranked according to the confidence score. miRDeep* is an integrated standalone application where sequence alignment, pre-miRNA secondary structure calculation and graphical display are purely Java coded. This application tool can be executed using a normal personal computer with 1.5 GB of memory. Further, we show that miRDeep* outperformed existing miRNA prediction tools using our LNCaP and other small RNAseq datasets. miRDeep* is freely available online at http://www.australianprostatecentre.org/research/software/mirdeep-star

Fundamentals of business process management

Encompasses the whole BPM lifecycle, including process identification, modelling, analysis, redesign, automation and monitoring Class-tested textbook complemented with additional teaching material on the accompanying website Covers both relevant conceptual background, industrial standards and actionable skills Business Process Management (BPM) is the art and science of how work should be performed in an organization in order to ensure consistent outputs and to take advantage of improvement opportunities, e.g. reducing costs, execution times or error rates. Importantly, BPM is not about improving the way individual activities are performed, but rather about managing entire chains of events, activities and decisions that ultimately produce added value for an organization and its customers. This textbook encompasses the entire BPM lifecycle, from process identification to process monitoring, covering along the way process modelling, analysis, redesign and automation. Concepts, methods and tools from business management, computer science and industrial engineering are blended into one comprehensive and inter-disciplinary approach. The presentation is illustrated using the BPMN industry standard defined by the Object Management Group and widely endorsed by practitioners and vendors worldwide. In addition to explaining the relevant conceptual background, the book provides dozens of examples, more than 100 hands-on exercises – many with solutions – as well as numerous suggestions for further reading. The textbook is the result of many years of combined teaching experience of the authors, both at the undergraduate and graduate levels as well as in the context of professional training. Students and professionals from both business management and computer science will benefit from the step-by-step style of the textbook and its focus on fundamental concepts and proven methods. Lecturers will appreciate the class-tested format and the additional teaching material available on the accompanying website fundamentals-of-bpm.org.

Enhancing security of linux-based android devices

Our daily lives become more and more dependent upon smartphones due to their increased capabilities. Smartphones are used in various ways from payment systems to assisting the lives of elderly or disabled people. Security threats for these devices become increasingly dangerous since there is still a lack of proper security tools for protection. Android emerges as an open smartphone platform which allows modification even on operating system level. Therefore, third-party developers have the opportunity to develop kernel-based low-level security tools which is not normal for smartphone platforms. Android quickly gained its popularity among smartphone developers and even beyond since it bases on Java on top of "open" Linux in comparison to former proprietary platforms which have very restrictive SDKs and corresponding APIs. Symbian OS for example, holding the greatest market share among all smartphone OSs, was closing critical APIs to common developers and introduced application certification. This was done since this OS was the main target for smartphone malwares in the past. In fact, more than 290 malwares designed for Symbian OS appeared from July 2004 to July 2008. Android, in turn, promises to be completely open source. Together with the Linux-based smartphone OS OpenMoko, open smartphone platforms may attract malware writers for creating malicious applications endangering the critical smartphone applications and owners� privacy. In this work, we present our current results in analyzing the security of Android smartphones with a focus on its Linux side. Our results are not limited to Android, they are also applicable to Linux-based smartphones such as OpenMoko Neo FreeRunner. Our contribution in this work is three-fold. First, we analyze android framework and the Linux-kernel to check security functionalities. We survey wellaccepted security mechanisms and tools which can increase device security. We provide descriptions on how to adopt these security tools on Android kernel, and provide their overhead analysis in terms of resource usage. As open smartphones are released and may increase their market share similar to Symbian, they may attract attention of malware writers. Therefore, our second contribution focuses on malware detection techniques at the kernel level. We test applicability of existing signature and intrusion detection methods in Android environment. We focus on monitoring events on the kernel; that is, identifying critical kernel, log file, file system and network activity events, and devising efficient mechanisms to monitor them in a resource limited environment. Our third contribution involves initial results of our malware detection mechanism basing on static function call analysis. We identified approximately 105 Executable and Linking Format (ELF) executables installed to the Linux side of Android. We perform a statistical analysis on the function calls used by these applications. The results of the analysis can be compared to newly installed applications for detecting significant differences. Additionally, certain function calls indicate malicious activity. Therefore, we present a simple decision tree for deciding the suspiciousness of the corresponding application. Our results present a first step towards detecting malicious applications on Android-based devices.

A variable step-size FxLMS algorithm for feedforward active noise control systems based on a new online secondary path modelling technique

Several approaches have been introduced in literature for active noise control (ANC) systems. Since FxLMS algorithm appears to be the best choice as a controller filter, researchers tend to improve performance of ANC systems by enhancing and modifying this algorithm. This paper proposes a new version of FxLMS algorithm. In many ANC applications an online secondary path modelling method using a white noise as a training signal is required to ensure convergence of the system. This paper also proposes a new approach for online secondary path modelling in feedfoward ANC systems. The proposed algorithm stops injection of the white noise at the optimum point and reactivate the injection during the operation, if needed, to maintain performance of the system. Benefiting new version of FxLMS algorithm and not continually injection of white noise makes the system more desirable and improves the noise attenuation performance. Comparative simulation results indicate effectiveness of the proposed approach.

First principle study of hydrogenation of MgB2 : an important step toward reversible hydrogen storage in the coupled LiBH4/MgH2 system

Recent experiments [F. E. Pinkerton, M. S. Meyer, G. P. Meisner, M. P. Balogh, and J. J. Vajo, J. Phys. Chem. C 111, 12881 (2007) and J. J. Vajo and G. L. Olson, Scripta Mater. 56, 829 (2007)] demonstrated that the recycling of hydrogen in the coupled LiBH4/MgH2 system is fully reversible. The rehydrogenation of MgB2 is an important step toward the reversibility. By using ab initio density functional theory calculations, we found that the activation barrier for the dissociation of H2 are 0.49 and 0.58 eV for the B and Mg-terminated MgB2(0001) surface, respectively. This implies that the dissociation kinetics of H2 on a MgB2 (0001) surface should be greatly improved compared to that in pure Mg materials. Additionally, the diffusion of dissociated H atom on the Mg-terminated MgB2(0001) surface is almost barrier-less. Our results shed light on the experimentally-observed reversibility and improved kinetics for the coupled LiBH4/MgH2 system.

Young men utilise limited neuromuscular prepartion to regulate post-impact knee mechanics during step landing

Purpose The neuromuscular mechanisms determining the mechanical behaviour of the knee during landing impact remain poorly understood. It was hypothesised that neuromuscular preparation is subject-specific and ranges along a continuum from passive to active. Methods A group of healthy men (N = 12) stepped-down from a knee-high platform for 60 consecutive trials. Surface EMG of the quadriceps and hamstrings was used to determine pre-impact onset timing, activation amplitude and cocontraction for each trial. Partial least squares regression was used to associate pre-impact preparation with post-impact knee stiffness and coordination. Results The group analysis revealed few significant changes in pre-impact preparation across trial blocks. Single-subject analyses revealed changes in muscle activity that varied in size and direction between individuals. Further, the association between pre-impact preparation and post-impact knee mechanics was subject-specific and ranged along a continuum of strategies. Conclusion The findings suggest that neuromuscular preparation during step landing is subject-specific and its association to post-impact knee mechanics occurs along a continuum, ranging from passive to active control strategies. Further work should examine the implications of these strategies on the distribution of knee forces in-vivo.

Accountable-eHealth systems : the next step forward for privacy

eHealth systems promise enviable benefits and capabilities for healthcare delivery. However, the technologies that make these capabilities possible introduce undesirable drawbacks such as information security related threats, which need to be appropriately addressed. Lurking in these threats are information privacy concerns. Addressing them has proven to be difficult because they often conflict with information access requirements of healthcare providers. Therefore, it is important to achieve an appropriate balance between these requirements. We contend that information accountability (IA) can achieve this balance. In this paper, we introduce accountable-eHealth (AeH) systems, which are eHealth systems that utilise IA as a measure of information privacy. We discuss how AeH system protocols can successfully achieve the aforementioned balance of requirements. As a means of implementation feasibility, we compare characteristics of AeH systems with Australia’s Personally Controlled Electronic Health Record (PCEHR) sys-tem and identify similarities and highlight the differences and the impact those differences would have to the eHealth domain.

Monitoring and benchmarking population diet quality globally : a step-wise approach

INFORMAS (International Network for Food and Obesity/non-communicable diseases Research, Monitoring and Action Support) aims to monitor and benchmark the healthiness of food environments globally. In order to assess the impact of food environments on population diets, it is necessary to monitor population diet quality between countries and over time. This paper reviews existing data sources suitable for monitoring population diet quality, and assesses their strengths and limitations. A step-wise framework is then proposed for monitoring population diet quality. Food balance sheets (FBaS), household budget and expenditure surveys (HBES) and food intake surveys are all suitable methods for assessing population diet quality. In the proposed ‘minimal’ approach, national trends of food and energy availability can be explored using FBaS. In the ‘expanded’ and ‘optimal’ approaches, the dietary share of ultra-processed products is measured as an indicator of energy-dense, nutrient-poor diets using HBES and food intake surveys, respectively. In addition, it is proposed that pre-defined diet quality indices are used to score diets, and some of those have been designed for application within all three monitoring approaches. However, in order to enhance the value of global efforts to monitor diet quality, data collection methods and diet quality indicators need further development work.

Exchanging data between Digital Human Modelling systems : a review of data formats

Digital human modeling (DHM) systems underwent significant development within the last years. They achieved constantly growing importance in the field of ergonomic workplace design, product development, product usability, ergonomic research, ergonomic education, audiovisual marketing and the entertainment industry. They help to design ergonomic products as well as healthy and safe socio-technical work systems. In the domain of scientific DHM systems, no industry specific standard interfaces are defined which could facilitate the exchange of 3D solid body data, anthropometric data or motion data. The focus of this article is to provide an overview of requirements for a reliable data exchange between different DHM systems in order to identify suitable file formats. Examples from the literature are discussed in detail. Methods: As a first step a literature review is conducted on existing studies and file formats for exchanging data between different DHM systems. The found file formats can be structured into different categories: static 3D solid body data exchange, anthropometric data exchange, motion data exchange and comprehensive data exchange. Each file format is discussed and advantages as well as disadvantages for the DHM context are pointed out. Case studies are furthermore presented, which show first approaches to exchange data between DHM systems. Lessons learnt are shortly summarized. Results: A selection of suitable file formats for data exchange between DHM systems is determined from the literature review.

Intercontinental haptic teleoperation of a flying vehicle : a step towards real-time applications

This paper describes the theory and practice for a stable haptic teleoperation of a flying vehicle. It extends passivity-based control framework for haptic teleoperation of aerial vehicles in the longest intercontinental setting that presents great challenges. The practicality of the control architecture has been shown in maneuvering and obstacle-avoidance tasks over the internet with the presence of significant time-varying delays and packet losses. Experimental results are presented for teleoperation of a slave quadrotor in Australia from a master station in the Netherlands. The results show that the remote operator is able to safely maneuver the flying vehicle through a structure using haptic feedback of the state of the slave and the perceived obstacles.

Are we there yet? A step closer to theorizing information systems success

The need for native Information Systems (IS) theories has been discussed by several prominent scholars. Contributing to their conjectural discussion, this research moves towards theorizing IS success as a native theory for the discipline. Despite being one of the most cited scholarly works to-date, IS success of DeLone and McLean (1992) has been criticized by some for lacking focus on the theoretical approach. Following theory development frameworks, this study improves the theoretical standing of IS success by minimizing interaction and inconsistency. The empirical investigation of theorizing IS success includes 1396 respondents, gathered through six surveys and a case study. The respondents represent 70 organisations, multiple Information Systems, and both private and public sector organizations.

Sensor Data Integrity : Multi-Sensor Perception for Unmanned Ground Vehicles

This document describes large, accurately calibrated and time-synchronised datasets, gathered in controlled environmental conditions, using an unmanned ground vehicle equipped with a wide variety of sensors. These sensors include: multiple laser scanners, a millimetre wave radar scanner, a colour camera and an infra-red camera. Full details of the sensors are given, as well as the calibration parameters needed to locate them with respect to each other and to the platform. This report also specifies the format and content of the data, and the conditions in which the data have been gathered. The data collection was made in two different situations of the vehicle: static and dynamic. The static tests consisted of sensing a fixed ’reference’ terrain, containing simple known objects, from a motionless vehicle. For the dynamic tests, data were acquired from a moving vehicle in various environments, mainly rural, including an open area, a semi-urban zone and a natural area with different types of vegetation. For both categories, data have been gathered in controlled environmental conditions, which included the presence of dust, smoke and rain. Most of the environments involved were static, except for a few specific datasets which involve the presence of a walking pedestrian. Finally, this document presents illustrations of the effects of adverse environmental conditions on sensor data, as a first step towards reliability and integrity in autonomous perceptual systems.

Structural characterization of glycerophospholipids by combinations of ozone- and collision-induced dissociation mass spectrometry: The next step towards "top-down" lipidomics

The complete structural elucidation of complex lipids, including glycerophospholipids, using only mass spectrometry represents a major challenge to contemporary analytical technologies. Here, we demonstrate that product ions arising from the collision-induced dissociation (CID) of the [M + Na] + adduct ions of phospholipids can be isolated and subjected to subsequent gas-phase ozonolysis-known as ozone-induced dissociation (OzID)-in a linear ion-trap mass spectrometer. The resulting CID/OzID experiment yields abundant product ions that are characteristic of the acyl substitution on the glycerol backbone (i.e., sn-position). This approach is shown to differentiate sn-positional isomers, such as the regioisomeric phosphatidylcholine pair of PC 16:0/18:1 and PC 18:1/16:0. Importantly, CID/OzID provides a sensitive diagnostic for the existence of an isomeric mixture in a given sample. This is of very high value for the analysis of tissue extracts since CID/OzID analyses can reveal changes in the relative abundance of isomeric constituents even within different tissues from the same animal. Finally, we demonstrate the ability to assign carbon-carbon double bond positions to individual acyl chains at specific backbone positions by adding subsequent CID and/or OzID steps to the workflow and that this can be achieved in a single step using a hybrid triple quadrupole-linear ion trap mass spectrometer. This unique approach represents the most complete and specific structural analysis of lipids by mass spectrometry demonstrated to date and is a significant step towards comprehensive top-down lipidomics. This journal is © The Royal Society of Chemistry 2014. Grant Number ARC/DP0986628, ARC/FT110100249, ARC/LP110200648

Multimedia : a necessary step in the evolution of research funding applications

Multimedia communication capabilities are rapidly expanding, and visual information is easily shared electronically, yet funding bodies still rely on paper grant proposal submissions. Incorporating modern technologies will streamline the granting process by increasing the fidelity of grant communication, improving the efficiency of review, and reducing the cost of the process.