A stereo-image analysis JAVA software with links to executable and source code

Scientists planning to use underwater stereoscopic image technologies are often faced with numerous problems during the methodological implementations: commercial equipment is too expensive; the setup or calibration is too complex; or the imaging processing (i.e. measuring objects in the stereo-images) is too complicated to be performed without a time-consuming phase of training and evaluation. The present paper addresses some of these problems and describes a workflow for stereoscopic measurements for marine biologists. It also provides instructions on how to assemble an underwater stereo-photographic system with two digital consumer cameras and gives step-by-step guidelines for setting up the hardware. The second part details a software procedure to correct stereo-image pairs for lens distortions, which is especially important when using cameras with non-calibrated optical units. The final part presents a guide to the process of measuring the lengths (or distances) of objects in stereoscopic image pairs. To reveal the applicability and the restrictions of the described systems and to test the effects of different types of camera (a compact camera and an SLR type), experiments were performed to determine the precision and accuracy of two generic stereo-imaging units: a diver-operated system based on two Olympus Mju 1030SW compact cameras and a cable-connected observatory system based on two Canon 1100D SLR cameras. In the simplest setup without any correction for lens distortion, the low-budget Olympus Mju 1030SW system achieved mean accuracy errors (percentage deviation of a measurement from the object's real size) between 10.2 and -7.6% (overall mean value: -0.6%), depending on the size, orientation and distance of the measured object from the camera. With the single lens reflex (SLR) system, very similar values between 10.1% and -3.4% (overall mean value: -1.2%) were observed. Correction of the lens distortion significantly improved the mean accuracy errors of either system. Even more, system precision (spread of the accuracy) improved significantly in both systems. Neither the use of a wide-angle converter nor multiple reassembly of the system had a significant negative effect on the results. The study shows that underwater stereophotography, independent of the system, has a high potential for robust and non-destructive in situ sampling and can be used without prior specialist training.

Sustainable assessment for large science classes : non-multiple choice, randomised assignments through a Learning Management System

This paper reports on the development of a tool that generates randomised, non-multiple choice assessment within the BlackBoard Learning Management System interface. An accepted weakness of multiple-choice assessment is that it cannot elicit learning outcomes from upper levels of Biggs’ SOLO taxonomy. However, written assessment items require extensive resources for marking, and are susceptible to copying as well as marking inconsistencies for large classes. This project developed an assessment tool which is valid, reliable and sustainable and that addresses the issues identified above. The tool provides each student with an assignment assessing the same learning outcomes, but containing different questions, with responses in the form of words or numbers. Practice questions are available, enabling students to obtain feedback on their approach before submitting their assignment. Thus, the tool incorporates automatic marking (essential for large classes), randomised tasks to each student (reducing copying), the capacity to give credit for working (feedback on the application of theory), and the capacity to target higher order learning outcomes by requiring students to derive their answers rather than choosing them. Results and feedback from students are presented, along with technical implementation details.

Implementing an enhanced repository statistics system for QUT ePrints

Queensland University of Technology (QUT) was one of the first universities in Australia to establish an institutional repository. Launched in November 2003, the repository (QUT ePrints) uses the EPrints open source repository software (from Southampton) and has enjoyed the benefit of an institutional deposit mandate since January 2004. Currently (April 2012), the repository holds over 36,000 records, including 17,909 open access publications with another 2,434 publications embargoed but with mediated access enabled via the ‘Request a copy’ button which is a feature of the EPrints software. At QUT, the repository is managed by the library.QUT ePrints (http://eprints.qut.edu.au) The repository is embedded into a number of other systems at QUT including the staff profile system and the University’s research information system. It has also been integrated into a number of critical processes related to Government reporting and research assessment. Internally, senior research administrators often look to the repository for information to assist with decision-making and planning. While some statistics could be drawn from the advanced search feature and the existing download statistics feature, they were rarely at the level of granularity or aggregation required. Getting the information from the ‘back end’ of the repository was very time-consuming for the Library staff. In 2011, the Library funded a project to enhance the range of statistics which would be available from the public interface of QUT ePrints. The repository team conducted a series of focus groups and individual interviews to identify and prioritise functionality requirements for a new statistics ‘dashboard’. The participants included a mix research administrators, early career researchers and senior researchers. The repository team identified a number of business criteria (eg extensible, support available, skills required etc) and then gave each a weighting. After considering all the known options available, five software packages (IRStats, ePrintsStats, AWStats, BIRT and Google Urchin/Analytics) were thoroughly evaluated against a list of 69 criteria to determine which would be most suitable. The evaluation revealed that IRStats was the best fit for our requirements. It was deemed capable of meeting 21 out of the 31 high priority criteria. Consequently, IRStats was implemented as the basis for QUT ePrints’ new statistics dashboards which were launched in Open Access Week, October 2011. Statistics dashboards are now available at four levels; whole-of-repository level, organisational unit level, individual author level and individual item level. The data available includes, cumulative total deposits, time series deposits, deposits by item type, % fulltexts, % open access, cumulative downloads, time series downloads, downloads by item type, author ranking, paper ranking (by downloads), downloader geographic location, domains, internal v external downloads, citation data (from Scopus and Web of Science), most popular search terms, non-search referring websites. The data is displayed in charts, maps and table format. The new statistics dashboards are a great success. Feedback received from staff and students has been very positive. Individual researchers have said that they have found the information to be very useful when compiling a track record. It is now very easy for senior administrators (including the Deputy Vice Chancellor-Research) to compare the full-text deposit rates (i.e. mandate compliance rates) across organisational units. This has led to increased ‘encouragement’ from Heads of School and Deans in relation to the provision of full-text versions.

Resource allocation in multiuser cooperative OFDM system using forced cost based decisions

A sub optimal resource allocation algorithm for Orthogonal Frequency Division Multiplexing (OFDM) based cooperative scheme is proposed. The system consists of multiple relays. Subcarrier space is divided into blocks and relays participating in cooperation are allocated specific blocks to be used with a user. To ensure unique subcarrier assignment system is constrained such that same block cannot be used by more than one user. Users are given fair block assignments while no restriction for maximum number of blocks a relay can employ is given. Forced cost based decisions [1] are used for block allocation. Simulation results show that this scheme outperforms a non cooperating scheme with sequential allocation with respect to power usage.

Strategies for gaining and maintaining academic support for the institutional open access repository

The impact of research can be measured by use or citation count. The more widely available that research outputs are; the more likely they are to be used, and the higher the impact. Making the author-manuscript version of research outputs freely available via the institutional repository greatly increases the availability of research outputs and can increase the impact. QUT ePrints, the open access institutional repository of research outputs at Queensland University of Technology (QUT), Australia, was established in 2003 and is managed by the QUT Library. The repository now contains over 39,000 records. More than 21,000 of these records have full-text copies attached as result of continuous effort to maintain momentum and encourage academic engagement. The full-text deposit rate has continued to increase over time and, in 2012 (August, at the time of writing), 88% of the records for works published in 2012 provide access to a full-text copy. Achieving success has required a long term approach to collaboration, open access advocacy, repository promotion, support for the deposit process, and ongoing system development. This paper discusses the various approaches adopted by QUT Library, in collaboration with other areas of the University, to achieve success. Approaches include mainstreaming the repository via having it report to the University Research and Innovation Committee; regular provision of deposit rate data to faculties; championing key academic supporters; and holding promotional competitions and events such as during Open Access Week. Support and training is provided via regular deposit workshops with academics and faculty research support groups and via the provision of online self-help information. Recent system developments have included the integration of citation data (from Scopus and Web of Science) and the development of a statistical reporting system which incentivise engagement.

How much is that data in the window? Advertising your research data with QUT Library

Queensland University of Technology (QUT) Library offers a range of resources and services to researchers as part of their research support portfolio. This poster will present key features of two of the data management services offered by research support staff at QUT Library. The first service is QUT Research Data Finder (RDF), a product of the Australian National Data Service (ANDS) funded Metadata Stores project. RDF is a data registry (metadata repository) that aims to publicise datasets that are research outputs arising from completed QUT research projects. The second is a software and code registry, which is currently under development with the sole purpose of improving discovery of source code and software as QUT research outputs. RESEARCH DATA FINDER As an integrated metadata repository, Research Data Finder aligns with institutional sources of truth, such as QUT’s research administration system, ResearchMaster, as well as QUT’s Academic Profiles system to provide high quality data descriptions that increase awareness of, and access to, shareable research data. The repository and its workflows are designed to foster better data management practices, enhance opportunities for collaboration and research, promote cross-disciplinary research and maximise the impact of existing research data sets. SOFTWARE AND CODE REGISTRY The QUT Library software and code registry project stems from concerns amongst researchers with regards to development activities, storage, accessibility, discoverability and impact, sharing, copyright and IP ownership of software and code. As a result, the Library is developing a registry for code and software research outputs, which will use existing Research Data Finder architecture. The underpinning software for both registries is VIVO, open source software developed by Cornell University. The registry will use the Research Data Finder service instance of VIVO and will include a searchable interface, links to code/software locations and metadata feeds to Research Data Australia. Key benefits of the project include:improving the discoverability and reuse of QUT researchers’ code and software amongst QUT and the QUT research community; increasing the profile of QUT research outputs on a national level by providing a metadata feed to Research Data Australia, and; improving the metrics for access and reuse of code and software in the repository.

Intrusion detection in distributed systems, an approach based on taint marking

This paper presents a new framework for distributed intrusion detection based on taint marking. Our system tracks information flows between applications of multiple hosts gathered in groups (i.e., sets of hosts sharing the same distributed information flow policy) by attaching taint labels to system objects such as files, sockets, Inter Process Communication (IPC) abstractions, and memory mappings. Labels are carried over the network by tainting network packets. A distributed information flow policy is defined for each group at the host level by labeling information and defining how users and applications can legally access, alter or transfer information towards other trusted or untrusted hosts. As opposed to existing approaches, where information is most often represented by two security levels (low/high, public/private, etc.), our model identifies each piece of information within a distributed system, and defines their legal interaction in a fine-grained manner. Hosts store and exchange security labels in a peer to peer fashion, and there is no central monitor. Our IDS is implemented in the Linux kernel as a Linux Security Module (LSM) and runs standard software on commodity hardware with no required modification. The only trusted code is our modified operating system kernel. We finally present a scenario of intrusion in a web service running on multiple hosts, and show how our distributed IDS is able to report security violations at each host level.

Design, implementation and multisite evaluation of a system suitability protocol for the quantitative assessment of instrument performance in liquid chromatography-multiple reaction monitoring-MS (LC-MRM-MS)

Multiple reaction monitoring (MRM) mass spectrometry coupled with stable isotope dilution (SID) and liquid chromatography (LC) is increasingly used in biological and clinical studies for precise and reproducible quantification of peptides and proteins in complex sample matrices. Robust LC-SID-MRM-MS-based assays that can be replicated across laboratories and ultimately in clinical laboratory settings require standardized protocols to demonstrate that the analysis platforms are performing adequately. We developed a system suitability protocol (SSP), which employs a predigested mixture of six proteins, to facilitate performance evaluation of LC-SID-MRM-MS instrument platforms, configured with nanoflow-LC systems interfaced to triple quadrupole mass spectrometers. The SSP was designed for use with low multiplex analyses as well as high multiplex approaches when software-driven scheduling of data acquisition is required. Performance was assessed by monitoring of a range of chromatographic and mass spectrometric metrics including peak width, chromatographic resolution, peak capacity, and the variability in peak area and analyte retention time (RT) stability. The SSP, which was evaluated in 11 laboratories on a total of 15 different instruments, enabled early diagnoses of LC and MS anomalies that indicated suboptimal LC-MRM-MS performance. The observed range in variation of each of the metrics scrutinized serves to define the criteria for optimized LC-SID-MRM-MS platforms for routine use, with pass/fail criteria for system suitability performance measures defined as peak area coefficient of variation <0.15, peak width coefficient of variation <0.15, standard deviation of RT <0.15 min (9 s), and the RT drift <0.5min (30 s). The deleterious effect of a marginally performing LC-SID-MRM-MS system on the limit of quantification (LOQ) in targeted quantitative assays illustrates the use and need for a SSP to establish robust and reliable system performance. Use of a SSP helps to ensure that analyte quantification measurements can be replicated with good precision within and across multiple laboratories and should facilitate more widespread use of MRM-MS technology by the basic biomedical and clinical laboratory research communities.

Primary control level of parallel distributed energy resources converters in system of multiple interconnected autonomous microgrids within self-healing networks

To minimise the number of load sheddings in a microgrid (MG) during autonomous operation, islanded neighbour MGs can be interconnected if they are on a self-healing network and an extra generation capacity is available in the distributed energy resources (DER) of one of the MGs. In this way, the total load in the system of interconnected MGs can be shared by all the DERs within those MGs. However, for this purpose, carefully designed self-healing and supply restoration control algorithm, protection systems and communication infrastructure are required at the network and MG levels. In this study, first, a hierarchical control structure is discussed for interconnecting the neighbour autonomous MGs where the introduced primary control level is the main focus of this study. Through the developed primary control level, this study demonstrates how the parallel DERs in the system of multiple interconnected autonomous MGs can properly share the load of the system. This controller is designed such that the converter-interfaced DERs operate in a voltage-controlled mode following a decentralised power sharing algorithm based on droop control. DER converters are controlled based on a per-phase technique instead of a conventional direct-quadratic transformation technique. In addition, linear quadratic regulator-based state feedback controllers, which are more stable than conventional proportional integrator controllers, are utilised to prevent instability and weak dynamic performances of the DERs when autonomous MGs are interconnected. The efficacy of the primary control level of the DERs in the system of multiple interconnected autonomous MGs is validated through the PSCAD/EMTDC simulations considering detailed dynamic models of DERs and converters.

Verifiable multi-secret sharing schemes for multiple threshold access structures

A multi-secret sharing scheme allows several secrets to be shared amongst a group of participants. In 2005, Shao and Cao developed a verifiable multi-secret sharing scheme where each participant’s share can be used several times which reduces the number of interactions between the dealer and the group members. In addition some secrets may require a higher security level than others involving the need for different threshold values. Recently Chan and Chang designed such a scheme but their construction only allows a single secret to be shared per threshold value. In this article we combine the previous two approaches to design a multiple time verifiable multi-secret sharing scheme where several secrets can be shared for each threshold value. Since the running time is an important factor for practical applications, we will provide a complexity comparison of our combined approach with respect to the previous schemes.

Where is the software? Building a Metadata Repository for Software and Code Generated by QUT Researchers

QUT Software Finder is a searchable repository of metadata describing software and source code, which has been created as a result of QUT research activities. It was launched in December 2013. https://researchdatafinder.qut.edu.au/scf The registry was designed to aid the discovery and visibility of QUT research outputs and encourage sharing and re-use of code and software throughout the research community, both nationally and internationally. The repository platform used is VIVO (an open source product initially developed at Cornell University). QUT Software Finder records that describe software or code are connected to information about researchers involved, the research groups, related publications and related projects. Links to where the software or code can be accessed from are also provided alongside licencing and re-use information.

A recommendation system for predicting risks across multiple business process instances

This paper proposes a recommendation system that supports process participants in taking risk-informed decisions, with the goal of reducing risks that may arise during process execution. Risk reduction involves decreasing the likelihood and severity of a process fault from occurring. Given a business process exposed to risks, e.g. a financial process exposed to a risk of reputation loss, we enact this process and whenever a process participant needs to provide input to the process, e.g. by selecting the next task to execute or by filling out a form, we suggest to the participant the action to perform which minimizes the predicted process risk. Risks are predicted by traversing decision trees generated from the logs of past process executions, which consider process data, involved resources, task durations and other information elements like task frequencies. When applied in the context of multiple process instances running concurrently, a second technique is employed that uses integer linear programming to compute the optimal assignment of resources to tasks to be performed, in order to deal with the interplay between risks relative to different instances. The recommendation system has been implemented as a set of components on top of the YAWL BPM system and its effectiveness has been evaluated using a real-life scenario, in collaboration with risk analysts of a large insurance company. The results, based on a simulation of the real-life scenario and its comparison with the event data provided by the company, show that the process instances executed concurrently complete with significantly fewer faults and with lower fault severities, when the recommendations provided by our recommendation system are taken into account.

Polymorphisms in the receptor tyrosine kinase MERTK gene are associated with Multiple Sclerosis susceptibility

Multiple sclerosis (MS) is a debilitating, chronic demyelinating disease of the central nervous system affecting over 2 million people worldwide. The TAM family of receptor tyrosine kinases (TYRO3, AXL and MERTK) have been implicated as important players during demyelination in both animal models of MS and in the human disease. We therefore conducted an association study to identify single nucleotide polymorphisms (SNPs) within genes encoding the TAM receptors and their ligands associated with MS. Analysis of genotype data from a genome-wide association study which consisted of 1618 MS cases and 3413 healthy controls conducted by the Australia and New Zealand Multiple Sclerosis Genetics Consortium (ANZgene) revealed several SNPs within the MERTK gene (Chromosome 2q14.1, Accession Number NG_011607.1) that showed suggestive association with MS. We therefore interrogated 28 SNPs in MERTK in an independent replication cohort of 1140 MS cases and 1140 healthy controls. We found 12 SNPs that replicated, with 7 SNPs showing p-values of less than 10-5 when the discovery and replication cohorts were combined. All 12 replicated SNPs were in strong linkage disequilibrium with each other. In combination, these data suggest the MERTK gene is a novel risk gene for MS susceptibility. © 2011 Ma et al.

Medical Data Access Accountability in EHR Systems, A Practical Perspective

The world has experienced a large increase in the amount of available data. Therefore, it requires better and more specialized tools for data storage and retrieval and information privacy. Recently Electronic Health Record (EHR) Systems have emerged to fulfill this need in health systems. They play an important role in medicine by granting access to information that can be used in medical diagnosis. Traditional systems have a focus on the storage and retrieval of this information, usually leaving issues related to privacy in the background. Doctors and patients may have different objectives when using an EHR system: patients try to restrict sensible information in their medical records to avoid misuse information while doctors want to see as much information as possible to ensure a correct diagnosis. One solution to this dilemma is the Accountable e-Health model, an access protocol model based in the Information Accountability Protocol. In this model patients are warned when doctors access their restricted data. They also enable a non-restrictive access for authenticated doctors. In this work we use FluxMED, an EHR system, and augment it with aspects of the Information Accountability Protocol to address these issues. The Implementation of the Information Accountability Framework (IAF) in FluxMED provides ways for both patients and physicians to have their privacy and access needs achieved. Issues related to storage and data security are secured by FluxMED, which contains mechanisms to ensure security and data integrity. The effort required to develop a platform for the management of medical information is mitigated by the FluxMED's workflow-based architecture: the system is flexible enough to allow the type and amount of information being altered without the need to change in your source code.