miRPlant : an integrated tool for identification of plant miRNA from RNA sequencing data

Background Small RNA sequencing is commonly used to identify novel miRNAs and to determine their expression levels in plants. There are several miRNA identification tools for animals such as miRDeep, miRDeep2 and miRDeep*. miRDeep-P was developed to identify plant miRNA using miRDeep’s probabilistic model of miRNA biogenesis, but it depends on several third party tools and lacks a user-friendly interface. The objective of our miRPlant program is to predict novel plant miRNA, while providing a user-friendly interface with improved accuracy of prediction. Result We have developed a user-friendly plant miRNA prediction tool called miRPlant. We show using 16 plant miRNA datasets from four different plant species that miRPlant has at least a 10% improvement in accuracy compared to miRDeep-P, which is the most popular plant miRNA prediction tool. Furthermore, miRPlant uses a Graphical User Interface for data input and output, and identified miRNA are shown with all RNAseq reads in a hairpin diagram. Conclusions We have developed miRPlant which extends miRDeep* to various plant species by adopting suitable strategies to identify hairpin excision regions and hairpin structure filtering for plants. miRPlant does not require any third party tools such as mapping or RNA secondary structure prediction tools. miRPlant is also the first plant miRNA prediction tool that dynamically plots miRNA hairpin structure with small reads for identified novel miRNAs. This feature will enable biologists to visualize novel pre-miRNA structure and the location of small RNA reads relative to the hairpin. Moreover, miRPlant can be easily used by biologists with limited bioinformatics skills.

An analysis of digital storytelling as a documentation tool for research in the creative and performing arts

This paper examines the capacity of digital storytelling to document research activity in the creative and performing arts. In particular, it seeks to identify the thought processes and methods that underpin this research and to capture them using the digital storytelling medium. Interest in this issue was prompted by the author’s work with the creative and performing artists from the Queensland Conservatorium and the Queensland College of Art as part of the Federal government’s Research Quality Framework (RQF) in 2007. The RQF compelled artists to address what it means to undertake research in their disciplines, to describe this, measure it and quantify it; for many practitioners this represents a significant challenge. These issues continue to be pertinent in the context of the Excellence in Research for Australia (ERA) initiative. This research is significant because it seeks to identify, in layman’s terms, the research methods and thought processes used by artists in their research practice. It seeks to do so free of the encumbrances of the professional doctorate policies, the higher education research quality frameworks, and the dense philosophical debates that have to-date dominated discussions of this issue. The research involves qualitative data collection methods including a detailed literature review, interviews with key practitioners and academics involved in the creative and performing arts, and three case studies. The literature review focuses on publications that explore issues of research practice and method in the creative and performing arts. The case studies involve three Queensland-based artists. Digital stories will be developed (and presented) with Marcus and Mafe using their visual materials and drawing on the issues identified in the literature review and interviews. Emmerson’s DVD provided a point of comparison with the digital stories. (Brief bios are attached)

Xenome--a tool for classifying reads from xenograft samples

Motivation Shotgun sequence read data derived from xenograft material contains a mixture of reads arising from the host and reads arising from the graft. Classifying the read mixture to separate the two allows for more precise analysis to be performed. Results We present a technique, with an associated tool Xenome, which performs fast, accurate and specific classification of xenograft-derived sequence read data. We have evaluated it on RNA-Seq data from human, mouse and human-in-mouse xenograft datasets.

Supporting residents’ expression of sexuality : the initial construction of a sexuality assessment tool for residential aged care facilities

Background: Sexuality is a key component of quality of life and well-being and a need to express one’s sexuality continues into old age. Staff and families in residential aged care facilities often find expressions of sexuality by residents, particularly those living with dementia, challenging and facilities often struggle to address individuals’ needs in this area. This paper describes the development of an assessment tool which enables residential aged care facilities to identify how supportive their organisation is of all residents’ expression of their sexuality, and thereby improve where required. Methods: Multi-phase design using qualitative methods and a Delphi technique. Tool items were derived from the literature and verified by qualitative interviews with aged care facility staff, residents and families. The final item pool was confirmed via a reactive Delphi process. Results: A final item pool of sixty-nine items grouped into seven key areas allows facilities to score their compliance with the areas identified as being supportive of older people’s expression of their sexuality in a residential aged care environment. Conclusions: The sexuality assessment tool (SexAT) guides practice to support the normalization of sexuality in aged care homes and assists facilities to identify where enhancements to the environment, policies, procedures and practices, information and education/training are required. The tool also enables facilities to monitor initiatives in these areas over time.

Human saliva as a tool to investigate intimate partner violence

Human saliva mirrors body’s health and well-being and many of the biomolecules present in blood or urine can also be found in salivary secretions. However, biomolecular concentrations in saliva are usually one tenth to one thousandth of the levels in blood (Pfaffe et al., 2011). Sensitive detection technology platforms are therefore required to detect biomolecules in saliva. Another road block to the advancement of salivary diagnostics is the lack of information related to healthy state saliva vs. a diseased saliva, baseline levels and reference ranges and diurnal variations. Saliva has numerous advantages over blood or urine as a diagnostic fluid: (a) the non-invasive nature of sample collection and the simple, safe, painless and cost-effective methods to collect it; (b) unskilled personnel can collect saliva samples at multiple time points; and (c) the total protein concentration is approximately a quarter of that is present in plasma, which makes it easier to investigate low abundance proteins (Pfaffe et al., 2011). Currently, saliva assays are routinely used to determine, diseases such as HIV, drugs and substances of abuse to provide information on exposure and give qualitative information on the type of illicit drug used (Kintz et al., 2009), cortisol levels for diagnosing Cushing’s syndrome (Doi et al., 2008), and use for biomonitoring of exposure to chemicals (Caporossi et al., 2010) to measure hormones (Gröschl, 2009)....

Near infrared spectroscopy for rapid determination of Mankin score components : a potential tool for quantitative characterization of articular cartilage at surgery

PURPOSE The purpose of this study was to demonstrate the potential of near infrared (NIR) spectroscopy for characterizing the health and degenerative state of articular cartilage based on the components of the Mankin score. METHODS Three models of osteoarthritic degeneration induced in laboratory rats by anterior cruciate ligament (ACL) transection, meniscectomy (MSX), and intra-articular injection of monoiodoacetate (1 mg) (MIA) were used in this study. Degeneration was induced in the right knee joint; each model group consisted of 12 rats (N = 36). After 8 weeks, the animals were euthanized and knee joints were collected. A custom-made diffuse reflectance NIR probe of 5-mm diameter was placed on the tibial and femoral surfaces, and spectral data were acquired from each specimen in the wave number range of 4,000 to 12,500 cm(-1). After spectral data acquisition, the specimens were fixed and safranin O staining (SOS) was performed to assess disease severity based on the Mankin scoring system. Using multivariate statistical analysis, with spectral preprocessing and wavelength selection technique, the spectral data were then correlated to the structural integrity (SI), cellularity (CEL), and matrix staining (SOS) components of the Mankin score for all the samples tested. RESULTS ACL models showed mild cartilage degeneration, MSX models had moderate degeneration, and MIA models showed severe cartilage degenerative changes both morphologically and histologically. Our results reveal significant linear correlations between the NIR absorption spectra and SI (R(2) = 94.78%), CEL (R(2) = 88.03%), and SOS (R(2) = 96.39%) parameters of all samples in the models. In addition, clustering of the samples according to their level of degeneration, with respect to the Mankin components, was also observed. CONCLUSIONS NIR spectroscopic probing of articular cartilage can potentially provide critical information about the health of articular cartilage matrix in early and advanced stages of osteoarthritis (OA). CLINICAL RELEVANCE This rapid nondestructive method can facilitate clinical appraisal of articular cartilage integrity during arthroscopic surgery.

Predicting the likelihood of non-healing : a venous leg ulcer risk assessment tool

This project developed, validated and tested reliability of a risk assessment tool to predict the risk of failure to heal of patients with venous leg ulcers within 24 weeks. The risk assessment tool will allow clinicians to be able to determine realistic outcomes for their patients, promote early healing and potentially avoid weeks of inappropriate therapy. The tool will also assist in addressing specific risk factors and guide decisions on early, alternative, tailored interventions.

Wood density : a tool to find complementary species for the design of mixed species plantations

The successful establishment and growth of mixed-species forest plantations requires that complementary or facilitatory species be identified. This can be difficult in many tropical areas because the growth characteristics of endemic species are often unknown, particularly when grown at potentially higher densities in plantations than in natural forests. Here, we investigate whether wood density is a useful and readily accessible trait for choosing complementary species for mixed species plantations. Wood density represents the carbon investment per unit volume of stem with a trade-off generally found between fast (low wood density) and slow (high wood density) growing species. To do this, we use data collected from 18 highly diverse mixed species plantations (4–23 mostly native species) aged from 6 to 11 years at the time of data collection located on Leyte Island, Philippines. We found significant negative correlations between wood densities and the height of the most abundant species, as well as with measures of overall stand growth and tree diameter size distribution. Not only do species with denser woods have slower growth rates, but also mixed-species plantations with higher average wood density and higher stem density were also less productive, at least in these young plantations. Similarly, stands with a high diversity in wood densities were less productive. There is growing interest in making greater use of native multi-species mixtures in smallholder and community planting programs in the tropics, and our results show databases of wood density values may help improve their design. In the early development stages of plantations, canopy closure and rapid height growth are usually key silvicultural targets, and wood density values can predict the rapid height development of species. If plantations are being grown for the livelihood of small landholders then the best target is to choose some species with different wood densities. This allows an early harvest of low-wood density species for early income, and will also reduce competition for slower growing trees with higher wood densities for later income generation.

A simple nutrition screening tool for paediatric inpatients

Background: Pediatric nutrition risk screening tools are not routinely implemented throughout many hospitals, despite prevalence studies demonstrating malnutrition is common in hospitalized children. Existing tools lack the simplicity of those used to assess nutrition risk in the adult population. This study reports the accuracy of a new, quick, and simple pediatric nutrition screening tool (PNST) designed to be used for pediatric inpatients. Materials and Methods: The pediatric Subjective Global Nutrition Assessment (SGNA) and anthropometric measures were used to develop and assess the validity of 4 simple nutrition screening questions comprising the PNST. Participants were pediatric inpatients in 2 tertiary pediatric hospitals and 1 regional hospital. Results: Two affirmative answers to the PNST questions were found to maximize the specificity and sensitivity to the pediatric SGNA and body mass index (BMI) z scores for malnutrition in 295 patients. The PNST identified 37.6% of patients as being at nutrition risk, whereas the pediatric SGNA identified 34.2%. The sensitivity and specificity of the PNST compared with the pediatric SGNA were 77.8% and 82.1%, respectively. The sensitivity of the PNST at detecting patients with a BMI z score of less than -2 was 89.3%, and the specificity was 66.2%. Both the PNST and pediatric SGNA were relatively poor at detecting patients who were stunted or overweight, with the sensitivity and specificity being less than 69%. Conclusion: The PNST provides a sensitive, valid, and simpler alternative to existing pediatric nutrition screening tools such as Screening Tool for the Assessment of Malnutrition in Pediatrics (STAMP), Screening Tool Risk on Nutritional status and Growth (STRONGkids), and Paediatric Yorkhill Malnutrition Score (PYMS) to ensure the early detection of hospitalized children at nutrition risk.

Large scale multiuser digital mind mapping tool : a study in usability

Project work can involve multiple people from varying disciplines coming together to solve problems as a group. Large scale interactive displays are presenting new opportunities to support such interactions with interactive and semantically enabled cooperative work tools such as intelligent mind maps. In this paper, we present a novel digital, touch-enabled mind-mapping tool as a first step towards achieving such a vision. This first prototype allows an evaluation of the benefits of a digital environment for a task that would otherwise be performed on paper or flat interactive surfaces. Observations and surveys of 12 participants in 3 groups allowed the formulation of several recommendations for further research into: new methods for capturing text input on touch screens; inclusion of complex structures; multi-user environments and how users make the shift from single- user applications; and how best to navigate large screen real estate in a touch-enabled, co-present multi-user setting.

A continental-scale tool for acoustic identification of European bats

Summary 1. Acoustic methods are used increasingly to survey and monitor bat populations. However, the use of acoustic methods at continental scales can be hampered by the lack of standardized and objective methods to identify all species recorded. This makes comparable continent-wide monitoring difficult, impeding progress towards developing biodiversity indicators, transboundary conservation programmes and monitoring species distribution changes. 2. Here we developed a continental-scale classifier for acoustic identification of bats, which can be used throughout Europe to ensure objective, consistent and comparable species identifications. We selected 1350 full-spectrum reference calls from a set of 15 858 calls of 34 European species, from EchoBank, a global echolocation call library. We assessed 24 call parameters to evaluate how well they distinguish between species and used the 12 most useful to train a hierarchy of ensembles of artificial neural networks to distinguish the echolocation calls of these bat species. 3. Calls are first classified to one of five call-type groups, with a median accuracy of 97·6%. The median species-level classification accuracy is 83·7%, providing robust classification for most European species, and an estimate of classification error for each species. 4. These classifiers were packaged into an online tool, iBatsID, which is freely available, enabling anyone to classify European calls in an objective and consistent way, allowing standardized acoustic identification across the continent. 5. Synthesis and applications. iBatsID is the first freely available and easily accessible continental- scale bat call classifier, providing the basis for standardized, continental acoustic bat monitoring in Europe. This method can provide key information to managers and conservation planners on distribution changes and changes in bat species activity through time.

From ideation to sculpture : digital sculpting as the primary 'ideation' tool for creature design

This research project examined the potential for circumventing drawing in the ideation process by adopting digital sculpture as the primary conceptual development and design tool for the digital sculpting of creature designs. Through a series of experimental research cycles, multiple frameworks were explored with the aim of identifying a methodology for creating '3D sculpted sketches' for the initial phases of the ideation process. This research project acknowledges that drawing still remains the predominant method of visualising design ideas for characters and creatures for many artists. However, alongside other ideation techniques digital sculpting can function as a rapid and responsive tool to visualize and explore forms in a digital sculpting environment for the conceptualisation of multiple creature design variations. The results of this study are significant for emerging digital sculptors who may not necessarily have a well-defined creative brief or initial concept.

Single-cell force spectroscopy, an emerging tool to quantify cell adhesion to biomaterials

Cell adhesion receptors play a central role in sensing and integrating signals provided by the cellular environment. Thus, understanding adhesive interactions at the cell-biomaterial interface is essential to improve the design of implants that should emulate certain characteristics of the cell's natural environment. Numerous cell adhesion assays have been developed; among these, atomic force microscopy-based single-cell force spectroscopy (AFM-SCFS) provides a versatile tool to quantify cell adhesion at physiological conditions. Here we discuss how AFM-SCFS can be used to quantify the adhesion of living cells to biomaterials and give examples of using AFM-SCFS in tissue engineering and regenerative medicine. We anticipate that in the near future, AFM-SCFS will be established in the biomaterial field as an important technique to quantify cell-biomaterial interactions and thereby will contribute to the optimization of implants, scaffolds, and medical devices.