An analytical tool that quantifies cellular morphology changes from three-dimensional fluorescence images

The most common software analysis tools available for measuring fluorescence images are for two-dimensional (2D) data that rely on manual settings for inclusion and exclusion of data points, and computer-aided pattern recognition to support the interpretation and findings of the analysis. It has become increasingly important to be able to measure fluorescence images constructed from three-dimensional (3D) datasets in order to be able to capture the complexity of cellular dynamics and understand the basis of cellular plasticity within biological systems. Sophisticated microscopy instruments have permitted the visualization of 3D fluorescence images through the acquisition of multispectral fluorescence images and powerful analytical software that reconstructs the images from confocal stacks that then provide a 3D representation of the collected 2D images. Advanced design-based stereology methods have progressed from the approximation and assumptions of the original model-based stereology(1) even in complex tissue sections(2). Despite these scientific advances in microscopy, a need remains for an automated analytic method that fully exploits the intrinsic 3D data to allow for the analysis and quantification of the complex changes in cell morphology, protein localization and receptor trafficking. Current techniques available to quantify fluorescence images include Meta-Morph (Molecular Devices, Sunnyvale, CA) and Image J (NIH) which provide manual analysis. Imaris (Andor Technology, Belfast, Northern Ireland) software provides the feature MeasurementPro, which allows the manual creation of measurement points that can be placed in a volume image or drawn on a series of 2D slices to create a 3D object. This method is useful for single-click point measurements to measure a line distance between two objects or to create a polygon that encloses a region of interest, but it is difficult to apply to complex cellular network structures. Filament Tracer (Andor) allows automatic detection of the 3D neuronal filament-like however, this module has been developed to measure defined structures such as neurons, which are comprised of dendrites, axons and spines (tree-like structure). This module has been ingeniously utilized to make morphological measurements to non-neuronal cells(3), however, the output data provide information of an extended cellular network by using a software that depends on a defined cell shape rather than being an amorphous-shaped cellular model. To overcome the issue of analyzing amorphous-shaped cells and making the software more suitable to a biological application, Imaris developed Imaris Cell. This was a scientific project with the Eidgenössische Technische Hochschule, which has been developed to calculate the relationship between cells and organelles. While the software enables the detection of biological constraints, by forcing one nucleus per cell and using cell membranes to segment cells, it cannot be utilized to analyze fluorescence data that are not continuous because ideally it builds cell surface without void spaces. To our knowledge, at present no user-modifiable automated approach that provides morphometric information from 3D fluorescence images has been developed that achieves cellular spatial information of an undefined shape (Figure 1). We have developed an analytical platform using the Imaris core software module and Imaris XT interfaced to MATLAB (Mat Works, Inc.). These tools allow the 3D measurement of cells without a pre-defined shape and with inconsistent fluorescence network components. Furthermore, this method will allow researchers who have extended expertise in biological systems, but not familiarity to computer applications, to perform quantification of morphological changes in cell dynamics.

Teaching planning beyond the national context : pedagogic analyses of international fieldtrip experiences

Urban and regional planners, in the era of globalization, require being equipped with skill sets to better deal with complex and rapidly changing economic, socio-cultural, political and environmental fabrics of cities and their regions. In order to provide such skill sets, urban and regional planning curriculum of Queensland University of Technology (Brisbane, Australia) offers regional planning practice in the international context. This paper reports the findings of the pedagogic analyses from the regional planning practice fieldtrips to Malaysia, Korea, Turkey, Taiwan, and discusses the opportunities and constraints of exposure of students to regional planning practice beyond the national context.

An assessment tool for selection of appropriate daylighting solutions for buildings in tropical and subtropical regions : Validation using radiance simulation

A new decision-making tool that will assist designers in the selection of appropriate daylighting solutions for buildings in tropical locations has been previously proposed by the authors. Through an evaluation matrix that prioritizes the parameters that best respond to the needs of tropical climates (e.g. reducing solar gain and protection from glare) the tool determines the most appropriate devices for specific climate and building inputs. The tool is effective in demonstrating the broad benefits and limitations of the different daylight strategies for buildings in the tropics. However for thorough analysis and calibration of the tool, validation is necessary. This paper presents a first step in the validation process. RADIANCE simulations were conducted to compare simulation performance with the performance predicted by the tool. To this end, an office building case study in subtropical Brisbane, Australia, and five different daylighting devices including openings, light guiding systems and light transport systems were simulated. Illuminance, light uniformity, daylight penetration and glare analysis were assessed for each device. The results indicate the tool can appropriately rank and recommend daylighting strategies based on specific building inputs for tropical and subtropical regions, making it a useful resource for designers.

The development of a supportive care needs assessment tool for Indigenous people with cancer

Background: Little is known about the supportive care needs of Indigenous people with cancer and to date, existing needs assessment tools have not considered cultural issues for this population. We aimed to adapt an existing supportive care needs assessment tool for use with Indigenous Australians with cancer. Methods: Face-to-face interviews with Indigenous cancer patients (n = 29) and five focus groups with Indigenous key-informants (n = 23) were conducted to assess the face and content validity, cultural acceptability, utility and relevance of the Supportive Care Needs Survey - Short Form 34 (SCNS-SF34) for use with Indigenous patients with cancer. Results: All items from the SCNS-SF34 were shortened and changed to use more appropriate language (e.g. the word 'anxiety' was substituted with 'worry'). Seven questions were omitted (e.g. items on death and future considerations) as they were deemed culturally inappropriate or irrelevant and 12 items were added (e.g. accessible transport). Optional instructions were added before the sexual items. The design and response format of the SCNS-SF34 was modified to make it easier to use for Indigenous cancer patients. Given the extensive modifications to the SCNS-SF34 and the liklihood of a different factor structure we consider this tool to be a new tool rather than a modification. The Supportive care needs assessment tool for Indigenous people (SCNAT-IP) shows promising face and content validity and will be useful in informing services where they need to direct their attention for these patients. Conclusions: Indigenous people with cancer have language, customs and specific needs that are not accommodated within the standard SCNS-SF34. Our SCNAT-IP improves acceptability, relevance and face validity for Indigenous-specific concerns. Our SCNAT-IP will allow screening for supportive care needs that are specific to Indigenous cancer patients' and greatly inform targeted policy development and practice.

Ecological footprinting : its potential as a tool for change in preservice teacher education

Environmental and sustainability issues pose challenges for society. Although education is seen as being a contributor to addressing sustainability, teacher education has been slow to act in preparing future teachers to teach sustainability. Recent Australian curriculum documents nominate sustainability as one of three cross-curriculum priorities. In one Australian university course, an Ecological Footprint Calculator tool has been employed to challenge preservice early childhood teachers to consider the sustainability of their lifestyles as a means for engaging them in learning and teaching for sustainability. Students enrolled in an integrated arts and humanities subject voluntarily engaged with the online calculator and shared their findings on an electronic discussion forum. These postings then became the basis of qualitative analysis and discussion. Data categories included reactions and reflections on reasons for the ‘heaviness’ of their footprints , student reactions leading to actions to reduce their footprints, reflections on the implications of the footprint results for future teaching, reactions that considered the need for societal change, and reflections on the integration of sustainability with the visual arts. The power of the tool’s application to stimulate interest in sustainability and education for sustainability more broadly in teacher education is explored.

GWCarb v1.0: carbonate speciation tool

This spreadsheet calculates carbonate speciation using carbonate equilibrium equations at standard conditions (T=25°C) with ionic strength corrections. The user will typically be able to calculate the different carbonate species by entering total alkalinity and pH. This spreadsheet contains additional tools to calculate the Langelier Index for calcium and the SAR of the water. Note that in this last calculation the potential for calcium precipitation is not taken into account. The last tool presented here is a carbonate speciation tool in open systems (e.g. open to the atmosphere) which takes into account atmospheric pressure.

HACC food service client cultural food preferences assessment tool

This assessment form is designed to help your HACC service provider arrange for the most appropriate food and meal services that they can. It includes questions relating to food preferences, health and nutrition, abilities to source and prepare foods as well as questions to highlight if you are at risk of not having adequate access to appropriate foods. It is understood that some people from certain cultures may not feel comfortable answering some of these questions. Therefore, please do not answer those questions with which you are not comfortable.

An automated tool for assessing security-critical designs and programs

This paper describes in detail our Security-Critical Program Analyser (SCPA). SCPA is used to assess the security of a given program based on its design or source code with regard to data flow-based metrics. Furthermore, it allows software developers to generate a UML-like class diagram of their program and annotate its confidential classes, methods and attributes. SCPA is also capable of producing Java source code for the generated design of a given program. This source code can then be compiled and the resulting Java bytecode program can be used by the tool to assess the program's overall security based on our security metrics.

Mobile social tool for supporting responsible drinking in yourng women

Binge drinking is an important issue in Australia and worldwide. Existing studies have shown that mobile tools provide an effective method to self-monitor drink sessions, whereas social tool such as Facebook, can be used to construct social drinker identity (thus normalizing binge drinking), but if used among a peer-support that promotes the importance of responsible drinking, it potentially can be effective in moderating alcohol consumption. To combine mobile and social tool approaches, the study involves two complementary and largely qualitative studies to inform a novel design of an engaging mobile social tool for supporting responsible drinking among young women: (1) a survey of literature and mobile tools on alcohol related studies and interventions; (2) an in-depth focus group interview among young women aged 18 to 24. The results and discussions provide some valuable insights for future research and development in the field.

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

Emerging from student to practitioner : a cumulative development tool for students

PURPOSE: This pilot project’s aim was to trial a tool and process for developing students’ ability to engage in self-assessment using reflection on their clinical experiences, including feedback from workplace learning, in order to aid them in linking theory to practice and develop strategies to improve performance. BACKGROUND: In nursing education, students can experience a mismatch in performance compared to theoretical learning, this is referred to as the ‘theory practice gap’ (Scully 2011, Chan Chan & Liu 2011). One specific contributing factor seems to be students’ inability to engage in meaningful reflection and self-correcting behaviours. A self-assessment strategy was implemented within a third year clinical unit to ameliorate this mismatch with encouraging results, as students developed self-direction in addressing learning needs. In this pilot project the above strategy was adapted for implementation between different clinical units, to create a whole of course approach to integrating workplace learning. METHOD: The methodology underpinning this project is a scaffolded, supported reflective practice process. Improved self-assessment skills is achieved by students reflecting on and engaging with feedback, then mapping this to learning outcomes to identify where performance can be improved. Evaluation of this project includes: collation of student feedback identifying successful strategies along with barriers encountered in implementation; feedback from students and teachers via above processes and tools; and comparison of the number of learning contracts issued in clinical nursing units with similar cohorts. RESULTS: Results will be complete by May 2012 and include analysis of the data collected via the above evaluation methods. Other outcomes will include the refined process and tool, plus resources that should improve cost effectiveness without reducing student support. CONCLUSION: Implementing these tools and processes over the entire student’s learning package, will assist them to demonstrate progressive development through the course. Students will have learnt to understand feedback and integrate these skills for life-long learning.

Transmission X-ray microscopy : a new tool in clay mineral floccules characterization

Effective flocculation and dewatering of mineral processing streams containing clays are microstructure dependent in clay-water systems. Initial clay flocculation is crucial in the design and for the development of a new methodology of gas exploitation. Microstructural engineering of clay aggregates using covalent cations and Keggin macromolecules have been monitored using the new state of the art Transmission X-ray Microscope (TXM) with 60 nm tomography resolution installed in a Taiwanese synchrotron. The 3-D reconstructions from TXM images show complex aggregation structures in montmorillonite aqueous suspensions after treatment with Na+, Ca2+ and Al13 Keggin macromolecules. Na-montmorillonite displays elongated, parallel, well-orientated and closed-void cellular networks, 0.5–3 μm in diameter. After treatment by covalent cations, the coagulated structure displays much smaller, randomly orientated and openly connected cells, 300–600 nm in diameter. The average distances measured between montmorillonite sheets was around 450 nm, which is less than half of the cell dimension measured in Na-montmorillonite. The most dramatic structural changes were observed after treatment by Al13 Keggin; aggregates then became arranged in compacted domains of a 300 nm average diameter composed of thick face-to-face oriented sheets, which forms porous aggregates with larger intra-aggregate open and connected voids.