Simulation and visualization of self-assembled nanodevice networks synthesized via plasma–surface interaction

Using advanced visualization techniques, a comprehensive visualization of all the stages of the self-organized growth of internetworked nanostructures on plasma-exposed surface has been made. Atomistic kinetic Monte Carlo simulation for the initial stage of deposition, with 3-D visualization of the whole system and half-tone visualization of the density field of the adsorbed atoms, makes it possible to implement a multiscale predictive modeling of the development of the nanoscale system.

Visualization of long-duration acoustic recordings of the environment

Acoustic recordings of the environment are an important aid to ecologists monitoring biodiversity and environmental health. However, rapid advances in recording technology, storage and computing make it possible to accumulate thousands of hours of recordings, of which, ecologists can only listen to a small fraction. The big-data challenge addressed in this paper is to visualize the content of long-duration audio recordings on multiple scales, from hours, days, months to years. The visualization should facilitate navigation and yield ecologically meaningful information. Our approach is to extract (at one minute resolution) acoustic indices which reflect content of ecological interest. An acoustic index is a statistic that summarizes some aspect of the distribution of acoustic energy in a recording. We combine indices to produce false-color images that reveal acoustic content and facilitate navigation through recordings that are months or even years in duration.

4DCT radiotherapy for NSCLC: A review of planning methods

Purpose To establish whether the use of a passive or active technique of planning target volume (PTV) definition and treatment methods for non-small cell lung cancer (NSCLC) deliver the most effective results. This literature review assesses the advantages and disadvantages in recent studies of each, while assessing the validity of the two approaches for planning and treatment. Methods A systematic review of literature focusing on the planning and treatment of radiation therapy to NSCLC tumours. Different approaches which have been published in recent articles are subjected to critical appraisal in order to determine their relative efficacy. Results Free-breathing (FB) is the optimal method to perform planning scans for patients and departments, as it involves no significant increase in cost, workload or education. Maximum intensity projection (MIP) is the fastest form of delineation, however it is noted to be less accurate than the ten-phase overlap approach for computed tomography (CT). Although gating has proven to reduce margins and facilitate sparing of organs at risk, treatment times can be longer and planning time can be as much as 15 times higher for intensity modulated radiation therapy (IMRT). This raises issues with patient comfort and stabilisation, impacting on the chance of geometric miss. Stereotactic treatments can take up to 3 hours to treat, along with increases in planning and treatment, as well as the additional hardware, software and training required. Conclusion Four-dimensional computed tomography (4DCT) is superior to 3DCT, with the passive FB approach for PTV delineation and treatment optimal. Departments should use a combination of MIP with visual confirmation ensuring coverage for stage 1 disease. Stages 2-3 should be delineated using ten-phases overlaid. Stereotactic and gated treatments for early stage disease should be used accordingly; FB-IMRT is optimal for latter stage disease.

Application of meshfree methods to numerically simulate microscale deformations of different plant food materials during drying

Plant food materials have a very high demand in the consumer market and therefore, improved food products and efficient processing techniques are concurrently being researched in food engineering. In this context, numerical modelling and simulation techniques have a very high potential to reveal fundamentals of the underlying mechanisms involved. However, numerical modelling of plant food materials during drying becomes quite challenging, mainly due to the complexity of the multiphase microstructure of the material, which undergoes excessive deformations during drying. In this regard, conventional grid-based modelling techniques have limited applicability due to their inflexible grid-based fundamental limitations. As a result, meshfree methods have recently been developed which offer a more adaptable approach to problem domains of this nature, due to their fundamental grid-free advantages. In this work, a recently developed meshfree based two-dimensional plant tissue model is used for a comparative study of microscale morphological changes of several food materials during drying. The model involves Smoothed Particle Hydrodynamics (SPH) and Discrete Element Method (DEM) to represent fluid and solid phases of the cellular structure. Simulation are conducted on apple, potato, carrot and grape tissues and the results are qualitatively and quantitatively compared and related with experimental findings obtained from the literature. The study revealed that cellular deformations are highly sensitive to cell dimensions, cell wall physical and mechanical properties, middle lamella properties and turgor pressure. In particular, the meshfree model is well capable of simulating critically dried tissues at lower moisture content and turgor pressure, which lead to cell wall wrinkling. The findings further highlighted the potential applicability of the meshfree approach to model large deformations of the plant tissue microstructure during drying, providing a distinct advantage over the state of the art grid-based approaches.

Rethinking the value of simulation methods in the information systems research field : a call for reconstructing contribution for a broader audience

The impact of simulation methods for social research in the Information Systems (IS) research field remains low. A concern is our field is inadequately leveraging the unique strengths of simulation methods. Although this low impact is frequently attributed to methodological complexity, we offer an alternative explanation – the poor construction of research value. We argue a more intuitive value construction, better connected to the knowledge base, will facilitate increased value and broader appreciation. Meta-analysis of studies published in IS journals over the last decade evidences the low impact. To facilitate value construction, we synthesize four common types of simulation research contribution: Analyzer, Tester, Descriptor, and Theorizer. To illustrate, we employ the proposed typology to describe how each type of value is structured in simulation research and connect each type to instances from IS literature, thereby making these value types and their construction visible and readily accessible to the general IS community.

Visualization of complex biological systems: An immune response model using OpenGL

In this paper we present an update on our novel visualization technologies based on cellular immune interaction from both large-scale spatial and temporal perspectives. We do so with a primary motive: to present a visually and behaviourally realistic environment to the community of experimental biologists and physicians such that their knowledge and expertise may be more readily integrated into the model creation and calibration process. Visualization aids understanding as we rely on visual perception to make crucial decisions. For example, with our initial model, we can visualize the dynamics of an idealized lymphatic compartment, with antigen presenting cells (APC) and cytotoxic T lymphocyte (CTL) cells. The visualization technology presented here offers the researcher the ability to start, pause, zoom-in, zoom-out and navigate in 3-dimensions through an idealised lymphatic compartment.

A Web-based system enabling the integration, analysis, and 3D sub-surface visualization of groundwater monitoring data and geological models

The 3D Water Chemistry Atlas is an intuitive, open source, Web-based system that enables the three-dimensional (3D) sub-surface visualization of ground water monitoring data, overlaid on the local geological model (formation and aquifer strata). This paper firstly describes the results of evaluating existing virtual globe technologies, which led to the decision to use the Cesium open source WebGL Virtual Globe and Map Engine as the underlying platform. Next it describes the backend database and search, filtering, browse and analysis tools that were developed to enable users to interactively explore the groundwater monitoring data and interpret it spatially and temporally relative to the local geological formations and aquifers via the Cesium interface. The result is an integrated 3D visualization system that enables environmental managers and regulators to assess groundwater conditions, identify inconsistencies in the data, manage impacts and risks and make more informed decisions about coal seam gas extraction, waste water extraction, and water reuse.

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

Agent-based simulation as a component of mixed methods in entrepreneurship research

As a new research method supplementing the existing qualitative and quantitative approaches, agent-based modelling and simulation (ABMS) may fit well within the entrepreneurship field because the core concepts and basic premises of entrepreneurship coincide with the characteristics of ABMS (McKelvey, 2004; Yang & Chandra, 2013). Agent-based simulation is a simulation method based on agent-based models. The agentbased models are composed of heterogeneous agents and their behavioural rules. By repeatedly carrying out agent-based simulations on a computer, the simulations reproduce each agent’s behaviour, their interactive process, and the emerging macroscopic phenomenon according to the flow of time. Using agent-based simulations, researchers may investigate temporal or dynamic effects of each agent’s behaviours.

Feasibility of perflutren microsphere contrast transthoracic echocardiography in the visualization of ventricular endocardium during venovenous extracorporeal membrane oxygenation in a validated ovine model

Background: Transthoracic echocardiography (TTE) during extra corporeal membrane oxygenation (ECMO) is important but can be technically challenging. Contrast-specific TTE can improve imaging in suboptimal studies. These contrast microspheres are hydrodynamically labile structures. This study assessed the feasibility of contrast echocardiography (CE) during venovenous (VV) ECMO in a validated ovine model. Method: Twenty-four sheep were commenced on VV ECMO. Parasternal long-axis (Plax) and short-axis (Psax) views were obtained pre- and postcontrast while on VV ECMO. Endocardial definition scores (EDS) per segment were graded: 1 = good, 2 = suboptimal 3 = not seen. Endocardial border definition score index (EBDSI) was calculated for each view. Endocardial length (EL) in the Plax view for the left ventricle (LV) and right ventricle (RV) was measured. Results: Summation EDS data for the LV and RV for unenhanced TTE (UE) versus CE TTE imaging: EDS 1 = 289 versus 346, EDS 2 = 38 versus 10, EDS 3 = 33 versus 4, respectively. Wilcoxon matched-pairs rank-sign tests showed a significant ranking difference (improvement) pre- and postcontrast for the LV (P < 0.0001), RV (P < 0.0001) and combined ventricular data (P < 0.0001). EBDSI for CE TTE was significantly lower than UE TTE for the LV (1.05 ± 0.17 vs. 1.22 ± 0.38, P = 0.0004) and RV (1.06 ± 0.22 vs. 1.42 ± 0.47, P = 0.0.0006) respectively. Visualized EL was significantly longer in CE versus UE for both the LV (58.6 ± 11.0 mm vs. 47.4 ± 11.7 mm, P < 0.0001) and the RV (52.3 ± 8.6 mm vs. 36.0 ± 13.1 mm, P < 0.0001), respectively. Conclusions: Despite exposure to destructive hydrodynamic forces, CE is a feasible technique in an ovine ECMO model. CE results in significantly improved EDS and increased EL.

Missing in space: An evaluation of imputation methods for missing data in spatial analysis of risk factors for type II diabetes

Background Spatial analysis is increasingly important for identifying modifiable geographic risk factors for disease. However, spatial health data from surveys are often incomplete, ranging from missing data for only a few variables, to missing data for many variables. For spatial analyses of health outcomes, selection of an appropriate imputation method is critical in order to produce the most accurate inferences. Methods We present a cross-validation approach to select between three imputation methods for health survey data with correlated lifestyle covariates, using as a case study, type II diabetes mellitus (DM II) risk across 71 Queensland Local Government Areas (LGAs). We compare the accuracy of mean imputation to imputation using multivariate normal and conditional autoregressive prior distributions. Results Choice of imputation method depends upon the application and is not necessarily the most complex method. Mean imputation was selected as the most accurate method in this application. Conclusions Selecting an appropriate imputation method for health survey data, after accounting for spatial correlation and correlation between covariates, allows more complete analysis of geographic risk factors for disease with more confidence in the results to inform public policy decision-making.

“I understand. I am a participant”: Navigating the ‘fuzzy’ boundaries of visual methods in qualitative longitudinal research

In this chapter we discuss how utilising the participatory visual methodology, photovoice, in an aged care context with its unique communal setting raised several ‘fuzzy boundary’ ethical dilemmas. To illustrate these challenges, we draw on immersive field notes from an ongoing qualitative longitudinal research (QLR) exploring the lived experience of aged care from the perspective of older residents, and focus on interactions with one participant, 81 year old Cassie. We explore how the camera, which is integral to the photovoice method, altered the researcher/participant ethical dynamics by becoming a continual ‘connector’ to the researcher. The camera took on a distinct agency, acting as a non-threatening ‘portal’ that lengthened contact, provided informal opportunities to alter the relationship dynamics and enabled unplanned participant revelation.

On the Cubicity of Interval Graphs

A k-cube (or ``a unit cube in k dimensions'') is defined as the Cartesian product R-1 x . . . x R-k where R-i (for 1 <= i <= k) is an interval of the form [a(i), a(i) + 1] on the real line. The k-cube representation of a graph G is a mapping of the vertices of G to k-cubes such that the k-cubes corresponding to two vertices in G have a non-empty intersection if and only if the vertices are adjacent. The cubicity of a graph G, denoted as cub(G), is defined as the minimum dimension k such that G has a k-cube representation. An interval graph is a graph that can be represented as the intersection of intervals on the real line - i. e., the vertices of an interval graph can be mapped to intervals on the real line such that two vertices are adjacent if and only if their corresponding intervals overlap. We show that for any interval graph G with maximum degree Delta, cub(G) <= inverted right perpendicular log(2) Delta inverted left perpendicular + 4. This upper bound is shown to be tight up to an additive constant of 4 by demonstrating interval graphs for which cubicity is equal to inverted right perpendicular log(2) Delta inverted left perpendicular.

A comparison of training methods to increase neck muscle strength

Objective To compare two neck strength training modalities. Background Neck injury in pilots flying high performance aircraft is a concern in aviation medicine. Strength training may be an effective means to strengthen the neck and decrease injury risk. Methods The cohort consisted of 32 age-height-weight matched participants, divided into two experimental groups; the Multi-Cervical Unit (MCU) and Thera-Band tubing groups (THER), and a control (CTRL) group. Ten weeks of training were undertaken and pre-and post isometric strength testing for all groups was performed on the MCU. Comparisons between the three groups were made using a Kruskal-Wallis test and effect sizes between the MCU and the THER groups and the THER and CTRL groups were also calculated. Results The MCU group displayed the greatest increase in isometric strength (flexion 64.4%, extension 62.9%, left lateral flexion 53.3%, right lateral flexion 49.1%) and differences were only statistically significant (p<0.05) when compared to the CTRL group. Increases in neck strength for the THER group were lower than that shown in the MCU group (flexion 42.0%, extension 29.9%, left lateral flexion 26.7%, right lateral flexion 24.1%). Moderate to large effect sizes were found between the MCU and THER as well as the THER and CTRL groups. Conclusions This study demonstrated that the MCU was the most effective training modality to increase isometric cervical muscle strength. Thera-Band tubing did however, produce moderate gains in isometric neck strength

Mechanical testing of internal fixation devices: A theoretical and practical examination of current methods

Successful healing of long bone fractures is dependent on the mechanical environment created within the fracture, which in turn is dependent on the fixation strategy. Recent literature reports have suggested that locked plating devices are too stiff to reliably promote healing. However, in vitro testing of these devices has been inconsistent in both method of constraint and reported outcomes, making comparisons between studies and the assessment of construct stiffness problematic. Each of the methods previously used in the literature were assessed for their effect on the bending of the sample and concordant stiffness. The choice of outcome measures used in in vitro fracture studies was also assessed. Mechanical testing was conducted on seven hole locked plated constructs in each method for comparison. Based on the assessment of each method the use of spherical bearings, ball joints or similar is suggested at both ends of the sample. The use of near and far cortex movement was found to be more comprehensive and more accurate than traditional centrally calculated inter fragmentary movement values; stiffness was found to be highly susceptible to the accuracy of deformation measurements and constraint method, and should only be used as a within study comparison method. The reported stiffness values of locked plate constructs from in vitro mechanical testing is highly susceptible to testing constraints and output measures, with many standard techniques overestimating the stiffness of the construct. This raises the need for further investigation into the actual mechanical behaviour within the fracture gap of these devices.