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The aim of this study is to investigate the potential anti-cancer activity of l-amino acid oxidase (CP-LAAO) purified from the venom of Cryptelytrops purpureomaculatus on SW480 and SW620 human colon cancer cells. Mass spectrometry guided purification was able to identify and purify CP-LAAO. Amino acid variations identified from the partial protein sequence of CP-LAAO may suggest novel variants of these proteins. The activity of the purified CP-LAAO was confirmed with o-phenyldiamine (OPD)-based spectrophotometric assay. CP-LAAO demonstrated time- and dose-dependent cytotoxic activity and the EC 50 value was determined at 13 µg/mL for both SW480 and SW620 cells. Significant increase of caspase-3 activity, reduction of Bcl-2 levels, as well as morphological changes consistent with apoptosis were demonstrated by CP-LAAO. Overall, these data provide evidence on the potential anti-cancer activity of CP-LAAO from the venom of Malaysian C. purpureomaculatus for therapeutic intervention of human colon cancer.

Purpose: Human epidermal growth factor receptor 2 (Erbb2/HER2) overexpression, which was previously detected in invasive breast cancer, has now been implicated in advanced gastric cancer (GC) and gastroesophageal junction cancer (GEC). A study was conducted to determine the rate of HER2 positivity in patients with locally advanced or metastatic GC and GEC in Malaysia and to assess the impact of various demographic and clinical parameters on HER2 positivity., Methods: A total of 228 adult patients with GC or GEC were enrolled from Subang Jaya Medical Centre, Malaysia, for retrospective (210) and prospective study. All patients were subjected to the HER2 immunohistochemistry test using an FDA-approved, standardized test kit. Carcinomas scoring 2+ on immunohistochemistry were further tested with HER2 in situ hybridization (ISH) using an FDA-approved test kit., Results: The overall rate of HER2 positivity in the population studied was 24.6% (n = 56). The rate was significantly higher in men than in women (29.6 vs. 16.3%; p = 0.024). HER2 overexpression was significantly more common in diffuse type than in intestinal type of tumors (39.8 vs. 14.9%; p < 0.001). In our study, out of 56 samples, 44 (78.6%) were considered for gene amplification testing, out of which 40 (90.1%) samples showed gene amplification. There was no statistically significant correlation between HER2 positivity and patient age, race, tumor location, tumor differentiation, and TNM staging., Conclusions: HER2 overexpression was evident in nearly 25% of the Malaysian patients with locally advanced or metastatic gastric cancer. The overexpression correlated significantly with male gender and diffuse-type tumors. The majority of the IHC-positive tumors demonstrated c-erb2 gene amplification and this finding reached statistical significance.

Patient-specific computer models have been developed representing a variety of aspects of the cardiovascular system spanning the disciplines of electrophysiology, electromechanics, solid mechanics, and fluid dynamics. These physiological mechanistic models predict macroscopic phenomena such as electrical impulse propagation and contraction throughout the entire heart as well as flow and pressure dynamics occurring in the ventricular chambers, aorta, and coronary arteries during each heartbeat. Such models have been used to study a variety of clinical scenarios including aortic aneurysms, coronary stenosis, cardiac valvular disease, left ventricular assist devices, cardiac resynchronization therapy, ablation therapy, and risk stratification. After decades of research, these models are beginning to be incorporated into clinical practice directly via marketed devices and indirectly by improving our understanding of the underlying mechanisms of health and disease within a clinical context.

Computational models of cardiac electrophysiology have a long history in basic science applications and device design and evaluation, but have significant potential for clinical applications in all areas of cardiovascular medicine, including functional imaging and mapping, drug safety evaluation, disease diagnosis, patient selection, and therapy optimisation or personalisation. For all stakeholders to be confident in model-based clinical decisions, cardiac electrophysiological (CEP) models must be demonstrated to be trustworthy and reliable. Credibility, that is, the belief in the predictive capability, of a computational model is primarily established by performing validation, in which model predictions are compared to experimental or clinical data. However, there are numerous challenges to performing validation for highly complex multi-scale physiological models such as CEP models. As a result, credibility of CEP model predictions is usually founded upon a wide range of distinct factors, including various types of validation results, underlying theory, evidence supporting model assumptions, evidence from model calibration, all at a variety of scales from ion channel to cell to organ. Consequently, it is often unclear, or a matter for debate, the extent to which a CEP model can be trusted for a given application. The aim of this article is to clarify potential rationale for the trustworthiness of CEP models by reviewing evidence that has been (or could be) presented to support their credibility. We specifically address the complexity and multi-scale nature of CEP models which makes traditional model evaluation difficult. In addition, we make explicit some of the credibility justification that we believe is implicitly embedded in the CEP modeling literature. Overall, we provide a fresh perspective to CEP model credibility, and build a depiction and categorisation of the wide-ranging body of credibility evidence for CEP models. This paper also represents a step toward the extension of model evaluation methodologies that are currently being developed by the medical device community, to physiological models.

Suspected virus-like symptoms were observed in cacao plants in Trinidad during 1943, and the viruses associated with these symptoms were designated as strains A and B of cacao Trinidad virus (CTV). However, viral etiology has not been demonstrated for either phenotype. Total DNA was isolated from symptomatic cacao leaves exhibiting the CTV A and B phenotypes and subjected to Illumina HiSeq and Sanger DNA sequencing. Based on de novo assembly, two apparently full-length badnavirus genomes of 7,533 and 7,454 nucleotides (nt) were associated with CTV strain A and B, respectively. The Trinidad badnaviral genomes contained four open reading frames, three of which are characteristic of other known badnaviruses, and a fourth that is present in only some badnaviruses. Both badnaviral genomes harbored hallmark caulimovirus-like features, including a tRNA Met priming site, a TATA box, and a polyadenylation-like signal. Pairwise comparisons of the RT-RNase H region indicated that the Trinidad isolates share 57-71% nt sequence identity with other known badnaviruses. Based on the system for badnavirus species demarcation in which viruses with less than 80% nt sequence identity in the RT-RNase gene are considered members of separate species, these isolates represent two previously unidentified badnaviruses, herein named cacao mild mosaic virus and cacao yellow vein banding virus, making them the first cacao-infecting badnaviruses identified thus far in the Western Hemisphere.

Head and neck squamous cell carcinoma (HNSCC) is generalized term that encompasses a diverse group of cancers that includes tumours of the oral cavity (OSCC), oropharynx (OPSCC) and nasopharynx (NPC). Genetic alterations that are common to all HNSCC types are likely to be important for squamous carcinogenesis. In this study, we have investigated the role of the homeodomain-only homeobox gene, HOPX, in the pathogenesis of HNSCC. We show that HOPX mRNA levels are reduced in OSCC and NPC cell lines and tissues and there is a general reduction of HOPX protein expression in these tumours and OPSCCs. HOPX promoter methylation was observed in a subset of HNSCCs and was associated with a worse overall survival in HPV negative tumours. RNAseq analysis of OSCC cells transfected with HOPX revealed a widespread deregulation of the transcription of genes related to epithelial homeostasis and ectopic over-expression of HOPX in OSCC and NPC cells inhibited cell proliferation, plating efficiency and migration, and enhanced sensitivity to UVA-induced apoptosis. Our results demonstrate that HOPX functions as a tumour suppressor in HNSCC and suggest a central role for HOPX in suppressing epithelial carcinogenesis.

Key Points: Mathematical and computational models of cardiac physiology have been an integral component of cardiac electrophysiology since its inception, and are collectively known as the Cardiac Physiome. We identify and classify the numerous sources of variability and uncertainty in model formulation, parameters and other inputs that arise from both natural variation in experimental data and lack of knowledge. The impact of uncertainty on the outputs of Cardiac Physiome models is not well understood, and this limits their utility as clinical tools. We argue that incorporating variability and uncertainty should be a high priority for the future of the Cardiac Physiome. We suggest investigating the adoption of approaches developed in other areas of science and engineering while recognising unique challenges for the Cardiac Physiome; it is likely that novel methods will be necessary that require engagement with the mathematics and statistics community., Abstract: The Cardiac Physiome effort is one of the most mature and successful applications of mathematical and computational modelling for describing and advancing the understanding of physiology. After five decades of development, physiological cardiac models are poised to realise the promise of translational research via clinical applications such as drug development and patient-specific approaches as well as ablation, cardiac resynchronisation and contractility modulation therapies. For models to be included as a vital component of the decision process in safety-critical applications, rigorous assessment of model credibility will be required. This White Paper describes one aspect of this process by identifying and classifying sources of variability and uncertainty in models as well as their implications for the application and development of cardiac models. We stress the need to understand and quantify the sources of variability and uncertainty in model inputs, and the impact of model structure and complexity and their consequences for predictive model outputs. We propose that the future of the Cardiac Physiome should include a probabilistic approach to quantify the relationship of variability and uncertainty of model inputs and outputs., (© 2016 The Authors. The Journal of Physiology published by John Wiley & Sons Ltd on behalf of The Physiological Society.)

The categorisation of lung disease into obstructive ventilatory defect (OVD) and tendency to a restrictive ventilatory defect (TRVD) patterns using spirometry is used to guide both prognostication and treatment. The effectiveness of categorisation depends upon having reference ranges that accurately represent the population they describe. The Global Lung Initiative 2012 (GLI 2012) has spirometry reference ranges drawn from the largest sample size to date. This study aimed to determine whether using spirometry reference ranges from the new GLI 2012 dataset, compared to the previously used National Health and Nutritional Examination Survey III (NHANES III) dataset, resulted in a change in diagnosis between OVD, TRVD and normal ventilatory pattern (NVP). Spirometry data were collected from 301 patients, aged 18-80 years, undergoing investigation at the Gold Coast Hospital and Health Service (GCHHS) throughout February and March 2014. OVD was defined as a forced expiratory volume in 1 second (FEV 1 ) divided by forced vital capacity (FVC) less than lower limit of normal (LLN). TRVD was defined as FEV 1 /FVC ≥ LLN, FEV 1 < LLN, and FVC < LLN. The LLN values were determined by equations from the GLI and NHANES datasets. Spirometry interpreted using the NHANES III equations showed: 102 individuals (33.9%) with normal spirometry, 136 (45.2%) with an OVD pattern, 52 (17.3%) with a TRVD pattern, and 11 (3.7%) with a mixed pattern. When the spirometry data were interpreted using the GLI 2012 equations 2 (0.7%) individuals changed from OVD to NVP, 2 (0.7%) changed from NVP to OVD and 14 (4.7%) changed from TRVD to NVP. Using the GLI 2012 reference range resulted in a change in diagnosis of lung disease in 5.9% of the individuals included in this study. This variance in diagnosis when changing reference ranges should be taken into account by clinicians as it may affect patient management., Competing Interests: The authors have no conflicts of interest to declare.

Tropidolaemus wagleri and Cryptelytrops purpureomaculatus are venomous pit viper species commonly found in Malaysia. Tandem mass spectrometry analysis of the crude venoms has detected different proteins in T. wagleri and C. purpureomaculatus . They were classified into 13 venom protein families consisting of enzymatic and nonenzymatic proteins. Enzymatic families detected in T. wagleri and C. purpureomaculatus venom were snake venom metalloproteinase, phospholipase A₂, ʟ-amino acid oxidase, serine proteases, 5'-nucleotidase, phosphodiesterase, and phospholipase B. In addition, glutaminyl cyclotransferase was detected in C. purpureomaculatus . C-type lectin-like proteins were common nonenzymatic components in both species. Waglerin was present and unique to T. wagleri -it was not in C. purpureomaculatus venom. In contrast, cysteine-rich secretory protein, bradykinin-potentiating peptide, and C-type natriuretic peptide were present in C. purpureomaculatus venom. Composition of the venom proteome of T. wagleri and C. purpureomaculatus provides useful information to guide production of effective antivenom and identification of proteins with potential therapeutic applications., Competing Interests: The authors declare no conflict of interest.

Elucidating the underlying mechanisms of fatal cardiac arrhythmias requires a tight integration of electrophysiological experiments, models, and theory. Existing models of transmembrane action potential (AP) are complex (resulting in over parameterization) and varied (leading to dissimilar predictions). Thus, simpler models are needed to elucidate the "minimal physiological requirements" to reproduce significant observable phenomena using as few parameters as possible. Moreover, models have been derived from experimental studies from a variety of species under a range of environmental conditions (for example, all existing rabbit AP models incorporate a formulation of the rapid sodium current, INa, based on 30 year old data from chick embryo cell aggregates). Here we develop a simple "parsimonious" rabbit AP model that is mathematically identifiable (i.e., not over parameterized) by combining a novel Hodgkin-Huxley formulation of INa with a phenomenological model of repolarization similar to the voltage dependent, time-independent rectifying outward potassium current (IK). The model was calibrated using the following experimental data sets measured from the same species (rabbit) under physiological conditions: dynamic current-voltage (I-V) relationships during the AP upstroke; rapid recovery of AP excitability during the relative refractory period; and steady-state INa inactivation via voltage clamp. Simulations reproduced several important "emergent" phenomena including cellular alternans at rates > 250 bpm as observed in rabbit myocytes, reentrant spiral waves as observed on the surface of the rabbit heart, and spiral wave breakup. Model variants were studied which elucidated the minimal requirements for alternans and spiral wave break up, namely the kinetics of INa inactivation and the non-linear rectification of IK.The simplicity of the model, and the fact that its parameters have physiological meaning, make it ideal for engendering generalizable mechanistic insight and should provide a solid "building-block" to generate more detailed ionic models to represent complex rabbit electrophysiology., Competing Interests: The authors have declared that no competing interests exist.

Cardiac electrophysiology models have been developed for over 50years, and now include detailed descriptions of individual ion currents and sub-cellular calcium handling. It is commonly accepted that there are many uncertainties in these systems, with quantities such as ion channel kinetics or expression levels being difficult to measure or variable between samples. Until recently, the original approach of describing model parameters using single values has been retained, and consequently the majority of mathematical models in use today provide point predictions, with no associated uncertainty. In recent years, statistical techniques have been developed and applied in many scientific areas to capture uncertainties in the quantities that determine model behaviour, and to provide a distribution of predictions which accounts for this uncertainty. In this paper we discuss this concept, which is termed uncertainty quantification, and consider how it might be applied to cardiac electrophysiology models. We present two case studies in which probability distributions, instead of individual numbers, are inferred from data to describe quantities such as maximal current densities. Then we show how these probabilistic representations of model parameters enable probabilities to be placed on predicted behaviours. We demonstrate how changes in these probability distributions across data sets offer insight into which currents cause beat-to-beat variability in canine APs. We conclude with a discussion of the challenges that this approach entails, and how it provides opportunities to improve our understanding of electrophysiology., (Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Background: APOBEC3B is a cytosine deaminase implicated in immune response to viral infection, cancer predisposition and carcinogenesis. Germline APOBEC3B deletion is more common in East Asian women and confers a modest risk to breast cancer in both East Asian and Caucasian women. Analysis of tumour samples from women of European descent has shown that germline APOBEC3B deletion is associated with an increased propensity to develop somatic mutations and with an enrichment for immune response-related gene sets. However, this has not been examined in Asian tumour samples, where population differences in genetic and dietary factors may have an impact on the immune system., Methods: In this study, we determined the prevalence of germline APOBEC3B deletion and its association with breast cancer risk in a cross-sectional hospital-based Asian multi-ethnic cohort of 1451 cases and 1442 controls from Malaysia. We compared gene expression profiles of breast cancers arising from APOBEC3B deletion carriers and non-carriers using microarray analyses. Finally, we characterised the overall abundance of tumour-infiltrating immune cells in breast cancers from TCGA and METABRIC using ESTIMATE and relative frequency of 22 immune cell subsets in breast cancers from METABRIC using CIBERSORT., Results: The minor allelic frequency of APOBEC3B deletion was estimated to be 0.35, 0.42 and 0.16 in female populations of Chinese, Malay and Indian descent, respectively, and that germline APOBEC3B deletion was associated with breast cancer risk with odds ratios of 1.23 (95 % CI: [1.05, 1.44]) for one-copy deletion and 1.38 (95 % CI: [1.10, 1.74]) for two-copy deletion compared to women with no deletion. Germline APOBEC3B deletion was not associated with any clinicopathologic features or the expression of any APOBEC family members but was associated with immune response-related gene sets (FDR q values < 0.05). Analysis of breast cancers from METABRIC revealed breast cancers from APOBEC3B deletion carriers to have significantly higher abundance of tumour-infiltrating immune cells (P < 0.001)., Conclusions: Taken together, our data suggests that tumour-infiltrating immune cells may be an important feature of breast cancers arising in women with APOBEC3B germline deletion, and that this may be of particular interest in Asian women where the germline deletion is more common.

The qualitative heterogeneity and increasing consumption of cocoa products require fast and efficient methods for quality assessment of fermented cocoa with regard to fermentation quality and flavor potential. To date, quality control is achieved by visual inspection (e.g., "cut test") and sensory testing. Chromatographic methods for quantification of flavor relevant substances are limited in their applicability in standard quality control due to laborious isolation and purification steps. Therefore, the aim of this study was the development of a near infrared spectroscopic (NIRS) method for routine analytical prediction of biochemical quality parameters. Different compound classes like phenolic substances (R(2)=0.93) or organic acids (R(2)=0.88) as well as individual substances like epicatechin (R(2)=0.93) or lactic acid (R(2)=0.87) could be precisely determined just as fermentation time (R(2)=0.92) and pH value (R(2)=0.94) presenting NIRS as fast and reliable alternative in routine quality assessment., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

Introduction: The efficacy of epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors in EGFR mutation-positive non-small-cell lung cancer (NSCLC) patients necessitates accurate, timely testing. Although EGFR mutation testing has been adopted by many laboratories in Asia, data are lacking on the proportion of NSCLC patients tested in each country, and the most commonly used testing methods., Methods: A retrospective survey of records from NSCLC patients tested for EGFR mutations during 2011 was conducted in 11 Asian Pacific countries at 40 sites that routinely performed EGFR mutation testing during that period. Patient records were used to complete an online questionnaire at each site., Results: Of the 22,193 NSCLC patient records surveyed, 31.8% (95% confidence interval: 31.2%-32.5%) were tested for EGFR mutations. The rate of EGFR mutation positivity was 39.6% among the 10,687 cases tested. The majority of samples were biopsy and/or cytology samples (71.4%). DNA sequencing was the most commonly used testing method accounting for 40% and 32.5% of tissue and cytology samples, respectively. A pathology report was available only to 60.0% of the sites, and 47.5% were not members of a Quality Assurance Scheme., Conclusions: In 2011, EGFR mutation testing practices varied widely across Asia. These data provide a reference platform from which to improve the molecular diagnosis of NSCLC, and EGFR mutation testing in particular, in Asia.

Undifferentiated nasopharyngeal carcinoma (NPC) is a highly metastatic disease that is consistently associated with Epstein-Barr virus (EBV) infection. In this study, we have investigated the contribution of lysophosphatidic acid (LPA) signalling to the pathogenesis of NPC. Here we demonstrate two distinct functional roles for LPA in NPC. First, we show that LPA enhances the migration of NPC cells and second, that it can inhibit the activity of EBV-specific cytotoxic T cells. Focusing on the first of these phenotypes, we show that one of the LPA receptors, LPA receptor 5 (LPAR5), is down-regulated in primary NPC tissues and that this down-regulation promotes the LPA-induced migration of NPC cell lines. Furthermore, we found that EBV infection or ectopic expression of the EBV-encoded LMP2A was sufficient to down-regulate LPAR5 in NPC cell lines. Our data point to a central role for EBV in mediating the oncogenic effects of LPA in NPC and identify LPA signalling as a potential therapeutic target in this disease., (Copyright © 2014 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.)

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common malignancy worldwide. Evidence suggests that miRNAs play an important role in progression, recurrence, metastasis and postoperative survival of HNSCC. Studies have investigated the utility of miRNAs as diagnostic/prognostic tools and as potential therapeutic targets and biomarkers that may improve the management and outcomes of HNSCC. The aim of this article is to review the current literature on aberrant expression profiles of miRNAs in biopsy samples of HNSCC and their role in cancer development, metastasis, prognosis and survival of these patients. This review gives an overview that miRNAs deregulation play major role in the development of HNSCC. They offer the potential to be used as biomarkers or novel therapeutic targets. Future research is required to test their use in both of these fields.

The mechanisms underlying ventricular fibrillation (VF) are not well understood. The electrical activity on the heart surface during VF has been recorded extensively in the experimental setting and in some cases clinically; however, corresponding transmural activation patterns are prohibitively difficult to measure. In this paper, we use a high-resolution biventricular heart model to study three-dimensional electrical activity during fibrillation, focusing on the driving sources of VF: "filaments," the organising centres of unstable reentrant scroll waves. We show, for the first time, specific 3D filament dynamics during simulated VF in a whole heart geometry that includes fine-scale anatomical structures. Our results suggest that transmural activity is much more complex than what would be expected from surface observations alone. We present examples of complex intramural activity, including filament breakup and reattachment, anchoring to the thin right ventricular apex; rapid transitions among various filament shapes; and filament lengths much greater than wall thickness. We also present evidence for anatomy playing a major role in VF development and coronary vessels and trabeculae influencing filament dynamics. Overall, our results indicate that intramural activity during simulated VF is extraordinarily complex and suggest that further investigation of 3D filaments is necessary to fully comprehend recorded surface patterns.

Perhaps the most mature area of multi-scale systems biology is the modelling of the heart. Current models are grounded in over fifty years of research in the development of biophysically detailed models of the electrophysiology (EP) of cardiac cells, but one aspect which is inadequately addressed is the incorporation of uncertainty and physiological variability. Uncertainty quantification (UQ) is the identification and characterisation of the uncertainty in model parameters derived from experimental data, and the computation of the resultant uncertainty in model outputs. It is a necessary tool for establishing the credibility of computational models, and will likely be expected of EP models for future safety-critical clinical applications. The focus of this paper is formal UQ of one major sub-component of cardiac EP models, the steady-state inactivation of the fast sodium current, INa. To better capture average behaviour and quantify variability across cells, we have applied for the first time an 'individual-based' statistical methodology to assess voltage clamp data. Advantages of this approach over a more traditional 'population-averaged' approach are highlighted. The method was used to characterise variability amongst cells isolated from canine epi and endocardium, and this variability was then 'propagated forward' through a canine model to determine the resultant uncertainty in model predictions at different scales, such as of upstroke velocity and spiral wave dynamics. Statistically significant differences between epi and endocardial cells (greater half-inactivation and less steep slope of steady state inactivation curve for endo) was observed, and the forward propagation revealed a lack of robustness of the model to underlying variability, but also surprising robustness to variability at the tissue scale. Overall, the methodology can be used to: (i) better analyse voltage clamp data; (ii) characterise underlying population variability; (iii) investigate consequences of variability; and (iv) improve the ability to validate a model. To our knowledge this article is the first to quantify population variability in membrane dynamics in this manner, and the first to perform formal UQ for a component of a cardiac model. The approach is likely to find much wider applicability across systems biology as current application domains reach greater levels of maturity., (Published by Elsevier Ltd.)

For computational models of cardiac activity to be used in safety-critical clinical decision-making, thorough and rigorous testing of the accuracy of predictions is required. The field of 'verification, validation and uncertainty quantification' has been developed to evaluate the credibility of computational predictions. The first stage, verification, is the evaluation of how well computational software correctly solves the underlying mathematical equations. The aim of this paper is to introduce novel methods for verifying multi-cellular electro-physiological solvers, a crucial first stage for solvers to be used with confidence in clinical applications. We define 1D-3D model problems with exact solutions for each of the monodomain, bidomain, and bidomain-with-perfusing-bath formulations of cardiac electro-physiology, which allow for the first time the testing of cardiac solvers against exact errors on fully coupled problems in all dimensions. These problems are carefully constructed so that they can be easily run using a general solver and can be used to greatly increase confidence that an implementation is correct, which we illustrate by testing one major solver, 'Chaste', on the problems. We then perform case studies on calculation verification (also known as solution verification) for two specific applications. We conclude by making several recommendations regarding verification in cardiac modelling., (Copyright © 2013 John Wiley & Sons, Ltd.)

Tissue microstructure, in particular the alignment of myocytes (fibre direction) and their lateral organisation into sheets, is fundamental to cardiac function. We studied the effect of microstructure on contraction in a computational model of rat left ventricular electromechanics. Different fibre models, globally rule-based or locally optimised to DT-MRI data, were compared, in order to understand whether a subject-specific fibre model would enhance the predictive power of our model with respect to the global ones. We also studied the impact of sheets on ventricular deformation by comparing: (a) a transversely isotropic versus an orthotropic material law and (b) a linear model with a bimodal model of sheet transmural variation. We estimated ejection fraction, wall thickening and base-to-apex shortening and compared them with measures from cine-MRI. We also evaluated Lagrangian strains as local metrics of cardiac deformation. Our results show that the subject-specific fibre model provides little improvement in the metric predictions with respect to global fibre models while material orthotropy allows closer agreement with measures than transverse isotropy. Nonetheless, the impact of sheets in our model is smaller than that of fibres. We conclude that further investigation of the modelling of sheet dynamics is necessary to fully understand the impact of tissue structure on cardiac deformation.

Background: Currently there is a paucity of information about biomarkers that can predict hospitalization for acute exacerbations of chronic obstructive pulmonary disease (AECOPD) patients presenting to the emergency department (ED). There is limited data on the consistency of ED management of AECOPD with local COPD guidelines. The aim of this study was to identify biomarkers associated with hospitalization in AECOPD patients and to determine if the ED management was concordant with local COPD guidelines., Materials and Methods: We performed a retrospective audit of consecutive AECOPD patients presenting to the Gold Coast Hospital ED over a 6-month period., Results: During the study period, 122 AECOPD patients (51% male, mean age (SE) 71 (±11) years) presented to the ED. Ninety-eight (80%) patients were hospitalized. Univariate analysis identified certain factors associated with hospitalization: Older age, former smokers, home oxygen therapy, weekday presentation, SpO2 < 92%, and raised inflammatory markers (white cell count (WCC) and C-reactive protein (CRP)). After adjustment for multiple variable, increased age was significantly associated with hospitalization (odds ratio (OR) 1.09; 95% confidence interval (CI): 1.00-1.18; P = 0.05). Radiology assessment and pharmacological management was in accordance with COPD guidelines. However, spirometry was performed in 17% of patients and 28% of patients with hypercapneic respiratory failure received noninvasive ventilation (NIV)., Conclusion: We identified several factors on univariate analysis that were associated with hospitalization. Further research is required to determine the utility of these biomarkers in clinical practice. Also, while overall adherence to local COPD guidelines was good, there is scope for improvement in performing spirometry and provision of NIV to eligible patients.

Background: Mutations in the tyrosine kinase domain of the epidermal growth factor receptor (EGFR) in non- small cell lung cancer (NSCLC) are predictive of response to EGFR-targeted therapy in advanced stages of disease. This study aimed to determine the frequency of EGFR mutations in NSCLCs and to correlate their presence with clinical characteristics in multiethnic Malaysian patients., Materials and Methods: In this prospective study, EGFR mutations in exons 18, 19, 20 and 21 in formalin-fixed paraffin-embedded biopsy specimens of consecutive NSCLC patients were asessed by real-time polymerase chain reaction., Results: EGFR mutations were detected in NSCLCs from 55 (36.4%) of a total of 151 patients, being significantly more common in females (62.5%) than in males (17.2%) [odds ratio (OR), 8.00; 95% confidence interval (CI), 3.77-16.98; p<0.001] and in never smokers (62.5%) than in ever smokers (12.7%) (OR, 11.50; 95%CI, 5.08-26.03; p<0.001). Mutations were more common in adenocarcinoma (39.4%) compared to non-adenocarcinoma NSCLCs (15.8%) (p=0.072). The mutation rates in patients of different ethnicities were not significantly different (p=0.08). Never smoking status was the only clinical feature that independently predicted the presence of EGFR mutations (adjusted OR, 5.94; 95%CI, 1.94- 18.17; p=0.002)., Conclusions: In Malaysian patients with NSCLC, the EGFR mutation rate was similar to that in other Asian populations. EGFR mutations were significantly more common in female patients and in never smokers. Never smoking status was the only independent predictor for the presence of EGFR mutations.

Computational models of cardiac electrophysiology have been used for over half a century to investigate physiological mechanisms and generate hypotheses for experimental testing, and are now starting to play a role in clinical applications. There is currently a great deal of interest in using models as diagnostic or therapeutic aids, for example using patient-specific whole-heart simulations to optimize cardiac resynchronization therapy, ablation therapy, and defibrillation. However, if models are to be used in safety-critical clinical decision making, the reliability of their predictions needs to be thoroughly investigated. In engineering and the physical sciences, the field of "verification, validation and uncertainty quantification" (VVUQ) [also known as "verification and validation" (V&V)] has been developed for rigorously evaluating the credibility of computational model predictions. In this article we first discuss why it is vital that cardiac models be developed and evaluated within a VVUQ framework, and then consider cardiac models in the context of each of the stages in VVUQ. We identify some of the major difficulties which may need to be overcome for cardiac models to be used in safely-critical clinical applications.

Context: Hospitalized patients with acute exacerbations of chronic obstructive pulmonary disease (AECOPD) may be managed by either respiratory specialists (RS) or general medicine physicians (GMP). While previous studies have audited the hospital AECOPD management of RS, only a small number of studies have evaluated the management of GMP., Aims: The aims of this study were to firstly examine the differences in AECOPD management of GMP and RS and secondly compare their care to national COPD guidelines., Methods: A retrospective review was undertaken of consecutive AECOPD patients admitted to two hospitals (one hospital where all AECOPD patients were managed by RS and another where all AECOPD patients were managed by GMP) over a 3-month period. Electronic medical records, medical case notes, pathology and radiology data for the admission were reviewed., Results: There were 201 COPD exacerbations in 169 patients (49.7% male, mean age 72.3). GMP managed 84 (41.7%) exacerbations. In comparison to RS, GMP performed fewer spirometry tests, blood gas analysis and less frequently treated patients with guideline-recommended medications. Referral to pulmonary rehabilitation was poor for both groups of clinicians. Median length of stay was shorter in GMP patients versus RS patients (3 days vs. 5 days, P = 0.001). There were no differences in the 12-month re-admission (41.7% vs. 38.5%, P = 0.664) and mortality rates (10.7% vs. 6%, P = 0.292) between both groups of patients., Conclusion: Our study found differences in the hospital AECOPD management of GMP and RS, but these did not translate into different clinical outcomes between their patients. We also found suboptimal adherence to national COPD guidelines, suggesting that there is scope for improvement in the AECOPD management of both groups of clinicians.

Lymphoepithelial carcinoma (LEC) of the parotid gland is rare. When it does occur, it is usually seen in Asians and Greenland Eskimos. An association with Epstein-Barr virus (EBV) infection has been documented. We report a case of EBV-associated LEC of the parotid gland in a 30-year-old Chinese woman. The patient underwent a total parotidectomy with preservation of the facial nerve, followed by postoperative radiotherapy. She recovered well without complications or recurrence. We present this case in view of the rarity of LEC, which has prevented extensive study of its clinical course, optimal treatment options, and overall prognosis.

Introduction: Despite available data from other Asian countries, the prevalence of epidermal growth factor receptor (EGFR) mutations among lung adenocarcinoma patients has not been reported in Malaysia. This study sought to determine the frequency of EGFR mutations among multiethnic Malaysian patients diagnosed with lung adenocarcinoma., Methods: Demographic and clinical information of patients whose lung adenocarcinoma biopsy specimens were submitted for EGFR mutation testing at Sime Darby Medical Center from 2009 to 2011 were analyzed. EGFR mutations at exons 18, 19, 20, and 21 were detected either through bidirectional sequencing or real-time polymerase chain reaction., Results: Among 812 patients in the study, 49% were female, 63.7% were ethnic Chinese, 29.4% Malay, 4.8% Indian, and 2.1% other ethnic groups. Mutations were present in the tumors of 321 patients (39.5%), with mutations at exons 19 (23.5%) and 21 (14.9%) being the most common. Mutations were significantly more frequent among women than in men (52.5% versus 27.8%, p < 0.001). Although mutations were more common among Chinese (40.8%) compared with Malay (37.2%) or Indian (33.3%) patients, the difference was not statistically significant (p = 0.591). Of 211 patients with smoking history records, never-smokers had a higher mutation rate compared with ever-smokers (54.8% versus 20.7%, p < 0.001)., Conclusion: EGFR mutations were present in 39.5% of patients. Mutations were more common in women and never-smokers with no differences in mutation frequency between different ethnicities. Because of the high mutation rates, reflex testing for EGFR mutation should be a routine practice for advanced lung adenocarcinoma patients in Malaysia.

A patient with a medial and posterior dislocation of the right sterno-clavicular (SC) joint and displacement of the trachea and brachiocephalic artery by the medial head of the clavicle underwent general anaesthetic in the operating theatre for an open reduction procedure. The surgeon initially attempted a closed reduction, but this required imaging to check SC alignment. The patient was transferred to an adjacent hybrid operating theatre for imaging. Cone beam computed tomography (CBCT) was performed, which successfully demonstrated a significant reduction in the dislocation of the SC joint. The trachea and brachiocephalic artery were no longer compressed or displaced. This case study demonstrates an alternative to the patient being transferred to the medical imaging department for multi-slice CT. It also describes a novel use of the hybrid operating theatre and its CBCT capabilities.

Background and Purpose: Understanding drug effects on the heart is key to safety pharmacology assessment and anti-arrhythmic therapy development. Here our goal is to demonstrate the ability of computational models to simulate the effect of drug action on the electrical activity of the heart, at the level of the ion-channel, cell, heart and ECG body surface potential., Experimental Approach: We use the state-of-the-art mathematical models governing the electrical activity of the heart. A drug model is introduced using an ion channel conductance block for the hERG and fast sodium channels, depending on the IC(50) value and the drug dose. We simulate the ECG measurements at the body surface and compare biomarkers under different drug actions., Key Results: Introducing a 50% hERG-channel current block results in 8% prolongation of the APD(90) and 6% QT interval prolongation, hERG block does not affect the QRS interval. Introducing 50% fast sodium current block prolongs the QRS and the QT intervals by 12% and 5% respectively, and delays activation times, whereas APD(90) is not affected., Conclusions and Implications: Both potassium and sodium blocks prolong the QT interval, but the underlying mechanism is different: for potassium it is due to APD prolongation; while for sodium it is due to a reduction of electrical wave velocity. This study shows the applicability of in silico models for the investigation of drug effects on the heart, from the ion channel to the ECG-based biomarkers., (© 2012 The Authors. British Journal of Pharmacology © 2012 The British Pharmacological Society.)

Chaste - Cancer, Heart And Soft Tissue Environment - is an open source C++ library for the computational simulation of mathematical models developed for physiology and biology. Code development has been driven by two initial applications: cardiac electrophysiology and cancer development. A large number of cardiac electrophysiology studies have been enabled and performed, including high-performance computational investigations of defibrillation on realistic human cardiac geometries. New models for the initiation and growth of tumours have been developed. In particular, cell-based simulations have provided novel insight into the role of stem cells in the colorectal crypt. Chaste is constantly evolving and is now being applied to a far wider range of problems. The code provides modules for handling common scientific computing components, such as meshes and solvers for ordinary and partial differential equations (ODEs/PDEs). Re-use of these components avoids the need for researchers to 're-invent the wheel' with each new project, accelerating the rate of progress in new applications. Chaste is developed using industrially-derived techniques, in particular test-driven development, to ensure code quality, re-use and reliability. In this article we provide examples that illustrate the types of problems Chaste can be used to solve, which can be run on a desktop computer. We highlight some scientific studies that have used or are using Chaste, and the insights they have provided. The source code, both for specific releases and the development version, is available to download under an open source Berkeley Software Distribution (BSD) licence at http://www.cs.ox.ac.uk/chaste, together with details of a mailing list and links to documentation and tutorials.

The bidomain framework has been extensively used to model tissue electrophysiology in a variety of applications. One limitation of the bidomain model is that it describes the activity of only one cell type interacting with the extracellular space. If more than one cell type contributes to the tissue electrophysiology, then the bidomain model is not sufficient. Recently, evidence has suggested that this is the case for at least two important applications: cardiac and gastrointestinal tissue electrophysiology. In the heart, fibroblasts ubiquitously interact with myocytes and are believed to play an important role in the organ electrophysiology. Along the GI tract, interstitial cells of Cajal (ICC) generate electrical waves that are passed on to surrounding smooth muscle cells (SMC), which are interconnected with the ICC and with each other. Because of the contribution of more than one cell type to the overall organ electrophysiology, investigators in different fields have independently proposed similar extensions of the bidomain model to incorporate multiple cell types and tested it on simplified geometries. In this paper, we provide a general derivation of such an extended bidomain framework applicable to any tissue and provide a generic and efficient implementation applicable to any geometry. Proof-of-concept results of tissue electrophysiology on realistic 3D organ geometries using the extended bidomain framework are presented for the heart and the stomach., (This journal is © The Royal Society of Chemistry 2012)

Theobroma cacao is an economically important tree of several tropical countries. Its genetic improvement is essential to provide protection against major diseases and improve chocolate quality. We discovered and mapped new expressed sequence tag-single nucleotide polymorphism (EST-SNP) and simple sequence repeat (SSR) markers and constructed a high-density genetic map. By screening 149 650 ESTs, 5246 SNPs were detected in silico, of which 1536 corresponded to genes with a putative function, while 851 had a clear polymorphic pattern across a collection of genetic resources. In addition, 409 new SSR markers were detected on the Criollo genome. Lastly, 681 new EST-SNPs and 163 new SSRs were added to the pre-existing 418 co-dominant markers to construct a large consensus genetic map. This high-density map and the set of new genetic markers identified in this study are a milestone in cocoa genomics and for marker-assisted breeding. The data are available at http://tropgenedb.cirad.fr.

Ongoing developments in cardiac modelling have resulted, in particular, in the development of advanced and increasingly complex computational frameworks for simulating cardiac tissue electrophysiology. The goal of these simulations is often to represent the detailed physiology and pathologies of the heart using codes that exploit the computational potential of high-performance computing architectures. These developments have rapidly progressed the simulation capacity of cardiac virtual physiological human style models; however, they have also made it increasingly challenging to verify that a given code provides a faithful representation of the purported governing equations and corresponding solution techniques. This study provides the first cardiac tissue electrophysiology simulation benchmark to allow these codes to be verified. The benchmark was successfully evaluated on 11 simulation platforms to generate a consensus gold-standard converged solution. The benchmark definition in combination with the gold-standard solution can now be used to verify new simulation codes and numerical methods in the future.

In this paper, we review multi-scale models of solid tumour growth and discuss a middle-out framework that tracks individual cells. By focusing on the cellular dynamics of a healthy colorectal crypt and its invasion by mutant, cancerous cells, we compare a cell-centre, a cell-vertex and a continuum model of cell proliferation and movement. All models reproduce the basic features of a healthy crypt: cells proliferate near the crypt base, they migrate upwards and are sloughed off near the top. The models are used to establish conditions under which mutant cells are able to colonize the crypt either by top-down or by bottom-up invasion. While the continuum model is quicker and easier to implement, it can be difficult to relate system parameters to measurable biophysical quantities. Conversely, the greater detail inherent in the multi-scale models means that experimentally derived parameters can be incorporated and, therefore, these models offer greater scope for understanding normal and diseased crypts, for testing and identifying new therapeutic targets and for predicting their impacts.

Simulation of cardiac electrical activity using the bi-domain equations can be a massively computationally demanding problem. This study provides a comprehensive guide to numerical bi-domain modelling. Each component of bi-domain simulations--discretization, ODE-solution, linear system solution, and parallelization--is discussed, and previously-used methods are reviewed, new methods are proposed, and issues which cause particular difficulty are highlighted. Particular attention is paid to the choice of stimulus currents, compatibility conditions for the equations, the solution of singular linear systems, and convergence of the numerical scheme., (2010 Elsevier Ltd. All rights reserved.)

Aim: Pleural procedures may cause patient discomfort and serious complications if performed inadequately. We surveyed junior doctors to provide information about training and experience., Methods: We surveyed 493 junior doctors working in departments involved in pleural procedures in three teaching hospitals via postal questionnaires in 2002., Results: The response rate was 66%. Formal training in the performance of pleural procedures was limited at undergraduate and postgraduate levels. Theoretical training at postgraduate level in pleural aspiration, chest drain insertion, and closed pleural biopsies was reported by 34%, 40%, and 14% of respondents respectively. Practical training using animal or artificial models occurred infrequently. Pleural aspiration, chest drain insertion, and pleural biopsy had been performed at least once by 91%, 66%, and 41% of respondents respectively. Most doctors felt they needed more training in chest drain insertion and pleural biopsy. Confidence in performing procedures was related to the number of times the procedure had been performed but not to formal teaching., Conclusions: This study provides a comprehensive survey of the background training, experience and confidence levels of junior medical staff in performing pleural procedures. Training in pleural procedures was limited and our results suggest the need for better training programmes and supervision of junior doctors.

Recent work has described the software engineering and computational infrastructure that has been set up as part of the Cancer, Heart and Soft Tissue Environment (CHASTE) project. CHASTE is an open source software package that currently has heart and cancer modelling functionality. This software has been written using a programming paradigm imported from the commercial sector and has resulted in a code that has been subject to a far more rigorous testing procedure than that is usual in this field. In this paper, we explain how new functionality may be incorporated into CHASTE. Whiteley has developed a numerical algorithm for solving the bidomain equations that uses the multi-scale (MS) nature of the physiology modelled to enhance computational efficiency. Using a simple geometry in two dimensions and a purpose-built code, this algorithm was reported to give an increase in computational efficiency of more than two orders of magnitude. In this paper, we begin by reviewing numerical methods currently in use for solving the bidomain equations, explaining how these methods may be developed to use the MS algorithm discussed above. We then demonstrate the use of this algorithm within the CHASTE framework for solving the monodomain and bidomain equations in a three-dimensional realistic heart geometry. Finally, we discuss how CHASTE may be developed to include new physiological functionality--such as modelling a beating heart and fluid flow in the heart--and how new algorithms aimed at increasing the efficiency of the code may be incorporated.

Aim: To determine the patient characteristics, referral patterns and delays in assessment and treatment of patients with primary lung cancer in South Auckland, New Zealand and compare with international standards., Methods: Retrospective review of the clinical records of 80 patients referred to a secondary care respiratory service and diagnosed with primary lung cancer in 2004., Results: Eighty-five percent of inpatient referrals and 48.5% of outpatient referrals were for advanced stage lung cancers. The median interval from receipt of outpatient referral to first chest physician assessment was 18 days, with median interval from the first chest physician assessment to bronchoscopy of 17 days and for staging CT chest of 16 days. For patients requiring a CT-guided percutaneous needle aspiration for diagnosis, there was a further median delay of 37 days after the initial CT scan. The median interval from the date of receipt of initial outpatient referral to diagnosis was 38 days, but for early stage lung cancers it was 54 days. The median interval to diagnosis for inpatient admissions was 6 days after the first respiratory assessment., Conclusion: The intervals for initial assessment, diagnosis and treatment of lung cancer in South Auckland do not meet the recommendations of international guidelines, especially for early stage lung cancers. Organisational and resource changes are required at each point in the diagnostic and management pathway to reduce delays.

Background and Objective: It has been suggested that pulmonary embolism (PE) is an under-recognized cause of pleural effusion. This study aimed to (i) establish the incidence and clinical relevance of pleural effusion in patients with pulmonary emboli; and (ii) determine if there is a relationship between development of pleural effusions and the location of emboli and number of pulmonary arteries involved., Methods: A retrospective analysis of all CT pulmonary angiograms (CTPA) performed over 12 months on adult patients with clinically suspected PE in a hospital which used CTPA as first-line imaging investigation for PE., Results: Of 285 CTPA, 60 patients (21%) had evidence of pulmonary emboli (38 had both central and peripheral clots and 22 peripheral emboli only). Emboli were bilateral in 39 cases and unilateral in 21 cases. Pleural effusion was present in almost one half (n = 29, 48%) of the patients with pulmonary emboli. Patients with pulmonary emboli were more likely to have a pleural effusion (OR 2.2 (95% CI: 1.1-4.7), P < 0.05) than patients without PE; however, the effusions were generally very small. Most (86%) of the effusions were present on the same side as the emboli. The location of emboli and number of arteries involved did not predict the presence of pleural effusions., Conclusions: Pleural effusion is common in patients with pulmonary emboli demonstrated on CTPA. These effusions are small and seldom alter clinical management. Clinicians should therefore have a high threshold of suspicion in attributing large or contralateral pleural effusions to embolic diseases without excluding alternative diagnoses.

Breast cancer is one of the biggest killers in the western world, and early diagnosis is essential for improved prognosis. The shape of the breast varies hugely between the scenarios of magnetic resonance (MR) imaging (patient lies prone, breast hanging down under gravity), X-ray mammography (breast strongly compressed) and ultrasound or biopsy/surgery (patient lies supine), rendering image fusion an extremely difficult task. This paper is concerned with the use of the finite-element method and nonlinear elasticity to build a 3-D, patient-specific, anatomically accurate model of the breast. The model is constructed from MR images and can be deformed to simulate breast shape and predict tumor location during mammography or biopsy/surgery. Two extensions of the standard elasticity problem need to be solved: an inverse elasticity problem (arising from the fact that only a deformed, stressed, state is known initially), and the contact problem of modeling compression. The model is used for craniocaudal mediolateral oblique mammographic image matching, and a number of numerical experiments are performed.

Cardiac modelling is the area of physiome modelling where the available simulation software is perhaps most mature, and it therefore provides an excellent starting point for considering the software requirements for the wider physiome community. In this paper, we will begin by introducing some of the most advanced existing software packages for simulating cardiac electrical activity. We consider the software development methods used in producing codes of this type, and discuss their use of numerical algorithms, relative computational efficiency, usability, robustness and extensibility. We then go on to describe a class of software development methodologies known as test-driven agile methods and argue that such methods are more suitable for scientific software development than the traditional academic approaches. A case study is a project of our own, Cancer, Heart and Soft Tissue Environment, which is a library of computational biology software that began as an experiment in the use of agile programming methods. We present our experiences with a review of our progress thus far, focusing on the advantages and disadvantages of this new approach compared with the development methods used in some existing packages. We conclude by considering whether the likely wider needs of the cardiac modelling community are currently being met and suggest that, in order to respond effectively to changing requirements, it is essential that these codes should be more malleable. Such codes will allow for reliable extensions to include both detailed mathematical models--of the heart and other organs--and more efficient numerical techniques that are currently being developed by many research groups worldwide.

An investigation was carried out to determine the diversity of 30 isolates of slow growing pigeonpea nodulating rhizobia based on variations in partial sequences of the 16S rRNA gene and numerical analysis of 80 phenotypic traits. Phylogenetic analysis using molecular sequences of 23 isolates showed that ARPE1 separated from the other isolates at an average distance of >14% divergence level. The other isolates were all within 5% divergence from each other but separated into four main groups, with group 1 containing 16 of the 23 isolates. Comparisons to sequences of reference strains revealed that the group 1 isolates were phylogenetically closely related to the slow growing soybean nodulating rhizobia belonging to Bradyrhizobium elkanii, although only three of these isolates were able to nodulate soybean. Numerical analysis of phenotypic data of 19 isolates showed that 14 isolates clustered together in one branch of the phenogram, which included the group 1, group 2 and group 4 isolates from the phylogenetic analysis. The group 3 isolates were highly variable in the phenogram with similarity levels lower than 50% among these isolates.