A clarion call for action based on refined DALY estimates for South Africa

Initial estimates of the burden of disease in South Africa in 20001 have been revised on the basis of additional data to estimate the disability-adjusted life-years (DALYs) for single causes for the first time in South Africa. The findings highlight the fact that despite uncertainty in the estimates, they provide important information to guide public health responses to improve the health of the nation...

Resistance to amoebic gill disease (AGD) is characterised by the transcriptional dysregulation of immune and cell cycle pathways

Amoebic gill disease (AGD) is a parasite-mediated proliferative gill disease capable of affecting a range of teleost hosts. While a moderate heritability for AGD resistance in Atlantic salmon has been reported previously, the mechanisms by which individuals resist the proliferative effects remain poorly understood. To gain more knowledge of this commercially important trait, we compared gill transcriptomes of two groups of Atlantic salmon, one designated putatively resistant, and one designated putatively susceptible to AGD. Utilising a 17k Atlantic salmon cDNA microarray we identified 196 transcripts that were differentially expressed between the two groups. Expression of 11 transcripts were further examined with real-time quantitative RT-PCR (qPCR) in the AGD-resistant and AGD-susceptible animals, as well as non-infected naïve fish. Gene expression determined by qPCR was in strong agreement with the microarray analysis. A large number of differentially expressed genes were involved in immune and cell cycle responses. Resistant individuals displayed significantly higher expression of genes involved in adaptive immunity and negative regulation of the cell cycle. In contrast, AGD-susceptible individuals showed higher expression of acute phase proteins and positive regulators of the cell cycle. Combined with the gill histopathology, our results suggest AGD resistance is acquired rather than innately present, and that this resistance is for the most part associated with the dysregulation of immune and cell cycle pathways. © 2008 Elsevier Ltd. All rights reserved.

Capturing natural-colour 3D models of insects for species discovery and diagnostics

Collections of biological specimens are fundamental to scientific understanding and characterization of natural diversity - past, present and future. This paper presents a system for liberating useful information from physical collections by bringing specimens into the digital domain so they can be more readily shared, analyzed, annotated and compared. It focuses on insects and is strongly motivated by the desire to accelerate and augment current practices in insect taxonomy which predominantly use text, 2D diagrams and images to describe and characterize species. While these traditional kinds of descriptions are informative and useful, they cannot cover insect specimens "from all angles" and precious specimens are still exchanged between researchers and collections for this reason. Furthermore, insects can be complex in structure and pose many challenges to computer vision systems. We present a new prototype for a practical, cost-effective system of off-the-shelf components to acquire natural-colour 3D models of insects from around 3 mm to 30 mm in length. ("Natural-colour" is used to contrast with "false-colour", i.e., colour generated from, or applied to, gray-scale data post-acquisition.) Colour images are captured from different angles and focal depths using a digital single lens reflex (DSLR) camera rig and two-axis turntable. These 2D images are processed into 3D reconstructions using software based on a visual hull algorithm. The resulting models are compact (around 10 megabytes), afford excellent optical resolution, and can be readily embedded into documents and web pages, as well as viewed on mobile devices. The system is portable, safe, relatively affordable, and complements the sort of volumetric data that can be acquired by computed tomography. This system provides a new way to augment the description and documentation of insect species holotypes, reducing the need to handle or ship specimens. It opens up new opportunities to collect data for research, education, art, entertainment, biodiversity assessment and biosecurity control. © 2014 Nguyen et al.

A new approach to estimating trends in chlamydia incidence

Objectives Directly measuring disease incidence in a population is difficult and not feasible to do routinely. We describe the development and application of a new method of estimating at a population level the number of incident genital chlamydia infections, and the corresponding incidence rates, by age and sex using routine surveillance data. Methods A Bayesian statistical approach was developed to calibrate the parameters of a decision-pathway tree against national data on numbers of notifications and tests conducted (2001-2013). Independent beta probability density functions were adopted for priors on the time-independent parameters; the shape parameters of these beta distributions were chosen to match prior estimates sourced from peer-reviewed literature or expert opinion. To best facilitate the calibration, multivariate Gaussian priors on (the logistic transforms of) the time-dependent parameters were adopted, using the Matérn covariance function to favour changes over consecutive years and across adjacent age cohorts. The model outcomes were validated by comparing them with other independent empirical epidemiological measures i.e. prevalence and incidence as reported by other studies. Results Model-based estimates suggest that the total number of people acquiring chlamydia per year in Australia has increased by ~120% over 12 years. Nationally, an estimated 356,000 people acquired chlamydia in 2013, which is 4.3 times the number of reported diagnoses. This corresponded to a chlamydia annual incidence estimate of 1.54% in 2013, increased from 0.81% in 2001 (~90% increase). Conclusions We developed a statistical method which uses routine surveillance (notifications and testing) data to produce estimates of the extent and trends in chlamydia incidence.

Calibration of treatment time intensity modulated EPID images for anatomical imaging

Intensity Modulated Radiotherapy (IMRT) is a well established technique for delivering highly conformal radiation dose distributions. The complexity of the delivery techniques and high dose gradients around the target volume make verification of the patient treatment crucial to the success of the treatment. Conventional treatment protocols involve imaging the patient prior to treatment, comparing the patient set-up to the planned set-up and then making any necessary shifts in the patient position to ensure target volume coverage. This paper presents a method for calibrating electronic portal imaging device (EPID) images acquired during IMRT delivery so that they can be used for verifying the patient set-up.

Multi-modal deformable medical image registration

Non-rigid image registration is an essential tool required for overcoming the inherent local anatomical variations that exist between images acquired from different individuals or atlases. Furthermore, certain applications require this type of registration to operate across images acquired from different imaging modalities. One popular local approach for estimating this registration is a block matching procedure utilising the mutual information criterion. However, previous block matching procedures generate a sparse deformation field containing displacement estimates at uniformly spaced locations. This neglects to make use of the evidence that block matching results are dependent on the amount of local information content. This paper presents a solution to this drawback by proposing the use of a Reversible Jump Markov Chain Monte Carlo statistical procedure to optimally select grid points of interest. Three different methods are then compared to propagate the estimated sparse deformation field to the entire image including a thin-plate spline warp, Gaussian convolution, and a hybrid fluid technique. Results show that non-rigid registration can be improved by using the proposed algorithm to optimally select grid points of interest.

Characterization of frequency‐dependent magnetic susceptibility in UXO electromagnetic geophysics

Soils at many locations that have their origin in volcanic parent material and have undergone extensive weathering often exhibit strong frequency-dependent magnetic susceptibilities. The presence of such susceptibility has a profound effect on electromagnetic induction data acquired in such environments. Their transient electromagnetic response is characterized by a t-1 decay that is strong enough to mask UXO responses. In a field study and associated laboratory work on characterizing the frequency-dependent magnetic susceptibility and its influence on transient electromagnetic data, we collected soil samples on the surface and in soil pits from the Island of Kaho'olawe, Hawaii, and measured their frequency dependent magnetic susceptibilities. We present the details of the field investigation, confirm previous theoretical work with field and laboratory measurements, characterize the susceptibility with a Cole-Cole model, and investigate the response specific to the measured susceptibility.

A critical evaluation of written discharge advice for people with mild traumatic brain injury : what should we be looking for?

Objective: To formally evaluate the written discharge advice for people with mild traumatic brain injury (mTBI). Methods: Eleven publications met the inclusion criteria: (1) intended for adults; (2) ≤two A4 pages; (3) published in English; (4) freely accessible; and (5) currently used (or suitable for use) in Australian hospital emergency departments or similar settings. Two independent raters evaluated the content and style of each publication against established standards. The readability of the publication, the diagnostic term(s) contained in it and a modified Patient Literature Usefulness Index (mPLUI) were also evaluated. Results: The mean content score was 19.18 ± 8.53 (maximum = 31) and the mean style score was 6.8 ± 1.34 (maximum = 8). The mean Flesch-Kincaid reading ease score was 66.42 ± 4.3. The mean mPLUI score was 65.86 ± 14.97 (maximum = 100). Higher scores on these metrics indicate more desirable properties. Over 80% of the publications used mixed diagnostic terminology. One publication scored optimally on two of the four metrics and highly on the others. Discussion: The content, style, readability and usefulness of written mTBI discharge advice was highly variable. The provision of written information to patients with mTBI is advised, but this variability in materials highlights the need for evaluation before distribution. Areas are identified to guide the improvement of written mTBI discharge advice.

Promiscuity, pheromones and pathogenicity : why all Enterococci are not created equal

Enterococcus faecalis is a Gram-positive, coccus shaped, lactic acid bacterium, with demonstrated ubiquity across multiple anatomical sites. Enterococcus faecalis isolates have been isolated from clinical samples as the etiological agent in patients with overt infections, and from body sites previously thought to be sterile but absent of signs and symptoms of infection. E. faecalis is implicated in both human health and disease, recognized as a commensal, a probiotic and an opportunistic multiply resistant pathogen. E. faecalis has emerged as a key pathogen in nosocomial infections. E. faecalis is well equipped to avert recognition by host cell immune mediators. Antigenic cell wall components including lipotechoic acids are concealed from immune detection by capsular polysaccharides produced by some strains. Thereby preventing complement activation, the pro-inflammatory response, opsonisation and phagocytosis. E. faecalis also produces a suite of enzymes including gelatinase and cytolysin, which aid in both virulence and host immune evasion. The ability of enterococci to form biofilms in vivo further increases virulence, whilst simultaneously preventing detection by host cells. E. faecalis exhibits high levels of both intrinsic and acquired antimicrobial resistance. The mobility of the E. faecalis genome is a significant contributor to antimicrobial resistance, with this species also transferring resistance to other Gram-positive bacteria. Whilst E. faecalis is of increasing concern in nosocomial infections, its role as a member of the endogenous microbiota cannot be underestimated. As a commensal and probiotic, E. faecalis plays an integral role in modulating the immune response, and in providing endogenous antimicrobial activity to enhance exclusion or inhibition of opportunistic pathogens in certain anatomical niches. In this chapter we will review possible mediators of enterococcal transition from commensal microbe to opportunistic pathogen, considering isolates obtained from patients diagnosed with pathogenic infections and those obtained from asymptomatic patients.

Prevalence of methicillin resistance and virulence determinants of Staphylococcus aureus in diabetic foot ulcers

Background Diabetic foot ulceration (DFU) is a multifactorial process and is responsible for considerable morbidity and contributes to the increasing cost of health care worldwide. The diagnosis and identification of these ulcers remains a complex problem. Bacterial infection is promoted in the diabetic foot wound by decreased vascular supply and impaired host immune response. As conventional clinical microbiological methods are time-consuming and only identifies about 1% of the wound microbiota, detection of bacteria present in DFUs using molecular methods is highly advantageous and efficient. The aim of this study was to assess the virulence and methicillin resistance profiles of Staphylococcus aureus detected in DFUs using DNA-based methods. Methods A total of 223 swab samples were collected from 30 patients from March to October 2012. Bacterial DNA was extracted from the swab samples using standard procedures and was used to perform polymerase chain reaction (PCR) using specific oligonucleotide primers. The products were visualized using agarose gel electrophoresis. Results S. aureus was detected in 44.8% of samples. 25% of the S. aureus was methicillin-resistant S. aureus harboring the mecA gene. The alpha-toxin gene was present in 85% of the S. aureus positive samples. 61% of the S. aureus present in DFU samples harbored the exfoliatin factor A gene. Both the fibronectin factor A and fibronectin factor B gene were detected in 71% and 74% of the S. aureus positive samples. Conclusions DNA-based detection and characterization of bacteria in DFUs are rapid and efficient and can assist in accurate, targeted antibiotic therapy of DFU infections. The majority of S. aureus detected in this study were highly virulent and also resistant to methicillin. Further studies are required to understand the role of S. aureus in DFU trajectory.

Spatial mapping of proteoglycan content in articular cartilage using near-infrared (NIR) spectroscopy

Diagnosis of articular cartilage pathology in the early disease stages using current clinical diagnostic imaging modalities is challenging, particularly because there is often no visible change in the tissue surface and matrix content, such as proteoglycans (PG). In this study, we propose the use of near infrared (NIR) spectroscopy to spatially map PG content in articular cartilage. The relationship between NIR spectra and reference data (PG content) obtained from histology of normal and artificially induced PG-depleted cartilage samples was investigated using principal component (PC) and partial least squares (PLS) regression analyses. Significant correlation was obtained between both data (R2 = 91.40%, p<0.0001). The resulting correlation was used to predict PG content from spectra acquired from whole joint sample, this was then employed to spatially map this component of cartilage across the intact sample. We conclude that NIR spectroscopy is a feasible tool for evaluating cartilage contents and mapping their distribution across mammalian joint

DNA molecules and human therapeutics

Nucleic acid molecules are championing a new generation of reverse engineered biopharmaceuticals. In terms of potential application in gene medicine, plasmid DNA (pDNA) vectors have exceptional therapeutic and immunological profiles as they are free from safety concerns associated with viral vectors, display non-toxicity and are simpler to develop. This review addresses the potential applications of pDNA molecules in vaccine design/development and gene therapy via recombinant DNA technology as well as a staged delivery mechanism for the introduction of plasmid-borne gene to target cells via the nasal route.

Scale adaptive tracking using mean shift and efficient feature matching

The mean shift tracker has achieved great success in visual object tracking due to its efficiency being nonparametric. However, it is still difficult for the tracker to handle scale changes of the object. In this paper, we associate a scale adaptive approach with the mean shift tracker. Firstly, the target in the current frame is located by the mean shift tracker. Then, a feature point matching procedure is employed to get the matched pairs of the feature point between target regions in the current frame and the previous frame. We employ FAST-9 corner detector and HOG descriptor for the feature matching. Finally, with the acquired matched pairs of the feature point, the affine transformation between target regions in the two frames is solved to obtain the current scale of the target. Experimental results show that the proposed tracker gives satisfying results when the scale of the target changes, with a good performance of efficiency.

Relocating a flood-affected community : good planning or good politics?

Problem, research strategy and findings: On January 10, 2011, the town of Grantham, Queensland (Australia), was inundated with a flash flood in which 12 of the town's 370 residents drowned. The overall damage bill in Queensland was AUD∃2.38 billion (USD∃2.4 billion) with 35 deaths, and more than three-quarters of the state was declared a flood disaster zone. In this study, we focus on the unusual and even rare decision to relocate Grantham in March 2011. The Lockyer Valley Regional Council (LVRC) acquired a 377-hectare (932-acre) site to enable a voluntary swap of equivalent-sized lots. In addition, planning regulations were set aside to streamline the relocation of a portion of the town. We review the natural hazard literature as it relates to community relocation, state and local government documents related to Grantham, and reports and newspaper articles related to the flood. We also analyze data from interviews with key stakeholders. We document the process of community relocation, assess the relocation process in Grantham against best practice, examine whether the process of community relocation can be upscaled and if the Grantham relocation is an example of good planning or good politics. Takeaway for practice: Our study reveals two key messages for practice. Community relocation (albeit a small one) is possible, and the process can be done quickly; some Grantham residents moved into their new, relocated homes in December 2012, just 11 months after the flood. Moreover, the role of existing planning regulations can be a hindrance to quick action; political leadership, particularly at the local level, is key to implementing the relocation.

An examination of isotherm generation : impact of bottle-point method upon potassium ion exchange with strong acid cation resin

This paper relates to the importance of impact of the chosen bottle-point method when conducting ion exchange equilibria experiments. As an illustration, potassium ion exchange with strong acid cation resin was investigated due to its relevance to the treatment of various industrial effluents and groundwater. The “constant mass” bottle-point method was shown to be problematic in that depending upon the resin mass used the equilibrium isotherm profiles were different. Indeed, application of common equilibrium isotherm models revealed that the optimal fit could be with either the Freundlich or Temkin equations, depending upon the conditions employed. It could be inferred that the resin surface was heterogeneous in character, but precise conclusions regarding the variation in the heat of sorption were not possible. Estimation of the maximum potassium loading was also inconsistent when employing the “constant mass” method. The “constant concentration” bottle-point method illustrated that the Freundlich model was a good representation of the exchange process. The isotherms recorded were relatively consistent when compared to the “constant mass” approach. Unification of all the equilibrium isotherm data acquired was achieved by use of the Langmuir Vageler expression. The maximum loading of potassium ions was predicted to be at least 116.5 g/kg resin.