Large-scale interlaboratory study to develop, analytically validate and apply highly multiplexed, quantitative peptide assays to measure cancer-relevant proteins in plasma

There is an increasing need in biology and clinical medicine to robustly and reliably measure tens-to-hundreds of peptides and proteins in clinical and biological samples with high sensitivity, specificity, reproducibility and repeatability. Previously, we demonstrated that LC-MRM-MS with isotope dilution has suitable performance for quantitative measurements of small numbers of relatively abundant proteins in human plasma, and that the resulting assays can be transferred across laboratories while maintaining high reproducibility and quantitative precision. Here we significantly extend that earlier work, demonstrating that 11 laboratories using 14 LC-MS systems can develop, determine analytical figures of merit, and apply highly multiplexed MRM-MS assays targeting 125 peptides derived from 27 cancer-relevant proteins and 7 control proteins to precisely and reproducibly measure the analytes in human plasma. To ensure consistent generation of high quality data we incorporated a system suitability protocol (SSP) into our experimental design. The SSP enabled real-time monitoring of LC-MRM-MS performance during assay development and implementation, facilitating early detection and correction of chromatographic and instrumental problems. Low to sub-nanogram/mL sensitivity for proteins in plasma was achieved by one-step immunoaffinity depletion of 14 abundant plasma proteins prior to analysis. Median intra- and inter-laboratory reproducibility was <20%, sufficient for most biological studies and candidate protein biomarker verification. Digestion recovery of peptides was assessed and quantitative accuracy improved using heavy isotope labeled versions of the proteins as internal standards. Using the highly multiplexed assay, participating laboratories were able to precisely and reproducibly determine the levels of a series of analytes in blinded samples used to simulate an inter-laboratory clinical study of patient samples. Our study further establishes that LC-MRM-MS using stable isotope dilution, with appropriate attention to analytical validation and appropriate quality c`ontrol measures, enables sensitive, specific, reproducible and quantitative measurements of proteins and peptides in complex biological matrices such as plasma.

Melanoma cell colony expansion parameters revealed by approximate Bayesian computation

In vitro studies and mathematical models are now being widely used to study the underlying mechanisms driving the expansion of cell colonies. This can improve our understanding of cancer formation and progression. Although much progress has been made in terms of developing and analysing mathematical models, far less progress has been made in terms of understanding how to estimate model parameters using experimental in vitro image-based data. To address this issue, a new approximate Bayesian computation (ABC) algorithm is proposed to estimate key parameters governing the expansion of melanoma cell (MM127) colonies, including cell diffusivity, D, cell proliferation rate, λ, and cell-to-cell adhesion, q, in two experimental scenarios, namely with and without a chemical treatment to suppress cell proliferation. Even when little prior biological knowledge about the parameters is assumed, all parameters are precisely inferred with a small posterior coefficient of variation, approximately 2–12%. The ABC analyses reveal that the posterior distributions of D and q depend on the experimental elapsed time, whereas the posterior distribution of λ does not. The posterior mean values of D and q are in the ranges 226–268 µm2h−1, 311–351 µm2h−1 and 0.23–0.39, 0.32–0.61 for the experimental periods of 0–24 h and 24–48 h, respectively. Furthermore, we found that the posterior distribution of q also depends on the initial cell density, whereas the posterior distributions of D and λ do not. The ABC approach also enables information from the two experiments to be combined, resulting in greater precision for all estimates of D and λ.

Design of a lightweight, modular robotic vehicle for the sustainable intensification of broadacre agriculture

This thesis presents the design process and the prototyping of a lightweight, modular robotic vehicle for the sustainable intensification of broadacre agriculture. Achieved by the joint operation of multiple autonomous vehicles to improve energy consumption, reduce labour, and increase efficiency in the application of inputs for the management of crops. The Small Robotic Farm Vehicle (SRFV) is a lightweight and energy efficient robotic vehicle with a configurable, modular design. It is capable of undertaking a range of agricultural tasks, including fertilising and weed management through mechanical intervention and precision spraying, whilst being more than an order of magnitude lower in weight than existing broadacre agricultural equipment.

A comparison land-water environment of maximal voluntary isometric contraction during manual muscle testing through surface electromyography

Background The aim of this study was to compare through surface electromyographic (sEMG) recordings of the maximum voluntary contraction (MVC) on dry land and in water by manual muscle test (MMT). Method Sixteen healthy right-handed subjects (8 males and 8 females) participated in measurement of muscle activation of the right shoulder. The selected muscles were the cervical erector spinae, trapezius, pectoralis, anterior deltoid, middle deltoid, infraspinatus and latissimus dorsi. The MVC test conditions were random with respect to the order on the land/in water. Results For each muscle, the MVC test was performed and measured through sEMG to determine differences in muscle activation in both conditions. For all muscles except the latissimus dorsi, no significant differences were observed between land and water MVC scores (p = 0.063–0.679) and precision (%Diff = 7–10%) were observed between MVC conditions in the muscles trapezius, anterior deltoid and middle deltoid. Conclusions If the procedure for data collection is optimal, under MMT conditions it appears that comparable MVC sEMG values were achieved on land and in water and the integrity of the EMG recordings were maintained during wáter immersion.

Combining meta- and mega-analytic approaches for multi-site diffusion imaging based genetic studies: From the enigma-DTI working group

Meta-analyses estimate a statistical effect size for a test or an analysis by combining results from multiple studies without necessarily having access to each individual study's raw data. Multi-site meta-analysis is crucial for imaging genetics, as single sites rarely have a sample size large enough to pick up effects of single genetic variants associated with brain measures. However, if raw data can be shared, combining data in a "mega-analysis" is thought to improve power and precision in estimating global effects. As part of an ENIGMA-DTI investigation, we use fractional anisotropy (FA) maps from 5 studies (total N=2, 203 subjects, aged 9-85) to estimate heritability. We combine the studies through meta-and mega-analyses as well as a mixture of the two - combining some cohorts with mega-analysis and meta-analyzing the results with those of the remaining sites. A combination of mega-and meta-approaches may boost power compared to meta-analysis alone.

Modeling of the hemodynamic responses in block design fMRI studies

The hemodynamic response function (HRF) describes the local response of brain vasculature to functional activation. Accurate HRF modeling enables the investigation of cerebral blood flow regulation and improves our ability to interpret fMRI results. Block designs have been used extensively as fMRI paradigms because detection power is maximized; however, block designs are not optimal for HRF parameter estimation. Here we assessed the utility of block design fMRI data for HRF modeling. The trueness (relative deviation), precision (relative uncertainty), and identifiability (goodness-of-fit) of different HRF models were examined and test-retest reproducibility of HRF parameter estimates was assessed using computer simulations and fMRI data from 82 healthy young adult twins acquired on two occasions 3 to 4 months apart. The effects of systematically varying attributes of the block design paradigm were also examined. In our comparison of five HRF models, the model comprising the sum of two gamma functions with six free parameters had greatest parameter accuracy and identifiability. Hemodynamic response function height and time to peak were highly reproducible between studies and width was moderately reproducible but the reproducibility of onset time was low. This study established the feasibility and test-retest reliability of estimating HRF parameters using data from block design fMRI studies.

Investigating brain connectivity heritability in a twin study using diffusion imaging data

Heritability of brain anatomical connectivity has been studied with diffusion-weighted imaging (DWI) mainly by modeling each voxel's diffusion pattern as a tensor (e.g., to compute fractional anisotropy), but this method cannot accurately represent the many crossing connections present in the brain. We hypothesized that different brain networks (i.e., their component fibers) might have different heritability and we investigated brain connectivity using High Angular Resolution Diffusion Imaging (HARDI) in a cohort of twins comprising 328 subjects that included 70 pairs of monozygotic and 91 pairs of dizygotic twins. Water diffusion was modeled in each voxel with a Fiber Orientation Distribution (FOD) function to study heritability for multiple fiber orientations in each voxel. Precision was estimated in a test-retest experiment on a sub-cohort of 39 subjects. This was taken into account when computing heritability of FOD peaks using an ACE model on the monozygotic and dizygotic twins. Our results confirmed the overall heritability of the major white matter tracts but also identified differences in heritability between connectivity networks. Inter-hemispheric connections tended to be more heritable than intra-hemispheric and cortico-spinal connections. The highly heritable tracts were found to connect particular cortical regions, such as medial frontal cortices, postcentral, paracentral gyri, and the right hippocampus.

Analyzing multi-fiber reconstruction in high angular resolution diffusion imaging using the tensor distribution function

High-angular resolution diffusion imaging (HARDI) can reconstruct fiber pathways in the brain with extraordinary detail, identifying anatomical features and connections not seen with conventional MRI. HARDI overcomes several limitations of standard diffusion tensor imaging, which fails to model diffusion correctly in regions where fibers cross or mix. As HARDI can accurately resolve sharp signal peaks in angular space where fibers cross, we studied how many gradients are required in practice to compute accurate orientation density functions, to better understand the tradeoff between longer scanning times and more angular precision. We computed orientation density functions analytically from tensor distribution functions (TDFs) which model the HARDI signal at each point as a unit-mass probability density on the 6D manifold of symmetric positive definite tensors. In simulated two-fiber systems with varying Rician noise, we assessed how many diffusionsensitized gradients were sufficient to (1) accurately resolve the diffusion profile, and (2) measure the exponential isotropy (EI), a TDF-derived measure of fiber integrity that exploits the full multidirectional HARDI signal. At lower SNR, the reconstruction accuracy, measured using the Kullback-Leibler divergence, rapidly increased with additional gradients, and EI estimation accuracy plateaued at around 70 gradients.

Text segmentation in unconstrained hand-drawings in whiteboard photos

In this paper we present a robust method to detect handwritten text from unconstrained drawings on normal whiteboards. Unlike printed text on documents, free form handwritten text has no pattern in terms of size, orientation and font and it is often mixed with other drawings such as lines and shapes. Unlike handwritings on paper, handwritings on a normal whiteboard cannot be scanned so the detection has to be based on photos. Our work traces straight edges on photos of the whiteboard and builds graph representation of connected components. We use geometric properties such as edge density, graph density, aspect ratio and neighborhood similarity to differentiate handwritten text from other drawings. The experiment results show that our method achieves satisfactory precision and recall. Furthermore, the method is robust and efficient enough to be deployed in a mobile device. This is an important enabler of business applications that support whiteboard-centric visual meetings in enterprise scenarios. © 2012 IEEE.

The grand philosopher of the Commons: In memory of Elinor Ostrom

The grand philosopher of the Commons, Elinor Ostrom, passed away on the 12th June 2012. She was a brilliant, creative polymath; a theoretician of fine precision and great intellectual power; a deviser of masterful empirical studies; and an energetic collaborator and networker. Ostrom posed a formidable intellectual challenge to the fields of economics and the social sciences - and the advocates of central regulation, privatization, and enclosure.

Investigating sea level rise due to global warming in the teaching laboratory using Archimedes’ principle

A teaching laboratory experiment is described that uses Archimedes’ principle to precisely investigate the effect of global warming on the oceans. A large component of sea level rise is due to the increase in the volume of water due to the decrease in water density with increasing temperature. Water close to 0 °C is placed in a beaker and a glass marble hung from an electronic balance immersed in the water. As the water warms, the weight of the marble increases as the water is less buoyant due to the decrease in density. In the experiment performed in this paper a balance with a precision of 0.1 mg was used with a marble 40.0 cm3 and mass of 99.3 g, yielding water density measurements with an average error of -0.008 ± 0.011%.

Visual openness in urban environments: Measuring visual openness and visibility to natural landscapes in a changing urban landscape in Gold Coast, Australia

The visual characteristics of urban environments have been changing dramatically with the growth of cities around the world. Protection and enhancement of landscape character in urban environments have been one of the challenges for policy makers in addressing sustainable urban growth. Visual openness and enclosure in urban environments are important attributes in perception of visual space which affect the human interaction with physical space and which can be often modified by new developments. Measuring visual openness in urban areas results in more accurate, reliable, and systematic approach to manage and control visual qualities in growing cities. Recent advances in techniques in geographic information systems (GIS) and survey systems make it feasible to measure and quantify this attribute with a high degree of realism and precision. Previous studies in this field do not take full advantage of these improvements. This paper proposes a method to measure the visual openness and enclosure in a changing urban landscape in Australia, on the Gold Coast, by using the improved functionality in GIS. Using this method, visual openness is calculated and described for all publicly accessible areas in the selected study area. A final map is produced which shows the areas with highest visual openness and visibility to natural landscape resources. The output of this research can be used by planners and decision-makers in managing and controlling views in complex urban landscapes. Also, depending on the availability of GIS data, this method can be applied to any region including non-urban landscapes to help planners and policy-makers manage views and visual qualities.

Emotional food design: From designing food products to designing food systems

Contemporary food systems promote the consumption of highly processed foods of limited nutrition, contributing to overweight and obesity, diet-related disease and significant financial burden on healthcare systems. In part, this has resulted from highly successful design, development and marketing strategies for processed foods. The successful application of such strategies to healthy food options, and the services and business plans that accompany them, could assist in enhancing health and alleviating burden on health care systems. Product designers have long been aware of the importance of intertwining emotional experiences with new products. However, a lack of theoretical precision exists for applying emotional design beyond food products, to the food systems, services and business models that drive them. This article explores emotional design within the context of food and food systems and proposes a new concept – Emotional Food Design (EFD), through which emotional design is integrated across levels of a food system. EFD complements the dominating deductive view of food systems research with an abductive iterative design approach contextualized within the creation of new food products, services and business models and their associated emotional attachments. This paper concludes by outlining what EFD can offer to reorient food systems to successfully promote healthy eating.

Determination of dimethyl sulfide in gas samples by single photon ionization time of flight mass spectrometry

It is difficult to determine sulfur-containing volatile organic compounds in the atmosphere because of their reactivity. Primary off-line techniques may suffer losses of analytes during the transportation from field to laboratory and sample preparation. In this study, a novel method was developed to directly measure dimethyl sulfide at parts-per-billion concentration levels in the atmosphere using vacuum ultraviolet single photon ionization time-of-flight mass spectrometry. This technique offers continuous sampling at a response rate of one measurement per second, or cumulative measurements over longer time periods. Laboratory prepared samples of different concentrations of dimethyl sulfide in pure nitrogen gas were analyzed at several sampling frequencies. Good precision was achieved using sampling periods of at least 60 seconds with a relative standard deviation of less than 25%. The detection limit for dimethyl sulfide was below the 3 ppb olfactory threshold. These results demonstrate that single photon ionization time-of-flight mass spectrometry is a valuable tool for rapid, real-time measurements of sulfur-containing organic compounds in the air.

A suitable method for journal bearing wear measurement

Purpose – Ideally, there is no wear in hydrodynamic lubrication regime. A small amount of wear occurs during start and stop of the machines and the amount of wear is so small that it is difficult to measure with accuracy. Various wear measuring techniques have been used where out-of-roundness was found to be the most reliable method of measuring small wear quantities in journal bearings. This technique was further developed to achieve higher accuracy in measuring small wear quantities. The method proved to be reliable as well as inexpensive. The paper aims to discuss these issues. Design/methodology/approach – In an experimental study, the effect of antiwear additives was studied on journal bearings lubricated with oil containing solid contaminants. The test duration was too long and the wear quantities achieved were too small. To minimise the test duration, short tests of about 90 min duration were conducted and wear was measured recording changes in variety of parameters related to weight, geometry and wear debris. The out-of-roundness was found to be the most effective method. This method was further refined by enlarging the out-of-roundness traces on a photocopier. The method was proved to be reliable and inexpensive. Findings – Study revealed that the most commonly used wear measurement techniques such as weight loss, roughness changes and change in particle count were not adequate for measuring small wear quantities in journal bearings. Out-of-roundness method with some refinements was found to be one of the most reliable methods for measuring small wear quantities in journal bearings working in hydrodynamic lubrication regime. By enlarging the out-of-roundness traces and determining the worn area of the bearing cross-section, weight loss in bearings was calculated, which was repeatable and reliable. Research limitations/implications – This research is a basic in nature where a rudimentary solution has been developed for measuring small wear quantities in rotary devices such as journal bearings. The method requires enlarging traces on a photocopier and determining the shape of the worn area on an out-of-roundness trace on a transparency, which is a simple but a crude method. This may require an automated procedure to determine the weight loss from the out-of-roundness traces directly. This method can be very useful in reducing test duration and measuring wear quantities with higher precision in situations where wear quantities are very small. Practical implications – This research provides a reliable method of measuring wear of circular geometry. The Talyrond equipment used for measuring the change in out-of-roundness due to wear of bearings indicates that this equipment has high potential to be used as a wear measuring device also. Measurement of weight loss from the traces is an enhanced capability of this equipment and this research may lead to the development of a modified version of Talyrond type of equipment for wear measurements in circular machine components. Originality/value – Wear measurement in hydrodynamic bearings requires long duration tests to achieve adequate wear quantities. Out-of-roundness is one of the geometrical parameters that changes with progression of wear in a circular shape components. Thus, out-of-roundness is found to be an effective wear measuring parameter that relates to change in geometry. Method of increasing the sensitivity and enlargement of out-of-roundness traces is original work through which area of worn cross-section can be determined and weight loss can be derived for materials of known density with higher precision.