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.

The contribution of three components of nutrition knowledge to socio-economic differences in food purchasing choices

Objectives: To assess socio-economic differences in three components of nutrition knowledge, i.e. knowledge of (i) the relationship between diet and disease, (ii) the nutrient content of foods and (iii) dietary guideline recommendations; furthermore, to determine if socio-economic differences in nutrition knowledge contribute to inequalities in food purchasing choices. Design: The cross-sectional study considered household food purchasing,nutrition knowledge, socio-economic and demographic information. Household food purchasing choices were summarised by three indices, based on self-reported purchasing of sixteen groceries, nineteen fruits and twenty-one vegetables. Socio-economic position (SEP) was measured by household income and education. Associations between SEP, nutrition knowledge and food purchasing were examined using general linear models adjusted for age, gender, household type and household size. Setting: Brisbane, Australia in 2000. Subjects: Main household food shoppers (n 1003, response rate 66?4 %), located in fifty small areas (Census Collectors Districts). Results: Shoppers in households of low SEP made food purchasing choices that were less consistent with dietary guideline recommendations: they were more likely to purchase grocery foods comparatively higher in salt, sugar and fat, and lower in fibre, and they purchased a narrower range of fruits and vegetables. Those of higher SEP had greater nutrition knowledge and this factor attenuated most associations between SEP and food purchasing choices. Among nutrition knowledge factors, knowledge of the relationship between diet and disease made the greatest and most consistent contribution to explaining socio-economic differences in food purchasing. Conclusions: Addressing inequalities in nutrition knowledge is likely to reduce socio-economic differences in compliance with dietary guidelines. Improving knowledge of the relationship between diet and disease appears to be a particularly relevant focus for health promotion aimed to reduce socio-economic differences in diet and related health inequalities.

Collaboration in Web N.0: Stigmergy and virtual pheromones

The aim of this project was to develop a general theory of stigmergy and a software design pattern to build collaborative websites. Stigmergy is a biological term used when describing some insect swarm-behaviour where 'food gathering' and 'nest building' activities demonstrate the emergence of self-organised societies achieved without an apparent management structure. The results of the project are an abstract model of stigmergy and a software design pattern for building Web 2.0 components exploiting this self-organizing phenomenon. A proof-of-concept implementation was also created demonstrating potential commercial viability for future website projects.

Opsin clines in butterflies suggest novel roles for insect photopigments

Opsins are ancient molecules that enable animal vision by coupling to a vitamin-derived chromophore to form lightsensitive photopigments. The primary drivers of evolutionary diversification in opsins are thought to be visual tasks related to spectral sensitivity and color vision. Typically, only a few opsin amino acid sites affect photopigment spectral sensitivity. We show that opsin genes of the North American butterfly Limenitis arthemis have diversified along a latitudinal cline, consistent with natural selection due to environmental factors. We sequenced single nucleotide(SNP) polymorphisms in the coding regions of the ultraviolet (UVRh), blue (BRh), and long-wavelength (LWRh) opsin genes from ten butterfly populations along the eastern United States and found that a majority of opsin SNPs showed significant clinal variation. Outlier detection and analysis of molecular variance indicated that many SNPs are under balancing selection and show significant population structure. This contrasts with what we found by analysing SNPs in the wingless and EF-1 alpha loci, and from neutral amplified fragment length polymorphisms, which show no evidence of significant locus-specific or genome-wide structure among populations. Using a combination of functional genetic and physiological approaches, including expression in cell culture, transgenic Drosophila, UV-visible spectroscopy, and optophysiology, we show that key BRh opsin SNPs that vary clinally have almost no effect on spectral sensitivity. Our results suggest that opsin diversification in this butterfly is more consistent with natural selection unrelated to spectral tuning. Some of the clinally varying SNPs may instead play a role in regulating opsin gene expression levels or the thermostability of the opsin protein. Lastly, we discuss the possibility that insect opsins might have important, yet-to-be elucidated, adaptive functions in mediating animal responses to abiotic factors, such as temperature or photoperiod.

Can larger-bodied cemented femoral components reduce periprosthetic fractures? A biomechanical study

Introduction: The risk for late periprosthetic femoral fractures is higher in patients treated for a neck of femur fracture compared to osteoarthritis. It has been hypothesised that osteopenia and consequent decreased stiffness of the proximal femur are responsible for this. We investigated whether a femoral component with a bigger body would increase the torque to failure in a biaxially loaded composite Sawbone model. Material and methods: A biomechanical bone analogue was used. Two different body sizes (Exeter 44-1 vs 44-4) of a polished tapered cemented femoral stem were implanted by an experienced surgeon in 7 bone analogues each and internally rotated at 40°/s until failure. Torque to fracture and fracture energy were measured using a biaxial materials testing device (Instron 8874, MI, USA). The data were non-parametric and therefore tested with the Mann-Whitney U-test. Results: The median torque to fracture was 156.7 Nm (IQR 19.7) for the 44-1 stem and 237.1 Nm (IQR 52.9) for the 44-4 stem (p=0.001). The median fracture energy was 8.5J (IQR 7.3) for the 44-1 stem and 19.5J (IQR 8.8) for the 44-4 stem (p=0.014). Conclusions: The use of a large body polished tapered cemented stems for neck of femur fractures increases the torque to failure in a biomechanical model and therefore is likely to reduce late periprosthetic fracture risk in this vulnerable cohort.

Multivariate variance-components analysis in DTI

Twin studies are a major research direction in imaging genetics, a new field, which combines algorithms from quantitative genetics and neuroimaging to assess genetic effects on the brain. In twin imaging studies, it is common to estimate the intraclass correlation (ICC), which measures the resemblance between twin pairs for a given phenotype. In this paper, we extend the commonly used Pearson correlation to a more appropriate definition, which uses restricted maximum likelihood methods (REML). We computed proportion of phenotypic variance due to additive (A) genetic factors, common (C) and unique (E) environmental factors using a new definition of the variance components in the diffusion tensor-valued signals. We applied our analysis to a dataset of Diffusion Tensor Images (DTI) from 25 identical and 25 fraternal twin pairs. Differences between the REML and Pearson estimators were plotted for different sample sizes, showing that the REML approach avoids severe biases when samples are smaller. Measures of genetic effects were computed for scalar and multivariate diffusion tensor derived measures including the geodesic anisotropy (tGA) and the full diffusion tensors (DT), revealing voxel-wise genetic contributions to brain fiber microstructure.

Re-valuing construction materials and components through design for disassembly

The construction industry accounts for a significant portion of the material consumption of our industrialised societies. That material consumption comes at an environmental cost, and when buildings and infrastructure projects are demolished and discarded, after their useful lifespan, that environmental cost remains largely unrecovered. The expected operational lifespan of modern buildings has become disturbingly short as buildings are replaced for reasons of changing cultural expectations, style, serviceability, locational obsolescence and economic viability. The same buildings however are not always physically or structurally obsolete; the materials and components within them are very often still completely serviceable. While there is some activity in the area of recycling of selected construction materials, such as steel and concrete, this is almost always in the form of down cycling or reprocessing. Very little of this material and component resource is reuse in a way that more effectively captures its potential. One significant impediment to such reuse is that buildings are not designed in a way that facilitates easy recovery of materials and components; they are designed and built for speed of construction and quick economic returns, with little or no consideration of the longer term consequences of their physical matter. This research project explores the potential for the recovery of materials and components if buildings were designed for such future recovery; a strategy of design for disassembly. This is not a new design philosophy; design for disassembly is well understood in product design and industrial design. There are also some architectural examples of design for disassembly; however these are specialist examples and there is no significant attempt to implement the strategy in the main stream construction industry. This paper presents research into the analysis of the embodied energy in buildings, highlighting its significance in comparison with operational energy. Analysis at material, component, and whole-of-building levels shows the potential benefits of strategically designing buildings for future disassembly to recover this embodied energy. Careful consideration at the early design stage can result in the deconstruction of significant portions of buildings and the recovery of their potential through higher order reuse and upcycling.

A novel near-infrared spectroscopy and chemometrics method for rapid analysis of several chemical components and antioxidant activity of mint (mentha haplocalyx briq.) samples

A novel near-infrared spectroscopy (NIRS) method has been researched and developed for the simultaneous analyses of the chemical components and associated properties of mint (Mentha haplocalyx Briq.) tea samples. The common analytes were: total polysaccharide content, total flavonoid content, total phenolic content, and total antioxidant activity. To resolve the NIRS data matrix for such analyses, least squares support vector machines was found to be the best chemometrics method for prediction, although it was closely followed by the radial basis function/partial least squares model. Interestingly, the commonly used partial least squares was unsatisfactory in this case. Additionally, principal component analysis and hierarchical cluster analysis were able to distinguish the mint samples according to their four geographical provinces of origin, and this was further facilitated with the use of the chemometrics classification methods-K-nearest neighbors, linear discriminant analysis, and partial least squares discriminant analysis. In general, given the potential savings with sampling and analysis time as well as with the costs of special analytical reagents required for the standard individual methods, NIRS offered a very attractive alternative for the simultaneous analysis of mint samples.

Errors in the knee joint forces and moments during gait depending on the foot and knee prosthetic components

Background Previously studies showed that inverse dynamics based on motion analysis and force-plate is inaccurate compared to direct measurements for individuals with transfemoral amputation (TFA). Indeed, direct measurements can appropriately take into account the absorption at the prosthetic foot and the resistance at the prosthetic knee. [1-3] However, these studies involved only a passive prosthetic knee. Aim The objective of the present study was to investigate if different types of prosthetic feet and knees can exhibit different levels of error in the knee joint forces and moments. Method Three trials of walking at self-selected speed were analysed for 9 TFAs (7 males and 2 females, 47±9 years old, 1.76±0.1 m 79±17 kg) with a motion analysis system (Qualisys, Goteborg, Sweden), force plates (Kitsler, Winterthur, Switzerland) and a multi-axial transducer (JR3, Woodland, USA) mounted above the prosthetic knee [1-17]. TFAs were all fitted with an osseointegrated implant system. The prostheses included different type of foot (N=5) and knee (N=3) components. The root mean square errors (RMSE) between direct measurements and the knee joint forces and moments estimated by inverse dynamics were computed for stance and swing phases of gait and expressed as a percentage of the measured amplitudes. A one-way Kruskal-Wallis ANOVA was performed (Statgraphics, Levallois-Perret, France) to analyse the effects of the prosthetic components on the RMSEs. Cross-effects and post-hoc tests were not analysed in this study. Results A significant effect (*) was found for the type of prosthetic foot on anterior-posterior force during swing (p=0.016), lateral-medial force during stance (p=0.009), adduction-abduction moment during stance (p=0.038), internal-external rotation moment during stance (p=0.014) and during swing (p=0.006), and flexion-extension moment during stance (p = 0.035). A significant effect (#) was found for the type of prosthetic knee on anterior-posterior force during swing (p=0.018) and adduction-abduction moment during stance (p=0.035). Discussion & Conclusion The RMSEs were larger during swing than during stance. It is because the errors on accelerations (as derived from motion analysis) become substantial with respect to the external loads. Thus, inverse dynamics during swing should be analysed with caution because the mean RMSEs are close to 50%. Conversely, there were fewer effects of the prosthetic components on RMSE during swing than during stance and, accordingly, fewer effects due to knees than feet. Thus, inverse dynamics during stance should be used with caution for comparison of different prosthetic components.

Condition monitoring and rating of bridge components in a rail or road network by using SHM systems within SRP

The safety and performance of bridges could be monitored and evaluated by Structural Health Monitoring (SHM) systems. These systems try to identify and locate the damages in a structure and estimate their severities. Current SHM systems are applied to a single bridge, and they have not been used to monitor the structural condition of a network of bridges. This paper propose a new method which will be used in Synthetic Rating Procedures (SRP) developed by the authors of this paper and utilizes SHM systems for monitoring and evaluating the condition of a network of bridges. Synthetic rating procedures are used to assess the condition of a network of bridges and identify their ratings. As an additional part of the SRP, the method proposed in this paper can continuously monitor the behaviour of a network of bridges and therefore it can assist to prevent the sudden collapses of bridges or the disruptions to their serviceability. The method could be an important part of a bridge management system (BMS) for managers and engineers who work on condition assessment of a network of bridges.

Body composition and components of energy expenditure in children with end-stage liver disease

Background: Better understanding of body composition and energy metabolism in pediatric liver disease may provide a scientific basis for improved medical therapy aimed at achieving optimal nutrition, slowing progression to end-stage liver disease (ESLD), and improving the outcome of liver transplantation. Methods: Twenty-one children less than 2 years of age with ESLD awaiting liver transplantation and 15 healthy, aged-matched controls had body compartment analysis using a four compartment model (body cell mass, fat mass, extracellular water, and extracellular solids). Subjects also had measurements of resting energy expenditure (REE) and respiratory quotient (RQ) by indirect calorimetry. Nine patients and 15 control subjects also had measurements of total energy expenditure (TEE) using doubly labelled water. Results: Mean weights and heights were similar in the two groups. Compared with control subjects, children with ESLD had higher relative mean body cell mass (33 ± 2% vs 29 ± 1% of body weight, P < 0.05), but had similar fat mass, extracellular water, and extracellular solid compartments (18% vs 20%, 41% vs 38%, and 7% vs 13% of body weight respectively). Compared with control subjects, children with ESLD had 27% higher mean REE/body weight (0.285 ± 0.013 vs 0.218. ± 0.013 mJ/kg/24h, P < 0.001), 16% higher REE/unit cell mass (P < 0.05); and lower mean RQ (P < 0.05). Mean TEE of patients was 4.70 ± 0.49 mJ/24h vs 3.19 ± 0.76 in controls, (P < 0.01). Conclusions: In children, ESLD is a hypermetabolic state adversely affecting the relationship between metabolic and non-metabolic body compartments. There is increased metabolic activity within the body cell mass with excess lipid oxidation during fasting and at rest. These findings have implications for the design of appropriate nutritional therapy.

Expression, Purification and Characterization of Peanut (Arachis hypogaea) Agglutinin (PNA) from Baculovirus Infected Insect Cells

Peanut (Arachis hypogaea) seed lectin, PNA is widely used to identify tumor specific antigen (T-antigen), Gal beta 1-3GalNAc on the eukaryotic cell surface. The functional amino acid coding region of a cDNA clone, pBSH-PN was PCR amplified and cloned downstream of the polyhedrin promoter in the Autographa californica nucleopolyhedrovirus (AcNPV) based transfer vector pVL1393. Co-transfection of Spodoptera frugiperda cells (Sf9) with the transfer vector, pAcPNA and AcRP6 (a recombinant AcNPV having B-gal downstream of the polyhedrin promoter) DNAs produced a recombinant virus, AcPNA which expresses PNA. Infection of suspension culture of Sf9 cells with plaque purified AcPNA produced as much as 9.8 mg PNA per liter (2.0 x 10(6) cells/ml) of serum-free medium. Intracellularly expressed protein (re-PNA) was purified to apparent homogeneity by affinity chromatography using ECD-Sepharose. Polyclonal antibodies against natural PNA (n-PNA) crossreacted with re-PNA. The subunit molecular weight (30 kDa), hemagglutination activity, and carbohydrate specificity of re-PNA were found to be identical to that of n-PNA, thus confirming the abundant production of a functionally active protein in the baculovirus expression system.

Food literacy: Definitions, components, learning and links to diet and health outcomes

Recently, the term ‘food literacy’ has emerged in policy, research and practice to describe the collection of knowledge, skills and behaviours required to practically meet food needs. This presentation will described research undertaken to empirically define the term and propose its impact on nutrition

Micro-scale anaerobic digestion of point source components of organic fraction of municipal solid waste

The fermentation characteristics of six specific types of the organic fraction of municipal solid waste (OFMSW) were examined, with an emphasis on properties that are needed when designing plug-flow type anaerobic bioreactors. More specifically, the decomposition patterns of a vegetable (cabbage), fruits (banana and citrus peels), fresh leaf litter of bamboo and teak leaves, and paper (newsprint) waste streams as feedstocks were studied. Individual OFMSW components were placed into nylon mesh bags and subjected to various fermentation periods (solids retention time, SRT) within the inlet of a functioning plug-flow biogas fermentor. These were removed at periodic intervals, and their composition was analyzed to monitor decomposition rates and changes in chemical composition. Components like cabbage waste, banana peels, and orange peels fermented rapidly both in a plug-flow biogas reactor (PFBR) as well as under a biological methane potential (BMP) assay, while other OFMSW components (leaf litter from bamboo and teak leaves and newsprint) fermented slowly with poor process stability and moderate biodegradation. For fruit and vegetable wastes (FVW), a rapid and efficient removal of pectins is the main cause of rapid disintegration of these feedstocks, which left behind very little compost forming residues (2–5%). Teak and bamboo leaves and newsprint decomposed only to 25–50% in 30 d. These results confirm the potential for volatile fatty acids accumulation in a PFBR’s inlet and suggest a modification of the inlet zone or operation of a PFBR with the above feedstocks.