Simulation of plant cell shrinkage during drying : A SPH–DEM approach

Plant based dried food products are popular commodities in global market where much research is focused to improve the products and processing techniques. In this regard, numerical modelling is highly applicable and in this work, a coupled meshfree particle-based two-dimensional (2-D) model was developed to simulate micro-scale deformations of plant cells during drying. Smoothed Particle Hydrodynamics (SPH) was used to model the viscous cell protoplasm (cell fluid) by approximating it to an incompressible Newtonian fluid. The visco-elastic characteristic of the cell wall was approximated to a Neo-Hookean solid material augmented with a viscous term and modelled with a Discrete Element Method (DEM). Compared to a previous work [H. C. P. Karunasena, W. Senadeera, Y. T. Gu and R. J. Brown, Appl. Math. Model., 2014], this study proposes three model improvements: linearly decreasing positive cell turgor pressure during drying, cell wall contraction forces and cell wall drying. The improvements made the model more comparable with experimental findings on dried cell morphology and geometric properties such as cell area, diameter, perimeter, roundness, elongation and compactness. This single cell model could be used as a building block for advanced tissue models which are highly applicable for product and process optimizations in Food Engineering.

A mass spectrometry study of XCO+, X = Si, Ge : Is SiCO+ a main group carbonyl? Comments on the bonding in ground state SiCO and the Si,C,O (+) potential energy surface

The cation\[Si,C,O](+) has been generated by 1) the electron ionisation (EI) of tetramethoxysilane and 2) chemical ionisation (CI) of a mixture of silane and carbon monoxide. Collisional activation (CA) experiments performed for mass-selected \[Si,C,O](+), generated by using both methods, indicate that the structure is not inserted OSiC+; however, a definitive structural assignment as Si+-CO, Si+-OC or some cyclic variant is impossible based on these results alone. Neutralisation-reionisation (+NR+) experiments for EI-generated \[Si,C,O](+) reveal a small peak corresponding to SiC+, but no detectable SiO+ signal, and thus establishes the existence of the Si+-CO isomer. CCSD(T)//B3LYP calculations employing a triple-zeta basis set have been used to explore the doublet and quartet potential-energy surfaces of the cation, as well as some important neutral states The results suggest that both Si+-CO and Si+ - OC isomers are feasible; however, the global minimum is (2)Pi SiCO+. Isomeric (2)Pi SiOC+ is 12.1 kcal mol(-1) less stable than (2)Pi SiCO+, and all quartet isomers are much higher in energy. The corresponding neutrals Si-CO and Si-OC are also feasible, but the lowest energy Si - OC isomer ((3)A") is bound by only 1.5 kcal mol(-1). We attribute most, if nor all, of the recovery signal in the +NR' experiment to SiCO+ survivor ions. The nature of the bonding in the lowest energy isomers of Si+ -(CO,OC) is interpreted with the aid of natural bond order analyses, and the ground stale bonding of SiCO+ is discussed in relation to classical analogues such as metal carbonyls and ketenes.

Implication of calcium hydroxide in the seawater neutralisation of bauxite refinery liquors

Tricalcium aluminate, hydrocalumite and residual lime have been identified as reversion contributing compounds after the seawater neutralisation of bauxite refinery residues. The formation of these compounds during the neutralisation process is dependent on the concentration of residual lime, pH and aluminate concentrations in the residue slurry. Therefore, the effect of calcium hydroxide (CaOH2) in bauxite refinery liquors was analysed and the degree of reversion monitored. This investigation found that the dissolution of tricalcium aluminate, hydrocalumite and CaOH2 caused reversion and continued to increase the pH of the neutralised residue until a state of equilibrium was reached at a solution pH of 10.5. The dissolution mechanism for each compound has been described and used to demonstrate the implications that this has on reversion in seawater neutralised Bayer liquor. This investigation describes the limiting factors for the dissolution and formation of these trigger compounds as well as confirming the formation of Bayer hydrotalcite (mixture of Mg6Al2(OH)16(CO32-,SO42-)•xH2O and Mg8Al2(OH)12(CO32-,SO42-)•xH2O) as the primary mechanism for reducing reversion during the neutralisation process. This knowledge then allowed for a simple but effective method (addition of magnesium chloride or increased seawater to Bayer liquor ratio) to be devised to reduce reversion occurring after the neutralisation of Bayer liquors. Both methods utilise the formation of Bayer hydrotalcite to permanently (stable in neutralised residue) remove hydroxyl (OH-) and aluminate (Al(OH)4-) ions from solution.

Characterization and novel activation of 72-kDa metalloproteinase in retinal interphotoreceptor matrix and Y-79 cell culture medium

Analysis of bovine interphotoreceptor matrix and conditioned medium from human Y-79 retinoblastoma cells by gelatin SDS-PAGE zymography reveals abundant activity of a 72-kDa M(r) gelatinase. The 72-kDa gelatinase from either source is inhibited by EDTA but not aprotinin or NEM, indicating that it is a metalloproteinase (MMP). The 72-kDa MMP is converted to a 62-kDa species with APMA treatment after gelatin sepharose affinity purification typical of previously described gelatinase MMP-2. The latent 72-kDa gelatinase from either bovine IPM or Y-79 media autoactivates without APMA in the presence of calcium and zinc after 72 hr at 37°C, producing a fully active mixture of proteinase species, 50 (48 in Y-79 medium), 38 and 35 kDa in size. The presence of inhibitory activity was examined in both whole bovine IPM and IPM fractions separated by SDS-PAGE. Whole IPM inhibited gelatinolytic activity of autoactivated Y-79-derived MMP in a dose-dependent manner. Inhibitory activities are observed in two protein fractions of 27-42 and 20-25 kDa. Western blots using antibodies to human tissue inhibitor of metalloproteinase 1 and 2 (TIMP-1 and -2) reveal the presence of two TIMP-1-like proteins at 21 and 29 kDa in inhibitory fractions of the bovine IPM. TIMP-2 was not detected in the inhibitory IPM fractions, consistent with the observed autoactivation of bovine IPM 72-kDa gelatinase. Potential roles for this IPM MMP-TIMP system include physiologic remodelling of the neural retina-RPE cell interface and digestion of shed rod outer segment as well as pathological processes such as retinal detachment, PE cell migration, neovascularization and tumor progression. Cultured Y-79 cells appear to be a good model for studying the production and regulation of this proteinase system.

Combined analysis of categorical and numerical descriptors of Australian groundnut accessions using nonlinear principal component analysis

For users of germplasm collections, the purpose of measuring characterization and evaluation descriptors, and subsequently using statistical methodology to summarize the data, is not only to interpret the relationships between the descriptors, but also to characterize the differences and similarities between accessions in relation to their phenotypic variability for each of the measured descriptors. The set of descriptors for the accessions of most germplasm collections consists of both numerical and categorical descriptors. This poses problems for a combined analysis of all descriptors because few statistical techniques deal with mixtures of measurement types. In this article, nonlinear principal component analysis was used to analyze the descriptors of the accessions in the Australian groundnut collection. It was demonstrated that the nonlinear variant of ordinary principal component analysis is an appropriate analytical tool because subspecies and botanical varieties could be identified on the basis of the analysis and characterized in terms of all descriptors. Moreover, outlying accessions could be easily spotted and their characteristics established. The statistical results and their interpretations provide users with a more efficient way to identify accessions of potential relevance for their plant improvement programs and encourage and improve the usefulness and utilization of germplasm collections.

Bioeconomic modelling and risk assessment of tiger prawn (Penaeus esculentus) stock enhancement in Exmouth Gulf, Australia

A bioeconomic model was developed to evaluate the potential performance of brown tiger prawn stock enhancement in Exmouth Gulf, Australia. This paper presents the framework for the bioeconomic model and risk assessment for all components of a stock enhancement operation, i.e. hatchery, grow-out, releasing, population dynamics, fishery, and monitoring, for a commercial scale enhancement of about 100 metric tonnes, a 25% increase in average annual catch in Exmouth Gulf. The model incorporates uncertainty in estimates of parameters by using a distribution for the parameter over a certain range, based on experiments, published data, or similar studies. Monte Carlo simulation was then used to quantify the effects of these uncertainties on the model-output and on the economic potential of a particular production target. The model incorporates density-dependent effects in the nursery grounds of brown tiger prawns. The results predict that a release of 21 million 1 g prawns would produce an estimated enhanced prawn catch of about 100 t. This scale of enhancement has a 66.5% chance of making a profit. The largest contributor to the overall uncertainty of the enhanced prawn catch was the post-release mortality, followed by the density-dependent mortality caused by released prawns. These two mortality rates are most difficult to estimate in practice and are much under-researched in stock enhancement.

Benthic metabolism as an indicator of stream ecosystem health

We tested direct and indirect measures of benthic metabolism as indicators of stream ecosystem health across a known agricultural land-use disturbance gradient in southeast Queensland, Australia. Gross primary production (GPP) and respiration (R24) in benthic chambers in cobble and sediment habitats, algal biomass (as chlorophyll a) from cobbles and sediment cores, algal biomass accrual on artificial substrates and stable carbon isotope ratios of aquatic plants and benthic sediments were measured at 53 stream sites, ranging from undisturbed subtropical rainforest to catchments where improved pasture and intensive cropping are major land-uses. Rates of benthic GPP and R24 varied by more than two orders of magnitude across the study gradient. Generalised linear regression modelling explained 80% or more of the variation in these two indicators when sediment and cobble substrate dominated sites were considered separately, and both catchment and reach scale descriptors of the disturbance gradient were important in explaining this variation. Model fits were poor for net daily benthic metabolism (NDM) and production to respiration ratio (P/R). Algal biomass accrual on artificial substrate and stable carbon isotope ratios of aquatic plants and benthic sediment were the best of the indirect indicators, with regression model R2 values of 50% or greater. Model fits were poor for algal biomass on natural substrates for cobble sites and all sites. None of these indirect measures of benthic metabolism was a good surrogate for measured GPP. Direct measures of benthic metabolism, GPP and R24, and several indirect measures were good indicators of stream ecosystem health and are recommended in assessing process-related responses to riparian and catchment land use change and the success of ecosystem rehabilitation actions.

Mixed data types and the use of pattern analysis on the Australian groundnut germplasm data

Data in germplasm collections contain a mixture of data types; binary, multistate and quantitative. Given the multivariate nature of these data, the pattern analysis methods of classification and ordination have been identified as suitable techniques for statistically evaluating the available diversity. The proximity (or resemblance) measure, which is in part the basis of the complementary nature of classification and ordination techniques, is often specific to particular data types. The use of a combined resemblance matrix has an advantage over data type specific proximity measures. This measure accommodates the different data types without manipulating them to be of a specific type. Descriptors are partitioned into their data types and an appropriate proximity measure is used on each. The separate proximity matrices, after range standardisation, are added as a weighted average and the combined resemblance matrix is then used for classification and ordination. Germplasm evaluation data for 831 accessions of groundnut (Arachis hypogaea L.) from the Australian Tropical Field Crops Genetic Resource Centre, Biloela, Queensland were examined. Data for four binary, five ordered multistate and seven quantitative descriptors have been documented. The interpretative value of different weightings - equal and unequal weighting of data types to obtain a combined resemblance matrix - was investigated by using principal co-ordinate analysis (ordination) and hierarchical cluster analysis. Equal weighting of data types was found to be more valuable for these data as the results provided a greater insight into the patterns of variability available in the Australian groundnut germplasm collection. The complementary nature of pattern analysis techniques enables plant breeders to identify relevant accessions in relation to the descriptors which distinguish amongst them. This additional information may provide plant breeders with a more defined entry point into the germplasm collection for identifying sources of variability for their plant improvement program, thus improving the utilisation of germplasm resources.

Managed livestock grazing is compatible with the maintenance of plant diversity in semidesert grasslands

Even when no baseline data are available, the impacts of 150 years of livestock grazing on natural grasslands can be assessed using a combined approach of grazing manipulation and regional-scale assessment of the flora. Here, we demonstrate the efficacy of this method across 18 sites in the semidesert Mitchell grasslands of northeastern Australia. Fifteen-year-old exclosures (ungrazed and macropod grazed) revealed that the dominant perennial grasses in the genus Astrebla do not respond negatively to grazing disturbance typical of commercial pastoralism. Neutral, positive, intermediate, and negative responses to grazing disturbance were recorded amongst plant species with no single life-form group associated with any response type. Only one exotic species, Cenchrus ciliaris, was recorded at low frequency. The strongest negative response was from a native annual grass, Chionachne hubbardiana, an example of a species that is highly sensitive to grazing disturbance. Herbarium records revealed only scant evidence that species with a negative response to grazing have declined through the period of commercial pastoralism. A regional analysis identified 14 from a total of 433 plant species in the regional flora that may be rare and potentially threatened by grazing disturbance. However, a targeted survey precluded grazing as a cause of decline for seven of these based on low palatability and positive responses to grazing and other disturbance. Our findings suggest that livestock grazing of semidesert grasslands with a short evolutionary history of ungulate grazing has altered plant composition, but has not caused declines in the dominant perennial grasses or in species richness as predicted by the preceding literature. The biggest impact of commercial pastoralism is the spread of woody leguminous trees that can transform grassland to thorny shrubland. The conservation of plant biodiversity is largely compatible with commercial pastoralism provided these woody weeds are controlled, but reserves strategically positioned within water remote areas are necessary to protect grazing-sensitive species. This study demonstrates that a combination of experimental studies and regional surveys can be used to understand anthropogenic impacts on natural ecosystems where reference habitat is not available.

Intercalation of dodecylamine into kaolinite and its layering structure investigated by molecular dynamics simulation

Dodecylamine was successfully intercalated into the layer space of kaolinite by utilizing the methanol treated kaolinite–dimethyl sulfoxide (DMSO) intercalation complex as an intermediate. The basal spacing of kaolinite, measured by X-ray diffraction (XRD), increased from 0.72 nm to 4.29 nm after the intercalation of dodecylamine. Also, the significant variation observed in the Fourier Transform Infrared Spectroscopy (FTIR) spectra of kaolinite when intercalated with dodecylamine verified the feasibility of intercalation of dodecylamine into kaolinite. Isothermal-isobaric (NPT) molecular dynamics simulation with the use of Dreiding force field was performed to probe into the layering behavior and structure of nanoconfined dodecylamine in the kaolinite gallery. The concentration profiles of the nitrogen atom, methyl group and methylene group of intercalated dodecylamine molecules in the direction perpendicular to the kaolinite basal surface indicated that the alkyl chains within the interlayer space of kaolinite exhibited an obvious layering structure. However, the unified bilayer, pseudo-trilayer, or paraffin-type arrangements of alkyl chains deduced based on their chain length combined with the measured basal spacing of organoclays were not found in this study. The alkyl chains aggregated to a mixture of ordered paraffin-type-like structure and disordered gauche conformation in the middle interlayer space of kaolinite, and some alkyl chains arranged in two bilayer structures, in which one was close to the silica tetrahedron surface, and the other was close to the alumina octahedron surface with their alkyl chains parallel to the kaolinite basal surface.

Constructions of cheating immune secret sharing

The work addresses the problem of cheating prevention in secret sharing. Two cheating scenarios are considered. In the first one, the cheaters always submit invalid shares to the combiner. In the second one, the cheaters collectively decide which shares are to be modified so the combiner gets a mixture of valid and invalid shares from the cheaters. The secret scheme is said to be k-cheating immune if any group of k cheaters has no advantage over honest participants. The paper investigates cryptographic properties of the defining function of secret sharing so the scheme is k-cheating immune. Constructions of secret sharing immune against k cheaters are given.

Plasma-enabled, catalyst-free growth of carbon nanotubes on mechanically-written Si features with arbitrary shape

Simple, rapid, catalyst-free synthesis of complex patterns of long, vertically aligned multiwalled carbon nanotubes, strictly confined within mechanically-written features on a Si(1 0 0) surface is reported. It is shown that dense arrays of the nanotubes can nucleate and fully fill the features when the low-temperature microwave plasma is in a direct contact with the surface. This eliminates additional nanofabrication steps and inevitable contact losses in applications associated with carbon nanotube patterns. Using metal catalyst has long been considered essential for the nucleation and growth of surface-supported carbon nanotubes (CNTs) [1] and [2]. Only very recently, the possibility of CNT growth using non-metallic (e.g., oxide [3] and SiC [4]) catalysts or artificially created carbon-enriched surface layers [5] has been demonstrated. However, successful integration of carbon nanostructures into Si-based nanodevice platforms requires catalyst-free growth, as the catalyst nanoparticles introduce contact losses, and their catalytic activity is very difficult to control during the growth [6]. Furthermore, in many applications in microfluidics, biological and molecular filters, electronic, sensor, and energy conversion nanodevices, the CNTs need to be arranged in specific complex patterns [7] and [8]. These patterns need to contain the basic features (e.g., lines and dots) written using simple procedures and fully filled with dense arrays of high-quality, straight, yet separated nanotubes. In this paper, we report on a completely metal or oxide catalyst-free plasma-based approach for the direct and rapid growth of dense arrays of long vertically-aligned multi-walled carbon nanotubes arranged into complex patterns made of various combinations of basic features on a Si(1 0 0) surface written using simple mechanical techniques. The process was conducted in a plasma environment [9] and [10] produced by a microwave discharge which typically generates the low-temperature plasmas at the discharge power below 1 kW [11]. Our process starts from mechanical writing (scribing) a pattern of arbitrary features on pre-treated Si(1 0 0) wafers. Before and after the mechanical feature writing, the Si(1 0 0) substrates were cleaned in an aqueous solution of hydrofluoric acid for 2 min to remove any possible contaminations (such as oil traces which could decompose to free carbon at elevated temperatures) from the substrate surface. A piece of another silicon wafer cleaned in the same way as the substrate, or a diamond scriber were used to produce the growth patterns by a simple arbitrary mechanical writing, i.e., by making linear scratches or dot punctures on the Si wafer surface. The results were the same in both cases, i.e., when scratching the surface by Si or a diamond scriber. The procedure for preparation of the substrates did not involve any possibility of external metallic contaminations on the substrate surface. After the preparation, the substrates were loaded into an ASTeX model 5200 chemical vapour deposition (CVD) reactor, which was very carefully conditioned to remove any residue contamination. The samples were heated to at least 800 °C to remove any oxide that could have formed during the sample loading [12]. After loading the substrates into the reactor chamber, N2 gas was supplied into the chamber at the pressure of 7 Torr to ignite and sustain the discharge at the total power of 200 W. Then, a mixture of CH4 and 60% of N2 gases were supplied at 20 Torr, and the discharge power was increased to 700 W (power density of approximately 1.49 W/cm3). During the process, the microwave plasma was in a direct contact with the substrate. During the plasma exposure, no external heating source was used, and the substrate temperature (∼850 °C) was maintained merely due to the plasma heating. The features were exposed to a microwave plasma for 3–5 min. A photograph of the reactor and the plasma discharge is shown in Fig. 1a and b.

Single-step, rapid low-temperature synthesis of Si quantum dots embedded in an amorphous SiC matrix in high-density reactive plasmas

A simple, effective and innovative approach based on low-pressure, thermally nonequilibrium, high-density inductively coupled plasmas is proposed to rapidly synthesize Si quantum dots (QDs) embedded in an amorphous SiC (a-SiC) matrix at a low substrate temperature and without any commonly used hydrogen dilution. The experimental results clearly demonstrate that uniform crystalline Si QDs with a size of 3-4 nm embedded in the silicon-rich (carbon content up to 10.7at.%) a-SiC matrix can be formed from the reactive mixture of silane and methane gases, with high growth rates of ∼1.27-2.34 nm s-1 and at a low substrate temperature of 200 °C. The achievement of the high-rate growth of Si QDs embedded in the a-SiC without any commonly used hydrogen dilution is discussed based on the unique properties of the inductively coupled plasma-based process. This work is particularly important for the development of the all-Si tandem cell-based third generation photovoltaic solar cells.

Use of reverse phase protein microarrays and reference standard development for molecular network analysis of metastatic ovarian carcinoma

Cancer can be defined as a deregulation or hyperactivity in the ongoing network of intracellular and extracellular signaling events. Reverse phase protein microarray technology may offer a new opportunity to measure and profile these signaling pathways, providing data on post-translational phosphorylation events not obtainable by gene microarray analysis. Treatment of ovarian epithelial carcinoma almost always takes place in a metastatic setting since unfortunately the disease is often not detected until later stages. Thus, in addition to elucidation of the molecular network within a tumor specimen, critical questions are to what extent do signaling changes occur upon metastasis and are there common pathway elements that arise in the metastatic microenvironment. For individualized combinatorial therapy, ideal therapeutic selection based on proteomic mapping of phosphorylation end points may require evaluation of the patient's metastatic tissue. Extending these findings to the bedside will require the development of optimized protocols and reference standards. We have developed a reference standard based on a mixture of phosphorylated peptides to begin to address this challenge.

One-step macroscopic alignment of conjugated polymer systems by epitaxial crystallization during spin-coating

The one-step preparation of highly anisotropic polymer semiconductor thin films directly from solution is demonstrated. The conjugated polymer poly(3-hexylthiophene) (P3HT) as well as P3HT:fullerene bulk-heterojunction blends can be spin-coated from a mixture of the crystallizable solvent 1,3,5-trichlorobenzene (TCB) and a second carrier solvent such as chlorobenzene. Solidification is initiated by growth of macroscopic TCB spherulites followed by epitaxial crystallization of P3HT on TCB crystals. Subsequent sublimation of TCB leaves behind a replica of the original TCB spherulites. Thus, highly ordered thin films are obtained, which feature square-centimeter-sized domains that are composed of one spherulite-like structure each. A combination of optical microscopy and polarized photoluminescence spectroscopy reveals radial alignment of the polymer backbone in case of P3HT, whereas P3HT:fullerene blends display a tangential orientation with respect to the center of spherulite-like structures. Moreover, grazing-incidence wide-angle X-ray scattering reveals an increased relative degree of crystallinity and predominantly flat-on conformation of P3HT crystallites in the blend. The use of other processing methods such as dip-coating is also feasible and offers uniaxial orientation of the macromolecule. Finally, the applicability of this method to a variety of other semi-crystalline conjugated polymer systems is established. Those include other poly(3-alkylthiophene)s, two polyfluorenes, the low band-gap polymer PCPDTBT, a diketopyrrolopyrrole (DPP) small molecule as well as a number of polymer:fullerene and polymer:polymer blends. Macroscopic spherulite-like structures of the conjugated polymer poly(3-hexylthiophene) (P3HT) grow directly during spin-coating. This is achieved by processing P3HT or P3HT:fullerene bulk heterojunction blends from a mixture of the crystallizable solvent 1,3,5-trichlorobenzene and a second carrier solvent such as chlorobenzene. Epitaxial growth of the polymer on solidified solvent crystals gives rise to circular-symmetric, spherulite-like structures that feature a high degree of anisotropy.