On the effective hydraulic conductivity and macrodispersivity for density-dependent groundwater flow

In this paper, semi-analytical expressions of the effective hydraulic conductivity ( KE) and macrodispersivity ( αE) for 3D steady-state density-dependent groundwater flow are derived using a stationary spectral method. Based on the derived expressions, we present the dependence of KE and αE on the density of fluid under different dispersivity and spatial correlation scale of hydraulic conductivity. The results show that the horizontal KE and αE are not affected by density-induced flow. However, due to gravitational instability of the fluid induced by density contrasts, both vertical KE and αE are found to be reduced slightly when the density factor ( γ ) is less than 0.01, whereas significant decreases occur when γ exceeds 0.01. Of note, the variation of KE and αE is more significant when local dispersivity is small and the correlation scale of hydraulic conductivity is large.

A two-Dimensional finite volume method for variable density flow and solute transport through saturated-unsaturated media

Extensive groundwater withdrawal has resulted in a severe seawater intrusion problem in the Gooburrum aquifers at Bundaberg, Queensland, Australia. Better management strategies can be implemented by understanding the seawater intrusion processes in those aquifers. To study the seawater intrusion process in the region, a two-dimensional density-dependent, saturated and unsaturated flow and transport computational model is used. The model consists of a coupled system of two non-linear partial differential equations. The first equation describes the flow of a variable-density fluid, and the second equation describes the transport of dissolved salt. A two-dimensional control volume finite element model is developed for simulating the seawater intrusion into the heterogeneous aquifer system at Gooburrum. The simulation results provide a realistic mechanism by which to study the convoluted transport phenomena evolving in this complex heterogeneous coastal aquifer.

Can hybridization cause local extinction : the case for demographic swamping of the Australian native, Senecio pinnatifolius, by the invasive, S. madagascariensis?

The outcome of interspecific hybridization between native and invasive species depends on the relative frequencies of parental taxa and viability of hybrid progeny. We investigated individual and population level consequences of hybridization between the Australian native, Senecio pinnatifolius, and the exotic S. madagascariensis, with AFLP markers and used this information to simulate the expected outcome of hybridization.A high frequency (range 8.3-75.6 %) of hybrids was detected in open pollinated seeds of both species, but mature hybrids were absent from sympatric populations indicating that sympatric populations represent tension zones. A hybridization advantage was observed for S. madagascariensis,where significantly more progeny than expected were sired based on proportional representation of the two species in sympatric populations. Simulations indicated S. pinnatifolius could be replaced in sympatric populations if hybridization was density dependent.For this native-exotic pair, prezygotic isolating barriers are weak, but low hybrid viability maintains a strong postzygotic barrier to introgression. Due to asymmetric hybridization, S. pinnatifolius appears under threat from demographic swamping, and local extinction is possible where it occurs in sympatry with S. madagascariensis.

Interaction of myxomatosis and Rabbit Haemorrhagic Disease in wild rabbit

Increasing resistance of rabbits to myxomatosis in Australia has led to the exploration of Rabbit Haemorrhagic Disease, also called Rabbit Calicivirus Disease (RCD) as a possible control agent. While the initial spread of RCD in Australia resulted in widespread rabbit mortality in affected areas, the possible population dynamic effects of RCD and myxomatosis operating within the same system have not been properly explored. Here we present early mathematical modelling examining the interaction between the two diseases. In this study we use a deterministic compartment model, based on the classical SIR model in infectious disease modelling. We consider, here, only a single strain of myxomatosis and RCD and neglect latent periods. We also include logistic population growth, with the inclusion of seasonal birth rates. We assume there is no cross-immunity due to either disease. The mathematical model allows for the possibility of both diseases to be simultaneously present in an individual, although results are also presented for the case where co infection is not possible, since co-infection is thought to be rare and questions exist as to whether it can occur. The simulation results of this investigation show that it is a crucial issue and should be part of future field studies. A single simultaneous outbreak of RCD and myxomatosis was simulated, while ignoring natural births and deaths, appropriate for a short timescale of 20 days. Simultaneous outbreaks may be more common in Queensland. For the case where co-infection is not possible we find that the simultaneous presence of myxomatosis in the population suppresses the prevalence of RCD, compared to an outbreak of RCD with no outbreak of myxomatosis, and thus leads to a less effective control of the population. The reason for this is that infection with myxomatosis removes potentially susceptible rabbits from the possibility of infection with RCD (like a vaccination effect). We found that the reduction in the maximum prevalence of RCD was approximately 30% for an initial prevalence of 20% of myxomatosis, for the case where there was no simultaneous outbreak of myxomatosis, but the peak prevalence was only 15% when there was a simultaneous outbreak of myxomatosis. However, this maximum reduction will depend on other parameter values chosen. When co-infection is allowed then this suppression effect does occur but to a lesser degree. This is because the rabbits infected with both diseases reduces the prevalence of myxomatosis. We also simulated multiple outbreaks over a longer timescale of 10 years, including natural population growth rates, with seasonal birth rates and density dependent(logistic) death rates. This shows how both diseases interact with each other and with population growth. Here we obtain sustained outbreaks occurring approximately every two years for the case of a simultaneous outbreak of both diseases but without simultaneous co-infection, with the prevalence varying from 0.1 to 0.5. Without myxomatosis present then the simulation predicts RCD dies out quickly without further introduction from elsewhere. With the possibility of simultaneous co-infection of rabbits, sustained outbreaks are possible but then the outbreaks are less severe and more frequent (approximately yearly). While further model development is needed, our work to date suggests that: 1) the diseases are likely to interact via their impacts on rabbit abundance levels, and 2) introduction of RCD can suppress myxomatosis prevalence. We recommend that further modelling in conjunction with field studies be carried out to further investigate how these two diseases interact in the population.

Phagocytosis of cross-linked gelatin matrix by human breast carcinoma cells correlates with their invasive capacity

During invasion and metastasis, cancer cells interact closely with the extracellular matrix molecules by attachment, degradation, and migration. We demonstrated previously the local degradation of fluorescently labeled gelatin matrix by cancer cells at invasive membrane protrusions, called invadopodia. Using the newly developed quantitative fluorescence-activated cell sorting-phagocytosis assay and image analysis of localized degradation of fluorescently labeled matrix, we document here that degradation and site- specific removal of cross-linked gelatin matrix is correlated with the extent of phagocytosis in human breast cancer cells. A higher phagocytic capacity is generally associated with increasing invasiveness, documented in other invasion and motility assays as well. Gelatin phagocytosis is time and cell density dependent, and it is mediated by the actin cytoskeleton. Most of the intracellular gelatin is routed to actively acidified vesicles, as demonstrated by the fluorescent colocalization of gelatin with acidic vesicles, indicating the intracellular degradation of the phagocytosed matrix in lysosomes. We show here that normal intracellular routing is blocked after treatment with acidification inhibitors. In addition, the need for partial proteolytic degradation of the matrix prior to phagocytosis is demonstrated by the inhibition of gelatin phagocytosis with different serine and metalloproteinase inhibitors and its stimulation by conditioned medium containing the matrix metalloproteinases MMP-2 and MMP-9. Our results demonstrate that phagocytosis of extracellular matrix is an inherent feature of breast tumor cells that correlates with and may even directly contribute to their invasive capacity. This assay is useful for screening and evaluating potential anti-invasive agents because it is fast, reproducible, and versatile.

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.

Time-Dependent Density Functional Molecular Orbital and Excited State Calculations on Bis(porphyrinyl)butadiynes in the Monocationic, Neutral, Monoanionic, and Dianionic Oxidation States

We report a theoretical study of the multiple oxidation states (1+, 0, 1−, and 2−) of a meso,meso-linked diporphyrin, namely bis[10,15,20-triphenylporphyrinatozinc(II)-5-yl]butadiyne (4), using Time-Dependent Density Functional Theory (TDDFT). The origin of electronic transitions of singlet excited states is discussed in comparison to experimental spectra for the corresponding oxidation states of the close analogue bis{10,15,20-tris[3‘,5‘-di-tert-butylphenyl]porphyrinatozinc(II)-5-yl}butadiyne (3). The latter were measured in previous work under in situ spectroelectrochemical conditions. Excitation energies and orbital compositions of the excited states were obtained for these large delocalized aromatic radicals, which are unique examples of organic mixed-valence systems. The radical cations and anions of butadiyne-bridged diporphyrins such as 3 display characteristic electronic absorption bands in the near-IR region, which have been successfully predicted with use of these computational methods. The radicals are clearly of the “fully delocalized” or Class III type. The key spectral features of the neutral and dianionic states were also reproduced, although due to the large size of these molecules, quantitative agreement of energies with observations is not as good in the blue end of the visible region. The TDDFT calculations are largely in accord with a previous empirical model for the spectra, which was based simplistically on one-electron transitions among the eight key frontier orbitals of the C4 (1,4-butadiyne) linked diporphyrins.

Temperature-dependent properties of nc-Si thin films synthesized in low-pressure, thermally nonequilibrium, high-density inductively coupled plasmas

Silicon thin films were synthesized simultaneously on single-crystal silicon and glass substrates by lowpressure, thermally nonequilibrium, high-density inductively coupled plasma-assisted chemical vapor deposition from the silane precursor gas without any additional hydrogen dilution in a broad range of substrate temperatures from 100 to 500 °C. The effect of the substrate temperature on the morphological, structural and optical properties of the synthesized silicon thin films is systematically studied by X-ray diffractometry, Raman spectroscopy, UV-vis spectroscopy, and scanning electron microscopy. It is shown that the formation of nanocrystalline silicon (nc-Si) occurs when the substrate temperature is higher than 200 °C and that all the deposited nc-Si films have a preferential growth along the (111) direction. However, the mean grain size of the (111) orientation slightly and gradually decreases while the mean grain size of the (220) orientation shows a monotonous increase with the increased substrate temperature from 200 to 500 °C. It is also found that the crystal volume fraction of the synthesized nc-Si thin films has a maximum value of ∼69.1% at a substrate temperature of 300 rather than 500 °C. This rather unexpected result is interpreted through the interplay of thermokinetic surface diffusion and hydrogen termination effects. Furthermore, we have also shown that with the increased substrate temperature from 100 to 500 °C, the optical bandgap is reduced while the growth rates tend to increase. The maximum rates of change of the optical bandgap and the growth rates occur when the substrate temperature is increased from 400 to 500 °C. These results are highly relevant to the development of photovoltaic thin-film solar cells, thin-film transistors, and flat-panel displays.

Sensitivity of proximal femoral stiffness and areal bone mineral density to changes in bone geometry and density

Areal bone mineral density (aBMD) is the most common surrogate measurement for assessing the bone strength of the proximal femur associated with osteoporosis. Additional factors, however, contribute to the overall strength of the proximal femur, primarily the anatomical geometry. Finite element analysis (FEA) is an effective and widely used computerbased simulation technique for modeling mechanical loading of various engineering structures, providing predictions of displacement and induced stress distribution due to the applied load. FEA is therefore inherently dependent upon both density and anatomical geometry. FEA may be performed on both three-dimensional and two-dimensional models of the proximal femur derived from radiographic images, from which the mechanical stiffness may be redicted. It is examined whether the outcome measures of two-dimensional FEA, two-dimensional, finite element analysis of X-ray images (FEXI), and three-dimensional FEA computed stiffness of the proximal femur were more sensitive than aBMD to changes in trabecular bone density and femur geometry. It is assumed that if an outcome measure follows known trends with changes in density and geometric parameters, then an increased sensitivity will be indicative of an improved prediction of bone strength. All three outcome measures increased non-linearly with trabecular bone density, increased linearly with cortical shell thickness and neck width, decreased linearly with neck length, and were relatively insensitive to neck-shaft angle. For femoral head radius, aBMD was relatively insensitive, with two-dimensional FEXI and threedimensional FEA demonstrating a non-linear increase and decrease in sensitivity, respectively. For neck anteversion, aBMD decreased non-linearly, whereas both two-dimensional FEXI and three dimensional FEA demonstrated a parabolic-type relationship, with maximum stiffness achieved at an angle of approximately 15o. Multi-parameter analysis showed that all three outcome measures demonstrated their highest sensitivity to a change in cortical thickness. When changes in all input parameters were considered simultaneously, three and twodimensional FEA had statistically equal sensitivities (0.41±0.20 and 0.42±0.16 respectively, p = ns) that were significantly higher than the sensitivity of aBMD (0.24±0.07; p = 0.014 and 0.002 for three-dimensional and two-dimensional FEA respectively). This simulation study suggests that since mechanical integrity and FEA are inherently dependent upon anatomical geometry, FEXI stiffness, being derived from conventional two-dimensional radiographic images, may provide an improvement in the prediction of bone strength of the proximal femur than currently provided by aBMD.

The effect of Tenofovir on vitamin D metabolism in HIV-infected adults is dependent on sex and ethnicity

Background: Tenofovir has been associated with renal phosphate wasting, reduced bone mineral density, and higher parathyroid hormone levels. The aim of this study was to carry out a detailed comparison of the effects of tenofovir versus non-tenofovir use on calcium, phosphate and, vitamin D, parathyroid hormone (PTH), and bone mineral density. Methods: A cohort study of 56 HIV-1 infected adults at a single centre in the UK on stable antiretroviral regimes comparing biochemical and bone mineral density parameters between patients receiving either tenofovir or another nucleoside reverse transcriptase inhibitor. Principal Findings: In the unadjusted analysis, there was no significant difference between the two groups in PTH levels (tenofovir mean 5.9 pmol/L, 95% confidence intervals 5.0 to 6.8, versus non-tenofovir; 5.9, 4.9 to 6.9; p = 0.98). Patients on tenofovir had significantly reduced urinary calcium excretion (median 3.01 mmol/24 hours) compared to non-tenofovir users (4.56; p,0.0001). Stratification of the analysis by age and ethnicity revealed that non-white men but not women, on tenofovir had higher PTH levels than non-white men not on tenofovir (mean difference 3.1 pmol/L, 95% CI 5.3 to 0.9; p = 0.007). Those patients with optimal 25-hydroxyvitamin D (.75 nmol/L) on tenofovir had higher 1,25-dihydroxyvitamin D [1,25(OH)2D] (median 48 pg/mL versus 31; p = 0.012), fractional excretion of phosphate (median 26.1%, versus 14.6;p = 0.025) and lower serum phosphate (median 0.79 mmol/L versus 1.02; p = 0.040) than those not taking tenofovir. Conclusions: The effects of tenofovir on PTH levels were modified by sex and ethnicity in this cohort. Vitamin D status also modified the effects of tenofovir on serum concentrations of 1,25(OH)2D and phosphate.

Synthesis of complementary RNA by RNA-dependent RNA polymerases in plant extracts is independent of an RNA primer

RNA-dependent RNA polymerase (RDR) activities were readily detected in extracts from cauliflower and broccoli florets, Arabidopsis thaliana (L.) Heynh callus tissue and broccoli nuclei. The synthesis of complementary RNA (cRNA) was independent of a RNA primer, whether or not the primer contained a 3′ terminal 2′-O-methyl group or was phosphorylated at the 5′ terminus. cRNA synthesis in plant extracts was not affected by loss-of-function mutations in the DICER-LIKE (DCL) proteins DCL2, DCL3, and DCL4, indicating that RDRs function independently of these DCL proteins. A loss-of-function mutation in RDR1, RDR2 or RDR6 did not significantly reduce the amount of cRNA synthesis. This indicates that these RDRs did not account for the bulk RDR activities in plant extracts, and suggest that either the individual RDRs each contribute a fraction of polymerase activity or another RDR(s) is predominant in the plant extract. © CSIRO 2008.

Composition-dependent structural and electronic properties of α-(Si1−xCx)3N4

The highly unusual structural and electronic properties of the α-phase of (Si1-xCx)3N4 are determined by density functional theory (DFT) calculations using the Generalized Gradient Approximation (GGA). The electronic properties of α-(Si 1-xCx)3N4 are found to be very close to those of α-C3N4. The bandgap of α-(Si 1-xCx)3N4 significantly decreases as C atoms are substituted by Si atoms (in most cases, smaller than that of either α-Si3N4 or α-C3N4) and attains a minimum when the ratio of C to Si is close to 2. On the other hand, the bulk modulus of α-(Si1-xCx)3N 4 is found to be closer to that of α-Si3N 4 than of α-C3N4. Plasma-assisted synthesis experiments of CNx and SiCN films are performed to verify the accuracy of the DFT calculations. TEM measurements confirm the calculated lattice constants, and FT-IR/XPS analysis confirms the formation and lengths of C-N and Si-N bonds. The results of DFT calculations are also in a remarkable agreement with the experiments of other authors.

Charge transport and density of trap states in balanced high mobility ambipolar organic thin-film transistors

We report on charge transport and density of trap states (trap DOS) in ambipolar diketopyrrolopyrrole-benzothiadiazole copolymer thin-film transistors. This semiconductor possesses high electron and hole field-effect mobilities of up to 0.6 cm 2/V-s. Temperature and gate-bias dependent field-effect mobility measurements are employed to extract the activation energies and trap DOS to understand its unique high mobility balanced ambipolar charge transport properties. The symmetry between the electron and hole transport characteristics, parameters and activation energies is remarkable. We believe that our work is the first charge transport study of an ambipolar organic/polymer based field-effect transistor with room temperature mobility higher than 0.1 cm 2/V-s in both electrons and holes.