Chromosomal gains and losses in ocular melanoma detected by comparative genomic hybridization in an Australian population-based study

To define the location of potential oncogenes and tumor suppressor genes in ocular melanoma we carried out comparative genomic hybridization (CGH) analysis on a population-based series of 25 formalin-fixed, paraffin-embedded primary tumors comprising 17 choroidal, 2 ciliary body, 4 iris, and 2 conjunctival melanomas. Twelve (48%) of the 25 melanomas showed no chromosomal changes and 13 (52%) had at least one chromosomal gain or loss. The mean number of CGH changes in all tumors was 3.3, with similar mean numbers of chromosomal gains (1.5) and losses (1.8). The highest number of chromosomal changes (i.e., nine) occurred in a conjunctival melanoma and included four changes not observed in tumors at any other ocular site (gains in 22q and 11p and losses in 6p and 17p). The most frequent gains in all primary ocular melanomas were on chromosome arm 8q (69%), 6p (31%) and 8p (23%) and the most frequent losses were on 6q (38%), 10q (23%), and 16q (23%). The most common pairing was gain in 8p and gain in 8q, implying a whole chromosome copy number increase; gains in 8p occurred only in conjunction with gains in 8q. The smallest regions of copy number alteration were mapped to gain of 8q21 and loss of 6q21, 10q21, and 16q22. Sublocalization of these chromosomal changes to single-band resolution should accelerate the identification of genes involved in the genesis of ocular melanoma.

Composition and quality of harvest residues and soil organic matter under windrow residue management in young hoop pine plantations as revealed by solid-state C-13 NMR spectroscopy

Solid-state C-13 nuclear magnetic resonance (NMR) with cross-polarisation (CP) and magic-angle-spinning (MAS) was used to: (a) examine the changes in carbon (C) composition of windrowed harvest residues during the first 3 years of hoop pine plantations in subtropical Australia; (b) assess the impacts of windrowed harvest residues on soil organic matter (SOM) composition and quality in the 0-10 cm soil layer. Harvest residues were collected from 0-, 1-, 2- and 3-year-old windrows of ca. 2.5 m width (15 m apart for 0-, 1- and 2-year-old sites and 10 m apart for 3-year-old site). Soils from the 0 to 10 cm soil layer were collected from the 1-, 2- and 3-year-old sites. The 13C NMR spectra of the harvest residues indicated the presence of lignin in the hoop pine wood, foliage and newly incorporated organic matter (NIOM). Condensed tannin structures were found in the decay-resistant bark, small wood and foliage, but were absent in other residue components and SOM. The NMR spectra of small wood samples contained condensed tannin structures because the outer layer of bark was not removed. NIOM showed a shift from foliage-like structures (celluloses) to lignin-type structures, indicating an incorporation of woody residues from the decomposing harvest residues. Suberins were also present in the small wood, foliage and bark. The 13C CP NMR spectra of SOM indicated that in areas where windrows were present, SOM did not show compositional changes. However, an increase in SOM quality under the windrows in the second year after their formation as characterised by the alkyl C/O-alkyl C (A/O-A) ratio was mainly due to inputs from the decomposition of the labile, readily available components of the windrowed harvest residues. (C) 2002 Published by Elsevier Science B.V.

Model-based analysis of anaerobic acetate uptake by a mixed culture of polyphosphate-accumulating and glycogen-accumulating organisms

An increasing number of studies shows that the glycogen-accumulating organisms (GAOs) can survive and may indeed proliferate under the alternating anaerobic/aerobic conditions found in EBPR systems, thus forming a strong competitor of the polyphosphate-accumulating organisms (PAOs). Understanding their behaviors in a mixed PAO and GAO culture under various operational conditions is essential for developing operating strategies that disadvantage the growth of this group of unwanted organisms. A model-based data analysis method is developed in this paper for the study of the anaerobic PAO and GAO activities in a mixed PAO and GAO culture. The method primarily makes use of the hydrogen ion production rate and the carbon dioxide transfer rate resulting from the acetate uptake processes by PAOs and GAOs, measured with a recently developed titration and off-gas analysis (TOGA) sensor. The method is demonstrated using the data from a laboratory-scale sequencing batch reactor (SBR) operated under alternating anaerobic and aerobic conditions. The data analysis using the proposed method strongly indicates a coexistence of PAOs and GAOs in the system, which was independently confirmed by fluorescent in situ hybridization (FISH) measurement. The model-based analysis also allowed the identification of the respective acetate uptake rates by PAOs and GAOs, along with a number of kinetic and stoichiometric parameters involved in the PAO and GAO models. The excellent fit between the model predictions and the experimental data not involved in parameter identification shows that the parameter values found are reliable and accurate. It also demonstrates that the current anaerobic PAO and GAO models are able to accurately characterize the PAO/GAO mixed culture obtained in this study. This is of major importance as no pure culture of either PAOs or GAOs has been reported to date, and hence the current PAO and GAO models were developed for the interpretation of experimental results of mixed cultures. The proposed method is readily applicable for detailed investigations of the competition between PAOs and GAOs in enriched cultures. However, the fermentation of organic substrates carried out by ordinary heterotrophs needs to be accounted for when the method is applied to the study of PAO and GAO competition in full-scale sludges. (C) 2003 Wiley Periodicals, Inc.

Integrated control of nitrate recirculation and external carbon addition in a predenitrification system

The integrated control of nitrate recirculation and external carbon addition in a predenitrification biological wastewater treatment system is studied. The proposed control structure consists of four feedback control loops, which manipulate the nitrate recirculation and the carbon dosage flows in a highly coordinated manner such that the consumption of external carbon is minimised while the nitrate discharge limits (based on both grab and composite samples) are met. The control system requires the measurement of the nitrate concentrations at the end of both the anoxic and the aerobic zones. Distinct from ordinary control systems, which typically minimise the variation in the controlled variables, the proposed control system essentially maximises the diurnal variation of the effluent nitrate concentration and through this maximises the use of influent COD for denitrification, thus minimising the requirement for external carbon source. Simulation studies using a commonly accepted simulation benchmark show that the controlled system consistently achieves the designated effluent quality with minimum costs.

SPAnDX: a process-based population dynamics model to explore management and climate change impacts on an invasive alien plant, Acacia nilotica

This paper describes a process-based metapopulation dynamics and phenology model of prickly acacia, Acacia nilotica, an invasive alien species in Australia. The model, SPAnDX, describes the interactions between riparian and upland sub-populations of A. nilotica within livestock paddocks, including the effects of extrinsic factors such as temperature, soil moisture availability and atmospheric concentrations of carbon dioxide. The model includes the effects of management events such as changing the livestock species or stocking rate, applying fire, and herbicide application. The predicted population behaviour of A. nilotica was sensitive to climate. Using 35 years daily weather datasets for five representative sites spanning the range of conditions that A. nilotica is found in Australia, the model predicted biomass levels that closely accord with expected values at each site. SPAnDX can be used as a decision-support tool in integrated weed management, and to explore the sensitivity of cultural management practices to climate change throughout the range of A. nilotica. The cohort-based DYMEX modelling package used to build and run SPAnDX provided several advantages over more traditional population modelling approaches (e.g. an appropriate specific formalism (discrete time, cohort-based, process-oriented), user-friendly graphical environment, extensible library of reusable components, and useful and flexible input/output support framework). (C) 2003 Published by Elsevier Science B.V.

Surface diffusion of strongly adsorbing vapors in activated carbon by a differential permeation method

Conventional methods to determine surface diffusion of adsorbed molecules are proven to be inadequate for strongly adsorbing vapors on activated carbon. Knudsen diffusion permeability (B-k) for strongly adsorbing vapors cannot be directly estimated from that of inert gases such as helium. In this paper three models are considered to elucidate the mechanism of surface diffusion in activated carbon. The transport mechanism in all three models is a combination of Knudsen diffusion, viscous flow and surface diffusion. The collision reflection factor f (which is the fraction of molecules undergoing collision to the solid surface over reflection from the surface) of the Knudsen diffusivity is assumed to be a function of loading. It was found to be 1.79 in the limit of zero loading, and decreases as loading increases. The surface diffusion permeability increases sharply at very low pressures and then starts to decrease after it has reached a maximum (B(mum)s) at a threshold pressure. The initial rapid increase in the total permeability is mainly attributed to surface diffusion. Interestingly the B(mum)s for all adsorbates appear at the same volumetric adsorbed phase concentration, suggesting that the volume of adsorbed molecules may play an important role in the surface diffusion mechanism in activated carbon. (C) 2003 Elsevier Ltd. All rights reserved.

Analysis of multicomponent adsorption kinetics on activated carbon

An integrated mathematical model for the kinetics of multicomponent adsorption on microporous carbon was developed. Transport in this bidisperse solid is represented by balance equations in the macropore and micropore phases, in which gas-phase diffusion dominates the mass transfer in the macropores, with the phenomenological diffusivities represented by the generalized Maxwell-Stefan (GMS) formulation. Viscous flow also contributes to the macropore fluxes and is included in the MS expressions. Diffusion of the adsorbed phase controls the mass transfer in the micro ore phase, p which is also described in a similar way by the MS method. The adsorption isotherms are represented by a new heterogeneous modified vacancy solution theory formulation of adsorption, which has proved to be a robust method for adsorption on activated carbons. The model is applied to the coadsorption and codesorption of C2H6 and C3H8 on Ajax and Norit carbon, as well as the displacement on Ajax carbon. The effect of the viscous flow in the macropore phase is not significant for the cases studied. The model accurately predicts the overshoot behavior and rollup of C2H6 during coadsorption. The prediction for the heavier compound C3H8 is always satisfactory, though at higher C3H8 mole fraction, the overshoot extent of C2H6 is overpredicted, possibly due to neglect of heat effects.

Osteoblast, fibroblast and in vivo biological response to poly(vinylidene fluoride) based composite materials

Electroactivematerials can be taken to advantage for the development of sensors and actuators as well as for novel tissue engineering strategies. Composites based on poly(vinylidenefluoride),PVDF,have been evaluated with respect to their biological response. Cell viability and proliferation were performed in vitro both with Mesenchymal Stem Cells differentiated to osteoblasts and Human Fibroblast Foreskin 1. In vivo tests were also performed using 6-week-old C57Bl/6 mice. It was concluded that zeolite and clay composites are biocompatible materials promoting cell response and not showing in vivo pro-inflammatory effects which renders both of them attractive for biological applications and tissue engineering, opening interesting perspectives to development of scaffolds from these composites. Ferrite and silver nanoparticle composites decrease osteoblast cell viability and carbon nanotubes decrease fibroblast viability. Further, carbon nanotube composites result in a significant increase in local vascularization accompanied an increase of inflammatory markers after implantation.

Temperature dependence of the electrical conductivity of vapor grown carbon nanofiber/epoxy composites with different filler dispersion levels

The influence of the dispersion of vapor grown carbon nanofibers (VGCNF) on the electrical properties of VGCNF/epoxy composites has been studied. A homogeneous dispersion of the VGCNF does not imply better electrical properties. The presence of well distributed clusters appears to be a key factor for increasing composite conductivity. It is also shown that the main conduction mechanism has an ionic nature for concentrations below the percolation threshold, while above the percolation threshold it is dominated by hopping between the fillers. Finally, using the granular system theory it is possible to explain the origin of conduction at low temperatures.

Modeling Carbon Nanotube Electrical Properties in CNT/Polymer Composites

In this work it is demonstrated that the capacitance between two cylinders increases with the rotation angle and it has a fundamental influence on the composite dielectric constant. The dielectric constant is lower for nematic materials than for isotropic ones and this can be attributed to the effect of the filler alignment in the capacitance. The effect of aspect ratio in the conductivity is also studied in this work. Finally, based on previous work and by comparing to results from the literature it is found that the electrical conductivity in this type of composites is due to hopping between nearest fillers resulting in a weak disorder regime that is similar to the single junction expression.

Coupling Mechanical and Electrical Behavior in the Multi-scale Simulation of Polymer-based CNT Nanocomposites

A numeric model has been proposed to investigate the mechanical and electrical properties of a polymeric/carbon nanotube (CNT) composite material subjected to a deformation force. The reinforcing phase affects the behavior of the polymeric matrix and depends on the nanofiber aspect ratio and preferential orientation. The simulations show that the mechanical behavior of a computer generated material (CGM) depends on fiber length and initial orientation in the polymeric matrix. It is also shown how the conductivity of the polymer/CNT composite can be calculated for each time step of applied stress, effectively providing the ability to simulate and predict strain-dependent electrical behavior of CNT nanocomposites.

Applying complex network theory to the understanding of high-aspect-ratio carbon-filled composites

This work demonstrates that the theoretical framework of complex networks typically used to study systems such as social networks or the World Wide Web can be also applied to material science, allowing deeper understanding of fundamental physical relationships. In particular, through the application of the network theory to carbon nanotubes or vapour-grown carbon nanofiber composites, by mapping fillers to vertices and edges to the gap between fillers, the percolation threshold has been predicted and a formula that relates the composite conductance to the network disorder has been obtained. The theoretical arguments are validated by experimental results from the literature.

The influence of matrix mediated hopping conductivity, filler concentration, aspect ratio and orientation on the electrical response of carbon nanotube/polymer nanocomposites

A model to simulate the conductivity of carbon nanotube/polymer nanocomposites is presented. The proposed model is based on hopping between the fillers. A parameter related to the influence of the matrix in the overall composite conductivity is defined. It is demonstrated that increasing the aspect ratio of the fillers will increase the conductivity. Finally, it is demonstrated that the alignment of the filler rods parallel to the measurement direction results in higher conductivity values, in agreement with results from recent experimental work.

Carbon Nanofiber Type and Content Dependence of the Physical Properties of Carbon Nanofiber Reinforced Polypropylene Composites

The variation of the physical properties of four differ- ent carbon nanofibers (CNFs), based-polymer nano- composites incorporated in the same polypropylene (PP) matrix by twin-screw extrusion process was investigated. Nanocomposites fabricated with CNFs with highly graphitic outer layer revealed electrical isolation-to-conducting behaviors as function of CNF’s content. Nanocomposites fabricated with CNFs with an outer layer consisting on a disordered pyro- litically stripped layer, in contrast, revealed better mechanical performance and enhanced thermal sta- bility. Further, CNF’s incorporation into the polymer increased the thermal stability and the degree of crystallinity of the polymer, independently on the filler content and type. In addition, dispersion of the CNFs’ clusters in PP was analyzed by transmitted light opti- cal microscopy, and grayscale analysis (GSA). The results showed a correlation between the filler concentration and the variance, a parameter which measures quantitatively the dispersion, for all composites. This method indicated a value of 1.4 vol% above which large clusters of CNFs cannot be dispersed effectively and as a consequence only slight changes in mechanical performance are observed. Finally, this study establishes that for tailoring the physical properties of CNF based-polymer nanocomposites, both adequate CNFs structure and content have to be chosen.

A Wireless EEG Acquisition Platform based on Embedded Systems

This paper proposes a wireless EEG acquisition platform based on Open Multimedia Architecture Platform (OMAP) embedded system. A high-impedance active dry electrode was tested for improving the scalp- electrode interface. It was used the sigma-delta ADS1298 analog-to-digital converter, and developed a “kernelspace” character driver to manage the communications between the converter unit and the OMAP’s ARM core. The acquired EEG signal data is processed by a “userspace” application, which accesses the driver’s memory, saves the data to a SD-card and transmits them through a wireless TCP/IP-socket to a PC. The electrodes were tested through the alpha wave replacement phenomenon. The experimental results presented the expected alpha rhythm (8-13 Hz) reactiveness to the eyes opening task. The driver spends about 725 μs to acquire and store the data samples. The application takes about 244 μs to get the data from the driver and 1.4 ms to save it in the SD-card. A WiFi throughput of 12.8Mbps was measured which results in a transmission time of 5 ms for 512 kb of data. The embedded system consumes about 200 mAh when wireless off and 400 mAh when it is on. The system exhibits a reliable performance to record EEG signals and transmit them wirelessly. Besides the microcontroller-based architectures, the proposed platform demonstrates that powerful ARM processors running embedded operating systems can be programmed with real-time constrains at the kernel level in order to control hardware, while maintaining their parallel processing abilities in high level software applications.