Successful development and testing of a Method for Aggregating The Reporting of Interventions in Complex Studies (MATRICS)

Objectives: To develop a tool for the accurate reporting and aggregation of findings from each of the multiple methods used in a complex evaluation in an unbiased way. Study Design and Setting: We developed a Method for Aggregating The Reporting of Interventions in Complex Studies (MATRICS) within a gastroenterology study [Evaluating New Innovations in (the delivery and organisation of) Gastrointestinal (GI) endoscopy services by the NHS Modernisation Agency (ENIGMA)]. We subsequently tested it on a different gastroenterology trial [Multi-Institutional Nurse Endoscopy Trial (MINuET)]. We created three layers to define the effects, methods, and findings from ENIGMA. We assigned numbers to each effect in layer 1 and letters to each method in layer 2. We used an alphanumeric code based on layers 1 and 2 to every finding in layer 3 to link the aims, methods, and findings. We illustrated analogous findings by assigning more than one alphanumeric code to a finding. We also showed that more than one effect or method could report the same finding. We presented contradictory findings by listing them in adjacent rows of the MATRICS. Results: MATRICS was useful for the effective synthesis and presentation of findings of the multiple methods from ENIGMA. We subsequently successfully tested it by applying it to the MINuET trial. Conclusion: MATRICS is effective for synthesizing the findings of complex, multiple-method studies.

Adiabatic eigenfunction-based approach for coherent excitation transfer: An almost analytical treatment of the Fenna-Matthews-Olson complex

We suggest a method of studying coherence in finite-level systems coupled to the environment and use it for the Hamiltonian that has been used to describe the light-harvesting pigment-protein complex. The method works with the adiabatic states and transforms the Hamiltonian to a form in which the terms responsible for decoherence and population relaxation are separated out. Decoherence is then accounted for nonperturbatively and population relaxation using a Markovian master equation. Almost analytical results can be obtained for the seven-level system, and the calculations are very simple for systems with more levels. We apply the treatment to the seven-level system, and the results are in excellent agreement with the exact numerical results of Nalbach et al. Nalbach, Braun, and Thorwart, Phys. Rev. E 84, 041926 (2011)]. Our approach is able to account for decoherence and population relaxation separately. It is found that decoherence causes only damping of oscillations and does not lead to transfer to the reaction center. Population relaxation is necessary for efficient transfer to the reaction center, in agreement with earlier findings. Our results show that the transformation to the adiabatic basis followed by a Redfield type of approach leads to results in good agreement with exact simulation.

Adiabatic Eigenfunction Based Approach to Coherent Transfer: Application to the Fenna-Matthews-Olson (FMO) Complex and the Role of Correlations in the Efficiency of Energy Transfer

We have recently suggested a method (Pallavi Bhattacharyya and K. L. Sebastian, Physical Review E 2013, 87, 062712) for the analysis of coherence in finite-level systems that are coupled to the surroundings and used it to study the process of energy transfer in the Fenna-Matthews-Olson (FMO) complex. The method makes use of adiabatic eigenstates of the Hamiltonian, with a subsequent transformation of the Hamiltonian into a form where the terms responsible for decoherence and population relaxation could be separated out at the lowest order. Thus one can account for decoherence nonperturbatively, and a Markovian type of master equation could be used for evaluating the population relaxation. In this paper, we apply this method to a two-level system as well as to a seven-level system. Comparisons with exact numerical results show that the method works quite well and is in good agreement with numerical calculations. The technique can be applied with ease to systems with larger numbers of levels as well. We also investigate how the presence of correlations among the bath degrees of freedom of the different bacteriochlorophyll a molecules of the FMO Complex affect the rate of energy transfer. Surprisingly, in the cases that we studied, our calculations suggest that the presence of anticorrelations, in contrast to correlations, make the excitation transfer more facile.

The preparation of phenolic resin/montmorillonite nanocomposites by suspension condensation polymerization and their morphology

Phenolic resin/clay nanocomposites were prepared using a suspension condensation polymerization method that was suitable to both novolac and resole. Natural montmorillonite and two kinds of organic modified montmorillonite were adopted to investigate the effect of modification on the final morphology of the nanocomposites. X-ray diffraction (XRD) measurements and Transmission Electron Microscope (TEM) observations showed that clay platelets were easier to be exfoliated or intercalated in novolac than in resole because novolac usually has a linear structure. The modifier with a phenyl ring was more compatible with novolac (or resole) than the aliphatic type modifier. The influence of curing on the morphology was studied as well. An exfoliation-adsorption and in situ condensation mechanism was proposed on the formation of the nanocomposites.

Synthesis, polymerization and wool coating studies of 3-iso-butylpyrrole and 3-iso-pentylpyrrole

In a four-step method starting from pyrrole, the synthesis of 3-iso-butylpyrrole and 3-iso-pentylpyrrole, was achieved in 45 and 44% yields, respectively. Polymerization studies of these branched alkyl pyrroles are described and the results compared with those obtained for the unbranched structural isomers n-butyl and n-pentylpyrrole. A series of conductive textiles were produced by the chemical polymerization of the iso-alkylpyrroles using both solution and vapour polymerization techniques. Fabrics coated with poly-iso-alkylpyrrole formed using the solution polymerization method had a lower surface resistance than those formed using the vapour polymerization method. These conductivity results were in direct contrast to those previously obtained for 3-n-alkylpyrroles on fabrics. A remarkable crystal-like growth on the surface of the textile fabric was observed when solution polymerization of 3-iso-pentylpyrrole was employed—reinforcing the notion that subtle changes in monomer structure can drastically affect bulk polymer properties.

Conducting nylon, cotton and wool yarns by continuous vapor polymerization of pyrrole

Conductive textile yarns were prepared by a continuous vapor polymerization method; the application of polypyrrole by the continuous vapor polymerization method used is designed for the easy adaptation into industrial procedures. The resultant conductive yarns were examined by longitudinal and cross-sectional views, clearly showing the varying levels of penetration of the polymer into the yarn structure. It was found that for wool the optimum specific resistance was achieved by using the 400 TPM yarn with a FeCl3 solution concentration of 80 g/L FeCl3 to produce 1.69 Ω g/cm2. For cotton yarn, the optimum specific resistance of 1.53 Ω g/cm2 was obtained with 80 g/L of a FeCl3 solution.

The role of unbound oligomers in the nucleation and growth of electrodeposited polypyrrole and method for preparing high strength, high conductivity films

Polypyrrole is a material with immensely useful properties suitable for a wide range of electrochemical applications, but its development has been hindered by cumbersome manufacturing processes. Here we show that a simple modification to the standard electrochemical polymerization method produces polypyrrole films of equivalently high conductivity and superior mechanical properties in one-tenth of the polymerization time. Preparing the film as a series of electrodeposited layers with thorough solvent washing between layering was found to produce excellent quality films even when layer deposition was accelerated by high current. The washing step between the sequentially polymerized layers altered the deposition mechanism, eliminating the typical dendritic growth and generating nonporous deposits. Solvent washing was shown to reduce the concentration of oligomeric species in the near-electrode region and hinder the three-dimensional growth mechanism that occurs by deposition of secondary particles from solution. As artificial muscles, the high density sequentially polymerized films produced the highest mechanical work output yet reported for polypyrrole actuators.

The effect of polymerization cycles on porosity of microwave-processed denture base resin

Statement of problem. Although most of the physical properties of denture base resin polymerized by microwave energy have been shown to be similar to resins polymerized by the conventional heat polymerization method, the presence of porosity is a problem.Purpose. This study evaluated the effect of different microwave polymerization cycles on the porosity of a denture base resin designed for microwave polymerization.Material and methods. Thirty-two rectangular resin specimens (65 X 40 X 5 mm) were divided into 3 experimental groups (A, B, and C; Onda-Cryl, microwave-polymerized resin) and I control group (T; Classico, heat-polymerized resin), according to the following polymerization cycles: (A) 500 W for 3 minutes, (B) 90 W for 13 minutes + 500 W for 90 seconds, (C) 320 W for 3 minutes + 0 W for 4 minutes + 720 W for 3 minutes, and (T) 74degreesC for 9 hours. Porosity was calculated by measurement of the specimen volume before and after its immersion in water. Data were analyzed using 1-way analysis of variance (alpha = .05).Results. The mean values and SDs of the percent mean porosity were: A = 1.05% +/- 0.28%, B = 0.91% +/- 0.15%, C = 0.88% +/- 0.23%, T = 0.93% +/- 0.23%. No significant differences were found in mean porosity among the groups evaluated.Conclusion. Within the limitations of this study, a denture base resin specifically designed for microwave Polymerization tested was not affected by different polymerization cycles. Porosity was similar to the conventional heat-polymerized denture base resin tested.

Studies on the formation of complex coacervates between chitosan and alginate during microparticles preparation

The formation of complex coacervates between chitosan and alginate was evaluated during microparticles formation. Mass ratio between polyelectrolytes and calcium chloride concentration were determinated by conductimetric analysis and by calcium ions quantification, respectively. Inert microparticles were prepared using a complex coacervation method in W/O emulsion and morphological analyses of microparticles were carried out. This method enabled the production of spherical particles, with slightly rough surface and narrow size distribution with maximal diameter of 10 μm.

Effect of polymerization methods and thermal cycling on color stability of acrylic resin denture teeth

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Fuzzy methods for analysis of microarrays and networks

Bioinformatics involves analyses of biological data such as DNA sequences, microarrays and protein-protein interaction (PPI) networks. Its two main objectives are the identification of genes or proteins and the prediction of their functions. Biological data often contain uncertain and imprecise information. Fuzzy theory provides useful tools to deal with this type of information, hence has played an important role in analyses of biological data. In this thesis, we aim to develop some new fuzzy techniques and apply them on DNA microarrays and PPI networks. We will focus on three problems: (1) clustering of microarrays; (2) identification of disease-associated genes in microarrays; and (3) identification of protein complexes in PPI networks. The first part of the thesis aims to detect, by the fuzzy C-means (FCM) method, clustering structures in DNA microarrays corrupted by noise. Because of the presence of noise, some clustering structures found in random data may not have any biological significance. In this part, we propose to combine the FCM with the empirical mode decomposition (EMD) for clustering microarray data. The purpose of EMD is to reduce, preferably to remove, the effect of noise, resulting in what is known as denoised data. We call this method the fuzzy C-means method with empirical mode decomposition (FCM-EMD). We applied this method on yeast and serum microarrays, and the silhouette values are used for assessment of the quality of clustering. The results indicate that the clustering structures of denoised data are more reasonable, implying that genes have tighter association with their clusters. Furthermore we found that the estimation of the fuzzy parameter m, which is a difficult step, can be avoided to some extent by analysing denoised microarray data. The second part aims to identify disease-associated genes from DNA microarray data which are generated under different conditions, e.g., patients and normal people. We developed a type-2 fuzzy membership (FM) function for identification of diseaseassociated genes. This approach is applied to diabetes and lung cancer data, and a comparison with the original FM test was carried out. Among the ten best-ranked genes of diabetes identified by the type-2 FM test, seven genes have been confirmed as diabetes-associated genes according to gene description information in Gene Bank and the published literature. An additional gene is further identified. Among the ten best-ranked genes identified in lung cancer data, seven are confirmed that they are associated with lung cancer or its treatment. The type-2 FM-d values are significantly different, which makes the identifications more convincing than the original FM test. The third part of the thesis aims to identify protein complexes in large interaction networks. Identification of protein complexes is crucial to understand the principles of cellular organisation and to predict protein functions. In this part, we proposed a novel method which combines the fuzzy clustering method and interaction probability to identify the overlapping and non-overlapping community structures in PPI networks, then to detect protein complexes in these sub-networks. Our method is based on both the fuzzy relation model and the graph model. We applied the method on several PPI networks and compared with a popular protein complex identification method, the clique percolation method. For the same data, we detected more protein complexes. We also applied our method on two social networks. The results showed our method works well for detecting sub-networks and give a reasonable understanding of these communities.

Efficiency comparison of Markov Chain Monte Carlo simulation with subset simulation (MCMC/ss) to standard Monte Carlo Simulation (sMC) for extreme event scenarios

Standard Monte Carlo (sMC) simulation models have been widely used in AEC industry research to address system uncertainties. Although the benefits of probabilistic simulation analyses over deterministic methods are well documented, the sMC simulation technique is quite sensitive to the probability distributions of the input variables. This phenomenon becomes highly pronounced when the region of interest within the joint probability distribution (a function of the input variables) is small. In such cases, the standard Monte Carlo approach is often impractical from a computational standpoint. In this paper, a comparative analysis of standard Monte Carlo simulation to Markov Chain Monte Carlo with subset simulation (MCMC/ss) is presented. The MCMC/ss technique constitutes a more complex simulation method (relative to sMC), wherein a structured sampling algorithm is employed in place of completely randomized sampling. Consequently, gains in computational efficiency can be made. The two simulation methods are compared via theoretical case studies.

Ionic transport in (PEG)x LiBr systems

Ionic conductivity in (PEG)(x)LiBr systems is measured using the complex impedance method in the temperature range -20 degrees C to 100 degrees C. For x = 6 and 10, above a certain concentration dependent temperature T-c, a power law fit based on mode coupling theory is seen to better explain the data than the Vogel-Tamman-Fulcher (VTF) expression. Li-7 NMR linewidth measurements indicate two regions of motional narrowing, one attributable to segmental motion and the other to translational diffusion.

Preparation, Structural, and Electrical Studies of Polyaniline/ZnFe2O4 Nanocomposites

Polyaniline/ZnFe2O4 nanocomposites were synthesized by a simple and inexpensive one-step in situ polymerization method in the presence of ZnFe2O4 nanoparticles. The structural, morphological, and electrical properties of the samples were characterized by wide angle X-ray diffraction (WAXD), Fourier transform infrared (FTIR) spectroscopy, scanning electron microscopy (SEM), and thermogravimetric analysis (TGA). WAXD and SEM revealed the formation of polyaniline/ZnFe2O4 nanocomposites. Infrared spectroscopy indicated that there was some interaction between the ZnFe2O4 nanoparticles and polyaniline. The dc electrical conductivity measurements were carried in the temperature range of 80 to 300 K. With increase in the doping concentration of ZnFe2O4, the conductivity of the nanocomposites found to be decreasing from 5.15 to 0.92 Scm(-1) and the temperature dependent resistivity follows ln rho(T) similar to T-1/2 behavior. The nanocomposites (80 wt % of ZnFe2O4) show a more negative magnetoresistance compared with that of pure polyaniline (PANI). These results suggest that the interaction between the polymer matrix PANI and zinc nanoparticles take place in these nanocomposites. (C) 2011 Wiley Periodicals, Inc. J Appl Polym Sci 120: 2856-2862, 2011

Effect of Multiwall Carbon Nanotubes on Electrical and Structural Properties of Polyaniline

Polyaniline (PANI) and PANI/CNT (multiwall carbon nanotubes, CNT) composites were prepared using an oxidative chemical polymerization method with ammonium persulfate and dodecyl benzene sulfonic acid as the oxidizing agent and surfactant, respectively. Fourier-transform infrared spectroscopy spectra illustrate the presence of PANI in the composite and show that some interaction exists between PANI and CNT. Embedding of CNT in the PANI matrix is confirmed by scanning electron micrography. Conductivity of the PANI/CNT composites was higher than that of pure PANI, and the maximum conductivity obtained was 4.44 S/cm at 20 wt.% CNT.