Atomistic origins of the phase transition mechanism in Ge(2)Sb(2)Te(5)

The fast and reversible phase transition mechanism between crystalline and amorphous phases of Ge(2)Sb(2)Te(5) has been in debate for several years. Through employing first-principles density functional theory calculations, we identify a direct structural link between the metastable crystalline and amorphous phases. The phase transition is driven by the displacement of Ge atoms along the rocksalt [111] direction from stable octahedron to high energy unstable tetrahedron sites close to the intrinsic vacancy regions, which generates a high energy intermediate phase between metastable and amorphous phases. Due to the instability of Ge at the tetrahedron sites, the Ge atoms naturally shift away from those sites, giving rise to the formation of local-ordered fourfold motifs and the long-range structural disorder. Intrinsic vacancies, which originate from Sb(2)Te(3), lower the energy barrier for Ge displacements, and hence, their distribution plays an important role in the phase transition. The high energy intermediate configuration can be obtained experimentally by applying an intense laser beam, which overcomes the thermodynamic barrier from the octahedron to tetrahedron sites. The high figure of merit of Ge(2)Sb(2)Te(5) is achieved from the optimal combination of intrinsic vacancies provided by Sb(2)Te(3) and the instability of the tetrahedron sites provided by GeTe.

LATENT RANK CHANGE DETECTION FOR ANALYSIS OF SPLICE-JUNCTION MICROARRAYS WITH NONLINEAR EFFECTS

Alternative splicing of gene transcripts greatly expands the functional capacity of the genome, and certain splice isoforms may indicate specific disease states such as cancer. Splice junction microarrays interrogate thousands of splice junctions, but data analysis is difficult and error prone because of the increased complexity compared to differential gene expression analysis. We present Rank Change Detection (RCD) as a method to identify differential splicing events based upon a straightforward probabilistic model comparing the over-or underrepresentation of two or more competing isoforms. RCD has advantages over commonly used methods because it is robust to false positive errors due to nonlinear trends in microarray measurements. Further, RCD does not depend on prior knowledge of splice isoforms, yet it takes advantage of the inherent structure of mutually exclusive junctions, and it is conceptually generalizable to other types of splicing arrays or RNA-Seq. RCD specifically identifies the biologically important cases when a splice junction becomes more or less prevalent compared to other mutually exclusive junctions. The example data is from different cell lines of glioblastoma tumors assayed with Agilent microarrays.

Structure, stability, depolarized light scattering, and vibrational spectra of fullerenols from all-electron density-functional-theory calculations

We have investigated the stability, electronic properties, Rayleigh (elastic), and Raman (inelastic) depolarization ratios, infrared and Raman absorption vibrational spectra of fullerenols [C(60)(OH)(n)] with different degrees of hydroxylation by using all-electron density-functional-theory (DFT) methods. Stable arrangements of these molecules were found by means of full geometry optimizations using Becke's three-parameter exchange functional with the Lee, Yang, and Parr correlation functional. This DFT level has been combined with the 6-31G(d,p) Gaussian-type basis set, as a compromise between accuracy and capability to treat highly hydroxylated fullerenes, e.g., C(60)(OH)(36). Thus, the molecular properties of fullerenols were systematically analyzed for structures with n=1, 2, 3, 4, 8, 10, 16, 18, 24, 32, and 36. From the electronic structure analysis of these molecules, we have evidenced an important effect related to the weak chemical reactivity of a possible C(60)(OH)(24) isomer. To investigate Raman scattering and the vibrational spectra of the different fullerenols, frequency calculations are carried out within the harmonic approximation. In this case a systematic study is only performed for n=1-4, 8, 10, 16, 18, and 24. Our results give good agreements with the expected changes in the spectral absorptions due to the hydroxylation of fullerenes.

The roles of xylan and lignin in oxalic acid pretreated corncob during separate enzymatic hydrolysis and ethanol fermentation

High yields of hemicellulosic and cellulosic sugars are critical in obtaining economical conversion of agricultural residues to ethanol. To optimize pretreatment conditions, we evaluated oxalic acid loading rates, treatment temperatures and times in a 2(3) full factorial design. Response-surface analysis revealed an optimal oxalic acid pretreatment condition to release sugar from the cob of Zea mays L ssp. and for Pichia stipitis CBS 6054. To ferment the residual cellulosic sugars to ethanol following enzymatic hydrolysis, highest saccharification and fermentation yields were obtained following pretreatment at 180 degrees C for 50 min with 0.024 g oxalic acid/g substrate. Under these conditions, only 7.5% hemicellulose remained in the pretreated substrate. The rate of cellulose degradation was significantly less than that of hemicellulose and its hydrolysis was not as extensive. Subsequent enzymatic saccharification of the residual cellulose was strongly affected by the pretreatment condition with cellulose hydrolysis ranging between 26.0% and 76.2%. The residual xylan/lignin ratio ranged from 0.31 to 1.85 depending on the pretreatment condition. Fermentable sugar and ethanol were maximal at the lowest ratio of xylan/lignin and at high glucan contents. The model predicts optimal condition of oxalic acid pretreatment at 168 degrees C, 74 min and 0.027 g/g of oxalic acid. From these findings, we surmised that low residual xylan was critical in obtaining maximal glucose yields from saccharification. Published by Elsevier Ltd.

Simultaneous saccharification and ethanol fermentation of oxalic acid pretreated corncob assessed with response surface methodology

Response surface methodology was used to evaluate optimal time, temperature and oxalic acid concentration for simultaneous saccharification and fermentation (SSF) of corncob particles by Pichia stipitis CBS 6054. Fifteen different conditions for pretreatment were examined in a 2(3) full factorial design with six axial points. Temperatures ranged from 132 to 180 degrees C, time from 10 to 90 min and oxalic acid loadings from 0.01 to 0.038 g/g solids. Separate maxima were found for enzymatic saccharification and hemicellulose fermentation, respectively, with the condition for maximum saccharification being significantly more severe. Ethanol production was affected by reaction temperature more than by oxalic acid and reaction time over the ranges examined. The effect of reaction temperature was significant at a 95% confidence level in its effect on ethanol production. Oxalic acid and reaction time were statistically significant at the 90% level. The highest ethanol concentration (20 g/l) was obtained after 48 h with an ethanol volumetric production rate of 0.42 g ethanol l(-1) h(-1). The ethanol yield after SSF with P. stipitis was significantly higher than predicted by sequential saccharification and fermentation of substrate pretreated under the same condition. This was attributed to the secretion of beta-glucosidase by P. stipitis. During SSF, free extracellular beta-glucosidase activity was 1.30 pNPG U/g with P. stipitis, while saccharification without the yeast was 0.66 pNPG U/g. Published by Elsevier Ltd.

Greenhouse gas emissions and energy balance of palm oil biofuel

The search for alternatives to fossil fuels is boosting interest in biodiesel production. Among the crops used to produce biodiesel, palm trees stand out due to their high productivity and positive energy balance. This work assesses life cycle emissions and the energy balance of biodiesel production from palm oil in Brazil. The results are compared through a meta-analysis to previous published studies: Wood and Corley (1991) [Wood BJ, Corley RH. The energy balance of oil palm cultivation. In: PORIM intl. palm oil conference agriculture; 1991.], Malaysia; Yusoff and Hansen (2005) [Yusoff S. Hansen SB. Feasibility study of performing an life cycle assessment on crude palm oil production in Malaysia. International Journal of Life Cycle Assessment 2007;12:50-8], Malaysia; Angarita et al. (2009) [Angarita EE, Lora EE, Costa RE, Torres EA. The energy balance in the palm oil-derived methyl ester (PME) life cycle for the cases in Brazil and Colombia. Renewable Energy 2009;34:2905-13], Colombia; Pleanjai and Gheewala (2009) [Pleanjai S. Gheewala SH. Full chain energy analysis of biodiesel production from palm oil in Thailand. Applied Energy 2009;86:S209-14], Thailand; and Yee et al. (2009) [Yee KF, Tan KT, Abdullah AZ, Lee la. Life cycle assessment of palm biodiesel: revealing facts and benefits for sustainability. Applied Energy 2009;86:S189-96], Malaysia. In our study, data for the agricultural phase, transport, and energy content of the products and co-products were obtained from previous assessments done in Brazil. The energy intensities and greenhouse gas emission factors were obtained from the Simapro 7.1.8. software and other authors. These factors were applied to the inputs and outputs listed in the selected studies to render them comparable. The energy balance for our study was 1:5.37. In comparison the range for the other studies is between 1:3.40 and 1:7.78. Life cycle emissions determined in our assessment resulted in 1437 kg CO(2)e/ha, while our analysis based on the information provided by other authors resulted in 2406 kg CO(2)e/ha, on average. The Angarita et al. (2009) [Angarita EE, Lora EE, Costa RE, Torres EA. The energy balance in the palm oil-derived methyl ester (PME) life cycle for the cases in Brazil and Colombia. Renewable Energy 2009:34:2905-13] study does not report emissions. When compared to diesel on a energy basis, avoided emissions due to the use of biodiesel account for 80 g CO(2)e/MJ. Thus, avoided life Cycle emissions associated with the use of biodiesel yield a net reduction of greenhouse gas emissions. We also assessed the carbon balance between a palm tree plantation, including displaced emissions from diesel, and a natural ecosystem. Considering the carbon balance outcome plus life cycle emissions the payback time for a tropical forest is 39 years. The result published by Gibbs et al. (2008) [Gibbs HK, Johnston M, Foley JA, Holloway T, Monfreda C, Ramankutty N, et al., Carbon payback times for crop-based biofuel expansion in the tropics: the effects of changing yield and technology. Environmental Research Letters 2008;3:10], which ignores life cycle emissions, determined a payback range for biodiesel production between 30 and 120 years. Crown Copyright (C) 2010 Published by Elsevier Ltd. All rights reserved.

Control charts for individual observations of a bivariate Poisson process

In this paper, three single-control charts are proposed to monitor individual observations of a bivariate Poisson process. The specified false-alarm risk, their control limits, and ARLs were determined to compare their performances for different types and sizes of shifts. In most of the cases, the single charts presented better performance rather than two separate control charts ( one for each quality characteristic). A numerical example illustrates the proposed control charts.

Diagnostic errors and repetitive sequential classifications in on-line process control by attributes

The procedure of on-line process control by attributes, known as Taguchi`s on-line process control, consists of inspecting the mth item (a single item) at every m produced items and deciding, at each inspection, whether the fraction of conforming items was reduced or not. If the inspected item is nonconforming, the production is stopped for adjustment. As the inspection system can be subject to diagnosis errors, one develops a probabilistic model that classifies repeatedly the examined item until a conforming or b non-conforming classification is observed. The first event that occurs (a conforming classifications or b non-conforming classifications) determines the final classification of the examined item. Proprieties of an ergodic Markov chain were used to get the expression of average cost of the system of control, which can be optimized by three parameters: the sampling interval of the inspections (m); the number of repeated conforming classifications (a); and the number of repeated non-conforming classifications (b). The optimum design is compared with two alternative approaches: the first one consists of a simple preventive policy. The production system is adjusted at every n produced items (no inspection is performed). The second classifies the examined item repeatedly r (fixed) times and considers it conforming if most classification results are conforming. Results indicate that the current proposal performs better than the procedure that fixes the number of repeated classifications and classifies the examined item as conforming if most classifications were conforming. On the other hand, the preventive policy can be averagely the most economical alternative rather than those ones that require inspection depending on the degree of errors and costs. A numerical example illustrates the proposed procedure. (C) 2009 Elsevier B. V. All rights reserved.

Effects of the preventive and corrective adjustments in economical designs for online process control for attributes with misclassification errors

The procedure for online process control by attributes consists of inspecting a single item at every m produced items. It is decided on the basis of the inspection result whether the process is in-control (the conforming fraction is stable) or out-of-control (the conforming fraction is decreased, for example). Most articles about online process control have cited the stoppage of the production process for an adjustment when the inspected item is non-conforming (then the production is restarted in-control, here denominated as corrective adjustment). Moreover, the articles related to this subject do not present semi-economical designs (which may yield high quantities of non-conforming items), as they do not include a policy of preventive adjustments (in such case no item is inspected), which can be more economical, mainly if the inspected item can be misclassified. In this article, the possibility of preventive or corrective adjustments in the process is decided at every m produced item. If a preventive adjustment is decided upon, then no item is inspected. On the contrary, the m-th item is inspected; if it conforms, the production goes on, otherwise, an adjustment takes place and the process restarts in-control. This approach is economically feasible for some practical situations and the parameters of the proposed procedure are determined minimizing an average cost function subject to some statistical restrictions (for example, to assure a minimal levelfixed in advanceof conforming items in the production process). Numerical examples illustrate the proposal.

Junctionless Multiple-Gate Transistors for Analog Applications

This paper presents the evaluation of the analog properties of nMOS junctionless (JL) multigate transistors, comparing their performance with those exhibited by inversion-mode (IM) trigate devices of similar dimensions. The study has been performed for devices operating in saturation as single-transistor amplifiers, and we have considered the dependence of the analog properties on fin width W(fin) and temperature T. Furthermore, this paper aims at providing a physical insight into the analog parameters of JL transistors. For that, in addition to device characterization, 3-D device simulations were performed. It is shown that, depending on gate voltage, JL devices can present both larger Early voltage V(EA) and larger intrinsic voltage gain A(V) than IM devices of similar dimensions. In addition, V(EA) and A(V) are always improved in JL devices when the temperature is increased, whereas they present a maximum value around room temperature for IM transistors.

Economic design of an X chart for short-run production

The aim of this paper is to present an economical design of an X chart for a short-run production. The process mean starts equal to mu(0) (in-control, State I) and in a random time it shifts to mu(1) > mu(0) (out-of-control, State II). The monitoring procedure consists of inspecting a single item at every m produced ones. If the measurement of the quality characteristic does not meet the control limits, the process is stopped, adjusted, and additional (r - 1) items are inspected retrospectively. The probabilistic model was developed considering only shifts in the process mean. A direct search technique is applied to find the optimum parameters which minimizes the expected cost function. Numerical examples illustrate the proposed procedure. (C) 2009 Elsevier B.V. All rights reserved.

Forecasting fuel ethanol consumption in Brazil by time series models: 2006-2012

This article analysed scenarios for Brazilian consumption of ethanol for the period 2006 to 2012. The results show that if the country`s GDP sustains a 4.6% a year growth, domestic consumption of fuel ethanol could increase to 25.16 billion liters in this period, which is a volume relatively close to the forecasted gasoline consumption of 31 billion liters. At a lower GDP growth of 1.22% a year, gasoline consumption would be reduced and domestic ethanol consumption in Brazil would be no higher than 18.32 billion liters. Contrary to the current situation, forecasts indicated that hydrated ethanol consumption could become much higher than anhydrous consumption in Brazil. The former is being consumed in cars moved exclusively by ethanol and flex-fuel cars, successfully introduced in the country at 2003. Flex cars allow Brazilian consumers to choose between gasoline and hydrated ethanol and immediately switch to whichever fuel presents the most favourable relative price.

A Log-Linear Regression Model for the Beta-Weibull Distribution

We introduce the log-beta Weibull regression model based on the beta Weibull distribution (Famoye et al., 2005; Lee et al., 2007). We derive expansions for the moment generating function which do not depend on complicated functions. The new regression model represents a parametric family of models that includes as sub-models several widely known regression models that can be applied to censored survival data. We employ a frequentist analysis, a jackknife estimator, and a parametric bootstrap for the parameters of the proposed model. We derive the appropriate matrices for assessing local influences on the parameter estimates under different perturbation schemes and present some ways to assess global influences. Further, for different parameter settings, sample sizes, and censoring percentages, several simulations are performed. In addition, the empirical distribution of some modified residuals are displayed and compared with the standard normal distribution. These studies suggest that the residual analysis usually performed in normal linear regression models can be extended to a modified deviance residual in the proposed regression model applied to censored data. We define martingale and deviance residuals to evaluate the model assumptions. The extended regression model is very useful for the analysis of real data and could give more realistic fits than other special regression models.

Cytotoxicity and Endothelial Cell Adhesion of Lyophilized and Irradiated Bovine Pericardium Modified With Silk Fibroin and Chitosan

Grafts of biological tissues have been used since the 1960s as an alternative to the mechanical heart prostheses. Nowadays, the most consolidated treatment to bovine pericardial (BP) bioprostheses is the crosslinking with glutaraldehyde (GA), although GA may induce calcification in vivo. In previous work, our group demonstrated that electron beam irradiation applied to lyophilized BP in the absence of oxygen promoted crosslinks among collagen fibers of BP tissue. In this work, the incorporation of silk fibroin (SF) and chitosan (CHIT) in the BP not treated with GA was studied. The samples were irradiated and then analyzed for their cytotoxicity and the ability of adhesion and growth of endothelial cells. Initially, all samples showed cytotoxicity. However, after a few washing cycles, the cytotoxicity due to acetic acid and ethanol residues was removed from the biomaterial making it suitable for the biofunctional test. The samples modified with SF/CHIT and electron beam irradiated favored the adhesion and growth of endothelial cells throughout the tissue.

Human Airway Epithelial Cell Responses to Neisseria lactamica and Purified Porin via Toll-Like Receptor 2-Dependent Signaling

The human airway epithelium is constantly exposed to microbial products from colonizing organisms. Regulation of Toll-like receptor (TLR) expression and specific interactions with bacterial ligands is thought to mitigate exacerbation of inflammatory processes induced by the commensal flora in these cells. The genus Neisseria comprises pathogenic and commensal organisms that colonize the human nasopharynx. Neisseria lactamica is not associated with disease, but N. meningitidis occasionally invades the host, causing meningococcal disease and septicemia. Upon colonization of the airway epithelium, specific host cell receptors interact with numerous Neisseria components, including the PorB porin, at the immediate bacterial-host cell interface. This major outer membrane protein is expressed by all Neisseria strains, regardless of pathogenicity, but its amino acid sequence varies among strains, particularly in the surface-exposed regions. The interaction of Neisseria PorB with TLR2 is essential for driving TLR2/TLR1-dependent cellular responses and is thought to occur via the porin`s surface-exposed loop regions. Our studies show that N. lactamica PorB is a TLR2 ligand but its binding specificity for TLR2 is different from that of meningococcal PorB. Furthermore, N. lactamica PorB is a poor inducer of proinflammatory mediators and of TLR2 expression in human airway epithelial cells. These effects are reproduced by whole N. lactamica organisms. Since the responsiveness of human airway epithelial cells to colonizing bacteria is in part regulated via TLR2 expression and signaling, commensal organisms such as N. lactamica would benefit from expressing a product that induces low TLR2-dependent local inflammation, likely delaying or avoiding clearance by the host.