Dual-orthogonal radial basis function networks for nonlinear time series prediction

A new structure of Radial Basis Function (RBF) neural network called the Dual-orthogonal RBF Network (DRBF) is introduced for nonlinear time series prediction. The hidden nodes of a conventional RBF network compare the Euclidean distance between the network input vector and the centres, and the node responses are radially symmetrical. But in time series prediction where the system input vectors are lagged system outputs, which are usually highly correlated, the Euclidean distance measure may not be appropriate. The DRBF network modifies the distance metric by introducing a classification function which is based on the estimation data set. Training the DRBF networks consists of two stages. Learning the classification related basis functions and the important input nodes, followed by selecting the regressors and learning the weights of the hidden nodes. In both cases, a forward Orthogonal Least Squares (OLS) selection procedure is applied, initially to select the important input nodes and then to select the important centres. Simulation results of single-step and multi-step ahead predictions over a test data set are included to demonstrate the effectiveness of the new approach.

Quantitative plant proteomics

Quantitation is an inherent requirement in comparative proteomics and there is no exception to this for plant proteomics. Quantitative proteomics has high demands on the experimental workflow, requiring a thorough design and often a complex multi-step structure. It has to include sufficient numbers of biological and technical replicates and methods that are able to facilitate a quantitative signal read-out. Quantitative plant proteomics in particular poses many additional challenges but because of the nature of plants it also offers some potential advantages. In general, analysis of plants has been less prominent in proteomics. Low protein concentration, difficulties in protein extraction, genome multiploidy, high Rubisco abundance in green tissue, and an absence of well-annotated and completed genome sequences are some of the main challenges in plant proteomics. However, the latter is now changing with several genomes emerging for model plants and crops such as potato, tomato, soybean, rice, maize and barley. This review discusses the current status in quantitative plant proteomics (MS-based and non-MS-based) and its challenges and potentials. Both relative and absolute quantitation methods in plant proteomics from DIGE to MS-based analysis after isotope labeling and label-free quantitation are described and illustrated by published studies. In particular, we describe plant-specific quantitative methods such as metabolic labeling methods that can take full advantage of plant metabolism and culture practices, and discuss other potential advantages and challenges that may arise from the unique properties of plants.

Anthropogenic greenhouse gas contribution to flood risk in England and Wales in autumn 2000

Interest in attributing the risk of damaging weather-related events to anthropogenic climate change is increasing1. Yet climate models used to study the attribution problem typically do not resolve the weather systems associated with damaging events2 such as the UK floods of October and November 2000. Occurring during the wettest autumn in England and Wales since records began in 17663, 4, these floods damaged nearly 10,000 properties across that region, disrupted services severely, and caused insured losses estimated at £1.3 billion (refs 5, 6). Although the flooding was deemed a ‘wake-up call’ to the impacts of climate change at the time7, such claims are typically supported only by general thermodynamic arguments that suggest increased extreme precipitation under global warming, but fail8, 9 to account fully for the complex hydrometeorology4, 10 associated with flooding. Here we present a multi-step, physically based ‘probabilistic event attribution’ framework showing that it is very likely that global anthropogenic greenhouse gas emissions substantially increased the risk of flood occurrence in England and Wales in autumn 2000. Using publicly volunteered distributed computing11, 12, we generate several thousand seasonal-forecast-resolution climate model simulations of autumn 2000 weather, both under realistic conditions, and under conditions as they might have been had these greenhouse gas emissions and the resulting large-scale warming never occurred. Results are fed into a precipitation-runoff model that is used to simulate severe daily river runoff events in England and Wales (proxy indicators of flood events). The precise magnitude of the anthropogenic contribution remains uncertain, but in nine out of ten cases our model results indicate that twentieth-century anthropogenic greenhouse gas emissions increased the risk of floods occurring in England and Wales in autumn 2000 by more than 20%, and in two out of three cases by more than 90%.

Surface chemistry of glycine on Pt{111} in different aqueous environments

Adsorption of glycine on Ptf111g under UHV conditions and in different aqueous environments was studied by XPS (UHV and ambient pressure) and NEXAFS. Under UHV conditions, glycine adsorbs in its neutral molecular state up to about 0.15 ML. Further deposition leads to the formation of an additional zwitterionic species, which is in direct contact with the substrate surface, followed by the growth of multilayers, which also consist of zwitterions. The neutral surface species is most stable and decomposes at 360 K through a multi-step process which includes the formation of methylamine and carbon monoxide. When glycine and water are co-adsorbed in UHV at low temperatures (< 170 K) inter-layer diffusion is inhibited and the surface composition depends on the adsorption sequence. Water adsorbed on top of a glycine layer does not lead to significant changes in its chemical state. When glycine is adsorbed on top of a pre-adsorbed chemisorbed water layer or thick ice layer, however, it is found in its zwitterionic state, even at low coverage. No difference is seen in the chemical state of glycine when the layers are exposed to ambient water vapor pressure up to 0.2 Torr at temperatures above 300 K. Also the decomposition temperature stays the same, 360 K, irrespective of the water vapor pressure. Only the reaction path of the decomposition products is affected by ambient water vapor.

Bootstrapping prediction intervals for autoregressive models

Methods of improving the coverage of Box–Jenkins prediction intervals for linear autoregressive models are explored. These methods use bootstrap techniques to allow for parameter estimation uncertainty and to reduce the small-sample bias in the estimator of the models’ parameters. In addition, we also consider a method of bias-correcting the non-linear functions of the parameter estimates that are used to generate conditional multi-step predictions.

A flow reactor process for the synthesis of peptides utilizing immobilized reagents, scavengers and catch and release protocols

A general flow process for the multi-step assembly of peptides has been developed and this procedure has been used to successfully construct a series of Boc, Cbz and Fmoc N-protected dipeptides in excellent yields and purities, including an extension of the method to enable the preparation of a tripeptide derivative.

Aircraft routing with minimal climate impact: the REACT4C climate cost function modelling approach (V1.0)

In addition to CO2, the climate impact of aviation is strongly influenced by non-CO2 emissions, such as nitrogen oxides, influencing ozone and methane, and water vapour, which can lead to the formation of persistent contrails in ice-supersaturated regions. Because these non-CO2 emission effects are characterised by a short lifetime, their climate impact largely depends on emission location and time; that is to say, emissions in certain locations (or times) can lead to a greater climate impact (even on the global average) than the same emission in other locations (or times). Avoiding these climate-sensitive regions might thus be beneficial to climate. Here, we describe a modelling chain for investigating this climate impact mitigation option. This modelling chain forms a multi-step modelling approach, starting with the simulation of the fate of emissions released at a certain location and time (time-region grid points). This is performed with the chemistry–climate model EMAC, extended via the two submodels AIRTRAC (V1.0) and CONTRAIL (V1.0), which describe the contribution of emissions to the composition of the atmosphere and to contrail formation, respectively. The impact of emissions from the large number of time-region grid points is efficiently calculated by applying a Lagrangian scheme. EMAC also includes the calculation of radiative impacts, which are, in a second step, the input to climate metric formulas describing the global climate impact of the emission at each time-region grid point. The result of the modelling chain comprises a four-dimensional data set in space and time, which we call climate cost functions and which describes the global climate impact of an emission at each grid point and each point in time. In a third step, these climate cost functions are used in an air traffic simulator (SAAM) coupled to an emission tool (AEM) to optimise aircraft trajectories for the North Atlantic region. Here, we describe the details of this new modelling approach and show some example results. A number of sensitivity analyses are performed to motivate the settings of individual parameters. A stepwise sanity check of the results of the modelling chain is undertaken to demonstrate the plausibility of the climate cost functions.

A physical organic chemistry approach to dissolution of cellulose: effects of cellulose mercerization on its properties and on the kinetics of its decrystallization

The effects of alkali treatment on the structural characteristics of cotton linters and sisal cellulose samples have been studied. Mercerization results in a decrease in the indices of crystallinity and the degrees of polymerization, and an increase in the alpha-cellulose contents of the samples. The relevance of the structural properties of cellulose to its dissolution is probed by studying the kinetics of cellulose decrystallization, prior to its solubilization in LiCl/N,N-dimethylacetamide (DMAc). Our data show that the decrystallization rate constants and activation parameters are only slightly dependent on the physico-chemical properties of the starting celluloses. This multi-step reaction is accompanied by a small enthalpy and large, negative, entropy of activation. These results are analyzed in terms of the interactions within the biopolymer chains during decrystallization, as well as those between the two ions of the electrolyte and both DMAc and cellulose.

The role of the TP53 gene during rat tongue carcinogenesis induced by 4-nitroquinoline 1-oxide

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

Human granulocyte colony stimulating factor (hG-CSF): cloning, overexpression, purification and characterization

Background: Biopharmaceutical drugs are mainly recombinant proteins produced by biotechnological tools. The patents of many biopharmaceuticals have expired, and biosimilars are thus currently being developed. Human granulocyte colony stimulating factor (hG-CSF) is a hematopoietic cytokine that acts on cells of the neutrophil lineage causing proliferation and differentiation of committed precursor cells and activation of mature neutrophils. Recombinant hG-CSF has been produced in genetically engineered Escherichia coli ( Filgrastim) and successfully used to treat cancer patients suffering from chemotherapy-induced neutropenia. Filgrastim is a 175 amino acid protein, containing an extra N-terminal methionine, which is needed for expression in E. coli. Here we describe a simple and low-cost process that is amenable to scaling-up for the production and purification of homogeneous and active recombinant hG-CSF expressed in E. coli cells.Results: Here we describe cloning of the human granulocyte colony-stimulating factor coding DNA sequence, protein expression in E. coli BL21(DE3) host cells in the absence of isopropyl-beta-D-thiogalactopyranoside ( IPTG) induction, efficient isolation and solubilization of inclusion bodies by a multi-step washing procedure, and a purification protocol using a single cationic exchange column. Characterization of homogeneous rhG-CSF by size exclusion and reverse phase chromatography showed similar yields to the standard. The immunoassay and N-terminal sequencing confirmed the identity of rhG-CSF. The biological activity assay, in vivo, showed an equivalent biological effect (109.4%) to the standard reference rhG-CSF. The homogeneous rhG-CSF protein yield was 3.2 mg of bioactive protein per liter of cell culture.Conclusion: The recombinant protein expression in the absence of IPTG induction is advantageous since cost is reduced, and the protein purification protocol using a single chromatographic step should reduce cost even further for large scale production. The physicochemical, immunological and biological analyses showed that this protocol can be useful to develop therapeutic bioproducts. In summary, the combination of different experimental strategies presented here allowed an efficient and cost-effective protocol for rhG-CSF production. These data may be of interest to biopharmaceutical companies interested in developing biosimilars and healthcare community.

Fatigue resistance of bovine teeth restored with resin-bonded fiber posts: Effect of post surface conditioning

This study evaluated the effect of post surface conditioning on the fatigue resistance of bovine teeth restored with resin-bonded fiber-reinforced composite (FRC). Root canals of 20 single-rooted bovine teeth (16 mm long) were prepared to 12 mm using a preparation drill of a double-tapered fiber post system. Using acrylic resin, each specimen was embedded (up to 3.0 mm from the cervical part of the specimen) in a PVC cylinder and allocated into one of two groups (n = 10) based on the post surface conditioning method: acid etching plus silanization or tribochemical silica coating (30 μm SiOx + silanization). The root canal dentin was etched (H2PO3 for 30 seconds), rinsed, and dried. A multi-step adhesive system was applied to the root dentin and the fiber posts were cemented with resin cement. The specimens were submitted to one million fatigue cycles. After fatigue testing, a score was given based on the number of fatigue cycles until fracture. All of the specimens were resistant to fatigue. No fracture of the root or the post and no loss of retention of the post were observed. The methodology and the results of this study indicate that tribochemical silica coating and acid etching performed equally well when dynamic mechanical loading was used.

Cementation of fiber post: influence of the cement insertion techniques on the bond strength of the fiber post-root dentin and the quality of the cement layer.

The aim of this study was to assess the influence of resin cement insertion methods on the bond strength of a fiber post to root dentin and quality of the cement layer. Forty bovine single-roots (length =16 mm) were randomly allocated into four groups, according to the cement insertion methods (N.=10): Gr1- Lentulo drill #40, Gr2- Centrix syringe, Gr3- Explorer #5, Gr4- fiber post. The root canals were prepared at 12 mm, using preparation bur # 3 of a cylinder quartz-FRC post (Aesthet post-plus, Bisco). The fiber posts were cemented using a multi-step etch-and-rinse adhesive system (All Bond 2®, Bisco) and a dual-cured resin cement (Duolink, Bisco). Each root was cut into seven samples: four samples of 1.8 mm thickness for push-out testing, and three with 0.5 mm for cement layer quality analyzing. One-way ANOVA was used for the push-out test values and the One-Way Kruskal-Wallis (P<0.05) and Dunn (10%) tests for the cement layer analyzes. ANOVA showed that the cement layer quality was affected by the cement insertion methods (P=0.0044): Gr1 (3.8 ± 1.3a), Gr2 (3.2 ± 1.3a), Gr3 (5.2 ± 1.5a,b) and Gr4 (5.2 ± 1.5b) (Dunn test), whereas the bond strength (MPa) was not affected by cement insertion methods: G1 (4.2 ± 1.3), G2 (3.2 ± 1.8), G3 (4.5 ± 0.9), G4 (3.1 ± 1.3). The fiber posts should be cemented with the assistance of the lentulo drill or centrix syringe to promote the best cement layer results.

Monitoramento do processo de densificação de compósitos termoestruturais de carbono reforçado com fibras de carbono por tomografia computadorizada e resistividade elétrica

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Pesagem em movimento e caracterização do tráfego ferroviário com uso da técnica B-WIM

Nesta dissertação é apresentado o desenvolvimento de algoritmos para aplicação do método Bridge-Weigh In Motion (B-WIM) para a pesagem em movimento de trens e para a caracterização do tráfego ferroviário, permitindo-se obter informações sobre a velocidade de passagem dos trens, número e espaçamento entre eixos. Os sistemas B-WIM a partir de uma simples instrumentação permitem determinar as cargas por eixo de veículos em movimento, eliminando o efeito dinâmico. Foram implementados os algoritmos para a determinação dos valores referentes a geometria do trem e das cargas, que foi validado a partir de um exemplo teórico, onde se simulou a passagem de um trem de características conhecidas sobre a ponte e as cargas por eixos foram determinadas com 100% de exatidão. Além disso, foi feito um exemplo numérico em elementos finitos, de um viaduto em concreto armado para aplicação do método, onde foi feita a determinação das cargas por eixo para diferentes velocidades de passagem do trem. A fim de reduzir o tempo de processamento nas análises do exemplo numérico, foi desenvolvido um algoritmo para a geração de cargas nodais no modelo numérico que reduziram o tempo de processamento em até 96% quando comparado com a análise de múltiplos passos (“Multi-Step”), que simula automaticamente a passagem do trem sobre a estrutura. Finalmente, o método foi testado em um caso real a partir de monitorações realizadas em um viaduto de concreto armado da Estrada de Ferro Carajás. Apesar de não ter sido possível a determinação das cargas por eixo da locomotiva, foi possível medir precisamente o peso bruto total da locomotiva quando se utilizou o modelo constitutivo de Collins & Mitchell (1991) para o concreto.

Peptídeos cíclicos em espécies do semiárido brasileiro e uma cultivada: caracterização e atividade biológica

Pós-graduação em Química - IQ