Computational differentiation of N-terminal signal peptides and transmembrane helices

Signal peptides and transmembrane helices both contain a stretch of hydrophobic amino acids. This common feature makes it difficult for signal peptide and transmembrane helix predictors to correctly assign identity to stretches of hydrophobic residues near the N-terminal methionine of a protein sequence. The inability to reliably distinguish between N-terminal transmembrane helix and signal peptide is an error with serious consequences for the prediction of protein secretory status or transmembrane topology. In this study, we report a new method for differentiating protein N-terminal signal peptides and transmembrane helices. Based on the sequence features extracted from hydrophobic regions (amino acid frequency, hydrophobicity, and the start position), we set up discriminant functions and examined them on non-redundant datasets with jackknife tests. This method can incorporate other signal peptide prediction methods and achieve higher prediction accuracy. For Gram-negative bacterial proteins, 95.7% of N-terminal signal peptides and transmembrane helices can be correctly predicted (coefficient 0.90). Given a sensitivity of 90%, transmembrane helices can be identified from signal peptides with a precision of 99% (coefficient 0.92). For eukaryotic proteins, 94.2% of N-terminal signal peptides and transmembrane helices can be correctly predicted with coefficient 0.83. Given a sensitivity of 90%, transmembrane helices can be identified from signal peptides with a precision of 87% (coefficient 0.85). The method can be used to complement current transmembrane protein prediction and signal peptide prediction methods to improve their prediction accuracies. (C) 2003 Elsevier Inc. All rights reserved.

Fast, scalable master equation solution algorithms. III. Direct time propagation accelerated by a diffusion approximation preconditioned iterative solver

In this paper we propose a novel fast and linearly scalable method for solving master equations arising in the context of gas-phase reactive systems, based on an existent stiff ordinary differential equation integrator. The required solution of a linear system involving the Jacobian matrix is achieved using the GMRES iteration preconditioned using the diffusion approximation to the master equation. In this way we avoid the cubic scaling of traditional master equation solution methods and maintain the low temperature robustness of numerical integration. The method is tested using a master equation modelling the formation of propargyl from the reaction of singlet methylene with acetylene, proceeding through long lived isomerizing intermediates. (C) 2003 American Institute of Physics.

Signal trait sexual dimorphism and mutual sexual selection in Drosophila serrata

The evolution of sexual dimorphism may occur when natural and sexual selection result in different optimum trait values for males and females. Perhaps the most prominent examples of sexual dimorphism occur in sexually selected traits, for which males usually display exaggerated trait levels, while females may show reduced expression of the trait. In some species, females also exhibit secondary sexual traits that may either be a consequence of a correlated response to sexual selection on males or direct sexual selection for female secondary sexual traits. In this experiment, we simultaneously measure the intersex genetic correlations and the relative strength of sexual selection on males and females for a set of cuticular hydrocarbons in Drosophila serrata. There was significant directional sexual selection on both male and female cuticular hydrocarbons: the strength of sexual selection did not differ among the sexes but males and females preferred different cuticular hydrocarbons. In contrast with many previous studies of sexual dimorphism, intersex genetic correlations were low. The evolution of sexual dimorphism in D. serrata appears to have been achieved by sex-limited expression of traits controlled by genes on the X chromosome and is likely to be in its final stages.

An advanced method for eliminating impacts from frequency deviations in power system signal processing

Frequency deviation is a common problem for power system signal processing. Many power system measurements are carried out in a fixed sampling rate assuming the system operates in its nominal frequency (50 or 60 Hz). However, the actual frequency may deviate from the normal value from time to time due to various reasons such as disturbances and subsequent system transients. Measurement of signals based on a fixed sampling rate may introduce errors under such situations. In order to achieve high precision signal measurement appropriate algorithms need to be employed to reduce the impact from frequency deviation in the power system data acquisition process. This paper proposes an advanced algorithm to enhance Fourier transform for power system signal processing. The algorithm is able to effectively correct frequency deviation under fixed sampling rate. Accurate measurement of power system signals is essential for the secure and reliable operation of power systems. The algorithm is readily applicable to such occasions where signal processing is affected by frequency deviation. Both mathematical proof and numerical simulation are given in this paper to illustrate robustness and effectiveness of the proposed algorithm. Crown Copyright (C) 2003 Published by Elsevier Science B.V. All rights reserved.

Constitutively active signal transducer and activator of transcription 5 can replace the requirement for growth hormone in adipogenesis of 3T3-F442A preadipocytes

Although it is the best characterized in vitro model of GH action, the mechanisms used by GH to induce differentiation of murine 3T3-F442A preadipocytes remain unclear. Here we have examined the role of three transcriptional regulators in adipogenesis. These regulators are either rapidly induced in response to GH [Stra13, signal transducer and activator of transcription (Stat) 3] or of central importance to GH signaling (Stat5). Retroviral transfection of 3T3-F442A preadipocytes was used to increase expression of Stra13, Stat3, and Stat5a. Only Stat5a transfection increased the expression of adipogenic markers peroxisome proliferator-activated receptor gamma, CCAAT enhancer binding protein (C/EBP)alpha, and adipose protein 2/fatty acid-binding protein in response to GH, as determined by quantitative RT-PCR. Transfection with constitutively active Stat3 and Stat5a revealed that constitutively active Stat5a but not Stat3 was able to replace the GH requirement for adipogenesis. Constitutively active Stat5a but not Stat3 was able to increase the formation of lipid droplets and expression of alpha-glycerol phosphate dehydrogenase toward levels seen in mature adipocytes. Constitutively active Stat5a was also able to increase the expression of transcripts for C/EBPalpha to similar levels as GH, and of C/EBPbeta, peroxisome proliferator-activated receptor gamma, and adipose protein 2/fatty acid-binding protein transcripts to a lesser extent. An in vivo role for GH in murine adipogenesis is supported by significantly decreased epididymal fat depot size in young GH receptor-deleted mice, before manifestation of the lipolytic actions of GH. We conclude that Stat5 is a critical factor in GH-induced, and potentially prolactin-induced, murine adipogenesis.

Simultaneous FT-NIR and ESR analyses to yield propagation rate coefficients for polymerization of methyl methacrylate based monomers

A hyphenated instrumental approach has been used to obtain reliable values for the propagation rate coefficients as a function of conversion for polymerizations of methyl methacrylate (MMA) and a mixture of MMA and ethyleneglycol dimethacrylate (EGDMA) with a 1:1 concentration of double bonds, from near the onset of the Trommsdorf region into the glass region. ESR spectroscopy was used to measure the radical concentration while FT-NIR fibre-optic spectroscopy was employed to measure instantaneously the double-bond concentration within the temperature-controlled cavity of the ESR instrument during polymerization. The advantage of this approach to the measurement of the rate coefficient is that it is equally applicable to branching and linear polymerizations. For the polymerization of methyl methacrylate, the values of the rate coefficient at the lowest conversions at which reliable values could be obtained were in agreement with recently reported values obtained by the PLP-SEC method. For the lowest conversions, the values obtained were 403 1 mol(-1) s(-1) at 306 K for MMA and 5201 mol(-1) s(-1) at 310 K for a 1:1 mixture of MMA and EGDMA. (C) 2003 Society of Chemical Industry.

Influence of leaf retention on cutting propagation of Lavandula dentata L.

Vegetative propagation of lavender offers several advantages over sexual propagation, among them crop homogeneity and yield of higher quality essential oil. However, Lavandula species have been propagated mostly by seeds and are said to be recalcitrant to rooting when propagated by cuttings. During cutting propagation, one of the important variables that influence the rooting capacity of cuttings is the leaf retention. The objective of this work was to evaluate the influence of leaf retention on rooting of L. dentata cuttings. Apical cuttings of L. dentata of 10 cm in length, keeping approximately 1/3, 1/2 or 2/3 of their leaves were planted in commercial substrate Plantmax HT® under intermittent mist. After two months, averages of root number, length of the longest root, root fresh and dry weights, and the survival percentage were evaluated. Root length and fresh weight were statistically greater with 2/3 of leaf retention and when fewer leaves were kept on the cuttings, lower means of root dry weight was observed. Under the conditions applied in this study, greater leaf retention was better for rooting of L. dentata cuttings.

Improving fECG signal acquisition in the evaluation of fetal well-being

The ability to monitor fetal heart rate is vital during late pregnancy and labor in order to evaluate fetal well-being. Current monitoring practice is essentially based on external cardiotocography and, less frequently, during labor, invasive fetal scalp electrocardiography. Many current and envisaged applications could benefi t from simpler devices using a 3-lead ECG confi guration. We are designing a maternity support belt with an embedded wireless 3-lead ECG sensor, and have investigated the infl uence of the ground electrode position on signal quality. Data from over 100 pregnant women was collected with the ground electrode placed in 3 locations in order to determine optimum electrode placement and belt form factor.

Chemical sterilization in in vitro propagation of Arundina bambusifolia Lindl. and Epidendrum ibaguense Kunth

There is a great demand for simpler and less costly laboratory techniques and for more accessible procedures for orchid breeders who do not have the necessary theoretical basis to use the traditional seed and clone production methods of orchids in vitro. The aim of this study was to assess the use of sodium hypochlorite (NaClO) as a decontaminant in the process of inoculating adult orchid explants of Arundina bambusifolia and Epidendrum ibaguenses. Solutions of NaClO (1.200, 2.400, 3.600, 4.800 and 6.000 mg L-1 - equivalent to 50, 100, 150, 200 and 250 mL L-1 of commercial bleach - CB) were sprayed on the explants (1.0 mL) and the culture medium (GB5), in the presence or absence of activated charcoal (2 g L-1). The explants used were nodal segments of field-grown adult plants. The procedures for inoculating the explants were conducted outside the laminar flow chamber (LFC), except for the control treatment (autoclaved medium and explant inoculation inside the LFC). The best results for fresh weight yield, height and number of shoots were obtained using NaClO in solution at 1.200 mg L-1 (equivalent to 50 mL L-1 commercial bleach) with activated charcoal in the culture medium. Fresh weight figures were 1.10 g/jar for Arundina bambusifolia and 0.16 g/jar for Epidendrum ibaguenses. Spraying the NaClO solutions controls the contamination of the culture medium already inoculated with the explants.

Rooting of hardwood cuttings of Roxo de Valinhos fig (Ficus carica L.) with different propagation strategies

The objective of this study was to evaluate the substrate, cuttings collection time, the position and the cutting depth, and the propagation environment on rooting of 'Purple Valinhos' fig tree cuttings in Southwestern Paraná, Brazil. Two experiments were carried out at UTFPR, Câmpus Dois Vizinhos, with hardwoods cuttings from Roxo de Valinhos fig tree. The first experiment used a randomized block design, in 3 x 3 x 2 factorial (substrate x environment x collection time), with four replications of 10 cuttings per plot. The cuttings were collected in the first fifteen days of July and August. The substrates were sand, soil and the mixture of these [1:1 (v / v)]. The environments used were open sky, tunnel with plastic cover and tunnel with half-shade black net cover. The second experiment used a randomized block design, 2 x 2 x 3 factorial (shoot cutting position x soil cover x shoot cutting depth), with four replications of 12 cuttings per plot. In the factor position, the vertically (0 º inclination) and inclined (45 º inclination) shoot cuttings were evaluated. Soil cover was tested with mulching plastic cover or not. The tested depths were 1/3, 1/2 and 2/3 in relation to the total length of the shoot cutting. In both experiments, the following were analyzed: rooting and mortality indices, number of leaves and primary shoots, length of the three largest roots per cutting. It was conclude that, the protected environment with plastic cover on sand as substrate must recommended for the rooting of fig estaca, collecting them in the first half of July. The inclination position and cutting depth of the estaca and the substrate coverage with plastic mulching did not influence the results.

Statistical classification of road pavements using near field vehicle rolling noise measurements

Low noise surfaces have been increasingly considered as a viable and cost-effective alternative to acoustical barriers. However, road planners and administrators frequently lack information on the correlation between the type of road surface and the resulting noise emission profile. To address this problem, a method to identify and classify different types of road pavements was developed, whereby near field road noise is analyzed using statistical learning methods. The vehicle rolling sound signal near the tires and close to the road surface was acquired by two microphones in a special arrangement which implements the Close-Proximity method. A set of features, characterizing the properties of the road pavement, was extracted from the corresponding sound profiles. A feature selection method was used to automatically select those that are most relevant in predicting the type of pavement, while reducing the computational cost. A set of different types of road pavement segments were tested and the performance of the classifier was evaluated. Results of pavement classification performed during a road journey are presented on a map, together with geographical data. This procedure leads to a considerable improvement in the quality of road pavement noise data, thereby increasing the accuracy of road traffic noise prediction models.

Avaliação dos sistemas WiMAX e GSM-R para ambientes ferroviários

Com este trabalho pretende-se estudar o desempenho das tecnologias GSM-R e WiMAX em ambientes ferroviários. Este tipo de estudo tem uma importância elevada devido grande interesse na reestruturação dos sistemas de comunicações vocacionados para aplicações ferroviárias. Estes sistemas são cada vez mais complexos, apresentando níveis mais elevados de exigência, como a segurança, suporte de sinalização, tráfego ferroviário e interoperabilidade entre sistemas de diferentes países. Com tudo isto é necessário explorar e conhecer o comportamento de diversas tecnologias para este tipo de aplicações. Neste trabalho foi efectuado um primeiro estudo abrangendo a tecnologia WiMAX (Norma IEEE 802.16d) em ambientes interiores de edifícios, de forma a estudar o seu comportamento com e sem linha de vista e em proximidade e afastamento da estação base. Este estudo foi conclusivo quanto há não adequação desta tecnologia em ambientes ferroviários, visto ter sido observado que em situações de ausência de linha de vista a degradação da qualidade do sinal não conseguiria suportar os níveis de exigência necessários para a aplicação do mesmo em ambientes ferroviários. Analisou-se em segundo lugar a tecnologia GSM-R, onde se efectuou um estudo de campo em ambientes reais. Para o estudo desta tecnologia foram utilizados ambientes diversificados de forma a obter um estudo mais aprofundado do seu comportamento. Como objectivo têm-se a criação de melhores métodos de planeamento, mais vocacionados para as características específicas dos ambientes ferroviários e exigências das aplicações dos sistemas de comunicações ferroviários. Através deste estudo foi possível obter conclusões relativamente à variação da potência do sinal para as diversas condições e ambientes de propagação a que o sistema GSM-R foi sujeito, tendo sido possível também caracterizar o tipo de ambientes característicos das linhas ferroviárias. Foi possível também concluir que este tipo de sistemas consegue responder aos níveis de exigência e aplicações dos sistemas de comunicação ferroviários, trazendo uma mais-valia relativamente aos existentes actualmente a nível nacional.

A two terminal optical signal and image processing p-i-n/p-i-n image and colour sensor

A two terminal optically addressed image processing device based on two stacked sensing/switching p-i-n a-SiC:H diodes is presented. The charge packets are injected optically into the p-i-n sensing photodiode and confined at the illuminated regions changing locally the electrical field profile across the p-i-n switching diode. A red scanner is used for charge readout. The various design parameters and addressing architecture trade-offs are discussed. The influence on the transfer functions of an a-SiC:H sensing absorber optimized for red transmittance and blue collection or of a floating anode in between is analysed. Results show that the thin a-SiC:H sensing absorber confines the readout to the switching diode and filters the light allowing full colour detection at two appropriated voltages. When the floating anode is used the spectral response broadens, allowing B&W image recognition with improved light-to-dark sensitivity. A physical model supports the image and colour recognition process.

New stacked photodevices for signal multiplexing and demultiplexing applications in the visible spectrum

Results on the use of a double a-SiC:H p-i-n heterostructure for signal multiplexing and demultiplexing applications in the visible range are presented. Pulsed monochromatic beams together (multiplexing mode), or a single polychromatic beam (demultiplexing mode) impinge on the device and are absorbed, accordingly to their wavelength. Red, green and blue pulsed input channels are transmitted together, each one with a specific transmission rate. The combined optical signal is analyzed by reading out, under different applied voltages, the generated photocurrent. Results show that in the multiplexing mode the output signal is balanced by the wavelength and transmission rate of each input channel, keeping the memory of the incoming optical carriers. In the demultiplexing mode the photocurrent is controlled by the applied voltage allowing regaining the transmitted information. A physical model supported by a numerical simulation gives insight into the device operation.

Implications of the LHC two-photon signal for two-Higgs-doublet models

We study the implications for two-Higgs-doublet models of the recent announcement at the LHC giving a tantalizing hint for a Higgs boson of mass 125 GeV decaying into two photons. We require that the experimental result be within a factor of 2 of the theoretical standard model prediction, and analyze the type I and type II models as well as the lepton-specific and flipped models, subject to this requirement. It is assumed that there is no new physics other than two Higgs doublets. In all of the models, we display the allowed region of parameter space taking the recent LHC announcement at face value, and we analyze the W+W-, ZZ, (b) over barb, and tau(+)tau(-) expectations in these allowed regions. Throughout the entire range of parameter space allowed by the gamma gamma constraint, the numbers of events for Higgs decays into WW, ZZ, and b (b) over bar are not changed from the standard model by more than a factor of 2. In contrast, in the lepton-specific model, decays to tau(+)tau(-) are very sensitive across the entire gamma gamma-allowed region.