Accurate estimation of isoelectric point of protein and peptide based on amino acid sequences

Motivation: In any macromolecular polyprotic system - for example protein, DNA or RNA - the isoelectric point - commonly referred to as the pI - can be defined as the point of singularity in a titration curve, corresponding to the solution pH value at which the net overall surface charge - and thus the electrophoretic mobility - of the ampholyte sums to zero. Different modern analytical biochemistry and proteomics methods depend on the isoelectric point as a principal feature for protein and peptide characterization. Protein separation by isoelectric point is a critical part of 2-D gel electrophoresis, a key precursor of proteomics, where discrete spots can be digested in-gel, and proteins subsequently identified by analytical mass spectrometry. Peptide fractionation according to their pI is also widely used in current proteomics sample preparation procedures previous to the LC-MS/MS analysis. Therefore accurate theoretical prediction of pI would expedite such analysis. While such pI calculation is widely used, it remains largely untested, motivating our efforts to benchmark pI prediction methods. Results: Using data from the database PIP-DB and one publically available dataset as our reference gold standard, we have undertaken the benchmarking of pI calculation methods. We find that methods vary in their accuracy and are highly sensitive to the choice of basis set. The machine-learning algorithms, especially the SVM-based algorithm, showed a superior performance when studying peptide mixtures. In general, learning-based pI prediction methods (such as Cofactor, SVM and Branca) require a large training dataset and their resulting performance will strongly depend of the quality of that data. In contrast with Iterative methods, machine-learning algorithms have the advantage of being able to add new features to improve the accuracy of prediction. Contact: yperez@ebi.ac.uk Availability and Implementation: The software and data are freely available at https://github.com/ypriverol/pIR. Supplementary information: Supplementary data are available at Bioinformatics online.

A study of magnetic non-linearity and finite length effects in solid iron subjected to a travelling MMF wave

This thesis describes an experimental and analytic study of the effects of magnetic non-linearity and finite length on the loss and field distribution in solid iron due to a travelling mmf wave. In the first half of the thesis, a two-dimensional solution is developed which accounts for the effects of both magnetic non-linearity and eddy-current reaction; this solution is extended, in the second half, to a three-dimensional model. In the two-dimensional solution, new equations for loss and flux/pole are given; these equations contain the primary excitation, the machine parameters and factors describing the shape of the normal B-H curve. The solution applies to machines of any air-gap length. The conditions for maximum loss are defined, and generalised torque/frequency curves are obtained. A relationship between the peripheral component of magnetic field on the surface of the iron and the primary excitation is given. The effects of magnetic non-linearity and finite length are combined analytically by introducing an equivalent constant permeability into a linear three-dimensional analysis. The equivalent constant permeability is defined from the non-linear solution for the two-dimensional magnetic field at the axial centre of the machine to avoid iterative solutions. In the linear three-dimensional analysis, the primary excitation in the passive end-regions of the machine is set equal to zero and the secondary end faces are developed onto the air-gap surface. The analyses, and the assumptions on which they are based, were verified on an experimental machine which consists of a three-phase rotor and alternative solid iron stators, one with copper end rings, and one without copper end rings j the main dimensions of the two stators are identical. Measurements of torque, flux /pole, surface current density and radial power flow were obtained for both stators over a range of frequencies and excitations. Comparison of the measurements on the two stators enabled the individual effects of finite length and saturation to be identified, and the definition of constant equivalent permeability to be verified. The penetration of the peripheral flux into the stator with copper end rings was measured and compared with theoretical penetration curves. Agreement between measured and theoretical results was generally good.

Two-wave mixing in BTO in the presence of detuning

The gain of a weak signal beam is measured in the usual two-wave mixing configuration in a photorefractive BTO crystal by varying a set of parameters, namely the applied electric field, the detuning, the beam ratio and the input intensity of the pump beam. All the experimental results are shown to be in good agreement with a theory based on that of Kukhtarev et al.

The use of ERS-1 crossovers and TOPEX/Poseidon repeat pass data for global sea surface variability studies

In previous sea-surface variability studies, researchers have failed to utilise the full ERS-1 mission due to the varying orbital characteristics in each mission phase, and most have simply ignored the Ice and Geodetic phases. This project aims to introduce a technique which will allow the straightforward use of all orbital phases, regardless of orbit type. This technique is based upon single satellite crossovers. Unfortunately the ERS-1 orbital height is still poorly resolved (due to higher air drag and stronger gravitational effects) when compared with that of TOPEX/Poseidon (T/P), so to make best use of the ERS-1 crossover data corrections to the ERS-1 orbital heights are calculated by fitting a cubic-spline to dual-crossover residuals with T/P. This correction is validated by comparison of dual satellite crossovers with tide gauge data. The crossover processing technique is validated by comparing the extracted sea-surface variability information with that from T/P repeat pass data. The two data sets are then combined into a single consistent data set for analysis of sea-surface variability patterns. These patterns are simplified by the use of an empirical orthogonal function decomposition which breaks the signals into spatial modes which are then discussed separately. Further studies carried out on these data include an analysis of the characteristics of the annual signal, discussion of evidence for Rossby wave propagation on a global basis, and finally analysis of the evidence for global mean sea level rise.

Low level feature detection in human vision

Influential models of edge detection have generally supposed that an edge is detected at peaks in the 1st derivative of the luminance profile, or at zero-crossings in the 2nd derivative. However, when presented with blurred triangle-wave images, observers consistently marked edges not at these locations, but at peaks in the 3rd derivative. This new phenomenon, termed ‘Mach edges’ persisted when a luminance ramp was added to the blurred triangle-wave. Modelling of these Mach edge detection data required the addition of a physiologically plausible filter, prior to the 3rd derivative computation. A viable alternative model was examined, on the basis of data obtained with short-duration, high spatial-frequency stimuli. Detection and feature-making methods were used to examine the perception of Mach bands in an image set that spanned a range of Mach band detectabilities. A scale-space model that computed edge and bar features in parallel provided a better fit to the data than 4 competing models that combined information across scale in a different manner, or computed edge or bar features at a single scale. The perception of luminance bars was examined in 2 experiments. Data for one image-set suggested a simple rule for perception of a small Gaussian bar on a larger inverted Gaussian bar background. In previous research, discriminability (d’) has typically been reported to be a power function of contrast, where the exponent (p) is 2 to 3. However, using bar, grating, and Gaussian edge stimuli, with several methodologies, values of p were obtained that ranged from 1 to 1.7 across 6 experiments. This novel finding was explained by appealing to low stimulus uncertainty, or a near-linear transducer.

A new fuzzy additive model for determining the common set of weights in Data Envelopment Analysis

The main advantage of Data Envelopment Analysis (DEA) is that it does not require any priori weights for inputs and outputs and allows individual DMUs to evaluate their efficiencies with the input and output weights that are only most favorable weights for calculating their efficiency. It can be argued that if DMUs are experiencing similar circumstances, then the pricing of inputs and outputs should apply uniformly across all DMUs. That is using of different weights for DMUs makes their efficiencies unable to be compared and not possible to rank them on the same basis. This is a significant drawback of DEA; however literature observed many solutions including the use of common set of weights (CSW). Besides, the conventional DEA methods require accurate measurement of both the inputs and outputs; however, crisp input and output data may not relevant be available in real world applications. This paper develops a new model for the calculation of CSW in fuzzy environments using fuzzy DEA. Further, a numerical example is used to show the validity and efficacy of the proposed model and to compare the results with previous models available in the literature.

Two-wave mixing in BTO in the presence of detuning

The gain of a weak signal beam is measured in the usual two-wave mixing configuration in a photorefractive BTO crystal by varying a set of parameters, namely the applied electric field, the detuning, the beam ratio and the input intensity of the pump beam. All the experimental results are shown to be in good agreement with a theory based on that of Kukhtarev et al.

Impact of inter-modal four-wave mixing on the performance of mode- and wavelength-division-multiplexing systems

In this paper, we investigate the impact of inter-modal four-wave mixing on mode- and wavelength-division-multiplexing systems. A set of coupled nonlinear Schrödinger equations, including linear mode coupling, is derived allowing to isolate the inter-modal four-wave mixing terms. The efficiency of inter-modal four-wave mixing between degenerate LP modes is found to be significantly higher than the intra-modal four-wave mixing efficiency. However, it is shown that the inter-modal four-wave mixing efficiency between degenerate modes is significantly reduced by the linear mode coupling.