Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes

Motivation: We compare phylogenetic approaches for inferring functional gene links. The approaches detect independent instances of the correlated gain and loss of pairs of genes from species' genomes. We investigate the effect on results of basing evidence of correlations on two phylogenetic approaches, Dollo parsminony and maximum likelihood (ML). We further examine the effect of constraining the ML model by fixing the rate of gene gain at a low value, rather than estimating it from the data. Results: We detect correlated evolution among a test set of pairs of yeast (Saccharomyces cerevisiae) genes, with a case study of 21 eukaryotic genomes and test data derived from known yeast protein complexes. If the rate at which genes are gained is constrained to be low, ML achieves by far the best results at detecting known functional links. The model then has fewer parameters but it is more realistic by preventing genes from being gained more than once. Availability: BayesTraits by M. Pagel and A. Meade, and a script to configure and repeatedly launch it by D. Barker and M. Pagel, are available at http://www.evolution.reading.ac.uk .

Retention time prediction and protein identification

Proteins are commonly identified through enzymatic digestion and generation of short sequence tags or fingerprints of peptide masses by mass spectrometry. Separation methods, such as liquid chromatography and electrophoresis, are often used to fractionate complex protein or peptide mixtures and these separations also provide information on the different species, such as molecular weight and isoelectric point from electrophoresis and hydrophobicity in reversed-phase chromatography. These are also properties that can be predicted from amino acid sequences derived from genomic sequences and used in protein identification. This chapter reviews recently introduced methods based on retention time prediction to extract information from chromatographic separations and the applications to protein identification in organisms with small and large genomes. Novel data on retention time prediction of posttranslationally modified peptides is also presented.

The measurement of maternal plasma corticotropin-releasing factor (CRF) and CRF-binding protein improves the early prediction of preeclampsia

In the present study we measured maternal plasma concentrations of two placental neurohormones, corticotropin-releasing factor (CRF) and CRF-binding protein (CRF-BP), in 58 at-risk pregnant women consecutively enrolled between 28 and 29 wk of pregnancy to evaluate whether their evaluation may predict third trimester-onset preeclampsia ( PE). The statistical significance was assessed by t test. The cut-off points for defining altered CRF and CRF-BP levels for prediction of PE were chosen by receiving operator characteristics curve analysis, and the probability of developing PE was calculated for several combinations of hormone testing results. CRF and CRF-BP levels were significantly ( both P < 0.0001) higher and lower, respectively, in the patients (n = 20) who later developed PE than in those who did not present PE at follow-up. CRF at the cut-off 425.95 pmol/liter achieved a sensitivity of 94.8% and a specificity of 96.9%, whereas CRF-BP at the cut-off 125.8 nmol/liter combined a sensitivity of 92.5% and a specificity of 82.5% as single markers for prediction of PE. The probability of PE was 34.5% in the whole study population, 93.75% when both CRF and CRF-BP levels were changed, and 0% if both hormone markers were unaltered. The measurement of CRF and CRF-BP levels may add significant prognostic information for predicting PE in at-risk pregnant women.

Discovery of three polymorphs of 7-fluoroisatin reveals challenges in using computational crystal structure prediction as a complement to experimental screening

A combined computational and experimental polymorph search was undertaken to establish the crystal forms of 7-fluoroisatin, a simple molecule with no reported crystal structures, to evaluate the value of crystal structure prediction studies as an aid to solid form discovery. Three polymorphs were found in a manual crystallisation screen, as well as two solvates. Form I ( P2(1)/c, Z0 1), found from the majority of solvent evaporation experiments, corresponded to the most stable form in the computational search of Z0 1 structures. Form III ( P21/ a, Z0 2) is probably a metastable form, which was only found concomitantly with form I, and has the same dimeric R2 2( 8) hydrogen bonding motif as form I and the majority of the computed low energy structures. However, the most thermodynamically stable polymorph, form II ( P1 , Z0 2), has an expanded four molecule R 4 4( 18) hydrogen bonding motif, which could not have been found within the routine computational study. The computed relative energies of the three forms are not in accord with experimental results. Thus, the experimental finding of three crystalline polymorphs of 7- fluoroisatin illustrates the many challenges for computational screening to be a tool for the experimental crystal engineer, in contrast to the results for an analogous investigation of 5- fluoroisatin.

Ab initio prediction of the infrared-absorption spectrum of the C2Cl radical

The three lowest (1(2)A('), 2(2)A('), and 1(2)A(')) potential-energy surfaces of the C2Cl radical, correlating at linear geometries with (2)Sigma(+) and (2)Pi states, have been studied ab initio using a large basis set and multireference configuration-interaction techniques. The electronic ground state is confirmed to be bent with a very low barrier to linearity, due to the strong nonadiabatic electronic interactions taking place in this system. The rovibronic energy levels of the (CCCl)-C-12-C-12-Cl-35 isotopomer and the absolute absorption intensities at a temperature of 5 K have been calculated, to an upper limit of 2000 cm(-1), using diabatic potential-energy and dipole moment surfaces and a recently developed variational method. The resulting vibronic states arise from a strong mixture of all the three electronic components and their assignments are intrinsically ambiguous. (c) 2005 American Institute of Physics.

Ab initio prediction of the infrared absorption spectrum of the C2Br radical

The first three electronic states (1(2)A', 2(2)A', 1(2)A '') of the C2Br radical, correlating at linear geometries with (2)Sigma(+) and (2)Pi states, have been studied ab initio, using Multi Reference Configuration Interaction techniques. The electronic ground state is found to have a bent equilibrium geometry, R-CC = 1.2621 angstrom, R-CBr = 1.7967 angstrom, < CCBr 156.1 degrees, with a very low barrier to linearity. Similarly to the valence isoelectronic radicals C2F and C2Cl, this anomalous behaviour is attributed to a strong three-state non-adiabatic electronic interaction. The Sigma, Pi(1/2), Pi(3/2) vibronic energy levels and their absolute infrared absorption intensities at a temperature of 5K have been calculated for the (CCBr)-C-12-C-12-Br-79 isotopomer, to an upper limit of 2000 cm(-1), using ab initio diabatic potential energy and dipole moment surfaces and a recently developed variational method.

Reliability in the whole life cycle of building systems

Purpose – The purpose of this research is to show that reliability analysis and its implementation will lead to an improved whole life performance of the building systems, and hence their life cycle costs (LCC). Design/methodology/approach – This paper analyses reliability impacts on the whole life cycle of building systems, and reviews the up-to-date approaches adopted in UK construction, based on questionnaires designed to investigate the use of reliability within the industry. Findings – Approaches to reliability design and maintainability design have been introduced from the operating environment level, system structural level and component level, and a scheduled maintenance logic tree is modified based on the model developed by Pride. Different stages of the whole life cycle of building services systems, reliability-associated factors should be considered to ensure the system's whole life performance. It is suggested that data analysis should be applied in reliability design, maintainability design, and maintenance policy development. Originality/value – The paper presents important factors in different stages of the whole life cycle of the systems, and reliability and maintainability design approaches which can be helpful for building services system designers. The survey from the questionnaires provides the designers with understanding of key impacting factors.

Critical reliability issues for building services systems

This paper addresses two critical issues associated with reliability and maintenance of building services systems. The first is the ratio of operating and/or maintenance costs to initial costs for building services systems. It is an important parameter for life cycle costing and maintenance policy development. The second is the proportion of items among building services systems that need preventive maintenance. In this paper, we estimate the ratios based on a cost dataset. It suggests that correctly estimating the ratio be important but using a constant ratio in life cycle costing may result in wrong decisions. It also estimates the proportion of preventive maintenance for building services systems on the basis of the distribution of failure patterns.

Prediction of Parkinson's disease tremor onset using artificial neural networks

In this paper we present the initial results using an artificial neural network to predict the onset of Parkinson's Disease tremors in a human subject. Data for the network was obtained from implanted deep brain electrodes. A tuned artificial neural network was shown to be able to identify the pattern of the onset tremor from these real time recordings.

OFDM joint data detection and phase noise cancellation based on minimum mean square prediction error

This paper proposes a new iterative algorithm for orthogonal frequency division multiplexing (OFDM) joint data detection and phase noise (PHN) cancellation based on minimum mean square prediction error. We particularly highlight the relatively less studied problem of "overfitting" such that the iterative approach may converge to a trivial solution. Specifically, we apply a hard-decision procedure at every iterative step to overcome the overfitting. Moreover, compared with existing algorithms, a more accurate Pade approximation is used to represent the PHN, and finally a more robust and compact fast process based on Givens rotation is proposed to reduce the complexity to a practical level. Numerical Simulations are also given to verify the proposed algorithm. (C) 2008 Elsevier B.V. All rights reserved.

An improved reliability Cuk based solar inverter with sliding mode control

Many photovoltaic inverter designs make use of a buck based switched mode power supply (SMPS) to produce a rectified sinusoidal waveform. This waveform is then unfolded by a low frequency switching structure to produce a fully sinusoidal waveform. The Cuk SMPS could offer advantages over the buck in such applications. Unfortunately the Cuk converter is considered to be difficult to control using classical methods. Correct closed loop design is essential for stable operation of Cuk converters. Due to these stability issues, Cuk converter based designs often require stiff low bandwidth control loops. In order to achieve this stable closed loop performance, traditional designs invariably need large, unreliable electrolytic capacitors. In this paper, an inverter with a sliding mode control approach is presented which enables the designer to make use of the Cuk converters advantages, while ameliorating control difficulties. This control method allows the selection of passive components based predominantly on ripple and reliability specifications while requiring only one state reference signal. This allows much smaller, more reliable non-electrolytic capacitors to be used. A prototype inverter has been constructed and results obtained which demonstrate the design flexibility of the Cuk topology when coupled with sliding mode control.