Experimental evidence for multivariate stabilizing sexual selection

Stabilizing selection is a fundamental concept in evolutionary biology. In the presence of a single intermediate optimum phenotype (fitness peak) on the fitness surface, stabilizing selection should cause the population to evolve toward such a peak. This prediction has seldom been tested, particularly for suites of correlated traits. The lack of tests for an evolutionary match between population means and adaptive peaks may be due, at least in part, to problems associated with empirically detecting multivariate stabilizing selection and with testing whether population means are at the peak of multivariate fitness surfaces. Here we show how canonical analysis of the fitness surface, combined with the estimation of confidence regions for stationary points on quadratic response surfaces, may be used to define multivariate stabilizing selection on a suite of traits and to establish whether natural populations reside on the multivariate peak. We manufactured artificial advertisement calls of the male cricket Teleogryllus commodus and played them back to females in laboratory phonotaxis trials to estimate the linear and nonlinear sexual selection that female phonotactic choice imposes on male call structure. Significant nonlinear selection on the major axes of the fitness surface was convex in nature and displayed an intermediate optimum, indicating multivariate stabilizing selection. The mean phenotypes of four independent samples of males, from the same population as the females used in phonotaxis trials, were within the 95% confidence region for the fitness peak. These experiments indicate that stabilizing sexual selection may play an important role in the evolution of male call properties in natural populations of T. commodus.

Prediction of BRCA1 status in patients with breast cancer using estrogen receptor and basal phenotype

Purpose: To investigate the proportion of breast cancers arising inpatients with germ line BRCA1 and BRCA2 mutations expressing basal markers and developing predictive tests for identification of high-risk patients. Experimental Design: Histopathologic material from 182 tumors in BRCA1 mutation carriers, 63 BRCA2 carriers, and 109 controls, collected as part of the international Breast Cancer Linkage Consortium were immunohistochemically stained for CK14, CK5/6, CK17, epidermal growth factor receptor (EGFR), and osteonectin. Results: All five basal markers were commoner in BRCA1 tumors than in control tumors (CK14: 61% versus 12%; CK5/6: 58% versus 7%; CK17: 53% versus 10%; osteonectin: 43% versus 19%; EGFR: 67% versus 21%; P < 0.0001 in each case). In a multivariate analysis, CK14, CK5/6, and estrogen receptor (ER) remained significant predictors of BRCA1 carrier status. In contrast, the frequency of basal markers in BRCA2 tumors did not differ significant from controls. Conclusion: The use of cytokeratin staining in combination with ER and morphology provides a more accurate predictor of BRCA1 mutation status than previously available, that may be useful in selecting patients for BRCA1 mutation testing. The high percentage of BRCA1 cases positive for EGFR suggests that specific anti-tyrosine kinase therapy may be of potential benefit in these patients.

Disease risk and mortality prediction in intensive care patients with pneumonia. Australian and New Zealand practice in intensive care (ANZPIC II)

This study of ventilated patients investigated pneumonia risk factors and outcome predictors in 476 episodes of pneumonia (48% community-acquired pneumonia, 24% hospital-acquired pneumonia, 28% ventilator-associated pneumonia) using a prospective survey in 14 intensive care units within Australia and New Zealand. For community acquired pneumonia, mortality increased with immunosuppression (OR 5.32, CI 95% 1.58-17.99, P < 0. 01), clinical signs of consolidation (OR 2.43, CI 95% 1.09-5.44, P = 0. 03) and Sepsis-Related Organ Failure Assessment (SOFA) scores (OR 1.19, CI 95% 1.08-1.30, P < 0. 001) but improved if appropriate antibiotic changes were made within three days of intensive care unit admission (OR 0.42, CI 95% 0.20-0.86, P = 0.02). For hospital-acquired pneumonia, immunosuppression (OR 6.98, CI 95% 1.16-42.2, P = 0.03) and non-metastatic cancer (OR 3.78, CI 95% 1.20-11.93, P = 0.02) were the principal mortality predictors. Alcoholism (OR 7.80, CI 95% 1.20-1750, P < 0.001), high SOFA scores (OR 1.44, CI 95% 1.20-1.75, P = 0.001) and the isolation of high risk organisms including Pseudomonas aeruginosa, Acinetobacter spp, Stenotrophomonas spp and methicillin resistant Staphylococcus aureus (OR 4.79, CI 95% 1.43-16.03, P = 0.01), were associated with increased mortality in ventilator-associated pneumonia. The use of non-invasive ventilation was independently protective against mortality for patients with community-acquired and hospital-acquired pneumonia (OR 0.35, CI 95% 0.18-0.68, P = 0.002). Mortality was similar for patients requiting both invasive and non-invasive ventilation and non-invasive ventilation alone (21% compared with 20% respectively, P = 0.56). Pneumonia risks and mortality predictors in Australian and New Zealand ICUs vary with pneumonia type. A history of alcoholism is a major risk factor for mortality in ventilator-associated pneumonia, greater in magnitude than the mortality effect of immunosuppression in hospital-acquired pneumonia or community-acquired pneumonia. Non-invasive ventilation is associated with reduced ICU mortality. Clinical signs of consolidation worsen, while rationalising antibiotic therapy within three days of ICU admission improves mortality for community-acquired pneumonia patients.

Prediction of Klason lignin and lignin thermal degradation products by Py-GC/MS in a collection of Lolium and Festuca grasses

A rapid method for the analysis of biomass feedstocks was established to identify the quality of the pyrolysis products likely to impact on bio-oil production. A total of 15 Lolium and Festuca grasses known to exhibit a range of Klason lignin contents were analysed by pyroprobe-GC/MS (Py-GC/MS) to determine the composition of the thermal degradation products of lignin. The identification of key marker compounds which are the derivatives of the three major lignin subunits (G, H, and S) allowed pyroprobe-GC/MS to be statistically correlated to the Klason lignin content of the biomass using the partial least-square method to produce a calibration model. Data from this multivariate modelling procedure was then applied to identify likely "key marker" ions representative of the lignin subunits from the mass spectral data. The combined total abundance of the identified key markers for the lignin subunits exhibited a linear relationship with the Klason lignin content. In addition the effect of alkali metal concentration on optimum pyrolysis characteristics was also examined. Washing of the grass samples removed approximately 70% of the metals and changed the characteristics of the thermal degradation process and products. Overall the data indicate that both the organic and inorganic specification of the biofuel impacts on the pyrolysis process and that pyroprobe-GC/MS is a suitable analytical technique to asses lignin composition. © 2007 Elsevier B.V. All rights reserved.

Predicting class I major histocompatibility complex (MHC) binders using multivariate statistics:comparison of discriminant analysis and multiple linear regression

The accurate in silico identification of T-cell epitopes is a critical step in the development of peptide-based vaccines, reagents, and diagnostics. It has a direct impact on the success of subsequent experimental work. Epitopes arise as a consequence of complex proteolytic processing within the cell. Prior to being recognized by T cells, an epitope is presented on the cell surface as a complex with a major histocompatibility complex (MHC) protein. A prerequisite therefore for T-cell recognition is that an epitope is also a good MHC binder. Thus, T-cell epitope prediction overlaps strongly with the prediction of MHC binding. In the present study, we compare discriminant analysis and multiple linear regression as algorithmic engines for the definition of quantitative matrices for binding affinity prediction. We apply these methods to peptides which bind the well-studied human MHC allele HLA-A*0201. A matrix which results from combining results of the two methods proved powerfully predictive under cross-validation. The new matrix was also tested on an external set of 160 binders to HLA-A*0201; it was able to recognize 135 (84%) of them.

BPROMPT:a consensus server for membrane protein prediction

Protein structure prediction is a cornerstone of bioinformatics research. Membrane proteins require their own prediction methods due to their intrinsically different composition. A variety of tools exist for topology prediction of membrane proteins, many of them available on the Internet. The server described in this paper, BPROMPT (Bayesian PRediction Of Membrane Protein Topology), uses a Bayesian Belief Network to combine the results of other prediction methods, providing a more accurate consensus prediction. Topology predictions with accuracies of 70% for prokaryotes and 53% for eukaryotes were achieved. BPROMPT can be accessed at http://www.jenner.ac.uk/BPROMPT.

Quantitative online prediction of peptide binding to the major histocompatibility complex

With its implications for vaccine discovery, the accurate prediction of T cell epitopes is one of the key aspirations of computational vaccinology. We have developed a robust multivariate statistical method, based on partial least squares, for the quantitative prediction of peptide binding to major histocompatibility complexes (MHC), the principal checkpoint on the antigen presentation pathway. As a service to the immunobiology community, we have made a Perl implementation of the method available via a World Wide Web server. We call this server MHCPred. Access to the server is freely available from the URL: http://www.jenner.ac.uk/MHCPred. We have exemplified our method with a model for peptides binding to the common human MHC molecule HLA-B*3501.

MHCPred : a server for quantitative prediction of peptide-MHC binding

Accurate T-cell epitope prediction is a principal objective of computational vaccinology. As a service to the immunology and vaccinology communities at large, we have implemented, as a server on the World Wide Web, a partial least squares-base multivariate statistical approach to the quantitative prediction of peptide binding to major histocom-patibility complexes (MHC), the key checkpoint on the antigen presentation pathway within adaptive,cellular immunity. MHCPred implements robust statistical models for both Class I alleles (HLA-A*0101, HLA-A*0201, HLA-A*0202, HLA-A*0203,HLA-A*0206, HLA-A*0301, HLA-A*1101, HLA-A*3301, HLA-A*6801, HLA-A*6802 and HLA-B*3501) and Class II alleles (HLA-DRB*0401, HLA-DRB*0401and HLA-DRB* 0701).

Application of the Heterogeneous System Prediction Method to Pattern Recognition Problem

* This work was financially supported by RFBR-04-01-00858.

Wind power forecasts using Gaussian processes and numerical weather prediction

Since wind at the earth's surface has an intrinsically complex and stochastic nature, accurate wind power forecasts are necessary for the safe and economic use of wind energy. In this paper, we investigated a combination of numeric and probabilistic models: a Gaussian process (GP) combined with a numerical weather prediction (NWP) model was applied to wind-power forecasting up to one day ahead. First, the wind-speed data from NWP was corrected by a GP, then, as there is always a defined limit on power generated in a wind turbine due to the turbine controlling strategy, wind power forecasts were realized by modeling the relationship between the corrected wind speed and power output using a censored GP. To validate the proposed approach, three real-world datasets were used for model training and testing. The empirical results were compared with several classical wind forecast models, and based on the mean absolute error (MAE), the proposed model provides around 9% to 14% improvement in forecasting accuracy compared to an artificial neural network (ANN) model, and nearly 17% improvement on a third dataset which is from a newly-built wind farm for which there is a limited amount of training data. © 2013 IEEE.

Deconstructing phonological tasks:the contribution of stimulus and response type to the prediction of early decoding skills

Abstract Phonological tasks are highly predictive of reading development but their complexity obscures the underlying mechanisms driving this association. There are three key components hypothesised to drive the relationship between phonological tasks and reading; (a) the linguistic nature of the stimuli, (b) the phonological complexity of the stimuli, and (c) the production of a verbal response. We isolated the contribution of the stimulus and response components separately through the creation of latent variables to represent specially designed tasks that were matched for procedure. These tasks were administered to 570 6 to 7-year-old children along with standardised tests of regular word and non-word reading. A structural equation model, where tasks were grouped according to stimulus, revealed that the linguistic nature and the phonological complexity of the stimulus predicted unique variance in decoding, over and above matched comparison tasks without these components. An alternative model, grouped according to response mode, showed that the production of a verbal response was a unique predictor of decoding beyond matched tasks without a verbal response. In summary, we found that multiple factors contributed to reading development, supporting multivariate models over those that prioritize single factors. More broadly, we demonstrate the value of combining matched task designs with latent variable modelling to deconstruct the components of complex tasks.

A comprehensive study of bankruptcy prediction: Accounting ratios, market variables, and microstructure

Bankruptcy prediction has been a fruitful area of research. Univariate analysis and discriminant analysis were the first methodologies used. While they perform relatively well at correctly classifying bankrupt and nonbankrupt firms, their predictive ability has come into question over time. Univariate analysis lacks the big picture that financial distress entails. Multivariate discriminant analysis requires stringent assumptions that are violated when dealing with accounting ratios and market variables. This has led to the use of more complex models such as neural networks. While the accuracy of the predictions has improved with the use of more technical models, there is still an important point missing. Accounting ratios are the usual discriminating variables used in bankruptcy prediction. However, accounting ratios are backward-looking variables. At best, they are a current snapshot of the firm. Market variables are forward-looking variables. They are determined by discounting future outcomes. Microstructure variables, such as the bid-ask spread, also contain important information. Insiders are privy to more information that the retail investor, so if any financial distress is looming, the insiders should know before the general public. Therefore, any model in bankruptcy prediction should include market and microstructure variables. That is the focus of this dissertation. The traditional models and the newer, more technical models were tested and compared to the previous literature by employing accounting ratios, market variables, and microstructure variables. Our findings suggest that the more technical models are preferable, and that a mix of accounting and market variables are best at correctly classifying and predicting bankrupt firms. Multi-layer perceptron appears to be the most accurate model following the results. The set of best discriminating variables includes price, standard deviation of price, the bid-ask spread, net income to sale, working capital to total assets, and current liabilities to total assets.

Multivariate analysis of regional-scale geochemical data for environmental monitoring

A compositional multivariate approach is used to analyse regional scale soil geochemical data obtained as part of the Tellus Project generated by the Geological Survey Northern Ireland (GSNI). The multi-element total concentration data presented comprise XRF analyses of 6862 rural soil samples collected at 20cm depths on a non-aligned grid at one site per 2 km2. Censored data were imputed using published detection limits. Using these imputed values for 46 elements (including LOI), each soil sample site was assigned to the regional geology map provided by GSNI initially using the dominant lithology for the map polygon. Northern Ireland includes a diversity of geology representing a stratigraphic record from the Mesoproterozoic, up to and including the Palaeogene. However, the advance of ice sheets and their meltwaters over the last 100,000 years has left at least 80% of the bedrock covered by superficial deposits, including glacial till and post-glacial alluvium and peat. The question is to what extent the soil geochemistry reflects the underlying geology or superficial deposits. To address this, the geochemical data were transformed using centered log ratios (clr) to observe the requirements of compositional data analysis and avoid closure issues. Following this, compositional multivariate techniques including compositional Principal Component Analysis (PCA) and minimum/maximum autocorrelation factor (MAF) analysis method were used to determine the influence of underlying geology on the soil geochemistry signature. PCA showed that 72% of the variation was determined by the first four principal components (PC’s) implying “significant” structure in the data. Analysis of variance showed that only 10 PC’s were necessary to classify the soil geochemical data. To consider an improvement over PCA that uses the spatial relationships of the data, a classification based on MAF analysis was undertaken using the first 6 dominant factors. Understanding the relationship between soil geochemistry and superficial deposits is important for environmental monitoring of fragile ecosystems such as peat. To explore whether peat cover could be predicted from the classification, the lithology designation was adapted to include the presence of peat, based on GSNI superficial deposit polygons and linear discriminant analysis (LDA) undertaken. Prediction accuracy for LDA classification improved from 60.98% based on PCA using 10 principal components to 64.73% using MAF based on the 6 most dominant factors. The misclassification of peat may reflect degradation of peat covered areas since the creation of superficial deposit classification. Further work will examine the influence of underlying lithologies on elemental concentrations in peat composition and the effect of this in classification analysis.

Multivariate statistical modeling of an anode backing furnace - Modélisation statistique multivariée du four à cuisson des anodes utilisées dans la fabrication d'aluminium primaire

La stratégie actuelle de contrôle de la qualité de l’anode est inadéquate pour détecter les anodes défectueuses avant qu’elles ne soient installées dans les cuves d’électrolyse. Des travaux antérieurs ont porté sur la modélisation du procédé de fabrication des anodes afin de prédire leurs propriétés directement après la cuisson en utilisant des méthodes statistiques multivariées. La stratégie de carottage des anodes utilisée à l’usine partenaire fait en sorte que ce modèle ne peut être utilisé que pour prédire les propriétés des anodes cuites aux positions les plus chaudes et les plus froides du four à cuire. Le travail actuel propose une stratégie pour considérer l’histoire thermique des anodes cuites à n’importe quelle position et permettre de prédire leurs propriétés. Il est montré qu’en combinant des variables binaires pour définir l’alvéole et la position de cuisson avec les données routinières mesurées sur le four à cuire, les profils de température des anodes cuites à différentes positions peuvent être prédits. Également, ces données ont été incluses dans le modèle pour la prédiction des propriétés des anodes. Les résultats de prédiction ont été validés en effectuant du carottage supplémentaire et les performances du modèle sont concluantes pour la densité apparente et réelle, la force de compression, la réactivité à l’air et le Lc et ce peu importe la position de cuisson.

Trajectory prediction uncertainty modelling for Air Traffic Management

The anticipated growth of air traffic worldwide requires enhanced Air Traffic Management (ATM) technologies and procedures to increase the system capacity, efficiency, and resilience, while reducing environmental impact and maintaining operational safety. To deal with these challenges, new automation and information exchange capabilities are being developed through different modernisation initiatives toward a new global operational concept called Trajectory Based Operations (TBO), in which aircraft trajectory information becomes the cornerstone of advanced ATM applications. This transformation will lead to higher levels of system complexity requiring enhanced Decision Support Tools (DST) to aid humans in the decision making processes. These will rely on accurate predicted aircraft trajectories, provided by advanced Trajectory Predictors (TP). The trajectory prediction process is subject to stochastic effects that introduce uncertainty into the predictions. Regardless of the assumptions that define the aircraft motion model underpinning the TP, deviations between predicted and actual trajectories are unavoidable. This thesis proposes an innovative method to characterise the uncertainty associated with a trajectory prediction based on the mathematical theory of Polynomial Chaos Expansions (PCE). Assuming univariate PCEs of the trajectory prediction inputs, the method describes how to generate multivariate PCEs of the prediction outputs that quantify their associated uncertainty. Arbitrary PCE (aPCE) was chosen because it allows a higher degree of flexibility to model input uncertainty. The obtained polynomial description can be used in subsequent prediction sensitivity analyses thanks to the relationship between polynomial coefficients and Sobol indices. The Sobol indices enable ranking the input parameters according to their influence on trajectory prediction uncertainty. The applicability of the aPCE-based uncertainty quantification detailed herein is analysed through a study case. This study case represents a typical aircraft trajectory prediction problem in ATM, in which uncertain parameters regarding aircraft performance, aircraft intent description, weather forecast, and initial conditions are considered simultaneously. Numerical results are compared to those obtained from a Monte Carlo simulation, demonstrating the advantages of the proposed method. The thesis includes two examples of DSTs (Demand and Capacity Balancing tool, and Arrival Manager) to illustrate the potential benefits of exploiting the proposed uncertainty quantification method.