An ensemble method for predicting subnuclear localizations from primary protein structures

Background Predicting protein subnuclear localization is a challenging problem. Some previous works based on non-sequence information including Gene Ontology annotations and kernel fusion have respective limitations. The aim of this work is twofold: one is to propose a novel individual feature extraction method; another is to develop an ensemble method to improve prediction performance using comprehensive information represented in the form of high dimensional feature vector obtained by 11 feature extraction methods. Methodology/Principal Findings A novel two-stage multiclass support vector machine is proposed to predict protein subnuclear localizations. It only considers those feature extraction methods based on amino acid classifications and physicochemical properties. In order to speed up our system, an automatic search method for the kernel parameter is used. The prediction performance of our method is evaluated on four datasets: Lei dataset, multi-localization dataset, SNL9 dataset and a new independent dataset. The overall accuracy of prediction for 6 localizations on Lei dataset is 75.2% and that for 9 localizations on SNL9 dataset is 72.1% in the leave-one-out cross validation, 71.7% for the multi-localization dataset and 69.8% for the new independent dataset, respectively. Comparisons with those existing methods show that our method performs better for both single-localization and multi-localization proteins and achieves more balanced sensitivities and specificities on large-size and small-size subcellular localizations. The overall accuracy improvements are 4.0% and 4.7% for single-localization proteins and 6.5% for multi-localization proteins. The reliability and stability of our classification model are further confirmed by permutation analysis. Conclusions It can be concluded that our method is effective and valuable for predicting protein subnuclear localizations. A web server has been designed to implement the proposed method. It is freely available at http://bioinformatics.awowshop.com/snlpr​ed_page.php.

Prediction of multilocus identity-by-descent

Previous studies have enabled exact prediction of probabilities of identity-by-descent (IBD) in randommating populations for a few loci (up to four or so), with extension to more using approximate regression methods. Here we present a precise predictor of multiple-locus IBD using simple formulas based on exact results for two loci. In particular, the probability of non-IBD X ABC at each of ordered loci A, B, and C can be well approximated by XABC = XABXBC/XB and generalizes to X123. . .k = X12X23. . .Xk-1,k/ Xk-2, where X is the probability of non-IBD at each locus. Predictions from this chain rule are very precise with population bottlenecks and migration, but are rather poorer in the presence of mutation. From these coefficients, the probabilities of multilocus IBD and non-IBD can also be computed for genomic regions as functions of population size, time, and map distances. An approximate but simple recurrence formula is also developed, which generally is less accurate than the chain rule but is more robust with mutation. Used together with the chain rule it leads to explicit equations for non-IBD in a region. The results can be applied to detection of quantitative trait loci (QTL) by computing the probability of IBD at candidate loci in terms of identity-by-state at neighboring markers.

Prediction of IBD based on population history for fine gene mapping

A novel multiple regression method (RM) is developed to predict identity-by-descent probabilities at a locus L (IBDL), among individuals without pedigree, given information on surrounding markers and population history. These IBDL probabilities are a function of the increase in linkage disequilibrium (LD) generated by drift in a homogeneous population over generations. Three parameters are sufficient to describe population history: effective population size (Ne), number of generations since foundation (T), and marker allele frequencies among founders (p). IBD L are used in a simulation study to map a quantitative trait locus (QTL) via variance component estimation. RM is compared to a coalescent method (CM) in terms of power and robustness of QTL detection. Differences between RM and CM are small but significant. For example, RM is more powerful than CM in dioecious populations, but not in monoecious populations. Moreover, RM is more robust than CM when marker phases are unknown or when there is complete LD among founders or Ne is wrong, and less robust when p is wrong. CM utilises all marker haplotype information, whereas RM utilises information contained in each individual marker and all possible marker pairs but not in higher order interactions. RM consists of a family of models encompassing four different population structures, and two ways of using marker information, which contrasts with the single model that must cater for all possible evolutionary scenarios in CM.

On the prediction of simultaneous inbreeding coefficients at multiple loci

A new deterministic method for predicting simultaneous inbreeding coefficients at three and four loci is presented. The method involves calculating the conditional probability of IBD (identical by descent) at one locus given IBD at other loci, and multiplying this probability by the prior probability of the latter loci being simultaneously IBD. The conditional probability is obtained applying a novel regression model, and the prior probability from the theory of digenic measures of Weir and Cockerham. The model was validated for a finite monoecious population mating at random, with a constant effective population size, and with or without selfing, and also for an infinite population with a constant intermediate proportion of selfing. We assumed discrete generations. Deterministic predictions were very accurate when compared with simulation results, and robust to alternative forms of implementation. These simultaneous inbreeding coefficients were more sensitive to changes in effective population size than in marker spacing. Extensions to predict simultaneous inbreeding coefficients at more than four loci are now possible.

Benefits and issues for bus travel time estimation and prediction

Bus travel time estimation and prediction are two important modelling approaches which could facilitate transit users in using and transit providers in managing the public transport network. Bus travel time estimation could assist transit operators in understanding and improving the reliability of their systems and attracting more public transport users. On the other hand, bus travel time prediction is an important component of a traveller information system which could reduce the anxiety and stress for the travellers. This paper provides an insight into the characteristic of bus in traffic and the factors that influence bus travel time. A critical overview of the state-of-the-art in bus travel time estimation and prediction is provided and the needs for research in this important area are highlighted. The possibility of using Vehicle Identification Data (VID) for studying the relationship between bus and cars travel time is also explored.

Investigation into the noise map based on traffic flow prediction in the citywide road network

As one of the measures for decreasing road traffic noise in a city, the control of the traffic flow and the physical distribution is considered. To conduct the measure effectively, the model for predicting the traffic flow in the citywide road network is necessary. In this study, the existing model named AVENUE was used as a traffic flow prediction model. The traffic flow model was integrated with the road vehicles' sound power model and the sound propagation model, and the new road traffic noise prediction model was established. As a case study, the prediction model was applied to the road network of Tsukuba city in Japan and the noise map of the city was made. To examine the calculation accuracy of the noise map, the calculated values of the noise at the main roads were compared with the measured values. As a result, it was found that there was a possibility that the high accuracy noise map of the city could be made by using the noise prediction model developed in this study.

Freeway travel time estimation & prediction : a literature review

This report is the second deliverable of the Real Time and Predictive Traveller Information project and the first deliverable of the Freeway Travel Time Information sub-project in the Integrated Traveller Information research Domain of the Smart Transport Research Centre. The primary objective of the Freeway Travel Time Information sub-project is to develop algorithms for real-time travel time estimation and prediction models for Freeway traffic. The objective of this report is to review the literature pertaining to travel time estimation and prediction models for freeway traffic.

Arterial travel time estimation & prediction : a literature review

This report is the fourth deliverable of the Real Time and Predictive Traveller Information project and the first deliverable of the Arterial Travel Time Information sub-project in the Integrated Traveller Information research Domain of the Smart Transport Research Centre. The primary objective of the Arterial Travel Time Information sub-project is to develop algorithms for real-time travel time estimation and prediction models for arterial traffic. The objective of this report is to review the literature pertaining to travel time estimation and prediction models for arterial traffic.

C-BN Single-Walled Nanotubes from Hybrid Connection of BN/C Nanoribbons: Prediction by ab initio Density Functional Calculations

We demonstrated for the first time by ab initio density functional calculation and molecular dynamics simulation that C0.5(BN)0.5 armchair single-walled nanotubes (NT) are gapless semiconductors and can be spontaneously formed via the hybrid connection of graphene/BN Nanoribbons (GNR/BNNR) at room temperature. The direct synthesis of armchair C0.5(BN)0.5 via the hybrid connection of GNR/BNNR is predicted to be both thermodynamically and dynamically stable. Such novel armchair C0.5(BN)0.5 NTs possess enhanced conductance as that observed in GNRs. Additionally, the zigzag C0.5(BN)0.5 SWNTs are narrow band gap semiconductors, which may have potential application for light emission. In light of recent experimental progress and the enhanced degree of control in the synthesis of GNRs and BNNR, our results highlight an interesting avenue for synthesizing a novel specific type of C0.5(BN)0.5 nanotube (gapless or narrow direct gap semiconductor), with potentially important applications in BNC-based nanodevices.

Character in the workplace : self directedness mediates harm avoidance in the prediction of job performance

The purpose of this study was to test a model of the relationship between temperament, character and job performance, in order to better understand the cause of stable individual differences in job performance. Personality was conceptualized in terms of Cloninger, Svrakic and Przybeck’s (1993) theoretical framework of personality. It was expected that Self Directedness (character) would mediate Harm Avoidance and Persistence (temperament) in the prediction of job performance. In order to test the hypotheses, a sample of 94 employee/supervisor pairs was recruited from several organizations across Australia. Participants completed a number of questionnaires online, regarding their personality traits (completed by employees) and Job Performance (completed by Supervisors). Consistent with the hypothesis, Self Directedness was found to be a moderate, direct predictor of job performance. Also consistent with the hypothesis, Self Directedness mediated Harm Avoidance in the prediction of job performance. Results show that character (Self Directedness) is important in the prediction of job performance, and also suggests that fearful, avoidant individuals are less likely to perform well in the workplace, based on their low level of character development.

Prediction of age at menopause from assessment of ovarian reserve may be improved by using body mass index and smoking status

Objective: Menopause is the consequence of exhaustion of the ovarian follicular pool. AMH, an indirect hormonal marker of ovarian reserve, has been recently proposed as a predictor for age at menopause. Since BMI and smoking status are relevant independent factors associated with age at menopause we evaluated whether a model including all three of these variables could improve AMH-based prediction of age at menopause. Methods: In the present cohort study, participants were 375 eumenorrheic women aged 19–44 years and a sample of 2,635 Italian menopausal women. AMH values were obtained from the eumenorrheic women. Results: Regression analysis of the AMH data showed that a quadratic function of age provided a good description of these data plotted on a logarithmic scale, with a distribution of residual deviates that was not normal but showed significant leftskewness. Under the hypothesis that menopause can be predicted by AMH dropping below a critical threshold, a model predicting menopausal age was constructed from the AMH regression model and applied to the data on menopause. With the AMH threshold dependent on the covariates BMI and smoking status, the effects of these covariates were shown to be highly significant. Conclusions: In the present study we confirmed the good level of conformity between the distributions of observed and AMH-predicted ages at menopause, and showed that using BMI and smoking status as additional variables improves AMH-based prediction of age at menopause.

Clinical data integration approach using SAS clinical data integration server (CDI) tools

The decisions people make about medical treatments have a great impact on their lives. Health care practitioners, providers and patients often make decisions about medical treatments without complete understanding of the circumstances. The main reason for this is that medical data are available in fragmented, disparate and heterogeneous data silos. Without a centralised data warehouse structure to integrate these data silos, it is highly unlikely and impractical for the users to get all the information required on time to make a correct decision. In this research paper, a clinical data integration approach using SAS Clinical Data Integration Server tools is presented.

Half metallicity in a zigzag double-walled nanotube nanodot : an Ab initio prediction

Ab initio density functional calculations were performed to study finite-length zigzag (7, 0) @ (16, 0) double-walled carbon nanotubes (DWCNTs) with H-termination at the open ends. We find that such a DWCNT nanodot displays a very large magnetic moment at the zigzag edges and the ground state displays symmetric anti-ferromagnetic coupling. When an external electric field is applied along the direction of tube axis, a gap is opened for one spin channel, whereas another spin channel remains metallic, i.e. half metallicity occurs. Our results suggest an important new avenue for the development of CNT-based spintronic materials with enhanced properties.

Half metallicity in finite-length zigzag single walled carbon nanotube : A first-principle prediction

We predict here from first-principle calculations that finite-length (n,0) single walled carbon nanotubes (SWCNTs) with H-termination at the open ends displaying antiferromagnetic coupling when n is greater than 6. An opposite local gating effect of the spin states, i.e., half metallicity, is found under the influence of an external electric field along the direction of tube axis. Remarkably, boron doping of unpassivated SWCNTs at both zigzag edges is found to favor a ferromagnetic ground state, with the B-doped tubes displaying half-metallic behavior even in the absence of an electric field. Aside of the intrinsic interest of these results, an important avenue for development of CNT-based spintronic is suggested.