Bayesian Calibration of a Stochastic Kinetic Computer Model Using Multiple Data Sources

Summary .  In this article, we describe a Bayesian approach to the calibration of a stochastic computer model of chemical kinetics. As with many applications in the biological sciences, the data available to calibrate the model come from different sources. Furthermore, these data appear to provide somewhat conflicting information about the model parameters. We describe a modeling framework that allows us to synthesize this conflicting information and arrive at a consensus inference. In particular, we show how random effects can be incorporated into the model to account for between-individual heterogeneity that may be the source of the apparent conflict.     

Robust Prediction of t‐Year Survival with Data from Multiple Studies

Summary Recently meta‐analysis has been widely utilized to combine information across multiple studies to evaluate a common effect. Integrating data from similar studies is particularly useful in genomic studies where the individual study sample sizes are not large relative to the number of parameters of interest. In this article, we are interested in developing robust prognostic rules for the prediction of t ‐year survival based on multiple studies. We propose to construct a composite score for prediction by fitting a stratified semiparametric transformation model that allows the studies to have related but not identical outcomes. To evaluate the accuracy of the resulting score, we provide point and interval estimators for the commonly used accuracy measures including the time‐specific receiver operating characteristic curves, and positive and negative predictive values. We apply the proposed procedures to develop prognostic rules for the 5‐year survival of breast cancer patients based on five breast cancer genomic studies.     

Asymmetric Contribution of Isotopically Contrasting Food Sources to Vertebrate Consumers in a Subtropical Semi‐arid Ecosystem

Habitat heterogeneity is a primary ecological factor that is particularly pronounced in arid ecosystems. The Tehuacán valley is a subtropical semi‐arid ecosystem in which several species of columnar cacti and agave (i.e., CAM plants) constitute the dominant elements accompanied by patches of trees and shrubs (i.e., C₃ plants). Vegetation in Tehuacán is isotopically heterogenous because CAM plants have less depleted δ¹³C values than C₃ plants. Fruits and flowers of cactus and agaves offer abundant food to vertebrates, but their leaves might be less attractive to insects than the leaves of C₃ plants. Therefore, we use carbon and nitrogen stable isotope analysis to test the hypothesis that C₃ and CAM food would contribute asymmetrically to different guilds of birds and bats. We predict that granivorous and frugivorous birds and nectarivorous and frugivorous bats will consume a CAM diet, whereas insectivorous birds and bats will consume a C₃ diet. Due to omnivory of bird and bat consumers, we predict that the importance of CAM food will decrease as the trophic level of the animal increases. Our results showed that CAM food predominated in plant‐eating birds and in some flower‐visiting bats, whereas C₃ food predominated in insect‐eating bats and birds and frugivorous bats. Habitat heterogeneity in Tehuacán is important for conservation due to the asymmetric role of CAM and C₃ food in the nutrition of different feeding guilds of vertebrates. Our study provides basic information to evaluate the potential impact of habitat loss on functional groups of consumers in a semi‐arid ecosystem.     

Plant cell calcium‐rich environment enhances thermostability of recombinantly produced α‐amylase from the hyperthermophilic bacterium Thermotoga maritime

In the industrial processing of starch for sugar syrup and ethanol production, a liquefaction step is involved where starch is initially solubilized at high temperature and partially hydrolyzed with a thermostable and thermoactive α‐amylase. Most amylases require calcium as a cofactor for their activity and stability, therefore calcium, along with the thermostable enzyme, are typically added to the starch mixture during enzymatic liquefaction, thereby increasing process costs. An attractive alternative would be to produce the enzyme directly in the tissue to be treated. In a proof of concept study, tobacco cell cultures were used as model system to test in planta production of a hyperthermophilic α‐amylase from Thermotoga maritima. While comparable biochemical properties to recombinant production in Escherichia coli were observed, thermostability of the plant‐produced α‐amylase benefited significantly from high intrinsic calcium levels in the tobacco cells. The plant‐made enzyme retained 85% of its initial activity after 3 h incubation at 100°C, whereas the E. coli‐produced enzyme was completely inactivated after 30 min under the same conditions. The addition of Ca²⁺ or plant cell extracts from tobacco and sweetpotato to the E. coli‐produced enzyme resulted in a similar stabilization, demonstrating the importance of a calcium‐rich environment for thermostability, as well as the advantage of producing this enzyme directly in plant cells where calcium is readily available. Biotechnol. Bioeng. 2009; 104: 947–956. © 2009 Wiley Periodicals, Inc.     

Bioprospecting of Saprobe Fungi from the Semi‐Arid North‐East of Brazil for the Control of Anthracnose on Sorghum

Anthracnose, caused by the hemiotrophic fungus Colletotrichum sublineolum, is one of the most important diseases affecting sorghum production worldwide. The main goal of this study was to select saprobe fungi from the semi‐arid north‐east of Brazil that could increase sorghum resistance to anthracnose and investigate this increased resistance at both physiological and biochemical levels. Plants were sprayed with Curvularia inaequalis, Gonytrichum macroladum, Memnoniella levispora, Pithomyces chartarum, Periconia hispidula, Phaeoisaria clematidia, Dictyochaeta heteroderae, Sarcopodium circinatum, Periconia byssoides, Moorella speciosa, Stachybotrys chartarum, Pseudobotrytis terrestres, Memnoniella echinata, Stachybotrys globosa and Gonytrichum clamydosporium 24 h before inoculation with C. sublineolum. Plants sprayed with water served as the control treatment. The area under the anthracnose progress curve was significantly reduced in comparison with the control treatment only for plants sprayed with C. inaequalis. Therefore, C. inaequalis was selected for physiological and biochemical evaluations. The peroxidases, chitinases and β‐1,3‐glucanases activities were significantly higher for plants sprayed with C. inaequalis and inoculated with C. sublineolum than for plants not sprayed with C. inaequalis and inoculated with C. sublineolum. There was no apparent decrease in the values of net carbon assimilation rate, stomatal conductance to water vapour or transpiration rate for plants sprayed with C. inaequalis and infected by C. sublineolum in comparison with plants not sprayed with C. inaequalis and infected by C. sublineolum. In conclusion, sorghum resistance against C. sublineolum infection was greatly potentiated by C. inaequalis without any apparent change in the photosynthetic capacity of the infected plants.     

Frailty‐Based Competing Risks Model for Multivariate Survival Data

Summary In this work, we provide a new class of frailty‐based competing risks models for clustered failure times data. This class is based on expanding the competing risks model of Prentice et al. (1978, Biometrics 34 , 541–554) to incorporate frailty variates, with the use of cause‐specific proportional hazards frailty models for all the causes. Parametric and nonparametric maximum likelihood estimators are proposed. The main advantages of the proposed class of models, in contrast to the existing models, are: (1) the inclusion of covariates; (2) the flexible structure of the dependency among the various types of failure times within a cluster; and (3) the unspecified within‐subject dependency structure. The proposed estimation procedures produce the most efficient parametric and semiparametric estimators and are easy to implement. Simulation studies show that the proposed methods perform very well in practical situations.     

Statistical Methods for Analyzing Right‐Censored Length‐Biased Data under Cox Model

Summary Length‐biased time‐to‐event data are commonly encountered in applications ranging from epidemiological cohort studies or cancer prevention trials to studies of labor economy. A longstanding statistical problem is how to assess the association of risk factors with survival in the target population given the observed length‐biased data. In this article, we demonstrate how to estimate these effects under the semiparametric Cox proportional hazards model. The structure of the Cox model is changed under length‐biased sampling in general. Although the existing partial likelihood approach for left‐truncated data can be used to estimate covariate effects, it may not be efficient for analyzing length‐biased data. We propose two estimating equation approaches for estimating the covariate coefficients under the Cox model. We use the modern stochastic process and martingale theory to develop the asymptotic properties of the estimators. We evaluate the empirical performance and efficiency of the two methods through extensive simulation studies. We use data from a dementia study to illustrate the proposed methodology, and demonstrate the computational algorithms for point estimates, which can be directly linked to the existing functions in S‐PLUS or R .     

Development of ELISA for the Determination of Transgenic Bt‐Cottons Using Antibodies against Cry1Ac Protein from Bacillus thuringiensis HD‐73

The area cultivated with Bt‐cottons expressing Cry1Ac gene increases year by year in China and other countries. To evaluate any potential adverse impacts on the environment from the release of Bt (Bacillus thuringiensis) technology, the development of a method for easily detecting the activity of the Cry1Ac toxins is of particular interest. The aim of this study was to develop sandwich‐ELISA for the detection of Cry1Ac protein in Bt‐cotton tissues. A specific antibody was obtained from rabbits inoculated with Cry1Ac protein derived from Bt strain HD‐73 and a secondary antibody conjugated to HRP could combine the Bt Cry1Ac protein specifically. The limit of detection was 5 ng/mL and there were no cross‐reactions between the positive control of Cry1Ab/1Ac, Cry1C, Cry2A, Cry3Bb1 and Cry9C. Extracts of proteins from cotton leaves were used to evaluate the suitability of the assay. Tris‐borate buffer and sodium carbonate buffer were employed for the extraction of protein, the limit absorbance of detection was 0.134 and 0.449, respectively, and the latter produced a higher background. The results showed that cultivars GK‐12, GK‐22, insect‐resistant cotton, bivalent transgenic cotton and shiyuan 321 assayed positively and NON was the negative sample. The PCR method was used for the validation of the developed assay. Although both methods allowed the same results to be obtained, ELISA needed simple equipment and took less time. The developed immunoassay method is considered reliable for the detection of Bt Cry1Ac protein.     

Tests for Monotonic Trend from Case‐Control Data: Cochran‐Armitage‐Mantel Trend Test,Isotonic Regression and Single and Multiple Contrast Tests

Tests for a monotonic trend between an ordered categorical exposure and disease status are routinely carried out from case‐control data using the Mantel‐extension trend test or the asymptotically equivalent Cochran‐Armitage test. In this study, we considered two alternative tests based on isotonic regression, namely an order‐restricted likelihood ratio test and an isotonic modification of the Mantel‐extension test extending the recent proposal by Mancuso, Ahn and Chen (2001) to case‐control data. Furthermore, we considered three tests based on contrasts, namely a single contrast (SC) test based on Schaafsma's coefficients, the Dosemeci and Benichou (DB) test, a multiple contrast (MC) test based on the Helmert, reverse‐Helmert and linear contrasts and we derived their case‐control versions. Using simulations, we compared the statistical properties of these five alternative tests to those of the Mantel‐extension test under various patterns including no relationship, as well as monotonic and non‐monotonic relationships between exposure and disease status. In the case of no relationship, all tests had close to nominal type I error except in situations combining a very unbalanced exposure distribution and small sample size, where the asymptotic versions of the three tests based on contrasts were highly anticonservative. The use of bootstrap instead of asymptotic versions corrected this anticonservatism. For monotonic patterns, all tests had close powers. For non monotonic patterns, the DB‐test showed the most favourable results as it was the least powerful test. The two tests based on isotonic regression were the most powerful tests and the Mantel‐extension test, the SC‐ and MC‐tests had in‐between powers. The six tests were applied to data from a case‐control study investigating the relationship between alcohol consumption and risk of laryngeal cancer in Turkey. In situations with no evidence of a monotonic relationship between exposure and disease status, the three tests based on contrasts did not conclude in favour of a significant trend whereas all the other tests did. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Attempted Integration of Multiple Species of Turaco Into a Mixed‐Species Aviary

Mixed‐species exhibits offer a variety of benefits but can be challenging to maintain due to difficulty in managing interspecific interactions. This is particularly true when little has been documented on the behavior of the species being mixed. This was the case when we attempted to house three species of turaco (family: Musophagidae) together with other species in a walk‐through aviary. To learn more about the behavior of great blue turacos, violaceous turacos, and white‐bellied gray go‐away birds, we supplemented opportunistic keeper observations with systematic data collection on their behavior, location, distance from other birds, and visibility to visitors. Keepers reported high levels of aggression among turacos, usually initiated by a go‐away bird or a violaceous turaco. Most aggression occurred during feedings or when pairs were defending nest sites. Attempts to reduce aggression by temporarily removing birds to holding areas and reintroducing them days later were ineffective. Systematic data collection revealed increased social behavior, including aggression, during breeding season in the violaceous turacos, as well as greater location fidelity. These behavioral cues may be useful in predicting breeding behavior in the future. Ultimately, we were only able to house three species of turaco together for a short time, and prohibitively high levels of conflict occurred when pairs were breeding. We conclude that mixing these three turaco species is challenging and may not be the most appropriate housing situation for them, particularly during breeding season. However, changes in turaco species composition, sex composition, or exhibit design may result in more compatible mixed‐turaco species groups. Zoo Biol. 32:216–221, 2013. © 2012 Wiley Periodicals, Inc.     

濒危植物明党参个体年龄非破坏性估测模型研究

探索了一种利用地上部性状以非破坏性途径估测濒危植物明党参（Changium smyrnioides Wolff)个体年龄的模型方法．首先利用根体积(Vt)与根体积年增长量(△V)的相关性,建立模型推断个体的年龄(t);进一步利用地上最大带柄叶长(L)和根体积(Vt)的相关性来估测个体年龄(t)该方法在种群年龄结构分析中十分有效,另外通过这些模型还可以初步判断出明党参根体积增长速度的转折点,因而具有重要的生物学意义．本方法对于植物生理生态学和种群生态学,特别对于难以估计年龄和不能大量破坏的多年生濒危植物的种群生态学研究具有重要意义。     

Production of N‐Acetyl‐Phosphinothricin: A Substance used for Inducing Male Sterility in Transgenic Plants

The non‐toxic compound N‐acetyl‐L‐phosphinothricin (N‐Ac‐L‐PPT) is used in a so‐called deacetylation system to induce male sterility in transgenic plants by tapetum specific deacetylation to the herbicide L‐phosphinothricin (L‐PPT). A procedure was developed to produce pure racemic and L‐isomeric N‐Ac‐PPT containing less than 30 ppm residual PPT. Experiments applied to wild type tobacco and PPT‐resistant tobacco showed that the maximal tolerated N‐Ac‐PPT concentration would be less than 45 mM of the L‐isomer. Otherwise unspecific deacetylation by several acylases, as well as by environmental conditions like higher temperatures or pHs beyond neutrality, increased the residual L‐PPT content to toxic concentrations. In contrast, N‐acetyl‐L‐phosphinothricyl‐alanyl‐alanine (N‐Ac‐L‐PPTT), a substance also occurring during the biosynthesis of phosphinothricyl‐alanyl‐alanine (PPTT) by some Streptomyces species, was tolerated up to 274 mM by wild type tobacco plants. However, the ArgE deacatylase from Escherichia coli originally used in the deacetylation system, as well as some other acylases, showed no activity towards N‐Ac‐L‐PPTT.     

Bayesian Modeling of ChIP‐chip Data Through a High‐Order Ising Model

Summary ChIP‐chip experiments are procedures that combine chromatin immunoprecipitation (ChIP) and DNA microarray (chip) technology to study a variety of biological problems, including protein–DNA interaction, histone modification, and DNA methylation. The most important feature of ChIP‐chip data is that the intensity measurements of probes are spatially correlated because the DNA fragments are hybridized to neighboring probes in the experiments. We propose a simple, but powerful Bayesian hierarchical approach to ChIP‐chip data through an Ising model with high‐order interactions. The proposed method naturally takes into account the intrinsic spatial structure of the data and can be used to analyze data from multiple platforms with different genomic resolutions. The model parameters are estimated using the Gibbs sampler. The proposed method is illustrated using two publicly available data sets from Affymetrix and Agilent platforms, and compared with three alternative Bayesian methods, namely, Bayesian hierarchical model, hierarchical gamma mixture model, and Tilemap hidden Markov model. The numerical results indicate that the proposed method performs as well as the other three methods for the data from Affymetrix tiling arrays, but significantly outperforms the other three methods for the data from Agilent promoter arrays. In addition, we find that the proposed method has better operating characteristics in terms of sensitivities and false discovery rates under various scenarios.     

Limited long‐term effectiveness of roller‐chopping for managing woody encroachment

The encroachment of woody plants into grasslands, woodland, and savanna has increased markedly over the past century, prompting the use of different physical methods to remove woody plants and restore grasses. Roller‐chopping is used extensively in the Americas, but little is known about its long‐term effectiveness for restoration, and whether its effectiveness varies with the intensity of encroachment. We compared the effects of roller‐chopping, under three treatment intensities (control, single treatment, double treatment), on woody plant density, ground cover, and groundstorey plants at sites of low, moderate, and high woody plant density in a semi‐arid eastern Australian woodland over 10 years. Both single and double treatment significantly altered the size distribution of Dodonaea viscosa, which comprised more than 85% of woody plants at all sites. Thus, roller‐chopping changed the size distribution of the community from an even‐size distribution to one dominated by shorter plants, irrespective of initial encroachment level. The effectiveness of roller‐chopping was strongly site‐specific, with significant reductions in density at low‐ and high‐density sites, but no clear trend in relation to the intensity of treatment (i.e. single cf. double treatment). The effectiveness of roller‐chopping was unsustained over the long term, with the suppressive effect on woody density diminishing over time. Grass cover increased with increasing intensity of woody removal, but only at the low‐density site and with some ill‐defined, variable, and short‐term effects on plant composition. Managers should consider that the short‐term effects may not adequately reflect the long‐term results of woody plant removal using the roller‐chopper.     

Time‐Varying Latent Effect Model for Longitudinal Data with Informative Observation Times

Summary In analysis of longitudinal data, it is not uncommon that observation times of repeated measurements are subject‐specific and correlated with underlying longitudinal outcomes. Taking account of the dependence between observation times and longitudinal outcomes is critical under these situations to assure the validity of statistical inference. In this article, we propose a flexible joint model for longitudinal data analysis in the presence of informative observation times. In particular, the new procedure considers the shared random‐effect model and assumes a time‐varying coefficient for the latent variable, allowing a flexible way of modeling longitudinal outcomes while adjusting their association with observation times. Estimating equations are developed for parameter estimation. We show that the resulting estimators are consistent and asymptotically normal, with variance–covariance matrix that has a closed form and can be consistently estimated by the usual plug‐in method. One additional advantage of the procedure is that it provides a unified framework to test whether the effect of the latent variable is zero, constant, or time‐varying. Simulation studies show that the proposed approach is appropriate for practical use. An application to a bladder cancer data is also given to illustrate the methodology.     

Plant‐derived recombinant immune complexes as self‐adjuvanting TB immunogens for mucosal boosting of BCG

Progress with protein‐based tuberculosis (TB) vaccines has been limited by poor availability of adjuvants suitable for human application. Here, we developed and tested a novel approach to molecular engineering of adjuvanticity that circumvents the need for exogenous adjuvants. Thus, we generated and expressed in transgenic tobacco plants the recombinant immune complexes (RICs) incorporating the early secreted Ag85B and the latency‐associated Acr antigen of Mycobacterium tuberculosis, genetically fused as a single polypeptide to the heavy chain of a monoclonal antibody to Acr. The RICs were formed by virtue of the antibody binding to Acr from adjacent molecules, thus allowing self‐polymerization of the complexes. TB‐RICs were purified from the plant extracts and shown to be biologically active by demonstrating that they could bind to C1q component of the complement and also to the surface of antigen‐presenting cells. Mice immunized with BCG and then boosted with two intranasal immunizations with TB‐RICs developed antigen‐specific serum IgG antibody responses with mean end‐point titres of 1 : 8100 (Acr) and 1 : 24 300 (Ag85B) and their splenocytes responded to in vitro stimulation by producing interferon gamma. 25% of CD4+ proliferating cells simultaneously produced IFN‐γ, IL‐2 and TNF‐α, a phenotype that has been linked with protective immune responses in TB. Importantly, mucosal boosting of BCG‐immunized mice with TB‐RICs led to a reduced M. tuberculosis infection in their lungs from log₁₀ mean = 5.69 ± 0.1 to 5.04 ± 0.2, which was statistically significant. We therefore propose that the plant‐expressed TB‐RICs represent a novel molecular platform for developing self‐adjuvanting mucosal vaccines.     

Database on Demand – An online tool for the custom generation of FASTA‐formatted sequence databases

In mass spectrometry‐based proteomics, most conventional search engines match spectral data to sequence databases. These search databases thus play a crucial role in the identification process. While search engines can derive peptides in silico from protein sequences, this is usually limited to standard digestion algorithms. Customized search databases that provide detailed control over the search space can vastly outperform such standard strategies, especially in gel‐free proteomics experiments. Here we present Database on Demand, an easy‐to‐use web tool that can quickly produce a wide variety of customized search databases.