Comparison of isotope-based linear and Bayesian mixing models in determining moisture recycling ratio

Stable water isotopes are natural tracers quantifying the contribution of moisture recycling to local precipitation,i.e.,the moisture recycling ratio,but various isotope-based models usually lead to different results,which affects the accuracy of local moisture recycling.In this study,a total of 18 stations from four typical areas in China were selected to compare the performance of isotope-based linear and Bayesian mixing models and to determine local moisture recycling ratio.Among the three vapor sources including advection,transpiration,and surface evaporation,the advection vapor usually played a dominant role,and the contribution of surface evaporation was less than that of transpiration.When the abnormal values were ignored,the arithmetic averages of differences between isotope-based linear and the Bayesian mixing models were 0.9%for transpiration,0.2%for surface evaporation,and–1.1%for advection,respectively,and the medians were 0.5%,0.2%,and–0.8%,respectively.The importance of transpiration was slightly less for most cases when the Bayesian mixing model was applied,and the contribution of advection was relatively larger.The Bayesian mixing model was found to perform better in determining an efficient solution since linear model sometimes resulted in negative contribution ratios.Sensitivity test with two isotope scenarios indicated that the Bayesian model had a relatively low sensitivity to the changes in isotope input,and it was important to accurately estimate the isotopes in precipitation vapor.Generally,the Bayesian mixing model should be recommended instead of a linear model.The findings are useful for understanding the performance of isotope-based linear and Bayesian mixing models under various climate backgrounds.

Adaptive Random Effects/Coefficients Modeling

Adaptive fractional polynomial modeling of general correlated outcomes is formulated to address nonlinearity in means, variances/dispersions, and correlations. Means and variances/dispersions are modeled using generalized linear models in fixed effects/coefficients. Correlations are modeled using random effects/coefficients. Nonlinearity is addressed using power transforms of primary (untransformed) predictors. Parameter estimation is based on extended linear mixed modeling generalizing both generalized estimating equations and linear mixed modeling. Models are evaluated using likelihood cross-validation (LCV) scores and are generated adaptively using a heuristic search controlled by LCV scores. Cases covered include linear, Poisson, logistic, exponential, and discrete regression of correlated continuous, count/rate, dichotomous, positive continuous, and discrete numeric outcomes treated as normally, Poisson, Bernoulli, exponentially, and discrete numerically distributed, respectively. Example analyses are also generated for these five cases to compare adaptive random effects/coefficients modeling of correlated outcomes to previously developed adaptive modeling based on directly specified covariance structures. Adaptive random effects/coefficients modeling substantially outperforms direct covariance modeling in the linear, exponential, and discrete regression example analyses. It generates equivalent results in the logistic regression example analyses and it is substantially outperformed in the Poisson regression case. Random effects/coefficients modeling of correlated outcomes can provide substantial improvements in model selection compared to directly specified covariance modeling. However, directly specified covariance modeling can generate competitive or substantially better results in some cases while usually requiring less computation time.

The Marginal Rao-Blackwellized Particle Filter for Mixed Linear/Nonlinear State Space Models

In this paper, the marginal Rao-Blackwellized particle filter （MRBPF）, which fuses the Rao-Blackwellized particle filter （RBPF） algorithm and the marginal particle filter （MPF） algorithm, is presented. The state space is divided into linear and non-linear parts, which can be estimated separately by the MPF and the optional Kalman filter. Through simulation in the terrain aided navigation （TAN） domain, it is demonstrated that, compared with the RBPF, the root mean square errors （RMSE） and the error variance of the nonlinear state estimations by the proposed MRBPF are respectively reduced by 29% and 96%, while the unique particle count is increased by 80%. It is also found that the MRBPF has better convergence properties, and analysis has shown that the existing RBPF is nothing more than a special case of the MRBPF.

Responses of River Runoff to Climate Change Based on Nonlinear Mixed Regression Model in Chaohe River Basin of Hebei Province, China

Taking the nonlinear nature of runoff system into account,and combining auto-regression method and multi-regression method,a Nonlinear Mixed Regression Model (NMR) was established to analyze the impact of temperature and precipitation changes on annual river runoff process. The model was calibrated and verified by using BP neural network with observed meteorological and runoff data from Daiying Hydrological Station in the Chaohe River of Hebei Province in 1956–2000. Compared with auto-regression model,linear multi-regression model and linear mixed regression model,NMR can improve forecasting precision remarkably. Therefore,the simulation of climate change scenarios was carried out by NMR. The results show that the nonlinear mixed regression model can simulate annual river runoff well.

IMPROVED ESTIMATES OF THE COVARIANCE MATRIX IN GENERAL LINEAR MIXED MODELS

In this article, the problem of estimating the covariance matrix in general linear mixed models is considered. Two new classes of estimators obtained by shrinking the eigenvalues towards the origin and the arithmetic mean, respectively, are proposed. It is shown that these new estimators dominate the unbiased estimator under the squared error loss function. Finally, some simulation results to compare the performance of the proposed estimators with that of the unbiased estimator are reported. The simulation results indicate that these new shrinkage estimators provide a substantial improvement in risk under most situations.

Impacts of the Minimum Purchase Price Policy for Grain on the Planting Area of Rice in Hubei Province Based on a Mixed Linear Model

Impacts of the minimum purchase price policy for grain on the planting area of rice in Hubei Province were analyzed based on a mixed linear model.After the indicator system containing the minimum purchase price policy and other factors influencing the planting area of rice was constructed,principal component analysis of the system was conducted,and then a mixed linear model where the planting area of rice was as the dependent variable was established.The results show that after the exclusion of the interference from other factors,the minimum purchase price policy for grain had a positive impact on the planting area of rice in Hubei Province.That is,the minimum purchase price policy significantly stimulated the growth of rice planting area in Hubei Province.

Nonparametric Estimation in Linear Mixed Models with Uncorrelated Homoscedastic Errors

Today, Linear Mixed Models (LMMs) are fitted, mostly, by assuming that random effects and errors have Gaussian distributions, therefore using Maximum Likelihood (ML) or REML estimation. However, for many data sets, that double assumption is unlikely to hold, particularly for the random effects, a crucial component in which assessment of magnitude is key in such modeling. Alternative fitting methods not relying on that assumption (as ANOVA ones and Rao’s MINQUE) apply, quite often, only to the very constrained class of variance components models. In this paper, a new computationally feasible estimation methodology is designed, first for the widely used class of 2-level (or longitudinal) LMMs with only assumption (beyond the usual basic ones) that residual errors are uncorrelated and homoscedastic, with no distributional assumption imposed on the random effects. A major asset of this new approach is that it yields nonnegative variance estimates and covariance matrices estimates which are symmetric and, at least, positive semi-definite. Furthermore, it is shown that when the LMM is, indeed, Gaussian, this new methodology differs from ML just through a slight variation in the denominator of the residual variance estimate. The new methodology actually generalizes to LMMs a well known nonparametric fitting procedure for standard Linear Models. Finally, the methodology is also extended to ANOVA LMMs, generalizing an old method by Henderson for ML estimation in such models under normality.

Linear Mixed Model Analysis of Worldwide Longitudinal Infant Mortality Rate Data and Association with Human Development Index

A linear mixed model is used to determine the explaining infant mortality rate data of United Nations countries. The HDI （human development index） has a significant negative linear relationship with infant mortality rate. United Nations data shows that the infant mortality rate has a descending trend over the period 1990-2010. This study aims to assess the value of the HDI as a predictor of infant mortality rate. Findings in the paper suggest that significant percentage reductions in infant mortality might be possible for countries for controlling the HDI.

A mixed integer linear programming approach for municipal solid waste management

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Combining Geographic Information Systems for Transportation and Mixed Integer Linear Programming in Facility Location-Allocation Problems

In this study, we aimed to assess the solution quality for location-allocation problems from facilities generated by the software TransCAD®?, a Geographic Information System for Transportation (GIS-T). Such facilities were obtained after using two routines together: Facility Location and Transportation Problem, when compared with optimal solutions from exact mathematical models, based on Mixed Integer Linear Programming (MILP), developed externally for the GIS. The models were applied to three simulations: the first one proposes opening factories and customer allocation in the state of Sao Paulo, Brazil;the second involves a wholesaler and a study of location and allocation of distribution centres for retail customers;and the third one involves the location of day-care centers and allocation of demand (0 - 3 years old children). The results showed that when considering facility capacity, the MILP optimising model presents results up to 37% better than the GIS and proposes different locations to open new facilities.

Detection of Alzheimer’s disease onset using MRI and PET neuroimaging:longitudinal data analysis and machine learning

The scientists are dedicated to studying the detection of Alzheimer’s disease onset to find a cure, or at the very least, medication that can slow the progression of the disease. This article explores the effectiveness of longitudinal data analysis, artificial intelligence, and machine learning approaches based on magnetic resonance imaging and positron emission tomography neuroimaging modalities for progression estimation and the detection of Alzheimer’s disease onset. The significance of feature extraction in highly complex neuroimaging data, identification of vulnerable brain regions, and the determination of the threshold values for plaques, tangles, and neurodegeneration of these regions will extensively be evaluated. Developing automated methods to improve the aforementioned research areas would enable specialists to determine the progression of the disease and find the link between the biomarkers and more accurate detection of Alzheimer’s disease onset.

Randomized MILP framework for Securing Virtual Machines from Malware Attacks

Cloud computing involves remote server deployments with public net-work infrastructures that allow clients to access computational resources.Virtual Machines(VMs)are supplied on requests and launched without interactions from service providers.Intruders can target these servers and establish malicious con-nections on VMs for carrying out attacks on other clustered VMs.The existing system has issues with execution time and false-positive rates.Hence,the overall system performance is degraded considerably.The proposed approach is designed to eliminate Cross-VM side attacks and VM escape and hide the server’s position so that the opponent cannot track the target server beyond a certain point.Every request is passed from source to destination via one broadcast domain to confuse the opponent and avoid them from tracking the server’s position.Allocation of SECURITY Resources accepts a safety game in a simple format as input andfinds the best coverage vector for the opponent using a Stackelberg Equilibrium(SSE)technique.A Mixed Integer Linear Programming(MILP)framework is used in the algorithm.The VM challenge is reduced by afirewall-based controlling mechanism combining behavior-based detection and signature-based virus detection.The pro-posed method is focused on detecting malware attacks effectively and providing better security for the VMs.Finally,the experimental results indicate that the pro-posed security method is efficient.It consumes minimum execution time,better false positive rate,accuracy,and memory usage than the conventional approach.

Estimating distribution of water uptake with depth of winter wheat by hydrogen and oxygen stable isotopes under different irrigation depths

Crop root system plays an important role in the water cycle of the soil-plant-atmosphere continuum. In this study, com- bined isotope techniques, root length density and root cell activity analysis were used to investigate the root water uptake mechanisms of winter wheat （Triticum aesfivum L.） under different irrigation depths in the North China Plain. Both direct inference approach and multisource linear mixing model were applied to estimate the distribution of water uptake with depth in six growing stages. Results showed that winter wheat under land surface irrigation treatment （Ts） mainly absorbed water from 10-20 cm soil layers in the wintering and green stages （66.9 and 72.0%, respectively）; 0-20 cm （57.0%） in the jointing stage; 0-40 （15.3%） and 80-180 cm （58.1%） in the heading stage; 60-80 （13.2%） and 180-220 cm （35.5%） in the filling stage; and 0-40 （46.8%） and 80-100 cm （31.0%） in the ripening stage. Winter wheat under whole soil layers irrigation treatment （Tw） absorbed more water from deep soil layer than Ts in heading, filling and ripening stages. Moreover, root cell activity and root length density of winter wheat under TW were significantly greater than that of Ts in the three stages. We concluded that distribution of water uptake with depth was affected by the availability of water sources, the root length density and root cell activity. Implementation of the whole soil layers irrigation method can affect root system distribution and thereby increase water use from deeper soil and enhance water use efficiency.

Assessment on Evaluating Parameters of Rice Core Collections Constructed by Genotypic Values and Molecular Marker Information

Eleven evaluating parameters for rice core collection were assessed based on genotypic values and molecular marke＇ information. Monte Carlo simulation combined with mixed linear model was used to eliminate the interference from environment in order to draw more reliable results. The coincidence rate of range （CR） was the optimal parameter. Mean Simpson index （MD）, mean Shannon-Weaver index of genetic diversity （M1） and mean polymorphism information content （MPIC） were important evaluating parameters. The variable rate of coefficient of variation （VR） could act as an important reference parameter for evaluating the variation degree of core collection. Percentage of polymorphic loci （p） could be used as a determination parameter for the size of core collection. Mean difference percentage （MD） was a determination parameter for the reliability judgment of core collection. The effective evaluating parameters for core collection selected in the research could be used as criteria for sampling percentage in different plant germplasm populations.

Genetic mapping of quantitative trait loci in crops

Dissecting the genetic architecture of complex traits is an ongoing challenge for geneticists.Two complementary approaches for genetic mapping,linkage mapping and association mapping have led to successful dissection of complex traits in many crop species.Both of these methods detect quantitative trait loci(QTL) by identifying marker–trait associations,and the only fundamental difference between them is that between mapping populations,which directly determine mapping resolution and power.Based on this difference,we first summarize in this review the advances and limitations of family-based mapping and natural population-based mapping instead of linkage mapping and association mapping.We then describe statistical methods used for improving detection power and computational speed and outline emerging areas such as large-scale meta-analysis for genetic mapping in crops.In the era of next-generation sequencing,there has arisen an urgent need for proper population design,advanced statistical strategies,and precision phenotyping to fully exploit high-throughput genotyping.

Assessment of different genetic distances in constructing cotton core subset by genotypic values

One hundred and sixty-eight genotypes of cotton from the same growing region were used as a germplasm group to study the validity of different genetic distances in constructing cotton core subset. Mixed linear model approach was employed to unbiasedly predict genotypic values of 20 traits for eliminating the environmental effect. Six commonly used genetic distances(Euclidean,standardized Euclidean,Mahalanobis,city block,cosine and correlation distances) combining four commonly used hierarchical cluster methods(single distance,complete distance,unweighted pair-group average and Ward's methods) were used in the least distance stepwise sampling(LDSS) method for constructing different core subsets. The analyses of variance(ANOVA) of different evaluating parameters showed that the validities of cosine and correlation distances were inferior to those of Euclidean,standardized Euclidean,Mahalanobis and city block distances. Standardized Euclidean distance was slightly more effective than Euclidean,Mahalanobis and city block distances. The principal analysis validated standardized Euclidean distance in the course of constructing practical core subsets. The covariance matrix of accessions might be ill-conditioned when Mahalanobis distance was used to calculate genetic distance at low sampling percentages,which led to bias in small-sized core subset construction. The standardized Euclidean distance is recommended in core subset construction with LDSS method.

Strategic mining options optimization:Open pit mining, underground mining or both

Near-surface deposits that extend to considerable depths are often amenable to both open pit mining and/or underground mining. This paper investigates the strategy of mining options for an orebody using a Mixed Integer Linear Programming(MILP) optimization framework. The MILP formulation maximizes the Net Present Value(NPV) of the reserve when extracted with(i) open pit mining,(ii) underground mining, and(iii) concurrent open pit and underground mining. Comparatively, implementing open pit mining generates a higher NPV than underground mining. However considering the investment required for these mining options, underground mining generates a better return on investment than open pit mining. Also, in the concurrent open pit and underground mining scenario, the optimizer prefers extracting blocks using open pit mining. Although the underground mine could access ore sooner, the mining cost differential for open pit mining is more than compensated for by the discounting benefits associated with earlier underground mining.

Saltmarsh vegetation and social environment influence flexible seasonal vigilance strategies for two sympatric migratory curlew species in adjacent coastal habitats

Background:Animals need to adjust their vigilance strategies when foraging between physically contrasting veg-etated and non-vegetated habitats.Vegetated habitats may pose a greater risk for some if vegetation characteristics function as a visual obstruction but benefit others if they serve as protective shelter.Variation in group size,presence of similar species,along with variation in environmental conditions and anthropogenic disturbance can also influence vigilance investment.Methods:In this study,we quantified the vigilance behaviour of two large-bodied,sympatric migratory curlew species-Far Eastern Curlew(Numenius madagascariensis)and Eurasian Curlew(N.arquata)-in vegetated Suaeda salsa saltmarsh and non-vegetated mudflat habitat in Liaohekou National Nature Reserve,China.We used linear mixed models to examine the effects of habitat type,season,tide time,flock size(conspecific and heterospecific),and human disturbance on curlew vigilance investment.Results:Both species spent a higher percentage of time under visual obstruction in S.salsa habitat compared to mudflat habitat but in response,only Far Eastern Curlew increased their percentage of vigilance time,indicating that visual obstruction in this habitat is only a concern for this species.There was no evidence that S.salsa vegetation served as a form of cryptic background colouration since neither species decreased their vigilance effect in S.salsa habitat in spring compared to the autumn migration season.The effect of curlew social environment(i.e.flock size)was habitat dependent since percentage of vigilance time by curlews in saltmarsh increased with both the number of individual curlews and number of other birds present,but not in mudflat habitat.Conclusions:We conclude that both migratory curlew species exhibit a flexible vigilance adjustment strategy to cope with the different environmental and social conditions of adjacent and sharply contrasting coastal habitats,and that the trade-off between the risks of foraging and the abundance of prey may be a relatively common phenom-enon in these and other shorebird populations.

Mapping Soil Organic Carbon Stocks of Northeastern China Using Expert Knowledge and GIS-based Methods

The main aim of this paper was to calculate soil organic carbon stock(SOCS) with consideration of the pedogenetic horizons using expert knowledge and GIS-based methods in northeastern China.A novel prediction process was presented and was referred to as model-then-calculate with respect to the variable thicknesses of soil horizons(MCV).The model-then-calculate with fixed-thickness(MCF),soil profile statistics(SPS),pedological professional knowledge-based(PKB) and vegetation type-based(Veg) methods were carried out for comparison.With respect to the similar pedological information,nine common layers from topsoil to bedrock were grouped in the MCV.Validation results suggested that the MCV method generated better performance than the other methods considered.For the comparison of polygon based approaches,the Veg method generated better accuracy than both SPS and PKB,as limited soil data were incorporated.Additional prediction of the pedogenetic horizons within MCV benefitted the regional SOCS estimation and provided information for future soil classification and understanding of soil functions.The intermediate product,that is,horizon thickness maps were fluctuant enough and reflected many details in space.The linear mixed model indicated that mean annual air temperature(MAAT) was the most important predictor for the SOCS simulation.The minimal residual of the linear mixed models was achieved in the vegetation type-based model,whereas the maximal residual was fitted in the soil type-based model.About 95% of SOCS could be found in Argosols,Cambosols and Isohumosols.The largest SOCS was found in the croplands with vegetation of Triticum aestivum L.,Sorghum bicolor(L.) Moench,Glycine max(L.) Merr.,Zea mays L.and Setaria italica(L.) P.Beauv.

Modeling Individual Patient Count/Rate Data over Time with Applications to Cancer Pain Flares and Cancer Pain Medication Usage

The purpose of this article is to investigate approaches for modeling individual patient count/rate data over time accounting for temporal correlation and non-constant dispersions while requiring reasonable amounts of time to search over alternative models for those data. This research addresses formulations for two approaches for extending generalized estimating equations (GEE) modeling. These approaches use a likelihood-like function based on the multivariate normal density. The first approach augments standard GEE equations to include equations for estimation of dispersion parameters. The second approach is based on estimating equations determined by partial derivatives of the likelihood-like function with respect to all model parameters and so extends linear mixed modeling. Three correlation structures are considered including independent, exchangeable, and spatial autoregressive of order 1 correlations. The likelihood-like function is used to formulate a likelihood-like cross-validation (LCV) score for use in evaluating models. Example analyses are presented using these two modeling approaches applied to three data sets of counts/rates over time for individual cancer patients including pain flares per day, as needed pain medications taken per day, and around the clock pain medications taken per day per dose. Means and dispersions are modeled as possibly nonlinear functions of time using adaptive regression modeling methods to search through alternative models compared using LCV scores. The results of these analyses demonstrate that extended linear mixed modeling is preferable for modeling individual patient count/rate data over time, because in example analyses, it either generates better LCV scores or more parsimonious models and requires substantially less time.