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Analysis of neighborhood dynamics of forest ecosystems using likelihood methods and modeling.

Advances in computing power in the past 20 years have led to a proliferation of spatially explicit, individual-based models of population and ecosystem dynamics. In forest ecosystems, the individual-based models encapsulate an emerging theory of "neighborhood" dynamics, in which fine-scale spatial interactions regulate the demography of component tree species. The spatial distribution of component species, in turn, regulates spatial variation in a whole host of community and ecosystem properties, with subsequent feedbacks on component species. The development of these models has been facilitated by development of new methods of analysis of field data, in which critical demographic rates and ecosystem processes are analyzed in terms of the spatial distributions of neighboring trees and physical environmental factors. The analyses are based on likelihood methods and information theory, and they allow a tight linkage between the models and explicit parameterization of the models from field data. Maximum likelihood methods have a long history of use for point and interval estimation in statistics. In contrast, likelihood principles have only more gradually emerged in ecology as the foundation for an alternative to traditional hypothesis testing. The alternative framework stresses the process of identifying and selecting among competing models, or in the simplest case, among competing point estimates of a parameter of a model. There are four general steps involved in a likelihood analysis: (1) model specification, (2) parameter estimation using maximum likelihood methods, (3) model comparison, and (4) model evaluation. Our goal in this paper is to review recent developments in the use of likelihood methods and modeling for the analysis of neighborhood processes in forest ecosystems. We will focus on a single class of processes, seed dispersal and seedling dispersion, because recent papers provide compelling evidence of the potential power of the approach, and illustrate some of the statistical challenges in applying the methods.

Computer Simulation↗

Observation and mathematical description of the acceleration phenomenon in batch respirograms associated with ammonium oxidation.

Two-step nitrification models are generally calibrated using short-term respirometric batch experiments. Important discrepancies appear between model predictions and experimental observations just after the pulse addition since a fast transient in the OUR profile is experimentally observed. Acceleration of the OUR appears ongoing between the substrate addition and attainment of the maximum OUR value. Among the several phenomena that could contribute to this observation, the most probable cause is the limitation of reducing equivalents required for maximal ammonia monooxygenase activity at the time of substrate addition. Ignoring acceleration would result in large parameter estimation errors from respirometric batch experiments. This work proposes a simple methodology to successfully describe (not to explain) the acceleration phenomenon estimating only two parameters. This methodology consists of introducing a Gaussian-like expression in the model.

Ammonia↗

Bioactuarial models of national mortality time series data.

The incidence and prevalence of chronic degenerative disease in America's elderly population are important determinants of the need for long-term care health services. Though a wide range of data on disease incidence and prevalence is available from a variety of different health studies, a Congressional Budget Office study (1977) concluded that data limitations are a major factor in the lack of precise national long-term care cost estimates. In this paper, we present a modeling strategy to make better use of existing data by using biomedically motivated actuarial models to integrate multiple data sources into a comprehensive model of population health dynamics. The development of a specific model for application to a disease of interest involves three distinct phases. First, biomedical evidence and data are used to specify a cohort model of chronic disease morbidity and mortality. Second, the model is fitted to cohort mortality data with estimates of its parameters being derived by maximum likelihood procedures. Third, the morbidity distribution in the national population is generated from the parameter estimates. The model is used to examine lung cancer morbidity and mortality patterns for U. S. white and non-white males in 1977. A review of these patterns suggests that, based on current concepts of lung cancer incidence and natural history, over 2 percent of white males in the United States have lung cancer at some stage of development, though most of this prevalence is pre-clinical.

Actuarial Analysis↗

[MEG inverse solution using Gauss-Newton algorithm modified by Moore-Penrose inversion].

In magnetoencephalogram(MEG) basic studies, it is an important issue to estimate magnetic source parameters by inverse solution. It is known that the magnetic field equations are nonlinear, thus explicit solutions are difficult to obtain. However optimization methods are available to this parameter estimation. In many usually used nonlinear local optimization algorithms, Gauss-Newton's is of fast convergent speed. When this algorithm is used, the singularity of the Jacobien matrix about the minimum least square error must be considered carefully. If the matrix is singular, the equation for searching direction has no general solution. One way to overcome this problem is to use negative gradient as searching direction, but it may cause descent of convergent speed. Another way is known as Levenberg-Marquardt algorithm which makes the matrix non-singular by adding some improved factors to it. In this paper we utilize Moore-Penrose inversion for the solution of iterative searching direction equation. In appendix we demonstrate that the searching direction obtained by the proposed method is successful. Computer simulation also demonstrates that by reasonable selection of initial iterative values, the modified Gauss-Newton algorithm is effective for MEG inverse solution in the case with one or two source dipoles.

Algorithms↗

Does plasma leptin concentration predict the nutritional status of hemodialyzed patients with chronic renal failure?

BACKGROUND: Patients with chronic renal failure are characterized by hyperleptinemia, and leptin is presumed to be an anorectogenic hormone. The aim of this prospective study was to analyze changes in body composition and parameters of nutritional status in relation to changes in plasma leptin concentration in uremic patients during the first year of hemodialysis therapy. MATERIAL/METHODS: 21 patients (10 F, 11 M, mean age 51+/- 3 years, BMI 24.3+/-1.1 kg/m2) were enrolled in this study. Nutritional status was evaluated by anthropometric parameters, estimation of body composition (DEXA method), and biochemical markers (plasma concentrations of albumin, cholesterol, triglycerides, transferrin) and plasma leptin concentration. Tests were performed twice: immediately after initiation of hemodialysis therapy and again 12 months later. RESULTS: After 12 months of hemodialysis therapy, the changes in body mass (-2.6+/-0.8 kg; p=0.23), total fat mass (TFM) (-0.3+/-0.8 kg; p=0.68) and total lean mass (TLM) (+0.5+/-0.8 kg; p=0.26) were insignificant. Plasma leptin concentration and estimated biochemical nutritional parameters did not change markedly. A significant positive correlation was noticed between TFM and plasma leptin concentration (R=0.521; p=0.02) at the beginning of hemodialysis therapy and between changes in TFM and plasma leptin concentration (R=0.466; p=0.04) after one year. CONCLUSIONS: Plasma leptin concentration does not predict forthcoming changes in body composition and changes of nutritional status in uremic patients after the first year of hemodialysis.

Body Composition↗

FEDMA--a simple algorithm for theoretical modeling of linear metabolic pathways: from fuzzy data sets to prediction and experiment.

A theoretical model of a chain of irreversible Michaelis-Menten reactions proceeding inside a living cell, taking cell growth, division and subcellular compartmentation into account, was proposed. It became a basis for the construction of a "fuzzy" enzymatic data-modeling algorithm (FEDMA) - a procedure allowing the estimation of missing parameter values for the modeled system, in accordance both with the derived theoretical rules and the available experimental data. The obtained tool was tested to model the heme biosynthesis pathway in Saccharomyces cerevisiae, where about 40% of parameters remain unknown. The missing parameters estimated by means of FEDMA fall in the range of expected values.

Algorithms↗

[Computerized image analysis in recognition and classification of aeroallergens].

UNLABELLED: In medical practice and research, it would be convenient to receive pollen identification and monitoring results in much shorter time than it comes from human identification. Image based analysis is one of the approaches to an automated identification scheme for pollens grain and pattern recognition on such images is widely used as a powerful tool. PURPOSE OF THE STUDY: The goal of such attempt is to provide accurate, fast recognition and classification and counting of pollen grains by computer system for monitoring. METHODS AND MATERIAL: The isolated pollen grain are objects extracted from microscopic image by CCD camera and PC computer under proper condition for further analysis. RESULTS: The algorithms are based on the knowledge from feature vector analysis of estimated parameters calculated from grain characteristics including morphological features, surface features and other applicable estimated characteristics. Segmentation algorithms specially tailored to pollen object characteristics provide exact descriptions of pollen characteristics (border and internal features) already used by human expert. The specific characteristics and its measures are statistically estimated for each object. Some low level statistics for estimated local and global measures of the features establish feature space. Some special care should be paid on choosing these feature and on constructing the feature space to optimize the number of subspaces for higher recognition rates in low-level classification for type differentiation of pollens grain. CONCLUSIONS: The results of estimated parameters of feature vector in low dimension space for some typical pollen types are presented as well as some effective and fast recognition results of performed experiments for different pollens. The findings show the evidence of using proper chosen estimators of tailored characteristics for good enough classification measures even for low dimensional classifiers for type differentiation of pollens grain.

Humans↗

Estimation of genetic parameters among reproductive and growth traits in yearling heifers.

Growth and reproductive data were obtained on 779 beef heifers at the San Juan Basin Research Center, Hesperus, Co. Genetic parameters were estimated for age of puberty (AOP), age of first calving (AOC), julian day of first calving (DOC), julian day of second calving (DOSC), birth weight, weaning weight, yearling weight, and average daily gain from weaning to yearling and to cycling weights. The least squares model included birth year, age of dam and breed as fixed effects, sire/breed as a random variable, and day of birth and percent inbreeding as covariates. Day of birth was not included in the analyses of AOC, DOC or DOSC. Paternal half-sib estimates of heritability were: AOP, .10 +/- .17; AOC, .01 +/- .12; DOC, .09 +/- .13 and DOSC, .36 +/- .18. Genetic and phenotypic correlations were generally favorable, but genetic correlations were variable with large standard errors. Inbreeding had a detrimental effect on reproductive traits, and a seasonal effect was present for AOP.

Age Factors↗

Pharmacodynamics and population pharmacokinetics of enalapril and lisinopril.

The di-acid metabolite of enalapril, enalaprilat, and its lysine analogue lisinopril are potent inhibitors of angiotensin converting enzyme (ACE); they do not contain sulphydryl groups. Both drugs can be assayed by high pressure liquid chromatography and by radioimmunoassay and plasma ACE inhibition remains stable under normal storage conditions. It is therefore possible to study their pharmacokinetics as well as their pharmacodynamic effects in man. Enalaprilat and lisinopril as well as ACE activity have been measured in blood taken during the course of two studies of the effects of these drugs on blood pressure and autonomic responsiveness. A population pharmacokinetic analysis approach applied to a few concentration-time data points in each of a relatively large number of subjects provided average population parameter estimates of the absorption rate constant, volume of distribution and clearance which correspond closely with the limited published data based on conventional pharmacokinetic approaches. It also provided estimates of pharmacodynamic parameters and the concentration of the drug required to produce a 50% ACE inhibition. Population drug concentration data obtained in the course of early clinical evaluations of new drugs may provide a rational basis for dosage regimens with improved efficacy and, in particular, reduced concentration-related toxic effects.

Adult↗

A likelihood ratio test for a patterned covariance matrix in a multivariate growth-curve model.

In a multivariate growth-curve model, the estimator of the parameter matrix is a function of the matrix of the sums of squares and of the cross-products due to error. However, if the assumption of a patterned covariance matrix is valid, then the parameter estimator does not depend on the error matrix. A likelihood ratio test of this patterned covariance matrix is constructed and its distribution is discussed. A numerical example is provided in which the design consists of two treatment groups, with three repeated measures being taken of the three response variables.

Growth↗

Likelihood-based inference for the genetic relative risk based on affected-sibling-pair marker data.

Using genetic marker data from affected sibling pairs, we study likelihood-based linkage analysis under quasi-recessive, quasi-dominant, and general single-locus models. We use an epidemiologic parameterization under a model where the marker locus is closely linked to the putative disease susceptibility gene. This model and parameterization allow inferences about the relative risk associated with the susceptible genotype. We base inferences on approximate likelihoods that focus on the affected siblings in the sibship and, using these likelihoods, we derive closed-form maximum likelihood estimators for model parameters and closed-form likelihood ratio statistics for tests that the relative risk associated with the susceptible genotype is one. Under the general single-locus model, our likelihood ratio test is the same as the iteratively computed triangle test proposed by Holmans (1993, American Journal of Human Genetics 52, 362-374) for the case where marker identity-by-descent is known; our derivation gives a closed form for the test statistic. We present quartiles of the distribution of parameter estimates and critical values for the exact null distribution of our likelihood ratio test statistics; we also give large-sample approximations to their null distributions. We show that the powers of our likelihood ratio tests exceed the powers of more commonly used nonparametric affected-sibling-pair tests when the data meet the inheritance model assumptions used to derive the test; we also show that our tests' powers are robust to violation of model assumptions. We conclude that our model-based inferences provide a practical alternative to more common affected-sibling-pair tests when investigators have some knowledge about the mode of inheritance of a disease and that our methods may sometimes be useful for comparing the genetic relative risk with environmental relative risks.

Disease Susceptibility↗

Including geophysical data in ground water model inverse calibration.

A nonlinear regression method is developed that can be used to estimate parameters of a ground waterflow model from a combination of observations of hydrological variables and observations of geophysical properties that are functionally related with the hydraulic conductivity. The procedure estimates: parameters characterizing the hydraulic conductivity field (e.g., zonal or pilot point values); geophysical properties that have been observed and that are functionally related with the hydraulic conductivity parameters; and a few parameters of the function that relates the hydraulic conductivity parameters with the geophysical properties (the type of function is assumed known). A fidelity factor, sigma(r)2, of a term of the minimized objective function reflects the faith one has in the validity of this functional relationship. The estimation methodology has been tested by means of synthetic models. The experimental results demonstrate that the number of estimated hydraulic conductivity parameters can be increased by adding geophysical observations to the set of hydrological observations that are traditionally used for model calibration. The improvement of the estimated hydraulic conductivity field and the simulated hydraulic head field can be significant but is dependent on the number, the locations, and the uncertainty of geophysical observations. The sensitivity of the estimation results to the value of sigma(r) is small for the studied problems except when the uncertainty of geophysical observations is high. In the latter case, a large sigma(r) value was found to be optimal to avoid that hydraulic conductivity estimates are closely tied to corresponding but highly uncertain geophysical observations.

Calibration↗

Comparing regression methods for the two-stage clonal expansion model of carcinogenesis.

In the statistical analysis of cohort data with risk estimation models, both Poisson and individual likelihood regressions are widely used methods of parameter estimation. In this paper, their performance has been tested with the biologically motivated two-stage clonal expansion (TSCE) model of carcinogenesis. To exclude inevitable uncertainties of existing data, cohorts with simple individual exposure history have been created by Monte Carlo simulation. To generate some similar properties of atomic bomb survivors and radon-exposed mine workers, both acute and protracted exposure patterns have been generated. Then the capacity of the two regression methods has been compared to retrieve a priori known model parameters from the simulated cohort data. For simple models with smooth hazard functions, the parameter estimates from both methods come close to their true values. However, for models with strongly discontinuous functions which are generated by the cell mutation process of transformation, the Poisson regression method fails to produce reliable estimates. This behaviour is explained by the construction of class averages during data stratification. Thereby, some indispensable information on the individual exposure history was destroyed. It could not be repaired by countermeasures such as the refinement of Poisson classes or a more adequate choice of Poisson groups. Although this choice might still exist we were unable to discover it. In contrast to this, the individual likelihood regression technique was found to work reliably for all considered versions of the TSCE model.

Adult↗

A QSPR study of the p solute polarity parameter to estimate retention in HPLC.

A Quantitative Structure-Property Relationship (QSPR) model is developed to calculate the solute polarity parameter p of a set of 233 compounds of a very different chemical nature. The proposed model, derived from multiple linear regression, contains four descriptors calculated from the molecular structure and the well-known hydrophobicity parameter log P(o/w). According to the statistics obtained with the prediction set, the model has a very good prediction capacity (R(2) = 0.954, F = 889, n = 45, and SD = 0.27). The study shows that log P(o/w) and hydrogen bond acidity of the solutes are the most relevant descriptors to predict p values. This p parameter is embodied in a general equation to predict retention in reversed-phase liquid chromatography (RP-HPLC). It describes analyte retention exclusively on the basis of mobile phase/analyte/stationary phase polar interactions. Equations and procedures to determine polarity of both chromatographic phases had been successfully developed previously. Therefore, the proposed QSPR model for p estimation becomes a very useful tool in RP-HPLC optimization of procedures and methods in the everyday analytical work.

Journal Article↗

NORA: a simple and reliable parameter for estimating renal output with or without frusemide challenge.

The aim of this study was to evaluate a simple parameter describing renal output, namely NORA (normalized residual activity). We first compared, in a simulated model, different parameters of transit to an ideal standard; we then compared, in a clinical study, NORA and output efficiency. 123I-hippurate, 99Tcm-DTPA and 99Tcm-MAG3 plasma curves, each with two levels of renal clearance, were convoluted by means of different types of simulated retention functions, with different mean transit times. On the reconstructed renograms, several parameters reflecting renal transit were determined and compared with mean transit time. In a second step, in 33 patients, we compared output efficiency and NORA (i.e. the residual renal activity), normalized by the renal activity at 2 min. These two parameters were calculated at the end of the renogram, at the end of the frusemide test and after the micturition phase. In the simulated model, both output efficiency and NORA were only slightly influenced by the level of overall renal function. In the clinical study, a good correlation was found between output efficiency and NORA, whatever part of the study considered (renogram, frusemide test, post-voiding image). NORA is a simple and reliable parameter that allows quantification of renal output; it is almost independent of the level of renal function and can be used whatever the timing of the frusemide injection.

Adolescent↗

STADEERS: a software package for the statistical design of experiments pertaining to the estimation of parameters in rate expressions that describe enzyme-catalyzed processes.

This paper describes a computational algorithm (STADEERS--STAtistical Design of Experiments in Enzyme ReactorS) for the statistical design of biochemical engineering experiments. The type of experiment that qualifies for this package involves a batch reaction catalyzed by a soluble enzyme where the activity of the enzyme decays with time. Assuming that both the catalytic action and the deactivation of the enzyme obey known rate expressions, the present code is helpful in the process of obtaining estimates of the kinetic parameters by providing as output the times at which samples should be withdrawn from the reacting mixture. Starting D-optimal design is used as a basis for the statistical approach. This BASIC code is a powerful tool when fitting a rate expression to data because it increases the effectiveness of experimentation by helping the biochemical kineticist obtain data points with the largest possible informational content.

Algorithms↗

Prediction of transmitting abilities for Holstein type traits.

Heritabilities and genetic and phenotypic correlations among 14 linear type traits were estimated from Holstein Association data by multiple trait REML. Data used for parameter estimation were records of 779,391 daughters of 871 sires included in the January 1988 sire evaluation. Each daughter was represented by her appraisal closest to 30 mo of age. Highest heritability was .37 for stature, and lowest was .10 for foot angle. Gains in reliability from using correlated traits in multiple trait prediction were large for some traits (up to 60% for foot angle for cows). Final score variance parameters were estimated from 953,596 records, which were 43% of records included in the national sire evaluation. Sire models that adjusted or did not adjust for merit of mates were compared. Heritability of final score was .27 with adjustment for merit of mates by subtraction of predicted transmitting ability of dam from daughter's record compared with .29 if mate was ignored. Evaluations for type for several popular older sires were reduced moderately by adjustment for merit of mates, but estimated genetic trend increased slightly. An improved genetic grouping procedure that considers group effects as inherited was adapted for use in sire models. Parameter estimates and models presented were implemented by the Holstein Association for computing July 1988 genetic evaluations for linear traits and final score.

Analysis of Variance↗