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PubMed2001

Genetic epidemiology and schizophrenia: a study of reproductive fitness.

Genetic epidemiological studies have demonstrated markedly reduced rates in reproduction among schizophrenic patients. According to evolutionary theory, behavioral and psychological phenotypes are selected based on ecological "fit". Where differential survival or reproductive success exists, genotype frequencies are altered in subsequent generations. In the case of schizophrenia, lower rates of reproduction constitute a negative selection factor that should reduce genes in the population associated with the expression of the disease--ultimately leading to decreases in prevalence. However, studies reveal a stable prevalence of about 1% over time. Attempts to explain the apparent contradiction between negative selection and stable prevalence have taken several forms. One explanation suggests that reproductive rates in relatives of schizophrenic patients are increased--compensating for reproductive loss in affected family members. Family data from schizophrenic patients at the Maryland Psychiatric Research Center were compared with those of healthy volunteers and volunteers with schizophrenia spectrum personality (SSP) disorders. Controlling for important socio-cultural and demographic variables, a multiple regression model revealed a significant increase in the number of siblings associated with schizophrenia. No differences in reproductive fitness were found among normal and SSP volunteers. This observed pattern in reproductive fitness provides one mechanism by which prevalence rates can remain stable despite lower reproductive rates among individuals with schizophrenia. Evidence of increased reproductive fitness in relatives suggests the need to consider the complex interactions of proximate and ultimate (evolutionary) mechanisms in the expression of schizophrenia.

Adult↗
PubMed1997

On the reliability of affinity and efficacy estimates obtained by direct operational model fitting of agonist concentration-effect curves following irreversible receptor inactivation.

Recently, Zernig and colleagues (1996) (J Pharmacol Toxicol Meth 35: 223-237) suggested that for the estimation of agonist affinity and efficacy, the method of simultaneously fitting of concentration-effect curves from control and irreversible antagonist-treated tissues to the operational model of agonism is superior to other analytical approaches. In the present study, we have evaluated the limitations of this simultaneous curve fitting method. Simulation studies showed that this method can be only employed with confidence when the upper asymptotes of the control curves display minimal variation between tissues, which makes its practical utility rather limited. The unreliability of the simultaneous fitting procedure was further underscored with the analysis of experimental data obtained from the interaction between noradrenaline and phenoxybenzamine in rat isolated aorta. The lack of robustness of the parameter estimates showed that under standard experimental conditions the outcomes of simultaneous model fitting are highly dependent on between-tissue variations of the upper asymptotes of the control curves and, therefore, may be unreliable. Therefore, whenever possible, a multiple curve design should be adopted, in which control and treated curves are obtained in one tissue and provide enough information for an independent estimation of affinity and efficacy that is free of intertissue differences.

Adrenergic alpha-Agonists↗
PubMed1997

Fast numerical algorithms for fitting multiresolution hybrid shape models to brain MRI.

In this paper, we present new and fast numerical algorithms for shape recovery from brain MRI using multiresolution hybrid shape models. In this modeling framework, shapes are represented by a core rigid shape characterized by a superquadric function and a superimposed displacement function which is characterized by a membrane spline discretized using the finite-element method. Fitting the model to brain MRI data is cast as an energy minimization problem which is solved numerically. We present three new computational methods for model fitting to data. These methods involve novel mathematical derivations that lead to efficient numerical solutions of the model fitting problem. The first method involves using the nonlinear conjugate gradient technique with a diagonal Hessian preconditioner. The second method involves the nonlinear conjugate gradient in the outer loop for solving global parameters of the model and a preconditioned conjugate gradient scheme for solving the local parameters of the model. The third method involves the nonlinear conjugate gradient in the outer loop for solving the global parameters and a combination of the Schur complement formula and the alternating direction-implicit method for solving the local parameters of the model. We demonstrate the efficiency of our model fitting methods via experiments on several MR brain scans.

Algorithms↗
PubMed1998

QTL mapping of genotype-environment interaction for fitness in Drosophila melanogaster.

A fundamental assumption of models for the maintenance of genetic variation by environmental heterogeneity is that selection favours alternative alleles in different environments. It is not clear, however, whether such antagonistic pleiotropy is common. We mapped quantitative trait loci (QTLs) causing variation for reproductive performance in each of three environmental treatments among a set of 98 recombinant inbred (RI) lines derived from a cross between two D. melanogaster laboratory strains. The three treatments were standard medium at 25 degrees C, ethanol-supplemented medium at 25 degrees C, and standard medium at 18 degrees C. The RI lines showed highly significant genotype-environment interaction for the fitness measure. Of six QTLs with significant effects on fitness in at least one of the environments, five had significantly different effects at the different temperatures. In each case, the QTL by temperature interaction arose because the QTL had stronger effects at one temperature than at the other. No evidence for QTLs with opposite fitness effects in different environments was found. These results, together with those of recent studies of crop plants, suggest that antagonistic pleiotropy is a relatively uncommon form of genotype-environment interaction for fitness, but additional studies of natural populations are needed to confirm this conclusion.

Animals↗
PubMed2005

Fitness effects and transmission routes of a microsporidian parasite infecting Drosophila and its parasitoids.

A microsporidian infection was discovered in laboratory cultures of Drosophila species. Ultrastructural examination suggested it belonged to the poorly characterized species Tubulinosema kingi, and morphological and sequence data are presented. We explored how T. kingi affected the fitness of Drosophila melanogaster and D. subobscura, as well as the fitness of 2 of their parasitoids, Asobara tabida and Pachycrepoideus vindemiae. In Drosophila, infections caused changes in most of the traits we looked at that were associated with fitness, in particular causing a 34-55% reduction in early-life fecundity. Parasitoid fitness was affected more severely by infection than that of their hosts, with pupal mortality in particular increasing by 75-89%. We investigated the most important routes of transmission for T. kingi in a laboratory setting. Letting Drosophila larvae feed on medium contaminated with spores from infected dead flies resulted in 100% infection. Low levels of transmission (<10%) were found between larvae, and vertically between mothers and their offspring. Parasitoids developing in infected hosts all became infected, but infected adults were neither able to transmit the pathogen to their offspring nor to their offspring's Drosophila host, either directly, or via contamination of the ovipositor or other body parts. A field survey of Drosophila and their parasitoids in southern England revealed no natural infections. We discuss the potential importance of Microsporidia in parasitoid-host interactions, and for those working with Drosophila in the laboratory.

Animals↗
PubMed1999

Fitting logistic IRT models: small wonder.

State-of-the-art item response theory (IRT) models use logistic functions exclusively as their item response functions (IRFs). Logistic functions meet the requirements that their range is the unit interval and that they are monotonically increasing, but they impose a parameter space whose dimensions can only be assigned a metaphorical interpretation in the context of testing. Applications of IRT models require obtaining the set of values for logistic function parameters that best fit an empirical data set. However, success in obtaining such set of values does not guarantee that the constructs they represent actually exist, for the adequacy of a model is not sustained by the possibility of estimating parameters. This article illustrates how mechanical adoption of off-the-shelf logistic functions as IRFs for IRT models can result in off-the-shelf parameter estimates and fits to data. The results of a simulation study are presented, which show that logistic IRT models can fit a set of data generated by IRFs other than logistic functions just as well as they fit logistic data, even though the response processes and parameter spaces involved in each case are substantially different. An explanation of why logistic functions work as they do is offered, the theoretical and practical consequences of their behavior are discussed, and a testable alternative to logistic IRFs is commented upon.

Humans↗
PubMed2002

Fluctuating asymmetry as an indicator of fitness: can we bridge the gap between studies?

There is growing evidence from both experimental and non-experimental studies that fluctuating asymmetry does not consistently index stress or fitness. The widely held--yet poorly substantiated--belief that fluctuating asymmetry can act as a universal measure of developmental stability and predictor of stress-mediated changes in fitness, therefore staggers. Yet attempts to understand why the reported relationships between fluctuating asymmetry, stress and fitness are so heterogeneous--i.e. whether the associations are truly weak or non-existent or whether they become confounded during different stages of the analytical pathways remain surprisingly scarce. Hence, we attempt to disentangle these causes, by reviewing the various statistical and conceptual factors that are suspected to confound potential relationships between fluctuating asymmetry, stress and fitness. Two main categories of factors are discerned: those associated with the estimation of developmental stability through fluctuating asymmetry and those associated with the effects of genotype and environment on developmental stability. Next, we describe a series of statistical tools that have recently been developed to help reduce this noise. We argue that the current lack of a theoretical framework that predicts if and when relationships with developmental stability can be expected, urges for further theoretical and empirical research, such as on the genetic architecture of developmental stability in stressed populations. If the underlying developmental mechanisms are better understood, statistical patterns of asymmetry variation may become a biologically meaningful tool.

Animals↗
PubMed2006

Biexponential fitting of diffusion-ordered NMR data: practicalities and limitations.

High resolution diffusion-ordered NMR spectroscopy (HR-DOSY) generally uses monoexponential fitting of the diffusional attenuation of pulsed-field gradient stimulated echo spectra and can, thus, only give proper separation of signals in the diffusion domain where the individual peaks are well-resolved in the spectral domain. In principle, it should be possible to resolve the decays of coincident spectral peaks by multiexponential fitting, but the well-known fundamental difficulties in such a separation are exacerbated by instrumental distortions of the signal decay. The limitations imposed on biexponential fitting by finite signal-to-noise ratio and by the distortion of the theoretical form of the signal attenuation as a result of pulsed-field gradient nonuniformity are explored, and the improvement in DOSY spectra produced using biexponential fitting afforded by compensating for the latter are illustrated.

1-Propanol↗
PubMedDate not supplied

Assessing model fit by cross-validation.

When QSAR models are fitted, it is important to validate any fitted model-to check that it is plausible that its predictions will carry over to fresh data not used in the model fitting exercise. There are two standard ways of doing this-using a separate hold-out test sample and the computationally much more burdensome leave-one-out cross-validation in which the entire pool of available compounds is used both to fit the model and to assess its validity. We show by theoretical argument and empiric study of a large QSAR data set that when the available sample size is small-in the dozens or scores rather than the hundreds, holding a portion of it back for testing is wasteful, and that it is much better to use cross-validation, but ensure that this is done properly.

Journal Article↗
PubMed2006

Fit of four curve-linear models to decay profiles for pest control substances in soil.

Experiments that investigate the pattern of degradation of pest control substances in soil are often undertaken to estimate the persistence of compounds in the environment. Mathematical models are typically fit to decay data to facilitate the interpretation of the results and make predictions concerning the environmental fate of xenobiotics in soil. Four mathematical models were fit to 61 data sets to compare their performance in conforming to empirical patterns of degradation of pest control substances in soil. The use of composite residual plots allowed comparisons of the performance of the different models over many data sets. While an exponential model, estimated using nonlinear regression, fit many data sets very well, a shift-log, biexponential, and Monod equation appears superior in many cases, and systematic deviations from data sets are often less evident with the latter models. A knowledge of the patterns of bias typically exhibited by each model across many data sets may be useful for selecting models with reduced bias when fitting individual data sets.

Linear Models↗
PubMed1998

Evolution of competitive fitness in experimental populations of E. coli: what makes one genotype a better competitor than another?

An important problem in microbial ecology is to identify those phenotypic attributes that are responsible for competitive fitness in a particular environment. Thousands of papers have been published on the physiology, biochemistry, and molecular genetics of Escherichia coli and other bacterial models. Nonetheless, little is known about what makes one genotype a better competitor than another even in such well studied systems. Here, we review experiments to identify the phenotypic bases of improved competitive fitness in twelve E. coli populations that evolved for thousands of generations in a defined environment, in which glucose was the limiting substrate. After 10,000 generations, the average fitness of the derived genotypes had increased by approximately 50% relative to the ancestor, based on competition experiments using marked strains in the same environment. The growth kinetics of the ancestral and derived genotypes showed that the latter have a shorter lag phase upon transfer into fresh medium and a higher maximum growth rate. Competition experiments were also performed in environments where other substrates were substituted for glucose. The derived genotypes are generally more fit in competition for those substrates that use the same mechanism of transport as glucose, which suggests that enhanced transport was an important target of natural selection in the evolutionary environment. All of the derived genotypes produce much larger cells than does the ancestor, even when both types are forced to grow at the same rate. Some but not all, of the derived genotypes also have greatly elevated mutation rates. Efforts are now underway to identify the genetic changes that underlie those phenotypic changes, especially substrate specificity and elevated mutation rate for which there are good candidate loci. Identification and subsequent manipulation of these genes may provide new insights into the reproducibility of adaptive evolution, the importance of co-adapted gene complexes, and the extent to which distinct phenotypes (e.g., substrate specificity and cell size) are affected by the same mutations.

Adaptation, Physiological↗
PubMed2002

Sensitivity of molecular docking to induced fit effects in influenza virus neuraminidase.

Many proteins undergo small side chain or even backbone movements on binding of different ligands into the same protein structure. This is known as induced fit and is potentially problematic for virtual screening of databases against protein targets. In this report we investigate the limits of the rigid protein approximation used by the docking program, GOLD, through cross-docking using protein structures of influenza neuraminidase. Neuraminidase is known to exhibit small but significant induced fit effects on ligand binding. Some neuraminidase crystal structures caused concern due to the bound ligand conformation and GOLD performed poorly on these complexes. A 'clean' set, which contained unique, unambiguous complexes, was defined. For this set, the lowest energy structure was correctly docked (i.e. RMSD < 1.5 A away from the crystal reference structure) in 84% of proteins, and the most promiscuous protein (1mwe) was able to dock all 15 ligands accurately including those that normally required an induced fit movement. This is considerably better than the 70% success rate seen with GOLD against general validation sets. Inclusion of specific water molecules involved in water-mediated hydrogen bonds did not significantly improve the docking performance for ligands that formed water-mediated contacts but it did prevent docking of ligands that displaced these waters. Our data supports the use of a single protein structure for virtual screening with GOLD in some applications involving induced fit effects, although care must be taken to identify the protein structure that performs best against a wide variety of ligands. The performance of GOLD was significantly better than the GOLD implementation of ChemScore and the reasons for this are discussed. Overall, GOLD has shown itself to be an extremely good, robust docking program for this system.

Algorithms↗
PubMed2002

A policy-capturing study of the simultaneous effects of fit with jobs, groups, and organizations.

The authors report an experimental policy-capturing study that examines the simultaneous impact of person-job (PJ), person-group (PG), and person-organization (PO) fit on work satisfaction. Using hierarchical linear modeling, the authors determined that all 3 types of fit had important, independent effects on satisfaction. Work experience explained systematic differences in how participants weighted each type of fit. Multiple interactions also showed participants used complex strategies for combining fit cues.

Adult↗
PubMed2005

Socialization tactics, employee proactivity, and person-organization fit.

This study examined the linkage between organizational socialization tactics and person-organization (P-O) fit and examined the moderating influence of employees' proactivity behaviors. Results from a sample of 279 employee-supervisor pairs from 7 organizations in South Korea revealed a positive relationship between institutionalized socialization tactics and P-O fit perceptions. However, the association between firms' socialization tactics and P-O fit was facilitated or negated by several proactive behaviors that employees used to gain control over their environment. For example, employees' positive framing harmonized with institutional tactics to create higher P-O fit, whereas employees who proactively developed strong relationships with their supervisors essentially replaced institutionalized socialization tactics.

Adult↗
PubMedDate not supplied

Relative fitness can decrease in evolving asexual populations of S. cerevisiae.

It is generally accepted from the darwinian theory of evolution that a progressive increase in population adaptation will occur in populations containing genetic variation in fitness, until a stable equilibrium is reached and/or the additive genetic variation is exhausted. However, the theoretical literature of population genetics documents exceptions where mean population fitness may decrease in response to evolutionary changes in gene frequency, due to varying selective coefficients, sexual selection or to epistatic interactions between loci. Until now, no examples of such exceptions have been documented from fitness estimates in either natural or experimental populations. We present here direct evidence that, as a result of epistatic interactions between adaptive mutations, mean population fitness can decrease in asexual evolving populations of the yeast Saccharomyces cerevisiae.

Biological Evolution↗
PubMed1996

Estimate of the genomic mutation rate deleterious to overall fitness in E. coli.

Mutations are a double-edged sword: they are the ultimate source of genetic variation upon which evolution depends, yet most mutations affecting fitness (viability and reproductive success) appear to be harmful. Deleterious mutations of small effect can escape natural selection, and should accumulate in small population. Reduced fitness from deleterious-mutation accumulation may be important in the evolution of sex, mate choice, and diploid life-cycles, and in the extinction of small populations. Few empirical data exist, however. Minimum estimates of the genomic deleterious-mutation rate for viability in Drosophila melanogaster are surprisingly high, leading to the conjecture that the rate for total fitness could exceed 1.0 mutation per individual per generation. Here we use Escherichia coli to provide an estimate of the genomic deleterious-mutation rate for total fitness in a microbe. We estimate that the per-microbe rate of deleterious mutations is in excess of 0.0002.

Animals↗
PubMed1988

The genetic variation and covariation among fitness components in Drosophila melanogaster females and males.

The results presented in this study indicate low to moderate level of heritable variation for the following fitness components in Drosophila melanogaster sampled from natural population: early and late fecundity of females, virility of males and longevity of females and males. The most striking exception from this are high additive genetic variances for preadult developmental duration in both sexes. Females exhibit significant negative genetic correlations between early and late components of fitness. In contrast to females, we did not observe any measurable correlations between components of fitness in males. Our data suggest that genetic covariance structure between fitness components differs by sex. We also observed significant negative correlations between virility of males and late components of female life history.

Animals↗
PubMed1993

A comparison of two in vitro methods for assessing the fitting accuracy of composite inlays.

Composite inlays were fabricated in standardised cavities cut into aluminum and perspex blocks using a computer controlled milling process. Four materials were used to construct the inlays. These were fabricated using an indirect technique following the manufacturers' recommendations, where applicable. In addition, for one of the composites, the fabrication procedures were modified. The fitting accuracy of the restorations was assessed by taking elastomeric impression wash replicas of the luting space and by examination of sectioned restored units using image analysis. The former method indicated significantly reduced fitting accuracy when either use of die spacer or secondary curing was omitted from restoration construction resulting in incomplete seating. The sectioning technique indicated that more factors appeared to significantly reduce fitting accuracy including bulk packing, alteration in curing time, omission to die spacer and the final polishing procedure. This method also provided more specific information concerning sites of premature contact. One material gave rise to significantly greater film thicknesses using both methods of assessment. No direct correlation was found between the two techniques of fit evaluation but both methods taken together provided complementary information.

Acrylic Resins↗