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PubMed1995

Prediction of protein secondary structure from circular dichroism spectra: an attempt to solve the problem of the best-fitting reference protein subsets.

In least-squares fitting of protein circular dichroism (CD) spectra using basis CD spectra for the respective secondary structure components, as given by reference proteins of known structural composition, good fits of the CD spectrum do not necessarily correspond to appropriate fits of the underlying structural composition of a test protein. In an attempt to overcome this problem, CD similarity measures were used to construct a subset of five reference CD spectra which permitted three-component fitting of the CD and prediction of the relative magnitude of total beta-sheet (antiparallel + parallel) and total other structure (beta-turn + remainder), relative to helix, in the test protein. A backpropagation neural network (BPN) was also trained to make this prediction. In subsequent five-component fitting of the CD spectrum, using a Monte Carlo method to generate subsets of reference proteins from the working data set, only those secondary structure fits which conformed to the consensus prediction of the CD similarity measures and the BPN were accepted. The method enhanced the fitting of antiparallel beta-sheet and beta-turn for 16 proteins, compared to the variable selection method of P. Manavalan and W. C. Johnson (1987, Anal. Biochem. 167, 76-85). Some other proteins were less well fitted. Improvement in results is expected with a larger representation of feasible basis CD spectra in the working reference proteins.

Circular Dichroism↗
PubMed2000

Pk-fit: a pharmacokinetic/pharmacodynamic and statistical data analysis software.

This paper presents a new software, Pk-fit, to fit nonlinear models to kinetic and dynamic data. Directly connected to the spreadsheet, a statistical software component manager is available. In the data manager, Pk-fit includes the noncompartmental analysis module, the compartmental analysis module, the nonlinear kinetic process module, the drug absorption module, the pharmacodynamic data modeling module, the simultaneous fitting module, and the user-defined library module. In this paper, we present a detailed comparison of the kinetic analysis using Pk-fit and common software packages, PCNONLIN, MODFIT, MKMODEL, NONMEM, and SIPHAR, based on the textbook published by Gabrielsson in 1992, "Compilation of Analyzed Data Sets for Pharmacokinetic Software Evaluation." The comparison of Pk-fit with the reference softwares revealed that the parameters and their dispersion found with Pk-fit are consistent with the ones estimated with the other programs. In conclusion, Pk-fit constituted a valid tool for pharmacokinetic/pharmacodynamic data analysis.

Data Interpretation, Statistical↗
PubMed1995

Adaptive walks with noisy fitness measurements.

Adaptive walks constitute an optimization technique for searching a space of possible solutions, for example, a space of different molecules. The goal is to find a point in space (a molecule) that is optimal or near-optimal in some property, generally referred to as the 'fitness', such as its ability to bind to a given receptor. Adaptive walking, an analog of natural selection, is a powerful technique for searching landscapes. However, errors in the measurements will cause errors in the adaptive walks. Mutant molecules of higher fitness may be ignored or mutants of lower fitness may be accepted. To examine the effect of measurement error on adaptive walks, we simulate single-agent hill-climbing walks on NK landscapes of varying ruggedness where Gaussian noise is added to the fitness values to model measurement error. We consider both constant measurement noise and noise whose variance decays exponentially with fitness. We show that fitness-independent noise can cause walks to 'melt' off the peaks in a landscape, wandering in larger regions as the noise increases. However, we also show that a small amount of noise actually helps the walk perform better than with no noise. For walks in which noise decreases exponentially with fitness, the most characteristic behavior is that the walk meanders throughout the landscape until it stumbles across a point of relatively high fitness, then it climbs the landscape towards the nearest peak. Finally, we characterize the balance between selection pressure and noise and show that there are several classes of walk dynamic behavior.

Algorithms↗
PubMed2003

Sociality and individual fitness in yellow-bellied marmots: insights from a long-term study (1962-2001).

Theoretical and empirical studies suggest that the age of first reproduction (the age at which reproduction begins) can have a substantial influence on population dynamics and individual fitness. Using complete survival and reproductive histories of 428 female yellow-bellied marmots (Marmota flaviventris) from a 40-year study (1962-2001), we investigated causes and fitness consequences of delayed maturity. Most females (86%) died without reproducing. The age of first reproduction of females that survived to reproduce at least once (n=60) ranged from 2 to 6 years. Females maturing later did not have a larger lifetime number of successful reproductive events or offspring production, nor did they experience improved survival. Females reproducing earlier had a higher fitness than those that delayed maturity. These results suggest that the net cost of early maturity was less than fitness benefits associated with early onset of reproduction, and that age of first reproduction in our study population is under substantial directional selection favoring early maturity. We conclude that female yellow-bellied marmots delay onset of reproduction not because of fitness benefits of foregoing reproduction at an earlier age, but due to the social suppression of reproduction by older, reproductive females, which enhances their own fitness to the detriment of the fitness of young females. Our results indicate that female yellow-bellied marmots that survive to reproduce may act to increase their own direct fitness, and that social suppression of reproduction of young females is a part of that strategy.

Adaptation, Physiological↗
PubMed1996

Reproductive fitness in familial schizophrenia.

BACKGROUND: Reproductive fitness is an important factor in understanding inheritance in genetic disorders. The purpose of this study was to determine whether fitness is reduced in familial schizophrenia (FS) and if fitness in siblings differs from the norm. METHOD: The number of offspring in 36 subjects with RDC schizophrenia or schizoaffective disorder (SZ) and their 101 siblings from large FS families was compared with age-adjusted census figures. RESULTS: Fitness in the SZ group was significantly reduced: 23% of expected in males and 51% of expected in females. Fitness of unaffected siblings was within census expectations. However, female siblings with schizophrenia spectrum features had increased fitness over census norms. Reduced fitness was correlated with low marital rates, poor functioning and positive symptoms. CONCLUSIONS: These results indicate that reduced fitness is an important genetic force in FS and is likely inherent to the illness. Sex differences are important and would need to be considered when examining maternal and paternal transmission of schizophrenia. The results support a proposed high mutation rate for schizophrenia, consistent with a dynamic mutation mechanism.

Adolescent↗
PubMed2004

Enhancement of initial stability of press-fit femoral stems using injectable calcium phosphate cement: an in vitro study in dog bones.

In this in vitro study we evaluated the initial stability of cementless femoral stems using an injectable calcium phosphate (Ca-P) cement. The cement was not used to form a cement mantle as is routinely done in PMMA cemented prostheses but functioned as an additive to fill the small gaps that exist between a press-fit placed titanium plasma sprayed implant and the bone bed. Six pair of Beagle femora were used in this study. In a random fashion, one femur of each pair was used for placement of a prosthesis without Ca-P cement, the contralateral was used for press-fit placement after injection of the calcium phosphate cement into the intramedullary canal. The reconstructions were placed in a MTS testing machine, tilted 15 degrees in varsus and 15 degrees of endorotation to obtain a physiological load on the femoral head. The load was applied stepwise from zero to a maximum of 100, 250 and 400 N, respectively. At each loading step the load was applied dynamically at a frequency of 1 Hz for 30 min. Between the loading steps, the load was removed for 10 min to allow elastic recovery. The stability of the stems was determined at each loading step with roentgen-stereophotogrammetric analysis. Results showed that with the prostheses without Ca-P cement the most important displacements were movement into varus (max. 818 microm under 400 N) and subsidence (max. 587 microm under 400 N). The displacements showed large variation. After unloading some elastic recovery occurred. In the specimens with Ca-P cement, displacements were negligible. As determined by an F-test the variations found were significantly smaller for the press-fit+Ca-P cement relative to the press-fit prosthesis at all loading steps (p<0.05). A paired t-test revealed significant differences in the mentioned displacements between the press-fit- and press-fit+Ca-P cement prosthesis at a loading with 400 N (P<0.05). On the basis of these results we conclude that the use of Ca-P cement increases the initial stability of press-fit inserted plasma-sprayed femoral prostheses and corrects for the high variability in displacements found with press-fit insertion of these femoral hip prostheses.

Adhesiveness↗
PubMed2004

Thermodynamical interpretation of evolutionary dynamics on a fitness landscape in a evolution reactor, I.

A theory for describing evolution as adaptive walks by a finite population with M walkers (M > or = 1) on an anisotropic Mt. Fuji-type fitness landscape is presented, from a thermodynamical point of view. Introducing the 'free fitness' as the sum of a fitness term and an entropy term and 'evolutionary force' as the gradient of free fitness on a fitness coordinate, we demonstrate that the behavior of these theoretical walkers is almost consistent with the thermodynamical schemes. The major conclusions are as follows: (1) an adaptive walk (=evolution) is driven by an evolutionary force in the direction in which free fitness increases; (2) the expectation of the climbing rate obeys an equation analogous to the Einstein relation in Brownian motion; (3) the standard deviation of the climbing rate is a quantity analogous to the mean thermal energy of a particle, kT (x constant). In addition, on the interpretation that the walkers climb the landscape by absorbing 'fitness information' from the surroundings, we succeeded in quantifying the fitness information and formulating a macroscopic scheme from an informational point of view.

Adaptation, Biological↗
PubMed2005

Thermodynamical interpretation of evolutionary dynamics on a fitness landscape in an evolution reactor, II.

In our previous report [Aita, T., Morinaga, S., Hosimi, Y., 2004. Thermodynamical interpretation of evolutionary dynamics on a fitness landscape in an evolution reactor I. Bull. Math. Biol. 66, 1371-1403], an analogy between thermodynamics and adaptive walks on a Mt. Fuji-type fitness landscape in an artificial selection system was presented. Introducing the 'free fitness' as the sum of a fitness term and an entropy term and 'evolutionary force' as the gradient of free fitness on a fitness coordinate, we demonstrated that the adaptive walk (=evolution) is driven by the evolutionary force in the direction in which free fitness increases. In this report, we examine the effect of various modifications of the original model on the properties of the adaptive walk. The modifications were as follows: first, mutation distance d was distributed obeying binomial distribution; second, the selection process obeyed the natural selection protocol; third, ruggedness was introduced to the landscape according to the NK model; fourth, a noise was included in the fitness measurement. The effect of each modification was described in the same theoretical framework as the original model by introducing 'effective' quantities such as the effective mutation distance or the effective screening size.

Algorithms↗
PubMed2003

Low dietary quality among older adults with self-perceived ill-fitting dentures.

OBJECTIVE: To examine dietary quality and nutrient intakes of participants wearing dentures with and without poor fit as determined by questionnaire and dental exam. DESIGN: Nutrient intakes, Healthy Eating Index (HEI) score, and serum nutrient values were examined among individuals wearing either adequate- or poor-fitting dentures and individuals who had at least 18 teeth. SUBJECTS/SETTING: Data was collected from 4,820 participants in the Third National Health and Nutrition Examination Survey ages 50 years and older with at least 18 teeth (n=3,207) or those wearing dentures (n=1,613), who responded to a questionnaire about denture fit and had their dentures evaluated by a dentist. STATISTICAL ANALYSES PERFORMED: Analysis of covariance and multivariate linear regression analyses were used to examine associations between individuals fully dentate, wearing good-or ill-fitting dentures, and nutritional status indicators. RESULTS: The group with self-perceived ill-fitting dentures compared with the group with natural teeth had significantly lower total HEI (66.5 vs 68.5 P<.002), vegetables (6.3 vs 6.8 P<.01), and variety scores (7.8 vs 8.2 P<.02); lower ascorbic acid (P<.009) and carotene intakes (P<.004). The group with self-perceived good-fitting dentures did not differ significantly from the dentate group. However, both groups wearing dentures had significantly lower serum levels of vitamins C and E, beta carotene, folate, lutein, and lycopene/zeaxanthin compared with the dentate group. APPLICATIONS/CONCLUSIONS: Dietary quality and intake of certain nutrients was poorer among the group with self-perceived ill-fitting dentures than among those wearing adequate dentures or those with natural teeth. Administering a simple questionnaire to patients about their perceptions of denture fit may be useful in identifying denture wearers at increased risk of dietary inadequacy.

Aged↗
PubMed2005

Predictive value of the user seal check in determining half-face respirator fit.

Guidelines issued by the Centers for Disease Control and Prevention and the World Health Organization state that healthcare workers should wear N95 masks or higher-level protection during all contact with suspected cases of severe acute respiratory syndrome. Before use, the manufacturer recommends performing a user seal check to ensure that the mask is fitted correctly. This study aimed to test the ability of the user seal check to detect poorly fitting masks. This study is a retrospective review of a mask-fitting programme carried out in the intensive care unit of the Prince of Wales Hospital in Hong Kong. In this programme, all staff were tested with two types of N95 mask and one type of N100 mask. The results of the documented user seal check were then compared with the formal fit-test results from a PortaCount. Using a PortaCount reading of 100 as the criterion for a correctly fitted mask, the user seal check wrongly indicated that the mask fitted on 18-31% of occasions, and wrongly indicated that it did not fit on 21-40% of occasions. These data indicate that the user seal check should not be used as a surrogate fit test. Its usefulness as a pre-use test must also be questioned.

Female↗
PubMed2006

Evaluation of left ventricular function with cardiac magnetic resonance imaging using Fourier fitting.

The aims of this study were to investigate the applicability of Fourier fitting in the magnetic resonance (MR) evaluation of left ventricular (LV) function and to determine the optimal number of harmonics for fitting. Cine cardiac MR imaging was performed in 10 subjects, and an LV time-volume curve was generated. Fourier fitting was applied to the original curve using 1-10 harmonics, and the qualities of the time-volume curve and first-derivative curve were evaluated. LV functional parameters were calculated from curves generated with and without fitting. The quality of the original time-volume curve was good, and Fourier fitting had no substantial effect on functional parameters obtained directly from the time-volume curve such as ejection fraction. The first-derivative curve generated without fitting showed substantial artificial fluctuation. The application of Fourier fitting depressed the fluctuation and tended to decrease estimates of peak ejection rate and peak filling rate. Five or six harmonics appeared to be appropriate for obtaining a high-quality first-derivative curve. In conclusion, Fourier fitting was indicated to aid in reducing the artificial fluctuation of the first-derivative curve generated from cine cardiac MR imaging and to contribute to the evaluation of functional parameters derived from the first-derivative curve.

Adult↗
PubMed2003

Thermodynamical interpretation of an adaptive walk on a Mt. Fuji-type fitness landscape: Einstein relation-like formula holds in a stochastic evolution.

We have theoretically studied the statistical properties of adaptive walks (or hill-climbing) on a Mt. Fuji-type fitness landscape in the multi-dimensional sequence space through mathematical analysis and computer simulation. The adaptive walk is characterized by the "mutation distance" d as the step-width of the walker and the "population size" N as the number of randomly generated d-fold point mutants to be screened. In addition to the fitness W, we introduced the following quantities analogous to thermodynamical concepts: "free fitness" G(W) is identical with W+T x S(W), where T is the "evolutionary temperature" T infinity square root of d/lnN and S(W) is the entropy as a function of W, and the "evolutionary force" X is identical with d(G(W)/T)/dW, that is caused by the mutation and selection pressure. It is known that a single adaptive walker rapidly climbs on the fitness landscape up to the stationary state where a "mutation-selection-random drift balance" is kept. In our interpretation, the walker tends to the maximal free fitness state, driven by the evolutionary force X. Our major findings are as follows: First, near the stationary point W*, the "climbing rate" J as the expected fitness change per generation is described by J approximately L x X with L approximately V/2, where V is the variance of fitness distribution on a local landscape. This simple relationship is analogous to the well-known Einstein relation in Brownian motion. Second, the "biological information gain" (DeltaG/T) through adaptive walk can be described by combining the Shannon's information gain (DeltaS) and the "fitness information gain" (DeltaW/T).

Animals↗
PubMed1992

Adaptedness, evolution and a hierarchical concept of fitness.

Fitness is a consequence of the adaptedness of an entity to its environment. The fitness of an evolutionary entity, when the entity is defined by a set of attributes determining how it interacts with its environment, is manifested as persistence of those attributes. Two measures of fitness are presented to explicate this concept: (1) an extensive measure of the persistence of the original set of attributes in the individual entity and its descendants, but corrected for evolution; this includes as a special case fitness as used in population genetics; and, (2) an intensive measure that is independent of the abundance of descendant exemplars. Fitness as conceived here is a function of survival time, degree of evolution, and when applicable, reproductive contribution. The rate of fitness increase of an entity will vary inversely with the degree of evolutionary change experienced by the entity, its descendants, or both through time. Adaptive evolution can increase the length of time that fitness accumulates by increasing the survival of descendants possessing all or some of the ancestral attributes. Reproduction, where possible, can increase the number of descendants. This concept of fitness is simple, unambiguous, coherent, and applicable to entities at any hierarchical level of interest to ecologists and evolutionary biologists.

Adaptation, Physiological↗
PubMed2001

Fitness to plead. A prospective study of the inter-relationships between expert opinion, legal criteria and specific symptomatology.

BACKGROUND: Psychiatrists are asked to give opinions as to fitness to plead, a legal concept. There is a dearth of research into fitness to plead in the UK, with no prospective studies and no studies involving the comparison of fit and unfit subjects. In particular, there have been no investigations into the meaning of 'unfit to plead' in terms of psychiatric symptomatology, or as to the relative importance of each legal fitness criterion in psychiatrists' conclusions as to fitness. METHOD: The study comprised a prospective evaluation of 479 consecutive referrals to psychiatrists at court. Individual legal fitness criteria were examined as predictors of unfitness. Associations of unfitness, and of individual legal fitness criteria, were examined with Brief Psychiatric Rating Scale (BPRS) symptom scores. RESULTS: The two most important of the legal criteria in clinical decisions as to unfitness were whether the person could follow the proceedings of the trial or give adequate instructions to their solicitor. The legal criteria concerning trial were more predictive of unfitness than those concerning plea. Unfitness was significantly associated with the presence of positive psychotic symptomatology, in particular conceptual disorganization and delusional thinking, but not with symptoms of anxiety, depression or withdrawal. CONCLUSION: Unfitness is most significantly associated with symptoms affecting comprehension and communication. The fitness criteria could be simplified without loss of power. These results, predominantly concerned with mental illness, may not generalize to the mentally impaired.

Adult↗
PubMed2000

Molecular electronic density fitting using elementary Jacobi rotations under atomic shell approximation

Fitted electron density functions constitute an important step in quantum similarity studies. This fact not only is presented in the published papers concerning quantum similarity measures (QSM), but also can be associated with the success of the developed fitting algorithms. As has been demonstrated in previous work, electronic density can be accurately fitted using the atomic shell approximation (ASA). This methodology expresses electron density functions as a linear combination of spherical functions, with the constraint that expansion coefficients must be positive definite, to preserve the statistical meaning of the density function as a probability distribution. Recently, an algorithm based on the elementary Jacobi rotations (EJR) technique was proven as an efficient electron density fitting procedure. In the preceding studies, the EJR algorithm was employed to fit atomic density functions, and subsequently molecular electron density was built in a promolecular way as a simple sum of atomic densities. Following previously established computational developments, in this paper the fitting methodology is applied to molecular systems. Although the promolecular approach is sufficiently accurate for quantum QSPR studies, some molecular properties, such as electrostatic potentials, cannot be described using such a level of approximation. The purpose of the present contribution is to demonstrate that using the promolecular ASA density function as the starting point, it is possible to fit ASA-type functions easily to the ab initio molecular electron density. A comparative study of promolecular and molecular ASA density functions for a large set of molecules using a fitted 6-311G atomic basis set is presented, and some application examples are also discussed.

Journal Article↗
PubMed2004

The validity of the Neale and Kendler model-fitting approach in examining the etiology of comorbidity.

Given that knowledge regarding the etiology of comorbidity between disorders can have a significant impact on research regarding the classification, treatment, and etiology of the disorders, the ability to reject incorrect hypotheses regarding the causes of comorbidity is very important. A simulation study was conducted to assess the validity of the Neale and Kendler (1995) model-fitting approach in examining the etiology of comorbidity between two disorders. First, data were simulated under the assumptions of the 13 alternative comorbidity models described by Neale and Kendler. Second, model-fitting analyses testing the comorbidity models were conducted on the simulated datasets. Thirteen sets of data with varying model parameters were simulated to test Neale and Kendler's assertion that their model-fitting approach is appropriate across a range of potential prevalences and degrees of familiality. The validity of the model-fitting approach in examining unselected twin data and a combination of selected family data and unselected family data was explored. The model-fitting approach successfully discriminated several classes of comorbidity models, although discrimination between models within classes of related models was less accurate. Results suggest that the model-fitting approach can be a useful tool in examining the etiology of the comorbidity between disorders if the caveats of the present study's results are considered carefully. As predicted by Neale and Kendler, variations in the disorder prevalences and familial correlations did not affect the validity of their model-fitting approach, but affected the power to discriminate the correct model. As suggested by Neale and Kendler, the model-fitting approach can be applied to both unselected and selected data and to both twin and family data.

Comorbidity↗
PubMed2002

When fit indices and residuals are incompatible.

Standard chi-square-based fit indices for factor analysis and related models have a little known property: They are more sensitive to misfit when unique variances are small than when they are large. Consequently, very small correlation residuals indicating excellent fit can be accompanied by indications of bad fit by the fit indices when unique variances are small. An empirical example of this incompatibility between residuals and fit indices is provided. For illustrative purposes, an artificial example is provided that yields exactly the same correlation residuals as the empirical example but has larger unique variances. For this example, the fit indices indicate excellent fit. A theoretical explanation for this phenomenon is provided using relationships between unique variances and eigenvalues of the fitted correlation matrix.

Humans↗
PubMed2000

How persuasive is a good fit? A comment on theory testing.

Quantitative theories with free parameters often gain credence when they closely fit data. This is a mistake. A good fit reveals nothing about the flexibility of the theory (how much it cannot fit), the variability of the data (how firmly the data rule out what the theory cannot fit), or the likelihood of other outcomes (perhaps the theory could have fit any plausible result), and a reader needs all 3 pieces of information to decide how much the fit should increase belief in the theory. The use of good fits as evidence is not supported by philosophers of science nor by the history of psychology; there seem to be no examples of a theory supported mainly by good fits that has led to demonstrable progress. A better way to test a theory with free parameters is to determine how the theory constrains possible outcomes (i.e., what it predicts), assess how firmly actual outcomes agree with those constraints, and determine if plausible alternative outcomes would have been inconsistent with the theory, allowing for the variability of the data.

Humans↗