Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Fitting”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,747 records · Page 97Linked to original sources
PubMed2006

Refinement of protein structures by iterative comparative modeling and CryoEM density fitting.

We developed a method for structure characterization of assembly components by iterative comparative protein structure modeling and fitting into cryo-electron microscopy (cryoEM) density maps. Specifically, we calculate a comparative model of a given component by considering many alternative alignments between the target sequence and a related template structure while optimizing the fit of a model into the corresponding density map. The method relies on the previously developed Moulder protocol that iterates over alignment, model building, and model assessment. The protocol was benchmarked using 20 varied target-template pairs of known structures with less than 30% sequence identity and corresponding simulated density maps at resolutions from 5A to 25A. Relative to the models based on the best existing sequence profile alignment methods, the percentage of C(alpha) atoms that are within 5A of the corresponding C(alpha) atoms in the superposed native structure increases on average from 52% to 66%, which is half-way between the starting models and the models from the best possible alignments (82%). The test also reveals that despite the improvements in the accuracy of the fitness function, this function is still the bottleneck in reducing the remaining errors. To demonstrate the usefulness of the protocol, we applied it to the upper domain of the P8 capsid protein of rice dwarf virus that has been studied by cryoEM at 6.8A. The C(alpha) root-mean-square deviation of the model based on the remotely related template, bluetongue virus VP7, improved from 8.7A to 6.0A, while the best possible model has a C(alpha) RMSD value of 5.3A. Moreover, the resulting model fits better into the cryoEM density map than the initial template structure. The method is being implemented in our program MODELLER for protein structure modeling by satisfaction of spatial restraints and will be applicable to the rapidly increasing number of cryoEM density maps of macromolecular assemblies.

Amino Acid Sequence↗
PubMed2004

Structural cost of shoot modules and its implications on plant potential fitness in a Mediterranean perennial shrub, Retama sphaerocarpa (L.) Boiss.

This paper introduces a methodology to analyse the structural costs on plant potential fitness, empirically exemplified in the hierarchical shoot system of a Mediterranean perennial plant, Retama sphaerocarpa (L.) Boiss. During growing season every year (March-August), the terminal shoot (which is the basic unit of growth) develops inflorescences, flowers and fruits, as well as new shoots (first-, second- and third-order branching shoots) which have the potential to "behave" as terminal shoots in the following year. Different morphological and demographical aspects of the modules within the terminal shoot were measured in 100 terminal shoots selected from different plants of a natural population of R. sphaerocarpa. Complementary samples of 100 shoots of different branching orders were collected to obtain biomass estimations of the terminal shoots. We propose a simple procedure to estimate structural cost (biomass investment) on plant potential fitness (flowering buds) as a methodology for interpreting and comparing the consequences on fitness of different plant growth patterns. The results of this study exemplify how differential allocation patterns among plant structural modules, depending on their position within the shoot system, can be quantified to estimate their influence upon plant potential fitness.

Biomass↗
PubMed2005

The distribution of fitness effects among beneficial mutations in Fisher's geometric model of adaptation.

Recent models of adaptation at the DNA sequence level assume that the fitness effects of new mutations show certain statistical properties. In particular, these models assume that the distribution of fitness effects among new mutations is in the domain of attraction of the so-called Gumbel-type extreme value distribution. This assumption has not, however, been justified on any biological or theoretical grounds. In this note, I study random mutation in one of the simplest models of mutation and adaptation-Fisher's geometric model. I show that random mutation in this model yields a distribution of mutational effects that belongs to the Gumbel type. I also show that the distribution of fitness effects among rare beneficial mutations in Fisher's model is asymptotically exponential. I confirm these analytic findings with exact computer simulations. These results provide some support for the use of Gumbel-type extreme value theory in studies of adaptation and point to a surprising connection between recent phenotypic- and sequence-based models of adaptation: in both, the distribution of fitness effects among rare beneficial mutations is approximately exponential.

Adaptation, Physiological↗
PubMed2006

Fitness of antimicrobial-resistant Campylobacter and Salmonella.

Campylobacter and Salmonella are the most commonly reported bacterial causes of human foodborne infections, and increasing proportions of these pathogens become resistant to medically important antimicrobial agents, imposing a burden on public health. Acquisition of resistance to antibiotics affects the adaptation and evolution of Salmonella and Campylobacter in various environments. Many resistance-conferring mutations entail a biological fitness cost, while others (e.g. fluoroquinolone resistance in Campylobacter) have no cost or even enhanced fitness. In Salmonella, the fitness disadvantage due to antimicrobial resistance can be restored by acquired compensatory mutations, which occur both in vitro and in vivo. The compensated or even enhanced fitness associated with antibiotic resistance may facilitate the spread and persistence of antimicrobial-resistant Salmonella and Campylobacter in the absence of selection pressure, creating a significant barrier for controlling antibiotic-resistant foodborne pathogens.

Animals↗
PubMed2007

Early clinical and radiological pulmonary complications following breast cancer radiation therapy: NTCP fit with four different models.

OBJECTIVE: To fit four different NTCP (Normal Tissue Complication Probability) models to prospectively collected data on short-term pulmonary complications following breast cancer radiotherapy (RT). MATERIALS/METHODS: Four hundred and seventy-five breast cancer patients, referred to the Radiotherapy Department at Stockholm Söder Hospital (1994-1998) for adjuvant post-operative RT were prospectively followed for pulmonary complications 1, 4 and 7 months after the completion of RT. Eighty-seven patients with complete dose-volume histogram (DVH) of the ipsilateral lung were selected for the present analysis. Mean dose to the ipsilateral lateral lung ranged from 2.5 to 18Gy (median 12Gy). Three different endpoints were considered: (1) clinical pneumonitis scored according to CTC-NCIC criteria: asymptomatic (grade 0) vs grade 1 and grade 2; (2) radiological changes assessed with diagnostic chest X-ray: no/slight radiological changes vs moderate/severe; (3) radiological changes assessed with CT: no/slight vs moderate/severe. Four NTCP models were used: the Lyman model with DVH reduced to the equivalent uniform dose (LEUD), the Logit model with DVH reduced to EUD, the Mean Lung Dose (MLD) model and the Relative Seriality (RS) model. The data fitting procedure was done using the maximum likelihood analysis. The analysis was done on the entire population (n=87) and on a subgroup of patients treated with loco-regional RT (n=44). RESULTS: 24/87 patients (28%) developed clinical pneumonitis; 28/81 patients (35%) had radiological side effects on chest X-rays and 11/75 patients (15%) showed radiological density changes on Computed Tomography (CT). The analysis showed that the risk of clinical pneumonitis was a smooth function of EUD (calculated from DVH using n=0.86+/-0.10, best fit result). With LEUD, the relationship between EUD and NTCP could be described with a D(50) of 16.4Gy+/-1.1Gy and a steepness parameter m of 0.36+/-0.7. The results found in the overall population were substantially confirmed in the subgroup of patients treated with loco-regional RT. CONCLUSIONS: A large group of prospective patient data (87 pts), including grade 1 pneumonitis, were analysed. The four NTCP models fit quite accurately the considered endpoints. EUD or the mean lung dose are robust and simple parameters correlated with the risk of pneumonitis. For all endpoints the D(50) values ranged in an interval between 10 and 20Gy.

Breast Neoplasms↗
PubMed2004

Curve-fitting of Fourier manipulated spectra comprising apodization, smoothing, derivation and deconvolution.

We present a general method for curve-fitting Fourier manipulated spectra, comprising apodized, smoothed, derivatised and deconvoluted spectra. The analytical expressions of Fourier manipulated bands in the spectral domain, needed for the curve-fitting, are usually very complex or do not even exist; hence an accurate curve-fit of Fourier manipulated spectra becomes unfeasible. Our strategy is to construct both the model and their derivatives in the Fourier domain, where they have simple and general expressions, and then Fourier transform them back to the spectral domain. The first benefit of this approach is the accurate curve-fitting of Fourier deconvoluted spectra, a main step in the secondary structure estimation of proteins by FTIR spectroscopy.

Models, Statistical↗
PubMed2004

Spatial interactions within modular organisms: genetic heterogeneity and organism fitness.

Modular organisms are composed of iterated units of construction that vary in their spatial arrangement. This variation is expected to affect the fitness of modular organisms due to interactions among neighboring modules and the potential for such organisms to be genetically heterogeneous. We devise a spatially explicit model to investigate how spatial interactions among neighboring modules affect organism fitness. We show that fitness is strongly dependent on the spatial arrangement of modules in both genetically homogeneous and heterogeneous organisms, and that the magnitude of the variation is dependent on the strength of interactions among modules. Organism fitness is more variable with interactions among modules that are symmetrical (each affects each other in the same directions) than with asymmetrical interactions (neighbors affect each other in different directions). We conclude by discussing potential extension of the present framework to a general dynamic model of spatially structured organism development.

Adaptation, Physiological↗
PubMed2005

Plasma leptin, ghrelin and adiponectin concentrations in young fit racehorses versus mature unfit standardbreds.

Concentrations of hormones related to energy homeostasis may differ between populations with varied body compositions, acting as signals to increase or decrease energy intake and/or expenditure. How these parameters correlate with body composition in horses and how they vary in fit (F) versus unfit (UF) Standardbred racehorses is unclear. The purpose of this study was to test the hypothesis that plasma concentrations of glucose (GLU), insulin (INS), cortisol (CORT), ghrelin (GHRL), adiponectin (ADIP) and leptin (LEP) would be correlated with body composition and differ in fit (F) versus unfit (UF) horses. Fasting plasma samples were taken from 12 unfit (11 +/- 2 years, 521 +/- 77 kg; mean +/- SD) and 34 fit (4 +/- 2 years, 475 +/- 83 kg) Standardbred horses. GHRL, LEP, ADIP, INS and CORT concentrations were measured using radioimmunoassay. GLU concentration was measured using colorometric kits. Body composition data included body weight, body condition score (BCS), and percent fat (%fat) calculated using rump fat thickness measured ultrasonically and the Westervelt equation. Data were analyzed using Pearson Product moment and Student's t tests. There were no differences (P>0.05) between F and UF horses for the plasma concentrations of CORT (69 +/- 14 versus 76 +/- 23 microg/dL), INS (7.2 +/- 3.5 versus 7.1 +/- 1.8 microIU/mL) or GLU (90 +/- 6 versus 86 +/- 7 mg/dL). Plasma GHRL and ADIP concentrations were greater (P<0.05) in F versus UF horses (54 +/- 27 versus 33 +/- 17 pg/mL and 1820 +/- 276 versus 1333 +/- 249 ng/mL, respectively), while plasma LEP was lower in F versus UF (1.0 +/- 0.6 versus 4.4 +/- 2.4 ng/mL, P<0.001). BCS and %fat were lower in F versus UF horses (4.8 +/- 0.3 versus 6.7 +/- 0.5 and 11.9 +/- 1.6 versus 15.4 +/- 2.5%, respectively), with no correlation between %fat and GHRL (-0.12, P>0.05), although there was a positive correlation between %fat and LEP (+0.72, P<0.05), and a negative correlation between %fat and ADIP (-0.40, P<0.05). The data show that in comparing fit and unfit horses, there are variations in body composition as well as concurrent and substantial differences in the concentrations of hormones, cytokines, and other parameters related to the control of appetite and feed intake.

Adiponectin↗
PubMed2005

A segmented form of foot-and-mouth disease virus interferes with standard virus: a link between interference and competitive fitness.

Serial passage of foot-and-mouth disease virus (FMDV) in BHK-21 cells at high multiplicity of infection resulted in dominance of particles containing defective RNAs that were infectious by complementation in the absence of standard viral RNA. In the present study, we show that the defective FMDV particles interfere with replication of the cognate standard virus. Coinfections of defective FMDV with standard FMDV mutants that differ up to 151-fold in relative fitness have documented that the degree of interference is higher for low fitness than for high fitness standard virus. These comparisons suggest a likely overlap between those mechanisms of intracellular competition that underlie viral interference and those expressed as fitness differences between two viruses when they coinfect the same cells. Interference may contribute to the selective pressures that help maintain dominance of segmented defective RNAs over the standard FMDV genome.

Animals↗
PubMed1999

Who participates in the Get Fit to Ski program?

The Get Fit to Ski program, run by the Australian Physiotherapy Association, is a pre-season conditioning program designed for, and marketed to, alpine sports participants. This paper describes the characteristics of Get Fit to Ski program participants in Melbourne during 1997. All participants were surveyed prior to commencement of the program to determine their demographics, skiing experience, recent injury history, self-perceived fitness level and expectations of the program. Descriptive statistics and chi-square tests were used to analyse the data. Mostly, participants are experienced skiers from a professional background who attend the program to improve their fitness and recovery for subsequent days of skiing. Understanding the characteristics of program participants helps with marketing and program development which could potentially result in a greater number of satisfied participants.

Journal Article↗
PubMed1999

Lack-of-fit testing of ion chromatographic calibration curves with inexact replicates.

Calibration studies involve the preparation and analysis of replicates for multiple concentrations of standards. Curves that are fitted through the data are evaluated for their adequacy of fit. A helpful test is a lack-of-fit procedure, which is performed easily by most statistical software. When coupled with Radj2, the procedure differentiates between data that are not linear and those that are simply noisy. The test requires data from exact replicates of the various standard levels involved. However, in ppt-level ion chromatography, the above condition may be impossible to meet. With the common anions (e.g., chloride, nitrite), the working standards must be prepared by mass and all liquids must be poured; transfer pipets contaminate at these concentrations. Since it is virtually impossible to pour out the desired mass exactly, final concentrations will vary slightly. Consequently, a different approach is needed for lack-of-fit testing. This paper discusses reasonable alternatives and applies them to actual data.

Analysis of Variance↗
PubMed1996

The response of bone in primates around unloaded dental implants supporting prostheses with different levels of fit.

Implant failure as a consequence of prosthetic loading following clinical determination of successful stage I healing is poorly understood. A basic premise of accepted prosthetic protocol is passive connection of multiunit prostheses to the implant support. To better understand mechanical factors related to implant failure, this basic passivity premise was experimentally tested prior to study of functional loading research. The purpose of this preliminary study was to measure the bone response around implants placed in the mandible of baboons that supported prostheses exhibiting two levels of fit and not loaded occlusally. Screw-retained prostheses that exhibited a mean linear distortion of 38 microns and 345 microns made up the fit and misfit groups respectively. The results failed to distinguish a difference in bone response between the two levels of prosthetic fit. Although the finding can be argued as a sample size limitation, the data strongly suggest an opposite response than is clinically expected and, consequently, does not warrant the use of additional animals in this initial study. Because the design of this study does not mimic the clinical application of misfitting prostheses (where dynamic functional loads are superimposed with misfit loads), it cannot be inferred that, in clinical application, fit does not alter the osseointegrated interface. Ongoing investigation of failure due to nonpassive connections under dynamic loading conditions of mastication will help clarify the clinical significance of passivity.

Analysis of Variance↗
PubMed1997

The effect of storage time of removable partial denture wax pattern on the accuracy of fit of the cast framework.

STATEMENT OF PROBLEM: Situations may arise in dental laboratories that could result in a time lapse between preparing the wax pattern of the removable partial denture framework and its casting into the cobalt-chromium alloy. PURPOSE: This study investigated the effect of storage time of the wax pattern before casting and the influence of the palatal major connector design on the accuracy of its fit on the master casts. MATERIAL AND METHODS: Forty-two frameworks were prepared with two designs of major connectors, which were divided into three subgroups according to the storage time of the wax patterns: 24 hours, 1 week, and 1 month. Discrepancies in the fit of the connectors to their respective casts were measured at specific locations for both connector designs. RESULTS: In both framework design groups, there was a significant deterioration in fit (p < 0.0005) of the major connectors with the increase in storage time of their wax patterns on their respective refractory casts. Gap discrepancies were more pronounced towards the center of the palate. CONCLUSIONS: The greatest discrepancies appeared at the middle sections of the connectors more than at the lateral section (p < 0.0005). Furthermore, frameworks with modified palatal plate major connectors exhibited greater inaccuracies in their fit than those with the anterior posterior palatal strap design, as evidenced by the increase in mean gap discrepancies under the palatal plate design (p < 0.0005).

Analysis of Variance↗
PubMed1988

Free fitness that always increases in evolution.

I here introduce a free fitness function in population biology, which monotonically increases with time and takes its maximum at the evolutionary equilibrium. By suitably defining an "index" for each state, the free fitness is expressed as the average index plus an entropy term. In many cases, the index has a biologically clear meaning, such as the logarithmic population mean fitness. The technique is applicable to any Markov process model (either continuous or discrete) with a positive steady state. I discuss four examples from various branches of population biology: (1) one-locus-two-allele system of population genetics with mutation, selection, and random genetic drift; (2) evolutionary dynamics of quantitative characters; (3) a molecular evolution model; and (4) an ecological succession model. Introducing free fitness clarifies the balance between systematic forces (e.g. natural selection or successional trend toward the climax) and disturbing processes (e.g. random drift).

Animals↗
PubMed1999

Sister chromatid exchange data fit with a mixture of Poisson distributions.

Bowman et al. [K.O. Bowman, Wesley Eddings, Marvin A. Kastenbaum, L. R. Shenton. Sister chromatid exchange data and Gram-Charlier series, Mutat. Res., 403 (1998) 159-169.] have shown that a Gram-Charlier modification of a negative binomial distribution gives a reasonable fit to counts of sister chromatid exchange (SCE) data originally presented by Bender et al. [M.A. Bender, R.J. Preston, R. C. Leonard, B.E. Pyatt, P.C. Gooch, On the distribution of spontaneous SCE in human peripheral blood lymphocytes, Mutat. Res., 281 (1992) 227-232. ]. Here we show that a mixture of a generalized Poisson distributions also fits the data. Advantages of the generalized Poisson mixture include a simplified model involving only four parameters which fits the data more closely according to the chi-squared goodness-of-fit criterion.

Female↗
PubMed1988

Breast cancer estrogen receptor assays: assessment of a direct hyperbolic fitting to analyse multipoint binding data.

Analysis of breast cancer estrogen receptor multipoint binding assay is performed by fitting experimental data to a hyperbolic model derived from the law of mass action. The calculations performed on a microcomputer are carried out from the total bound and free ligand concentrations. The parameters estimated by hyperbolic fitting, receptor concentration N and constant of dissociation K, well agree with those obtained by Scatchard's transformation. N and K derived from hyperbolic analysis are much less susceptible to the influence of experimental errors. The method is more reliable at low receptor concentrations. The main advantage of the hyperbolic fitting is to simplify the technical methodology in clinical laboratory practice; there is no need to determine the non-specific bindings experimentally. Calculations can be easily automated on any laboratory microcomputer. Assays of any kind of receptor could be analysed by the hyperbolic fitting when the physical-chemical equilibrium between receptor, nonsaturable component and ligand can be approximated by a two-component model.

Breast Neoplasms↗
PubMed2001

Quantifying amorphous content of lactose using parallel beam X-ray powder diffraction and whole pattern fitting.

The objective of this study was to demonstrate the applicability of parallel beam X-ray powder diffraction (XRPD) and a new method for whole pattern fitting to the quantification of the residual amount of amorphous content in a pharmaceutical solid using lactose as a model system. Lactose monohydrate, prepared by slurry conversion of anhydrous lactose, was mixed with different amounts of amorphous lactose produced by lyophilization. X-ray powder diffractograms of each mixture were recorded and analyzed by whole pattern fitting using Percentage Crystallinity Determination Software from Kratos Analytical Inc. The polycapillary X-ray optic, which provides a parallel beam of X-radiation, has advantages over Bragg-Brentano Optics with respect to sample height artifacts. Significant shifts in peak position with changes in sample height of lactose monohydrate were observed using Bragg-Brentano Optics while no change was detected for the polycapillary X-ray optic. A technique to normalize all diffractograms to have the same total integrated intensity was necessary to eliminate tube fluctuation effects. After normalization, the amorphous content of lactose in the range of 1-10% was reproducibly predicted (small standard deviation between samplings) using whole pattern fitting. The limit of detection was calculated to be 0.37% amorphous content. The results indicated that parallel beam XRPD and whole pattern fitting can provide accurate analysis of relatively small amounts of amorphous content in pharmaceuticals compared to typical XRPD analysis.

Lactose↗
PubMed1999

Empirical fitting with polycon II lenses.

Historically, rigid gas permeable (RGP) lens parameters have been determined through trial fitting. Nevertheless, practitioners would likely welcome the opportunity to empirically fit RGP lenses if they could be confident of the outcome. This clinical investigation sought to evaluate the potential success of empirically fitting 9.0 mm Polycon II lenses. Based on both objective and subjective outcomes, this study suggests that empirically fitting the larger 9.5 mm Polycon II design, in combination with a lid attachment approach, would yield greater initial patient satisfaction.

Journal Article↗