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PubMed2006

[Possibilities and limitations of statistical regression models for the calculation of threshold values for minimum provider volumes].

Inadequate statistical procedures are often applied for the derivation of threshold values in various medical research areas. The frequently applied method to establish threshold values on the basis of simple comparisons between arbitrarily defined low-volume and high-volume groups may be misleading because the result depends on the preceding classification. In this paper, the possibilities and limitations of statistical regression models for the calculation of threshold values are described. The features of these models for the selection of minimum volumes for hospitals or physicians are discussed. Simulated data examples are used to demonstrate that the definition of a useful minimum provider volume should not be based upon a calculated value of purely mathematical meaning without clinically assessing the risk curve. In the application of statistical regression models to retrospective observational data it should be noticed that calculated threshold values are only of a hypothesis-generating character. In order to verify that a minimum provider volume leads to the expected quality improvement, a prospective intervention study is required.

Data Interpretation, Statistical↗
PubMed2006

Modeling of protein interactions with surface-grafted charged polymers. Correlations between statistical molecular modeling and a mean field approach.

Ion exchange media involving charge groups attached to flexible polymers are widely used for protein purification. Such media often provide enhanced target protein purity and yield. Yet, little is understood about protein interaction with such media at the molecular level, or how different media architectures might affect separation performance. To gain a better understanding of such adsorptive systems, statistical mechanical perturbation calculations, utilizing a Debye-Hückel potential, were performed on surface-grafted charged polymers and their interaction with model proteins. The studied systems were weakly charged, and the polymers were linear and relatively short (degree of polymerization is 30). Segment distributions from the surface were also determined. The interaction of spherical model protein particles of 12-30 A radius were investigated with respect to polymer grafting density, distance from matrix surface, protein charge, and ionic strength. The partitioning coefficient of the model proteins was determined for different distances from the surface. An empirical mean field theory that scales the entropy of the protein with the square of the protein radius correlates well to Monte Carlo statistical modeling results. Upon adsorption to the polymer layers, the model proteins exhibit a critical surface charge density that is proportional to the ionic strength, independent of the grafting density, and appears to be a fundamental determinant of protein adsorption. Partitioning of protein-like nanoparticles to the charged polymer surface is only favored above the particle critical charge density.

Ions↗
PubMed2000

Novel techniques for characterizing complex water use patterns within a network based statistical hydrological model

Information on the magnitude and variability of flow regimes at the river reach scale is a central component of most aspects of water resource and water quality management. Within the UK, river stretches with permanent gauging stations represent less than one percent of the total number of river stretches mapped at a scale of 1:50,000 and fewer than 20% of gauged catchments can be regarded as having natural flow regimes. This paper is the second of two papers that describe the development and application of hydrological models for estimating the variability and magnitude of natural and artificially influenced flow regimes at ungauged sites. The development of the models for estimating statistical descriptions of both the natural and artificially influenced flow regimes at ungauged river reaches is described by Young et al. (Young AR, Gustard A, Bullock A, Sekulin AE, Croker KM. Sci Total Environ 2000: this issue). This paper describes a pragmatic approach for applying the model to a complex river basin and characterizing the impacts of water use in the basin through example. The basin selected for the application contains the Aire and the Calder catchments within south Yorkshire.

Journal Article↗
PubMed1997

[Statistical analysis of pharmacological data: use of cumulative chi-squared statistic].

The cumulative chi-squared statistic has been proposed for testing against ordered alternatives in various statistical models. As usual statistical tests of ordered column categorical data, the chi 2 test, Fisher's exact test and Wilcoxon test are used. Pharmacological studies often are performed by multiple dosing. Data obtained from these studies are called ordered categorical data. The cumulative chi-squared statistic, which has been proposed by Hirotsu and Shibuya for testing against ordered alternatives in various statistical models, is little used in spite of its good applicability in the field of pharmacology. This method was too difficult for the general pharmacologist and biological scientists because it requires the use of a complex matrix and a powerful computer to carry out the analysis. However since a more simple method was proposed by Matsumoto and Yoshimura this method has been used more frequently in the biological sciences. In this paper, the one way cumulative chi-squared statistic test and two way chi-squared statistic test are compared with the chi-squared statistic test and Wilcoxon test.

Data Interpretation, Statistical↗
PubMed2004

Statistical-acoustics models of energy decay in systems of coupled rooms and their relation to geometrical acoustics.

An improved statistical-acoustics model of high-frequency sound fields in coupled rooms is developed by incorporating into prior models geometrical-acoustics corrections for both energy decay within subrooms and energy transfer between subrooms. The conditions under which statistical-acoustics models of coupled rooms are valid approximations to geometrical acoustics are examined by comparison of computational geometrical-acoustics predictions of decay curves in two- and three-room systems with those of both improved and prior statistical-acoustics models. The accuracy of the decay model used within subrooms is found to have a primary influence on the accuracy of predictions in coupled systems. Likewise, nondiffuse transfer of energy is shown to significantly affect decay of energy in systems of coupled rooms. The decrease in energy density of the reverberant field with distance from the source, which is predicted by geometrical acoustics, is found to result in spatial dependence of decay-curve shape for certain coupling geometries. Geometrical effects are shown to contribute to the failure of statistical-acoustics models in the case of strong coupling between subrooms; thus, previously proposed statistical-acoustics criteria cannot predict the point at which the models break down with consistent accuracy.

Acoustics↗
PubMed2006

Analyses of simulations of three-dimensional lattice proteins in comparison with a simplified statistical mechanical model of protein folding.

Folding and unfolding simulations of three-dimensional lattice proteins were analyzed using a simplified statistical mechanical model in which their amino acid sequences and native conformations were incorporated explicitly. Using this statistical mechanical model, under the assumption that only interactions between amino acid residues within a local structure in a native state are considered, the partition function of the system can be calculated for a given native conformation without any adjustable parameter. The simulations were carried out for two different native conformations, for each of which two foldable amino acid sequences were considered. The native and non-native contacts between amino acid residues occurring in the simulations were examined in detail and compared with the results derived from the theoretical model. The equilibrium thermodynamic quantities (free energy, enthalpy, entropy, and the probability of each amino acid residue being in the native state) at various temperatures obtained from the simulations and the theoretical model were also examined in order to characterize the folding processes that depend on the native conformations and the amino acid sequences. Finally, the free energy landscapes were discussed based on these analyses.

Amino Acid Sequence↗
PubMed2004

How can statistical approaches enhance transdisciplinary study of drug misuse prevention?

Application of statistical techniques in transdisciplinary research includes statistical model selection and model specification. This paper presents statistical models used in drug misuse prevention research. The historical roots of these models are discussed to illustrate the numerous disciplines from which different techniques originated. Single and multilevel approaches are described to illustrate methods of synthesizing perspectives from different scientific arenas. Using single-level approaches in transdisciplinary research, these models can easily incorporate broader theoretical considerations and more integrated hypotheses by representing each discipline with a set of variables. Simultaneous testing of every set of variables obtained from different disciplines may provide more comparable results to identify critical factors associated with substance-use behavior. Using multilevel approaches, more powerful syntheses across disciplines can be achieved by representing each discipline at a different level.

Biomedical Research↗
PubMed2000

Estimating the probability for a protein to have a new fold: A statistical computational model.

Structural genomics aims to solve a large number of protein structures that represent the protein space. Currently an exhaustive solution for all structures seems prohibitively expensive, so the challenge is to define a relatively small set of proteins with new, currently unknown folds. This paper presents a method that assigns each protein with a probability of having an unsolved fold. The method makes extensive use of protomap, a sequence-based classification, and scop, a structure-based classification. According to protomap, the protein space encodes the relationship among proteins as a graph whose vertices correspond to 13,354 clusters of proteins. A representative fold for a cluster with at least one solved protein is determined after superposition of all scop (release 1.37) folds onto protomap clusters. Distances within the protomap graph are computed from each representative fold to the neighboring folds. The distribution of these distances is used to create a statistical model for distances among those folds that are already known and those that have yet to be discovered. The distribution of distances for solved/unsolved proteins is significantly different. This difference makes it possible to use Bayes' rule to derive a statistical estimate that any protein has a yet undetermined fold. Proteins that score the highest probability to represent a new fold constitute the target list for structural determination. Our predicted probabilities for unsolved proteins correlate very well with the proportion of new folds among recently solved structures (new scop 1.39 records) that are disjoint from our original training set.

Amino Acid Sequence↗
PubMed2006

[Developing a statistical conceptual model for pre-chlorination process in waterworks].

Aiming at a method of risk analysis for drinking water treatment, a statistical conceptual model was developed to simulate the pre-chlorination process in waterworks, which involved the reactions among chlorine residuals, ammonia nitrogen, bromide and organic matter. The model was calibrated and verified with field data from a typical waterworks. The model could well predict the probability distribution of the concentration of permanganate index, ammonia nitrogen, chloroform, bromodichloromethane, chlorodibromomethane and bromoform in the pre-chlorination process.

Chlorine Compounds↗
PubMed2004

Five hierarchical levels of sequence-structure correlation in proteins.

This article reviews recent work towards modelling protein folding pathways using a bioinformatics approach. Statistical models have been developed for sequence-structure correlations in proteins at five levels of structural complexity: (i) short motifs; (ii) extended motifs; (iii) nonlocal pairs of motifs; (iv) 3-dimensional arrangements of multiple motifs; and (v) global structural homology. We review statistical models, including sequence profiles, hidden Markov models (HMMs) and interaction potentials, for the first four levels of structural detail. The I-sites (folding Initiation sites) Library models short local structure motifs. Each succeeding level has a statistical model, as follows: HMMSTR (HMM for STRucture) is an HMM for extended motifs; HMMSTR-CM (Contact Maps) is a model for pairwise interactions between motifs; and SCALI-HMM (HMMs for Structural Core ALIgnments) is a set of HMMs for the spatial arrangements of motifs. The parallels between the statistical models and theoretical models for folding pathways are discussed in this article; however, global sequence models are not discussed because they have been extensively reviewed elsewhere. The data used and algorithms presented in this article are available at http://www.bioinfo.rpi.edu/~bystrc/ (click on "servers" or "downloads") or by request to bystrc@rpi.edu .

Algorithms↗
PubMed2002

Methodology to predict long-term cancer survival from short-term data using Tobacco Cancer Risk and Absolute Cancer Cure models.

Three parametric statistical models have been fully validated for cancer of the larynx for the prediction of long-term 15, 20 and 25 year cancer-specific survival fractions when short-term follow-up data was available for just 1-2 years after the end of treatment of the last patient. In all groups of cases the treatment period was only 5 years. Three disease stage groups were studied, T1N0, T2N0 and T3N0. The models are the Standard Lognormal (SLN) first proposed by Boag (1949 J. R. Stat. Soc. Series B 11 15-53) but only ever fully validated for cancer of the cervix, Mould and Boag (1975 Br. J. Cancer 32 529-50), and two new models which have been termed Tobacco Cancer Risk (TCR) and Absolute Cancer Cure (ACC). In each, the frequency distribution of survival times of defined groups of cancer deaths is lognormally distributed: larynx only (SLN), larynx and lung (TCR) and all cancers (ACC). All models each have three unknown parameters but it was possible to estimate a value for the lognormal parameter S a priori. By reduction to two unknown parameters the model stability has been improved. The material used to validate the methodology consisted of case histories of 965 patients, all treated during the period 1944-1968 by Dr Manuel Lederman of the Royal Marsden Hospital, London, with follow-up to 1988. This provided a follow-up range of 20-44 years and enabled predicted long-term survival fractions to be compared with the actual survival fractions, calculated by the Kaplan and Meier (1958 J. Am. Stat. Assoc. 53 457-82) method. The TCR and ACC models are better than the SLN model and for a maximum short-term follow-up of 6 years, the 20 and 25 year survival fractions could be predicted. Therefore the numbers of follow-up years saved are respectively 14 years and 19 years. Clinical trial results using the TCR and ACC models can thus be analysed much earlier than currently possible. Absolute cure from cancer was also studied, using not only the prediction models which incorporate a parameter for a statistically cured fraction of patients C(SLN), C(TCR) and C(ACC), but because of the long follow-up range of 20-44 years, also by complete life analysis. The survival experience of those who did not die of their original cancer of the larynx was compared to the expected survival experience of a population with the same age, birth cohort and sex structure. To date it has been generally assumed for early stage disease that although for some 5-10 years after treatment the survival experience of this patient subgroup might be no different from that expected in the matched group, thereafter the death rate of this subgroup becomes lower than that of the matched group. This implies that surviving cancer patients cured of their disease tend to die of other conditions at a higher than normal rate as they become older, and therefore cancer is never totally cured. Our conclusion is that at least for cancer of the glottic larynx, the answer to the question: 'Can cancer totally be cured?' is 'Yes to at least 15-years post-treatment and also probably to 25 years.'

Disease-Free Survival↗
PubMed2005

Nonequilibrium statistical mechanical models for cytoskeletal assembly: towards understanding tensegrity in cells.

The cytoskeleton is not an equilibrium structure. To develop theoretical tools to investigate such nonequilibrium assemblies, we study a statistical physical model of motorized spherical particles. Though simple, it captures some of the key nonequilibrium features of the cytoskeletal networks. Variational solutions of the many-body master equation for a set of motorized particles accounts for their thermally induced Brownian motion as well as for the motorized kicking of the structural elements. These approximations yield stability limits for crystalline phases and for frozen amorphous structures. The methods allow one to compute the effects of nonequilibrium behavior and adhesion (effective cross-linking) on the mechanical stability of localized phases as a function of density, adhesion strength, and temperature. We find that nonequilibrium noise does not necessarily destabilize mechanically organized structures. The nonequilibrium forces strongly modulate the phase behavior and have comparable effect as the adhesion due to cross-linking. Modeling transitions such as these allows the mechanical properties of cytoskeleton to rapidly and adaptively change. The present model provides a statistical mechanical underpinning for a tensegrity picture of the cytoskeleton.

Animals↗
PubMedDate not supplied

Assessment of shape variation of the levator ani with optimal scan planning and statistical shape modeling.

OBJECTIVE: To capture 3D shape variation of the levator ani during straining with open access MR imaging. METHODS: Optimal scan-planning based on statistical shape modeling is developed for recovering the entire 3D structure of the levator ani from a limited number of 2D imaging planes. Statistical shape modeling ensures optimum material correspondence, and Subspace Reprojection is used to identify the optimum orientation of the imaging plans. The accuracy of the method in using limited 2D imaging planes to instantiate the dynamic structure of the levator ani is assessed with data acquired from 10 asymptomatic subjects. RESULTS: Leave-one-out analysis was performed whereby a model based on a training set consisting of all but one surface was used to instantiate the dynamic surface structure from the corresponding optimal planes. The mean surface distance error for the proposed Subspace Reprojection method is 3.989 +/- 0.790 mm, which is significantly smaller than other approaches. CONCLUSIONS: Surfaces of the levator ani may be instantiated using a limited number of imaging planes as well as a statistical shape model based on a training set of subjects. The proposed technique offers a new way forward for studying dynamic shape changes of 3D structures where complete volumetric imaging is prohibited by the inherent temporal resolution of the scanning technique.

Adult↗
PubMed1976

The worth of a screening program: an application of a statistical decision model for the benefit evaluation of screening projects.

A statistical decision model is applied to the benefit evaluation of screening projects to derive an expression which provides upper and lower limits for average benefits in terms of prevalance rates of screen positives and negatives, and the average cost of screening and referral. Possible applications of such a technique are discussed and a numerical example is given.

Bayes Theorem↗
PubMed2005

Statistical coil model of the unfolded state: resolving the reconciliation problem.

An unfolded state ensemble is generated by using a self-avoiding statistical coil model that is based on backbone conformational frequencies in a coil library, a subset of the Protein Data Bank. The model reproduces two apparently contradicting behaviors observed in the chemically denatured state for a variety of proteins, random coil scaling of the radius of gyration and the presence of significant amounts of local backbone structure (NMR residual dipolar couplings). The most stretched members of our unfolded ensemble dominate the residual dipolar coupling signal, whereas the uniformity of the sign of the couplings follows from the preponderance of polyproline II and beta conformers in the coil library. Agreement with the NMR data substantially improves when the backbone conformational preferences include correlations arising from the chemical and conformational identity of neighboring residues. Although the unfolded ensembles match the experimental observables, they do not display evidence of native-like topology. By providing an accurate representation of the unfolded state, our statistical coil model can be used to improve thermodynamic and kinetic modeling of protein folding.

Computational Biology↗
PubMed1995

Assessment of developmental toxicity potential of chemicals by quantitative structure-toxicity relationship models.

Statistically significant quantitative structure-toxicity relationship (QSTR) models have been developed for assessing developmental toxicity potential (DTP) of chemicals. Three submodels, one each for aliphatic, heteroaromatic and carboaromatic compounds, have been cross-validated to ascertain their robustness. The specificities of the models range from 86% to 97%, and their sensitivities between 86% and 89%. For convenient computer-assisted application, the models are installed in a toxicity assessment software package, TOPKAT, which has been recently enhanced with algorithms to identify whether or not a query structure is inside the optimum prediction space (OPS) of a QSTR model. Different functionalities of the TOPKAT program have been explained by assessing the DTP of a number of compounds not used in the model training sets. The DTP of 18 existing drugs was assessed using these models; the DT assay results were available for 5 of these. Three of these 5 molecules were identified to be inside the OPS and their TOPKAT assessment matched their experimental assignment.

Algorithms↗
PubMed2004

A statistical-thermodynamic model of viral budding.

We present a simple statistical thermodynamic model for budding of viral nucleocapsids at the cell membrane. The membrane is modeled as a flexible lipid bilayer embedding linker (spike) proteins, which serve to anchor and thus wrap the membrane around the viral capsids. The free energy of a single bud is expressed as a sum of the bending energy of its membrane coat, the spike-mediated capsid-membrane adhesion energy, and the line energy associated with the bud's rim, all depending on the extent of wrapping (i.e., bud size), and density of spikes in the curved membrane. This self-energy is incorporated into a simple free energy functional for the many-bud system, allowing for different spike densities, and hence entropy, in the curved (budding) and planar membrane regions, as well as for the configurational entropy of the polydisperse bud population. The equilibrium spike densities in the coexisting, curved and planar, membrane regions are calculated as a function of the membrane bending energy and the spike-mediated adhesion energy, for different spike and nucleocapsid concentrations in the membrane plane, as well as for several values of the bud's rim energy. We show that complete budding (full wrapping of nucleocapsids) can only take place if the adhesion energy exceeds a certain, critical, bending free energy. Whenever budding takes place, the spike density in the mature virions is saturated, i.e., all spike adhesion sites are occupied. The rim energy plays an important role in determining the size distribution of buds. The fraction of fully wrapped buds increases as this energy increases, resulting eventually in an all-or-nothing mechanism, whereby nucleocapsids at the plasma membrane are either fully enveloped or completely naked (just touching the membrane). We also find that at low concentrations all capsids arriving at the membrane get tightly and fully enveloped. Beyond a certain concentration, corresponding approximately to a stoichiometric spike/capsid ratio, newly arriving capsids cannot be fully wrapped; i.e., the budding yield decreases.

Algorithms↗