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PubMed2006

Mathematics of protein pathological misfolding.

"Protein folding is defined as a process by which a polypeptide chain performs a search in conformational space with the objective of achieving the so-called native conformation to global free-energy minimum under a given set of physiochemical conditions of the medium." Misfolding then, is the process by which this objective is not achieved. Protein Folding Quality Assessment (PFQA), is characterized by a three-parameter distribution function Phi(T) referred to as the PFQA function. It uses results of protein folding processes to assess the output quality of protein folding. Protein misfolding is implicated in the initial cause of many conformational diseases. Folding of cytosolic protein can be regarded as the performance of the protein after it is produced or manufactured by the synthesis processes. Protein folding through different mechanisms and pathways has been extensively covered in [J.D. Bryngelson, P.G. Wolynes, Spin glass and statistical mechanics of protein folding, Proc. Natl. Acad. Sci. USA 84 (1987) 7524; J. Wang, Statistics, pathways and dynamics of single molecule folding, J. Chem. Phys. 118 (2) (2003) 953; N.D. Socci, J.N. Onuchic, P.G. Wolynes, Diffusive dynamics of the reaction coordinates for protein folding funnels, J. Chem. Phys. 104 (14) (1996); D. Thirumalai, From minimal models to real proteins, time scales for protein folding kinetics, J. Phys. I France 5 (1995) 1457]. The model is based on growth models of Ratkowsky, Richards, etc. [D.A. Ratkowski, T.J. Reeds, Choosing near-linear parameters logistic model for radio-ligand and related assays, Biometrics 42 (1986) 575] for a three-parameters model to handle the quality assessment of the folding process. Thus a complete distribution can be found, thanks to the scale, location and shape parameters.

Algorithms↗

PubMed1990

Logistic analysis of the defense reaction induced by electrical stimulation of the rat mesencephalic tectum.

Subliminal and threshold functions of behavioral output to electrical stimulation of the rat mesencephalic tectum were fitted using the logistic model. The results suggest the existence of isotopic albeit anisotropic freezing and flight mechanisms in the dorsal periaqueductal gray and deep layers of the superior colliculus. Moreover, the marked parallelism of immobility and running threshold functions indicates the probable coupling of these mechanisms through a kind of negative feedback. Finally, the good fitting to the model suggests that the behavioral output to electrical stimulation of these areas follows a logistic function of the logarithm of the stimulus intensity.

Aggression↗

PubMed1995

Models based on variable fractional digestion rates to describe ruminal in situ digestion.

Using a first-order model to describe ruminal in situ digestion implies that the rate of digestion is affected only by the quantity of potentially digestible substrate remaining. Other factors, like the microbial efficacy for digesting substrate, are assumed to be constant. However, microbes are not only the cause but also the result of digestion, being one of the digestion end-products. Two sigmoidal models (a logistic and a Gompertz-like model) were derived from a general digestion function in which the rate of digestion equals the product of the quantity of potentially digestible substrate remaining and a non-constant fractional rate of digestion (microbial efficacy function). The models were compared with a first-order model with a discrete lag time. The logistic model specifically accounted for the conversion of substrate mass to microbial mass, but did not describe microbial migration between the substrate and the ruminal fluid. In contrast, the Gompertz-like model assumed that the change in microbial efficacy was only time-dependent. There was little difference between models in estimates of scale parameters, but the asymptotic microbial efficacy was consistently higher for the logistic model than for the other models. Estimates of discrete lag time in the first-order model were biased towards obtaining values identical to the independent variable. Scale estimators appeared to be more robust than kinetic estimators. Lack-of-fit was present for most model-data set combinations. The similar patterns of residuals between models suggested that a four-parameter model may be insufficient to describe the data. It was concluded that if a four-parameter model is to be used, the model with a discrete lag time would be the least biologically appropriate.

Animal Feed↗

PubMed2003

Interaction as departure from additivity in case-control studies: a cautionary note.

It has been argued that assessment of interaction should be based on departures from additive rates or risks. The corresponding fundamental interaction parameter cannot generally be estimated from case-control studies. Thus, surrogate measures of interaction based on relative risks from logistic models have been proposed, such as the relative excess risk due to interaction (RERI), the attributable proportion due to interaction (AP), and the synergy index (S). In practice, it is usually necessary to include covariates such as age and gender to control for confounding. The author uncovers two problems associated with surrogate interaction measures in this case: First, RERI and AP vary across strata defined by the covariates, whereas the fundamental interaction parameter is unvarying. S does not vary across strata, which suggests that it is the measure of choice. Second, a misspecification problem implies that measures based on logistic regression only approximate the true measures. This problem can be rectified by using a linear odds model, which also enables investigators to test whether the fundamental interaction parameter is zero. A simulation study reveals that coverage is much improved by using the linear odds model, but bias may be a concern regardless of whether logistic regression or the linear odds model is used.

Case-Control Studies↗

PubMed1991

Using ordinal logistic regression to estimate the likelihood of colorectal neoplasia.

The utility of ordinal logistic regression in the prediction of colorectal neoplasia was demonstrated in a group of 461 consecutive patients undergoing colonoscopy in a community practice. One hundred twenty-nine patients had adenomatous polyps and 34 had colorectal adenocarcinoma. An ordinal logistic regression model developed in a random subset (292 patients) identified five predictors of colorectal neoplasia. Colorectal neoplasia risk could be predicted using the patient's age, sex, hematocrit, fecal occult blood test result and indication for colonoscopy. The risk of colorectal neoplasia in the remaining subset of patients (169) could be reliably estimated from the model. Ordinal logistic regression analysis in this select group of patients can accurately estimate the likelihood of colorectal neoplasia. Because the generalizability of our findings are unknown, the model should not be applied to other patients. However, application of this technique to an unselected group of patients not already referred for colonoscopy could provide unbiased estimates of colorectal neoplasia risk in individual patients.

Adenocarcinoma↗

PubMed1999

Validation procedures in radiologic diagnostic models. Neural network and logistic regression.

OBJECTIVE: To compare the performance of two predictive radiologic models, logistic regression (LR) and neural network (NN), with five different resampling methods. METHODS: One hundred sixty-seven patients with proven calvarial lesions as the only known disease were enrolled. Clinical and CT data were used for LR and NN models. Both models were developed with cross-validation, leave-one-out, and three different bootstrap algorithms. The final results of each model were compared with error rate and the area under receiver operating characteristic curves (Az). RESULTS: The NN obtained statistically higher Az values than LR with cross-validation. The remaining resampling validation methods did not reveal statistically significant differences between LR and NN rules. CONCLUSIONS: The NN classifier performs better than the one based on LR. This advantage is well detected by three-fold cross-validation but remains unnoticed when leave-one-out or bootstrap algorithms are used.

Adolescent↗

PubMed2001

Social dimensions of adolescent substance use.

OBJECTIVES: The aim of this study was to explore in detail the relationship between various social aspects of young people's lives and substance use and differences in the degree of influence exerted by the different social factors as a function of age. Design, setting, participants. The study was a survey of pupils aged 11-16 in a stratified sample of five English schools. Data from 4516 participants were obtained in relation to their cigarette, alcohol and illicit drug use and their contact with the police, perceived academic achievements and future expectations, religious beliefs, family structure, the importance of family versus peer opinions and suspension from school. MEASURES: Cumulative, age-specific preferences of substance misuse were compared. Logistic regression was used to rank the various risk factors. RESULTS: Substantial differences were found between substance users and non-users and the various risk factors being examined. For example, of those who had only been in trouble with the police, 18.8% used illegal drugs compared with 1.6% of those who had not had a police contact and who had no other risk factors. Many of these relationships were age-sensitive. For instance, the negative relationship between belief in God and illicit drug use became stronger as age increased (non-believers: y = 8.1886x - 9.16 R(2) = 0.9484; believers: y = 5.1514x - 8.08 R(2) = 0.9247). These results suggest that, within this sample of English adolescents, there was a strong relationship between substance use and the social factors examined. Although there were differences depending upon whether cigarette, alcohol or illicit drug use was being modelled, logistic regression indicated that the social factors could be ranked in the following order of importance: concurrent use of the second and third substances, having been in trouble with the police, perceived poor academic performance and low future academic expectations, a lack of religious belief, coming from a non-intact family, favouring peer over family opinion and having been suspended from school. Many of these relationships were age-sensitive with substance use peaking at age 15. CONCLUSION: The models and relationships presented in this paper show that a constellation of behaviours are related to adolescent substance use. Also demonstrated is that behaviours cannot be considered in isolation, but need to be examined from an holistic or biopsychosocial standpoint. These relationships are complex and future research should consider not only causality of adolescent substance use, but also of the aetiology of the satellite behaviours.

Adolescent↗

PubMed2004

Risk factors for colonization and infection in a hospital outbreak caused by a strain of Klebsiella pneumoniae with reduced susceptibility to expanded-spectrum cephalosporins.

Between February 2001 and January 2002, an increase in the number of Klebsiella pneumoniae isolates with reduced susceptibility to expanded-spectrum cephalosporins (RSKp) was detected in the neonatal unit of the Juan Canalejo Hospital, and 21 patients were either colonized or infected by the bacterial isolates. The current "gold standard" method for typing K. pneumoniae isolates is pulsed-field gel electrophoresis. However, this technique is expensive and time-consuming. In a search for faster and accurate alternatives to this method, we investigated PCR-based fingerprinting techniques (enterobacterial repetitive intergenic consensus sequence PCR [ERIC-PCR], repetitive extragenic palindromic sequence-based PCR [REP-PCR], and RAPD [randomly amplified polymorphic DNA]) for their ability to characterize K. pneumoniae isolates. The causal agent of the nosocomial outbreak was characterized by these techniques and was found to be a single epidemic strain (RSKp). A multiple regression logistic model was developed to identify potential independent factors associated with colonization and/or infection by RSKp. Logistic regression analysis was applied to all significant variables (P < 0.05) in the univariate analysis, and it was revealed that intubation (odds ratio [OR], 27.0; 95% confidence interval [95%CI], 5.39 to 135.14) and prematurity (OR, 4.4; 95%CI, 0.89 to 21.89) were such independent factors. Moreover, oxime cephalosporins did not appear to be statistically significant. Overall, the results showed that PCR-based techniques are expeditious and useful methods for typing K. pneumoniae isolates. Of the techniques studied, ERIC-PCR showed the highest discriminatory index (D = 0.828), followed by RAPD (D = 0.826) and REP-PCR (D = 0.773)

Cephalosporins↗

PubMed1994

Leukemia risk associated with benzene exposure in the pliofilm cohort. II. Risk estimates.

The detailed work histories of the individual workers composing the Pliofilm cohort represent a unique resource for estimating the dose-response for leukemia that may follow occupational exposure to benzene. In this paper, we report the results of analyzing the updated Pliofilm cohort using the proportional hazards model, a more sophisticated technique that uses more of the available exposure data than the conditional logistic model used by Rinsky et al. The more rigorously defined exposure estimates derived by Paustenbach et al. are consistent with those of Crump and Allen in giving estimates of the slope of the leukemogenic dose-response that are not as steep as the slope resulting from the exposure estimates of Rinsky et al. We consider estimates of 0.3-0.5 additional leukemia deaths per thousand workers with 45 ppm-years of cumulative benzene exposure to be the best estimates currently available of leukemia risk from occupational exposure to benzene. These risks were estimated in the proportional hazards model when the exposure estimates of Crump and Allen or of Paustenbach et al. were used to derive a cumulative concentration-by-time metric.

Aged↗

PubMedDate not supplied

Diagnostic value of combined evaluation of neopterin and anti-DNA antibody levels for assessment of disease activity in systemic lupus erythematosus.

OBJECTIVE: The present study was designed to investigate whether the combined evaluation of laboratory tests could improve their diagnostic value. Laboratory parameters of systemic lupus erythematosus (SLE), such as anti-dsDNA, neopterin, soluble IL-2 receptor (sIL-2R), C3, C4, and complement haemolytic activity (CH50), and a logistic model that provides the probable clinical activity (PCA) of a given patient, calculated by stepwise multiple logistic regression analysis from the parameters mentioned above--were evaluated as SLE activation markers. METHODS: Serum samples from 101 patients were assayed by ELISA (neopterin, sIL-2R, anti-dsDNA), radial immunodiffusion (C3, C4) and haemolytic complement assay (CH50). RESULTS: Among the parameters investigated, PCA showed the greatest difference between the values representing active and inactive stages of the disease (p < 0.001), the highest correlation with SLEDAI (p < 0.001) and the highest sensitivity and specificity values (0.91, 0.88, respectively). Moreover, this value of PCA was the most useful in discriminating between active and inactive sample pairs. CONCLUSION: We conclude that PCA is more useful in evaluating SLE activity than the single parameters studied.

Adult↗

PubMed1993

Relative risk, risk difference and rate difference models for sparse stratified data: a pseudo likelihood approach.

We consider a relative risk and a risk difference model for binomial data, and a rate difference model for Poisson (person year) data. It is assumed that the data are stratified in a large number of small strata. If each stratum has its own parameter in the model, then, due to the large number of parameters, straightforward maximum likelihood leads to inconsistent estimates of the relevant parameters. By contrast to the logistic model, conditioning on the number of events per stratum does not help in eliminating the stratum nuisance parameters. We propose a pseudo likelihood method to overcome these consistency problems. The resulting pseudo maximum likelihood estimates can easily be computed with standard statistical software. Our approach gives a more general framework for the Mantel-Haenszel type estimators proposed in the literature. In the special case of a series of 2 x 2 tables, for the risk and rate difference models, our approach yields exactly these ad hoc Mantel-Haenszel estimators, while for the relative risk model it gives a close approximation of the Mantel-Haenszel relative risk estimator. For the regression models corresponding to the association measures relative risk, risk difference and rate difference, our method provides analogues of conditional logistic regression, which were not previously available.

Analysis of Variance↗

PubMed2006

Prediction of distal radius fracture in children, using a biomechanical impact model and case-control data on playground free falls.

OBJECTIVES: To assess the ability of a biomechanical impact model to predict the likelihood of distal radius fracture in children using data gathered for a previous epidemiological case-control study of falls from playground equipment. METHODOLOGY: Factor of Risk (FR) values were generated for each of selected subjects from the case-control study using a biomechanical model. Logistic regression curves were fitted to examine the relationship between the FR values and the probability of radius fracture. RESULTS: Forty-five cases and thirty-one controls were selected. The logistic regression analyses showed a significant association between the probability of fracture and FR. CONCLUSIONS: The biomechanical model distinguished between children who fractured their distal radius and those who did not. The model can be used to test how risk factors, such as fall height and ground surface type, affect physical stresses transmitted through the arm and their relation to the fracture tolerance of the distal radius.

Accidental Falls↗

PubMed1987

Relationship between plant virus concentration and infectivity: a 'growth curve' model.

A logistic ('growth curve') model is formulated and applied to the relationship between numbers of infections (local lesions) produced by a virus on inoculated plants and the concentration of the virus in the inoculum. This model has the advantages of being simple, data-based and therefore not founded on limiting postulates, and of being applicable to a wide range of infection-dilution series, including those obtained from multicomponent viruses. Here, it is applied to common tobacco mosaic virus. Examples of infection-dilution series taken from the literature are fitted more closely and more objectively than they were fitted by the original authors. A limiting number for lesions is estimated by minimizing chi 2 values for differences between observed lesion numbers and those calculated from the logistic equation. The complete fitting procedure can be programmed on a hand-held calculator.

Models, Biological↗

PubMed1988

Selection of high-risk groups for breast cancer screening. Evidence from an Italian multicentric case control study.

In recent years techniques for the selection of risk groups for high priority breast screening have been evaluated. We used data from a large multicentric case control study in Italy, recently published, to fit a reduced logistic model for predictive purposes, using variables which are easily collected. The predicted probability of being a case obtained through the logistic analysis was then used to classify the same set of data by calculating values of sensitivity and specificity at different cutoff points of the predicted probability. The results showed the low predictive power of the model. The selection of higher risk groups in a screening population program is discussed.

Adult↗

PubMed2005

Dose response and factors related to interstitial pneumonitis after bone marrow transplant.

PURPOSE: Total body irradiation (TBI) and chemotherapy are common components of conditioning regimens for bone marrow transplantation. Interstitial pneumonitis (IP) is a known regimen-related complication. Using published data of IP in a multivariate logistic regression, this study sought to identify the parameters in the bone marrow transplantation conditioning regimen that were significantly associated with IP and to establish a radiation dose-response function. METHODS AND MATERIALS: A retrospective review was conducted of articles that reported IP incidence along with lung dose, fractionation, dose rate, and chemotherapy regimen. In the final analysis, 20 articles (n = 1090 patients), consisting of 26 distinct TBI/chemotherapy regimens, were included in the analysis. Multivariate logistic regression was performed to determine dosimetric and chemotherapeutic factors that influenced the incidence of IP. RESULTS: A logistic model was generated from patients receiving daily fractions of radiation. In this model, lung dose, cyclophosphamide dose, and the addition of busulfan were significantly associated with IP. An incidence of 3%-4% with chemotherapy-only conditioning regimens is estimated from the models. The alpha/beta value of the linear-quadratic model was estimated to be 2.8 Gy. The dose eliciting a 50% incidence, D50, for IP after 120 mg/kg of cyclophosphamide was 8.8 Gy; in the absence of chemotherapy, the estimated D50 is 10.6 Gy. No dose rate effect was observed. The use of busulfan as a substitute for radiation is equivalent to treating with 14.8 Gy in 4 fractions with 50% transmission blocks shielding the lung. The logistic regression failed to find a model that adequately fit the multiple-fraction-per-day data. CONCLUSIONS: Dose responses for both lung radiation dose and cyclophosphamide dose were identified. A conditioning regimen of 12 Gy TBI in 6 daily fractions induces an IP incidence of about 11% in the absence of lung shielding. Shielding the lung to receive 50% of this dose lowers the estimated incidence to about 2.3%. Because the lungs can be adequately shielded, we recommend against using busulfan as a substitute for fractionated TBI with cyclophosphamide.

Algorithms↗

PubMed2006

Examining the role of partner status in an HIV prevention trial targeting HIV-positive gay and bisexual men: the seropositive urban men's intervention trial (SUMIT).

The goal of this analysis was to examine whether partner status impacted behavioral outcomes from the Seropositive Urban Men's Intervention Trial (SUMIT). We contrasted sample characteristics of HIV-positive gay and bisexual men with and without main partners and then examined differences in sexual behaviors among men participating in an enhanced HIV prevention intervention compared to those in a standard condition. Logistic regression analyses were performed to differentiate characteristics of men with and without main partners and mixed-model logistic regression analyses were performed to test for intervention effects. Men with main partners showed a greater likelihood of having unprotected anal sex with any partner, although the number of male sexual partners was higher for men without a main partner. SUMIT generally produced few differences in sexual risk behaviors and did not affect several potential mediator variables of the relationship between the intervention and sexual behaviors with main and nonmain partners.

Bisexuality↗

PubMed1993

Benzene toxicity and risk assessment, 1972-1992: implications for future regulation.

Acute and chronic exposure to benzene vapors poses a number of health hazards to humans. To evaluate the probability that a specific degree of exposure will produce an adverse effect, risk assessment methods must be used. This paper reviews much of the published information and evaluates the various risk assessments for benzene that have been conducted over the past 20 years. There is sufficient evidence that chronic exposure to relatively high concentrations of benzene can produce an increased incidence of acute myelogenous leukemia (AML). Some studies have indicated that benzene may cause other leukemias, but due to the inconsistency of results, the evidence is not conclusive. To predict the leukemogenic risk for humans exposed to much lower doses of benzene than those observed in most epidemiology studies, a model must be used. Although several models could yield plausible results, to date most risk assessments have used the linear-quadratic or conditional logistic models. These appear to be the most appropriate ones for providing the cancer risk for airborne concentrations of 1 ppb to 10 ppm, the range most often observed in the community and workplace. Of the seven major epidemiology studies that have been conducted, there is a consensus that the Pliofilm cohort (rubber workers) is the best one for estimating the cancer potency because it is the only one with good exposure and incidence of disease data. The current EPA, OSHA, and ACGIH cancer potency estimates for benzene are based largely on this cohort. A retrospective exposure assessment and an analysis of the incidence of disease in these workers were completed in 1991. All of these issues are discussed and the implications evaluated in this paper. The range of benzene exposures to which Americans are commonly exposed and the current regulatory criteria are also presented.

Animals↗

PubMed1997

Acute respiratory effects on workers exposed to metalworking fluid aerosols in an automotive transmission plant.

Exposure to metalworking fluids has been linked to modest cross-shift reductions in FEV1 and occupational asthma. To identify responsible agents, we measured personal exposures to thoracic particulate (TP), viable plus nonviable thoracic bacteria (BAC), and vapor phase nicotine (VPN) (as a surrogate for tobacco particulate) among 83 machinists exposed to soluble oils and 46 dry assemblers working in an automotive transmission machining plant using biocides infrequently. The participants completed interviews and performed pre- and postshift spirometry on Monday and Thursday of the same week in each of three rounds of data collection (June 1992, January 1993, June 1993). Generalized estimating equations were used to combine information across rounds in multiple regression models of cross-shift and cross-week changes in forced expiratory volume, I second (FEV1) and forced vital capacity (FVC). Mean seniority was 19 years among machinists. Mean personal TP levels were 0.41 mg/m3 in machinists and 0.13 mg/m3 in assemblers. Six of the 83 machinists and none of the 46 assemblers experienced a greater than 19% cross-shift decrement in FEV1 or FVC at least once (p = .07). In regression models using either TP or BAC, among subjects with lower baseline (Monday preshift) FEV1/FVC ratios, increasing exposure was significantly associated with increasing cross-shift decrements in FEV1 and FVC in linear models, and with increased likelihood of a 10% or greater cross-shift decrement in FEV1 or FVC in logistic models. Adjustment of TP for VPN did not affect models significantly. We conclude that clinically important cross-shift decrements in pulmonary function are associated with exposure to metalworking fluid aerosols within a high-seniority population.

Adult↗