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PubMed2005

Process development for a Cuban cholera vaccine based on the attenuated strain Vibrio cholerae 638.

Genetically modified Vibrio cholerae strain 638 (biotype El Tor, serotype Ogawa) has previously been shown to be immunogenic in animal models and in human trials. Our objective in the work reported herein was to describe the process development methods for the production of the 638 attenuated cholera vaccine. Cell seed bank, culture of biomass, lyophilization and final formulation were processes were developed. The results show kinetics of culture that fulfils a logistical model. The microbiological properties, colonizing capability, immunogenicity and non-toxigenicity of the final product were indistinguishable from the properties of the working seed lot. We conclude that the non-reactogenic, immunogenic and protective strain 638 is robust and can withstand the fermentation processes required for large-scale production of a vaccine.

Animals↗
PubMed2006

Interval mapping for loci affecting unordered categorical traits.

Many traits including shapes and colors of flowers, fruits and seeds in plants, as well as coat colors and some behavioral properties in animals, are recorded in discrete categories. If categories are ordered, genetic analyses of the categorical traits are often performed using the threshold model, which considers a latent continuous variable, called the liability, underlying a trait and assumes the monotonic relationship between the phenotype and the liability. In some categorical traits, however, descriptions of phenotypes are purely nominal and the phenotypic scores cannot be ordered. The threshold model is unreasonable for the analyses of such unordered categorical traits. In this study, we developed a method for interval mapping of loci affecting unordered categorical traits with more than two categories. The probability of the phenotype of an individual falling in each of the categories was expressed by a polychotomous logistic model, in which the log-odds for each category relative to the reference category were assumed to follow a linear model including genotype at a locus affecting a trait as covariate. Based on the model, the interval mapping using a maximum likelihood method was devised for the analysis of complex categorical traits described with unordered categories. We confined ourselves to the case of F2 populations derived from a cross between two inbred lines, although this approach can easily be extended to the analyses for other populations of general structures. As results of analyses of simulated data show, the method showed high efficiency in detecting the loci affecting unordered categorical traits.

Animals↗
PubMed2002

Complications of endoscopic sphincterotomy: results from a single tertiary referral center.

BACKGROUND AND STUDY AIMS: Complications of endoscopic sphincterotomy (ES) have been assessed in recent multicenter studies. The aim of this series was to report and identify risk factors for complications of ES at a single tertiary referral center. PATIENTS AND METHODS: Between 1996 and 2000, 1159 consecutive endoscopic retrograde cholangiopancreatographies (ERCP) procedures were performed and their related complications were assessed. A total of 658 patients (57 %) underwent ES. All the clinical, radiological and biological data were carefully recorded within the 30 days following the procedure. Multivariate analysis was performed using a stepwise logistic model. RESULTS: The morbidity rate for ES was 7.7 %, being moderate to severe in 5 %. Morbidity included acute pancreatitis (3.5 %), perforations (1.8 %), sepsis (1.2 %) and bleeding (1.2 %). The 30-day mortality was 0.9 %. In the 1159 ERCP procedures, 231 patients underwent precut papillotomy (20 %) followed by sphincterotomy in 174 cases. Using logistic regression analysis, the risk factors for ES were precut papillotomy (relative risk, RR 2.76), confidence interval, (CI 1.39 - 5.49) and the presence of sphincter of Oddi dysfunction (RR, 7.72, CI 3.2 - 18.4). CONCLUSIONS: In this single-center series, we found a complication rate of ES in about 7 %, comparable to that in multicenter series. Precut papillotomy and sphincter of Oddi dysfunction were the main independent risk factors for ES.

Female↗
PubMed1996

Effect of dimethoate on body growth of representatives of the soil living mesofauna.

For the elucidation of effects of a pesticide on life-cycle parameters of arthropods, applicable in the development of ecotoxicological test procedures with soil living animals, attention was drawn to body growth, which has previously been described as a sensitive parameter in Collembola. Body growth of the following three soil-dwelling arthropods was studied under the influence of dimethoate: Folsomia fimetaria (L.), Hypogastrura assimilis Krausbauer, and Hypoaspis aculeifer Canestrini. The effect of this insecticide and acaricide proved to be sex and species specific. Two models were compared for modeling individual body length. The logistic growth model fitted data for all species, whereas the growth model of von Bertalanffy was less applicable for F. fimetaria and H. aculeifer. The growth rate coefficient of the logistic model proved to be a robust parameter useful for predicting effects of dimethoate on juvenile growth of F. fimetaria and H. aculeifer. Adverse effect concentrations on growth for these species were the following: EC10 = 0.11 mg dimethoate/kg dry soil for F. fimetaria and EC10 = 0.59 mg dimethoate/kg dry soil for H. aculeifer. For H. assimilis, no adverse effects on growth were observed at the tested concentrations. The results are compared to other life-cycle parameters (end-points).

Analysis of Variance↗
PubMedDate not supplied

A multiphasic approach for describing serial height data of Fels children: a hexaphasic-logistic-additive growth model.

In this paper, we reported the results obtained from fitting a new growth model to serial height data of 80 Fels children. The model assumed that human height growth curves are due to the combined effects of six macroscopic logistic growth processes, each reaching the same asymptotic height value. It was named the Walker and Walker-Hexaphasic-Logistic-Additive (WWHLA) growth model. An advantage to using this model is that it allowed us to easily fit entire growth curves with 14 biologically interpretable parameters. We tested the model using a computerized nonlinear least squares technique. The results showed that the new model worked extremely well. The fits resulted in high R, R2, and adjusted R2 values, large F values, relatively low residual mean squares, Durbin-Watson statistics that were very close to 2, and relatively small standard error estimates for the model parameters. In addition, the normality and constant variance test passed for more than 95 percent of the children, and the graphs of the residuals essentially showed no model bias. The new model identified the six growth components or processes in both male and female growth curves. The processes were named according to when they reached their peak height velocity: neonatal, infantile, early-childhood, middle-childhood, late-childhood, and pubertal. Preliminary results suggest that the WWHLA model appears to be the best that is currently available at this time for describing the human growth curve.

Body Height↗
PubMed2003

Factors associated with growth faltering in children from rural Saudi Arabia.

Recent studies on the growth of children in Saudi Arabia have revealed that children under two years of age suffer from faltering growth when compared with the American reference population. The present study aims to identify parental and child characteristics associated with faltering growth among the children in a rural area of Saudi Arabia. A cross-sectional study of all women with a child less than three years of age in a rural community in NorthWestern part of Saudi Arabia was undertaken. Anthropometric measurements, socio-demographic and fertility variables were collected using a structured questionnaire. The indicators of growth were derived from the data and univariate and logistic models fitted to determine potential risk factors. There were 332 children, sex ratio 1.35 and 94.3% were less than 2 years of age. A low frequency (1.5%) had low weight for height, 11.4% low weight for age and 36.1% low height for age when compared with the American NCHS reference population. Multiple logistic regression suggested birth space > 2 years (OR = 0.44, 95% CI = 0.25 - 0.77), father's with primary or intermediate education (OR = 0.45, 95% CI = 0.25-0.90), birth weight > 2500 gms. (OR = 0.8, 95% CI = 0.03-0.75), male birth (OR = 2.60, 95%. CI = 1.54-4.59) were variables statistically and independently associated with faltering growth. The pattern of growth of children under 2 years deviated negatively from their NCHS-WHO reference. This is similar to the previous findings from urban communities in Saudi Arabia. This growth faltering could be attributed partly to the inadequacy of the reference to compare growth pattern of children in all geographical areas, of the world. While the effects of different dietary habits may not be ruled out, it may be important to develop a different anthropometrics and nutrients growth chart that could be more appropriate to compare variation of infant growth in all nations of the world.

Adolescent↗
PubMed2001

A probability model for predicting BRCA1 and BRCA2 mutations in breast and breast-ovarian cancer families.

Germline mutations in BRCA1 and BRCA2 genes predispose to hereditary breast and ovarian cancer. Our aim was to find associations between the clinical characteristics and positive mutation status in 148 breast cancer families in order to predict the probability of finding a BRCA mutation in a family. Several factors were associated with mutations in univariate analysis, whereas in multivariate analysis (logistic regression with backward selection) only the age of the youngest breast cancer patient and the number of ovarian cancer cases in a family were independent predictors of BRCA mutations. A logistic model was devised to estimate the probability for a family of harbouring a mutation in either BRCA1 or BRCA2. Altogether, 63 out of 148 families (43%) and 28 out of 29 (97%) mutation carrier families obtained probabilities over 10%. The mean probability was 55% for mutation-positive families and 11% for mutation-negative families. The models by Couch et al (1997) and Shattuck-Eidens et al (1997) previously designed for BRCA1 were also tested for their applicability to distinguish carrier families with mutations in either gene. The probability model should be a useful tool in genetic counselling and focusing the mutation analyses, and thus increasing also the cost-effectiveness of the genetic screening.

Adult↗
PubMed2005

Predictive model for congenital muscular torticollis: analysis of 1021 infants with sonography.

OBJECTIVE: To construct a predictive model to foretell congenital muscular torticollis (CMT) on the basis of clinical correlates. DESIGN: Correlation study. SETTING: Regional hospital. PARTICIPANTS: A consecutive series of 1021 newborn infants. INTERVENTIONS: Not applicable. MAIN OUTCOME MEASURE: Participants underwent portable ultrasonography to diagnose CMT. Significant clinical correlates were identified to construct a predictive model using the logistic regression model. RESULTS: Forty of 1021 infants were diagnosed with CMT using ultrasonography, yielding an overall incidence of 3.92%. Birth body length (odds ratio [OR]=1.38; 95% confidence interval [CI], 1.49-2.38), facial asymmetry (OR=21.75; 95% CI, 6.6-71.7), plagiocephaly (OR=22.3; 95% CI, 7.01-70.95), perineal trauma during delivery (OR=4.26; 95% CI, 1.25-14.52), and primiparity (OR=6.32; 95% CI, 2.34-17.04) were significant correlates. A predictive logistic regression model with the incorporation of these 4 correlates was developed. We used cross-validation with a receiver operating characteristic curve to validate the predictive model. CONCLUSIONS: Our study successfully developed a quantitative predictive model for estimating the risk of CMT on the basis of clinical correlates only. This model has good discriminative ability for classifying CMT and non-CMT by yielding acceptable values of false-negative and false-positive cases.

Female↗
PubMed1984

Predictability of pregnancy outcome in preterm delivery.

Multivariate models have great potential value in enhancing the understanding of why some pregnancies have poor outcomes. Recently, such models have been advocated as a basis for predictive scoring systems that attempt to classify patients into high-risk and low-risk groups. In this report the usefulness of such an approach was assessed by studying the predictability of preterm delivery at The Johns Hopkins Hospital during 1980, using a multiple logistic model. Choosing a cutoff point (or probability of preterm delivery) of 10%, 697 of 2865 patients were placed in the high-risk group. The sensitivity, specificity, and positive predictive value of the model, as applied to this select population, were 62.2, 79.4, and 22.7%, respectively. Thus, only 23% of patients predicted to have preterm deliveries in fact delivered preterm. The predictive value could have been improved by increasing the cutoff point, but only at the expense of markedly reducing the sensitivity of the model. It was concluded that the potential value of multivariate analyses of pregnancy outcome as a predictive, risk-classification technique is limited. Nevertheless, such studies may aid the clinical evaluation of each individual patient by providing a better understanding of the etiologies of poor outcome.

Abortion, Incomplete↗
PubMed1995

Nomograms for determining the probability of axillary node involvement in women with breast cancer.

We have previously reported that a history of pregnancy is independently associated with axillary node involvement in breast cancer patients. We have now studied additional women with breast cancer and have used our data and the logistic model to produce nomograms for determining the risk of axillary node involvement, based on tumor size, age, and number of pregnancies. There was an increase in the incidence of axillary node involvement in women with a history of pregnancy. To exclude the confounding effect that tumor size or age might have on node involvement, logistic regression was performed. Pregnancy, tumor size, and age were the three independent variables. History of pregnancy had a significant effect on node involvement (P = 0.036) that was independent of tumor size and age. Nomograms were constructed from these data. Surgeons do not perform an axillary dissection in every breast cancer patient. If the axilla is clinically negative and the tumor small, the surgeon, medical oncologist, and radiation oncologist may decide that a dissection need not be done. The nomograms in this article may allow for a more methodical choice of patients for axillary dissection. Moreover, a radiation oncologist might use the nomograms to help decide whether to irradiate an undissected axilla.

Adult↗
PubMed1989

Regression models for time to seroconversion following experimental bovine leukaemia virus infection.

This paper develops a parametric model for time to seroconversion after experimental bovine leukaemia virus (BLV) infection, and examines the effects of inoculation route, volume of inoculum, type of inoculation material, and antigen status of donor on seroconversion time. We used parametric and nonparametric statistical methodology to analyse interval data on 150 animals from 13 published reports. The log-logistic model fitted the observed times to seroconversion better than the log-normal or Weibull models, which were the considered alternatives.

Animals↗
PubMed1995

Modelling covariate effects in observer agreement studies: the case of nominal scale agreement.

Correction for chance-expected agreement has become an accepted technique in the analysis of observer agreement data and may be particularly useful when the level of agreement achieved in different populations is compared. However, formal methods for making comparisons of chance-corrected agreement or, more generally, for studying the effects of covariates on chance-corrected agreement have not received much attention. For nominal scale agreement data we show how Tanner and Young's model for observer agreement can be applied to this problem. The models discussed can be fitted using existing software and certain model parameters have interpretations in terms of positive and negative agreement odds ratios. The proposed methodology facilitates investigation of issues such as confounding of covariate effects and interaction between covariates in their effect on chance-corrected agreement. The methods outlined therefore allow observer agreement data to be analyzed in a manner strongly analogous to the logistic modelling of the association between disease and suspected risk factors. The methods are illustrated using data on the comparability of primary and proxy respondent reports of the primary respondents participation in physically vigorous leisure time activity.

Analysis of Variance↗
PubMed1987

A quantitative analysis of palliative care decisions in acute nonlymphocytic leukemia.

With the increasing incidence of cancer in elderly patients, decisions to adopt palliative care become particularly relevant to this patient population. In order to define characteristics of decisions to adopt palliative care, including those factors influencing whether a particular patient received palliation, the frequency of this therapeutic posture, and the duration of this treatment period, we performed a retrospective analytical survey of all patients with acute nonlymphocytic leukemia (ANLL) treated at Duke University Medical Center over the past ten years. Logistic regression analysis identified several potentially significant variables influencing the decision to adopt palliative care. Using a stepwise logistic model, the only independent variable associated with adoption of palliative therapy was initial treatment off a research protocol (P = 0.0001). Initial treatment off a research protocol was itself associated with older age (P = 0.0002), nonspontaneous onset of leukemia (P = 0.005), female sex (P = 0.003), and the absence of dependent children (P = 0.01) when examined by multivariate logistic regression. The palliative treatment interval was defined as the time between the discontinuation of aggressive treatment and the patient's death. Fifty-one percent, 119 of 235 patients, received palliative care; of these, 47% were palliated from the time of diagnosis and 53% were palliated only after receiving remission induction therapy. The median duration for the palliative care period was 46 days (50 days for the initially palliated group, 24 days for the group receiving aggressive therapy.(ABSTRACT TRUNCATED AT 250 WORDS)

Aged↗
PubMed2006

Does disturbance enhance genotypic diversity in clonal organisms? A field test in the marine angiosperm Zostera marina.

Physical disturbance has often been invoked to control genotypic diversity in sessile clonal organisms, yet experimental evidence is lacking. I studied the effects of physical disturbance on genet dynamics and genotypic diversity in a clonal marine angiosperm, Zostera marina (eelgrass). In replicated plots of 1 m2, the vegetation canopy was removed in gaps of zero (control), 25%, 50% and 75% of the area (n = 6 replicates). Before removal and during two consecutive years, the genotypic composition was determined using genetic markers (DNA microsatellites) in a 5 x 5 pixel grid per plot. An aggregate index of genet dynamics summarizing recruitment, increase, loss and decrease of clones was maximal at intermediate disturbance levels (quadratic polynomial P = 0.02). Physical disturbance also increased the occurrence of new genotypes, possibly reflecting recruitment (linear model, P < 0.05). Contrary to expectations, there was no competitive advantage of more heterozygous genotypes over less heterozygous ones. In the absence of disturbance, in particular, clones with lower individual heterozygosity were more likely to increase in area over a 1-year time period than more heterozygous ones, while there was no such correlation in plots with disturbance (logistic model, P(disturbance x heterozygosity) = 0.036). Undisturbed plots revealed background recruitment independent of canopy gaps, suggesting that Z. marina exhibits a strategy of continual recruitment. Effects of experimental disturbance (linear or quadratic) on clonal diversity were not detectable. Instead, initial (pretreatment) clonal diversity accounted for between 68% and 91% of the variance in diversity, indicating remarkable resilience of genotypic diversity in the face of physical disturbance.

Environment↗
PubMed1993

A simple multiple system organ failure scoring system predicts mortality of patients who have sepsis syndrome.

A simple multiple system organ failure (MSOF) score may predict mortality of patients who have sepsis syndrome. Using an MSOF scoring system, we prospectively determined the presence or absence of respiratory, cardiovascular, renal, hepatic, gastrointestinal, hematologic, and neurologic organ failure on day 1 of sepsis syndrome in 154 consecutive patients who had sepsis syndrome in the ICU of a tertiary care, teaching hospital. We used 30-day hospital mortality as the primary outcome variable. Overall 30-day mortality was 34 percent. There was a strong linear association between number of organ system failures and 30-day mortality (p < 0.0001). Mortality was 20 percent in patients who had less than 3 organ system failures (n = 111) and 70 percent in patients who had 3 or more organ system failures (n = 43). Survival was assessed using the Cox proportional hazards model and was found to be significantly different (p < 0.01) between the two groups defined by the aforementioned dichotomy after adjustment for age and sex using time to death as the primary outcome. The increase in relative risk of death associated with 3 or more organ system failures was 2.77 (95 percent confidence interval, 2.74 to 2.83). Using logistic regression, the adjusted odds ratios (OR) for covariates most predictive of mortality were hematologic (OR = 6.2), neurologic (OR = 4.4), hepatic (OR = 3.4), cardiovascular (OR = 2.6), and age (1.05 per year). The logistic model using the seven organ system failures and age as covariates accurately predicted outcome 75 percent of the time with a sensitivity of 51 percent and specificity of 87 percent. In conclusion, a simple scoring system tabulating the number of organ system failures present on day 1 of sepsis syndrome predicts the mortality of patients who have sepsis syndrome with reasonable accuracy.

Adult↗
PubMedDate not supplied

Withholding or starting antibiotic treatment in patients with dementia and pneumonia: prediction of mortality with physicians' judgment of illness severity and with specific prognostic models.

BACKGROUND: To help decision makers plan treatment, the authors assessed clinical predictors of mortality from nursing home-acquired pneumonia in patients with dementia. METHODS: Pneumonia patients treated without (n = 165) or with antibiotics (n = 541) were enrolled in a prospective cohort study in 61 nursing homes. RESULTS: In both groups, clinical judgment of illness severity was a strong predictor for 1-week mortality. Despite large differences in frailty and mortality (83% in untreated patients and 15% in treated patients), separate multivariable logistic models included similar specific predictors. DISCUSSION: Despite profound differences between the 2 independent groups, predictors for short-term mortality were largely similar. We found that, when combined with physicians' clinical judgment, 3 readily assessed predictors (respiratory rate, fluid intake, and eating dependency) helped predict mortality. Our results, if confirmed in an independent population, can help make decision making about antibiotic treatment of pneumonia in patients with dementia more evidence-based.

Aged↗
PubMed2003

Log-linear models for assessing gene-age interaction and their application to case-control studies of the apolipoprotein E (apoE) gene in Alzheimer's disease.

Case-control studies provide a powerful approach for detecting disease-susceptibility genes or assessing gene-environment interactions. We investigated the situation in which the gene being studied plays a role in several diseases, and the allele frequency among subjects free of the disease of interest consequently decreases with age as subjects die from other diseases. The logistic model is one approach frequently used for analyzing case-control data, but it cannot accommodate this dependence of genotype and age. Using a log-linear model, we therefore proposed a hierarchical procedure that could be used as a valid method for assessing interactions in such situations. We then applied this procedure to observed data on Alzheimer's disease and the apolipoprotein E gene in Japan. We were able to derive an appropriate inference on whether the interaction was a gene-age interaction or merely a bias due to death from other diseases.

Age Factors↗
PubMed1989

Environmental and behavioural factors affecting the prevalence of foot lameness in New Zealand dairy herds - a case-control study.

A case-control study of environmental and behavioural factors influencing foot lameness was undertaken on 62 dairy herds comprising an average of 185 milking cows in Taranaki, New Zealand. Thirty two case herds were identified as having had at least 10 per cent of the cows lame during the milking season in which the herd was studied, and thirty control herds were selected on the basis that no more than 3 per cent of cows in these herds had been lame per year for at least two years immediately prior to investigation. Each herd was visited at both a morning and an afternoon milking, and 58 risk factors were measured between the time the farmer began to assemble the cows for milking and the completion of milking. Comparison of single variables between case and control herds identified 24 which showed differences (p<0.10). These variables were then subjected to stepwise multivariate logistic regression, and statistically significant variables in this analysis were used to create a tentative path diagram of possible causal web relationships between the various risk factors and the outcome variable, the lameness prevalence level. Information from a review of the published literature was used to include further variables to the 24 into the initial (or null hypothesis) path model. Logistic path analysis was then used to eliminate non-significant paths from the diagram, leaving 19 arrows joining 13 variables in the final path diagram, compared with 33 joining 20 variables in the initial version. The most influential variables in explaining variation between case and control herds were the average level of maintenance of the track and the degree of patience shown by the farmer in bringing the cows in for milking. Overall, factors associated with the movement of animals to the milking shed explained 40 per cent of the variation (deviance) with regard to the lameness prevalence level. Risk factors associated with characteristics of the milking process explain 24 per cent, and risk factors associated with characteristics of the cows in the herd explain 9.5 per cent. Recommendations are made on management changes which deserve further investigation as ways of reducing lameness problems in dairy herds.

Journal Article↗