A model-based framework for chronic hepatitis C prevalence estimation.
Ontology highlight
ABSTRACT:
SUBMITTER: Hamadeh A
PROVIDER: S-EPMC6874092 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:BackgroundA common approach to the application of epidemiological models is to determine a single (point estimate) parameterisation using the information available in the literature. However, in many cases there is considerable uncertainty about parameter values, reflecting both the incomplete nature of current knowledge and natural variation, for example between farms. Furthermore model outcomes may be highly sensitive to different parameter values. Paratuberculosis is an infection for which many of the key parameter values are poorly understood and highly variable, and for such infections there is a need to develop and apply statistical techniques which make maximal use of available data.ResultsA technique based on Latin hypercube sampling combined with a novel reweighting method was developed which enables parameter uncertainty and variability to be incorporated into a model-based framework for estimation of prevalence. The method was evaluated by applying it to a simulation of paratuberculosis in dairy herds which combines a continuous time stochastic algorithm with model features such as within herd variability in disease development and shedding, which have not been previously explored in paratuberculosis models. Generated sample parameter combinations were assigned a weight, determined by quantifying the model's resultant ability to reproduce prevalence data. Once these weights are generated the model can be used to evaluate other scenarios such as control options. To illustrate the utility of this approach these reweighted model outputs were used to compare standard test and cull control strategies both individually and in combination with simple husbandry practices that aim to reduce infection rates.ConclusionsThe technique developed has been shown to be applicable to a complex model incorporating realistic control options. For models where parameters are not well known or subject to significant variability, the reweighting scheme allowed estimated distributions of parameter values to be combined with additional sources of information, such as that available from prevalence distributions, resulting in outputs which implicitly handle variation and uncertainty. This methodology allows for more robust predictions from modelling approaches by allowing for parameter uncertainty and combining different sources of information, and is thus expected to be useful in application to a large number of disease systems.
| S-EPMC3544565 | biostudies-literature
Project description:One of the most important and critical factors in software projects is the proper cost estimation. This activity, which has to be done prior to the beginning of a project in the initial stage, always encounters several challenges and problems. However, due to the high significance and impact of the proper cost estimation, several approaches and methods have been proposed regarding how to perform cost estimation, in which the analogy-based approach is one of the most popular ones. In recent years, many attempts have been made to employ suitable techniques and methods in this approach in order to improve estimation accuracy. However, achieving improved estimation accuracy in these techniques is still an appropriate research topic. To improve software development cost estimation, the current study has investigated the effect of the LEM algorithm on optimization of features weighting and proposed a new method as well. In this research, the effectiveness of this algorithm has been examined on two datasets, Desharnais and Maxwell. Then, MMRE, PRED (0.25), and MdMRE criteria have been used to evaluate and compare the proposed method against other evolutionary algorithms. Employing the proposed method showed considerable improvement in estimating software cost estimation.
| S-EPMC8771765 | biostudies-literature
Project description:BackgroundModel-based small area estimation methods can help generate parameter estimates at the district level, where planned population survey sample sizes are not large enough to support direct estimates of HIV prevalence with adequate precision. We computed district-level HIV prevalence estimates and their 95% confidence intervals for districts in Uganda.MethodsOur analysis used direct survey and model-based estimation methods, including Fay-Herriot (area-level) and Battese-Harter-Fuller (unit-level) small area models. We used regression analysis to assess for consistency in estimating HIV prevalence. We use a ratio analysis of the mean square error and the coefficient of variation of the estimates to evaluate precision. The models were applied to Uganda Population-Based HIV Impact Assessment 2016/2017 data with auxiliary information from the 2016 Lot Quality Assurance Sampling survey and antenatal care data from district health information system datasets for unit-level and area-level models, respectively.ResultsEstimates from the model-based and the direct survey methods were similar. However, direct survey estimates were unstable compared with the model-based estimates. Area-level model estimates were more stable than unit-level model estimates. The correlation between unit-level and direct survey estimates was (β1 = 0.66, r2 = 0.862), and correlation between area-level model and direct survey estimates was (β1 = 0.44, r2 = 0.698). The error associated with the estimates decreased by 37.5% and 33.1% for the unit-level and area-level models, respectively, compared to the direct survey estimates.ConclusionsAlthough the unit-level model estimates were less precise than the area-level model estimates, they were highly correlated with the direct survey estimates and had less standard error associated with estimates than the area-level model. Unit-level models provide more accurate and reliable data to support local decision-making when unit-level auxiliary information is available.
| S-EPMC8345831 | biostudies-literature
Project description:BackgroundThe development of a successful COVID-19 control strategy requires a thorough understanding of the trends in geographic and demographic distributions of disease burden. In terms of the estimation of the population prevalence, this includes the crucial process of unravelling the number of patients who remain undiagnosed.ObjectiveThis study estimates the period prevalence of COVID-19 between March 1, 2020, and November 30, 2020, and the proportion of the infected population that remained undiagnosed in the Canadian provinces of Quebec, Ontario, Alberta, and British Columbia.MethodsA model-based mathematical framework based on a disease progression and transmission model was developed to estimate the historical prevalence of COVID-19 using provincial-level statistics reporting seroprevalence, diagnoses, and deaths resulting from COVID-19. The framework was applied to three different age cohorts (< 30; 30-69; and ≥70 years) in each of the provinces studied.ResultsThe estimates of COVID-19 period prevalence between March 1, 2020, and November 30, 2020, were 4.73% (95% CI 4.42%-4.99%) for Quebec, 2.88% (95% CI 2.75%-3.02%) for Ontario, 3.27% (95% CI 2.72%-3.70%) for Alberta, and 2.95% (95% CI 2.77%-3.15%) for British Columbia. Among the cohorts considered in this study, the estimated total number of infections ranged from 2-fold the number of diagnoses (among Quebecers, aged ≥70 years: 26,476/53,549, 49.44%) to 6-fold the number of diagnoses (among British Columbians aged ≥70 years: 3108/18,147, 17.12%).ConclusionsOur estimates indicate that a high proportion of the population infected between March 1 and November 30, 2020, remained undiagnosed. Knowledge of COVID-19 period prevalence and the undiagnosed population can provide vital evidence that policy makers can consider when planning COVID-19 control interventions and vaccination programs.
| S-EPMC8432517 | biostudies-literature
Project description:Estimation of disease prevalence at sub-city neighborhood scale allows early and targeted interventions that can help save lives and reduce public health burdens. However, the cost-prohibitive nature of highly localized data collection and sparsity of representative signals, has made it challenging to identify neighborhood scale prevalence of disease. To overcome this challenge, we utilize alternative data sources, which are both less sparse and representative of localized disease prevalence: using query data from a large commercial search engine, we identify the prevalence of respiratory illness in the United States, localized to census tract geographic granularity. Focusing on asthma and Chronic Obstructive Pulmonary Disease (COPD), we construct a set of features based on searches for symptoms, medications, and disease-related information, and use these to identify illness rates in more than 23 thousand tracts in 500 cities across the United States. Out of sample model estimates from search data alone correlate with ground truth illness rate estimates from the CDC at 0.69 to 0.76, with simple additions to these models raising those correlations to as high as 0.84. We then show that in practice search query data can be added to other relevant data such as census or land cover data to boost results, with models that incorporate all data sources correlating with ground truth data at 0.91 for asthma and 0.88 for COPD.
| S-EPMC8189491 | biostudies-literature
Project description:BACKGROUND:Genetic variation in IL28B and other factors are associated with sustained virological response (SVR) after pegylated-interferon/ribavirin treatment for chronic hepatitis C (CHC). Using data from the HALT-C Trial, we developed a model to predict a patient's probability of SVR based on IL28B genotype and clinical variables. METHODS:HALT-C enrolled patients with advanced CHC who had failed previous interferon-based treatment. Subjects were re-treated with pegylated-interferon/ribavirin during trial lead-in. We used step-wise logistic regression to calculate adjusted odds ratios (aOR) and create the predictive model. Leave-one-out cross-validation was used to predict a priori probabilities of SVR and determine area under the receiver operator characteristics curve (AUC). RESULTS:Among 646 HCV genotype 1-infected European American patients, 14.2% achieved SVR. IL28B rs12979860-CC genotype was the strongest predictor of SVR (aOR, 7.56; p<.0001); the model also included HCV RNA (log10 IU/ml), AST:ALT ratio, Ishak fibrosis score and prior ribavirin treatment. For this model AUC was 78.5%, compared to 73.0% for a model restricted to the four clinical predictors and 60.0% for a model restricted to IL28B genotype (p<0.001). Subjects with a predicted probability of SVR <10% had an observed SVR rate of 3.8%; subjects with a predicted probability >10% (43.3% of subjects) had an SVR rate of 27.9% and accounted for 84.8% of subjects actually achieving SVR. To verify that consideration of both IL28B genotype and clinical variables is required for treatment decisions, we calculated AUC values from published data for the IDEAL Study. CONCLUSION:A clinical prediction model based on IL28B genotype and clinical variables can yield useful individualized predictions of the probability of treatment success that could increase SVR rates and decrease the frequency of futile treatment among patients with CHC.
| S-EPMC3132753 | biostudies-literature
Project description:This SuperSeries is composed of the following subset Series: GSE36533: Transcriptomic analysis of the woodchuck model of chronic hepatitis B: Liver gene expression in uninfected, resolved and chronically infected woodchucks GSE36541: Transcriptomic analysis of the woodchuck model of chronic hepatitis B: Kidney gene expression in uninfected, resolved and chronically infected woodchucks GSE36544: Transcriptomic analysis of the woodchuck model of chronic hepatitis B: Spleen gene expression in uninfected, resolved and chronically infected woodchucks GSE36545: Transcriptomic analysis of the woodchuck model of chronic hepatitis B: Liver gene expression in tumor and non-tumor samples from chronically infected woodchucks Refer to individual Series
2012-04-10 | E-GEOD-36250 | biostudies-arrayexpress
Project description:BackgroundThe clinical mitigation of intracranial hypertension due to traumatic brain injury requires timely knowledge of intracranial pressure to avoid secondary injury or death. Noninvasive intracranial pressure (nICP) estimation that operates sufficiently fast at multihour timescales and requires only common patient measurements is a desirable tool for clinical decision support and improving traumatic brain injury patient outcomes. However, existing model-based nICP estimation methods may be too slow or require data that are not easily obtained.ObjectiveThis work considers short- and real-time nICP estimation at multihour timescales based on arterial blood pressure (ABP) to better inform the ongoing development of practical models with commonly available data.MethodsWe assess and analyze the effects of two distinct pathways of model development, either by increasing physiological integration using a simple pressure estimation model, or by increasing physiological fidelity using a more complex model. Comparison of the model approaches is performed using a set of quantitative model validation criteria over hour-scale times applied to model nICP estimates in relation to observed ICP.ResultsThe simple fully coupled estimation scheme based on windowed regression outperforms a more complex nICP model with prescribed intracranial inflow when pulsatile ABP inflow conditions are provided. We also show that the simple estimation data requirements can be reduced to 1-minute averaged ABP summary data under generic waveform representation.ConclusionsStronger performance of the simple bidirectional model indicates that feedback between the systemic vascular network and nICP estimation scheme is crucial for modeling over long intervals. However, simple model reduction to ABP-only dependence limits its utility in cases involving other brain injuries such as ischemic stroke and subarachnoid hemorrhage. Additional methodologies and considerations needed to overcome these limitations are illustrated and discussed.
| S-EPMC8077603 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below.
2012-04-11 | GSE36250 | GEO
Project description:The analysis of genome-wide genetic association studies generally starts with univariate statistical tests of each single-nucleotide polymorphism. The standard approach is the Cochran-Armitage trend test or its logistic regression equivalent although this approach can lose considerable power if the underlying genetic model is not additive. An alternative is the MAX test, which is robust against the three basic modes of inheritance. Here, the asymptotic distribution of the MAX test is derived using the generalized linear model together with the Delta method and multiple contrasts. The approach is applicable to binary, quantitative, and survival traits. It may be used for unrelated individuals, family-based studies, and matched pairs. The approach provides point and interval effect estimates and allows selecting the most plausible genetic model using the minimum P-value. R code is provided. A Monte-Carlo simulation study shows that the asymptotic MAX test framework meets type I error levels well, has good power, and good model selection properties for minor allele frequencies ≥0.3. Pearson's χ(2)-test is superior for lower minor allele frequencies with low frequencies for the rare homozygous genotype. In these cases, the model selection procedure should be used with caution. The use of the MAX test is illustrated by reanalyzing findings from seven genome-wide association studies including case-control, matched pairs, and quantitative trait data.
| S-EPMC3820468 | biostudies-literature