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Empirical Bayesian Approach to Testing Homogeneity of Several Means of Inflated Poisson Distributions (IPD)

Open Journal of Statistics 2023年第3期13卷 285-299页

作者： Mohamed M. Shoukri Maha Aleid Department of Epidemiology and Biostatistics Schulich School of Medicine and Dentistry University of Western Ontario London Canada Knowledge Translation Department Saudi National Institute of Health Riyadh Saudi Arabia

Objectives: We introduce a special form of the Generalized Poisson Distribution. The distribution has one parameter, yet it has a variance that is larger than the mean a phenomenon known as “over dispersion”. We discuss potential applications of the distribution as a model of counts, and under the assumption of independence we will perform statistical inference on the ratio of two means, with generalization to testing the homogeneity of several means. Methods: Bayesian methods depend on the choice of the prior distributions of the population parameters. In this paper, we describe a Bayesian approach for estimation and inference on the parameters of several independent Inflated Poisson (IPD) distributions with two possible priors, the first is the reciprocal of the square root of the Poisson parameter and the other is a conjugate Gamma prior. The parameters of Gamma distribution are estimated in the empirical Bayesian framework using the maximum likelihood (ML) solution using nonlinear mixed model (NLMIXED) in SAS. With these priors we construct the highest posterior confidence intervals on the ratio of two IPD parameters and test the homogeneity of several populations. Results: We encountered convergence problem in estimating the hyperparameters of the posterior distribution using the NLMIXED. However, direct maximization of the predictive density produced solutions to the maximum likelihood equations. We apply the methodologies to RNA-SEQ read count data of gene expression values.

关键词： Distributions of Over-Dispersed Counts Lagrange Class of Distributions Knowledge Transfer Gamma Prior Posterior Inference Wilson-Hilferty Transformation RNA_SEQ Read Counts Data

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Non-alcoholic steatohepatitis and the risk of myocardial infarction: Apopulation-based national study

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World Journal of Hepatology 2020年第7期12卷 378-388页

作者： Sara Ghoneim Aneesh Dhorepatil Aun Raza Shah Ganesh Ram Subhan Ahmad Chang Kim Imad Asaad Department of Internal medicine Case Western Reserve University at MetroHealth Medical CenterClevelandOH 44109United States Department of Pain Management The Schulich School of Medicine and DentistryLondonOntario N6A 5C1Canada Division of Gastroenterology Case Western Reserve University at MetroHealth Medical CenterClevelandOH 44109United States

BACKGROUNDNon-alcoholic fatty liver disease (NAFLD) is a systemic disease with bidirectionalrelationships with cardiovascular disease (CVD). Non-alcoholic steatohepatitis(NASH) is a more severe subtype of NAFLD. Patients with NASH exhibit moreintra and extrahepatic inflammation, procoagulant imbalances andproatherogenic lipid profiles. Whether NASH increases the risk of ischemic heartdisease is currently *** investigate the relationship between acute myocardial infarction (MI) andNASH in a large cohort of subjects in the United *** reviewed data from a large commercial database (Explorys IBM) thataggregates electronic health records from 26 large nationwide healthcare *** systemized nomenclature of clinical medical terms (SNOMED CT), weidentified adult with the diagnosis of NASH from 1999-2019. We includedpatients with the diagnosis of acute MI from 2018-2019. Comorbidities known tobe associated with NASH and MI such as obesity, diabetes mellitus,hyperlipidemia, smoking, male gender, and hypertension were *** and multivariable analyses were performed to investigate whetherNASH is independently associated with the risk of *** of 55099280 patients, 43170 were diagnosed with NASH (0.08%) and 107000(0.194%) had a MI within 2018-2019. After adjusting for traditional risk factors,NASH conferred greater odds of MI odds ratio (OR) 1.5 [95% confidence interval(CI): 1.40-1.62]. Hyperlipidemia had the strongest association with MI OR 8.39(95%CI: 8.21-8.58) followed by hypertension OR 3.11 (95%CI: 3.05-3.17) andsmoking OR 2.83 (95%CI: 2.79-2.87). NASH had a similar association with MI asthe following traditional risk factors like age above 65 years OR 1.47 (95%CI: 1.45-1.49), male gender OR 1.53 (95%CI: 1.51-1.55) diabetes mellitus OR 1.89 (95%CI:1.86-1.91).CONCLUSIONMI appears to be a prevalent disease in NASH. Patients with NASH may needearly identification and aggressive cardiovascular risk modification.

关键词： Non-alcoholic steatohepatitis Myocardial infarction Non-alcoholic fatty liver disease Ischemic cardiovascular disease United States population Atherosclerosis

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On the Index of Repeatability: Estimation and Sample Size Requirements

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Open Journal of Statistics 2019年第4期9卷 530-541页

作者： Maha Al-Eid Mohamed M. Shoukri Department of Biostatistics Epidemiology and Scientific Computing King Faisal Specialist Hospital and Research Center Riyadh KSA Department of Epidemiology and Biostatistics Schulich School of Medicine and Dentistry London Ontario Canada

Background: Repeatability is a statement on the magnitude of measurement error. When biomarkers are used for disease diagnoses, they should be measured accurately. Objectives: We derive an index of repeatability based on the ratio of two variance components. Estimation of the index is derived from the one-way Analysis of Variance table based on the one-way random effects model. We estimate the large sample variance of the estimator and assess its adequacy using bootstrap methods. An important requirement for valid estimation of repeatability is the availability of multiple observations on each subject taken by the same rater and under the same conditions. Methods: We use the delta method to derive the large sample variance of the estimate of repeatability index. The question related to the number of required repeats per subjects is answered by two methods. In first methods we estimate the number of repeats that minimizes the variance of the estimated repeatability index, and the second determine the number of repeats needed under cost-constraints. Results and Novel Contribution: The situation when the measurements do not follow Gaussian distribution will be dealt with. It is shown that the required sample size is quite sensitive to the relative cost. We illustrate the methodologies on the Serum Alanine-aminotransferase (ALT) available from hospital registry data for samples of males and females. Repeatability is higher among females in comparison to males.

关键词： Measurements Errors Functions of Variance Components Delta Method Lagrange Multiplier Bootstrap Technique

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Early Stage Triple Negative Breast Cancer Has Significantly Better Outcomes than More Advanced Disease: A Single Centre Retrospective Review

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Journal of Cancer Therapy 2016年第10期7卷 665-674页

作者： Caroline Hamm Swati Kulkarni Rasna Gupta Amin Kay John Mathews Khalid Hirmiz Indryas Woldie Akmal Ghafoor Tarek Elfiki Sindu Kanjeekal Ming Pan Kenneth Schneider Junaid Yousuf Mohammad Jarrar Colvin Springer Maher El-Masri schulich school of medicine Western University London ON Canada University of Windsor Windsor ON Canada

A retrospective, serial analysis of 181 triple negative breast cancer (TNBC) patients was undertaken at a regional cancer centre in Canada. The primary focus of the analysis was to investigate the effect of presenting stage in patients with TNBC on progression free and overall survival. We were able to demonstrate that patients presenting with an earlier stage breast cancer had a significantly superior progression free and overall survival when compared to more advanced stage. The adjusted multivariate cox-regression analyses for the overall and progression free survival suggest that the hazard of death was significantly lower for patients with stages I (HR = 0.09;95% CI 0.03 - 0.24) and II (HR = 0.29;95% CI 0.16 - 0.54) than for patients with stage III. The only other predictor of progression free survival besides stage, was receipt of radiotherapy (HR = 0.39;95% CI 0.22 - 0.69) in the adjusted cox regression analysis. Less than 2% of patients presented with stage IV disease. The small numbers presenting with stage IV disease may have impact on the development of clinical and translational trials. Certainly there may be stage migration if staging included more standardized or more sensitive investigations such as PET scans, and this might an important consideration in developing clinical trials. Twenty-five percent of patients presented with stage I disease. It is important for patients with TNBC presenting with earlier stages of disease that they are aware that they will have a better prognosis than their counterparts with more advanced disease. It is important that we are aware of this patient population, as their treatment recommendations are unclear and a source of a fair amount of controversy currently.

关键词： Triple Negative Breast Cancer Prognostic Factors Stage

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Estimating Benefits from Immunesuppressive Treatment in Diffuse Cutaneous Systemic Sclerosis: Data from the Canadian Scleroderma Research Group

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Open Journal of Rheumatology and Autoimmune Diseases 2014年第4期4卷 248-253页

作者： Tommy Choy Murray Baron Janet E. Pope schulich school of medicine & dentistry University of Western Ontario London Ontario Canada McGill University Montreal Canada Department of medicine Division of Rheumatology St. Joseph’s Health Care London Ontario Canada

Objective: To determine the efficacy of immunesuppressive treatment over 1 year in early diffuse cutaneous systemic sclerosis (dcSSc). Methods: dcSSc patients with less than 3 years disease duration and at least one year of data enrolled in the CSRG database were included. Regression analyses for achieving at least minimal important differences (MID) for 5 outcomes over one year were done to determine baseline predictors of change and if immunesuppressive treatment yielded the attainment of the MID. Results: 124 patients (mean age 52.3 years;79.2% female) were included. Variables associated with MID at one year were often the baseline variable and for some outcomes, age, sex, smoking, restrictive lung disease and treatment type. Treatment with immunesuppressive was not found to be associated with achieving MIDs in multivariate analyses. Conclusion: Treatment was associated with achieving a MID change at 1 year using univariate statistics, but not in multivariate models. These observational data do not support improvement with immunesuppressives over one year but there could be confounding or biases comparing with those prescribed immunesuppressives vs. those who don’t.

关键词： Immunesuppressive Treatment Diffuse Cutaneous Systemic Sclerosis

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3D Shape Reconstruction of Lumbar Vertebra From Two X-ray Images and a CT Model

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IEEE/CAA Journal of Automatica Sinica 2020年第4期7卷 1124-1133页

作者： Longwei Fang Zuowei Wang Zhiqiang Chen Fengzeng Jian Shuo Li Huiguang He the Research Center for Brain-Inspired Intelligence&National Laboratory of Pattern Recognition Institute of AutomationChinese Academy of SciencesBeijing 100190 the University of Chinese Academy of Sciences Beijing 100049China the Department of Neurosurgery Xuanwu HospitalCapital Medical UniversityDivision of SpineChina International Neurological InstituteBeijing 100053 Department of Neurosurgery Beijing HospitalNational Center of GerontologyBeijing 100730China the Department of Neurosurgery Xuanwu HospitalCapital Medical UniversityDivision of SpineChina International Neurological Institute Beijing 100053China the Department of Medical Biophysics Schulich School of Medical and Dentistryand also with the Department of Medical ImagingSchulich School of Medical and DentistryUniversity of Western OntarioON N6A 4V2Canada the University of Chinese Academy of Sciences Beijing 100049 the Center for Excellence in Brain Science and Intelligence Technology Chinese Academy of SciencesBeijing 100190China

Structure reconstruction of 3 D anatomy from biplanar X-ray images is a challenging topic. Traditionally, the elastic-model-based method was used to reconstruct 3 D shapes by deforming the control points on the elastic mesh. However, the reconstructed shape is not smooth because the limited control points are only distributed on the edge of the elastic ***, statistical-model-based methods, which include shape-model-based and intensity-model-based methods, are introduced due to their smooth reconstruction. However, both suffer from limitations. With the shape-model-based method, only the boundary profile is considered, leading to the loss of valid intensity information. For the intensity-based-method, the computation speed is slow because it needs to calculate the intensity distribution in each iteration. To address these issues, we propose a new reconstruction method using X-ray images and a specimen’s CT data. Specifically, the CT data provides both the shape mesh and the intensity model of the vertebra. Intensity model is used to generate the deformation field from X-ray images, while the shape model is used to generate the patient specific model by applying the calculated deformation *** on the public synthetic dataset and clinical dataset show that the average reconstruction errors are 1.1 mm and1.2 mm, separately. The average reconstruction time is 3 minutes.

关键词： 2D/2D registration 2D/3D registration 3D reconstruction vertebra model X-ray image

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Hepatocellular carcinoma in non-alcoholic fatty liver disease from a clinical and public health perspective

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Hepatobiliary Surgery and Nutrition 2022年第5期11卷 755-758页

作者： Luis Antonio Díaz Marco Arrese Juan Pablo Arab Departamento de Gastroenterología Escuela de MedicinaPontificia Universidad Católica de ChileSantiagoChile Division of Gastroenterology Department of MedicineSchulich School of MedicineWestern University&London Health Sciences CentreLondonONCanada Alimentiv LondonONCanada

Non-alcoholic fatty liver disease(NAFLD)is the leading cause of chronic liver disease in the western world(1).Currently,the global prevalence of NAFLD is estimated at 30%and is notably higher in South America and the Middle East(1).NAFLD prevalence has been rising during the last decades,and cases of decompensated NAFLD cirrhosis could increase by 168%in 2030(Figure 1A)(2).These trends are probably explained by several factors including the decrease in viral hepatitis incidence and the increasing prevalence of obesity and type 2 diabetes mellitus(T2DM)among the general population(2).

关键词： prevalence NAFLD liver

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Optimization of Image Quality in Retrospective Respiratory-Gated Micro-CT for Quantitative Measurements of Lung Function in Free-Breathing Rats

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Journal of Biomedical Science and Engineering 2014年第4期7卷 157-172页

作者： Nancy L. Ford Andrew Jeklin Karen Yip Darren Yohan David W. Holdsworth Maria Drangova Department of Oral Biological and Medical Sciences The University of British Columbia Vancouver Canada Department of Physics Ryerson University Toronto Canada schulich school of medicine & dentistry The University of Western Ontario London Canada

Objective: To optimize scan time and X-ray dose with no loss of image quality for retrospectively gated micro-CT scans of free-breathing rats. Methods: Five free-breathing rats were scanned using a dynamic micro-CT scanner over 10 continuous gantry rotations (50 seconds and entrance dose of 0.28 Gy). The in-phase projection views were selected and reconstructed, representing peak inspiration and end expiration from all 10 rotations and progressively fewer rotations. A least error method was also used to ensure that all angular positions were filled. Image quality and reproducibility for physiological measurements were compared for the two techniques. Results: The least error approach underestimated the lung volume, air content in the lung at peak inspiration, and tidal volume. Other measurements showed no differences between the projection-sorting techniques. Conclusions: Seven gantry rotations (35 seconds and 0.2 Gy dose) proved to be the optimal protocol for both the in-phase images and the least error images.

关键词： Respiratory-Gating Micro-CT Lung Imaging Free-Breathing Rats Tidal Volume

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Quasi-Binomial Regression Model for the Analysis of Data with Extra-Binomial Variation

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Open Journal of Statistics 2022年第1期12卷 1-14页

作者： Mohamed M. Shoukri Maha M. Aleid Department of Epidemiology and Biostatistics Schulich School of Medicine and Dentistry University of Western Ontario London Ontario Canada Department of Biostatistics Epidemiology and Scientific Computing King Faisal Specialist Hospital and Research Center Riyadh KSA

Objectives: Developing inference procedures on the quasi-binomial distribution and the regression model. Methods: Score testing and the method of maximum likelihood for regression parameters estimation. Data: Several examples are included, based on published data. Results: A quasi-binomial model is used to model binary response data which exhibit extra-binomial variation. A partial score test on the binomial hypothesis versus the quasi-binomial alternative is developed and illustrated on three data sets. The extended logit transformation on the binomial parameter is introduced and the large sample dispersion matrix of the estimated parameters is derived. The Nonlinear Mixed Procedure (NLMIXED) in SAS is shown to be very appropriate for the estimation of nonlinear regression.

关键词： Quasi-Binomial Distribution Extra Binomial Variations Score Test Quasi-Binomial Regression Model COVID-19 Case Fatality Data

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Quasi-Negative Binomial: Properties, Parametric Estimation, Regression Model and Application to RNA-SEQ Data

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Open Journal of Statistics 2022年第2期12卷 216-237页

作者： Mohamed M. Shoukri Maha M. Aleid Department of Epidemiology and Biostatistics Schulich School of Medicine and Dentistry University of Western Ontario London Canada Department of Biostatistics Epidemiology and Scientific Computing King Faisal Specialist Hospital and Research Center Riyadh Saudi Arabia

Background: The Poisson and the Negative Binomial distributions are commonly used to model count data. The Poisson is characterized by the equality of mean and variance whereas the Negative Binomial has a variance larger than the mean and therefore both models are appropriate to model over-dispersed count data. Objectives: A new two-parameter probability distribution called the Quasi-Negative Binomial Distribution (QNBD) is being studied in this paper, generalizing the well-known negative binomial distribution. This model turns out to be quite flexible for analyzing count data. Our main objectives are to estimate the parameters of the proposed distribution and to discuss its applicability to genetics data. As an application, we demonstrate that the QNBD regression representation is utilized to model genomics data sets. Results: The new distribution is shown to provide a good fit with respect to the “Akaike Information Criterion”, AIC, considered a measure of model goodness of fit. The proposed distribution may serve as a viable alternative to other distributions available in the literature for modeling count data exhibiting overdispersion, arising in various fields of scientific investigation such as genomics and biomedicine.

关键词： Queuing Models Overdispersion Moment Estimators Delta Method Bootstrap Maximum Likelihood Estimation Fisher’s Information Orthogonal Polynomials Regression Models RNE-Seq Data

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