scholarly journals Bayesian model-based tight clustering for time course data

2009 ◽  
Vol 25 (1) ◽  
pp. 17-38 ◽  
Author(s):  
Yongsung Joo ◽  
George Casella ◽  
James Hobert
2017 ◽  
Vol 122 (5) ◽  
pp. 1292-1303
Author(s):  
Charles H. Van Brackle ◽  
Ryan A. Harris ◽  
K. Melissa Hallow

The brachial artery flow-mediated dilation (FMD) test is the most widely utilized method to evaluate endothelial function noninvasively in humans by calculating the percent change in diameter (FMD%). However, the underutilized velocity and diameter time course data, coupled with confounding influences in shear exposure, noise, and upward bias, make the FMD test less desirable. In this study, we developed an exposure-response, model-based approach that not only quantifies FMD based on the rich velocity and diameter data, it overcomes previously acknowledged challenges. FMD data were obtained from 15 apparently healthy participants, each exposed to four different cuff occlusion durations. The velocity response following cuff release was described by an exponential model with two parameters defining peak velocity and rate of decay. Shear exposure derived from velocity was used to drive the diameter response model, which consists of additive constriction and dilation terms. Three parameters describing distinct aspects of the vascular response to shear (magnitude of the initial constriction response, and magnitude and time constant of the dilation response) were estimated for both the individuals and population. These parameters are independent of shear exposure. Thus this approach produces identifiable and physiologically meaningful parameters that may provide additional information for comparing differences between experimental groups or over time, and provides a means to completely account for shear exposure. NEW & NOTEWORTHY While flow-mediated dilation (FMD) is a valuable tool for evaluating endothelial function, analytical challenges include confounding influences of shear exposure, upward bias, and underutilization of rich time course data collected during FMD testing. We have developed an exposure-response, model-based approach that quantifies endothelial function based on the velocity and diameter data and fully accounts for shear exposure. It produces physiologically meaningful parameters that may provide useful information for comparing differences between experimental groups or over time.


2018 ◽  
Vol 12 (3) ◽  
pp. e0006339 ◽  
Author(s):  
Caetano Souto-Maior ◽  
Gabriel Sylvestre ◽  
Fernando Braga Stehling Dias ◽  
M. Gabriela M. Gomes ◽  
Rafael Maciel-de-Freitas

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Arika Fukushima ◽  
Masahiro Sugimoto ◽  
Satoru Hiwa ◽  
Tomoyuki Hiroyasu

Abstract Background Historical and updated information provided by time-course data collected during an entire treatment period proves to be more useful than information provided by single-point data. Accurate predictions made using time-course data on multiple biomarkers that indicate a patient’s response to therapy contribute positively to the decision-making process associated with designing effective treatment programs for various diseases. Therefore, the development of prediction methods incorporating time-course data on multiple markers is necessary. Results We proposed new methods that may be used for prediction and gene selection via time-course gene expression profiles. Our prediction method consolidated multiple probabilities calculated using gene expression profiles collected over a series of time points to predict therapy response. Using two data sets collected from patients with hepatitis C virus (HCV) infection and multiple sclerosis (MS), we performed numerical experiments that predicted response to therapy and evaluated their accuracies. Our methods were more accurate than conventional methods and successfully selected genes, the functions of which were associated with the pathology of HCV infection and MS. Conclusions The proposed method accurately predicted response to therapy using data at multiple time points. It showed higher accuracies at early time points compared to those of conventional methods. Furthermore, this method successfully selected genes that were directly associated with diseases.


2017 ◽  
Vol 14 (2) ◽  
Author(s):  
Qihua Tan ◽  
Mads Thomassen ◽  
Mark Burton ◽  
Kristian Fredløv Mose ◽  
Klaus Ejner Andersen ◽  
...  

AbstractModeling complex time-course patterns is a challenging issue in microarray study due to complex gene expression patterns in response to the time-course experiment. We introduce the generalized correlation coefficient and propose a combinatory approach for detecting, testing and clustering the heterogeneous time-course gene expression patterns. Application of the method identified nonlinear time-course patterns in high agreement with parametric analysis. We conclude that the non-parametric nature in the generalized correlation analysis could be an useful and efficient tool for analyzing microarray time-course data and for exploring the complex relationships in the omics data for studying their association with disease and health.


2018 ◽  
Vol 105 (4) ◽  
pp. 970-978 ◽  
Author(s):  
Yupeng Ren ◽  
Liang Li ◽  
Susan Kirshner ◽  
Yaning Wang ◽  
Chandrahas Sahajwalla ◽  
...  

2013 ◽  
Vol 104 (8) ◽  
pp. 1676-1684 ◽  
Author(s):  
Max Puckeridge ◽  
Bogdan E. Chapman ◽  
Arthur D. Conigrave ◽  
Stuart M. Grieve ◽  
Gemma A. Figtree ◽  
...  

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