scholarly journals A new efficient approach to fit stochastic models on the basis of high-throughput experimental data using a model of IRF7 gene expression as case study

2017 ◽  
Vol 11 (1) ◽  
Author(s):  
Luis U. Aguilera ◽  
Christoph Zimmer ◽  
Ursula Kummer
Keyword(s):  
Gene Expression ◽  
Experimental Data ◽  
High Throughput ◽  
Stochastic Models ◽  
Efficient Approach

Use of Posterior Probabilities to Evaluate Methods of Discriminant Analysis

1981 ◽  
Vol 20 (04) ◽  
pp. 207-212 ◽  
Author(s):  
J. Hermans ◽  
B. van Zomeren ◽  
J. W. Raatgever ◽  
P. J. Sterk ◽  
J. D. F. Habbema
Keyword(s):  
Experimental Data ◽  
Discriminant Analysis ◽  
Posterior Probabilities

By means of a case study the choice between several methods of discriminant analysis is presented. Experimental data of a two-groups problem with one or two variables is analysed. The different methods are compared according to posterior probabilities which can be computed for each subject and which are the basis of discriminant analysis. These posterior probabilities are analysed graphically as well as numerically.

Effects of Over Fire Air on the Combustion and NOx Emission Characteristics of a 600 MW Opposed Swirling Fired Boiler

2012 ◽  
Vol 512-515 ◽  
pp. 2135-2142 ◽  
Author(s):  
Yu Peng Wu ◽  
Zhi Yong Wen ◽  
Yue Liang Shen ◽  
Qing Yan Fang ◽  
Cheng Zhang ◽  
...  
Keyword(s):  
Fluid Dynamics ◽  
Experimental Data ◽  
Empirical Method ◽  
Nox Emission ◽  
Emission Characteristics ◽  
Cfd Model ◽  
Nitrogen Release ◽  
Computational Fluid Dynamics Cfd ◽  
Low Nox Emission

A computational fluid dynamics (CFD) model of a 600 MW opposed swirling coal-fired utility boiler has been established. The chemical percolation devolatilization (CPD) model, instead of an empirical method, has been adapted to predict the nitrogen release during the devolatilization. The current CFD model has been validated by comparing the simulated results with the experimental data obtained from the boiler for case study. The validated CFD model is then applied to study the effects of ratio of over fire air (OFA) on the combustion and nitrogen oxides (NOx) emission characteristics. It is found that, with increasing the ratio of OFA, the carbon content in fly ash increases linearly, and the NOx emission reduces largely. The OFA ratio of 30% is optimal for both high burnout of pulverized coal and low NOx emission. The present study provides helpful information for understanding and optimizing the combustion of the studied boiler

scholarly journals Principled Decision-Making Workflow with Hierarchical Bayesian Models of High-Throughput Dose-Response Measurements

Entropy ◽  
2021 ◽  
Vol 23 (6) ◽  
pp. 727
Author(s):  
Eric J. Ma ◽  
Arkadij Kummer
Keyword(s):  
Decision Making ◽  
High Throughput ◽  
Noisy Data ◽  
Hierarchical Bayesian ◽  
Hierarchical Bayesian Models ◽  
Melting Temperatures ◽  
Hierarchical Bayesian Estimation ◽  
The Face ◽  
Point Data

We present a case study applying hierarchical Bayesian estimation on high-throughput protein melting-point data measured across the tree of life. We show that the model is able to impute reasonable melting temperatures even in the face of unreasonably noisy data. Additionally, we demonstrate how to use the variance in melting-temperature posterior-distribution estimates to enable principled decision-making in common high-throughput measurement tasks, and contrast the decision-making workflow against simple maximum-likelihood curve-fitting. We conclude with a discussion of the relative merits of each workflow.

scholarly journals Comprehensive high-throughput meta-analysis of differentially expressed microRNAs in transcriptomic datasets reveals significant disruption of MAPK/JNK signal transduction pathway in Adult T-cell leukemia/lymphoma

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Shahrzad Shadabi ◽  
Nargess Delrish ◽  
Mehdi Norouzi ◽  
Maryam Ehteshami ◽  
Fariba Habibian-Sezavar ◽  
...  
Keyword(s):  
Gene Expression ◽  
Signal Transduction ◽  
T Cell ◽  
Network Analysis ◽  
High Throughput ◽  
Target Gene ◽  
Differentially Expressed ◽  
Cell Leukemia ◽  
Adult T Cell Leukemia ◽  
Healthy Donors

Abstract Background Human T-lymphotropic virus 1 (HTLV-1) infection may lead to the development of Adult T-cell leukemia/lymphoma (ATLL). To further elucidate the pathophysiology of this aggressive CD4+ T-cell malignancy, we have performed an integrated systems biology approach to analyze previous transcriptome datasets focusing on differentially expressed miRNAs (DEMs) in peripheral blood of ATLL patients. Methods Datasets GSE28626, GSE31629, GSE11577 were used to identify ATLL-specific DEM signatures. The target genes of each identified miRNA were obtained to construct a protein-protein interactions network using STRING database. The target gene hubs were subjected to further analysis to demonstrate significantly enriched gene ontology terms and signaling pathways. Quantitative reverse transcription Polymerase Chain Reaction (RTqPCR) was performed on major genes in certain pathways identified by network analysis to highlight gene expression alterations. Results High-throughput in silico analysis revealed 9 DEMs hsa-let-7a, hsa-let-7g, hsa-mir-181b, hsa-mir-26b, hsa-mir-30c, hsa-mir-186, hsa-mir-10a, hsa-mir-30b, and hsa-let-7f between ATLL patients and healthy donors. Further analysis revealed the first 5 of DEMs were directly associated with previously identified pathways in the pathogenesis of HTLV-1. Network analysis demonstrated the involvement of target gene hubs in several signaling cascades, mainly in the MAPK pathway. RT-qPCR on human ATLL samples showed significant upregulation of EVI1, MKP1, PTPRR, and JNK gene vs healthy donors in MAPK/JNK pathway. Discussion The results highlighted the functional impact of a subset dysregulated microRNAs in ATLL on cellular gene expression and signal transduction pathways. Further studies are needed to identify novel biomarkers to obtain a comprehensive mapping of deregulated biological pathways in ATLL.

scholarly journals Fast and Efficient 5′P Degradome Library Preparation for Analysis of Co-Translational Decay in Arabidopsis

Plants ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 466
Author(s):  
Marie-Christine Carpentier ◽  
Cécile Bousquet-Antonelli ◽  
Rémy Merret
Keyword(s):  
Gene Expression ◽  
Quality Control ◽  
Transcriptional Regulation ◽  
High Throughput ◽  
Library Preparation ◽  
Working Day ◽  
Set Up ◽  
Post Transcriptional Regulation ◽  
Commercial Kit

The recent development of high-throughput technologies based on RNA sequencing has allowed a better description of the role of post-transcriptional regulation in gene expression. In particular, the development of degradome approaches based on the capture of 5′monophosphate decay intermediates allows the discovery of a new decay pathway called co-translational mRNA decay. Thanks to these approaches, ribosome dynamics could now be revealed by analysis of 5′P reads accumulation. However, library preparation could be difficult to set-up for non-specialists. Here, we present a fast and efficient 5′P degradome library preparation for Arabidopsis samples. Our protocol was designed without commercial kit and gel purification and can be easily done in one working day. We demonstrated the robustness and the reproducibility of our protocol. Finally, we present the bioinformatic reads-outs necessary to assess library quality control.

scholarly journals High-throughput identification of protein functional similarities using a gene-expression-based siRNA screen

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Beth K. Neilsen ◽  
David L. Kelly ◽  
Binita Chakraborty ◽  
Hyun Seok Kim ◽  
Michael A. White ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Throughput ◽  
Sirna Screen
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