A comparative assessment on gene expression classification methods of RNA-seq data generated using next-generation sequencing (NGS).

Next-generation sequencing or massively parallel sequencing have revolutionized genomic research. RNA sequencing (RNA-Seq) can profile the gene-expression used for molecular diagnosis, disease classification and providing potential markers of diseases. For classification of gene expressions, several methods that have been proposed are based on microarray data which is a continuous scale or require a normal distribution assumption. As the RNA-Seq data do not meet those requirements, these methods cannot be applied directly. In this study, we compare several classifiers including Logistic Regression, Support Vector Machine, Classification and Regression Trees and Random Forest. A simulation study with different parameters such as over dispersion, differential expression rate is conducted and the results are compared with two mRNA experimental datasets. To measure predictive accuracy six performance indicators are used: Percentage Correctly Classified, Area Under Receiver Operating Characteristic (ROC) Curve, Kolmogorov Smirnov Statistics, Partial Gini Index, H-measure and Brier Score. The result shows that Random Forest outperforms the other classification algorithms.

Retraction: The Role of Heat Shock Proteins in Cellular Homeostasis and Cell Survival.

[This retracts the article DOI: 10.7759/cureus.18316.].

Correction: The Role of Heat Shock Proteins in Cellular Homeostasis and Cell Survival.

[This corrects the article DOI: 10.7759/cureus.18316.].

The Role of Heat Shock Proteins in Cellular Homeostasis and Cell Survival.

This review article has been necessitated by the limited number of studies on the role of heat shock proteins (HSPs) in cellular functions. The analysis is performed by reviewing evidence in various literary works concerning the topic. The main function of HSPs is to prevent the formation of non-functional proteins and facilitate protein folding. They also enhance the survival of cells in addition to being clinically significant. HSPs protect proteins from stress factors such as temperature, pH, and low levels of oxygen. Some of the common types of HSPs include HSP70, HSP90, HSP27, and HSP100. These proteins have different weights and other features which make them suit for different cellular functions. However, they have numerous similar features which make them perform almost the same functions, yet they vary in the degree of protection that they provide for the cells. The release of HSPs is controlled by four types of HSF depending on the type of stress that a cell is subjected to. HSF1 is responsible for identifying stress factors, especially heat. HSF2 performs almost similar functions as HSF1 in addition to cellular development. HSF3 is released when the stress conditions are extreme and, hence, cannot be effectively controlled by HSF1 and HSF2. HSF4 functions by inducing negative DNA transcriptions. Other tasks of HSPs include enhancing the immune system. The cells help in the management of Alzheimer's disease and other similar complications by forming protective tissues around brain cells. The cells also help in controlling cancer and heart diseases. However, their roles are more enhanced in managing cancer, extending to diagnosis and prediction. Further research on the HSPs and HSFs may extend their application to curing tumorous cells.

Evidence for Field-Evolved Resistance of Striacosta albicosta (Lepidoptera: Noctuidae) to Cry1F Bacillus thuringiensis Protein and Transgenic Corn Hybrids in Ontario, Canada.

Western bean cutworm, Striacosta albicosta (Smith) (Lepidoptera: Noctuidae), is a pest of corn (Zea mays L.) that has recently expanded its range into Ontario, Canada. Control of S. albicosta damage to corn hybrids containing event TC1507-expressing Cry1F Bacillus thuringiensis protein alone or pyramided with event MON 89034 expressing Cry1A.105 and Cry2Ab2 Bt proteins was tested in 2011-2015 in Ontario in small- and large-scale field plots with natural infestation. In 2011, significantly lower incidence and severity of kernel damage was sustained by Cry1F × Cry1A.105 + Cry2Ab2 corn compared with a non-Bt near-isogenic hybrid. However, from 2012 to 2015, there was no difference in incidence or severity of damage comparing non-Bt hybrids with Cry1F hybrids alone or pyramided with Cry1A.105 and Cry2Ab2 planted as a pure stand or with an integrated refuge (95% Bt: 5% non-Bt seeds). In 2015, neonate larvae derived from Ontario field-collections were tested in concentration-response diet-overlay bioassays with lyophilized Cry1F protein at concentrations up to 75 µg cm-2. The concentrations at which mortality of 50% (LC50) of the collections occurred ranged from approximately 10 µg cm-2 (F0) to >28 µg cm-2 (F1) in a 7-d bioassay, indicating relative insensitivity to Cry1F. Results from field experiments, laboratory bioassays, and the history of exposure to Cry1F in corn show that S. albicosta in Ontario are not controlled by Cry1F-expressing corn hybrids and provide evidence for the conclusion that the evolution of resistance to Cry1F has occurred.