MLSeq: Machine learning interface for RNA-sequencing data

Background and Objective: In the last decade, RNA-sequencing technology has become method-of-choice and prefered to microarray technology for gene expression based classification and differential expression analysis since it produces less noisy data. Although there are many algorithms proposed for microarray data, the number of available algorithms and programs are limited for classification of RNA-sequencing data. For this reason, we developed MLSeq, to bring not only frequently used classification algorithms but also novel approaches together and make them available to be used for classification of RNA sequencing data. This package is developed using R language environment and distributed through BIOCONDUCTOR network

Power of diaphragm ultrasonography to predict weaning success

Purpose: The aim of this study; to evaluate the effects of diaphragm thickness on weaning with ultrasonography (USG)

Validation of the five-item version of the Geriatric Depression Scale (GDS-5) in a Turkish elderly population

Background Late-life depression is a geriatric syndrome which should be taken seriously. Many clinical scales have been developed for the screening of geriatric depression. Most of these have been validated at different times and in diverse populations. A five-question version of the Geriatric Depression Scale (GDS-5) was developed in 1997. This test has been validated and used in different populations. In the present study, we plan to validate the GDS-5 for the Turkish elderly population. Methods Patients aged 60 years and older who applied to the Geriatrics Clinic of our hospital between November 2018 and November 2019 were included in the study. We compared the effectiveness of Yesavage Geriatric Depression Scale-30 (YGDS-30) and GDS-5 in screening depression, based on Diagnostic and Statistical Manual of Mental Disorders Fifth Edition (DSM-5) depression criteria. Results Four hundred participants were included in the study. A significant positive correlation was found between the DSM-5 scale and the GDS-5 scale (rho = 0.726, P = 2, the sensitivity, specificity, positive predictive and negative predictive values for the GDS-5 scale were determined as 96%, 68%, 54%, and 98%, respectively. We obtained these diagnostic measures with 95% confidence intervals. Conclusion This study demonstrated the validity and reliability of the GDS-5 for Turkish elderly populations. This five-question scale will be significant in daily use to screen for depression in elderly individuals with multiple problems

Genewise dispersion estimations for real datasets.

<p>Genewise dispersion estimations for real datasets.</p

Results obtained from real datasets.

<p>Figure shows the performance results of classifiers for datasets with changing number of most significant number of genes. Note that PLDA and NBLDA methods are not performed on the transformed data. However, the results for both transformed and non-transformed data are given in the same figure for the comparison purpose.</p

Simulation results for <i>k</i> = 2, <i>d</i>_<i>kj</i> = 10%, transformation: rlog.

<p>Figure shows the performance results of classifiers with changing parameters of sample size (<i>n</i>), number of genes (<i>p</i>) and type of dispersion (<i>φ = 0</i>.<i>01</i>: very slight, <i>φ = 0</i>.<i>1</i>: substantial, <i>φ = 1</i>: very high).</p

RNA-Seq classification workflow.

<p>RNA-Seq classification workflow.</p

Description of real RNA-Seq datasets used in this study.

<p>Description of real RNA-Seq datasets used in this study.</p

Biomarker potential of the GRP78 cell-free RNA in endometrial cancer

Background Circulating tumor cells represent an opportunity for the assessment of early recurrent disease or for real-time tracing of cancer. Glucose Regulated Protein 78 (GRP78) is known in the literature as a stress factor in endometrial cancer. We aimed to investigate the importance of the gene by targeting tumor traces circulating in the cell fluids of patients with Type 1 endometrial cancer, examining cell-free RNAs in patients' samples and performing ROC analysis. Methodology In this study, 32 endometrial cancer patients and 20 controls were included. This in vitro study evaluated, the GRP78 cell-free mRNA expression levels in endometrial cancer patients, by quantitative real-time polymerase chain reaction qRT-PCR Light Cycler. Receiver operating characteristic (ROC) analysis is a tool used to identify the precision of a diagnostic test or prediction model. In our study, we investigated whether the expression levels of cell-free GRP78 mRNA could be used as a diagnostic criterion. Results The ROC curve results for endometrial cancer diagnostic criterion of cfRNA GRP78 mRNA indicated quite a significant value (p < 0.001). Conclusion Current findings show that cell-free mRNA GRP78 is now a criterion that can be used together with smear mRNA GRP78 without the need for invasive methods in endometrial cancer studies