Semiparametric methods for identification of tumor progression genes from microarray data

The use of microarray data has become quite commonplace in medical and scientific experiments. We focus here on microarray data generated from cancer studies. It is potentially important for the discovery of biomarkers to identify genes whose expression levels correlate with tumor progression. In this article, we develop statistical procedures for the identification of such genes, which we term tumor progression genes. Two methods are considered in this paper. The first is use of a proportional odds procedure, combined with false discovery rate estimation techniques to adjust for the multiple testing problem. The second method is based on order-restricted estimation procedures. The proposed methods are applied to data from a prostate cancer study. In addition, their finite-sample properties are compared using simulated data

Reliability Estimation Model for Software Components Using CEP

This paper presents a graphical complexity measure based approach with an illustration for estimating the reliability of software component. This paper also elucidates how the graph-theory concepts are applied in the field of software programming. The control graphs of several actual software components are described and the correlation between intuitive complexity and the graph-theoretic complexity are illustrated. Several properties of the graph theoretic complexity are presented which shows that the software component complexity depends only on the decision structure. A symbolic reliability model for component based software systems from the execution path of software components connected in series, parallel or mixed configuration network structure is presented with a crisp narration of the factors which influence computation of the overall reliability of component based software systems. In this paper, reliability estimation model for software components using Component Execution Paths (CEP) based on graph theory is elucidated

A comparative analysis of chronic obstructive pulmonary disease using machine learning, and deep learning

Chronic obstructive pulmonary disease (COPD) is a general clinical issue in numerous countries considered the fifth reason for inability and the third reason for mortality on a global scale within 2021. From recent reviews, a deep convolutional neural network (CNN) is used in the primary analysis of the deadly COPD, which uses the computed tomography (CT) images procured from the deep learning tools. Detection and analysis of COPD using several image processing techniques, deep learning models, and machine learning models are notable contributions to this review. This research aims to cover the detailed findings on pulmonary diseases or lung diseases, their causes, and symptoms, which will help treat infections with high performance and a swift response. The articles selected have more than 80% accuracy and are tabulated and analyzed for sensitivity, specificity, and area under the curve (AUC) using different methodologies. This research focuses on the various tools and techniques used in COPD analysis and eventually provides an overview of COPD with coronavirus disease 2019 (COVID-19) symptoms.

Empirical Bayes Identication of Tumor Progression Genes from Microarray Data

The use of microarray data has become quite commonplace in medical and scientific experiments. We focus here on microarray data generated from cancer studies. It is potentially important for the discovery of biomarkers to identify genes whose expression levels correlate with tumor progression. In this article, we propose a simple procedure for the identification of such genes, which we term tumor progression genes. The first stage involves estimation based on the proportional odds model. At the second stage, we calculate two quantities: a q -value, and a shrinkage estimator of the test statistic is constructed to adjust for the multiple testing problem. The relationship between the proposed method with the false discovery rate is studied. The proposed methods are applied to data from a prostate cancer microarray study. (© 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/55946/1/68_ftp.pd

Classification and Selection of Biomarkers in Genomic Data Using LASSO

High-throughput gene expression technologies such as microarrays have been utilized in a variety of scientific applications. Most of the work has been done on assessing univariate associations between gene expression profiles with clinical outcome (variable selection) or on developing classification procedures with gene expression data (supervised learning). We consider a hybrid variable selection/classification approach that is based on linear combinations of the gene expression profiles that maximize an accuracy measure summarized using the receiver operating characteristic curve. Under a specific probability model, this leads to the consideration of linear discriminant functions. We incorporate an automated variable selection approach using LASSO. An equivalence between LASSO estimation with support vector machines allows for model fitting using standard software. We apply the proposed method to simulated data as well as data from a recently published prostate cancer study

PubMed QUEST: The PubMed Query Search Tool. An informatics tool to aid cancer centers and cancer investigators in searching the PubMed databases

Searching PubMed for citations related to a specific cancer center or group of authors can be labor-intensive. We have created a tool, PubMed QUEST, to aid in the rapid searching of PubMed for publications of interest. It was designed by taking into account the needs of entire cancer centers as well as individual investigators. The experience of using the tool by our institution’s cancer center administration and investigators has been favorable and we believe it could easily be adapted to other institutions. Use of the tool has identified limitations of automated searches for publications based on an author’s name, especially for common names. These limitations could likely be solved if the PubMed database assigned a unique identifier to each author

A case of abdominal tuberculosis: a challenging diagnosis

Tuberculosis continues to intimidate the human race since traditional for an extremely long time not only due to its effects as a medical ailment, but also it impacts as a social and economic burden. Tuberculosis is a major health problem in developing countries. Abdominal tuberculosis is most common extra pulmonary tuberculosis. Tuberculosis can suspect in endemic countries like India, and can have various presentations and complications, it can mislead the diagnosis. Here, this case it involves small bowel, large bowel and peritoneum with different presentation

Anthelmintic activity of leaves extracts of Olea europaea on Pheretima posthuma

Parasitic roundworms (nematodes) cause substantial morbidity and mortality in livestock animals globally and considerable productivity losses to farmers. The control of these nematodes has relied largely on the use of a limited number of anthelmintics. However, resistance to many of these anthelmintics is now widespread, and, therefore, there is a need to find new drugs to ensure sustained and effective treatment and control into the future. The present study was undertaken to evaluate the anthelmintic activity of crude aqueous, Petroleum ether, chloroform and methanol extract Olea europaea leaves using Pheretima posthuma as test worms. Single concentration (5%) of extracts was tested in the bioassay, which involved the determination of the time of paralysis (P) and time of death (D) of the worms. Piperazine citrate was included as a standard reference and distilled water as a control. The results of the present study indicated that Olea europaea leaves extracts were exhibited anthelmintic activity significantly when compared with the standard (Piperazine citrate) group. Further studies are in process to isolate the active principles responsible for the activity

Prognostic meta-signature of breast cancer developed by two-stage mixture modeling of microarray data

BACKGROUND: An increasing number of studies have profiled tumor specimens using distinct microarray platforms and analysis techniques. With the accumulating amount of microarray data, one of the most intriguing yet challenging tasks is to develop robust statistical models to integrate the findings. RESULTS: By applying a two-stage Bayesian mixture modeling strategy, we were able to assimilate and analyze four independent microarray studies to derive an inter-study validated "meta-signature" associated with breast cancer prognosis. Combining multiple studies (n = 305 samples) on a common probability scale, we developed a 90-gene meta-signature, which strongly associated with survival in breast cancer patients. Given the set of independent studies using different microarray platforms which included spotted cDNAs, Affymetrix GeneChip, and inkjet oligonucleotides, the individually identified classifiers yielded gene sets predictive of survival in each study cohort. The study-specific gene signatures, however, had minimal overlap with each other, and performed poorly in pairwise cross-validation. The meta-signature, on the other hand, accommodated such heterogeneity and achieved comparable or better prognostic performance when compared with the individual signatures. Further by comparing to a global standardization method, the mixture model based data transformation demonstrated superior properties for data integration and provided solid basis for building classifiers at the second stage. Functional annotation revealed that genes involved in cell cycle and signal transduction activities were over-represented in the meta-signature. CONCLUSION: The mixture modeling approach unifies disparate gene expression data on a common probability scale allowing for robust, inter-study validated prognostic signatures to be obtained. With the emerging utility of microarrays for cancer prognosis, it will be important to establish paradigms to meta-analyze disparate gene expression data for prognostic signatures of potential clinical use