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Glioblastoma multiforme (GBM) is the most malignant brain tumor with rapid relapse, and an early biomarker identification in GBM is of high importance. We introduced our computational methodologies to identify serum microRNAs (miRNAs) as novel biomarkers in GBM. Differentially expressed miRNAs (DEMs) in GBM were analyzed from the Gene Expression Omnibus (GEO) repository; we then combined Venn diagrams...
With the development of deep sequencing technology, isomiRs (isoform of miRNA) are consistently observed in a variety of cell types, tissues, and different cell development stages. miRNA isoforms as the products of miRNA genes, are variants which are different from mature miRNAs in length and position. Recently, many studies emphasized on isomiR and found its subtypes are differentially expression...
Identifying effective cancer biomarkers is crucial in precision medicine. Based on the high-throughput available omics data such as microarray, this paper aims to identify potential biomarker genes for hepatocellular carcinoma by bioinformatics and machine learning. We describe the gene coexpressions with network model and detect out the genes that are closely related to liver cancer infected by hepatitis...
This study reports a magnetic-bead based microfluidic system to capture cholangiocarcinoma cells by using structurally well-defined heparan sulfate (HS) octasaccharides. Ten synthetic HS octasaccharides (from SCH-43 to SCH-52) were coated on magnetic beads for this study, respectively. An integrated microfluidic system equipped with micromixers, normally-closed valves, and microchambers was developed...
Lung adenocarcinoma is the leading cause of cancer deaths in the United States. This subtype of lung cancer shows an average five-year survival rate of 15–17%, which is mainly due to late diagnosis and specific prognostic evaluation for therapy recommendation. There is an urgent need for developing reliable prognostic biomarkers to predict the success of the therapy and devise effective treatment...
The CD13/aminopeptidase N cell surface peptidase was originally identified as a marker for tumors of the hematopoietic system. Recent evidence however extends the role of CD13/APN to solid tumors as well where it is postulated to regulate angiogenesis and tumor metastasis.
Cholangiocarcinoma (CCA) is a cancer of bile duct, which possesses a high mortality rate and poor prognosis owing to its difficulties in early diagnosis and a lack of effective treatment. To improve the clinical detection, one of promising approaches is to find specific biomarkers to detect CCA cells. However, the existing screening processes are usually time-consuming and lab-intensive. In this study,...
Angiogenesis plays a vital role in tumor growth and progression. Discovering the molecular underpinnings of tumor angiogenesis has led to the development of many targeted therapies. Some of these therapies have improved patient survival, but their overall impact has been blunted by relatively modest efficacy and the eventual emergence of adaptive resistance. Developing new therapies and identifying...
In order to improve colorectal cancer (CRC) stratification, researches made before were using biomarkers, biomarker combinations or gene expression profile (GEP) clustering individually for patient classification. This study was trying to use both biomarker and GEP for the colon cancer (CC) classification. GEPs were adopted as an approach in selecting and combining biomarkers for patient classification...
Reagents binding specifically to target molecules are essential tools for clinical diagnosis and targeted therapy. Screening of target cell-surface specific affinity reagents with bench-top methods has some drawbacks, including time-consuming, labor-intensive and requirement of large-scale instrument. Microfluidic platforms may overcome these drawbacks because they could automate and complete the...
Centrosome amplification leads to the loss of regulated chromosome segregation, aneuploidy, and chromosome instability and has the possibility to be a biomarker of cancer prognosis. To explore this feasibility, resected, stage I non-small cell lung cancer (NSCLC) tissues from six survivor and six fatal cases were immunostained and scanned. Regions of interest were selected to include one cell and...
Cancer is the second leading cause of death in the United States. It is believed that many people develop cancers in their lifetime but the immune system kills these cells without the need for outside treatments. In cancer progression, however, tumor cells may evade the immune system by a mechanism that is not fully understood. Soluble fibrin (sFn), a marker for disseminated intravascular coagulation,...
Explosive compounds such as TNT and RDX have various toxicological effects on the natural environment. The goal of the earthworm microarray experiment is to unearth the biomarker for toxicity evaluation. We propose a novel recursive gene selection method which can handle the multi-class setting effectively and efficiently. The selection is performed iteratively. In each iteration, a linear multi-class...
Despite various efforts to develop new predictive models for early detection of tumor local failure in locally advanced non-small cell lung cancer (NSCLC), many patients still suffer from a high local failure rate after radiotherapy. Based on recent studies of biomarker proteins' role in predicting tumor response following radiotherapy, we hypothesize that incorporation of physical and biological...
In this paper, we present a practical algorithm to deal with the data specific classification problem when there are datasets with different properties. We proposed to integrate error rate, missing values and expert judgment as factors for determining data specific pruning to form Expert Knowledge Based Pruning (EKBP). We conduct an extensive experimental study on openly available 40 real world datasets...
Parametric estimation of perfusion using [15O]-H2O is an important biomarker for assessing treatment response in oncology clinical trials involving anti-vascular and anti-angiogenic agents. Traditionally the set of dynamic images are reconstructed independently, followed by post-reconstruction kinetic modelling. This methodology results in sub-optimal and often noisy end point parameters if voxel-by-voxel...
We developed a quantitative detection method that can reflect the degree of visceral cell oxidative DNA damage induced by exogenous compound exposures using 8-OHdG as a biomarker in vitro. In this study formaldehyde (FA) was used as a model exogenous compound and malondialdehyde (MDA) was used as a reference indicator. Rat liver cell suspension was applied in this in vitro exposure experiments as...
Glioblastomas are very aggressive cerebral tumors which are characterized by strong proliferative activity which is often assessed using the Ki-67 staining method. We propose a novel clustering method that exhibits high performance to detect Ki-67 hot-spots on immunohistochemical slides of glioblastomas.
The identification of effective biomarkers for preventive intervention or targeted therapies will increase survival rate of cancer patients dramatically. However, the unclear molecular mechanism of carcinogenesis still blocks the discovery process of effective cancer biomarkers. Network-based analyses have been introduced into computational biomarker discovery for many years. The random walks ranking...
In this paper, we investigated the use of gene coexpression network analyses to identify potential biomarkers for breast carcinoma prognosis. The network mining algorithm CODENSE is used to identify highly connected genome-wide gene co-expression networks among a variety of cancer types, and the resulted gene clusters are applied to a series of breast cancer microarray sets to categorize the patients...
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