Altered platelet activating factor metabolism in insulin dependent diabetes mellitus

Diabetes mellitus is associated with several abnormalities of platelet function. Recent studies have shown that the blood level of platelet activating factor (PAF), a potent inducer of platelet aggregation, is elevated in insulin dependent diabetes mellitus (IDDM) and remains unchanged in non-insulin dependent diabetes mellitus (NIDDM) patients. However, the mechanism of this increase in PAF levels has not been determined. In this study we have measured the activity of plasma PAF acetylhydrolase (an enzyme that regulates PAF levels) and lipoprotein levels in control subjects and diabetic patients. The data presented show that plasma PAF acetylhydrolase activity is significantly decreased in IDDM and is not altered in NIDDM patients. The lipoprotein levels were similar in control and diabetic subjects and there was no correlation between lipoprotein levels and PAF acetylhydrolase activity. These results suggest that the elevated levels of PAF in IDDM patients could be due to a decrease in plasma PAF acetylhydrolase activity

A hybrid algorithm to improve the accuracy of support vector machines on skewed data-sets

Over the past few years, has been shown that generalization power of Support Vector Machines (SVM) falls dramatically on imbalanced data-sets. In this paper, we propose a new method to improve accuracy of SVM on imbalanced data-sets. To get this outcome, firstly, we used undersampling and SVM to obtain the initial SVs and a sketch of the hyperplane. These support vectors help to generate new artificial instances, which will take part as the initial population of a genetic algorithm. The genetic algorithm improves the population in artificial instances from one generation to another and eliminates instances that produce noise in the hyperplane. Finally, the generated and evolved data were included in the original data-set for minimizing the imbalance and improving the generalization ability of the SVM on skewed data-sets

WTEN: An advanced coupled tensor factorization strategy for learning from imbalanced data

© Springer International Publishing AG 2016. Learning from imbalanced and sparse data in multi-mode and high-dimensional tensor formats efficiently is a significant problem in data mining research. On one hand,Coupled Tensor Factorization (CTF) has become one of the most popular methods for joint analysis of heterogeneous sparse data generated from different sources. On the other hand,techniques such as sampling,cost-sensitive learning,etc. have been applied to many supervised learning models to handle imbalanced data. This research focuses on studying the effectiveness of combining advantages of both CTF and imbalanced data learning techniques for missing entry prediction,especially for entries with rare class labels. Importantly,we have also investigated the implication of joint analysis of the main tensor and extra information. One of our major goals is to design a robust weighting strategy for CTF to be able to not only effectively recover missing entries but also perform well when the entries are associated with imbalanced labels. Experiments on both real and synthetic datasets show that our approach outperforms existing CTF algorithms on imbalanced data

Advanced Detection Tool for PDF Threats

In this paper we introduce an efficient application for malicious PDF detection: ADEPT. With targeted attacks rising over the recent past, exploring a new detection and mitigation paradigm becomes mandatory. The use of malicious PDF files that exploit vulnerabilities in well-known PDF readers has become a popular vector for targeted at- tacks, for which few efficient approaches exist. Although simple in theory, parsing followed by analysis of such files is resource-intensive and may even be impossible due to several obfuscation and reader-specific artifacts. Our paper describes a new approach for detecting such malicious payloads that leverages machine learning techniques and an efficient feature selection mechanism for rapidly detecting anomalies. We assess our approach on a large selection of malicious files and report the experimental performance results for the developed prototype

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons’ Data

We present a systematic analysis of the effects of synchronizing a large-scale, deeply characterized, multi-omic dataset to the current human reference genome, using updated software, pipelines, and annotations. For each of 5 molecular data platforms in The Cancer Genome Atlas (TCGA)—mRNA and miRNA expression, single nucleotide variants, DNA methylation and copy number alterations—comprehensive sample, gene, and probe-level studies were performed, towards quantifying the degree of similarity between the ‘legacy’ GRCh37 (hg19) TCGA data and its GRCh38 (hg38) version as ‘harmonized’ by the Genomic Data Commons. We offer gene lists to elucidate differences that remained after controlling for confounders, and strategies to mitigate their impact on biological interpretation. Our results demonstrate that the hg19 and hg38 TCGA datasets are very highly concordant, promote informed use of either legacy or harmonized omics data, and provide a rubric that encourages similar comparisons as new data emerge and reference data evolve. Gao et al. performed a systematic analysis of the effects of synchronizing the large-scale, widely used, multi-omic dataset of The Cancer Genome Atlas to the current human reference genome. For each of the five molecular data platforms assessed, they demonstrated a very high concordance between the ‘legacy’ GRCh37 (hg19) TCGA data and its GRCh38 (hg38) version as ‘harmonized’ by the Genomic Data Commons

The Integrated Genomic Landscape of Thymic Epithelial Tumors

Thymic epithelial tumors (TETs) are one of the rarest adult malignancies. Among TETs, thymoma is the most predominant, characterized by a unique association with autoimmune diseases, followed by thymic carcinoma, which is less common but more clinically aggressive. Using multi-platform omics analyses on 117 TETs, we define four subtypes of these tumors defined by genomic hallmarks and an association with survival and World Health Organization histological subtype. We further demonstrate a marked prevalence of a thymoma-specific mutated oncogene, GTF2I, and explore its biological effects on multi-platform analysis. We further observe enrichment of mutations in HRAS, NRAS, and TP53. Last, we identify a molecular link between thymoma and the autoimmune disease myasthenia gravis, characterized by tumoral overexpression of muscle autoantigens, and increased aneuploidy

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin