MOTIVATION: MicroRNA (miRNA) is a set of newly discovered non-coding small RNA molecules. Its significant effects have contributed to a number of critical biological events including cell proliferation, apoptosis development, as well as tumorigenesis. High-dimensional genomic discovery platforms (e.g. microarray) have been employed to evaluate the important roles of miRNAs by analyzing their expression profiling. However, because of the small total number of miRNAs and the absence of well-known endogenous controls, the traditional normalization methods for messenger RNA (mRNA) profiling analysis could not offer a suitable solution for miRNA analysis. The need for the establishment of new adaptive methods has come to the forefront. RESULTS: Locked nucleic acid (LNA)-based miRNA array was employed to profile miRNAs using colorectal cancer cell lines under different treatments. The expression pattern of overall miRNA profiling was pre-evaluated by a panel of miRNAs using Taqman-based quantitative real-time polymerase chain reaction (qRT-PCR) miRNA assays. A logistic regression model was built based on qRT-PCR results and then applied to the normalization of miRNA array data. The expression levels of 20 additional miRNAs selected from the normalized list were post-validated. Compared with other popularly used normalization methods, the logistic regression model efficiently calibrates the variance across arrays and improves miRNA microarray discovery accuracy. AVAILABILITY: Datasets and R package are available at http://gauss.usouthal.edu/publ/logit/.

This paper describes the design and implementation of a protocol scrubber, a transparent interposition mechanism for explicitly removing network attacks at both the transport and application protocol layers. The transport scrubber supports downstream passive network-based intrusion detection systems; whereas the application scrubbing mechanism supports transparent fail-closed active network-based intrusion detection systems. The transport scrubber's role is to convert ambiguous network flows into well-behaved flows that are unequivocally interpreted by all downstream endpoints. As an example, this paper presents the implementation of a TCP/IP scrubber that eliminates insertion and evasion attacks-attacks that use ambiguities to subvert detection-on passive network-based intrusion detection systems, while preserving high performance. The application protocol scrubbing mechanism is used as a substrate for building fail-closed active network based intrusion detections systems that can respond to attacks by eluding or modifying application data flows in real-time. This paper presents the high performance implementation of a general purpose transparent application-level scrubbing toolkit in the FreeBSD kernel.