Classification and regression trees are machine-learning methods for constructing prediction models from data. The models are obtained by recursively partitioning the data space and fitting a simple prediction model within each partition. As a result, the partitioning can be represented graphically as a decision tree. Classification trees are designed for dependent variables that take a finite number of unordered values, with prediction error measured in terms of misclassification cost. Regression trees are for dependent variables that take continuous or ordered discrete values, with prediction error typically measured by the squared difference between the observed and predicted values. This article gives an introduction to the subject by reviewing some widely available algorithms and comparing their capabilities, strengths, and weakness in two examples. © 2011 John Wiley & Sons, Inc. WIREs Data Mining Knowl Discov 2011 1 14-23 DOI: 10.1002/widm.8

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Technologies > Classification
Technologies > Machine Learning
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Classification and regression trees

RNA interference (RNAi) is the process of sequence-specific, post-transcriptional gene silencing in animals and plants, initiated by double-stranded RNA (dsRNA) that is homologous in sequence to the silenced gene. The mediators of sequence-specific messenger RNA degradation are 21- and 22-nucleotide small interfering RNAs (siRNAs) generated by ribonuclease III cleavage from longer dsRNAs. Here we show that 21-nucleotide siRNA duplexes specifically suppress expression of endogenous and heterologous genes in different mammalian cell lines, including human embryonic kidney (293) and HeLa cells. Therefore, 21-nucleotide siRNA duplexes provide a new tool for studying gene function in mammalian cells and may eventually be used as gene-specific therapeutics.

Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells

One of the mechanisms by which the innate immune system senses the invasion of pathogenic microorganisms is through the Toll-like receptors (TLRs), which recognize specific molecular patterns that are present in microbial components. Stimulation of different TLRs induces distinct patterns of gene expression, which not only leads to the activation of innate immunity but also instructs the development of antigen-specific acquired immunity. Here, we review the rapid progress that has recently improved our understanding of the molecular mechanisms that mediate TLR signalling.

Toll-like receptor signalling

The innate immune system in drosophila and mammals senses the invasion of microorganisms using the family of Toll receptors, stimulation of which initiates a range of host defense mechanisms. In drosophila antimicrobial responses rely on two signaling pathways: the Toll pathway and the IMD pathway. In mammals there are at least 10 members of the Toll-like receptor (TLR) family that recognize specific components conserved among microorganisms. Activation of the TLRs leads not only to the induction of inflammatory responses but also to the development of antigen-specific adaptive immunity. The TLR-induced inflammatory response is dependent on a common signaling pathway that is mediated by the adaptor molecule MyD88. However, there is evidence for additional pathways that mediate TLR ligand-specific biological responses.

Toll-like receptors.

Since the first application of the surface plasmon resonance (SPR) phenomenon for sensing almost two decades ago, this method has made great strides both in terms of instrumentation development and applications. SPR sensor technology has been commercialized and SPR biosensors have become a central tool for characterizing and quantifying biomolecular interactions. This paper attempts to review the major developments in SPR technology. Main application areas are outlined and examples of applications of SPR sensor technology are presented. Future prospects of SPR sensor technology are discussed.

Surface plasmon resonance sensors: review

Observation of molecular ions from large peptides using fast heavy ion induced desorption

An αß T cell receptor structure at 2.5 A and its orientation in the TCR-MHC complex. Science. 1996. 274: 209-219.

The tentative amino acid sequence of pooled, papain-solubilized HLA antigen heavy chains has been determined. The amino acid sequence comprises 273 residues. As the structural analyses were performed on HLA antigen heavy chains comprising a mixture of several allelic forms derived from the A, B, and possibly C loci, multiple residues were encountered in several positions. However, a quantitatively dominating residue could always be easily identified. The present data suggest that the amino acid variability of the HLA-A, -B, and -C antigens is found in restricted regions of the molecule. The COOH-terminal third of the HLA antigen heavy chain appears to be less variable than other regions of the molecule. Previous work has shown that the HLA antigen heavy chain contains two immunoglobulin-like disulphide loops. The COOH-terminal third of the heavy chain was shown to be similar in primary structure to beta 2-microglobulin and the immunoglobulin G constant domains.

Primary structure of pooled, papain-solubilized HLA-A, -B, and -C antigens.

CD40 ligand (CD40L) expression on T cells is known to play a crucial role in B cell responses. Some evidence also supports a role for CD40L-CD40 interactions in T cell responses, at least in vivo. Whether the T cell requirement for these interactions is an invariable finding, however, is less clear. Here, we provide evidence that the Ag specificity of T cells influences the requirement for CD40L. T cell hybridomas with dual reactivity for two different Ags, allo-H2-Ap and Mls(a) superantigens, display a differential requirement for CD40L expression. Whereas the response to splenic APC expressing Mls(a) Ags requires CD40L expression, the response to alloantigen-bearing APC does not. The requirement for CD40L expression for the Mls(a) response appears to reflect a strong dependence of this response on ICAM-1 (intercellular adhesion molecule-1) and the ability of CD40-mediated signals to regulate ICAM-1 expression. These findings demonstrate that CD40L-CD40-mediated cross-talk is important for some but not all T cell responses and is influenced by both the type of Ag recognized and the type of APC.

Antigen specificity of dual reactive T hybridomas determines the requirement for CD40 ligand-CD40 interactions.

Determination of attachment sites for N-linked carbohydrate groups of class II histocompatibility α-chain and analysis of possible o-linked glycosylation of α- and γ-chains

Per A. Peterson

Papers

Observation of molecular ions from large peptides using fast heavy ion induced desorption

An αß T cell receptor structure at 2.5 A and its orientation in the TCR-MHC complex. Science. 1996. 274: 209-219.

Primary structure of pooled, papain-solubilized HLA-A, -B, and -C antigens.

Antigen specificity of dual reactive T hybridomas determines the requirement for CD40 ligand-CD40 interactions.

Determination of attachment sites for N-linked carbohydrate groups of class II histocompatibility α-chain and analysis of possible o-linked glycosylation of α- and γ-chains