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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Technologies > Statistical Fundamentals

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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

A rat monoclonal antibody (McAb 21:9) reactive with the human invariant gamma-chain of class II major histocompatibility complex (MHC)-encoded antigens was isolated and was shown to react with the carbohydrate-carrying, COOH-terminal part of the gamma-chain. The McAb 21:9 binds to a molecule that is identified as the gamma-chain for the following reasons: it has an apparent m.w. of 33,000, similar to that of the gamma-chain; it has a two-dimensional gel migration pattern identical to that of the gamma-chain; and it associates with immature, but not processed class II antigens. When used for immunohistochemical staining on sections of normal human skin, only dendritic, class II MHC antigen, and anti-Leu-6 reactive Langerhans cells are labeled in the epidermis. HLA-DR-expressing keratinocytes present in the tuberculin reaction, cutaneous T cell lymphoma, and lichen planus, however, did not react with the anti-gamma-chain antibody, nor with a HLA-DQ-reactive antibody. Cell surface expression of the gamma-chain was observed on 1 to 3% of normal viable epidermal cells in suspension. By using double indirect immunofluorescence, it was possible to demonstrate the simultaneous binding of anti-gamma-chain, anti-HLA-DR, anti-Leu-10, and anti-Leu-6 antibodies, respectively, on the same cells, thus confirming their identity as Langerhans cells. The presence of the gamma-chain on the surface of the immunocompetent Langerhans cells may indicate that the cell surface, not the cytoplasm as has been suggested, is the site of the primary function of the gamma-chain.

Cell surface expression of invariant gamma-chain of class II histocompatibility antigens in human skin.

Isolation and partial characterization of papain-solubilized murine H-2 antigens

Earlier findings that human activated T blasts display HLA-DR determinants have been confirmed. After phytohemagglutinin activation, Percoll gradient-purified blast cells were cultured for two weeks in mitogen-derived supernatants from human lymphocyte cultures. Using purified T blasts and internal labeling procedures, it was established that T blasts actively produced HLA-DR-like chains, as assessed by sodium dodecyl sulfate polyacrylamide gel electrophoresis. Further, HLA-DR chains obtained from Epstein-Barr virus-transformed B cells and from T blasts of the same donor were compared. Two-dimensional gel electrophoretic comparisons indicated a striking homology between 29 kD and 35kD chains, obtained from the two different cell types. Peptide map analysis and preliminary amino acid sequence comparisons further supported this similarity. A more complete analysis would, however, be required to prove actual identity. The fact that human T blasts produce and display HLA-DR molecules very similar, if not identical, to those present on B cells must then be incorporated into models discussing major histocompatibility complex-restricted collaborations involving HLA-DR molecules.

Biochemical comparison of HLA-DR molecules derived from autologous human T and B lymphoblasts

A bovine adrenal cDNA library was constructed and a clone corresponding to cellular retinoic-acid-binding protein (CRABP) mRNA was isolated and sequenced. The insert of the clone corresponds to 75 bp of the 5′ untranslated portion, the whole translated and the complete 3′ untranslated portion of the bovine CRABP mRNA. A genomic Southern blot, probed with CRABP cDNA, indicated that only one copy of the gene is present in the human genome. Hybridizing bands in restricted chicken and fish DNA were also observed. Using the CRABP cDNA as probe we have located the human CRABP gene to chromosome 3 in hybridizations to mouse-human, hamster-human and rat-human cell hybrids. In situ hybridizations on rat testis cells probed with CRABP and cellular retinol-binding protein antisense mRNA indicate that both proteins are expressed in tubuli cells.

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1432-1033.1988.tb13964.x

Isolation and characterization of a cDNA clone corresponding to bovine cellular retinoic-acid-binding protein and chromosomal localization of the corresponding human gene.

Per A. Peterson

Papers

Cell surface expression of invariant gamma-chain of class II histocompatibility antigens in human skin.

Isolation and partial characterization of papain-solubilized murine H-2 antigens

Biochemical comparison of HLA-DR molecules derived from autologous human T and B lymphoblasts

Isolation and characterization of a cDNA clone corresponding to bovine cellular retinoic-acid-binding protein and chromosomal localization of the corresponding human gene.

Crystallization of and preliminary X-ray data for an intracellular vitamin A-binding protein from rat liver.