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

Deoxycholate-solubilized HLA antigens have been isolated from platelets and comprised a mixture of 43,000- and 39,000-dalton polypeptide chains associated with beta2-microglobulin. Limited proteolysis experiments suggested that the 39,000-dalton chain is a fragment of the intact 43,000-dalton chain. Further proteolysis of the 39,000-dalton fragment yields a 33,000-dalton component. The 39,000-dalton molecule is more acidic than both the 43,000- and the 33,000-dalton chains. Differences in the amino acid compositions of the 43,000- and 39,000-dalton species demonstrate that the peptide(s) released on generation of the 39,000-dalton component are charged. The proteolytic split most probably occurs in the COOH-terminal end, which, owing to its content of charged amino acids, most probably is not integrated into the hydrocarbon matrix of the membrane. The 39,000- and 43,000-dalton components bind detergent in micellar form and can be incorporated into liposomes. The 33,000-dalton fragment has lost the ability to bind detergent micelles and is not incorporated into liposomes.

Isolation and Properties of Detergent-Solubilized HLA Antigens Obtained from Platelets

The central event in the cellular immune response to invading pathogens is the presentation of non-self antigenic peptides by major histocompatibility complex (MHC) class I molecules to cytotoxic T lymphocytes (CTLs). As peptide binding and transport proteins, MHC class I molecules have evolved distinct biochemical and cellular strategies for acquiring antigenic peptides, providing CTLs an extracellular representation of the intracellular antigen content. Whereas efficient generation of MHC class I binding peptides depends on the intracellular, immunoproteasome-mediated proteolysis machinery, translocation of peptides into the lumen of the endoplasmic reticulum requires the endoplasmic reticulum-resident, adenosine 5'-triphosphate (ATP) binding cassette transporter associated with antigen processing (TAP). Here we show, for the first time, that immunoproteasomes, TAP complexes, and MHC class I molecules are physically associated, providing an effective means of transporting MHC class I binding peptides from their sites of generation into the lumen of the endoplasmic reticulum for loading onto MHC class I molecules. In this review, we assess the current understanding of the functional regulation of immunoproteasomes and transporter associated with antigen processing.

Functional regulation of immunoproteasomes and transporter associated with antigen processing.

In vivo regulation of the assembly and intracellular transport of class I major histocompatibility complex molecules.

Significance of the expression of HLA-DR antigen on epidermal Langerhans cells.

Papain-solubilized HLA-A, HLA-B and HLA-C antigens (referred to as HLA antigens) were cleaved by limited proteolysis to yield two large fragments. The NH2-terminal 20000-M, fragment contains one immunoglobulin-like disulfide bridge which encompasses some 55 - 60 amino acid residues. The other fragment, with a molecular weight of about 12000, is devoid of carbohydrate but contains an immunoglobulin-like disulfide bond. Fragments of similar sizes were also obtained when the isolated HLA antigen heavy chain was subjected to acid cleavage in 70% formic acid. The combined amino acid content of the isolated 22000-M, and 11 000-M, acid cleavage fragments was very similar, if not identical, to that of the intact 33000-M, HLA antigen heavy chain. These data suggested that the acid preferentially cleaved a single aspartyl-prolyl bond in the heavy chain, as supported by the fact that the 11 000-M, fragment had proline as its NH2-teirrlirial residue. Each one of the two acid cleavage fragments contained an immunoglobulin-like disulfide bridge. While the 41 NHz-terminal residues of the intact HLA antigen heavy chain did not display any homology with immunoglobulin sequences, the 31 NH2-terniinal residues of the 11 000-M, acid cleavage fragment displayed as much homology with Pz-microglobulin and the constant immunoglobulin homology regions as they did among themselves. This information strongly suggests that immunoglobulins, Pz-microglobulin and the HLA antigen heavy chains have had a related evolution. Moreover, the HLA antigen heavy chain has most probably arisen by a gene duplication event involving the same ancestral gene which gave rise to the immunoglobulin chains.

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1432-1033.1979.tb12962.x

Per A. Peterson

Papers

Isolation and Properties of Detergent-Solubilized HLA Antigens Obtained from Platelets

Functional regulation of immunoproteasomes and transporter associated with antigen processing.

In vivo regulation of the assembly and intracellular transport of class I major histocompatibility complex molecules.

Significance of the expression of HLA-DR antigen on epidermal Langerhans cells.

Similarities between immunoglobulins and transplantation antigens in amino-acid sequence and disulfide-bond distribution.