Methods in molecular biology
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This chapter gives a brief overview of text-mining techniques to extract knowledge from large text collections. It describes the basis pipeline of how to come from text to relationships between biological concepts and the problems that are encountered at each step in the pipeline. We first explain how words in text are recognized as concepts. ⋯ This we call implicit information extraction. Fourth, the validation techniques to evaluate a text-mining system such as ROC curves and retrospective studies are discussed. We conclude by examining how text information can be combined with other non-textual data sources such as microarray expression data and what the future directions are for text-mining within the Internet.
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Presence of foreign tissue in a host's body would immediately lead to a strong immune response directed to destroy the alloantigens present in fetus and placenta. However, during pregnancy, the semiallogeneic fetus is allowed to grow within the maternal uterus due to multiple mechanisms of immune tolerance, which are discussed in this chapter.
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Tissue microarrays (TMAs) are produced by taking small punches from a series of paraffin-embedded (donor) tissue blocks and transferring these tissue cores into a positionally encoded array in a recipient paraffin block. Though TMAs are not used for clinical diagnosis, they have several advantages over using conventional whole histological sections for research. Tissue from multiple patients or blocks can be examined on the same slide, and only a very small amount of reagent is required to stain or label an entire array. ⋯ These advantages allow the use of TMAs in high-throughput procedures, such as screening antibodies for diagnostics and validating prognostic markers that are impractical using conventional whole tissue sections. TMAs can be used for immunohistochemistry, immunofluorescence, in situ hybridization, and conventional histochemical staining. Finally, several tissue cores may be taken without -consuming the tissue block, allowing the donor block to be returned to its archive for any additional studies.
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Human pluripotent stem cells (PSCs), which include human embryonic stem cells (ESCs) as well as induced pluripotent stem cells (iPSCs), represent an important source of cellular therapies in regenerative medicine and the study of early human development. As such, it is becoming increasingly important to develop methods for the large-scale banking of human PSC lines. There are several well-established methods for the propagation of human PSCs. ⋯ Nevertheless, as the field develops, it will no doubt become increasingly important to produce a bank of cells for clinical use without xenogeneic reagents, particularly nonhuman feeder cells which might harbor viruses with potential risk to human health or cell product integrity. Thus, even for cell lines previously exposed to xenogeneic reagents, it is important to minimize any subsequent exposure of the cell lines to additional adventitious agents. We have specifically described procedures for the growth of hESCs on Matrigel, an animal-matrix, and CELLstart, an animal-free matrix, and these can be used to produce hESCs as part of a clinical manufacturing process.
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Septic syndromes represent a major, although largely under-recognized, healthcare problem worldwide accounting for thousands of deaths every year. Although flow cytometry (FCM) remains a relatively confidential diagnostic tool, it is useful at every step of intensive care unit (ICU) patients' management. This review will focus on biomarkers measurable by FCM on a routine standardized basis and usable for the diagnosis of sepsis and for prediction of adverse outcome, occurrence of secondary nosocomial infections or guidance of putative immunotherapy relative to innate and adaptive immune dysfunctions in ICU patients. ⋯ In the specific clinical context of ICU patients' monitoring, the increasing potential of FCM is further illustrated by the use of the biomarkers listed above as stratification tools in preliminary clinical studies. The next critical step is to use these standardized FCM protocols in large multicentric clinical trials testing individualized immunotherapy. Importantly, many other markers of immune dysfunction are currently under development that could further enable the administration of targeted individualized therapy in ICU patients.