Methods in molecular biology
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Over the past 20 years, advances in high-throughput biological techniques and the availability of computational resources including fast Internet access have resulted in an explosion of large genome-scale data sets "big data." While such data are readily available for download and personal use and analysis from a variety of repositories, often such analysis requires access to seldom-available computational skills. As a result a number of databases have emerged to provide scientists with online tools enabling the interrogation of data without the need for sophisticated computational skills beyond basic knowledge of Internet browser utility. This chapter focuses on the Eukaryotic Pathogen Databases (EuPathDB: http://eupathdb.org) Bioinformatic Resource Center (BRC) and illustrates some of the available tools and methods.
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The diagnosis of sepsis, and especially its differentiation from sterile inflammation, may be challenging. TREM-1, the triggering receptor expressed on myeloid cells-1, is an amplifier of the innate immune response. ⋯ In this chapter, we review the numerous studies that have evaluated the usefulness of sTREM-1 concentration determination for the diagnosis and the prognosis evaluation of sepsis or localized infection. Nowadays, sandwich ELISA kits are available and the assay is described.
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Metabolites, the chemical entities that are transformed during metabolism, provide a functional readout of cellular biochemistry that offers the best prediction of the phenotype and the nature of a disease. Mass spectrometry now allows thousands of metabolites to be quantitated. ⋯ These sophisticated statistical techniques are computationally intensive. This chapter reviews techniques applicable to metabolomics approaches to disease.
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In a normal spontaneous menstrual cycle, the luteal phase is characterized by the production and secretion of estradiol (E) and progesterone (P) from the corpus luteum (CL) in an episodic manner. The steroidogenesis of the CL is dependent on continued tonic luteinizing hormone (LH) secretion (Fritz and Speroff, Clinical gynecologic endocrinology and infertility, 8th edn. Wolters Kluwer, Lippincott Williams & Wilkins, Philadelphia, 2011). ⋯ Progesterone concentrations normally rise sharply after ovulation, reaching a peak approximately 8 days after the LH surge. Since the secretion of E and P during the luteal phase is episodic and correlates closely with LH pulses, relatively low mid-luteal progesterone levels can be found in the course of a totally normal luteal phase (Fritz and Speroff, Clinical gynecologic endocrinology and infertility, 8th edn. Wolters Kluwer, Lippincott Williams & Wilkins, Philadelphia, 2011).
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Multiple sequence alignment (MSA) is a fundamental and ubiquitous technique in bioinformatics used to infer related residues among biological sequences. Thus alignment accuracy is crucial to a vast range of analyses, often in ways difficult to assess in those analyses. ⋯ We outline a set of desirable characteristics for effective benchmarking, and evaluate each strategy in light of them. We conclude that there is currently no universally applicable means of benchmarking MSA, and that developers and users of alignment tools should base their choice of benchmark depending on the context of application-with a keen awareness of the assumptions underlying each benchmarking strategy.