Methods in molecular biology
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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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iRefWeb is a bioinformatics resource that offers access to a large collection of data on protein-protein interactions in over a thousand organisms. This collection is consolidated from 14 major public databases that curate the scientific literature. ⋯ Users of iRefWeb are able to retrieve all curated interactions for a given organism or those involving a given protein (or a list of proteins), narrow down their search results based on different supporting evidence, and assess the reliability of these interactions using various criteria. They may also examine all data and annotations related to any publication that described the interaction-detection experiments. iRefWeb is freely available to the research community worldwide at http://wodaklab.org/iRefWeb .
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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.
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Targeted intrathecal (IT) drug delivery systems (IDDS) are an option in algorithms for the treatment of patients with moderate to severe chronic refractory pain when more conservative options fail. This therapy is well established and supported by several publications. ⋯ Recent technological advances, new therapeutic applications, reported complications, and the costs as well as maintenance required for this therapy require the need to stay up-to-date about new recommendations that may improve outcomes. This chapter reviews all technological issues regarding IDDS implantation with follow-up, and pharmacological recommendations published during recent years that provide evidence-based decision making process in the management of chronic pain and spasticity in patients.