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Data and Text Processing for Health and Life Sciences

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Book Series: Advances in Experimental Medicine and Biology ISBN: 9783030138455 Year: Pages: 98 DOI: 10.1007/978-3-030-13845-5 Language: English
Publisher: Springer Nature
Subject: Medicine (General) --- Computer Science
Added to DOAB on : 2020-02-05 11:21:03
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This open access book is a step-by-step introduction on how shell scripting can help solve many of the data processing tasks that Health and Life specialists face everyday with minimal software dependencies. The examples presented in the book show how simple command line tools can be used and combined to retrieve data and text from web resources, to filter and mine literature, and to explore the semantics encoded in biomedical ontologies. To store data this book relies on open standard text file formats, such as TSV, CSV, XML, and OWL, that can be open by any text editor or spreadsheet application. The first two chapters, Introduction and Resources, provide a brief introduction to the shell scripting and describe popular data resources in Health and Life Sciences. The third chapter, Data Retrieval, starts by introducing a common data processing task that involves multiple data resources. Then, this chapter explains how to automate each step of that task by introducing the required commands line tools one by one. The fourth chapter, Text Processing, shows how to filter and analyze text by using simple string matching techniques and regular expressions. The last chapter, Semantic Processing, shows how XPath queries and shell scripting is able to process complex data, such as the graphs used to specify ontologies. Besides being almost immutable for more than four decades and being available in most of our personal computers, shell scripting is relatively easy to learn by Health and Life specialists as a sequence of independent commands. Comprehending them is like conducting a new laboratory protocol by testing and understanding its procedural steps and variables, and combining their intermediate results. Thus, this book is particularly relevant to Health and Life specialists or students that want to easily learn how to process data and text, and which in return may facilitate and inspire them to acquire deeper bioinformatics skills in the future.

Cancer Biomarkers and Targets in Digestive Organs

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ISBN: 9783039214631 9783039214648 Year: Pages: 146 DOI: 10.3390/books978-3-03921-464-8 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Medicine (General)
Added to DOAB on : 2019-12-09 11:49:15
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Identification and development of cancer biomarkers and targets have greatly accelerated progress towards precision medicine in oncology. Studies of tumor biology have not only provided insights into the mechanisms underlying carcinogenesis, but also led to discovery of molecules that have been developed into cancer biomarkers and targets. Multi-platforms for molecular characterization of tumors using next-generation genomic sequencing, immunohistochemistry, in situ hybridization, and blood-based biopsies have greatly expanded the portfolio of potential biomarkers and targets. These cancer biomarkers have been developed for diagnosis, early detection, prognosis, and prediction of treatment response. The molecular targets have been exploited for anti-cancer therapy and delivery of therapeutic agents. This Special Issue of Biomedicines focuses on recent advances in the discovery, characterization, translation, and clinical application of cancer biomarkers and targets in malignant diseases of the digestive system. The goal is to stimulate basic and translational research and clinical collaboration in this exciting field with the hope of developing strategies for prevention and early detection/diagnosis of cancer in digestive organs, and improving therapeutic and psychosocial outcomes in patients with these malignant diseases.

Keywords

colorectal cancer --- intestinal disorder --- intestinal tumors --- zebrafish --- stereotactic body radiation therapy --- immunotherapy --- biomarkers --- Asian Cancer Research Group (ACRG) --- gastric carcinoma --- molecular profiling --- precision therapy --- pembrolizumab --- predictive biomarkers --- ramucirumab --- The Cancer Genome Atlas (TCGA) --- therapeutic targets --- trastuzumab --- biliary tract carcinoma --- chemotherapy --- clinical trial --- colorectal carcinoma --- gastric carcinoma --- gastrointestinal oncology --- hepatocellular carcinoma --- immunotherapy --- pancreatic carcinoma --- targeted therapy --- Liver transplantation --- liver graft injury --- intragraft gene expression profiles --- cell adhesion molecules --- CD274 --- HFE --- hepatocellular carcinoma --- immunohistochemistry --- molecular profiling --- next-generation sequencing --- precision medicine --- predictive biomarkers --- gastrointestinal oncology --- pancreatic carcinoma --- hepatocellular carcinoma --- biliary tract carcinoma --- gastric carcinoma --- colorectal carcinoma --- stereotactic body radiation therapy --- liver transplant --- targeted therapy --- psychosocial support --- G protein–coupled receptors --- cholecystokinin --- gastrin --- gastrin-releasing peptide --- bombesin --- neurokinin --- neurotensin --- somatostatin --- circulating tumor cells --- colorectal carcinoma --- CAM invasion assay --- phenotypic mosaics --- tumor progenitor --- biomarker --- gastrointestinal malignancies --- immunotherapy --- n/a

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