Clonorchis sinensis and Clonorchiasis: The Relevance of Exploring Genetic Variation.

Parasitic trematodes (flukes) cause substantial mortality and morbidity in humans. The Chinese liver fluke, Clonorchis sinensis, is one of the most destructive parasitic worms in humans in China, Vietnam, Korea and the Russian Far East. Although C. sinensis infection can be controlled relatively well using anthelmintics, the worm is carcinogenic, inducing cholangiocarcinoma and causing major suffering in ~15 million people in Asia. This chapter provides an account of C. sinensis and clonorchiasis research-covering aspects of biology, epidemiology, pathogenesis and immunity, diagnosis, treatment and control, genetics and genomics. It also describes progress in the area of molecular biology (genetics, genomics, transcriptomics and proteomics) and highlights challenges associated with comparative genomics and population genetics. It then reviews recent advances in the sequencing and characterisation of the mitochondrial and nuclear genomes for a Korean isolate of C. sinensis and summarises salient comparative genomic work and the implications thereof. The chapter concludes by considering how advances in genomic and informatics will enable research on the genetics of C. sinensis and related parasites, as well as the discovery of new fluke-specific intervention targets.

An Approach for Some in Advanced Pharmacy Informatics Education.

Computerization is transforming health care while the quantity and complexity of biomedical knowledge rapidly grows. Today, all clinicians use health information technology (HIT), but only some pharmacists need to be cross-trained in "all" that advanced informatics entails so they can devise new and better information systems to support the pharmacy practice of the future. We propose a dual approach to informatics education in pharmacy: incorporate fundamental informatics education into pharmacy curricula for all students; and train some students interested in becoming informatics experts to design, develop, implement, and evaluate novel HIT for pharmacy. This commentary focuses specifically on the latter. It discusses the advanced pharmacy informatics training needed by some pharmacists to support innovation of HIT and to enable a shift to a more fully system-supported pharmacy practice.

A Large-Scale Informatics Database to Advance Research and Discovery of the Effects of Mild Traumatic Brain Injury.

Clinical research advances in traumatic brain injury (TBI) and behavioral health have always been restricted by the quantity and quality of the data as well as the difficulty of collecting standardized clinical elements. Those barriers, together with the complexity of evaluating TBI, have resulted in serious challenges for clinicians, researchers, and organizations interested in analyzing the short- and long-term effects of TBI. In an effort to raise awareness about existing and cost-effective ways to collect clinical data within the Department of Defense, this article describes some of the steps taken to quickly build a large-scale informatics database to facilitate collection of standardized clinical data and obtain trends of the longitudinal outcomes of service members diagnosed with mild TBI. The database was built following the Defense of Health Agency guidelines and currently has millions of longitudinal clinical data points, Department of Defense-wide clinical data for service members diagnosed with mild TBI to support population studies, and multiple built-in analytical applications to enable interactive data exploration and analysis.

Systems Medicine: The Future of Medical Genomics, Healthcare, and Wellness.

Recent advances in genomics have led to the rapid and relatively inexpensive collection of patient molecular data including multiple types of omics data. The integration of these data with clinical measurements has the potential to impact on our understanding of the molecular basis of disease and on disease management. Systems medicine is an approach to understanding disease through an integration of large patient datasets. It offers the possibility for personalized strategies for healthcare through the development of a new taxonomy of disease. Advanced computing will be an important component in effectively implementing systems medicine. In this chapter we describe three computational challenges associated with systems medicine: disease subtype discovery using integrated datasets, obtaining a mechanistic understanding of disease, and the development of an informatics platform for the mining, analysis, and visualization of data emerging from translational medicine studies.

What's hot, what's new at WTC--basic science.

The World Transplant Congress of 2014 presented a broad swath of science that touched on many disparate aspects of cell and organ transplantation, molecular and cellular immunology, systems biology, development, technology and translation into humans. A number of themes emerged this year. B cell biology and antibody chemistry were prominent, as they have been for several years. T cells, co-stimulatory blockade and regulatory T cells continue to dominate many aspects of immune research. Many new aspects of monocyte, macrophage, NK cell and NK T cell development, biology and regulation are now being explored. Diverse aspects of organ injury and the acute and chronic responses to injury are being investigated with new techniques, new targets and a resurgent vigor. Novel advances in xenotransplantation and experimental tolerance garnered much attention. Newer investigations in microbiota and nanotechnology promise significant gains in the near future. Lastly the 'omics of DNA, RNA, proteins, metabolites, bacteria and enzyme actions promise new understanding in biological systems and how to control those systems.

Neuroinformatics of the Allen Mouse Brain Connectivity Atlas.

The Allen Mouse Brain Connectivity Atlas is a mesoscale whole brain axonal projection atlas of the C57Bl/6J mouse brain. Anatomical trajectories throughout the brain were mapped into a common 3D space using a standardized platform to generate a comprehensive and quantitative database of inter-areal and cell-type-specific projections. This connectivity atlas has several desirable features, including brain-wide coverage, validated and versatile experimental techniques, a single standardized data format, a quantifiable and integrated neuroinformatics resource, and an open-access public online database (http://connectivity.brain-map.org/). Meaningful informatics data quantification and comparison is key to effective use and interpretation of connectome data. This relies on successful definition of a high fidelity atlas template and framework, mapping precision of raw data sets into the 3D reference framework, accurate signal detection and quantitative connection strength algorithms, and effective presentation in an integrated online application. Here we describe key informatics pipeline steps in the creation of the Allen Mouse Brain Connectivity Atlas and include basic application use cases.

Open-access biorepository for idiopathic pulmonary fibrosis. The way forward.

Although widespread use of animal modeling has transformed pulmonary research, the overarching goal of biomedical research is to enhance our understanding of human physiology and pathology. Thus, we believe that future gains in understanding human lung disease will be enhanced when studying patient-derived samples becomes an integral part of the investigational process. For idiopathic pulmonary fibrosis (IPF), investigators need quality human specimens, collected in a standardized fashion, along with carefully annotated, long-term clinical and outcomes data to address current knowledge gaps. Access to human lung tissues through commercial entities or the Lung Tissue Resource Consortium, an NHLBI-funded consortium, has demonstrated the feasibility of this approach. However, these samples are not always well annotated or collected uniformly and are limited in their breadth to address future IPF research needs. Therefore, we propose leveraging ongoing and future studies in IPF to establish a biorepository that will meet current and future needs of IPF investigations. Specifically, we propose that blood, cell, and lung samples, linked to robust longitudinal clinical phenotyping generated from future industry, federally sponsored, and investigator-initiated clinical studies be prospectively and uniformly collected and stored in a biorepository and linked registry. Here we outline standardized methodologies that would allow specimens and clinical data collected from different studies to be integrated and accessible to the IPF research community for investigations that will inform future basic and translational research in IPF. Such a biorepository needs the combined efforts of all stakeholders, to be driven by projected future scientific needs and to be available to all qualified researchers. We believe this infrastructure is crucial, is feasible, and would accelerate research in IPF.

Trends in information theory-based chemical structure codification.

This report offers a chronological review of the most relevant applications of information theory in the codification of chemical structure information, through the so-called information indices. Basically, these are derived from the analysis of the statistical patterns of molecular structure representations, which include primitive global chemical formulae, chemical graphs, or matrix representations. Finally, new approaches that attempt to go "back to the roots" of information theory, in order to integrate other information-theoretic measures in chemical structure coding are discussed.