tranSMART-XNAT Connector tranSMART-XNAT connector-image selection based on clinical phenotypes and genetic profiles.

Motivation: TranSMART has a wide range of functionalities for translational research and a large user community, but it does not support imaging data. In this context, imaging data typically includes 2D or 3D sets of magnitude data and metadata information. Imaging data may summarise complex feature descriptions in a less biased fashion than user defined plain texts and numeric numbers. Imaging data also is contextualised by other data sets and may be analysed jointly with other data that can explain features or their variation. Results: Here we describe the tranSMART-XNAT Connector we have developed. This connector consists of components for data capture, organisation and analysis. Data capture is responsible for imaging capture either from PACS system or directly from an MRI scanner, or from raw data files. Data are organised in a similar fashion as tranSMART and are stored in a format that allows direct analysis within tranSMART. The connector enables selection and download of DICOM images and associated resources using subjects' clinical phenotypic and genotypic criteria. Availability and Implementation: tranSMART-XNAT connector is written in Java/Groovy/Grails. It is maintained and available for download at https://github.com/sh107/transmart-xnat-connector.git. Contact: sijin@ebi.ac.uk.

Opportunities and considerations for visualising neuroimaging data on very large displays.

Neuroimaging experiments can generate impressive volumes of data and many images of the results. This is particularly true of multi-modal imaging studies that use more than one imaging technique, or when imaging is combined with other assessments. A challenge for these studies is appropriate visualisation of results in order to drive insights and guide accurate interpretations. Next-generation visualisation technology therefore has much to offer the neuroimaging community. One example is the Imperial College London Data Observatory; a high-resolution (132 megapixel) arrangement of 64 monitors, arranged in a 313 degree arc, with a 6 metre diameter, powered by 32 rendering nodes. This system has the potential for high-resolution, large-scale display of disparate data types in a space designed to promote collaborative discussion by multiple researchers and/or clinicians. Opportunities for the use of the Data Observatory are discussed, with particular reference to applications in Multiple Sclerosis (MS) research and clinical practice. Technical issues and current work designed to optimise the use of the Data Observatory for neuroimaging are also discussed, as well as possible future research that could be enabled by the use of the system in combination with eye-tracking technology.

IBC's 23rd Annual Antibody Engineering, 10th Annual Antibody Therapeutics international conferences and the 2012 Annual Meeting of The Antibody Society: December 3-6, 2012, San Diego, CA.

The 23rd Annual Antibody Engineering, 10th Annual Antibody Therapeutics international conferences, and the 2012 Annual Meeting of The Antibody Society, organized by IBC Life Sciences with contributions from The Antibody Society and two Scientific Advisory Boards, were held December 3-6, 2012 in San Diego, CA. The meeting drew over 800 participants who attended sessions on a wide variety of topics relevant to antibody research and development. As a prelude to the main events, a pre-conference workshop held on December 2, 2012 focused on intellectual property issues that impact antibody engineering. The Antibody Engineering Conference was composed of six sessions held December 3-5, 2012: (1) From Receptor Biology to Therapy; (2) Antibodies in a Complex Environment; (3) Antibody Targeted CNS Therapy: Beyond the Blood Brain Barrier; (4) Deep Sequencing in B Cell Biology and Antibody Libraries; (5) Systems Medicine in the Development of Antibody Therapies/Systematic Validation of Novel Antibody Targets; and (6) Antibody Activity and Animal Models. The Antibody Therapeutics conference comprised four sessions held December 4-5, 2012: (1) Clinical and Preclinical Updates of Antibody-Drug Conjugates; (2) Multifunctional Antibodies and Antibody Combinations: Clinical Focus; (3) Development Status of Immunomodulatory Therapeutic Antibodies; and (4) Modulating the Half-Life of Antibody Therapeutics. The Antibody Society's special session on applications for recording and sharing data based on GIATE was held on December 5, 2012, and the conferences concluded with two combined sessions on December 5-6, 2012: (1) Development Status of Early Stage Therapeutic Antibodies; and (2) Immunomodulatory Antibodies for Cancer Therapy.

Guidelines for information about therapy experiments: a proposal on best practice for recording experimental data on cancer therapy.

BACKGROUND: Biology, biomedicine and healthcare have become data-driven enterprises, where scientists and clinicians need to generate, access, validate, interpret and integrate different kinds of experimental and patient-related data. Thus, recording and reporting of data in a systematic and unambiguous fashion is crucial to allow aggregation and re-use of data. This paper reviews the benefits of existing biomedical data standards and focuses on key elements to record experiments for therapy development. Specifically, we describe the experiments performed in molecular, cellular, animal and clinical models. We also provide an example set of elements for a therapy tested in a phase I clinical trial. FINDINGS: We introduce the Guidelines for Information About Therapy Experiments (GIATE), a minimum information checklist creating a consistent framework to transparently report the purpose, methods and results of the therapeutic experiments. A discussion on the scope, design and structure of the guidelines is presented, together with a description of the intended audience. We also present complementary resources such as a classification scheme, and two alternative ways of creating GIATE information: an electronic lab notebook and a simple spreadsheet-based format. Finally, we use GIATE to record the details of the phase I clinical trial of CHT-25 for patients with refractory lymphomas. The benefits of using GIATE for this experiment are discussed. CONCLUSIONS: While data standards are being developed to facilitate data sharing and integration in various aspects of experimental medicine, such as genomics and clinical data, no previous work focused on therapy development. We propose a checklist for therapy experiments and demonstrate its use in the 131Iodine labeled CHT-25 chimeric antibody cancer therapy. As future work, we will expand the set of GIATE tools to continue to encourage its use by cancer researchers, and we will engineer an ontology to annotate GIATE elements and facilitate unambiguous interpretation and data integration.

Establishing a knowledge trail from molecular experiments to clinical trials.

During the development cycle of a new antibody therapy, the therapeutic agent will be tested on subsequently more biologically complex models. New experiments' designs are based upon data gathered from prior models. New researchers who inherit the data and researchers from groups with different cultures or expertise are often called upon to interpret these data. Experiments which are not recorded consistently or employ ambiguous terminology can make interpreting these results difficult. The researcher who had originally collected the data may not be at hand to correct any misunderstanding or offer clarification and data can be unknowingly misused. This introduces an element of risk into the therapy development process. We have developed a reporting guideline for recording therapy experiments. This guideline consists of a checklist of data to be recorded from antibody therapy experiments performed in molecular, cellular, animal and clinical model.

Best use of experimental data in cancer informatics.

The welcome attitude of the 'omics community, journals and funders of research towards data sharing, coupled with successful implementations of data standards, has resulted in resource dissemination and a better understanding of many diseases, including cancer. Sharing experiment data is beneficial in terms of knowledge generation, allowing reproduction and validation of results. An adherence to a reporting guideline enables full-value extraction from costly data; this is an inexpensive method to increased quality without incurring disproportionate costs. For therapy data in particular, easy access to the range of new approaches and the ability to perform valid comparisons between these approaches would be especially useful. We discuss initiatives that support resource sharing and summarize three reporting guidelines for experiment data that have been adopted successfully. Finally, we introduce a new guideline that encompasses the diverse data types in therapeutic experiments, which is intended to be of use to the cancer therapeutics community.

Biliary pleural fistula detected by hepatobiliary scintigraphy.

A biliary pleural fistula is a rare complication secondary to trauma, infection, malignancy, biliary disease, malignancies, or percutaneous procedures. Its presence may be suggested by the development of a right pleural effusion in a patient with such history and can be confirmed with a hepatobiliary scan or endoscopic retrograde cholangiopancreatography. Patients are treated with antibiotics and the fistula usually spontaneously closes. If after 2 weeks the fistula persists, percutaneous drainage, sphincterotomy, or biliary stent placement can be performed to promote healing of the fistula. In complicated cases, open thoracic surgery or video-assisted thoracic surgery may be required.

The importance of paternal family history in hereditary breast cancer is underappreciated by health care professionals.

OBJECTIVES: Cancer genetics clinics have been established in many major oncology centers worldwide in recent years. For such specialized clinics to fulfill their function, primary care physicians need to identify high-risk patients for referral. METHODS: We conducted a survey to evaluate the level of awareness of breast cancer risk factors and hereditary breast cancer among health care providers and patients. RESULTS: 284 health care professionals, 221 medical students, 104 breast cancer patients and 177 cancer-free women participated in the study. Less than half of the patients with breast cancer were aware of their risk for another breast cancer or of the increased breast cancer risk of their sisters and daughters. Less than one quarter of the health care professionals and medical students knew the importance of paternal family history in the evaluation for hereditary breast cancer. Only about half of the health care professionals and medical students and less than one third of the breast cancer patients and cancer-free women knew about genetic testing and prophylactic mastectomy as options for women at risk for hereditary breast cancer. CONCLUSIONS: Health care providers and medical students lack basic genetic knowledge and are not aware of emerging diagnostic and preventive options for hereditary breast cancer. Inclusion of cancer genetics in the continuing medical education of health care providers is important to promote such awareness.