Informatic system for a global tissue–fluid biorepository with a graph theory–oriented graphical user interface

The Richard Floor Biorepository supports collaborative studies of extracellular vesicles (EVs) found in human fluids and tissue specimens. The current emphasis is on biomarkers for central nervous system neoplasms but its structure may serve as a template for collaborative EV translational studies in other fields. The informatic system provides specimen inventory tracking with bar codes assigned to specimens and containers and projects, is hosted on globalized cloud computing resources, and embeds a suite of shared documents, calendars, and video-conferencing features. Clinical data are recorded in relation to molecular EV attributes and may be tagged with terms drawn from a network of externally maintained ontologies thus offering expansion of the system as the field matures. We fashioned the graphical user interface (GUI) around a web-based data visualization package. This system is now in an early stage of deployment, mainly focused on specimen tracking and clinical, laboratory, and imaging data capture in support of studies to optimize detection and analysis of brain tumour–specific mutations. It currently includes 4,392 specimens drawn from 611 subjects, the majority with brain tumours. As EV science evolves, we plan biorepository changes which may reflect multi-institutional collaborations, proteomic interfaces, additional biofluids, changes in operating procedures and kits for specimen handling, novel procedures for detection of tumour-specific EVs, and for RNA extraction and changes in the taxonomy of EVs. We have used an ontology-driven data model and web-based architecture with a graph theory–driven GUI to accommodate and stimulate the semantic web of EV science

Geological relationships and laser ablation ICP-MS U-Pb geochronology of the Saint George Batholith, southwestern New Brunswick, Canada: implications for its tectonomagmatic evolution

  The Late Silurian to Late Devonian Saint George Batholith in southwestern New Brunswick is a large composite intrusion (2000 km2) emplaced into the continental margin of the peri-Gondwanan microcontinent of Ganderia. The batholith includes: (1) Bocabec Gabbro; (2) equigranular Utopia and Wellington Lake biotite granites; (3) Welsford, Jake Lee Mountain, and Parks Brook peralkaline granites; (4) two-mica John Lee Brook Granite; (6) Jimmy Hill and Magaguadavic megacrystic granites; and (6) rapakivi Mount Douglas Granite. New LA ICP-MS in situ analyses of six samples from the Saint George Batholith are as follows: (1) U-Pb monazite crystallization age of 425.5 ± 2.1 Ma for the Utopia Granite in the western part of the batholith (2) U-Pb zircon crystallization ages of 420.4 ± 2.4 Ma and 420.0 ± 3.5 Ma for two samples of the Utopia Granite from the central part of the batholith; (3) U-Pb zircon crystallization age of 418.0 ± 2.3 Ma for the Jake Lee Mountain Granite; (4) U-Pb zircon crystallization age of 415.5 ± 2.1 Ma for the Wellington Lake Granite; and (5) U-Pb monazite crystallization age of 413.3 ± 2.1 Ma for the John Lee Brook Granite. The new geochronological together with new and existing geochemical data suggest that the protracted magmatic evolution of the Late Silurian to Early Devonian plutonic rocks is related to the transition of the Silurian Kingston arc-Mascarene backarc system from an extensional to compressional tectonic environment during collision of the Avalonian microcontinent with Laurentia followed by slab break-off.

Differentiation of Vascular Characteristics Using Contrast-Enhanced Ultrasound Imaging

Ultrasound contrast imaging has been used to assess tumour growth and regression by assessing the flow through the macro- and micro-vasculature. Our aim was to differentiate the blood kinetics of vessels such as veins, arteries and microvasculature within the limits of the spatial resolution of contrast-enhanced ultrasound imaging. The highly vascularised ovine ovary was used as a biological model. Perfusion of the ovary with SonoVue was recorded with a Philips iU22 scanner in contrast imaging mode. One ewe was treated with prostaglandin to induce vascular regression. Time-intensity curves (TIC) for different regions of interest were obtained, a lognormal model was fitted and flow parameters calculated. Parametric maps of the whole imaging plane were generated for 2 × 2 pixel regions of interest. Further analysis of TICs from selected locations helped specify parameters associated with differentiation into four categories of vessels (arteries, veins, medium-sized vessels and micro-vessels). Time-dependent parameters were associated with large veins, whereas intensity-dependent parameters were associated with large arteries. Further development may enable automation of the technique as an efficient way of monitoring vessel distributions in a clinical setting using currently available scanners.Agência financiadora Medical Research Council UK (MRC) 30800896 Science & Technology Facilities Council (STFC) ST/M007804/1 British Heart Foundation PG/10/021/28254 Life Sciences Discovery Fund 3292512 United States Department of Defense CA160415/PRCRPinfo:eu-repo/semantics/publishedVersio

Multicenter data acquisition made easy

<p>Abstract</p> <p>Background</p> <p>The process for data collection in multicenter trials may be troublesome and expensive. We report our experience with the spreadsheet function in Googledocs for this purpose.</p> <p>Methods</p> <p>In Googledocs the data manager creates a form similar to the paper case record form, which will function as a decentral data entry module. When the forms are submitted, they are presented in a spreadsheet in Googledocs, which can be exported to different standard spreadsheet formats.</p> <p>Results</p> <p>For a multicenter randomized clinical trial with five different participating hospitals we created a decentral data entry module using the spreadsheet function in Googledocs. The study comprised 332 patients (clinicaltrials.gov identifier: NCT00815698) with five visits per patient. One person at each study site entered data from the original paper based case report forms which were kept at the study sites as originals. We did not experience any technical problems using the system.</p> <p>Conclusions</p> <p>The system allowed for decentral data entry, and it was easy to use, safe, and free of charge. The spreadsheet function in Googledocs may potentially replace current expensive solutions for data acquisition in multicenter trials.</p> <p>Trial registration</p> <p>clinicaltrials.gov NCT00815698</p