The Digital Anatomist Foundational Model Server

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Distributed Queries for Quality Control Checks in Clinical Trials

Operational Quality Control (QC) checks are standard practice in clinical trials and ensure ongoing compliance with the study protocol, standard operating procedures (SOPs) and Good Clinical Practice (GCP). We present a method for defining QC checks as distributed queries over case report forms (CRF) and clinical imaging data- sources. Our distributed query system can integrate time-sensitive information in order to populate QC checks that can facilitate discrepancy resolution workflow in clinical trials

Study of an automatic trajectory following control system

It is shown that the estimator part of the Modified Partitioned Adaptive Controller, (MPAC) developed for nonlinear aircraft dynamics of a small jet transport can adapt to sensor failures. In addition, an investigation is made into the potential usefulness of the configuration detection technique used in the MPAC and the failure detection filter is developed that determines how a noise plant output is associated with a line or plane characteristic of a failure. It is shown by computer simulation that the estimator part and the configuration detection part of the MPAC can readily adapt to actuator and sensor failures and that the failure detection filter technique cannot detect actuator or sensor failures accurately for this type of system because of the plant modeling errors. In addition, it is shown that the decision technique, developed for the failure detection filter, can accurately determine that the plant output is related to the characteristic line or plane in the presence of sensor noise

Lightweight distributed XML-based integration of translational data

A distributed XQuery engine sends sub queries to separate XML data sources, and then combines the results into a single XML composite result. The system is lightweight in that it is very simple to add a new data source. An illustrative example is given for integrating data from an electronic data capture (EDC) system and a separate specimen management system

Complete Atrioventricular Heart Block From an Epilepsy Treatment

Atrioventricular (AV) heart block without adequate escape rhythm can result in sudden cardiac arrest and death. We report complete (third degree) AV block in a 16 year-old boy as a late effect of vagus nerve stimulation (VNS). He experienced brief, daily, complex partial seizures, treated with lamotrigine, levetiracetam, and the placement of Model 102 VNS at age 4. Electroencephalography (EEG) showed generalized slow spike-and-wave discharges consistent with Lennox-Gastaut syndrome. At age 12, his VNS was changed to Model 303 PereniaDURA/Model 103 Demipulse generator, set at an output current of 2.25 mA on a standard 30 seconds on, 5 minutes off paradigm. At age 16, he experienced episodes of sudden collapse followed by unconsciousness. Holter monitor showed 15 second symptomatic complete AV block without escape (Figure 1). The patient was taking psychotropic medication with potential cardiac side effects: methylphenidate (tachycardia), guanfacine (first degree AV block), and haloperidol (prolonged QT interval, Torsades de Pointes). Haloperidol, methylphenidate, and VNS were stopped without further symptoms. Off these medications, the VNS was resumed at reduced current (1.25 mA), with re-occurrence of symptomatic AV block. Again, the VNS was stopped and symptoms/heart block ceased. Psychotropic medication was resumed without any side effects

A Partnership Approach for Electronic Data Capture in Small-Scale Clinical Trials

The data collection process for clinical trials can be a tedious and error-prone process, and even a barrier to initiating small-scale studies. Electronic Data Capture (EDC) software can meet the need for faster and more reliable collection of data, but these informatics solutions can also be difficult to for researchers to set up. Establishing a full-featured commercial Clinical Trials Management System (CTMS) ecosystem is not realistic due to current institutional resource constraints. As an alternative solution, our Biomedical Informatics core (BMI) provided the technical expertise to pilot each EDC system in partnership with research teams and performed a qualitative evaluation using criteria we had established with prior research.1 When we began our pilot process, we assumed that each system’s EDC functionality would be the most important aspect and we produced a whitepaper focused on functionality.2 However, as we worked with various study teams it became clear they were willing to work around limitations since any web-based EDC software was a step up from paper forms. In our evaluation we found that the design of the Catalyst Web Tools3 made it difficult to use for clinical trials. OpenClinica4 has the most advanced functionality, for example in site management and complex CRF design, but what documentation is available is written in less user-friendly technical language. REDCap5 had a very clear advantage due to its ease of use extensive tutorials, and online training materials. In early 2010, BMI decided on REDCap as the preferred EDC software to support for small-scale studies. Since then usage has steadily increased. As of August 2010 there were 98 active REDCap users and 16 production studies at the University of Washington, Seattle Children’s, Fred Hutchinson Cancer Research Center, and Bastyr University, with collaborators from many other institutions. Post-evaluation, in addition to maintaining our installation of REDCap we are concentrating on future work in two areas: partnerships with investigators to enhance the local usage of REDCap, and informatics research to solve problems in data integration and interoperability. BMI members have contributed to the Ontology of Clinical Research.7 Additionally through our i2b2 Cross-Institutional Clinical Translational Research (CICTR) project we have identified use cases for moving data between REDCap and i2b2.8 Lastly, in keeping with our “bottom up” philosophy we are applying lightweight data integration techniques to query across REDCap and other systems, such as freezer inventory

Lightweight XML-based query, integration and visualization of distributed, multimodality brain imaging data

A need of many neuroimaging researchers is to integrate multimodality brain data that may be stored in separate databases. To address this need we have developed a framework that provides a uniform XML-based query interface across multiple online data sources. The development of this framework is driven by the need to integrate neurosurgical and neuroimaging data related to language. The data sources for the language studies are 1) a web-accessible relational database of neurosurgical cortical stimulation mapping data (CSM) that includes patient-specific 3-D coordinates of each stimulation site mapped to an MRI reconstruction of the patient brain surface; and 2) an XML database of fMRI and structural MRI data and analysis results, created automatically by a batch program we have embedded in SPM. To make these sources available for querying each is wrapped as an XML view embedded in a web service. A top level web application accepts distributed XQueries over the sources, which are dispatched to the underlying web services. Returned results can be displayed as XML, HTML, CSV (Excel format), a 2-D schematic of a parcellated brain, or a 3-D brain visualization. In the latter case the CSM patient-specific coordinates returned by the query are sent to a transformation web-service for conversion to normalized space, after which they are sent to our 3-D visualization program MindSeer, which is accessed via Java WebStart through a generated link. The anatomical distribution of pooled CSM sites can then be visualized using various surfaces derived from brain atlases. As this framework is further developed and generalized we believe it will have appeal for researchers who wish to query, integrate and visualize results across their own databases as well as those of collaborators

Profile of the Offshore Bird Assemblage in Support for the Cape Charles Wind Project

In recent years, near shore areas of the Atlantic Coast have been recognized in their ability to support significant wind resources. Offshore wind development has become one of the fastest growing energy sectors in the world and the focus of the clean energy movement of the United States. The growth of the wind industry will require the development of new technologies, and the construction of new infrastructures. Along the way will be the establishment of new government policies and guidelines to, among many issues, protect significant biological resources including migratory birds and birds of special conservation concern. Minimizing population exposure to a potential hazard is a critical for reducing negative impacts to bird populations. For wind farms, selecting a location that is away from bird concentration areas can reduce the exposure of populations to direct collision mortality and indirect disturbances that reduce the carrying capacity of their habitats. This study provides a spatially explicit profile of an offshore bird concentration area at Cape Charles, VA that can be used to detail the distribution of expected impacts for this location. The specific objectives of this project were to collect information that 1) details the spatial distribution of birds in relation to height above the water and distance from the shoreline within the proposed construction area, 2) provide a relative estimate of abundance for species detected, and 3) provide a sampling of the diversity of species utilizing the proposed area. Bird surveys were conducted on 75 days between 17 October 2011 and 15 May 2012 to encompass the fall, winter, and spring seasons. All surveys began at sunrise and lasted until 1400 EST. Birds were surveyed using a transect line that was oriented perpendicular to the shoreline and extended outward 5 km. A total of 298,519 bird observations of 110 species were made across the three survey seasons (Appendix 1). The Northern Gannet was the numerically dominant species observed and accounted for 49% of all detections. This species was followed in rank order of abundance by the Red-throated Loon, Laughing Gull, and Surf Scoter (15.7, 5.3, and 3.4 % of all detections, respectively). The remaining observations were divided between 106 additional species that included various waterfowl (ducks and geese), waterbirds (gulls, terns, and skimmers), wading birds (herons, ibis), shorebirds (sandpipers, plovers), raptors, and landbirds. We found that groups of species used the study area differently from one another. Some species were predominantly distributed within 1 km of the shoreline, some species were distributed relatively further away from shore, and other species utilized both near and far shore environments uniformly. Moreover, the overwhelming majority of birds were distributed within 30 m of the water surface and did not appear to shift their relative height use in relation to shoreline proximity

Are prices of new dwellings different? A spectral analysis of UK property vintages

The work makes two contributions to Hui’s (2011) dynamic house price classification. First, a house price ripple in cycles from Modern to Older dwellings is revealed and, second, as New housing is shown to have lower volatility than the other two. Using spectral analysis, it is argued that there is a 7½-year repeat buyer-second-hand cycle and a five year, first time buyer-New housing cycle, common to three house price vintages. These cycles reinforce each other every fifteen years, which corresponds with a Minsky super-cycle in housing finance. The equity of the owner-occupier is fortified by higher house prices whereas new builds extract embedded equity from the market. Government should support builders and facilitate access to market to first time buyers and through programmes like Help-to-Buy 1. However, to address the greater price instability that should follow, Government should impose a capital gains tax on the house seller