Citations

Abstract Motivation: The Biological Reference Repository (BioR) is a toolkit for annotating variants. BioR stores public and user-specific annotation sources in indexed JSON-encoded flat files (catalogs). The BioR toolkit provides the functionality to combine and retrieve annotation from these catalogs via the command-line interface. Several catalogs from commonly used annotation sources and instructions for creating user-specific catalogs are provided. Commands from the toolkit can be combined with other UNIX commands for advanced annotation processing. We also provide instructions for the development of custom annotation pipelines. Availability and implementation: The package is implemented in Java and makes use of external tools written in Java and Perl. The toolkit can be executed on Mac OS X 10.5 and above or any Linux distribution. The BioR application, quickstart, and user guide documents and many biological examples are available at http://bioinformaticstools.mayo.edu . Contact: Kocher.JeanPierre@mayo.edu Supplementary information: Supplementary data are available at Bioinformatics online.

SummaryObjectiveTo better understand the relationship between efficacy and perampanel dose, integrated actual (last) dose data from three phase III trials and an extension study (blinded Conversion Period; open‐label Maintenance Period) were analyzed.MethodsSeizure frequency data were analyzed in patients who were randomized to and completed the 13‐week Maintenance Period of the phase III studies on perampanel 8 mg, and who received an actual (last) dose of 12 mg during (1) the extension 16‐week blinded Conversion Period or (2) weeks 1–13 of the extension Maintenance Period. Due to a treatment‐by‐region interaction (p = 0.042), analyses excluded patients from the Latin America region (n = 162/1,480; 10.9% of the treated cohort).ResultsOf 372 patients randomized to 8 mg in the phase III studies, 273 completed the Maintenance Period at 8 mg and 267 entered the extension study. In patients who then had an actual (last) dose of 12 mg during the extension blinded Conversion Period (n = 217), median percent change in seizure frequency per 28 days improved from −32.4% (8 mg, phase III Maintenance Period) to −44.2% (12 mg, extension blinded Conversion Period); 50% responder rates increased slightly from 37.3% to 42.9%. In patients who completed the phase III studies on 8 mg and had an actual (last) dose of 12 mg during weeks 1–13 of the extension Maintenance Period (n = 181), median percent change in seizure frequency per 28 days improved from −34.1% (phase III Maintenance Period) to −46.0% (weeks 1–13 extension Maintenance Period); 50% responder rates were 39.2% and 46.4%. Seizure control remained substantially unchanged in patients who completed the phase III studies at 12 mg and continued on that dose during the extension.SignificanceIncreasing perampanel dose from 8 to 12 mg can produce additional benefits in seizure control in at least some patients who tolerate the higher dose.

Background: The current systems of healthcare delivery in the United States suffer from problems that often leave patients with inadequate quality of care. In their report entitled “Crossing the Quality Chasm,” the Institute of Medicine (IOM) identified reasons for poor and/or inconsistent quality of healthcare delivery and provided recommendations to improve it. The purpose of this review is to describe features of an innovative web-based program called the Thyroid Cancer Care Collaborative (TCCC) and see how it addresses IOM recommendations to improve the quality of healthcare delivery. Summary: The TCCC addresses the three actionable IOM recommendations directed at healthcare organizations and clinicians to redesign the care process. It does so by exploiting information technology (IT) in ways suggested by the IOM, and it fits within a set of 10 rules provided by the IOM. Some features of the TCCC include: (i) automated disease staging based on three validated scoring systems; (ii) highly illustrated educational videos on all aspects of thyroid cancer care; (iii) personalized clinical decision-making modules for clinicians and physicians; (iv) portability of data to share among treating physicians; (v) virtual tumor boards, “ask the expert,” and frequently asked questions modules; (vi) physician workflow integration; and (vii) data for comprehensive analysis to answer difficult questions in thyroid cancer management. Conclusion: The TCCC has the potential to improve thyroid cancer care delivery and offers several benefits to patients, clinicians, and researchers. The TCCC is a valuable example of how IOM initiatives can improve the healthcare system.

Objectives/Hypothesis Pharyngocutaneous fistulae (PCF) are known to occur in nearly one‐third of patients after salvage total laryngectomy (STL). PCF has severe impact on duration of admission and costs and quality of life and can even cause severe complications such as bleeding, infection and death. Many patients need further surgical procedures. The implications for functional outcome and survival are less clear. Several studies have shown that using vascularized tissue from outside the radiation field reduces the risk of PCFs following STL. This review and meta‐analysis aims to identify the evidence base to support this hypothesis. Data Sources English language literature from 2004 to 2013 Review Methods We searched the English language literature for articles published on the subject from 2004 to 2013. Results Adequate data was available to identify pooled incidence rates from seven articles. The pooled relative risk derived from 591 patients was 0.63 (95% CI: 0.47 to 0.85), indicating that patients who have flap reconstruction/reinforcement reduced their risk of PCF by one‐third. Conclusion This pooled analysis suggests that there is a clear advantage in using vascularized tissue from outside the radiation field in the laryngectomy defect. While some studies show a clear reduction in PCF rates, others suggest that the fistulae that occur are smaller and rarely need repair. Laryngoscope , 124:1848–1853, 2014

AbstractBackgroundWell‐differentiated thyroid cancer (WDTC) recurs in up to 30% of patients. Guidelines from the American Thyroid Association (ATA) and the National Comprehensive Cancer Network (NCCN) provide valuable parameters for the management of recurrent disease, but fail to guide the clinician as to the multitude of factors that should be taken into account. The Thyroid Cancer Care Collaborative (TCCC) is a web‐based repository of a patient's clinical information. Ten clinical decision‐making modules (CDMMs) process this information and display individualized treatment recommendations.MethodsWe conducted a review of the literature and analysis of the management of patients with recurrent/persistent WDTC.ResultsSurgery remains the most common treatment in recurrent/persistent WDTC and can be performed with limited morbidity in experienced hands. However, careful observation may be the recommended course in select patients. Reoperation yields biochemical remission rates between 21% and 66%. There is a reported 1.2% incidence of permanent unexpected nerve paralysis and a 3.5% incidence of permanent hypoparathyroidism. External beam radiotherapy and percutaneous ethanol ablation have been reported as therapeutic alternatives. Radioactive iodine as a primary therapy has been reported previously for metastatic lymph nodes, but is currently advocated by the ATA as an adjuvant to surgery.ConclusionThe management of recurrent lymph nodes is a multifactorial decision and is best determined by a multidisciplinary team. The CDMMs allow for easy adoption of contemporary knowledge, making this information accessible to both patient and clinician. © 2014 Wiley Periodicals, Inc. Head Neck 37: 605–614, 2015

Abstract Objective Risk scores and accelerated diagnostic protocols can identify chest pain patients with low risk of major adverse cardiac event who could be discharged early from the ED , saving time and costs. We aimed to derive and validate a chest pain score and accelerated diagnostic protocol ( ADP ) that could safely increase the proportion of patients suitable for early discharge. Methods Logistic regression identified statistical predictors for major adverse cardiac events in a derivation cohort. Statistical coefficients were converted to whole numbers to create a score. Clinician feedback was used to improve the clinical plausibility and the usability of the final score (Emergency Department Assessment of Chest pain Score [ EDACS ]). EDACS was combined with electrocardiogram results and troponin results at 0 and 2 h to develop an ADP ( EDACS‐ADP ). The score and EDACS‐ADP were validated and tested for reproducibility in separate cohorts of patients. Results In the derivation ( n = 1974) and validation ( n = 608) cohorts, the EDACS‐ADP classified 42.2% (sensitivity 99.0%, specificity 49.9%) and 51.3% (sensitivity 100.0%, specificity 59.0%) as low risk of major adverse cardiac events, respectively. The intra‐class correlation coefficient for categorisation of patients as low risk was 0.87. Conclusion The EDACS‐ADP identified approximately half of the patients presenting to the ED with possible cardiac chest pain as having low risk of short‐term major adverse cardiac events, with high sensitivity. This is a significant improvement on similar, previously reported protocols. The EDACS‐ADP is reproducible and has the potential to make considerable cost reductions to health systems.