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Eckermann S.,University of Wollongong | Willan A.R.,SickKids Research Institute | Willan A.R.,University of Toronto
PharmacoEconomics | Year: 2013

Risk sharing arrangements relate to adjusting payments for new health technologies given evidence of their performance over time. Such arrangements rely on prospective information regarding the incremental net benefit of the new technology, and its use in practice. However, once the new technology has been adopted in a particular jurisdiction, randomized clinical trials within that jurisdiction are likely to be infeasible and unethical in the cases where they would be most helpful, i.e. with current evidence of positive while uncertain incremental health and net monetary benefit. Informed patients in these cases would likely be reluctant to participate in a trial, preferring instead to receive the new technology with certainty. Consequently, informing risk sharing arrangements within a jurisdiction is problematic given the infeasibility of collecting prospective trial data. To overcome such problems, we demonstrate that global trials facilitate trialling post adoption, leading to more complete and robust risk sharing arrangements that mitigate the impact of costs of reversal on expected value of information in jurisdictions who adopt while a global trial is undertaken. More generally, optimally designed global trials offer distinct advantages over locally optimal solutions for decision makers and manufacturers alike: avoiding opportunity costs of delay in jurisdictions that adopt; overcoming barriers to evidence collection; and improving levels of expected implementation. Further, the greater strength and translatability of evidence across jurisdictions inherent in optimal global trial design reduces barriers to translation across jurisdictions characteristic of local trials. Consequently, efficiently designed global trials better align the interests of decision makers and manufacturers, increasing the feasibility of risk sharing and the expected strength of evidence over local trials, up until the point that current evidence is globally sufficient. © 2013 Springer International Publishing Switzerland.

Douda D.N.,SickKids Research Institute | Douda D.N.,Hospital for Sick Children | Douda D.N.,Harvard University | Khan M.A.,SickKids Research Institute | And 4 more authors.
Proceedings of the National Academy of Sciences of the United States of America | Year: 2015

Neutrophils cast neutrophil extracellular traps (NETs) to defend the host against invading pathogens. Although effective against microbial pathogens, a growing body of literature now suggests that NETs have negative impacts on many inflammatory and autoimmune diseases. Identifying mechanisms that regulate the process termed "NETosis" is important for treating these diseases. Although two major types of NETosis have been described to date, mechanisms regulating these forms of cell death are not clearly established. NADPH oxidase 2 (NOX2) generates large amounts of reactive oxygen species (ROS), which is essential for NOX-dependent NETosis. However, major regulators of NOX-independent NETosis are largely unknown. Here we show that calcium activated NOX-independent NETosis is fast and mediated by a calcium-activated small conductance potassium (SK) channel member SK3 and mitochondrial ROS. Although mitochondrial ROS is needed for NOX-independent NETosis, it is not important for NOX-dependent NETosis. We further demonstrate that the activation of the calcium-activated potassium channel is sufficient to induce NOX-independent NETosis. Unlike NOX-dependent NETosis, NOX-independent NETosis is accompanied by a substantially lower level of activation of ERK and moderate level of activation of Akt, whereas the activation of p38 is similar in both pathways. ERK activation is essential for the NOX-dependent pathway, whereas its activation is not essential for the NOX-independent pathway. Despite the differential activation, both NOX-dependent and -independent NETosis require Akt activity. Collectively, this study highlights key differences in these two major NETosis pathways and provides an insight into previously unknown mechanisms for NOX-independent NETosis.

Jin L.,Louisiana State University | Batra S.,Louisiana State University | Douda D.N.,SickKids Research Institute | Douda D.N.,University of Toronto | And 4 more authors.
Journal of Immunology | Year: 2014

Severe bacterial sepsis leads to a proinflammatory condition that can manifest as septic shock, multiple organ failure, and death. Neutrophils are critical for the rapid elimination of bacteria; however, the role of neutrophil chemoattractant CXCL1 in bacterial clearance during sepsis remains elusive. To test the hypothesis that CXCL1 is critical to host defense during sepsis, we used CXCL1- deficient mice and bone marrow chimeras to demonstrate the importance of this molecule in sepsis. We demonstrate that CXCL1 plays a pivotal role in mediating host defense to polymicrobial sepsis after cecal ligation and puncture in gene-deficient mice. CXCL1 appears to be essential for restricting bacterial outgrowth and death in mice. CXCL1 derived from both hematopoietic and resident cells contributed to bacterial clearance. Moreover, CXCL1 is essential for neutrophil migration, expression of proinflammatory mediators, activation of NF-kB and MAPKs, and upregulation of adhesion molecule ICAM-1. rIL-17 rescued impaired host defenses in cxcl1-/-mice. CXCL1 is important for IL-17A production via Th17 differentiation. CXCL1 is essential for NADPH oxidase-mediated reactive oxygen species production and neutrophil extracellular trap formation. This study reveals a novel role for CXCL1 in neutrophil recruitment via modulating T cell function and neutrophil-related bactericidal functions. These studies suggest that modulation of CXCL1 levels in tissues and blood could reduce bacterial burden in sepsis. © 2014 by The American Association of Immunologists, Inc.

Burrell K.,SickKids Research Institute | Hill R.P.,Ontario Cancer Institute | Hill R.P.,University of Toronto | Zadeh G.,University of Toronto | Zadeh G.,University of Western Ontario
PLoS ONE | Year: 2012

Radiation therapy (RT) is a widely accepted treatment strategy for many central nervous system (CNS) pathologies. However, despite recognized therapeutic success, significant negative consequences are associated with cranial irradiation (CR), which manifests months to years post-RT. The pathophysiology and molecular alterations that culminate in the long-term detrimental effects of CR are poorly understood, though it is thought that endothelial injury plays a pivotal role in triggering cranial injury. We therefore explored the contribution of bone marrow derived cells (BMDCs) in their capacity to repair and contribute to neo-vascularization following CR. Using high-resolution in vivo optical imaging we have studied, at single-cell resolution, the spatio-temporal response of BMDCs in normal brain following CR. We demonstrate that BMDCs are recruited specifically to the site of CR, in a radiation dose and temporal-spatial manner. We establish that BMDCs do not form endothelial cells but rather they differentiate predominantly into inflammatory cells and microglia. Most notably we provide evidence that more than 50% of the microglia in the irradiated region of the brain are not resident microglia but recruited from the bone marrow following CR. These results have invaluable therapeutic implications as BMDCs may be a primary therapeutic target to block acute and long-term inflammatory response following CR. Identifying the critical steps involved in the sustained recruitment and differentiation of BMDCs into microglia at the site of CR can provide new insights into the mechanisms of injury following CR offering potential therapeutic strategies to counteract the long-term adverse effects of CR. © 2012 Burrell et al.

Chen M.H.,University of Toronto | Willan A.R.,SickKids Research Institute
Statistics in Medicine | Year: 2014

Value-of-information methods are applied to assess the evidence in support of a new diagnostic test and, where the evidence is insufficient for decision making, to determine the optimal sample size for future studies. Net benefit formulations are derived under various diagnostic and treatment scenarios. The expressions for the expected opportunity loss of adopting strategies that include the new test are given. Expressions for the expected value of information from future studies are derived. One-sample and two-sample designs, with or without known prevalence, are considered. An example is given. © 2014 John Wiley & Sons, Ltd.

Li Y.,University of Toronto | Goldenberg A.,University of Toronto | Goldenberg A.,SickKids Research Institute | Wong K.-C.,University of Toronto | Zhang Z.,University of Toronto
Bioinformatics | Year: 2014

Motivation: Systematic identification of microRNA (miRNA) targets remains a challenge. The miRNA overexpression coupled with genome-wide expression profiling is a promising new approach and calls for a new method that integrates expression and sequence information.Results: We developed a probabilistic scoring method called targetScore. TargetScore infers miRNA targets as the transformed fold-changes weighted by the Bayesian posteriors given observed target features. To this end, we compiled 84 datasets from Gene Expression Omnibus corresponding to 77 human tissue or cells and 113 distinct transfected miRNAs. Comparing with other methods, targetScore achieves significantly higher accuracy in identifying known targets in most tests. Moreover, the confidence targets from targetScore exhibit comparable protein downregulation and are more significantly enriched for Gene Ontology terms. Using targetScore, we explored oncomir-oncogenes network and predicted several potential cancer-related miRNA-messenger RNA interactions. © 2013 The Author 2013. Published by Oxford University Press. All rights reserved.

Wang B.,SickKids Research Institute | Wang B.,Stanford University | Mezlini A.M.,SickKids Research Institute | Mezlini A.M.,University of Toronto | And 10 more authors.
Nature Methods | Year: 2014

Recent technologies have made it cost-effective to collect diverse types of genome-wide data. Computational methods are needed to combine these data to create a comprehensive view of a given disease or a biological process. Similarity network fusion (SNF) solves this problem by constructing networks of samples (e.g., patients) for each available data type and then efficiently fusing these into one network that represents the full spectrum of underlying data. For example, to create a comprehensive view of a disease given a cohort of patients, SNF computes and fuses patient similarity networks obtained from each of their data types separately, taking advantage of the complementarity in the data. We used SNF to combine mRNA expression, DNA methylation and microRNA (miRNA) expression data for five cancer data sets. SNF substantially outperforms single data type analysis and established integrative approaches when identifying cancer subtypes and is effective for predicting survival. © 2014 Nature America, Inc.

Chen M.H.,SickKids Research Institute | Chen M.H.,University of Toronto | Willan A.R.,SickKids Research Institute | Willan A.R.,University of Toronto
Clinical Trials | Year: 2013

Background Most often, sample size determinations for randomized clinical trials are based on frequentist approaches that depend on somewhat arbitrarily chosen factors, such as type I and II error probabilities and the smallest clinically important difference. As an alternative, many authors have proposed decision-theoretic (full Bayesian) approaches, often referred to as value of information methods that attempt to determine the sample size that maximizes the difference between the trials expected utility and its expected cost, referred to as the expected net gain. Taking an industry perspective, Willan proposes a solution in which the trials utility is the increase in expected profit. Furthermore, Willan and Kowgier, taking a societal perspective, show that multistage designs can increase expected net gain. Purpose The purpose of this article is to determine the optimal sample size using value of information methods for industry-based, multistage adaptive randomized clinical trials, and to demonstrate the increase in expected net gain realized. At the end of each stage, the trials sponsor must decide between three actions: continue to the next stage, stop the trial and seek regulatory approval, or stop the trial and abandon the drug. Methods A model for expected total profit is proposed that includes consideration of per-patient profit, disease incidence, time horizon, trial duration, market share, and the relationship between trial results and probability of regulatory approval. The proposed method is extended to include multistage designs with a solution provided for a two-stage design. An example is given. Results Significant increases in the expected net gain are realized by using multistage designs. Limitations The complexity of the solutions increases with the number of stages, although far simpler near-optimal solutions exist. The method relies on the central limit theorem, assuming that the sample size is sufficiently large so that the relevant statistics are normally distributed. Conclusion From a value of information perspective, the use of multistage designs in industry trials leads to significant gains in the expected net gain. © 2012 The Author(s).

Cheng O.Z.,SickKids Research Institute | Cheng O.Z.,University of Toronto | Palaniyar N.,SickKids Research Institute | Palaniyar N.,University of Toronto
Frontiers in Immunology | Year: 2013

Neutrophil extracellular traps (NETs) are beneficial antimicrobial defense structures that can help fight against invading pathogens in the host. However, recent studies reveal that NETs exert adverse effects in a number of diseases including those of the lung. Many inflammatory lung diseases are characterized with a massive influx of neutrophils into the airways. Neutrophils contribute to the pathology of these diseases. To date, NETs have been identified in the lungs of cystic fibrosis (CF), acute lung injury (ALI), allergic asthma, and lungs infected with bacteria, virus, or fungi. These microbes and several host factors can stimulate NET formation, or NETosis. Different forms of NETosis have been identified and are dependent on varying types of stimuli. All of these pathways however appear to result in the formation of NETs that contain DNA, modified extracellular histones, proteases, and cytotoxic enzymes. Some of the NET components are immunogenic and damaging to host tissue. Innate immune collectins, such as pulmonary surfactant protein D (SP-D), bind NETs, and enhance the clearance of dying cells and DNA by alveolar macrophages. In many inflammatory lung diseases, bronchoalveolar SP-D levels are altered and its deficiency results in the accumulation of DNA in the lungs. Some of the other therapeutic molecules under consideration for treating NET-related diseases include DNases, antiproteases, myeloperoxidase (MPO) inhibitors, peptidylarginine deiminase-4 inhibitors, and anti-histone antibodies. NETs could provide important biological advantage for the host to fight against certain microbial infections. However, too much of a good thing can be a bad thing. Maintaining the right balance of NET formation and reducing the amount of NETs that accumulate in tissues are essential for harnessing the power of NETs with minimal damage to the hosts. © 2013 Cheng and Palaniyar.

Douglas G.M.,University of Toronto | Wilson M.D.,SickKids Research Institute | Wilson M.D.,University of Toronto | Moses A.M.,University of Toronto
Molecular Biology and Evolution | Year: 2016

Characteristics of pseudogene degeneration at the coding level are well-known, such as a shift toward neutral rates of nonsynonymous substitutions and gain of frameshift mutations. In contrast, degeneration of pseudogene transcriptional regulation is not well understood. Here, we test two predictions of regulatory degeneration along a pseudogenized lineage: 1) Decreased transcription factor (TF) binding and 2) accelerated evolution in putative cis-regulatory regions. We find evidence for decreased TF binding levels nearby two primate pseudogenes compared with functional liver genes. However, the majority of TF-bound sequences nearby pseudogenes do not show evidence for lineage-specific accelerated rates of evolution. We conclude that decreases in TF binding level could be a marker for regulatory degeneration, while sequence degeneration in primate cis-regulatory modules may be obscured by background rates of TF binding site turnover. © 2016 The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

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