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1.  Host-directed therapy of tuberculosis based on interleukin-1 and type I interferon crosstalk 
Nature  2014;511(7507):99-103.
Tuberculosis remains second only to HIV/AIDS as the leading cause of mortality worldwide due to a single infectious agent1. Despite chemotherapy, the global tuberculosis epidemic has intensified because of HIV co-infection, the lack of an effective vaccine and the emergence of multi-drug-resistant bacteria2–5. Alternative host-directed strategies could be exploited to improve treatment efficacy and outcome, contain drug-resistant strains and reduce disease severity and mortality6. The innate inflammatory response elicited by Mycobacterium tuberculosis (Mtb) represents a logical host target7. Here we demonstrate that interleukin-1 (IL-1) confers host resistance through the induction of eicosanoids that limit excessive type I interferon (IFN) production and foster bacterial containment. We further show that, in infected mice and patients, reduced IL-1 responses and/or excessive type I IFN induction are linked to an eicosanoid imbalance associated with disease exacerbation. Host-directed immunotherapy with clinically approved drugs that augment prostaglandin E2 levels in these settings prevented acute mortality of Mtb-infected mice. Thus, IL-1 and type I IFNs represent two major counter-regulatory classes of inflammatory cytokines that control the outcome of Mtb infection and are functionally linked via eicosanoids. Our findings establish proof of concept for host-directed treatment strategies that manipulate the host eicosanoid network and represent feasible alternatives to conventional chemotherapy.
PMCID: PMC4809146  PMID: 24990750
2.  Data discipline in electronic medical records 
Canadian Family Physician  2015;61(12):e570-e576.
To evaluate the transformation in smoking status documentation after implementing a standardized intake tool as part of a primary care smoking cessation program.
A before-and-after evaluation of smoking status documentation was conducted following implementation of a smoking assessment tool. To evaluate the effect of the intervention, the Canadian Primary Care Sentinel Surveillance Network was used to extract aggregate smoking data on the study cohort.
Academic primary care clinic in Kingston, Ont.
A total of 7312 primary care patients.
As the first phase in a primary care smoking cessation program, a standardized intake tool was developed as part of a vital signs screening process.
Main outcome measures
Documented smoking status of patients before implementation of the intake tool and documented smoking status of patients in the 6 months after its implementation.
Following the implementation of the standardized intake tool, there was a 55% (P < .001; 95% CI 0.53 to 0.56) increase in the proportion of patients with a completed smoking status; more than 1100 former smokers were identified and the documented smoking rate in this cohort increased from 4.4% to 16.2%.
This study shows that the implementation of an intake tool, integrated into existing clinical operational structures, is an effective way to standardize clinical documentation and promotes the optimization of electronic medical records.
PMCID: PMC4677960  PMID: 27035007
3.  Type I IFN Induction via Poly-ICLC Protects Mice against Cryptococcosis 
PLoS Pathogens  2015;11(8):e1005040.
Cryptococcus neoformans is the most common cause of fungal meningoencephalitis in AIDS patients. Depletion of CD4 cells, such as occurs during advanced AIDS, is known to be a critical risk factor for developing cryptococcosis. However, the role of HIV-induced innate inflammation in susceptibility to cryptococcosis has not been evaluated. Thus, we sought to determine the role of Type I IFN induction in host defense against cryptococci by treatment of C. neoformans (H99) infected mice with poly-ICLC (pICLC), a dsRNA virus mimic. Unexpectedly, pICLC treatment greatly extended survival of infected mice and reduced fungal burdens in the brain. Protection from cryptococcosis by pICLC-induced Type I IFN was mediated by MDA5 rather than TLR3. PICLC treatment induced a large, rapid and sustained influx of neutrophils and Ly6Chigh monocytes into the lung while suppressing the development of eosinophilia. The pICLC-mediated protection against H99 was CD4 T cell dependent and analysis of CD4 T cell polyfunctionality showed a reduction in IL-5 producing CD4 T cells, marginal increases in Th1 cells and dramatic increases in RORγt+ Th17 cells in pICLC treated mice. Moreover, the protective effect of pICLC against H99 was diminished in IFNγ KO mice and by IL-17A neutralization with blocking mAbs. Furthermore, pICLC treatment also significantly extended survival of C. gattii infected mice with reduced fungal loads in the lungs. These data demonstrate that induction of type I IFN dramatically improves host resistance against the etiologic agents of cryptococcosis by beneficial alterations in both innate and adaptive immune responses.
Author Summary
Meningoencephalitis due to Cryptococcus neoformans is the leading cause of mortality in AIDS patients in the developing world. It has been known that depletion of CD4 T cells is the most critical predisposing factor to cryptococcosis in HIV infected patients. What has not been clear is the effect of HIV-induced innate inflammation in susceptibility to cryptococcosis. We treated C. neoformans infected mice with poly-ICLC (pICLC), a dsRNA virus mimic, to study the role of virus-induced type I IFN in host defense against cryptococcosis. PICLC treatment induced type I IFN in C. neoformans infected mice via MDA5 and significantly prolonged the survival of mice with reduced fungal burden in the brain. PICLC also protected mice from cryptococcosis caused by C. gattii. PICLC treatment recruited large numbers of neutrophils and Ly6Chigh monocytes into the lung parenchyma and suppressed eosinophilia. PICLC-mediated protection against C. neoformans required CD4 T cells and was associated with suppressed Th2 and enhanced Th17 responses. IFNγ and IL-17A were also important for pICLC-induced protection of infected mice. Our study demonstrates that induction of type I IFN dramatically improves host resistance against cryptococci by beneficial alterations in both innate and adaptive immune responses as long as CD4 cells are not depleted.
PMCID: PMC4529209  PMID: 26252005
4.  Defining Features of Protective CD4 T cell responses to Mycobacterium tuberculosis 
CD4 T cells are critical for control of Mycobacterium tuberculosis (Mtb) infection and represent the best hope for vaccine-elicited protection. However, little is understood about the properties of Mtb-specific CD4 T cells that mediate control, and the lack of correlates of protection present a significant barrier to the rational development of new vaccination and therapeutic strategies which are sorely needed. Here we discuss the features of protective CD4 T cells including recent evidence for IFN-γ dependent and independent mechanisms of protection, poor protection by terminally differentiated cells and the importance of T cell migratory capacity for the control of Mtb infection.
PMCID: PMC4122329  PMID: 25000593
5.  Intravascular staining for discrimination of vascular and tissue leukocytes 
Nature protocols  2014;9(1):209-222.
Characterization of the cellular participants in tissue immune responses is crucial to understanding infection, cancer, autoimmunity, allergy, graft rejection and other immunological processes. previous reports indicate that leukocytes in lung vasculature fail to be completely removed by perfusion. several studies suggest that intravascular staining may discriminate between tissue-localized and blood-borne cells in the mouse lung. Here we outline a protocol for the validation and use of intravascular staining to define innate and adaptive immune cells in mice. We demonstrate application of this protocol to leukocyte analyses in many tissues and we describe its use in the contexts of lymphocytic choriomeningitis virus and Mycobacterium tuberculosis infections or solid tumors. Intravascular staining and organ isolation usually takes 5–30 min per mouse, with additional time required for any subsequent leukocyte isolation, staining and analysis. In summary, this simple protocol should help enable interpretable analyses of tissue immune responses.
PMCID: PMC4428344  PMID: 24385150
6.  Control of Mycobacterium tuberculosis infection by a subset of lung parenchyma homing CD4 T cells 
Th1 cells are critical for containment of Mycobacterium tuberculosis (Mtb) infection, but little else is known about the properties of protective CD4 T cell responses. Here we show that pulmonary Th1 response against Mtb is composed of two populations that are either CXCR3hi and localize to lung parenchyma or are CX3CR1hiKLRG1hi and retained within lung blood vasculature. Mtb-specific parenchymal CD4 T cells rapidly migrate back into the lung parenchyma upon adoptive transfer, while the intravascular effectors produce the highest levels of IFNγ in vivo. Importantly, parenchymal T cells displayed greater control of infection compared to the intravascular counterparts upon transfer into susceptible T cell deficient hosts. Thus, we have identified a subset of naturally generated Mtb-specific CD4 T cells with enhanced protective capacity, and show that control of Mtb correlates with the ability of CD4 T cells to efficiently enter the lung parenchyma rather than produce high levels of IFNγ.
PMCID: PMC4010124  PMID: 24591367
7.  CD4 T Cells Promote Rather than Control Tuberculosis in the Absence of PD-1–Mediated Inhibition 
Although CD4 T cells are required for host resistance to Mycobacterium tuberculosis, they may also contribute to pathology. In this study, we examine the role of the inhibitory receptor PD-1 and its ligand PD-L1 during M. tuberculosis infection. After aerosol exposure, PD-1 knockout (KO) mice develop high numbers of M. tuberculosis-specific CD4 T cells but display markedly increased susceptibility to infection. Importantly, we show that CD4 T cells themselves drive the increased bacterial loads and pathology seen in infected PD-1 KO mice, and PD-1 deficiency in CD4 T cells is sufficient to trigger early mortality. PD-L1 KO mice also display enhanced albeit less severe susceptibility, indicating that T cells are regulated by multiple PD ligands during M. tuberculosis infection. M. tuberculosis-specific CD8 T cell responses were normal in PD-1 KO mice, and CD8 T cells only had a minor contribution to the exacerbated disease in the M. tuberculosis-infected PD-1 KO and PD-L1 KO mice. Thus, in the absence of the PD-1 pathway, M. tuberculosis benefits from CD4 T cell responses, and host resistance requires inhibition by PD-1 to prevent T cell-driven exacerbation of the infection.
PMCID: PMC4059388  PMID: 21172867
8.  Cord factor and peptidoglycan recapitulate the Th17-promoting adjuvant activity of mycobacteria through Mincle/CARD9 signaling and the inflammasome 
Although adjuvants are critical vaccine components, their modes of action are poorly understood. Here, we investigated the mechanisms by which the heat-killed mycobacteria in complete Freund’s adjuvant (CFA) promote T helper 17 (Th17) CD4+ T cell responses. We found that IL-17 secretion by CD4+ T cells following CFA immunization requires MyD88 and IL-1β/IL-1 receptor (IL-1R) signaling. Through measurement of antigen-specific responses after adoptive transfer of OTII cells, we confirmed that MyD88-dependent signaling controls Th17 differentiation rather than simply production of IL-17. Additional experiments showed that CFA-induced Th17 differentiation involves IL-1β processing by the inflammasome, as mice lacking caspase 1, ASC, or NLRP3 exhibit partially defective responses after immunization. Biochemical fractionation studies further revealed that peptidoglycan is the major component of heat-killed mycobacteria responsible for inflammasome activation. By assaying Il1b transcripts in the injection site skin of CFA-immunized mice, we found that signaling through the adaptor molecule CARD9 plays a major role in triggering pro-IL-1β expression. Moreover, we demonstrated that recognition of the mycobacterial glycolipid trehalose dimycolate (cord factor) by the C type lectin receptor mincle partially explains this CARD9 requirement. Importantly, purified peptidoglycan and cord factor administered in mineral oil synergized to recapitulate the Th17-promoting activity of CFA, and, as expected, this response was diminished in caspase 1-and CARD9-deficient mice. Taken together, these findings suggest a general strategy for the rational design of Th17-skewing adjuvants by combining agonists of the CARD9 pathway with inflammasome activators.
PMCID: PMC3719989  PMID: 23630357
9.  Plasma Heme Oxygenase-1 Levels Distinguish Latent or Successfully Treated Human Tuberculosis from Active Disease 
PLoS ONE  2013;8(5):e62618.
Tuberculosis (TB) is associated with oxidative stress and the induction of host anti-oxidants to counteract this response. Heme oxygenase-1 (HO-1) is a critical promoter of cytoprotection in diverse disease models including mycobacterial infection. Nevertheless, the pattern of expression of HO-1 in human tuberculosis has not been studied. Here, we examine expression of HO-1 in M. tuberculosis-exposed and -infected individuals and test its ability to distinguish active from latent and successfully treated TB cases. In addition, we assess correlations between plasma levels of HO-1 and cytokines closely associated with the immunopathogenesis of TB.
Cross-sectional and longitudinal analyses of levels of HO-1, acute phase proteins and pro-inflammatory cytokines were performed in plasma samples from individuals with active pulmonary, extra-pulmonary or latent TB infection and healthy controls as part of a prospective cohort study in South India.
Systemic levels of HO-1 were dramatically increased in individuals with active pulmonary and extra-pulmonary tuberculosis and particularly those with bilateral lung lesions and elevated bacillary loads in sputum. HO-1 levels effectively discriminated active from latent tuberculosis with higher predictive values than either C-reactive protein or serum amyloid protein. Moreover, there was a marked reduction in HO-1 levels in active TB cases following anti-tuberculous therapy but not in those who failed treatment. Pulmonary TB patients displaying the highest concentrations of HO-1 in plasma exhibited significantly elevated plasma levels of interleukin (IL)-10, interferon (IFN)-γ and IL-17 and diminished levels of tumor necrosis factor (TNF)-α.
These findings establish HO-1 levels as a potentially useful parameter for distinguishing active from latent or treated pulmonary tuberculosis, that is superior in this respect to the measurement of other acute inflammatory proteins.
PMCID: PMC3646008  PMID: 23671613
10.  Innate and adaptive interferons suppress IL-1α and IL-1β production by distinct pulmonary myeloid subsets during Mycobacterium tuberculosis infection 
Immunity  2011;35(6):1023-1034.
Interleukin-1 (IL-1) receptor signaling is required for control of Mycobacterium tuberculosis (Mtb) infection, yet the role of its two ligands, IL-1α and IL-1β, and the regulation of their expression in vivo are poorly understood. Here we show that in addition to IL-1β, IL-1α was independently required for host resistance. We identified two multifunctional inflammatory monocyte-macrophage and DC populations that co-expressed both IL-1 species at the single cell level in lungs of Mtb infected mice. Moreover, we demonstrated that interferons (IFNs) played important roles in fine-tuning IL-1 production by these cell populations in vivo. Type I IFNs inhibited IL-1 production by both subsets while CD4+ T cell derived IFNγ suppressed IL-1 expression selectively in inflammatory monocytes. These data provide a cellular basis for the anti-inflammatory effects of IFNs as well as pro-bacterial functions of type I IFNs during Mtb infection and reveal differential regulation of IL-1 induction by specialized cellular sources as an additional layer of complexity in the activity of IL-1 in vivo.
PMCID: PMC3246221  PMID: 22195750
11.  Cutting Edge: Caspase-1 Independent IL-1β Production Is Critical for Host Resistance to Mycobacterium tuberculosis and Does Not Require TLR Signaling In Vivo 
To investigate the respective contributions of TLR versus IL-1R mediated signals in MyD88 dependent control of Mycobacterium tuberculosis, we compared the outcome of M. tuberculosis infection in MyD88, TRIF/MyD88, IL-1R1, and IL-1β-deficient mice. All four strains displayed acute mortality with highly increased pulmonary bacterial burden suggesting a major role for IL-1β signaling in determining the MyD88 dependent phenotype. Unexpectedly, the infected MyD88 and TRIF/MyD88-deficient mice, rather than being defective in IL-1β expression, displayed increased cytokine levels relative to wild-type animals. Similarly, infected mice deficient in caspase-1 and ASC, which have critical functions in inflammasome-mediated IL-1β maturation, showed unimpaired IL-1β production and importantly, were considerably less susceptible to infection than IL-1β deficient mice. Together our findings reveal a major role for IL-1β in host resistance to M. tuberculosis and indicate that during this infection the cytokine can be generated by a mechanism that does not require TLR signaling or caspase-1. The Journal of Immunology, 2010, 184: 3326–3330.
PMCID: PMC3420351  PMID: 20200276
12.  An in vitro screening cascade to identify neuroprotective antioxidants in ALS 
Free Radical Biology & Medicine  2009;46(8):1127-1138.
Amyotrophic lateral sclerosis (ALS) is an adult-onset neurodegenerative disease, characterized by progressive dysfunction and death of motor neurons. Although evidence for oxidative stress in ALS pathogenesis is well described, antioxidants have generally shown poor efficacy in animal models and human clinical trials. We have developed an in vitro screening cascade to identify antioxidant molecules capable of rescuing NSC34 motor neuron cells expressing an ALS-associated mutation of superoxide dismutase 1. We have tested known antioxidants and screened a library of 2000 small molecules. The library screen identified 164 antioxidant molecules, which were refined to the 9 most promising molecules in subsequent experiments. Analysis of the in silico properties of hit compounds and a review of published literature on their in vivo effectiveness have enabled us to systematically identify molecules with antioxidant activity combined with chemical properties necessary to penetrate the central nervous system. The top-performing molecules identified include caffeic acid phenethyl ester, esculetin, and resveratrol. These compounds were tested for their ability to rescue primary motor neuron cultures after trophic factor withdrawal, and the mechanisms of action of their antioxidant effects were investigated. Subsequent in vivo studies can be targeted using molecules with the greatest probability of success.
PMCID: PMC2742740  PMID: 19439221
5-LOX, 5-lipoxygenase; AAPH, 2,2′-azobis(2-methylpropionamidine) dihydrochloride; ALS, amyotrophic lateral sclerosis; ARE, antioxidant response element; BBB, blood–brain barrier; CAPE, caffeic acid phenethyl ester; CNS, central nervous system; DCF, dichlorofluorescein; DMSO, dimethyl sulfoxide; Esc, esculetin; EthD1, ethidium homodimer-1; EGFP, enhanced green fluorescent protein; LTB4, leukotriene B4; MN, motor neuron; MTT, methylthiazolyldiphenyl tetrazolium bromide; NDGA, nordihydroguaiaretic acid; Nrf2, nuclear factor erythroid 2-related factor 2; OTCA, 2-oxo-l-thiazolidine-4-carboxylic acid; PBS, phosphate-buffered saline; PI, prediction interval; PSA, polar surface area; Res, resveratrol; R-PE, R-phycoerythrin; SOD1, superoxide dismutase 1; TK, thymidine kinase promoter; TRAP, total radical-trapping antioxidant parameter.; Antioxidant; Amyotrophic lateral sclerosis; Mouse; NSC34; Superoxide dismutase; Free radicals
13.  Prevention of renal injury after induction of ozone tolerance in rats submitted to warm ischaemia. 
Mediators of Inflammation  1999;8(1):37-41.
On the basis that ozone (O3) can upregulate cellular antioxidant enzymes, a morphological, biochemical and functional renal study was performed in rats undergoing a prolonged treatment with O3 before renal ischaemia. Rats were divided into four groups: (1) control, a medial abdominal incision was performed to expose the kidneys; (2) ischaemia, in animals undergoing a bilateral renal ischaemia (30 min), with subsequent reperfusion (3 h); (3) O3 + ischaemia, as group 2, but with previous treatment with O3 (0.5 mg/kg per day given in 2.5 ml O2) via rectal administration for 15 treatments; (4) O2 + ischaemia, as group 3, but using oxygen (O2) alone. Biochemical parameters as fructosamine level, phospholipase A, and superoxide dismutases (SOD) activities, as well as renal plasma flow (RPF) and glomerular filtration rate (GFR), were measured by means of plasma clearance of p-amino-hippurate and inulin, respectively. In comparison with groups 1 and 3, the RPF and GFR were significantly decreased in groups 2 and 4. Interestingly, renal homogenates of the latter groups yielded significantly higher values of phospholipase A activity and fructosamine level in comparison with either the control (1) and the O3 (3) treated groups. Moreover renal SOD activity showed a significant increase in group 3 without significant differences among groups 1, 2 and 4. Morphological alterations of the kidney were present in 100%, 88% and 30% of the animals in groups 2, 4 and 3, respectively. It is proposed that the O3 protective effect can be ascribed to the substantial possibility of upregulating the antioxidant defence system capable of counteracting the damaging effect of ischaemia. These findings suggest that, whenever possible, ozone preconditioning may represent a prophylactic approach for minimizing renal damage before transplantation.
PMCID: PMC1781776  PMID: 10704088
14.  Disruption of the autoinhibited state primes the E3 ligase parkin for activation and catalysis 
The EMBO Journal  2015;34(20):2506-2521.
The PARK2 gene is mutated in 50% of autosomal recessive juvenile parkinsonism (ARJP) cases. It encodes parkin, an E3 ubiquitin ligase of the RBR family. Parkin exists in an autoinhibited state that is activated by phosphorylation of its N-terminal ubiquitin-like (Ubl) domain and binding of phosphoubiquitin. We describe the 1.8 Å crystal structure of human parkin in its fully inhibited state and identify the key interfaces to maintain parkin inhibition. We identify the phosphoubiquitin-binding interface, provide a model for the phosphoubiquitin–parkin complex and show how phosphorylation of the Ubl domain primes parkin for optimal phosphoubiquitin binding. Furthermore, we demonstrate that the addition of phosphoubiquitin leads to displacement of the Ubl domain through loss of structure, unveiling a ubiquitin-binding site used by the E2∼Ub conjugate, thus leading to active parkin. We find the role of the Ubl domain is to prevent parkin activity in the absence of the phosphorylation signals, and propose a model for parkin inhibition, optimization for phosphoubiquitin recruitment, release of inhibition by the Ubl domain and engagement with an E2∼Ub conjugate. Taken together, this model provides a mechanistic framework for activating parkin.
PMCID: PMC4609183  PMID: 26254304
enzyme mechanism; Parkinson's disease; phosphorylation; ubiquitination; ubiquitin ligase
15.  Comparative Study of Outcome Measures and Analysis Methods for Traumatic Brain Injury Trials 
Journal of Neurotrauma  2015;32(8):581-589.
Batteries of functional and cognitive measures have been proposed as alternatives to the Extended Glasgow Outcome Scale (GOSE) as the primary outcome for traumatic brain injury (TBI) trials. We evaluated several approaches to analyzing GOSE and a battery of four functional and cognitive measures. Using data from a randomized trial, we created a “super” dataset of 16,550 subjects from patients with complete data (n=331) and then simulated multiple treatment effects across multiple outcome measures. Patients were sampled with replacement (bootstrapping) to generate 10,000 samples for each treatment effect (n=400 patients/group). The percentage of samples where the null hypothesis was rejected estimates the power. All analytic techniques had appropriate rates of type I error (≤5%). Accounting for baseline prognosis either by using sliding dichotomy for GOSE or using regression-based methods substantially increased the power over the corresponding analysis without accounting for prognosis. Analyzing GOSE using multivariate proportional odds regression or analyzing the four-outcome battery with regression-based adjustments had the highest power, assuming equal treatment effect across all components. Analyzing GOSE using a fixed dichotomy provided the lowest power for both unadjusted and regression-adjusted analyses. We assumed an equal treatment effect for all measures. This may not be true in an actual clinical trial. Accounting for baseline prognosis is critical to attaining high power in Phase III TBI trials. The choice of primary outcome for future trials should be guided by power, the domain of brain function that an intervention is likely to impact, and the feasibility of collecting outcome data.
PMCID: PMC4394163  PMID: 25317951
Glasgow Outcome Scale; outcome measures; research design; statistical data analysis; traumatic brain injury
16.  A systematic review and meta-analysis of thiazide-induced hyponatraemia: time to reconsider electrolyte monitoring regimens after thiazide initiation? 
Hyponatraemia is one of the major adverse effects of thiazide and thiazide-like diuretics and the leading cause of drug-induced hyponatraemia requiring hospital admission. We sought to review and analyze all published cases of this important condition.
Ovid Medline, Embase, Web of Science and PubMed electronic databases were searched to identify all relevant articles published before October 2013. A proportions meta-analysis was undertaken.
One hundred and two articles were identified of which 49 were single patient case reports. Meta-analysis showed that mean age was 75 (95% CI 73, 77) years, 79% were women (95% CI 74, 82) and mean body mass index was 25 (95% CI 20, 30) kg m−2. Presentation with thiazide-induced hyponatraemia occurred a mean of 19 (95% CI 8, 30) days after starting treatment, with mean trough serum sodium concentration of 116 (95% CI 113, 120) mm and serum potassium of 3.3 (95% CI 3.0, 3.5) mm. Mean urinary sodium concentration was 64 mm (95% CI 47, 81). The most frequently reported drugs were hydrochlorothiazide, indapamide and bendroflumethiazide.
Patients with thiazide-induced hyponatraemia were characterized by advanced age, female gender, inappropriate saliuresis and mild hypokalaemia. Low BMI was not found to be a significant risk factor, despite previous suggestions. The time from thiazide initiation to presentation with hyponatraemia suggests that the recommended practice of performing a single investigation of serum biochemistry 7–14 days after thiazide initiation may be insufficient or suboptimal. Further larger and more systematic studies of thiazide-induced hyponatraemia are required.
PMCID: PMC4386942  PMID: 25139696
hypokalaemia; hypokalemia; hyponatraemia; hyponatremia; thiazide; thiazide-like
17.  Human Wound Infection with Mannheimia glucosida following Lamb Bite 
Journal of Clinical Microbiology  2015;53(10):3374-3376.
Mannheimia spp. are veterinary pathogens that can cause mastitis and pneumonia in domestic cattle and sheep. While Mannheimia glucosida can be found as normal flora in oral and respiratory mucosa in sheep, there have been no reported cases of human infection with this organism.
PMCID: PMC4572521  PMID: 26202121
18.  What’s in a Name? Effect of Breed Perceptions & Labeling on Attractiveness, Adoptions & Length of Stay for Pit-Bull-Type Dogs 
PLoS ONE  2016;11(3):e0146857.
Previous research has indicated that certain breeds of dogs stay longer in shelters than others. However, exactly how breed perception and identification influences potential adopters' decisions remains unclear. Current dog breed identification practices in animal shelters are often based upon information supplied by the relinquishing owner, or staff determination based on the dog's phenotype. However, discrepancies have been found between breed identification as typically assessed by welfare agencies and the outcome of DNA analysis. In Study 1, the perceived behavioral and adoptability characteristics of a pit-bull-type dog were compared with those of a Labrador Retriever and Border Collie. How the addition of a human handler influenced those perceptions was also assessed. In Study 2, lengths of stay and perceived attractiveness of dogs that were labeled as pit bull breeds were compared to dogs that were phenotypically similar but were labeled as another breed at an animal shelter. The latter dogs were called "lookalikes." In Study 3, we compared perceived attractiveness in video recordings of pit-bull-type dogs and lookalikes with and without breed labels. Lastly, data from an animal shelter that ceased applying breed labeling on kennels were analyzed, and lengths of stay and outcomes for all dog breeds, including pit bulls, before and after the change in labeling practice were compared. In total, these findings suggest that breed labeling influences potential adopters' perceptions and decision-making. Given the inherent complexity of breed assignment based on morphology coupled with negative breed perceptions, removing breed labels is a relatively low-cost strategy that will likely improve outcomes for dogs in animal shelters.
PMCID: PMC4805246  PMID: 27008213
19.  Utility of linking primary care electronic medical records with Canadian census data to study the determinants of chronic disease: an example based on socioeconomic status and obesity 
Electronic medical records (EMRs) used in primary care contain a breadth of data that can be used in public health research. Patient data from EMRs could be linked with other data sources, such as a postal code linkage with Census data, to obtain additional information on environmental determinants of health. While promising, successful linkages between primary care EMRs with geographic measures is limited due to ethics review board concerns. This study tested the feasibility of extracting full postal code from primary care EMRs and linking this with area-level measures of the environment to demonstrate how such a linkage could be used to examine the determinants of disease. The association between obesity and area-level deprivation was used as an example to illustrate inequalities of obesity in adults.
The analysis included EMRs of 7153 patients aged 20 years and older who visited a single, primary care site in 2011. Extracted patient information included demographics (date of birth, sex, postal code) and weight status (height, weight). Information extraction and management procedures were designed to mitigate the risk of individual re-identification when extracting full postal code from source EMRs. Based on patients’ postal codes, area-based deprivation indexes were created using the smallest area unit used in Canadian censuses. Descriptive statistics and socioeconomic disparity summary measures of linked census and adult patients were calculated.
The data extraction of full postal code met technological requirements for rendering health information extracted from local EMRs into anonymized data. The prevalence of obesity was 31.6 %. There was variation of obesity between deprivation quintiles; adults in the most deprived areas were 35 % more likely to be obese compared with adults in the least deprived areas (Chi-Square = 20.24(1), p < 0.0001). Maps depicting spatial representation of regional deprivation and obesity were created to highlight high risk areas.
An area based socio-economic measure was linked with EMR-derived objective measures of height and weight to show a positive association between area-level deprivation and obesity. The linked dataset demonstrates a promising model for assessing health disparities and ecological factors associated with the development of chronic diseases with far reaching implications for informing public health and primary health care interventions and services.
PMCID: PMC4788841  PMID: 26969124
Socio-economic factors; Population health; BMI-Body Mass Index; EMR-electronic medical record; Obesity; Public health
20.  Robot Guided ‘Pen Skill’ Training in Children with Motor Difficulties 
PLoS ONE  2016;11(3):e0151354.
Motor deficits are linked to a range of negative physical, social and academic consequences. Haptic robotic interventions, based on the principles of sensorimotor learning, have been shown previously to help children with motor problems learn new movements. We therefore examined whether the training benefits of a robotic system would generalise to a standardised test of ‘pen-skills’, assessed using objective kinematic measures [via the Clinical Kinematic Assessment Tool, CKAT]. A counterbalanced, cross-over design was used in a group of 51 children (37 male, aged 5–11 years) with manual control difficulties. Improved performance on a novel task using the robotic device could be attributed to the intervention but there was no evidence of generalisation to any of the CKAT tasks. The robotic system appears to have the potential to support motor learning, with the technology affording numerous advantages. However, the training regime may need to target particular manual skills (e.g. letter formation) in order to obtain clinically significant improvements in specific skills such as handwriting.
PMCID: PMC4788189  PMID: 26967993
21.  Robust production of recombinant phosphoproteins using cell-free protein synthesis 
Nature communications  2015;6:8168.
Understanding the functional and structural consequences of site-specific protein phosphorylation has remained limited by our inability to produce phosphoproteins at high yields. Here, we address this limitation by developing a cell-free protein synthesis (CFPS) platform that employs crude extracts from a genomically recoded strain of Escherichia coli for site-specific, co-translational incorporation of phosphoserine into proteins. We apply this system to the robust production of up to milligram quantities of human MEK1 kinase. Then, we recapitulate a physiological signaling cascade in vitro to evaluate the contributions of site-specific phosphorylation of mono- and doubly-phosphorylated forms on MEK1 activity. We discover that only one phosphorylation event is necessary and sufficient for MEK1 activity. Our work sets the stage for using CFPS as a rapid high-throughput technology platform for direct expression of programmable phosphoproteins containing multiple phosphorylated residues. This work will facilitate study of phosphorylation-dependent structure-function relationships, kinase signaling networks, and kinase inhibitor drugs.
PMCID: PMC4566161  PMID: 26350765
synthetic biology; in vitro; cell-free protein synthesis; protein phosphorylation; non-standard amino acids
22.  A flexible codon in genomically recoded Escherichia coli permits programmable protein phosphorylation 
Nature communications  2015;6:8130.
Biochemical investigation of protein phosphorylation events is limited by inefficient production of the phosphorylated and non-phosphorylated forms of full-length proteins. Here, using a genomically recoded strain of E. coli with a flexible UAG codon we produce site-specific serine- or phosphoserine-containing proteins, with purities approaching 90%, from a single recombinant DNA. Specifically, we synthesize human MEK1 kinase with two serines or two phosphoserines, from one DNA template, and demonstrate programmable kinase activity. Programmable protein phosphorylation is poised to help reveal the structural and functional information encoded in the phosphoproteome.
PMCID: PMC4566969  PMID: 26350500
23.  Perioperative blood loss in total hip and knee arthroplasty: Outcomes associated with intravenous tranexamic acid use in an academic medical center 
SAGE Open Medicine  2016;4:2050312116637024.
Clinical trials have reported decreased blood loss with the use of tranexamic acid during joint reconstruction. The purpose of this study was to assess the individual practice implications of tranexamic acid use in joint replacement surgery.
Health records of adults undergoing total knee arthroplasty and total hip arthroplasty over a 12-month period were retrospectively reviewed. The treatment group comprised patients who received intravenous tranexamic acid perioperatively. The control group comprised patients who did not receive tranexamic acid.
Patients in the treatment group (n = 64) and the control group (n = 99) were well matched for demographics, orthopedic diagnosis, and comorbidities. In-hospital postsurgical mean decreases in hemoglobin concentrations were −4.05 g/dL and −4.94 g/dL in the treatment and control groups, respectively (p < 0.001). Postsurgical mean decreases in hematocrit levels were −11.2% and −14.2% in the treatment and control groups, respectively (p < 0.001). Three patients in the treatment group (5%) and 21 patients in the control group (21%) received red blood cell transfusions (p = 0.006). As compared to control, the relative risk of transfusion in the treatment group was 0.23 (95% confidence interval = 0.07–0.76) and the number needed to treat to avoid one transfusion was 7.0 (95% confidence interval = 3.8–14.4). No evidence of thromboembolism or other serious complications were observed in either group.
In patients undergoing joint replacement surgery, perioperative administration of tranexamic acid was associated with diminished blood loss and lesser resource utilization.
PMCID: PMC4790417  PMID: 27026800
Knee; hip; arthroplasty; transfusion; tranexamic acid
24.  Why two heads apart are better than two heads together: Multiple mechanisms underlie the collaborative inhibition effect in memory 
Although a group of people working together remembers more than any one individual, they recall less than their predicted potential. This finding is known as collaborative inhibition, and is generally thought to arise due to retrieval disruption. However, there is growing evidence that is inconsistent with the retrieval disruption account, suggesting that additional mechanisms also contribute to collaborative inhibition. In the current studies, we examined two alternate mechanisms -- retrieval inhibition and retrieval blocking. To identify the contributions of retrieval disruption, retrieval inhibition, and retrieval blocking we tested how collaborative recall of entirely unshared information influences subsequent individual recall and individual recognition memory. If collaborative inhibition is due solely to retrieval disruption, then there should be a release from the negative effects of collaboration on subsequent individual recall and recognition tests. If it is due to retrieval inhibition, then the negative effects of collaboration should persist on both individual recall and recognition memory tests. Finally, if it is due to retrieval blocking, then the impairment should persist on subsequent individual free recall, but not recognition, tests. Novel to the current study, results suggest that retrieval inhibition plays a role in the collaborative inhibition effect. The negative effects of collaboration persisted on a subsequent, always-individual, free recall test (Experiment 1) and also on a subsequent, always-individual, recognition test (Experiment 2). However, consistent with the retrieval disruption account, this deficit was attenuated (Experiment 1). Together, these results suggest that, in addition to retrieval disruption, multiple mechanisms play a role in collaborative inhibition.
PMCID: PMC4309738  PMID: 25068855
collaborative inhibition; retrieval disruption; retrieval inhibition; retrieval blocking; part-set cuing
25.  Cytokine and lipid mediator networks in tuberculosis 
Immunological reviews  2015;264(1):264-275.
A major approach for immunologic intervention in tuberculosis involves redirecting the outcome of the host immune response from the induction of disease to pathogen control. Cytokines and lipid mediators known as eicosanoids play key roles in regulating this balance and as such represent important targets for immunologic intervention. While the evidence for cytokine/eicosanoid function derives largely from the investigation of murine and zebra fish experimental infection models, clinical studies have confirmed the existence of many of the same pathways in tuberculosis patients. Here we summarize new data that reveal important intersections between the cytokine and eicosanoid networks in the host response to mycobacteria and discuss how targeting this crosstalk can promote resistance to lethal Mycobacterium tuberculosis infection. This approach could lead to new host-directed therapies to be used either as an adjunct for improving the efficacy of standard antibiotic treatment or for the management of drug-resistant infections.
PMCID: PMC4339232  PMID: 25703565
tuberculosis; cytokines; eicosanoids; lipoxins; prostaglandins; host-directed therapy

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