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1.  No Laughing Matter 
The Permanente Journal  2015;19(1):94-95.
A cough, then breathlessness; laughter then breathlessness. Is the cause the tubes or the gut?
PMCID: PMC4315388  PMID: 25663214
2.  Neurovirulence and Immunogenicity of Attenuated Recombinant Vesicular Stomatitis Viruses in Nonhuman Primates 
Journal of Virology  2014;88(12):6690-6701.
In previous work, a prototypic recombinant vesicular stomatitis virus Indiana serotype (rVSIV) vector expressing simian immunodeficiency virus (SIV) gag and human immunodeficiency virus type 1 (HIV-1) env antigens protected nonhuman primates (NHPs) from disease following challenge with an HIV-1/SIV recombinant (SHIV). However, when tested in a stringent NHP neurovirulence (NV) model, this vector was not adequately attenuated for clinical evaluation. For the work described here, the prototypic rVSIV vector was attenuated by combining specific G protein truncations with either N gene translocations or mutations (M33A and M51A) that ablate expression of subgenic M polypeptides, by incorporation of temperature-sensitive mutations in the N and L genes, and by deletion of the VSIV G gene to generate a replicon that is dependent on trans expression of G protein for in vitro propagation. When evaluated in a series of NHP NV studies, these attenuated rVSIV variants caused no clinical disease and demonstrated a very significant reduction in neuropathology compared to wild-type VSIV and the prototypic rVSIV vaccine vector. In spite of greatly increased in vivo attenuation, some of the rVSIV vectors elicited cell-mediated immune responses that were similar in magnitude to those induced by the much more virulent prototypic vector. These data demonstrate novel approaches to the rational attenuation of VSIV NV while retaining vector immunogenicity and have led to identification of an rVSIV N4CT1gag1 vaccine vector that has now successfully completed phase I clinical evaluation.
IMPORTANCE The work described in this article demonstrates a rational approach to the attenuation of vesicular stomatitis virus neurovirulence. The major attenuation strategy described here will be most likely applicable to other members of the Rhabdoviridae and possibly other families of nonsegmented negative-strand RNA viruses. These studies have also enabled the identification of an attenuated, replication-competent rVSIV vector that has successfully undergone its first clinical evaluation in humans. Therefore, these studies represent a major milestone in the development of attenuated rVSIV, and likely other vesiculoviruses, as a new vaccine platform(s) for use in humans.
PMCID: PMC4054374  PMID: 24696472
3.  Garlic Revisited: Antimicrobial Activity of Allicin-Containing Garlic Extracts against Burkholderia cepacia Complex 
PLoS ONE  2014;9(12):e112726.
The antimicrobial activities of garlic and other plant alliums are primarily based on allicin, a thiosulphinate present in crushed garlic bulbs. We set out to determine if pure allicin and aqueous garlic extracts (AGE) exhibit antimicrobial properties against the Burkholderia cepacia complex (Bcc), the major bacterial phytopathogen for alliums and an intrinsically multiresistant and life-threatening human pathogen. We prepared an AGE from commercial garlic bulbs and used HPLC to quantify the amount of allicin therein using an aqueous allicin standard (AAS). Initially we determined the minimum inhibitory concentrations (MICs) of the AGE against 38 Bcc isolates; these MICs ranged from 0.5 to 3% (v/v). The antimicrobial activity of pure allicin (AAS) was confirmed by MIC and minimum bactericidal concentration (MBC) assays against a smaller panel of five Bcc isolates; these included three representative strains of the most clinically important species, B. cenocepacia. Time kill assays, in the presence of ten times MIC, showed that the bactericidal activity of AGE and AAS against B. cenocepacia C6433 correlated with the concentration of allicin. We also used protein mass spectrometry analysis to begin to investigate the possible molecular mechanisms of allicin with a recombinant form of a thiol-dependent peroxiredoxin (BCP, Prx) from B. cenocepacia. This revealed that AAS and AGE modifies an essential BCP catalytic cysteine residue and suggests a role for allicin as a general electrophilic reagent that targets protein thiols. To our knowledge, we report the first evidence that allicin and allicin-containing garlic extracts possess inhibitory and bactericidal activities against the Bcc. Present therapeutic options against these life-threatening pathogens are limited; thus, allicin-containing compounds merit investigation as adjuncts to existing antibiotics.
PMCID: PMC4249831  PMID: 25438250
4.  The Temporal Rating of Emergency Non-Technical skills (TRENT) index for self and others: psychometric properties and emotional responses 
BMC Medical Education  2014;14:240.
To enhance the non-technical skills (NTS) assessment literature by developing a reliable and valid peer and self-assessment tool for NTS in a simulated ward setting to include emotional reactions: the Temporal Rating of Emergency Non-Technical skills (TRENT) Index. The paper aims to document (1) the psychometric properties of the TRENT index (e.g., reliability, idiosyncrasy biases) and (2) its validity in terms of performance-emotional associations in the high fidelity simulated ward environment.
Two samples of doctors (Ns =150 & 90) taking part in emergency simulations provided both self and peer-assessment of NTS, with the second sample also providing self-assessments of mood. The psychometric properties of the TRENT were explored for self- and peer-assessment, and pre- and post-simulation environment mood was used to assess validity.
A psychometrically reliable and valid 5-factor assessment of NTS was developed. While there was evidence for both intra-rater and inter-rater reliability, inter-rater idiosyncrasy was also observed. Self-rated, but not peer-rated, negative performance was positively associated with post simulation negative mood.
These are the first results that pertain to inter-, intra-rater reliability as well as idiosyncratic biases in NTS assessment and the first to show that simulator performance can influence mood after assessment. Potential clinical carry-over effects of mood are discussed.
Electronic supplementary material
The online version of this article (doi:10.1186/s12909-014-0240-y) contains supplementary material, which is available to authorized users.
PMCID: PMC4330940  PMID: 25431182
Self-assessment; Peer-assessment; Performance; Stress; Emotions; Reliability; Inter-rater
5.  Multiple Nuclear Localization Signals Mediate Nuclear Localization of the GATA Transcription Factor AreA 
Eukaryotic Cell  2014;13(4):527-538.
The Aspergillus nidulans GATA transcription factor AreA activates transcription of nitrogen metabolic genes in response to nitrogen limitation and is known to accumulate in the nucleus during nitrogen starvation. Sequence analysis of AreA revealed multiple nuclear localization signals (NLSs), five putative classical NLSs conserved in fungal AreA orthologs but not in the Saccharomyces cerevisiae functional orthologs Gln3p and Gat1p, and one putative noncanonical RRX33RXR bipartite NLS within the DNA-binding domain. In order to identify the functional NLSs in AreA, we constructed areA mutants with mutations in individual putative NLSs or combinations of putative NLSs and strains expressing green fluorescent protein (GFP)-AreA NLS fusion genes. Deletion of all five classical NLSs individually or collectively did not affect utilization of nitrogen sources or AreA-dependent gene expression and did not prevent AreA nuclear localization. Mutation of the bipartite NLS conferred the inability to utilize alternative nitrogen sources and abolished AreA-dependent gene expression likely due to effects on DNA binding but did not prevent AreA nuclear localization. Mutation of all six NLSs simultaneously prevented AreA nuclear accumulation. The bipartite NLS alone strongly directed GFP to the nucleus, whereas the classical NLSs collaborated to direct GFP to the nucleus. Therefore, AreA contains multiple conserved NLSs, which show redundancy and together function to mediate nuclear import. The noncanonical bipartite NLS is conserved in GATA factors from Aspergillus, yeast, and mammals, indicating an ancient origin.
PMCID: PMC4000105  PMID: 24562911
6.  Measuring the Absolute Abundance of the Smad Transcription Factors Using Quantitative Immunoblotting 
In the age of systems biology, biologists seek to quantify the absolute number of molecules in experimentally treated samples. Immunoblotting remains a technique of choice for assessing the relative differences between the protein levels in different samples. Here we discuss how to exploit immunoblotting for estimating the number of Smad transcription factor molecules per cell. We focus on describing the calculations needed to analyze the data. Our methods are generally applicable to the quantification of other cellular proteins.
PMCID: PMC4168016  PMID: 20694679
Transforming Growth Factor-β; Smad; Cell signaling; Quantitative; Immunoblot; Western blot
7.  Thoracic Endometriosis Syndrome: Case Report and Review of the Literature 
The Permanente Journal  2014;18(3):61-65.
Thoracic endometriosis syndrome is the presence of endometrial tissue in or around the lung. Thoracic endometriosis syndrome consists of four distinct clinical entities: catamenial pneumothorax, catamenial hemothorax, hemoptysis, and pulmonary nodules. Thoracic endometriosis syndrome is a rare and complex condition, and diagnosis is often delayed or missed by clinicians, which can result in recurrent hospitalizations and other complications. Current treatments include hormone therapy and, where warranted, surgical intervention. We report the case of a 48-year-old woman with endometriosis causing bowel obstruction and concurrent catamenial pneumothorax.
PMCID: PMC4116267  PMID: 25102519
8.  Variation in Outcomes for Risk-Stratified Pediatric Cardiac Surgical Operations: An Analysis of the STS Congenital Heart Surgery Database 
The Annals of thoracic surgery  2012;94(2):564-572.
We evaluated outcomes for groups of risk-stratified operations in The Society of Thoracic Surgeons Congenital Heart Surgery Database to provide contemporary benchmarks and examine variation between centers.
Patients undergoing surgery from 2005 to 2009 were included. Centers with more than 10% missing data were excluded. Discharge mortality and postoperative length of stay (PLOS) among patients discharged alive were calculated for groups of risk-stratified operations using the five Society of Thoracic Surgeons-European Association for Cardio-Thoracic Surgery Congenital Heart Surgery mortality categories (STAT Mortality Categories). Power for analyzing between-center differences in outcome was determined for each STAT Mortality Category. Variation was evaluated using funnel plots and Bayesian hierarchical modeling.
In this analysis of risk-stratified operations, 58,506 index operations at 73 centers were included. Overall discharge mortality (interquartile range among programs with more than 10 cases) was as follows: STAT Category 1 = 0.55% (0% to 1.0%), STAT Category 2 = 1.7% (1.0% to 2.2%), STAT Category 3 = 2.6% (1.1% to 4.4%), STAT Category 4 = 8.0% (6.3% to 11.1%), and STAT Category 5 = 18.4% (13.9% to 27.9%). Funnel plots with 95% prediction limits revealed the number of centers characterized as outliers by STAT Mortality Categories was as follows: Category 1 = 3 (4.1%), Category 2 = 1 (1.4%), Category 3 = 7 (9.7%), Category 4 = 13 (17.8%), and Category 5 = 13 (18.6%). Between-center variation in PLOS was analyzed for all STAT Categories and was greatest for STAT Category 5 operations.
This analysis documents contemporary benchmarks for risk-stratified pediatric cardiac surgical operations grouped by STAT Mortality Categories and the range of outcomes among centers. Variation was greatest for the more complex operations. These data may aid in the design and planning of quality assessment and quality improvement initiatives.
PMCID: PMC4006082  PMID: 22704799
9.  Structural Transition from Helices to Hemihelices 
PLoS ONE  2014;9(4):e93183.
Helices are amongst the most common structures in nature and in some cases, such as tethered plant tendrils, a more complex but related shape, the hemihelix forms. In its simplest form it consists of two helices of opposite chirality joined by a perversion. A recent, simple experiment using elastomer strips reveals that hemihelices with multiple reversals of chirality can also occur, a richness not anticipated by existing analyses. Here, we show through analysis and experiments that the transition from a helical to a hemihelical shape, as well as the number of perversions, depends on the height to width ratio of the strip's cross-section. Our findings provides the basis for the deterministic manufacture of a variety of complex three-dimensional shapes from flat strips.
PMCID: PMC3997338  PMID: 24759785
10.  Introducing structured caregiver training in stroke care: findings from the TRACS process evaluation study 
BMJ Open  2014;4(4):e004473.
To evaluate the process of implementation of the modified London Stroke Carers Training Course (LSCTC) in the Training Caregivers After Stroke (TRACS) cluster randomised trial and contribute to the interpretation of the TRACS trial results. The LSCTC was a structured competency-based training programme designed to help develop the knowledge and skills (eg, patient handling or transfer skills) essential for the day-to-day management of disabled survivors of stroke. The LSCTC comprised 14 components, 6 were mandatory (and delivered to all) and 8 non-mandatory, to be delivered based on individual assessment of caregiver need.
Process evaluation using non-participant observation, documentary analysis and semistructured interviews.
Patients with stroke (n=38), caregivers (n=38), stroke unit staff (n=53).
10 of the 36 stroke units participating in the TRACS trial in four English regions (Yorkshire, North West, South East and South West, Peninsula).
Preparatory cascade training on delivery of the LSCTC did not reach all staff and did not lead to multidisciplinary team (MDT) wide understanding of, engagement with or commitment to the LSCTC. Although senior therapists in most intervention units observed developed ownership of the LSCTC, MDT working led to separation rather than integration of delivery of LSCTC elements. Organisational features of stroke units and professionals’ patient-focused practices limited the involvement of caregivers. Caregivers were often invited to observe therapy or care being provided by professionals but had few opportunities to make sense of, or to develop knowledge and stroke-specific skills provided by the LSCTC. Where provided, caregiver training came very late in the inpatient stay. Assessment and development of caregiver competence was not commonly observed.
Contextual factors including service improvement pressures and staff perceptions of the necessity for and work required in caregiver training impacted negatively on implementation of the caregiver training intervention. Structured caregiver training programmes such as the LSCTC are unlikely to be practical in settings with short inpatient stays. Stroke units where early supported discharge is in place potentially offer a more effective vehicle for introducing competency based caregiver training.
LINKED TRACS Cluster randomised controlled trial number
PMCID: PMC4010820  PMID: 24736035
Qualitative Research; Rehabilitation
11.  Effects of pretesting implicit self-determined motivation on behavioral engagement: evidence for the mere measurement effect at the implicit level 
Research into individuals’ intended behavior and performance has traditionally adopted explicitly measured, self-report constructs, and outcomes. More recently, research has shown that completing explicit self-report measures of constructs may effect subsequent behavior, termed the “mere measurement” effect. The aim of the present experiment was to investigate whether implicit measures of motivation showed a similar mere measurement effect on subsequent behavior. It may be the case that measuring the implicit systems affects subsequent implicit interventions (e.g., priming), observable on subsequent behavior. Priming manipulations were also given to participants in order to investigate the interaction between measurement and priming of motivation. Initially, a 2 [implicit association test (IAT: present vs. absent) ×2 (Prime: autonomous vs. absent) and a 2 (IAT: present vs. absent) × 2 (Prime: controlled vs. absent)] between participants designs were conducted, these were them combined into a 2 (IAT: present vs. absent) ×3 (Prime: autonomous vs. controlled vs. absent) between participants design, with attempts at a novel task taken as the outcome measure. Implicit measure completion significantly decreased behavioral engagement. Priming autonomous motivation significantly facilitated, and controlled motivation significantly inhibited performance. Finally, there was a significant implicit measurement × priming interaction, such that priming autonomous motivation only improved performance in the absence of the implicit measure. Overall, this research provides an insight into the effects of implicit measurement and priming of motivation and the combined effect of completing both tasks on behavior.
PMCID: PMC3923262  PMID: 24592249
implicit measurement; mere measurement effect; self-determination theory; implicit association test; priming
12.  The INSPIRED study: a randomised controlled trial of the Whole Person Model of disease self-management for people with type 2 diabetes 
BMC Public Health  2014;14:134.
The prevalence of type 2 diabetes has increased dramatically in the last decade, and is continuing to rise. It is a chronic condition, often related to obesity, diet and sedentary lifestyles, and can lead to significant health complications, disability and early death. Diabetes is commonly associated with depression, which can impact significantly on a person’s ability to manage their illness and, consequently, on disease outcomes. Disease self-management is fundamental in diabetes and requires support from multiple health professionals and the active participation of the person, including in maintaining a healthy lifestyle. The Whole Person Model was developed in order to integrate emotional and behavioural aspects into a self-management program for people with type 2 diabetes. Here we describe a study designed to test the efficacy of the Whole Person Model of disease self-management in type 2 diabetes.
In a parallel-group randomised trial, 180 people with type 2 diabetes of between 2–10 years duration will be recruited via invitation through the Australian National Diabetes Services Scheme. Participants will undergo baseline assessment, followed by randomisation to either intervention or control condition. Control participants will receive fact sheets containing key information about diabetes self-management. The intervention group will receive the INSPIRED (Individual Support & Resources for Diabetes) Manual and be assigned a Health Coach. The INSPIRED Manual consists of six modules that provide key information about diabetes and disease management using the Whole Person Model. Engagement is facilitated by interactive tasks and contact with a Health Coach over seven weeks – an introductory face-to-face session, and six subsequent contacts by phone following each module. Follow-up assessments occur at 13 weeks (post-intervention) and 26 weeks. Primary outcomes include blood glucose management (HbA1c), weight and mood. Secondary outcomes include level of exercise, confidence to manage diabetes, and psychosocial well-being.
The Whole Person Model is designed to enable health professionals to address mood disturbance without pathologizing any disorders and, in the context of the chronic illness, empowering behavior change and self-management. If proven effective, this model will strengthen capacity of the healthcare workforce to foster and support effective diabetes self-management.
Trial registration
Australia and New Zealand Clinical Trials Register, ACTRN12613000391774
PMCID: PMC3933337  PMID: 24507417
Type 2 diabetes mellitus; Diabetes; Self-management; Depression; Support; Resources
13.  The Expression of stlA in Photorhabdus luminescens Is Controlled by Nutrient Limitation 
PLoS ONE  2013;8(11):e82152.
Photorhabdus is a genus of Gram-negative entomopathogenic bacteria that also maintain a mutualistic association with nematodes from the family Heterorhabditis. Photorhabdus has an extensive secondary metabolism that is required for the interaction between the bacteria and the nematode. A major component of this secondary metabolism is a stilbene molecule, called ST. The first step in ST biosynthesis is the non-oxidative deamination of phenylalanine resulting in the production of cinnamic acid. This reaction is catalyzed by phenylalanine-ammonium lyase, an enzyme encoded by the stlA gene. In this study we show, using a stlA-gfp transcriptional fusion, that the expression of stlA is regulated by nutrient limitation through a regulatory network that involves at least 3 regulators. We show that TyrR, a LysR-type transcriptional regulator that regulates gene expression in response to aromatic amino acids in E. coli, is absolutely required for stlA expression. We also show that stlA expression is modulated by σS and Lrp, regulators that are implicated in the regulation of the response to nutrient limitation in other bacteria. This work is the first that describes pathway-specific regulation of secondary metabolism in Photorhabdus and, therefore, our study provides an initial insight into the complex regulatory network that controls secondary metabolism, and therefore mutualism, in this model organism.
PMCID: PMC3838401  PMID: 24278476
14.  Evaluating the impact of depression, anxiety & autonomic function on health related quality of life, vocational functioning and health care utilisation in acute coronary syndrome patients: the ADVENT study protocol 
Depression and anxiety are highly prevalent and co-morbid in acute coronary syndrome patients. Somatic and cognitive subtypes of depression and anxiety in acute coronary syndrome have been shown to be associated with mortality although their association with patient outcomes is unknown, as are the mechanisms that underpin these associations. We are conducting a prospective cohort study which aims to examine in acute coronary syndrome patients: (1) the role of somatic subtypes of depression and anxiety as predictors of health related quality of life outcomes; (2) how somatic subtypes of depression and anxiety relate to long term vocational functioning and healthcare utilisation; and (3) the role of the autonomic nervous system assessed by heart rate variability as a moderator of these associations.
Patients are being screened after index admission for acute coronary syndrome at a single, high volume centre, MonashHeart, Monash Health, Victoria, Australia. The inclusion criterion is all patients aged > 21 years old and fluent in English admitted to MonashHeart, Monash Health with a diagnosis of acute coronary syndrome. The primary outcome is mean health related quality of life (Short Form-36) Physical and Mental Health Summary scores at 12 and 24 months in subtypes with somatic symptoms of depression and anxiety. Depressive domains are assessed by the Beck Depression Inventory II and the Cardiac Depression Scale. Anxiety is measured using the Speilberger State-Trait Anxiety Inventory and the Crown Crisp Phobic Anxiety questionnaire. Secondary outcomes include clinical variables, healthcare service utilisation and vocational functioning.
This manuscript presents the protocol for a prospective cohort study which will investigate the role of somatic subtypes of depression and anxiety as predictors of health related quality of life, long-term vocational functioning and health service use, and the role of the autonomic nervous system in moderating these associations. Findings from the study have the potential to inform more effective pharmacological, psychological and behavioural interventions and better guide health policy on the use of health care resources.
PMCID: PMC4225620  PMID: 24237848
Depression; Anxiety; Heart rate variability; Protocol
World journal for pediatric & congenital heart surgery  2013;4(1):10.1177/2150135112461924.
Several distinct definitions of postoperative death have been used in various quality reporting programs. Some have defined a postoperative mortality as a patient who expires while still in the hospital, while others have considered all deaths occurring within a predetermined, standardized time interval after surgery. While if continues to collect mortality data using both these individual definitions, the Society of Thoracic Surgeons (STS) believes that either alone may be inadequate. Accordingly, the STS prefers a more encompassing metric, Operative Mortality, which is defined as (1) all deaths occurring during the hospitalization in which the operation was performed, even if after 30 days; and (2) all deaths occurring after discharge from the hospital, but before the end of the thirtieth postoperative day. This manuscript provides clarification for some uncommon but important scenarios where the correct application of this definition may be problematic.
PMCID: PMC3828200  PMID: 23799748
cardiac disease; thoracic disease; congenital heart disease; outcomes analysis; quality improvement; database; mortality
16.  An empirically based tool for analyzing morbidity associated with operations for congenital heart disease 
The Journal of thoracic and cardiovascular surgery  2012;145(4):10.1016/j.jtcvs.2012.06.029.
Congenital heart surgery outcomes analysis requires reliable methods of estimating the risk of adverse outcomes. Contemporary methods focus primarily on mortality or rely on expert opinion to estimate morbidity associated with different procedures. We created an objective, empirically based index that reflects statistically estimated risk of morbidity by procedure.
Morbidity risk was estimated using data from 62,851 operations in the Society of Thoracic Surgeons Congenital Heart Surgery Database (2002-2008). Model-based estimates with 95% Bayesian credible intervals were calculated for each procedure’s average risk of major complications and average postoperative length of stay. These 2 measures were combined into a composite morbidity score. A total of 140 procedures were assigned scores ranging from 0.1 to 5.0 and sorted into 5 relatively homogeneous categories.
Model-estimated risk of major complications ranged from 1.0% for simple procedures to 38.2% for truncus arteriosus with interrupted aortic arch repair. Procedure-specific estimates of average postoperative length of stay ranged from 2.9 days for simple procedures to 42.6 days for a combined atrial switch and Rastelli operation. Spearman rank correlation between raw rates of major complication and average postoperative length of stay was 0.82 in procedures with n greater than 200. Rate of major complications ranged from 3.2% in category 1 to 30.0% in category 5. Aggregate average postoperative length of stay ranged from 6.3 days in category 1 to 34.0 days in category 5.
Complication rates and postoperative length of stay provide related but not redundant information about morbidity. The Morbidity Scores and Categories provide an objective assessment of risk associated with operations for congenital heart disease, which should facilitate comparison of outcomes across cohorts with differing case mixes.
PMCID: PMC3824389  PMID: 22835225
17.  Initial application in the EACTS and STS Congenital Heart Surgery Databases of an empirically derived methodology of complexity adjustment to evaluate surgical case mix and results† 
Outcomes evaluation is enhanced by assignment of operative procedures to appropriate categories based upon relative average risk. Formal risk modelling is challenging when a large number of operation types exist, including relatively rare procedures. Complexity stratification provides an alternative methodology. We report the initial application in the Congenital Heart Surgery Databases of the Society of Thoracic Surgeons (STS) and the European Association for Cardio-thoracic Surgery (EACTS) of an empirically derived system of complexity adjustment to evaluate surgical case mix and results.
Complexity stratification is a method of analysis in which the data are divided into relatively homogeneous groups (called strata). A complexity stratification tool named the STS–EACTS Congenital Heart Surgery Mortality Categories (STAT Mortality Categories) was previously developed based on the analysis of 77 294 operations entered in the Congenital Heart Surgery Databases of EACTS (33 360 operations) and STS (43 934 patients). Procedure-specific mortality rate estimates were calculated using a Bayesian model that adjusted for small denominators. Operations were sorted by increasing risk and grouped into five categories (the STAT Mortality Categories) that were designed to minimize within-category variation and maximize between-category variation. We report here the initial application of this methodology in the EACTS Congenital Heart Surgery Database (47 187 operations performed over 4 years: 2006–09) and the STS Congenital Heart Surgery Database (64 307 operations performed over 4 years: 2006–09).
In the STS Congenital Heart Surgery Database, operations classified as STAT Mortality Categories 1–5 were (1): 17332, (2): 20114, (3): 9494, (4): 14525 and (5): 2842. Discharge mortality was (1): 0.54%, (2): 1.6%, (3): 2.4%, (4): 7.5% and (5): 17.8%. In the EACTS Congenital Heart Surgery Database, operations classified as STAT Mortality Categories 1–5 were (1): 19874, (2): 12196, (3): 5614, (4): 8287 and (5): 1216. Discharge mortality was (1): 0.99%, (2): 2.9%, (3): 5.0%, (4): 10.3% and (5): 25.0%.
The STAT Mortality Categories facilitate analysis of outcomes across the wide spectrum of distinct congenital heart surgery operations including infrequently performed procedures.
PMCID: PMC3858079  PMID: 22700597
Database; Outcomes; Quality assessment; Quality improvement
18.  Drug Rescue Distinguishes between Different Structural Models of Human P-Glycoprotein 
Biochemistry  2013;52(41):7167-7169.
There is no high-resolution crystal structure of the human P-glycoprotein (P-gp) drug pump. Homology models of human P-gp based on the crystal structures of mouse or Caenorhabditis elegans P-gps show large differences in the orientation of transmembrane segment 5 (TM5). TM5 is one of the most important transmembrane segments involved in drug–substrate interactions. Drug rescue of P-gp processing mutants containing an arginine at each position in TM5 was used to identify positions facing the lipid or internal aqueous chamber. Only the model based on the C. elegans P-gp structure was compatible with the drug rescue results.
PMCID: PMC3798097  PMID: 24083983
19.  Hydrophobic Fluorescent Probes Introduce Artifacts into Single Molecule Tracking Experiments Due to Non-Specific Binding 
PLoS ONE  2013;8(9):e74200.
Single-molecule techniques are powerful tools to investigate the structure and dynamics of macromolecular complexes; however, data quality can suffer because of weak specific signal, background noise and dye bleaching and blinking. It is less well-known, but equally important, that non-specific binding of probe to substrates results in a large number of immobile fluorescent molecules, introducing significant artifacts in live cell experiments. Following from our previous work in which we investigated glass coating substrates and demonstrated that the main contribution to this non-specific probe adhesion comes from the dye, we carried out a systematic investigation of how different dye chemistries influence the behaviour of spectrally similar fluorescent probes. Single-molecule brightness, bleaching and probe mobility on the surface of live breast cancer cells cultured on a non-adhesive substrate were assessed for anti-EGFR affibody conjugates with 14 different dyes from 5 different manufacturers, belonging to 3 spectrally homogeneous bands (491 nm, 561 nm and 638 nm laser lines excitation). Our results indicate that, as well as influencing their photophysical properties, dye chemistry has a strong influence on the propensity of dye-protein conjugates to adhere non-specifically to the substrate. In particular, hydrophobicity has a strong influence on interactions with the substrate, with hydrophobic dyes showing much greater levels of binding. Crucially, high levels of non-specific substrate binding result in calculated diffusion coefficients significantly lower than the true values. We conclude that the physic-chemical properties of the dyes should be considered carefully when planning single-molecule experiments. Favourable dye characteristics such as photostability and brightness can be offset by the propensity of a conjugate for non-specific adhesion.
PMCID: PMC3774629  PMID: 24066121
20.  Implementing a training intervention to support caregivers after stroke: a process evaluation examining the initiation and embedding of programme change 
Medical Research Council (MRC) guidance identifies implementation as a key element of the development and evaluation process for complex healthcare interventions. Implementation is itself a complex process involving the mobilization of human, material, and organizational resources to change practice within settings that have pre-existing structures, historical patterns of relationships, and routinized ways of working. Process evaluations enable researchers and clinicians to understand how implementation proceeds and what factors impact on intended program change. A qualitative process evaluation of the pragmatic cluster randomized controlled trial; Training Caregivers after Stroke was conducted to examine how professionals were engaged in the work of delivering training; how they reached and involved caregivers for whom the intervention was most appropriate; how did those on whom training was targeted experience and respond to it. Normalization Process Theory, which focuses attention on implementing and embedding program change, was used as a sensitizing framework to examine selected findings.
Contextual factors including organizational history and team relationships, external policy, and service development initiatives, impinged on implementation of the caregiver training program in unintended ways that could not have been predicted through focus on mechanisms of individual and collective action at unit level. Factors that facilitated or impeded the effectiveness of the cascade training model used, whether and how stroke unit teams made sense of and engaged individually and collectively with a complex caregiver training intervention, and what impact these factors had on embedding the intervention in routine stroke unit practice were identified.
Where implementation of complex interventions depends on multiple providers, time needs to be invested in reaching agreement on who will take responsibility for delivery of specific components and in determining how implementation and its effectiveness will be monitored. This goes beyond concern with intervention fidelity; explicit consideration also needs to be given to the implementation process in terms of how program change can be effected at organizational, practice, and service delivery levels. Normalization Process Theory’s constructs help identify vulnerable features of implementation processes in respect of the work involved in embedding complex interventions.
PMCID: PMC3765868  PMID: 23972027
Process evaluation; Implementation theory; Stroke; Caregiver training; Normalization process theory
21.  Bithiazole Correctors Rescue CFTR Mutants by Two Different Mechanisms 
Biochemistry  2013;52(31):5161-5163.
Better correctors are needed to repair cystic fibrosis transmembrane conductance regulator (CFTR) processing mutants that cause cystic fibrosis. Determining where the correctors bind to CFTR would aid in the development of new correctors. A recent study reported that the second nucleotide-binding domain (NBD2) was involved in binding of bithiazole correctors. Here, we show that bithiazole correctors could also rescue CFTR mutants that lacked NBD2. These results suggest that bithiazoles rescue CFTR mutants by two different mechanisms.
PMCID: PMC3737597  PMID: 23865422
22.  30 Days in the Life: Daily Nutrient Balancing in a Wild Chacma Baboon 
PLoS ONE  2013;8(7):e70383.
For most animals, the ability to regulate intake of specific nutrients is vital to fitness. Recent studies have demonstrated nutrient regulation in nonhuman primates over periods of one observation day, though studies of humans indicate that such regulation extends to longer time frames. Little is known about longer-term regulation in nonhuman primates, however, due to the challenges of multiple-day focal follows. Here we present the first detailed study of nutrient intake across multiple days in a wild nonhuman primate. We conducted 30 consecutive all day follows on one female chacma baboon (Papio hamadryas ursinus) in the Cape Peninsula of South Africa. We documented dietary composition, compared the nutritional contribution of natural and human-derived foods to the diet, and quantified nutrient intake using the geometric framework of nutrition. Our focus on a single subject over consecutive days allowed us to examine daily dietary regulation within an individual over time. While the amounts varied daily, our subject maintained a strikingly consistent balance of protein to non-protein (fat and carbohydrate) energy across the month. Human-derived foods, while contributing a minority of the diet, were higher in fat and lower in fiber than naturally-derived foods. Our results demonstrate nutrient regulation on a daily basis in our subject, and demonstrate that she was able to maintain a diet with a constant proportional protein content despite wide variation in the composition of component foods. From a methodological perspective, the results of this study suggest that nutrient intake is best estimated over at least an entire day, with longer-term regulatory patterns (e.g., during development and reproduction) possibly requiring even longer sampling. From a management and conservation perspective, it is notable that nearly half the subject’s daily energy intake derived from exotic foods, including those currently being eradicated from the study area for replacement by indigenous vegetation.
PMCID: PMC3722187  PMID: 23894645
23.  Thiorhodamines Containing Amide and Thioamide Functionality as Inhibitors of the ATP-Binding Cassette Drug Transporter P-glycoprotein (ABCB1) 
Bioorganic & medicinal chemistry  2012;20(14):4290-4302.
Twelve thiorhodamine derivatives have been examined for their ability to stimulate the ATPase activity of purified human P-glycoprotein (P-gp)-His10, to promote uptake of calcein AM and vinblastine into multidrug-resistant, P-gp-overexpressing MDCKII-MDR1 cells, and for their rates of transport in monolayers of multidrug-resistant, P-gp-overexpressing MDCKII-MDR1 cells. The thiorhodamine derivatives have structural diversity from amide and thioamide functionality (N,N-diethyl and N-piperidyl) at the 5-position of a 2-thienyl substituent on the thiorhodamine core and from diversity at the 3-amino substituent with N,N-dimethylamino, fused azadecalin (julolidyl), and fused N-methylcyclohexylamine (half-julolidyl) substituents. The julolidyl and half-julolidyl derivatives were more effective inhibitors of P-gp than the dimethylamino analogues. Amide-containing derivatives were transported much more rapidly than thioamide-containing derivatives.
PMCID: PMC3400123  PMID: 22727780
Multidrug resistance; P-glycoprotein; thiorhodamine; transport inhibition; ATPase stimulation
24.  Inhibition of the PLP-dependent enzyme serine palmitoyltransferase by cycloserine: evidence for a novel decarboxylative mechanism of inactivation 
Molecular bioSystems  2010;6(9):1682-1693.
Cycloserine (CS, 4-amino-3-isoxazolidone) is a cyclic amino acid mimic that is known to inhibit many essential pyridoxal 5′-phosphate (PLP)-dependent enzymes. Two CS enantiomers are known; d-cycloserine (DCS, also known as Seromycin), is a natural product that is used to treat resistant Mycobacterium tuberculosis infections as well as neurological disorders since it is a potent NMDA receptor agonist, and l-cycloserine (LCS), is a synthetic enantiomer whose usefulness as a drug has been hampered by its inherent toxicity arising through inhibition of sphingolipid metabolism. Previous studies on various PLP-dependent enzymes revealed a common mechanism of inhibition by both enantiomers of CS; the PLP cofactor is disabled by forming a stable 3-hydroxyisoxazole/pyridoxamine 5′-phosphate (PMP) adduct at the active site where the cycloserine ring remains intact. Here we describe a novel mechanism of CS inactivation of the PLP-dependent enzyme serine palmitoyltransferase (SPT) from Sphingomonas paucimobilis. SPT catalyses the condensation of l-serine and palmitoyl-CoA, the first step in the de novo sphingolipid biosynthetic pathway. We have used a range of kinetic, spectroscopic and structural techniques to postulate that both LCS and DCS inactivate SPT by transamination to form a free pyridoxamine 5′-phosphate (PMP) and β-aminooxyacetaldehyde that remain bound at the active site. We suggest this occurs by ring opening of the cycloserine ring followed by decarboxylation. Enzyme kinetics show that inhibition is reversed by incubation with excess PLP and that LCS is a more effective SPT inhibitor than DCS. UV-visible spectroscopic data, combined with site-directed mutagenesis, suggest that a mobile Arg378 residue is involved in cycloserine inactivation of SPT.
PMCID: PMC3670083  PMID: 20445930
25.  A Salt Bridge in Intracellular Loop 2 Is Essential for Folding of Human P-Glycoprotein 
Biochemistry  2013;52(19):3194-3196.
There is no high-resolution structure of the human P-glycoprotein (P-gp, ABCB1) drug pump. Homology models based on the crystal structures of mouse and Caenorhabditis elegans P-gps show extensive contacts between intracellular loop 2 (ICL2, in the first transmembrane domain) and the second nucleotide-binding domain. Human P-gp modeled on these P-gp structures yields different ICL2 structures. Only the model based on the C. elegans P-gp structure predicts the presence of a salt bridge. We show that the Glu256–Arg276 salt bridge was critical for P-gp folding.
PMCID: PMC3656768  PMID: 23634976

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