Showing papers by "University of Auckland published in 2013"

Guidelines for perioperative care in elective colonic surgery: Enhanced recovery after surgery (ERAS®) society recommendations

Abstract: This is the fourth updated Enhanced Recovery After Surgery (ERAS®) Society guideline presenting a consensus for optimal perioperative care in colorectal surgery and providing graded recommendations for each ERAS item within the ERAS® protocol. A wide database search on English literature publications was performed. Studies on each item within the protocol were selected with particular attention paid to meta-analyses, randomised controlled trials and large prospective cohorts and examined, reviewed and graded according to Grading of Recommendations, Assessment, Development and Evaluation (GRADE) system. All recommendations on ERAS® protocol items are based on best available evidence; good-quality trials; meta-analyses of good-quality trials; or large cohort studies. The level of evidence for the use of each item is presented accordingly. The evidence base and recommendation for items within the multimodal perioperative care pathway are presented by the ERAS® Society in this comprehensive consensus review.

Systematic identification of trans eQTLs as putative drivers of known disease associations

Abstract: Identifying the downstream effects of disease-associated SNPs is challenging. To help overcome this problem, we performed expression quantitative trait locus (eQTL) meta-analysis in non-transformed peripheral blood samples from 5,311 individuals with replication in 2,775 individuals. We identified and replicated trans eQTLs for 233 SNPs (reflecting 103 independent loci) that were previously associated with complex traits at genome-wide significance. Some of these SNPs affect multiple genes in trans that are known to be altered in individuals with disease: rs4917014, previously associated with systemic lupus erythematosus (SLE), altered gene expression of C1QB and five type I interferon response genes, both hallmarks of SLE. DeepSAGE RNA sequencing showed that rs4917014 strongly alters the 3' UTR levels of IKZF1 in cis, and chromatin immunoprecipitation and sequencing analysis of the trans-regulated genes implicated IKZF1 as the causal gene. Variants associated with cholesterol metabolism and type 1 diabetes showed similar phenomena, indicating that large-scale eQTL mapping provides insight into the downstream effects of many trait-associated variants.

Development of a Single-Sided Flux Magnetic Coupler for Electric Vehicle IPT Charging Systems

Abstract: Inductive power transfer is a practical method for recharging electric vehicles because it is safe, convenient, and reliable. The performance of the magnetic couplers that transfer power determines the overall feasibility of a complete system. Circular couplers are the most common topology in the literature; however, they have fundamentally limited coupling. Their flux patterns necessarily limit the operational air gap as well as tolerance to horizontal misalignment. A new polarized coupler topology [referred to as a double D (DD)] is presented, which overcomes these difficulties. DDs provide a charge zone five times larger than that possible with circular pads for a similar material cost and are smaller. A 0.31-m2 DD enables 2 kW of power transfer over an oval area measuring 540 mm × 800 mm with a 200-mm air gap. Leakage magnetic fields have been investigated and show that circular and DD couplers operating under similar power transfer conditions produce similar levels. Both topologies can be designed and operated to ensure compliance with international guidelines.

Modern Trends in Inductive Power Transfer for Transportation Applications

Abstract: Inductive power transfer (IPT) has progressed to be a power distribution system offering significant benefits in modern automation systems and particularly so in stringent environments. Here, the same technology may be used in very dirty environments and in a clean room manufacture. This paper reviews the development of simple factory automation (FA) IPT systems for both today's complex applications and onward to a much more challenging application-IPT roadway. The underpinning of all IPT technology is two strongly coupled coils operating at resonance to transfer power efficiently. Over time the air-gap, efficiency, coupling factor, and power transfer capability have significantly improved. New magnetic concepts are introduced to allow misalignment, enabling IPT systems to migrate from overhead monorails to the floor. However, the demands of IPT roadway bring about significant challenges. Here, compared with the best FA practice, air-gaps need to be 100 times larger, power levels greater than ten times, system losses ten times lower to meet efficiency requirements, and systems from different manufacturers must be interoperable over the full range of operation. This paper describes how roadway challenges are being met and outlines the problems that still exist and the solutions designers are finding to them.

Inductive Power Transfer

Abstract: Inductive power transfer (IPT) was an engineering curiosity less than 30 years ago, but, at that time, it has grown to be an important technology in a variety of applications. The paper looks at the background to IPT and how its development was based on sound engineering principles leading on to factory automation and growing to a $1 billion industry in the process. Since then applications for the technology have diversified and at the same time become more technically challenging, especially for the static and dynamic charging of electric vehicles (EVs), where IPT offers possibilities that no other technology can match. Here, systems that are ten times more powerful, more tolerant of misalignment, safer, and more efficient may be achievable, and if they are, IPT can transform our society. The challenges are significant but the technology is promising.

Predicting survival in heart failure: a risk score based on 39 372 patients from 30 studies.

Abstract: Aims Using a large international database from multiple cohort studies, the aim is to create a generalizable easily used risk score for mortality in patients with heart failure (HF). Methods and results The MAGGIC meta-analysis includes individual data on 39 372 patients with HF, both reduced and preserved left-ventricular ejection fraction (EF), from 30 cohort studies, six of which were clinical trials. 40.2% of patients died during a median follow-up of 2.5 years. Using multivariable piecewise Poisson regression methods with stepwise variable selection, a final model included 13 highly significant independent predictors of mortality in the following order of predictive strength: age, lower EF, NYHA class, serum creatinine, diabetes, not prescribed beta-blocker, lower systolic BP, lower body mass, time since diagnosis, current smoker, chronic obstructive pulmonary disease, male gender, and not prescribed ACE-inhibitor or angiotensin-receptor blockers. In preserved EF, age was more predictive and systolic BP was less predictive of mortality than in reduced EF. Conversion into an easy-to-use integer risk score identified a very marked gradient in risk, with 3-year mortality rates of 10 and 70% in the bottom quintile and top decile of risk, respectively. Conclusion In patients with HF of both reduced and preserved EF, the influences of readily available predictors of mortality can be quantified in an integer score accessible by an easy-to-use website [www.heartfailurerisk.org][1]. The score has the potential for widespread implementation in a clinical setting. [1]: http://www.heartfailurerisk.org

Genome-Wide Association Study of Retinopathy in Individuals Without Diabetes

Abstract: Background Mild retinopathy (microaneurysms or dot-blot hemorrhages) is observed in persons without diabetes or hypertension and may reflect microvascular disease in other organs. We conducted a genome-wide association study (GWAS) of mild retinopathy in persons without diabetes.

Using biochar for remediation of soils contaminated with heavy metals and organic pollutants

Abstract: Soil contamination with heavy metals and organic pollutants has increasingly become a serious global environmental issue in recent years. Considerable efforts have been made to remediate contaminated soils. Biochar has a large surface area, and high capacity to adsorb heavy metals and organic pollutants. Biochar can potentially be used to reduce the bioavailability and leachability of heavy metals and organic pollutants in soils through adsorption and other physicochemical reactions. Biochar is typically an alkaline material which can increase soil pH and contribute to stabilization of heavy metals. Application of biochar for remediation of contaminated soils may provide a new solution to the soil pollution problem. This paper provides an overview on the impact of biochar on the environmental fate and mobility of heavy metals and organic pollutants in contaminated soils and its implication for remediation of contaminated soils. Further research directions are identified to ensure a safe and sustainable use of biochar as a soil amendment for remediation of contaminated soils.

Observation of a new boson with mass near 125 GeV in pp collisions at $ \sqrt{s}=7 $ and 8 TeV

Abstract: A detailed description is reported of the analysis used by the CMS Collaboration in the search for the standard model Higgs boson in pp collisions at the LHC, which led to the observation of a new boson. The data sample corresponds to integrated luminosities up to 5.1 inverse femtobarns at sqrt(s) = 7 TeV, and up to 5.3 inverse femtobarns at sqrt(s) = 8 TeV. The results for five Higgs boson decay modes gamma gamma, ZZ, WW, tau tau, and bb, which show a combined local significance of 5 standard deviations near 125 GeV, are reviewed. A fit to the invariant mass of the two high resolution channels, gamma gamma and ZZ to 4 ell, gives a mass estimate of 125.3 +/- 0.4 (stat) +/- 0.5 (syst) GeV. The measurements are interpreted in the context of the standard model Lagrangian for the scalar Higgs field interacting with fermions and vector bosons. The measured values of the corresponding couplings are compared to the standard model predictions. The hypothesis of custodial symmetry is tested through the measurement of the ratio of the couplings to the W and Z bosons. All the results are consistent, within their uncertainties, with the expectations for a standard model Higgs boson.

Incidence of traumatic brain injury in New Zealand: a population-based study

Abstract: Summary Background Traumatic brain injury (TBI) is the leading cause of long-term disability in children and young adults worldwide. However, accurate information about its incidence does not exist. We aimed to estimate the burden of TBI in rural and urban populations in New Zealand across all ages and TBI severities. Methods We did a population-based incidence study in an urban (Hamilton) and rural (Waikato District) population in New Zealand. We registered all cases of TBI (admitted to hospital or not, fatal or non-fatal) that occurred in the population between March 1, 2010, and Feb 28, 2011, using multiple overlapping sources of information. We calculated incidence per 100 000 person-years with 95% CIs using a Poisson distribution. We calculated rate ratios [RRs] to compare the age-standardised rates between sex, ethnicity, and residency (urban, rural) groups. We used direct standardisation to age-standardise the rates to the world population. Results The total incidence of TBI per 100 000 person-years was 790 cases (95% CI 749–832); incidence per 100 000 person-years of mild TBI was 749 cases (709–790) and of moderate to severe TBI was 41 cases (31–51). Children (aged 0–14 years) and adolescents and young adults (aged 15–34 years) constituted almost 70% of all TBI cases. TBI affected boys and men more than women and girls (RR 1·77, 95% CI 1·58–1·97). Most TBI cases were due to falls (38% [516 of 1369]), mechanical forces (21% [288 of 1369]), transport accidents (20% [277 of 1369]), and assaults (17% [228 of 1369]). Compared with people of European origin, Maori people had a greater risk of mild TBI (RR 1·23, 95% CI 1·08–1·39). Incidence of moderate to severe TBI in the rural population (73 per 100 000 person-years [95% CI 50–107) was almost 2·5 times greater than in the urban population (31 per 100 000 person-years [23–42]). Interpretation Our findings suggest that the incidence of TBI, especially mild TBI, in New Zealand is far greater than would be estimated from the findings of previous studies done in other high-income countries. Our age-specific and residency-specific data for TBI incidence overall and by mechanism of injury should be considered when planning prevention and TBI care services. Funding Health Research Council of New Zealand.

Modeling of octave-spanning Kerr frequency combs using a generalized mean-field Lugiato-Lefever model.

Abstract: A generalized Lugiato-Lefever equation is numerically solved with a Newton-Raphson method to model Kerr frequency combs. We obtain excellent agreement with past experiments, even for an octave-spanning comb. Simulations are much faster than with any other technique despite including more modes than ever before. Our study reveals that Kerr combs are associated with temporal cavity solitons and dispersive waves, and opens up new avenues for the understanding of Kerr-comb formation.

Can We Name Earth's Species Before They Go Extinct?

Abstract: Some people despair that most species will go extinct before they are discovered. However, such worries result from overestimates of how many species may exist, beliefs that the expertise to describe species is decreasing, and alarmist estimates of extinction rates. We argue that the number of species on Earth today is 5 ± 3 million, of which 1.5 million are named. New databases show that there are more taxonomists describing species than ever before, and their number is increasing faster than the rate of species description. Conservation efforts and species survival in secondary habitats are at least delaying extinctions. Extinction rates are, however, poorly quantified, ranging from 0.01 to 1% (at most 5%) per decade. We propose practical actions to improve taxonomic productivity and associated understanding and conservation of biodiversity.

The International Study of Asthma and Allergies in Childhood (ISAAC) Phase Three: A global synthesis

Abstract: This ISAAC Phase Three synthesis provides summarised information on the main findings of the study, regional tables and figures related to the prevalence and severity of current symptoms of asthma, rhinoconjunctivitis and eczema in the main regions of the world. The large number of surveyed children (≈1,200,000), the large number of centres (233) and countries (98) that participated in ISAAC Phase Three makes this study the most comprehensive survey of these diseases ever undertaken. Globally, the prevalence for current asthma, rhinoconjunctivitis and eczema in the 13-14-year age group was 14.1%, 14.6% and 7.3%, respectively. In the 6-7-year age group the prevalence for current asthma, rhinoconjunctivitis and eczema was 11.7%, 8.5% and 7.9%, respectively. The study shows a wide variability in the prevalence and severity of asthma, rhinoconjunctivitis and eczema which occurs not just between regions and countries but between centres in the same country and centres in the same city. This study definitively establishes that the prevalence of those diseases can be very high in non-affluent centres with low socioeconomic conditions. The large variability also suggests a crucial role of local environment characteristics to determine the differences in prevalence between one place and another. Thus, ISAAC Phase Three has provided a large body of epidemiological information on asthma, rhinoconjunctivitis and eczema in childhood from contrasting environments which is expected to yield new clues about the aetiology of those conditions and reasons for their marked global variability.

Birth–death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV)

Abstract: Phylogenetic trees can be used to infer the processes that generated them. Here, we introduce a model, the Bayesian birth–death skyline plot, which explicitly estimates the rate of transmission, recovery, and sampling and thus allows inference of the effective reproductive number directly from genetic data. Our method allows these parameters to vary through time in a piecewise fashion and is implemented within the BEAST2 software framework. The method is a powerful alternative to the existing coalescent skyline plot, providing insight into the differing roles of incidence and prevalence in an epidemic. We apply this method to data from the United Kingdom HIV-1 epidemic and Egyptian hepatitis C virus (HCV) epidemic. The analysis reveals temporal changes of the effective reproductive number that highlight the effect of past public health interventions.

INFORMAS (International Network for Food and Obesity/non-communicable diseases Research, Monitoring and Action Support): overview and key principles

Abstract: 20 Global Alliance for Improved Nutrition (GAIN), Geneva, Switzerland Summary Non-communicable diseases (NCDs) dominate disease burdens globally and poor nutrition increasingly contributes to this global burden. Compre- hensive monitoring of food environments, and evaluation of the impact of public and private sector policies on food environments is needed to strengthen accountability systems to reduce NCDs. The International Network for Food and Obesity/NCDs Research, Monitoring and Action Support (INFORMAS) is a global network of public-interest organizations and researchers that aims to monitor, benchmark and support public and private sector actions to create healthy food environments and reduce obesity, NCDs and their related inequalities. The INFORMAS framework includes two 'process' modules, that monitor the policies and actions of the public and private sectors, seven 'impact' modules that monitor the key characteristics of food environments and three 'outcome' modules that monitor dietary quality, risk factors and NCD morbidity and mortality. Monitoring frameworks and indicators have been developed for 10 modules to provide consistency, but allowing for stepwise approaches ('minimal', 'expanded', 'optimal') to data collection and analysis. INFORMAS data will enable benchmarking of food environments between countries, and monitoring of progress over time within countries. Through monitoring and benchmarking, INFORMAS will strengthen the account- ability systems needed to help reduce the burden of obesity, NCDs and their related inequalities.

The effect of virtual achievements on student engagement

Abstract: Badge-based achievement systems are being used increasingly to drive user participation and engagement across a variety of platforms and contexts. Despite positive anecdotal reports, there is currently little empirical evidence to support their efficacy in particular domains. With the recent rapid growth of tools for online learning, an interesting open question for educators is the extent to which badges can positively impact student participation. In this paper, we report on a large-scale (n > 1000) randomized, controlled experiment measuring the impact of incorporating a badge-based achievement system within an online learning tool. We discover a highly significant positive effect on the quantity of students' contributions, without a corresponding reduction in their quality, as well as on the period of time over which students engaged with the tool. Students enjoyed being able to earn badges, and indicated a strong preference for having them available in the user interface.

Antibiotics for the common cold and acute purulent rhinitis.

Abstract: Background It has long been believed that antibiotics have no role in the treatment of common colds yet they are often prescribed in the belief that they may prevent secondary bacterial infections. Objectives To determine the efficacy of antibiotics compared with placebo for reducing general and specific nasopharyngeal symptoms of acute upper respiratory tract infections (URTIs) (common colds). To determine if antibiotics have any influence on the outcomes for acute purulent rhinitis and acute clear rhinitis lasting less than 10 days before the intervention. To determine whether there are significant adverse outcomes associated with antibiotic therapy for participants with a clinical diagnosis of acute URTI or acute purulent rhinitis. Search methods For this 2013 update we searched CENTRAL 2013, Issue 1, MEDLINE (March 2005 to February week 2, 2013), EMBASE (January 2010 to February 2013), CINAHL (2005 to February 2013), LILACS (2005 to February 2013) and Biosis Previews (2005 to February 2013). Selection criteria Randomised controlled trials (RCTs) comparing any antibiotic therapy against placebo in people with symptoms of acute upper respiratory tract infection for less than seven days, or acute purulent rhinitis less than 10 days in duration. Data collection and analysis Both review authors independently assessed trial quality and extracted data. Main results This updated review included 11 studies. Six studies contributed to one or more analyses related to the common cold, with up to 1047 participants. Five studies contributed to one or more analyses relating to purulent rhinitis, with up to 791 participants. One study contributed only to data on adverse events and one met the inclusion criteria but reported only summary statistics without providing any numerical data that could be included in the meta-analyses. Interpretation of the combined data is limited because some studies included only children, or only adults, or only males; a wide range of antibiotics were used and outcomes were measured in different ways. There was a moderate risk of bias because of unreported methods details or because an unknown number of participants were likely to have chest or sinus infections. Participants receiving antibiotics for the common cold did no better in terms of lack of cure or persistence of symptoms than those on placebo (risk ratio (RR) 0.95, 95% confidence interval (CI) 0.59 to 1.51, (random-effects)), based on a pooled analysis of six trials with a total of 1047 participants. The RR of adverse effects in the antibiotic group was 1.8, 95% CI 1.01 to 3.21, (random-effects). Adult participants had a significantly greater risk of adverse effects with antibiotics than with placebo (RR 2.62, 95% CI 1.32 to 5.18) (random-effects) while there was no greater risk in children (RR 0.91, 95% CI 0.51 to 1.63). The pooled RR for persisting acute purulent rhinitis with antibiotics compared to placebo was 0.73 (95% CI 0.47 to 1.13) (random-effects), based on four studies with 723 participants. There was an increase in adverse effects in the studies of antibiotics for acute purulent rhinitis (RR 1.46, 95% CI 1.10 to 1.94). Authors' conclusions There is no evidence of benefit from antibiotics for the common cold or for persisting acute purulent rhinitis in children or adults. There is evidence that antibiotics cause significant adverse effects in adults when given for the common cold and in all ages when given for acute purulent rhinitis. Routine use of antibiotics for these conditions is not recommended.

From knowledge to action: Bridging gaps in disaster risk reduction

Abstract: A large amount of studies have been produced on disaster-related issues over the last century of research, yet there continues to be gaps in translating knowledge into action. This paper discusses ...

Oxygen Saturation and Outcomes in Preterm Infants

Abstract: Background The clinically appropriate range for oxygen saturation in preterm infants is unknown. Previous studies have shown that infants had reduced rates of retinopathy of prematurity when lower targets of oxygen saturation were used. Methods In three international randomized, controlled trials, we evaluated the effects of targeting an oxygen saturation of 85 to 89%, as compared with a range of 91 to 95%, on disability-free survival at 2 years in infants born before 28 weeks' gestation. Halfway through the trials, the oximeter-calibration algorithm was revised. Recruitment was stopped early when an interim analysis showed an increased rate of death at 36 weeks in the group with a lower oxygen saturation. We analyzed pooled data from patients and now report hospital-discharge outcomes. Results A total of 2448 infants were recruited. Among the 1187 infants whose treatment used the revised oximeter-calibration algorithm, the rate of death was significantly higher in the lower-target group than in the highe...

Aberrant splicing of HTT generates the pathogenic exon 1 protein in Huntington disease

Abstract: Huntington disease (HD) is a devastating, late-onset, inherited neurodegenerative disorder that manifests with personality changes, movement disorders, and cognitive decline. It is caused by a CAG repeat expansion in exon 1 of the HTT gene that translates to a polyglutamine tract in the huntingtin protein (HTT). The formation of HTT fragments has been implicated as an essential step in the molecular pathogenesis of HD and several proteases that cleave HTT have been identified. However, the importance of smaller N-terminal fragments has been highlighted by their presence in HD postmortem brains and by the fact that nuclear inclusions are only detected by antibodies to the N terminus of HTT. Despite an intense research effort, the precise length of these fragments and the mechanism by which they are generated remains unknown. Here we show that CAG repeat length–dependent aberrant splicing of exon 1 HTT results in a short polyadenylated mRNA that is translated into an exon 1 HTT protein. Given that mutant exon 1 HTT proteins have consistently been shown to be highly pathogenic in HD mouse models, the aberrant splicing of HTT mRNA provides a mechanistic basis for the molecular pathogenesis of HD. RNA-targeted therapeutic strategies designed to lower the levels of HTT are under development. Many of these approaches would not prevent the production of exon 1 HTT and should be reviewed in light of our findings.

Where do people die? An international comparison of the percentage of deaths occurring in hospital and residential aged care settings in 45 populations, using published and available statistics

Abstract: Place of death, specifically the percentage who die in hospital or residential aged care, is largely unreported. This paper presents a cross-national comparison of location of death information from published reports and available data. Reports of deaths occurring in hospitals, residential aged care facilities, and other locations for periods since 2001 were compiled. Over 16 million deaths are reported in 45 populations. Half reported 54 % or more of all deaths occurred in hospitals, ranging from Japan (78 %) to China (20 %). Of 21 populations reporting deaths of older people, a median of 18 % died in residential aged care, with percentages doubling with each 10-year increase in age, and 40 % higher among women. This place of death study includes more populations than any other known. In many populations, residential aged care was an important site of death for older people, indicating the need to optimise models of end-of-life care in this setting. For many countries, more standardised reporting of place of death would inform policies and planning of services to support end-of-life care.

Plant-Symbiotic Fungi as Chemical Engineers: Multi-Genome Analysis of the Clavicipitaceae Reveals Dynamics of Alkaloid Loci

Abstract: The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive and bioprotective alkaloids. The family includes grass symbionts in the epichloae clade (Epichloe and Neotyphodium species), which are extraordinarily diverse both in their host interactions and in their alkaloid profiles. Epichloae produce alkaloids of four distinct classes, all of which deter insects, and some—including the infamous ergot alkaloids—have potent effects on mammals. The exceptional chemotypic diversity of the epichloae may relate to their broad range of host interactions, whereby some are pathogenic and contagious, others are mutualistic and vertically transmitted (seed-borne), and still others vary in pathogenic or mutualistic behavior. We profiled the alkaloids and sequenced the genomes of 10 epichloae, three ergot fungi (Claviceps species), a morning-glory symbiont (Periglandula ipomoeae), and a bamboo pathogen (Aciculosporium take), and compared the gene clusters for four classes of alkaloids. Results indicated a strong tendency for alkaloid loci to have conserved cores that specify the skeleton structures and peripheral genes that determine chemical variations that are known to affect their pharmacological specificities. Generally, gene locations in cluster peripheries positioned them near to transposon-derived, AT-rich repeat blocks, which were probably involved in gene losses, duplications, and neofunctionalizations. The alkaloid loci in the epichloae had unusual structures riddled with large, complex, and dynamic repeat blocks. This feature was not reflective of overall differences in repeat contents in the genomes, nor was it characteristic of most other specialized metabolism loci. The organization and dynamics of alkaloid loci and abundant repeat blocks in the epichloae suggested that these fungi are under selection for alkaloid diversification. We suggest that such selection is related to the variable life histories of the epichloae, their protective roles as symbionts, and their associations with the highly speciose and ecologically diverse cool-season grasses.

El Niño modulations over the past seven centuries

Abstract: The El Nino/Southern Oscillation exhibits considerable natural variability on interdecadal to centennial timescales making it difficult to understand how climate change affects it. A reconstruction now shows there has been anomalously high activity in the late twentieth century, relative to the past seven centuries. This is suggestive of a response to global warming, and will provide constraints to improve climate models and projections.