Showing papers by "University of Sydney published in 2007"

Consolidated criteria for reporting qualitative research (COREQ): a 32-item checklist for interviews and focus groups

Abstract: Background. Qualitative research explores complex phenomena encountered by clinicians, health care providers, policy makers and consumers. Although partial checklists are available, no consolidated reporting framework exists for any type of qualitative design. Objective. To develop a checklist for explicit and comprehensive reporting of qualitative studies (indepth interviews and focus groups). Methods. We performed a comprehensive search in Cochrane and Campbell Protocols, Medline, CINAHL, systematic reviews of qualitative studies, author or reviewer guidelines of major medical journals and reference lists of relevant publications for existing checklists used to assess qualitative studies. Seventy-six items from 22 checklists were compiled into a comprehensive list. All items were grouped into three domains: (i) research team and reflexivity, (ii) study design and (iii) data analysis and reporting. Duplicate items and those that were ambiguous, too broadly defined and impractical to assess were removed. Results. Items most frequently included in the checklists related to sampling method, setting for data collection, method of data collection, respondent validation of findings, method of recording data, description of the derivation of themes and inclusion of supporting quotations. We grouped all items into three domains: (i) research team and reflexivity, (ii) study design and (iii) data analysis and reporting. Conclusions. The criteria included in COREQ, a 32-item checklist, can help researchers to report important aspects of the research team, study methods, context of the study, findings, analysis and interpretations.

Physical Activity and Public Health Updated Recommendation for Adults From the American College of Sports Medicine and the American Heart Association

Abstract: Summary—In 1995 the American College of Sports Medicine and the Centers for Disease Control and Prevention published national guidelines on Physical Activity and Public Health The Committee on Exercise and Cardiac Rehabilitation of the American Heart Association endorsed and supported these recommendations The purpose of the present report is to update and clarify the 1995 recommendations on the types and amounts of physical activity needed by healthy adults to improve and maintain health Development of this document was by an expert panel of scientists, including physicians, epidemiologists, exercise scientists, and public health specialists This panel reviewed advances in pertinent physiologic, epidemiologic, and clinical scientific data, including primary research articles and reviews published since the original recommendation was issued in 1995 Issues considered by the panel included new scientific evidence relating physical activity to health, physical activity recommendations by various organizations in the interim, and communications issues Key points related to updating the physical activity recommendation were outlined and writing groups were formed A draft manuscript was prepared and circulated for review to the expert panel as well as to outside experts Comments were integrated into the final recommendation Primary Recommendation—To promote and maintain health, all healthy adults aged 18 to 65 yr need moderate-intensity aerobic (endurance) physical activity for a minimum of 30 min on five days each week or vigorous-intensity aerobic physical activity for a minimum of 20 min on three days each week [I (A)] Combinations of moderate- and vigorous-intensity activity can be performed to meet this recommendation [IIa (B)] For example, a person can meet the recommendation by walking briskly for 30 min twice during the week and then jogging for 20 min on two other days Moderate-intensity aerobic activity, which is generally equivalent to a brisk walk and noticeably accelerates the heart rate, can be accumulated toward the 30-min minimum by performing bouts each lasting 10 or more minutes [I (B)] Vigorous-intensity activity is exemplified by jogging, and causes rapid breathing and a substantial increase in heart rate In addition, every adult should perform activities that maintain or increase muscular strength and endurance a minimum of two days each week [IIa (A)] Because of the dose-response relation between physical activity and health, persons who wish to further improve their personal fitness, reduce their risk for chronic diseases and disabilities or prevent unhealthy weight gain may benefit by exceeding the minimum recommended amounts of physical activity [I (A)] (Circulation 2007;116:1081-1093)

Physical activity and public health: updated recommendation for adults from the American College of Sports Medicine and the American Heart Association.

Abstract: Summary: In 1995 the American College of Sports Medicine and the Centers for Disease Control and Prevention published national guidelines on Physical Activity and Public Health. The Committee on Exercise and Cardiac Rehabilitation of the American Heart Association endorsed and supported these recommendations. The purpose of the present report is to update and clarify the 1995 recommendations on the types and amounts of physical activity needed by healthy adults to improve and maintain health. Development of this document was by an expert panel of scientists, including physicians, epidemiologists, exercise scientists, and public health specialists. This panel reviewed advances in pertinent physiologic, epidemiologic, and clinical scientific data, including primary research articles and reviews published since the original recommendation was issued in 1995. Issues considered by the panel included new scientific evidence relating physical activity to health, physical activity recommendations by various organizations in the interim, and communications issues. Key points related to updating the physical activity recommendation were outlined and writing groups were formed. A draft manuscript was prepared and circulated for review to the expert panel as well as to outside experts. Comments were integrated into the final recommendation. Primary Recommendation: To promote and maintain health, all healthy adults aged 18 to 65 yr need moderate-intensity aerobic (endurance) physical activity for a minimum of 30 min on five days each week or vigorous-intensity aerobic physical activity for a minimum of 20 min on three days each week. [I (A)] Combinations of moderate- and vigorous-intensity activity can be performed to meet this recommendation. [IIa (B)] For example, a person can meet the recommendation by walking briskly for 30 min twice during the week and then jogging for 20 min on two other days. Moderate-intensity aerobic activity, which is generally equivalent to a brisk walk and noticeably accelerates the heart rate, can be accumulated toward the 30-min minimum by performing bouts each lasting 10 or more minutes. [I (B)] Vigorous-intensity activity is exemplified by jogging, and causes rapid breathing and a substantial increase in heart rate. In addition, every adult should perform activities that maintain or increase muscular strength and endurance a minimum of two days each week. [IIa (A)] Because of the dose-response relation between physical activity and health, persons who wish to further improve their personal fitness, reduce their risk for chronic diseases and disabilities or prevent unhealthy weight gain may benefit by exceeding the minimum recommended amounts of physical activity. [I (A)]

Patterns of somatic mutation in human cancer genomes

Abstract: Cancers arise owing to mutations in a subset of genes that confer growth advantage. The availability of the human genome sequence led us to propose that systematic resequencing of cancer genomes for mutations would lead to the discovery of many additional cancer genes. Here we report more than 1,000 somatic mutations found in 274 megabases (Mb) of DNA corresponding to the coding exons of 518 protein kinase genes in 210 diverse human cancers. There was substantial variation in the number and pattern of mutations in individual cancers reflecting different exposures, DNA repair defects and cellular origins. Most somatic mutations are likely to be 'passengers' that do not contribute to oncogenesis. However, there was evidence for 'driver' mutations contributing to the development of the cancers studied in approximately 120 genes. Systematic sequencing of cancer genomes therefore reveals the evolutionary diversity of cancers and implicates a larger repertoire of cancer genes than previously anticipated.

An Evaluation of Harmonic Vibrational Frequency Scale Factors

Abstract: Scale factors for obtaining fundamental vibrational frequencies, low-frequency vibrational frequencies, zeropoint vibrational energies (ZPVEs), and thermal contributions to enthalpy and entropy have been derived through a least-squares approach from harmonic frequencies determined at more than 100 levels of theory. Wave function procedures (HF, MP2, QCISD, QCISD(T), CCSD, and CCSD(T)) and a large and representative range of density functional theory (DFT) approaches (B3-LYP, BMK, EDF2, M05-2X, MPWB1K, O3-LYP, PBE, TPSS, etc.) have been examined in conjunction with basis sets such as 6-31G(d), 6-31+G(d,p), 6-31G(2df,p), 6-311+G(d,p), and 6-311+G(2df,p). The vibrational frequency scale factors were determined by a comparison of theoretical harmonic frequencies with the corresponding experimental fundamentals utilizing a standard set of 1066 individual vibrations. ZPVE scale factors were generally obtained from a comparison of the computed ZPVEs with experimental ZPVEs for a smaller standard set of 39 molecules, though the effect of expansion to a 48 molecule data set was also examined. In addition to evaluating the scale factors for a wide range of levels of theory, we have also probed the effect on scale factors of varying the percentage of incorporated exact exchange in hybrid DFT calculations using a modified B3-LYP functional. This has revealed a near-linear relationship between the magnitude of the scale factor and the proportion of exact exchange. Finally, we have investigated the effect of basis set size on HF, MP2, B3-LYP, and BMK scale factors by deriving values with basis sets ranging from 6-31G(d) up to 6-311++G(3df,3pd) as well as with basis sets in the cc-pVnZ and aug-cc-pVnZ series and with the TZV2P basis.

Management of Thyroid Dysfunction during Pregnancy and Postpartum: An Endocrine Society Clinical Practice Guideline

Abstract: Objective: The aim was to update the guidelines for the management of thyroid dysfunction during pregnancy and postpartum published previously in 2007. A summary of changes between the 2007 and 2012 version is identified in the Supplemental Data (published on The Endocrine Society's Journals Online web site at http://jcem.endojournals.org). Evidence: This evidence-based guideline was developed according to the U.S. Preventive Service Task Force, grading items level A, B, C, D, or I, on the basis of the strength of evidence and magnitude of net benefit (benefits minus harms) as well as the Grading of Recommendations, Assessment, Development, and Evaluation (GRADE) system to describe both the strength of recommendations and the quality of evidence. Consensus Process: The guideline was developed through a series of e-mails, conference calls, and one face-to-face meeting. An initial draft was prepared by the Task Force, with the help of a medical writer, and reviewed and commented on by members of The Endocri...

Justifying Knowledge, Justifying Method, Taking Action: Epistemologies, Methodologies, and Methods in Qualitative Research

Abstract: In this article, the authors clarify a framework for qualitative research, in particular for evaluating its quality, founded on epistemology, methodology, and method. They define these elements and discuss their respective contributions and interrelationships. Epistemology determines and is made visible through method, particularly in the participant- researcher relationship, measures of research quality, and form, voice, and representation in analysis and writing. Epistemology guides methodological choices and is axiological. Methodology shapes and is shaped by research objectives, questions, and study design. Methodologies can prescribe choices of method, resonate with particular academic disciplines, and encourage or discourage the use and/or development of theory. Method is constrained by and makes visible methodological and epistemic choices. If we define good quality qualitative research as research that attends to all three elements and demonstrates internal consistency between them, standardized checklists can be transcended and innovation and diversity in qualitative research practice facilitated.

Genome-wide profiling identifies epithelial cell genes associated with asthma and with treatment response to corticosteroids

Abstract: Airway inflammation and epithelial remodeling are two key features of asthma. IL-13 and other cytokines produced during T helper type 2 cell-driven allergic inflammation contribute to airway epithelial goblet cell metaplasia and may alter epithelial–mesenchymal signaling, leading to increased subepithelial fibrosis or hyperplasia of smooth muscle. The beneficial effects of corticosteroids in asthma could relate to their ability to directly or indirectly decrease epithelial cell activation by inflammatory cells and cytokines. To identify markers of epithelial cell dysfunction and the effects of corticosteroids on epithelial cells in asthma, we studied airway epithelial cells collected from asthmatic subjects enrolled in a randomized controlled trial of inhaled corticosteroids, from healthy subjects and from smokers (disease control). By using gene expression microarrays, we found that chloride channel, calcium-activated, family member 1 (CLCA1), periostin, and serine peptidase inhibitor, clade B (ovalbumin), member 2 (serpinB2) were up-regulated in asthma but not in smokers. Corticosteroid treatment down-regulated expression of these three genes and markedly up-regulated expression of FK506-binding protein 51 (FKBP51). Whereas high baseline expression of CLCA1, periostin, and serpinB2 was associated with a good clinical response to corticosteroids, high expression of FKBP51 was associated with a poor response. By using airway epithelial cells in culture, we found that IL-13 increased expression of CLCA1, periostin, and serpinB2, an effect that was suppressed by corticosteroids. Corticosteroids also induced expression of FKBP51. Taken together, our findings show that airway epithelial cells in asthma have a distinct activation profile and identify direct and cell-autonomous effects of corticosteroid treatment on airway epithelial cells that relate to treatment responses and can now be the focus of specific mechanistic studies.

Accuracy of procalcitonin for sepsis diagnosis in critically ill patients: systematic review and meta-analysis

Abstract: Procalcitonin is widely reported as a useful biochemical marker to diff erentiate sepsis from other non-infectious causes of systemic infl ammatory response syndrome. In this systematic review, we estimated the diagnostic accuracy of procalcitonin in sepsis diagnosis in critically ill patients. 18 studies were included in the review. Overall, the diagnostic performance of procalcitonin was low, with mean values of both sensitivity and specifi city being 71% (95% CI 67–76) and an area under the summary receiver operator characteristic curve of 0·78 (95% CI 0·73–0·83). Studies were grouped into phase 2 studies (n=14) and phase 3 studies (n=4) by use of Sackett and Haynes’ classifi cation. Phase 2 studies had a low pooled diagnostic odds ratio of 7·79 (95% CI 5·86–10·35). Phase 3 studies showed signifi cant heterogeneity because of variability in sample size (meta-regression coeffi cient –0·592, p=0·017), with diagnostic performance upwardly biased in smaller studies, but moving towards a null eff ect in larger studies. Procalcitonin cannot reliably diff erentiate sepsis from other non-infectious causes of systemic infl ammatory response syndrome in critically ill adult patients. The fi ndings from this study do not lend support to the widespread use of the procalcitonin test in critical care settings.

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

Abstract: We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in protein-coding genes seems to be relatively rare, with lineage-specific differences being largely due to diversification and rapid turnover in gene families involved in environmental interactions. In contrast, about 20% of eutherian conserved non-coding elements (CNEs) are recent inventions that postdate the divergence of Eutheria and Metatheria. A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation.

Mutations in smooth muscle α-actin ( ACTA2 ) lead to thoracic aortic aneurysms and dissections

Abstract: Mutations in smooth muscle α-actin ( ACTA2 ) lead to thoracic aortic aneurysms and dissections

Reference frames, superselection rules, and quantum information

Abstract: Recently, there has been much interest in a new kind of ``unspeakable'' quantum information that stands to regular quantum information in the same way that a direction in space or a moment in time stands to a classical bit string: the former can only be encoded using particular degrees of freedom while the latter are indifferent to the physical nature of the information carriers. The problem of correlating distant reference frames, of which aligning Cartesian axes and synchronizing clocks are important instances, is an example of a task that requires the exchange of unspeakable information and for which it is interesting to determine the fundamental quantum limit of efficiency. There have also been many investigations into the information theory that is appropriate for parties that lack reference frames or that lack correlation between their reference frames, restrictions that result in global and local superselection rules. In the presence of these, quantum unspeakable information becomes a new kind of resource that can be manipulated, depleted, quantified, etc. Methods have also been developed to contend with these restrictions using relational encodings, particularly in the context of computation, cryptography, communication, and the manipulation of entanglement. This paper reviews the role of reference frames and superselection rules in the theory of quantum-information processing.

Screening for colorectal cancer using the faecal occult blood test, hemoccult.

Abstract: Background Colorectal cancer is a leading cause of morbidity and mortality, especially in the Western world. The human and financial costs have prompted considerable research to evaluate screening tests to detect the cancer at an early curable stage. Tests that have been considered for population screening include the faecal occult blood test (FOBT), flexible sigmoidoscopy and colonoscopy. Reducing mortality from colorectal cancer (CRC) may be achieved by the introduction of population-based screening programmes. Objectives To determine whether screening for colorectal cancer using the faecal occult blood test (guaiac or immunochemical) reduces colorectal cancer mortality and to consider the benefits and harms of screening. Search methods Published and unpublished data for this review were identified by: Reviewing studies included in the previous Cochrane review; Searching several electronic databases (Cochrane Library, Medline, Embase, CINAHL, PsychInfo, Amed, SIGLE, HMIC); and Writing to the principal investigators of potentially eligible trials. Selection criteria We included all randomised trials of screening for colorectal cancer that compared faecal occult blood test (guaiac or immunochemical) on more than one occasion with no screening and reported colorectal cancer mortality. Data collection and analysis Data from the eligible trials were independently extracted by two reviewers. The primary data analysis was performed using the group participants were originally randomised to ('intention to screen'), whether or not they attended screening; a secondary analysis adjusted for non-attendance. We calculated the relative risks and risk differences for each trial, and then overall, using fixed and random effects models (including testing for heterogeneity of effects). We identified nine articles concerning four randomised controlled trials and two controlled trials involving over 320,000 participants with follow-up ranging from 8 to 18 years. Main results Combined results from the 4 eligible randomised controlled trials shows that participants allocated to FOBT screening had a statistically significant 16% reduction in the relative risk of colorectal cancer mortality (RR 0.84; CI: 0.78-0.90). In the 3 studies that used biennial screening (Funen, Minnesota, Nottingham) there was a 15% relative risk reduction (RR 0.85, CI: 0.78-0.92) in colorectal cancer mortality. When adjusted for mean screening attendance in the individual studies, there was a 25% relative risk reduction (RR 0.75, CI: 0.66 - 0.84) for those attending at least one round of screening using the faecal occult blood test. Authors' conclusions Benefits of screening include a modest reduction in colorectal cancer mortality, a possible reduction in cancer incidence through the detection and removal of colorectal adenomas, and potentially, the less invasive surgery that earlier treatment of colorectal cancers may involve. Harmful effects of screening include the psycho-social consequences of receiving a false-positive result, the potentially significant complications of colonoscopy or a false-negative result, the possibility of overdiagnosis (leading to unnecessary investigations or treatment) and the complications associated with treatment.

Saline or Albumin for Fluid Resuscitation in Patients with Traumatic Brain Injury

Abstract: A b s t r ac t Background The Saline versus Albumin Fluid Evaluation study suggested that patients with traumatic brain injury resuscitated with albumin had a higher mortality rate than those resuscitated with saline. We conducted a post hoc follow-up study of patients with traumatic brain injury who were enrolled in the study. Methods For patients with traumatic brain injury (i.e., a history of trauma, evidence of head trauma on a computed tomographic [CT] scan, and a score of ≤13 on the Glasgow Coma Scale [GCS]), we recorded baseline characteristics from case-report forms, clinical records, and CT scans and determined vital status and functional neurologic outcomes 24 months after randomization. Results We followed 460 patients, of whom 231 (50.2%) received albumin and 229 (49.8%) received saline. The subgroup of patients with GCS scores of 3 to 8 were classified as having severe brain injury (160 [69.3%] in the albumin group and 158 [69.0%] in the saline group). Demographic characteristics and indexes of severity of brain injury were similar at baseline. At 24 months, 71 of 214 patients in the albumin group (33.2%) had died, as compared with 42 of 206 in the saline group (20.4%) (relative risk, 1.63; 95% confidence interval [CI], 1.17 to 2.26; P = 0.003). Among patients with severe brain injury, 61 of 146 patients in the albumin group (41.8%) died, as compared with 32 of 144 in the saline group (22.2%) (relative risk, 1.88; 95% CI, 1.31 to 2.70; P<0.001); among patients with GCS scores of 9 to 12, death occurred in 8 of 50 patients in the albumin group (16.0%) and 8 of 37 in the saline group (21.6%) (relative risk, 0.74; 95% CI, 0.31 to 1.79; P = 0.50). Conclusions In this post hoc study of critically ill patients with traumatic brain injury, fluid resuscitation with albumin was associated with higher mortality rates than was resuscitation with saline. (Current Controlled Trials number, ISRCTN76588266.)

Grand challenges in chronic non-communicable diseases

Abstract: The top 20 policy and research priorities for conditions such as diabetes, stroke and heart disease.

Simultaneous Localization, Mapping and Moving Object Tracking

Abstract: Simultaneous localization, mapping and moving object tracking (SLAMMOT) involves both simultaneous localization and mapping (SLAM) in dynamic environments and detecting and tracking these dynamic objects. In this paper, a mathematical framework is established to integrate SLAM and moving object tracking. Two solutions are described: SLAM with generalized objects, and SLAM with detection and tracking of moving objects (DATMO). SLAM with generalized objects calculates a joint posterior over all generalized objects and the robot. Such an approach is similar to existing SLAM algorithms, but with additional structure to allow for motion modeling of generalized objects. Unfortunately, it is computationally demanding and generally infeasible. SLAM with DATMO decomposes the estimation problem into two separate estimators. By maintaining separate posteriors for stationary objects and moving objects, the resulting estimation problems are much lower dimensional than SLAM with generalized objects. Both SLAM and moving object tracking from a moving vehicle in crowded urban areas are daunting tasks. Based on the SLAM with DATMO framework, practical algorithms are proposed which deal with issues of perception modeling, data association, and moving object detection. The implementation of SLAM with DATMO was demonstrated using data collected from the CMU Navlab11 vehicle at high speeds in crowded urban environments. Ample experimental results shows the feasibility of the proposed theory and algorithms.

Breakage mechanics—Part I: Theory

Abstract: Different measures have been suggested for quantifying the amount of fragmentation in randomly compacted crushable aggregates. A most effective and popular measure is to adopt variants of Hardin's [1985. Crushing of soil particles. J. Geotech. Eng. ASCE 111(10), 1177–1192] definition of relative breakage ‘ B r ’. In this paper we further develop the concept of breakage to formulate a new continuum mechanics theory for crushable granular materials based on statistical and thermomechanical principles. Analogous to the damage internal variable ‘ D ’ which is used in continuum damage mechanics (CDM), here the breakage internal variable ‘ B ’ is adopted. This internal variable represents a particular form of the relative breakage ‘ B r ’ and measures the relative distance of the current grain size distribution from the initial and ultimate distributions. Similar to ‘ D ’, ‘ B ’ varies from zero to one and describes processes of micro-fractures and the growth of surface area. However, unlike damage that is most suitable to tensioned solid-like materials, the breakage is aimed towards compressed granular matter. While damage effectively represents the opening of micro-cavities and cracks, breakage represents comminution of particles. We term the new theory continuum breakage mechanics (CBM), reflecting the analogy with CDM. A focus is given to developing fundamental concepts and postulates, and identifying the physical meaning of the various variables. In this part of the paper we limit the study to describe an ideal dissipative process that includes breakage without plasticity. Plastic strains are essential, however, in representing aspects that relate to frictional dissipation, and this is covered in Part II of this paper together with model examples.

Preparing for Critical Infrastructure Breakdowns: The Limits of Crisis Management and the Need for Resilience

Abstract: Modern societies are widely considered to harbour an increased propensity for breakdowns of their critical infrastructure (CI) systems. While such breakdowns have proven rather rare, Hurricane Katrina has demonstrated the catastrophic consequences of such breakdowns. This article explores how public authorities can effectively prepare to cope with these rare events. Drawing from the literature on crisis and disaster management, we examine the strengths and weaknesses of traditional approaches to crisis preparation and crisis response. We argue that the established ways of organising for critical decision-making will not suffice in the case of a catastrophic breakdown. In the immediate aftermath of such a breakdown, an effective response will depend on the adaptive behaviour of citizens, front-line workers and middle managers. In this article, we formulate a set of strategies that enhance societal resilience and identify the strong barriers to their implementation.