Archiving primary data: Solutions for long-term studies

The recent trend for journals to require open access to primary data included in publications has been embraced by many biologists, but has caused apprehension amongst researchers engaged in long-term ecological and evolutionary studies. A worldwide survey of 73 principal investigators (Pls) with long-term studies revealed positive attitudes towards sharing data with the agreement or involvement of the PI, and 93% of PIs have historically shared data. Only 8% were in favor of uncontrolled, open access to primary data while 63% expressed serious concern. We present here their viewpoint on an issue that can have non-trivial scientific consequences. We discuss potential costs of public data archiving and provide possible solutions to meet the needs of journals and researchers.

The correlation between reading and mathematics ability at age twelve has a substantial genetic component

Dissecting how genetic and environmental influences impact on learning is helpful for maximizing numeracy and literacy. Here we show, using twin and genome-wide analysis, that there is a substantial genetic component to children’s ability in reading and mathematics, and estimate that around one half of the observed correlation in these traits is due to shared genetic effects (so-called Generalist Genes). Thus, our results highlight the potential role of the learning environment in contributing to differences in a child’s cognitive abilities at age twelve.

Global, regional, and national disability-adjusted life years (DALYs) for 306 diseases and injuries and healthy life expectancy (HALE) for 188 countries, 1990–2013: Quantifying the epidemiological transition

Background The Global Burden of Disease Study 2013 (GBD 2013) aims to bring together all available epidemiological data using a coherent measurement framework, standardised estimation methods, and transparent data sources to enable comparisons of health loss over time and across causes, age–sex groups, and countries. The GBD can be used to generate summary measures such as disability-adjusted life-years (DALYs) and healthy life expectancy (HALE) that make possible comparative assessments of broad epidemiological patterns across countries and time. These summary measures can also be used to quantify the component of variation in epidemiology that is related to sociodemographic development. Methods We used the published GBD 2013 data for age-specific mortality, years of life lost due to premature mortality (YLLs), and years lived with disability (YLDs) to calculate DALYs and HALE for 1990, 1995, 2000, 2005, 2010, and 2013 for 188 countries. We calculated HALE using the Sullivan method; 95% uncertainty intervals (UIs) represent uncertainty in age-specific death rates and YLDs per person for each country, age, sex, and year. We estimated DALYs for 306 causes for each country as the sum of YLLs and YLDs; 95% UIs represent uncertainty in YLL and YLD rates. We quantified patterns of the epidemiological transition with a composite indicator of sociodemographic status, which we constructed from income per person, average years of schooling after age 15 years, and the total fertility rate and mean age of the population. We applied hierarchical regression to DALY rates by cause across countries to decompose variance related to the sociodemographic status variable, country, and time. Findings Worldwide, from 1990 to 2013, life expectancy at birth rose by 6·2 years (95% UI 5·6–6·6), from 65·3 years (65·0–65·6) in 1990 to 71·5 years (71·0–71·9) in 2013, HALE at birth rose by 5·4 years (4·9–5·8), from 56·9 years (54·5–59·1) to 62·3 years (59·7–64·8), total DALYs fell by 3·6% (0·3–7·4), and age-standardised DALY rates per 100 000 people fell by 26·7% (24·6–29·1). For communicable, maternal, neonatal, and nutritional disorders, global DALY numbers, crude rates, and age-standardised rates have all declined between 1990 and 2013, whereas for non–communicable diseases, global DALYs have been increasing, DALY rates have remained nearly constant, and age-standardised DALY rates declined during the same period. From 2005 to 2013, the number of DALYs increased for most specific non-communicable diseases, including cardiovascular diseases and neoplasms, in addition to dengue, food-borne trematodes, and leishmaniasis; DALYs decreased for nearly all other causes. By 2013, the five leading causes of DALYs were ischaemic heart disease, lower respiratory infections, cerebrovascular disease, low back and neck pain, and road injuries. Sociodemographic status explained more than 50% of the variance between countries and over time for diarrhoea, lower respiratory infections, and other common infectious diseases; maternal disorders; neonatal disorders; nutritional deficiencies; other communicable, maternal, neonatal, and nutritional diseases; musculoskeletal disorders; and other non-communicable diseases. However, sociodemographic status explained less than 10% of the variance in DALY rates for cardiovascular diseases; chronic respiratory diseases; cirrhosis; diabetes, urogenital, blood, and endocrine diseases; unintentional injuries; and self-harm and interpersonal violence. Predictably, increased sociodemographic status was associated with a shift in burden from YLLs to YLDs, driven by declines in YLLs and increases in YLDs from musculoskeletal disorders, neurological disorders, and mental and substance use disorders. In most country-specific estimates, the increase in life expectancy was greater than that in HALE. Leading causes of DALYs are highly variable across countries. Interpretation Global health is improving. Population growth and ageing have driven up numbers of DALYs, but crude rates have remained relatively constant, showing that progress in health does not mean fewer demands on health systems. The notion of an epidemiological transition—in which increasing sociodemographic status brings structured change in disease burden—is useful, but there is tremendous variation in burden of disease that is not associated with sociodemographic status. This further underscores the need for country-specific assessments of DALYs and HALE to appropriately inform health policy decisions and attendant actions.

The reader-assembled narrative: Representing the random in print fiction

The growing interest in co-created reading experiences in both digital and print formats raises interesting questions for creative writers who work in the space of interactive fiction. This essay argues that writers have not abandoned experiments with co-creation in print narratives in favour of the attractions of the digital environment, as might be assumed by the discourse on digital development. Rather, interactive print narratives, in particular ‘reader-assembled narratives’ demonstrate a rich history of experimentation and continue to engage writers who wish to craft individual reading experiences for readers and to experiment with their own creative process as writers. The reader-assembled narrative has been used for many different reasons and for some writers, such as BS Johnson it is a method of problem solving, for others, like Robert Coover, it is a way to engage the reader in a more playful sense. Authors such as Marc Saporta, BS Johnson, and Robert Coover have engaged with this type of narrative play. This examination considers the narrative experimentation of these authors as a way of offering insights into creative practice for contemporary creative writers.

Finite Element Solution Of Surface-Tension Driven Flows In Laser Surface-Melting

Lasers are very efficient in heating localized regions and hence they find a wide application in surface treatment processes. The surface of a material can be selectively modified to give superior wear and corrosion resistance. In laser surface-melting and welding problems, the high temperature gradient prevailing in the free surface induces a surface-tension gradient which is the dominant driving force for convection (known as thermo-capillary or Marangoni convection). It has been reported that the surface-tension driven convection plays a dominant role in determining the melt pool shape. In most of the earlier works on laser-melting and related problems, the finite difference method (FDM) has been used to solve the Navier Stokes equations [1]. Since the Reynolds number is quite high in these cases, upwinding has been used. Though upwinding gives physically realistic solutions even on a coarse grid, the results are inaccurate. McLay and Carey have solved the thermo-capillary flow in welding problems by an implicit finite element method [2]. They used the conventional Galerkin finite element method (FEM) which requires that the pressure be interpolated by one order lower than velocity (mixed interpolation). This restricts the choice of elements to certain higher order elements which need numerical integration for evaluation of element matrices. The implicit algorithm yields a system of nonlinear, unsymmetric equations which are not positive definite. Computations would be possible only with large mainframe computers.Sluzalec [3] has modeled the pulsed laser-melting problem by an explicit method (FEM). He has used the six-node triangular element with mixed interpolation. Since he has considered the buoyancy induced flow only, the velocity values are small. In the present work, an equal order explicit FEM is used to compute the thermo-capillary flow in the laser surface-melting problem. As this method permits equal order interpolation, there is no restriction in the choice of elements. Even linear elements such as the three-node triangular elements can be used. As the governing equations are solved in a sequential manner, the computer memory requirement is less. The finite element formulation is discussed in this paper along with typical numerical results.

Working covariance model selection for generalized estimating equations

We investigate methods for data-based selection of working covariance models in the analysis of correlated data with generalized estimating equations. We study two selection criteria: Gaussian pseudolikelihood and a geodesic distance based on discrepancy between model-sensitive and model-robust regression parameter covariance estimators. The Gaussian pseudolikelihood is found in simulation to be reasonably sensitive for several response distributions and noncanonical mean-variance relations for longitudinal data. Application is also made to a clinical dataset. Assessment of adequacy of both correlation and variance models for longitudinal data should be routine in applications, and we describe open-source software supporting this practice.

Criteria for working-correlation-structure selection in GEE: Assessment via simulation

Efficiency of analysis using generalized estimation equations is enhanced when intracluster correlation structure is accurately modeled. We compare two existing criteria (a quasi-likelihood information criterion, and the Rotnitzky-Jewell criterion) to identify the true correlation structure via simulations with Gaussian or binomial response, covariates varying at cluster or observation level, and exchangeable or AR(l) intracluster correlation structure. Rotnitzky and Jewell's approach performs better when the true intracluster correlation structure is exchangeable, while the quasi-likelihood criteria performs better for an AR(l) structure.

Unbiased estimating equations from working correlation models for irregularly timed repeated measures

The method of generalized estimating equation-, (GEEs) has been criticized recently for a failure to protect against misspecification of working correlation models, which in some cases leads to loss of efficiency or infeasibility of solutions. However, the feasibility and efficiency of GEE methods can be enhanced considerably by using flexible families of working correlation models. We propose two ways of constructing unbiased estimating equations from general correlation models for irregularly timed repeated measures to supplement and enhance GEE. The supplementary estimating equations are obtained by differentiation of the Cholesky decomposition of the working correlation, or as score equations for decoupled Gaussian pseudolikelihood. The estimating equations are solved with computational effort equivalent to that required for a first-order GEE. Full details and analytic expressions are developed for a generalized Markovian model that was evaluated through simulation. Large-sample ".sandwich" standard errors for working correlation parameter estimates are derived and shown to have good performance. The proposed estimating functions are further illustrated in an analysis of repeated measures of pulmonary function in children.

Working correlation structure misspecification, estimation and covariate design: Implications for generalised estimating equations performance

The method of generalised estimating equations for regression modelling of clustered outcomes allows for specification of a working matrix that is intended to approximate the true correlation matrix of the observations. We investigate the asymptotic relative efficiency of the generalised estimating equation for the mean parameters when the correlation parameters are estimated by various methods. The asymptotic relative efficiency depends on three-features of the analysis, namely (i) the discrepancy between the working correlation structure and the unobservable true correlation structure, (ii) the method by which the correlation parameters are estimated and (iii) the 'design', by which we refer to both the structures of the predictor matrices within clusters and distribution of cluster sizes. Analytical and numerical studies of realistic data-analysis scenarios show that choice of working covariance model has a substantial impact on regression estimator efficiency. Protection against avoidable loss of efficiency associated with covariance misspecification is obtained when a 'Gaussian estimation' pseudolikelihood procedure is used with an AR(1) structure.

Drops That Open Worlds : Image of Water in the Poetry of Euphrase Kezilahabi

Euphrase Kezilahabi on tansanialainen kirjailija, joka ensimmäisenä julkaisi swahilinkielisen vapaalla mitalla kirjoitetun runokokoelman. Perinteisessä swahilirunoudessa tiukat muotosäännöt ovat tärkeitä, ja teos synnytti kiivasta keskustelua. Runoteokset Kichomi ( Viilto , Kipu , 1974) ja Karibu Ndani ( Tervetuloa sisään , 1988) sekä Kezilahabin muu tuotanto voidaan nähdä uuden sukupolven taiteena. Kezilahabi on arvostettu runoilija, mutta hänen runojaan ei aiemmin ole käännetty englanniksi (yksittäisiä säkeitä lukuunottamatta), eikä juurikaan tutkittu yksityiskohtaisesti. Yleiskuvaan pyrkivissä lausunnoissa Kezilahabin runouden on hyvin usein määritelty olevan poliittista. Monet Kezilahabin runoista ottavatkin kantaa yhteiskunnallisiin kysymyksiin, mutta niiden pohdinta on kuitenkin runoissa vain yksi taso. Sen lisäksi Kezilahabin lyriikassa on paljon muuta ennen kartoittamatonta tämä tutkimus keskittyy veden kuvaan (the image of water). Kezilahabi vietti lapsuutensa saarella Victoria-järven keskellä, ja hänen vesikuvastonsa on rikasta. Tutkimuskysymyksenä on, mitä veden kuva runoteoksissa Kichomi ja Karibu Ndani esittää. Runojen analysoinnissa ja tulkinnassa on tarkasteltu myös sitä, miten äänteellinen taso osallistuu kuvien luomiseen. Tutkimuksen määritelmä kuvasta pohjautuu osittain Hugh Kennerin näkemykseen, jonka mukaan oleellista kuvassa on kirjaimellinen taso. Kennerin lähtökohtaan on yhdistetty John Shoptawin teoriaa, joka korostaa runon äänteellisen puolen tärkeyttä merkityksen muodostumisessa. Foneemien analyysissä vaikutteena on ollut Reuven Tsurin teoria. Analyysiosio osoittaa, että veden kuva edustaa ja käsittelee teoksissa lukuisia teemoja: elämää, kuolemaa, fyysistä vetovoimaa, runoutta, mielikuvitusta ja (ali)tajuntaa sekä moraalia. Veden kuvan tutkimuksen pohjalta on nähtävissä, että Kezilahabin filosofia asettuu elävä/kuollut- ja elämä/kuolema dikotomioiden ulkopuolelle.

The Context-integrity of the global carbon regime: The relevance and impact of the World Trade Organization

In the study of the integrity of the global carbon regime there are a number of institutions that must be considered for their impacts on this system. In particular, the subject matter of this chapter is concerned with the main international institution for trade, the World Trade Organization (the WTO). Otherwise stated, this chapter is concerned with how the institutional integrity of the global carbon regime aligns with the values and policy objectives of the WTO. This is done with a view to consider whether the global carbon regime aligns with these values and objectives in a way demonstrative of context-integrity. This alignment is not a single-sided undertaking and, therefore, it is essential that the underlying values of the WTO themselves align with the global carbon regime. I suggest this is particularly crucial given the importance of the objectives of the climate change regime, and the scientific predictions of the current climate projections.

Urinary tract infection of mice to model human disease: Practicalities, implications and limitations

Urinary tract infections (UTIs) are among the most common bacterial infections in humans. Murine models of human UTI are vital experimental tools that have helped to elucidate UTI pathogenesis and advance knowledge of potential treatment and infection prevention strategies. Fundamentally, several variables are inherent in different murine models, and understanding the limitations of these variables provides an opportunity to understand how models may be best applied to research aimed at mimicking human disease. In this review, we discuss variables inherent in murine UTI model studies and how these affect model usage, data analysis and data interpretation. We examine recent studies that have elucidated UTI host–pathogen interactions from the perspective of gene expression, and review new studies of biofilm and UTI preventative approaches. We also consider potential standards for variables inherent in murine UTI models and discuss how these might expand the utility of models for mimicking human disease and uncovering new aspects of pathogenesis

Uropathogenic Escherichia Coli engages CD14-dependent signaling to enable bladder-macrophage-dependent control of acute urinary tract infection

Background CD14, a coreceptor for several pattern recognition receptors and a widely used monocyte/macrophage marker, plays a key role in host responses to gram-negative bacteria. Despite the central role of CD14 in the inflammatory response to lipopolysaccharide and other microbial products and in the dissemination of bacteria in some infections, the signaling networks controlled by CD14 during urinary tract infection (UTI) are unknown. Methods We used uropathogenic Escherichia coli (UPEC) infection of wild-type (WT) C57BL/6 and Cd14−/− mice and RNA sequencing to define the CD14-dependent transcriptional signature and the role of CD14 in host defense against UTI in the bladder. Results UPEC induced the upregulation of Cd14 and the monocyte/macrophage-related genes Emr1/F4/80 and Csf1r/c-fms, which was associated with lower UPEC burdens in WT mice, compared with Cd14−/− mice. Exacerbation of infection in Cd14−/− mice was associated with the absence of a 491-gene transcriptional signature in the bladder that encompassed multiple host networks not previously associated with this receptor. CD14-dependent pathways included immune cell trafficking, differential cytokine production in macrophages, and interleukin 17 signaling. Depletion of monocytes/macrophages in the bladder by administration of liposomal clodronate led to higher UPEC burdens. Conclusions This study identifies new host protective and signaling roles for CD14 in the bladder during UPEC UTI.

Characterisation of the efficacy of endodontic medications using a three-dimensional fluorescent tooth model: An ex vivo study

The purpose of this study was to establish a three-dimensional fluorescent tooth model to investigate bacterial viability against intra-canal medicaments across the thickness and surface of root dentine. Dental microbial biofilms (Enterococcus faecalis and Streptococcus mutans) were established on the external root surface and bacterial kill was monitored over time against intra-canal medicament (Ca(OH)2 ) using fluorescent microscopy in conjunction with BacLight SYTO9 and propidium iodide stains. An Olympus digital camera fitted to SZX16 fluorescent microscope captured images of bacterial cells in biofilms on the external root surface. Viability of biofilm was measured by calculating the total pixel area of green (viable bacteria) and red (non-viable bacteria) for each image using ImageJ® software. All data generated were assessed for normality and then analysed using a Mann-Whitney t-test. The viability of S. mutans biofilm following Ca(OH)2 treatment showed a significant decline compared with the untreated group (P = 0.0418). No significant difference was seen for E. faecalis biofilm between the Ca(OH)2 and untreated groups indicating Ca(OH)2 medicament is ineffective against E. faecalis biofilm. This novel three-dimensional fluorescent biofilm model provides a new clinically relevant tool for testing of medicaments against dental biofilms.

Dispelling Myths about Doctorates in the Australian Public Service

Many doctoral candidates pursue their studies with the goal of ultimately securing an academic position in a university. There are, however, many other career options for doctoral graduates in non-academic positions, including a career in the public service, either at the state or national level. Public service managers are interested in people who can demonstrate a range of skills and capacities, and most doctoral graduates will have developed a range of these skills.