Extending the Latent Multinomial Model with Complex Error Processes and Dynamic Markov Bases

The latent multinomial model (LMM) model of Link et al. (2010) provided a general framework for modelling mark-recapture data with potential errors in identification. Key to this approach was a Markov chain Monte Carlo (MCMC) scheme for sampling possible configurations of the counts true capture histories that could have generated the observed data. This MCMC algorithm used vectors from a basis for the kernel of the linear map between the true and observed counts to move between the possible configurations of the true data. Schofield and Bonner (2015) showed that a strict basis was sufficient for some models of the errors, including the model presented by Link et al. (2010), but a larger set called a Markov basis may be required for more complex models. We address two further challenges with this approach: 1) that models with more complex error mechanisms do not fit easily within the LMM and 2) that the Markov basis can be difficult or impossible to compute for even moderate sized studies. We address these issues by extending the LMM to separately model the capture/demographic process and the error process and by developing a new MCMC sampling scheme using dynamic Markov bases. Our work is motivated by a study of Queen snakes (Regina septemvittata) in Kentucky, USA, and we use simulation to compare the use of PIT tags, with perfect identification, and brands, which are prone to error, when estimating survival rates

Life, Death and Preferential Attachment

Scientific communities are characterized by strong stratification. The highly skewed frequency distribution of citations of published scientific papers suggests a relatively small number of active, cited papers embedded in a sea of inactive and uncited papers. We propose an analytically soluble model which allows for the death of nodes. This model provides an excellent description of the citation distributions for live and dead papers in the SPIRES database. Further, this model suggests a novel and general mechanism for the generation of power law distributions in networks whenever the fraction of active nodes is small.Comment: 5 pages, 2 figure

Linking discrete event simulation models using HLA

The increasing usage of discrete event simulation packages for modeling and analyzing manufacturing and logistics has led to a need for connecting simulation models together at runtime. One such methodology for linking discrete event simulation models together has been developed for this research and this paper demonstrates the usage of this linking method. A unified simulation model is developed from two submodels developed using different simulation packages. <br /

The impact of individualised cardiovascular disease (CVD) risk estimates and lifestyle advice on physical activity in individuals at high risk of CVD: a pilot 2 x 2 factorial understanding risk trial.

BACKGROUND: There is currently much interest in encouraging individuals to increase physical activity in order to reduce CVD risk. This study has been designed to determine if personalised CVD risk appreciation can increase physical activity in adults at high risk of CVD. METHODS/DESIGN: In a 2 x 2 factorial design participants are allocated at random to a personalised 10-year CVD risk estimate or numerical CVD risk factor values (systolic blood pressure, LDL cholesterol and fasting glucose) and, simultaneously, to receive a brief lifestyle advice intervention targeting physical activity, diet and smoking cessation or not. We aim to recruit 200 participants from Oxfordshire primary care practices. Eligibility criteria include adults age 40-70 years, estimated 10-year CVD risk > or =20%, ability to read and write English, no known CVD and no physical disability or other condition reducing the ability to walk. Primary outcome is physical activity measured by ActiGraph accelerometer with biochemical, anthropometrical and psychological measures as additional outcomes. Primary analysis is between group physical activity differences at one month powered to detect a difference of 30,000 total counts per day of physical activity between the groups. Additional analyses will seek to further elucidate the relationship between the provision of risk information, and intention to change behaviour and to determine the impact of both interventions on clinical and anthropometrical measures including fasting and 2 hour plasma glucose, fructosamine, serum cotinine, plasma vitamin C, body fat percentage and blood pressure. DISCUSSION: This is a pilot trial seeking to demonstrate in a real world setting, proof of principal that provision of personalised risk information can contribute to behaviour changes aimed at reducing CVD risk. This study will increase our understanding of the links between the provision of risk information and behaviour change and if successful, could be used in clinical practice with little or no modification.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Correlations in Networks associated to Preferential Growth

Combinations of random and preferential growth for both on-growing and stationary networks are studied and a hierarchical topology is observed. Thus for real world scale-free networks which do not exhibit hierarchical features preferential growth is probably not the main ingredient in the growth process. An example of such real world networks includes the protein-protein interaction network in yeast, which exhibits pronounced anti-hierarchical features.Comment: 4 pages, 4 figure

Rac Activation Induces NADPH Oxidase Activity in Transgenic COSphox Cells and Level of Superoxide Production is Exchange Factor-Dependent

Transient expression of constitutively active Rac1 derivatives, (G12V) or (Q61L), was sufficient to induce phagocyte NADPH oxidase activity in a COS-7 cell model in which human cDNAs for essential oxidase components, gp91phox, p22phox, p47phox, and p67phox, were expressed as stable transgenes. Expression of constitutively active Rac1 in “COSphox” cells induced translocation of p47phox and p67phox to the membrane. Furthermore, translocation of p47phox was induced in the absence of p67phox expression, even though Rac does not directly bind p47phox. Rac effector domain point substitutions (A27K, G30S, D38A, Y40C), which can selectively eliminate interaction with different effector proteins, impaired Rac1V12-induced superoxide production. Activation of endogenous Rac1 by expression of constitutively active Rac-guanine nucleotide exchange factor (GEF) derivatives was sufficient to induce high level NADPH oxidase activity in COSphox cells. The constitutively active form of the hematopoietic-specific GEF, Vav1, was the most effective at activating superoxide production, despite detection of higher levels of Rac1-GTP upon expression of constitutively active Vav2 or Tiam1 derivatives. These data suggest that Rac can play a dual role in NADPH oxidase activation, both by directly participating in the oxidase complex and by activating signaling events leading to oxidase assembly, and that Vav1 may be the physiologically relevant GEF responsible for activating this Rac-regulated complex

Epidemiology and individual, household and geographical risk factors of podoconiosis in ethiopia: results from the first nationwide mapping

Although podoconiosis is one of the major causes of tropical lymphoedema and is endemic in Ethiopia its epidemiology and risk factors are poorly understood. Individual-level data for 129,959 individuals from 1,315 communities in 659 woreda (districts) were collected for a nationwide integrated survey of lymphatic filariasis and podoconiosis. Blood samples were tested for circulating Wuchereria bancrofti antigen using immunochromatographic card tests. A clinical algorithm was used to reach a diagnosis of podoconiosis by excluding other potential causes of lymphoedema of the lower limb. Bayesian multilevel models were used to identify individual and environmental risk factors. Overall, 8,110 of 129,959 (6.2%, 95% confidence interval [CI] 6.1-6.4%) surveyed individuals were identified with lymphoedema of the lower limb, of whom 5,253 (4.0%, 95% CI 3.9-4.1%) were confirmed to be podoconiosis cases. In multivariable analysis, being female, older, unmarried, washing the feet less frequently than daily, and being semiskilled or unemployed were significantly associated with increased risk of podoconiosis. Attending formal education and living in a house with a covered floor were associated with decreased risk of podoconiosis. Podoconiosis exhibits marked geographical variation across Ethiopia, with variation in risk associated with variation in rainfall, enhanced vegetation index, and altitude

Mutli-objective optimisation of GENIE Earth system models

Overview:•GENIE Project•Multi-objective Optimisation•Surrogate Modelling•Grid Computing Infrastructure•Parameter Estimation for a new Ocean Mixing Scheme•Conclusion