Model Selection and Adaptive Markov chain Monte Carlo for Bayesian Cointegrated VAR model

This paper develops a matrix-variate adaptive Markov chain Monte Carlo (MCMC) methodology for Bayesian Cointegrated Vector Auto Regressions (CVAR). We replace the popular approach to sampling Bayesian CVAR models, involving griddy Gibbs, with an automated efficient alternative, based on the Adaptive Metropolis algorithm of Roberts and Rosenthal, (2009). Developing the adaptive MCMC framework for Bayesian CVAR models allows for efficient estimation of posterior parameters in significantly higher dimensional CVAR series than previously possible with existing griddy Gibbs samplers. For a n-dimensional CVAR series, the matrix-variate posterior is in dimension $3n^2 + n$, with significant correlation present between the blocks of matrix random variables. We also treat the rank of the CVAR model as a random variable and perform joint inference on the rank and model parameters. This is achieved with a Bayesian posterior distribution defined over both the rank and the CVAR model parameters, and inference is made via Bayes Factor analysis of rank. Practically the adaptive sampler also aids in the development of automated Bayesian cointegration models for algorithmic trading systems considering instruments made up of several assets, such as currency baskets. Previously the literature on financial applications of CVAR trading models typically only considers pairs trading (n=2) due to the computational cost of the griddy Gibbs. We are able to extend under our adaptive framework to $n >> 2$ and demonstrate an example with n = 10, resulting in a posterior distribution with parameters up to dimension 310. By also considering the rank as a random quantity we can ensure our resulting trading models are able to adjust to potentially time varying market conditions in a coherent statistical framework.Comment: to appear journal Bayesian Analysi

A new approach to evaluate forest structure restoration needs across Oregon and Washington, USA

Widespread habitat degradation and uncharacteristic fire, insect, and disease outbreaks in forests across the western United States have led to highly publicized calls to increase the pace and scale of forest restoration. Despite these calls, we frequently lack a comprehensive understanding of forest restoration needs. In this study we demonstrate a new approach for evaluating where, how much, and what types of restoration are needed to move present day landscape scale forest structure towards a Natural Range of Variability (NRV) across eastern Washington, eastern Oregon, and southwestern Oregon. Our approach builds on the conceptual framework of the LANDFIRE and Fire Regime Condition Class programs. Washington–Oregon specific datasets are used to assess the need for changes to current forest structure resulting from disturbance and/or succession at watershed and regional scales. Across our analysis region we found that changes in current structure would be needed on an estimated 4.7 million+ ha (40% of all coniferous forests) in order to restore forest structure approximating NRV at the landscape scale. Both the overall level and the type of restoration need varied greatly between forested biophysical settings. Regional restoration needs were dominated by the estimated 3.8+ million ha in need of thinning and/or low severity fire in forests that were historically maintained by frequent low or mixed severity fire (historical Fire Regime Group I and III biophysical settings). However, disturbance alone cannot restore NRV forest structure. We found that time to transition into later development structural classes through successional processes was required on approximately 3.2 million ha (over 25% of all coniferous forests). On an estimated 2.3 million ha we identified that disturbance followed by succession was required to restore NRV forest structure. The results of this study are intended to facilitate the ability of local land managers to incorporate regional scale, multi-ownership context into local forest management and restoration. Meeting the region-wide restoration needs identified in this study will require a substantial increase in the pace and scale of restoration treatments and coordination amongst governments, agencies, and landowners.Keywords: Landfire, Fire Regime Condition Class, Gradient nearest neighbor, Natural range of variation, Ecological restoration, Pacific Northwes

F.J. Turner’s ‘frontier thesis’: the ruse of American ‘character'

American society was transformed by the expansion of capital Westward and the explosion in opportunities that ensued for land grabbing and agricultural and industrial investment. In Turner’s (1961) frontier thesis this was portrayed as resulting in the emergence of ‘the new man’ i.e. the fulfilment of American character. The frontier thesis is a neo-Darwinian contribution. It posits exceptionalism and transcendence as the keys to American character. The gene pool of the Americans, thriving in a new geographical and social environment, is depicted as achieving a higher level of development than the stratified societies of Old Europe. What the thesis ignores is the importance of orthodox Eurocentric strategies of colonization and land appropriation. Turner portrays pioneer/settler society as a heroic departure, but in many ways, it is a continuation of European precedents. Analogously, the proposition that the push West crystallized American character obscures the role of personality, especially in urban-industrial settings, in establishing the parameters of American life. Turner conceived of character as emerging from a struggle with the spatial frontier. But the struggles of personality with the social frontier of repression and establishment values is no less significant. The paper examines the tensions between character and personality by using some ideas developed by Carl Schmitt on the significance of ‘the opportunity’ in competitive advantage. The importance of the opportunity and personality in developing the American way of life are examined by the vaudeville and celebrity traditions. The exploitation of contingency for personal advantage, the use of melodrama to engineer social impact, the social validation of forthright behaviour are examined in the context of the careers of the film actress Mae West and the comedian Bob Hope

Putting the Whole Grain Puzzle Together: Health Benefits Associated with Whole Grains—Summary of American Society for Nutrition 2010 Satellite Symposium123

The symposium “Putting the Whole Grain Puzzle Together: Health Benefits Associated with Whole Grains” sponsored by the ASN brought together researchers to review the evidence regarding the health benefits associated with whole grains. Current scientific evidence indicates that whole grains play an important role in lowering the risk of chronic diseases, such as coronary heart disease, diabetes, and cancer, and also contribute to body weight management and gastrointestinal health. The essential macro- and micronutrients, along with the phytonutrients present in whole grains, synergistically contribute to their beneficial effects. Current evidence lends credence to the recommendations to incorporate whole grain foods into a healthy diet and lifestyle program. The symposium also highlighted the need for further research to examine the role of whole grain foods in disease prevention and management to gain a better understanding of their mechanisms of action

Ten-year mortality, disease progression, and treatment-related side effects in men with localised prostate cancer from the ProtecT randomised controlled trial according to treatment received

Background The ProtecT trial reported intention-to-treat analysis of men with localised prostate cancer randomly allocated to active monitoring (AM), radical prostatectomy, and external beam radiotherapy. Objective To report outcomes according to treatment received in men in randomised and treatment choice cohorts. Design, setting, and participants This study focuses on secondary care. Men with clinically localised prostate cancer at one of nine UK centres were invited to participate in the treatment trial comparing AM, radical prostatectomy, and radiotherapy. Intervention Two cohorts included 1643 men who agreed to be randomised and 997 who declined randomisation and chose treatment. Outcome measurements and statistical analysis Analysis was carried out to assess mortality, metastasis and progression and health-related quality of life impacts on urinary, bowel, and sexual function using patient-reported outcome measures. Analysis was based on comparisons between groups defined by treatment received for both randomised and treatment choice cohorts in turn, with pooled estimates of intervention effect obtained using meta-analysis. Differences were estimated with adjustment for known prognostic factors using propensity scores. Results and limitations According to treatment received, more men receiving AM died of PCa (AM 1.85%, surgery 0.67%, radiotherapy 0.73%), whilst this difference remained consistent with chance in the randomised cohort (p = 0.08); stronger evidence was found in the exploratory analyses (randomised plus choice cohort) when AM was compared with the combined radical treatment group (p = 0.003). There was also strong evidence that metastasis (AM 5.6%, surgery 2.4%, radiotherapy 2.7%) and disease progression (AM 20.35%, surgery 5.87%, radiotherapy 6.62%) were more common in the AM group. Compared with AM, there were higher risks of sexual dysfunction (95% at 6 mo) and urinary incontinence (55% at 6 mo) after surgery, and of sexual dysfunction (88% at 6 mo) and bowel dysfunction (5% at 6 mo) after radiotherapy. The key limitations are the potential for bias when comparing groups defined by treatment received and changes in the protocol for AM during the lengthy follow-up required in trials of screen-detected PCa. Conclusions Analyses according to treatment received showed increased rates of disease-related events and lower rates of patient-reported harms in men managed by AM compared with men managed by radical treatment, and stronger evidence of greater PCa mortality in the AM group. Patient summary More than 95 out of every 100 men with low or intermediate risk localised prostate cancer do not die of prostate cancer within 10 yr, irrespective of whether treatment is by means of monitoring, surgery, or radiotherapy. Side effects on sexual and bladder function are better after active monitoring, but the risks of spreading of prostate cancer are more common

Functional and quality of life outcomes of localised prostate cancer treatments (prostate testing for cancer and treatment [ProtecT] study)

Objective To investigate the functional and quality of life (QoL) outcomes of treatments for localised prostate cancer and inform treatment decision-making. Patients and Methods Men aged 50–69 years diagnosed with localised prostate cancer by prostate-specific antigen testing and biopsies at nine UK centres in the Prostate Testing for Cancer and Treatment (ProtecT) trial were randomised to, or chose one of, three treatments. Of 2565 participants, 1135 men received active monitoring (AM), 750 a radical prostatectomy (RP), 603 external-beam radiotherapy (EBRT) with concurrent androgen-deprivation therapy (ADT) and 77 low-dose-rate brachytherapy (BT, not a randomised treatment). Patient-reported outcome measures (PROMs) completed annually for 6 years were analysed by initial treatment and censored for subsequent treatments. Mixed effects models were adjusted for baseline characteristics using propensity scores. Results Treatment-received analyses revealed different impacts of treatments over 6 years. Men remaining on AM experienced gradual declines in sexual and urinary function with age (e.g., increases in erectile dysfunction from 35% of men at baseline to 53% at 6 years and nocturia similarly from 20% to 38%). Radical treatment impacts were immediate and continued over 6 years. After RP, 95% of men reported erectile dysfunction persisting for 85% at 6 years, and after EBRT this was reported by 69% and 74%, respectively (P < 0.001 compared with AM). After RP, 36% of men reported urinary leakage requiring at least 1 pad/day, persisting for 20% at 6 years, compared with no change in men receiving EBRT or AM (P < 0.001). Worse bowel function and bother (e.g., bloody stools 6% at 6 years and faecal incontinence 10%) was experienced by men after EBRT than after RP or AM (P < 0.001) with lesser effects after BT. No treatment affected mental or physical QoL. Conclusion Treatment decision-making for localised prostate cancer can be informed by these 6-year functional and QoL outcomes

25th annual computational neuroscience meeting: CNS-2016

The same neuron may play different functional roles in the neural circuits to which it belongs. For example, neurons in the Tritonia pedal ganglia may participate in variable phases of the swim motor rhythms [1]. While such neuronal functional variability is likely to play a major role the delivery of the functionality of neural systems, it is difficult to study it in most nervous systems. We work on the pyloric rhythm network of the crustacean stomatogastric ganglion (STG) [2]. Typically network models of the STG treat neurons of the same functional type as a single model neuron (e.g. PD neurons), assuming the same conductance parameters for these neurons and implying their synchronous firing [3, 4]. However, simultaneous recording of PD neurons shows differences between the timings of spikes of these neurons. This may indicate functional variability of these neurons. Here we modelled separately the two PD neurons of the STG in a multi-neuron model of the pyloric network. Our neuron models comply with known correlations between conductance parameters of ionic currents. Our results reproduce the experimental finding of increasing spike time distance between spikes originating from the two model PD neurons during their synchronised burst phase. The PD neuron with the larger calcium conductance generates its spikes before the other PD neuron. Larger potassium conductance values in the follower neuron imply longer delays between spikes, see Fig. 17.Neuromodulators change the conductance parameters of neurons and maintain the ratios of these parameters [5]. Our results show that such changes may shift the individual contribution of two PD neurons to the PD-phase of the pyloric rhythm altering their functionality within this rhythm. Our work paves the way towards an accessible experimental and computational framework for the analysis of the mechanisms and impact of functional variability of neurons within the neural circuits to which they belong

Model Selection and Adaptive Markov chain Monte Carlo for Bayesian Cointegrated VAR model

This paper develops a matrix-variate adaptive Markov chain Monte Carlo (MCMC) methodology for Bayesian Cointegrated Vector Auto Regressions (CVAR). We replace the popular approach to sampling Bayesian CVAR models, involving griddy Gibbs, with an automated efficient alternative, based on the Adaptive Metropolis algorithm of Roberts and Rosenthal, (2009). Developing the adaptive MCMC framework for Bayesian CVAR models allows for efficient estimation of posterior parameters in significantly higher dimensional CVAR series than previously possible with existing griddy Gibbs samplers. For a n-dimensional CVAR series, the matrix-variate posterior is in dimension $3n^2 + n$, with significant correlation present between the blocks of matrix random variables. We also treat the rank of the CVAR model as a random variable and perform joint inference on the rank and model parameters. This is achieved with a Bayesian posterior distribution defined over both the rank and the CVAR model parameters, and inference is made via Bayes Factor analysis of rank. Practically the adaptive sampler also aids in the development of automated Bayesian cointegration models for algorithmic trading systems considering instruments made up of several assets, such as currency baskets. Previously the literature on financial applications of CVAR trading models typically only considers pairs trading (n=2) due to the computational cost of the griddy Gibbs. We are able to extend under our adaptive framework to $n >> 2$ and demonstrate an example with n = 10, resulting in a posterior distribution with parameters up to dimension 310. By also considering the rank as a random quantity we can ensure our resulting trading models are able to adjust to potentially time varying market conditions in a coherent statistical framework.