Bayesian model selection for exponential random graph models via adjusted pseudolikelihoods

Models with intractable likelihood functions arise in areas including network analysis and spatial statistics, especially those involving Gibbs random fields. Posterior parameter es timation in these settings is termed a doubly-intractable problem because both the likelihood function and the posterior distribution are intractable. The comparison of Bayesian models is often based on the statistical evidence, the integral of the un-normalised posterior distribution over the model parameters which is rarely available in closed form. For doubly-intractable models, estimating the evidence adds another layer of difficulty. Consequently, the selection of the model that best describes an observed network among a collection of exponential random graph models for network analysis is a daunting task. Pseudolikelihoods offer a tractable approximation to the likelihood but should be treated with caution because they can lead to an unreasonable inference. This paper specifies a method to adjust pseudolikelihoods in order to obtain a reasonable, yet tractable, approximation to the likelihood. This allows implementation of widely used computational methods for evidence estimation and pursuit of Bayesian model selection of exponential random graph models for the analysis of social networks. Empirical comparisons to existing methods show that our procedure yields similar evidence estimates, but at a lower computational cost.Comment: Supplementary material attached. To view attachments, please download and extract the gzzipped source file listed under "Other formats

Whey protein and sphingomyelin but not casein contribute to α-tocopherol bioaccessibility in skim milk

Bioaccessibility, or the extent to which nutrients can be taken up by enterocytes, is an important predictor of nutrient bioavailability. Despite being fat-soluble, the relatively high bioaccessibility of α-tocopherol (α-T) is unaffected by the fat content of dairy milk. This suggests that physiochemical properties of dairy milk independent of fat are functionally responsible for promoting α-T bioaccessibility. We therefore hypothesized that the emulsifying properties of whey protein (WP) and micellarized casein (CAS) and an amphiphilic phospholipid, sphingomyelin (SM), are responsible for α-T bioaccessibility. To test this, simulated digestions in vitro were performed to define the independent and additive contributions of WP, CAS, and SM relative to non-fat milk on α-T bioaccessibility. Digestions containing 15 mg α-T were performed in non-fat milk (245 mL) or water (245 mL) containing milk-matched levels of WP (1.6 g), SM (16.1 mg), and CAS (6.6 g), alone or in combination (WP+SM+CAS). α-T recovery was evaluated by HPLCECD following the gastric through intestinal phases of digestion. α-T bioaccessibility was expressed as the ratio of α-T recovered in the aqueous fraction relative to that in chyme. α-T bioaccessibility differed in response to treatments as follows (means ± SEM; P skim milk (57.4 ± 1.8%) > CAS (35.9 ± 2.3%) = WP+SM+CAS (33.6 ± 1.1%). Lower bioaccessibility in WP+SM+CAS treatment compared to skim milk suggests that other components of milk may also contribute to α-T bioaccessibility. Relative to skim milk, isolated SM and WP potentiate α-T bioaccessibility while CAS is inhibitory. These findings suggest that WP and SM partially contribute to α-T bioaccessibility while other factors may also have a potentiating role.OARDC SEEDSNo embargoAcademic Major: Animal Science

Statistical Network Analysis with Bergm

Recent advances in computational methods for intractable models have made network data increasingly amenable to statistical analysis. Exponential random graph models (ERGMs) emerged as one of the main families of models capable of capturing the complex dependence structure of network data in a wide range of applied contexts. The Bergm package for R has become a popular package to carry out Bayesian parameter inference, missing data imputation, model selection and goodness-of-fit diagnostics for ERGMs. Over the last few years, the package has been considerably improved in terms of efficiency by adopting some of the state-of-the-art Bayesian computational methods for doubly-intractable distributions. Recently, version 5 of the package has been made available on CRAN having undergone a substantial makeover, which has made it more accessible and easy to use for practitioners. New functions include data augmentation procedures based on the approximate exchange algorithm for dealing with missing data, adjusted pseudo-likelihood and pseudo-posterior procedures, which allow for fast approximate inference of the ERGM parameter posterior and model evidence for networks on several thousands nodes.Comment: 22 pages, 5 figure

Technology and dementia: the future is now

Background: Technology has multiple potential applications to dementia from diagnosis and assessment to care delivery and supporting ageing in place. Objectives: To summarise key areas of technology development in dementia and identify future directions and implications. Method: Members of the US Alzheimer’s Association Technology Professional Interest Area involved in delivering the annual pre-conference summarised existing knowledge on current and future technology developments in dementia. Results: The main domains of technology development are as follows: (i) diagnosis, assessment and monitoring, (ii) maintenance of functioning, (iii) leisure and activity, (iv) caregiving and management. Conclusions: The pace of technology development requires urgent policy, funding and practice change, away from a narrow medical approach, to a holistic model that facilitates future risk reduction and pre- vention strategies, enables earlier detection and supports implementation at scale for a meaningful and fulfilling life with dementia

The crucial role of sulfur in a phytoremediation process : Lessons from the Poaceae species as phytoremediants : a review

Among living organisms plants are the most tolerant to pollution. This fact, emphasizes their utility for phytoremediation, a promising technology for environmental cleanup. Many botanical families include multiple species which exhibit a notable phytoremediation potential. Each of these species enjoys certain advantages, but at the same encounters some limitations with respect to its application as phytoremediants. Careful selection of the appropriate family and genotype to match the particular pollutant and environment is crucial for successful phytoremediation; the Poaceae family seems to be one of the most important for this technology. Phytoremediation of inorganic and organic pollutants largely depends on sulfur (S) metabolism. Therefore, S sufficient conditions and efficient S metabolism constitute the prerequisites for the effectiveness of the process. In the modern societies, heavy-metal pollution of soils is causing ever greater problems, exacerbated by the fact that most heavy metals accumulated in plants may, either directly or indirectly, find their way into animals and human beings. Wheat, rice and maize are among the world\u2019s most prominent crops, whilst cadmium (Cd) and nickel (Ni) are among the most toxic metals. Therefore, the physiological adaptations induced in cereals, by Cd for example, are alarming and subsequently, the responsiveness of these species has been studied extensively as model plants. Studies with Arundo donax as phytoremediant have proven that this species is tolerant to increased concentrations of Cd and Ni in its rhizosphere, and as a consequence, it can be cultivated in contaminated areas for phytoremediation and energy production purposes. S-deficiency of crops is frequently reported, especially during the past two decades, worldwide. The main reasons for this deficiency are: the reduction of sulfur dioxide emission from power plants and various industrial sources, the ever increasing use of high-analysis low-S-containing fertilizers and the decreasing use of S-containing fertilizers, S-containing fungicides, pesticides and high-yielding varieties. A sufficient S supply of cereal crops is required in early growth stages, which cannot be fully compensated by S fertilization during later growth. Elemental S proved to contribute continuously to the crop\u2019s S nutrition due to its constant release after oxidation. Therefore, the early diagnosis of S deficiency, the profiling of S forms in the soil of the phytoremediation site and the prediction of S-fertilizer requirements are of key importance for achieving a successful process

Distinct mechanisms for aerenchyma formation in leaf sheaths of rice genotypes displaying a quiescence or escape strategy for flooding tolerance

Background and Aims Rice is one of the few crops able to withstand periods of partial or even complete submergence. One of the adaptive traits of rice is the constitutive presence and further development of aerenchyma which enables oxygen to be transported to submerged organs. The development of lysigenous aerenchyma is promoted by ethylene accumulating within the submerged plant tissues, although other signalling mechanisms may also co-exist. In this study, aerenchyma development was analysed in two rice (Oryza sativa) varieties, ‘FR13A’ and ‘Arborio Precoce’, which show opposite traits in flooding response in terms of internode elongation and survival. Methods The growth and survival of rice varieties under submergence was investigated in the leaf sheath of ‘FR13A’ and ‘Arborio Precoce’. The possible involvement of ethylene and reactive oxygen species (ROS) was evaluated in relation to aerenchyma formation. Cell viability and DNA fragmentation were determined by FDA/FM4-64 staining and TUNEL assay, respectively. Ethylene production was monitored by gas chromatography and by analysing ACO gene expression. ROS production was measured by using Amplex Red assay kit and the fluorescent dye DCFH2-DA. The expression of APX1 was also evaluated. AVG and DPI solutions were used to test the effect of inhibiting ethylene biosynthesis and ROS production, respectively. Key Results Both the varieties displayed constitutive lysigenous aerenchyma formation, which was further enhanced when submerged. ‘Arborio Precoce’, which is characterized by fast elongation when submerged, showed active ethylene biosynthetic machinery associated with increased aerenchymatous areas. ‘FR13A’, which harbours the Sub1A gene that limits growth during oxygen deprivation, did not show any increase in ethylene production after submersion but still displayed increased aerenchyma. Hydrogen peroxide levels increased in ‘FR13A’ but not in ‘Arborio Precoce’. Conclusions While ethylene controls aerenchyma formation in the fast-elongating ‘Arborio Precoce’ variety, in ‘FR13A’ ROS accumulation plays an important role

One tissue, two fates: different roles of megagametophyte cells during Scots pine embryogenesis

In the Scots pine (Pinus sylvestris L.) seed, embryos grow and develop within the corrosion cavity of the megagametophyte, a maternally derived haploid tissue, which houses the majority of the storage reserves of the seed. In the present study, histochemical methods and quantification of the expression levels of the programmed cell death (PCD) and DNA repair processes related genes (MCA, TAT-D, RAD51, KU80, and LIG) were used to investigate the physiological events occurring in the megagametophyte tissue during embryo development. It was found that the megagametophyte was viable from the early phases of embryo development until the early germination of mature seeds. However, the megagametophyte cells in the narrow embryo surrounding region (ESR) were destroyed by cell death with morphologically necrotic features. Their cell wall, plasma membrane, and nuclear envelope broke down with the release of cell debris and nucleic acids into the corrosion cavity. The occurrence of necrotic-like cell death in gymnosperm embryogenesis provides a favourable model for the study of developmental cell death with necrotic-like morphology and suggests that the mechanism underlying necrotic cell death is evolutionary conserved