A Four Dimensional Spatio-Temporal Analysis of an Agricultural Dataset

While a variety of statistical models now exist for the spatio-temporal analysis of two-dimensional (surface) data collected over time, there are few published examples of analogous models for the spatial analysis of data taken over four dimensions: latitude, longitude, height or depth, and time. When taking account of the autocorrelation of data within and between dimensions, the notion of closeness often differs for each of the dimensions. Here, we consider a number of approaches to the analysis of such a dataset, which arises from an agricultural experiment exploring the impact of different cropping systems on soil moisture. The proposed models vary in their representation of the spatial correlation in the data, the assumed temporal pattern and choice of conditional autoregressive (CAR) and other priors. In terms of the substantive question, we find that response cropping is generally more effective than long fallow cropping in reducing soil moisture at the depths considered (100 cm to 220 cm). Thus, if we wish to reduce the possibility of deep drainage and increased groundwater salinity, the recommended cropping system is response cropping.     

Characterising Uncertainty in Expert Assessments: Encoding Heavily Skewed Judgements

When limited or no observed data are available, it is often useful to obtain expert knowledge about parameters of interest, including point estimates and the uncertainty around these values. However, it is vital to elicit this information appropriately in order to obtain valid estimates. This is particularly important when the experts’ uncertainty about these estimates is strongly skewed, for instance when their best estimate is the same as the lowest value they consider possible. Also this is important when interest is in the aggregation of elicited values. In this paper, we compare alternative distributions for describing such estimates. The distributions considered include the lognormal, mirror lognormal, Normal and scaled Beta. The case study presented here involves estimation of the number of species in coral reefs, which requires eliciting counts within broader taxonomic groups, with highly skewed uncertainty estimates. This paper shows substantial gain in using the scaled Beta distribution, compared with Normal or lognormal distributions. We demonstrate that, for this case study on counting species, applying the novel encoding methodology developed in this paper can facilitate the acquisition of more rigorous estimates of (hierarchical) count data and credible bounds. The approach can also be applied to the more general case of enumerating a sampling frame via elicitation.     

Herpes Simplex Virus type 1 infects Langerhans cells and the novel epidermal dendritic cell,Epi-cDC2s,via different entry pathways

Skin mononuclear phagocytes (MNPs) provide the first interactions of invading viruses with the immune system. In addition to Langerhans cells (LCs), we recently described a second epidermal MNP population, Epi-cDC2s, in human anogenital epidermis that is closely related to dermal conventional dendritic cells type 2 (cDC2) and can be preferentially infected by HIV. Here we show that in epidermal explants topically infected with herpes simplex virus (HSV-1), both LCs and Epi-cDC2s interact with HSV-1 particles and infected keratinocytes. Isolated Epi-cDC2s support higher levels of infection than LCs in vitro, inhibited by acyclovir, but both MNP subtypes express similar levels of the HSV entry receptors nectin-1 and HVEM, and show similar levels of initial uptake. Using inhibitors of endosomal acidification, actin and cholesterol, we found that HSV-1 utilises different entry pathways in each cell type. HSV-1 predominantly infects LCs, and monocyte-derived MNPs, via a pH-dependent pathway. In contrast, Epi-cDC2s are mainly infected via a pH-independent pathway which may contribute to the enhanced infection of Epi-cDC2s. Both cells underwent apoptosis suggesting that Epi-cDC2s may follow the same dermal migration and uptake by dermal MNPs that we have previously shown for LCs. Thus, we hypothesize that the uptake of HSV and infection of Epi-cDC2s will stimulate immune responses via a different pathway to LCs, which in future may help guide HSV vaccine development and adjuvant targeting.     

A climatic stability approach to prioritizing global conservation investments

Climate change is impacting species and ecosystems globally. Many existing templates to identify the most important areas to conserve terrestrial biodiversity at the global scale neglect the future impacts of climate change. Unstable climatic conditions are predicted to undermine conservation investments in the future. This paper presents an approach to developing a resource allocation algorithm for conservation investment that incorporates the ecological stability of ecoregions under climate change. We discover that allocating funds in this way changes the optimal schedule of global investments both spatially and temporally. This allocation reduces the biodiversity loss of terrestrial endemic species from protected areas due to climate change by 22% for the period of 2002-2052, when compared to allocations that do not consider climate change. To maximize the resilience of global biodiversity to climate change we recommend that funding be increased in ecoregions located in the tropics and/or mid-elevation habitats, where climatic conditions are predicted to remain relatively stable. Accounting for the ecological stability of ecoregions provides a realistic approach to incorporating climate change into global conservation planning, with potential to save more species from extinction in the long term.     

Urokinase-type plasminogen activator and arthritis progression: role in systemic disease with immune complex involvement

Introduction  

Urokinase-type plasminogen activator (u-PA) has been implicated in fibrinolysis, cell migration, latent cytokine activation, cell activation, T-cell activation, and tissue remodeling, all of which are involved in the development of rheumatoid arthritis. Previously, u-PA has been reported to play a protective role in monoarticular arthritis models involving mBSA as the antigen, but a deleterious role in the systemic polyarticular collagen-induced arthritis (CIA) model. The aim of the current study is to determine how u-PA might be acting in systemic arthritis models.     

Complete genome sequence of Staphylothermus marinus Stetter and Fiala 1986 type strain F1

Staphylothermus marinus Fiala and Stetter 1986 belongs to the order Desulfurococcales within the archaeal phylum Crenarchaeota. S. marinus is a hyperthermophilic, sulfur-dependent, anaerobic heterotroph. Strain F1 was isolated from geothermally heated sediments at Vulcano, Italy, but S. marinus has also been isolated from a hydrothermal vent on the East Pacific Rise. We report the complete genome of S. marinus strain F1, the type strain of the species. This is the fifth reported complete genome sequence from the order Desulfurococcales.     

Detection, isolation, and characterization of helicobacter species from the gastrointestinal tract of the brushtail possum

The presence of Helicobacter species in Australian marsupials was examined systematically using microscopy, culture, and PCR in different regions of the gastrointestinal tract (GIT) and in the liver of brushtail possums (BTPs) (Trichosurus vulpecula), a common Australian marsupial that feeds on eucalyptus leaves. The spatial distribution of Helicobacter species in the GIT sections also was examined microscopically in silver-stained sections and by fluorescent in situ hybridization (FISH) using a Helicobacter genus-specific probe. Helicobacter species were found colonizing the lower bowel of all BTPs studied. Good agreement was observed between the detection of Helicobacter species using culture and PCR, which was supported by the microscopic examination of silver-stained sections and FISH. The lower bowel of BTPs were colonized by one to three morphologically different (a comma-shaped species with no apparent flagella, a fusiform-shaped species entwined with periplasmic fibers and a bipolar sheathed flagella, and an S-shaped species with bipolar sheathed flagella) and potentially novel Helicobacter species, as well as in one case with a potentially novel Campylobacter species, which was a tightly coiled rod with bipolar unsheathed flagella. The isolation and characterization of these Helicobacter species in BTPs provides important information regarding the specific natural niche of these bacteria and their corelationship within their host, and it increases our understanding of the ecology of Helicobacter species.