The effects of mobile real-time information on rural passengers

The research described here is supported by the award made by the RCUK Digital Economy programme to the dot.rural Digital Economy Research Hub; award reference: EP/G066051/1/.

A Naturalist Abroad in the Museum of Ontology : Phillipe Descola's Beyond Nature and Culture

Peer reviewed

Major Histocompatibility Complex (MHC) Class II sequence polymorphism in long-finned pilot whale (Globicephala melas) from the North Atlantic

Funding Silvia S. Monteiro and Marisa Ferreira were supported by a Ph.D. grant from Fundação para a Ciência e Tecnologia (ref SFRH/BD/38735/2007 and SFRH/BD/30240/2006, respectively). Alfredo López was supported by a postdoctoral grant from Fundação para a Ciência e Tecnologia (ref SFRH/BPD/82407/2011). Catarina Eira is supported by CESAM (UID/AMB/50017), from FCT/MEC through national funds and FEDER (PT2020, Compete 2020). The work related with strandings and tissue collection in Portugal was partially supported by the SafeSea Project EEAGrants PT 0039 (supported by Iceland, Liechtenstein and Norway through the EEA Financial Mechanism), by the Project MarPro–Life09 NAT/PT/000038 (funded by the European Union–Program Life+) and by the project CetSenti FCT RECI/AAG-GLO/0470/2012; FCOMP-01-0124-FEDER-027472 (Funded by the Program COMPETE and Fundação para a Ciência e Tecnologia).

The geological and microbiological controls on the occurrence, mobility and concentration of Se and Te in coal and black shales

© 2016 Institute of Materials, Minerals and Mining and The AusIMM Published by Taylor & Francis on behalf of the Institute and The AusIMM

The influence of religion and ethnonationalism on public attitudes towards amnesty : Northern Ireland as a case study

Peer reviewed

Models and empirical data for the production of referring expressions

Article Accepted Date: 29 May 2014 Acknowledgements The authors gratefully acknowledge the support of the Cognitive Science Society for the organisation of the Workshop on Production of Referring Expressions: Bridging the Gap between Cognitive and Computational Approaches to Reference, from which this special issue originated. Funding Emiel Krahmer and Albert Gatt thank The Netherlands Organisation for Scientific Research (NWO) for VICI grant Bridging the Gap between Computational Linguistics and Psycholinguistics: The Case of Referring Expressions (grant number 277-70-007).

The administration route is decisive for the ability of the vaccine adjuvant CAF09 to induce antigen-specific CD8+ T-cell responses:the immunological consequences of the biodistribution profile

A prerequisite for vaccine-mediated induction of CD8+ T-cell responses is the targeting of dendritic cell (DC) subsets specifically capable of cross-presenting antigen epitopes to CD8+ T cells. Administration of a number of cationic adjuvants via the intraperitoneal (i.p.) route has been shown to result in strong CD8+ T-cell responses, whereas immunization via e.g. the intramuscular (i.m.) or subcutaneous (s.c.) routes often stimulate weak CD8+ T-cell responses. The hypothesis for this is that self-drainage of the adjuvant/antigen to the lymphoid organs, which takes place upon i.p. immunization, is required for the subsequent activation of cross-presenting lymphoid organ-resident CD8α+ DCs. In contrast, s.c. or i.m. immunization usually results in the formation of a depot at the site of injection (SOI), which hinders the self-drainage and targeting of the vaccine to cross-presenting CD8α+ DCs. We investigated this hypothesis by correlating the biodistribution pattern and the adjuvanticity of the strong CD8+ T-cell inducing liposomal cationic adjuvant formulation 09 (CAF09), which is composed of dimethyldioctadecylammonium bromide/monomycoloyl glycerol liposomes with polyinosinic:polycytidylic acid electrostatically adsorbed to the surface. Biodistribution studies with radiolabeled CAF09 and a surface-adsorbed model antigen [ovalbumin (OVA)] showed that a significantly larger fraction of the vaccine dose localized in the draining lymph nodes (dLNs) and the spleen 6 h after i.p. immunization, as compared to after i.m. immunization. Studies with fluorescently labelled OVA + CAF09 demonstrated a preferential association of OVA + CAF09 to DCs/monocytes, as compared to macrophages and B cells, following i.p. immunization. Administration of OVA + CAF09 via the i.p. route did also result in DC activation, whereas no DC activation could be measured within the same period with unadjuvanted OVA and OVA + CAF09 administered via the s.c. or i.m. routes. In the dLNs, the highest level of activated, cross-presenting CD8α+ DCs was detected at 24 h post immunization, whereas an influx of activated, migrating and cross-presenting CD103+ DCs to the dLNs could be measured after 48 h. This suggests that the CD8α+ DCs are activated by self-draining OVA + CAF09 in the lymphoid organs, whereas the CD103+ DCs are stimulated by the OVA + CAF09 at the SOI. These results support the hypothesis that the self-drainage of OVA + CAF09 to the draining LNs is required for the activation of CD8α+ DCs, while the migratory CD103+ DCs may play a role in sustaining the subsequent induction of strong CD8+ T-cell responses.

Global distributions of diazotrophs abundance, biomass and nitrogen fixation rates - Gridded data product (NetCDF) - Contribution to the MAREDAT World Ocean Atlas of Plankton Functional Types

The MAREDAT atlas covers 11 types of plankton, ranging in size from bacteria to jellyfish. Together, these plankton groups determine the health and productivity of the global ocean and play a vital role in the global carbon cycle. Working within a uniform and consistent spatial and depth grid (map) of the global ocean, the researchers compiled thousands and tens of thousands of data points to identify regions of plankton abundance and scarcity as well as areas of data abundance and scarcity. At many of the grid points, the MAREDAT team accomplished the difficult conversion from abundance (numbers of organisms) to biomass (carbon mass of organisms). The MAREDAT atlas provides an unprecedented global data set for ecological and biochemical analysis and modeling as well as a clear mandate for compiling additional existing data and for focusing future data gathering efforts on key groups in key areas of the ocean. This is a gridded data product about diazotrophic organisms . There are 6 variables. Each variable is gridded on a dimension of 360 (longitude) * 180 (latitude) * 33 (depth) * 12 (month). The first group of 3 variables are: (1) number of biomass observations, (2) biomass, and (3) special nifH-gene-based biomass. The second group of 3 variables is same as the first group except that it only grids non-zero data. We have constructed a database on diazotrophic organisms in the global pelagic upper ocean by compiling more than 11,000 direct field measurements including 3 sub-databases: (1) nitrogen fixation rates, (2) cyanobacterial diazotroph abundances from cell counts and (3) cyanobacterial diazotroph abundances from qPCR assays targeting nifH genes. Biomass conversion factors are estimated based on cell sizes to convert abundance data to diazotrophic biomass. Data are assigned to 3 groups including Trichodesmium, unicellular diazotrophic cyanobacteria (group A, B and C when applicable) and heterocystous cyanobacteria (Richelia and Calothrix). Total nitrogen fixation rates and diazotrophic biomass are calculated by summing the values from all the groups. Some of nitrogen fixation rates are whole seawater measurements and are used as total nitrogen fixation rates. Both volumetric and depth-integrated values were reported. Depth-integrated values are also calculated for those vertical profiles with values at 3 or more depths.

THE HERPESVIRUS NUCLEAR EGRESS COMPLEX COMPONENT, UL31, IS RECRUITED TO SITES OF DNA DAMAGE THROUGH POLY(ADP-RIBOSE) BINDING

The herpes simplex virus (HSV) UL31 gene encodes a conserved member of the herpesvirus nuclear egress complex that not only functions in the egress of DNA-containing capsids from the nucleus, but is also required for optimal viral genome expression, replication and packaging into capsids. Here, we report that the UL31 protein from HSV-2 and the orthologous protein, ORF69, from Kaposi's sarcoma-associated herpesvirus (KSHV) are recruited to sites of DNA damage. Recruitment of UL31 to sites of DNA damage occurred in HSV-2 infected cells, but did not require other viral proteins. The N-terminus of UL31 contains sequences resembling a poly(ADP-ribose) (PAR) binding motif. As protein poly-ADP ribosylation (PARylation) is a hallmark of the DNA damage response we examined the relationship between PARylation and UL31 recruitment to DNA damage. While the PAR polymerase (PARP)1/2 inhibitor, olaparib, prevented UL31 recruitment to damaged DNA, KU55933 inhibition of signaling through the ataxia telangiectasia mutated (ATM) DNA damage response pathway had no effect. These findings were further supported by experiments demonstrating direct and specific interaction between HSV-2 UL31 and PAR using purified components. Co-transfection with the viral kinase Us3, known to phosphorylate UL31, inhibited UL31 recruitment to DNA damage but also prevented the recruitment of other proteins recruited to DNA damage sites. The viral E3 ubiquitin ligase ICP0 was observed to co-localize with UL31 in transfected cells in a manner that is independent of the PAR-binding ability of UL31. However, inhibition of PARP1/2/3 did not reduce the ability of HSV-2 to replicate and we observed reduced PAR levels in the nuclei of infected cells. This study reveals a previously unrecognized function for UL31 orthologs and may suggest that the recognition of PAR by UL31 is coupled to the nuclear egress of herpesvirus capsids, influences viral DNA replication and packaging, or possibly modulates the DNA damage response mounted by virally infected cells.

Resistance is futile: the borg, the hive, and corporate hegemony

The Borg, a collective of humanoid cyborgs linked together in a hive-mind and modeled on the earthly superorganisms of ant colonies and beehives, has been the most feared alien race in the Star Trek universe. The formidable success of the Borg in assimilating their foes corresponds to the astounding success of superorganisms in our own biosphere. Yet the Borg also serves as a metaphor for another collective of biological entities known as the corporation. In the Anthropocene epoch, corporations have become the most powerful force on the planet; their influence on the social world and the environment exceeds any government and may determine the continued sustainability of human life. Corporations have been described as people and as machines, but neither metaphor accurately describes their essence or contributes to an understanding that might resist their power. This paper reframes our understanding of the corporation by examining the metaphors that are used to describe it, and by suggesting an entirely new metaphor viewing the Borg and the corporation through the lens of sociobiology. I will argue that the corporation is a new form of superorganism that has become the dominant species on the planet and that the immense, intractable power of a globalized, corporate hive-mind has become the principal obstacle to addressing the planetary emergency of climate change. Reframing our metaphoric understanding of corporations as biological entities in the planetary biosphere may enable us to imagine ways to resist their increasing dominance and create a sustainable future. 

Mapping social values of ecosystem services: What is behind the map?

A growing interest in mapping the social value of ecosystem services (ES) is not yet methodologically aligned with what is actually being mapped. We critically examine aspects of the social value mapping process that might influence map outcomes and limit their practical use in decision making. We rely on an empirical case of participatory mapping, for a single ES (recreation opportunities), which involves diverse stakeholders such as planners, researchers, and community representatives. Value elicitation relied on an individual open-ended interview and a mapping exercise. Interpretation of the narratives and GIS calculations of proximity, centrality, and dispersion helped in exploring the factors driving participants’ answers. Narratives reveal diverse value types. Whereas planners highlighted utilitarian and aesthetic values, the answers from researchers revealed naturalistic values as well. In turn community representatives acknowledged symbolic values. When remitted to the map, these values were constrained to statements toward a much narrower set of features of the physical (e.g., volcanoes) and built landscape (e.g., roads). The results suggest that mapping, as an instrumental approach toward social valuation, may capture only a subset of relevant assigned values. This outcome is the interplay between participants’ characteristics, including their acquaintance with the territory and their ability with maps, and the mapping procedure itself, including the proxies used to represent the ES and the value typology chosen, the elicitation question, the cartographic features displayed on the base map, and the spatial scale.

Assessing the resilience of a real-world social-ecological system: lessons from a multidisciplinary evaluation of a South African pastoral system

In the past decades, social-ecological systems (SESs) worldwide have undergone dramatic transformations with often detrimental consequences for livelihoods. Although resilience thinking offers promising conceptual frameworks to understand SES transformations, empirical resilience assessments of real-world SESs are still rare because SES complexity requires integrating knowledge, theories, and approaches from different disciplines. Taking up this challenge, we empirically assess the resilience of a South African pastoral SES to drought using various methods from natural and social sciences. In the ecological subsystem, we analyze rangelands’ ability to buffer drought effects on forage provision, using soil and vegetation indicators. In the social subsystem, we assess households’ and communities’ capacities to mitigate drought effects, applying agronomic and institutional indicators and benchmarking against practices and institutions in traditional pastoral SESs. Our results indicate that a decoupling of livelihoods from livestock-generated income was initiated by government interventions in the 1930s. In the post-apartheid phase, minimum-input strategies of herd management were adopted, leading to a recovery of rangeland vegetation due to unintentionally reduced stocking densities. Because current livelihood security is mainly based on external monetary resources (pensions, child grants, and disability grants), household resilience to drought is higher than in historical phases. Our study is one of the first to use a truly multidisciplinary resilience assessment. Conflicting results from partial assessments underline that measuring narrow indicator sets may impede a deeper understanding of SES transformations. The results also imply that the resilience of contemporary, open SESs cannot be explained by an inward-looking approach because essential connections and drivers at other scales have become relevant in the globalized world. Our study thus has helped to identify pitfalls in empirical resilience assessment and to improve the conceptualization of SES dynamics.

This battle was not over: Parade’s End as a transitional text in the development of ‘disenchanted’ First World War literature.

This chapter argues that the novels of Ford's Parade's End tetralogy occupy a significant place in the development of "disenchanted" fiction about the First World War. The values of Ernest Raymond's patriotic Tell England are contrasted with those of C. E Montague's Disenchantment, providing a brief synopsis of the early 1920s response to the conflict. Parade's End is seen as introducing several key themes in to the post-First World War discursive field, including national identity, psychology, memory, and time. The presentation of these aligned with the formal aspects of the novel, allows it to push the boundaries of the readerly horizon of expectations. Frayn argues that Ford's readership, though moderately-sized, was influential from a literary point of view, and thus facilitated the reception of later, more vitriolic, criticisms of war.

A novel mechanism of action of HER2 targeted immunotherapy is explained by inhibition of NRF2 function in ovarian cancer cells

Nuclear erythroid related factor-2 (NRF2) is known to promote cancer therapeutic detoxification and crosstalk with growth promoting pathways. HER2 receptor tyrosine kinase is frequently overexpressed in cancers leading to uncontrolled receptor activation and signaling. A combination of HER2 targeting monoclonal antibodies shows greater anticancer efficacy than the single targeting antibodies, however, its mechanism of action is largely unclear. Here we report novel actions of anti-HER2 drugs, Trastuzumab and Pertuzumab, involving NRF2. HER2 targeting by antibodies inhibited growth in association with persistent generation of reactive oxygen species (ROS), glutathione (GSH) depletion, reduction in NRF2 levels and inhibition of NRF2 function in ovarian cancer cell lines. The combination of antibodies produced more potent effects than single alone; downregulated NRF2 substrates by repressing the Antioxidant Response (AR) pathway with concomitant transcriptional inhibition of NRF2. We showed the antibody combination produced increased methylation at the NRF2 promoter consistent with repression of NRF2 antioxidant function, as HDAC and methylation inhibitors reversed such produced transcriptional effects. These findings demonstrate a novel mechanism and role for NRF2 in mediating the response of cancer cells to the combination of Trastuzumab and Pertuzumab and reinforce the importance of NRF2 in drug resistance and as a key anticancer target.

The importance of improving diet in 'Securing Scotland's Health': exploring differences in dietary intake between Scotland and England

Background: Various factors have been investigated to account for the higher premature death rates in Scotland compared to England. Higher levels of deprivation in Scotland provide a partial explanation for these differences but recent work comparing areas of the UK with similar deprivation profiles and low life expectancy has shown that this is not the only reason. One hypothesis yet to be tested adequately is differences in diet and nutrition. Objective: To conduct a comparative analysis of dietary intake between Scotland and England using pooled food purchase data from the Living Costs and Food Survey (LCFS) from 2001 to 2012 and to assess differences in equivalised income quintiles (controlling for survey year, age of household reference person, and age household reference person left full-time education). Results: Lower intakes of fruit and vegetables, oil rich fish, fibre, vitamin A, folate, vitamin C and vitamin D and higher intakes of red and processed meat, whole milk, butter, savoury snacks, confectionary, soft drinks, saturated fat and NMES (added sugar and sugar in fruit juice), sodium and alcohol were found for Scotland compared to England. Differences between Scotland and England were higher for those on lower incomes for dietary components known to be related to health outcomes. For example fruit consumption was 14g/day lower for the lowest income quintile compared to 4 g/day lower in the highest quintile for Scotland versus England. Conclusions: A poorer diet in Scotland compared to England, particularly among disadvantaged groups, is likely to be one of the reasons for excess mortality. The current evidence on the continued poor diet in Scotland, particularly in disadvantaged groups, should not be ignored. Identifying effective, culturally appropriate approaches to improve diet across the population and notably in the most deprived areas needs further investment. Funded by NHS Health Scotland. Data provided by DEFRA, ONS and the UK Data Archive.