Interdisciplinary perspectives on the development, integration and application of cognitive ontologies

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data

Establishment and operation of a Good Manufacturing Practice-compliant allogeneic Epstein-Barr virus (EBV)-specific cytotoxic cell bank for the treatment of EBV-associated lymphoproliferative disease

Funded by Wellcome Trust Translational Award SNBTSPeer reviewedPublisher PD

Detection of hot, metal-enriched outflowing gas around z≈ z\approx\,2.3 star-forming galaxies in the Keck Baryonic Structure Survey

We use quasar absorption lines to study the physical conditions in the circumgalactic medium of redshift $z\approx 2.3$ star-forming galaxies taken from the Keck Baryonic Structure Survey (KBSS). In Turner et al. 2014 we used the pixel optical depth technique to show that absorption by HI and the metal ions OVI, NV, CIV, CIII and SiIV is strongly enhanced within $|\Delta v|\lesssim170$ km/s and projected distances $|d|\lesssim180$ proper kpc from sightlines to the background quasars. Here we demonstrate that the OVI absorption is also strongly enhanced at fixed HI, CIV, and SiIV optical depths, and that this enhancement extends out to $\sim350$ km/s. At fixed HI the increase in the median OVI optical depth near galaxies is 0.3-0.7 dex and is detected at 2--3-$\sigma$ confidence for all seven HI bins that have $\log_{10}\tau_{\rm HI}\ge-1.5$. We use ionization models to show that the observed strength of OVI as a function of HI is consistent with enriched, photoionized gas for pixels with $\tau_{\rm HI}\gtrsim10$. However, for pixels with $\tau_{\rm HI} \lesssim 1$ this would lead to implausibly high metallicities at low densities if the gas were photoionized by the background radiation. This indicates that the galaxies are surrounded by gas that is sufficiently hot to be collisionally ionized ($T > 10^5\,$K) and that a substantial fraction of the hot gas has a metallicity $\gtrsim 10^{-1}$ of solar. Given the high metallicity and large velocity extent (out to $\sim1.5\times v_{\rm circ}$) of this gas, we conclude that we have detected hot, metal enriched outflows arising from star-forming galaxies.Comment: Accepted for publication in MNRAS, 14 pages, 9 figures (not including appendices

Cytometric analysis of T cell phenotype using cytokine profiling for improved manufacturing of an EBV-specific T cell therapy

Acknowledgements We gratefully acknowledge the voluntary donations of peripheral blood and leukapheresis samples used in this study. This study was supported by the staff of the Scottish National Blood Transfusion Service (SNBTS) Clinical Apheresis Unit, Aberdeen and medical colleagues at the New Zealand Blood Transfusion Service for collection of the donor leukapheresis material for the second iteration of the EBV-T cell bank. This work was supported by a Wellcome Trust Translational Award. The ongoing operation of the UK EBV-specific T cell bank is supported by cost-recovery fees and supported by SNBTS. Contributions RSC and AK were responsible for the acquisition and analysis of data, and RSC wrote the principal manuscript; GW and MV were involved in supply of material and interpretation of data; MLT, JDMC and ARF were responsible for study conception and design, data analysis and interpretation, and revision of the final manuscript.Peer reviewedPublisher PD

Preferred and actual place of death in haematological malignancies : a report from the UK haematological malignancy research network

Objectives Hospital death is comparatively common in people with haematological cancers, but little is known about patient preferences. This study investigated actual and preferred place of death, concurrence between these and characteristics of preferred place discussions. Methods Set within a population-based haematological malignancy patient cohort, adults (≥18 years) diagnosed 2004–2012 who died 2011–2012 were included (n=963). Data were obtained via routine linkages (date, place and cause of death) and abstraction of hospital records (diagnosis, demographics, preferred place discussions). Logistic regression investigated associations between patient and clinical factors and place of death, and factors associated with the likelihood of having a preferred place discussion. Results Of 892 patients (92.6%) alive 2 weeks after diagnosis, 58.0% subsequently died in hospital (home, 20.0%; care home, 11.9%; hospice, 10.2%). A preferred place discussion was documented for 453 patients (50.8%). Discussions were more likely in women (p=0.003), those referred to specialist palliative care (p<0.001), and where cause of death was haematological cancer (p<0.001); and less likely in those living in deprived areas (p=0.005). Patients with a discussion were significantly (p<0.05) less likely to die in hospital. Last recorded preferences were: home (40.6%), hospice (18.1%), hospital (17.7%) and care home (14.1%); two-thirds died in their final preferred place. Multiple discussions occurred for 58.3% of the 453, with preferences varying by proximity to death and participants in the discussion. Conclusion Challenges remain in ensuring that patients are supported to have meaningful end-of-life discussions, with healthcare services that are able to respond to changing decisions over time

Metal-line absorption around z ≈ 2.4 star-forming galaxies in the Keck Baryonic Structure Survey

We study metal absorption around 854 z ≈ 2.4 star-forming galaxies taken from the Keck Baryonic Structure Survey. The galaxies examined in this work lie in the fields of 15 hyperluminous background quasi-stellar objects, with galaxy impact parameters ranging from 35 proper kpc (pkpc) to 2 proper Mpc (pMpc). Using the pixel optical depth technique, we present the first galaxy-centred 2D maps of the median absorption by O VI, N V, C IV, C III, and Si IV, as well as updated results for H I. At small galactocentric radii we detect a strong enhancement of the absorption relative to randomly located regions that extend out to at least 180 pkpc in the transverse direction, and ±240 km s^(−1) along the line of sight (LOS, ∼1 pMpc in the case of pure Hubble flow) for all ions except N V. For C IV (and H I) we detect a significant enhancement of the absorption signal out to 2 pMpc in the transverse direction, corresponding to the maximum impact parameter in our sample. After normalizing the median absorption profiles to account for variations in line strengths and detection limits, in the transverse direction we find no evidence for a sharp drop-off in metals distinct from that of H I. We argue instead that non-detection of some metal-line species in the extended circumgalactic medium is consistent with differences in the detection sensitivity. Along the LOS, the normalized profiles reveal that the enhancement in the absorption is more extended for O VI, C IV, and Si IV than for H I. We also present measurements of the scatter in the pixel optical depths, covering fractions, and equivalent widths as a function of projected galaxy distance. Limiting the sample to the 340 galaxies with redshifts measured from nebular emission lines does not decrease the extent of the enhancement along the LOS compared to that in the transverse direction. This rules out redshift errors as the source of the observed redshift-space anisotropy and thus implies that we have detected the signature of gas peculiar velocities from infall, outflows, or virial motions for H I, O VI, C IV, C III, and Si IV

Habitat associations of day-flying Lepidoptera and their foodplants within nature reserves in Bedfordshire, UK

Species often associate with specific habitat characteristics, resulting in patchy distributions, whereby they only occupy a proportion of available habitat. Understanding which characteristics species require is a valuable tool for informing conservation management. We investigated the associations of eleven species of day-flying Lepidoptera larvae and their foodplants with habitat characteristics within calcareous grassland reserves in Bedfordshire, UK, across two scales relevant to land managers and target species: the reserve (cardinal aspect, vegetation type) and foodplant patch scale (foodplant height and density). We investigated whether ecological traits (habitat specialism, as defined at a national-scale, and overwintering life stage) influenced the strength of associations. At the reserve scale, we found variation in associations with habitat characteristics across species, with species that overwinter at non-adult life stages having more restricted associations, indicating that they may be more vulnerable to environmental change. Associations were generally stronger with vegetation type than aspect, which can be manipulated more easily by land managers. Seven species had similar associations with habitat characteristics to their foodplants, implying that management to benefit foodplants will also benefit larvae. However, the remaining four species had different associations to their foodplants, and may require alternative management approaches. At the foodplant patch scale, four species were associated with foodplant characteristics, which could be used to inform effective fine-scale management. Implications for insect conservation: Diverse habitat associations imply that topographic and vegetation variation are valuable for supporting diverse assemblages of butterflies and their foodplants