IPD - the Immuno Polymorphism Database

The Immuno Polymorphism Database (IPD) (http://www.ebi.ac.uk/ipd/) is a set of specialist databases related to the study of polymorphic genes in the immune system. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of Killer-cell Immunoglobulin-like Receptors; IPD-MHC, a database of sequences of the Major Histocompatibility Complex of different species; IPD-HPA, alloantigens expressed only on platelets; and IPD-ESTAB, which provides access to the European Searchable Tumour Cell-Line Database, a cell bank of immunologically characterized melanoma cell lines. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. Those sections with similar data, such as IPD-KIR and IPD-MHC share the same database structure. The sharing of a common database structure makes it easier to implement common tools for data submission and retrieval. The data are currently available online from the website and ftp directory; files will also be made available in different formats to download from the website and ftp server. The data will also be included in SRS, BLAST and FASTA search engines at the European Bioinformatics Institute

Mental model updating and team adaptation

In this article, we build on theories of team adaptation by exploring the role of team members' cognitive knowledge structures in team adaptation to a changing task context. We introduce the notion of mental model updating as the extent to which team members update their mental models in reaction to a change in the task situation. In a laboratory study we investigate the relations between initial mental model similarity and accuracy, team mental model updating, the development of novel interaction patterns, and postchange team performance. The results indicate that mental model updating is positively related to postchange team performance. Also, team adaptation patterns accounted for the effect of mental model updating on postchange team performance. We did not find evidence for a positive relation between initial mental model similarity and accuracy and mental model updating

Anticancer activity and DNA interaction of bis(pyridyl)allene-derived metal complexes

The constant need for novel drugs has prompted the scientific community to explore alternative structures to natural products and small and medium size organic compounds used in classic medicinal and pharmaceutical chemistry. Since the discovery of cisplatin, organometallic compounds have revealed great potential as metallodrugs and their development has exponentially grown in recent years. In this manuscript, we describe our efforts towards the synthesis of new metallodrugs by reaction of bis(pyridyl)allenes and metal complexes. Two classes of compounds are presented: one in which the allene structure is intact and the metal (Pd(II), Pt(IV) or Au(III)) coordinates to the pyridine-nitrogens; and another, in which one of the pyridines cyclises into a gold-activated allene to form β-N-stabilised gold carbenes. Both classes of compounds are active catalysts in important organic reactions, and are also promising antimicrobial, antifungal and anticancer agents. In this work, we describe the promising anticancer activity, against breast cancer cells, of the gold carbene complexes, and preliminary studies of their interaction with DNA, including non-canonical DNA structures. Our results have revealed an unusual selective stabilisation of hTeloC i-motif by one of the Au(III) carbene complexes, that opens up exciting opportunities for further development of novel DNA-binding metallodrugs

Pollen signals of ground flora in managed woodlands

This paper explores the vegetation signals contained in the non-arboreal pollen and spore (NAPS) components of pollen assemblages from Tauber traps placed in woodlands subject to rotational cutting (coppicing) in lowland England. Sets of three Tauber traps were placed in compartments of different ages at multiple locations within each woodland for 1 year, and pollen assemblages recorded along with a vegetation survey using a modified pin-frame method in an area of 10 m radius around each trap array. Cluster analysis suggests that, as expected, the ground layer vegetation broadly reflects the different environmental conditions in the three woods, with the main subdivisions within woods apparently driven by changes in ground cover between the early and late stages of the coppice cycle. Non-arboreal pollen and spores (NAPS) assemblages group according to woodland of origin, with subdivisions which relate to pollen abundance but lack a simple relationship with years since cutting. Indices of Association between NAPS records and plant presence in the area around each array were calculated using presence–absence data for multiple distances of vegetation survey. All values tend towards an asymptote, which is interpreted as implying an effective source area for the single taxon presence–absence indicator values of ground flora taxa in coppiced woodlands on the order of a 10 m radius. Only four taxa, Poaceae, Ranunculus acris-type, Cyperaceae, and Scilla-type, have an Index of Association (A) greater than 0.5, implying that the presence of pollen can be interpreted in terms of the local presence of the relevant plant taxon with some confidence. Estimates of Pollen Productivity relative to Poaceae are presented for five taxa: Apiaceae, Asteraceae (Cardueae), Cyperaceae, Mercurialis perennis, and Scilla-type. Years since cutting does affect the ground vegetation and NAPS assemblage trapped in these woods, but that the effect is more clearly seen at an assemblage level in the vegetation than in the pollen assemblages. The interpretative significance of NAPS taxa does not seem to be in providing information about the local conditions around the sampling point, but in reflecting the ground flora of the wider woodland

A quasi-diagonal approach to the estimation of Lyapunov spectra for spatio-temporal systems from multivariate time series

We describe methods of estimating the entire Lyapunov spectrum of a spatially extended system from multivariate time-series observations. Provided that the coupling in the system is short range, the Jacobian has a banded structure and can be estimated using spatially localised reconstructions in low embedding dimensions. This circumvents the ``curse of dimensionality'' that prevents the accurate reconstruction of high-dimensional dynamics from observed time series. The technique is illustrated using coupled map lattices as prototype models for spatio-temporal chaos and is found to work even when the coupling is not strictly local but only exponentially decaying.Comment: 13 pages, LaTeX (RevTeX), 13 Postscript figs, to be submitted to Phys.Rev.

Approaches to quantitative reconstruction of woody vegetation in managed woodlands from pollen records

There has been increasing interest in developing quantitative methods for reconstructing the dynamics of cultural landscapes over the last 15 years. This paper adds to this literature by using various approaches to reconstruct the vegetation of two woodlands subject to rotational coppicing (the periodic cutting of broadleaved trees and shrubs for wood products). Pollen deposition at ground level was determined at both sites using ‘Tauber’ traps placed near to the centre of 14 compartments of differing age in the coppice rotation. For the main woody taxa, Relative Pollen Productivity (RPP) estimates were derived using linear regression for pollen influx data and Extended R-value analysis for percentage data. The vegetation around three ponds was reconstructed by applying four methods (inverting the two RPP estimate approaches, the modern analogue technique and correction for pollen productivity using the linear regression estimated RPP values) to pollen data obtained from the uppermost sample of sediment from the ponds. To determine whether these methods gave better estimates of the vegetation composition than the original pollen proportions, the results were compared with the surveyed vegetation around each pond using the Bray–Curtis Index. Linear regression of pollen influx produced RPP values which are comparable with previous European studies, whilst for some taxa the Extended R-value analysis produced estimates which are orders of magnitude different both from values derived from the linear regression and previous work. No single approach performed equally well at reconstructing the vegetation around the ponds, and at two of the three locations the uncorrected pollen proportions were most similar to the surveyed vegetation.We conclude that applying quantitative reconstruction methods to individual small sites is, currently, not likely to be useful in complex cultural landscapes. In the context of coppiced woodland, deficiencies in our understanding of pollen taphonomy and the impact of the practice on pollen production first need to be rectified, and we identify strategies to address this situation

Hepatitis transmission risk IN kidney Transplantation (the HINT study); a cross-sectional survey of transplant clinicians in Australian and New Zealand

Background Interpreting hepatitis serology and virus transmission risk in transplantation can be challenging. Decisions must balance opportunity to transplant against potential infection transmission. We aimed to survey understanding among the Australian and New Zealand medical transplant workforce of hepatitis risk in kidney donors and recipients. Methods An anonymous, self-completed, cross-sectional survey was distributed via electronic mailing lists to Australian and New Zealand clinicians involved in kidney transplantation (2014-2015). We compared interpretation of clinical scenarios with paired donor and recipient hepatitis B virus and hepatitis C virus serology to recommendations in clinical practice guidelines. We used logistic regression modeling to investigate characteristics associated with decisions on transplant suitability in scenarios with poor (<50%) guideline concordance (odds ratios [OR]). Results One hundred ten respondents had representative workforce demographics: most were male (63%) nephrologists (74%) aged 40 to 49 years. Although donor and recipient hepatitis status was largely well understood, transplant suitability responses varied among respondents. For a hepatitis B virus surface antigen-positive donor and vaccinated recipient, 44% suggested this was unsuitable for transplant (guideline concordant) but 35% suggested this was suitable with prophylaxis (guideline divergent). In 4 scenarios with transplant suitability guideline concordance less than 50%, acute transplant care involvement predicted guideline concordant responses (OR, 1.69; P = 0.04). Guideline concordant responses were chosen less by hepatologists, intensive care doctors (OR, 0.23, 0.35, respectively; P = 0.01), and New Zealanders (guideline concordant responses OR, 0.17; P < 0.01; alternative responses OR, 4.31; P < 0.01). Conclusions Despite broadly consistent interpretations of hepatitis serology, transplant suitability decisions varied and often diverged from guidelines. Improved decision support may reduce clinician variability

Responses of Southern Ocean seafloor habitats and communities to global and local drivers of change

Knowledge of life on the Southern Ocean seafloor has substantially grown since the beginning of this century with increasing ship-based surveys and regular monitoring sites, new technologies and greatly enhanced data sharing. However, seafloor habitats and their communities exhibit high spatial variability and heterogeneity that challenges the way in which we assess the state of the Southern Ocean benthos on larger scales. The Antarctic shelf is rich in diversity compared with deeper water areas, important for storing carbon (“blue carbon”) and provides habitat for commercial fish species. In this paper, we focus on the seafloor habitats of the Antarctic shelf, which are vulnerable to drivers of change including increasing ocean temperatures, iceberg scour, sea ice melt, ocean acidification, fishing pressures, pollution and non-indigenous species. Some of the most vulnerable areas include the West Antarctic Peninsula, which is experiencing rapid regional warming and increased iceberg-scouring, subantarctic islands and tourist destinations where human activities and environmental conditions increase the potential for the establishment of non-indigenous species and active fishing areas around South Georgia, Heard and MacDonald Islands. Vulnerable species include those in areas of regional warming with low thermal tolerance, calcifying species susceptible to increasing ocean acidity as well as slow-growing habitat-forming species that can be damaged by fishing gears e.g., sponges, bryozoan, and coral species. Management regimes can protect seafloor habitats and key species from fishing activities; some areas will need more protection than others, accounting for specific traits that make species vulnerable, slow growing and long-lived species, restricted locations with optimum physiological conditions and available food, and restricted distributions of rare species. Ecosystem-based management practices and long-term, highly protected areas may be the most effective tools in the preservation of vulnerable seafloor habitats. Here, we focus on outlining seafloor responses to drivers of change observed to date and projections for the future. We discuss the need for action to preserve seafloor habitats under climate change, fishing pressures and other anthropogenic impacts

p53 mutation with frequent novel codons but not a mutator phenotype in BRCA1- and BRCA2-associated breast tumours

The status of p53 was investigated in breast tumours arising in germ-line carriers of mutant alleles of BRCA1 and BRCA2 and in a control series of sporadic breast tumours. p53 expression was detected in 20/26 (77%) BRCA1-, 10/22 (45%) BRCA2-associated and 25/72 (35%) grade-matched sporadic tumours. Analysis of p53 sequence revealed that the gene was mutant in 33/50 (66%) BRCA-associated tumours, whereas 7/20 (35%) sporadic grade-matched tumours contained p53 mutation (P < 0.05). A number of the mutations detected in the BRCA-associated tumours have not been previously described in human cancer databases, whilst others occur extremely rarely. Analysis of additional genes, p16(INK4), Ki-ras and β-globin revealed absence or very low incidence of mutations, suggesting that the higher frequency of p53 mutation in the BRCA-associated tumours does not reflect a generalized increase in susceptibility to the acquisition of somatic mutation. Furthermore, absence of frameshift mutations in the polypurine tracts present in the coding sequence of the TGF β type II receptor (TGF β IIR) and Bax implies that loss of function of BRCA1 or BRCA2 does not confer a mutator phenotype such as that found in tumours with microsatellite instability (MSI). p21(Waf1) was expressed in BRCA-associated tumours regardless of p53 status and, furthermore, some tumours expressing wild-type p53 did not express detectable p21(Waf1). These data do not support, therefore, the simple model based on studies of BRCA-/- embryos, in which mutation of p53 in BRCA-associated tumours results in loss of p21(Waf1) expression and deregulated proliferation. Rather, they imply that proliferation of such tumours will be subject to multiple mechanisms of growth regulation