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

The IMGT/HLA database

It is 12 years since the IMGT/HLA database was first released, providing the HLA community with a searchable repository of highly curated HLA sequences. The HLA complex is located within the 6p21.3 region of human chromosome 6 and contains more than 220 genes of diverse function. Many of the genes encode proteins of the immune system and are highly polymorphic. The naming of these HLA genes and alleles and their quality control is the responsibility of the WHO Nomenclature Committee for Factors of the HLA System. Through the work of the HLA Informatics Group and in collaboration with the European Bioinformatics Institute, we are able to provide public access to this data through the web site http://www.ebi.ac.uk/imgt/hla/. Regular updates to the web site ensure that new and confirmatory sequences are dispersed to the HLA community, and the wider research and clinical communities

Popular culture, participation and progression in the literacy classroom

In this paper, I share an account of what happens when a teacher values children's experiences of popular culture in a classroom activity. Drawing on a socio-cultural approach to learning, I suggest that children are not simply enthused when their lived cultures are valued in the classroom but more fundamentally that they are motivated because they can participate in (and are not excluded from) the learning that is constructed. Drawing on data from a recent media literacy research project, I aim to demonstrate the necessity of including popular culture experiences in literacy teaching in order to ensure that children are able to articulate and develop key conceptual understandings. Furthermore, I suggest that interrogatory pedagogic strategies, including practical productions, are key to ensuring that children are able to make explicit, and then organise and develop their conceptual understandings

LEARNS: A creative approach to analysing and representing narrative data incorporating photo-elicitation techniques

© 2018, The Author(s) 2018. Background: Diversity exists in how storied data gathered in narrative inquiry is analysed and represented, more so when there is a need to combine multiple data collection methods, including photographs. Aim: This paper discusses the use of an analytical framework entitled LEARNS developed as part of a PhD study that has potential to fill this gap. Results: The step-by-step framework presented in this paper was developed in order to analyse the data collected in this research study and gives understanding and insight into the experience of mothers whose babies are removed at birth. The LEARNS framework provides transparency and credibility; it also negates the need to restrict findings to broad themes via content/thematic analysis. Conclusions: LEARNS could offer other researchers a reliable framework to use for future social science research

The role of salt bridges, charge density, and subunit flexibility in determining disassembly routes of protein complexes

Mass spectrometry can be used to characterize multiprotein complexes, defining their subunit stoichiometry and composition following solution disruption and collision-induced dissociation (CID). While CID of protein complexes in the gas phase typically results in the dissociation of unfolded subunits, a second atypical route is possible wherein compact subunits or subcomplexes are ejected without unfolding. Because tertiary structure and subunit interactions may be retained, this is the preferred route for structural investigations. How can we influence which pathway is adopted? By studying properties of a series of homomeric and heteromeric protein complexes and varying their overall charge in solution, we found that low subunit flexibility, higher charge densities, fewer salt bridges, and smaller interfaces are likely to be involved in promoting dissociation routes without unfolding. Manipulating the charge on a protein complex therefore enables us to direct dissociation through structurally informative pathways that mimic those followed in solution

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. 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. 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-ESTDAB, which provides access to the European Searchable Tumour Cell-Line Database, a cell bank of immunologically characterized melanoma cell lines. The data is currently available online from the website and FTP directory. This article describes the latest updates and additional tools added to the IPD project

Near-Infrared Light Curves of the Black Hole Binary A0620-00

We measured the near-infrared orbital light curve of the black hole binary A0620-00 in 1995 and 1996. The light curves show an asymmetric, double-humped modulation with extra emission in the peak at orbital phase 0.75. There were no significant changes in the shape of the light curve over the one-year observation period. There were no sharp dips in the light curves nor reversals of the asymmetry between the two peaks as seen in earlier observations. The light curves are well fit by models incorporating ellipsoidal variations from the mass-losing K-type star plus a beamed bright spot on the accretion disk around the compact star. The long-term stability of the light curve shape rules out superhumps and star spots as sources of asymmetry when we observed A0620-00. The ellipsoidal variations yield a lower limit i >= 38 deg on the orbital inclination. The light curves show no eclipse features, which places an upper limit i <= 75 deg. This range of inclinations constrains the mass of the compact object to 3.3 < M_1 < 13.6 Msun. The light curves do not further constrain the orbital inclination because the contribution of the accretion disk to the observed flux is unknown. We argue that a previous attempt to measure the near-infrared flux from the accretion disk using the dilution of the 12CO(2,0) bandhead in the spectrum of the K star is not reliable because the band strength depends strongly on surface gravity.Comment: Accepted for publication in the Astronomical Journal. 17 pages, 4 figures. Prepared using AASTEX V. 5.

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

The HLA diversity of the Anthony Nolan register

While the success of allogeneic stem cell transplantation depends on a high degree of HLA compatibility between donor and patient, finding a suitable donor remains challenging due to the hyperpolymorphic nature of HLA genes. We calculated high‐resolution allele, haplotype and phenotype frequencies for HLA‐A, ‐C, ‐B, ‐DRB1 and ‐DQB1 for 10 subpopulations of the Anthony Nolan (AN) register using an in‐house expectation‐maximisation (EM) algorithm run on mixed resolution HLA data, covering 676 155 individuals. Sample sizes range from 599 410 for British/Irish North West European (BINWE) individuals, the largest subpopulation in the United Kingdom to 1105 for the British Bangladeshi population. Calculation of genetic distance between the subpopulations based on haplotype frequencies shows three broad clusters, each following a major continental group: European, African and Asian. We further analysed the HLA haplotype and phenotype diversity of each subpopulation, and found that 35.52% of BINWE individuals ranging to 98.34% of Middle Eastern individuals on the register had a unique phenotype within their subpopulation. These analyses and the allele, haplotype and phenotype frequency data of the subpopulation on the AN register are a valuable resource in understanding the HLA diversity in the United Kingdom and can be used to improve the accuracy of match likelihoods and to inform future donor recruitment strategies