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  • Lees, William, et al. (författare)
  • OGRDB : a reference database of inferred immune receptor genes
  • 2020
  • Ingår i: Nucleic Acids Research. - Oxford University Press. - 1362-4962. ; 48:D1, s. 964-970
  • Tidskriftsartikel (refereegranskat)abstract
    • High-throughput sequencing of the adaptive immune receptor repertoire (AIRR-seq) is providing unprecedented insights into the immune response to disease and into the development of immune disorders. The accurate interpretation of AIRR-seq data depends on the existence of comprehensive germline gene reference sets. Current sets are known to be incomplete and unrepresentative of the degree of polymorphism and diversity in human and animal populations. A key issue is the complexity of the genomic regions in which they lie, which, because of the presence of multiple repeats, insertions and deletions, have not proved tractable with short-read whole genome sequencing. Recently, tools and methods for inferring such gene sequences from AIRR-seq datasets have become available, and a community approach has been developed for the expert review and publication of such inferences. Here, we present OGRDB, the Open Germline Receptor Database (https://ogrdb.airr-community.org), a public resource for the submission, review and publication of previously unknown receptor germline sequences together with supporting evidence.
  • Ljung, R. C., et al. (författare)
  • Intron 22 Inversions and haemophilia
  • 1994
  • Ingår i: The Lancet. - Elsevier. - 0140-6736. ; 343:8900, s. 791-792
  • Tidskriftsartikel (refereegranskat)
  • Loley, Christina, et al. (författare)
  • No Association of Coronary Artery Disease with X-Chromosomal Variants in Comprehensive International Meta-Analysis
  • 2016
  • Ingår i: Scientific Reports. - 2045-2322 .- 2045-2322. ; 6
  • Tidskriftsartikel (refereegranskat)abstract
    • In recent years, genome-wide association studies have identified 58 independent risk loci for coronary artery disease (CAD) on the autosome. However, due to the sex-specific data structure of the X chromosome, it has been excluded from most of these analyses. While females have 2 copies of chromosome X, males have only one. Also, one of the female X chromosomes may be inactivated. Therefore, special test statistics and quality control procedures are required. Thus, little is known about the role of X-chromosomal variants in CAD. To fill this gap, we conducted a comprehensive X-chromosome-wide meta-analysis including more than 43,000 CAD cases and 58,000 controls from 35 international study cohorts. For quality control, sex-specific filters were used to adequately take the special structure of X-chromosomal data into account. For single study analyses, several logistic regression models were calculated allowing for inactivation of one female X-chromosome, adjusting for sex and investigating interactions between sex and genetic variants. Then, meta-analyses including all 35 studies were conducted using random effects models. None of the investigated models revealed genome-wide significant associations for any variant. Although we analyzed the largest-to-date sample, currently available methods were not able to detect any associations of X-chromosomal variants with CAD.
  • Lund, B, et al. (författare)
  • Novel cluster of alpha-interferon gene sequences in a placental cosmid DNA library.
  • 1984
  • Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - 0027-8424. ; 81:8, s. 2435-9
  • Tidskriftsartikel (refereegranskat)abstract
    • A human cosmid library was constructed and probed with a human alpha interferon (IFN-alpha) cDNA clone. One clone giving a strong hybridizing signal was isolated and characterized. The cosmid DNA insert represents a section of the human genome containing three regions of IFN-alpha-like sequences. The DNA was characterized with restriction endonuclease mapping, thereby allowing comparison to similar linkage groups reported recently and determination of homologous regions on the known physical map. The three IFN-alpha-like sequences were analyzed by a partial sequence analysis. Mapping and sequence data establish this section as a not-yet-described cluster of IFN-alpha sequences in the human genome; however, a part of the section matches to some degree to a previously described genomic region. The region described here could represent genetic polymorphism or a duplicated segment.
  • Maes, Dirk, et al. (författare)
  • Integrating national Red Lists for prioritising conservation actions for European butterflies
  • 2019
  • Ingår i: Journal of Insect Conservation. - Springer. - 1366-638X. ; 23:2, s. 301-330
  • Tidskriftsartikel (refereegranskat)abstract
    • Red Lists are very valuable tools in nature conservation at global, continental and (sub-) national scales. In an attempt to prioritise conservation actions for European butterflies, we compiled a database with species lists and Red Lists of all European countries, including the Macaronesian archipelagos (Azores, Madeira and Canary Islands). In total, we compiled national species lists for 42 countries and national Red Lists for 34 of these. The most species-rich countries in Europe are Italy, Russia and France with more than 250 species each. Endemic species are mainly found on the Macaronesian archipelagos and on the Mediterranean islands. By attributing numerical values proportionate to the threat statuses in the different national Red List categories, we calculated a mean Red List value for every country (cRLV) and a weighted Red List value for every species (wsRLV) using the square root of the country’s area as a weighting factor. Countries with the highest cRLV were industrialised (NW) European countries such as the Netherlands, Belgium, the Czech Republic and Denmark, whereas large Mediterranean countries such as Spain and Italy had the lowest cRLV. Species for which a Red List assessment was available in at least two European countries and with a relatively high wsRLV (≥ 50) are Colias myrmidone, Pseudochazara orestes, Tomares nogelii, Colias chrysotheme and Coenonympha oedippus. We compared these wsRLVs with the species statuses on the European Red List to identify possible mismatches. We discuss how this complementary method can help to prioritise butterfly conservation on the continental and/or the (sub-)national scale.
  • Mandal, Pankaj K, et al. (författare)
  • Efficient Ablation of Genes in Human Hematopoietic Stem and Effector Cells using CRISPR/Cas9.
  • 2014
  • Ingår i: Cell Stem Cell. - Cell Press. - 1934-5909. ; 15:5, s. 643-652
  • Tidskriftsartikel (refereegranskat)abstract
    • Genome editing via CRISPR/Cas9 has rapidly become the tool of choice by virtue of its efficacy and ease of use. However, CRISPR/Cas9-mediated genome editing in clinically relevant human somatic cells remains untested. Here, we report CRISPR/Cas9 targeting of two clinically relevant genes, B2M and CCR5, in primary human CD4(+) T cells and CD34(+) hematopoietic stem and progenitor cells (HSPCs). Use of single RNA guides led to highly efficient mutagenesis in HSPCs but not in T cells. A dual guide approach improved gene deletion efficacy in both cell types. HSPCs that had undergone genome editing with CRISPR/Cas9 retained multilineage potential. We examined predicted on- and off-target mutations via target capture sequencing in HSPCs and observed low levels of off-target mutagenesis at only one site. These results demonstrate that CRISPR/Cas9 can efficiently ablate genes in HSPCs with minimal off-target mutagenesis, which could have broad applicability for hematopoietic cell-based therapy.
  • Martins, C., et al. (författare)
  • Development of a long pulse high power klystron modulator for the ESS linac based on the Stack Multi-Level topology
  • 2016
  • Ingår i: 7th International Particle Accelerator Conference, IPAC 2016,Busan, Korea, Republic of,2016-05-08 - 2016-05-13. - Joint Accelerator Conferences Website (JACoW).
  • Konferensbidrag (refereegranskat)abstract
    • A novel Stacked Multi-Level (SML) modulator topology optimized for long pulse and high average power applications has been developed at ESS. It utilizes six identical modules connected in series at the HV output side and fed in parallel from the low voltage side. Each one is formed by one HF inverter, one step-up transformer, one HV rectifier bridge and one HV passive filter. They are supplied, in groups of two, from three capacitor banks which in turn will be charged from the low voltage electrical grid by using three groups of active AC/DC and DC/DC converters. Industrial standard power electronic components are used at the primary stage, which are placed in conventional electrical cabinets. Only few special components (transformers, rectifiers, filters) are required to be placed in an oil tank. A technology demonstrator rated for 115kV/20A and 3.5ms/14Hz is at the final phase of construction. The main power conversion circuit and regulation principles will be described and details on the design and construction of the main subsystems will be given. Simulation and experimental results will be given showing the achieved performance in terms of HV pulse quality and AC grid power quality.
  • Masciari, S., et al. (författare)
  • Germline E-cadherin mutations in familial lobular breast cancer
  • 2007
  • Ingår i: Journal of Medical Genetics. - BMJ Publishing Group. - 0022-2593. ; 44:11, s. 726-731
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: The cell surface glycoprotein E-cadherin (CDH1) is a key regulator of adhesive properties in epithelial cells. Germline mutations in CDH1 are well established as the defects underlying hereditary diffuse gastric cancer (HDGC) syndrome, and an increased risk of lobular breast cancer (LBC) has been described in HDGC kindreds. However, germline CDH1 mutations have not been described in patients with LBC in non-HDGC families. This study aimed to investigate the frequency of germline CDH1 mutations in patients with LBC with early onset disease or family histories of breast cancer without DGC. Methods: Germline DNA was analysed in 23 women with invasive lobular or mixed ductal and lobular breast cancers who had at least one close relative with breast cancer or had themselves been diagnosed before the age of 45 years, had tested negative for a germline BRCA1 or BRCA2 mutation, and reported no personal or family history of diffuse gastric cancer. The full coding sequence of CDH1 including splice junctions was amplified using PCR and screened for mutations using DHPLC and sequencing. Results: A novel germline CDH1 truncating mutation in the extracellular portion of the protein (517insA) was identified in one woman who had LBC at the age of 42 years and a first degree relative with invasive LBC. Conclusions: Germline CDH1 mutations can be associated with invasive LBC in the absence of diffuse gastric cancer. The finding, if confirmed, may have implications for management of individuals at risk for this breast cancer subtype. Clarification of the cancer risks in the syndrome is essential.
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