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  • 1
    Publication Date: 2016-02-06
    Description: Motivation: Analysing the joint association between a large set of responses and predictors is a fundamental statistical task in integrative genomics, exemplified by numerous expression Quantitative Trait Loci (eQTL) studies. Of particular interest are the so-called ‘ hotspots ’ , important genetic variants that regulate the expression of many genes. Recently, attention has focussed on whether eQTLs are common to several tissues, cell-types or, more generally, conditions or whether they are specific to a particular condition. Results: We have implemented MT-HESS, a Bayesian hierarchical model that analyses the association between a large set of predictors, e.g. SNPs, and many responses, e.g. gene expression, in multiple tissues, cells or conditions. Our Bayesian sparse regression algorithm goes beyond ‘ one-at-a-time ’ association tests between SNPs and responses and uses a fully multivariate model search across all linear combinations of SNPs, coupled with a model of the correlation between condition/tissue-specific responses. In addition, we use a hierarchical structure to leverage shared information across different genes, thus improving the detection of hotspots. We show the increase of power resulting from our new approach in an extensive simulation study. Our analysis of two case studies highlights new hotspots that would remain undetected by standard approaches and shows how greater prediction power can be achieved when several tissues are jointly considered. Availability and implementation: C ++ source code and documentation including compilation instructions are available under GNU licence at http://www.mrc-bsu.cam.ac.uk/software/ . Contact: sylvia.richardson@mrc-bsu.cam.ac.uk or lb664@cam.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 2
    Publication Date: 2015-07-15
    Description: Progesterone receptor (PR) expression is used as a biomarker of oestrogen receptor-alpha (ERalpha) function and breast cancer prognosis. Here we show that PR is not merely an ERalpha-induced gene target, but is also an ERalpha-associated protein that modulates its behaviour. In the presence of agonist ligands, PR associates with ERalpha to direct ERalpha chromatin binding events within breast cancer cells, resulting in a unique gene expression programme that is associated with good clinical outcome. Progesterone inhibited oestrogen-mediated growth of ERalpha(+) cell line xenografts and primary ERalpha(+) breast tumour explants, and had increased anti-proliferative effects when coupled with an ERalpha antagonist. Copy number loss of PGR, the gene coding for PR, is a common feature in ERalpha(+) breast cancers, explaining lower PR levels in a subset of cases. Our findings indicate that PR functions as a molecular rheostat to control ERalpha chromatin binding and transcriptional activity, which has important implications for prognosis and therapeutic interventions.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4650274/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4650274/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mohammed, Hisham -- Russell, I Alasdair -- Stark, Rory -- Rueda, Oscar M -- Hickey, Theresa E -- Tarulli, Gerard A -- Serandour, Aurelien A -- Birrell, Stephen N -- Bruna, Alejandra -- Saadi, Amel -- Menon, Suraj -- Hadfield, James -- Pugh, Michelle -- Raj, Ganesh V -- Brown, Gordon D -- D'Santos, Clive -- Robinson, Jessica L L -- Silva, Grace -- Launchbury, Rosalind -- Perou, Charles M -- Stingl, John -- Caldas, Carlos -- Tilley, Wayne D -- Carroll, Jason S -- 242664/European Research Council/International -- 5P30CA142543/CA/NCI NIH HHS/ -- A10178/Cancer Research UK/United Kingdom -- England -- Nature. 2015 Jul 16;523(7560):313-7. doi: 10.1038/nature14583. Epub 2015 Jul 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK. ; Dame Roma Mitchell Cancer Research Laboratories and the Adelaide Prostate Cancer Research Centre, School of Medicine, Hanson Institute Building, University of Adelaide, Adelaide, South Australia 5005, Australia. ; Department of Urology, University of Texas, Southwestern Medical Center at Dallas, Dallas, Texas 75390, USA. ; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 450 West Drive, CB7295, Chapel Hill, North Carolina 27599, USA. ; 1] Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK [2] Cambridge Breast Unit, Addenbrooke's Hospital, Cambridge University Hospital NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 2QQ, UK [3] Cambridge Experimental Cancer Medicine Centre, Cambridge CB2 0RE, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26153859" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Breast Neoplasms/drug therapy/*genetics/*metabolism/pathology ; Cell Line, Tumor ; Cell Proliferation/drug effects ; Chromatin/drug effects/genetics/metabolism ; DNA Copy Number Variations/genetics ; Disease Progression ; Estrogen Receptor alpha/antagonists & inhibitors/*metabolism ; Estrogens/metabolism/pharmacology ; Female ; *Gene Expression Regulation, Neoplastic/drug effects ; Humans ; Ligands ; Mice ; Progesterone/metabolism/pharmacology ; Protein Binding/drug effects ; Receptors, Progesterone/genetics/*metabolism ; Transcription, Genetic/drug effects ; Xenograft Model Antitumor Assays
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2015-08-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mohammed, Hisham -- Russell, I Alasdair -- Stark, Rory -- Rueda, Oscar M -- Hickey, Theresa E -- Tarulli, Gerard A -- Serandour, Aurelien A -- Birrell, Stephen N -- Bruna, Alejandra -- Saadi, Amel -- Menon, Suraj -- Hadfield, James -- Pugh, Michelle -- Raj, Ganesh V -- Brown, Gordon D -- D'Santos, Clive -- Robinson, Jessica L L -- Silva, Grace -- Launchbury, Rosalind -- Perou, Charles M -- Stingl, John -- Caldas, Carlos -- Tilley, Wayne D -- Carroll, Jason S -- England -- Nature. 2015 Oct 1;526(7571):144. doi: 10.1038/nature14959. Epub 2015 Aug 5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26245370" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
    Electronic Resource
    Electronic Resource
    Bradford : Emerald
    Compel 15 (1996), S. 48-62 
    ISSN: 0332-1649
    Source: Emerald Fulltext Archive Database 1994-2005
    Topics: Electrical Engineering, Measurement and Control Technology , Mathematics
    Notes: Presents a new method to compute simultaneously the near and the far field in electromagnetic 3D scattering problems. In this approach a bounded spherical domain contains all the inhomogeneous objects and divides the whole space into two different regions. In both regions the field is expressed as a linear expansion with the same unknown coefficients. Gives the field as an exact infinite expansion of vector spherical harmonics in the outer region. Computes the basis functions using finite elements in the inner region. Finally, obtains the coefficients of the two expansions by matching the inner and the outer fields on the spherical interface.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Amsterdam : Elsevier
    Comparative Biochemistry and Physiology -- Part B: Biochemistry and 100 (1991), S. 153-159 
    ISSN: 0305-0491
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    Amsterdam : Elsevier
    Mechanisms of Development 43 (1993), S. 49-56 
    ISSN: 0925-4773
    Keywords: Forelimb development ; Forelimb regeneration ; Myosin isoform ; Thyroid hormone regulation
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology
    Type of Medium: Electronic Resource
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  • 7
    ISSN: 0014-5793
    Keywords: Anguilla anguilla ; Gel eleetrophoresis ; Myosin ; Myosin subunit composition
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology , Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    Springer
    Human genetics 〈Berlin〉 55 (1980), S. 23-29 
    ISSN: 1432-1203
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary Sequential cytogenetic studies of four patients with ataxia telangiectasia showed the progressive development of lymphocyte clones, each marked with a rearranged chromosome 14. Initial studies had shown random chromosomal breaks and rearrangements. Later studies in all patients showed nonrandom rearrangement of chromosome 14 with a breakpoint at 14q12 and with the distal segment translocated to either chromosome 14 or 7. The proportion of circulating lymphocytes carrying the marker tended to increase with time, accounting for the majority of the lymphocytes eventually in one case. The marked lymphocyte clones evolved further, as a result of loss of the small centric portions of the rearranged chromosome 14 (14pter→14q12). Perhaps the abnormal clones in ataxia telangiectasia escape immunologic surveillance and flourish in an immunologically impaired environment. Subsequent to the loss of the centric portion of the rearranged chromosome 14, the cells may acquire additional capabilities that enhance malignant transformation.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    Springer
    Journal of thermal analysis and calorimetry 34 (1988), S. 269-277 
    ISSN: 1572-8943
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Description / Table of Contents: Zusammenfassung Aus einer Aluminiumnitratlösung wurde mit Ammoniaklösung durch Präzipitation Aluminiumhydroxid gefertigt. Mittels TG, DTA und DTG wurde die thermische Zersetzung des festen Hydroxides untersucht. Die Probe wurde Temperaturen zwischen 200 °C und 1000 °C ausgesetzt. Die Phasenzusammensetzung der erhaltenen Produkte wurde mittels Röntgenphasenanalyse untersucht und die Oberflächenstrukturen verglichen.
    Abstract: Резюме Методами ТГ, ДТГ и ДТА и зучено термическое разложение осажденн ой гидроокиси алюминия, полученной из растворов нитрата алюминия и аммиака. Образец терм ически обрабатывался в темп ературном интервале 200–1000°. Фазовый состав образ ующихся при этом продуктов был изучен с помощью рентгенофа зового анализа и сопоставле на их удельная площадь поверхности.
    Notes: Abstract Aluminium hydroxide was prepared by precipitation from aluminium nitrate solution with ammonia solution. Thermal decomposition of the solid hydroxide was studied by means of TG, DTG and DTA. The sample was thermally treated in the temperature interval between 200 °C and 1000 °C. X-ray phase analysis was used to study the phase compositions of the resulting products, and their surface areas were compared.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    Hoboken, NJ : Wiley-Blackwell
    AIChE Journal 27 (1981), S. 754-761 
    ISSN: 0001-1541
    Keywords: Chemistry ; Chemical Engineering
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The phase equilibria of the systems are discussed: (i)n-butanol-acetic acid-water and n-heptane(ii)Water-acetic acid-benzene and carbon tetrachloride(iii)Water-methanol-p.cresol and methyl naphthalene have been studied and a correlating procedure has been developed that utilizes binary and ternary experimental data to predict the composition of the quaternary equilibrium mixtures. Allowance is made for the different salting effects and the agreement between the experimental and predicted quaternary data is in all cases very good.
    Additional Material: 13 Ill.
    Type of Medium: Electronic Resource
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