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  • 1
    Publication Date: 2013-06-06
    Description: Motivation: As RNA interference is becoming a standard method for targeted gene perturbation, computational approaches to reverse engineer parts of biological networks based on measurable effects of RNAi become increasingly relevant. The vast majority of these methods use gene expression data, but little attention has been paid so far to other data types. Results : Here we present a method, which can infer gene networks from high-dimensional phenotypic perturbation effects on single cells recorded by time-lapse microscopy. We use data from the Mitocheck project to extract multiple shape, intensity and texture features at each frame. Features from different cells and movies are then aligned along the cell cycle time. Subsequently we use Dynamic Nested Effects Models (dynoNEMs) to estimate parts of the network structure between perturbed genes via a Markov Chain Monte Carlo approach. Our simulation results indicate a high reconstruction quality of this method. A reconstruction based on 22 gene knock downs yielded a network, where all edges could be explained via the biological literature. Availability : The implementation of dynoNEMs is part of the Bioconductor R-package nem . Contact: frohlich@bit.uni-bonn.de 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: 2012-06-24
    Description: Motivation: There have been many successful experimental and bioinformatics efforts to elucidate transcription factor (TF)-target networks in several organisms. For many organisms, these annotations are complemented by miRNA-target networks of good quality. Attempts that use these networks in combination with gene expression data to draw conclusions on TF or miRNA activity are, however, still relatively sparse. Results: In this study, we propose Bayesian inference of regulation of transcriptional activity ( BIRTA ) as a novel approach to infer both, TF and miRNA activities, from combined miRNA and mRNA expression data in a condition specific way. That means our model explains mRNA and miRNA expression for a specific experimental condition by the activities of certain miRNAs and TFs, hence allowing for differentiating between switches from active to inactive (negative switch) and inactive to active (positive switch) forms. Extensive simulations of our model reveal its good prediction performance in comparison to other approaches. Furthermore, the utility of BIRTA is demonstrated at the example of Escherichia coli data comparing aerobic and anaerobic growth conditions, and by human expression data from pancreas and ovarian cancer. Availability and implementation: The method is implemented in the R package birta , which is freely available for Bio-conductor (〉=2.10) on http://www.bioconductor.org/packages/release/bioc/html/birta.html . Contact: frohlich@bit.uni-bonn.de 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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  • 3
    Publication Date: 2009-05-30
    Description: Chronic viral infection is often associated with the dysfunction of virus-specific T cells. Our studies using Il21r-deficient (Il21r-/-) mice now suggest that interleukin-21 (IL-21) is critical for the long-term maintenance and functionality of CD8+ T cells and the control of chronic lymphocytic choriomeningitis virus infection in mice. Cell-autonomous IL-21 receptor (IL-21R)-dependent signaling by CD8+ T cells was required for sustained cell proliferation and cytokine production during chronic infection. Il21r-/- mice showed normal CD8+ T cell expansion, effector function, memory homeostasis, and recall responses during acute and after resolved infection with several other nonpersistent viruses. These data suggest that IL-21R signaling is required for the maintenance of polyfunctional T cells during chronic viral infections and have implications for understanding the immune response to other persisting antigens, such as tumors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Frohlich, Anja -- Kisielow, Jan -- Schmitz, Iwana -- Freigang, Stefan -- Shamshiev, Abdijapar T -- Weber, Jacqueline -- Marsland, Benjamin J -- Oxenius, Annette -- Kopf, Manfred -- New York, N.Y. -- Science. 2009 Jun 19;324(5934):1576-80. doi: 10.1126/science.1172815. Epub 2009 May 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Biomedicine, Institute of Integrative Biology, ETH Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19478140" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; CD8-Positive T-Lymphocytes/*immunology ; Chronic Disease ; Humans ; Immunologic Memory ; Interferon-gamma/biosynthesis ; Lymphocytic Choriomeningitis/*immunology ; Mice ; Mice, Inbred C57BL ; Peptide Fragments/biosynthesis ; Receptors, Interleukin-21/*immunology ; Signal Transduction
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2010-07-21
    Description: The Centre for the AIDS Program of Research in South Africa (CAPRISA) 004 trial assessed the effectiveness and safety of a 1% vaginal gel formulation of tenofovir, a nucleotide reverse transcriptase inhibitor, for the prevention of HIV acquisition in women. A double-blind, randomized controlled trial was conducted comparing tenofovir gel (n = 445 women) with placebo gel (n = 444 women) in sexually active, HIV-uninfected 18- to 40-year-old women in urban and rural KwaZulu-Natal, South Africa. HIV serostatus, safety, sexual behavior, and gel and condom use were assessed at monthly follow-up visits for 30 months. HIV incidence in the tenofovir gel arm was 5.6 per 100 women-years (person time of study observation) (38 out of 680.6 women-years) compared with 9.1 per 100 women-years (60 out of 660.7 women-years) in the placebo gel arm (incidence rate ratio = 0.61; P = 0.017). In high adherers (gel adherence 〉 80%), HIV incidence was 54% lower (P = 0.025) in the tenofovir gel arm. In intermediate adherers (gel adherence 50 to 80%) and low adherers (gel adherence 〈 50%), the HIV incidence reduction was 38 and 28%, respectively. Tenofovir gel reduced HIV acquisition by an estimated 39% overall, and by 54% in women with high gel adherence. No increase in the overall adverse event rates was observed. There were no changes in viral load and no tenofovir resistance in HIV seroconverters. Tenofovir gel could potentially fill an important HIV prevention gap, especially for women unable to successfully negotiate mutual monogamy or condom use.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3001187/" 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/PMC3001187/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Abdool Karim, Quarraisha -- Abdool Karim, Salim S -- Frohlich, Janet A -- Grobler, Anneke C -- Baxter, Cheryl -- Mansoor, Leila E -- Kharsany, Ayesha B M -- Sibeko, Sengeziwe -- Mlisana, Koleka P -- Omar, Zaheen -- Gengiah, Tanuja N -- Maarschalk, Silvia -- Arulappan, Natasha -- Mlotshwa, Mukelisiwe -- Morris, Lynn -- Taylor, Douglas -- CAPRISA 004 Trial Group -- AI51794/AI/NIAID NIH HHS/ -- D43 TW000231/TW/FIC NIH HHS/ -- D43 TW000231-17/TW/FIC NIH HHS/ -- D43TW00231/TW/FIC NIH HHS/ -- U01 AI068619/AI/NIAID NIH HHS/ -- U01AI068633/AI/NIAID NIH HHS/ -- U01AI46749/AI/NIAID NIH HHS/ -- U19 AI051794/AI/NIAID NIH HHS/ -- U19 AI051794-05/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2010 Sep 3;329(5996):1168-74. doi: 10.1126/science.1193748. Epub 2010 Jul 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for the AIDS Program of Research in South Africa (CAPRISA), Durban 4013, South Africa. caprisa@ukzn.ac.za〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20643915" target="_blank"〉PubMed〈/a〉
    Keywords: Adenine/administration & dosage/adverse effects/*analogs & ; derivatives/therapeutic use ; Administration, Intravaginal ; Adolescent ; Adult ; Anti-HIV Agents/*administration & dosage/adverse effects/therapeutic use ; Anti-Infective Agents, Local/administration & dosage/adverse effects/therapeutic ; use ; Double-Blind Method ; Drug Resistance, Viral ; Female ; HIV Infections/epidemiology/*prevention & control ; HIV-1/*drug effects/physiology ; Humans ; Incidence ; Organophosphonates/*administration & dosage/adverse effects/therapeutic use ; Patient Compliance ; Pregnancy ; Pregnancy Outcome ; Rural Population/statistics & numerical data ; Sexual Behavior ; South Africa/epidemiology ; Tenofovir ; Urban Population/statistics & numerical data ; Vaginal Creams, Foams, and Jellies ; Viral Load ; Young Adult
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2014-07-22
    Description: FOXP3(+) regulatory T cells (Treg cells) are abundant in the intestine, where they prevent dysregulated inflammatory responses to self and environmental stimuli. It is now appreciated that Treg cells acquire tissue-specific adaptations that facilitate their survival and function; however, key host factors controlling the Treg response in the intestine are poorly understood. The interleukin (IL)-1 family member IL-33 is constitutively expressed in epithelial cells at barrier sites, where it functions as an endogenous danger signal, or alarmin, in response to tissue damage. Recent studies in humans have described high levels of IL-33 in inflamed lesions of inflammatory bowel disease patients, suggesting a role for this cytokine in disease pathogenesis. In the intestine, both protective and pathological roles for IL-33 have been described in murine models of acute colitis, but its contribution to chronic inflammation remains ill defined. Here we show in mice that the IL-33 receptor ST2 is preferentially expressed on colonic Treg cells, where it promotes Treg function and adaptation to the inflammatory environment. IL-33 signalling in T cells stimulates Treg responses in several ways. First, it enhances transforming growth factor (TGF)-beta1-mediated differentiation of Treg cells and, second, it provides a necessary signal for Treg-cell accumulation and maintenance in inflamed tissues. Strikingly, IL-23, a key pro-inflammatory cytokine in the pathogenesis of inflammatory bowel disease, restrained Treg responses through inhibition of IL-33 responsiveness. These results demonstrate a hitherto unrecognized link between an endogenous mediator of tissue damage and a major anti-inflammatory pathway, and suggest that the balance between IL-33 and IL-23 may be a key controller of intestinal immune responses.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4339042/" 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/PMC4339042/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schiering, Chris -- Krausgruber, Thomas -- Chomka, Agnieszka -- Frohlich, Anja -- Adelmann, Krista -- Wohlfert, Elizabeth A -- Pott, Johanna -- Griseri, Thibault -- Bollrath, Julia -- Hegazy, Ahmed N -- Harrison, Oliver J -- Owens, Benjamin M J -- Lohning, Max -- Belkaid, Yasmine -- Fallon, Padraic G -- Powrie, Fiona -- 086335/Wellcome Trust/United Kingdom -- 095688/Wellcome Trust/United Kingdom -- 097109/Wellcome Trust/United Kingdom -- 099814/Wellcome Trust/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2014 Sep 25;513(7519):564-8. doi: 10.1038/nature13577. Epub 2014 Jul 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK [2] Division of Molecular Immunology, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK (C.S.); Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, University at Buffalo (SUNY), Buffalo, New York 14214-3000, USA (E.A.W.). [3]. ; 1] Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK [2]. ; Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK. ; Experimental Immunology, Department of Rheumatology and Clinical Immunology, Charite - University Medicine Berlin, and German Rheumatism Research Center (DRFZ), D-10117 Berlin, Germany. ; 1] Program in Barrier Immunity and Repair, Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA [2] Division of Molecular Immunology, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK (C.S.); Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, University at Buffalo (SUNY), Buffalo, New York 14214-3000, USA (E.A.W.). ; Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK. ; Program in Barrier Immunity and Repair, Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA. ; Trinity Biomedical Sciences Institute, Trinity College Dublin, Pearse Street, Dublin 2, Ireland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25043027" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Colitis/immunology/pathology ; Colon/cytology/immunology/pathology ; Disease Models, Animal ; Female ; Immunity, Mucosal ; Inflammation/immunology/metabolism/pathology ; Interleukin-23/immunology ; Interleukin-33 ; Interleukins/antagonists & inhibitors/*immunology/metabolism ; Intestines/*cytology/*immunology/pathology ; Male ; Mice ; Mice, Inbred C57BL ; Receptors, Interleukin/metabolism ; Signal Transduction/immunology ; T-Lymphocytes, Regulatory/cytology/*immunology ; Thymus Gland/cytology ; Transforming Growth Factor beta/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 6
    Publication Date: 2012-02-11
    Description: Pathogen-associated molecular patterns decisively influence antiviral immune responses, whereas the contribution of endogenous signals of tissue damage, also known as damage-associated molecular patterns or alarmins, remains ill defined. We show that interleukin-33 (IL-33), an alarmin released from necrotic cells, is necessary for potent CD8(+) T cell (CTL) responses to replicating, prototypic RNA and DNA viruses in mice. IL-33 signaled through its receptor on activated CTLs, enhanced clonal expansion in a CTL-intrinsic fashion, determined plurifunctional effector cell differentiation, and was necessary for virus control. Moreover, recombinant IL-33 augmented vaccine-induced CTL responses. Radio-resistant cells of the splenic T cell zone produced IL-33, and efficient CTL responses required IL-33 from radio-resistant cells but not from hematopoietic cells. Thus, alarmin release by radio-resistant cells orchestrates protective antiviral CTL responses.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bonilla, Weldy V -- Frohlich, Anja -- Senn, Karin -- Kallert, Sandra -- Fernandez, Marylise -- Johnson, Susan -- Kreutzfeldt, Mario -- Hegazy, Ahmed N -- Schrick, Christina -- Fallon, Padraic G -- Klemenz, Roman -- Nakae, Susumu -- Adler, Heiko -- Merkler, Doron -- Lohning, Max -- Pinschewer, Daniel D -- New York, N.Y. -- Science. 2012 Feb 24;335(6071):984-9. doi: 10.1126/science.1215418. Epub 2012 Feb 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology and Immunology, University of Geneva, 1 rue Michel Servet, 1211 Geneva 4, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22323740" target="_blank"〉PubMed〈/a〉
    Keywords: Adoptive Transfer ; Animals ; Arenaviridae Infections/*immunology/pathology ; Cell Differentiation ; Gene Expression Profiling ; Herpesviridae Infections/*immunology ; Interleukin-33 ; Interleukins/genetics/immunology/*metabolism ; Lymphocyte Activation ; Lymphocytic choriomeningitis virus/*immunology/physiology ; Mice ; Mice, Transgenic ; Necrosis ; Receptors, Interleukin/genetics/metabolism ; Recombinant Proteins/immunology ; Rhadinovirus/*immunology ; Signal Transduction ; Stromal Cells/immunology/metabolism ; T-Lymphocytes, Cytotoxic/*immunology/transplantation ; Tumor Virus Infections/immunology ; Up-Regulation ; Vaccinia virus/immunology ; Virus Replication
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 1971-01-01
    Print ISSN: 0029-554X
    Electronic ISSN: 1878-3759
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Physics
    Published by Elsevier
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  • 8
    Publication Date: 1971-12-01
    Print ISSN: 0029-554X
    Electronic ISSN: 1878-3759
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Physics
    Published by Elsevier
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  • 9
    Publication Date: 2015-04-01
    Description: During infection, the release of damage-associated molecular patterns, so-called “alarmins,” orchestrates the immune response. The alarmin IL-33 plays a role in a wide range of pathologies. Upon release, IL-33 signals through its receptor ST2, which reportedly is expressed only on CD4+ T cells of the Th2 and regulatory subsets. Here...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 10
    Publication Date: 1989-01-01
    Print ISSN: 0090-4341
    Electronic ISSN: 1432-0703
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Medicine
    Published by Springer
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