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  • 1
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    Induction of AIDS in rhesus monkeys by molecularly cloned simian immunodeficiency virus (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-06-01
    Description: Better understanding of the pathogenesis of acquired immunodeficiency syndrome (AIDS) would be greatly facilitated by a relevant animal model that uses molecularly cloned virus of defined sequence to induce the disease. Such a system would also be of great value for AIDS vaccine research. An infectious molecular clone of simian immunodeficiency virus (SIV) was identified that induces AIDS in common rhesus monkeys in a time frame suitable for laboratory investigation. These results provide another strong link in the chain of evidence for the viral etiology of AIDS. More importantly, they define a system for molecular dissection of the determinants of AIDS pathogenesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kestler, H -- Kodama, T -- Ringler, D -- Marthas, M -- Pedersen, N -- Lackner, A -- Regier, D -- Sehgal, P -- Daniel, M -- King, N -- AI25328/AI/NIAID NIH HHS/ -- RR00168/RR/NCRR NIH HHS/ -- RR00169/RR/NCRR NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1990 Jun 1;248(4959):1109-12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉New England Regional Primate Research Center, Harvard Medical School, Southborough, MA 01772.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2160735" target="_blank"〉PubMed〈/a〉
    Keywords: *Acquired Immunodeficiency Syndrome ; Animals ; Antibodies, Viral/biosynthesis ; Cloning, Molecular ; *Disease Models, Animal ; Leukocytes, Mononuclear/microbiology ; Macaca mulatta ; Macrophages/microbiology ; Opportunistic Infections/etiology ; *Retroviridae Infections/complications/immunology ; *Simian Immunodeficiency Virus/genetics/immunology/isolation & ; purification/pathogenicity ; Transfection ; Virus Replication
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
    Electronic Resource
    Electronic Resource
    The Listeria monocytogenesiap gene as an indicator gene for the study of PrfA-dependent regulation (1997)
    Springer
    Molecular genetics and genomics 256 (1997), S. 54-62 
    Details
    ISSN: 1617-4623
    Keywords: Key wordsListeria monocytogenes ; p60 protein ; PrfA protein ; Regulation of gene expression ; Cell division
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The iap gene of Listeria monocytogenes encodes the extracellular protein p60, which possesses a murein hydrolase activity necessary for septum separation. We constructed L. monocytogenes EGD strains harbouring plasmids that carry the iap gene under the control of the PrfA-regulated promoters of the L. monocytogenes genes hly, mpl, and actA. After insertional inactivation of the chromosomal iap gene in L. monocytogenes EGD, p60 synthesis was strictly dependent on PrfA. Elevated temperature (40 °C) enhanced synthesis of p60 in L. monocytogenes when the iap gene was under the control of the hly promoter; this appeared to be associated with increased synthesis of PrfA at this temperature. Synthesis of p60 in L. monocytogenes was significantly lower when the iap gene was placed under the control of the actA or the mpl promoter. Transcription of the iap gene was repressed in L. monocytogenes in the presence of PrfA when iap expression was under the control of the prfA promoter P2. Under the control of the hly promoter the gene produced low levels of secreted p60 in the presence of low amounts of PrfA, and this in turn led to the generation of long listerial cell filaments consisting of bacteria that had failed to separate. Overexpression of p60 in the presence of high levels of PrfA caused formation of single cells, which showed reduced viability depending on the level of secreted p60. These data suggest that the iap gene may be a valuable tool for monitoring virulence gene regulation by PrfA under in vivo conditions, without disturbing the integrity of the infected host cells.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004380050545
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    Paper (German National Licenses)
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  • 3
    Electronic Resource
    Electronic Resource
    Thenef gene of SIVmac239 is necessary for efficient growth in H9 cells (1996)
    Springer
    Journal of biomedical science 3 (1996), S. 422-434 
    Details
    ISSN: 1423-0127
    Keywords: nef ; SIVmac239 ; H9 ; Replication ; CD4
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract AIDS viruses require an intact functionalnef gene in order to inducedisease. The nonpathogenic molecular cloned virus SIVmac239nef-deletion encodes a truncatednef gene. This attenuated reading frame is expressed both in vitro and in a virus-infected animal in vivo. Encoding the first 58 amino acids of Nef, the reading frame retained its ability to down-modulate CD4 from the surface of T cells. CD4-down-modulated stable cell lines expressing full-length and truncatednef genes were significantly less infected by SIV. SIV-mac239nef-open and SIVmacnef-deletion encoding a truncatednef clearly differed in replication kinetics in H9 cells and H9-derived cell lines. SIV-mac239nef-deletion replication was delayed in H9.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02258046
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  • 4
    Electronic Resource
    Electronic Resource
    Cardiac vulnerability assessment from electrical microvariability of high-resolution electrocardiogram (2000)
    Springer
    Medical & biological engineering & computing 38 (2000), S. 88-92 
    Details
    ISSN: 1741-0444
    Keywords: High-resolution ECG ; QRS variability ; ST-T variability ; adaptive filtering ; ventricular tachycardia
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Notes: Abstract Patients susceptible to malignant arrhythmias often have an increased beat-to-beat variation of the T-wave of the electrocardiogram. Variability analysis of the T-wave is increasingly used for non-invasive risk assessment. The aim of this study is to evaluate intra-QRS beat-to-beat signal variation and to compare it to ST-T variation. The beat-to-beat, microvolt variation of the QRS and the ST-T segment from 44 patients with coronary heart disease at high risk of suffering from malignant arrhythmias and from 51 healthy volunteers are compared. Variation analysis is carried out on 250 consecutive sinus beats from high-resolution electrocardiograms. The individual beats are filtered using a waveform-independent, cubic spline-filter. A variability index of the QRS and ST-T segments is calculated as the integrated standard deviation of corresponding samples inside the area of interest. Patients at risk of suffering from malignant arrhythmias have a significantly higher variability index of both the QRS (median 44.5 ms against 34.7 ms, p〈0.001) and the ST-T segment (median 20.5 ms against 9.8 ms, p〈0.001) compared to the group of healthy subjects. The discriminative ability of the odds variability indices of the QRS and ST-T segments are not statistically different, the ratios being 7.8 (QRS) and 12.6 (ST-T). We conclude that patients at high risk of suffering from malignant arrhythmias are characterised by an increased beat-to-beat microvolt variation of both the QRS and the ST-T segment. Further studies are necessary to evaluate the prognostic potential of depolarisation variability.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02344694
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  • 5
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    A candidate live inactivatable attenuated vaccine for AIDS. (1996)
    National Academy of Sciences
    Details
    Publication Date: 1996-09-03
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 6
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    Automated array-based genomic profiling in chronic lymphocytic leukemia: Development of a clinical tool and discovery of recurrent genomic alterations (2004)
    National Academy of Sciences
    Details
    Publication Date: 2004-01-16
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 7
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    GiANT: gene set uncertainty in enrichment analysis (2016)
    Oxford University Press
    Details
    Publication Date: 2016-06-16
    Description: : Over the past years growing knowledge about biological processes and pathways revealed complex interaction networks involving many genes. In order to understand these networks, analysis of differential expression has continuously moved from single genes towards the study of gene sets. Various approaches for the assessment of gene sets have been developed in the context of gene set analysis (GSA). These approaches are bridging the gap between raw measurements and semantically meaningful terms. We present a novel approach for assessing uncertainty in the definition of gene sets. This is an essential step when new gene sets are constructed from domain knowledge or given gene sets are suspected to be affected by uncertainty. Quantification of uncertainty is implemented in the R-package GiANT. We also included widely used GSA methods, embedded in a generic framework that can readily be extended by custom methods. The package provides an easy to use front end and allows for fast parallelization. Availability and implementation: The package GiANT is available on CRAN. Contacts: hans.kestler@leibniz-fli.de or hans.kestler@uni-ulm.de
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 8
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    Sputnik: ad hoc distributed computation (2015)
    Oxford University Press
    Details
    Publication Date: 2015-04-12
    Description: Motivation : In bioinformatic applications, computationally demanding algorithms are often parallelized to speed up computation. Nevertheless, setting up computational environments for distributed computation is often tedious. Aim of this project were the lightweight ad hoc set up and fault-tolerant computation requiring only a Java runtime, no administrator rights, while utilizing all CPU cores most effectively. Results: The Sputnik framework provides ad hoc distributed computation on the Java Virtual Machine which uses all supplied CPU cores fully. It provides a graphical user interface for deployment setup and a web user interface displaying the current status of current computation jobs. Neither a permanent setup nor administrator privileges are required. We demonstrate the utility of our approach on feature selection of microarray data. Availability and implementation : The Sputnik framework is available on Github http://github.com/sysbio-bioinf/sputnik under the Eclipse Public License. Contact : hkestler@fli-leibniz.de or hans.kestler@uni-ulm.de Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 9
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    BiTrinA--multiscale binarization and trinarization with quality analysis (2016)
    Oxford University Press
    Details
    Publication Date: 2016-02-02
    Description: Motivation: When processing gene expression profiles or other biological data, it is often required to assign measurements to distinct categories (e.g. ‘high’ and ‘low’ and possibly ‘intermediate’). Subsequent analyses strongly depend on the results of this quantization. Poor quantization will have potentially misleading effects on further investigations. We propose the BiTrinA package that integrates different multiscale algorithms for binarization and for trinarization of one-dimensional data with methods for quality assessment and visualization of the results. By identifying measurements that show large variations over different time points or conditions, this quality assessment can determine candidates that are related to the specific experimental setting. Availability and implementation: BiTrinA is freely available on CRAN. Contact: hans.kestler@leibniz-fli.de or hans.kestler@uni-ulm.de Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 10
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    Cooperative development of logical modelling standards and tools with CoLoMoTo (2015)
    Oxford University Press
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    Publication Date: 2015-04-03
    Description: The identification of large regulatory and signalling networks involved in the control of crucial cellular processes calls for proper modelling approaches. Indeed, models can help elucidate properties of these networks, understand their behaviour and provide (testable) predictions by performing in silico experiments. In this context, qualitative, logical frameworks have emerged as relevant approaches, as demonstrated by a growing number of published models, along with new methodologies and software tools. This productive activity now requires a concerted effort to ensure model reusability and interoperability between tools. Following an outline of the logical modelling framework, we present the most important achievements of the Consortium for Logical Models and Tools, along with future objectives. Our aim is to advertise this open community, which welcomes contributions from all researchers interested in logical modelling or in related mathematical and computational developments. Contact: contact@colomoto.org
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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