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On the excitation of ULF waves by solar wind pressure enhancements

P. T. I. Eriksson, L. G. Blomberg, S. Schaefer, K.-H. Glassmeier
2006 Annales Geophysicae  
</strong> We study the onset and development of an ultra low frequency (ULF) pulsation excited by a storm sudden commencement.  ...  On 30 August 2001, 14:10 UT, the Cluster spacecraft are located in the dayside magnetosphere and observe the excitation of a ULF pulsation by a threefold enhancement in the solar wind dynamic pressure.  ...  Eriksson et al.: ULF oscillations with Cluster P. T. I.Eriksson et al.: ULF oscillations with Cluster  ... 
doi:10.5194/angeo-24-3161-2006 fatcat:cvoohmhvmfeahbgckxqo4qbhje

Rekommunalisierung: Renaissance öffentlicher Unternehmen?

Felix Höffler, Christina Schaefer, Ulf Papenfuß, Martin T. W. Rosenfeld, Gerd Landsberg
2013 Wirtschaftsdienst  
Christina Schaefer, Ulf Papenfuß Renaissance öffentlicher Unternehmen?  ...  Ulf Papenfuß ist dort wissen- schaftlicher Mitarbeiter.  ... 
doi:10.1007/s10273-013-1489-1 fatcat:gq7qzzvi4fgydn6qtshdd3aqfy

dPORE-miRNA: Polymorphic Regulation of MicroRNA Genes

Sebastian Schmeier, Ulf Schaefer, Cameron R. MacPherson, Vladimir B. Bajic, Christos Ouzounis
2011 PLoS ONE  
MicroRNAs (miRNAs) are short non-coding RNA molecules that act as post-transcriptional regulators and affect the regulation of protein-coding genes. Mostly transcribed by PolII, miRNA genes are regulated at the transcriptional level similarly to protein-coding genes. In this study we focus on human miRNAs. These miRNAs are involved in a variety of pathways and can affect many diseases. Our interest is on possible deregulation of the transcription initiation of the miRNA encoding genes, which is
more » ... facilitated by variations in the genomic sequence of transcriptional control regions (promoters). Methodology: Our aim is to provide an online resource to facilitate the investigation of the potential effects of single nucleotide polymorphisms (SNPs) on miRNA gene regulation. We analyzed SNPs overlapped with predicted transcription factor binding sites (TFBSs) in promoters of miRNA genes. We also accounted for the creation of novel TFBSs due to polymorphisms not present in the reference genome. The resulting changes in the original TFBSs and potential creation of new TFBSs were incorporated into the Dragon Database of Polymorphic Regulation of miRNA genes (dPORE-miRNA). Conclusions: The dPORE-miRNA database enables researchers to explore potential effects of SNPs on the regulation of miRNAs. dPORE-miRNA can be interrogated with regards to: a/miRNAs (their targets, or involvement in diseases, or biological pathways), b/SNPs, or c/transcription factors. dPORE-miRNA can be accessed at http://cbrc.kaust.edu.sa/ dpore and http://apps.sanbi.ac.za/dpore/. Its use is free for academic and non-profit users.
doi:10.1371/journal.pone.0016657 pmid:21326606 pmcid:PMC3033892 fatcat:liyqzxhgrvbeth7lm7yyh3u5fi

4.-8. März 2019

Jurica Seva, Julian Goetze, Mario Lamping, Damian Tobias Rieke, Reinhold Schaefer, Ulf Leser
2019 Datenbanksysteme für Business, Technologie und Web  
Diagnosis and treatment decisions in cancer increasingly depend on a detailed analysis of the mutational status of a patient's genome. This analysis relies on previously published information regarding the association of variations to disease progression and possible interventions. Clinicians to a large degree use biomedical search engines to obtain such information; however, the vast majority of search results in the common search engines focuses on basic science and is clinically irrelevant.
more » ... e developed the Variant-Information Search Tool, a search engine designed for the targeted search of clinically relevant publications given a mutation profile. VIST indexes all PubMed abstracts, applies advanced text mining to identify mentions of genes and variants and uses machine-learning based scoring to judge the relevancy of documents. Its functionality is available through a fast and intuitive web interface. We also performed a comparative evaluation, showing that VIST's ranking is superior to that of PubMed or vector space models.
doi:10.18420/btw2019-39 dblp:conf/btw/SevaGLRSL19 fatcat:mtnn64we6nah3mepuhguot7234

Parallel Monte-Carlo Tree Search for HPC Systems [chapter]

Tobias Graf, Ulf Lorenz, Marco Platzner, Lars Schaefers
2011 Lecture Notes in Computer Science  
Monte-Carlo Tree Search (MCTS) is a simulation-based search method that brought about great success to applications such as Computer-Go in the past few years. The power of MCTS strongly depends on the number of simulations computed per time unit and the amount of memory available to store data gathered during simulation. High-performance computing systems such as large compute clusters provide vast computation and memory resources and thus seem to be natural targets for running MCTS. However,
more » ... far only few publications deal with parallelizing MCTS for distributed memory machines. In this paper, we present a novel approach for the parallelization of MCTS which allows for an equally distributed spreading of both the work and memory load among all compute nodes within a distributed memory HPC system. We describe our approach termed UCT-Treesplit and evaluate its performance on the example of a state-of-the-art Go engine.
doi:10.1007/978-3-642-23397-5_36 fatcat:z5wfwg5tirfhhcsoacyyivdure

Mercury methylating microbial communities of boreal forest soils [article]

Jingying Xu, Moritz Buck, Karin Eklof, Omneya Ahmed Osman, Jeffra K Schaefer, Kevin Bishop, Erik Björn, Ulf Skyllberg, Stefan Bertilsson, Andrea G Bravo
2018 bioRxiv   pre-print
Skyllberg ULF, Qian JIN, Frech W, Xia K. 2002.  ...  Schaefer JK, Kronberg R-M, Morel FMM, Skyllberg U. 2014. Detection of a key Hg methylation 506 gene, hgcA , in wetland soils. Environ Microbiol Rep n/a-n/a. 507 35.  ... 
doi:10.1101/299248 fatcat:qsbrcpvwhnhnzi75jumr7q4ihu

Network analysis of microRNAs and their regulation in human ovarian cancer

Sebastian Schmeier, Ulf Schaefer, Magbubah Essack, Vladimir B Bajic
2011 BMC Systems Biology  
MicroRNAs (miRNAs) are small non-coding RNA molecules that repress the translation of messenger RNAs (mRNAs) or degrade mRNAs. These functions of miRNAs allow them to control key cellular processes such as development, differentiation and apoptosis, and they have also been implicated in several cancers such as leukaemia, lung, pancreatic and ovarian cancer (OC). Unfortunately, the specific machinery of miRNA regulation, involving transcription factors (TFs) and transcription co-factors (TcoFs),
more » ... is not well understood. In the present study we focus on computationally deciphering the underlying network of miRNAs, their targets, and their control mechanisms that have an influence on OC development. Results: We analysed experimentally verified data from multiple sources that describe miRNA influence on diseases, miRNA targeting of mRNAs, and on protein-protein interactions, and combined this data with ab initio transcription factor binding site predictions within miRNA promoter regions. From these analyses, we derived a network that describes the influence of miRNAs and their regulation in human OC. We developed a methodology to analyse the network in order to find the nodes that have the largest potential of influencing the network's behaviour (network hubs). We further show the potentially most influential miRNAs, TFs and TcoFs, showing subnetworks illustrating the involved mechanisms as well as regulatory miRNA network motifs in OC. We find an enrichment of miRNA targeted OC genes in the highly relevant pathways cell cycle regulation and apoptosis. Conclusions: We combined several sources of interaction and association data to analyse and place miRNAs within regulatory pathways that influence human OC. These results represent the first comprehensive miRNA regulatory network analysis for human OC. This suggests that miRNAs and their regulation may play a major role in OC and that further directed research in this area is of utmost importance to enhance our understanding of the molecular mechanisms underlying human cancer development and OC in particular.
doi:10.1186/1752-0509-5-183 pmid:22050994 pmcid:PMC3219655 fatcat:r7463u5jyzbqfm2irx6xbvjbsy

Mechanoenzymatics and Protective Mechanisms of Titins' Catalytic and IG Domains

Ulf Hensen, Lars Schaefer, Frauke Graeter, Joao M. Nunes, Daniel J. Mueller, Helmut Grubmueller
2010 Biophysical Journal  
1 , Lars Schaefer 1 , Frauke Graeter 1 , Joao M.  ...  Schematic showing the observed helical rearrangements during the photocycle of bacteriorhodopsin. 1176-Plat Mechanoenzymatics and Protective Mechanisms of Titins' Catalytic and IG Domains Ulf Hensen  ... 
doi:10.1016/j.bpj.2009.12.1223 fatcat:qhog2e7bcreuzbt36bghwogkke

Mutations and Binding Sites of Human Transcription Factors

Frederick Kinyua Kamanu, Yulia A. Medvedeva, Ulf Schaefer, Boris R. Jankovic, John A. C. Archer, Vladimir B. Bajic
2012 Frontiers in Genetics  
† Frederick Kinyua Kamanu and Yulia A. Medvedeva have contributed equally to this work. Mutations in any genome may lead to phenotype characteristics that determine ability of an individual to cope with adaptation to environmental challenges. In studies of human biology, among the most interesting ones are phenotype characteristics that determine responses to drug treatments, response to infections, or predisposition to specific inherited diseases. Most of the research in this field has been
more » ... used on the studies of mutation effects on the final gene products, peptides, and their alterations. Considerably less attention was given to the mutations that may affect regulatory mechanism(s) of gene expression, although these may also affect the phenotype characteristics. In this study we make a pilot analysis of mutations observed in the regulatory regions of 24,667 human RefSeq genes. Our study reveals that out of eight studied mutation types, "insertions" are the only one that in a statistically significant manner alters predicted transcription factor binding sites (TFBSs). We also find that 25 families of TFBSs have been altered by mutations in a statistically significant manner in the promoter regions we considered. Moreover, we find that the related transcription factors are, for example, prominent in processes related to intracellular signaling; cell fate; morphogenesis of organs and epithelium; development of urogenital system, epithelium, and tube; neuron fate commitment. Our study highlights the significance of studying mutations within the genes regulatory regions and opens way for further detailed investigations on this topic, particularly on the downstream affected pathways.
doi:10.3389/fgene.2012.00100 pmid:22670148 pmcid:PMC3365286 fatcat:lo2saco3bjgydo6ymnpgagk3my

DDEC: Dragon database of genes implicated in esophageal cancer

Magbubah Essack, Aleksandar Radovanovic, Ulf Schaefer, Sebastian Schmeier, Sundararajan V Seshadri, Alan Christoffels, Mandeep Kaur, Vladimir B Bajic
2009 BMC Cancer  
Esophageal cancer ranks eighth in order of cancer occurrence. Its lethality primarily stems from inability to detect the disease during the early organ-confined stage and the lack of effective therapies for advanced-stage disease. Moreover, the understanding of molecular processes involved in esophageal cancer is not complete, hampering the development of efficient diagnostics and therapy. Efforts made by the scientific community to improve the survival rate of esophageal cancer have resulted
more » ... a wealth of scattered information that is difficult to find and not easily amendable to data-mining. To reduce this gap and to complement available cancer related bioinformatic resources, we have developed a comprehensive database (Dragon Database of Genes Implicated in Esophageal Cancer) with esophageal cancer related information, as an integrated knowledge database aimed at representing a gateway to esophageal cancer related data. Description: Manually curated 529 genes differentially expressed in EC are contained in the database. We extracted and analyzed the promoter regions of these genes and complemented gene-related information with transcription factors that potentially control them. We further, precompiled text-mined and data-mined reports about each of these genes to allow for easy exploration of information about associations of EC-implicated genes with other human genes and proteins, metabolites and enzymes, toxins, chemicals with pharmacological effects, disease concepts and human anatomy. The resulting database, DDEC, has a useful feature to display potential associations that are rarely reported and thus difficult to identify. Moreover, DDEC enables inspection of potentially new 'association hypotheses' generated based on the precompiled reports. Conclusion: We hope that this resource will serve as a useful complement to the existing public resources and as a good starting point for researchers and physicians interested in EC genetics. DDEC is freely accessible to academic and non-profit users at http://apps.sanbi.ac.za/ddec/. DDEC will be updated twice a year.
doi:10.1186/1471-2407-9-219 pmid:19580656 pmcid:PMC2711974 fatcat:djgjbgajurc4dl5khhtc4x4rhu

DDESC: Dragon database for exploration of sodium channels in human

Sunil Sagar, Mandeep Kaur, Adam Dawe, Sundararajan Seshadri, Alan Christoffels, Ulf Schaefer, Aleksandar Radovanovic, Vladimir B Bajic
2008 BMC Genomics  
Sodium channels are heteromultimeric, integral membrane proteins that belong to a superfamily of ion channels. The mutations in genes encoding for sodium channel proteins have been linked with several inherited genetic disorders such as febrile epilepsy, Brugada syndrome, ventricular fibrillation, long QT syndrome, or channelopathy associated insensitivity to pain. In spite of these significant effects that sodium channel proteins/genes could have on human health, there is no publicly available
more » ... resource focused on sodium channels that would support exploration of the sodium channel related information. Results: We report here Dragon Database for Exploration of Sodium Channels in Human (DDESC), which provides comprehensive information related to sodium channels regarding different entities, such as "genes and proteins", "metabolites and enzymes", "toxins", "chemicals with pharmacological effects", "disease concepts", "human anatomy", "pathways and pathway reactions" and their potential links. DDESC is compiled based on text-and data-mining. It allows users to explore potential associations between different entities related to sodium channels in human, as well as to automatically generate novel hypotheses. Conclusion: DDESC is first publicly available resource where the information related to sodium channels in human can be explored at different levels. This database is freely accessible for academic and non-profit users via the worldwide web http://apps.sanbi.ac.za/ddesc.
doi:10.1186/1471-2164-9-622 pmid:19099596 pmcid:PMC2631582 fatcat:ch4vigfp2bay3kjaguowpciqlm

High Sensitivity TSS Prediction: Estimates of Locations Where TSS Cannot Occur

Ulf Schaefer, Rimantas Kodzius, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Vladimir B. Bajic, Timothy Ravasi
2010 PLoS ONE  
Although transcription in mammalian genomes can initiate from various genomic positions (e.g., 39UTR, coding exons, etc.), most locations on genomes are not prone to transcription initiation. It is of practical and theoretical interest to be able to estimate such collections of non-TSS locations (NTLs). The identification of large portions of NTLs can contribute to better focusing the search for TSS locations and thus contribute to promoter and gene finding. It can help in the assessment of 59
more » ... ompleteness of expressed sequences, contribute to more successful experimental designs, as well as more accurate gene annotation. Methodology: Using comprehensive collections of Cap Analysis of Gene Expression (CAGE) and other transcript data from mouse and human genomes, we developed a methodology that allows us, by performing computational TSS prediction with very high sensitivity, to annotate, with a high accuracy in a strand specific manner, locations of mammalian genomes that are highly unlikely to harbor transcription start sites (TSSs). The properties of the immediate genomic neighborhood of 98,682 accurately determined mouse and 113,814 human TSSs are used to determine features that distinguish genomic transcription initiation locations from those that are not likely to initiate transcription. In our algorithm we utilize various constraining properties of features identified in the upstream and downstream regions around TSSs, as well as statistical analyses of these surrounding regions. Conclusions: Our analysis of human chromosomes 4, 21 and 22 estimates ,46%, ,41% and ,27% of these chromosomes, respectively, as being NTLs. This suggests that on average more than 40% of the human genome can be expected to be highly unlikely to initiate transcription. Our method represents the first one that utilizes high-sensitivity TSS prediction to identify, with high accuracy, large portions of mammalian genomes as NTLs. The server with our algorithm implemented is available at http://cbrc.kaust.edu.sa/ddm/.
doi:10.1371/journal.pone.0013934 pmid:21085627 pmcid:PMC2981523 fatcat:lfs5my5xv5cejmeknfquytfmwe

Reconceptualizing Moral Disengagement as a Process: Transcending Overly Liberal and Overly Conservative Practice in the Field

Ulf Schaefer, Onno Bouwmeester
2020 Journal of Business Ethics  
Moral disengagement was initially conceptualized as a process through which people reconstrue unethical behaviors, with the effect of deactivating self-sanctions and thereby clearing the way for ethical transgressions. Our article challenges how researchers now conceptualize moral disengagement. The current literature is overly liberal, in that it mixes two related but distinct constructs-process moral disengagement and the propensity to morally disengage-creating ambiguity in the findings. It
more » ... s overly conservative, as it adopts a challengeable classification scheme of "four points in moral self-regulation" and perpetuates defining moral disengagement via a set of eight psychological mechanisms, narrowing our understanding of the phenomenon. To address these problems, we propose to define process moral disengagement intensionally (specifying the necessary and sufficient conditions for correct application of the term) as intrapsychic cognitive reasoning processes through which people selectively reconstrue a moral judgment "behavior B by actor A is morally wrong" and shift it toward becoming "behavior B is not morally wrong" or "actor A is not responsible for behavior B." This definition achieves disambiguation and increased concept clarity. We leverage the definition to motivate a classification scheme for psychological mechanisms of moral disengagement along two dimensions-reconstruing morality and reconstruing agency-and to initiate an open inventory of psychological mechanisms that specify how process moral disengagement operates.
doi:10.1007/s10551-020-04520-6 fatcat:b4epysex5vckrghwb54qcezjam

MOST: a modified MLST typing tool based on short read sequencing

Rediat Tewolde, Timothy Dallman, Ulf Schaefer, Carmen L. Sheppard, Philip Ashton, Bruno Pichon, Matthew Ellington, Craig Swift, Jonathan Green, Anthony Underwood
2016 PeerJ  
. • Ulf Schaefer analyzed the data, contributed reagents/materials/analysis tools, reviewed drafts of the paper. • Carmen L.  ... 
doi:10.7717/peerj.2308 pmid:27602279 pmcid:PMC4991843 fatcat:6nuz7qycx5gjjfxabbwy5q3ea4

Mercury methylating microbial communities of boreal forest soils

Jingying Xu, Moritz Buck, Karin Eklöf, Omneya O. Ahmed, Jeffra K. Schaefer, Kevin Bishop, Ulf Skyllberg, Erik Björn, Stefan Bertilsson, Andrea G. Bravo
2019 Scientific Reports  
The formation of the potent neurotoxic methylmercury (MeHg) is a microbially mediated process that has raised much concern because MeHg poses threats to wildlife and human health. Since boreal forest soils can be a source of MeHg in aquatic networks, it is crucial to understand the biogeochemical processes involved in the formation of this pollutant. High-throughput sequencing of 16S rRNA and the mercury methyltransferase, hgcA, combined with geochemical characterisation of soils, were used to
more » ... etermine the microbial populations contributing to MeHg formation in forest soils across Sweden. The hgcA sequences obtained were distributed among diverse clades, including Proteobacteria, Firmicutes, and Methanomicrobia, with Deltaproteobacteria, particularly Geobacteraceae, dominating the libraries across all soils examined. Our results also suggest that MeHg formation is also linked to the composition of non-mercury methylating bacterial communities, likely providing growth substrate (e.g. acetate) for the hgcA-carrying microorganisms responsible for the actual methylation process. While previous research focused on mercury methylating microbial communities of wetlands, this study provides some first insights into the diversity of mercury methylating microorganisms in boreal forest soils.
doi:10.1038/s41598-018-37383-z pmid:30679728 pmcid:PMC6345997 fatcat:ndys52jy5veqjnfwupcdm7x7oe
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