572 research outputs found
Detection of viral sequence fragments of HIV-1 subfamilies yet unknown
No full textAbstract Background Methods of determining whether or not any particular HIV-1 sequence stems - completely or in part - from some unknown HIV-1 subtype are important for the design of vaccines and molecular detection systems, as well as for epidemiological monitoring. Nevertheless, a single algorithm only, the Branching Index (BI), has been developed for this task so far. Moving along the genome of a query sequence in a sliding window, the BI computes a ratio quantifying how closely the query sequence clusters with a subtype clade. In its current version, however, the BI does not provide predicted boundaries of unknown fragments. Results We have developed Unknown Subtype Finder (USF), an algorithm based on a probabilistic model, which automatically determines which parts of an input sequence originate from a subtype yet unknown. The underlying model is based on a simple profile hidden Markov model (pHMM) for each known subtype and an additional pHMM for an unknown subtype. The emission probabilities of the latter are estimated using the emission frequencies of the known subtypes by means of a (position-wise) probabilistic model for the emergence of new subtypes. We have applied USF to SIV and HIV-1 sequences formerly classified as having emerged from an unknown subtype. Moreover, we have evaluated its performance on artificial HIV-1 recombinants and non-recombinant HIV-1 sequences. The results have been compared with the corresponding results of the BI. Conclusions Our results demonstrate that USF is suitable for detecting segments in HIV-1 sequences stemming from yet unknown subtypes. Comparing USF with the BI shows that our algorithm performs as good as the BI or better.</p
Ingo Plag, Word-Formation in English (2
No full text1. General observations Ingo Plag is Professor of English Linguistics at Heinrich-Heine-Universität Düsseldorf. He has published articles in specialized journals like Linguistics, Language or English Language and Linguistics and in works like the Yearbook of Morphology [2001], Word-Formation: An International Handbook of the Languages of Europe [2016] or Word Knowledge and Word Usage: A Cross-Disciplinary Guide to the Mental Lexicon [2017]. He is the author of Morphological Productivity: Stru..
MarVis-Pathway: integrative and exploratory pathway analysis of non-targeted metabolomics data
No full textA central aim in the evaluation of non-targeted metabolomics data is the detection of intensity patterns that differ between experimental conditions as well as the identification of the underlying metabolites and their association with metabolic pathways. In this context, the identification of metabolites based on non-targeted mass spectrometry data is a major bottleneck. In many applications, this identification needs to be guided by expert knowledge and interactive tools for exploratory data analysis can significantly support this process. Additionally, the integration of data from other omics platforms, such as DNA microarray-based transcriptomics, can provide valuable hints and thereby facilitate the identification of metabolites via the reconstruction of related metabolic pathways. We here introduce the MarVis-Pathway tool, which allows the user to identify metabolites by annotation of pathways from cross-omics data. The analysis is supported by an extensive framework for pathway enrichment and meta-analysis. The tool allows the mapping of data set features by ID, name, and accurate mass, and can incorporate information from adduct and isotope correction of mass spectrometry data. MarVis-Pathway was integrated in the MarVis-Suite (http://marvis.gobics.de), which features the seamless highly interactive filtering, combination, clustering, and visualization of omics data sets. The functionality of the new software tool is illustrated using combined mass spectrometry and DNA microarray data. This application confirms jasmonate biosynthesis as important metabolic pathway that is upregulated during the wound response of Arabidopsis plants
Remarks on Early Medieval legal charters — The legend of “dux Ingo” and his “carta sine litteris”
No full textEnea Silvio Piccolomini in his work entitled
De Europa
written in 1458, tells an interesting story defined as a legend in terms of genre about a duke called Ingo, who lived during the reign of Charlemagne. This narrative claims that in 790
dux gentis
Ingo held a feast for the inhabitants of his province where food was served to the peasants allowed to appear before him in golden and silver bowls, while to the dignitaries standing further away from him in bowls made of clay. The researchers’ attention is deservedly raised by the query how come that this parabolical story with biblical tone was included in Enea Silvio’s work; if it had been borrowed who the
auctor
might have been he borrowed it from. The answer seems to be very simple: from the
Conversio Bagoariorum et Carantanorum
drafted regarding the lawsuit proceeded against Methodius. In the case narrated in the
Conversio
Ingo sent a charter or much rather a parchment without any writing, or letters on it
(carta sine litteris)
, which provided his legate with sufficient authenticity to demand obedience from the people.In this study-after having compared the two narratives and outlined the place of De Europa in Enea Silvio Piccolomini’s oeuvre and the circumstances of the drafting and tendencies of the Conversio Bagoariorum et Carantanorum-the author attempts to answer the following questions. To what extent can duke Ingo, mentioned by Enea Silvio and not questioned in the literature for long centuries, be considered a real historical person? Does the Conversio refer to Ingo as a duke, and if it does, what is his existence as a duke and introduction in the literature as a duke owing to? What could the meaning of carta sine litteris referred to in Conversio have been, and why did Enea Silvio not take this item over although he could have put it forward as a further proof of Ingo’s dignity? To what literary prefigurations can the description of the feast held by Ingo be traced back to, and what role did it play in the Conversio? Regarding the borrowing of the Ingo story by Enea Silvio, what possible intermediary writing and author can be reckoned with
The role of recombination in the emergence of a complex and dynamic HIV epidemic
No full textAbstract Background Inter-subtype recombinants dominate the HIV epidemics in three geographical regions. To better understand the role of HIV recombinants in shaping the current HIV epidemic, we here present the results of a large-scale subtyping analysis of 9435 HIV-1 sequences that involve subtypes A, B, C, G, F and the epidemiologically important recombinants derived from three continents. Results The circulating recombinant form CRF02_AG, common in West Central Africa, appears to result from recombination events that occurred early in the divergence between subtypes A and G, followed by additional recent recombination events that contribute to the breakpoint pattern defining the current recombinant lineage. This finding also corrects a recent claim that G is a recombinant and a descendant of CRF02, which was suggested to be a pure subtype. The BC and BF recombinants in China and South America, respectively, are derived from recent recombination between contemporary parental lineages. Shared breakpoints in South America BF recombinants indicate that the HIV-1 epidemics in Argentina and Brazil are not independent. Therefore, the contemporary HIV-1 epidemic has recombinant lineages of both ancient and more recent origins. Conclusions Taken together, we show that these recombinant lineages, which are highly prevalent in the current HIV epidemic, are a mixture of ancient and recent recombination. The HIV pandemic is moving towards having increasing complexity and higher prevalence of recombinant forms, sometimes existing as "families" of related forms. We find that the classification of some CRF designations need to be revised as a consequence of (1) an estimated > 5% error in the original subtype assignments deposited in the Los Alamos sequence database; (2) an increasing number of CRFs are defined while they do not readily fit into groupings for molecular epidemiology and vaccine design; and (3) a dynamic HIV epidemic context.</p
jpHMM: recombination analysis in viruses with circular genomes such as the hepatitis B virus
No full textjpHMM is a very accurate and widely used tool for recombination detection in genomic sequences of HIV-1. Here, we present an extension of jpHMM to analyze recombinations in viruses with circular genomes such as the hepatitis B virus (HBV). Sequence analysis of circular genomes is usually performed on linearized sequences using linear models. Since linear models are unable to model dependencies between nucleotides at the 5'- and 3'-end of a sequence, this can result in inaccurate predictions of recombination breakpoints and thus in incorrect classification of viruses with circular genomes. The proposed circular jpHMM takes into account the circularity of the genome and is not biased against recombination breakpoints close to the 5'- or 3'-end of the linearized version of the circular genome. It can be applied automatically to any query sequence without assuming a specific origin for the sequence coordinates. We apply the method to genomic sequences of HBV and visualize its output in a circular form. jpHMM is available online at http://jphmm.gobics.de for download and as a web server for HIV-1 and HBV sequences.Open-Access-Publikationsfonds 201
jpHMM: Improving the reliability of recombination prediction in HIV-1
No full textPreviously, we developed jumping profile hidden Markov model (jpHMM), a new method to detect recombinations in HIV-1 genomes. The jpHMM predicts recombination breakpoints in a query sequence and assigns to each position of the sequence one of the major HIV-1 subtypes. Since incorrect subtype assignment or recombination prediction may lead to wrong conclusions in epidemiological or vaccine research, information about the reliability of the predicted parental subtypes and breakpoint positions is valuable. For this reason, we extended the output of jpHMM to include such information in terms of 'uncertainty' regions in the recombination prediction and an interval estimate of the breakpoint. Both types of information are computed based on the posterior probabilities of the subtypes at each query sequence position. Our results show that this extension strongly improves the reliability of the jpHMM recombination prediction. The jpHMM is available online at http://jphmm.gobics.de/
Constructing symmetric generalized FGM copulas by means of certain univariate distributions
No full textIn this paper we focus on symmetric generalized Fairlie-Gumbel-Morgenstern (or symmetric Sarmanov) copulas which are characterized by means of so-called generator functions. In particular, we introduce a class of generator functions which is based on univariate distributions with certain properties. Some of the generator functions from the literature are recovered. Moreover two new generators are suggested, implying two new copulas. Finally, the opposite way around, it is exemplarily shown how to calculate the univariate distribution which belongs to a given copula generator function. --
[Schauspielhaus Düsseldorf] / Peer Gynt : zweiter Teil ; Freitag, den 4. Februar 1916, abends 7 1/2 Uhr ; ein dramatisches Gedicht
No full textvon Henrik Ibsen. In der Uebertragung von Christian Morgenstern. Musik von Edvard Grieg. Leiter der Aufführung: Gustav Lindemann. Künstlerischer Beirat: Knut Ström. Musikalische Leitung: Hans Ebert. Personen des Stückes: Otto Stoeckel, Gertud Hackelderg, Peter Esser, Ingo Krauß, Paul Kaufmann, Ferry Dittrich, Eugen Keller, Eugen Dumont, Olivia Veit, Paul Henckels, Fritz Sander, Julius Herrmann, Theodor Kigler, Friedrich Wörnle, Carl Walter Schott, Emil Lind, Oscar Fuch
[Schauspielhaus Düsseldorf] / Peer Gynt : zweiter Teil ; Dienstag, den 1. Februar 1916, abends 7 1/2 Uhr ; ein dramatisches Gedicht
No full textvon Henrik Ibsen. In der Uebertragung von Christian Morgenstern. Musik von Edvard Grieg. Leiter der Aufführung: Gustav Lindemann. Künstlerischer Beirat: Knut Ström. Musikalische Leitung: Hans Ebert. Personen des Stückes: Peter Esser, Ingo Krauß, Paul Kaufmann, Ferry Dittrich, Eugen Keller, Eugen Dumont, Olivia Veit, Paul Henckels, Fritz Sander, Julius Herrmann, Theodor Kigler, Friedrich Wörnle, Carl Walter Schott, Emil Lin
- …
