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Schirmer S, Korner-Nievergelt F, von Rönn JAC, Liebscher V. Estimating survival in continuous space from mark-dead-recovery data - Towards a continuous version of the multinomial dead recovery model. J Theor Biol 2023; 574:111625. [PMID: 37748534 DOI: 10.1016/j.jtbi.2023.111625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 08/15/2023] [Accepted: 09/18/2023] [Indexed: 09/27/2023]
Abstract
Understanding spatially varying survival is crucial for understanding the ecology and evolution of migratory animals, which may ultimately help to conserve such species. We develop an approach to estimate an annual survival probability function varying continuously in geographic space, if the recovery probability is constant over space. This estimate is based on a density function over continuous geographic space and the discrete age at death obtained from dead recovery data. From the same density function, we obtain an estimate for animal distribution in space corrected for survival, i.e., migratory connectivity. This is possible, when migratory connectivity can be separated from recovery probability. In this article, we present the method how spatially and continuously varying survival and the migratory connectivity corrected for survival can be obtained, if a constant recovery probability can be assumed reasonably. The model is a stepping stone in developing a model allowing for disentangling spatially heterogeneous survival and migratory connectivity corrected for survival from a spatially heterogeneous recovery probability. We implement the method using kernel density estimates in the R-package CONSURE. Any other density estimation technique can be used as an alternative. In a simulation study, the estimators are unbiased but show edge effects in survival and migratory connectivity. Applying the method to a real-world data set of European robins Erithacus rubecula results in biologically reasonable continuous heat-maps for survival and migratory connectivity.
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Affiliation(s)
- Saskia Schirmer
- Department of Mathematics and Computer Science, University of Greifswald, Walther-Rathenau-Straße 47, 17489 Greifswald, Germany; Swiss Ornithological Institute, Seerose 1, 6204 Sempach, Switzerland; Zoological Institute and Museum, University of Greifswald, Loitzer Straße 26, 17489 Greifswald, Germany.
| | | | - Jan A C von Rönn
- Swiss Ornithological Institute, Seerose 1, 6204 Sempach, Switzerland
| | - Volkmar Liebscher
- Department of Mathematics and Computer Science, University of Greifswald, Walther-Rathenau-Straße 47, 17489 Greifswald, Germany
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2
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Klosa J, Simon N, Liebscher V, Wittenburg D. A Fitted Sparse-Group Lasso for Genome-Based Evaluations. IEEE/ACM Trans Comput Biol Bioinform 2023; 20:30-38. [PMID: 35254989 DOI: 10.1109/tcbb.2022.3156805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
In life sciences, high-throughput techniques typically lead to high-dimensional data and often the number of covariates is much larger than the number of observations. This inherently comes with multicollinearity challenging a statistical analysis in a linear regression framework. Penalization methods such as the lasso, ridge regression, the group lasso, and convex combinations thereof, which introduce additional conditions on regression variables, have proven themselves effective. In this study, we introduce a novel approach by combining the lasso and the standardized group lasso leading to meaningful weighting of the predicted ("fitted") outcome which is of primary importance, e.g., in breeding populations. This "fitted" sparse-group lasso was implemented as a proximal-averaged gradient descent method and is part of the R package "seagull" available at CRAN. For the evaluation of the novel method, we executed an extensive simulation study. We simulated genotypes and phenotypes which resemble data of a dairy cattle population. Genotypes at thousands of genomic markers were used as covariates to fit a quantitative response. The proximity of markers on a chromosome determined grouping. In the majority of simulated scenarios, the new method revealed improved prediction abilities compared to other penalization approaches and was able to localize the signals of simulated features.
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3
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Schirmer S, Korner-Nievergelt F, von Rönn JAC, Liebscher V. Estimation in the multinomial reencounter model - Where do migrating animals go and how do they survive in their destination area? J Theor Biol 2022; 543:111108. [PMID: 35367238 DOI: 10.1016/j.jtbi.2022.111108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 11/25/2022]
Abstract
Spatial variation in survival has individual fitness consequences and influences population dynamics. Which space animals use during the annual cycle determines how they are affected by this spatial variability. Therefore, knowing spatial patterns of survival and space use is crucial to understand demography of migrating animals. Extracting information on survival and space use from observation data, in particular dead recovery data, requires explicitly identifying the observation process. We build a fully stochastic model for animals marked in populations of origin, which were found dead in spatially discrete destination areas. The model acts on the population level and includes parameters for use of space, survival and recovery probability. It is based on the division coefficient and the multinomial reencounter model. We use a likelihood-based approach, derive Restricted Maximum Likelihood-like estimates for all parameters and prove their existence and uniqueness. In a simulation study we demonstrate the performance of the model by using Bayesian estimators derived by the Markov chain Monte Carlo method. We obtain unbiased estimates for survival and recovery probability if the sample size is large enough. Moreover, we apply the model to real-world data of European robins Erithacus rubecula ringed at a stopover site. We obtain annual survival estimates for different spatially discrete non-breeding areas. Additionally, we can reproduce already known patterns of use of space for this species.
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Affiliation(s)
- Saskia Schirmer
- Department of Mathematics and Computer Science, University of Greifswald, Walther-Rathenau-Straße 47, 17489 Greifswald, Germany; Swiss Ornithological Institute, Seerose 1, 6204 Sempach, Switzerland.
| | | | - Jan A C von Rönn
- Swiss Ornithological Institute, Seerose 1, 6204 Sempach, Switzerland
| | - Volkmar Liebscher
- Department of Mathematics and Computer Science, University of Greifswald, Walther-Rathenau-Straße 47, 17489 Greifswald, Germany
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4
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Vitense P, Kasbohm E, Klassen A, Gierschner P, Trefz P, Weber M, Miekisch W, Schubert JK, Möbius P, Reinhold P, Liebscher V, Köhler H. Detection of Mycobacterium avium ssp. paratuberculosis in Cultures From Fecal and Tissue Samples Using VOC Analysis and Machine Learning Tools. Front Vet Sci 2021; 8:620327. [PMID: 33614764 PMCID: PMC7887282 DOI: 10.3389/fvets.2021.620327] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 01/13/2021] [Indexed: 12/17/2022] Open
Abstract
Analysis of volatile organic compounds (VOCs) is a novel approach to accelerate bacterial culture diagnostics of Mycobacterium avium subsp. paratuberculosis (MAP). In the present study, cultures of fecal and tissue samples from MAP-infected and non-suspect dairy cattle and goats were explored to elucidate the effects of sample matrix and of animal species on VOC emissions during bacterial cultivation and to identify early markers for bacterial growth. The samples were processed following standard laboratory procedures, culture tubes were incubated for different time periods. Headspace volume of the tubes was sampled by needle trap-micro-extraction, and analyzed by gas chromatography-mass spectrometry. Analysis of MAP-specific VOC emissions considered potential characteristic VOC patterns. To address variation of the patterns, a flexible and robust machine learning workflow was set up, based on random forest classifiers, and comprising three steps: variable selection, parameter optimization, and classification. Only a few substances originated either from a certain matrix or could be assigned to one animal species. These additional emissions were not considered informative by the variable selection procedure. Classification accuracy of MAP-positive and negative cultures of bovine feces was 0.98 and of caprine feces 0.88, respectively. Six compounds indicating MAP presence were selected in all four settings (cattle vs. goat, feces vs. tissue): 2-Methyl-1-propanol, 2-methyl-1-butanol, 3-methyl-1-butanol, heptanal, isoprene, and 2-heptanone. Classification accuracies for MAP growth-scores ranged from 0.82 for goat tissue to 0.89 for cattle feces. Misclassification occurred predominantly between related scores. Seventeen compounds indicating MAP growth were selected in all four settings, including the 6 compounds indicating MAP presence. The concentration levels of 2,3,5-trimethylfuran, 2-pentylfuran, 1-propanol, and 1-hexanol were indicative for MAP cultures before visible growth was apparent. Thus, very accurate classification of the VOC samples was achieved and the potential of VOC analysis to detect bacterial growth before colonies become visible was confirmed. These results indicate that diagnosis of paratuberculosis can be optimized by monitoring VOC emissions of bacterial cultures. Further validation studies are needed to increase the robustness of indicative VOC patterns for early MAP growth as a pre-requisite for the development of VOC-based diagnostic analysis systems.
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Affiliation(s)
- Philipp Vitense
- Institute of Mathematics and Computer Science, University of Greifswald, Greifswald, Germany
| | - Elisa Kasbohm
- Institute of Mathematics and Computer Science, University of Greifswald, Greifswald, Germany
| | - Anne Klassen
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut, Jena, Germany
| | - Peter Gierschner
- Department of Anaesthesia and Intensive Care, University Medicine Rostock, Rostock, Germany
| | - Phillip Trefz
- Department of Anaesthesia and Intensive Care, University Medicine Rostock, Rostock, Germany
| | - Michael Weber
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut, Jena, Germany
| | - Wolfram Miekisch
- Department of Anaesthesia and Intensive Care, University Medicine Rostock, Rostock, Germany
| | - Jochen K Schubert
- Department of Anaesthesia and Intensive Care, University Medicine Rostock, Rostock, Germany
| | - Petra Möbius
- National Reference Laboratory for Paratuberculosis, Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut, Jena, Germany
| | - Petra Reinhold
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut, Jena, Germany
| | - Volkmar Liebscher
- Institute of Mathematics and Computer Science, University of Greifswald, Greifswald, Germany
| | - Heike Köhler
- National Reference Laboratory for Paratuberculosis, Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut, Jena, Germany
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Klosa J, Simon N, Westermark PO, Liebscher V, Wittenburg D. Seagull: lasso, group lasso and sparse-group lasso regularization for linear regression models via proximal gradient descent. BMC Bioinformatics 2020; 21:407. [PMID: 32933477 PMCID: PMC7493359 DOI: 10.1186/s12859-020-03725-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 08/31/2020] [Indexed: 11/15/2022] Open
Abstract
Background Statistical analyses of biological problems in life sciences often lead to high-dimensional linear models. To solve the corresponding system of equations, penalization approaches are often the methods of choice. They are especially useful in case of multicollinearity, which appears if the number of explanatory variables exceeds the number of observations or for some biological reason. Then, the model goodness of fit is penalized by some suitable function of interest. Prominent examples are the lasso, group lasso and sparse-group lasso. Here, we offer a fast and numerically cheap implementation of these operators via proximal gradient descent. The grid search for the penalty parameter is realized by warm starts. The step size between consecutive iterations is determined with backtracking line search. Finally, seagull -the R package presented here- produces complete regularization paths. Results Publicly available high-dimensional methylation data are used to compare seagull to the established R package SGL. The results of both packages enabled a precise prediction of biological age from DNA methylation status. But even though the results of seagull and SGL were very similar (R2 > 0.99), seagull computed the solution in a fraction of the time needed by SGL. Additionally, seagull enables the incorporation of weights for each penalized feature. Conclusions The following operators for linear regression models are available in seagull: lasso, group lasso, sparse-group lasso and Integrative LASSO with Penalty Factors (IPF-lasso). Thus, seagull is a convenient envelope of lasso variants.
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Affiliation(s)
- Jan Klosa
- Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology, 18196, Dummerstorf, Germany
| | - Noah Simon
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Pål Olof Westermark
- Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology, 18196, Dummerstorf, Germany
| | - Volkmar Liebscher
- Institute of Mathematics and Computer Science, University of Greifswald, 17489, Greifswald, Germany
| | - Dörte Wittenburg
- Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology, 18196, Dummerstorf, Germany.
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6
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Petersen I, Schlüter R, Hoff KJ, Liebscher V, Bange G, Riedel K, Pané-Farré J. Non-invasive and label-free 3D-visualization shows in vivo oligomerization of the staphylococcal alkaline shock protein 23 (Asp23). Sci Rep 2020; 10:125. [PMID: 31924851 PMCID: PMC6954212 DOI: 10.1038/s41598-019-56907-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 12/04/2019] [Indexed: 11/26/2022] Open
Abstract
Fluorescence-tags, commonly used to visualize the spatial distribution of proteins within cells, can influence the localization of the tagged proteins by affecting their stability, interaction with other proteins or the induction of oligomerization artifacts. To circumvent these obstacles, a protocol was developed to generate 50 nm thick serial sections suitable for immunogold labeling and subsequent reconstruction of the spatial distribution of immuno-labeled native proteins within individual bacterial cells. Applying this method, we show a cellular distribution of the staphylococcal alkaline shock protein 23 (Asp23), which is compatible with filament formation, a property of Asp23 that we also demonstrate in vitro.
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Affiliation(s)
- Inga Petersen
- University of Greifswald, Institute of Microbiology, Felix-Hausdorff-Str. 8, 17489, Greifswald, Germany.,Center for Functional Genomics of Microbes, Felix-Hausdorff-Str. 8, 17489, Greifswald, Germany
| | - Rabea Schlüter
- University of Greifswald, Imaging Center of the Department of Biology, Friedrich-Ludwig-Jahn-Str. 15, 17489, Greifswald, Germany
| | - Katharina J Hoff
- University of Greifswald, Institute of Mathematics and Computer Science, Walther-Rathenau-Str. 47, 17489, Greifswald, Germany.,Center for Functional Genomics of Microbes, Felix-Hausdorff-Str. 8, 17489, Greifswald, Germany
| | - Volkmar Liebscher
- University of Greifswald, Institute of Mathematics and Computer Science, Walther-Rathenau-Str. 47, 17489, Greifswald, Germany
| | - Gert Bange
- Philipps-University Marburg, SYNMIKRO Research Center and Department of Chemistry, Hans-Meerwein-Strasse 6, C07, 35043, Marburg, Germany
| | - Katharina Riedel
- University of Greifswald, Institute of Microbiology, Felix-Hausdorff-Str. 8, 17489, Greifswald, Germany.,Center for Functional Genomics of Microbes, Felix-Hausdorff-Str. 8, 17489, Greifswald, Germany
| | - Jan Pané-Farré
- University of Greifswald, Institute of Microbiology, Felix-Hausdorff-Str. 8, 17489, Greifswald, Germany. .,Center for Functional Genomics of Microbes, Felix-Hausdorff-Str. 8, 17489, Greifswald, Germany. .,Philipps-University Marburg, SYNMIKRO Research Center and Department of Chemistry, Hans-Meerwein-Strasse 6, C07, 35043, Marburg, Germany.
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7
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Gellert M, Hossain MF, Berens FJF, Bruhn LW, Urbainsky C, Liebscher V, Lillig CH. Substrate specificity of thioredoxins and glutaredoxins - towards a functional classification. Heliyon 2019; 5:e02943. [PMID: 31890941 PMCID: PMC6928294 DOI: 10.1016/j.heliyon.2019.e02943] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 11/15/2019] [Accepted: 11/25/2019] [Indexed: 12/13/2022] Open
Abstract
The spatio-temporal reduction and oxidation of protein thiols is an essential mechanism in signal transduction in all kingdoms of life. Thioredoxin (Trx) family proteins efficiently catalyze thiol-disulfide exchange reactions and the proteins are widely recognized for their importance in the operation of thiol switches. Trx family proteins have a broad and at the same time very distinct substrate specificity – a prerequisite for redox switching. Despite of multiple efforts, the true nature for this specificity is still under debate. Here, we comprehensively compare the classification/clustering of various redoxins from all domains of life based on their similarity in amino acid sequence, tertiary structure, and their electrostatic properties. We correlate these similarities to the existence of common interaction partners, identified in various previous studies and suggested by proteomic screenings. These analyses confirm that primary and tertiary structure similarity, and thereby all common classification systems, do not correlate to the target specificity of the proteins as thiol-disulfide oxidoreductases. Instead, a number of examples clearly demonstrate the importance of electrostatic similarity for their target specificity, independent of their belonging to the Trx or glutaredoxin subfamilies.
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Affiliation(s)
- Manuela Gellert
- Institute for Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Germany
| | - Md Faruq Hossain
- Institute for Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Germany
| | - Felix Jacob Ferdinand Berens
- Institute for Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Germany.,Institute for Mathematics and Informatics, University of Greifswald, Germany
| | - Lukas Willy Bruhn
- Institute for Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Germany.,Institute for Mathematics and Informatics, University of Greifswald, Germany
| | - Claudia Urbainsky
- Institute for Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Germany
| | - Volkmar Liebscher
- Institute for Mathematics and Informatics, University of Greifswald, Germany
| | - Christopher Horst Lillig
- Institute for Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Germany
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8
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Siems T, Hellmuth M, Liebscher V. Simultaneous Credible Regions for Multiple Changepoint Locations. J Comput Graph Stat 2018. [DOI: 10.1080/10618600.2018.1513366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Tobias Siems
- aDepartment of Mathematics and Computer Science, University of Greifswald, Greifswald, Germany
| | - Marc Hellmuth
- aDepartment of Mathematics and Computer Science, University of Greifswald, Greifswald, Germany
| | - Volkmar Liebscher
- aDepartment of Mathematics and Computer Science, University of Greifswald, Greifswald, Germany
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9
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Wittenburg D, Liebscher V. An approximate Bayesian significance test for genomic evaluations. Biom J 2018; 60:1096-1109. [PMID: 30101421 PMCID: PMC6282823 DOI: 10.1002/bimj.201700219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 03/06/2018] [Accepted: 04/10/2018] [Indexed: 11/12/2022]
Abstract
Genomic information can be used to study the genetic architecture of some trait. Not only the size of the genetic effect captured by molecular markers and their position on the genome but also the mode of inheritance, which might be additive or dominant, and the presence of interactions are interesting parameters. When searching for interacting loci, estimating the effect size and determining the significant marker pairs increases the computational burden in terms of speed and memory allocation dramatically. This study revisits a rapid Bayesian approach (fastbayes). As a novel contribution, a measure of evidence is derived to select markers with effect significantly different from zero. It is based on the credibility of the highest posterior density interval next to zero in a marginalized manner. This methodology is applied to simulated data resembling a dairy cattle population in order to verify the sensitivity of testing for a given range of type-I error levels. A real data application complements this study. Sensitivity and specificity of fastbayes were similar to a variational Bayesian method, and a further reduction of computing time could be achieved. More than 50% of the simulated causative variants were identified. The most complex model containing different kinds of genetic effects and their pairwise interactions yielded the best outcome over a range of type-I error levels. The validation study showed that fastbayes is a dual-purpose tool for genomic inferences - it is applicable to predict future outcome of not-yet phenotyped individuals with high precision as well as to estimate and test single-marker effects. Furthermore, it allows the estimation of billions of interaction effects.
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Affiliation(s)
- Dörte Wittenburg
- Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, D-18196, Dummerstorf, Germany
| | - Volkmar Liebscher
- Department of Mathematics and Computer Science, University of Greifswald, Walther-Rathenau-Str. 47, D-17489, Greifswald, Germany
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10
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Kruff N, Lax C, Liebscher V, Walcher S. The Rosenzweig-MacArthur system via reduction of an individual based model. J Math Biol 2018; 78:413-439. [PMID: 30094616 DOI: 10.1007/s00285-018-1278-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 07/31/2018] [Indexed: 10/28/2022]
Abstract
The Rosenzweig-MacArthur system is a particular case of the Gause model, which is widely used to describe predator-prey systems. In the classical derivation, the interaction terms in the differential equation are essentially derived from considering handling time vs. search time, and moreover there exist derivations in the literature which are based on quasi-steady state assumptions. In the present paper we introduce a derivation of this model from first principles and singular perturbation reductions. We first establish a simple stochastic mass action model which leads to a three-dimensional ordinary differential equation, and systematically determine all possible singular perturbation reductions (in the sense of Tikhonov and Fenichel) to two-dimensional systems. Among the reductions obtained we find the Rosenzweig-MacArthur system for a certain choice of small parameters as well as an alternative to the Rosenzweig-MacArthur model, with density dependent death rates for predators. The arguments to obtain the reductions are intrinsically mathematical; no heuristics are employed.
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Affiliation(s)
- Niclas Kruff
- Lehrstuhl A für Mathematik, RWTH Aachen University, 52056, Aachen, Germany
| | - Christian Lax
- Lehrstuhl A für Mathematik, RWTH Aachen University, 52056, Aachen, Germany
| | - Volkmar Liebscher
- Institute of Mathematics and Computer Science, University Greifswald, 17487, Greifswald, Germany.
| | - Sebastian Walcher
- Lehrstuhl A für Mathematik, RWTH Aachen University, 52056, Aachen, Germany
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11
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Liebscher V. New Gromov-Inspired Metrics on Phylogenetic Tree Space. Bull Math Biol 2018; 80:493-518. [DOI: 10.1007/s11538-017-0385-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 12/19/2017] [Indexed: 11/29/2022]
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12
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Kasbohm E, Fischer S, Küntzel A, Oertel P, Bergmann A, Trefz P, Miekisch W, Schubert JK, Reinhold P, Ziller M, Fröhlich A, Liebscher V, Köhler H. Strategies for the identification of disease-related patterns of volatile organic compounds: prediction of paratuberculosis in an animal model using random forests. J Breath Res 2017; 11:047105. [PMID: 28768897 DOI: 10.1088/1752-7163/aa83bb] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Modern statistical methods which were developed for pattern recognition are increasingly being used for data analysis in studies on emissions of volatile organic compounds (VOCs). With the detection of disease-related VOC profiles, novel non-invasive diagnostic tools could be developed for clinical applications. However, it is important to bear in mind that not all statistical methods are equally suitable for the investigation of VOC profiles. In particular, univariate methods are not able to discover VOC patterns as they consider each compound separately. The present study demonstrates this fact in practice. Using VOC samples from a controlled animal study on paratuberculosis, the random forest classification method was applied for pattern recognition and disease prediction. This strategy was compared with a prediction approach based on single compounds. Both methods were framed within a cross-validation procedure. A comparison of both strategies based on these VOC data reveals that random forests achieves higher sensitivities and specificities than predictions based on single compounds. Therefore, it will most likely be more fruitful to further investigate VOC patterns instead of single biomarkers for paratuberculosis. All methods used are thoroughly explained to aid the transfer to other data analyses.
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Affiliation(s)
- Elisa Kasbohm
- Institute of Epidemiology, Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany. Department of Mathematics and Computer Science, University of Greifswald, Germany
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13
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Singh NK, Ernst M, Liebscher V, Fuellen G, Taher L. Revealing complex function, process and pathway interactions with high-throughput expression and biological annotation data. Mol Biosyst 2016; 12:3196-208. [PMID: 27507577 DOI: 10.1039/c6mb00280c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The biological relationships both between and within the functions, processes and pathways that operate within complex biological systems are only poorly characterized, making the interpretation of large scale gene expression datasets extremely challenging. Here, we present an approach that integrates gene expression and biological annotation data to identify and describe the interactions between biological functions, processes and pathways that govern a phenotype of interest. The product is a global, interconnected network, not of genes but of functions, processes and pathways, that represents the biological relationships within the system. We validated our approach on two high-throughput expression datasets describing organismal and organ development. Our findings are well supported by the available literature, confirming that developmental processes and apoptosis play key roles in cell differentiation. Furthermore, our results suggest that processes related to pluripotency and lineage commitment, which are known to be critical for development, interact mainly indirectly, through genes implicated in more general biological processes. Moreover, we provide evidence that supports the relevance of cell spatial organization in the developing liver for proper liver function. Our strategy can be viewed as an abstraction that is useful to interpret high-throughput data and devise further experiments.
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Affiliation(s)
- Nitesh Kumar Singh
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Ernst-Heydemann-Str. 8, 18057 Rostock, Germany.
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14
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Zühlke D, Dörries K, Bernhardt J, Maaß S, Muntel J, Liebscher V, Pané-Farré J, Riedel K, Lalk M, Völker U, Engelmann S, Becher D, Fuchs S, Hecker M. Costs of life - Dynamics of the protein inventory of Staphylococcus aureus during anaerobiosis. Sci Rep 2016; 6:28172. [PMID: 27344979 PMCID: PMC4921807 DOI: 10.1038/srep28172] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 05/31/2016] [Indexed: 01/19/2023] Open
Abstract
Absolute protein quantification was applied to follow the dynamics of the cytoplasmic proteome of Staphylococcus aureus in response to long-term oxygen starvation. For 1,168 proteins, the majority of all expressed proteins, molecule numbers per cell have been determined to monitor the cellular investments in single branches of bacterial life for the first time. In the presence of glucose the anaerobic protein pattern is characterized by increased amounts of glycolytic and fermentative enzymes such as Eno, GapA1, Ldh1, and PflB. Interestingly, the ferritin-like protein FtnA belongs to the most abundant proteins during anaerobic growth. Depletion of glucose finally leads to an accumulation of different enzymes such as ArcB1, ArcB2, and ArcC2 involved in arginine deiminase pathway. Concentrations of 29 exo- and 78 endometabolites were comparatively assessed and have been integrated to the metabolic networks. Here we provide an almost complete picture on the response to oxygen starvation, from signal transduction pathways to gene expression pattern, from metabolic reorganization after oxygen depletion to beginning cell death and lysis after glucose exhaustion. This experimental approach can be considered as a proof of principle how to combine cell physiology with quantitative proteomics for a new dimension in understanding simple life processes as an entity.
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Affiliation(s)
- Daniela Zühlke
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany
| | - Kirsten Dörries
- Institute of Biochemistry, Ernst-Moritz-Arndt-University Greifswald, Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany
| | - Jörg Bernhardt
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany
| | - Sandra Maaß
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany
| | - Jan Muntel
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany
| | - Volkmar Liebscher
- Department of Mathematics and Informatics, Ernst-Moritz-Arndt-University Greifswald, Walther-Rathenau-Strasse 47, D-17487 Greifswald, Germany
| | - Jan Pané-Farré
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany
| | - Katharina Riedel
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany
| | - Michael Lalk
- Institute of Biochemistry, Ernst-Moritz-Arndt-University Greifswald, Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15 a, D-17487 Greifswald, Germany
| | - Susanne Engelmann
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany.,Institute of Microbiology, Technical University Braunschweig, Inhoffenstrasse 7, D-38124 Braunschweig, Germany.,Helmholtz Institute for Infection Research, Microbial Proteomics, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
| | - Dörte Becher
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany
| | - Stephan Fuchs
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany.,Robert Koch Institute, FG13 Nosocomial Pathogens and Antibiotic Resistance, Burgstrasse 37, D-38855 Wernigerode, Germany
| | - Michael Hecker
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany
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15
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Abstract
A classical result about Markov jump processes states that a certain class of dynamical systems given by ordinary differential equations are obtained as the limit of a sequence of scaled Markov jump processes. This approach fails if the scaling cannot be carried out equally across all entities. In the present paper we present a convergence theorem for such an unequal scaling. In contrast to an equal scaling the limit process is not purely deterministic but still possesses randomness. We show that these processes constitute a rich subclass of piecewise-deterministic processes. Such processes apply in molecular biology where entities often occur in different scales of numbers.
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16
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Ivanovska T, Laqua R, Wang L, Schenk A, Yoon JH, Hegenscheid K, Völzke H, Liebscher V. An efficient level set method for simultaneous intensity inhomogeneity correction and segmentation of MR images. Comput Med Imaging Graph 2015; 48:9-20. [PMID: 26741125 DOI: 10.1016/j.compmedimag.2015.11.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 10/21/2015] [Accepted: 11/30/2015] [Indexed: 11/30/2022]
Abstract
Intensity inhomogeneity (bias field) is a common artefact in magnetic resonance (MR) images, which hinders successful automatic segmentation. In this work, a novel algorithm for simultaneous segmentation and bias field correction is presented. The proposed energy functional allows for explicit regularization of the bias field term, making the model more flexible, which is crucial in presence of strong inhomogeneities. An efficient minimization procedure, attempting to find the global minimum, is applied to the energy functional. The algorithm is evaluated qualitatively and quantitatively using a synthetic example and real MR images of different organs. Comparisons with several state-of-the-art methods demonstrate the superior performance of the proposed technique. Desirable results are obtained even for images with strong and complicated inhomogeneity fields and sparse tissue structures.
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Affiliation(s)
| | - René Laqua
- Ernst-Moritz-Arndt University, Greifswald, Germany
| | - Lei Wang
- Fraunhofer Institute for Medical Image Computing MEVIS, Bremen, Germany
| | - Andrea Schenk
- Fraunhofer Institute for Medical Image Computing MEVIS, Bremen, Germany
| | - Jeong Hee Yoon
- Department of Radiology, Seoul National University Hospital, Seoul, Republic of Korea
| | | | - Henry Völzke
- Ernst-Moritz-Arndt University, Greifswald, Germany
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17
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Ameling S, Kacprowski T, Chilukoti RK, Malsch C, Liebscher V, Suhre K, Pietzner M, Friedrich N, Homuth G, Hammer E, Völker U. Associations of circulating plasma microRNAs with age, body mass index and sex in a population-based study. BMC Med Genomics 2015; 8:61. [PMID: 26462558 PMCID: PMC4604724 DOI: 10.1186/s12920-015-0136-7] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 09/20/2015] [Indexed: 01/08/2023] Open
Abstract
Background Non-cellular blood circulating microRNAs (plasma miRNAs) represent a promising source for the development of prognostic and diagnostic tools owing to their minimally invasive sampling, high stability, and simple quantification by standard techniques such as RT-qPCR. So far, the majority of association studies involving plasma miRNAs were disease-specific case-control analyses. In contrast, in the present study, plasma miRNAs were analysed in a sample of 372 individuals from a population-based cohort study, the Study of Health in Pomerania (SHIP). Methods Quantification of miRNA levels was performed by RT-qPCR using the Exiqon Serum/Plasma Focus microRNA PCR Panel V3.M covering 179 different miRNAs. Of these, 155 were included in our analyses after quality-control. Associations between plasma miRNAs and the phenotypes age, body mass index (BMI), and sex were assessed via a two-step linear regression approach per miRNA. The first step regressed out the technical parameters and the second step determined the remaining associations between the respective plasma miRNA and the phenotypes of interest. Results After regressing out technical parameters and adjusting for the respective other two phenotypes, 7, 15, and 35 plasma miRNAs were significantly (q < 0.05) associated with age, BMI, and sex, respectively. Additional adjustment for the blood cell parameters identified 12 and 19 miRNAs to be significantly associated with age and BMI, respectively. Most of the BMI-associated miRNAs likely originate from liver. Sex-associated differences in miRNA levels were largely determined by differences in blood cell parameters. Thus, only 7 as compared to originally 35 sex-associated miRNAs displayed sex-specific differences after adjustment for blood cell parameters. Conclusions These findings emphasize that circulating miRNAs are strongly impacted by age, BMI, and sex. Hence, these parameters should be considered as covariates in association studies based on plasma miRNA levels. The established experimental and computational workflow can now be used in future screening studies to determine associations of plasma miRNAs with defined disease phenotypes. Electronic supplementary material The online version of this article (doi:10.1186/s12920-015-0136-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sabine Ameling
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, , Friedrich-Ludwig-Jahn-Str. 15A, D-17475, Greifswald, Germany. .,DZHK (German Centre for Cardiovascular Research), partner site Greifswald, Greifswald, Germany.
| | - Tim Kacprowski
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, , Friedrich-Ludwig-Jahn-Str. 15A, D-17475, Greifswald, Germany.
| | - Ravi Kumar Chilukoti
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, , Friedrich-Ludwig-Jahn-Str. 15A, D-17475, Greifswald, Germany.
| | - Carolin Malsch
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, , Friedrich-Ludwig-Jahn-Str. 15A, D-17475, Greifswald, Germany.
| | - Volkmar Liebscher
- Institute of Mathematics and Informatics, Ernst-Moritz-Arndt-University, Greifswald, Germany.
| | - Karsten Suhre
- Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Education City, PO Box 24144, Doha, Qatar. .,Helmholtz Zentrum München, Germany, Research Centre for Environmental Health, Neuherberg, Germany.
| | - Maik Pietzner
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany.
| | - Nele Friedrich
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany. .,DZHK (German Centre for Cardiovascular Research), partner site Greifswald, Greifswald, Germany.
| | - Georg Homuth
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, , Friedrich-Ludwig-Jahn-Str. 15A, D-17475, Greifswald, Germany.
| | - Elke Hammer
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, , Friedrich-Ludwig-Jahn-Str. 15A, D-17475, Greifswald, Germany. .,DZHK (German Centre for Cardiovascular Research), partner site Greifswald, Greifswald, Germany.
| | - Uwe Völker
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, , Friedrich-Ludwig-Jahn-Str. 15A, D-17475, Greifswald, Germany. .,DZHK (German Centre for Cardiovascular Research), partner site Greifswald, Greifswald, Germany.
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18
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Kloppot P, Selle M, Kohler C, Stentzel S, Fuchs S, Liebscher V, Müller E, Kale D, Ohlsen K, Bröker BM, Zipfel PF, Kahl BC, Ehricht R, Hecker M, Engelmann S. Microarray-based identification of human antibodies against Staphylococcus aureus antigens. Proteomics Clin Appl 2015; 9:1003-11. [PMID: 25676254 DOI: 10.1002/prca.201400123] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 01/06/2015] [Accepted: 02/05/2015] [Indexed: 02/03/2023]
Abstract
PURPOSE The mortality rate of patients with Staphylococcus aureus infections is alarming and urgently demands new strategies to attenuate the course of these infections or to detect them at earlier stages. EXPERIMENTAL DESIGN To study the adaptive immune response to S. aureus antigens in healthy human volunteers, a protein microarray containing 44 S. aureus proteins was developed using the ArrayStrip platform technology. RESULTS Testing plasma samples from 15 S. aureus carriers and 15 noncarriers 21 immunogenic S. aureus antigens have been identified. Seven antigens were recognized by antibodies present in at least 60% of the samples, representing the core S. aureus immunome of healthy individuals. S. aureus-specific serum immunoglobulin G (IgG) levels were significantly lower in noncarriers than in carriers specifically anti-IsaA, anti-SACOL0479, and anti-SACOL0480 IgGs were found at lower frequencies and quantities. Twenty-two antigens present on the microarray were encoded by all S. aureus carrier isolates. Nevertheless, the immune system of the carriers was responsive to only eight of them and with different intensities. CONCLUSION AND CLINICAL RELEVANCE The established protein microarray allows a broad profiling of the S. aureus-specific antibody response and can be used to identify S. aureus antigens that might serve as vaccines or diagnostic markers.
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Affiliation(s)
- Peggy Kloppot
- Institut für Mikrobiologie, Universität Greifswald, Greifswald, Germany
| | - Martina Selle
- Institut für Molekulare Infektionsbiologie, Universität Würzburg, Würzburg, Germany
| | - Christian Kohler
- Institut für Mikrobiologie, Universität Greifswald, Greifswald, Germany
| | - Sebastian Stentzel
- Institut für Immunologie und Transfusionsmedizin, Universitätsmedizin Greifswald, Greifswald, Germany
| | - Stephan Fuchs
- Institut für Mikrobiologie, Universität Greifswald, Greifswald, Germany
| | - Volkmar Liebscher
- Institut für Mathematik und Informatik, Universität Greifswald, Greifswald, Germany
| | | | - Devika Kale
- Institut für Medizinische Mikrobiologie, Universitätsklinikum Münster, Münster, Germany
| | - Knut Ohlsen
- Institut für Molekulare Infektionsbiologie, Universität Würzburg, Würzburg, Germany
| | - Barbara M Bröker
- Institut für Immunologie und Transfusionsmedizin, Universitätsmedizin Greifswald, Greifswald, Germany
| | - Peter F Zipfel
- Infektionsbiologie, Hans-Knöll-Institut Jena, Münster, Germany.,Friedrich Schiller Universität, Jena, Germany
| | - Barbara C Kahl
- Institut für Medizinische Mikrobiologie, Universitätsklinikum Münster, Münster, Germany
| | | | - Michael Hecker
- Institut für Mikrobiologie, Universität Greifswald, Greifswald, Germany
| | - Susanne Engelmann
- Institut für Mikrobiologie, Universität Greifswald, Greifswald, Germany.,Institut für Mikrobiologie, TU Braunschweig, Braunschweig, Germany.,Mikrobielle Proteomik, Helmholtzzentrum für Infektionsforschung, Braunschweig, Germany
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19
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Ivanovska T, Laqua R, Wang L, Liebscher V, Völzke H, Hegenscheid K. A level set based framework for quantitative evaluation of breast tissue density from MRI data. PLoS One 2014; 9:e112709. [PMID: 25422942 PMCID: PMC4244105 DOI: 10.1371/journal.pone.0112709] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 10/14/2014] [Indexed: 11/29/2022] Open
Abstract
Breast density is a risk factor associated with the development of breast cancer. Usually, breast density is assessed on two dimensional (2D) mammograms using the American College of Radiology (ACR) classification. Magnetic resonance imaging (MRI) is a non-radiation based examination method, which offers a three dimensional (3D) alternative to classical 2D mammograms. We propose a new framework for automated breast density calculation on MRI data. Our framework consists of three steps. First, a recently developed method for simultaneous intensity inhomogeneity correction and breast tissue and parenchyma segmentation is applied. Second, the obtained breast component is extracted, and the breast-air and breast-body boundaries are refined. Finally, the fibroglandular/parenchymal tissue volume is extracted from the breast volume. The framework was tested on 37 randomly selected MR mammographies. All images were acquired on a 1.5T MR scanner using an axial, T1-weighted time-resolved angiography with stochastic trajectories sequence. The results were compared to manually obtained groundtruth. Dice's Similarity Coefficient (DSC) as well as Bland-Altman plots were used as the main tools for evaluation of similarity between automatic and manual segmentations. The average Dice's Similarity Coefficient values were and for breast and parenchymal volumes, respectively. Bland-Altman plots showed the mean bias () standard deviation equal for breast volumes and for parenchyma volumes. The automated framework produced sufficient results and has the potential to be applied for the analysis of breast volume and breast density of numerous data in clinical and research settings.
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Affiliation(s)
- Tatyana Ivanovska
- Institute of Community Medicine, University Medicine Greifswald, Greifswald, Germany
- * E-mail:
| | - René Laqua
- Institute of Diagnostic Radiology and Neuroradiology, University Medicine Greifswald, Greifswald, Germany
| | - Lei Wang
- Fraunhofer Institute for Medical Image Computing MEVIS, Bremen, Germany
| | - Volkmar Liebscher
- Institute of Mathematics and Informatics, Ernst-Moritz-Arndt University, Greifswald, Germany
| | - Henry Völzke
- Institute of Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Katrin Hegenscheid
- Institute of Diagnostic Radiology and Neuroradiology, University Medicine Greifswald, Greifswald, Germany
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20
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Siatkowski M, Liebscher V, Fuellen G. CellFateScout - a bioinformatics tool for elucidating small molecule signaling pathways that drive cells in a specific direction. Cell Commun Signal 2013; 11:85. [PMID: 24206562 PMCID: PMC3833265 DOI: 10.1186/1478-811x-11-85] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 10/29/2013] [Indexed: 12/12/2022] Open
Abstract
Background Small molecule effects can be represented by active signaling pathways within functional networks. Identifying these can help to design new strategies to utilize known small molecules, e.g. to trigger specific cellular transformations or to reposition known drugs. Results We developed CellFateScout that uses the method of Latent Variables to turn differential high-throughput expression data and a functional network into a list of active signaling pathways. Applying it to Connectivity Map data, i.e., differential expression data describing small molecule effects, we then generated a Human Small Molecule Mechanisms Database. Finally, using a list of active signaling pathways as query, a similarity search can identify small molecules from the database that may trigger these pathways. We validated our approach systematically, using expression data of small molecule perturbations, yielding better predictions than popular bioinformatics tools. Conclusions CellFateScout can be used to select small molecules for their desired effects. The CellFateScout Cytoscape plugin, a tutorial and the Human Small Molecule Mechanisms Database are available at https://sourceforge.net/projects/cellfatescout/ under LGPLv2 license.
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Affiliation(s)
| | | | - Georg Fuellen
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, University of Rostock, Ernst Heydemann Strasse 8, D-18057 Rostock, Germany.
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21
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Stahnke N, Liebscher V, Staubach C, Ziller M. An approach to model monitoring and surveillance data of wildlife diseases—Exemplified by Classical Swine Fever in wild boar. Prev Vet Med 2013; 112:355-69. [DOI: 10.1016/j.prevetmed.2013.07.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 07/29/2013] [Accepted: 07/31/2013] [Indexed: 10/26/2022]
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22
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Klaere S, Liebscher V. An algebraic analysis of the two state Markov model on tripod trees. Math Biosci 2012; 237:38-48. [PMID: 22430560 DOI: 10.1016/j.mbs.2012.03.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2010] [Revised: 02/22/2012] [Accepted: 03/02/2012] [Indexed: 11/15/2022]
Abstract
Methods of phylogenetic inference use more and more complex models to generate trees from data. However, even simple models and their implications are not fully understood. Here, we investigate the two-state Markov model on a tripod tree, inferring conditions under which a given set of observations gives rise to such a model. This type of investigation has been undertaken before by several scientists from different fields of research. In contrast to other work we fully analyse the model, presenting conditions under which one can infer a model from the observation or at least get support for the tree-shaped interdependence of the leaves considered. We also present all conditions under which the results can be extended from tripod trees to quartet trees, a step necessary to reconstruct at least a topology. Apart from finding conditions under which such an extension works we discuss example cases for which such an extension does not work.
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Affiliation(s)
- Steffen Klaere
- Department of Statistics and School of Biological Sciences, The University of Auckland, Auckland, New Zealand.
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23
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Gloger O, Tönies KD, Liebscher V, Kugelmann B, Laqua R, Völzke H. Prior shape level set segmentation on multistep generated probability maps of MR datasets for fully automatic kidney parenchyma volumetry. IEEE Trans Med Imaging 2012; 31:312-325. [PMID: 21937343 DOI: 10.1109/tmi.2011.2168609] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Fully automatic 3-D segmentation techniques for clinical applications or epidemiological studies have proven to be a very challenging task in the domain of medical image analysis. 3-D organ segmentation on magnetic resonance (MR) datasets requires a well-designed segmentation strategy due to imaging artifacts, partial volume effects, and similar tissue properties of adjacent tissues. We developed a 3-D segmentation framework for fully automatic kidney parenchyma volumetry that uses Bayesian concepts for probability map generation. The probability map quality is improved in a multistep refinement approach. An extended prior shape level set segmentation method is then applied on the refined probability maps. The segmentation quality is improved by incorporating an exterior cortex edge alignment technique using cortex probability maps. In contrast to previous approaches, we combine several relevant kidney parenchyma features in a sequence of segmentation techniques for successful parenchyma delineation on native MR datasets. Furthermore, the proposed method is able to recognize and exclude parenchymal cysts from the parenchymal volume. We analyzed four different quality measures showing better results for right parenchymal tissue than for left parenchymal tissue due to an incorporated liver part removal in the segmentation framework. The results show that the outer cortex edge alignment approach successfully improves the quality measures.
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Affiliation(s)
- Oliver Gloger
- Institute for Community Medicine, Ernst Moritz Arndt University of Greifswald, 17475 Greifswald, Germany.
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24
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Affiliation(s)
- G. Winkler
- a Institute of Biomathematics and Biometrics, GSF , National Research Center for Environment and Health , Postfach 1129, Oberschleißheim , D-85758 , Germany E-mail:
| | - V. Liebscher
- b Institute of Biomathematics and Biometrics, GSF , National Research Center for Environment and Health , Postfach 1129, Oberschleißheim , D-85758 , Germany E-mail:
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25
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Gotzen B, Liebscher V, Walcher S. On a class of deterministic population models with stochastic foundation. Bull Math Biol 2010; 73:1559-82. [PMID: 20827511 DOI: 10.1007/s11538-010-9581-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Accepted: 08/13/2010] [Indexed: 10/19/2022]
Abstract
Generalising a site-based stochastic model due to Royama, Solé et al. and Sumpter et al., we investigate competition in a single species with discrete, non-overlapping generations. We show that the deterministic limit of the dynamics depends on a few easily interpretable parameters only. Further, we discuss qualitative properties and limit sets of the corresponding difference equations, and we relate these to modes of competition. Moreover, a detailed analysis of stochastic effects in some relevant scenarios indicates that the behaviour of the stochastic model is very sensitive to further details of the model.
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Affiliation(s)
- Bernd Gotzen
- Lehrstuhl A für Mathematik, RWTH Aachen, Aachen, Germany
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26
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Müller J, Kuttler C, Hense BA, Zeiser S, Liebscher V. Transcription, intercellular variability and correlated random walk. Math Biosci 2009; 216:30-9. [PMID: 18762199 DOI: 10.1016/j.mbs.2008.08.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2007] [Revised: 07/29/2008] [Accepted: 08/02/2008] [Indexed: 01/03/2023]
Abstract
We develop a simple model for the random distribution of a gene product. It is assumed that the only source of variance is due to switching transcription on and off by a random process. Under the condition that the transition rates between on and off are constant we find that the amount of mRNA follows a scaled Beta distribution. Additionally, a simple positive feedback loop is considered. The simplicity of the model allows for an explicit solution also in this setting. These findings in turn allow, e.g., for easy parameter scans. We find that bistable behavior translates into bimodal distributions. These theoretical findings are in line with experimental results.
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Affiliation(s)
- Johannes Müller
- Technische Universität München, Centre for Mathematical Sciences, Boltzmannstrasse 3, 85748 Garching/Munich, Germany.
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27
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Boysen L, Kempe A, Liebscher V, Munk A, Wittich O. Consistencies and rates of convergence of jump-penalized least squares estimators. Ann Stat 2009. [DOI: 10.1214/07-aos558] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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28
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Zeiser S, Franz U, Müller J, Liebscher V. Hybrid Modeling of Noise Reduction by a Negatively Autoregulated System. Bull Math Biol 2009; 71:1006-24. [DOI: 10.1007/s11538-008-9391-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2007] [Accepted: 12/02/2008] [Indexed: 01/03/2023]
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Abstract
Somitogenesis describes the segmentation of vertebrate embryonic bodies, which is thought to be induced by ultradian clocks (i.e., clocks with relatively short cycles compared to circadian clocks). One candidate for such a clock is the bHLH factor Hes1, forming dimers which repress the transcription of its own encoding gene. Most models for such small autoregulative networks are based on delay equations where a Hill function represents the regulation of transcription. The aim of the present paper is to estimate the Hill coefficient in the switch of an Hes1 oscillator and to suggest a more detailed model of the autoregulative network. The promoter of Hes1 consists of three to four binding sites for Hes1 dimers. Using the sparse data from literature, we find, in contrast to other statements in literature, that there is not much evidence for synergistic binding in the regulatory region of Hes1, and that the Hill coefficient is about three. As a model for the negative feedback loop, we use a Goodwin system and find sustained oscillations for systems with a large enough number of linear differential equations. By a suitable variation of the number of equations, we provide a rational lower bound for the Hill coefficient for such a system. Our results suggest that there exist additional nonlinear processes outside of the regulatory region of Hes1.
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Affiliation(s)
- Stefan Zeiser
- GSF-National Research Centre for Environment and Health, Institute of Biomathematics and Biometry, Oberschleissheim, Germany.
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Zeiser S, Franz U, Wittich O, Liebscher V. Simulation of genetic networks modelled by piecewise deterministic Markov processes. IET Syst Biol 2008; 2:113-35. [DOI: 10.1049/iet-syb:20070045] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Wagenstaller J, Spranger S, Lorenz-Depiereux B, Kazmierczak B, Nathrath M, Wahl D, Heye B, Glaser D, Liebscher V, Meitinger T, Strom TM. Copy-number variations measured by single-nucleotide-polymorphism oligonucleotide arrays in patients with mental retardation. Am J Hum Genet 2007; 81:768-79. [PMID: 17847001 PMCID: PMC2227926 DOI: 10.1086/521274] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2007] [Accepted: 06/26/2007] [Indexed: 12/31/2022] Open
Abstract
Whole-genome analysis using high-density single-nucleotide-polymorphism oligonucleotide arrays allows identification of microdeletions, microduplications, and uniparental disomies. We studied 67 children with unexplained mental retardation with normal karyotypes, as assessed by G-banded chromosome analyses. Their DNAs were analyzed with Affymetrix 100K arrays. We detected 11 copy-number variations that most likely are causative of mental retardation, because they either arose de novo (9 cases) and/or overlapped with known microdeletions (2 cases). The eight deletions and three duplications varied in size from 200 kb to 7.5 Mb. Of the 11 copy-number variations, 5 were flanked by low-copy repeats. Two of those, on chromosomes 15q25.2 and Xp22.31, have not been described before and have a high probability of being causative of new deletion and duplication syndromes, respectively. In one patient, we found a deletion affecting only a single gene, MBD5, which codes for the methyl-CpG-binding domain protein 5. In addition to the 67 children, we investigated 4 mentally retarded children with apparent balanced translocations and detected four deletions at breakpoint regions ranging in size from 1.1 to 14 Mb.
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Affiliation(s)
- Janine Wagenstaller
- Institute of Human Genetics, GSF National Research Center for Environment and Health, Munich-Neuherberg, Germany
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Drobyshev AL, Machka C, Horsch M, Seltmann M, Liebscher V, Hrabé de Angelis M, Beckers J. Specificity assessment from fractionation experiments (SAFE): a novel method to evaluate microarray probe specificity based on hybridisation stringencies. Nucleic Acids Res 2003; 31:E1-1. [PMID: 12527790 PMCID: PMC140526 DOI: 10.1093/nar/gng001] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The cDNA-chip technology is a highly versatile tool for the comprehensive analysis of gene expression at the transcript level. Although it has been applied successfully in expression profiling projects, there is an ongoing dispute concerning the quality of such expression data. The latter critically depends on the specificity of hybridisation. SAFE (specificity assessment from fractionation experiments) is a novel method to discriminate between non- specific cross-hybridisation and specific signals. We applied in situ fractionation of hybridised target on DNA-chips by means of repeated washes with increasing stringencies. Different fractions of hybridised target are washed off at defined stringencies and the collected fluorescence intensity data at each step comprise the fractionation curve. Based on characteristic features of the fractionation curve, unreliable data can be filtered and eliminated from subsequent analyses. The approach described here provides a novel experimental tool to identify probes that produce specific hybridisation signals in DNA-chip expression profiling approaches. The iterative use of the SAFE procedure will result in increasingly reliable sets of probes for microarray experiments and significantly improve the overall efficiency and reliability of RNA expression profiling data from DNA-chip experiments.
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Affiliation(s)
- Alexei L Drobyshev
- Institute of Experimental Genetics, GSF-National Research Centre for Environment and Health, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
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Liebscher V. Diagonal versions and quantum stochastic integrals on the symmetric Fock space with nonadapted integrands. Probab Theory Relat Fields 1998. [DOI: 10.1007/s004400050190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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