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arXiv 2024年

作者： Ingham, John F. Hutchings, Frances Zuliani, Paolo Wang, Yujiang Soudjani, Sadegh Taylor, Peter N. Interdisciplinary Computing and Complex BioSystems Group School of Computing Newcastle University Newcastle upon Tyne United Kingdom Faculty of Medical Sciences Newcastle University Newcastle upon Tyne United Kingdom UCL Queen Square Institute of Neurology Queen Square London United Kingdom Dipartimento di Informatica Università di Roma "La Sapienza" Rome Italy Max Planck Institute for Software Systems Kaiserslautern Germany

Vagus Nerve Stimulation (VNS) is an established palliative treatment for drug resistant epilepsy. While effective for many patients, its mechanism of action is incompletely understood. Predicting individuals’ response, or optimum stimulation parameters, is challenging. Computational modelling has informed other problems in epilepsy but, to our knowledge, has not been applied to VNS. We started with an established, four-population neural mass model (NMM), capable of reproducing the seizure-like dynamics of a thalamocortical circuit. We extended this to include 18 further neural populations, representing nine other brain regions relevant to VNS, with connectivity based on existing literature. We modelled stimulated afferent vagal fibres as projecting to the nucleus tractus solitarius (NTS), which receives input from the vagus nerve in vivo. Bifurcation analysis of a deterministic version of the model showed higher background NTS input made the model monostable at a fixed point (FP), representing normal activity, while lower inputs produce bistability between the FP and a limit cycle (LC), representing the seizure state. Adding noise produced transitions between seizure and normal states. This stochastic model spent decreasing time in the seizure state with increasing background NTS input, until seizures were abolished, consistent with the deterministic model. Simulated VNS stimulation, modelled as a 30 Hz square wave, was summed with the background input to the NTS and was found to reduce total seizure duration in a dose-dependent manner, similar to expectations in vivo. We have successfully produced an in silico model of VNS in epilepsy, capturing behaviour seen in vivo. This may aid understanding therapeutic mechanisms of VNS in epilepsy and provides a starting point to (i) determine which patients might respond best to VNS, and (ii) optimise individuals’ treatments. Copyright © 2024, The Authors. All rights reserved.

关键词： Stochastic models

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Carbogen inhalation during non-convulsive status epilepticus: A quantitative analysis of EEG recordings

arXiv

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arXiv 2019年

作者： Ramaraju, S. Reichert, S. Wang, Y. Forsyth, R. Taylor, P.N. Interdisciplinary Computing and Complex Bio-Systems Group School of Computing Science Newcastle University United Kingdom Department of Electrical Engineering Medical Engineering and Computer Science Offenburg University of Applied Sciences Germany Institute of Neuroscience Faculty of Medical Science Newcastle University United Kingdom

Objective: To quantify the effect of inhaled 5% carbon-dioxide/95% oxygen on EEG recordings from patients in non-convulsive status epilepticus (NCSE). Methods: Five children of mixed aetiology in NCSE were given high flow of inhaled carbogen (5% carbon dioxide/95% oxygen) using a face mask for maximum 120s. EEG was recorded concurrently in all patients. The effects of inhaled carbogen on patient EEG recordings were investigated using band-power, functional connectivity and graph theory measures. Carbogen effect was quantified by measuring effect size (Cohen's d) between "before", "during" and "after" carbogen delivery states. Results: Carbogen's apparent effect on EEG band-power and network metrics across all patients for "before-during" and "before-after" inhalation comparisons was inconsistent across the five patients. Conclusion: The changes in different measures suggest a potentially non-homogeneous effect of carbogen on the patients' EEG. Different aetiology and duration of the inhalation may underlie these non-homogeneous effects. Tuning the carbogen parameters (such as ratio between CO2 and O2, duration of inhalation) on a personalised basis may improve seizure suppression in future. Copyright © 2019, The Authors. All rights reserved.

关键词： Carbon dioxide

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Independent components of human brain morphology

arXiv

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arXiv 2020年

作者： Wang, Yujiang Ludwig, Tobias Little, Bethany Necus, Joe H. Winston, Gavin Vos, Sjoerd B. de Tisi, Jane Duncan, John S. Taylor, Peter N. Mota, Bruno Interdisciplinary Complex Systems Group School of Computing Newcastle University Newcastle upon Tyne United Kingdom Faculty of Medical Sciences Newcastle University Newcastle upon Tyne United Kingdom UCL Queen Square Institute of Neurology London United Kingdom Graduate Training Center of Neuroscience University of Tübingen Tübingen Germany University College London London United Kingdom Department of Clinical and Experimental Epilepsy University College London London United Kingdom Department of Medicine Division of Neurology Queens University Kingston Canada Epilepsy Society MRI Unit Chalfont St Peter United Kingdom Institute of Physics Federal University of Rio de Janeiro Brazil

Quantification of brain morphology has become an important cornerstone in understanding brain structure. Measures of cortical morphology such as thickness and surface area are frequently used to compare groups of subjects or characterise longitudinal changes. However, such measures are often treated as independent from each other. A recently described scaling law, derived from a statistical physics model of cortical folding, demonstrates that there is a tight covariance between three commonly used cortical morphology measures: cortical thickness, total surface area, and exposed surface area. We show that assuming the independence of cortical morphology measures can hide features and potentially lead to misinterpretations. Using the scaling law, we account for the covariance between cortical morphology measures and derive novel independent measures of cortical morphology. By applying these new measures, we show that new information can be gained;in our example we show that distinct morphological alterations underlie healthy ageing compared to temporal lobe epilepsy, even on the coarse level of a whole hemisphere. We thus provide a conceptual framework for characterising cortical morphology in a statistically valid and interpretable manner, based on theoretical reasoning about the shape of the cortex. Copyright © 2020, The Authors. All rights reserved.

关键词： Morphology

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Reliability and comparability of human brain structural covariance networks

arXiv

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arXiv 2019年

作者： Carmon, Jona Heege, Jil Necus, Joe H. Owen, Thomas W. Pipa, Gordon Kaiser, Marcus Taylor, Peter N. Wang, Yujiang Institute of Cognitive Science Osnabrueck University Osnabrueck Germany Humboldt University Berlin Berlin Germany Interdisciplinary Complex Systems Group School of Computing Newcastle University Newcastle upon Tyne United Kingdom Institute of Neuroscience Faculty of Medical Sciences Newcastle University Newcastle upon Tyne United Kingdom Institute of Neurology University College London United Kingdom School of Medicine Shanghai Jiao Tong University Shanghai China

Structural covariance analysis is a promising and increasingly used structural Magnetic Resonance Imaging (MRI) analysis method which characterises the co-relations of morphology between brain regions over a group of subjects. However, to our knowledge, little has been investigated in terms of the comparability of results between different data sets of healthy human subjects as well as the reliability of results over different rescan sessions and FreeSurfer versions. Our results show (significant) differences of structural covariance between two data sets of age- and sex-matched healthy human adults. This low comparability is unaltered by site correction, and is most severe when using average cortical thickness as a measure of cortical morphology. The low comparability further extends to significant differences in graph theoretic measures. Similar results of low reliability were found when comparing rescan sessions of the same subjects, and even between different FreeSurfer versions of the same scans. To understand our observations of low reliability, we estimated a measurement error covariance, and we show that it is largest in cortical thickness. On simulated data we further demonstrated that stronger errors cause stronger attenuation of correlations and proportionally decreases reliability, which agrees with associations we observed in the real data. To our knowledge this study is the first highlight the problem of reliability and comparability in structural covariance. Practically, we suggest that (1) combining data from different scanners and sites for structural covariance analysis in a naive manner should be avoided, (2) surface area and volume should be preferred as morphological measures of structural covariance over cortical thickness, and (3) some analysis of robustness of the results should be performed for every structural covariance study. Copyright © 2019, The Authors. All rights reserved.

关键词： Brain

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Complete edge-colored permutation graphs

arXiv

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arXiv 2020年

作者： Hartmann, Tom Bannach, Max Middendorf, Martin Stadler, Peter F. Wieseke, Nicolas Hellmuth, Marc Bioinformatics Group Department of Computer Science & Interdisciplinary Center for Bioinformatics Universität Leipzig Härtelstraße 16–18 LeipzigD-04107 Germany Institute for Theoretical Computer Science Universität zu Lübeck Ratzeburger Allee 160 LübeckD-23562 Germany Swarm Intelligence and Complex Systems Group Faculty of Mathematics and Computer Science University of Leipzig Augustusplatz 10 LeipzigD-04109 Germany Halle-Jena-Leipzig Competence Center for Scalable Data Services and Solutions Dresden-Leipzig Leipzig Research Center for Civilization Diseases Centre for Biotechnology and Biomedicine at Leipzig University Universität Leipzig Max Planck Institute for Mathematics in the Sciences Inselstraße 22 LeipzigD-04103 Germany Institute for Theoretical Chemistry University of Vienna Währingerstrasse 17 WienA-1090 Austria Facultad de Ciencias Universidad National de Colombia Sede Bogotá Colombia Santa Fe Insitute 1399 Hyde Park Rd. Santa FeNM87501 United States School of Computing University of Leeds EC Stoner Building LeedsLS2 9JT United Kingdom

We introduce the concept of complete edge-colored permutation graphs as complete graphs that are the edge-disjoint union of "classical" permutation graphs. We show that a graph G = (V, E) is a complete edge-colored permutation graph if and only if each monochromatic subgraph of G is a "classical" permutation graph and G does not contain a triangle with 3 different colors. Using the modular decomposition as a framework we demonstrate that complete edge-colored permutation graphs are characterized in terms of their strong prime modules, which induce also complete edge-colored permutation graphs. This leads to an O(|V |2)-time recognition algorithm. We show, moreover, that complete edge-colored permutation graphs form a superclass of so-called symbolic ultrametrics and that the coloring of such graphs is always a Gallai coloring. Copyright © 2020, The Authors. All rights reserved.

关键词： Graphic methods

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Forbidden time travel: Characterization of time-consistent tree reconciliation maps 17

Forbidden time travel: Characterization of time-consistent t...

引用

17th International Workshop on Algorithms in Bioinformatics, WABI 2017

作者： Nøjgaard, Nikolai Geiß, Manuela Merkle, Daniel Stadler, Peter F. Wieseke, Nicolas Hellmuth, Marc Department of Mathematics and Computer Science University of Greifswald Greifswald Germany Department of Mathematics and Computer Science University of Southern Denmark Denmark Bioinformatics Group Department of Computer Science Interdisciplinary Center of Bioinformatics University of Leipzig Leipzig Germany Max-Planck-Institute for Mathematics in the Sciences Leipzig Germany Institute for Theoretical Chemistry University of Vienna Vienna Austria Santa Fe Institute Santa FeNM United States Parallel Computing and Complex Systems Group Department of Computer Science Leipzig University Leipzig Germany Saarland University Center for Bioinformatics Saarbrücken Germany

ISBN: (纸本)9783959770507

Motivation: In the absence of horizontal gene transfer it is possible to reconstruct the history of gene families from empirically determined orthology relations, which are equivalent to eventlabeled gene trees. Knowledge of the event labels considerably simplifies the problem of reconciling a gene tree T with a species trees S, relative to the reconciliation problem without prior knowledge of the event types. It is well-known that optimal reconciliations in the unlabeled case may violate time-consistency and thus are not biologically feasible. Here we investigate the mathematical structure of the event labeled reconciliation problem with horizontal transfer. Results: We investigate the issue of time-consistency for the event-labeled version of the reconciliation problem, provide a convenient axiomatic framework, and derive a complete characterization of time-consistent reconciliations. This characterization depends on certain weak conditions on the event-labeled gene trees that reflect conditions under which evolutionary events are observable at least in principle. We give an O(|V (T)| log(|V (S)|))-time algorithm to decide whether a time-consistent reconciliation map exists. It does not require the construction of explicit timing maps, but relies entirely on the comparably easy task of checking whether a small auxiliary graph is acyclic. Significance: The combinatorial characterization of time consistency and thus biologically feasible reconciliation is an important step towards the inference of gene family histories with horizontal transfer from orthology data, i.e., without presupposed gene and species trees. The fast algorithm to decide time consistency is useful in a broader context because it constitutes an attractive component for all tools that address tree reconciliation problems. © Nikolai Nøjgaard, Manuela Geiß, Daniel Merkle, Peter F. Stadler, Nicolas Wieseke, and Marc Hellmuth.

关键词： Genes

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From event labeled gene trees to species trees

arXiv

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arXiv 2017年

作者： Hernandez-Rosales, Maribel Hellmuth, Marc Wieseke, Nicolas Huber, Katharina T. Moulton, Vincent Stadler, Peter F. Dpt. of Mathematics and Computer Science University of Greifswald Walther- Rathenau-Strasse 47 GreifswaldD-17487 Saarland University Center for Bioinformatics Building e 2.1 P.O. Box 151150 SaarbrückenD-66041 Bioinformatics Group Department of Computer Science Interdisciplinary Center of Bioinformatics University of Leipzig Härtelstraße 16-18 LeipzigD-04107 Germany School of Computing Sciences University of East Anglia NorwichNR4 7TJ United Kingdom Max-Planck-Institute for Mathematics in the Sciences Inselstraße 22 LeipzigD-04103 Germany Inst. F. Theoretical Chemistry University of Vienna Währingerstraße 17 WienA-1090 Austria Santa Fe Institute 1399 Hyde Park Rd. Santa Fe United States Parallel Computing and Complex Systems Group Department of Computer Science Leipzig University Augustusplatz 10 Leipzig04109 Germany

Background: Tree reconciliation problems have long been studied in phylogenetics. A particular variant of the reconciliation problem for a gene tree T and a species tree S assumes that for each interior vertex x of T it is known whether x represents a speciation or a duplication. This problem appears in the context of analyzing orthology data. Results: We show that S is a species tree for T if and only if S displays all rooted triples of T that have three distinct species as their leaves and are rooted in a speciation vertex. A valid reconciliation map can then be found in polynomial time. Simulated data shows that the event-labeled gene trees convey a large amount of information on underlying species trees, even for a large percentage of losses. Conclusions: The knowledge of event labels in a gene tree strongly constrains the possible species tree and, for a given species tree, also the possible reconciliation maps. Nevertheless, many degrees of freedom remain in the space of feasible solutions. In order to disambiguate the alternative solutions additional external constraints as well as optimization criteria could be employed. Copyright © 2017, The Authors. All rights reserved.

关键词： Polynomial approximation

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Forbidden time travel: Characterization of time-consistent tree reconciliation maps

arXiv

引用

arXiv 2017年

作者： Nøjgaard, Nikolai Geiß, Manuela Stadler, Peter F. Merkle, Daniel Wieseke, Nicolas Hellmuth, Marc Dpt. of Mathematics and Computer Science University of Greifswald Walther- Rathenau-Strasse 47 GreifswaldD-17487 Saarland University Center for Bioinformatics Building e 2.1 P.O. Box 151150 SaarbrückenD-66041 Bioinformatics Group Department of Computer Science Interdisciplinary Center of Bioinformatics University of Leipzig Härtelstraße 16-18 LeipzigD-04107 Germany Department of Mathematics and Computer Science University of Southern Denmark Max-Planck-Institute for Mathematics in the Sciences Inselstraße 22 LeipzigD-04103 Germany Inst. F. Theoretical Chemistry University of Vienna Währingerstraße 17 WienA-1090 Austria Santa Fe Institute 1399 Hyde Park Rd. Santa Fe United States Parallel Computing and Complex Systems Group Department of Computer Science Leipzig University Augustusplatz 10 Leipzig04109 Germany

Motivation: In the absence of horizontal gene transfer it is possible to reconstruct the history of gene families from empirically determined orthology relations, which are equivalent to eventlabeled gene trees. Knowledge of the event labels considerably simplifies the problem of reconciling a gene tree T with a species trees S, relative to the reconciliation problem without prior knowledge of the event types. It is well-known that optimal reconciliations in the unlabeled case may violate time-consistency and thus are not biologically feasible. Here we investigate the mathematical structure of the event labeled reconciliation problem with horizontal transfer. Results: We investigate the issue of time-consistency for the event-labeled version of the reconciliation problem, provide a convenient axiomatic framework, and derive a complete characterization of time-consistent reconciliations. This characterization depends on certain weak conditions on the event-labeled gene trees that reflect conditions under which evolutionary events are observable at least in principle. We give an O(|V(T)|log(|V (S)|))-time algorithm to decide whether a time-consistent reconciliation map exists. It does not require the construction of explicit timing maps, but relies entirely on the comparably easy task of checking whether a small auxiliary graph is acyclic. Significance: The combinatorial characterization of time consistency and thus biologically feasible reconciliation is an important step towards the inference of gene family histories with horizontal transfer from orthology data, i.e., without presupposed gene and species trees. The fast algorithm to decide time consistency is useful in a broader context because it constitutes an attractive component for all tools that address tree reconciliation problems. Copyright © 2017, The Authors. All rights reserved.

关键词： Genes

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Reconstructing gene trees from Fitch's xenology relation

arXiv

引用

arXiv 2017年

作者： Geiß, Manuela Anders, John Stadler, Peter F. Wieseke, Nicolas Hellmuth, Marc Bioinformatics Group Department of Computer Science Interdisciplinary Center of Bioinformatics University of Leipzig Härtelstraße 16-18 LeipzigD-04107 Germany Dpt. of Mathematics and Computer Science University of Greifswald Walther- Rathenau-Strasse 47 GreifswaldD-17487 Germany Saarland University Center for Bioinformatics Building E 2.1 P.O. Box 151150 SaarbrückenD-66041 Germany Max-Planck-Institute for Mathematics in the Sciences Inselstraße 22 LeipzigD-04103 Germany Inst. f. Theoretical Chemistry University of Vienna Währingerstraße 17 WienA-1090 Austria Santa Fe Institute 1399 Hyde Park Rd. Santa Fe United States Parallel Computing and Complex Systems Group Department of Computer Science Leipzig University Augustusplatz 10 Leipzig04109 Germany

Two genes are xenologs in the sense of Fitch if they are separated by at least one horizontal gene transfer event. Horizonal gene transfer is asymmetric in the sense that the transferred copy is distinguished from the one that remains within the ancestral lineage. Hence xenology is more precisely thought of as a non-symmetric relation: y is xenologous to x if y has been horizontally transferred at least once since it diverged from the least common ancestor of x and y. We show that xenology relations are characterized by a small set of forbidden induced subgraphs on three vertices. Furthermore, each xenology relation can be derived from a unique least-resolved edge-labeled phylogenetic tree. We provide a linear-time algorithm for the recognition of xenology relations and for the construction of its least-resolved edge-labeled phylogenetic tree. The fact that being a xenology relation is a heritable graph property, finally has far-reaching consequences on approximation problems associated with xenology relations. Copyright © 2017, The Authors. All rights reserved.

关键词： Clustering algorithms

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Cograph editing: Merging modules is equivalent to editing P4s

arXiv

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arXiv 2017年

作者： Fritz, Adrian Hellmuth, Marc Wieseke, Nicolas Stadler, Peter F. Computational Biology of Infection Research Helmholtz Centre for Infection Research Inhoffenstraße 7 BraunschweigD-38124 Germany University of Greifswald Dpt. of Mathematics and Computer Science Walther- Rathenau-Strasse 47 GreifswaldD-17487 Germany Saarland University Center for Bioinformatics Building e 2.1 P.O. Box 151150 SaarbrückenD-66041 Germany Parallel Computing and Complex Systems Group Department of Computer Science University of Leipzig Augustusplatz 10 LeipzigD-04109 Germany Bioinformatics Group Department of Computer Science Interdisciplinary Center of Bioinformatics University of Leipzig Härtelstraße 16-18 LeipzigD-04107 Germany Max-Planck-Institute for Mathematics in the Sciences Inselstraße 22 LeipzigD-04103 Germany Inst. F. Theoretical Chemistry University of Vienna Währingerstraße 17 WienA-1090 Austria Santa Fe Institute 1399 Hyde Park Rd. Santa FeNM87501 United States

The modular decomposition of a graph G = (V;E) does not contain prime modules if and only if G is a cograph, that is, if no quadruple of vertices induces a simple connected path P4. The cograph editing problem consists in inserting into and deleting from G a set F of edges so that H = (V,EΔF) is a cograph and |F| is minimum. This NP-hard combinatorial optimization problem has recently found applications, e.g., in the context of phylogenetics. Efficient heuristics are hence of practical importance. The simple characterization of cographs in terms of their modular decomposition suggests that instead of editing G one could operate directly on the modular decomposition. We show here that editing the induced P4s is equivalent to resolving prime modules by means of a suitable defined merge operation on the submodules. Moreover, we characterize so-called module-preserving edit sets and demonstrate that optimal pairwise sequences of module-preserving edit sets exist for every non-cograph. This eventually leads to an exact algorithm for the cograph editing problem. In addition, we provide two heuristics with time complexity O(|V|3), resp., O(|V|2). Copyright © 2017, The Authors. All rights reserved.

关键词： Graph theory

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