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Persistent network homology

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https://www.readbyqxmd.com/read/29174401/the-gut-microbiota-facilitates-drifts-in-the-genetic-diversity-and-infectivity-of-bacterial-viruses
#1
Luisa De Sordi, Varun Khanna, Laurent Debarbieux
The intestinal microbiota and human health are intimately linked, but interactions between bacteria and bacteriophages in the context of the mammalian intestine remain largely unexplored. We used comparative population genomics to study a tripartite network consisting of a virulent bacteriophage, its bacterial host, and a phage-insensitive bacterial strain both in vitro and within the murine gut. The bacteriophage adapted to infect the insensitive strain when the three partners co-existed in the gut of conventional mice, but not in dixenic mice or in planktonic cultures...
November 16, 2017: Cell Host & Microbe
https://www.readbyqxmd.com/read/29115375/persistent-stat5-mediated-ros-production-and-involvement-of-aberrant-p53-apoptotic-signaling-in-the-resistance-of-chronic-myeloid-leukemia-to-imatinib
#2
Yanhong Cheng, Yingchan Hao, Aimei Zhang, Chaojie Hu, Xiaoxiao Jiang, Quan Wu, Xiucai Xu
The persistent activation of signal transducer and activator of transcription 5 (STAT5) may principally be attributed to breakpoint cluster region (BCR)-Abelson murine leukemia viral oncogene homolog 1 (ABL1), and have multi-faceted effects in the development of chronic myeloid leukemia (CML). The p53 protein network regulates important mechanisms in DNA damage repair, cell cycle regulation/checkpoints, and cell senescence and apoptosis, as demonstrated by its ability to positively regulate the expression of various pro-apoptotic genes, including B-cell lymphoma-2 (Bcl-2) and Bcl-2-associated X protein (Bax)...
October 20, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29075089/exact-topological-inference-for-paired-brain-networks-via-persistent-homology
#3
Moo K Chung, Victoria Vilalta-Gil, Hyekyoung Lee, Paul J Rathouz, Benjamin B Lahey, David H Zald
We present a novel framework for characterizing paired brain networks using techniques in hyper-networks, sparse learning and persistent homology. The framework is general enough for dealing with any type of paired images such as twins, multimodal and longitudinal images. The exact nonparametric statistical inference procedure is derived on testing monotonic graph theory features that do not rely on time consuming permutation tests. The proposed method computes the exact probability in quadratic time while the permutation tests require exponential time...
June 2017: Information Processing in Medical Imaging: Proceedings of the ... Conference
https://www.readbyqxmd.com/read/29062589/integration-of-canonical-and-noncanonical-pathways-in-tlr4-signaling-complex-regulation-of-the-wound-repair-program
#4
REVIEW
Paula J McKeown-Longo, Paul J Higgins
Significance: Chronic inflammation and maladaptive repair contribute to the development of fibrosis that negatively impacts quality of life and organ function. The toll-like receptor (TLR) system is a critical node in the tissue response to both exogenous (pathogen-associated) and endogenous (damage-associated) molecular pattern factors (PAMPs and DAMPs, respectively). The development of novel TLR ligand-, pathway-, and/or target gene-specific therapeutics may have clinical utility in the management of the exuberant inflammatory/fibrotic tissue response to injury without compromising the host defense to pathogens...
October 1, 2017: Advances in Wound Care
https://www.readbyqxmd.com/read/29027203/phylogenetically-persistent-purinergic-modulation-of-central-pattern-generators-for-breathing-in-lamprey-and-mammals
#5
Gregory D Funk
Vertebrate behaviours are produced by neuroglial networks that evolved from a common set of ancestral (homologous) traits, as well as unique specializations that created opportunities for new behaviours and exploitation of novel environments. This article is protected by copyright. All rights reserved.
October 13, 2017: Journal of Physiology
https://www.readbyqxmd.com/read/28866539/clique-community-persistence-a-topological-visual-analysis-approach-for-complex-networks
#6
Bastian Rieck, Ulderico Fugacci, Jonas Lukasczyk, Heike Leitte
Complex networks require effective tools and visualizations for their analysis and comparison. Clique communities have been recognized as a powerful concept for describing cohesive structures in networks. We propose an approach that extends the computation of clique communities by considering persistent homology, a topological paradigm originally introduced to characterize and compare the global structure of shapes. Our persistence-based algorithm is able to detect clique communities and to keep track of their evolution according to different edge weight thresholds...
August 29, 2017: IEEE Transactions on Visualization and Computer Graphics
https://www.readbyqxmd.com/read/28749969/topologynet-topology-based-deep-convolutional-and-multi-task-neural-networks-for-biomolecular-property-predictions
#7
Zixuan Cang, Guo-Wei Wei
Although deep learning approaches have had tremendous success in image, video and audio processing, computer vision, and speech recognition, their applications to three-dimensional (3D) biomolecular structural data sets have been hindered by the geometric and biological complexity. To address this problem we introduce the element-specific persistent homology (ESPH) method. ESPH represents 3D complex geometry by one-dimensional (1D) topological invariants and retains important biological information via a multichannel image-like representation...
July 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28456167/persistent-homology-of-time-dependent-functional-networks-constructed-from-coupled-time-series
#8
Bernadette J Stolz, Heather A Harrington, Mason A Porter
We use topological data analysis to study "functional networks" that we construct from time-series data from both experimental and synthetic sources. We use persistent homology with a weight rank clique filtration to gain insights into these functional networks, and we use persistence landscapes to interpret our results. Our first example uses time-series output from networks of coupled Kuramoto oscillators. Our second example consists of biological data in the form of functional magnetic resonance imaging data that were acquired from human subjects during a simple motor-learning task in which subjects were monitored for three days during a five-day period...
April 2017: Chaos
https://www.readbyqxmd.com/read/28451879/dynamical-persistence-of-active-sites-identified-in-maltose-binding-protein
#9
Dragan Nikolić, Violeta Kovačev-Nikolić
This study identifies dynamical properties of maltose-binding protein (MBP) useful in unveiling active site residues susceptible to ligand binding. The described methodology has been previously used in support of novel topological techniques of persistent homology and statistical inference in complex, multi-scale, high-dimensional data often encountered in computational biophysics. Here we outline a computational protocol that is based on the anisotropic elastic network models of 14 all-atom three-dimensional protein structures...
May 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28169281/gating-of-memory-encoding-of-time-delayed-cross-frequency-meg-networks-revealed-by-graph-filtration-based-on-persistent-homology
#10
Jarang Hahm, Hyekyoung Lee, Hyojin Park, Eunjoo Kang, Yu Kyeong Kim, Chun Kee Chung, Hyejin Kang, Dong Soo Lee
To explain gating of memory encoding, magnetoencephalography (MEG) was analyzed over multi-regional network of negative correlations between alpha band power during cue (cue-alpha) and gamma band power during item presentation (item-gamma) in Remember (R) and No-remember (NR) condition. Persistent homology with graph filtration on alpha-gamma correlation disclosed topological invariants to explain memory gating. Instruction compliance (R-hits minus NR-hits) was significantly related to negative coupling between the left superior occipital (cue-alpha) and the left dorsolateral superior frontal gyri (item-gamma) on permutation test, where the coupling was stronger in R than NR...
February 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28046127/structure-function-network-mapping-and-its-assessment-via-persistent-homology
#11
Hualou Liang, Hongbin Wang
Understanding the relationship between brain structure and function is a fundamental problem in network neuroscience. This work deals with the general method of structure-function mapping at the whole-brain level. We formulate the problem as a topological mapping of structure-function connectivity via matrix function, and find a stable solution by exploiting a regularization procedure to cope with large matrices. We introduce a novel measure of network similarity based on persistent homology for assessing the quality of the network mapping, which enables a detailed comparison of network topological changes across all possible thresholds, rather than just at a single, arbitrary threshold that may not be optimal...
January 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/27930309/sox2-progenitors-in-sharks-link-taste-development-with-the-evolution-of-regenerative-teeth-from-denticles
#12
Kyle J Martin, Liam J Rasch, Rory L Cooper, Brian D Metscher, Zerina Johanson, Gareth J Fraser
Teeth and denticles belong to a specialized class of mineralizing epithelial appendages called odontodes. Although homology of oral teeth in jawed vertebrates is well supported, the evolutionary origin of teeth and their relationship with other odontode types is less clear. We compared the cellular and molecular mechanisms directing development of teeth and skin denticles in sharks, where both odontode types are retained. We show that teeth and denticles are deeply homologous developmental modules with equivalent underlying odontode gene regulatory networks (GRNs)...
December 20, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27911727/role-of-the-bone-morphogenic-protein-pathway-in-developmental-haemopoiesis-and-leukaemogenesis
#13
REVIEW
Parto Toofan, Helen Wheadon
Myeloid leukaemias share the common characteristics of being stem cell-derived clonal diseases, characterised by excessive proliferation of one or more myeloid lineage. Chronic myeloid leukaemia (CML) arises from a genetic alteration in a normal haemopoietic stem cell (HSC) giving rise to a leukaemic stem cell (LSC) within the bone marrow (BM) 'niche'. CML is characterised by the presence of the oncogenic tyrosine kinase fusion protein breakpoint cluster region-abelson murine leukaemia viral oncogene homolog 1 (BCR-ABL), which is responsible for driving the disease through activation of downstream signal transduction pathways...
October 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27877115/insights-into-brain-architectures-from-the-homological-scaffolds-of-functional-connectivity-networks
#14
Louis-David Lord, Paul Expert, Henrique M Fernandes, Giovanni Petri, Tim J Van Hartevelt, Francesco Vaccarino, Gustavo Deco, Federico Turkheimer, Morten L Kringelbach
In recent years, the application of network analysis to neuroimaging data has provided useful insights about the brain's functional and structural organization in both health and disease. This has proven a significant paradigm shift from the study of individual brain regions in isolation. Graph-based models of the brain consist of vertices, which represent distinct brain areas, and edges which encode the presence (or absence) of a structural or functional relationship between each pair of vertices. By definition, any graph metric will be defined upon this dyadic representation of the brain activity...
2016: Frontiers in Systems Neuroscience
https://www.readbyqxmd.com/read/27859919/integrated-multimodal-network-approach-to-pet-and-mri-based-on-multidimensional-persistent-homology
#15
Hyekyoung Lee, Hyejin Kang, Moo K Chung, Seonhee Lim, Bung-Nyun Kim, Dong Soo Lee
Finding underlying relationships among multiple imaging modalities in a coherent fashion is one of the challenging problems in multimodal analysis. In this study, we propose a novel approach based on multidimensional persistence. In the extension of the previous threshold-free method of persistent homology, we visualize and discriminate the topological change of integrated brain networks by varying not only threshold but also mixing ratio between two different imaging modalities. The multidimensional persistence is implemented by a new bimodal integration method called 1D projection...
November 17, 2016: Human Brain Mapping
https://www.readbyqxmd.com/read/27793055/personalized-anticancer-therapy-selection-using-molecular-landscape-topology-and-thermodynamics
#16
Edward A Rietman, Jacob G Scott, Jack A Tuszynski, Giannoula Lakka Klement
Personalized anticancer therapy requires continuous consolidation of emerging bioinformatics data into meaningful and accurate information streams. The use of novel mathematical and physical approaches, namely topology and thermodynamics can enable merging differing data types for improved accuracy in selecting therapeutic targets. We describe a method that uses chemical thermodynamics and two topology measures to link RNA-seq data from individual patients with academically curated protein-protein interaction networks to select clinically relevant targets for treatment of low-grade glioma (LGG)...
March 21, 2017: Oncotarget
https://www.readbyqxmd.com/read/27650055/disrupted-brain-metabolic-connectivity-in-a-6-ohda-induced-mouse-model-of-parkinson-s-disease-examined-using-persistent-homology-based-analysis
#17
Hyung-Jun Im, Jarang Hahm, Hyejin Kang, Hongyoon Choi, Hyekyoung Lee, Do Won Hwang, E Edmund Kim, June-Key Chung, Dong Soo Lee
Movement impairments in Parkinson's disease (PD) are caused by the degeneration of dopaminergic neurons and the consequent disruption of connectivity in the cortico-striatal-thalamic loop. This study evaluated brain metabolic connectivity in a 6-Hydroxydopamine (6-OHDA)-induced mouse model of PD using (18)F-fluorodeoxy glucose positron emission tomography (FDG PET). Fourteen PD-model mice and ten control mice were used for the analysis. Voxel-wise t-tests on FDG PET results yielded no significant regional metabolic differences between the PD and control groups...
September 21, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27647921/molecular-organization-of-cytokinesis-nodes-and-contractile-rings-by-super-resolution-fluorescence-microscopy-of-live-fission-yeast
#18
Caroline Laplante, Fang Huang, Irene R Tebbs, Joerg Bewersdorf, Thomas D Pollard
Cytokinesis in animals, fungi, and amoebas depends on the constriction of a contractile ring built from a common set of conserved proteins. Many fundamental questions remain about how these proteins organize to generate the necessary tension for cytokinesis. Using quantitative high-speed fluorescence photoactivation localization microscopy (FPALM), we probed this question in live fission yeast cells at unprecedented resolution. We show that nodes, protein assembly precursors to the contractile ring, are discrete structural units with stoichiometric ratios and distinct distributions of constituent proteins...
October 4, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27544206/unity-and-disunity-in-evolutionary-sciences-process-based-analogies-open-common-research-avenues-for-biology-and-linguistics
#19
REVIEW
Johann-Mattis List, Jananan Sylvestre Pathmanathan, Philippe Lopez, Eric Bapteste
BACKGROUND: For a long time biologists and linguists have been noticing surprising similarities between the evolution of life forms and languages. Most of the proposed analogies have been rejected. Some, however, have persisted, and some even turned out to be fruitful, inspiring the transfer of methods and models between biology and linguistics up to today. Most proposed analogies were based on a comparison of the research objects rather than the processes that shaped their evolution...
2016: Biology Direct
https://www.readbyqxmd.com/read/27520814/understanding-the-streptococcus-mutans-cid-lrg-system-through-cidb-function
#20
Sang-Joon Ahn, Kelly C Rice
The Streptococcus mutans lrgAB and cidAB operons have been previously described as a potential model system to dissect the complexity of biofilm development and virulence of S. mutans Herein, we have attempted to further characterize the Cid/Lrg system by focusing on CidB, which has been shown to be critical for the ability of S. mutans to survive and persist in a nonpreferred oxygen-enriched condition. We have found that the expression level of cidB is critical to oxidative stress tolerance of S. mutans, most likely by impacting lrg expression...
October 15, 2016: Applied and Environmental Microbiology
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