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Persistent network homology

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https://www.readbyqxmd.com/read/29550052/airway-pathological-heterogeneity-in-asthma-visualization-of-disease-microclusters-using-topological-data-analysis
#1
Salman Siddiqui, Aarti Shikotra, Matthew Richardson, Emma Doran, David Choy, Alex Bell, Cary D Austin, Jeffrey Eastham-Anderson, Beverley Hargadon, Joseph R Arron, Andrew Wardlaw, Christopher E Brightling, Liam G Heaney, Peter Bradding
BACKGROUND: Asthma is a complex chronic disease underpinned by pathological changes within the airway wall. How variations in structural airway pathology and cellular inflammation contribute to the expression and severity of asthma are poorly understood. OBJECTIVES: Therefore we evaluated pathological heterogeneity using topological data analysis (TDA) with the aim of visualizing disease clusters and microclusters. METHODS: A discovery population of 202 adult patients (142 asthmatic patients and 60 healthy subjects) and an external replication population (59 patients with severe asthma) were evaluated...
March 7, 2018: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/29529083/pleiotropic-roles-of-clostridium-difficile-sin-locus
#2
Brintha Parasumanna Girinathan, Junjun Ou, Bruno Dupuy, Revathi Govind
Clostridium difficile is the primary cause of nosocomial diarrhea and pseudomembranous colitis. It produces dormant spores, which serve as an infectious vehicle responsible for transmission of the disease and persistence of the organism in the environment. In Bacillus subtilis, the sin locus coding SinR (113 aa) and SinI (57 aa) is responsible for sporulation inhibition. In B. subtilis, SinR mainly acts as a repressor of its target genes to control sporulation, biofilm formation, and autolysis. SinI is an inhibitor of SinR, so their interaction determines whether SinR can inhibit its target gene expression...
March 12, 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29497364/vulnerable-parkin-loss-of-function-drosophila-dopaminergic-neurons-have-advanced-mitochondrial-aging-mitochondrial-network-loss-and-transiently-reduced-autophagosome-recruitment
#3
Juliana Cackovic, Susana Gutierrez-Luke, Gerald B Call, Amber Juba, Stephanie O'Brien, Charles H Jun, Lori M Buhlman
Selective degeneration of substantia nigra dopaminergic (DA) neurons is a hallmark pathology of familial Parkinson's disease (PD). While the mechanism of degeneration is elusive, abnormalities in mitochondrial function and turnover are strongly implicated. An Autosomal Recessive-Juvenile Parkinsonism (AR-JP) Drosophila melanogaster model exhibits DA neurodegeneration as well as aberrant mitochondrial dynamics and function. Disruptions in mitophagy have been observed in parkin loss-of-function models, and changes in mitochondrial respiration have been reported in patient fibroblasts...
2018: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/29448328/granular-response-to-impact-topology-of-the-force-networks
#4
T Takahashi, Abram H Clark, T Majmudar, L Kondic
The impact of an intruder on granular matter leads to the formation of mesoscopic force networks, which were seen particularly clearly in the recent experiments carried out with photoelastic particles [Clark et al., Phys. Rev. Lett. 114, 144502 (2015)PRLTAO0031-900710.1103/PhysRevLett.114.144502]. These force networks are characterized by complex structure and evolve on fast time scales. While it is known that total photoelastic activity in the granular system is correlated with the acceleration of the intruder, it is not known how the structure of the force network evolves during impact, and if there are dominant features in the networks that can be used to describe the intruder's dynamics...
January 2018: Physical Review. E
https://www.readbyqxmd.com/read/29408792/on-the-reliability-of-individual-brain-activity-networks
#5
Ben Cassidy, F DuBois Bowman, Caroline Rae, Victor Solo
There is intense interest in fMRI research on whole-brain functional connectivity, and however, two fundamental issues are still unresolved: the impact of spatiotemporal data resolution (spatial parcellation and temporal sampling) and the impact of the network construction method on the reliability of functional brain networks. In particular, the impact of spatiotemporal data resolution on the resulting connectivity findings has not been sufficiently investigated. In fact, a number of studies have already observed that functional networks often give different conclusions across different parcellation scales...
February 2018: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/29391478/disrupted-resting-state-network-of-fibromyalgia-in-theta-frequency
#6
Mi Kyung Choe, Manyoel Lim, June Sic Kim, Dong Soo Lee, Chun Kee Chung
Fibromyalgia (FM), chronic widespread pain, exhibits spontaneous pain without external stimuli and is associated with altered brain activities during resting state. To understand the topological features of brain network in FM, we employed persistent homology which is a multiple scale network modeling framework not requiring thresholding. Spontaneous magnetoencephalography (MEG) activity was recorded in 19 healthy controls (HCs) and 18 FM patients. Barcode, single linkage dendrogram and single linkage matrix were generated based on the proposed modeling framework...
February 1, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29381889/alteration-in-the-local-and-global-functional-connectivity-of-resting-state-networks-in-parkinson-s-disease
#7
Maryam Ghahremani, Jaejun Yoo, Sun Ju Chung, Kwangsun Yoo, Jong C Ye, Yong Jeong
OBJECTIVE: Parkinson's disease (PD) is a neurodegenerative disorder that mainly leads to the impairment of patients' motor function, as well as of cognition, as it progresses. This study tried to investigate the impact of PD on the resting state functional connectivity of the default mode network (DMN), as well as of the entire brain. METHODS: Sixty patients with PD were included and compared to 60 matched normal control (NC) subjects. For the local connectivity analysis, the resting state fMRI data were analyzed by seed-based correlation analyses, and then a novel persistent homology analysis was implemented to examine the connectivity from a global perspective...
January 2018: Journal of Movement Disorders
https://www.readbyqxmd.com/read/29339459/novel-two-component-system-of-streptococcus-sanguinis-affecting-functions-associated-with-viability-in-saliva-and-biofilm-formation
#8
Tarsila M Camargo, Rafael N Stipp, Lívia A Alves, Erika N Harth-Chu, José F Höfling, Renata O Mattos-Graner
Streptococcus sanguinis is a pioneer species of teeth and a common opportunistic pathogen of infective endocarditis. In this study, we identified a two-component system, S. sanguinis SptRS (SptRS Ss ), affecting S. sanguinis survival in saliva and biofilm formation. Isogenic mutants of sptRSs (SKsptR) and sptSSs (SKsptS) showed reduced cell counts in ex vivo assays of viability in saliva compared to those of parent strain SK36 and complemented mutants. Reduced counts of the mutants in saliva were associated with reduced growth rates in nutrient-poor medium (RPMI) and increased susceptibility to the deposition of C3b and the membrane attach complex (MAC) of the complement system, a defense component of saliva and serum...
April 2018: Infection and Immunity
https://www.readbyqxmd.com/read/29314829/quantitative-toxicity-prediction-using-topology-based-multitask-deep-neural-networks
#9
Kedi Wu, Guo-Wei Wei
The understanding of toxicity is of paramount importance to human health and environmental protection. Quantitative toxicity analysis has become a new standard in the field. This work introduces element specific persistent homology (ESPH), an algebraic topology approach, for quantitative toxicity prediction. ESPH retains crucial chemical information during the topological abstraction of geometric complexity and provides a representation of small molecules that cannot be obtained by any other method. To investigate the representability and predictive power of ESPH for small molecules, ancillary descriptors have also been developed based on physical models...
February 26, 2018: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/29174401/the-gut-microbiota-facilitates-drifts-in-the-genetic-diversity-and-infectivity-of-bacterial-viruses
#10
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...
December 13, 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
#11
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
#12
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
#13
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
#14
Gregory D Funk
No abstract text is available yet for this article.
December 1, 2017: Journal of Physiology
https://www.readbyqxmd.com/read/28866539/clique-community-persistence-a-topological-visual-analysis-approach-for-complex-networks
#15
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...
January 2018: 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
#16
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
#17
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
#18
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
#19
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
#20
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
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