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Persistent network homology

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...
2016: Scientific Reports
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
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
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...
October 15, 2016: Applied and Environmental Microbiology
Jakob Dohrmann, Rahul Singh
MOTIVATION: Alignments of protein-protein interaction networks (PPIN) can be used to predict protein function, study conserved aspects of the interactome, and to establish evolutionary correspondences. Within this problem context, determining multiple network alignments (MNA) is a significant challenge that involves high computational complexity. A limited number of public MNA implementations are available currently and the majority of the pairwise network alignment (PNA) algorithms do not have MNA counterparts...
July 4, 2016: Bioinformatics
Yasuaki Hiraoka, Takenobu Nakamura, Akihiko Hirata, Emerson G Escolar, Kaname Matsue, Yasumasa Nishiura
This article proposes a topological method that extracts hierarchical structures of various amorphous solids. The method is based on the persistence diagram (PD), a mathematical tool for capturing shapes of multiscale data. The input to the PDs is given by an atomic configuration and the output is expressed as 2D histograms. Then, specific distributions such as curves and islands in the PDs identify meaningful shape characteristics of the atomic configuration. Although the method can be applied to a wide variety of disordered systems, it is applied here to silica glass, the Lennard-Jones system, and Cu-Zr metallic glass as standard examples of continuous random network and random packing structures...
June 28, 2016: Proceedings of the National Academy of Sciences of the United States of America
Helen L Carlson, Zeanna Jadavji, Aleksandra Mineyko, Omar Damji, Jacquie Hodge, Jenny Saunders, Mia Hererro, Michele Nowak, Rebecca Patzelt, Anya Mazur-Mosiewicz, Frank P MacMaster, Adam Kirton
Expressive dysphasia accompanies left inferior frontal gyrus (IFG/Broca) injury. Recovery may relate to interhemispheric balance with homologous, contralesional IFG but is unexplored in children. We evaluated effects of inhibitory rTMS to contralesional IFG combined with intensive speech therapy (SLT). A 15year-old, right-handed male incurred a left middle cerebral artery stroke. After 30months, severe non-fluent dysphasia impacted quality of life. Language networks, neuronal metabolism and white matter pathways were explored using MRI...
August 2016: Brain and Language
Slobodan Maletić, Yi Zhao, Milan Rajković
Inspired by an early work of Muldoon et al., Physica D 65, 1-16 (1993), we present a general method for constructing simplicial complex from observed time series of dynamical systems based on the delay coordinate reconstruction procedure. The obtained simplicial complex preserves all pertinent topological features of the reconstructed phase space, and it may be analyzed from topological, combinatorial, and algebraic aspects. In focus of this study is the computation of homology of the invariant set of some well known dynamical systems that display chaotic behavior...
May 2016: Chaos
Violeta Kovacev-Nikolic, Peter Bubenik, Dragan Nikolić, Giseon Heo
Persistent homology captures the evolution of topological features of a model as a parameter changes. The most commonly used summary statistics of persistent homology are the barcode and the persistence diagram. Another summary statistic, the persistence landscape, was recently introduced by Bubenik. It is a functional summary, so it is easy to calculate sample means and variances, and it is straightforward to construct various test statistics. Implementing a permutation test we detect conformational changes between closed and open forms of the maltose-binding protein, a large biomolecule consisting of 370 amino acid residues...
March 2016: Statistical Applications in Genetics and Molecular Biology
Alexandra Jacunski, Scott J Dixon, Nicholas P Tatonetti
Synthetic lethality is a genetic interaction wherein two otherwise nonessential genes cause cellular inviability when knocked out simultaneously. Drugs can mimic genetic knock-out effects; therefore, our understanding of promiscuous drugs, polypharmacology-related adverse drug reactions, and multi-drug therapies, especially cancer combination therapy, may be informed by a deeper understanding of synthetic lethality. However, the colossal experimental burden in humans necessitates in silico methods to guide the identification of synthetic lethal pairs...
October 2015: PLoS Computational Biology
Kelin Xia, Zhixiong Zhao, Guo-Wei Wei
Although persistent homology has emerged as a promising tool for the topological simplification of complex data, it is computationally intractable for large datasets. We introduce multiresolution persistent homology to handle excessively large datasets. We match the resolution with the scale of interest so as to represent large scale datasets with appropriate resolution. We utilize flexibility-rigidity index to access the topological connectivity of the data set and define a rigidity density for the filtration analysis...
October 7, 2015: Journal of Chemical Physics
Andrew Gaddis, Keri S Rosch, Benjamin Dirlikov, Deana Crocetti, Lindsey MacNeil, Anita D Barber, John Muschelli, Brian Caffo, James J Pekar, Stewart H Mostofsky
Motor overflow is a developmental phenomenon that typically disappears by late childhood. Abnormal persistence of motor overflow is often present in children with attention-deficit/hyperactivity disorder (ADHD). This study employed functional magnetic resonance imaging (fMRI) during a finger-sequencing task to examine whether excessive motor overflow in children with ADHD is associated with decreased extent of motor circuit activation. Thirty-four right-handed children (18 typically developing controls, 16 ADHD) completed fMRI while performing a finger-sequencing task...
September 30, 2015: Psychiatry Research
Jason A Bubier, Charles A Phillips, Michael A Langston, Erich J Baker, Elissa J Chesler
A persistent challenge lies in the interpretation of consensus and discord from functional genomics experimentation. Harmonizing and analyzing this data will enable investigators to discover relations of many genes to many diseases, and from many phenotypes and experimental paradigms to many diseases through their genomic substrates. The system provides a platform for cross-species integration and interrogation of heterogeneous curated and experimentally derived functional genomics data. GeneWeaver enables researchers to store, share, analyze, and compare results of their own genome-wide functional genomics experiments in an environment containing rich companion data obtained from major curated repositories, including the Mouse Genome Database and other model organism databases, along with derived data from highly specialized resources, publications, and user submissions...
October 2015: Mammalian Genome: Official Journal of the International Mammalian Genome Society
Md Anayet Hasan, Md Habibul Hasan Mazumder, Afrin Sultana Chowdhury, Amit Datta, Md Arif Khan
BACKGROUND: Malaria has been a major life threatening mosquito borne disease from long since. Unavailability of any effective vaccine and recent emergence of multi drug resistant strains of malaria pathogen Plasmodium falciparum continues to cause persistent deaths in the tropical and sub-tropical region. As a result, demands for new targets for more effective anti-malarial drugs are escalating. Transketolase is an enzyme of the pentose phosphate pathway; a novel pathway which is involved in energy generation and nucleic acid synthesis...
2015: Source Code for Biology and Medicine
Sebastian Benzekry, Jack A Tuszynski, Edward A Rietman, Giannoula Lakka Klement
BACKGROUND: The ever-increasing expanse of online bioinformatics data is enabling new ways to, not only explore the visualization of these data, but also to apply novel mathematical methods to extract meaningful information for clinically relevant analysis of pathways and treatment decisions. One of the methods used for computing topological characteristics of a space at different spatial resolutions is persistent homology. This concept can also be applied to network theory, and more specifically to protein-protein interaction networks, where the number of rings in an individual cancer network represents a measure of complexity...
2015: Biology Direct
Heejung Kim, Jarang Hahm, Hyekyoung Lee, Eunjoo Kang, Hyejin Kang, Dong Soo Lee
The human brain naturally integrates audiovisual information to improve speech perception. However, in noisy environments, understanding speech is difficult and may require much effort. Although the brain network is supposed to be engaged in speech perception, it is unclear how speech-related brain regions are connected during natural bimodal audiovisual or unimodal speech perception with counterpart irrelevant noise. To investigate the topological changes of speech-related brain networks at all possible thresholds, we used a persistent homological framework through hierarchical clustering, such as single linkage distance, to analyze the connected component of the functional network during speech perception using functional magnetic resonance imaging...
May 2015: Brain Connectivity
Miroslav Kramár, Arnaud Goullet, Lou Kondic, Konstantin Mischaikow
We discuss sets of measures with the goal of describing dynamical properties of force networks in dense particulate systems. The presented approach is based on persistent homology and allows for extracting precise, quantitative measures that describe the evolution of geometric features of the interparticle forces, without necessarily considering the details related to individual contacts between particles. The networks considered emerge from discrete element simulations of two-dimensional particulate systems consisting of compressible frictional circular disks...
November 2014: Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
G Petri, P Expert, F Turkheimer, R Carhart-Harris, D Nutt, P J Hellyer, F Vaccarino
Networks, as efficient representations of complex systems, have appealed to scientists for a long time and now permeate many areas of science, including neuroimaging (Bullmore and Sporns 2009 Nat. Rev. Neurosci. 10, 186-198. (doi:10.1038/nrn2618)). Traditionally, the structure of complex networks has been studied through their statistical properties and metrics concerned with node and link properties, e.g. degree-distribution, node centrality and modularity. Here, we study the characteristics of functional brain networks at the mesoscopic level from a novel perspective that highlights the role of inhomogeneities in the fabric of functional connections...
December 6, 2014: Journal of the Royal Society, Interface
S Ardanza-Trevijano, Iker Zuriguel, Roberto Arévalo, Diego Maza
We use the first Betti number of a complex to analyze the morphological structure of granular samples in mechanical equilibrium. We investigate two-dimensional granular packings after a tapping process by means of both simulations and experiments. States with equal packing fraction obtained with different tapping intensities are distinguished after the introduction of a filtration parameter which determines the particles (nodes in the network) that are joined by an edge. This is accomplished by just using the position of the particles obtained experimentally and no other information about the possible contacts, or magnitude of forces...
May 2014: Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
Hyekyoung Lee, Moo K Chung, Hyejin Kang, Dong Soo Lee
Recent studies have found that the modular structure of functional brain network is disrupted during the progress of Alzheimer's is the most basic topological disease. The modular structure of network invariant in determining the shape of network in the view of algebraic topology. In this study, we propose a new method to find another higher order topological invariant, hole, based on persistent homology. If a hole exists in the network, the information can be inefficiently delivered between regions. If we can localize the hole in the network, we can infer the reason of network inefficiency...
2014: Medical Image Computing and Computer-assisted Intervention: MICCAI ..
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