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Persistent network homology

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https://www.readbyqxmd.com/read/27911727/role-of-the-bone-morphogenic-protein-pathway-in-developmental-haemopoiesis-and-leukaemogenesis
#1
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
#2
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
#3
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
#4
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)...
October 26, 2016: 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
#5
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
https://www.readbyqxmd.com/read/27647921/molecular-organization-of-cytokinesis-nodes-and-contractile-rings-by-super-resolution-fluorescence-microscopy-of-live-fission-yeast
#6
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
#7
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
#8
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
https://www.readbyqxmd.com/read/27378297/the-smal-web-server-global-multiple-network-alignment-from-pairwise-alignments
#9
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
https://www.readbyqxmd.com/read/27298351/hierarchical-structures-of-amorphous-solids-characterized-by-persistent-homology
#10
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
https://www.readbyqxmd.com/read/27262774/treatment-of-dysphasia-with-rtms-and-language-therapy-after-childhood-stroke-multimodal-imaging-of-plastic-change
#11
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
https://www.readbyqxmd.com/read/27249945/persistent-topological-features-of-dynamical-systems
#12
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
https://www.readbyqxmd.com/read/26812805/using-persistent-homology-and-dynamical-distances-to-analyze-protein-binding
#13
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
https://www.readbyqxmd.com/read/26451775/connectivity-homology-enables-inter-species-network-models-of-synthetic-lethality
#14
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
https://www.readbyqxmd.com/read/26450288/multiresolution-persistent-homology-for-excessively-large-biomolecular-datasets
#15
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
https://www.readbyqxmd.com/read/26272039/motor-overflow-in-children-with-attention-deficit-hyperactivity-disorder-is-associated-with-decreased-extent-of-neural-activation-in-the-motor-cortex
#16
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
https://www.readbyqxmd.com/read/26092690/geneweaver-finding-consilience-in-heterogeneous-cross-species-functional-genomics-data
#17
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 GeneWeaver.org 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
https://www.readbyqxmd.com/read/26089981/molecular-docking-study-of-malaria-drug-target-enzyme-transketolase-in-plasmodium-falciparum-3d7-portends-the-novel-approach-to-its-treatment
#18
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
https://www.readbyqxmd.com/read/26018239/design-principles-for-cancer-therapy-guided-by-changes-in-complexity-of-protein-protein-interaction-networks
#19
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
https://www.readbyqxmd.com/read/25495216/brain-networks-engaged-in-audiovisual-integration-during-speech-perception-revealed-by-persistent-homology-based-network-filtration
#20
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
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