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1,406 | journal.pcbi.1006637 | 2,018 | Dynamical anchoring of distant arrhythmia sources by fibrotic regions via restructuring of the activation pattern | Many clinically relevant cardiac arrhythmias are conjectured to be organized by rotors ., A rotor is an extension of the concept of a reentrant source of excitation into two or three dimensions with an area of functional block in its center , referred to as the core ., Rapid and complex reentry arrhythmias such as atri... | Introduction, Materials and methods, Results, Discussion | Rotors are functional reentry sources identified in clinically relevant cardiac arrhythmias , such as ventricular and atrial fibrillation ., Ablation targeting rotor sites has resulted in arrhythmia termination ., Recent clinical , experimental and modelling studies demonstrate that rotors are often anchored around fib... | Rotors are waves of cardiac excitation like a tornado causing cardiac arrhythmia ., Recent research shows that they are found in ventricular and atrial fibrillation ., Burning ( via ablation ) the site of a rotor can result in the termination of the arrhythmia ., Recent studies showed that rotors are often anchored to ... | dermatology, medicine and health sciences, diagnostic radiology, engineering and technology, cardiovascular anatomy, cardiac ventricles, fibrosis, magnetic resonance imaging, developmental biology, electrocardiography, bioassays and physiological analysis, cardiology, research and analysis methods, scars, arrhythmia, i... | null |
2,233 | journal.pcbi.1002283 | 2,011 | Chemotaxis when Bacteria Remember: Drift versus Diffusion | The bacterium E . coli moves by switching between two types of motions , termed ‘run’ and ‘tumble’ 1 ., Each results from a distinct movement of the flagella ., During a run , flagella motors rotate counter-clockwise ( when looking at the bacteria from the back ) , inducing an almost constant forward velocity of about ... | Introduction, Models, Results, Discussion | Escherichia coli ( E . coli ) bacteria govern their trajectories by switching between running and tumbling modes as a function of the nutrient concentration they experienced in the past ., At short time one observes a drift of the bacterial population , while at long time one observes accumulation in high-nutrient regi... | The chemotaxis of Escherichia coli is a prototypical model of navigational strategy ., The bacterium maneuvers by switching between near-straight motion , termed runs , and tumbles which reorient its direction ., To reach regions of high nutrient concentration , the run-durations are modulated according to the nutrient... | physics, statistical mechanics, theoretical biology, biophysics theory, biology, computational biology, biophysics simulations, biophysics | null |
4 | journal.pcbi.1005644 | 2,017 | A phase transition induces chaos in a predator-prey ecosystem with a dynamic fitness landscape | In many natural ecosystems , at least one constituent species evolves quickly enough relative to its population growth that the two effects become interdependent ., This phenomenon can occur when selection forces are tied to such sudden environmental effects as algal blooms or flooding 1 , or it can arise from more sub... | Introduction, Model, Results, Discussion | In many ecosystems , natural selection can occur quickly enough to influence the population dynamics and thus future selection ., This suggests the importance of extending classical population dynamics models to include such eco-evolutionary processes ., Here , we describe a predator-prey model in which the prey popula... | Evolution is usually thought to occur very gradually , taking millennia or longer in order to appreciably affect a species survival mechanisms ., Conversely , demographic shifts due to predator invasion or environmental change can occur relatively quickly , creating abrupt and lasting effects on a species survival ., H... | ecology and environmental sciences, predator-prey dynamics, population dynamics, systems science, mathematics, population biology, thermodynamics, computer and information sciences, ecosystems, dynamical systems, free energy, community ecology, physics, population metrics, ecology, predation, natural selection, trophic... | null |
1,522 | journal.pgen.1000098 | 2,008 | Evaluating Statistical Methods Using Plasmode Data Sets in the Age of Massive Public Databases: An Illustration Using False Discovery Rates | “Omic” technologies ( genomic , proteomic , etc . ) have led to high dimensional experiments ( HDEs ) that simultaneously test thousands of hypotheses ., Often these omic experiments are exploratory , and promising discoveries demand follow-up laboratory research ., Data from such experiments require new ways of thinki... | Introduction, Results, Discussion, Methods | Plasmode is a term coined several years ago to describe data sets that are derived from real data but for which some truth is known ., Omic techniques , most especially microarray and genomewide association studies , have catalyzed a new zeitgeist of data sharing that is making data and data sets publicly available on ... | Plasmode is a term used to describe a data set that has been derived from real data but for which some truth is known ., Statistical methods that analyze data from high dimensional experiments ( HDEs ) seek to estimate quantities that are of interest to scientists , such as mean differences in gene expression levels an... | biotechnology, mathematics, science policy, computational biology, molecular biology, genetics and genomics | null |
931 | journal.pcbi.1006166 | 2,018 | Variability in pulmonary vein electrophysiology and fibrosis determines arrhythmia susceptibility and dynamics | Success rates for catheter ablation of persistent atrial fibrillation ( AF ) patients are currently low; however , there is a subset of patients for whom pulmonary vein isolation ( PVI ) alone is a successful treatment strategy 1 ., PVI ablation may work by preventing triggered beats from entering the left atrial body ... | Introduction, Materials and methods, Results, Discussion | Success rates for catheter ablation of persistent atrial fibrillation patients are currently low; however , there is a subset of patients for whom electrical isolation of the pulmonary veins alone is a successful treatment strategy ., It is difficult to identify these patients because there are a multitude of factors a... | Atrial fibrillation is the most commonly encountered cardiac arrhythmia , affecting a significant portion of the population ., Currently , ablation is the most effective treatment but success rates are less than optimal , being 70% one-year post-treatment ., There is a large effort to find better ablation strategies to... | medicine and health sciences, engineering and technology, cardiovascular anatomy, fibrosis, electrophysiology, endocardium, simulation and modeling, developmental biology, epicardium, research and analysis methods, cardiology, arrhythmia, atrial fibrillation, rotors, mechanical engineering, anatomy, physiology, biology... | null |
900 | journal.pntd.0006075 | 2,017 | Development and preliminary evaluation of a multiplexed amplification and next generation sequencing method for viral hemorrhagic fever diagnostics | Outbreaks of viral hemorrhagic fever ( VHF ) occur in many parts of the world 1 , 2 ., VHFs are caused by various single-stranded RNA viruses , the majority of which are classified in Arenaviridae , Filoviridae , and Flaviviridae families and Bunyavirales order 3 ., Human infections show high morbidity and mortality ra... | Introduction, Methods, Results, Discussion | We describe the development and evaluation of a novel method for targeted amplification and Next Generation Sequencing ( NGS ) -based identification of viral hemorrhagic fever ( VHF ) agents and assess the feasibility of this approach in diagnostics ., An ultrahigh-multiplex panel was designed with primers to amplify a... | Viral hemorrhagic fever is a severe and potentially lethal disease , characterized by fever , malaise , vomiting , mucosal and gastrointestinal bleeding , and hypotension , in which multiple organ systems are affected ., Due to modern transportation and global trade , outbreaks of viral hemorrhagic fevers have the pote... | sequencing techniques, medicine and health sciences, rift valley fever virus, pathology and laboratory medicine, togaviruses, pathogens, tropical diseases, microbiology, alphaviruses, viruses, next-generation sequencing, chikungunya virus, rna viruses, genome analysis, neglected tropical diseases, molecular biology tec... | null |
1,279 | journal.pcbi.1007284 | 2,019 | Fast and near-optimal monitoring for healthcare acquired infection outbreaks | "Since the time of Hippocrates , the “father of western medicine” , a central tenet of medical c(...TRUNCATED) | Introduction, Materials and methods, Results, Discussion | "According to the Centers for Disease Control and Prevention ( CDC ) , one in twenty five hospital p(...TRUNCATED) | "Healthcare acquired infections ( HAIs ) lead to significant losses of lives and result in heavy eco(...TRUNCATED) | "medicine and health sciences, gut bacteria, medical personnel, sociology, social sciences, health c(...TRUNCATED) | null |
1,891 | journal.pcbi.1003705 | 2,014 | Rethinking Transcriptional Activation in the Arabidopsis Circadian Clock | "The task of the circadian clock is to synchronize a multitude of biological processes to the daily (...TRUNCATED) | Introduction, Results, Methods, Discussion | "Circadian clocks are biological timekeepers that allow living cells to time their activity in antic(...TRUNCATED) | "Like most living organisms , plants are dependent on sunlight , and evolution has endowed them with(...TRUNCATED) | "systems biology, physiological processes, computer and information sciences, network analysis, phys(...TRUNCATED) | null |
521 | journal.pcbi.1006080 | 2,018 | "Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted s(...TRUNCATED) | "The emergence and maturation of next-generation sequencing technologies , including whole genome se(...TRUNCATED) | Introduction, Results, Discussion, Materials and methods | "Somatic copy number variations ( CNVs ) play a crucial role in development of many human cancers .,(...TRUNCATED) | "We present Bamgineer , a software program to introduce user-defined , haplotype-specific copy numbe(...TRUNCATED) | "sequencing techniques, alleles, genetic mapping, genome analysis, copy number variation, molecular (...TRUNCATED) | null |
2,225 | journal.pcbi.1006772 | 2,019 | "A component overlapping attribute clustering (COAC) algorithm for single-cell RNA sequencing data a(...TRUNCATED) | "Single cell ribonucleic acid sequencing ( scRNA-seq ) offers advantages for characterization of cel(...TRUNCATED) | Introduction, Results, Discussion, Methods and materials | "Recent advances in next-generation sequencing and computational technologies have enabled routine a(...TRUNCATED) | "Single-cell RNA sequencing ( scRNA-seq ) can reveal complex and rare cell populations , uncover gen(...TRUNCATED) | "biotechnology, medicine and health sciences, clinical research design, engineering and technology, (...TRUNCATED) | null |
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