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Neurotoxicity in all prion disorders is believed to result from the accumulation of PrP-scrapie ( PrPSc ) , a β-sheet rich isoform of a normal cell-surface glycoprotein , the prion protein ( PrPC ) . Limited reports suggest imbalance of brain iron homeostasis as a significant associated cause of neurotoxicity in prion-...	Prion disorders are neurodegenerative conditions of humans and animals that are invariably fatal . The main agent responsible for neurotoxicity in all prion disorders is PrP-scrapie ( PrPSc ) , a β-sheet rich isoform of a normal cell-surface glycoprotein , the prion protein ( PrPC ) . Deposits of PrPSc in the brain par...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neurological", "disorders/prion", "diseases" ]	2009	Abnormal Brain Iron Homeostasis in Human and Animal Prion Disorders
Chromosomal location has a significant effect on the evolutionary dynamics of genes involved in sexual dimorphism , impacting both the pattern of sex-specific gene expression and the rate of duplication and protein evolution for these genes . For nearly all non-model organisms , however , knowledge of chromosomal gene ...	The distribution and organization of genes on chromosomes vary widely among animals . Chromosomes can change in number and size , as well as gene composition , over short evolutionary time scales . Furthermore , chromosome location can influence how genes are expressed in various tissues and how they evolve . The sex c...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/comparative", "genomics", "genetics", "and", "genomics/chromosome", "biology", "evolutionary", "biology/genomics" ]	2010	Comparative Genomic Hybridization (CGH) Reveals a Neo-X Chromosome and Biased Gene Movement in Stalk-Eyed Flies (Genus Teleopsis)
The granulomatous lesion resulting from infection with the fungus Paracoccidioides brasiliensis is characterized by a compact aggregate of mature cells , surrounded by a fibroblast- and collagen-rich content . Granuloma formation requires signaling elicited by inflammatory molecules such as members of the interleukin-1...	After infectious insults , the release of intracellular molecules from dying cells , such as IL-1α , provokes a local inflammation as an alert of tissue damage . In this study , we investigated the steps necessary for IL-1α-mediated inflammation and its implications after fungal infection . We identified a molecular me...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "yeast", "infections", "pathology", "and", "laboratory", "medicine", "immune", "physiology", "cytokines", "pathogens", "immunology", "microbiology", "cell", "di...	2019	Caspase-11-dependent IL-1α release boosts Th17 immunity against Paracoccidioides brasiliensis
Campylobacter jejuni is the major cause of bacterial food-borne illness in the USA and Europe . An important virulence attribute of this bacterial pathogen is its ability to enter and survive within host cells . Here we show through a quantitative proteomic analysis that upon entry into host cells , C . jejuni undergoe...	Campylobacter jejuni is one of the most common causes of food-borne illness in the United States and a major cause of diarrheal diseases in developing countries . This pathogen can invade intestinal epithelial cells , which is very important for its ability to cause disease . Once it gains access to epithelial cells , ...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2012	Quantitative Proteomics of Intracellular Campylobacter jejuni Reveals Metabolic Reprogramming
Since its discovery in 1969 , enterovirus 71 ( EV71 ) has emerged as a serious worldwide health threat . This human pathogen of the picornavirus family causes hand , foot , and mouth disease , and also has the capacity to invade the central nervous system to cause severe disease and death . Upon binding to a host recep...	In a picornavirus capsid structural integrity must not be compromised until a key mechanism triggers genome release into a permissive cell . It has long been established that the majority of members of the picornavirus family solve this dilemma with a two-step uncoating process initiated by receptor recognition . For h...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology", "emerging", "viral", "diseases", "biology", "microbiology", "viral", "structure" ]	2013	The Enterovirus 71 A-particle Forms a Gateway to Allow Genome Release: A CryoEM Study of Picornavirus Uncoating
Although lactic acidosis is a prominent feature of solid tumors , we still have limited understanding of the mechanisms by which lactic acidosis influences metabolic phenotypes of cancer cells . We compared global transcriptional responses of breast cancer cells in response to three distinct tumor microenvironmental st...	Solid tumors usually have many differences in their chemical environments , such as low oxygen , depletion of glucose , high acidity ( low pH ) , and accumulation of lactate , from normal tissues . These changes are usually called tumor microenvironmental stresses . In this study , we have used microarrays to compare t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/cancer", "genetics", "pathology/molecular", "pathology" ]	2010	Lactic Acidosis Triggers Starvation Response with Paradoxical Induction of TXNIP through MondoA
Polarized membrane trafficking is essential for the construction and maintenance of multiple plasma membrane domains of cells . Highly polarized Drosophila photoreceptors are an excellent model for studying polarized transport . A single cross-section of Drosophila retina contains many photoreceptors with 3 clearly dif...	Cells in animal bodies have multiple plasma membrane domains; this polarized characteristic of cells is essential for their specific functions . Selective membrane transport pathways play key roles in the construction and maintenance of polarized structures . Drosophila photoreceptors with multiple plasma membrane doma...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "vesicles", "cell", "processes", "social", "sciences", "neuroscience", "membrane", "proteins", "golgi", "apparatus", "eyes", "cellular", "structures", "and", "organelles", "endosomes", "research", "and", "analysis", "methods", ...	2016	Rab6 Is Required for Multiple Apical Transport Pathways but Not the Basolateral Transport Pathway in Drosophila Photoreceptors
This cross-sectional study aimed to investigate the current prevalence and risk factors associated with intestinal polyparasitism ( the concurrent infection with multiple intestinal parasite species ) among Orang Asli school children in the Lipis district of Pahang state , Malaysia . Fecal samples were collected from 4...	Intestinal parasitic infections ( IPI ) are still a major public health problem worldwide , with more than 2 billion people infected with at least one parasite species . Despite efforts to improve the quality of life of the Orang Asli population in rural Malaysia , IPI are still highly prevalent and of serious concern ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "cryptosporidiosis", "helminth", "infections", "infectious", "diseases", "medicine", "and", "health", "sciences", "amebiasis", "parasitic", "intestinal", "diseases", "giardiasis", "neglected", "tropical", "diseases", "tropical", "diseases", "protozoan", "infections", "soil-...	2014	Epidemiology of Intestinal Polyparasitism among Orang Asli School Children in Rural Malaysia
From genomic association studies , quantitative trait loci analysis , and epigenomic mapping , it is evident that significant efforts are necessary to define genetic-epigenetic interactions and understand their role in disease susceptibility and progression . For this reason , an analysis of the effects of genetic vari...	The placenta is a critical organ playing multiple roles including oxygen and metabolite transfer from mother to fetus , hormone production , and vascular perfusion . With this study , we aimed to deliver a placenta-specific regulatory map based on a combination of publicly available and newly generated data . To comple...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome-wide", "association", "studies", "gene", "regulation", "regulatory", "proteins", "dna-binding", "proteins", "alleles", "dna", "transcription", "mathematics", "genome", "analysis", "transcription", "factors", "epigenetics", "dna", "dna", "methylation", "chromatin", ...	2018	Genetic variants influence on the placenta regulatory landscape
Plant morphogenesis is strongly dependent on the directional growth and the subsequent oriented division of individual cells . It has been shown that the plant cortical microtubule array plays a key role in controlling both these processes . This ordered structure emerges as the collective result of stochastic interact...	In contrast to animal cells , plant cells are encased in a rigid cell wall providing among others the necessary rigidity to contain the turgor pressure that allows the plant as a whole to raise itself against gravity . In order to maintain this mechanical integrity while growing requires plant cells to rigorously contr...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "plant", "anatomy", "microtubules", "pavement", "cells", "cell", "cycle", "and", "cell", "division", "plant", "cell", "biology", "cell", "processes", "brassica", "condensed", "matter", "physics", "plant", "science", "model", "organisms", "experimental", "organism", ...	2018	A computational framework for cortical microtubule dynamics in realistically shaped plant cells
A mutated KRAS protein is frequently observed in human cancers . Traditionally , the oncogenic properties of KRAS missense mutants at position 12 ( G12X ) have been considered as equal . Here , by assessing the probabilities of occurrence of all KRAS G12X mutations and KRAS dynamics we show that this assumption does no...	The oncogene KRAS is frequently mutated in various cancers . When the amino acid glycine 12 is mutated , KRAS protein acquires oncogenic properties that result in tumor cell-growth and cancer progression . These mutations prevail especially in the pancreatic ductal adenocarcinoma , which is a cancer with an exceptional...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "crystal", "structure", "markov", "models", "condensed", "matter", "physics", "multivariate", "analysis", "mutation", "mathematics", "statistics", "(mathematics)", "mutation", "databases", "crystallography", "research", "and", "ana...	2018	Assessment of mutation probabilities of KRAS G12 missense mutants and their long-timescale dynamics by atomistic molecular simulations and Markov state modeling
[PSI+] is an amyloid-based prion of Sup35p , a subunit of the translation termination factor . Prion “strains” or “variants” are amyloids with different conformations of a single protein sequence , conferring different phenotypes , but each relatively faithfully propagated . Wild Saccharomyces cerevisiae isolates have ...	The [PSI+] prion ( infectious protein ) of yeast is a self-propagating amyloid ( filamentous protein polymer ) of the Sup35 protein , a subunit of the translation termination factor . A single protein can form many biologically distinct prions , called prion variants . Wild yeast strains have three groups of Sup35 sequ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "epigenetics", "biology", "genetics", "of", "disease", "genetics", "and", "genomics" ]	2013	The [PSI+] Prion Exists as a Dynamic Cloud of Variants
Eukaryotic chromosomes initiate DNA synthesis from multiple replication origins . The machinery that initiates DNA synthesis is highly conserved , but the sites where the replication initiation proteins bind have diverged significantly . Functional comparative genomics is an obvious approach to study the evolution of r...	DNA replication is an evolutionarily conserved , cell cycle–regulated , spatially and temporally coordinated mechanism in eukaryotes . It is initiated by the binding of the Origin Recognition Complex ( ORC ) to multiple replication origins . While the ORC is highly conserved , its DNA binding specificity and the primar...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "genetics", "and", "genomics/comparative", "genomics", "genetics", "and", "genomics/functional", "genomics", "genetics", "and", "genomics/chromosome", "biology", ...	2010	A Comprehensive Genome-Wide Map of Autonomously Replicating Sequences in a Naive Genome
Merkel cell carcinoma ( MCC ) frequently contains integrated copies of Merkel cell polyomavirus DNA that express a truncated form of Large T antigen ( LT ) and an intact Small T antigen ( ST ) . While LT binds RB and inactivates its tumor suppressor function , it is less clear how ST contributes to MCC tumorigenesis . ...	Merkel cell carcinoma ( MCC ) is a highly aggressive , neuroendocrine cancer of the skin . MCC frequently contains integrated copies of Merkel cell polyomavirus DNA and expresses two viral transcripts including a truncated form of Large T antigen ( LT ) and an intact Small T antigen ( ST ) . While LT binds the Retinobl...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biotechnology", "genome", "engineering", "medicine", "and", "health", "sciences", "engineering", "and", "technology", "synthetic", "biology", "crispr", "synthetic", "bioengineering", "oncology", "immunoprecipitation", "stem", "cells", "induced", "pluripotent", "stem", "c...	2017	Merkel cell polyomavirus recruits MYCL to the EP400 complex to promote oncogenesis
Plants are continuously exposed to a myriad of abiotic and biotic stresses . However , the molecular mechanisms by which these stress signals are perceived and transduced are poorly understood . To begin to identify primary stress signal transduction components , we have focused on genes that respond rapidly ( within 5...	Plants are sessile organisms constantly challenged by a wide spectrum of biotic and abiotic stresses . These stresses cause considerable losses in crop yields worldwide , while the demand for food and energy is on the rise . Understanding the molecular mechanisms driving stress responses is crucial to devising targeted...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "arabidopsis", "(thale", "cress)", "plant", "biology" ]	2007	Mechanical Stress Induces Biotic and Abiotic Stress Responses via a Novel cis-Element
Natural immunity or resistance to pathogens most often relies on the genetic make-up of the host . In a LEW rat model of refractoriness to toxoplasmosis , we previously identified on chromosome 10 the Toxo1 locus that directs toxoplasmosis outcome and controls parasite spreading by a macrophage-dependent mechanism . No...	Toxoplasmosis is a ubiquitous parasitic infection causing a wide spectrum of diseases . It is usually asymptomatic but can lead to severe ocular and neurological disorders . The host factors that determine natural resistance to toxoplasmosis are yet poorly characterized . Among the animal models to study susceptibility...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "genome", "expression", "analysis", "innate", "immune", "system", "medicine", "and", "health", "sciences", "animal", "genetics", "pathology", "and", "laboratory", "medicine", "immunology", "microbiology", "vertebrates", "animals", "mammals", ...	2014	A Highly Conserved Toxo1 Haplotype Directs Resistance to Toxoplasmosis and Its Associated Caspase-1 Dependent Killing of Parasite and Host Macrophage
The intra-S phase checkpoint kinase of metazoa and yeast , ATR/MEC1 , protects chromosomes from DNA damage and replication stress by phosphorylating subunits of the replicative helicase , MCM2-7 . Here we describe an unprecedented ATR-dependent pathway in Tetrahymena thermophila in which the essential pre-replicative c...	DNA damage and replication stress activate cell cycle checkpoint responses that protect the integrity of eukaryotic chromosomes . A well-conserved response involves the reversible phosphorylation of the replicative helicase , MCM2-7 , which together with the origin recognition complex ( ORC ) dictates when and where re...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Checkpoint Activation of an Unconventional DNA Replication Program in Tetrahymena
In this paper we used a general stochastic processes framework to derive from first principles the incidence rate function that characterizes epidemic models . We investigate a particular case , the Liu-Hethcote-van den Driessche's ( LHD ) incidence rate function , which results from modeling the number of successful t...	Nonlinearity in the infection incidence is one of the main components that shape seasonal epidemics . Here , we revisit classical incidence and propose a first principles derivation of the infection incidence rate . A qualitative analysis of the SIRS model with both the classical and the proposed incidence rate showed ...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "ecology/theoretical", "ecology", "computational", "biology/population", "genetics", "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "mathematics/statistics" ]	2011	First Principles Modeling of Nonlinear Incidence Rates in Seasonal Epidemics
Human papillomaviruses infect stratified epithelia and link their productive life cycle to the differentiation state of the host cell . Productive viral replication or amplification is restricted to highly differentiated suprabasal cells and is dependent on the activation of the ATM DNA damage pathway . The ATM pathway...	Over 120 types of human papillomavirus ( HPV ) have been identified , and approximately one-third of these infect epithelial cells of the genital mucosa . Infection by a subset of HPV types is responsible for the development of cervical and other anogenital cancers . The infectious life cycle of HPV is dependent on dif...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Human Papillomaviruses Activate and Recruit SMC1 Cohesin Proteins for the Differentiation-Dependent Life Cycle through Association with CTCF Insulators
This article presents the integration of brain injury biomechanics and graph theoretical analysis of neuronal connections , or connectomics , to form a neurocomputational model that captures spatiotemporal characteristics of trauma . We relate localized mechanical brain damage predicted from biofidelic finite element s...	According to the Centers for Disease Control and Prevention in the United States , approximately 1 . 7 million people , on average , sustain a traumatic brain injury annually . During the last few decades , brain neurotrauma biomechanics has been an active area of research involving medical clinicians and a broad range...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "tissue", "mechanics", "medicine", "mechanics", "classical", "mechanics", "dynamics", "(mechanics)", "neuroscience", "biomechanics", "biophysics", "simulations", "neuroimaging", "biology", "head", "injury", "biophysics", "continuum", "mechanics", "connectomics", "physics", ...	2012	Combining the Finite Element Method with Structural Connectome-based Analysis for Modeling Neurotrauma: Connectome Neurotrauma Mechanics
The Caenorhabditis elegans left and right AWC olfactory neurons communicate to establish stochastic asymmetric identities , AWCON and AWCOFF , by inhibiting a calcium-mediated signaling pathway in the future AWCON cell . NSY-4/claudin-like protein and NSY-5/innexin gap junction protein are the two parallel signals that...	Cell identity determination requires a competition between the induction of cell type–specific genes and the suppression of genes that promote an alternative cell type . In the nematode C . elegans , a specific sensory neuron pair communicates to establish stochastic asymmetric identities by inhibiting a calcium signal...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "developmental", "biology", "caenorhabditis", "elegans", "developmental", "neuroscience", "model", "organisms", "biology", "neuroscience", "cell", "fate", "determination" ]	2012	The MicroRNA mir-71 Inhibits Calcium Signaling by Targeting the TIR-1/Sarm1 Adaptor Protein to Control Stochastic L/R Neuronal Asymmetry in C. elegans
The grey mould fungus Botrytis cinerea causes losses of commercially important fruits , vegetables and ornamentals worldwide . Fungicide treatments are effective for disease control , but bear the risk of resistance development . The major resistance mechanism in fungi is target protein modification resulting in reduce...	Bacterial and fungal pathogens cause diseases in humans and plants alike . Antibiotics and fungicides are used for disease control , but the microbes are able to adapt quickly to these drugs by mutation . Multiple drug resistance ( MDR ) is well investigated in human pathogens and causes increasing problems with antibi...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "microbiology/plant-biotic", "interactions", "microbiology/microbial", "growth", "and", "development", "microbiology/microbial", "evolution", "and", "genomics" ]	2009	Fungicide-Driven Evolution and Molecular Basis of Multidrug Resistance in Field Populations of the Grey Mould Fungus Botrytis cinerea
The immune state of wild animals is largely unknown . Knowing this and what affects it is important in understanding how infection and disease affects wild animals . The immune state of wild animals is also important in understanding the biology of their pathogens , which is directly relevant to explaining pathogen spi...	The immune state of wild animals—and the factors that affect this—is largely unknown . Knowing this is important in understanding how infection and disease affects wild animals , and the biology of their pathogens . The paucity of knowledge about wild animals' immune state is in stark contrast to our exquisitely detail...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "animal", "types", "medicine", "and", "health", "sciences", "animal", "pathogens", "immune", "cells", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "population", "genetics", "animals", "clinical", "m...	2018	The ecology of immune state in a wild mammal, Mus musculus domesticus
Viral immune evasion by sequence variation is a major hindrance to HIV-1 vaccine design . To address this challenge , our group has developed a computational model , rooted in physics , that aims to predict the fitness landscape of HIV-1 proteins in order to design vaccine immunogens that lead to impaired viral fitness...	At least 70 million people have been infected with HIV since the beginning of the epidemic and an effective vaccine remains elusive . The high mutation rate and diversity of HIV strains enables the virus to effectively evade host immune responses , presenting a significant challenge for HIV vaccine design . We have dev...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "immunodeficiency", "viruses", "infectious", "diseases", "medicine", "and", "health", "sciences", "medical", "microbiology", "hiv", "viral", "pathogens", "genetics", "microbial", "pathogens", "biology", "and", "life", "sciences", "immunology", "microbiology", "computation...	2014	The Fitness Landscape of HIV-1 Gag: Advanced Modeling Approaches and Validation of Model Predictions by In Vitro Testing
The process of fertilization is critically dependent on the mutual recognition of gametes and in Plasmodium , the male gamete surface protein P48/45 is vital to this process . This protein belongs to a family of 10 structurally related proteins , the so called 6-cys family . To identify the role of additional members o...	Sexual reproduction for malaria parasites is an essential process and is necessary for parasite transmission between hosts . Fertilisation between female and male gametes occurs in the midgut of the mosquito and proteins on the surface of gametes are principle targets in transmission blocking strategies . Despite their...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "cell", "biology/microbial", "growth", "and", "development", "microbiology/parasitology", "infectious", "diseases/protozoal", "infections", "infectious", "diseases/tropical", "and", "travel-associated", "d...	2010	Three Members of the 6-cys Protein Family of Plasmodium Play a Role in Gamete Fertility
The inoculum effect ( IE ) is an increase in the minimum inhibitory concentration ( MIC ) of an antibiotic as a function of the initial size of a microbial population . The IE has been observed in a wide range of bacteria , implying that antibiotic efficacy may depend on population density . Such density dependence cou...	The pace of antibiotic discovery has rapidly slowed in the last few decades , creating an urgent need to reevaluate and optimize therapies based on current drugs . In this work , we combine quantitative laboratory experiments on bacterial populations with mathematical models of antimicrobial therapies to demonstrate th...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "antimicrobials", "medicine", "and", "health", "sciences", "classical", "mechanics", "pathology", "and", "laboratory", "medicine", "fluid", "mechanics", "pathogens", "drugs", "microbiology", "antibiotic", "resistance", "pharmaceutics", "antibiotics", "enterococcus", "pharma...	2016	Population Density Modulates Drug Inhibition and Gives Rise to Potential Bistability of Treatment Outcomes for Bacterial Infections
Soil- and waterborne bacteria such as Pseudomonas aeruginosa are constantly challenging body surfaces . Since infections of healthy skin are unexpectedly rare , we hypothesized that the outermost epidermis , the stratum corneum , and sweat glands directly control the growth of P . aeruginosa by surface-provided antimic...	Pseudomonas aeruginosa is able to cause severe infections that increasingly threaten patients with cystic fibrosis and burns . The emerging antibiotic resistance of those bacteria exigently necessitates the development of new effective drugs . Since healthy skin is unexpectedly resistant towards P . aeruginosa infectio...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[]	2015	Skin-Derived C-Terminal Filaggrin-2 Fragments Are Pseudomonas aeruginosa-Directed Antimicrobials Targeting Bacterial Replication
Cardiac fibrosis occurs in many forms of heart disease and is considered to be one of the main arrhythmogenic factors . Regions with a high density of fibroblasts are likely to cause blocks of wave propagation that give rise to dangerous cardiac arrhythmias . Therefore , studies of the wave propagation through these re...	Cardiac arrhythmias are one of the major causes of death in the industrialized world . The most dangerous ones are often caused by the blocks of propagation of electrical signals . One of the common factors that contribute to the likelihood of these blocks , is a condition called cardiac fibrosis . In fibrosis , excita...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "statistical", "mechanics", "muscle", "tissue", "fibroblasts", "connective", "tissue", "cells", "waves", "cellular", "structures", "and", "organelles", "cytoskeleton", "cardiology", "contractile", "proteins", "actins", "computer", ...	2019	Self-organization of conducting pathways explains electrical wave propagation in cardiac tissues with high fraction of non-conducting cells
Trachoma is endemic in several Pacific Island states . Recent surveys across the Solomon Islands indicated that whilst trachomatous inflammation—follicular ( TF ) was present at levels warranting intervention , the prevalence of trachomatous trichiasis ( TT ) was low . We set out to determine the relationship between c...	Trachoma is the most common infectious cause blindness worldwide , and the target of a global elimination initiative . A package of community-wide interventions is recommended to treat trachoma , which aim to reduce transmission of the causative agent Chlamydia trachomatis . These interventions require significant , pr...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "sequencing", "techniques", "medicine", "and", "health", "sciences", "solomon", "islands", "pathology", "and", "laboratory", "medicine", "chlamydia", "trachomatis", "pathogens", "immunology", "tropical", "diseases", "geographical", "locations", "microbiology", "bacterial", ...	2016	Low Prevalence of Conjunctival Infection with Chlamydia trachomatis in a Treatment-Naïve Trachoma-Endemic Region of the Solomon Islands
We model the regulatory role of proteins bound to looped DNA using a simulation in which dsDNA is represented as a self-avoiding chain , and proteins as spherical protrusions . We simulate long self-avoiding chains using a sequential importance sampling Monte-Carlo algorithm , and compute the probabilities for chain lo...	Biological regulation-at-a-distance , whereby a transcription factor ( TF ) is able to generate susbstantial regulatory effects on gene expression even though it may be bound a large distance away from its target ( 500 bp–1 Mbp ) , is only partially understood . Using a biophysical model and a computer simulation that ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "invertebrates", "gene", "regulation", "radii", "geometry", "animals", "simulation", "and", "modeling", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "mathematics", "materials", "science", "experimental", "organism", "systems", "epigenetics", "ma...	2017	A Looping-Based Model for Quenching Repression
Chronic viral infections lead to CD8+ T cell exhaustion , characterized by impaired cytokine secretion . Presence of the immune-regulatory cytokine IL-10 promotes chronicity of Lymphocytic Choriomeningitis Virus ( LCMV ) Clone 13 infection , while absence of IL-10/IL-10R signaling early during infection results in vira...	Chronic viral infections like Hepatitis B and C Virus ( HBV and HCV ) and Human Immunodeficiency Virus ( HIV ) in humans affect more than 500 million people worldwide . While a robust T cell response is a hallmark of many acute infections one hurdle inhibiting the clearance of chronic viral infections is that the immun...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Macrophage and T Cell Produced IL-10 Promotes Viral Chronicity
The SV40 small t antigen ( ST ) is a potent oncoprotein that perturbs the function of protein phosphatase 2A ( PP2A ) . ST directly interacts with the PP2A scaffolding A subunit and alters PP2A activity by displacing regulatory B subunits from the A subunit . We have determined the crystal structure of full-length ST i...	The study of how DNA tumor viruses induce malignant transformation has led to the identification of key pathways that also play a role in spontaneously arising cancers . One such virus , simian virus 40 ( SV40 ) , produces two proteins , the large T and small t antigens , that bind and inactivate tumor suppressor genes...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "biochemistry", "infectious", "diseases", "virology", "in", "vitro", "chemistry", "chemical", "biology" ]	2007	Structural Basis of PP2A Inhibition by Small t Antigen
Phlebotomine sand flies are vectors of human leishmaniases , important neglected tropical diseases . In this study , we investigated diel patterns of oviposition behavior , effects of visual cues on oviposition-site selection , and whether these affect the attraction of gravid Phlebotomus papatasi ( Scopoli ) , the vec...	Sand flies are vectors of human leishmaniases , an important neglected tropical disease . An alternative approach to the conventional delivery of an insecticide to the vector is to bring the vector to the insecticide using oviposition ( egg-laying ) -site attractants . Olfactory cues originating from organic matter hav...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "laboratory", "equipment", "engineering", "and", "technology", "social", "sciences", "sand", "flies", "light", "neuroscience", "animals", "electromagnetic", "radiation", "reproductive", "physiology", "artificial", ...	2019	Diel periodicity and visual cues guide oviposition behavior in Phlebotomus papatasi, vector of old-world cutaneous leishmaniasis
Lactase persistence ( LP ) is common among people of European ancestry , but with the exception of some African , Middle Eastern and southern Asian groups , is rare or absent elsewhere in the world . Lactase gene haplotype conservation around a polymorphism strongly associated with LP in Europeans ( −13 , 910 C/T ) ind...	Most adults worldwide do not produce the enzyme lactase and so are unable to digest the milk sugar lactose . However , most people in Europe and many from other populations continue to produce lactase throughout their life ( lactase persistence ) . In Europe , a single genetic variant , −13 , 910*T , is strongly associ...	[ "Abstract", "Introduction", "Discussion", "Material", "and", "Methods" ]	[ "evolutionary", "biology/evolutionary", "and", "comparative", "genetics", "evolutionary", "biology/human", "evolution", "nutrition", "computational", "biology/molecular", "genetics", "computational", "biology/evolutionary", "modeling" ]	2009	The Origins of Lactase Persistence in Europe
Cohesin is crucial for genome stability , cell division , transcription and chromatin organization . Its functions critically depend on NIPBL , the cohesin-loader protein that is found to be mutated in >60% of the cases of Cornelia de Lange syndrome ( CdLS ) . Other mutations are described in the cohesin subunits SMC1A...	The most frequent mutations in the human developmental disorder Cornelia de Lange Syndrome ( CdLS ) occur in the NIPBL gene . NIPBL is critical for chromatin-association of the cohesin complex and has a dual role as transcription factor . The regulation of the NIPBL gene is of great interest since organisms are very se...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "gene", "regulation", "messenger", "rna", "dna-binding", "proteins", "cloning", "long", "non-coding", "rnas", "dna", "transcription", "molecular", "biology", "techniques", "research", "and", "analysis", "methods", "transcriptional", "control", "proteins", "gene", "expre...	2017	Regulation of the cohesin-loading factor NIPBL: Role of the lncRNA NIPBL-AS1 and identification of a distal enhancer element
Scrapie is a transmissible spongiform encephalopathy ( TSE ) in sheep and goats . In recent years , atypical scrapie cases were identified that differed from classical scrapie in the molecular characteristics of the disease-associated pathological prion protein ( PrPsc ) . In this study , we analyze the molecular and n...	In the view of concerns that bovine spongiform encephalopathy has entered the small ruminant population , comprehensive active surveillance programs for transmissible spongiform encephalopathies ( TSEs ) in sheep and goats were implemented worldwide . In these , previously unrecognized atypical scrapie cases were ident...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "infectious", "diseases", "sheep", "none", "vertebrates", "animals", "mammals" ]	2007	Diversity in Neuroanatomical Distribution of Abnormal Prion Protein in Atypical Scrapie
In nearly all picornaviruses the precursor of the smallest capsid protein VP4 undergoes co-translational N-terminal myristoylation by host cell N-myristoyltransferases ( NMTs ) . Curtailing this modification by mutation of the myristoylation signal in poliovirus has been shown to result in severe assembly defects and v...	Picornaviruses are important human and animal pathogens . Protective vaccines are only available against very few representatives . Furthermore , antiviral drugs have not made it to the market because of serious side effects and viral mutational escape . We here show that pharmacological inhibition of cellular myristoy...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "hela", "cells", "biological", "cultures", "microbiology", "viral", "structure", "viruses", "rna", "viruses", "cell", "cultures", "rhinovirus", "infection", "microbial", "genomics", "research", "and", "analysis", "methods", "in...	2018	Cellular N-myristoyltransferases play a crucial picornavirus genus-specific role in viral assembly, virion maturation, and infectivity
Complex gene expression patterns in animal development are generated by the interplay of transcriptional activators and repressors at cis-regulatory DNA modules ( CRMs ) . How repressors work is not well understood , but often involves interactions with co-repressors . We isolated mutations in the brakeless gene in a s...	Nuclear receptors play important roles in embryonic development and cellular differentiation by regulating gene expression at the level of transcription . The functions of transcriptional repressors , including nuclear receptors , are often mediated by other proteins , so-called co-repressors . We performed a genetic s...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "developmental", "biology", "homo", "(human)", "drosophila", "molecular", "biology", "genetics", "and", "genomics" ]	2007	Drosophila Brakeless Interacts with Atrophin and Is Required for Tailless-Mediated Transcriptional Repression in Early Embryos
Distal arthrogryposis type 2B ( DA2B ) is an important genetic disorder in humans . However , the mechanisms governing this disease are not clearly understood . In this study , we generated knock-in mice carrying a DA2B mutation ( K175del ) in troponin I type 2 ( skeletal , fast ) ( TNNI2 ) , which encodes a fast-twitc...	Distal arthrogryposis type 2B ( DA2B ) is an autosomal dominant genetic disorder . The typical clinical features of DA2B include hand and/or foot contracture and shortness of stature in patients . To date , mutations in TNNI2 can explain approximately 20% of familial incidences of DA2B . TNNI2 encodes a subunit of the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mutation", "genetics", "biology", "and", "life", "sciences", "human", "genetics", "genetics", "of", "disease" ]	2014	A Gain-of-Function Mutation in Tnni2 Impeded Bone Development through Increasing Hif3a Expression in DA2B Mice
Over the past several years fungal infections have shown an increasing incidence in the susceptible population , and caused high mortality rates . In parallel , multi-resistant fungi are emerging in human infections . Therefore , the identification of new potential antifungal targets is a priority . The first task of t...	Some fungi have become pathogenic to plants and in a lesser extent to animals . Under certain conditions their presence in the human body can prove a threat for human health , especially for immunocompromised patients . Yet , some fungi can also infect healthy individuals . The low sensitivity of the antifungal drugs a...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "biotechnology", "biomacromolecule-ligand", "interactions", "sequencing", "techniques", "medicine", "and", "health", "sciences", "functional", "genomics", "small", "molecules", "molecular", "biology", "techniques", "pharmacology", "sequence", "analysis", "genome", "complexity...	2014	Analysis of the Protein Domain and Domain Architecture Content in Fungi and Its Application in the Search of New Antifungal Targets
DJ-1 is one of the causative genes for early onset familiar Parkinson’s disease ( PD ) and is also considered to influence the pathogenesis of sporadic PD . DJ-1 has various physiological functions which converge on controlling intracellular reactive oxygen species ( ROS ) levels . In RNA-sequencing analyses searching ...	The molecular pathogenesis of Parkinson’s disease ( PD ) is still elusive even though many causative genes for the disease have been identified . In this study , we demonstrated that isocitrate dehydrogenase ( IDH ) , the enzyme responsible for converting isocitrate into α-ketoglutarate , is critical for the pathogenes...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "oxidative", "stress", "neurodegenerative", "diseases", "neuroscience", "animals", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "experimental", "organism", "systems", "genome", "analysis", ...	2017	Isocitrate protects DJ-1 null dopaminergic cells from oxidative stress through NADP+-dependent isocitrate dehydrogenase (IDH)
Collective cell migration plays an important role in development . Here , we study the posterior lateral line primordium ( PLLP ) a group of about 100 cells , destined to form sensory structures , that migrates from head to tail in the zebrafish embryo . We model mutually inhibitory FGF-Wnt signalling network in the PL...	Collective migration of a group of cells plays an important role in the development of an organism . Here we study a specific example in the zebrafish embryo , where a group of about 100 cells ( the posterior lateral line primordium , PLLP ) , destined to form sensory structures , migrates from head to tail . We model ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "signal", "transduction", "signal", "inhibition", "computer", "and", "information", "sciences", "cell", "motility", "developmental", "biology", "cell", "biology", "simulation", "and", "modeling", "network", "analysis", "cell", "migration", "chemokines", "biology", "and"...	2017	Polarization and migration in the zebrafish posterior lateral line system
The various roles that aggregation prone regions ( APRs ) are capable of playing in proteins are investigated here via comprehensive analyses of multiple non-redundant datasets containing randomly generated amino acid sequences , monomeric proteins , intrinsically disordered proteins ( IDPs ) and catalytic residues . R...	Biotechnology requires the large-scale expression , yield , and storage of recombinant proteins . Each step in protein production has the potential to cause aggregation as proteins , not evolved to exist outside the cell , endure the various steps involved in commercial manufacturing processes . Mechanistic studies int...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[]	2013	On the Role of Aggregation Prone Regions in Protein Evolution, Stability, and Enzymatic Catalysis: Insights from Diverse Analyses
An ability to sense pathogens by a number of specialized cell types including the dendritic cells plays a central role in host's defenses . Activation of these cells through the stimulation of the pathogen-recognition receptors induces the production of a number of cytokines including Type I interferons ( IFNs ) that m...	We have previously observed and reported that the activation of unfolded protein responses during infection with some viruses such as vesicular stomatitis virus and hepatitis C virus compromises the cellular responses to the cytokines that belong to family of Type I interferons ( IFNα/β ) . These effects apparently rel...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2011	Pathogen Recognition Receptor Signaling Accelerates Phosphorylation-Dependent Degradation of IFNAR1
Circadian clocks control the timing of animal behavioral and physiological rhythms . Fruit flies anticipate daily environmental changes and exhibit two peaks of locomotor activity around dawn and dusk . microRNAs are small non-coding RNAs that play important roles in post-transcriptional regulation . Here we identify D...	Circadian clocks control the timing of animal physiology . Drosophila has been a powerful model in understanding the mechanisms of circadian regulation . Fruit flies anticipate daily environmental changes and exhibit two peaks of locomotor activity around dawn and dusk . Here we identify miR-210 as a critical regulator...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "natural", "antisense", "transcripts", "gene", "regulation", "neuroscience", "biological", "locomotion", "animals", "circadian", "oscillators", "animal", "models", "micrornas", "model", "organisms", "drosophila", "...	2019	miR-210 controls the evening phase of circadian locomotor rhythms through repression of Fasciclin 2
Expanded polyglutamine ( polyQ ) proteins are known to be the causative agents of a number of human neurodegenerative diseases but the molecular basis of their cytoxicity is still poorly understood . PolyQ tracts may impede the activity of the proteasome , and evidence from single cell imaging suggests that the sequest...	Neurodegenerative diseases feature concentration of misfolded or damaged proteins into inclusion bodies . There is controversy over whether these entities are protective , detrimental , or relatively benign . The formation of inclusion bodies may be accelerated by inefficient protein degradation and may promote activat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/post-translational", "regulation", "of", "gene", "expression", "cell", "biology/cellular", "death", "and", "stress", "responses", "neurological", "disorders", "biochemistry/cell", "signaling", "and", "trafficking", "structures", "biochemistry/macromolecula...	2010	Experimental and Computational Analysis of Polyglutamine-Mediated Cytotoxicity
The inhibitory receptor programmed death-1 ( PD-1 ) has the capacity to maintain peripheral tolerance and limit immunopathological damage; however , its precise role in fulminant viral hepatitis ( FH ) has yet to be described . Here , we investigated the functional mechanisms of PD-1 as related to FH pathogenesis induc...	The principal characteristic of fulminant viral hepatitis ( FH ) induced by the murine hepatitis virus strain-3 ( MHV-3 ) is severe hepatocellular necrosis , which is mediated by the fibrinogen-like protein 2 ( FGL2 ) , a molecule that has the capacity to promote fibrinogen deposition and activate the coagulation casca...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/animal", "models", "of", "infection", "pathology/immunology", "virology/effects", "of", "virus", "infection", "on", "host", "gene", "expression", "immunology/immunity", "to", "infections", "pathology/molecular", "pathology" ]	2011	Programmed Death (PD)-1-Deficient Mice Are Extremely Sensitive to Murine Hepatitis Virus Strain-3 (MHV-3) Infection
Macrolides are used to treat various inflammatory diseases owing to their immunomodulatory properties; however , little is known about their precise mechanism of action . In this study , we investigated the functional significance of the expansion of myeloid-derived suppressor cell ( MDSC ) -like CD11b+Gr-1+ cells in r...	Myeloid-derived suppressor cells ( MDSCs ) are a heterogeneous population of anti-inflammatory myeloid progenitors that expand in response to acute and chronic inflammation as well as in various diseases , such as autoimmune diseases and cancer . The macrolide antibiotic clarithromycin has immunomodulatory effects in v...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "flow", "cytometry", "medicine", "and", "health", "sciences", "immune", "physiology", "immune", "cells", "spleen", "drugs", "immunology", "pulmonology", "immunosuppressives", "animal", "models", "pneumonia", "routes", "of", "administration", "model", ...	2018	Clarithromycin expands CD11b+Gr-1+ cells via the STAT3/Bv8 axis to ameliorate lethal endotoxic shock and post-influenza bacterial pneumonia
Integrins are heterodimeric ( αβ ) cell surface receptors that are activated to a high affinity state by the formation of a complex involving the α/β integrin transmembrane helix dimer , the head domain of talin ( a cytoplasmic protein that links integrins to actin ) , and the membrane . The talin head domain contains ...	Transmission of signals across the cell membrane is an essential process for all living organisms . Integrins are one example of cell surface receptors ( αβ ) which , uniquely , form a bidirectional signalling pathway across the membrane . Integrins are crucial for many cellular processes and play key roles in patholog...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[]	2013	Conformational Changes in Talin on Binding to Anionic Phospholipid Membranes Facilitate Signaling by Integrin Transmembrane Helices
Mitochondrial DNA ( mtDNA ) variants have been traditionally used as markers to trace ancient population migrations . Although experiments relying on model organisms and cytoplasmic hybrids , as well as disease association studies , have served to underline the functionality of certain mtDNA SNPs , only little is known...	The mitochondrion is an organelle found in all cells of our body and plays a significant role in the energy and heat production . This is the only organelle in animal cells harboring its own genome outside of the nucleus . Mitochondrial DNA ( mtDNA ) variants have been traditionally used as neutral markers to trace anc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "transfer", "rna", "rna-binding", "proteins", "mitochondrial", "dna", "gene", "regulation", "population", "genetics", "non-coding", "rna", "forms", "of", "dna", "mitochondria", "dna", "bioenergetics", "population", "biology", "molecular", "bi...	2016	Ancient Out-of-Africa Mitochondrial DNA Variants Associate with Distinct Mitochondrial Gene Expression Patterns
Transcription factors ( TFs ) regulate gene expression through specific interactions with short promoter elements . The same regulatory protein may recognize a variety of related sequences . Moreover , once they are detected it is hard to predict whether highly similar sequence motifs will be recognized by the same TF ...	A prime mode of control of transcription is the binding of transcription factors to promoter elements . These elements are often imprecise – often more than one , yet typically not all , of the nucleotides may be tolerated . In another field of protein structures , only some of the amino acid substitutions are tolerate...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/functional", "genomics", "genetics", "and", "genomics/gene", "expression", "computational", "biology/genomics", "computational", "biology/transcriptional", "regulation" ]	2008	Functional Characterization of Variations on Regulatory Motifs
Shoot apical meristems ( SAM ) are resistant to most plant viruses due to RNA silencing , which is restrained by viral suppressors of RNA silencing ( VSRs ) to facilitate transient viral invasion of the SAM . In many cases chronic symptoms and long-term virus recovery occur , but the underlying mechanisms are poorly un...	In many virus-infected plants , the development of viral symptoms on the upper leaves gradually decline , until finally the top leaves appear normal and become resistant to secondary infection . Many documented cases suggest that symptom recovery is accompanied with antiviral RNA silencing . Most plant viruses encode v...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "plant", "anatomy", "rna-binding", "proteins", "rna", "interference", "gene", "regulation", "rna", "extraction", "brassica", "plant", "physiology", "plant", "science", "model", "organisms", "experimental", "organism", "systems", "epigenetics", "plants", "extraction", "t...	2017	Cucumber mosaic virus coat protein modulates the accumulation of 2b protein and antiviral silencing that causes symptom recovery in planta
Recent reports have questioned the accepted dogma that mammalian mitochondrial DNA ( mtDNA ) is strictly maternally inherited . In humans , the argument hinges on detecting a signature of inter-molecular recombination in mtDNA sequences sampled at the population level , inferring a paternal source for the mixed haploty...	Emerging evidence raises the possibility that human mitochondrial DNA ( mtDNA ) is not strictly maternally inherited , but it has not been technically possible to test this hypothesis directly . We identified trios with discordant mtDNA haplotypes , parent-offspring trios were validated using polymorphic microsatellite...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Extreme-Depth Re-sequencing of Mitochondrial DNA Finds No Evidence of Paternal Transmission in Humans
As cells proceed along their developmental pathways they make a series of sequential cell fate decisions . Each of those decisions needs to be made in a robust manner so there is no ambiguity in the state of the cell as it proceeds to the next stage . Here we examine the decision made by the Drosophila R7 precursor cel...	Animals are made from a vast diversity of different cell types , and understanding how they are specified is a major goal of developmental biology . In this study we use the Drosophila R7 photoreceptor as a model system for understanding how cell fate specification occurs . We examine the step when the R7 precursor cel...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "gene", "regulation", "regulatory", "proteins", "precursor", "cells", "social", "sciences", "dna-binding", "proteins", "cloning", "neuroscience", "dna", "transcription", "gene", "function", "transcription", "factors", "molecular", ...	2016	R7 Photoreceptor Specification in the Developing Drosophila Eye: The Role of the Transcription Factor Deadpan
Inhibition of nitric oxide ( NO ) signaling may contribute to pathological activation of the vascular endothelium during severe malaria infection . Dimethylarginine dimethylaminohydrolase ( DDAH ) regulates endothelial NO synthesis by maintaining homeostasis between asymmetric dimethylarginine ( ADMA ) , an endogenous ...	During a malaria infection , the vascular endothelium becomes more adhesive , permeable , and prone to trigger blood clotting . These changes help the parasite adhere to blood vessels , but endanger the host by obstructing blood flow through small vessels . Endothelial nitric oxide ( NO ) would normally counteract thes...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Plasmodium Infection Is Associated with Impaired Hepatic Dimethylarginine Dimethylaminohydrolase Activity and Disruption of Nitric Oxide Synthase Inhibitor/Substrate Homeostasis
Atrial fibrillation , a common cardiac arrhythmia , often progresses unfavourably: in patients with long-term atrial fibrillation , fibrillatory episodes are typically of increased duration and frequency of occurrence relative to healthy controls . This is due to electrical , structural , and contractile remodeling pro...	Atrial fibrillation is an abnormal heart rhythm characterized by rapid and irregular activation of the upper chambers of the heart . Atrial fibrillation often shows a natural progression towards longer and more frequently occurring episodes and often occurs in patients with existing heart disease ( s ) . Because atrial...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "physiology", "biology", "anatomy", "and", "physiology", "biophysics", "computational", "biology", "cardiovascular" ]	2012	Effects of Electrical and Structural Remodeling on Atrial Fibrillation Maintenance: A Simulation Study
The architecture of iso-orientation domains in the primary visual cortex ( V1 ) of placental carnivores and primates apparently follows species invariant quantitative laws . Dynamical optimization models assuming that neurons coordinate their stimulus preferences throughout cortical circuits linking millions of cells s...	In the primary visual cortex of primates and carnivores , local visual stimulus features such as edge orientation are processed by neurons arranged in arrays of iso-orientation domains . Large-scale comparative studies have uncovered that the spatial layout of these domains and their topological defects follows species...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Random Wiring, Ganglion Cell Mosaics, and the Functional Architecture of the Visual Cortex
Dengue virus ( DENV ) infection of an individual human or mosquito host produces a dynamic population of closely-related sequences . This intra-host genetic diversity is thought to offer an advantage for arboviruses to adapt as they cycle between two very different host species , but it remains poorly characterized . T...	Dengue virus ( DENV ) is transmitted between humans through the bite of infected female Aedes aegypti mosquitoes . Virus populations experience significant drops in size and are subject to differing selection pressures as they cycle between human and mosquito hosts . Subsequent changes in viral intra-host genetic diver...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Tracking Dengue Virus Intra-host Genetic Diversity during Human-to-Mosquito Transmission
Circulation is an important delivery method for both natural and synthetic molecules , but microenvironment interactions , regulated by endothelial cells and critical to the molecule's fate , are difficult to interpret using traditional approaches . In this work , we analyzed and predicted growth factor capture under f...	In this work we have investigated the role of a family of cell surface molecules , proteoglycans , in blood vessel capture of proteins important to normal and diseased states under flow conditions . We developed a computer model to analyze and predict these events and , using an experimental system incorporating endoth...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "cell", "biology", "computational", "biology" ]	2010	Endothelial Cell Capture of Heparin-Binding Growth Factors under Flow
Many critical events in the Plasmodium life cycle rely on the controlled release of Ca2+ from intracellular stores to activate stage-specific Ca2+-dependent protein kinases . Using the motility of Plasmodium berghei ookinetes as a signalling paradigm , we show that the cyclic guanosine monophosphate ( cGMP ) -dependent...	Malaria , caused by Plasmodium spp . parasites , is a profound human health problem . Plasmodium parasites progress through a complex life cycle as they move between infected humans and blood-feeding mosquitoes . We know that tight regulation of calcium ion levels within the cytosol of the parasite is critical to contr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "second", "messenger", "system", "mechanisms", "of", "signal", "transduction", "cgmp", "signaling", "host-pathogen", "interaction", "microbiology", "parasitology", "parasite", "physiology", "phosphoinositide", "signal", "transduction", "crosstalk", "cell", "movement", "sign...	2014	Phosphoinositide Metabolism Links cGMP-Dependent Protein Kinase G to Essential Ca2+ Signals at Key Decision Points in the Life Cycle of Malaria Parasites
Antiretroviral therapy ( ART ) has reduced morbidity and mortality in HIV-1 infection; however HIV-1-associated neurocognitive disorders ( HAND ) persist despite treatment . The reasons for the limited efficacy of ART in the brain are unknown . Here we used functional genomics to determine ART effectiveness in the brai...	HAND is a common complication of HIV-1 infection in the nervous system presenting a varied spectrum of clinical manifestations with cognitive , motor and behavioral symptoms . Introduction of ART has greatly reduced morbidity and mortality in HIV-1 infection; however HAND persists and its overall prevalence appears to ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "neurobiology", "of", "disease", "and", "regeneration", "functional", "genomics", "retrovirology", "and", "hiv", "immunopathogenesis", "microbiology", "neuroscience", "infectious", "diseases", "hiv", "biology", "dementia", "virology", "neurology", "neurological"...	2011	Significant Effects of Antiretroviral Therapy on Global Gene Expression in Brain Tissues of Patients with HIV-1-Associated Neurocognitive Disorders
We identified a non-synonymous mutation in Oas2 ( I405N ) , a sensor of viral double-stranded RNA , from an ENU-mutagenesis screen designed to discover new genes involved in mammary development . The mutation caused post-partum failure of lactation in healthy mice with otherwise normally developed mammary glands , char...	Using ENU-mutagenesis in mice we discovered a pedigree with lactation failure . Mammary development through puberty and pregnancy appeared normal in mutant animals , but the activation of lactation failed in the immediate post partum period and no milk reached the pups . Failure of lactation was accompanied by greatly ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "milk", "reproductive", "system", "body", "fluids", "maternal", "health", "nucleases", "enzymes", "gene", "regulation", "dna-binding", "proteins", "enzymology", "diet", "reproductive", "physiology", "endocrine", "physiology", "ep...	2017	A mutation in the viral sensor 2’-5’-oligoadenylate synthetase 2 causes failure of lactation
Sequencing of whole cancer genomes has revealed an abundance of recurrent mutations in gene-regulatory promoter regions , in particular in melanoma where strong mutation hotspots are observed adjacent to ETS-family transcription factor ( TF ) binding sites . While sometimes interpreted as functional driver events , the...	Cancer is caused by somatic mutations that typically occur in protein-coding genes . However , the advent of whole genome sequencing has made it possible to venture beyond protein-coding DNA in search of non-coding mutations with putative cancer driver roles . Indeed , recent studies , in particular in skin cancers , d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cancer", "genomics", "sequencing", "techniques", "medicine", "and", "health", "sciences", "chemical", "compounds", "cancers", "and", "neoplasms", "basic", "cancer", "research", "organic", "compounds", "oncology", "genome", "sequencing", "mutation", "pyrimidines", "sequ...	2018	Elevated pyrimidine dimer formation at distinct genomic bases underlies promoter mutation hotspots in UV-exposed cancers
Energy metabolism is central to cellular biology . Thus , genome-scale models of heterotrophic unicellular species must account appropriately for the utilization of external nutrients to synthesize energy metabolites such as ATP . However , metabolic models designed for flux-balance analysis ( FBA ) may contain thermod...	Genome-scale metabolic models are routinely used to simulate the growth of unicellular organisms , and are likely to become an important tool in the medical sciences . The most popular method employed for this task is flux balance analysis ( FBA ) , a simplified mathematical description able to describe the simultaneou...	[ "Abstract", "Introduction", "Results", "and", "discussions", "Materials", "and", "methods" ]	[ "protons", "medicine", "and", "health", "sciences", "metabolic", "networks", "physiological", "processes", "metabolites", "network", "analysis", "genome", "analysis", "bioenergetics", "thermodynamics", "research", "and", "analysis", "methods", "computer", "and", "informat...	2017	Erroneous energy-generating cycles in published genome scale metabolic networks: Identification and removal
Recent studies found that mutations in the human SLC30A10 gene , which encodes a manganese ( Mn ) efflux transporter , are associated with hypermanganesemia with dystonia , polycythemia , and cirrhosis ( HMDPC ) . However , the relationship between Mn metabolism and HMDPC is poorly understood , and no specific treatmen...	Impaired function of the manganese transporter SLC30A10 has been implicated in HMDPC ( hypermanganesemia with dystonia , polycythemia , and cirrhosis ) , an early-onset metabolic disorder clinically characterized by increased systemic Mn levels , neurological impairment , polycythemia , and hepatic injury . No specific...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "chemical", "bonding", "medicine", "and", "health", "sciences", "manganese", "hela", "cells", "biological", "cultures", "cell", "processes", "vertebrates", "animals", "biological", "locomotion", "animal", "models", "osteichthyes", "organisms", "developmental", "biology", ...	2017	Zebrafish slc30a10 deficiency revealed a novel compensatory mechanism of Atp2c1 in maintaining manganese homeostasis
For more than a century , the origin of metazoan animals has been debated . One aspect of this debate has been centered on what the hypothetical “urmetazoon” bauplan might have been . The morphologically most simply organized metazoan animal , the placozoan Trichoplax adhaerens , resembles an intriguing model for one o...	Following one of the basic principles in evolutionary biology that complex life forms derive from more primitive ancestors , it has long been believed that the higher animals , the Bilateria , arose from simpler ( diploblastic ) organisms such as the cnidarians ( corals , polyps , and jellyfishes ) . A large number of ...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology", "evolutionary", "biology" ]	2009	Concatenated Analysis Sheds Light on Early Metazoan Evolution and Fuels a Modern “Urmetazoon” Hypothesis
Implantation of a blastocyst in the uterus is a multistep process tightly controlled by an intricate regulatory network of interconnected ovarian , uterine , and embryonic factors . Bone morphogenetic protein ( BMP ) ligands and receptors are expressed in the uterus of pregnant mice , and BMP2 has been shown to be a ke...	A couple is defined as infertile when failing to become pregnant after one year of regular , unprotected intercourse . Infertility affects more than 10% of couples . The implantation of the embryo in the uterus is one of the most critical steps of pregnancy , and it has been estimated that 75% of pregnancy fails becaus...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Activin-Like Kinase 2 Functions in Peri-implantation Uterine Signaling in Mice and Humans
Nematode-trapping fungi ( NTF ) are a large and diverse group of fungi , which may switch from a saprotrophic to a predatory lifestyle if nematodes are present . Different fungi have developed different trapping devices , ranging from adhesive cells to constricting rings . After trapping , fungal hyphae penetrate the w...	Nematode-trapping fungi are fascinating microorganisms , because they are able to switch from saprotrophic growth to a predatory lifestyle . Duddingtonia flagrans forms adhesive trap systems and conidia and resistant chlamydospores . Chlamydospores are ideal for dissemination in the environment to control nematode popu...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "caenorhabditis", "fungal", "genetics", "rna", "extraction", "parasitic", "diseases", "animals", "nematode", "infections", "animal", "models", "fungi", "caenorhabditis", "elegans", "model", "organisms", "experiment...	2019	Intercellular communication is required for trap formation in the nematode-trapping fungus Duddingtonia flagrans
In eukaryotic cells , most mRNAs are exported from the nucleus by the transcription export ( TREX ) complex , which is loaded onto mRNAs after their splicing and capping . We have studied in mammalian cells the nuclear export of mRNAs that code for secretory proteins , which are targeted to the endoplasmic reticulum me...	In eukaryotic cells , precursors of messenger RNAs ( mRNAs ) are synthesized and processed in the nucleus . During processing , noncoding introns are spliced out , and a cap and poly-adenosine sequence are added to the beginning and end of the transcript , respectively . The resulting mature mRNA is exported from the n...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "cell", "biology", "computational", "biology", "molecular", "biology" ]	2007	The Signal Sequence Coding Region Promotes Nuclear Export of mRNA
A systematic assessment of global neural network connectivity through direct electrophysiological assays has remained technically infeasible , even in simpler systems like dissociated neuronal cultures . We introduce an improved algorithmic approach based on Transfer Entropy to reconstruct structural connectivity from ...	Unraveling the general organizing principles of connectivity in neural circuits is a crucial step towards understanding brain function . However , even the simpler task of assessing the global excitatory connectivity of a culture in vitro , where neurons form self-organized networks in absence of external stimuli , rem...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "circuit", "models", "connectomics", "calcium", "imaging", "developmental", "neuroscience", "computer", "science", "neuroanatomy", "neural", "networks", "computational", "neuroscience", "biology", "computerized", "simulations", "neuroscience", "neural", "circuit", "formation"...	2012	Model-Free Reconstruction of Excitatory Neuronal Connectivity from Calcium Imaging Signals
In Africa , relapsing fevers are neglected arthropod-borne infections caused by closely related Borrelia species . They cause mild to deadly undifferentiated fever particularly severe in pregnant women . Lack of a tool to genotype these Borrelia organisms limits knowledge regarding their reservoirs and their epidemiolo...	In Africa , relapsing fevers are caused by four cultured species: Borrelia crocidurae , Borrelia duttonii , Borrelia hispanica and Borrelia recurrentis . These borreliae are transmitted by the bite of Ornithodoros soft ticks except for B . recurrentis which is transmitted by louse Pediculus humanus . They cause potenti...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "bacterial", "diseases", "infectious", "diseases", "borrelia", "infection", "zoonoses", "neglected", "tropical", "diseases" ]	2012	Multispacer Sequence Typing Relapsing Fever Borreliae in Africa
The Complementarity Determining Regions ( CDRs ) of antibodies are assumed to account for the antigen recognition and binding and thus to contain also the antigen binding site . CDRs are typically discerned by searching for regions that are most different , in sequence or in structure , between different antibodies . H...	Antibodies are a primary adaptive defence mechanism against infection , and function by recognizing and binding to non-self antigens . While most of the sequence of all antibodies of a given individual is identical , relatively small variations turn each antibody into a specific binder of one antigen . It is widely ass...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology", "biology", "computational", "biology" ]	2012	Structural Consensus among Antibodies Defines the Antigen Binding Site
Bacteria form dense surface-associated communities known as biofilms that are central to their persistence and how they affect us . Biofilm formation is commonly viewed as a cooperative enterprise , where strains and species work together for a common goal . Here we explore an alternative model: biofilm formation is a ...	Bacteria often attach to each other and to surfaces and make biofilms . These dense communities occur everywhere , including on us and inside us , where they are central to both health and disease . Biofilm formation is often viewed as the coordinated action of multiple strains that work together in order to prosper an...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Conclusions", "Methods" ]	[]	2015	Biofilm Formation As a Response to Ecological Competition
Mitochondrial membrane biogenesis and lipid metabolism require phospholipid transfer from the endoplasmic reticulum ( ER ) to mitochondria . Transfer is thought to occur at regions of close contact of these organelles and to be nonvesicular , but the mechanism is not known . Here we used a novel genetic screen in S . c...	Mitochondrial membrane biogenesis and lipid metabolism depend on the transfer of phospholipid from the endoplasmic reticulum to mitochondria . This transfer is thought to occur at regions where these organelles are in close contact , and , although the process is thought not to involve vesicles , the mechanism is not k...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences" ]	2014	A Conserved Endoplasmic Reticulum Membrane Protein Complex (EMC) Facilitates Phospholipid Transfer from the ER to Mitochondria
Wolbachia is an intracellular bacterium that infects a remarkable range of insect hosts . Insects such as mosquitos act as vectors for many devastating human viruses such as Dengue , West Nile , and Zika . Remarkably , Wolbachia infection provides insect hosts with resistance to many arboviruses thereby rendering the i...	Insects such as mosquitos act as vectors to spread devastating human diseases such as Dengue , West Nile , and Zika . It is critical to develop control strategies to prevent the transmission of these diseases to human populations . A novel strategy takes advantage of an endosymbiotic bacterium Wolbachia pipientis . The...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "rna", "interference", "pathology", "and", "laboratory", "medicine", "cell", "processes", "genomic", "library", "screening", "animals", "wolbachia", "invertebrate", "genomics", "animal", "models", "drosophila", "...	2018	Whole genome screen reveals a novel relationship between Wolbachia levels and Drosophila host translation
Chronic liver infection by hepatitis C virus ( HCV ) is a major public health concern . Despite partly successful treatment options , several aspects of intrahepatic HCV infection dynamics are still poorly understood , including the preferred mode of viral propagation , as well as the proportion of infected hepatocytes...	Around 170 million people worldwide are chronically infected with the hepatitis C virus ( HCV ) . Although partly successful treatment options are available , several aspects of HCV infection dynamics within the liver are still poorly understood . How many hepatocytes are infected during chronic HCV infection ? How doe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "hepatitis", "c", "infectious", "diseases", "medicine", "and", "health", "sciences", "infectious", "hepatitis", "simulation", "and", "modeling", "population", "modeling", "gastroenterology", "and", "hepatology", "biology", "and", "life", "sciences", "infectious", "disea...	2014	Inferring Viral Dynamics in Chronically HCV Infected Patients from the Spatial Distribution of Infected Hepatocytes
The C-terminal domain ( CTD ) of RNA polymerase II ( RNAPII ) is composed of heptapeptide repeats , which play a key regulatory role in gene expression . Using genetic interaction , chromatin immunoprecipitation followed by microarrays ( ChIP-on-chip ) and mRNA expression analysis , we found that truncating the CTD res...	RNA Polymerase II ( RNAPII ) is the enzyme responsible for the transcription of all protein-coding genes . It has a unique extended domain called the C-terminal domain ( CTD ) . This domain is highly conserved across species and is composed of repeats of a seven amino acid sequence . The CTD functions as a recruiting p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	High-Throughput Genetic and Gene Expression Analysis of the RNAPII-CTD Reveals Unexpected Connections to SRB10/CDK8
Failure to establish an appropriate balance between pro- and anti-inflammatory immune responses is believed to contribute to pathogenesis of severe malaria . To determine whether this balance is maintained by classical regulatory T cells ( CD4+ FOXP3+ CD127−/low; Tregs ) we compared cellular responses between Gambian c...	While Tregs have been implicated in regulation of the immune response to chronic infections , their potential in determining disease outcome in acute infections is unclear . In this study we have found that Tregs are unable to control the florid inflammation during acute , severe P . falciparum malaria infections , sug...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/immunomodulation", "infectious", "diseases/tropical", "and", "travel-associated", "diseases", "immunology/immunity", "to", "infections", "infectious", "diseases/protozoal", "infections" ]	2009	Distinct Roles for FOXP3+ and FOXP3− CD4+ T Cells in Regulating Cellular Immunity to Uncomplicated and Severe Plasmodium falciparum Malaria
Exome sequencing is becoming a standard tool for mapping Mendelian disease-causing ( or pathogenic ) non-synonymous single nucleotide variants ( nsSNVs ) . Minor allele frequency ( MAF ) filtering approach and functional prediction methods are commonly used to identify candidate pathogenic mutations in these studies . ...	Sequencing the coding regions of the human genome is becoming a standard approach in identifying causal genes for human Mendelian diseases . Researchers often rely on multiple functional prediction methods/tools to separate the candidate causal mutation ( s ) from other rare mutations in these studies . In this paper ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "sequencing", "genomics", "genetic", "mutation", "genetics", "biology", "human", "genetics", "genetics", "of", "disease", "genetics", "and", "genomics" ]	2013	Predicting Mendelian Disease-Causing Non-Synonymous Single Nucleotide Variants in Exome Sequencing Studies
Isogenic cells sensing identical external signals can take markedly different decisions . Such decisions often correlate with pre-existing cell-to-cell differences in protein levels . When not neglected in signal transduction models , these differences are accounted for in a static manner , by assuming randomly distrib...	TRAIL induces apoptosis selectively in cancer cells and is currently tested in clinics . Having a mechanistic understanding of TRAIL resistance could help to limit its apparition . Several observations suggested that protein level fluctuations play an important role in TRAIL resistance and its acquisition . However , q...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry", "biochemical", "simulations", "cell", "death", "signal", "transduction", "mathematics", "cell", "biology", "apoptosis", "gene", "expression", "genetics", "biology", "and", "life", "sciences", "cell", "processes", "physical", "sciences", "computational", ...	2014	Modeling Dynamics of Cell-to-Cell Variability in TRAIL-Induced Apoptosis Explains Fractional Killing and Predicts Reversible Resistance
Loci identified in genome-wide association studies ( GWAS ) of cardio-metabolic traits account for a small proportion of the traits' heritability . To date , most association studies have not considered parent-of-origin effects ( POEs ) . Here we report investigation of POEs on adiposity and glycemic traits in young ad...	To date , genetic variants identified in large-scale genetic studies using recent technical and methodological advances explain only a small proportion of the genetic basis of obesity , diabetes and other cardiovascular risk factors . These studies were typically conducted in samples of unrelated individuals . Here we ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Parent-of-Origin Effects of the APOB Gene on Adiposity in Young Adults
Dengue virus ( DENV ) infection causes dengue fever , dengue hemorrhagic fever and dengue shock syndrome . It is estimated that a third of the world’s population is at risk for infection , with an estimated 390 million infections annually . Dengue virus serotype 2 ( DENV2 ) causes severe epidemics , and the leading tet...	Dengue viruses ( DENV ) are flaviviruses transmitted by mosquitos . There are approximately 390 million DENV infections every year , making dengue virus a major global public health concern . While there is a recently licensed DENV vaccine , it has low efficacy against preventing DENV2 infections . Individuals that are...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "serum", "dengue", "virus", "medicine", "and", "health", "sciences", "chemical", "characterization", "immune", "physiology", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "body", "fluids", "pathogens", "immunology", "microbiology"...	2018	Human dengue virus serotype 2 neutralizing antibodies target two distinct quaternary epitopes
Despite elimination efforts , the number of Mycobacterium leprae ( M . leprae ) infected individuals who develop leprosy , is still substantial . Solid evidence exists that individuals living in close proximity to patients are at increased risk to develop leprosy . Early diagnosis of leprosy in endemic areas requires f...	Leprosy is an infectious disease caused by the bacterium Mycobacterium leprae , which causes skin and nerve damage . Despite worldwide efforts to eliminate leprosy , the number of infected individuals who develop leprosy , is still substantial . Household contacts of new leprosy patients are especially at risk . Early ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "mycobacterium", "leprae", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "laboratory", "equipment", "engineering", "and", "technology", "tropical", "diseases", "geographical", "locations", "biomarkers...	2017	Longitudinal assessment of anti-PGL-I serology in contacts of leprosy patients in Bangladesh
Timely resolution of inflammation is critical for the restoration of homeostasis in injured or infected tissue . Chronic inflammation is often characterized by a persistent increase in the concentrations of inflammatory cells and molecular mediators , whose distinct amount and timing characteristics offer an opportunit...	A recent approach to quantitatively characterize the timing and intensity of the inflammatory response relies on the use of four quantities termed inflammation indices . The values of the inflammation indices may reflect the differences between normal and pathological inflammation , and may be used to gauge the effects...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Computational Identification of Mechanistic Factors That Determine the Timing and Intensity of the Inflammatory Response
Unlike the core structural elements of a protein like regular secondary structure , template based modeling ( TBM ) has difficulty with loop regions due to their variability in sequence and structure as well as the sparse sampling from a limited number of homologous templates . We present a novel , knowledge-based meth...	A protein's structure consists of elements of regular secondary structure connected by less regular stretches of loop segments . The irregularity of the loop structure makes loop modeling quite challenging . More accurate sampling of these loop conformations has a direct impact on protein modeling , design , function c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "mathematics", "statistics", "biology", "computational", "biology" ]	2011	Near-Native Protein Loop Sampling Using Nonparametric Density Estimation Accommodating Sparcity
Reassortments and point mutations are two major contributors to diversity of Influenza A virus; however , the link between these two processes is unclear . It has been suggested that reassortments provoke a temporary increase in the rate of amino acid changes as the viral proteins adapt to new genetic environment , but...	Influenza A is a rapidly evolving virus with genome composed of eight distinct RNA molecules called segments . This genetic structure allows formation of new combinations of segments when a cell is coinfected by multiple viral strains , in a process called reassortment . While “antigenic drift” – the process of continu...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "organismal", "evolution", "genome", "evolution", "population", "genetics", "microbiology", "parallel", "evolution", "mutation", "microbial", "evolution", "forms", "of", "evolution", "comparative", "genomics", "biology", "evolutionary", "theory", "evolutionary", "genetics",...	2014	Intrasubtype Reassortments Cause Adaptive Amino Acid Replacements in H3N2 Influenza Genes
The Ufm1 conjugation system is an ubiquitin-like modification system that consists of Ufm1 , Uba5 ( E1 ) , Ufc1 ( E2 ) , and less defined E3 ligase ( s ) and targets . The biological importance of this system is highlighted by its essential role in embryogenesis and erythroid development , but the underlying mechanism ...	Protein modification by Ubiquitin ( Ub ) and Ubiquitin-like proteins ( Ubl ) plays pivotal roles in a wide range of cellular functions and signaling pathways . The Ufm1 conjugation system is a novel ubiquitin-like system , yet its biological functions and working mechanism remains poorly understood . UFBP1 is a putativ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	UFBP1, a Key Component of the Ufm1 Conjugation System, Is Essential for Ufmylation-Mediated Regulation of Erythroid Development
Previous studies have shown that EBLV-1 strains exclusively hosted by Eptesicus isabellinus bats in the Iberian Peninsula cluster in a specific monophyletic group that is related to the EBLV-1b lineage found in the rest of Europe . More recently , enhanced passive surveillance has allowed the detection of the first EBL...	Rabies is caused by at least fourteen different viruses of the genus Lyssavirus . Although the classical rabies virus transmitted by the dog accounts for most human cases , most lyssaviruses are hosted by bats , which are able to transmit the disease to humans . The European bat lyssaviruses 1 ( EBLV-1 ) and 2 ( EBLV-2...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "and", "discussion" ]	[ "taxonomy", "organismal", "evolution", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "geographical", "locations", "microbiology", "vertebrates", "animals", "mammals", "genetic", "mapping", "viruses", "phylogenetics", "...	2018	First cases of European bat lyssavirus type 1 in Iberian serotine bats: Implications for the molecular epidemiology of bat rabies in Europe
Electrophysiological evidence suggested primarily the involvement of the middle temporal ( MT ) area in depth cue integration in macaques , as opposed to human imaging data pinpointing area V3B/kinetic occipital area ( V3B/KO ) . To clarify this conundrum , we decoded monkey functional MRI ( fMRI ) responses evoked by ...	In everyday life , we interact with a three-dimensional world that we perceive via our two-dimensional retinas . Our brain can reconstruct the third dimension from these flat retinal images using multiple sources of visual information , or cues . The horizontal displacement of the two retinal images , known as binocula...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "diagnostic", "radiology", "functional", "magnetic", "resonance", "imaging", "brain", "vertebrates", "social", "sciences", "neuroscience", "animals", "mammals", "magnetic", "resonance", "imaging", "primates", "brain", "mapping", ...	2019	Areal differences in depth cue integration between monkey and human
Cytomegaloviruses ( CMVs ) encode cellular homologs to evade host immune functions . In this study , we analyzed the roles of GP33 , a guinea pig CMV ( GPCMV ) -encoded G protein-coupled receptor ( GPCR ) homolog , in cellular signaling , viral growth and pathogenesis . The cDNA structure of GP33 was determined by RACE...	Cytomegalovirus ( CMV ) is a major pathogen that causes congenital diseases , including birth defects and developmental abnormalities in newborns . Better understanding of the immune evasion mechanisms may open the way to the development of new types of live attenuated vaccines for congenital CMV infection . In contras...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "innate", "immune", "system", "medicine", "and", "health", "sciences", "reproductive", "system", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "spleen", "immunology", "microbiology", "vert...	2018	Roles of GP33, a guinea pig cytomegalovirus-encoded G protein-coupled receptor homolog, in cellular signaling, viral growth and inflammation in vitro and in vivo
With the rising development of bacterial resistance the search for new medical treatments beyond conventional antimicrobials has become a key aim of public health research . Possible innovative strategies include the inhibition of bacterial virulence . However , consideration must be given to the evolutionary and envir...	With the rising development of antibiotic resistance and rapid spread of nosocomial pathogens , the search for new treatments beyond conventional antibiotics becomes a key aim of public health research . As such , anti-virulence therapies might be alternative antimicrobial strategies . However , consideration must be g...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology/microbial", "evolution", "and", "genomics", "ecology/evolutionary", "ecology", "infectious", "diseases/nosocomial", "and", "healthcare-associated", "infections", "microbiology/microbial", "evolution", "and", "genomics", "microbiology", "infectious", "dise...	2010	Quorum Sensing Inhibition Selects for Virulence and Cooperation in Pseudomonas aeruginosa
Biomarker discovery aims to find small subsets of relevant variables in ‘omics data that correlate with the clinical syndromes of interest . Despite the fact that clinical phenotypes are usually characterized by a complex set of clinical parameters , current computational approaches assume univariate targets , e . g . ...	Many infectious diseases such as tuberculosis and malaria are challenging both for scientists trying to understand the biochemical basis of the diseases and for medical doctors making diagnosis . The challenges arise both from the dependence of the diseases on sets of proteins and from the complexity of the symptoms . ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "algorithms", "systems", "biology", "medicine", "infectious", "diseases", "computer", "science", "bacterial", "diseases", "mycobacterium", "diagnostic", "medicine", "tuberculosis", "global", "health", "biology", "computational", "biology", "malaria", "parasitic", "diseases"...	2013	Biomarker Discovery by Sparse Canonical Correlation Analysis of Complex Clinical Phenotypes of Tuberculosis and Malaria
Cortisol , secreted in the adrenal cortex in response to stress , is an informative biomarker that distinguishes anxiety disorders such as major depression and post-traumatic stress disorder ( PTSD ) from normal subjects . Yehuda et al . proposed a hypothesis that , in humans , the hypersensitive hypothalamus-pituitary...	PTSD is an anxiety disorder that occurs among persons exposed to a traumatic event involving life threat and injury . This is a co-morbid psychiatric disorder that occurs along with depression . Cortisol is an informative endocrine biomarker that can distinguish PTSD from other co-morbid disorders . In comparison to no...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "systems", "biology", "biology", "genetics", "and", "genomics" ]	2012	Modeling Cortisol Dynamics in the Neuro-endocrine Axis Distinguishes Normal, Depression, and Post-traumatic Stress Disorder (PTSD) in Humans
Despite the overall decrease in visceral leishmaniasis ( VL ) incidence on the Indian subcontinent , there remain spatiotemporal clusters or ‘hotspots’ of new cases . The characteristics of these hotspots , underlying transmission dynamics , and their importance for shaping control strategies are not yet fully understo...	Visceral leishmaniasis ( VL ) is the deadliest vector-borne parasitic disease after malaria worldwide and is one of the neglected tropical diseases targeted for elimination and control by the World Health Organization . Despite the overall decrease in VL incidence in Bihar , India , a region previously highly endemic f...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "kala-azar", "medicine", "and", "health", "sciences", "immunology", "tropical", "diseases", "geographical", "locations", "india", "age", "distribution", "sand", "flies", "parasitic", "diseases", "geoinformatics", "age", "groups", "neglected", "tropical", "diseases", "po...	2018	Visceral leishmaniasis: Spatiotemporal heterogeneity and drivers underlying the hotspots in Muzaffarpur, Bihar, India
Two classes of antiviral drugs , neuraminidase inhibitors and adamantanes , are approved for prophylaxis and therapy against influenza virus infections . A major concern is that antiviral resistant viruses emerge and spread in the human population . The 2009 pandemic H1N1 virus is already resistant to adamantanes . Rec...	Recently , a pandemic A/H1N1 influenza virus was isolated from an immune compromised patient with a novel antiviral resistance pattern to the neuraminidase inhibitor class of drugs . This virus had an amino acid change in the viral neuraminidase enzyme; an isoleucine at position 223 was substituted by an arginine ( I22...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "protein", "chemistry", "drugs", "and", "devices", "influenza", "pharmacology", "biology", "viral", "diseases", "drug", "interactions", "biophysics" ]	2012	H1N1 2009 Pandemic Influenza Virus: Resistance of the I223R Neuraminidase Mutant Explained by Kinetic and Structural Analysis
The balance between pro-inflammatory and regulatory immune responses in determining optimal T cell activation is vital for the successful resolution of microbial infections . This balance is maintained in part by the negative regulators of T cell activation , CTLA-4 and PD-1/PD-L , which dampen effector responses durin...	T cells are part of the body's defense system in response to infection . However , once the infection has been suitably controlled , these T cells must be switched off . Inhibitory pathways , such as CTLA-4 and PD-1 , are known to send the ‘turn off’ signal to T cells during chronic infections . However , their roles i...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "immune", "cells", "immunity", "immunology", "biology", "parasitic", "diseases", "immune", "system" ]	2012	The CTLA-4 and PD-1/PD-L1 Inhibitory Pathways Independently Regulate Host Resistance to Plasmodium-induced Acute Immune Pathology
Passive acoustic sensing has emerged as a powerful tool for quantifying anthropogenic impacts on biodiversity , especially for echolocating bat species . To better assess bat population trends there is a critical need for accurate , reliable , and open source tools that allow the detection and classification of bat cal...	There is a critical need for robust and accurate tools to scale up biodiversity monitoring and to manage the impact of anthropogenic change . For example , the monitoring of bat species and their population dynamics can act as an important indicator of ecosystem health as they are particularly sensitive to habitat conv...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion", "Data", "reporting" ]	[ "acoustics", "medicine", "and", "health", "sciences", "neural", "networks", "engineering", "and", "technology", "audio", "signal", "processing", "applied", "mathematics", "signal", "processing", "vertebrates", "neuroscience", "animals", "mammals", "animal", "signaling", ...	2018	Bat detective—Deep learning tools for bat acoustic signal detection
Human red blood cells ( RBCs ) lose ∼30% of their volume and ∼20% of their hemoglobin ( Hb ) content during their ∼100-day lifespan in the bloodstream . These observations are well-documented , but the mechanisms for these volume and hemoglobin loss events are not clear . RBCs shed hemoglobin-containing vesicles during...	Red blood cell concentration ( RBC ) , mean volume ( MCV ) , and hemoglobin content ( MCH ) are routinely measured in the complete blood count , a fundamental clinical test essential for the screening , diagnosis , and management of most diseases . Variation in MCV and MCH is associated with many important clinical con...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "population", "dynamics", "blood", "counts", "integrative", "physiology", "blood", "volume", "mathematics", "population", "modeling", "population", "biology", "stochastic", "processes", "theoretical", "biology", ...	2014	In Vivo Volume and Hemoglobin Dynamics of Human Red Blood Cells
The ( asymptotic ) degree distributions of the best-known “scale-free” network models are all similar and are independent of the seed graph used; hence , it has been tempting to assume that networks generated by these models are generally similar . In this paper , we observe that several key topological features of suc...	The interactions among proteins in an organism can be represented as a protein–protein interaction ( PPI ) network , where each protein is represented with a node , and each interaction is represented with an edge between two nodes . As PPI networks of several model organisms become available , their topological featur...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "saccharomyces", "computational", "biology" ]	2007	Not All Scale-Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Evolution
Immunity-related GTPases ( IRG ) play an important role in defense against intracellular pathogens . One member of this gene family in humans , IRGM , has been recently implicated as a risk factor for Crohn's disease . We analyzed the detailed structure of this gene family among primates and showed that most of the IRG...	The IRG gene family plays an important role in defense against intracellular bacteria , and genome-wide association studies have implicated structural variants of the single-copy human IRGM locus as a risk factor for Crohn's disease . We reconstruct the evolutionary history of this region among primates and show that t...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/comparative", "genomics", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics", "evolutionary", "biology/human", "evolution", "genetics", "and", "genomics/functional", "genomics", "immunology/innate", "immunity", "molecular", "bi...	2009	Death and Resurrection of the Human IRGM Gene

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