Split (3)

train · 24.8k rows

Search is not available for this dataset

article stringlengths 4.36k 149k	summary stringlengths 32 3.35k	section_headings listlengths 1 91	keywords listlengths 0 141	year stringclasses 13 values	title stringlengths 20 281
Systemic sclerosis ( SSc ) is an orphan , complex , inflammatory disease affecting the immune system and connective tissue . SSc stands out as a severely incapacitating and life-threatening inflammatory rheumatic disease , with a largely unknown pathogenesis . We have designed a two-stage genome-wide association study ...	Systemic sclerosis ( SSc ) is a connective tissue disease characterized by generalized microangiopathy , severe immunologic alterations , and massive deposits of matrix components in the connective tissue . Epidemiological investigations indicate that SSc follows a pattern of multifactorial inheritance; however , only ...	[ "Abstract", "Introduction", "Results/Discussion", "Material", "and", "Methods" ]	[ "medicine", "rheumatology", "public", "health", "and", "epidemiology", "cytokines", "immunology", "rheumatoid", "arthritis", "genetic", "epidemiology", "systemic", "lupus", "erythematosus", "inflammatory", "and", "psoriatic", "arthritis", "disease", "mapping", "scleroderma"...	2011	Genome-Wide Scan Identifies TNIP1, PSORS1C1, and RHOB as Novel Risk Loci for Systemic Sclerosis
Deep brain stimulation ( DBS ) of the subthalamic nucleus ( STN ) is modeled to explore the mechanisms of this effective , but poorly understood , treatment for motor symptoms of drug-refractory Parkinson’s disease and dystonia . First , a neural field model of the corticothalamic-basal ganglia ( CTBG ) system is devel...	Pathological 13-30 Hz ( beta ) oscillations within the basal ganglia are a characteristic feature of human Parkinson’s disease which seem to correlate with symptom severity . The origin of these oscillations and the suppressive mechanism of effective deep brain stimulation treatments remains to be shown . We formulate ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "myoclonus", "pathology", "and", "laboratory", "medicine", "neurodegenerative", "diseases", "membrane", "potential", "brain", "electrophysiology", "electrophysiology", "neuroscience", "surgical", "and", "invasive", "medical", "proced...	2018	Quantitative theory of deep brain stimulation of the subthalamic nucleus for the suppression of pathological rhythms in Parkinson’s disease
In malaria-naïve individuals , Plasmodium falciparum infection results in high levels of parasite-infected red blood cells ( iRBCs ) that trigger systemic inflammation and fever . Conversely , individuals in endemic areas who are repeatedly infected are often asymptomatic and have low levels of iRBCs , even young child...	Malaria remains a major cause of disease and death worldwide . When mosquitoes infect people with malaria parasites for the first time , the parasite rapidly multiplies in the blood and the body responds by producing molecules that cause inflammation and fever , and sometimes the infection progresses to life-threatenin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "medicine", "and", "health", "sciences", "protozoans", "malarial", "parasites", "clinical", "immunology", "biology", "and", "life", "sciences", "immunology", "microbiology", "protozoology", "plasmodium", "falciparum", "parasitic", "diseases", "im...	2014	Exposure-Dependent Control of Malaria-Induced Inflammation in Children
Insulators are DNA sequences that control the interactions among genomic regulatory elements and act as chromatin boundaries . A thorough understanding of their location and function is necessary to address the complexities of metazoan gene regulation . We studied by ChIP–chip the genome-wide binding sites of 6 insulat...	The spatiotemporal specificity of gene expression is controlled by interactions among regulatory proteins , cis-regulatory elements , chromatin modifications , and genes . These interactions can occur over large distances , and the mechanisms by which they are controlled are poorly understood . Insulators are DNA seque...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/histone", "modification", "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/functional", "genomics", "genetics", "and", "genomics/epigenetics", "genetics", "and", "genomics" ]	2010	A Comprehensive Map of Insulator Elements for the Drosophila Genome
Mammalian Argonaute proteins ( EIF2C1−4 ) play an essential role in RNA-induced silencing . Here , we show that the loss of eIF2C2 ( Argonaute2 or Ago2 ) results in gastrulation arrest , ectopic expression of Brachyury ( T ) , and mesoderm expansion . We identify a genetic interaction between Ago2 and T , as Ago2 haplo...	Gastrulation is a developmental phase that delineates the three embryonic germ layers: ectoderm , endoderm , and mesoderm . The gene Brachyury is essential for mesoderm development , and short-tail mice , which were later found to be carrying a Brachyury mutation , have been known since 1927 . In this study , we found ...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "developmental", "biology", "none", "cell", "biology", "mammals", "eukaryotes", "vertebrates", "mus", "(mouse)", "genetics", "and", "genomics" ]	2007	Argonaute2 Is Essential for Mammalian Gastrulation and Proper Mesoderm Formation
There is growing interest in understanding the nature and consequences of interactions among infectious agents . Pathogen interactions can be operational at different scales , either within a co-infected host or in host populations where they co-circulate , and can be either cooperative or competitive . The detection o...	It is becoming increasingly evident that pathogens associated with infectious diseases interact amongst themselves . Pathogen interactions can occur in a co-infected host , or in host populations where they co-circulate , and they can be cooperative or competitive . Four serotypes of dengue virus , for example , can ex...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "population", "ecology", "mathematics", "ecology", "population", "modeling", "statistics", "theoretical", "ecology", "biology", "computational", "biology", "infectious", "disease", "modeling", "statistical", "methods" ]	2011	Statistical Inference for Multi-Pathogen Systems
Residue interaction networks and loop motions are important for catalysis in dihydrofolate reductase ( DHFR ) . Here , we investigate the effects of ligand binding and chain connectivity on network communication in DHFR . We carry out systematic network analysis and molecular dynamics simulations of the native DHFR and...	The cooperative movements within a protein concerning the binding and dissociation of the reactants and products could be important for protein function . Communication among the various parts of an enzyme can be achieved by the networks connecting amino acids through peptide backbone connections and nonbonded amino ac...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "none", "molecular", "biology", "computational", "biology" ]	2007	Ligand Binding and Circular Permutation Modify Residue Interaction Network in DHFR
Chromatin assembly mutants accumulate recombinogenic DNA damage and are sensitive to genotoxic agents . Here we have analyzed why impairment of the H3K56 acetylation-dependent CAF1 and Rtt106 chromatin assembly pathways , which have redundant roles in H3/H4 deposition during DNA replication , leads to genetic instabili...	Loss of replication fork integrity is a primary source of genetic instability . In eukaryotes DNA synthesis is rapidly followed by its assembly into chromatin , and these two processes are tightly connected . Defective chromatin assembly mutants accumulate DNA damage and are sensitive to genotoxic agents , even though ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "biology", "molecular", "cell", "biology", "genetics", "and", "genomics" ]	2011	Histone H3K56 Acetylation, CAF1, and Rtt106 Coordinate Nucleosome Assembly and Stability of Advancing Replication Forks
Joint genetic models for multiple traits have helped to enhance association analyses . Most existing multi-trait models have been designed to increase power for detecting associations , whereas the analysis of interactions has received considerably less attention . Here , we propose iSet , a method based on linear mixe...	Genetic effects on phenotypes can depend on external contexts , including environment . Statistical tests for identifying such interactions are important to understand how individual genetic variants may act in different contexts . Interaction effects can either be studied using measurements of a given phenotype in dif...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "c-reactive", "proteins", "immune", "cells", "protein", "interactions", "built", "structures", "engineering", "and", "technology", "immunology", "random", "variables", "covariance", "simulation", "and", "modelin...	2017	Joint genetic analysis using variant sets reveals polygenic gene-context interactions
Bacteria can survive antibiotic treatment without acquiring heritable antibiotic resistance . We investigated persistence to the fluoroquinolone ciprofloxacin in Escherichia coli . Our data show that a majority of persisters to ciprofloxacin were formed upon exposure to the antibiotic , in a manner dependent on the SOS...	The frequent failure of antibiotic treatments is an acute public health problem . Bacteria can escape the lethal action of antibiotics by a mutation in the cell's DNA , leading to antibiotic resistance . Alternatively , they can enter a physiological state in which the antibiotics do not affect them . This phenomenon ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/epigenetics", "microbiology/microbial", "evolution", "and", "genomics", "infectious", "diseases/antimicrobials", "and", "drug", "resistance", "microbiology" ]	2009	SOS Response Induces Persistence to Fluoroquinolones in Escherichia coli
Plants with facultative crassulacean acid metabolism ( CAM ) maximize performance through utilizing C3 or C4 photosynthesis under ideal conditions while temporally switching to CAM under water stress ( drought ) . While genome-scale analyses of constitutive CAM plants suggest that time of day networks are shifted , or ...	Crassulacean acid metabolism ( CAM ) photosynthesis represents an important adaptation to arid environments as CAM plants take up CO2 at night when evapotranspiration rates are lower . Genomes and large-scale datasets are available for several plants with constitutive CAM activity , but they provided little insight on ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "ecology", "and", "environmental", "sciences", "c3", "photosynthesis", "genetic", "networks", "water", "resources", "chemical", "compounds", "carbohydrates", "departures", "from", "diploidy", "organic", "compounds", "circadian", "oscillators", "plant", "science", "tetrapl...	2019	Time of day and network reprogramming during drought induced CAM photosynthesis in Sedum album
Robustly predicting outcome for cancer patients from gene expression is an important challenge on the road to better personalized treatment . Network-based outcome predictors ( NOPs ) , which considers the cellular wiring diagram in the classification , hold much promise to improve performance , stability and interpret...	Cancer is caused by disrupted activity of several pathways . Therefore , to predict cancer patient prognosis from gene expression profiles , it may be beneficial to consider the cellular interactome ( e . g . the protein interaction network ) . These so-called Network based Outcome Predictors ( NOPs ) hold the potentia...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "genetic", "networks", "breast", "tumors", "statistics", "protein", "interaction", "networks", "cancers", "and", "neoplasms", "oncology", "mathematics", "forecasting", "network", "analysis", "genome", "analysis", "research", "and...	2019	A data-driven interactome of synergistic genes improves network-based cancer outcome prediction
Myxococcus xanthus cells self-organize into aligned groups , clusters , at various stages of their lifecycle . Formation of these clusters is crucial for the complex dynamic multi-cellular behavior of these bacteria . However , the mechanism underlying the cell alignment and clustering is not fully understood . Motivat...	Many bacterial species are capable of collectively moving and reorganizing themselves into a variety of multi-cellular structures . However , the mechanisms behind this self-organization behavior are not completely understood . The majority of previous studies focused on biochemical signaling among cells . However , me...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[]	2015	Mechanism for Collective Cell Alignment in Myxococcus xanthus Bacteria
All organisms have developed mechanisms to respond to organ or tissue damage that may appear during development or during the adult life . This process of regeneration is a major long-standing problem in Developmental Biology . We are using the Drosophila melanogaster wing imaginal disc to study the response to major d...	The study of how organs or tissues regenerate after damage is a classic topic in Developmental Biology . We are studying this process in the developing wing imaginal disc of Drosophila melanogaster , using genetic methods to inflict massive damage in the region destined to form the wing blade . We find that the lesion ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "growth", "control", "organism", "development", "regeneration", "biology", "morphogenesis", "cell", "fate", "determination", "limb", "development" ]	2013	Tissue Homeostasis in the Wing Disc of Drosophila melanogaster: Immediate Response to Massive Damage during Development
Nonsense-mediated mRNA decay ( NMD ) prevents the accumulation of transcripts bearing premature termination codons . Here we show that Saccharomyces cerevisiae NMD mutants accumulate 5′–extended RNAs ( CD-CUTs ) of many subtelomeric genes . Using the subtelomeric ZRT1 and FIT3 genes activated in response to zinc and ir...	Precise expression of genes relies on their accurate and timely transcription and on turning off these genes when production of the proteins is not required . Our study describes that in the baker's yeast , S . cerevisiae , repression of many genes relies on transcription of long extended RNAs upstream from where trans...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "biology", "genomics", "genetics", "and", "genomics" ]	2011	Cryptic Transcription Mediates Repression of Subtelomeric Metal Homeostasis Genes
The p75 neurotrophin receptor , a member of the tumor necrosis factor receptor superfamily , is required as a co-receptor for the Nogo receptor ( NgR ) to mediate the activity of myelin-associated inhibitors such as Nogo , MAG , and OMgp . p45/NRH2/PLAIDD is a p75 homologue and contains a death domain ( DD ) . Here we ...	Injuries to the brain and spinal cord often result in paralysis due to the fact that the injured nerves cannot regrow to reach their normal targets and carry out their functions . At the injury sites , there are proteins released from the damaged myelin that bind the Nogo receptor ( NgR ) on the nerve and inhibit its r...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences" ]	2014	Heterodimerization of p45–p75 Modulates p75 Signaling: Structural Basis and Mechanism of Action
In January 2011 , human cases with hemorrhagic manifestations in the hospital staff were reported from a tertiary care hospital in Ahmadabad , India . This paper reports a detailed epidemiological investigation of nosocomial outbreak from the affected area of Ahmadabad , Gujarat , India . Samples from 3 suspected cases...	A nosocomial outbreak of CCHFV occurred in January 2011 , in a tertiary care hospital in Ahmadabad , Gujarat State in western India . Out of a total five cases reported , contact transmission occurred to three treating medical professionals , all of whom succumbed to the disease . The only survivor was the husband of t...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biology" ]	2012	Detection, Isolation and Confirmation of Crimean-Congo Hemorrhagic Fever Virus in Human, Ticks and Animals in Ahmadabad, India, 2010–2011
An important step in understanding gene regulation is to identify the DNA binding sites recognized by each transcription factor ( TF ) . Conventional approaches to prediction of TF binding sites involve the definition of consensus sequences or position-specific weight matrices and rely on statistical analysis of DNA se...	An important step in characterizing the genetic regulatory network of a cell is to identify the DNA binding sites recognized by each transcription factor ( TF ) protein encoded in the genome . Current computational approaches to TF binding site prediction rely exclusively on DNA sequence analysis . In this manuscript ,...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "molecular", "biology/bioinformatics", "mathematics/statistics", "computational", "biology/sequence", "motif", "analysis", "computational", "biology/transcriptional", "regulation" ]	2010	Using Sequence-Specific Chemical and Structural Properties of DNA to Predict Transcription Factor Binding Sites
Genome size and complexity vary tremendously among eukaryotic species and their organelles . Comparisons across deeply divergent eukaryotic lineages have suggested that variation in mutation rates may explain this diversity , with increased mutational burdens favoring reduced genome size and complexity . The discovery ...	A fundamental challenge in evolutionary biology is to explain why organisms exhibit dramatic variation in genome size and complexity . One hypothesis predicts that high rates of mutation in DNA sequence create selection against large and complex genomes , which are more susceptible to mutational disruption . Species of...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "genomics", "evolutionary", "biology", "genetics", "and", "genomics" ]	2012	Rapid Evolution of Enormous, Multichromosomal Genomes in Flowering Plant Mitochondria with Exceptionally High Mutation Rates
This paper demonstrates a previously unreported property of deoxyribonucleic acid—the ability of dye-labeled , solid-state DNA dried onto a surface to detect odors delivered in the vapor phase by changes in fluorescence . This property is useful for engineering systems to detect volatiles and provides a way for artific...	Biological systems can provide engineering guidance on how evolution has solved particular problems . In the context of detecting chemicals in either the aqueous or vapor phase , two general biological approaches have emerged . The first relies on individual highly specific single receptors ( sensors ) , each tuned to ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "chemistry", "neuroscience", "molecular", "biology" ]	2008	Solid-State, Dye-Labeled DNA Detects Volatile Compounds in the Vapor Phase
Coordinated cardiomyocyte growth , differentiation , and morphogenesis are essential for heart formation . We demonstrate that the bHLH transcription factors Hand1 and Hand2 play critical regulatory roles for left ventricle ( LV ) cardiomyocyte proliferation and morphogenesis . Using an LV-specific Cre allele ( Hand1LV...	The left ventricle of the heart drives blood flow throughout the body . Impaired left ventricle function , associated either with heart failure or with certain , severe cardiac birth defects , constitutes a significant cause of mortality . Understanding how heart muscle grows is vital to developing improved treatments ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "death", "medicine", "and", "health", "sciences", "cardiovascular", "physiology", "in", "situ", "hybridization", "molecular", "probe", "techniques", "cardiovascular", "anatomy", "cardiac", "ventricles", "cell", "processes", "developmental", "biology", "molecular",...	2017	Hand factor ablation causes defective left ventricular chamber development and compromised adult cardiac function
We examined relationships between schistosome infection , HIV transmission or acquisition , and all-cause death . We retrospectively tested baseline sera from a heterosexual HIV-discordant couple cohort in Lusaka , Zambia with follow-up from 1994–2012 in a nested case-control design . Schistosome-specific antibody leve...	This study explored the association between schistosome infections ( a disease caused by parasitic flatworms , also known as ‘snail fever’ , which is very common throughout sub-Saharan Africa ) and human immunodeficiency virus ( HIV ) . We found in Lusaka , the capital of Zambia , that schistosome infections were assoc...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma", "mansoni", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "helminths", "pathogens", ...	2018	Schistosomiasis is associated with incident HIV transmission and death in Zambia
Yersinia enterocolitica ( Ye ) evades the immune system of the host by injection of Yersinia outer proteins ( Yops ) via a type three secretion system into host cells . In this study , a reporter system comprising a YopE-β-lactamase hybrid protein and a fluorescent staining sensitive to β-lactamase cleavage was used to...	An important strategy of Yersinia enterocolitica ( Ye ) to suppress the immune defense is to inject bacterial proteins ( Yersinia outer proteins , Yops ) after cell contact directly into host cells , which affects their functions . However , tracking of cells in which Yop injection occurred has only been described for ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/immunity", "to", "infections", "microbiology/innate", "immunity", "immunology/immunity", "to", "infections", "microbiology", "microbiology/cellular", "microbiology", "and", "pathogenesis" ]	2009	Yersinia enterocolitica Targets Cells of the Innate and Adaptive Immune System by Injection of Yops in a Mouse Infection Model
The diversity and geographical distribution of fleas parasitizing small mammals have been poorly investigated on Indian Ocean islands with the exception of Madagascar where endemic plague has stimulated extensive research on these arthropod vectors . In the context of an emerging flea-borne murine typhus outbreak that ...	Fleas are blood-feeding parasites involved in the transmission of several arthropod borne pathogens . Rat-fleas ( Xenopsylla spp . ) are known vectors of bubonic plague together with other human diseases receiving less attention such as murine typhus . This latter disease was recorded for the first time in 2011 on Reun...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "taxonomy", "invertebrates", "medicine", "and", "health", "sciences", "typhus", "of", "rickettsiae", "animals", "animal", "phylogenetics", "phylogenetics", "emerging", "infectious", "diseases", "fleas", "veterinary", "science", "infectious", "diseases", "veterinary", "dis...	2014	Fleas of Small Mammals on Reunion Island: Diversity, Distribution and Epidemiological Consequences
Cortical activity has distinct features across scales , from the spiking statistics of individual cells to global resting-state networks . We here describe the first full-density multi-area spiking network model of cortex , using macaque visual cortex as a test system . The model represents each area by a microcircuit ...	The mammalian cortex fulfills its complex tasks by operating on multiple temporal and spatial scales from single cells to entire areas comprising millions of cells . These multi-scale dynamics are supported by specific network structures at all levels of organization . Since models of cortex hitherto tend to concentrat...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "action", "potentials", "medicine", "and", "health", "sciences", "diagnostic", "radiology", "functional", "magnetic", "resonance", "imaging", "neural", "networks", "nervous", "system", "membrane", "potential", "vertebrates", "electrophysiology", "neuroscience", "animals", ...	2018	A multi-scale layer-resolved spiking network model of resting-state dynamics in macaque visual cortical areas
While three countries in South Asia decided to eliminate anthroponotic visceral leishmaniasis ( VL ) by 2015 , its control in other regions seems fraught with difficulties . Is there a scope for more effective VL control in the Americas where transmission is zoonotic ? We reviewed the evidence on VL control strategies ...	Visceral leishmaniasis is a vector-borne disease characterized by fever , spleen and liver enlargement , and low blood cell counts . In the Americas VL is zoonotic , with domestic dogs as main animal reservoirs , and is caused by the intracellular parasite Leishmania infantum ( syn . Leishmania chagasi ) . Humans acqui...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/protozoal", "infections", "infectious", "diseases/neglected", "tropical", "diseases", "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases" ]	2010	Control of Visceral Leishmaniasis in Latin America—A Systematic Review
Many bacterial pathogens and symbionts use type III secretion machines to interact with their hosts by injecting bacterial effector proteins into host target cells . A central component of this complex machine is the cytoplasmic sorting platform , which orchestrates the engagement and preparation of type III secreted p...	Many pathogenic and symbiotic gram-negative bacteria utilize type III secretion systems to deliver bacterial proteins , known as effectors , directly into the host cell cytosol to promote their survival and the colonization of tissues . Type III secretion systems or injectisomes are large , multiprotein complexes compo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "bacteriology", "antimicrobials", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "drugs", "microbiology", "bacterial", "diseases", "physiological", "processes", "mutation", "secretion", "systems", "immunoprecipitation", "...	2019	Role of SpaO in the assembly of the sorting platform of a Salmonella type III secretion system
Staphylococcus aureus exhibits many defenses against host innate immunity , including the ability to replicate in the presence of nitric oxide ( NO· ) . S . aureus NO· resistance is a complex trait and hinges on the ability of this pathogen to metabolically adapt to the presence of NO· . Here , we employed deep sequenc...	The human pathogen Staphylococcus aureus is remarkably resistant to many facets of the host immune response , including the antibacterial radical nitric oxide ( NO· ) . The mechanism underlying this resistance is complex and comprises many gene products . Here we employ an approach that involves transposon mutagenesis ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "protons", "medicine", "and", "health", "sciences", "neurochemistry", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "respiratory", "infections", "enzymes", "pathogens", "microbiology", "enzymology", "carbohydrates", "neuroscience", "staphylococcus", ...	2018	Genetic requirements for Staphylococcus aureus nitric oxide resistance and virulence
Plasmacytoid dendritic cells ( pDC ) are innate immune cells that sense viral nucleic acids through endosomal Toll-like receptor ( TLR ) 7/9 to produce type I interferon ( IFN ) and to differentiate into potent antigen presenting cells ( APC ) . Engagement of TLR7/9 in early endosomes appears to trigger the IRF7 pathwa...	Plasmacytoid dendritic cells ( pDC ) are innate immune cells that are specialized to produce type I interferon ( IFN ) and to activate adaptive immune responses . Although IFN is an anti-viral cytokine , it may contribute more to pathogenesis than to protection during chronic viral infections , including chronic HIV in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "lysosomes", "vesicles", "pathology", "and", "laboratory", "medicine", "hek", "293", "cells", "influenza", "pathogens", "biological", "cultures", "microbiology", "retroviruses", "viruses", "immunodeficiency", "viruses", "immune", ...	2016	CD4 Receptor is a Key Determinant of Divergent HIV-1 Sensing by Plasmacytoid Dendritic Cells
Rabies in China remains a public health problem . In 2014 , nearly one thousand rabies-related deaths were reported while rabies geographic distribution has expanded for the recent years . This report used surveillance data to describe the epidemiological characteristics of human rabies in China including determining h...	China is a high-risk environment for rabies , with human rabies cases second only to India globally . This paper reviews 55 years of rabies epidemiology in mainland China , and detailed analysis of data in recent years . In this study , notifiable surveillance data were analyzed and found that rabies still remains a se...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "china", "pathogens", "immunology", "tropical", "diseases", "geographical", "locations", "microbiology", "vertebrates", "animals", "mammals", "dogs", "viruses", "preventive", "medicine"...	2016	Human Rabies in China, 1960-2014: A Descriptive Epidemiological Study
Chikungunya virus causes mosquito-transmitted infection that leads to extensive morbidity affecting substantial quality of life . Disease associated morbidity , quality of life , and financial loss are seldom reported in resources limited countries , such as Bangladesh . We reported the acute clinical profile , quality...	A major outbreak of chikungunya virus occurred for the first time in Dhaka , Bangladesh between May and September 2017 . In this study , a face-to-face interview with a structured questionnaire was conducted to collect data to investigate the clinical symptoms , quality of life , and economic aspects of 1 , 326 chikung...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "togaviruses", "chikungunya", "infection", "economic", "analysis", "pathogens", "tropical", "diseases", "microbiology", "geographical", "locations", "social", "sciences", "alphaviruses", ...	2018	Chikungunya outbreak (2017) in Bangladesh: Clinical profile, economic impact and quality of life during the acute phase of the disease
Mycetoma is a chronic granulomatous disease . It is classified into eumycetoma caused by fungi and actinomycetoma due to filamentous actinomycetes . Mycetoma can be found in geographic areas in close proximity to the Tropic of Cancer . Mexico is one of the countries in which this disease is highly endemic . In this ret...	Mycetoma is a chronic , subcutaneous granulomatous disease that usually begins after traumatic inoculation with causative microorganisms . Based on its etiology , mycetoma is referred to eumycetoma when the infection is caused by filamentous fungi , and actinomycetoma when the infection is due to aerobic actinomycetes ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "subcutaneous", "mycoses", "medicine", "and", "health", "sciences", "mycetoma", "neglected", "tropical", "diseases", "tropical", "diseases", "fungal", "diseases" ]	2014	Mycetoma: Experience of 482 Cases in a Single Center in Mexico
Epstein-Barr virus ( EBV ) , a ubiquitous B-lymphotropic herpesvirus , ectopically infects T or NK cells to cause severe diseases of unknown pathogenesis , including chronic active EBV infection ( CAEBV ) and EBV-associated hemophagocytic lymphohistiocytosis ( EBV-HLH ) . We developed xenograft models of CAEBV and EBV-...	Epstein-Barr virus ( EBV ) is a ubiquitous human herpesvirus that infects more than 90% of the adult human population in the world . EBV usually infects B lymphocytes and does not produce symptoms in infected individuals , but in rare occasions it infects T or NK lymphocytes and causes severe diseases such as chronic a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "hematologic", "cancers", "and", "related", "disorders", "medicine", "infectious", "diseases", "myelomas", "and", "lymphoproliferative", "diseases", "lymphomas", "viral", "diseases", "hematology", "epstein-barr", "virus", "infectious", "mononucleosis" ]	2011	Novel Mouse Xenograft Models Reveal a Critical Role of CD4+ T Cells in the Proliferation of EBV-Infected T and NK Cells
Triggering receptor expressed on myeloid cells-1 ( TREM-1 ) is a potent amplifier of pro-inflammatory innate immune reactions . While TREM-1-amplified responses likely aid an improved detection and elimination of pathogens , excessive production of cytokines and oxygen radicals can also severely harm the host . Studies...	Triggering receptor expressed on myeloid cells-1 ( TREM-1 ) is an immune receptor expressed by myeloid cells that has the capacity to augment pro-inflammatory responses in the context of a microbial infection . While a TREM-1-amplified response likely serves the efficient clearance of pathogens , it also bears the pote...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunopathology", "pathogenesis", "inflammation", "immune", "cells", "cytokines", "monocytes", "immunity", "immune", "activation", "t", "cells", "immune", "defense", "immunology", "immunity", "to", "infections", "biology", "microbiology", "host-pathogen", "interaction", ...	2014	TREM-1 Deficiency Can Attenuate Disease Severity without Affecting Pathogen Clearance
The slime mold Dictyostelium discoideum is one of the model systems of biological pattern formation . One of the most successful answers to the challenge of establishing a spiral wave pattern in a colony of homogeneously distributed D . discoideum cells has been the suggestion of a developmental path the cells follow (...	Spatio-temporal pattern formation is a core discipline of theoretical biology . Formation of large-scale patterns from local interactions can very prominently be observed in the swarming behavior of fish and birds , in animal markings or bacterial growth patterns . It also plays a critical role in the life cycle of the...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biophysics/cell", "signaling", "and", "trafficking", "structures", "biophysics/theory", "and", "simulation", "computational", "biology/systems", "biology" ]	2009	Predicting the Distribution of Spiral Waves from Cell Properties in a Developmental-Path Model of Dictyostelium Pattern Formation
Advances in sequencing have generated a large number of complete genomes . Traditionally , phylogenetic analysis relies on alignments of orthologs , but defining orthologs and separating them from paralogs is a complex task that may not always be suited to the large datasets of the future . An alternative to traditiona...	Due to their lack of distinct morphological features , bacteria and archaea were extremely difficult to classify until technology was developed to obtain their DNA sequences; these sequences could then be compared to estimate evolutionary relationships . Now , due to technological advances , there is a flood of availab...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "taxonomy", "horizontal", "gene", "transfer", "split-decomposition", "method", "microbiology", "gene", "transfer", "multiple", "alignment", "calculation", "phylogenetics", "data", "management", "phylogenetic", "analysis", "genetic", "elements", "...	2016	Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer
Methamphetamine ( Meth ) is abused by over 35 million people worldwide . Chronic Meth abuse may be particularly devastating in individuals who engage in unprotected sex with multiple partners because it is associated with a 2-fold higher risk for obtaining HIV and associated secondary infections . We report the first s...	There is a new population of HIV+ men who are developing AIDS over months instead of years as typical . It has recently become popular among gay and bisexual men to consume very high levels of Meth . Unsafe sex together with Meth abuse has been suspected to lead to rapid disease progression . While studies show exacerb...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viruses", "infectious", "diseases", "public", "health", "and", "epidemiology", "virology", "yeast", "and", "fungi", "in", "vitro", "immunology", "mus", "(mouse)", "homo", "(human)" ]	2008	Methamphetamine Inhibits Antigen Processing, Presentation, and Phagocytosis
Trachoma is the leading infectious cause of blindness in the world , and for endemic communities , mass treatment with azithromycin reduces the pool of infection . High coverage is essential , especially in children as they are the infectious reservoir . However , infection remains post-mass treatment . We sought to de...	Trachoma control programs aim for high coverage of endemic communities with oral azithromycin to reduce the pool of infection with Chlamydia trachomatis . However , even with high coverage , infection is seen following treatment . In four communities in Tanzania , we followed every child aged under ten years from basel...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases" ]	2011	Risk Factors for Ocular Infection with Chlamydia trachomatis in Children 6 Months following Mass Treatment in Tanzania
Nuclear receptor ligand binding domains ( LBDs ) convert ligand binding events into changes in gene expression by recruiting transcriptional coregulators to a conserved activation function-2 ( AF-2 ) surface . While most nuclear receptor LBDs form homo- or heterodimers , the human nuclear receptor pregnane X receptor (...	Long-range motions play essential roles in protein function but are difficult to appreciate from static crystal structures . We sought to understand how macromolecular motion affects the formation of transcriptional complexes central to controlling gene expression . Using 20- to 30-ns molecular dynamics simulations , w...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/molecular", "dynamics", "computational", "biology/macromolecular", "structure", "analysis", "diabetes", "and", "endocrinology/endocrinology" ]	2008	Active Nuclear Receptors Exhibit Highly Correlated AF-2 Domain Motions
Thromboembolic events were described in patients with Chagas disease without cardiomyopathy . We aim to confirm if there is a hypercoagulable state in these patients and to determine if there is an early normalization of hemostasis factors after antiparasitic treatment . Ninety-nine individuals from Chagas disease-ende...	The manuscript describes the results of a study whose aim was to assess the tendency to coagulate in people suffering from a parasitic infection frequent in Latin America named T . cruzi infection or Chagas disease , by the study of several coagulation factors . According to the state of the art in this topic , specifi...	[ "Abstract", "Introduction", "Methods", "Results", "and", "Discussion" ]	[]	2016	Altered Hypercoagulability Factors in Patients with Chronic Chagas Disease: Potential Biomarkers of Therapeutic Response
During the intracellular life of Salmonella enterica , a unique membrane-bound compartment termed Salmonella-containing vacuole , or SCV , is formed . By means of translocated effector proteins , intracellular Salmonella also induce the formation of extensive , highly dynamic membrane tubules termed Salmonella-induced ...	Salmonella enterica is an invasive , facultative intracellular bacterial pathogen . Within mammalian host cells , Salmonella inhabits a specialized membrane-bound compartment , the Salmonella-containing vacuole ( SCV ) , redirects host cell vesicular transport and massively remodels the endosomal system . These activit...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "host-pathogen", "interactions", "medical", "microbiology", "microbial", "pathogens", "biology", "and", "life", "sciences", "microbiology", "pathogenesis" ]	2014	Reorganization of the Endosomal System in Salmonella-Infected Cells: The Ultrastructure of Salmonella-Induced Tubular Compartments
The circadian clock is a set of regulatory steps that oscillate with a period of approximately 24 hours influencing many biological processes . These oscillations are robust to external stresses , and in the case of genotoxic stress ( i . e . DNA damage ) , the circadian clock responds through phase shifting with prima...	Many physiological processes are regulated by the circadian clock , and we are continuing to learn about the role of the circadian clock in disease . Research in recent years has begun to shed light on the feedback mechanisms that exist between circadian regulation and other processes , including metabolism and the res...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Predicted Role of NAD Utilization in the Control of Circadian Rhythms during DNA Damage Response
Chagas disease is a parasitic disorder caused by the infection with the flagellated protozoan Trypanosoma cruzi . According to the World Health Organization , more than six million people are currently infected in endemic regions . Genetic factors have been proposed to influence predisposition to infection and developm...	Chagas disease is a parasitic disorder caused by the infection with the protozoan Trypanosoma cruzi . In Latin America , this disease represents a major public health concern , as almost 6 million people are currently infected . During the last years , great efforts have been made in health policy to control the diseas...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "cardiomyopathies", "medicine", "and", "health", "sciences", "population", "genetics", "tropical", "diseases", "variant", "genotypes", "parasitic", "diseases", "parasitic", "protozoans", "genetic", "mapping", "genetic", "predisposition", "protozoans", "neglected", "tropical...	2016	IL18 Gene Variants Influence the Susceptibility to Chagas Disease
There is a current interest in quantifying time-varying connectivity ( TVC ) based on neuroimaging data such as fMRI . Many methods have been proposed , and are being applied , revealing new insight into the brain’s dynamics . However , given that the ground truth for TVC in the brain is unknown , many concerns remain ...	Time-varying connectivity attempts to quantify the fluctuating covariance relationship between two or more regions through time . In recent years , it has become popular to do this with fMRI neuroimaging data . There have been many methods proposed to quantify time-varying connectivity , but very few attempts to system...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "diagnostic", "radiology", "functional", "magnetic", "resonance", "imaging", "markov", "models", "neural", "networks", "random", "variables", "neuroscience", "covariance", "simulation", "and", "modeling", "magnetic", "resonance", ...	2018	Simulations to benchmark time-varying connectivity methods for fMRI
Meta-analysis of genetic association studies increases sample size and the power for mapping complex traits . Existing methods are mostly developed for datasets without missing values , i . e . the summary association statistics are measured for all variants in contributing studies . In practice , genotype imputation i...	It is of great interest to estimate the joint effects of multiple variants from large scale meta-analyses , in order to fine-map causal variants and understand the genetic architecture for complex traits . The summary association statistics from participating studies in a meta-analysis often contain missing values at s...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "genome-wide", "association", "studies", "variant", "genotypes", "random", "variables", "covariance", "genetic", "mapping", "mathematics", "statistics", "(mathematics)", "genome", "analysis", "research", "and", "analysis", "methods", "genome", "complexity", "genomics", "m...	2018	Proper conditional analysis in the presence of missing data: Application to large scale meta-analysis of tobacco use phenotypes
Although they have become a widely used experimental technique for identifying differentially expressed ( DE ) genes , DNA microarrays are notorious for generating noisy data . A common strategy for mitigating the effects of noise is to perform many experimental replicates . This approach is often costly and sometimes ...	Though the use of microarrays to identify differentially expressed ( DE ) genes has become commonplace , it is still not a trivial task . Microarray data are notorious for being noisy , and current DE gene methods do not fully utilize pre-existing biological knowledge to help control this noise . One such source of kno...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/systems", "biology", "genetics", "and", "genomics/gene", "expression", "computational", "biology/genomics", "genetics", "and", "genomics/bioinformatics", "diabetes", "and", "endocrinology/type", "2", "diabetes" ]	2010	Using Pre-existing Microarray Datasets to Increase Experimental Power: Application to Insulin Resistance
A fundamental question in understanding neuronal computations is how dendritic events influence the output of the neuron . Different forms of integration of neighbouring and distributed synaptic inputs , isolated dendritic spikes and local regulation of synaptic efficacy suggest that individual dendritic branches may f...	Neurons were originally divided into three morphologically distinct compartments: the dendrites receive the synaptic input , the soma integrates it and communicates the output of the cell to other neurons via the axon . Although several lines of evidence challenged this oversimplified view , neurons are still considere...	[ "Abstract", "Introduction", "Model", "Results", "Discussion", "Methods" ]	[ "neuroscience/theoretical", "neuroscience", "computational", "biology/computational", "neuroscience" ]	2009	Parallel Computational Subunits in Dentate Granule Cells Generate Multiple Place Fields
Even with identification of multiple causal genetic variants for common human diseases , understanding the molecular processes mediating the causal variants’ effect on the disease remains a challenge . This understanding is crucial for the development of therapeutic strategies to prevent and treat disease . While stati...	The causal path from a genetic variant to a complex phenotype such as disease progression is often not known . Studying gene expression variation is one approach to identify the mediating genes , however , it is difficult to distinguish causative from correlative genes . This becomes a challenge especially when studyin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[]	2015	Temporal Expression Profiling Identifies Pathways Mediating Effect of Causal Variant on Phenotype
The variation in the expression patterns of the gap genes in the blastoderm of the fruit fly Drosophila melanogaster reduces over time as a result of cross regulation between these genes , a fact that we have demonstrated in an accompanying article in PLoS Biology ( see Manu et al . , doi:10 . 1371/journal . pbio . 100...	C . H . Waddington predicted in 1942 that networks of chemical reactions in embryos can counteract the effects of variable developmental conditions to produce reliable outcomes . The experimental signature of this process , called “canalization , ” is the reduction of the variation of the concentrations of molecular de...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "developmental", "biology", "computational", "biology/transcriptional", "regulation", "mathematics", "developmental", "biology/pattern", "formation", "computational", "biology", "evolutionary", "biology", "computational", "biology/systems", "biology" ]	2009	Canalization of Gene Expression and Domain Shifts in the Drosophila Blastoderm by Dynamical Attractors
Understanding the mechanisms of cell function and drug action is a major endeavor in the pharmaceutical industry . Drug effects are governed by the intrinsic properties of the drug ( i . e . , selectivity and potency ) and the specific signaling transduction network of the host ( i . e . , normal vs . diseased cells ) ...	Cells are complex functional units . Signal transduction refers to the underlying mechanism that regulates cell function , and it is usually depicted on signaling pathways maps . Each cell type has distinct signaling transduction mechanisms , and several diseases arise from alterations on the signaling pathways . Small...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "pharmacology/drug", "development", "computer", "science/numerical", "analysis", "and", "theoretical", "computing", "pharmacology/drug", "interactions", "oncology/gastrointestinal", "cancers", "computational", "biology/signaling", "networks", "computational", "biology", "computatio...	2009	Identifying Drug Effects via Pathway Alterations using an Integer Linear Programming Optimization Formulation on Phosphoproteomic Data
Vaccinia virus interferes with early events of the activation pathway of the transcriptional factor NF-kB by binding to numerous host TIR-domain containing adaptor proteins . We have previously determined the X-ray structure of the A46 C-terminal domain; however , the structure and function of the A46 N-terminal domain...	Viruses possess mechanisms to interfere with the host immune system to enhance their replication . Vaccinia virus , the viral vaccine used to eradicate smallpox , synthesizes many such proteins . The vaccinia virus protein A46 is one of a series of proteins preventing expression of host proteins that induce an anti-vir...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "crystal", "structure", "condensed", "matter", "physics", "crystals", "materials", "science", "protein", "structure", "crystallography", "materials", "by", "structure", "lipids", "computer", "and", "information", "sciences", "solid", "state", "physics", "protein", "stru...	2016	Vaccinia Virus Immunomodulator A46: A Lipid and Protein-Binding Scaffold for Sequestering Host TIR-Domain Proteins
We captured , ectoparasite-combed , and blood-sampled cave-roosting Madagascan fruit bats ( Eidolon dupreanum ) and tree-roosting Madagascan flying foxes ( Pteropus rufus ) in four single-species roosts within a sympatric geographic foraging range for these species in central Madagascar . We describe infection with nov...	Bartonella spp . are bacteria that inhabit the red blood cells of both human and animal hosts . Among humans , Bartonella spp . are known to cause several febrile illnesses , including Carrion’s disease ( Bartonella bacilliformis ) , trench fever ( Bartonella quintana ) , and cat scratch fever ( Bartonella henselae ) ,...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Bartonella spp. in Fruit Bats and Blood-Feeding Ectoparasites in Madagascar
The RIG-I-like RNA helicase ( RLR ) -mediated interferon ( IFN ) response plays a pivotal role in the hepatic antiviral immunity . The hepatitis A virus ( HAV ) and the hepatitis C virus ( HCV ) counter this response by encoding a viral protease that cleaves the mitochondria antiviral signaling protein ( MAVS ) , a com...	HEV infection is a common cause for acute viral hepatitis worldwide . Approximately 20 millions of people are infected annually . In immunocompetent hosts the infection is self-limited and mostly asymptomatic , but the virus frequently persists when immunity is compromised leading to increased risk for cirrhosis . Curr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "transfection", "phosphorylation", "medicine", "and", "health", "sciences", "luciferase", "pathology", "and", "laboratory", "medicine", "hepacivirus", "pathogens", "enzymes", "microbiology", "enzymology", "viruses", "rna", "viruses", "molecular", "biology", "techniques", ...	2017	Hepatitis E virus persists in the presence of a type III interferon response
Genome mosaicism in temperate bacterial viruses ( bacteriophages ) is so great that it obscures their phylogeny at the genome level . However , the precise molecular processes underlying this mosaicism are unknown . Illegitimate recombination has been proposed , but homeologous recombination could also be at play . To ...	Temperate bacterial viruses alternate between a dormant state , during which viral DNA remains integrated in the host genome , and a lytic state of phage multiplication . Temperate viruses have a characteristic genome organisation known as ‘mosaic’ – they contain ‘foreign’ segments that originate from related viruses ....	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/bioinformatics", "molecular", "biology/recombination", "microbiology/microbial", "evolution", "and", "genomics" ]	2008	The λ Red Proteins Promote Efficient Recombination between Diverged Sequences: Implications for Bacteriophage Genome Mosaicism
During active somatosensation , neural signals expected from movement of the sensors are suppressed in the cortex , whereas information related to touch is enhanced . This tactile suppression underlies low-noise encoding of relevant tactile features and the brain’s ability to make fine tactile discriminations . Layer (...	We study how information is transformed between connected brain areas: the thalamus , the gateway to the cortex , and layer 4 ( L4 ) in cortex , which is the first station to process sensory input from the thalamus . When mice perform an active object localization task with their whiskers , thalamic neurons and inhibit...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "action", "potentials", "medicine", "and", "health", "sciences", "neural", "networks", "nervous", "system", "membrane", "potential", "social", "sciences", "electrophysiology", "neuroscience", "animal", "anatomy", "interneurons", "zoology", "computer", "and", "information"...	2017	Mechanisms underlying a thalamocortical transformation during active tactile sensation
Patterns of trait distribution among competing species can potentially reveal the processes that allow them to coexist . It has been recently proposed that competition may drive the spontaneous emergence of niches comprising clusters of similar species , in contrast with the dominant paradigm of greater-than-chance spe...	Species traits determine how they compete with each other . As such , patterns in the distributions of traits in a community of competing species may reveal the processes responsible for coexistence . One central idea in theoretical ecology is that the strength of competition relates to similarity in species needs and ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "community", "ecology", "population", "metrics", "ecological", "metrics", "ecology", "and", "environmental", "sciences", "ecological", "niches", "species", "diversity", "ecology", "species", "delimitation", "community", "structure", "speciation", "habitats", "biology", "a...	2019	Generalizing clusters of similar species as a signature of coexistence under competition
Pentameric ligand-gated ion channels are activated by the binding of agonists to a site distant from the ion conduction path . These membrane proteins consist of distinct ligand-binding and pore domains that interact via an extended interface . Here , we have investigated the role of residues at this interface for chan...	The pentameric ligand-gated ion channels constitute a large family of membrane proteins that are expressed in animals and certain bacteria . Their molecular architecture and function is conserved throughout the family . In mammals , they operate as receptors of the neurotransmitters acetylcholine , serotonin , GABA , a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "crystal", "structure", "chemical", "compounds", "aliphatic", "amino", "acids", "condensed", "matter", "physics", "vertebrates", "organic", "compounds", "animals", "xenopus", "germ", "cells", "animal", "models", "mutation", "oocytes", "model", "organisms", "amphibians",...	2016	Signal Transduction at the Domain Interface of Prokaryotic Pentameric Ligand-Gated Ion Channels
Natural isolates of Burkholderia pseudomallei ( Bp ) , the causative agent of melioidosis , can exhibit significant ecological flexibility that is likely reflective of a dynamic genome . Using whole-genome Bp microarrays , we examined patterns of gene presence and absence across 94 South East Asian strains isolated fro...	Melioidosis is a serious infectious disease of humans caused by Burkholderia pseudomallei , a soil bacterium endemic to many areas in South East Asia . Besides humans , B . pseudomallei is also capable of infecting many other species and can be isolated from diverse environmental sources including soil , water , and ai...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "microbiology/environmental", "microbiology", "microbiology/microbial", "evolution", "and", "genomics" ]	2008	The Core and Accessory Genomes of Burkholderia pseudomallei: Implications for Human Melioidosis
Interleukin-4 receptor ( IL-4Rα ) is critical for the initiation of type-2 immune responses and implicated in the pathogenesis of experimental schistosomiasis . IL-4Rα mediated type-2 responses are critical for the control of pathology during acute schistosomiasis . However , type-2 responses tightly associate with fib...	Liver fibroproliferative diseases drive a considerable fraction of the overall human mortality . This is closely linked to the absence of efficient control measures against such diseases . Schistosomiasis , a chronic disease that affects humans , preferentially causes liver fibrosis and is responsible for devastating e...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "schistosoma", "invertebrates", "schistosoma", "mansoni", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "enzyme-linked", "immunoassays", "helminths", "spleen", "immunology", "tropical", "diseases", "parasitic", "dise...	2017	Host regulation of liver fibroproliferative pathology during experimental schistosomiasis via interleukin-4 receptor alpha
The treatment of leishmaniasis relies mostly on parenteral drugs with potentially serious adverse effects . Additionally , parasite resistance in the treatment of leishmaniasis has been demonstrated for the majority of drugs available , making the search for more effective and less toxic drugs and treatment regimens a ...	Cutaneous and visceral leishmaniasis are part of the group we call neglected diseases . They are serious conditions that afflict millions in vast regions of the world . These diseases are very difficult to treat . This is due to the scanty choice of effective drugs together with their potentially severe side effects . ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "veterinary", "diseases", "zoonoses", "medicine", "and", "health", "sciences", "clinical", "medicine", "drug", "research", "and", "development", "leishmaniasis", "neglected", "tropical", "diseases", "biology", "and", "life", "sciences", "pharma...	2014	Antileishmanial Activity of the Estrogen Receptor Modulator Raloxifene
Despite control efforts , human schistosomiasis remains prevalent throughout Africa , Asia , and South America . The global schistosomiasis burden has changed little since the new anthelmintic drug , praziquantel , promised widespread control . We evaluated large-scale schistosomiasis control attempts over the past cen...	Schistosomiasis is a parasitic disease infecting more than 250 million people worldwide , with almost 800 million at risk . Over the past century , nations undertook schistosomiasis control programs , with outcomes varying from little effect to elimination . The biggest hope for elimination began about 40 years ago wit...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "engineering", "and", "technology", "cancer", "treatment", "clinical", "oncology", "tropical", "diseases", "parasitic", "diseases", "animals", "health", "care", "oncology", "control", "engineering", "clinical", "...	2016	Global Assessment of Schistosomiasis Control Over the Past Century Shows Targeting the Snail Intermediate Host Works Best
Type 1A topoisomerases ( topos ) are the only ubiquitous topos . E . coli has two type 1A topos , topo I ( topA ) and topo III ( topB ) . Topo I relaxes negative supercoiling in part to inhibit R-loop formation . To grow , topA mutants acquire compensatory mutations , base substitutions in gyrA or gyrB ( gyrase ) or am...	DNA topoisomerases are nicking closing enzymes with strand passage activity that solves the topological problems inherent to the double-helical structure of DNA . Topos of the type 1A family are the only ubiquitous topos . They are classified in two subfamilies , topo I and topo III respectively found in bacteria only ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "sequencing", "techniques", "medicine", "and", "health", "sciences", "immune", "cells", "nucleases", "enzymes", "immunology", "dna-binding", "proteins", "enzymology", "next-generation", "sequencing", "mutation", "dna", "replication", "genome", "analysis"...	2018	Topoisomerases I and III inhibit R-loop formation to prevent unregulated replication in the chromosomal Ter region of Escherichia coli
In multiple studies DNA methylation has proven to be an accurate biomarker of age . To develop these biomarkers , the methylation of multiple CpG sites is typically linearly combined to predict chronological age . By contrast , in this study we apply the Universal PaceMaker ( UPM ) model to investigate changes in DNA m...	DNA methylation is an important component of the epigenetic code that defines and maintains the state of cells . Recently , it has been found that certain sites in the genome undergo methylation changes at different rates during aging . The seminal work of Steve Horvath found that the methylation of a couple hundred Cp...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biotechnology", "medicine", "and", "health", "sciences", "genome", "evolution", "simulation", "and", "modeling", "optimization", "methylation", "mathematics", "algebra", "pacemakers", "epigenetics", "dna", "dna", "methylation", "chromatin", "polynomials", "research", "an...	2016	A Statistical Framework to Identify Deviation from Time Linearity in Epigenetic Aging
Crimean-Congo hemorrhagic fever ( CCHF ) is a serious disease with a high fatality rate reported in many countries . The first case of CCHF in Oman was detected in 1995 and serosurveys have suggested widespread infection of humans and livestock throughout the country . Cases of CCHF reported to the Ministry of Health (...	Crimean-Congo hemorrhagic fever , an often fatal tick-borne viral disease , has made an impact in the Sultanate of Oman—affecting nationals and expatriates alike—for the past 20 years . In this retrospective review of the epidemiology and outcomes of cases in Oman from 1995 to 2017 , we identified 4 sporadic cases in 1...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "death", "rates", "reverse", "transcriptase-polymerase", "chain", "reaction", "taxonomy", "invertebrates", "livestock", "sequencing", "techniques", "medicine", "and", "health", "sciences", "ixodes", "crimean-congo", "hemorrhagic", "fever", "tropical", "diseases", "geographi...	2019	Clinical and molecular epidemiology of Crimean-Congo hemorrhagic fever in Oman
Blastomyces dermatitidis belongs to a group of human pathogenic fungi that exhibit thermal dimorphism . At 22°C , these fungi grow as mold that produce conidia or infectious particles , whereas at 37°C they convert to budding yeast . The ability to switch between these forms is essential for virulence in mammals and ma...	The dimorphic fungi are the most common cause of invasive fungal disease worldwide . In the soil , these fungi grow as mold that produce infectious spores; when inhaled into the warmer lungs of a mammalian host , the spores convert into yeast , which cause infection . The change in shape between mold and yeast is a cru...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/fungal", "infections", "microbiology/medical", "microbiology" ]	2010	SREB, a GATA Transcription Factor That Directs Disparate Fates in Blastomyces dermatitidis Including Morphogenesis and Siderophore Biosynthesis
A biophysical model that captures molecular homeostatic control of ions at the perisynaptic cradle ( PsC ) is of fundamental importance for understanding the interplay between astroglial and neuronal compartments . In this paper , we develop a multi-compartmental mathematical model which proposes a novel mechanism wher...	During periods of neuronal activity , ionic homeostasis in the surrounding extracellular space ( ECS ) is disturbed . To provide a healthy environment for continued neuronal function , excess ions such as potassium must be buffered away from the ECS; a vital supportive role provided by astrocyte cells . It has long bee...	[ "Abstract", "Introduction", "Models", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "neurochemistry", "nervous", "system", "astrocytes", "membrane", "potential", "ions", "electrophysiology", "neuroscience", "macroglial", "cells", "sodium", "neurotransmitters", "cations", "physical", "chemistry", "animal", "cells", ...	2018	Potassium and sodium microdomains in thin astroglial processes: A computational model study
Slow-cycling subpopulations exist in bacteria , yeast , and mammalian systems . In the case of cancer , slow-cycling subpopulations have been proposed to give rise to drug resistance . However , the origin of slow-cycling human cells is poorly studied , in large part due to lack of markers to identify these rare cells ...	Even within a genetically identical population , some cells proliferate more slowly than others . Slow-cycling cells have been implicated in resistance to antibiotics , antifungals , and cancer therapies , yet the origin of the slow-cycling state remains poorly understood . Here , we isolate a naturally slow-cycling su...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "sequencing", "techniques", "cellular", "stress", "responses", "anaphase", "gene", "regulation", "cell", "cycle", "and", "cell", "division", "cell", "processes", "cloning", "dna", "damage", "mitosis", "molecular", "biology", "techniques", "dna", "rna", "sequencing", ...	2019	Spontaneously slow-cycling subpopulations of human cells originate from activation of stress-response pathways
Treatment with nifurtimox ( NF ) for Chagas disease is discouraged during breast-feeding because no information on NF transfer into breast milk is available . NF is safe and effective for paediatric and adult Chagas disease . We evaluated the degree of NF transfer into breast milk in lactating women with Chagas disease...	It is not known whether Nifurtimox , a drug for Chagas disease , is significantly transferred into breast milk , and no clinical trials were conducted to evaluate this topic . Treatment with nifurtimox is safe and effective in children and newborns with Chagas disease . Treatment of young women before pregnancy prevent...	[ "Abstract", "Introduction", "Population", "and", "methods", "Results", "Discussion", "Conclusion" ]	[ "neonatology", "children", "medicine", "and", "health", "sciences", "milk", "breast", "milk", "body", "fluids", "maternal", "health", "liquid", "chromatography", "tropical", "diseases", "diet", "parasitic", "diseases", "pediatrics", "age", "groups", "nutrition", "wome...	2019	Negligible exposure to nifurtimox through breast milk during maternal treatment for Chagas Disease
Many broadly neutralizing antibodies ( bNAbs ) against human immunodeficiency virus type 1 ( HIV-1 ) were shown effective in animal models , and are currently evaluated in clinical trials . However , use of these antibodies in humans is hampered by the rapid emergence of resistant viruses . Here we show that soft-rando...	Several potent antibodies against human immunodeficiency virus type 1 ( HIV-1 ) have been evaluated in clinical trials . Use of these antibodies in humans , however , is problematic , because easy viral escape remains a major concern . To gain greater insights , we sought to develop an approach to rapidly assess the li...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "microbial", "mutation", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "cloning", "retroviruses", "viruses", "immunodeficiency", "viruses", "mutation", "substitution"...	2018	Diverse pathways of escape from all well-characterized VRC01-class broadly neutralizing HIV-1 antibodies
A dengue early warning system aims to prevent a dengue outbreak by providing an accurate prediction of a rise in dengue cases and sufficient time to allow timely decisions and preventive measures to be taken by local authorities . This study seeks to identify the optimal lead time for warning of dengue cases in Singapo...	A dengue early warning system that would provide an accurate forecast could enhance the effectiveness of dengue control , but only if it is given in sufficient time for local authorities to implement those control operations . In this study , we have suggested the optimal timing for issuing a warning of a dengue outbre...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "epidemiology", "global", "health", "neglected", "tropical", "diseases", "infectious", "disease", "control", "infectious", "disease", "modeling", "public", "health" ]	2012	Optimal Lead Time for Dengue Forecast
Genome-scale metabolic network reconstructions ( GENREs ) are repositories of knowledge about the metabolic processes that occur in an organism . GENREs have been used to discover and interpret metabolic functions , and to engineer novel network structures . A major barrier preventing more widespread use of GENREs , pa...	Metabolism is the driving force behind all biological activity . Genome-scale metabolic network reconstructions ( GENREs ) are representations of metabolic systems that can be analyzed mathematically to make predictions about how a system will behave , as well as to design systems with new properties . GENREs have trad...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "biotechnology", "medicine", "and", "health", "sciences", "chemical", "compounds", "pneumococcus", "pathology", "and", "laboratory", "medicine", "small", "molecules", "pathogens", "metabolic", "networks", "microbiology", "organic", "compounds", "pseudomonas", "aeruginosa", ...	2017	Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA
Accurately measuring the neural correlates of consciousness is a grand challenge for neuroscience . Despite theoretical advances , developing reliable brain measures to track the loss of reportable consciousness during sedation is hampered by significant individual variability in susceptibility to anaesthetics . We add...	Though scientific understanding of how brain networks generate consciousness has seen rapid advances in recent years , application of this knowledge to accurately track transitions to unconsciousness during general anaesthesia has proven difficult due to considerable variability in this gradual process across individua...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2016	Brain Connectivity Dissociates Responsiveness from Drug Exposure during Propofol-Induced Transitions of Consciousness
Age patterns in asymptomatic and symptomatic infection with Leishmania donovani , the causative agent of visceral leishmaniasis ( VL ) in the Indian subcontinent ( ISC ) , are currently poorly understood . Age-stratified serology and infection incidence have been used to assess transmission levels of other diseases , w...	As the elimination target for visceral leishmaniasis ( VL ) in the Indian subcontinent ( <1 case/10 , 000 people/year ) is approached , there is a growing need for surveillance tools with which to monitor transmission to ensure the target is sustained , especially given the large proportion of infections which are asym...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "immunology", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "age", "groups", "protozoans", "leishm...	2018	Age trends in asymptomatic and symptomatic Leishmania donovani infection in the Indian subcontinent: A review and analysis of data from diagnostic and epidemiological studies
Vocal learning , the substrate of human language acquisition , has rarely been described in other mammals . Often , group-specific vocal dialects in wild populations provide the main evidence for vocal learning . While social learning is often the most plausible explanation for these intergroup differences , it is usua...	The spontaneous acquisition of speech by human infants is considered a keystone of human language , but the ability to reproduce vocalizations acquired by hearing is not commonly described in other mammals . This skill , termed vocal learning , is challenging to study in nonhuman animals since such investigation requir...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "learning", "acoustics", "vocalization", "linguistics", "linear", "discriminant", "analysis", "social", "sciences", "vertebrates", "neuroscience", "animals", "mammals", "learning", "and", "memory", "animal", "signaling", "and", "communication", "cognitive", "psychology", ...	2017	Crowd vocal learning induces vocal dialects in bats: Playback of conspecifics shapes fundamental frequency usage by pups
Fragile X-associated tremor/ataxia syndrome ( FXTAS ) , a late-onset neurodegenerative disorder , has been recognized in older male fragile X premutation carriers and is uncoupled from fragile X syndrome . Using a Drosophila model of FXTAS , we previously showed that transcribed premutation repeats alone are sufficient...	Fragile X–associated tremor/ataxia syndrome ( FXTAS ) is an adult-onset neurodegenerative disorder , usually affecting males over 50 years of age . FXTAS patients are the carriers of fragile X premutation alleles . Using a FXTAS Drosophila model , we previously demonstrated that fragile X premutation rCGG repeats alone...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "neurological", "disorders", "neurology", "cerebellar", "disorders" ]	2012	MicroRNA-277 Modulates the Neurodegeneration Caused by Fragile X Premutation rCGG Repeats
The lipid kinase phosphatidylinositol 4-kinase III alpha ( PI4KIIIα ) is an essential host factor of hepatitis C virus ( HCV ) replication . PI4KIIIα catalyzes the synthesis of phosphatidylinositol 4-phosphate ( PI4P ) accumulating in HCV replicating cells due to enzyme activation resulting from its interaction with no...	Hepatitis C virus ( HCV ) infections affect about 170 million people worldwide and often result in severe chronic liver disease . HCV is a positive-strand RNA virus inducing massive rearrangements of intracellular membranes to generate the sites of genome replication , designated the membranous web . The complex biogen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "enzymes", "microbiology", "hepatitis", "lipid", "metabolism", "hepatitis", "c", "infectious", "diseases", "lipids", "virulence", "factors", "and", "mechanisms", "proteins", "enzyme", "regulation", "membranes", "and", "sorting", "biology", "viral", "replicat...	2013	The Lipid Kinase Phosphatidylinositol-4 Kinase III Alpha Regulates the Phosphorylation Status of Hepatitis C Virus NS5A
The loss of HIV-specific CD8+ T cell cytolytic function is a primary factor underlying progressive HIV infection , but whether HIV-specific CD8+ T cells initially possess cytolytic effector capacity , and when and why this may be lost during infection , is unclear . Here , we assessed CD8+ T cell functional evolution f...	Previous studies have demonstrated that HIV-specific CD8+ T cells are critical for the initial control of HIV infection . However , this control is typically incomplete , being able to neither clear infection nor maintain plasma viremia below undetectable levels . Mounting evidence has implicated CD8+ T cell cytotoxic ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "hiv", "infections", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "pathogens", "immunology", "microbiology", "cloning", "neuroscience", "learning"...	2016	Temporal Dynamics of CD8+ T Cell Effector Responses during Primary HIV Infection
Recent studies suggest that some monoclonal antibodies ( mAbs ) specific for ebolavirus glycoprotein ( GP ) can protect experimental animals against infections . Most mAbs isolated from ebolavirus survivors appeared to target the glycan cap or the stalk region of the viral GP , which is the envelope protein and the onl...	Recent progress in isolation of mAbs from survivors of filovirus infections suggests that the human adaptive immune system is capable of producing strong antibody responses . However , the effects of mAbs with different epitope specificity on individual steps of filovirus infection are still unclear . We evaluated a pa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "flow", "cytometry", "medicine", "and", "health", "sciences", "immune", "physiology", "immune", "cells", "viral", "transmission", "and", "infection", "immunology", "cell", "processes", "microbiology", "viral", "structure", "fluorophotometry", "antibodi...	2018	Asymmetric antiviral effects of ebolavirus antibodies targeting glycoprotein stem and glycan cap
Entry into mitosis is triggered by cyclinB/Cdk1 , whose activity is abruptly raised by a positive feedback loop . The Greatwall kinase phosphorylates proteins of the endosulfine family and allows them to bind and inhibit the main Cdk1-counteracting PP2A-B55 phosphatase , thereby promoting mitotic entry . In contrast to...	In all eukaryotic cells chromosome partition during mitosis requires a number of processes , including the formation of the mitotic spindle , i . e . the machinery that drives chromosome segregation to the daughter cells . Mitotic entry requires a delicate balance between protein phosphorylation , driven by cyclin-depe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "cell", "biology", "genetics", "biology", "model", "organisms" ]	2013	Budding Yeast Greatwall and Endosulfines Control Activity and Spatial Regulation of PP2ACdc55 for Timely Mitotic Progression
Vascular endothelial cells act as gatekeepers that protect underlying tissue from blood-borne toxins and pathogens . Nevertheless , endothelial cells are able to internalize large fibrin clots and apoptotic debris from the bloodstream , although the precise mechanism of such phagocytosis-like uptake is unknown . We sho...	Vascular endothelial cells , which line the lumen of blood vessels , are conventionally viewed as a restrictive barrier that protects underlying tissue from blood-borne toxins and pathogens . Nonetheless , even highly restrictive endothelial cells can internalize micron-sized objects , such as blood clots , raising the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "evolutionary", "biology", "gene", "regulation", "pathogens", "endothelial", "cells", "focal", "adhesions", "population", "genetics", "microbiolog...	2016	Endothelial Cells Use a Formin-Dependent Phagocytosis-Like Process to Internalize the Bacterium Listeria monocytogenes
Copper ions play an important role in ethylene receptor biogenesis and proper function . The copper transporter RESPONSIVE-TO-ANTAGONIST1 ( RAN1 ) is essential for copper ion transport in Arabidopsis thaliana . However it is still unclear how copper ions are delivered to RAN1 and how copper ions affect ethylene recepto...	Copper ions are cofactors of protein functions , and their disorder is closely related to many human diseases which drive to develop new copper chelator related drugs . In plants , copper ions are essential for ethylene receptors , but many details are unclear . Researchers need novel specific copper chelators to study...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "plant", "anatomy", "chemical", "compounds", "plant", "growth", "and", "development", "ethylene", "signaling", "cascade", "ethylene", "plant", "embryo", "anatomy", "brassica", "organic", "compounds", "hormones", "developmental", "biology", "plant", "science", "model", ...	2017	Triplin, a small molecule, reveals copper ion transport in ethylene signaling from ATX1 to RAN1
Orientia tsutsugamushi , the etiologic agent of scrub typhus , is a mite-borne rickettsia transmitted by the parasitic larval stage of trombiculid mites . Approximately one-third of the world's population is at risk of infection with Orientia tsutsugamushi , emphasizing its importance in global health . In order to stu...	Scrub typhus is a disease found in Southeast Asia that infects over 1 million people each year . This disease is caused by the intracellular pathogen Orientia tsutsugamushi transmitted by the bite of chigger mites . Scrub typhus is characterized by pulmonary disease and in severe cases , multiorgan system failure . The...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "typhus", "medicine", "and", "health", "sciences", "liver", "immunology", "tropical", "diseases", "microbiology", "lungs", "bacterial", "diseases", "histology", "respiratory", "system", "immunochemistry", "emerging", "infectious", "diseases", "population", "modeling", "ne...	2014	A Hematogenously Disseminated Orientia tsutsugamsushi-Infected Murine Model of Scrub Typhus
The inner structural Gag proteins and the envelope ( Env ) glycoproteins of human immunodeficiency virus ( HIV-1 ) traffic independently to the plasma membrane , where they assemble the nascent virion . HIV-1 carries a relatively low number of glycoproteins in its membrane , and the mechanism of Env recruitment and vir...	Newly formed HIV-1 particles assemble at the plasma membrane of virus producing cells . The inner structural protein Gag and the envelope glycoprotein Env , which are both essential components of infectious virus particles , traffic to the membrane via different pathways . Attached to the inner side of the membrane , G...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology", "biology", "microbiology" ]	2013	Super-Resolution Microscopy Reveals Specific Recruitment of HIV-1 Envelope Proteins to Viral Assembly Sites Dependent on the Envelope C-Terminal Tail
EBNA3C , one of the Epstein-Barr virus ( EBV ) -encoded latent antigens , is essential for primary B-cell transformation . Cyclin D1 , a key regulator of G1 to S phase progression , is tightly associated and aberrantly expressed in numerous human cancers . Previously , EBNA3C was shown to bind to Cyclin D1 in vitro alo...	Epstein-Barr virus ( EBV ) , a ubiquitous human herpesvirus , is linked to the development of multiple cancers , including lymphomas and epithelial carcinomas . EBNA3C , one of its essential latent antigens encoded by EBV , is expressed in EBV-associated lymphomas and contributes to aberrant cell growth after EBV infec...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/viral", "infections", "virology/viruses", "and", "cancer", "oncology/hematological", "malignancies", "microbiology/cellular", "microbiology", "and", "pathogenesis" ]	2011	Epstein-Barr Virus Nuclear Antigen 3C Facilitates G1-S Transition by Stabilizing and Enhancing the Function of Cyclin D1
The repair of DNA double-strand breaks must be accurate to avoid genomic rearrangements that can lead to cell death and disease . This can be accomplished by promoting homologous recombination between correctly aligned sister chromosomes . Here , using a unique system for generating a site-specific DNA double-strand br...	Genetic recombination is critically important for the repair of DNA double-strand breaks and is the only repair mechanism available to the bacterium Escherichia coli . Repair requires that the appropriate location on an unbroken sister chromosome is recognised as a repair template , and this can be accomplished by a sy...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "cell", "biology", "nucleic", "acids", "biology", "and", "life", "sciences", "dna", "dna", "recombination", "molecular", "cell", "biology" ]	2014	Branch Migration Prevents DNA Loss during Double-Strand Break Repair
The pathogenic fungus Cryptococcus neoformans exhibits morphological changes in cell size during lung infection , producing both typical size 5 to 7 μm cells and large titan cells ( > 10 μm and up to 100 μm ) . We found and optimized in vitro conditions that produce titan cells in order to identify the ancestry of tita...	Cryptococcus neoformans is a yeast that is capable of morphological change upon interaction with the host . Particularly , in the lungs of infected mice , a subpopulation of yeast enlarges , producing cells up to 100 μm in cell body diameter–referred to as titan cells . Along with their large size , the titan cells hav...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "flow", "cytometry", "cell", "physiology", "chitin", "cell", "walls", "cryptococcus", "neoformans", "medicine", "and", "health", "sciences", "cryptococcus", "yeast", "infections", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "cell", "format...	2018	Titan cells formation in Cryptococcus neoformans is finely tuned by environmental conditions and modulated by positive and negative genetic regulators
Schistosomiasis affects more than 200 million individuals worldwide , with a further 650 million living at risk of infection , constituting a severe health problem in developing countries . Even though an effective treatment exists , it does not prevent re-infection , and the development of an effective vaccine still r...	Schistosomiasis is a parasitic disease causing serious chronic morbidity in tropical countries . Together with the publication of the transcriptome database , a series of new vaccine candidates were proposed based on their functional classification . However , the prediction of vaccine candidates from sequence informat...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biotechnology", "infectious", "diseases/helminth", "infections", "molecular", "biology", "immunology" ]	2010	Schistosoma mansoni Stomatin Like Protein-2 Is Located in the Tegument and Induces Partial Protection against Challenge Infection
APE1 is a multifunctional protein with a DNA base excision repair function in its C-terminal domain and a redox activity in its N-terminal domain . The redox function of APE1 converts certain transcription factors from inactive oxidized to active reduced forms . Given that among the APE1-regulated transcription factors...	As a major AIDS-associated malignancy , Kaposi’s sarcoma ( KS ) is caused by Kaposi’s sarcoma-associated herpesvirus ( KSHV ) . Currently there is no definitive cure for KS . In this study , we identified a cellular protein , namely APE1 , as an effective therapeutic target for blocking KSHV replication and inhibiting ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "cardiovascular", "physiology", "pathogens", "immunology", "microbiology", "cancers", "and", "neoplasms", "viral", "...	2017	An APE1 inhibitor reveals critical roles of the redox function of APE1 in KSHV replication and pathogenic phenotypes
The growing availability of high-quality genomic annotation has increased the potential for mechanistic insights when the specific variants driving common genome-wide association signals are accurately localized . A range of fine-mapping strategies have been advocated , and specific successes reported , but the overall...	Over the last few years , several approaches for fine-mapping genome-wide association studies ( GWAS ) loci have been proposed and used to localize potential causal variants . However , the performance of these types of tests is often poorly characterized . In this study , we used extensive simulations to show that sta...	[ "Abstract", "Introduction", "Results", "Methods" ]	[]	2015	Evaluating the Performance of Fine-Mapping Strategies at Common Variant GWAS Loci
Hypomethylating agents reactivate tumor suppressor genes that are epigenetically silenced in cancer . Inevitably these genes are resilenced , leading to drug resistance . Using the MLH1 tumor suppressor gene as a model , we showed that decitabine-induced re-expression was dependent upon demethylation and eviction of pr...	Hypomethylating agents are emerging as effective cancer therapies . However , their therapeutic effects are transient and drug resistance inevitably develops . While resistance is associated with resilencing of genes initially demethylated by the drug , the mechanism underlying this resilencing is unknown . We provide ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology", "medicine", "epigenetic", "therapy", "gene", "expression", "genetics", "cancer", "treatment", "epigenetics", "biology", "dna", "modification", "molecular", "cell", "biology", "chromatin", "dna", "transcription", "histone", "modification" ]	2013	Reassembly of Nucleosomes at the MLH1 Promoter Initiates Resilencing Following Decitabine Exposure
Reproduction is a defining feature of living systems . To reproduce , aggregates of biological units ( e . g . , multicellular organisms or colonial bacteria ) must fragment into smaller parts . Fragmentation modes in nature range from binary fission in bacteria to collective-level fragmentation and the production of u...	Mode of reproduction is a defining trait of all organisms , including colonial bacteria and multicellular organisms . To produce offspring , aggregates must fragment by splitting into two or more groups . The particular way that a given group fragments defines the life cycle of the organism . For instance , insect colo...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "death", "rates", "organismal", "evolution", "cell", "division", "analysis", "cell", "cycle", "and", "cell", "division", "cell", "processes", "developmental", "biology", "bioassays", "and", "physiological", "analysis", "population", "biology", "fecundity", "research", ...	2017	Fragmentation modes and the evolution of life cycles
Systems biology models are used to understand complex biological and physiological systems . Interpretation of these models is an important part of developing this understanding . These models are often fit to experimental data in order to understand how the system has produced various phenomena or behaviour that are s...	Systems biology models are mathematical representations of biological processes that reproduce the overall behaviour of a biological system . They are comprised by a number of parameters representing biological information . We use them to understand the behaviour of biological systems , such as the brain . We do this ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Discussion" ]	[ "medicine", "and", "health", "sciences", "oxygen", "integrative", "physiology", "simulation", "and", "modeling", "oxygen", "metabolism", "systems", "science", "mathematics", "physiological", "parameters", "near-infrared", "spectroscopy", "research", "and", "analysis", "me...	2019	A Bayesian framework for the analysis of systems biology models of the brain
The high-risk HPV E6 and E7 proteins cooperate to immortalize primary human cervical cells and the E7 protein can independently transform fibroblasts in vitro , primarily due to its ability to associate with and degrade the retinoblastoma tumor suppressor protein , pRb . The binding of E7 to pRb is mediated by a conser...	Human papillomaviruses ( HPVs ) are estimated to cause the most common sexually transmitted infection in the world , and these infections are recognized as the major cause of cervical cancer . One of the papillomavirus oncoproteins , E7 , plays a major role in both the viral life cycle and progression to cancer . In ce...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "virology/viral", "replication", "and", "gene", "regulation", "virology/virus", "evolution", "and", "symbiosis", "virology/animal", "models", "of", "infection", "virology/emerging", "viral", "diseases", "virology", "virology/viruses", "and", "cancer", "virology/effects", "o...	2010	The Canine Papillomavirus and Gamma HPV E7 Proteins Use an Alternative Domain to Bind and Destabilize the Retinoblastoma Protein
Malignant carcinomas that recur following therapy are typically de-differentiated and multidrug resistant ( MDR ) . De-differentiated cancer cells acquire MDR by up-regulating reactive oxygen species ( ROS ) –scavenging enzymes and drug efflux pumps , but how these genes are up-regulated in response to de-differentiati...	The development of multidrug resistance is the primary obstacle to treating cancers . High-grade tumors that are less differentiated typically respond poorly to therapy and carry a much worse prognosis than well-differentiated low-grade tumors . Therapy-resistant cancer cells often overexpress antioxidants or efflux pr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cellular", "stress", "responses", "cell", "biology", "gene", "expression", "genetics", "cellular", "types", "biology", "and", "life", "sciences", "cell", "processes", "molecular", "cell", "biology" ]	2014	De-Differentiation Confers Multidrug Resistance Via Noncanonical PERK-Nrf2 Signaling
The Arabidopsis COP1/SPA E3 ubiquitin ligase is a key negative regulator that represses light signaling in darkness by targeting transcription factors involved in the light response for degradation . The COP1/SPA complex consists of COP1 and members of the four-member SPA protein family ( SPA1-SPA4 ) . Genetic analysis...	Plants have evolved photoreceptors that initiate a signaling cascade to adjust growth and development to the ambient light environment . The CUL4-dependent COP1/SPA E3 ubiquitin ligase is a key negative regulator of light signaling whose function is repressed by light . Recent research has identified mechanisms that ar...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Photoreceptor Specificity in the Light-Induced and COP1-Mediated Rapid Degradation of the Repressor of Photomorphogenesis SPA2 in Arabidopsis
Adaptation in response to selection on polygenic phenotypes may occur via subtle allele frequencies shifts at many loci . Current population genomic techniques are not well posed to identify such signals . In the past decade , detailed knowledge about the specific loci underlying polygenic traits has begun to emerge fr...	The process of adaptation is of fundamental importance in evolutionary biology . Within the last few decades , genotyping technologies and new statistical methods have given evolutionary biologists the ability to identify individual regions of the genome that are likely to have been important in this process . When ada...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "genetic", "polymorphism", "natural", "selection", "genome", "analysis", "genetics", "biology", "and", "life", "sciences", "evolutionary", "adaptation", "population", "genetics", "computational", "biology", "evolutionary", "biology",...	2014	A Population Genetic Signal of Polygenic Adaptation
Mosquitoes host communities of microbes in their digestive tract that consist primarily of bacteria . We previously reported that Aedes aegypti larvae colonized by a native community of bacteria and gnotobiotic larvae colonized by only Escherichia coli develop very similarly into adults , whereas axenic larvae never mo...	Several mosquito species including Aedes aegypti transmit pathogens as adults that cause disease in humans and other vertebrates . It has also long been known that mosquitoes host bacteria in their digestive tract , which are primarily acquired during the larval stage and transstadially transmitted to adults . Our rece...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion", "Data", "Deposition" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "enzymes", "enzymology", "diet", "animals", "physiological", "processes", "developmental", "biology", "nutrition", "insect", "vectors", "bacteria", "digestive", "system", "molting", "aedes", "aegypti", "proteins", ...	2017	Transcriptome Sequencing Reveals Large-Scale Changes in Axenic Aedes aegypti Larvae
Echolocating bats rely on active sound emission ( echolocation ) for mapping novel environments and navigating through them . Many theoretical frameworks have been suggested to explain how they do so , but few attempts have been made to build an actual robot that mimics their abilities . Here , we present the ‘Robat’—a...	Many animals are able of mapping a new environment even while moving through it for the first time . Bats can do this by emitting sound and extracting information from the echoes reflected from objects in their surroundings . In this study , we mimicked this ability by developing a robot that emits sound like a bat and...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "acoustics", "medicine", "and", "health", "sciences", "engineering", "and", "technology", "ears", "vertebrates", "robots", "animals", "mammals", "echoes", "remote", "sensing", "robotics", "bioacoustics", "head", "physics", "mechanical", "engineering", "eukaryota", "anat...	2018	A fully autonomous terrestrial bat-like acoustic robot
Macrophage cells that are stimulated by two different ligands that bind to G-protein-coupled receptors ( GPCRs ) usually respond as if the stimulus effects are additive , but for a minority of ligand combinations the response is synergistic . The G-protein-coupled receptor system integrates signaling cues from the envi...	The G protein signal transduction system transmits a wide variety of extracellular signals including light , odors , and hormones , to intracellular effectors in diverse cell types in eukaryotes . G-protein-coupled receptors are involved in many diseases including inflammation , cardiac dysfunction , and diabetes , and...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/cell", "signaling", "biophysics/theory", "and", "simulation", "mathematics/statistics", "biophysics/cell", "signaling", "and", "trafficking", "structures", "computational", "biology/systems", "biology" ]	2008	A Dual Receptor Crosstalk Model of G-Protein-Coupled Signal Transduction
Attenuated viral vaccines can be generated by targeting essential pathogenicity factors . We report here the rational design of an attenuated recombinant coronavirus vaccine based on a deletion in the coding sequence of the non-structural protein 1 ( nsp1 ) . In cell culture , nsp1 of mouse hepatitis virus ( MHV ) , li...	Prevention of viral diseases by vaccination aims for controlled induction of protective immune responses against viral pathogens . Live viral vaccines consist of attenuated , replication-competent viruses that are believed to be superior in the induction of broad immune responses , including cell-mediated immunity . Th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "viruses", "infectious", "diseases", "virology", "immunology", "mus", "(mouse)", "homo", "(human)", "mammals" ]	2007	Coronavirus Non-Structural Protein 1 Is a Major Pathogenicity Factor: Implications for the Rational Design of Coronavirus Vaccines

Subsets and Splits

No community queries yet

The top public SQL queries from the community will appear here once available.