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RNA interference ( RNAi ) requires RNA-dependent RNA polymerases ( RdRPs ) in many eukaryotes , and RNAi amplification constitutes the only known function for eukaryotic RdRPs . Yet in animals , classical model organisms can elicit RNAi without possessing RdRPs , and only nematode RNAi was shown to require RdRPs . Here...	RNA interference ( RNAi ) is a conserved gene regulation system in eukaryotes . In non-animal eukaryotes , it necessitates RNA-dependent RNA polymerases ( “RdRPs” ) . Among animals , only nematodes appear to require RdRPs for RNAi . Yet additional animal clades have RdRPs and it is assumed that they participate in RNAi...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "cdna", "libraries", "rna", "interference", "gene", "regulation", "animals", "small", "nuclear", "rna", "genome", "analysis", "forms", "of", "dna", "dna", "libraries", "epigenetics", "dna", "amphioxus", "small", "interfering", "rnas", "genomic", "libraries", "genomi...	2019	Functional lability of RNA-dependent RNA polymerases in animals
In most transmissible spongiform encephalopathies prions accumulate in the lymphoreticular system ( LRS ) long before they are detectable in the central nervous system . While a considerable body of evidence showed that B lymphocytes and follicular dendritic cells play a major role in prion colonization of lymphoid org...	Prions , rogue proteins that cause the fatal brain disease CJD in humans and BSE in cattle are not only found in the brain , but also in other tissues , particularly in lymphoid organs , long before they are detectable in the central nervous system . It is of great interest to better characterize how prions colonize th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "neurological", "disorders", "neurology", "biology", "neuroscience" ]	2012	Plasmacytoid Dendritic Cells Sequester High Prion Titres at Early Stages of Prion Infection
Estimating the difficulty of a decision is a fundamental process to elaborate complex and adaptive behaviour . In this paper , we show that the movement time of behaving monkeys performing a decision-making task is correlated with decision difficulty and that the activity of a population of neurons in ventral Premotor ...	Understanding how the brain produces complex cognitive functions has been a crucial question since ancient philosophical inquiries . The encoding of decision difficulty in the brain is fundamental for complex and adaptive behaviour , and can provide valuable information in uncertain environments where the future outcom...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	The Encoding of Decision Difficulty and Movement Time in the Primate Premotor Cortex
The entomopathogenic fungus Beauveria bassiana has a wide host range and is used as a biocontrol agent against arthropod pests . Mycoviruses have been described in phytopathogenic fungi while in entomopathogenic fungi their presence has been reported only rarely . Here we show that 21 . 3% of a collection of B . bassia...	Virus diversity is constantly increasing and the findings often challenge our perceptions of the virosphere , enhance our understanding of the global ecology and evolution of viruses and virus-like elements and offer a range of new tools . Here we describe a fungal viral family , provisionally designated as Polymycovir...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "fungal", "genetics", "computational", "biology", "microbiology", "fungi", "agarose", "gel", "electrophoresis", "genome", "analysis", "sequence", "motif", "analysis", "gel", "electrophoresis", "microbial", "genomics", "research", "and", "analysis", "methods", "sequence", ...	2017	Studies on the Virome of the Entomopathogenic Fungus Beauveria bassiana Reveal Novel dsRNA Elements and Mild Hypervirulence
Giardia intestinalis is a ubiquitous parasitic protist that is the causative agent of giardiasis , one of the most common protozoan diarrheal diseases in the world . Giardia trophozoites attach to the intestinal epithelium using a specialized and elaborate microtubule structure , the ventral disc . Surrounding the vent...	Giardia is a unicellular intestinal parasite that infects millions of people worldwide each year . Colonization of the small intestine is a critical stage in Giardia infection . Giardia colonizes the intestinal wall using a specialized suction cup-like structure , the ventral disc . Little is known about the protein co...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biology", "microbiology", "parasitology" ]	2011	Novel Structural Components of the Ventral Disc and Lateral Crest in Giardia intestinalis
The use of antibiotics targeting the obligate bacterial endosymbiont Wolbachia of filarial parasites has been validated as an approach for controlling filarial infection in animals and humans . Availability of genomic sequences for the Wolbachia ( wBm ) present in the human filarial parasite Brugia malayi has enabled g...	Filarial nematode parasites are responsible for a number of devastating diseases in humans and animals . These include lymphatic filariasis and onchocerciasis that afflict 150 million people in the tropics and threaten the health of over one billion . The parasites possess intracellular bacteria , Wolbachia , which are...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "public", "health", "medicine", "biochemistry", "infectious", "diseases", "public", "health", "and", "epidemiology", "drug", "research", "and", "development", "drugs", "and", "devices", "global", "health", "neglected", "tropical", "diseases", "pharmacology", "biology", ...	2011	Targeting the Wolbachia Cell Division Protein FtsZ as a New Approach for Antifilarial Therapy
Staphylococcus epidermidis and Staphylococcus aureus are leading causes of hospital-acquired infections that have become increasingly difficult to treat due to the prevalence of antibiotic resistance in these organisms . The ability of staphylococci to produce biofilm is an important virulence mechanism that allows bac...	Biofilm is an agglomeration of microbes bound together by a slimy matrix composed of excreted proteins and polysaccharide polymers . Most bacteria in the environment reside in biofilms , as do 80% or more of those causing human infections , according to some estimates . During infection , biofilm matrix acts as a safe ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "caenorhabditis", "immunology", "microbiology", "eubacteria" ]	2007	Staphylococcal Biofilm Exopolysaccharide Protects against Caenorhabditis elegans Immune Defenses
miR-155 plays critical roles in numerous physiological and pathological processes , however , its function in the regulation of blood glucose homeostasis and insulin sensitivity and underlying mechanisms remain unknown . Here , we reveal that miR-155 levels are downregulated in serum from type 2 diabetes ( T2D ) patien...	In the present study , we provide evidence for the first time showing that miR-155 is a positive regulator of insulin sensitivity in mice . Here , we determine that miR-155 levels are downregulated in serum from type 2 diabetes ( T2D ) patients , and shows a negative correlation with HOMA-IR , suggesting that miR-155 m...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "carbohydrate", "metabolism", "medicine", "and", "health", "sciences", "diabetic", "endocrinology", "gene", "regulation", "brown", "adipose", "tissue", "glucose", "metabolism", "hormones", "animal", "models", "glucose", "tolerance", "diabetes", "mellitus", "micrornas", ...	2016	MiR-155 Enhances Insulin Sensitivity by Coordinated Regulation of Multiple Genes in Mice
The leucine transporter ( LeuT ) has recently commanded exceptional attention due mainly to two distinctions; it provides the only crystal structures available for a protein homologous to the pharmacologically relevant neurotransmitter: sodium symporters ( NSS ) , and , it exhibits a hallmark 5-TM inverted repeat ( “Le...	Elucidating the mechanism of active transport across the membrane is relevant not only to the understanding of physiological processes but also to the rational design of drugs that modulate these processes . In the cell membrane , specialized proteins known as secondary transporters utilize the energy stored in the ele...	[ "Abstract", "Introduction", "Methods", "Results/Discussion" ]	[ "computational", "biology/molecular", "dynamics", "biophysics", "biochemistry/membrane", "proteins", "and", "energy", "transduction", "biophysics/membrane", "proteins", "and", "energy", "transduction" ]	2010	Modeling and Dynamics of the Inward-Facing State of a Na+/Cl− Dependent Neurotransmitter Transporter Homologue
Sleep is essential for optimal brain functioning and health , but the biological substrates through which sleep delivers these beneficial effects remain largely unknown . We used a systems genetics approach in the BXD genetic reference population ( GRP ) of mice and assembled a comprehensive experimental knowledge base...	Sleep is essential for optimal brain functioning and health , but the biological substrates through which sleep delivers these beneficial effects remain largely unknown . We used a systems genetics approach in a large , diverse reference population of mice and assembled a comprehensive experimental knowledge base compr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "methods", "and", "resources", "quantitative", "trait", "loci", "sleep", "brain", "electrophysiology", "electrophysiology", "neuroscience", "physiological", "processes", "clinical", "medicine", "metabolites", "brain", "mapping", "b...	2018	A systems genetics resource and analysis of sleep regulation in the mouse
Trypanosomatids are flagellated protozoan parasites that are very unusual in terms of cytoskeleton organization but also in terms of cell death . Most of the Trypanosomatid cytoskeleton consists of microtubules , forming different substructures including a subpellicular corset . Oddly , the actin network appears struct...	Leishmania are unique unicellular organisms in terms of cytoskeleton organization and mechanisms of cell death . For example , the major cytoskeletal components of these parasites are microtubules , which form a subpellicular corset . In terms of cell death , an apoptotic phenotype has been characterized in Leishmania ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "cell", "death", "autophagic", "cell", "death", "medicine", "and", "health", "sciences", "microtubules", "pathology", "and", "laboratory", "medicine", "pathogens", "cell", "processes", "parasitic", "protozoans", "protozoans", "leishmania", "molecular", "biology", "techn...	2019	(De)glutamylation and cell death in Leishmania parasites
G-quadruplex ( G4 ) , formed by repetitive guanosine-rich sequences , is known to play various key regulatory roles in cells . Herpesviruses containing a large double-stranded DNA genome show relatively higher density of G4-forming sequences in their genomes compared to human and mouse . However , it remains poorly und...	Although a number of G4-forming sequences are predicted in the herpesviral genomes and some G4s are characterized individually , why so many G4s are present in the genome and whether they are all functional are not yet clear . Our genome-wide bioinformatic sequence analyses and biophysical stability and structure assay...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "luciferase", "gene", "regulation", "enzymes", "enzymology", "microbiology", "sequence", "motif", "analysis", "mammalian", "genomics", "dna", "microbial", "genetics", "promoter", "regions", "research", "and", "analysis", "methods", "sequence", "analysis", "bioinformatics"...	2018	Genome-wide analysis of regulatory G-quadruplexes affecting gene expression in human cytomegalovirus
Protein misfolding cyclic amplification ( PMCA ) provides faithful replication of mammalian prions in vitro and has numerous applications in prion research . However , the low efficiency of conversion of PrPC into PrPSc in PMCA limits the applicability of PMCA for many uses including structural studies of infectious pr...	Protein misfolding cyclic amplification ( PMCA ) provides faithful replication of mammalian prions in vitro . While PMCA has become an important tool in prion research , its application is limited because of low yield , poor efficiency and , sometimes , stochastic behavior . The current study introduces a new PMCA form...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "infectious", "diseases/prion", "diseases" ]	2011	Highly Efficient Protein Misfolding Cyclic Amplification
The human liver fluke , Opisthorchis viverrini , is designated as a group 1 carcinogen , and is the major risk factor for cholangiocarcinoma in endemic countries throughout Southeast Asia . Proteins in the excretory-secretory products and tegumental surface membranes of the fluke have been proposed to play pivotal role...	Liver fluke infection is a fish borne disease that afflicts millions of residents in Thailand and Laos . Infection results from eating undercooked freshwater fish contaminated with larvae of the worm Opisthorchis viverrini . Infection can lead to cancer of the bile ducts ( cholangiocarcinoma ) . Indeed , O . viverrini ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "molecular", "cell", "biology", "rna", "interference", "gene", "expression", "biology", "microbiology", "molecular", "biology", "parasitology" ]	2012	Molecular Characterization of a Tetraspanin from the Human Liver Fluke, Opisthorchis viverrini
Cutaneous leishmaniasis is a vector-borne disease that is in Ethiopia mainly caused by the parasite Leishmania aethiopica . This neglected tropical disease is common in rural areas and causes serious morbidity . Persistent nonhealing cutaneous leishmaniasis has been associated with poor T cell mediated responses; howev...	The leishmaniases are a complex of diseases caused by Leishmania parasites . Currently , the diseases affect an estimated 12 million people in 88 countries , and approximately 350 million more people are at risk . The leishmaniases belong to the most neglected tropical diseases , affecting the poorest populations , for...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "neglected", "tropical", "diseases", "immunology", "biology", "parasitic", "diseases", "immunomodulation", "immune", "response" ]	2012	Local Increase of Arginase Activity in Lesions of Patients with Cutaneous Leishmaniasis in Ethiopia
The Chemical Master Equation ( CME ) is a cornerstone of stochastic analysis and simulation of models of biochemical reaction networks . Yet direct solutions of the CME have remained elusive . Although several approaches overcome the infinite dimensional nature of the CME through projections or other means , a common f...	Stochastic models of chemical networks are necessary to quantitatively describe random fluctuations and other probabilistic phenomena within living cells . The Chemical Master Equation ( CME ) describes the time evolution of molecular abundance probabilities in these models , and is a basis for many stochastic simulati...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "applied", "mathematics", "synthetic", "biology", "algorithms", "mathematical", "computing", "probability", "distribution", "mathematics", "algebra", "stochastic", "processes", "biophysics", "simulations", "biochemistry", "simulations", "probability", "density", "regulatory", ...	2014	Direct Solution of the Chemical Master Equation Using Quantized Tensor Trains
Profilin is an actin monomer binding protein that provides ATP-actin for incorporation into actin filaments . In contrast to higher eukaryotic cells with their large filamentous actin structures , apicomplexan parasites typically contain only short and highly dynamic microfilaments . In apicomplexans , profilin appears...	The malaria parasite Plasmodium has two invasive forms that migrate across different tissue barriers , the ookinete and the very rapidly migrating sporozoite . Previous work has shown that the motility of these and related parasites ( e . g . Toxoplasma gondii ) depends on a highly dynamic actin cytoskeleton and retrog...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "chemical", "bonding", "cell", "motility", "parasite", "groups", "actin", "filaments", "plasmodium", "cell", "processes", "parasitology", "developmental", "biology", "apicomplexa", "hydrogen", "bonding", "physical", "chemistry", "contractile", "proteins", "polymer", "chem...	2017	A unique profilin-actin interface is important for malaria parasite motility
Statistical analysis of alignments of large numbers of protein sequences has revealed “sectors” of collectively coevolving amino acids in several protein families . Here , we show that selection acting on any functional property of a protein , represented by an additive trait , can give rise to such a sector . As an il...	Proteins play crucial parts in all cellular processes , and their functions are encoded in their amino-acid sequences . Recently , statistical analyses of protein sequence alignments have demonstrated the existence of “sectors” of collectively correlated amino acids . What is the origin of these sectors ? Here , we pro...	[ "Abstract", "Introduction", "Model", "and", "methods", "Results", "Discussion" ]	[ "classical", "mechanics", "statistics", "random", "variables", "covariance", "amino", "acid", "sequence", "analysis", "multivariate", "analysis", "mathematics", "algebra", "damage", "mechanics", "research", "and", "analysis", "methods", "sequence", "analysis", "sequence",...	2019	Revealing evolutionary constraints on proteins through sequence analysis
Whereas the majority of pathogenic Salmonella serovars are capable of infecting many different animal species , typically producing a self-limited gastroenteritis , serovars with narrow host-specificity exhibit increased virulence and their infections frequently result in fatal systemic diseases . In our study , a gene...	The process of Salmonella host-adaptation is traditionally considered to involve acquisition of novel genetic elements encoding specific virulence factors or loss of genes representing liability for the more pathogenic strains . Here , by analysis of the mannose-sensitive fimbrial adhesin FimH , we demonstrate that in ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "microbial", "mutation", "microbial", "evolution", "microbial", "pathogens", "biology", "evolutionary", "biology", "microbiology", "bacterial", "evolution", "evolutionary", "processes", "bacterial", "pathogens", "host-pathogen", "interaction", "pathogenesis" ]	2012	Evolution of Salmonella enterica Virulence via Point Mutations in the Fimbrial Adhesin
We report the identification of a novel polyomavirus present in respiratory secretions from human patients with symptoms of acute respiratory tract infection . The virus was initially detected in a nasopharyngeal aspirate from a 3-year-old child from Australia diagnosed with pneumonia . A random library was generated f...	We have identified a novel virus , referred to as WU virus , in the family Polyomaviridae by screening of human respiratory secretions . Two human polyomaviruses , BK and JC , were identified in 1971 and infect the majority of humans around the world . These two viruses are closely related to each other and are both ar...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "viruses", "homo", "(human)", "infectious", "diseases", "virology" ]	2007	Identification of a Novel Polyomavirus from Patients with Acute Respiratory Tract Infections
Recently , genetic association findings for nicotine dependence , smoking behavior , and smoking-related diseases converged to implicate the chromosome 15q25 . 1 region , which includes the CHRNA5-CHRNA3-CHRNB4 cholinergic nicotinic receptor subunit genes . In particular , association with the nonsynonymous CHRNA5 SNP ...	Nicotine binds to cholinergic nicotinic receptors , which are composed of a variety of subunits . Genetic studies for smoking behavior and smoking-related diseases have implicated a genomic region that encodes the alpha5 , alpha3 , and beta4 subunits . We examined genetic data across this region for over 38 , 000 smoke...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "genetics", "and", "genomics/genetics", "of", "disease", "genetics", "and", "genomics/complex", "traits" ]	2010	Multiple Independent Loci at Chromosome 15q25.1 Affect Smoking Quantity: a Meta-Analysis and Comparison with Lung Cancer and COPD
Galileo described the concept of motion relativity—motion with respect to a reference frame—in 1632 . He noted that a person below deck would be unable to discern whether the boat was moving . Embryologists , while recognizing that embryonic tissues undergo large-scale deformations , have failed to account for relative...	Swirling dance-like patterns of cellular motion accompany the formation of a vital embryonic structure in birds and mammals called the primitive streak , which is located where the future vertebral column will form . The primitive streak is considered the “organizing center” of the embryo , because during early embryon...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology", "developmental", "biology" ]	2008	The ECM Moves during Primitive Streak Formation—Computation of ECM Versus Cellular Motion
A polygenic model of inheritance , whereby hundreds or thousands of weakly associated variants contribute to a trait’s heritability , has been proposed to underlie the genetic architecture of complex traits . However , relatively few genetic variants have been positively identified so far and they collectively explain ...	It is widely accepted that genetics influences a broad range of human traits and diseases , yet only a few genetic variants are known to determine these traits and their impact is modest . In this report , we made the hypothesis that combining information from a large number of genetic variants would help better explai...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Contribution of Large Region Joint Associations to Complex Traits Genetics
Recent evidence demonstrates a role for paternal aging on offspring disease susceptibility . It is well established that various neuropsychiatric disorders ( schizophrenia , autism , etc . ) , trinucleotide expansion associated diseases ( myotonic dystrophy , Huntington's , etc . ) and even some forms of cancer have in...	There is a striking trend of delayed parenthood in developed countries due to secular and socioeconomic pressures . As a result , physicians commonly consult with concerned patients inquiring about the impact of advanced age on their ability to conceive healthy offspring . The concern has more frequently surrounded the...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "urology", "medicine", "and", "health", "sciences", "genetics", "epigenetics", "biology", "and", "life", "sciences", "infertility" ]	2014	Age-Associated Sperm DNA Methylation Alterations: Possible Implications in Offspring Disease Susceptibility
The function of AarF domain-containing kinase 1 ( ADCK1 ) has not been thoroughly revealed . Here we identified that ADCK1 utilizes YME1-like 1 ATPase ( YME1L1 ) to control optic atrophy 1 ( OPA1 ) and inner membrane mitochondrial protein ( IMMT ) in regulating mitochondrial dynamics and cristae structure . We firstly ...	Mitochondria function as energy producing factories in the cell , and thus the malfunctioning of mitochondria becomes the causes of many diseases . Especially in muscles that continuously require a vast amount of energy , dysfunction of mitochondria leads to abnormalities in muscles . Mitochondria maintain their homeos...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "fluorescence", "imaging", "invertebrates", "cell", "death", "medicine", "and", "health", "sciences", "rna", "interference", "hela", "cells", "biological", "cultures", "cell", "processes", "animals", "animal", "models", "drosophila", "melanogaster", "model", "organisms"...	2019	Drosophila ADCK1 is critical for maintaining mitochondrial structures and functions in the muscle
Protein phosphorylation is a common post-translational modification in eukaryotic cells and has a wide range of functional effects . Here , we used mass spectrometry to search for phosphorylated residues in all the proteins of influenza A and B viruses – to the best of our knowledge , the first time such a comprehensiv...	Eukaryotic cells regulate the function of many of their proteins through the reversible phosphorylation of serine , threonine or tyrosine residues . It is known that some influenza virus proteins are phosphorylated , but few sites of phosphorylation have been identified . We used mass spectrometry to identify 39 sites ...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "sequence", "analysis", "biochemistry", "virology", "peptide", "mapping", "biology", "microbiology", "viral", "replication", "viral", "structure", "host-pathogen", "interaction", "proteomics" ]	2012	Mapping the Phosphoproteome of Influenza A and B Viruses by Mass Spectrometry
A major goal of evolutionary biology is to unravel the molecular genetic mechanisms that underlie functional diversification and adaptation . We investigated how changes in gene regulation and coding sequence contribute to sensory diversification in two replicate radiations of cichlid fishes . In the clear waters of La...	The molecular mechanisms that generate biodiversity remain largely elusive . We examined how two of these mechanisms , changes in gene expression and changes in gene coding sequence , have generated an incredibly diverse set of visual systems in rapidly speciating African cichlids . We found large differences in cone o...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology/evolutionary", "ecology", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics", "molecular", "biology/molecular", "evolution", "evolutionary", "biology", "ecology/physiological", "ecology" ]	2009	The Eyes Have It: Regulatory and Structural Changes Both Underlie Cichlid Visual Pigment Diversity
Aspergillus fumigatus is the most important airborne fungal pathogen causing life-threatening infections in immunocompromised patients . Macrophages and neutrophils are known to kill conidia , whereas hyphae are killed mainly by neutrophils . Since hyphae are too large to be engulfed , neutrophils possess an array of e...	The fungus Aspergillus fumigatus grows on decaying organic matter and produces large numbers of spores , called conidia , which are constantly inhaled by humans . This is harmless , because we have a functioning defence system of immune cells called neutrophil granulocytes , but people with too few or non-functioning n...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/cellular", "microbiology", "and", "pathogenesis", "microbiology/immunity", "to", "infections", "immunology/immunity", "to", "infections", "immunology/innate", "immunity", "microbiology/cellular", "microbiology", "and", "pathogenesis" ]	2010	Production of Extracellular Traps against Aspergillus fumigatus In Vitro and in Infected Lung Tissue Is Dependent on Invading Neutrophils and Influenced by Hydrophobin RodA
Buruli ulcer ( BU ) is described as a relatively painless condition; however clinical observations reveal that patients do experience pain during their treatment . Knowledge on current pain assessment and treatment in BU is necessary to develop and implement a future guideline on pain management in BU . A mixed methods...	Buruli ulcer ( BU ) is considered relatively painless . Nevertheless , observations suggested that patients experience pain during wound care dressings . This study explored views on pain , along with pain assessment and treatment practices . Medical records were reviewed on prescribed pain medication and health care p...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Assessment and Treatment of Pain during Treatment of Buruli Ulcer
Microbes can be metabolically engineered to produce biofuels and biochemicals , but rerouting metabolic flux toward products is a major hurdle without a systems-level understanding of how cellular flux is controlled . To understand flux rerouting , we investigated a panel of Saccharomyces cerevisiae strains with progre...	An important strategy for sustainable energy is microbial production of biofuels from non-food plant material . However , many microbes , including yeast , cannot use the xylose comprising ~30% of hemicellulosic sugars , especially under anaerobic conditions . Although cells can be engineered with required enzymes , th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "chemical", "compounds", "metabolic", "processes", "carbohydrates", "organic", "compounds", "glucose", "plasmid", "construction", "fermentation", "xylose", "fungi", "hypoxia", "dna", "construction", "molecular", "biology", "techniques", "alcohols", "resea...	2019	Rewired cellular signaling coordinates sugar and hypoxic responses for anaerobic xylose fermentation in yeast
RNA-directed DNA methylation ( RdDM ) and histone H3 lysine 9 dimethylation ( H3K9me2 ) are related transcriptional silencing mechanisms that target transposable elements ( TEs ) and repeats to maintain genome stability in plants . RdDM is mediated by small and long noncoding RNAs produced by the plant-specific RNA pol...	DNA topoisomerase is an enzyme that releases the torsional stress in DNA generated during DNA replication or transcription . Here , we uncovered an unexpected role of DNA topoisomerase 1α ( TOP1α ) in the maintenance of genome stability . Eukaryotic genomes are usually littered with transposable elements ( TEs ) and re...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences" ]	2014	DNA Topoisomerase 1α Promotes Transcriptional Silencing of Transposable Elements through DNA Methylation and Histone Lysine 9 Dimethylation in Arabidopsis
Woolly mammoths ( Mammuthus primigenius ) populated Siberia , Beringia , and North America during the Pleistocene and early Holocene . Recent breakthroughs in ancient DNA sequencing have allowed for complete genome sequencing for two specimens of woolly mammoths ( Palkopoulou et al . 2015 ) . One mammoth specimen is fr...	We observe an excess of detrimental mutations , consistent with genomic meltdown in woolly mammoths on Wrangel Island just prior to extinction . We observe an excess of deletions , an increase in the proportion of deletions affecting gene sequences , and an excess of premature stop codons in response to evolution under...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "heterozygosity", "deletion", "mutation", "genome", "evolution", "population", "genetics", "vertebrates", "animals", "mammals", "mutation", "effective", "population", "size", "mammalian", "genomics", "population", "biology", "molecular", "evolution", "comparative", "genomic...	2017	Excess of genomic defects in a woolly mammoth on Wrangel island
Lymphocytic choriomeningitis virus ( LCMV ) causes a systemic infection in mice with virus replication occurring in both peripheral tissues and secondary lymphoid organs . Because of the rapid systemic dissemination of the virus , the secondary lymphoid organs responsible for the induction of the LCMV-specific CD8 T ce...	CD8 T cells are required for the elimination of infected host cells following an acute virus infection . In addition , memory CD8 T cells provide immunity to the host against a secondary infection . Much is known about the priming of CD8 T cells towards viruses that induce a localized infection , however the site respo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immune", "cells", "t", "cells", "immunology", "biology", "immune", "response" ]	2012	The Initial Draining Lymph Node Primes the Bulk of the CD8 T Cell Response and Influences Memory T Cell Trafficking after a Systemic Viral Infection
Actin and nuclear myosin 1c ( NM1 ) cooperate in RNA polymerase I ( pol I ) transcription . NM1 is also part of a multiprotein assembly , B-WICH , which is involved in transcription . This assembly contains the chromatin remodeling complex WICH with its subunits WSTF and SNF2h . We report here that NM1 binds SNF2h with...	Actin and myosin are key regulators of several processes that occur in the cell nucleus . In rRNA biogenesis , actin in complex with nuclear myosin 1c ( NM1 ) is involved in several phases of rDNA transcription . Further , NM1 interacts with the chromatin remodelling complex WICH , with the subunits WSTF and SNF2h . Th...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry", "gene", "expression", "biology", "molecular", "cell", "biology", "molecular", "biology", "dna", "transcription", "histone", "modification" ]	2013	Nuclear Myosin 1c Facilitates the Chromatin Modifications Required to Activate rRNA Gene Transcription and Cell Cycle Progression
Infection with Zika virus ( ZIKV ) is associated with human congenital fetal anomalies . To model fetal outcomes in nonhuman primates , we administered Asian-lineage ZIKV subcutaneously to four pregnant rhesus macaques . While non-pregnant animals in a previous study contemporary with the current report clear viremia w...	Maternal ZIKV infection in pregnancy is associated with severe fetal anomalies , including microcephaly . It has been shown that infection manifests differently in pregnancy than in the non-pregnant state , with prolonged maternal viremia . ZIKV is spread by mosquitos and through sexual contact and since its first dete...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "diagnostic", "radiology", "pathology", "and", "laboratory", "medicine", "maternal", "health", "obstetrics", "and", "gynecology", "pathogens", "microbiology", "vertebrates", "animals", "mammals", "magnetic", "re...	2017	Highly efficient maternal-fetal Zika virus transmission in pregnant rhesus macaques
PAX5 , one of nine members of the mammalian paired box ( PAX ) family of transcription factors , plays an important role in B cell development . Approximately one-third of individuals with pre-B acute lymphoblastic leukemia ( ALL ) acquire heterozygous inactivating mutations of PAX5 in malignant cells , and heterozygou...	Mutations inactivating PAX5 disrupt B cell differentiation and occur frequently in ALL . Others have previously shown that restoring PAX5 expression normalizes B cell differentiation and leads to disease remission in a mouse model of ALL . We found that exogenous expression of PAX5’s intact and closely related gene fam...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "flow", "cytometry", "leukemias", "medicine", "and", "health", "sciences", "immune", "cells", "gene", "regulation", "regulatory", "proteins", "immunology", "cancers", "and", "neoplasms", "dna-binding", "proteins", "paired", "box", "cell", "differenti...	2018	Activating PAX gene family paralogs to complement PAX5 leukemia driver mutations
It is poorly understood how progressive brain swelling in experimental cerebral malaria ( ECM ) evolves in space and over time , and whether mechanisms of inflammation or microvascular sequestration/obstruction dominate the underlying pathophysiology . We therefore monitored in the Plasmodium berghei ANKA-C57BL/6 murin...	Brain swelling is difficult to detect ex vivo and has recently been identified as a strong predictor of death not only in experimental cerebral malaria ( ECM ) , but also in human cerebral malaria . As whole-brain in-vivo imaging methods have been widely underutilized in this disease model , little is known about the s...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "diagnostic", "radiology", "pathology", "and", "laboratory", "medicine", "immunology", "tropical", "diseases", "brain", "parasitic", "diseases", "microglial", "cells", "magnetic", "resonance", "imaging", "signs", "and", "symptoms...	2016	Experimental Cerebral Malaria Spreads along the Rostral Migratory Stream
Genital granulomas induced by Schistosoma haematobium eggs can manifest as different lesion types visible by colposcopy; rubbery papules ( RP ) , homogenous sandy patches ( HSP ) and grainy sandy patches ( GSP ) . Pronounced tissue eosinophilia is a candidate marker for active S . haematobium pathology , as viable schi...	The blood-dwelling fluke Schistosoma haematobium produce eggs which can inflict lesions both in the urinary and genital tract . Lesions in the female genital tract have been hypothesised to confer higher risk of contraction of HIV and other genital infections . These epithelial genital lesions are visibly different and...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "public", "and", "occupational", "health", "helminth", "infections", "infectious", "diseases", "schistosomiasis", "medicine", "and", "health", "sciences", "global", "health", "neglected", "tropical", "diseases", "tropical", "diseases", "parasitic", "diseases" ]	2014	Eosinophil Granule Proteins ECP and EPX as Markers for a Potential Early-Stage Inflammatory Lesion in Female Genital Schistosomiasis (FGS)
Immunity to one of the four dengue virus ( DV ) serotypes can increase disease severity in humans upon subsequent infection with another DV serotype . Serotype cross-reactive antibodies facilitate DV infection of myeloid cells in vitro by promoting virus entry via Fcγ receptors ( FcγR ) , a process known as antibody-de...	Dengue is the most common vector-borne viral disease of humans , with over 3 billion people at risk for infection and 50–100 million infections in tropical and subtropical regions each year . Dengue virus ( DV ) causes a spectrum of clinical disease ranging from an acute debilitating , self-limited febrile illness ( DF...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/viral", "infections", "immunology/immunity", "to", "infections", "virology/new", "therapies,", "including", "antivirals", "and", "immunotherapy", "virology/animal", "models", "of", "infection" ]	2010	Lethal Antibody Enhancement of Dengue Disease in Mice Is Prevented by Fc Modification
Chloride homeostasis is a critical determinant of the strength and robustness of inhibition mediated by GABAA receptors ( GABAARs ) . The impact of changes in steady state Cl− gradient is relatively straightforward to understand , but how dynamic interplay between Cl− influx , diffusion , extrusion and interaction with...	Fast synaptic inhibition relies on chloride current to hyperpolarize the neuron or to prevent depolarization caused by concurrent excitatory input . Both scenarios necessarily involve chloride flux into the cell and , thus , a change in intracellular chloride concentration . The vast majority of models neglect changes ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neurobiology", "of", "disease", "and", "regeneration", "neuroscience", "homeostatic", "mechanisms", "ion", "channels", "computational", "neuroscience", "neurotransmitters", "biophysics", "simulations", "theoretical", "biology", "biophysics", "theory", "biology", "biophysics"...	2011	Efficacy of Synaptic Inhibition Depends on Multiple, Dynamically Interacting Mechanisms Implicated in Chloride Homeostasis
In somatic cells , recombination between the homologous chromosomes followed by equational segregation leads to loss of heterozygosity events ( LOH ) , allowing the expression of recessive alleles and the production of novel allele combinations that are potentially beneficial upon Darwinian selection . However , inter-...	The genetic diversity of eukaryotes relies on the diversification of the parental information , mostly occurring by recombination during gamete formation . Homologous chromosomes also recombine in somatic cells , though much less frequently . Here , we sequenced the genome of S . cerevisiae hybrid diploid cells that en...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "meiosis", "cell", "cycle", "and", "cell", "division", "variant", "genotypes", "cell", "processes", "chromatids", "genetic", "mapping", "dna", "homologous", "recombination", "chromosome", "biology", "biochemistry", "cell", "biology", "nucleic", "acids", "heredity", "g...	2016	Extensive Recombination of a Yeast Diploid Hybrid through Meiotic Reversion
Bacteria that live in the environment have evolved pathways specialized to defend against eukaryotic organisms or other bacteria . In this manuscript , we systematically examined the role of the five type VI secretion systems ( T6SSs ) of Burkholderia thailandensis ( B . thai ) in eukaryotic and bacterial cell interact...	Many bacteria encounter both eukaryotic cells and other bacterial species as a part of their lifestyles . In order to compete and survive , these bacteria have evolved specialized pathways that target these distinct cell types . Type VI secretion systems ( T6SSs ) are bacterial protein export machines postulated to pun...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/environmental", "microbiology", "microbiology/microbial", "growth", "and", "development", "microbiology/microbial", "evolution", "and", "genomics", "microbiology/cellular", "microbiology", "and", "pathogenesis" ]	2010	Burkholderia Type VI Secretion Systems Have Distinct Roles in Eukaryotic and Bacterial Cell Interactions
The Gram-negative human pathogen N . gonorrhoeae ( Ngo ) quickly attaches to epithelial cells , and large numbers of the bacteria remain on the cell surface for prolonged periods . Ngo invades cells but few viable intracellular bacteria are recovered until later stages of infection , leading to the assumption that Ngo ...	Neisseria gonorrhoeae ( Ngo ) , which causes the sexually transmitted disease of gonorrhea , primarily infects the uorgenital epithelium . It attaches to the epithelial surface for lengthy periods . It also invades epithelial cells , but few viable intracellular bacteria are recovered until later stages of infection . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "death", "autophagic", "cell", "death", "medicine", "and", "health", "sciences", "lysosomes", "pathology", "and", "laboratory", "medicine", "intracellular", "pathogens", "molecular", "probe", "techniques", "gene", "regulation", "pathogens", "cell", "processes", ...	2019	Neisseria gonorrhoeae evades autophagic killing by downregulating CD46-cyt1 and remodeling lysosomes
Endemic areas for soil-transmitted helminthiases often lack the tools and trained personnel necessary for point-of-care diagnosis . This study pilots the use of smartphone microscopy and an artificial neural network-based ( ANN ) object detection application named Kankanet to address those two needs . A smartphone was ...	For rainforest-enshrouded rural villages of Madagascar , soil-transmitted helminthiases are more the rule than the exception . However , the microscopy equipment and lab technicians needed for diagnosis are a distance of several days’ hike away . We piloted a solution for these communities by leveraging resources the v...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "engineering", "and", "technology", "helminths", "tropical", "diseases", "hookworms", "geographical", "locations", "parasitic", "diseases", "animals", "cell", "phones", "neuroscience", "artificial", "neural", "netw...	2019	Kankanet: An artificial neural network-based object detection smartphone application and mobile microscope as a point-of-care diagnostic aid for soil-transmitted helminthiases
The nonhuman primate ( NHP ) -related injuries in rabies-enzootic countries is a public health problem of increasing importance . The aims of this work are to collect data concerning rabies transmission from NHPs to humans; to collate medical practices regarding rabies postexposure prophylaxis ( PEP ) in different coun...	No international consensus or even a consensus among existing national recommendations about rabies postexposure prophylaxis ( PEP ) following a nonhuman primate ( NHP ) -related injury currently exists . Epidemiologic studies and reports collated in this review indicate that the number of rabies case reported in NHPs ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "rabies", "veterinary", "diseases", "zoonoses", "medicine", "and", "health", "sciences", "epidemiology", "neglected", "tropical", "diseases", "biology", "and", "life", "sciences", "tropical", "diseases", "veterinary", "science" ]	2014	Rabies in Nonhuman Primates and Potential for Transmission to Humans: A Literature Review and Examination of Selected French National Data
Despite extensive work on the mechanisms that generate plasma membrane furrows , understanding how cells are able to dynamically regulate furrow dimensions is an unresolved question . Here , we present an in-depth characterization of furrow behaviors and their regulation in vivo during early Drosophila morphogenesis . ...	One of the primary events that must occur repeatedly throughout a complex animal’s lifetime is the ingression of a plasma membrane furrow . Furrow formation and ingression are requisite elements of cell division , and drive the physical separation of one cell into two cells . However , the mechanisms that permit an emb...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "metaphase", "cell", "cycle", "and", "cell", "division", "cell", "processes", "animals", "invertebrate", "genomics", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "experimental", "organism", "systems",...	2018	Differentially-dimensioned furrow formation by zygotic gene expression and the MBT
Two major human diseases caused by filariid nematodes are onchocerciasis , or river blindness , and lymphatic filariasis , which can lead to elephantiasis . The drugs ivermectin , diethylcarbamazine ( DEC ) , and albendazole are used in control programs for these diseases , but are mainly effective against the microfil...	Onchocerciasis or river blindness , and lymphatic filariasis , which can lead to disfiguring elephantiasis , are two neglected tropical diseases that affect millions of people , primarily in developing countries . Both diseases are caused by filariid nematodes; onchocerciasis is caused by Onchocerca volvulus and lympha...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Repurposing Auranofin as a Lead Candidate for Treatment of Lymphatic Filariasis and Onchocerciasis
The flexibility in the structure of calmodulin ( CaM ) allows its binding to over 300 target proteins in the cell . To investigate the structure-function relationship of CaM , we combined methods of computer simulation and experiments based on circular dichroism ( CD ) to investigate the structural characteristics of C...	Proteins are workhorses for driving biological functions inside cells . Calmodulin ( CaM ) is a protein that can carry cellular signals by triggered conformational changes due to calcium binding that alters target binding . Interestingly , CaM is able to bind over 300 targets . One of the challenges in characterizing C...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "macromolecular", "assemblies", "protein", "folding", "protein", "structure", "biophysics", "simulations", "physical", "chemistry", "biophysics", "theory", "chemistry", "biology", "biophysics", "physics", "biochemistry", "biophysic", "al", "simulations", "computational", "c...	2011	The Effect of Macromolecular Crowding, Ionic Strength and Calcium Binding on Calmodulin Dynamics
The competence of the tsetse fly Glossina pallidipes ( Diptera; Glossinidae ) to acquire salivary gland hypertrophy virus ( SGHV ) , to support virus replication and successfully transmit the virus depends on complex interactions between Glossina and SGHV macromolecules . Critical requisites to SGHV transmission are it...	Tsetse fly ( Diptera; Glossinidae ) transmits two devastating diseases to farmers ( human African Trypanosomiasis; HAT ) and their livestock ( Animal African Trypanosomiasis; AAT ) in 37 sub-Saharan African countries . During the rainy seasons , vast areas of fertile , arable land remain uncultivated as farmers flee th...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "biology", "veterinary", "science", "agriculture" ]	2011	The Salivary Secretome of the Tsetse Fly Glossina pallidipes (Diptera: Glossinidae) Infected by Salivary Gland Hypertrophy Virus
Communication between distant sites often defines the biological role of a protein: amino acid long-range interactions are as important in binding specificity , allosteric regulation and conformational change as residues directly contacting the substrate . The maintaining of functional and structural coupling of long-r...	Fine analyses of families of protein sequences reveal the existence of networks of coevolved amino acids . These networks are clusters of residues often entering in physical contact one with the other , and they relate residues which are located far apart on the three dimensional structure . Coevolved residues often pl...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "computational", "biology/macromolecular", "structure", "analysis", "computational", "biology/comparative", "sequence", "analysis", "computational", "biology/macromolecular", "sequence", "analysis", "evolutionary", "biology/bioinformatics", "computational", "biology" ]	2009	A Combinatorial Approach to Detect Coevolved Amino Acid Networks in Protein Families of Variable Divergence
Bacteria lose or gain genetic material and through selection , new variants become fixed in the population . Here we provide the first , genome-wide example of a single bacterial strain's evolution in different deliberately colonized patients and the surprising insight that hosts appear to personalize their microflora ...	Bacterial virulence results from the interaction between bacteria and their hosts . This interaction provides selection pressure for bacterial adaptation towards increased fitness or virulence . Basic mechanisms involved in bacterial adaptation at the genetic level are point mutations and recombination . As bacterial g...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "infectious", "diseases/urological", "infections", "infectious", "diseases", "genetics", "and", "genomics/comparative", "genomics", "genetics", "and", "genomics/functional", "genomics", "microbiology/micro...	2010	Host Imprints on Bacterial Genomes—Rapid, Divergent Evolution in Individual Patients
Human respiratory syncytial virus ( RSV ) is a major cause of severe respiratory illness in children and susceptible adults . RSV blocks the development of the innate antiviral immune response and can grow to high titers in the respiratory tract . Here we demonstrate that immunostimulatory defective viral genomes ( iDV...	Respiratory syncytial virus is a major cause of chronic lung damage , asthma exacerbations , and hospitalizations of infants , elders , and high-risk adults . Currently , there is no effective vaccine or treatment available to protect the general population from RSV infection . Here , we demonstrate that defective form...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Immunostimulatory Defective Viral Genomes from Respiratory Syncytial Virus Promote a Strong Innate Antiviral Response during Infection in Mice and Humans
Aquaglyceroporins ( AQPs ) transport water and glycerol and play important roles in drug-uptake in pathogenic trypanosomatids . For example , AQP2 in the human-infectious African trypanosome , Trypanosoma brucei gambiense , is responsible for melarsoprol and pentamidine-uptake , and melarsoprol treatment-failure has be...	Protein channels in cell membranes transport specific molecules in and out of cells , and can also facilitate drug-uptake . One such protein , known as an aquaglyceroporin ( AQP ) , allows parasitic African trypanosomes , the cause of lethal diseases in humans and livestock , to accumulate an arsenic-based drug known a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "respiratory", "infections", "molecular", "probe", "techniques", "immunology", "marker", "genes", "parasitic", "diseases", "parasitic", "protozoans", "pulmonology", "monomers", "(chemistry)", ...	2017	Aquaglyceroporin-null trypanosomes display glycerol transport defects and respiratory-inhibitor sensitivity
Generally , the second messenger bis- ( 3’-5’ ) -cyclic dimeric GMP ( c-di-GMP ) regulates the switch between motile and sessile lifestyles in bacteria . Here , we show that c-di-GMP is an essential regulator of multicellular development in the social bacterium Myxococcus xanthus . In response to starvation , M . xanth...	The nucleotide-based second messenger c-di-GMP is ubiquitous in bacteria and generally regulates the switch between motile and sessile lifestyles . We show that c-di-GMP regulates multicellular morphogenesis and cellular differentiation during the starvation-induced developmental program that culminates in fruiting bod...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "cell", "motility", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "pathogens", "microbiology", "dna", "transcription", "bacterial", "sporulation", "regulator", "genes", "gene", "types", "micr...	2016	A Minimal Threshold of c-di-GMP Is Essential for Fruiting Body Formation and Sporulation in Myxococcus xanthus
In 1995 , one of the largest outbreaks of human toxoplasmosis occurred in the Pacific Northwest region of North America . Genetic typing identified a novel Toxoplasma gondii strain linked to the outbreak , in which a wide spectrum of human disease was observed . For this globally-distributed , water-borne zoonosis , st...	Severity of toxoplasmosis , a water-borne zoonosis , varies widely from chronic and benign to acutely fatal . Here , we investigate polyparasitism ( infection with multiple parasite species ) as one factor governing the spectrum of disease in Toxoplasma gondii infections . This study utilized wild marine mammals as sen...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology", "infectious", "disease", "epidemiology", "population", "genetics", "microbiology", "marine", "biology", "model", "organisms", "population", "biology", "veterinary", "science", "veterinary", "diseases", "veterinary", "epidemiology",...	2011	Polyparasitism Is Associated with Increased Disease Severity in Toxoplasma gondii-Infected Marine Sentinel Species
When blood flows through a bifurcation , red blood cells ( RBCs ) travel into side branches at different hematocrit levels , and it is even possible that all RBCs enter into one branch only , leading to a complete separation of plasma and RBCs . To quantify this phenomenon via particle-based mesoscopic simulations , we...	Blood tests , which provide a wealth of information on the state of human health , are often performed on cell-free samples . Therefore , blood-plasma separation needs to be achieved . A simple but effective solution for isolating plasma from blood utilizes capillary bifurcations . In a particle-based simulation study ...	[ "Abstract", "Introduction", "Methods", "Results/Discussion" ]	[]	2015	Inflow/Outflow Boundary Conditions for Particle-Based Blood Flow Simulations: Application to Arterial Bifurcations and Trees
Buruli Ulcer ( BU ) is a neglected tropical disease caused by Mycobacterium ulcerans . Former BU patients may experience participation restrictions due to physical limitations , stigmatization and other social factors . A scale that measures participation restrictions among children , who represent almost half of the a...	Buruli Ulcer is a neglected tropical disease caused by infection with Mycobacterium ulcerans . While treatment has largely improved , former BU patients may experience participation restrictions after treatment , due to physical limitations , stigmatization or other social factors . With more than half of the BU patien...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "children", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "education", "sociology", "tropical", "diseases", "geographical", "locations", "social", "sciences", "pediatrics", "bacterial", "diseases", "age", "groups", "signs", "and"...	2019	The paediatric participation scale measuring participation restrictions among former Buruli Ulcer patients under the age of 15 in Ghana and Benin: Development and first validation results
The chicken ovalbumin upstream promoter-transcription factors ( COUP-TFI and II ) make up the most conserved subfamily of nuclear receptors that play key roles in angiogenesis , neuronal development , organogenesis , cell fate determination , and metabolic homeostasis . Although the biological functions of COUP-TFs hav...	Unlike other classes of receptors , nuclear receptors can bind directly to DNA and act as transcription factors , playing key roles in embryonic development and cellular metabolism . Most nuclear receptors are activated by signal-triggering molecules ( ligands ) and can regulate their activity by recruiting coactivator...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "biophysics", "molecular", "biology" ]	2008	Identification of COUP-TFII Orphan Nuclear Receptor as a Retinoic Acid–Activated Receptor
Given the highly dynamic and complex nature of the human gut microbial community , the ability to identify and predict time-dependent compositional patterns of microbes is crucial to our understanding of the structure and functions of this ecosystem . One factor that could affect such time-dependent patterns is microbi...	The ability to characterize and predict temporal trajectories of the microbial community in the human gut is crucial to our understanding of the structure and functions of this ecosystem . In this study we develop MTV-LMM , a method for modeling time-series microbial community data . Using MTV-LMM we find that in contr...	[ "Abstract", "Introduction", "Results", "Materials", "and", "methods", "Discussion" ]	[ "taxonomy", "children", "ecology", "and", "environmental", "sciences", "microbiome", "community", "structure", "statistics", "microbiology", "multivariate", "analysis", "age", "groups", "phylogenetics", "data", "management", "non-coding", "rna", "mathematics", "infants", ...	2019	Modeling the temporal dynamics of the gut microbial community in adults and infants
The WHO definition of trachomatous trichiasis ( TT ) is “at least one eyelash touching the globe , or evidence of recent epilation of in-turned eyelashes” , reflecting the fact that epilation is used as a self-management tool for TT . In Fiji’s Western Division , a high TT prevalence ( 8 . 7% in those aged ≥15 years ) ...	Trachoma , caused by infection with ocular strains of Chlamydia trachomatis , represents a major public health issue , and is targeted for global elimination as a public health problem by the year 2020 . Until recently , data on trachoma in the Pacific Island states have been sparse , with marked variability in the fin...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "skin", "medicine", "and", "health", "sciences", "pruritus", "integumentary", "system", "fijians", "tropical", "diseases", "geographical", "locations", "social", "sciences", "neuroscience", "habits", "ethnicities", "bacterial", "diseases", "eye", "diseases", "neglected", ...	2017	Eyelash Epilation in the Absence of Trichiasis: Results of a Population-Based Prevalence Survey in the Western Division of Fiji
Taenia solium taeniosis/cysticercosis was declared eradicable by the International Task Force for Disease Eradication in 1993 , but remains a neglected zoonosis . To assist in the attempt to regionally eliminate this parasite , we developed cystiSim , an agent-based model for T . solium transmission and control . The m...	Taenia solium is the leading cause of preventable epilepsy and the highest ranking foodborne parasite in terms of disease burden worldwide . Currently there are no large scale control programmes implemented against T . solium , but efficacious intervention tools are there , making control programmes the next step forwa...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "livestock", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pig", "models", "immunology", "tropical", "diseases", "vertebrates", "parasitic", "diseases", "animals", "mammals", "simulation", "and", "modeling", "an...	2016	CystiSim – An Agent-Based Model for Taenia solium Transmission and Control
Serovar identification of clinical isolates of Leptospira is generally not performed on a routine basis , yet the identity of an infecting serovar is valuable from both epidemiologic and public health standpoints . Only a small number of reference laboratories worldwide have the capability to perform the cross agglutin...	Leptospirosis is an infection caused by Leptospira bacteria , and is probably the most widespread zoonosis in the world . It is carried by a wide range of animals that contaminate the environment by shedding organisms in their urine . Humans become infected when they come into contact with contaminated urine or water i...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases" ]	2010	Application and Validation of PFGE for Serovar Identification of Leptospira Clinical Isolates
Infections of humans and livestock with African trypanosomes are treated with drugs introduced decades ago that are not always fully effective and often have severe side effects . Here , the trypanosome haptoglobin-haemoglobin receptor ( HpHbR ) has been exploited as a route of uptake for an antibody-drug conjugate ( A...	Here we show that antibody-drug conjugates ( ADCs ) can be re-purposed from cancer immunotherapeutics to anti-protozoals by changing the specificity of the immunoglobulin to target a trypanosome cell surface receptor . Trypanosomes were used as a model system due to the availability of receptor null cell lines that all...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "toxins", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "animal", "models", "of", "disease", "immunology", "microbiology", "parasitic", "diseases", "parasitic", "protozoans", "toxicology", "toxic", "agents...	2019	A single dose of antibody-drug conjugate cures a stage 1 model of African trypanosomiasis
Lens epithelium–derived growth factor ( LEDGF/p75 ) is a cellular cofactor of HIV-1 integrase ( IN ) that interacts with IN through its IN binding domain ( IBD ) and tethers the viral pre-integration complex to the host cell chromatin . Here we report the generation of a human somatic LEDGF/p75 knockout cell line that ...	Like other viruses , HIV has a limited genome and needs to exploit the machinery of the host cell to complete its replication cycle . The elucidation of virus-host interactions not only sheds light on pathogenesis but also provides opportunities in a limited number of cases to develop novel antiviral drugs . A prototyp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "drug", "research", "and", "development", "drugs", "and", "devices", "hiv", "pharmacology", "viral", "diseases" ]	2012	LEDGF/p75-Independent HIV-1 Replication Demonstrates a Role for HRP-2 and Remains Sensitive to Inhibition by LEDGINs
HIV has a high mutation rate , which contributes to its ability to evolve quickly . However , we know little about the fitness costs of individual HIV mutations in vivo , their distribution and the different factors shaping the viral fitness landscape . We calculated the mean frequency of transition mutations at 870 si...	HIV’s high mutation rate allows it to evolve quickly . However , most mutations probably reduce the virus’ ability to replicate —they are costly to the virus . Until now , the actual cost of mutations is not well understood . We used within-patient mutation frequencies to estimate the cost of 870 HIV mutations in vivo ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "microbial", "mutation", "pathology", "and", "laboratory", "medicine", "evolutionary", "biology", "enzymes", "pathogens", "microbiology", "enzymology", "retroviruses", "viruses", "immunodeficiency", "viruses", "mutation", "rna", "v...	2018	Within-patient mutation frequencies reveal fitness costs of CpG dinucleotides and drastic amino acid changes in HIV
Reverse engineering of gene regulatory networks ( GRNs ) is a central task in systems biology . Most of the existing methods for GRN inference rely on gene co-expression analysis or TF-target binding information , where the determination of co-expression is often unreliable merely based on gene expression levels , and ...	Gene expression images , with abundant spatial expression patterns , have become an important resource for identifying gene regulatory networks ( GRNs ) , while the computational methods for image-based GRN reconstruction have been very few . In spite of the difference in experimental types and conditions , we utilize ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "gene", "regulation", "animals", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "sense", "organ", "development", "organism", "development", "eye", "development", "experimental", "organism", "systems", "...	2019	Predicting gene regulatory interactions based on spatial gene expression data and deep learning
Understanding the genetic pathways that regulate how pathogenic fungi respond to their environment is paramount to developing effective mitigation strategies against disease . Carbon catabolite repression ( CCR ) is a global regulatory mechanism found in a wide range of microbial organisms that ensures the preferential...	To succeed as pathogens , fungi such as the rice blast fungus M . oryzae must adapt their metabolism to nutrient availability within the host , but little is known about the genetic regulatory mechanisms involved . M . oryzae destroys enough rice to feed 60 million people annually , and understanding how the infection ...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "genetics", "biology", "microbiology", "genetics", "and", "genomics" ]	2012	Principles of Carbon Catabolite Repression in the Rice Blast Fungus: Tps1, Nmr1-3, and a MATE–Family Pump Regulate Glucose Metabolism during Infection
Atypical hemolytic uremic syndrome ( aHUS ) is associated with defective complement regulation . Disease-associated mutations have been described in the genes encoding the complement regulators complement factor H , membrane cofactor protein , factor B , and factor I . In this study , we show in two independent cohorts...	Hemolytic uremic syndrome ( HUS ) is a severe kidney disease , which is characterized by hemolytic anemia , thrombocytopenia , and acute renal failure . The nondiarrhea-associated form , also known as atypical HUS ( aHUS ) , is rare , sometimes familial , often recurrent , and has a poor outcome . Several studies have ...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "homo", "(human)", "genetics", "and", "genomics", "immunology" ]	2007	Deletion of Complement Factor H–Related Genes CFHR1 and CFHR3 Is Associated with Atypical Hemolytic Uremic Syndrome
Coronary artery disease ( CAD ) has a significant genetic contribution that is incompletely characterized . To complement genome-wide association ( GWA ) studies , we conducted a large and systematic candidate gene study of CAD susceptibility , including analysis of many uncommon and functional variants . We examined 4...	Coronary artery disease ( CAD ) has a strong genetic basis that remains poorly characterised . Using a custom-designed array , we tested the association with CAD of almost 50 , 000 common and low frequency variants in ∼2 , 000 genes of known or suspected cardiovascular relevance . We genotyped the array in 15 , 596 CAD...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "coronary", "artery", "disease", "medicine", "public", "health", "and", "epidemiology", "cardiovascular", "disease", "epidemiology", "genetic", "association", "studies", "epidemiology", "genetics", "biology", "human", "genetics", "genetics", "of", "disease", "genetics", ...	2011	Large-Scale Gene-Centric Analysis Identifies Novel Variants for Coronary Artery Disease
Buruli ulcer may induce severe disabilities impacting on a person's well-being and quality of life . Information about long-term disabilities and participation restrictions is scanty . The objective of this study was to gain insight into participation restrictions among former Buruli ulcer patients in Ghana and Benin ....	Disabilities among Buruli ulcer patients remain a problem . Previous studies revealed contractures , deformities and functional limitations in daily life after treatment . According to the International Classification of Functioning , Disability and Health , disabilities occur not only at the physical and activity leve...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "physiotherapy", "infectious", "diseases", "medicine", "and", "health", "sciences", "health", "care" ]	2014	Persisting Social Participation Restrictions among Former Buruli Ulcer Patients in Ghana and Benin
Venezuelan equine encephalitis viruses ( VEEV ) are responsible for human diseases in the Americas , producing severe or mild illness with symptoms indistinguishable from dengue and other arboviral diseases . For this reason , many cases remain without certain diagnosis . Seroprevalence studies for VEEV subtypes IAB , ...	Venezuelan equine encephalitis viruses ( VEEV ) are responsible for human diseases in the Americas . They produce severe or mild illnesses with symptoms indistinguishable from dengue and other arboviral diseases; for this reason , many cases remain undiagnosed . We detected neutralizing antibodies ( NTAbs ) against VEE...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2013	Venezuelan Equine Encephalitis Viruses (VEEV) in Argentina: Serological Evidence of Human Infection
Autism is a highly heritable neurodevelopmental disorder , yet the genetic underpinnings of the disorder are largely unknown . Aberrant brain overgrowth is a well-replicated observation in the autism literature; but association , linkage , and expression studies have not identified genetic factors that explain this tra...	Autism is a disorder characterized by aberrant social , communication , and restricted and repetitive behaviors . It develops clinically in the first years of life . Toddlers and children with autism often exhibit early brain enlargement and excess neuron numbers in the prefrontal cortex . Adults with autism generally ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "genetics", "biology", "genomics", "neuroscience", "genetics", "and", "genomics" ]	2012	Age-Dependent Brain Gene Expression and Copy Number Anomalies in Autism Suggest Distinct Pathological Processes at Young Versus Mature Ages
In Brazil , as in many other affected countries , a large proportion of visceral leishmaniasis ( VL ) occurs in remote locations and treatment is often performed on basis of clinical suspicion . This study aimed at developing predictive models to help with the clinical management of VL in patients with suggestive clini...	Visceral leishmaniasis ( VL ) is a neglected tropical disease endemic to 65 countries , including Brazil , where the disease frequently occurs in remote locations and treatment is often performed on the basis of clinical suspicion . Predictive models based on scoring systems could be a helpful tool for the clinical man...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "public", "health" ]	2012	Predictive Models for the Diagnostic of Human Visceral Leishmaniasis in Brazil
Despite historical evidence of blinding trachoma , there have been no widespread contemporary surveys of trachoma prevalence in the northern states of Sudan . We aimed to conduct district-level surveys in this vast region in order to map the extent of the problem and estimate the need for trachoma control interventions...	Trachoma is an infectious disease which is caused by a bacterium , Chlamydia trachomatis and is the leading cause of preventable blindness , estimated to be responsible for 2 . 9% of blindness globally . The World Health Organization ( WHO ) recommends an integrated strategy for control and elimination of blinding trac...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "eye", "infections", "medicine", "disease", "mapping", "public", "health", "and", "epidemiology", "survey", "methods", "epidemiology", "ophthalmology", "trachoma" ]	2011	The Prevalence of Blinding Trachoma in Northern States of Sudan
The evolution of ever increasing complex life forms has required innovations at the molecular level in order to overcome existing barriers . For example , evolving processes for cell differentiation , such as epigenetic mechanisms , facilitated the transition to multicellularity . At the same time , studies using gene ...	Understanding the transition to multicellularity remains a key unanswered question in evolutionary biology . The transition required three essential cellular features to evolve: adhesion , signaling and differentiation . In particular , cell differentiation requires sensitivity to environmental cues to create distinct ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "systems", "biology", "evolutionary", "modeling", "regulatory", "networks", "biology", "computational", "biology", "evolutionary", "biology", "evolutionary", "theory" ]	2014	Epigenetics Decouples Mutational from Environmental Robustness. Did It Also Facilitate Multicellularity?
In the Americas , yellow fever virus transmission is a latent threat due to the proximity between urban and wild environments . Although yellow fever has nearly vanished from North and Central America , there are still 13 countries in the Americas considered endemic by the World Health Organization . Human cases usuall...	Yellow fever ( YF ) is a zoonotic disease caused by yellow fever virus ( YFV ) , which is transmitted to humans through the bite of an infected mosquito . Sylvatic and urban cycles have been present in different periods , but currently most cases result from human exposure to jungle or forested environments . The World...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "immunology", "geographical", "locations", "vertebrates", "social", "sciences", "animals", "mammals", "primates", "preventive", "medicine", "land", "use", "vaccination", "and", "immu...	2017	Geographic patterns and environmental factors associated with human yellow fever presence in the Americas
We have investigated to what extent natural transformation acting on free DNA substrates can facilitate transfer of mobile elements including transposons , integrons and/or gene cassettes between bacterial species . Naturally transformable cells of Acinetobacter baylyi were exposed to DNA from integron-carrying strains...	Genetic elements , such as transposons and integrons , frequently carry antimicrobial resistance determinants and can be found widely disseminated among pathogenic bacteria . Their distribution pattern suggests dissemination through horizontal gene transfer . The role of natural transformation in horizontal transfer of...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "bacteriology", "genetic", "mutation", "genome", "evolution", "microbiology", "mutation", "types", "emerging", "infectious", "diseases", "microbial", "evolution", "biology", "heredity", "genetics", "gene", "flow", "genomics", "bacterial", "evolution", "genetics", "and", ...	2012	Natural Transformation Facilitates Transfer of Transposons, Integrons and Gene Cassettes between Bacterial Species
Zika virus ( ZIKV ) infection during pregnancy in humans is associated with an increased incidence of congenital anomalies including microcephaly as well as fetal death and miscarriage and collectively has been referred to as Congenital Zika Syndrome ( CZS ) . Animal models for ZIKV infection in pregnancy have been dev...	Zika virus is endemic in the Americas , primarily spread through mosquitos and sexual contact . Zika virus infection during pregnancy in women is associated with a variety of fetal pathologies now referred to as Congenital Zika Syndrome ( CZS ) , with the most severe pathology being fetal microcephaly . Developing mode...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "reproductive", "system", "pathology", "and", "laboratory", "medicine", "maternal", "health", "obstetrics", "and", "gynecology", "nervous", "system", "pathogens", "microbiology", "vertebrates", "brain", "animals", "mammals", "pri...	2019	Zika virus infection at mid-gestation results in fetal cerebral cortical injury and fetal death in the olive baboon
Identifying natural allelic variation that underlies quantitative trait variation remains a fundamental problem in genetics . Most studies have employed either simple synthetic populations with restricted allelic variation or performed association mapping on a sample of naturally occurring haplotypes . Both of these ap...	Most traits of economic and evolutionary interest vary quantitatively and have multiple genes affecting their expression . Dissecting the genetic basis of such traits is crucial for the improvement of crops and management of diseases . Here , we develop a new resource to identify genes underlying such quantitative trai...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/complex", "traits", "plant", "biology/plant", "growth", "and", "development", "plant", "biology/plant", "genetics", "and", "gene", "expression" ]	2009	A Multiparent Advanced Generation Inter-Cross to Fine-Map Quantitative Traits in Arabidopsis thaliana
Familiar cancers represent a privileged point of view for studying the complex cellular events inducing tumor transformation . Von Hippel-Lindau syndrome , a familiar predisposition to develop cancer is a clear example . Here , we present our efforts to decipher the role of von Hippel-Lindau tumor suppressor protein ( ...	Cancer is generally caused by a series of mutations accumulating over time in a healthy tissue , which becomes re-programmed to proliferate at the expense of the hosting organism . This process is difficult to follow and understand as events in a multitude of different genes can lead to similar outcomes without apparen...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "phosphorylation", "renal", "cell", "carcinoma", "medicine", "and", "health", "sciences", "endocrine", "tumors", "carcinomas", "cancers", "and", "neoplasms", "genitourinary", "tract", "tumors", "oncology", "neurological", "tumors", "mutation", "substitution", "mutation", ...	2019	Genotype-phenotype relations of the von Hippel-Lindau tumor suppressor inferred from a large-scale analysis of disease mutations and interactors
STAT2 is the quintessential transcription factor for type 1 interferons ( IFNs ) , where it functions as a heterodimer with STAT1 . However , the human and murine STAT2-deficient phenotypes suggest important additional and currently unidentified type 1 IFN-independent activities . Here , we show that STAT2 constitutive...	For more than a quarter century , we have known that STAT1 and STAT2 are essential for the classic host immune defense system against viral infections known as the type 1 interferon response . While STAT1 has since been assigned multiple additional roles , STAT2 is thought to function exclusively as the principal partn...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "phosphorylation", "nuclear", "import", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "cytokines", "immunology", "cell", "processes", "parasitic", "diseases", "developmental", "biology...	2016	STAT2 Is a Pervasive Cytokine Regulator due to Its Inhibition of STAT1 in Multiple Signaling Pathways
Botulinum neurotoxins ( BoNTs ) are produced by Clostridium botulinum and cause the fatal disease botulism , a flaccid paralysis of the muscle . BoNTs are released together with several auxiliary proteins as progenitor toxin complexes ( PTCs ) to become highly potent oral poisons . Here , we report the structure of a ∼...	Food-borne botulinum neurotoxin ( BoNT ) poisoning results in fatal muscle paralysis . But how can BoNT–a large protein released by the bacteria clostridia–survive the hostile gastrointestinal ( GI ) tract to gain access to neurons that control muscle contraction ? Here , we report the complete structure of a bimodular...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Structure of a Bimodular Botulinum Neurotoxin Complex Provides Insights into Its Oral Toxicity
Individual perception of vaccine safety is an important factor in determining a person's adherence to a vaccination program and its consequences for disease control . This perception , or belief , about the safety of a given vaccine is not a static parameter but a variable subject to environmental influence . To compli...	A frequently made assumption in population models is that individuals make decisions in a standard way , which tends to be fixed and set according to the modeler's view on what is the most likely way individuals should behave . In this paper we acknowledge the importance of modeling behavioral changes ( in the form of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mathematics/statistics", "computational", "biology/ecosystem", "modeling", "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases" ]	2009	Dynamic Modeling of Vaccinating Behavior as a Function of Individual Beliefs
RNA viruses typically occur in genetically diverse populations due to their error-prone genome replication . Genetic diversity is thought to be important in allowing RNA viruses to explore sequence space , facilitating adaptation to changing environments and hosts . Some arboviruses that infect both a mosquito vector a...	The ability of arboviruses to perpetuate in nature given that they must infect two disparate hosts ( the mosquito vector and the vertebrate host ) remains a mystery . We studied how viral genetic diversity is impacted by the dual host transmission cycle . Our studies of an enzootic cycle using Venezuelan equine encepha...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viral", "evolution", "rna", "viruses", "emerging", "infectious", "diseases", "virology", "viral", "classification", "emerging", "viral", "diseases", "biology", "evolutionary", "biology", "microbiology", "evolutionary", "genetics" ]	2012	Vector-Borne Transmission Imposes a Severe Bottleneck on an RNA Virus Population
The observation , by Alter et al . , of the enrichment of NK cell “escape” variants in individuals carrying certain Killer-cell Immunoglobulin-like Receptor ( KIR ) genes is compelling evidence that natural killer ( NK ) cells exert selection pressure on HIV-1 . Alter et al hypothesise that variant peptide , in complex...	In our opinion , some of the best evidence that natural killer ( NK ) cells contribute to the control of HIV-1 infection is the identification of 22 virus variants , “KIR footprints” , that were hypothesised to escape the NK cell response ( Nature , 2011 ) . The authors ( Alter , Heckerman , Schneidewind , Fadda et al ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "engineering", "and", "technology", "pathogens", "immunology", "microbiology", "alleles", "telecommunications", "retroviruses", "viruses", "immunode...	2017	HIV-1 adaptation to NK cell-mediated immune pressure
Multiple sclerosis ( MS ) and type 1 diabetes ( T1D ) are organ-specific autoimmune disorders with significant heritability , part of which is conferred by shared alleles . For decades , the Human Leukocyte Antigen ( HLA ) complex was the only known susceptibility locus for both T1D and MS , but loci outside the HLA co...	Multiple sclerosis ( MS ) and type 1 diabetes ( T1D ) are common , organ-specific inflammatory disorders that continue to increase in global prevalence . The processes leading to both T1D and MS are genetically determined and are thought to involve an autoimmune mechanism . After decades of research into the genetic ba...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genetics", "of", "disease", "genetics", "and", "genomics/complex", "traits", "genetics", "and", "genomics/genetics", "of", "the", "immune", "system" ]	2009	IL2RA Genetic Heterogeneity in Multiple Sclerosis and Type 1 Diabetes Susceptibility and Soluble Interleukin-2 Receptor Production
Oncomelania hupensis is the unique intermediate host of Schistosoma japonicum , which causes schistosomiasis endemic in the Far East , and especially in mainland China . O . hupensis largely determines the parasite's geographical range . How O . hupensis's genetic diversity is distributed geographically in mainland Chi...	The intermediate host of Schistosoma japonicum in Asia is the snail Oncomelania hupensis , which can be separated phenotypically into ribbed- and smooth-shelled morphotypes . In China , the typical morphotype is ribbed-shelled , with its distribution restricted to mainland China . Smooth-shelled snails with varix are a...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "evolutionary", "biology/evolutionary", "ecology", "infectious", "diseases/neglected", "tropical", "diseases", "molecular", "biology/molecular", "evolution", "infectious", "diseases/helminth", "infections", "ecology/population", "ecology" ]	2010	Distinct Genetic Diversity of Oncomelania hupensis, Intermediate Host of Schistosoma japonicum in Mainland China as Revealed by ITS Sequences
The potential benefit in using IL-2 in immunotherapy for cancer and autoimmunity has been linked to the modulation of immune responses , which partly relies on a direct effect on Tregs populations . Here , we revisited the role of IL-2 in HIV infection and investigated whether its use as an adjuvant with therapeutic va...	Interleukin-2 ( IL-2 ) has been used in immunotherapy for cancer and autoimmunity and its beneficial effect has been linked to the modulation of immune responses , which partly relies on a direct effect on Tregs populations . In this study , we assessed the role of IL-2 in HIV infection and investigated whether its use...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "highly-active", "antiretroviral", "therapy", "viral", "transmission", "and", "infection", "antiviral", "therapy", "pathogens", "immunology", "mic...	2017	Negative modulation of suppressive HIV-specific regulatory T cells by IL-2 adjuvanted therapeutic vaccine
Rac1 is a small GTPase involved in actin cytoskeleton organization and polarized cell growth in many organisms . In this study , we investigate the biological function of MgRac1 , a Rac1 homolog in Magnaporthe grisea . The Mgrac1 deletion mutants are defective in conidial production . Among the few conidia generated , ...	The fungus Magnaporthe grisea ( M . grisea ) is an important pathogen in plants and has a great impact on agriculture . Its infection of rice causes one of the most destructive diseases , the rice blast disease , around the world . M . grisea starts infection by producing conidia , which generate infectious structures ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/plant-biotic", "interactions" ]	2008	Rac1 Is Required for Pathogenicity and Chm1-Dependent Conidiogenesis in Rice Fungal Pathogen Magnaporthe grisea
Multiple factors over the lifetime of an individual , including diet , geography , and physiologic state , will influence the microbial communities within the primate gut . To determine the source of variation in the composition of the microbiota within and among species , we investigated the distal gut microbial commu...	The microbial communities that inhabit the gastrointestinal tract of humans and other mammals are complex , dynamic , and critical to both health and disease . The composition and constituents of these communities are influenced by multiple factors such as host diet , geography , physiology , and disease state . Given ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology/human", "evolution", "microbiology/environmental", "microbiology", "evolutionary", "biology/microbial", "evolution", "and", "genomics" ]	2010	Evolutionary Relationships of Wild Hominids Recapitulated by Gut Microbial Communities
Mammalian chromosomes initiate DNA replication at multiple sites along their length during each S phase following a temporal replication program . The majority of genes on homologous chromosomes replicate synchronously . However , mono-allelically expressed genes such as imprinted genes , allelically excluded genes , a...	Mammalian chromosomes are duplicated every cell cycle during a precise temporal DNA replication program . Thus , every chromosome contains regions that are replicated early and other regions that are replicated late during each S phase . Most of the genes , present in two copies on homologous chromosomes , replicate sy...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "genetics", "biology", "genomics", "molecular", "cell", "biology", "genetics", "and", "genomics" ]	2013	Asynchronous Replication, Mono-Allelic Expression, and Long Range Cis-Effects of ASAR6
The Saccharomyces cerevisiae Fkh1 protein has roles in cell-cycle regulated transcription as well as a transcription-independent role in recombination donor preference during mating-type switching . The conserved FHA domain of Fkh1 regulates donor preference by juxtaposing two distant regions on chromosome III to promo...	Specific chromosomal interactions between distal regions of the genome allow for DNA transactions necessary for normal cell function , but the protein-protein interfaces that regulate such interactions remain largely unknown . The budding yeast Fkh1 protein uses its evolutionarily conserved phosphothreonine-binding FHA...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "phosphorylation", "protein", "interactions", "chemical", "compounds", "dna-binding", "proteins", "threonine", "organic", "compounds", "dna", "transcription", "immunoprecipitation", "amino", "acids", "co-immunoprecipitation", "research", "and", "analysis", "methods", "protein...	2016	Binding of the Fkh1 Forkhead Associated Domain to a Phosphopeptide within the Mph1 DNA Helicase Regulates Mating-Type Switching in Budding Yeast
Bisphenol A ( BPA ) and other endocrine disrupting chemicals have been reported to induce negative effects on a wide range of physiological processes , including reproduction . In the female , BPA exposure increases meiotic errors , resulting in the production of chromosomally abnormal eggs . Although numerous studies ...	During the past several decades , the incidence of human male reproductive abnormalities such as hypospadias , undescended testicles , testicular cancer , and low sperm counts has increased . Environmental factors—and in particular , exposure to environmental estrogens—have been implicated as contributing factors and ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Estrogenic Exposure Alters the Spermatogonial Stem Cells in the Developing Testis, Permanently Reducing Crossover Levels in the Adult
Genetic and environmental factors shape host susceptibility to infection , but how and how rapidly environmental variation might alter the susceptibility of mammalian genotypes remains unknown . Here , we investigate the impacts of seminatural environments upon the nematode susceptibility profiles of inbred C57BL/6 mic...	The environment in which an individual resides is likely to change how she or he responds to infection . However , most of our understanding about host responses to infection arises from experimental studies conducted under uniform environmental conditions in the laboratory . We wished to investigate whether findings i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "gut", "bacteria", "microbiome", "helminths", "immunology", "microbiology", "parasitic", "diseases", "animals", "nematode", "infections", "developm...	2018	Rapid environmental effects on gut nematode susceptibility in rewilded mice
Kaposi's sarcoma ( KS ) , an enigmatic endothelial cell vascular neoplasm , is characterized by the proliferation of spindle shaped endothelial cells , inflammatory cytokines ( ICs ) , growth factors ( GFs ) and angiogenic factors . KSHV is etiologically linked to KS and expresses its latent genes in KS lesion endothel...	Kaposi's sarcoma associated herpes virus ( KSHV ) , with a 160 kb DNA genome , has evolved with two distinct life cycle phases , namely latency and lytic replication . KS , a complex angioproliferative disease , is regulated by a balance between pro-angiogenic and anti-angiogenic factors . In our previous study , we sh...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "virology/effects", "of", "virus", "infection", "on", "host", "gene", "expression", "virology" ]	2010	Kaposi's Sarcoma Associated Herpes Virus (KSHV) Induced COX-2: A Key Factor in Latency, Inflammation, Angiogenesis, Cell Survival and Invasion
Retrotransposon sequences are positioned throughout the genome of almost every eukaryote that has been sequenced . As mobilization of these elements can have detrimental effects on the transcriptional regulation and stability of an organism's genome , most organisms have evolved mechanisms to repress their movement . H...	Condensins are conserved complexes that are well known for their roles in promoting the efficient condensation of chromosomes during early mitosis . Previously , we have shown that the Drosophila Condensin II subunit , dCAP-D3 , also functions to regulate transcription in somatic cells during the later stages of develo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Condensin II Subunit dCAP-D3 Restricts Retrotransposon Mobilization in Drosophila Somatic Cells
Little is known about how the mode of respiratory virus transmission determines the dynamics of primary infection and protection from reinfection . Using non-invasive imaging of murine parainfluenza virus 1 ( Sendai virus ) in living mice , we determined the frequency , timing , dynamics , and virulence of primary infe...	Parainfluenza viruses are highly contagious , a leading cause of acute respiratory infection ( ARI ) in children , often reoccurring , and currently controlled by non-pharmaceutical interventions . We tracked infection and reinfection of a prototypic murine parainfluenza virus after contact or airborne transmission . O...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2013	Mode of Parainfluenza Virus Transmission Determines the Dynamics of Primary Infection and Protection from Reinfection
In the vertebrate nervous system , myelination of axons for rapid impulse propagation requires the synthesis of large amounts of lipids and proteins by oligodendrocytes and Schwann cells . Myelin membranes are thought to be cell-autonomously assembled by these axon-associated glial cells . Here , we report the surprisi...	The myelin membrane is a highly specialized plasma membrane that enwraps axons , acts as an insulator , and is thus important for fast conduction of action potentials . It is thereby critical for proper functioning of the nervous system . Myelin in the central nervous system is synthesized by oligodendrocytes . Because...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "nervous", "system", "astrocytes", "brain", "diet", "neuroscience", "macroglial", "cells", "nutrition", "nerve", "fibers", "physical", "chemistry", "surface", "chemistry", "lipids", "animal", "cells", "axons", "chemistry", "cor...	2017	Oligodendroglial myelination requires astrocyte-derived lipids
DNA interstrand crosslinks ( ICLs ) are among the most toxic types of damage to a cell . For this reason , many ICL-inducing agents are effective therapeutic agents . For example , cisplatin and nitrogen mustards are used for treating cancer and psoralen plus UVA ( PUVA ) is useful for treating psoriasis . However , re...	Crosslinks , linking the complementary stands of the DNA double helix , can lead to cell death , because they are so effective at interfering with normal genomic transactions such as DNA replication . This property of crosslinking agents has long been utilized in cancer therapy . The purpose of our research is to under...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/cellular", "death", "and", "stress", "responses", "cell", "biology/cell", "signaling", "genetics", "and", "genomics/nuclear", "structure", "and", "function", "biochemistry/replication", "and", "repair", "genetics", "and", "genomics/gene", "function", "gen...	2008	Human MLH1 Protein Participates in Genomic Damage Checkpoint Signaling in Response to DNA Interstrand Crosslinks, while MSH2 Functions in DNA Repair
Chronic hepatitis B virus ( HBV ) infection is associated with functionally impaired virus-specific T cell responses . Although the myeloid-derived suppressor cells ( MDSCs ) are known to play a critical role in impairing antiviral T cell responses , viral factors responsible for the expansion of MDSCs in chronic hepat...	HBeAg is not a structural component of HBV and is not essential for viral DNA replication , however , HBeAg positivity is associated with high levels of viremia in patients . HBeAg may represent a viral strategy to establish persistent infection , but the mechanism remains largely ambiguous . Growing evidence suggests ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "flow", "cytometry", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "immune", "suppression", "mic...	2019	Hepatitis B e antigen induces the expansion of monocytic myeloid-derived suppressor cells to dampen T-cell function in chronic hepatitis B virus infection

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