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Intestinal parasitoses are a major concern for public health , especially in children from middle and low-income populations of tropical and subtropical areas . We examined the presence and co-infection of parasites in humans as well as parasitic environmental contamination in Puerto Iguazú , Argentina . We explored th...	Enteroparasites are among the main issues in public health arena , especially in children of vulnerable communities from developing countries . We performed a combined analysis of the factors that describe parasite prevalence in children and their environment . Our result evidenced a combined effect of socio-demographi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "children", "medicine", "and", "health", "sciences", "vertebrates", "parasitic", "diseases", "animals", "mammals", "parasitology", "dogs", "age", "groups", "families", "public", "and", "occupational", "health", "infectious", "diseases", "parasitic", "intestinal", "disea...	2017	Environmental and socio-demographic individual, family and neighborhood factors associated with children intestinal parasitoses at Iguazú, in the subtropical northern border of Argentina
The control of Mycobacterium tuberculosis ( Mtb ) infection is heavily dependent on the adaptive Th1 cellular immune response . Paradoxically , optimal priming of the Th1 response requires activation of priming dendritic cells with Th1 cytokine IFN-γ . At present , the innate cellular mechanisms required for the genera...	Mycobacterium tuberculosis ( Mtb ) infects about one-third of the world's population . Most people who are exposed remain healthy , but control of this intracellular bacterium requires a robust cellular immune response . Production of the pro-inflammatory cytokine IFN-γ from cells in the adaptive immune response is cri...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "immunology", "homo", "(human)", "eubacteria" ]	2008	Human Innate Mycobacterium tuberculosis–Reactive αβTCR+ Thymocytes
To establish correlates of human immunity to the live plague vaccine ( LPV ) , we analyzed parameters of cellular and antibody response to the plasminogen activator Pla of Y . pestis . This outer membrane protease is an essential virulence factor that is steadily expressed by Y . pestis . PBMCs and sera were obtained f...	Yersinia pestis , the causative agent of plague , has been recognized as one of the most devastating pathogen experienced by mankind . It remains endemic in many parts of the world , and is considered emerging pathogen . A live attenuated Y . pestis strain EV line NIIEG has been used for decades in the former Soviet Un...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "plagues", "enzyme-linked", "immunoassays", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "vaccines", "preventive", "medicine", "bacterial", "diseases", "drug", "de...	2018	Humoral and cellular immune responses to Yersinia pestis Pla antigen in humans immunized with live plague vaccine
Recent studies have established that the highly condensed and transcriptionally silent heterochromatic domains in budding yeast are virtually dynamic structures . The underlying mechanisms for heterochromatin dynamics , however , remain obscure . In this study , we show that histones are dynamically acetylated on H4K12...	The genetic material in eukaryotes is packaged into chromatin . The chromatin structure is orchestrated such that euchromatic regions are relatively uncondensed and accessible to factors that bind DNA , whereas heterochromatic regions are densely packaged into higher-order conformations . The compact nature for heteroc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/histone", "modification", "molecular", "biology/chromatin", "structure" ]	2011	Histone H4 Lysine 12 Acetylation Regulates Telomeric Heterochromatin Plasticity in Saccharomyces cerevisiae
Animal and human trypanosomiasis are constraints to both animal and human health in Sub-Saharan Africa , but there is little recent evidence as to how these parasites circulate in wild hosts in natural ecosystems . The Luangwa Valley in Zambia supports high densities of tsetse flies ( Glossina species ) and is recognis...	Animal and human trypanosomiasis are constraints to both animal and human health in Sub-Saharan Africa , but there is little recent evidence as to how these parasites circulate in natural hosts in natural ecosystems . A cross-sectional survey of trypanosome prevalence in 418 wildlife hosts was conducted in the Luangwa ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "biology", "veterinary", "science" ]	2011	Characterisation of the Wildlife Reservoir Community for Human and Animal Trypanosomiasis in the Luangwa Valley, Zambia
Viral entry into the host cell is the first step towards successful infection . Viral entry starts with virion attachment , and binding to receptors . Receptor binding viruses either directly release their genome into the cell , or enter cells through endocytosis . For DNA viruses and a few RNA viruses , the endocytose...	White Spot Syndrome Virus ( WSSV ) is one of the most virulent pathogens in shrimp farming . Several viral candidate receptors , or attachment factors were reported in previous studies , however , most of them are not authentic transmembrane proteins . In particular , the protein receptor ( s ) required the intracellul...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "shrimp", "invertebrates", "medicine", "and", "health", "sciences", "immune", "cells", "rna", "interference", "immune", "physiology", "293t", "cells", "immunology", "cell", "processes", "biological", "cultures", "animals", "crustaceans", "epigenetics",...	2019	The polymeric immunoglobulin receptor-like protein from Marsupenaeus japonicus is a receptor for white spot syndrome virus infection
Plant leaves are arranged around the stem in a beautiful geometry that is called phyllotaxis . In the majority of plants , phyllotaxis exhibits a distichous , Fibonacci spiral , decussate , or tricussate pattern . To explain the regularity and limited variety of phyllotactic patterns , many theoretical models have been...	Phyllotaxis , the beautiful geometry of plant-leaf arrangement around the stem , has long attracted the attention of researchers of biological-pattern formation . Many mathematical models , as typified by those of Douady and Couder ( alternate-specific form , DC1; more generalized form , DC2 ) , have been proposed for ...	[ "Abstract", "Introduction", "Material,", "methods,", "and", "models", "Results", "Discussion" ]	[ "plant", "anatomy", "buds", "computerized", "simulations", "mathematical", "models", "hormones", "plant", "science", "plant", "hormones", "microscopy", "plants", "flowering", "plants", "research", "and", "analysis", "methods", "computer", "and", "information", "sciences...	2019	Mathematical model studies of the comprehensive generation of major and minor phyllotactic patterns in plants with a predominant focus on orixate phyllotaxis
Axon injury can lead to several cell survival responses including increased stability and axon regeneration . Using an accessible Drosophila model system , we investigated the regulation of injury responses and their relationship . Axon injury stabilizes the rest of the cell , including the entire dendrite arbor . Afte...	Unlike many other cell types , most neurons last a lifetime . When injured , these cells often activate survival and repair strategies rather than dying . One such response is regeneration of the axon after it is injured . Axon regeneration is a conserved process activated by the same signaling cascade in worms , flies...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "rna", "interference", "microtubules", "microtubule", "dynamics", "cell", "processes", "neuroscience", "animals", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "nerve", "fibers", "mitochondria", "epigenetics", "bioenergetics", "mic...	2016	Mitochondria and Caspases Tune Nmnat-Mediated Stabilization to Promote Axon Regeneration
SCYX-7158 , an oxaborole , is currently in Phase I clinical trials for the treatment of human African trypanosomiasis . Here we investigate possible modes of action against Trypanosoma brucei using orthogonal chemo-proteomic and genomic approaches . SILAC-based proteomic studies using an oxaborole analogue immobilised ...	The mode of action of a new class of boron-containing chemicals ( the oxaboroles ) , currently under development for the treatment of human African trypanosomiasis , is unknown . Here we identify a number of potential candidate proteins that could be involved either in the mode of action of these compounds or in the me...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[]	2015	Genomic and Proteomic Studies on the Mode of Action of Oxaboroles against the African Trypanosome
Biological networks entail important topological features and patterns critical to understanding interactions within complicated biological systems . Despite a great progress in understanding their structure , much more can be done to improve our inference and network analysis . Spectral methods play a key role in many...	Networks are a representation of choice for many problems in biology and medicine including protein interactions , metabolic pathways , evolutionary biology , cancer subtyping and disease modeling to name a few . The key to much of network analysis lies in the spectrum decomposition represented by eigenvectors of the n...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "protein", "interaction", "networks", "mathematics", "algebra", "network", "analysis", "protein", "structure", "computer", "and", "information", "sciences", "proteins", "algebraic", "structures", "proteomics", "protein", "structure", "networks", "molecular", "biology", "p...	2017	Vicus: Exploiting local structures to improve network-based analysis of biological data
When growing populations of bacteria are confronted with bactericidal antibiotics , the vast majority of cells are killed , but subpopulations of genetically susceptible but phenotypically resistant bacteria survive . In accord with the prevailing view , these “persisters” are non- or slowly dividing cells randomly gen...	Because of its importance to therapy , a great deal of effort has been devoted to understanding the mechanisms responsible for and the genetic basis of persistence in inherently susceptible but phenotypically antibiotic-resistant subpopulations of bacteria . Much of this research is based on the premise that persisters...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "microbial", "evolution", "biology", "microbiology", "evolutionary", "biology", "population", "biology", "infectious", "disease", "control", "infectious", "disease", "modeling" ]	2013	Pharmacodynamics, Population Dynamics, and the Evolution of Persistence in Staphylococcus aureus
Culture is the gold standard for the detection of environmental B . pseudomallei . In general , soil specimens are cultured in enrichment broth for 2 days , and then the culture broth is streaked on an agar plate and incubated further for 7 days . However , identifying B . pseudomallei on the agar plates among other so...	Burkholderia pseudomallei is an environmental Gram-negative bacillus and the causative agent of melioidosis . Culture and PCR assays are standard diagnostic tools used to detect B . pseudomallei in the environment . However , those tests require experienced microbiologists and are regularly conducted only in a few rese...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "lao", "people", "burkholderia", "pseudomallei", "pathology", "and", "laboratory", "medicine", "melioidosis", "pathogens", "microbiology", "ethnicities", "bacterial", "diseases", "cereal", "crops", "fungi", "rice", "experimental", ...	2016	Utility of a Lateral Flow Immunoassay (LFI) to Detect Burkholderia pseudomallei in Soil Samples
At the core of amyloid fibrils is the cross-β spine , a long tape of β-sheets formed by the constituent proteins . Recent high-resolution x-ray studies show that the unit of this filamentous structure is a β-sheet bilayer with side chains within the bilayer forming a tightly interdigitating “steric zipper” interface . ...	Accumulation of amyloid fibrils is a salient feature of various protein misfolding diseases . Recent advances in precision experiments have begun to reveal their atomistic structures . Quantitative elucidation of how the observed structures are selected over other possible filament patterns would provide much insight i...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neurological", "disorders/alzheimer", "disease", "neurological", "disorders/prion", "diseases", "computational", "biology/molecular", "dynamics", "biophysics/protein", "folding" ]	2009	Thermodynamic Selection of Steric Zipper Patterns in the Amyloid Cross-β Spine
The emergence of replicases that can replicate themselves is a central issue in the origin of life . Recent experiments suggest that such replicases can be realized if an RNA polymerase ribozyme is divided into fragments short enough to be replicable by the ribozyme and if these fragments self-assemble into a functiona...	How evolution got started is a crucial question in the origin of life . One possibility is that RNA molecules gained the ability to catalyze self-replication . Researchers recently proposed how this possibility might have been realized: a long RNA catalyst was divided into short replicable fragments , and these fragmen...	[ "Abstract", "Introduction", "Model", "Results", "Discussions" ]	[ "nucleic", "acid", "synthesis", "enzymes", "cell", "cycle", "and", "cell", "division", "cell", "processes", "enzymology", "dna-binding", "proteins", "ribozymes", "systems", "science", "mathematics", "polymerases", "rna", "amplification", "rna", "synthesis", "chemical", ...	2019	Horizontal transfer between loose compartments stabilizes replication of fragmented ribozymes
Transmission of Yersinia pestis by flea bite can occur by two mechanisms . After taking a blood meal from a bacteremic mammal , fleas have the potential to transmit the very next time they feed . This early-phase transmission resembles mechanical transmission in some respects , but the mechanism is unknown . Thereafter...	The ecology of plague is complex and its epidemiology is enigmatic . Many different flea species are able to transmit Yersinia pestis , the plague bacillus , and they can transmit in two different ways . Early-phase transmission can occur during the first week after a flea has fed on a diseased animal . Thereafter , tr...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "death", "rates", "united", "states", "invertebrates", "medicine", "and", "health", "sciences", "plagues", "body", "fluids", "pathology", "and", "laboratory", "medicine", "demography", "pathogens", "geographical", "locations", "microbiology", "vector-borne", "diseases", ...	2017	Comparative Ability of Oropsylla montana and Xenopsylla cheopis Fleas to Transmit Yersinia pestis by Two Different Mechanisms
Obstacles to bacterial survival and replication in the cytosol of host cells , and the mechanisms used by bacterial pathogens to adapt to this niche are not well understood . Listeria monocytogenes is a well-studied Gram-positive foodborne pathogen that has evolved to invade and replicate within the host cell cytosol; ...	Infection with intracellular pathogens causes a majority of the global infectious disease associated mortality . A number of intracellular pathogens must directly access the host cytosol in order to cause disease; however , non-cytosol adapted bacteria do not survive or replicate upon access to the cytosol . The mechan...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "phosphorylation", "cell", "walls", "cell", "physiology", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "cell", "metabolism", "monomers", "(chemistry...	2016	The Listeria monocytogenes PASTA Kinase PrkA and Its Substrate YvcK Are Required for Cell Wall Homeostasis, Metabolism, and Virulence
Visceral leishmaniasis is a lethal parasitic disease transmitted by phlebotomine sand flies . The largest focus of VL in Ethiopia is located in the lowland region bordering Sudan , where the epidemiology is complicated by the presence of thousands of seasonal agricultural workers who live under precarious conditions . ...	Visceral leishmaniasis is a lethal parasitic disease transmitted by sand flies . The largest focus of VL in Ethiopia is located in the lowland region bordering Sudan , where hundreds of thousands of agricultural workers migrate for work every year during the planting and harvest seasons . We conducted two parallel stud...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2013	Risk Factors for Visceral Leishmaniasis among Residents and Migrants in Kafta-Humera, Ethiopia
Planar cell polarity ( PCP ) is the mechanism by which cells orient themselves in the plane of an epithelium or during directed cell migration , and is regulated by a highly conserved signalling pathway . Mutations in the PCP gene Vangl2 , as well as in other key components of the pathway , cause a spectrum of cardiac ...	Congenital heart defects are common , affecting almost 1% of all live births . Many of these affect the outflow region , where the aorta and pulmonary trunk connect with the main ventricular chambers . Congenital heart defects arise from disruption of normal developmental processes and can be modelled in mice . Thus , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biology", "and", "life", "sciences", "developmental", "biology" ]	2014	Vangl2-Regulated Polarisation of Second Heart Field-Derived Cells Is Required for Outflow Tract Lengthening during Cardiac Development
To ensure genomic integrity , the genome must be duplicated exactly once per cell cycle . Disruption of replication licensing mechanisms may lead to re-replication and genomic instability . Cdt1 , also known as Double-parked ( Dup ) in Drosophila , is a key regulator of the assembly of the pre-replicative complex ( pre...	Catastrophic consequences may occur if the cell fails to either completely copy the genome or if it duplicates some regions of the genome more than once in a cell cycle . The cell must coordinate thousands of DNA replication start sites ( origins ) to ensure that the entire genome is copied and that no replication orig...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/epigenetics", "molecular", "biology/chromosome", "structure", "molecular", "biology/dna", "replication", "genetics", "and", "genomics/chromosome", "biology" ]	2010	Preferential Re-Replication of Drosophila Heterochromatin in the Absence of Geminin
Understanding the genetic basis of reproductive isolation promises insight into speciation and the origins of biological diversity . While progress has been made in identifying genes underlying barriers to reproduction that function after fertilization ( post-zygotic isolation ) , we know much less about earlier acting...	Barriers to reproduction are necessary for generating new species . Little is known about the genes underlying reproductive barriers , particularly those that function prior to fertilization , but their identity is of great interest as they offer insight into the genetic mechanisms and evolutionary forces generating bi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Selection on Plant Male Function Genes Identifies Candidates for Reproductive Isolation of Yellow Monkeyflowers
Choosing the right nutrients to consume is essential to health and wellbeing across species . However , the factors that influence these decisions are poorly understood . This is particularly true for dietary proteins , which are important determinants of lifespan and reproduction . We show that in Drosophila melanogas...	What animals , including humans , choose to eat has a tremendous impact on health and wellbeing . Though intake of dietary proteins and amino acids is essential for animals , excessive consumption of these nutrients is known to have detrimental effects . Many animals , therefore , execute precise control over the intak...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "microbiome", "chemical", "compounds", "disaccharides", "appetite", "microbiology", "diet", "carbohydrates", "organic", "compounds", "physiological", "processes", "fungi", "nutrition", "eating", "bacteria", "microbial", "genomics", ...	2017	Commensal bacteria and essential amino acids control food choice behavior and reproduction
Salivary components from disease vectors help arthropods to acquire blood and have been shown to enhance pathogen transmission in different model systems . Here we show that two salivary enzymes from Lutzomyia longipalpis have a synergist effect that facilitates a more efficient blood meal intake and diffusion of other...	Blood-feeding is key to sand flies reproductive success and an important link in Leishmania spp . transmission . While the sand flies attempt to modify the bite site to enhance blood feeding success , the host’s ability to react to injury becomes compromised and could facilitate pathogen invasion . In our model , sever...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "cell", "motility", "medicine", "and", "health", "sciences", "body", "fluids", "immune", "physiology", "immune", "cells", "ears", "immunology", "sand", "flies", "parasitic", "diseases", "antibodies", "insect", "vectors", "neutrophils", "immune", "s...	2018	Immunity to LuloHya and Lundep, the salivary spreading factors from Lutzomyia longipalpis, protects against Leishmania major infection
Ribonucleotide reductase ( RNR ) provides the precursors for the generation of dNTPs , which are required for DNA synthesis and repair . Here , we investigated the function of the major RNR subunits Rnr1 and Rnr3 in telomere elongation in budding yeast . We show that Rnr1 is essential for the sustained elongation of sh...	Telomeres protect the ends of eukaryotic chromosomes and as such determine the replicative capacity of a cell . In budding yeast and approximately 80% of human tumors the enzyme telomerase maintains telomere length by adding newly synthesized repeats to telomeres using dNTPs generated by Ribonucleotide reductase ( RNR ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "fungal", "spores", "chromosome", "structure", "and", "function", "molecular", "probe", "techniques", "cell", "cycle", "and", "cell", "division", "cell", "processes", "dna", "damage", "telomeres", "fungi", "model", "organisms", "experimental", "organism", "systems", ...	2017	Rnr1, but not Rnr3, facilitates the sustained telomerase-dependent elongation of telomeres
Olfactory sensory neurons connect to the antennal lobe of the fly to create the primary units for processing odor cues , the glomeruli . Unique amongst antennal-lobe neurons is an identified wide-field serotonergic neuron , the contralaterally-projecting , serotonin-immunoreactive deutocerebral neuron ( CSDn ) . The CS...	Serotonin , a major neuromodulatory transmitter , regulates diverse behaviours . Serotonergic dysfunction is implicated in various neuropsychological disorders , such as anxiety and depression , as well as in neurodegenerative disorders . In the central nervous systems , across taxa , serotonergic neurons are often sma...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "developmental", "neuroscience", "cellular", "neuroscience", "behavioral", "neuroscience", "neuronal", "morphology", "genetics", "biology", "neuroscience", "neural", "circuit", "formation" ]	2013	Sensory Neuron-Derived Eph Regulates Glomerular Arbors and Modulatory Function of a Central Serotonergic Neuron
Transcriptional regulation in human cells is a complex process involving a multitude of regulatory elements encoded by the genome . Recent studies have shown that distinct chromatin signatures mark a variety of functional genomic elements and that subtle variations of these signatures mark elements with different funct...	Recent studies have observed that histone tails can be modified in a variety of ways . Analyzing a collection of 21 histone modifications , we attempted to determine what common signatures are associated with different classes of regulatory elements and whether they mark places of distinct function . Indeed , at promot...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/functional", "genomics", "genetics", "and", "genomics/gene", "expression", "computational", "biology/alternative", "splicing", "computational", "biology/genomics", "genetics", "and", "genomics/epigenetics", "genetics", "and", "genomics/bioinformatics"...	2009	Discovery and Annotation of Functional Chromatin Signatures in the Human Genome
There is still no safe and effective vaccine against dengue virus infection . Epidemics of dengue virus infection are increasingly a threat to human health around the world . Antibodies generated in response to dengue infection have been shown to impact disease development and effectiveness of dengue vaccine . In this ...	Dengue virus ( DENV ) is a leading cause of human illness in the tropics and subtropics , with about 40% of the world’s population living in areas at risk for infection . There are four DENV serotypes . Patients who have previously been infected by one dengue serotype may develop more severe symptoms such as bleeding a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "dengue", "virus", "medicine", "and", "health", "sciences", "immune", "physiology", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "vertebrates", "cloning", "animals", "mammals", "viruses", "primat...	2019	Potent neutralizing antibodies elicited by dengue vaccine in rhesus macaque target diverse epitopes
Terpenoid synthases construct the carbon skeletons of tens of thousands of natural products . To predict functions and specificity of triterpenoid synthases , a mechanism-based , multi-intermediate docking approach is proposed . In addition to enzyme function prediction , other potential applications of the current app...	The rapid growth in the number of protein sequences presents challenges for enzyme function assignment . Computational methods , such as bioinformatics , homology modeling and docking , are becoming increasingly important for predicting of enzyme functions from protein sequences . Terpenoids are one of largest classes ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry", "simulation", "and", "modeling", "biology", "and", "life", "sciences", "enzymology", "enzyme", "chemistry", "research", "and", "analysis", "methods" ]	2014	Predicting the Functions and Specificity of Triterpenoid Synthases: A Mechanism-Based Multi-intermediate Docking Approach
Kaposi sarcoma-associated herpesvirus ( KSHV ) has been linked to Kaposi sarcoma and B-cell malignancies . Mechanisms of KSHV-induced oncogenesis remain elusive , however , in part due to lack of reliable in vivo models . Recently , we showed that transgenic mice expressing the KSHV latent genes , including all viral m...	Kaposi’s sarcoma-associated herpesvirus ( KSHV ) is associated with Kaposi sarcoma as well as the B-cell malignancies primary effusion lymphoma ( PEL ) and multicentric Castleman’s disease ( MCD ) . Only a few KSHV genes , including all micro RNAs , are expressed in latent infection of B cells . We already showed that ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	KSHV Latency Locus Cooperates with Myc to Drive Lymphoma in Mice
Echinostome metacercariae are the infective stage for humans and animals . The identification of echinostomes has been based until recently on morphology but molecular techniques using sequences of ribosomal RNA and mitochondrial DNA have indicated major clades within the group . In this study we have used the ITS2 reg...	Infections by food-borne trematodes are estimated to infect over 40 million people worldwide , although infections by echinostomes make up only a portion of these cases , usually in regions where their prevalence is high . In South East Asia and in the far east of Asia , human infection is associated with cultural and ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "gene", "identification", "and", "analysis", "genetics", "biology", "and", "life", "sciences", "molecular", "genetics", "zoology", "parasitology" ]	2014	Molecular Analysis of Echinostome Metacercariae from Their Second Intermediate Host Found in a Localised Geographic Region Reveals Genetic Heterogeneity and Possible Cryptic Speciation
Recent experimental and clinical studies have provided diverse insight into the mechanisms of human focal seizure initiation and propagation . Often these findings exist at different scales of observation , and are not reconciled into a common understanding . Here we develop a new , multiscale mathematical model of cor...	According to the WHO fact sheet , epilepsy is a neurological disorder affecting about 50 million people worldwide . Even today 30% of epilepsy patients do not respond well to drug therapies . Neocortical focal epilepsy is a particular type of epilepsy in which drug treatments fail and surgical success rate is low . Hen...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "epilepsy", "medicine", "and", "health", "sciences", "computational", "neuroscience", "neurology", "biology", "and", "life", "sciences", "computational", "biology" ]	2014	Dynamic Mechanisms of Neocortical Focal Seizure Onset
Proteins containing DUF59 domains have roles in iron-sulfur ( FeS ) cluster assembly and are widespread throughout Eukarya , Bacteria , and Archaea . However , the function ( s ) of this domain is unknown . Staphylococcus aureus SufT is composed solely of a DUF59 domain . We noted that sufT is often co-localized with s...	Iron-sulfur ( FeS ) clusters are inorganic cofactors that are used for diverse cellular processes including cellular respiration , DNA replication and repair , antibiotic resistance , and dinitrogen fixation . A failure to properly assemble FeS clusters in proteins results in widespread metabolic disorders , metabolic ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biofilms", "antimicrobials", "sequencing", "techniques", "medicine", "and", "health", "sciences", "neurochemistry", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "pathogens", "drugs", "microbiology", "operons", "carbohydrates", "neuroscience", "sta...	2016	The DUF59 Containing Protein SufT Is Involved in the Maturation of Iron-Sulfur (FeS) Proteins during Conditions of High FeS Cofactor Demand in Staphylococcus aureus
In recent years , there has been growing awareness of the significant burden of Chagas disease in the United States ( US ) . However , epidemiological data on both prevalence and access to care for this disease are limited . The objective of this study is to provide an updated national estimate of Chagas disease preval...	Chagas disease is a parasitic infection that primarily affects poor populations in Latin America . However , awareness of this disease in the United States has increased in recent years . In this study , we utilize data from the American Community Survey and the World Health Organization to estimate the number of cases...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "united", "states", "medicine", "and", "health", "sciences", "body", "fluids", "hispanic", "people", "tropical", "diseases", "geographical", "locations", "parasitic", "diseases", "parasitic", "protozoans", "ethnicities", "north", "america", "protozoans", "neglected", "t...	2016	Estimating the Burden of Chagas Disease in the United States
Type I interferon ( IFN-I ) plays a critical role in the homeostasis of hematopoietic stem cells and influences neutrophil influx to the site of inflammation . IFN-I receptor knockout ( Ifnar1−/− ) mice develop significant defects in the infiltration of Ly6Chi monocytes in the lung after influenza infection ( A/PR/8/34...	Type I interferon ( IFN-I ) was originally reported as a molecule that interferes with influenza virus replication . Various IFN-I inducible antiviral proteins contribute to dampening virus replication and dissemination . Thus , loss of IFN-I signaling attenuates antiviral response and aggravates disease . Recent studi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "respiratory", "medicine/respiratory", "infections", "microbiology/immunity", "to", "infections", "microbiology/innate", "immunity", "immunology/innate", "immunity", "infectious", "diseases/viral", "infections", "virology/host", "antiviral", "responses" ]	2011	Type I Interferon Signaling Regulates Ly6Chi Monocytes and Neutrophils during Acute Viral Pneumonia in Mice
Eosinophil responses typify both allergic and parasitic helminth disease . In helminthic disease , the role of eosinophils can be both protective in immune responses and destructive in pathological responses . To investigate whether eosinophils are involved in both protection and pathology during filarial nematode infe...	Eosinophil recruitment is a classic characteristic of both allergic and parasitic helminth diseases . Elucidation of the role of eosinophils in these diseases is of pivotal importance for understanding the mechanisms of protection and the development of pathology . In the last few years , the part played by eosinophils...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunopathology", "immunity", "innate", "immunity", "immunity", "to", "infections", "immune", "defense", "immunology", "biology" ]	2014	Eosinophils Are Important for Protection, Immunoregulation and Pathology during Infection with Nematode Microfilariae
How did evolution generate the extraordinary diversity of vertebrates on land ? Zero species are known prior to ~380 million years ago , and more than 30 , 000 are present today . An expansionist model suggests this was achieved by large and unbounded increases , leading to substantially greater diversity in the presen...	Vertebrates invaded the land more than 360 million years ago . Since then , they diversified to more than 30 , 000 tetrapod species today , including birds , mammals , squamates , and amphibians . The fossil record provides our best window onto diversification across such long spans of time , but is unevenly sampled . ...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "biogeography", "geologic", "time", "ecology", "and", "environmental", "sciences", "population", "genetics", "paleoecology", "biodiversity", "fossil", "record", "geology", "speciation", "paleontology", "population", "biology", "ecological", "metrics", "geography", "paleogeo...	2016	Near-Stasis in the Long-Term Diversification of Mesozoic Tetrapods
Adjunctive vitamin D treatment for pulmonary tuberculosis enhances resolution of inflammation but has modest effects on bacterial clearance . Sodium 4-phenylbutyrate ( PBA ) is in clinical use for a range of conditions and has been shown to synergise with vitamin D metabolites to upregulate cathelicidin antimicrobial p...	Tuberculosis ( TB ) is the world’s leading bacterial cause of death . Effective treatment currently requires a minimum of 4 drugs taken for at least 6 months . While these drugs kill the TB causing bacteria ( Mtb ) , they do not directly resolve the inmmunopathology associated with morbidity . Immunomodulatory agents t...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Phenylbutyrate Is Bacteriostatic against Mycobacterium tuberculosis and Regulates the Macrophage Response to Infection, Synergistically with 25-Hydroxy-Vitamin D₃
How can we explain the uneven decline of syphilis around the world following the introduction of penicillin ? In this paper we use antenatal syphilis prevalence ( ASP ) to investigate how syphilis prevalence varied worldwide in the past century , and what risk factors correlate with this variance . 1 ) A systematic rev...	Syphilis rates have varied tremendously between different populations around the world . We conducted a systematic review of syphilis prevalence in pregnant women in 13 populations with available data for the last 100 years . Our findings were that in most populations syphilis prevalence dropped to under 1% before 1960...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "antimicrobials", "urology", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "maternal", "health", "obstetrics", "and", "gynecology", "pathogens", "drugs", "tropical", "diseases", "geographical", "loc...	2016	The Global Epidemiology of Syphilis in the Past Century – A Systematic Review Based on Antenatal Syphilis Prevalence
Nuclear factor κB ( NF-κB ) is a transcription factor important for regulating innate and adaptive immunity , cellular proliferation , apoptosis , and senescence . Dysregulation of NF-κB and its upstream regulator IκB kinase ( IKK ) contributes to the pathogenesis of multiple inflammatory and degenerative diseases as w...	Aberrant up-regulation of the transcription factor nuclear factor κB ( NF-κB ) and the IκB kinase ( IKK ) that regulates NF-κB is associated with a variety of inflammatory and degenerative diseases in humans , including aging . Thus , development of effective and specific drugs able to decrease IKK/NF-κB activity has s...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biotechnology", "group-specific", "staining", "innate", "immune", "system", "medicine", "and", "health", "sciences", "luciferase", "immune", "physiology", "cytokines", "chemical", "compounds", "pathology", "and", "laboratory", "medicine", "protein", "interactions", "elec...	2018	Development of novel NEMO-binding domain mimetics for inhibiting IKK/NF-κB activation
Johne's disease ( JD ) , a persistent and slow progressing infection of ruminants such as cows and sheep , is caused by slow replicating bacilli Mycobacterium avium subspecies paratuberculosis ( MAP ) infecting macrophages in the gut . Infected animals initially mount a cell-mediated CD4 T cell response against MAP whi...	Mycobacterium avium subsp . paratuberculosis ( MAP ) is the causative agent of Johne's disease , a chronic enteric disease of ruminants such as sheep and cows . Due to early culling and reduction in milk production of affected animals , MAP inflicts high economic cost to diary farms . MAP infection has a long incubatio...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "immune", "cells", "antigen-presenting", "cells", "immunology", "host-pathogen", "interaction", "microbiology", "mathematics", "population", "modeling", "bacterial", "pathogens", "theoretical", "biology", "t", "cells", "infectious", "disease", "modeling", "biology", "pathog...	2014	Competition for Antigen between Th1 and Th2 Responses Determines the Timing of the Immune Response Switch during Mycobaterium avium Subspecies paratuberulosis Infection in Ruminants
To develop new approaches to control HIV-1 replication , we examined the capacity of recently described small molecular modulators of RNA splicing for their effects on viral RNA metabolism . Of the drugs tested , digoxin was found to induce a dramatic inhibition of HIV-1 structural protein synthesis , a response due , ...	Antiretroviral therapies ( ART ) for HIV/AIDS are successful in slowing disease progression by inhibiting viral proteins . However , the ability of HIV to adapt to ARTs has given rise to drug-resistant virus strains that now represent ≥16% of newly infected people . This development calls for the generation of new trea...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "microbiology", "molecular", "cell", "biology" ]	2013	Digoxin Suppresses HIV-1 Replication by Altering Viral RNA Processing
Antagonistic interactions are likely important driving forces of the evolutionary process underlying bacterial genome complexity and diversity . We hypothesized that the ability of evolved bacteria to escape specific components of host innate immunity , such as phagocytosis and killing by macrophages ( MΦ ) , is a crit...	The selective pressure imposed by the host immune system is an important component of microbial adaptation from commensalism to pathogenicity . We used experimental evolution to study the initial steps of the adaptation of Escherichia coli to cells of the innate immune system , i . e . , macrophages . Our results demon...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	The Genetic Basis of Escherichia coli Pathoadaptation to Macrophages
Loop-mediated isothermal amplification ( LAMP ) is at the forefront of the search for innovative diagnostics for human African trypanosomiasis ( HAT ) . Several simple endpoint detection methods have been developed for LAMP and here we compare four of these: ( i ) visualization of turbidity; ( ii ) addition of hydroxyn...	Human African trypanosomiasis ( HAT ) is a disease of the rural poor in sub-Saharan Africa where diagnostic laboratories are scarce and often ill equipped . Specific LAMP ( loop-mediated isothermal amplification ) tests for HAT have been developed and represent a significant step forward in the search for simple , sens...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "evidence-based", "healthcare/methods", "for", "diagnostic", "and", "therapeutic", "studies", "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases" ]	2010	LAMP for Human African Trypanosomiasis: A Comparative Study of Detection Formats
Genes involved in the same function tend to have similar evolutionary histories , in that their rates of evolution covary over time . This coevolutionary signature , termed Evolutionary Rate Covariation ( ERC ) , is calculated using only gene sequences from a set of closely related species and has demonstrated potentia...	Molecular evolution has informed our understanding of gene function; however , classical methods have largely been static in their implementation , focusing on single genes . Here , we present and prove the utility of a dynamic , network-based understanding of molecular evolution to infer relationships between genes as...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Evolutionary Signatures amongst Disease Genes Permit Novel Methods for Gene Prioritization and Construction of Informative Gene-Based Networks
Ghana started its national programme to eliminate lymphatic filariasis ( LF ) in 2000 , with mass drug administration ( MDA ) with ivermectin and albendazole as main strategy . We review the progress towards elimination that was made by 2016 for all endemic districts of Ghana and analyze microfilaria ( mf ) prevalence ...	Lymphatic filariasis ( LF ) control in Ghana has relied on ivermectin and albendazole since the year 2000 when the Ghana Filariasis Elimination Programme started . We analyzed trends in microfilaraemia prevalence during MDA , reported coverage , and transmission assessment survey using data obtained from the Ghana Heal...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "cancer", "detection", "and", "diagnosis", "invertebrates", "medicine", "and", "health", "sciences", "lymphatic", "mapping", "education", "sociology", "geographical", "locations", "tropical", "diseases", "social", "sciences", "parasitic", "diseases", "animals", "parasitol...	2019	Progress towards lymphatic filariasis elimination in Ghana from 2000-2016: Analysis of microfilaria prevalence data from 430 communities
The partitioning and subsequent inheritance of cellular factors like proteins and RNAs is a ubiquitous feature of cell division . However , direct quantitative measures of how such nongenetic inheritance affects subsequent changes in gene expression have been lacking . We tracked families of the yeast Saccharomyces cer...	When cells divide , not only DNA but an entire pattern of gene expression can be passed from mother to daughter cell . Once cell division is complete , random processes cause this pattern to change , with closely related cells growing less similar over time . We measured inheritance of a dynamic gene-expression state i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mathematics", "yeast", "and", "fungi", "biophysics", "genetics", "and", "genomics" ]	2007	Heritable Stochastic Switching Revealed by Single-Cell Genealogy
Harnessing genetic differences between cancerous and noncancerous cells offers a strategy for the development of new therapies . Extrapolating from yeast genetic interaction data , we used cultured human cells and siRNA to construct and evaluate a synthetic lethal interaction network comprised of chromosome instability...	Anticancer therapeutic discovery is a major challenge in cancer research . Because cancer is a disease caused by somatic genetic mutations , the search for anticancer therapeutics is often driven by the ability to exploit genetic differences specific to tumor cells . Recently , cancer therapeutic development has sought...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "dna", "metabolism", "cancer", "genetics", "genetic", "networks", "drugs", "and", "devices", "enzymes", "microbiology", "chemical", "biology", "genome", "analysis", "tools", "genome", "databases", "model", "organisms", "dna", "replication", "nuclease", "dn...	2013	An Evolutionarily Conserved Synthetic Lethal Interaction Network Identifies FEN1 as a Broad-Spectrum Target for Anticancer Therapeutic Development
Effective transfer of genetic information during cell division requires a major reorganization of chromosome structure . This process is triggered by condensin , a conserved pentameric ATPase essential for chromosome condensation . How condensin harnesses the energy of ATP hydrolysis to promote chromatin reorganization...	In eukaryotes , the deletion of a single copy of most genes shows little or no detectable phenotype under standard proliferative conditions . This implies that a large reduction in the level of a gene product can be tolerated by eukaryotic organisms and that a “reserve capacity” is built in the protein machinery that d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "condensation", "chromosome", "structure", "and", "function", "molecular", "probe", "techniques", "enzymes", "condensed", "matter", "physics", "enzymology", "phosphatases", "sequence", "motif", "analysis", "molecular", "biology", "techniques", "epigenetics", "chromatin", ...	2018	Condensin ATPase motifs contribute differentially to the maintenance of chromosome morphology and genome stability
Skin-penetrating parasitic nematodes infect approximately one billion people worldwide and are responsible for some of the most common neglected tropical diseases . The infective larvae of skin-penetrating nematodes are thought to search for hosts using sensory cues , yet their host-seeking behavior is poorly understoo...	Parasitic worms are a significant public health problem . Skin-penetrating worms such as hookworms and the human threadworm Strongyloides stercoralis dwell in the soil before infecting their host . However , how they locate and identify appropriate hosts is not understood . Here we investigated the host-seeking behavio...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "ecology", "biology", "and", "life", "sciences", "sensory", "perception", "neuroscience", "parasitology", "behavioral", "ecology" ]	2014	Diverse Host-Seeking Behaviors of Skin-Penetrating Nematodes
Oak galls are spectacular extended phenotypes of gallwasp genes in host oak tissues and have evolved complex morphologies that serve , in part , to exclude parasitoid natural enemies . Parasitoids and their insect herbivore hosts have coevolved to produce diverse communities comprising about a third of all animal speci...	Herbivorous insects , such as the wasps that induce trees to make galls , and the parasitoids that attack ( and ultimately kill ) the wasps comprise about a third of all animal species , but it remains unclear what determines the structure of these complex coevolving communities . Here , we analyzed 48 parasitoid commu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "ecology/evolutionary", "ecology", "ecology/behavioral", "ecology", "evolutionary", "biology/evolutionary", "ecology", "ecology", "evolutionary", "biology/animal", "behavior", "ecology/community", "ecology", "and", "biodiversity", "evolutionary", "biology" ]	2009	Host Niches and Defensive Extended Phenotypes Structure Parasitoid Wasp Communities
Enteric fever , a systemic infection caused by the bacteria Salmonella Typhi and Salmonella Paratyphi A , is endemic in Kathmandu , Nepal . Previous work identified proximity to poor quality water sources as a community-level risk for infection . Here , we sought to examine individual-level risk factors related to hygi...	Enteric fever , caused by ingestion of bacteria Salmonella Typhi or Salmonella Paratyphi A , is common in regions with poor water quality and sanitation . We sought to identify individual-level risks for infection in Kathmandu , Nepal , a region endemic for enteric fever . In this study , we enrolled patients presentin...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "bacterial", "diseases", "infectious", "diseases", "infectious", "disease", "epidemiology", "epidemiology", "infectious", "disease", "control", "gastrointestinal", "infections", "salmonella" ]	2013	Differential Epidemiology of Salmonella Typhi and Paratyphi A in Kathmandu, Nepal: A Matched Case Control Investigation in a Highly Endemic Enteric Fever Setting
The epithelial-mesenchymal transition ( EMT ) is an embryonic transdifferentiation process consisting of conversion of polarized epithelial cells to motile mesenchymal ones . EMT–inducing transcription factors are aberrantly expressed in multiple tumor types and are known to favor the metastatic dissemination process ....	The epithelial-mesenchymal transition ( EMT ) is essential to germ layer formation and cell migration in the early vertebrate embryo . EMT is aberrantly reactivated under pathological conditions , including fibrotic disease and cancer progression . In the latter process , EMT is known to promote invasion and metastatic...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biology" ]	2012	EMT Inducers Catalyze Malignant Transformation of Mammary Epithelial Cells and Drive Tumorigenesis towards Claudin-Low Tumors in Transgenic Mice
Immunization programs have often been impeded by vaccine scares , as evidenced by the measles-mumps-rubella ( MMR ) autism vaccine scare in Britain . A “free rider” effect may be partly responsible: vaccine-generated herd immunity can reduce disease incidence to such low levels that real or imagined vaccine risks appea...	“Herd immunity” is a phenomenon whereby an entire population—including unvaccinated individuals—can be protected from infection by vaccinating only a certain percentage of the population . This suggests that immunization programs can be victims of their own success: past vaccinations can drive disease incidence to such...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "mathematics", "theoretical", "biology", "applied", "mathematics", "biology", "population", "biology" ]	2012	Evolutionary Game Theory and Social Learning Can Determine How Vaccine Scares Unfold
Rheumatic heart disease ( RHD ) is considered a major public health problem in developing countries , although scarce data are available to substantiate this . Here we quantify mortality from RHD in Fiji during 2008–2012 in people aged 5–69 years . Using 1 , 773 , 999 records derived from multiple sources of routine cl...	Rheumatic heart disease is the result of an abnormal immune response to the bacteria Streptococcus pyogenes . The disease causes permanent scarring of the heart values , which results in heart failure , stroke and early death . It primarily affects the world’s poorest and most disadvantaged populations and despite the ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Rheumatic Heart Disease-Attributable Mortality at Ages 5–69 Years in Fiji: A Five-Year, National, Population-Based Record-Linkage Cohort Study
Identifying the ancestry of chromosomal segments of distinct ancestry has a wide range of applications from disease mapping to learning about history . Most methods require the use of unlinked markers; but , using all markers from genome-wide scanning arrays , it should in principle be possible to infer the ancestry of...	The genomes of individuals from admixed populations consist of chromosomal segments of distinct ancestry . For example , the genomes of African American individuals contain segments of both African and European ancestry , so that a specific location in the genome may inherit 0 , 1 , or 2 copies of European ancestry . I...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "genetics", "and", "genomics/genetics", "of", "disease", "mathematics/statistics", "genetics", "and", "genomics/bioinformatics", "genetics", "and", "genomics/population", "genetics" ]	2009	Sensitive Detection of Chromosomal Segments of Distinct Ancestry in Admixed Populations
We previously showed that fusion between hepatocytes lacking a crucial liver enzyme , fumarylacetoacetate hydrolase ( FAH ) , and wild-type blood cells resulted in hepatocyte reprogramming . FAH expression was restored in hybrid hepatocytes and , upon in vivo expansion , ameliorated the effects of FAH deficiency . Here...	The liver comprises many different types of cells , including hepatocytes . Hepatocytes perform numerous physiological functions , such as detoxification , metabolism , and protein synthesis . Hepatocytes have the ability to fuse with blood cells , generating hybrid hepatocytes that contain nuclei from both fusion part...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "biology/cell", "growth", "and", "division", "gastroenterology", "and", "hepatology/hepatology", "developmental", "biology/stem", "cells" ]	2009	Ploidy Reductions in Murine Fusion-Derived Hepatocytes
Trachomatous trichiasis ( TT ) , inturned eyelashes from repeated infection with Chlamydia trachomatis , is the leading infectious cause of blindness in the world . Though surgery will correct entropion caused by trachoma , uptake of TT surgery remains low . In this case-control study , we identify barriers that preven...	The burden of trachomatis trichiasis ( TT ) , a complication of trachoma , is largest in the poorest societies of our world . One part of the World Health Organization ( WHO ) strategy to eliminate blinding trachoma is surgery for patients with TT , and trachoma programs in endemic countries have worked to increase the...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "tropical", "diseases", "geographical", "locations", "social", "sciences", "neuroscience", "surgical", "and", "invasive", "medical", "procedures", "bacterial", "diseases", "tanzania", "eye", "diseases", "neglected", "tropical", "...	2017	Identifying Patient Perceived Barriers to Trichiasis Surgery in Kongwa District, Tanzania
The availability of a diagnostic test to detect subclinical leprosy cases is crucial to interrupt the transmission of M . leprae . In this study we assessed the minimum sensitivity level of such a ( hypothetical ) diagnostic test and the optimal testing strategy in order to effectively reduce the new case detection rat...	The annual number of new leprosy cases has been stable in the past decade , indicating that transmission has not been yet been interrupted . As current control seems to be insufficient to bring down the number of cases , there is a need for novel tools to interrupt transmission . A diagnostic that permitted diagnosis o...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusions" ]	[ "humoral", "immunity", "mycobacterium", "leprae", "medicine", "and", "health", "sciences", "immunology", "tropical", "diseases", "geographical", "locations", "bacterial", "diseases", "neglected", "tropical", "diseases", "infectious", "disease", "control", "bacteria", "ban...	2018	Minimum requirements and optimal testing strategies of a diagnostic test for leprosy as a tool towards zero transmission: A modeling study
To investigate the underlying mechanisms of T2D pathogenesis , we looked for diabetes susceptibility genes that increase the risk of type 2 diabetes ( T2D ) in a Han Chinese population . A two-stage genome-wide association ( GWA ) study was conducted , in which 995 patients and 894 controls were genotyped using the Ill...	Type 2 diabetes ( T2D ) is a complex disease that involves many genes and environmental factors . Genome-wide and candidate-gene association studies have thus far identified at least 19 regions containing genes that may confer a risk for T2D . However , most of these studies were conducted with patients of European des...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/complex", "traits", "genetics", "and", "genomics/genetics", "of", "disease", "genetics", "and", "genomics/population", "genetics", "diabetes", "and", "endocrinology", "genetics", "and", "genomics", "diabetes", "and", "endocrinology/type", "2",...	2010	A Genome-Wide Association Study Identifies Susceptibility Variants for Type 2 Diabetes in Han Chinese
Histone tails play an important role in nucleosome structure and dynamics . Here we investigate the effect of truncation of histone tails H3 , H4 , H2A and H2B on nucleosome structure with 100 ns all-atom molecular dynamics simulations . Tail domains of H3 and H2B show propensity of -helics formation during the intact ...	Histone tails are the most common sites of post-translational modifications . Tail modifications alter both inter and intra nucleosomal interactions to disrupt the condensed chromatin structure , thereby playing crucial role in gene access . Here we investigated histone tail functions on the stability of a single nucle...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "physics", "biophysic", "al", "simulations", "macromolecular", "assemblies", "biology", "computational", "biology", "biophysics", "simulations", "biophysics" ]	2011	Role of Histone Tails in Structural Stability of the Nucleosome
In an effort to suppress microbial outgrowth , the host sequesters essential nutrients in a process termed nutritional immunity . However , inflammatory responses to bacterial insult can restore nutritional resources . Given that nutrient availability modulates virulence factor production and biofilm formation by other...	Clinical management of upper and lower respiratory tract diseases caused by nontypeable Haemophilus influenzae ( NTHI ) is a significant socioeconomic burden . Therapies targeting the pathogenic lifestyle of NTHI remain non-existent due to a lack of understanding of host microenvironmental cues and bacterial responses ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Haemophilus Responses to Nutritional Immunity: Epigenetic and Morphological Contribution to Biofilm Architecture, Invasion, Persistence and Disease Severity
It is generally acknowledged that biological vision presents nonlinear characteristics , yet linear filtering accounts of visual processing are ubiquitous . The template-matching operation implemented by the linear-nonlinear cascade ( linear filter followed by static nonlinearity ) is the most widely adopted computatio...	Any attempt to model human vision must first ask: can it be approximated by a process that linearly matches the visual stimulus with an internal template ? We often take this approximation for granted without properly checking its validity . Even if we assume that the approximation is valid under specific conditions , ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	The Elementary Operations of Human Vision Are Not Reducible to Template-Matching
Parasitic nematodes are of medical and veterinary importance , adversely affecting human health and animal welfare . Ascaris suum is a gastrointestinal parasite of pigs; in addition to its veterinary significance it is a good model of the human parasite Ascaris lumbricoides , estimated to infect ∼1 . 4 billion people g...	Ascarid nematodes are major pathogens of humans and livestock . The major method of control is by the use of anthelmintic drugs , many of which target the nervous system . Drugs such as levamisole , pyrantel and oxantel target the nicotinic acetylcholine receptors present on muscle . Nematodes have several such recepto...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/helminth", "infections", "infectious", "diseases/neglected", "tropical", "diseases" ]	2009	The Nicotinic Acetylcholine Receptors of the Parasitic Nematode Ascaris suum: Formation of Two Distinct Drug Targets by Varying the Relative Expression Levels of Two Subunits
Recombination and mutagenesis are elevated by active transcription . The correlation between transcription and genome instability is largely explained by the topological and structural changes in DNA and the associated physical obstacles generated by the transcription machinery . However , such explanation does not dir...	Uracil in DNA , a major source of spontaneous mutations , can occur through the deamination of cytosine residues or through the direct incorporation of dUTP by DNA polymerases . Recent studies in yeast have shown that the uracil-associated mutations occur more frequently at highly transcribed regions . Because the redu...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "and", "materials" ]	[ "nucleic", "acid", "synthesis", "chemical", "compounds", "nucleobases", "nucleotides", "organic", "compounds", "dna", "transcription", "dna", "damage", "mutation", "fungi", "dna", "replication", "uracils", "pyrimidines", "dna", "dna", "synthesis", "chemical", "synthesis...	2018	Unscheduled DNA synthesis leads to elevated uracil residues at highly transcribed genomic loci in Saccharomyces cerevisiae
Murine models of urinary tract infection ( UTI ) have provided substantial data identifying uropathogenic E . coli ( UPEC ) virulence factors and assessing their expression in vivo . However , it is unclear how gene expression in these animal models compares to UPEC gene expression during UTI in humans . To address thi...	Animal models of infection have been used extensively to study how bacteria and other pathogens cause disease . These models provide valuable information and have led to the development of numerous vaccines and antimicrobial therapies . However , it is important to recognize how these animal models compare to human inf...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/bacterial", "infections", "infectious", "diseases/urological", "infections", "microbiology/cellular", "microbiology", "and", "pathogenesis" ]	2010	Escherichia coli Global Gene Expression in Urine from Women with Urinary Tract Infection
Leishmania amastigotes manipulate the activity of macrophages to favor their own success . However , very little is known about the role of innate recognition and signaling triggered by amastigotes in this host-parasite interaction . In this work we developed a new infection model in adult Drosophila to take advantage ...	Leishmaniasis is caused by Leishmania parasites and transmitted to humans by sandflies . After the establishment of infection , the intracellular parasite form , known as an amastigote , preferentially infects and replicates in macrophages , cells otherwise specialized for killing microbes . To overcome macrophage leth...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "immunology", "microbiology", "parasitic", "diseases", "protozoan", "life", "cycles", "parasitic", "protozoans", "developmental", "biology", "protozoans", "leishmania", "membrane", "receptor", ...	2016	Leishmania amazonensis Engages CD36 to Drive Parasitophorous Vacuole Maturation
Despite mounting evidence that epigenetic abnormalities play a key role in cancer biology , their contributions to the malignant phenotype remain poorly understood . Here we studied genome-wide DNA methylation in normal B-cell populations and subtypes of B-cell non-Hodgkin lymphoma: follicular lymphoma and diffuse larg...	Follicular lymphomas and diffuse large B-cell lymphomas are the most common non-Hodgkin lymphomas . Although these diseases share many mutant alleles , the underlying cause of the different phenotypes remains unclear . We show that direct comparison of DNA methylation patterning provides insights about gene deregulatio...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "oncology", "medicine" ]	2013	Aberration in DNA Methylation in B-Cell Lymphomas Has a Complex Origin and Increases with Disease Severity
Bacterial porins are water-filled β-barrel channels that allow translocation of solutes across the outer membrane . They feature a constriction zone , contributed by the plunging of extracellular loop 3 ( L3 ) into the channel lumen . Porins are generally in the open state , but undergo gating in response to external v...	Porins are the main conduits for hydrophilic nutrients and ions uptake into the periplasm of Gram-negative bacteria . Their translocation permeability is determined by the amino-acid distribution on their extracellular loop L3 . Bacterial porin channels have long been known to undergo step-wise gating , under the appli...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Understanding Voltage Gating of Providencia stuartii Porins at Atomic Level
Centromere is a specialized chromatin domain that plays a vital role in chromosome segregation . In most eukaryotes , centromere is surrounded by the epigenetically distinct heterochromatin domain . Heterochromatin has been shown to contribute to centromere function , but the precise role of heterochromatin in centrome...	Centromere is a specialized chromosomal domain that is essential for faithful chromosome segregation during mitosis and meiosis . In most eukaryotes , centromeres are surrounded by the densely packed heterochromatin . The exact role of heterochromatin in centromere assembly remains elusive . Centromeres in most eukaryo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "chromosome", "structure", "and", "function", "centromeres", "fungi", "model", "organisms", "immunoprecipitation", "fungal", "evolution", "experimental", "organism", "systems", "epigenetics", "chromatin", "schizosaccharomyces", "research", "and", "analysis", "methods", "het...	2018	Heterochromatin and RNAi regulate centromeres by protecting CENP-A from ubiquitin-mediated degradation
The parasitic liver fluke Fasciola hepatica infests mainly ruminants , but it can also cause fasciolosis in people , who ingest the metacercariae encysted on plants . The drug of choice to treat fasciolosis is triclabendazole ( TBZ ) , which has been on the market for several decades . This is also true for the other a...	The liver fluke F . hepatica imposes an economic burden by infesting domestic ruminants . In addition , the WHO classified human fasciolosis as a disease of vital global public health importance , because several million people worldwide are infested by this trematode . Because it is currently not possible to vaccinate...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "taxonomy", "invertebrates", "biliary", "system", "medicine", "and", "health", "sciences", "liver", "body", "fluids", "chemical", "compounds", "helminths", "bile", "animals", "invertebrate", "genomics", "trematodes", "phylogenetics", "data", "management", "phylogenetic", ...	2018	Identification and characterization of the Fasciola hepatica sodium- and chloride-dependent taurine transporter
To preserve genome integrity , the S-phase checkpoint senses damaged DNA or nucleotide depletion and when necessary , arrests replication progression and delays cell division . Previous studies , based on two pol2 mutants have suggested the involvement of DNA polymerase epsilon ( Pol ε ) in sensing DNA replication accu...	The viability of living organisms depends on the integrity of their genomes . Each cell has to constantly monitor DNA replication and coordinate it with cell division to avoid genomic instability . This is achieved through pathways known as cell cycle checkpoints . Therefore , upon replication perturbation , DNA synthe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "phosphorylation", "flow", "cytometry", "cellular", "stress", "responses", "cell", "cycle", "and", "cell", "division", "cell", "processes", "fungi", "model", "organisms", "dna", "replication", "experimental", "organism", "systems", "dna", "synthesis", "phase", "resear...	2017	Mutations in the Non-Catalytic Subunit Dpb2 of DNA Polymerase Epsilon Affect the Nrm1 Branch of the DNA Replication Checkpoint
Mycetoma is a devastating neglected tropical disease , caused by various fungal and bacterial pathogens . Correct diagnosis to the species level is mandatory for proper treatment . In endemic areas , various diagnostic tests and techniques are in use to achieve that , and that includes grain culture , surgical biopsy h...	In mycetoma endemic regions , the medical and health settings are commonly suboptimal , and only a few diagnostic tests and techniques are available . That had badly affected the patients’ proper diagnosis and management and thus the late presentation of patients with advanced disease . In this retrospective study , th...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "cytology", "pathology", "and", "laboratory", "medicine", "biopsy", "mycetoma", "pathogens", "tropical", "diseases", "microbiology", "surgical", "and", "invasive", "medical", "procedures", "actinomadura", "histology", "nocardia", ...	2019	The Accuracy of Histopathological and Cytopathological Techniques in the Identification of the Mycetoma Causative Agents
Synaptic receptors in the human brain consist of multiple protein subunits , many of which have multiple variants , coded by different genes , and are differentially expressed across brain regions and developmental stages . The brain can tune the electrophysiological properties of synapses to regulate plasticity and in...	Synapses change their properties during development affecting information processing and learning . Most synaptic receptors consist of several proteins , each having several variants coded by closely related genes . These protein variants are similar in structure , yet often differ slightly in their biophysical attribu...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Gene Expression Switching of Receptor Subunits in Human Brain Development
The human monoclonal antibody ( mAb ) HK20 neutralizes a broad spectrum of primary HIV-1 isolates by targeting the highly conserved heptad repeat 1 ( HR1 ) of gp41 , which is transiently exposed during HIV-1 entry . Here we present the crystal structure of the HK20 Fab in complex with a gp41 mimetic 5-Helix at 2 . 3 Å ...	The HIV-1 envelope glycoprotein composed of the receptor binding subunit gp120 and the fusion protein gp41 is the prime target for neutralizing antibodies . Receptor binding induces a conformational change in gp41 that transiently exposes the conserved heptad repeat 1 ( HR1 ) region . We have previously isolated the hu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/hiv", "infection", "and", "aids", "immunology/antigen", "processing", "and", "recognition", "biochemistry/biomacromolecule-ligand", "interactions", "virology/antivirals,", "including", "modes", "of", "action", "and", "resistance" ]	2010	Crystal Structure and Size-Dependent Neutralization Properties of HK20, a Human Monoclonal Antibody Binding to the Highly Conserved Heptad Repeat 1 of gp41
NK cells are important immune effectors for preventing microbial invasion and dissemination , through natural cytotoxicity and cytokine secretion . Bacillus anthracis spores can efficiently drive IFN-γ production by NK cells . The present study provides insights into the mechanisms of cytokine and cellular signaling th...	NK cells are important immune effectors that perform a surveillance task and react to transformed , stressed , and virally infected cells . They represent a first-line defence against cancer and pathogen invasion . Different pathogens trigger distinct NK-cell activation pathways . The Bacillus anthracis spore is the hi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immune", "cells", "cytokines", "immune", "activation", "immunity", "to", "infections", "immunology", "microbiology", "host-pathogen", "interaction", "bacterial", "pathogens", "biology", "immune", "response", "gram", "positive", "immune", "system", "nk", "cells", "immun...	2012	Mechanisms of NK Cell-Macrophage Bacillus anthracis Crosstalk: A Balance between Stimulation by Spores and Differential Disruption by Toxins
Naïve anti-viral CD8+ T cells ( TCD8+ ) are activated by the presence of peptide-MHC Class I complexes ( pMHC-I ) on the surface of professional antigen presenting cells ( pAPC ) . Increasing the number of pMHC-I in vivo can increase the number of responding TCD8+ . Antigen can be presented directly or indirectly ( cro...	To induce a protective cell type ( CD8+ T cells ) following virus infection , it is necessary to present degraded fragments of viral protein in complex with self molecules on the surface of so-called antigen presenting cells ( APC ) . This process can occur in infected or uninfected APC and has been studied and quantif...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Peptide-MHC-I from Endogenous Antigen Outnumber Those from Exogenous Antigen, Irrespective of APC Phenotype or Activation
G protein–coupled receptors ( GPCRs ) play an important role in physiology and disease and represent the most productive drug targets . Orphan GPCRs , with their endogenous ligands unknown , were considered a source of drug targets and consequently attract great interest to identify their endogenous cognate ligands for...	The current model on G protein–coupled receptors ( GPCRs ) is that they have at least one endogenous ligand for the activation of the heterotrimeric G proteins that controls lots of physiological functions . Currently , 140 out of approximately 800 GPCRs are referred to as orphan because of a lack of knowledge about th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "luciferase", "assay", "luciferase", "enzymes", "enzymology", "vertebrates", "animals", "mammals", "biochemical", "analysis", "enzyme", "assays", "amniotes", "bioassays", "and", "physiological", "analysis", "calcium", "signaling", "g", "protein", "coupled", "receptors", ...	2019	Constitutively active BRS3 is a genuinely orphan GPCR in placental mammals
Hsp90 from Giardia lamblia is expressed by splicing of two independently transcribed RNA molecules , coded by genes named HspN and HspC located 777 kb apart . The reasons underlying such unique trans-splicing based generation of GlHsp90 remain unclear . In this study using mass-spectrometry we identify the sequence of ...	Giardia lamblia is one of the most common causes of diarrhoea across the globe . The disease can result in fatalities especially in small children . The parasite is transmitted by contaminated food through faeco-oral route due to unhygienic habits . The parasite exhibits two stages during its lifecycle; namely cysts an...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "spectrometric", "identification", "of", "proteins", "cellular", "stress", "responses", "giardia", "enzymes", "cell", "processes", "enzymology", "microbiology", "parasitic", "protozoans", "protozoans", "chaperone", "proteins", "enzyme", "kinetics", "giardia", "lamblia", "...	2014	Trans-spliced Heat Shock Protein 90 Modulates Encystation in Giardia lamblia
Genomic instability is a major driver of intra-tumor heterogeneity . However , unstable genomes often exhibit different molecular and clinical phenotypes , which are associated with distinct mutational processes . Here , we algorithmically inferred the clonal phylogenies of ~6 , 000 human tumors from 32 tumor types to ...	Cancer is characterized by cells accumulating molecular alterations promoting specific phenotypic features , such as uncontrolled proliferation and survival . Cancer cells sometimes exhibit a high number of such alterations , often driven by defects of the DNA repair pathway or by external mutagens , such as tobacco sm...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cancer", "genomics", "taxonomy", "medicine", "and", "health", "sciences", "genetic", "networks", "chromosome", "structure", "and", "function", "basic", "cancer", "research", "cloning", "oncology", "mutation", "phylogenetics", "data", "management", "phylogenetic", "anal...	2018	Pan-cancer inference of intra-tumor heterogeneity reveals associations with different forms of genomic instability
In the nematode Caenorhabditis elegans , cholinergic motor neurons stimulate muscle contraction as well as activate GABAergic motor neurons that inhibit contraction of the contralateral muscles . Here , we describe the composition of an ionotropic acetylcholine receptor that is required to maintain excitation of the ch...	Neuronal acetylcholine receptors modulate a wide range of activities in vertebrates and invertebrates . The activity and sensitivity of these receptors to particular pharmacological agents is determined by the subunit composition of the receptors . A rich diversity of acetylcholine receptors are expressed in the nervou...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience/behavioral", "neuroscience", "genetics", "and", "genomics/gene", "function" ]	2009	A Neuronal Acetylcholine Receptor Regulates the Balance of Muscle Excitation and Inhibition in Caenorhabditis elegans
Dengue virus is endemic in peninsular Malaysia . The clinical manifestations vary depending on the incubation period of the virus as well as the immunity of the patients . Glucose-6-phosphate dehydrogenase ( G6PD ) deficiency is prevalent in Malaysia where the incidence is 3 . 2% . It has been noted that some G6PD-defi...	An estimated 50 to 100 million cases of dengue fever occur each year worldwide . Among these , there are 200 , 000 to 500 , 000 cases of life-threatening dengue hemorrhagic fever ( DHF ) and dengue shock syndrome ( DSS ) . Factors contributing to the development of DHF/DSS are not yet fully identified . Glucose-6-phosp...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "genetics", "immunology", "biology", "microbiology", "molecular", "cell", "biology" ]	2014	Dengue Virus Type 2 (DENV2)-Induced Oxidative Responses in Monocytes from Glucose-6-Phosphate Dehydrogenase (G6PD)-Deficient and G6PD Normal Subjects
Foxp3+ regulatory T ( Treg ) cells are essential for the maintenance of immune homeostasis and tolerance . During viral infections , Treg cells can limit the immunopathology resulting from excessive inflammation , yet potentially inhibit effective antiviral T cell responses and promote virus persistence . We report her...	T cell exhaustion represents a state of T cell dysfunction associated with clinically relevant diseases , such as persistent viral infections or cancer . Although the molecular signature of exhausted T cells has been characterized in detail at the functional and transcriptional level , the immunological mechanisms that...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunopathology", "medicine", "infectious", "diseases", "lymphocytic", "choriomeningitis", "immunology", "biology", "viral", "diseases" ]	2013	IL-21 Restricts Virus-driven Treg Cell Expansion in Chronic LCMV Infection
Sequence conservation and co-variation of base pairs are hallmarks of structured RNAs . For certain RNAs ( e . g . riboswitches ) , a single sequence must adopt at least two alternative secondary structures to effectively regulate the message . If alternative secondary structures are important to the function of an RNA...	RNA ( Ribonucleic Acid ) is a messenger of genetic information , master regulator , and catalyst in the cell . To carry out its function , RNA can fold into complex three-dimensional structures . Certain classes of RNAs , called riboswitches , adopt at least two alternative structures to act as a switch . We set out to...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "rna", "rna", "structure", "molecular", "cell", "biology", "nucleic", "acids", "biology", "evolutionary", "biology", "ribozymes" ]	2013	Evolutionary Evidence for Alternative Structure in RNA Sequence Co-variation
The polysaccharide capsule of Streptococcus pneumoniae defines over ninety serotypes , which differ in their carriage prevalence and invasiveness for poorly understood reasons . Recently , an inverse correlation between carriage prevalence and oligosaccharide structure of a given capsule has been described . Our previo...	Streptococcus pneumoniae bacteria are responsible for serious human infections including meningitis , pneumonia and bacteraemia and are a common cause of otitis media ( ear infection ) in children . However , they most often reside harmlessly in the infant nasopharynx . An association has long been observed between the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "bacterial", "diseases", "infectious", "diseases", "biology", "microbiology" ]	2012	Capsule Type of Streptococcus pneumoniae Determines Growth Phenotype
The Global Program to Eliminate Lymphatic Filariasis ( LF ) has a target date of 2020 . This program is progressing well in many countries . However , progress has been slow in some countries , and others have not yet started their mass drug administration ( MDA ) programs . Acceleration is needed . We studied how incr...	The Global Program to Eliminate Lymphatic Filariasis ( LF ) employs annual mass drug administration ( MDA ) of antifilarial drugs to reduce infection rates in populations and interrupt transmission . While this program is working well in many countries , progress has been slow in others , and some countries have not ye...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "social", "and", "behavioral", "sciences", "preventive", "medicine", "non-clinical", "medicine", "population", "modeling", "global", "health", "neglected", "tropical", "diseases", "cost", "effectiveness", "infectious"...	2013	Modeling the Impact and Costs of Semiannual Mass Drug Administration for Accelerated Elimination of Lymphatic Filariasis
CD1d-restricted invariant natural killer T ( iNKT ) cells represent a heterogeneous population of lipid-reactive T cells that are involved in many immune responses , mediated through T-cell receptor ( TCR ) –dependent and/or independent activation . Although numerous microbial lipid antigens ( Ags ) have been identifie...	Invariant natural killer T ( iNKT ) cells are a population of unconventional T lymphocytes that activate rapidly during inflammation due to their innate-like features . They are unconventional since they do not react to peptidic antigens ( Ags ) presented by classical major histocompatibility complex ( MHC ) molecules;...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "glycolipids", "medicine", "and", "health", "sciences", "immune", "physiology", "immune", "cells", "sphingolipids", "antigen-presenting", "cells", "biological", "cultures", "immunology", "dendritic", "cells", "hybridomas", "research", "and", "analysis", "methods", "immune...	2019	TLR9-mediated dendritic cell activation uncovers mammalian ganglioside species with specific ceramide backbones that activate invariant natural killer T cells
Type I interferon response plays a prominent role against viral infection , which is frequently disrupted by viruses . Here , we report Bcl-2 associated transcription factor 1 ( Bclaf1 ) is degraded during the alphaherpesvirus Pseudorabies virus ( PRV ) and Herpes simplex virus type 1 ( HSV-1 ) infections through the v...	Alphaherpesvirus , such as Pseudorabies virus ( PRV ) and Herpes simplex virus type 1 ( HSV-1 ) , can establish persistent infection and cause various diseases in hosts . Interferon ( IFN ) response is hosts’ first defense system against viral infection . Here , we report alphaherpesvirus induces degradation of a host ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "hela", "cells", "pathogens", "biological", "cultures", "microbiology", "plasmid", "construction", "viruses", "immunoprecipitation", "dna", "viruses", "cell", "cultur...	2019	Bclaf1 critically regulates the type I interferon response and is degraded by alphaherpesvirus US3
Non-Typhoidal Salmonella ( NTS ) is an important cause of invasive bacterial disease and associated with mortality in Africa . However , little is known about the environmental reservoirs and predominant modes of transmission . Our study aimed to study the role of domestic animals in the transmission of NTS to humans i...	Salmonellosis is a neglected tropical disease causing serious dysentery and septicaemia particularly in young infants , elderly and immunocompromised individuals such as HIV patients and associated with substantial mortality in developing countries . Salmonellosis also constitutes a major public health problem as it is...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "biology", "veterinary", "science", "agriculture" ]	2011	Clonal Differences between Non-Typhoidal Salmonella (NTS) Recovered from Children and Animals Living in Close Contact in The Gambia
The mechanisms involved in the recognition of microbial pathogens and activation of the immune system have been extensively studied . However , the mechanisms involved in the recovery phase of an infection are incompletely characterized at both the cellular and physiological levels . Here , we establish a Caenorhabditi...	Infections by bacterial pathogens often produce substantial tissue damage and alter metabolism in the host that , if left unchecked , could be detrimental to overall fitness . The cellular and systemic responses that resolve these alterations in the host are not well defined . Here , we examine transcriptional networks...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "immune", "system", "invertebrates", "caenorhabditis", "elegans", "infectious", "disease", "immunology", "model", "organisms", "innate", "immune", "system", "clinical", "immunology", "immunity", "caenorhabditis", "nematoda", "biology", "and", "life", ...	2014	Recovery from an Acute Infection in C. elegans Requires the GATA Transcription Factor ELT-2
Ephrins and Eph receptors are involved in the establishment of vertebrate tissue boundaries . The complexity of the system is puzzling , however in many instances , tissues express multiple ephrins and Ephs on both sides of the boundary , a situation that should in principle cause repulsion between cells within each ti...	How embryonic tissues separate from each other to shape the developing organism is a fundamental question in developmental biology . In vertebrates , this process relies on local repulsive reactions specifically generated at contacts between cells of different types . These reactions are triggered by typical repulsive ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology", "biology", "and", "life", "sciences", "developmental", "biology" ]	2014	Variable Combinations of Specific Ephrin Ligand/Eph Receptor Pairs Control Embryonic Tissue Separation
Human brucellosis is considered to be an important but typically under-diagnosed cause of febrile illness in many low and middle-income countries . In Kenya , and throughout East Africa , laboratory diagnosis for the disease is based primarily on the febrile antigen Brucella agglutination test ( FBAT ) , yet few studie...	Brucellosis is a debilitating disease of people caused by infection with one of a number of different Brucella species . In almost all cases , people acquire the infection through exposure to infected animals or contaminated animal products . Human brucellosis is well known for its wide range of symptoms , and is often...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "livestock", "medicine", "and", "health", "sciences", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "tropical", "diseases", "microbiology", "geographical", "locations", "brucellosis", "bacterial", "diseases", "veterinary", ...	2017	Poor performance of the rapid test for human brucellosis in health facilities in Kenya
Leishmania major cutaneous leishmaniasis is an infectious zoonotic disease . It is produced by a digenetic parasite , which resides in the phagolysosomal compartment of different mammalian macrophage populations . There is an urgent need to develop new therapies ( drugs ) against this neglected disease that hits develo...	Leishmaniasis is a parasitic disease that is far from eradication . The lack of an efficacious vaccine and treatment failures are major factors in its intractable worldwide prevalence . A non-invasive imaging technique using genetically engineered parasites that expressed fluorescent proteins could give to researchers ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "parastic", "protozoans", "medicine", "infectious", "diseases", "leishmania", "leishmaniasis", "neglected", "tropical", "diseases", "protozoology", "biology", "microbiology", "parasitic", "diseases" ]	2012	Appraisal of a Leishmania major Strain Stably Expressing mCherry Fluorescent Protein for Both In Vitro and In Vivo Studies of Potential Drugs and Vaccine against Cutaneous Leishmaniasis
Variability , stochastic or otherwise , is a central feature of neural activity . Yet the means by which estimates of variation and uncertainty are derived from noisy observations of neural activity is often heuristic , with more weight given to numerical convenience than statistical rigour . For two-photon imaging dat...	There are many sources of noise in recordings of neural activity , and the first challenge in neural data analysis is to separate this noise from experimentally relevant variation . This is particularly problematic for two-photon imaging data . Two-photon imaging uses fluorescent indicators to measure changes in the co...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "fluorescence", "imaging", "cluster", "analysis", "neurochemistry", "statistical", "noise", "statistics", "hierarchical", "clustering", "neuroscience", "kernel", "functions", "mathematics", "nerve", "fibers", "neurotransmitters", "calcium", "signaling", "research", "and", "...	2019	Bayesian hypothesis testing and experimental design for two-photon imaging data
The relationship between the underlying contact network over which a pathogen spreads and the pathogen phylogenetic trees that are obtained presents an opportunity to use sequence data to learn about contact networks that are difficult to study empirically . However , this relationship is not explicitly known and is us...	Understanding whether and how transmission patterns are revealed by branching patterns in phylogenetic trees for pathogens remains a challenging research question . Besides the diversification of the pathogen , branching patterns depend strongly on the host contact structure as it shapes opportunities for the pathogen ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "taxonomy", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "statistics", "pathogens", "microbiology", "retroviruses", "viruses", "immunodeficiency", "viruses", "multivariate", "analysis", "phylogenetics", "data", "management", "mathem...	2019	Phylogenies from dynamic networks
The creation of restriction enzymes with programmable DNA-binding and -cleavage specificities has long been a goal of modern biology . The recently discovered Type IIL MmeI family of restriction-and-modification ( RM ) enzymes that possess a shared target recognition domain provides a framework for engineering such new...	Type II restriction endonucleases ( REases ) are the bedrock of modern biotechnology . Type II REases were essential for the recombinant DNA revolution and the development of gene technology . However , despite the discovery of more than 4 , 000 REases , the DNA recognition specificities are limited to only ~365 . The ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "crystal", "structure", "condensed", "matter", "physics", "enzymology", "nucleotides", "amino", "acid", "sequence", "analysis", "sequence", "motif", "analysis", "dna", "dna", "structure", "crystallography", "molecular", "biology", "techniques",...	2016	Structure of Type IIL Restriction-Modification Enzyme MmeI in Complex with DNA Has Implications for Engineering New Specificities
We simulate deformable red blood cells in the microcirculation using the immersed boundary method with a cytoskeletal model that incorporates structural details revealed by tomographic images . The elasticity of red blood cells is known to be supplied by both their lipid bilayer membranes , which resist bending and loc...	Red blood cells are responsible for delivering oxygen to tissues throughout the body . These terminally differentiated cells have developed a fascinating flexibility and resiliency that is critical to navigating the circulatory system . Far from being rigid bodies , red blood cells adopt biconcave disk shapes at equili...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "cell", "physiology", "junctional", "complexes", "spectrins", "simulation", "and", "modeling", "red", "blood", "cells", "materials", "science", "cellular", "structures", "and", "organelles", "macromolecules", "cytoskeleton", "materials", "by", "structu...	2017	Image-based model of the spectrin cytoskeleton for red blood cell simulation
New Caledonia and French Polynesia are areas in which arboviruses circulate extensively . A large serological survey among horses from New Caledonia and French Polynesia was carried out to investigate the seroprevalence of flaviviruses in the horse population . Here , 293 equine sera samples were screened for flaviviru...	New Caledonia and French Polynesia , located in the South Pacific , are facing circulation of dengue virus ( DENV ) for a long time and emergence of Zika virus ( ZIKV ) since 2013 . A large serosurvey among horses’ population from these two islands was carried out to investigate the seroprevalence of the main flaviviru...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "geomorphology", "dengue", "virus", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "landforms", "pathogens", "topography", "geographical", "locations", "microbiology", "vertebrates", "animals", "mammals", "viruses", "rna", "viruses"...	2019	Serological evidence of infection with dengue and Zika viruses in horses on French Pacific Islands
The Catabolite Activator Protein ( CAP ) is a showcase example for entropic allostery . For full activation and DNA binding , the homodimeric protein requires the binding of two cyclic AMP ( cAMP ) molecules in an anti-cooperative manner , the source of which appears to be largely of entropic nature according to previo...	The Catabolite Activator Protein ( CAP ) is a well-studied example for how cellular catabolite levels are integrated into the gene regulation . Its affinity for a specific stretch of DNA can be switched on by the binding of two nucleotide molecules termed cAMP to its two protomers . Even though the nucleotides occupy s...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[]	2015	Dynamic Allostery of the Catabolite Activator Protein Revealed by Interatomic Forces
Recent studies led to the proposal that meiotic gene conversion can result after transient engagement of the donor chromatid and subsequent DNA synthesis-dependent strand annealing ( SDSA ) . Double Holliday junction ( dHJ ) intermediates were previously proposed to form both reciprocal crossover recombinants ( COs ) a...	In organisms that reproduce sexually , sex cells ( gametes ) are produced by the specialized cell division called meiosis , which halves the number of chromosomes from two sets ( diploid ) to one ( haploid ) . During meiosis , homologous DNA molecules exchange genetic material in a process called homologous recombinati...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics" ]	2007	Synthesis-Dependent Strand Annealing in Meiosis
Adaptation is at the heart of sensation and nowhere is it more salient than in early visual processing . Light adaptation in photoreceptors is doubly dynamical: it depends upon the temporal structure of the input and it affects the temporal structure of the response . We introduce a non-linear dynamical adaptation mode...	Photoreceptors constitute the interface between the visual world and the cerebral world , as they convert light inputs into neural signals . This conversion is subject to continuous adaptation: response gain and time scale vary as a function of input history . This adaptation is ‘dynamical’ both because it depends upon...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	Dynamical Adaptation in Photoreceptors
Glucose is a major energy source and is a key regulator of metabolism but excessive dietary glucose is linked to several disorders including type 2 diabetes , obesity and cardiac dysfunction . Dietary intake greatly influences organismal survival but whether the effects of nutritional status are transmitted to the offs...	Nutritional state has major effects on health and longevity , and investigations into the mechanisms of dietary restriction have taken the lion's share of recent genetic discoveries . We used Caenorhabditis elegans to investigate the role of diet on nematode physiology and report the surprising finding that exposure to...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "caenorhabditis", "neurodegenerative", "diseases", "animals", "animal", "models", "caenorhabditis", "elegans", "model", "organisms", "glucose", "signaling", "epigenetics", "motor", "neuron", "diseases", "research", ...	2014	Heritable Transmission of Stress Resistance by High Dietary Glucose in Caenorhabditis elegans

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