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A fundamental question in human susceptibility to bacterial infections is to what extent variability is a function of differences in the pathogen species or in individual humans . To focus on the pathogen species , we compared in the same individual the human adaptive T and B cell immune response to multiple strains of...	We address a fundamental question regarding the variability in human susceptibility to bacterial infection . Recent attention has been directed to human immune variation as the major element in infection susceptibility , however , our study focuses on the contribution of the pathogenic bacteria . To separate the contri...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "bacteriology", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "staphylococcus", "aureus", "streptococcus", "pyogenes", "bacterial", "genetics", "microb...	2018	Strains of bacterial species induce a greatly varied acute adaptive immune response: The contribution of the accessory genome
Telomerase is a ribonucleoprotein complex involved in the maintenance of telomeres , a protective structure at the distal ends of chromosomes . The enzyme complex contains two main components , telomerase reverse transcriptase ( TERT ) , the catalytic subunit , and telomerase RNA ( TR ) , which serves as a template for...	The enzyme complex telomerase , with its two main components telomerase reverse transcriptase and telomerase RNA , plays an important role in telomere maintenance . Perturbation of telomere length regulation can ultimately result in cellular senescence ( telomere shortening ) and is also observed in tumor cells ( incre...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "virology/persistence", "and", "latency", "virology/virulence", "factors", "and", "mechanisms", "virology/animal", "models", "of", "infection", "virology", "virology/viruses", "and", "cancer" ]	2010	Herpesvirus Telomerase RNA(vTR)-Dependent Lymphoma Formation Does Not Require Interaction of vTR with Telomerase Reverse Transcriptase (TERT)
Here we present the development and implementation of a genome-wide reverse genetic screen in the budding yeast , Saccharomyces cerevisiae , that couples high-throughput strain growth , robotic RNA isolation and cDNA synthesis , and quantitative PCR to allow for a robust determination of the level of nearly any cellula...	The coding portions of most eukaryotic genes are interrupted by non-coding regions termed introns that must be excised prior to their translation . The excision of introns from precursor messenger RNA ( pre–mRNA ) , is catalyzed by the spliceosome , a large macromolecule composed of both RNA and protein components . Se...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "analysis", "tools", "chromosome", "biology", "gene", "expression", "genetics", "biology", "genomics", "genetics", "and", "genomics" ]	2012	A Quantitative, High-Throughput Reverse Genetic Screen Reveals Novel Connections between Pre–mRNA Splicing and 5′ and 3′ End Transcript Determinants
Large spatial and temporal fluctuations in the population density of living organisms have profound consequences for biodiversity conservation , food production , pest control and disease control , especially vector-borne disease control . Chagas disease vector control based on insecticide spraying could benefit from i...	Chagas disease , or American trypanosomiasis , is mainly transmitted to humans by insects that dwell in human habitations and structures closely associated with human habitations , such as kitchen out-buildings , chicken coops , goat corrals , and grain storage bins . Widespread in the Americas , the disease causes chr...	[ "Abstract", "Introduction", "Methods", "and", "materials", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "tropical", "diseases", "vertebrates", "chickens", "parasitic", "diseases", "animals", "habitats", "neglected", "tropical", "diseases", "population", "biology", "infectious", "disease"...	2017	Chagas disease vector control and Taylor's law
Phenotypic resistance describes a bacterial population that becomes transiently resistant to an antibiotic without requiring a genetic change . We here investigated the role of the small regulatory RNA ( sRNA ) RyhB , a key contributor to iron homeostasis , in the phenotypic resistance of Escherichia coli to various cl...	Understanding the mechanisms at work behind bacterial antibiotic resistance has become a major health issue in the face of the antibiotics crisis . Here , we show that RyhB , a bacterial small regulatory RNA , decreases the sensitivity of Escherichia coli to the antibiotic gentamicin when iron is scarce , an environmen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "antimicrobials", "cell", "physiology", "medicine", "and", "health", "sciences", "drugs", "microbiology", "operons", "antibiotic", "resistance", "mutation", "antibiotics", "pharmacology", "dna", "molecular", "biology", "techniques", "research", "and", "analysis", "methods...	2019	A small RNA controls bacterial sensitivity to gentamicin during iron starvation
Accurate inference of molecular and functional interactions among genes , especially in multicellular organisms such as Drosophila , often requires statistical analysis of correlations not only between the magnitudes of gene expressions , but also between their temporal-spatial patterns . The ISH ( in-situ-hybridizatio...	As high-throughput technologies for molecular abundance profiling are becoming more inexpensive and accessible , computational inference of gene interaction networks from such data based on well-founded statistical principles is imperative to advance the understanding of regulatory mechanisms in various biological syst...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2013	GINI: From ISH Images to Gene Interaction Networks
Pathogens have developed diverse strategies to infect their hosts and evade the host defense systems . Many pathogens reside within host phagocytic cells , thus evading much of the host immune system . For dimorphic fungal pathogens which grow in a multicellular hyphal form , a central attribute which facilitates growt...	Dimorphic fungal pathogens pose significant health and agricultural problems worldwide . These fungi have the capacity to switch between a multicellular hyphal growth form and a unicellular yeast growth form . Often one form is pathogenic , found in infected hosts , and the other is not . Many dimorphic fungal pathogen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/morphogenesis", "and", "cell", "biology", "infectious", "diseases/fungal", "infections", "cell", "biology/microbial", "growth", "and", "development", "genetics", "and", "genomics/gene", "function", "microbiology/microbial", "growth", "and", "development", "...	2009	In Vivo Yeast Cell Morphogenesis Is Regulated by a p21-Activated Kinase in the Human Pathogen Penicillium marneffei
The detection of epistatic interactive effects of multiple genetic variants on the susceptibility of human complex diseases is a great challenge in genome-wide association studies ( GWAS ) . Although methods have been proposed to identify such interactions , the lack of an explicit definition of epistatic effects , tog...	Although genome-wide association studies ( GWAS ) have been quite popular due to recent advances in low-cost genotyping techniques , most of the reported studies only analyze single-locus effects because traditional multi-locus methods are not computationally practical in the detection of epistatic interactive effects ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "computational", "biology/population", "genetics", "genetics", "and", "genomics/complex", "traits", "genetics", "and", "genomics/disease", "models", "genetics", "and", "genomics/genetics", "of", "disease", "mathematics/statistics", "genetics", "and", "genomics/population", "g...	2009	Epistatic Module Detection for Case-Control Studies: A Bayesian Model with a Gibbs Sampling Strategy
Systemic sclerosis ( SSc ) is a rare systemic autoimmune disease characterized by skin and organ fibrosis . The pathogenesis of SSc and its progression are poorly understood . The SSc intrinsic gene expression subsets ( inflammatory , fibroproliferative , normal-like , and limited ) are observed in multiple clinical co...	Systemic sclerosis ( SSc ) is a rare autoimmune disease characterized by skin thickening ( fibrosis ) and progressive organ failure . Previous studies of SSc skin biopsies have identified molecular subsets of SSc based upon gene expression termed the inflammatory , fibroproliferative , normal-like , and limited intrins...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "genetics", "biology", "and", "life", "sciences", "genomics", "computational", "biology" ]	2015	Systems Level Analysis of Systemic Sclerosis Shows a Network of Immune and Profibrotic Pathways Connected with Genetic Polymorphisms
During sprouting angiogenesis in the vertebrate vascular system , and primary branching in the Drosophila tracheal system , specialized tip cells direct branch outgrowth and network formation . When tip cells lumenize , they form subcellular ( seamless ) tubes . How these seamless tubes are made , shaped and maintained...	Biological tubes adopt a variety of shapes to carry out their functions . In addition to multicellular tubes , single epithelial or endothelial cells build unicellular lumens lined by an apical membrane devoid of cell junctions , or seams . Such seamless tubes are highly conserved from invertebrates to vertebrate organ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "chitin", "medicine", "and", "health", "sciences", "cloning", "alleles", "developmental", "biology", "respiratory", "system", "materials", "science", "molecular", "biology", "techniques", "embryos", "trachea", "macromolecules", "cellular", "structures", "and", "organelles...	2018	An Ichor-dependent apical extracellular matrix regulates seamless tube shape and integrity
The vegetative insecticidal proteins ( Vip ) , secreted by many Bacillus thuringiensis strains during their vegetative growth stage , are genetically distinct from known insecticidal crystal proteins ( ICPs ) and represent the second-generation insecticidal toxins . Compared with ICPs , the insecticidal mechanisms of V...	Bacillus thuringiensis Vip3A has potential in control of Lepidopteran pest and has been used in transgenic plants . However , studies of the insecticidal mechanisms of Vip3A are rare , and none of their definite receptors have been reported so far , which seriously restricts the study of its insecticidal mechanism and ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "toxins", "pathology", "and", "laboratory", "medicine", "cell", "processes", "animals", "toxic", "agents", "toxicology", "plasmid", "construction", "animal", "models", "membrane", "proteins", "developmental", "bi...	2018	Scavenger receptor-C acts as a receptor for Bacillus thuringiensis vegetative insecticidal protein Vip3Aa and mediates the internalization of Vip3Aa via endocytosis
Natural killer ( NK ) cells are circulating lymphocytes that play an important role in the control of viral infections and tumors . Their functions are regulated by several activating and inhibitory receptors . A subset of these receptors in human NK cells are the killer immunoglobulin-like receptors ( KIRs ) , which i...	Human natural killer ( NK ) cells patrol peripheral tissue , monitoring changes on the surface of body cells . They express a network of activating and inhibitory receptors called the killer immunoglobulin-like receptors ( KIRs ) . The main ligands of inhibitory KIRs are MHC class I molecules , which present viral pept...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Virus Encoded MHC-Like Decoys Diversify the Inhibitory KIR Repertoire
Gene duplication provides much of the raw material from which functional diversity evolves . Two evolutionary mechanisms have been proposed that generate functional diversity: neofunctionalization , the de novo acquisition of function by one duplicate , and subfunctionalization , the partitioning of ancestral functions...	Molecular evolution studies have shown that the redundancy intrinsic to gene duplication may allow one gene duplicate to acquire a new function ( neofunctionalization ) or for both duplicates to each assume a subset of the ancestral gene's functions ( subfunctionalization ) . Studies of networks of interacting proteins...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/evolutionary", "modeling", "computational", "biology/systems", "biology" ]	2009	Questioning the Ubiquity of Neofunctionalization
The pathogen Mycobacterium tuberculosis employs a range of ESX-1 substrates to manipulate the host and build a successful infection . Although the importance of ESX-1 secretion in virulence is well established , the characterization of its individual components and the role of individual substrates is far from complete...	M . tuberculosis is a facultative intracellular pathogen that has an intimate relationship with host macrophages . Proteins secreted by the ESX-1 secretion system play an important role in this interaction , for instance by orchestrating the escape from the phagosome into the cytosol of the macrophage . However , the e...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "bacteriology", "protein", "transport", "blood", "cells", "medicine", "and", "health", "sciences", "fish", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "cell", "processes", "immunology", "microbiology", "vertebrates", "animals", "animal"...	2018	EspH is a hypervirulence factor for Mycobacterium marinum and essential for the secretion of the ESX-1 substrates EspE and EspF
Gut immunity is regulated by intricate and dynamic mechanisms to ensure homeostasis despite a constantly changing microbial environment . Several regulatory factors have been described to participate in feedback responses to prevent aberrant immune activity . Little is , however , known about how transcriptional progra...	The numerous human diseases caused by aberrations in intestinal immunity and integrity urge a better understanding of the regulatory interactions that balance the output of host-microbe interactions . In this study , we discovered a novel phenomenon of transcriptional antagonism exerted via two isoforms encoded from th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "rna", "interference", "gene", "regulation", "immunology", "dna", "transcription", "sequence", "motif", "analysis", "molecular", "biology", "techniques", "epigenetics", "research", "and", "analysis", "methods", "sequence", "analy...	2018	Nubbin isoform antagonism governs Drosophila intestinal immune homeostasis
Evolutionary innovation in eukaryotes and especially animals is at least partially driven by genome rearrangements and the resulting emergence of proteins with new domain combinations , and thus potentially novel functionality . Given the random nature of such rearrangements , one could expect that proteins with partic...	Most proteins in eukaryotes are composed of two or more domains , evolutionary independent units with ( often ) their own individual functions . The specific repertoire of multidomain proteins in a given species defines the topology of pathways and networks that carry out its metabolic and regulatory processes . When p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "computational", "biology", "evolutionary", "biology" ]	2012	This Déjà Vu Feeling—Analysis of Multidomain Protein Evolution in Eukaryotic Genomes
Polycomb ( PcG ) regulation has been thought to produce stable long-term gene silencing . Genomic analyses in Drosophila and mammals , however , have shown that it targets many genes , which can switch state during development . Genetic evidence indicates that critical for the active state of PcG target genes are the h...	Polycomb ( PcG ) regulation has been thought to produce stable long-term gene silencing . Genomic analyses in Drosophila and mammals , however , have shown that it targets many genes that can switch state during development . Here we analyze the repertoire of alternative states in which PcG target genes are found in di...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/chromatin", "structure", "molecular", "biology/histone", "modification", "molecular", "biology/transcription", "initiation", "and", "activation", "genetics", "and", "genomics/functional", "genomics", "molecular", "biology/bioinformatics", "genetics", "and", ...	2010	Alternative Epigenetic Chromatin States of Polycomb Target Genes
Previously , we showed Leishmania donovani Ufm1 has a Gly residue conserved at the C-terminal region with a unique 17 amino acid residue extension that must be processed prior to conjugation to target proteins . In this report , we describe for the first time the isolation and characterization of the Leishmania Ufm1-sp...	Ubiquitin and ubiquitin like proteins ( Ubls ) and the enzymes that mediate the conjugation/deconjugation reactions have not been well studied in protozoan parasites despite their widely recognized importance in a broad range of cellular functions in eukaryotes . We have previously reported that Ufm1 has distinct prote...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "parasitology", "biology", "microbiology" ]	2014	Deletion of Ubiquitin Fold Modifier Protein Ufm1 Processing Peptidase Ufsp in L. donovani Abolishes Ufm1 Processing and Alters Pathogenesis
Huntington's disease ( HD ) is one of several neurodegenerative disorders caused by expansion of CAG repeats in a coding gene . Somatic CAG expansion rates in HD vary between organs , and the greatest instability is observed in the brain , correlating with neuropathology . The fundamental mechanisms of somatic CAG repe...	Huntington's disease ( HD ) is a genetically determined neurodegenerative disorder identified by the presence of a mutation for a long series of CAG repeats ( >36 repeats ) in the Huntingtin ( HTT ) gene . Longer repeat sequences cause disease onset at a younger age . The mutation encodes an expanded glutamine tract wi...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/disease", "models", "genetics", "and", "genomics/genetics", "of", "disease", "biochemistry/replication", "and", "repair", "mathematics/statistics", "genetics", "and", "genomics", "molecular", "biology/dna", "repair" ]	2010	Continuous and Periodic Expansion of CAG Repeats in Huntington's Disease R6/1 Mice
Autozygosity occurs when two chromosomal segments that are identical from a common ancestor are inherited from each parent . This occurs at high rates in the offspring of mates who are closely related ( inbreeding ) , but also occurs at lower levels among the offspring of distantly related mates . Here , we use runs of...	Inbreeding occurs when genetic relatives have offspring . Because all humans are related to one another , even if very distantly , all people are inbred to various degrees . From a genetic standpoint , it is well known that inbreeding increases the risk that a child will have a rare recessive genetic disease , but ther...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome-wide", "association", "studies", "medicine", "psychoses", "mental", "health", "population", "genetics", "schizophrenia", "biology", "evolutionary", "genetics", "psychiatry", "haplotypes", "genetics", "human", "genetics", "evolutionary", "biology", "genetics", "and",...	2012	Runs of Homozygosity Implicate Autozygosity as a Schizophrenia Risk Factor
We describe a consanguineous Iraqi family in which affected siblings had mild mental retardation and congenital ataxia characterized by quadrupedal gait . Genome-wide linkage analysis identified a 5 . 8 Mb interval on chromosome 8q with shared homozygosity among the affected persons . Sequencing of genes contained in t...	We identified a homozygous missense mutation ( S100P ) in the gene encoding carbonic anhydrase VIII in a consanguineous Iraqi family in which affected siblings had mild mental retardation and congenital ataxia characterized by quadrupedal gait . The affected persons walk on their hands and feet with their legs held str...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/gene", "discovery", "genetics", "and", "genomics/medical", "genetics" ]	2009	CA8 Mutations Cause a Novel Syndrome Characterized by Ataxia and Mild Mental Retardation with Predisposition to Quadrupedal Gait
Ubiquitination , a post-translational modification , mediates diverse cellular functions including endocytic transport of molecules . Kaposi's sarcoma-associated herpesvirus ( KSHV ) , an enveloped herpesvirus , enters endothelial cells primarily through clathrin-mediated endocytosis . Whether ubiquitination and protea...	Ubiquitination , a post-translational modification , mediates important cellular functions including endocytic transport of molecules . Kaposi's sarcoma-associated herpesvirus ( KSHV ) is a gammaherpesvirus linked to the development of Kaposi's sarcoma , an endothelial malignancy commonly found in AIDS patients , and s...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biology" ]	2012	The Ubiquitin/Proteasome System Mediates Entry and Endosomal Trafficking of Kaposi's Sarcoma-Associated Herpesvirus in Endothelial Cells
Trypanosomatid parasites are notorious for the human diseases they cause throughout Africa and South America . However , non-pathogenic trypanosomatids are also found worldwide , infecting a wide range of hosts . One example is Trypanosoma ( Megatrypanum ) theileri , a ubiquitous protozoan commensal of bovids , which i...	Single-celled parasites of the order Kinetoplastida are responsible for devastating diseases of humans and animals , including African trypanosomiasis , Chagas' disease and leishmaniasis . However , there are also many species of trypanosomatids that do not cause disease and are distributed globally . One example is Tr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "veterinary", "diseases", "molecular", "cell", "biology", "veterinary", "parasitology", "immunity", "immunology", "biology", "microbiology", "veterinary", "science", "parasitology" ]	2011	Targeting Cattle-Borne Zoonoses and Cattle Pathogens Using a Novel Trypanosomatid-Based Delivery System
Successful infection of the host requires secretion of effector proteins to evade or suppress plant immunity . Secretion of effectors in root-infecting fungal pathogens , however , remains unexplored . We previously reported that Verticillium dahliae , a root-infecting phytopathogenic fungus , develops a penetration pe...	Pathogens secrete effector proteins as molecular weapons to evade or suppress plant immunity . However , the mechanism ( s ) by which root-infecting fungal pathogens secrete secretory effector proteins remains unexplored . We previously reported that Verticillium dahliae , a root-infecting phytopathogenic fungus , form...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "protein", "transport", "cell", "processes", "light", "microscopy", "fungal", "structure", "fungi", "plant", "science", "microscopy", "septins", "plant", "pathology", "research", "and", "analysis", "methods", "mycology", "proteins", "fluorescence", "recovery", "after", ...	2017	Secretory proteins are delivered to the septin-organized penetration interface during root infection by Verticillium dahliae
Dengue virus ( DENV ) is a mosquito-borne flavivirus , and symptoms of infection range from asymptomatic to the severe dengue hemorrhagic fever/dengue shock syndrome ( DHF/DSS ) . High viral loads correlate with disease severity , and both type I & II interferons ( IFNs ) are crucial for controlling viral replication ....	Dengue virus ( DENV ) is a mosquito-borne pathogen present in the tropical and sub-tropical regions of the world , and an estimated 2 . 5 billion people are at risk of infection . Interferon ( IFN ) mediated innate responses in the host are critical for limiting viral spread following DENV infection . We have previousl...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/virulence", "factors", "and", "mechanisms", "virology/viral", "replication", "and", "gene", "regulation", "infectious", "diseases/neglected", "tropical", "diseases", "virology/animal", "models", "of", "infection", "virology", "immunology/innate", "immunity", "infect...	2011	STAT2 Mediates Innate Immunity to Dengue Virus in the Absence of STAT1 via the Type I Interferon Receptor
Yellow fever ( Yf ) outbreak was recently reported in South Omo of Southern Ethiopia . This area was also highly affected by Yf outbreak in the 1960s . However , there is no reliable information on the level of community knowledge attitudes and practices about the disease in the area . The objective of the current stud...	Yellow fever is becoming one of the most important re-emerging mosquito-borne viral diseases in many African countries despite the availability of an effective vaccine . Hence , assessing information on what a community knows about Yellow fever would contribute to the design of appropriate control strategies in additio...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "vomiting", "immunology", "tropical", "diseases", "parasitic", "diseases", "animals", "vaccines", "preventive", "medicine", "physiological", "processe...	2018	Community knowledge, attitudes and practices on Yellow fever in South Omo area, Southern Ethiopia
Prion strains are characterized by differences in the outcome of disease , most notably incubation period and neuropathological features . While it is established that the disease specific isoform of the prion protein , PrPSc , is an essential component of the infectious agent , the strain-specific relationship between...	Prion diseases are a group of infectious fatal neurodegenerative diseases that affect animals including humans . This unique infectious agent is the result of a post-translational conformational change of the normal form of the prion protein , PrPC , to an infectious form of the prion protein , PrPSc . Different strain...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/prion", "diseases" ]	2011	The Strain-Encoded Relationship between PrPSc Replication, Stability and Processing in Neurons is Predictive of the Incubation Period of Disease
Brazilian spotted fever ( BSF ) , caused by the bacterium Rickettsia rickettsii , has been associated with the transmission by the tick Amblyomma sculptum , and one of its main hosts , the capybara ( Hydrochoerus hydrochaeris ) . During 2015–2019 , we captured capybaras and ticks in seven highly anthropic areas of São ...	Brazilian spotted fever ( BSF ) , caused by the bacterium Rickettsia rickettsii , is the deadliest tick-borne disease of the New World . In southeastern Brazil , where 489 patients succumbed to the disease from 2001 to 2018 , R . rickettsii is transmitted to humans mainly by the tick Amblyomma sculptum , which uses the...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusions" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "ixodes", "pathology", "and", "laboratory", "medicine", "pathogens", "geographical", "locations", "microbiology", "rickettsia", "animals", "developmental", "biology", ...	2019	Epidemiology of capybara-associated Brazilian spotted fever
Apoptosis is regulated by several signaling pathways which are extensively linked by crosstalks . Boolean or logical modeling has become a promising approach to capture the qualitative behavior of such complex networks . Here we built a large-scale literature-based Boolean model of the central intrinsic and extrinsic a...	Apoptosis is one of the most investigated topics in the life sciences , especially as this kind of programmed cell death has been linked to several diseases . The strong desire to understand the function and regulation of apoptosis is unfortunately confronted with its complexity and its high degree of cross linking wit...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/cellular", "death", "and", "stress", "responses", "computational", "biology/systems", "biology", "cell", "biology/cell", "signaling" ]	2009	ON/OFF and Beyond - A Boolean Model of Apoptosis
Microbes are predominantly found in surface-attached and spatially structured polymicrobial communities . Within these communities , microbial cells excrete a wide range of metabolites , setting the stage for interspecific metabolic interactions . The links , however , between metabolic and ecological interactions ( fu...	Understanding the structure and functioning of polymicrobial communities is a major challenge in biology , as witnessed by the dramatic yet mysterious roles played by the human microbiome in human health . Microbial multispecies communities often show complex spatial structures and patterns of metabolic exchange , yet ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	Metabolic and Demographic Feedbacks Shape the Emergent Spatial Structure and Function of Microbial Communities
A rare subset of HIV-infected individuals , designated viremic non-progressors ( VNP ) , remain asymptomatic and maintain normal levels of CD4+ T-cells despite persistently high viremia . To identify mechanisms potentially responsible for the VNP phenotype , we compared VNPs ( average >9 years of HIV infection ) to HIV...	Here we assessed correlates of protection from disease progression in a rare subset of HIV-infected individuals , viremic non-progressors ( VNP ) . These individuals have high viral load for several years . In contrast to the majority of infected individuals , however , these individuals do not progress to AIDS . Here ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "immunodeficiency", "viruses", "infectious", "diseases", "medicine", "and", "health", "sciences", "immune", "cells", "diagnostic", "medicine", "cell", "biology", "animal", "cells", "clinical", "immunology", "medical", "microbiology", "hiv", "viral", "pathogens", "hiv", ...	2014	Limited HIV Infection of Central Memory and Stem Cell Memory CD4+ T Cells Is Associated with Lack of Progression in Viremic Individuals
Atypical porcine reproductive and respiratory syndrome ( PRRS ) , which is caused by the Chinese highly pathogenic PRRS virus ( HP-PRRSV ) , has resulted in large economic loss to the swine industry since its outbreak in 2006 . However , to date , the region ( s ) within the viral genome that are related to the fatal v...	PRRS is a considerable threat to the pig industry worldwide . A large-scale atypical PRRS caused by highly pathogenic PRRSV ( HP-PRRSV ) that emerged in 2006 has resulted in considerable economic loss to Chinese pig production . The disease is characterized by a high body temperature ( 41°C–42°C ) , morbidity and by mo...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "veterinary", "microbiology", "biology", "and", "life", "sciences", "veterinary", "science" ]	2014	Nsp9 and Nsp10 Contribute to the Fatal Virulence of Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus Emerging in China
A national mapping of Schistosoma haematobium was conducted in Sierra Leone before the mass drug administration ( MDA ) with praziquantel . Together with the separate mapping of S . mansoni and soil-transmitted helminths , the national control programme was able to plan the MDA strategies according to the World Health ...	Two forms of schistosomiasis or bilharzia ( intestinal and urogenital ) exist in Sierra Leone . The main control strategy for this disease currently is through mass drug administration ( MDA ) according to the World Health Organization recommended anthelminthic chemotherapy guidelines , and others include snail control...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "disease", "mapping", "infectious", "diseases", "public", "health", "and", "epidemiology", "epidemiology", "infectious", "disease", "epidemiology", "neglected", "tropical", "diseases", "infectious", "disease", "control", "parasitic", "diseases" ]	2012	Combined Spatial Prediction of Schistosomiasis and Soil-Transmitted Helminthiasis in Sierra Leone: A Tool for Integrated Disease Control
Comparative genomics revealed in the last decade a scenario of rampant horizontal gene transfer ( HGT ) among prokaryotes , but for fungi a clearly dominant pattern of vertical inheritance still stands , punctuated however by an increasing number of exceptions . In the present work , we studied the phylogenetic distrib...	Genes are commonly vertically inherited , meaning that they share the evolutionary history of the organisms in which they are found . However , they can also be transmitted between species with overlapping niches , a phenomenon known as horizontal gene transfer ( HGT ) that can occur between closely related species but...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "organismal", "evolution", "genomics", "adaptation", "microbial", "evolution", "comparative", "genomics", "hybridization", "biology", "evolutionary", "biology", "genomic", "evolution", "evolutionary", "processes", "evolutionary", "genetics" ]	2013	Extensive Intra-Kingdom Horizontal Gene Transfer Converging on a Fungal Fructose Transporter Gene
Epilepsy is one of the most common signs of Neurocysticercosis ( NCC ) . In this study , spatial and temporal variations in the incidence of hospitalized cases ( IHC ) of epilepsy and NCC in Ecuadorian municipalities were analyzed . Additionally , potential socio-economic and landscape indicators were evaluated in orde...	T . solium neurocysticercosis is considered the most important parasitic disease of the central nervous system in humans; it is estimated to be responsible for at least one third of acquired epilepsies in developing countries . In Ecuador , the relationship between acquired epilepsy and neurocysticercosis remains uncle...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Distribution and Potential Indicators of Hospitalized Cases of Neurocysticercosis and Epilepsy in Ecuador from 1996 to 2008
Infantile beriberi ( thiamine deficiency ) occurs mainly in infants breastfed by mothers with inadequate intake of thiamine , typically among vulnerable populations . We describe possible and probable cases of infantile thiamine deficiency in northern Laos . Three surveys were conducted in Luang Namtha Province . First...	Infantile thiamine deficiency ( beriberi ) , is rarely seen today after decades of strong public health attention . Infantile beriberi occurs mainly in infants breastfed by mothers with inadequate intake of thiamine . There is evidence of the persistence of infantile thiamine deficiency in Vientiane , the capital of La...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Beriberi (Thiamine Deficiency) and High Infant Mortality in Northern Laos
Paracoccidioides lutzii is a new agent of paracoccidioidomycosis ( PCM ) and has its epicenter localized to the Central-West region of Brazil . Serological diagnosis of PCM caused by P . lutzii has not been established . This study aimed to develop new antigenic preparations from P . lutzii and to apply them in serolog...	Tropical diseases , such as paracoccidioidomycosis , are the most common type of neglected diseases . From 1980 to 1995 , 3 , 181 deaths from paracoccidioidomycosis occurred in Brazil , representing the eighth most common cause of death from predominantly chronic or recurrent types of infectious and parasitic diseases ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "mycology", "immunoassays", "biology", "and", "life", "sciences", "immunology", "microbiology", "immunologic", "techniques", "research", "and", "analysis", "methods" ]	2014	Serology of Paracoccidioidomycosis Due to Paracoccidioides lutzii
Ebola and other filoviruses pose significant public health and conservation threats by causing high mortality in primates , including humans . Preventing future outbreaks of ebolavirus depends on identifying wildlife reservoirs , but extraordinarily high biodiversity of potential hosts in temporally dynamic environment...	Preventing future outbreaks of ebolaviruses in humans and other vulnerable animal populations will require identifying the natural reservoirs of filoviruses . Accumulating indirect evidence points to certain bat species as prime suspects . To guide the search for natural filovirus reservoirs , we mined intrinsic biolog...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[ "geographical", "locations", "vertebrates", "animals", "mammals", "viruses", "filoviruses", "mathematics", "rna", "viruses", "phylogenetic", "analysis", "molecular", "biology", "techniques", "africa", "fruit", "bats", "discrete", "mathematics", "research", "and", "analysi...	2016	Undiscovered Bat Hosts of Filoviruses
Differential transcription in Ascaris suum was investigated using a genomic-bioinformatic approach . A cDNA archive enriched for molecules in the infective third-stage larva ( L3 ) of A . suum was constructed by suppressive-subtractive hybridization ( SSH ) , and a subset of cDNAs from 3075 clones subjected to microarr...	In the present study , we constructed a cDNA library enriched for molecules of the infective third-stage larva ( L3 ) of Ascaris suum , the common roundworm of pigs . Using the method of suppressive-subtractive hybridization ( SSH ) , we explored transcription of a subset of molecules by microarray analysis and conduct...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biotechnology", "genetics", "and", "genomics/genomics", "computational", "biology/transcriptional", "regulation", "computational", "biology/molecular", "genetics", "genetics", "and", "genomics/bioinformatics" ]	2008	Genomic-Bioinformatic Analysis of Transcripts Enriched in the Third-Stage Larva of the Parasitic Nematode Ascaris suum
Global genome nucleotide excision repair removes DNA damage from transcriptionally silent regions of the genome . Relatively little is known about the molecular events that initiate and regulate this process in the context of chromatin . We've shown that , in response to UV radiation–induced DNA damage , increased hist...	Protection against genotoxic insult requires a network of DNA damage responses , including DNA repair . Inherited DNA repair defects cause severe clinical consequences including extreme cancer susceptibility . Despite detailed mechanistic understanding of the core reactions , little is known about the molecular events ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "nucleic", "acids", "dna", "biology", "molecular", "cell", "biology", "dna", "repair", "molecular", "biology" ]	2011	How Chromatin Is Remodelled during DNA Repair of UV-Induced DNA Damage in Saccharomyces cerevisiae
Vector-borne diseases account for more than 17% of all infectious diseases , causing more than one million deaths annually . Malaria remains one of the most important public health problems worldwide . These vectors are bloodsucking insects , which can transmit disease-producing microorganisms during a blood meal . The...	In the era of malaria elimination , novel surveillance strategies are needed in order to achieve and sustain malaria free status in the region . New malaria infection burden surveillance strategies should be simple to implement , technologically uncomplicated , cost-effective and applicable to areas where malaria cases...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "parasite", "groups", "body", "fluids", "plasmodium", "tropical", "diseases", "vector-borne", "diseases", "parasitic", "diseases", "animals", "parasitic", "protozoans", "parasitology", "apicomplexa", "protozoans", ...	2018	Use of anthropophilic culicid-based xenosurveillance as a proxy for Plasmodium vivax malaria burden and transmission hotspots identification
Nipah virus is a zoonotic pathogen that causes severe disease in humans . The mechanisms of pathogenesis are not well described . The first Nipah virus outbreak occurred in Malaysia , where human disease had a strong neurological component . Subsequent outbreaks have occurred in Bangladesh and India and transmission an...	Nipah virus causes severe disease in humans and outbreaks have occurred in two geographic regions , Malaysia and Bangladesh , and viruses have been isolated during outbreaks from both of these regions ( NiV-M and NiV-B , respectively ) . The original outbreak of Nipah virus occurred in Malaysia and caused severe enceph...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "animal", "models", "of", "infection", "viral", "transmission", "and", "infection", "virology", "emerging", "viral", "diseases", "immunology", "biology", "microbiology", "viral", "replication" ]	2013	Comparison of the Pathogenicity of Nipah Virus Isolates from Bangladesh and Malaysia in the Syrian Hamster
The Global Program to Eliminate Lymphatic Filariasis aims to interrupt transmission of lymphatic filariasis and manage morbidity in people currently living with the disease . A component of morbidity management is improving health-related quality of life ( HRQoL ) in patients . Measurement of HRQoL in current managemen...	Lymphatic filariasis affects approximately 120 million people and is the second leading cause of life-long disability worldwide . Because lymphatic filariasis is one of the World Health Organization's six eradicable diseases , much effort has been placed into reducing transmission of the disease and managing morbidity ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "filariasis", "tropical", "diseases", "(non-neglected)", "neglected", "tropical", "diseases", "parasitic", "diseases", "lymphatic", "filariasis" ]	2014	Comparison of Three Quality of Life Instruments in Lymphatic Filariasis: DLQI, WHODAS 2.0, and LFSQQ
Francisella tularensis causes the disease tularemia . Human pulmonary exposure to the most virulent form , F . tularensis subsp . tularensis ( Ftt ) , leads to high morbidity and mortality , resulting in this bacterium being classified as a potential biothreat agent . However , a closely-related species , F . novicida ...	Francisella tularensis is a bacterium that causes the infectious disease tularemia . F . tularensis has been developed as a biothreat agent , because it causes high morbidity and mortality when spread by aerosol . There is currently no approved vaccine for human use , making mankind vulnerable to the illicit use of thi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "medicine", "and", "health", "sciences", "biology", "and", "life", "sciences", "immunology", "microbiology" ]	2014	Live Attenuated Francisella novicida Vaccine Protects against Francisella tularensis Pulmonary Challenge in Rats and Non-human Primates
Patients with localized tuberculoid and generalized lepromatous leprosy show respectively Th1 and Th2 cytokine profile . Additionally , other patients in both types of leprosy also show a non discriminating Th0 cytokine profile with both interferon-γ and IL-4 . The present study investigated the role of Th17 cells whic...	Leprosy caused by Mycobacterium leprosy continues to be a public health challenge in developing countries . It manifests as a leprosy spectrum with varied clinical forms of localized ( tuberculoid ) and generalized ( lepromatous ) disease . Consensus on the immunological basis for leprosy spectrum is lacking . T helper...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "immunopathology", "immune", "cells", "t", "cells", "immunology", "biology", "immune", "response" ]	2013	CD4+ Th17 Cells Discriminate Clinical Types and Constitute a Third Subset of Non Th1, Non Th2 T Cells in Human Leprosy
Polyomavirus BKV is highly prevalent among humans . The virus establishes an asymptomatic persistent infection in the urinary system in healthy people , but uncontrolled productive infection of the virus in immunocompromised patients can lead to serious diseases . In spite of its high prevalence , our knowledge regardi...	Infection by polyomavirus BKV is common and mostly harmless in healthy populations but can cause severe damages to kidney and bladder in transplant recipients . The infection by BKV usually occurs in early childhood and persists chronically in the urinary system throughout life . Our data show that this virus has the a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "respiratory", "infections", "endothelial", "cells", "immunology", "bladder", "cell", "processes", "pulmonology", "epithelial", "cells", "cell", "proliferation", "animal", "cells", "proteins", "gene", "expression", "biological", ...	2019	Human polyomavirus BKV infection of endothelial cells results in interferon pathway induction and persistence
The viral family Arenaviridae includes a number of viruses that can cause hemorrhagic fever in humans . Arenavirus infection often involves multiple organs and can lead to capillary instability , impaired hemostasis , and death . Preclinical testing for development of antiviral or therapeutics is in part hampered due t...	Arenaviruses are carried by rodents , and in South America and West Africa can cause a fatal hemorrhagic fever syndrome in humans . Food , water or household items contaminated with rodent urine can be a source for transmission . General supportive care , anti-fever medication and the antiviral drug Ribaviran are used ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "and", "Methods" ]	[ "immune", "cells", "immunity", "to", "infections", "immunology", "microbiology", "host-pathogen", "interaction", "animal", "models", "model", "organisms", "inflammation", "t", "cells", "biology", "mouse", "immune", "response", "immunopathology", "immunity", "virology" ]	2012	Lymphocytic Choriomeningitis Virus Infection in FVB Mouse Produces Hemorrhagic Disease
Ornithodoros turicata is a veterinary and medically important argasid tick that is recognized as a vector of the relapsing fever spirochete Borrelia turicatae and African swine fever virus . Historic collections of O . turicata have been recorded from Latin America to the southern United States . However , the geograph...	Argasid ticks are understudied vectors of significant human and veterinary pathogens . The life-cycle and feeding behavior of the tick poses challenges when attempting to understand the vector’s distribution . These ticks reside in dens , nests , and cave cavities , and are indiscriminant nocturnal feeders . They also ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "united", "states", "invertebrates", "livestock", "medicine", "and", "health", "sciences", "ixodes", "pathology", "and", "laboratory", "medicine", "atmospheric", "science", "pathogens", "geographical", "locations", "vertebrates", "animals", "mammals", "north", "america", ...	2016	Assessment of the Geographic Distribution of Ornithodoros turicata (Argasidae): Climate Variation and Host Diversity
Alveolar echinococcosis ( AE ) is a parasitic zoonosis resembling malignancy due to its clinically silent infiltrative growth , predominately in the liver . The comorbid psychological burden and fear of disease progression in AE patients have hardly been examined to date . The aim of this study was to evaluate depressi...	Alveolar echinococcosis ( AE ) is a parasitic zoonosis resembling malignancy due to its clinically silent infiltrative growth , predominately in the liver . For some somatic diseases , comorbid psychological burden predicts the course of disease . However , as far as we are aware , little is known about comorbid psycho...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "neuropsychiatric", "disorders", "medicine", "and", "health", "sciences", "psychotherapy", "anxiety", "disorders", "post-traumatic", "stress", "disorder", "tropical", "diseases", "social", "sciences", "parasitic", "diseases", "health", "care", "mental", "health", "therapi...	2019	Psychological burden and resilience factors in patients with Alveolar Echinococcosis – A cross-sectional study
Spider silk fibers are produced from soluble proteins ( spidroins ) under ambient conditions in a complex but poorly understood process . Spidroins are highly repetitive in sequence but capped by nonrepetitive N- and C-terminal domains ( NT and CT ) that are suggested to regulate fiber conversion in similar manners . B...	The spinning process of spider silk is crucial for making webs or other complex constructions to catch spider's prey . The main components of the silk are spidroins , which are large and repetitive proteins that have conserved nonrepetitive terminal domains ( NT and CT ) . Spiders manage both to store the highly aggreg...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "physiological", "processes", "proteins", "protein", "folding", "physiology", "protein", "structure", "biology", "and", "life", "sciences", "biophysics" ]	2014	Carbonic Anhydrase Generates CO2 and H+ That Drive Spider Silk Formation Via Opposite Effects on the Terminal Domains
Retrograde axonal transport requires an intricate interaction between the dynein motor and its cargo . What mediates this interaction is largely unknown . Using forward genetics and a novel in vivo imaging approach , we identified JNK-interacting protein 3 ( Jip3 ) as a direct mediator of dynein-based retrograde transp...	To form and maintain connections , neurons require the active transport of proteins and organelles between the neuronal cell body and axon terminals . Inhibition of this “axonal” transport has been linked to neurodegenerative diseases . Despite the importance of this process , to date there was no vertebrate model syst...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "developmental", "biology", "zebrafish", "developmental", "neuroscience", "model", "organisms", "biology", "neuroscience" ]	2013	JNK-Interacting Protein 3 Mediates the Retrograde Transport of Activated c-Jun N-Terminal Kinase and Lysosomes
Rift Valley fever ( RVF ) outbreaks are recurrent , occurring at irregular intervals of up to 15 years at least in East Africa . Between outbreaks disease inter-epidemic activities exist and occur at low levels and are maintained by female Aedes mcintoshi mosquitoes which transmit the virus to their eggs leading to dis...	Rift Valley fever ( RVF ) is a relatively novel vector-borne zoonotic disease , with long and irregular periods between outbreaks . Although outbreaks are highly correlated with occurrence of abnormal rainfall and flooding regimes , there have been instances with above normal rainfall where no disease outbreaks were re...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "livestock", "medicine", "and", "health", "sciences", "rift", "valley", "fever", "virus", "pathology", "and", "laboratory", "medicine", "infectious", "disease", "epidemiology", "pathogens", "vector-borne", "diseases", "microbiology", "tropical", "diseases...	2016	Predicting Rift Valley Fever Inter-epidemic Activities and Outbreak Patterns: Insights from a Stochastic Host-Vector Model
Although the malaria burden in the Lao PDR has gradually decreased , the elimination of malaria by 2030 presents many challenges . Microscopy and malaria rapid diagnostic tests ( RDTs ) are used to diagnose malaria in the Lao PDR; however , some studies have reported the prevalence of sub-microscopic Plasmodium infecti...	The Lao People’s Democratic Republic ( Laos ) is a country in the Greater Mekong Subregion . In Laos , the numbers of reported cases of malaria and deaths due to malaria have been gradually decreasing . Recently , the Lao government adopted a goal of eliminating malaria by 2030 . To achieve this goal , we must understa...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "parasite", "groups", "medicine", "and", "health", "sciences", "lao", "people", "pathology", "and", "laboratory", "medicine", "plasmodium", "tropical", "diseases", "plasmodium", "falciparum", "parasitic", "diseases", "parasitic", "protozoans", "parasitology", "ethnicities...	2017	The detection of cryptic Plasmodium infection among villagers in Attapeu province, Lao PDR
Host defence peptides ( HDPs ) are expressed throughout the animal and plant kingdoms . They have multifunctional roles in the defence against infectious agents of mammals , possessing both bactericidal and immune-modulatory activities . We have identified a novel family of molecules secreted by helminth parasites ( he...	In mammals , secreted host defence peptides ( HDPs ) protect against a wide range of infectious pathogens . They also perform a range of immune modulatory functions which regulate the immune response to pathogens , ensuring that the protective inflammatory response is not exacerbated and that post-infection repair mech...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "immunology", "biology" ]	2013	Cathelicidin-like Helminth Defence Molecules (HDMs): Absence of Cytotoxic, Anti-microbial and Anti-protozoan Activities Imply a Specific Adaptation to Immune Modulation
Rapid pathogen identification during an acute febrile illness is a critical first step for providing appropriate clinical care and patient isolation . Primary screening using sensitive and specific assays , such as real-time PCR and ELISAs , can rapidly test for known circulating infectious diseases . If the initial te...	Identifying the causative agent in an acute febrile illness can be challenging diagnostically , especially when organisms in a particular region have overlapping clinical presentation or when that pathogen’s presence is unexpected . Ebola virus , for example , was not considered in an acute febrile illness differential...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "dengue", "virus", "medicine", "and", "health", "sciences", "parasite", "groups", "pathology", "and", "laboratory", "medicine", "togaviruses", "plasmodium", "pathogens", "microbiology", "orthomyxoviruses", "alphaviruses", "parasitology", "viruses", "organisms", "apicomplexa...	2018	A highly multiplexed broad pathogen detection assay for infectious disease diagnostics
Alignments of orthologous protein sequences convey a complex picture . Some positions are utterly conserved whilst others have diverged to variable degrees . Amongst the latter , many are non-exchangeable between extant sequences . How do functionally critical and highly conserved residues diverge ? Why and how did the...	Orthologs are proteins in different species sharing the same function and structure . However , the mechanisms that underline the divergence of different sequences from a single ancestor remain unclear , particularly because many amino acid exchanges between orthologs result in loss of function ( incompatibility ) . We...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "biochemistry", "genetics", "biology", "genomics", "evolutionary", "biology" ]	2013	Mechanisms of Protein Sequence Divergence and Incompatibility
MRP4 ( multidrug resistance-associated protein 4 ) is a member of the MRP/ABCC subfamily of ATP-binding cassette ( ABC ) transporters that are essential for many cellular processes requiring the transport of substrates across cell membranes . Although MRP4 has been implicated as a detoxification protein by transport of...	The drug transporters are often known for their ability to transport different physiological-related compounds across cell membranes . Although the abnormal up-regulation of some these transporters is believed to be the common cause of the clinic problem called drug resistance , the biological functions of these transp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "biology", "and", "life", "sciences" ]	2014	A Drosophila ABC Transporter Regulates Lifespan
Glossina fuscipes fuscipes is the main vector of human and animal trypanosomiasis in Africa , particularly in Uganda . Attempts to control/eradicate this species using biological methods require knowledge of its reproductive biology . An important aspect is the number of times a female mates in the wild as this influen...	Glossina fuscipes fuscipes is the most common tsetse species in Uganda where it is responsible for transmitting Trypanosoma brucei rhodensiense and Trypanosoma brucei gambiense parasites causing sleeping sickness in humans in addition to related trypanosomes that cause Nagana in cattle . An understanding of the reprodu...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "statistics", "population", "genetics", "gene", "pool", "mathematical", "computing", "mathematics", "effective", "population", "size", "population", "modeling", "theoretical", "ecology", "population", "biology", "biostatistics", "genetic", "polymorphism", "biology", "popula...	2011	Polyandry Is a Common Event in Wild Populations of the Tsetse Fly Glossina fuscipes fuscipes and May Impact Population Reduction Measures
Encounters between human neutrophils and zymosan elicit an initially protrusive cell response that is distinct from the thin lamella embracing antibody-coated targets . Recent experiments have led us to hypothesize that this behavior has its mechanistic roots in the modulation of interactions between membrane and cytos...	Recent micropipette experiments have provided a unique live view of “one-on-one” interactions between human neutrophils and their phagocytic targets . Our results revealed surprising differences between two prominent immunological pathways: the response to fungal targets ( mimicked using zymosan particles ) , and antib...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biophysics/theory", "and", "simulation", "immunology/immune", "response", "immunology/innate", "immunity", "computational", "biology", "physics/interdisciplinary", "physics" ]	2011	Protrusive Push versus Enveloping Embrace: Computational Model of Phagocytosis Predicts Key Regulatory Role of Cytoskeletal Membrane Anchors
Many chronic infections , including malaria and HIV , are associated with a large expansion of CD21−CD27− ‘atypical’ memory B cells ( MBCs ) that exhibit reduced B cell receptor ( BCR ) signaling and effector functions . Little is known about the conditions or transcriptional regulators driving atypical MBC differentia...	Antibodies are proteins in blood that help kill microbes such as viruses , bacteria and parasites . Antibodies are produced by B cells with the help of T follicular helper ( Tfh ) cells . Some microbes for which we have no effective vaccines , such as HIV and malaria , establish chronic infections that are not cleared ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "chemical", "bonding", "innate", "immune", "system", "medicine", "and", "health", "sciences", "children", "immune", "cells", "immune", "physiology", "cytokines", "immunology", "tropical", "diseases", "parasitic", "diseases", "cell", "differentiation", ...	2017	Malaria-induced interferon-γ drives the expansion of Tbethi atypical memory B cells
In 2008 a nosocomial outbreak of five cases of viral hemorrhagic fever due to a novel arenavirus , Lujo virus , occurred in Johannesburg , South Africa . Lujo virus is only the second pathogenic arenavirus , after Lassa virus , to be recognized in Africa and the first in over 40 years . Because of the remote , resource...	Viral hemorrhagic fever is a syndrome often associated with high fatality and risk of secondary transmission . In 2008 , an outbreak of a novel hemorrhagic fever virus called Lujo occurred in Johannesburg , South Africa , with secondary transmission from the index patient to four healthcare workers . Four of the five p...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "viral", "diseases", "infectious", "diseases", "medicine", "and", "health", "sciences" ]	2014	Clinical Features and Patient Management of Lujo Hemorrhagic Fever
Salmonella Typhi and Salmonella Paratyphi A are the agents of enteric ( typhoid ) fever; both can establish chronic carriage in the gallbladder . Chronic Salmonella carriers are typically asymptomatic , intermittently shedding bacteria in the feces , and contributing to disease transmission . Detecting chronic carriers...	Enteric fever , caused by typhoidal Salmonella serovars , remains a substantial public health problem in many low- and middle-income countries . The human-restricted nature of these organisms combined with the development of new vaccines suggests that regional elimination of enteric fever should be possible . However ,...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biliary", "system", "medicine", "and", "health", "sciences", "liver", "pathology", "and", "laboratory", "medicine", "gallbladder", "pathogens", "microbiology", "biomarkers", "salmonella", "typhi", "surgical", "and", "invasive", "medical", "procedures", "multivariate", ...	2018	Diagnostic metabolite biomarkers of chronic typhoid carriage
The main constraint to the fight against container-breeding mosquito vectors of human arboviruses is the difficulty in targeting the multiplicity of larval sources , mostly represented by small man-made water containers . The aim of this work is to assess the feasibility of the “auto-dissemination” approach , already t...	Aedes albopictus ( the Asian Tiger mosquito ) is one of the most invasive and aggressive disease vectors in the world . It is a serious public nuisance and a public health risk , due to its ability to transmit pathogens to humans . The control of this mosquito is complicated by the difficulty in targeting either juveni...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "ecology", "biology", "public", "health" ]	2012	The “Auto-Dissemination” Approach: A Novel Concept to Fight Aedes albopictus in Urban Areas
Effective T cell responses can decisively influence the outcome of retroviral infection . However , what constitutes protective T cell responses or determines the ability of the host to mount such responses is incompletely understood . Here we studied the requirements for development and induction of CD4+ T cells that ...	Our immune systems defend against viral infection . However , the immune response to a virus often differs substantially between individuals , as does the outcome of infection . The antiviral immune response relies on recognition of viral proteins by T lymphocytes using T cell antigen receptors ( TCRs ) . TCRs are crea...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "adaptive", "immunity", "immune", "cells", "immunity", "t", "cells", "immunity", "to", "infections", "immunology", "biology", "immune", "response" ]	2012	Negative Selection by an Endogenous Retrovirus Promotes a Higher-Avidity CD4+ T Cell Response to Retroviral Infection
Buruli ulcer , an emerging tropical disease caused by Mycobacterium ulcerans ( MU ) , is characterized by disfiguring skin necrosis and high morbidity . Relatively little is understood about the mode of transmission , pathogenesis , or host immune responses to MU infection . Due to significant reduction in quality of l...	Buruli ulcer , caused by subcutaneous infection with Mycobacterium ulcerans , is a highly disfiguring flesh-eating skin disease with significant morbidity . Besides surgical intervention , 8-week combination antibiotics is the standard of care . However , problems with resistance and toxicity warrant their replacement ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Recombinant BCG Expressing Mycobacterium ulcerans Ag85A Imparts Enhanced Protection against Experimental Buruli ulcer
Eastern equine encephalitis ( EEE ) virus ( Togaviridae , Alphavirus ) is a highly pathogenic mosquito-borne zoonosis that is responsible for occasional outbreaks of severe disease in humans and equines , resulting in high mortality and neurological impairment in most survivors . In the past , human disease outbreaks i...	Eastern equine encephalitis ( EEE ) is a highly pathogenic mosquito-borne virus responsible for outbreaks of severe disease in humans and equines , causing high mortality and neurological impairment in most survivors . In the past , human disease outbreaks in the northeastern U . S . occurred sporadically with no appar...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2016	Dynamics of Vector-Host Interactions in Avian Communities in Four Eastern Equine Encephalitis Virus Foci in the Northeastern U.S.
Hybrid incompatibilities play a critical role in the evolution and maintenance of species . We have discovered a simple genetic incompatibility that causes lethality in hybrids between two closely related species of yellow monkeyflower ( Mimulus guttatus and M . nasutus ) . This hybrid incompatibility , which causes on...	The evolution of hybrid incompatibilities ( gene interactions that cause hybrids to be sterile or inviable ) is a common outcome of genomic divergence between lineages . However , evaluating the importance of hybrid incompatibilities for speciation requires that we identify the causal genes and evolutionary forces in r...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "plant", "cell", "biology", "brassica", "chloroplasts", "alleles", "plant", "science", "model", "organisms", "genome", "analysis", "experimental", "organism", "systems", "seedlings", "plants", "cellular", "structures", "and", "organelles", "arabidopsis", "thaliana", "re...	2018	Gene duplicates cause hybrid lethality between sympatric species of Mimulus
Dimensionality is a fundamental component that can have profound implications on the characteristics of physical systems . In cell biology , however , the majority of studies on cell physical properties , from rheology to force generation to migration , have been performed on 2D substrates , and it is not clear how a m...	Biomechanical properties at the cellular and subcellular levels are important in providing proper biological functions , from cell migratory capabilities to intracellular transport . Deregulation in these properties can lead to disease states such as cancer metastasis . We develop and demonstrate an integrated experime...	[ "Abstract", "Introduction", "Methods", "Results", "and", "Discussion" ]	[ "biotechnology", "bioengineering", "biology", "and", "life", "sciences", "cell", "mechanics", "biophysics", "biomechanics" ]	2014	Impact of Dimensionality and Network Disruption on Microrheology of Cancer Cells in 3D Environments
Current therapies for cutaneous leishmaniasis are limited by poor efficacy , long-term course of treatment , and the development of resistance . We evaluated if pentavalent antimony ( an anti-parasitic drug ) combined with imiquimod ( an immunomodulator ) was more effective than pentavalent antimony alone in patients w...	Neglected tropical diseases ( NTDs ) are a group of tropical infections including trypanosomiasis , filariasis , schistosomiasis , onchocerciasis , leishmaniasis and other such diseases of poverty . Of the classic neglected diseases , leishmaniasis has among the highest level of morbidity and mortality . Infection with...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "microbiology/immunity", "to", "infections" ]	2009	First-Line Therapy for Human Cutaneous Leishmaniasis in Peru Using the TLR7 Agonist Imiquimod in Combination with Pentavalent Antimony
The molecular events leading to the development of the bat wing remain largely unknown , and are thought to be caused , in part , by changes in gene expression during limb development . These expression changes could be instigated by variations in gene regulatory enhancers . Here , we used a comparative genomics approa...	The limb is a classic example of vertebrate homology and is represented by a large range of morphological structures such as fins , legs and wings . The evolution of these structures could be driven by alterations in gene regulatory elements that have critical roles during development . To identify elements that may co...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "split-decomposition", "method", "vertebrates", "animals", "mammals", "multiple", "alignment", "calculation", "developmental", "biology", "sequence", "motif", "analysis", "molecular", "biology", "techniques", "mammalian", "genomics", "embryos", "...	2016	Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the HoxD Locus
Neural Mass Models provide a compact description of the dynamical activity of cell populations in neocortical regions . Moreover , models of regional activity can be connected together into networks , and inferences made about the strength of connections , using M/EEG data and Bayesian inference . To date , however , B...	The activity of populations of neurons in the human brain can be described using a set of differential equations known as a neural mass model . These models can then be connected to describe activity in multiple brain regions and , by fitting them to human brain imaging data , statistical inferences can be made about c...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "engineering", "and", "technology", "applied", "mathematics", "signal", "processing", "neuroscience", "simulation", "and", "modeling", "algorithms", "regression", "analysis", "optimization", "mathematics", "statistics", "(mathematics)", "neuroimaging", "research", "and", "a...	2016	Annealed Importance Sampling for Neural Mass Models
The replication terminus region ( Ter ) of the unique chromosome of most bacteria locates at mid-cell at the time of cell division . In several species , this localization participates in the necessary coordination between chromosome segregation and cell division , notably for the selection of the division site , the l...	The genome of Vibrio cholerae is divided into two circular chromosomes , chrI and chrII . ChrII is derived from a horizontally acquired mega-plasmid , which raised questions on the necessary coordination of the processes that ensure its segregation with the cell division cycle . Here , we show that the MatP/matS macrod...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "biology", "genetics", "biology", "and", "life", "sciences", "microbiology", "molecular", "cell", "biology" ]	2014	Differential Management of the Replication Terminus Regions of the Two Vibrio cholerae Chromosomes during Cell Division
Coalescent theory is routinely used to estimate past population dynamics and demographic parameters from genealogies . While early work in coalescent theory only considered simple demographic models , advances in theory have allowed for increasingly complex demographic scenarios to be considered . The success of this a...	Mathematical models play an important role in our understanding of what processes drive the complex population dynamics of infectious pathogens . Yet developing statistical methods for fitting models to epidemiological data is difficult . Epidemiological data is often noisy , incomplete , aggregated across different sc...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "mathematics", "statistics", "(mathematics)", "epidemiology", "population", "dynamics", "biology", "and", "life", "sciences", "population", "genetics", "population", "biology", "physical", "sciences", "evolutionary", "biology", "st...	2014	Phylodynamic Inference for Structured Epidemiological Models
The vast majority of meiotic recombination events ( crossovers ( COs ) and non-crossovers ( NCOs ) ) cluster in narrow hotspots surrounded by large regions devoid of recombinational activity . Here , using a new molecular approach in plants , called “pollen-typing” , we detected and characterized hundreds of CO and NCO...	During meiosis , genomes are reshuffled by recombination between homologous chromosomes . Reciprocal recombination events called crossovers are clustered in several kilobase-wide regions called hotspots , where their frequency is greatly enhanced compared to adjacent regions . Our understanding of hotspot organization ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Contrasted Patterns of Crossover and Non-crossover at Arabidopsis thaliana Meiotic Recombination Hotspots
Seasonal influenza virus infections can cause significant morbidity and mortality , but the threat from the emergence of a new pandemic influenza strain might have potentially even more devastating consequences . As such , there is intense interest in isolating and characterizing potent neutralizing antibodies that tar...	Influenza viruses cause severe respiratory infections on a global scale annually . Vaccine efforts are hampered by the virus’s naturally high mutation rate , which results in wide variation between influenza strains of the antigens that are produced and recognized by antibodies , particularly in the surface glycoprotei...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "chemical", "characterization", "immune", "physiology", "crystal", "structure", "pathology", "and", "laboratory", "medicine", "influenza", "pathogens", "immunology", "condensed", "matter", "physics", "microbiology", "orthomyxoviruses...	2019	Potent anti-influenza H7 human monoclonal antibody induces separation of hemagglutinin receptor-binding head domains
A drug exerts its effects typically through a signal transduction cascade , which is non-linear and involves intertwined networks of multiple signaling pathways . Construction of such a signaling pathway network ( SPNetwork ) can enable identification of novel drug targets and deep understanding of drug action . Howeve...	A deep understanding of a drug’s mechanisms of actions is essential not only in the discovery of new treatments but also in minimizing adverse effects . Here , we develop a computational framework , the Drug-specific Signaling Pathway Network ( DSPathNet ) , to reconstruct a comprehensive signaling pathway network ( SP...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action
Enterovirus 71 ( EV71 ) causes hand , foot and mouth disease , a mild and self-limited illness that is sometimes associated with severe neurological complications . EV71 neurotropic determinants remain ill-defined to date . We previously identified a mutation in the VP1 capsid protein ( L97R ) that was acquired over th...	Enterovirus 71 ( EV71 ) has been the cause of major hand-foot-and-mouth disease outbreaks , particularly in the Asia-Pacific region . However , the recent emergence of severe neurological cases associated with EV71 infection in Europe and the lack of an efficient vaccine or antiviral agent to fight EV71 infections high...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "binding", "cell", "physiology", "medicine", "and", "health", "sciences", "chemical", "characterization", "respiratory", "infections", "biological", "cultures", "microbiology", "neuroscience", "pulmonology", "caco-2", "cells", "digestive", "system", "research", "a...	2018	A VP1 mutation acquired during an enterovirus 71 disseminated infection confers heparan sulfate binding ability and modulates ex vivo tropism
Ciliopathies are genetic disorders arising from dysfunction of microtubule-based cellular appendages called cilia . Different cilia types possess distinct stereotypic microtubule doublet arrangements with non-motile or ‘primary’ cilia having a 9+0 and motile cilia have a 9+2 array of microtubule doublets . Primary cili...	Growth-Arrest Specific 8 ( Gas8 ) is implicated in dual roles at both the primary cilium to regulate hedgehog signaling and in motile cilia to coordinate cilia movement . To investigate these roles in vivo , we created a Gas8 genetrap mutant mouse . Though no overt primary cilia phenotypes were evident in the Gas8 gene...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "microtubules", "pathogens", "alleles", "animal", "models", "respiratory", "system", "model", "organisms", "trachea", "cellular", "structures", "and", "organelles", "cytoskeleton", "r...	2016	Mutation of Growth Arrest Specific 8 Reveals a Role in Motile Cilia Function and Human Disease
Coronavirus replication takes place in the host cell cytoplasm and triggers inflammatory gene expression by poorly characterized mechanisms . To obtain more insight into the signals and molecular events that coordinate global host responses in the nucleus of coronavirus-infected cells , first , transcriptome dynamics w...	Coronaviruses are major human and animal pathogens . They belong to a family of plus-strand RNA viruses that have extremely large genomes and encode a variety of proteins involved in virus-host interactions . The four common coronaviruses ( HCoV-229E , NL63 , OC43 , HKU1 ) cause mainly upper respiratory tract infection...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "viral", "transmission", "and", "infection", "gene", "regulation", "microbiology", "dna", "transcription", "epigenetics", "microbial", "genetics", "chromatin", "chromosome", "biology", "proteins", "gene", "expression", "viral", "replication", "viral", "...	2017	The NF-κB-dependent and -independent transcriptome and chromatin landscapes of human coronavirus 229E-infected cells
To maintain a particular cell fate , a unique set of genes should be expressed while another set is repressed . One way to repress gene expression is through Polycomb group ( PcG ) proteins that compact chromatin into a silent configuration . In addition to cell fate maintenance , PcG proteins also maintain normal cell...	Genetic information is stored in our genomic DNA , and different cells retrieve distinct sets of information from our genome . While it is important to activate genomic regions encoding proteins that are essential for a given cell type , it is equally important to silence genomic regions encoding proteins that are pote...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "gene", "regulation", "dna-binding", "proteins", "cloning", "dna", "transcription", "mutation", "developmental", "biology", "molecular", "biology", "techniques", "eyes", "morphogenesis", "research", "and", "analysis", "methods", ...	2016	dBRWD3 Regulates Tissue Overgrowth and Ectopic Gene Expression Caused by Polycomb Group Mutations
Enteropathogenic and enterohemorrhagic Escherichia coli ( EPEC/EHEC ) are human intestinal pathogens responsible for diarrhea in both developing and industrialized countries . In research laboratories , EPEC and EHEC are defined on the basis of their pathogenic features; nevertheless , their identification in routine l...	A rapid and low-cost diagnosis for EPEC/EHEC infections is extremely required considering their global prevalence , the severity of the diseases associated with them , and the fact that the use of antibiotics to treat EHEC infections can be harmful . For EHEC , the detection of Stx toxins has already been developed , b...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "bacterial", "diseases", "infectious", "diseases", "medicine", "and", "health", "sciences", "diagnostic", "medicine", "antigen-antibody", "reaction", "analysis", "emerging", "infectious", "diseases", "antibody", "production", "serodiagnosis", "immunoassays", "antibody", "is...	2014	Development of a Rapid Agglutination Latex Test for Diagnosis of Enteropathogenic and Enterohemorrhagic Escherichia coli Infection in Developing World: Defining the Biomarker, Antibody and Method
Mutated NLRP3 assembles a hyperactive inflammasome , which causes excessive secretion of interleukin ( IL ) -1β and IL-18 and , ultimately , a spectrum of autoinflammatory disorders known as cryopyrinopathies of which neonatal-onset multisystem inflammatory disease ( NOMID ) is the most severe phenotype . NOMID mice ph...	The NLRP3 inflammasome plays an important role in the maturation of interleukin ( IL ) -1β and IL-18 . Accordingly , NLRP3 gain-of-function mutations , which cause a spectrum of autoinflammatory disorders known as cryopyrin-associated periodic syndromes ( CAPS ) , are associated with excessive IL-1β and IL-18 productio...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]	[ "flow", "cytometry", "inflammatory", "diseases", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "spleen", "immunology", "animal", "models", "bone", "marrow", "ce...	2018	Gasdermin D mediates the pathogenesis of neonatal-onset multisystem inflammatory disease in mice
Why are mitochondria almost always inherited from one parent during sexual reproduction ? Current explanations for this evolutionary mystery include conflict avoidance between the nuclear and mitochondrial genomes , clearing of deleterious mutations , and optimization of mitochondrial-nuclear coadaptation . Mathematica...	Mitochondria contain genes that encode the machinery needed to power cells . Unlike the nuclear genome , the mitochondrial genome is typically inherited from one parent only ( uniparental inheritance ) . The most common explanation for uniparental inheritance is the genomic conflict theory , which states that uniparent...	[ "Abstract", "Introduction", "Results", "Discussion", "Model" ]	[]	2015	Selection against Heteroplasmy Explains the Evolution of Uniparental Inheritance of Mitochondria
Mosquitoes are incriminated as vectors for many crippling diseases , including malaria , West Nile fever , Dengue fever , and other neglected tropical diseases ( NTDs ) . microRNAs ( miRNAs ) can interact with multiple target genes to elicit biological functions in the mosquitoes . However , characterization and functi...	Millions of human infections are caused by mosquito-borne diseases , so understanding the molecular and genetic mechanisms that determine variability in transmission efficiency and insect susceptibility may assist with novel vector control strategies . Recently , microRNAs ( miRNAs ) have been studied as post-transcrip...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "chikungunya", "infection", "gene", "regulation", "tropical", "diseases", "animals", "wolbachia", "micrornas", "neglected", "tropical", "diseases", "infectious", "disease", "control", "insect", ...	2018	microRNA profiles and functions in mosquitoes
Myeloid dendritic cells ( DCs ) can capture HIV-1 via the receptor CD169/Siglec-1 that binds to the ganglioside , GM3 , in the virus particle membrane . In turn , HIV-1 particles captured by CD169 , an I-type lectin , whose expression on DCs is enhanced upon maturation with LPS , are protected from degradation in CD169...	Dendritic cells ( DCs ) are professional antigen presenting cells , and their sentinel roles are important to elicit a potent antiviral immunity . However , HIV-1 has exploited DCs to spread infection by several mechanisms . One such mechanism is the DC-mediated trans-infection pathway , whereby DCs transmit captured v...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	CD169-Mediated Trafficking of HIV to Plasma Membrane Invaginations in Dendritic Cells Attenuates Efficacy of Anti-gp120 Broadly Neutralizing Antibodies
It is often supposed that a protein's rate of evolution and its amino acid content are determined by the function and anatomy of the protein . Here we examine an alternative possibility , namely that the requirement to specify in the unprocessed RNA , in the vicinity of intron–exon boundaries , information necessary fo...	Most of the DNA in our genes is actually not involved in the specification of proteins . Rather , the bits with the protein-coding information ( exons ) are separated from each other by noncoding bits , introns . Before a gene can be translated into protein these introns are removed and the exons are spliced back toget...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "none", "computational", "biology", "evolutionary", "biology", "genetics", "and", "genomics" ]	2007	Splicing and the Evolution of Proteins in Mammals
Long-term memories are likely stored in the synaptic weights of neuronal networks in the brain . The storage capacity of such networks depends on the degree of plasticity of their synapses . Highly plastic synapses allow for strong memories , but these are quickly overwritten . On the other hand , less labile synapses ...	Memory is critical to virtually all aspects of behavior , which may explain why memory is such a complex phenomenon involving numerous interacting mechanisms that operate across multiple brain regions . Many of these mechanisms cooperate to transform initially fragile memories into more permanent ones ( memory consolid...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience", "learning", "and", "memory", "biology", "computational", "neuroscience" ]	2013	Efficient Partitioning of Memory Systems and Its Importance for Memory Consolidation
Schistosomiasis and opisthorchiasis are of public health importance in Southeast Asia . Praziquantel ( PZQ ) is the drug of choice for morbidity control but few dose comparisons have been made . Ninety-three schoolchildren were enrolled in an area of Lao PDR where Schistosoma mekongi and Opisthorchis viverrini coexist ...	Parasitic worm infections are of public health importance in Southeast Asia . Particularly , the blood-dwelling Schistosoma mekongi worm , which is acquired by skin contact with the infectious cercariae in freshwater , can lead to liver enlargement . An infection with Opisthorchis viverrini is obtained by consumption o...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "clinical", "research", "design", "infectious", "disease", "epidemiology", "parasitic", "diseases", "food-borne", "trematodes", "parasitology", "preventive", "medicine", "neglected", "tropical", "diseases", "infectious"...	2012	Efficacy of Praziquantel against Schistosoma mekongi and Opisthorchis viverrini: A Randomized, Single-Blinded Dose-Comparison Trial
The replication time of Saccharomyces cerevisiae telomeres responds to TG1–3 repeat length , with telomeres of normal length replicating late during S phase and short telomeres replicating early . Here we show that Tel1 kinase , which is recruited to short telomeres , specifies their early replication , because we find...	The ends of chromosomes are protected by specialized structures called telomeres , which prevent their recognition as DNA breaks and enable recruitment of telomerase , the reverse transcriptase that maintains telomere length by replacing terminal TG-repeat sequences lost during successive rounds of DNA replication . Ch...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "cell", "biology", "cell", "biology", "biology", "and", "life", "sciences", "chromosome", "biology" ]	2014	At Short Telomeres Tel1 Directs Early Replication and Phosphorylates Rif1
Cockayne syndrome is an inherited premature aging disease associated with numerous developmental and neurological defects , and mutations in the gene encoding the CSB protein account for the majority of Cockayne syndrome cases . Accumulating evidence suggests that CSB functions in transcription regulation , in addition...	Cockayne syndrome is a devastating inherited disease , in which patients appear to age prematurely , have sun sensitivity and suffer from profound neurological and developmental defects . Mutations in the CSB gene account for the majority of Cockayne syndrome cases . CSB is an ATP-dependent chromatin remodeler , and th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "cell", "biology", "genetics", "biology", "and", "life", "sciences", "genomics", "molecular", "cell", "biology" ]	2014	The Sequence-Specific Transcription Factor c-Jun Targets Cockayne Syndrome Protein B to Regulate Transcription and Chromatin Structure
Replication fork stalling and collapse is a major source of genome instability leading to neoplastic transformation or cell death . Such stressed replication forks can be conservatively repaired and restarted using homologous recombination ( HR ) or non-conservatively repaired using micro-homology mediated end joining ...	The cell itself damages its own DNA throughout the cell cycle as a result of oxidative metabolism , and this damage creates barriers for replication fork progression . Thus , DNA replication is not a smooth and continuous process , but rather one of stalls and restarts . Therefore , proper replication fork restart is c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	EEPD1 Rescues Stressed Replication Forks and Maintains Genome Stability by Promoting End Resection and Homologous Recombination Repair
Kynurenines , the main products of tryptophan catabolism , possess both prooxidant and anioxidant effects . Having multiple neuroactive properties , kynurenines are implicated in the development of neurological and cognitive disorders , such as Alzheimer's , Parkinson's , and Huntington's diseases . Autoxidation of 3-h...	Kynurenines , the tryptophan metabolites with multiple biological activities , regulate the production of reactive oxygen species ( ROS ) during several neurodegenerative diseases . Many experiments show that kynurenines can be both prooxidants and antioxidants depending on their concentration , mode of action , and ce...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "chemical", "compounds", "density", "functional", "theory", "solutions", "enthalpy", "materials", "science", "chemical", "radicals", "quantum", "mechanics", "thermodynamics", "materials", "by", "structure", "physical", "chemistry", "chemistry", "free", "radicals", "oxidat...	2016	Antioxidant Properties of Kynurenines: Density Functional Theory Calculations
Staphylococcus aureus requires branched-chain amino acids ( BCAAs; isoleucine , leucine , valine ) for protein synthesis , branched-chain fatty acid synthesis , and environmental adaptation by responding to their availability via the global transcriptional regulator CodY . The importance of BCAAs for S . aureus physiol...	To infect its human host , the bacterial pathogen Staphylococcus aureus must either take up nutrients from the surrounding environment or produce them itself . Previous studies have reported that S . aureus does not produce the amino acids leucine and valine , despite it possessing the genes to do so . In this study , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "pathogens", "split-decomposition", "method", "microbiology", "operons", "staphylococcus", "aureus", "multiple", "alignment", "calculation", "mutation", "sequence", ...	2018	Repression of branched-chain amino acid synthesis in Staphylococcus aureus is mediated by isoleucine via CodY, and by a leucine-rich attenuator peptide
We suggest for the first time that the action of multivalent cations on microtubule dynamics can result from facilitated diffusion of GTP-tubulin to the microtubule ends . Facilitated diffusion can promote microtubule assembly , because , upon encountering a growing nucleus or the microtubule wall , random GTP-tubulin ...	Interactions between biomolecules ( DNA , proteins , sugar , etc . ) represent the link between genome information and function of living organisms . For effective competition between organisms and adaptation to environmental changes , these interactions have to take place at very high rates . As such interactions requ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biophysics/macromolecular", "assemblies", "and", "machines", "biochemistry/experimental", "biophysical", "methods", "biophysics/experimental", "biophysical", "methods", "biophysics/biomacromolecule-ligand", "interactions", "biochemistry/macromolecular", "assemblies", "and", "machines"...	2009	Polyamine Sharing between Tubulin Dimers Favours Microtubule Nucleation and Elongation via Facilitated Diffusion
Synapses are dynamic molecular assemblies whose sizes fluctuate significantly over time-scales of hours and days . In the current study , we examined the possibility that the spontaneous microscopic dynamics exhibited by synaptic molecules can explain the macroscopic size fluctuations of individual synapses and the sta...	Neurons communicate through specialized sites of cell–cell contact known as synapses . This vast set of connections is believed to be crucial for sensory processing , motor function , learning and memory . Experimental data from recent years suggest that synapses are not static structures , but rather dynamic assemblie...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "engineering", "and", "technology", "nervous", "system", "condensed", "matter", "physics", "electrophysiology", "neuroscience", "simulation", "and", "modeling", "probability", "distribution", "mathematics", "statistics", "(mathematic...	2017	Cooperative stochastic binding and unbinding explain synaptic size dynamics and statistics
Human filarial infection is characterized by downregulated parasite-antigen specific T cell responses but distinct differences exist between patients with longstanding infection ( endemics ) and those who acquired infection through temporary residency or visits to filarial-endemic regions ( expatriates ) . To character...	Infection with the filarial parasite Loa loa causes a parasite-specific downregulation of T cell responses . However , differences exist ( clinical and immunologic ) between patients born and living in filarial endemic regions ( endemics ) and those who become infected during travel or short-term residency ( expatriate...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "biology", "molecular", "cell", "biology", "parasitic", "diseases" ]	2012	Regulation of Global Gene Expression in Human Loa loa Infection Is a Function of Chronicity
Wnt proteins regulate many developmental processes and are required for tissue homeostasis in adult animals . The cellular responses to Wnts are manifold and are determined by the respective Wnt ligand and its specific receptor complex in the plasma membrane . Wnt receptor complexes contain a member of the Frizzled fam...	Wnts are secreted , growth factor-like proteins that are important for the development of many tissues and organs in animals . They are also required in adult animals and humans for controlling the balance between growth and differentiation . Wnts are bound at the cell surface by Wnt receptors , which are dimers compos...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "histology", "developmental", "biology", "medicine", "and", "health", "sciences", "urology", "model", "organisms", "anatomy", "cell", "biology", "evolutionary", "biology", "genetics", "biology", "and", "life", "sciences", "genomics", "molecular", "cell",...	2014	The PTK7-Related Transmembrane Proteins Off-track and Off-track 2 Are Co-receptors for Drosophila Wnt2 Required for Male Fertility
Natively unstructured regions are a common feature of eukaryotic proteomes . Between 30% and 60% of proteins are predicted to contain long stretches of disordered residues , and not only have many of these regions been confirmed experimentally , but they have also been found to be essential for protein function . In th...	As a result of high throughput sequencing technologies , there is a growing need to provide fast and accurate computational tools to predict the function of proteins from amino acid sequence . Most methods that attempt to do this rely on transferring function annotations between closely related proteins; however , a la...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "none", "molecular", "biology", "computational", "biology", "homo", "(human)" ]	2007	Inferring Function Using Patterns of Native Disorder in Proteins
Forkhead box p3 ( Foxp3 ) -expressing regulatory T cells are key mediators of peripheral tolerance suppressing undesirable immune responses . Ectopic expression of Foxp3 confers regulatory T cell phenotype to conventional T cells , lending itself to therapeutic use in the prevention of autoimmunity and transplant rejec...	Autoimmune diseases come in many diverse forms—such as rheumatoid arthritis , type I diabetes , multiple sclerosis , and inflammatory bowel disease—yet all share the same underlying cause , the launch of a detrimental immune response . In healthy individuals , a specialized immune cell type called regulatory T cells pr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology", "rheumatology" ]	2008	Specific Immunosuppression with Inducible Foxp3-Transduced Polyclonal T cells
It was shown recently using experimental data that it is possible under certain conditions to determine whether a person with known genotypes at a number of markers was part of a sample from which only allele frequencies are known . Using population genetic and statistical theory , we show that the power of such identi...	It was shown recently by Homer and colleagues that it may be possible to determine whether a person with known genotypes at a number of markers was part of a pool of DNA from which only frequencies of alleles at the markers are known . In this study , we quantify how well such identification can work in practice . The ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "genetics", "and", "genomics/population", "genetics" ]	2009	The Limits of Individual Identification from Sample Allele Frequencies: Theory and Statistical Analysis

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