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Orientia tsutsugamushi is a clinically important but neglected obligate intracellular bacterial pathogen of the Rickettsiaceae family that causes the potentially life-threatening human disease scrub typhus . In contrast to the genome reduction seen in many obligate intracellular bacteria , early genetic studies of Orie...	Orientia tsutsugamushi is an obligate intracellular bacterial pathogen , and the causative agent of the human disease scrub typhus . This vector-borne bacterial infection can be life-threatening if not treated rapidly with appropriate antibiotics . Orientia is endemic across large parts of Asia and is estimated to infe...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "bacteriology", "sequencing", "techniques", "geomorphology", "taxonomy", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "landforms", "intracellular", "pathogens", "pathogens", "topography", "microbiology", "genome", "sequencing", "phy...	2018	Long-read whole genome sequencing and comparative analysis of six strains of the human pathogen Orientia tsutsugamushi
We developed a bacterial genetic system based on translation of the his operon leader peptide gene to determine the relative speed at which the ribosome reads single or multiple codons in vivo . Low frequency effects of so-called “silent” codon changes and codon neighbor ( context ) effects could be measured using this...	The central dogma of molecular biology states that DNA is transcribed into RNA , which is translated into protein . The process of translation from messenger RNA ( mRNA ) into protein by the ribosome is a complicated process involving transfer RNA intermediates with attached amino acids that must recognize 3 base codon...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences" ]	2014	The Effects of Codon Context on In Vivo Translation Speed
Shigella infection , the cause of bacillary dysentery , induces caspase-1 activation and cell death in macrophages , but the precise mechanisms of this activation remain poorly understood . We demonstrate here that caspase-1 activation and IL-1β processing induced by Shigella are mediated through Ipaf , a cytosolic pat...	Shigella are bacterial pathogens that are the cause of bacillary dysentery known as shigellosis . A crucial aspect of the propensity of Shigella to cause diseases lies in its ability to invade the cytoplasm of epithelial cells as well as macrophages . The bacterial invasion of macrophages induces pyroptosis , the proin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "cell", "biology", "mammals", "immunology", "mus", "(mouse)", "eubacteria" ]	2007	Differential Regulation of Caspase-1 Activation, Pyroptosis, and Autophagy via Ipaf and ASC in Shigella-Infected Macrophages
Scrub typhus is a common and underdiagnosed cause of febrile illness in Southeast Asia , caused by infection with Orientia tsutsugamushi . Inoculation of the organism at a cutaneous mite bite site commonly results in formation of a localized pathological skin reaction termed an eschar . The site of development of the o...	Scrub typhus is an infectious disease common in Southeast Asia , caused by the intracellular bacteria Orientia tsutsugamushi . These microorgansims infect humans through chigger mite bites , after which O . tsutsugamushi invades cells in the dermis , causing an inflammatory lesion called an eschar . Other rickettsia ca...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "dermatology", "infectious", "diseases", "clinical", "immunology", "immunology" ]	2012	Orientia tsutsugamushi in Human Scrub Typhus Eschars Shows Tropism for Dendritic Cells and Monocytes Rather than Endothelium
Influenza disease is a global health issue that causes significant morbidity and mortality through seasonal epidemics . Currently , inactivated influenza virus vaccines given intramuscularly or live attenuated influenza virus vaccines administered intranasally are the only approved options for vaccination against influ...	Influenza virus remains a global health risk causing significant morbidity and mortality each year , with the elderly ( >65 years ) and the very young particularly prone to severe respiratory disease . Scientists are working to develop highly efficacious vaccines capable of eliciting broad cross-clade protection from i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "humoral", "immunity", "medicine", "immune", "cells", "immune", "activation", "influenza", "immunity", "to", "infections", "immunology", "adaptive", "immunity", "immune", "defense", "immunoregulation", "infectious", "disease", "control", "immunomodulation", "immunotherapy",...	2014	Intranasal Vaccination Promotes Detrimental Th17-Mediated Immunity against Influenza Infection
Natural Killer ( NK ) cells are crucial in early resistance to murine cytomegalovirus ( MCMV ) infection . In B6 mice , the activating Ly49H receptor recognizes the viral m157 glycoprotein on infected cells . We previously identified a mutant strain ( MCMVG1F ) whose variant m157 also binds the inhibitory Ly49C recepto...	We previously identified a viral murine cytomegalovirus ( MCMV ) strain whose variant m157 immunoevasin can bind the inhibitory Ly49C NK cell receptor in addition to activating Ly49H receptor in B6 mice . Here we show that simultaneous engagement of the two receptors by m157 hampers NK cell activation . Most Ly49H+ NK ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "immune", "activation", "immunology", "microbiology", "cytomegalovirus", "infection", "infectious", "disease", "cont...	2014	Ly49C-Dependent Control of MCMV Infection by NK Cells Is Cis-Regulated by MHC Class I Molecules
Protein production , genomic RNA replication , and virion assembly during infection by picornaviruses like human rhinovirus and poliovirus take place in the cytoplasm of infected human cells , making them the quintessential cytoplasmic pathogens . However , a growing body of evidence suggests that picornavirus replicat...	We explored the dynamics of host cell protein relocalization from the nucleus to the cytoplasm during an infection by human rhinovirus using quantitative mass spectrometry , confocal imaging , and Western blot analysis . We discovered a highly selective re-equilibration of proteins with known mRNA splicing and transpor...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "hela", "cells", "gene", "regulation", "enzymes", "pathogens", "biological", "cultures", "microbiology", "enzymology", "viruses", "rna", "viruses", "cell", "cultures", "rhinovirus", ...	2018	Exploitation of nuclear functions by human rhinovirus, a cytoplasmic RNA virus
To provide tight spatiotemporal signaling control , the cyclic adenosine monophosphate ( cAMP ) -dependent protein kinase ( PKA ) holoenzyme typically nucleates a macromolecular complex or a “PKA signalosome . ” Using the RIIβ holoenzyme as a prototype , we show how autophosphorylation/dephosphorylation of the RIIβ sub...	Kinases are important regulators in many cellular signaling processes . They bind to and phosphorylate different substrates to affect distinct signaling events . Usually , a kinase releases its substrate quickly after phosphorylation to ensure fast signaling . However , we find that this is not always true for the prot...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Single Turnover Autophosphorylation Cycle of the PKA RIIβ Holoenzyme
Neurobeachin ( Nbea ) regulates neuronal membrane protein trafficking and is required for the development and functioning of central and neuromuscular synapses . In homozygous knockout ( KO ) mice , Nbea deficiency causes perinatal death . Here , we report that heterozygous KO mice haploinsufficient for Nbea have highe...	Body weight and energy balance are under very complex neural , endocrine , and metabolic control . Correspondingly , recent research suggests that hundreds of genes contribute to human obesity and that only a small proportion of them have as yet been identified . Neurobeachin ( Nbea ) is a protein specifically expresse...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "medicine", "non-clinical", "medicine", "nutrition", "genetics", "genetics", "and", "genomics", "biology", "neuroscience", "metabolic", "disorders", "clinical", "genetics" ]	2012	Neurobeachin, a Regulator of Synaptic Protein Targeting, Is Associated with Body Fat Mass and Feeding Behavior in Mice and Body-Mass Index in Humans
Soil-transmitted helminths ( STH ) infect nearly 1 . 5 billion individuals globally , and contribute to poor physical and cognitive development in children . STH control programs typically consist of regular delivery of anthelminthic drugs , targeting school-aged children . Expanding STH control programs community-wide...	Soil-transmitted helminth ( STH ) infections are widespread globally , and their health impacts include poor growth and impaired cognitive development in children . STH control programs therefore usually focus on delivering deworming medications to school-aged children . However , expanding such programs to the whole c...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "children", "medicine", "and", "health", "sciences", "education", "helminths", "sociology", "tropical", "diseases", "hookworms", "social", "sciences", "parasitic", "diseases", "animals", "necator", "americanus", "health", "care", "physiological", "process...	2018	(S)WASH-D for Worms: A pilot study investigating the differential impact of school- versus community-based integrated control programs for soil-transmitted helminths
Congress created the tropical disease priority review voucher program to stimulate new drug development for tropical diseases . An analysis of the pharmaceutical pipeline indicates that the development of drugs for these tropical diseases has increased . However , the effects of the program are not uniform across all d...	Offering priority review vouchers ( PRVs ) as a reward for developing a drug to treat a tropical or other understudied disease was first introduced by Ridley et al ( 2006 ) . The idea has become popular with lawmakers because it provides a perceived valuable incentive ( vouchers have sold for as much as $350 million ) ...	[ "Abstract", "Introduction", "Background", "Study", "data", "and", "methods", "Study", "results", "Discussion" ]	[ "bacterial", "diseases", "infectious", "diseases", "medicine", "and", "health", "sciences", "drug", "research", "and", "development", "pharmaceutics", "tuberculosis", "epidemiology", "pharmacology", "tropical", "diseases", "malaria", "drug", "therapy", "parasitic", "disea...	2018	Is the priority review voucher program stimulating new drug development for tropical diseases?
CCL3 is a ligand for the HIV-1 co-receptor CCR5 . There have recently been conflicting reports in the literature concerning whether CCL3-like gene ( CCL3L ) copy number variation ( CNV ) is associated with resistance to HIV-1 acquisition and with both viral load and disease progression following infection with HIV-1 . ...	Host genetic factors are important in determining why some individuals maintain effective control of HIV-1 replication while others do not . Genes implicated in this control include a number associated with the development of classical immune effector responses against HIV-1 infection and others associated with viral e...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/hiv", "infection", "and", "aids", "virology/effects", "of", "virus", "infection", "on", "host", "gene", "expression", "virology/animal", "models", "of", "infection", "virology" ]	2010	Contributions of Mamu-A*01 Status and TRIM5 Allele Expression, But Not CCL3L Copy Number Variation, to the Control of SIVmac251 Replication in Indian-Origin Rhesus Monkeys
Genome sequencing data have recently demonstrated that eukaryote evolution has been remarkably influenced by the acquisition of a large number of genes by horizontal gene transfer ( HGT ) across different kingdoms . However , in depth-studies on the physiological traits conferred by these accidental DNA acquisitions ar...	Parasitic wasps are important insect biocontrol agents . These insects are beneficial for the ecological service they provide , which largely contributes to the control of natural populations of their hosts . Paradoxically , they can be beneficial also for non-host individuals attacked by mistake , if these survive aft...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "organismal", "evolution", "parasite", "evolution", "cell", "processes", "microbiology", "animals", "parasitology", "developmental", "biology", "microbial", "evolution", "spodoptera", "research", "and", "analysis", "methods", "sequence", "analysis", "sequen...	2019	Evolution of an insect immune barrier through horizontal gene transfer mediated by a parasitic wasp
We have mapped a protein interaction network of human homologs of proteins that modify longevity in invertebrate species . This network is derived from a proteome-scale human protein interaction Core Network generated through unbiased high-throughput yeast two-hybrid searches . The longevity network is composed of 175 ...	Studies of longevity in model organisms such as baker's yeast , roundworm , and fruit fly have clearly demonstrated that a diverse array of genetic mutations can result in increased life span . In fact , large-scale genetic screens have identified hundreds of genes that when mutated , knocked down , or deleted will sig...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/functional", "genomics", "computational", "biology/signaling", "networks", "genetics", "and", "genomics/gene", "expression", "biotechnology/protein", "chemistry", "and", "proteomics" ]	2009	A Human Protein Interaction Network Shows Conservation of Aging Processes between Human and Invertebrate Species
Inactivation of the Transforming Growth Factor Beta ( TGFβ ) tumor suppressor pathway contributes to the progression of Pancreatic Ductal AdenoCarcinoma ( PDAC ) since it is inactivated in virtually all cases of this malignancy . Genetic lesions inactivating this pathway contribute to pancreatic tumor progression in mo...	Inactivation of the TGFβ tumor suppressor pathway contributes to the progression of Pancreatic Ductal AdenoCarcinoma ( PDAC ) , a devastating malignancy . Transcriptional Intermediary Factor 1γ ( TIF1γ ) has recently been proposed to be involved in TGFβ signaling , a pathway inactivated in virtually all cases of this m...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/disease", "models", "genetics", "and", "genomics/cancer", "genetics", "gastroenterology", "and", "hepatology/pancreas" ]	2009	Inactivation of TIF1γ Cooperates with KrasG12D to Induce Cystic Tumors of the Pancreas
Tuberculosis ( TB ) granulomas are organized collections of immune cells comprised of macrophages , lymphocytes and other cells that form in the lung as a result of immune response to Mycobacterium tuberculosis ( Mtb ) infection . Formation and maintenance of granulomas are essential for control of Mtb infection and ar...	Tuberculosis is a common and deadly infectious disease caused by a highly successful bacterium , Mycobacterium tuberculosis ( Mtb ) . Multiple host immune factors control the formation of a self-organizing aggregate of immune cells termed a granuloma in the lungs after inhalation of Mtb . One such factor , tumor necros...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biophysics", "infectious", "diseases", "immunology", "computational", "biology/systems", "biology" ]	2010	Identification of Key Processes that Control Tumor Necrosis Factor Availability in a Tuberculosis Granuloma
The Caenorhabditis elegans pharynx ( or foregut ) functions as a pump that draws in food ( bacteria ) from the environment . While the “organ identity factor” PHA-4 is critical for formation of the C . elegans pharynx as a whole , little is known about the specification of distinct cell types within the pharynx . Here ...	To make an organ , cells must be instructed to be part of a common structure yet must also be assigned specific roles or identities within that structure . For example , the stomach contains a variety of different kinds of cells , including muscles , nerves , and glands . This same complexity is seen even in relatively...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/sequence", "motif", "analysis", "genetics", "and", "genomics/gene", "expression", "developmental", "biology/cell", "differentiation", "genetics", "and", "genomics/gene", "function", "developmental", "biology/molecular", "development", "developmental", ...	2008	The HLH-6 Transcription Factor Regulates C. elegans Pharyngeal Gland Development and Function
Enterobacter sp . 638 is an endophytic plant growth promoting gamma-proteobacterium that was isolated from the stem of poplar ( Populus trichocarpa×deltoides cv . H11-11 ) , a potentially important biofuel feed stock plant . The Enterobacter sp . 638 genome sequence reveals the presence of a 4 , 518 , 712 bp chromosome...	Poplar is considered as the model tree species for the production of lignocellulosic biomass destined for biofuel production . The plant growth promoting endophytic bacterium Enterobacter sp . 638 can improve the growth of poplar on marginal soils by as much as 40% . This prompted us to sequence the genome of this stra...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/plant-biotic", "interactions", "microbiology/environmental", "microbiology", "genetics", "and", "genomics/genome", "projects", "microbiology", "genetics", "and", "genomics" ]	2010	Genome Sequence of the Plant Growth Promoting Endophytic Bacterium Enterobacter sp. 638
The pathological outcomes of schistosomiasis are largely dependent on the molecular and cellular mechanisms of the host immune response . In this study , we investigated the contribution of variations in host gene expression to the contrasting hepatic pathology observed between two inbred mouse strains following Schist...	Schistosomiasis is a significant cause of morbidity and mortality in the tropical world although its true burden has been historically underestimated . Millions of people currently endure severe pathology as a result of schistosome infections , although some individuals appear to be less susceptible to infection despit...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "genome", "expression", "analysis", "immunology", "microbiology", "host-pathogen", "interaction", "parasitic", "diseases", "parasitology", "neglected", "tropical", "diseases", "infectious", "diseases", "gene", "expression", "biology", "pathogenesis", "molecular", ...	2011	Differential Expression of Chemokine and Matrix Re-Modelling Genes Is Associated with Contrasting Schistosome-Induced Hepatopathology in Murine Models
Drosophila brains contain numerous neurons that form complex circuits . These neurons are derived in stereotyped patterns from a fixed number of progenitors , called neuroblasts , and identifying individual neurons made by a neuroblast facilitates the reconstruction of neural circuits . An improved MARCM ( mosaic analy...	A brain consists of numerous , potentially individually unique neurons that derive from a limited number of progenitors . It has been shown in various model organisms that specific neurons arise in a lineage made by a repeatedly renewing progenitor at specific times of development . However , except in the worm C . ele...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience/neurodevelopment" ]	2010	A Complete Developmental Sequence of a Drosophila Neuronal Lineage as Revealed by Twin-Spot MARCM
Schistosomiasis is a parasitic disease which affects almost 300 million people worldwide each year . It is highly endemic in Mozambique . Prevention and control of schistosomiasis relies mainly on mass drug administration ( MDA ) , as well as adoption of basic sanitation practices . Individual and community perceptions...	Schistosomiasis is one of the 17 ‘neglected tropical diseases’ as classified by the World Health Organization . It is a parasitic disease of poverty that affects around 300 million people each year , causing chronic ill-health and severe morbidity . The disease , which is spread through contact with freshwater contamin...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "children", "medicine", "and", "health", "sciences", "education", "sociology", "tropical", "diseases", "social", "sciences", "parasitic", "diseases", "age", "groups", "research", "design", "pharmaceutics", "neglected", "tropical", "diseases", "surveys", "infectious", "d...	2016	Have You Heard of Schistosomiasis? Knowledge, Attitudes and Practices in Nampula Province, Mozambique
Recombination is an essential process in eukaryotes , which increases diversity by disrupting genetic linkage between loci and ensures the proper segregation of chromosomes during meiosis . In the human genome , recombination events are clustered in hotspots , whose location is determined by the PRDM9 protein . There i...	In eukaryotic genomes , recombination plays a central role by ensuring the proper segregation of chromosomes during meiosis and increasing genetic diversity at the population scale . Recombination events are not uniformly distributed along chromosomes , but cluster in narrow regions called hotspots . The absence of ove...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry", "genomics", "genetic", "polymorphism", "genome", "evolution", "human", "genomics", "genetics", "biology", "and", "life", "sciences", "dna", "population", "genetics", "dna", "recombination", "evolutionary", "biology", "molecular", "evolution", "computationa...	2014	The Red Queen Model of Recombination Hotspots Evolution in the Light of Archaic and Modern Human Genomes
Genetic recombination shapes the diversity of RNA viruses , including enteroviruses ( EVs ) , which frequently have mosaic genomes . Pathogenic circulating vaccine-derived poliovirus ( cVDPV ) genomes consist of mutated vaccine poliovirus ( PV ) sequences encoding capsid proteins , and sequences encoding nonstructural ...	Recombination shapes viral genomes , including those of the pathogenic circulating vaccine-derived polioviruses ( cVDPVs ) , responsible for poliomyelitis outbreaks . The genomes of cVDPVs consist of sequences from vaccine poliovirus ( PV ) and other enteroviruses ( EVs ) . We investigated the plasticity of cVDPV genom...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Evolution and Emergence of Enteroviruses through Intra- and Inter-species Recombination: Plasticity and Phenotypic Impact of Modular Genetic Exchanges in the 5’ Untranslated Region
Cystic echinococcosis ( CE ) caused by the Echinococcus granulosus , is a major public health problem worldwide , including India . The different genotypes of E . granulosus responsible for human hydatidosis have been reported from endemic areas throughout the world . However , the genetic characterization of E . granu...	Cystic echinococcosis caused by Echinococcus granulosus is a widespread zoonotic disease . This cestode parasite is a complex of genetic variants and to date , ten distinct genotypes ( genotypes G1–G10 ) have been identified on the basis of mitochondrial DNA sequences . The strain variation in E . granulosus may influe...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "biology" ]	2013	Molecular Characterization of Echinococcus granulosus Cysts in North Indian Patients: Identification of G1, G3, G5 and G6 Genotypes
The current millennium has seen a steep rise in the number , size and case-fatalities of cholera outbreaks in many African countries . Over 40 , 000 cases of cholera were reported from Nigeria in 2010 . Variants of Vibrio cholerae O1 El Tor biotype have emerged but very little is known about strains causing cholera out...	Cholera is acute watery diarrhoea , severely dehydrating , caused by Vibrio cholerae , a bacterium ubiquitous in aquatic environments . Cholera is a global threat , particularly , in areas where sanitary conditions , such as drinking water and sewage , are not available . Seven cholera pandemics , all originating in As...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "bacteriology", "medicine", "public", "health", "and", "epidemiology", "infectious", "disease", "epidemiology", "microbiology", "clinical", "epidemiology", "molecular", "genetics", "bacterial", "pathogens", "genetic", "epidemiology", "molecular", "epidemiology", "epidemiology...	2013	Cholera Outbreaks in Nigeria Are Associated with Multidrug Resistant Atypical El Tor and Non-O1/Non-O139 Vibrio cholerae
Klebsiella pneumoniae causes significant morbidity and mortality worldwide , particularly amongst hospitalized individuals . The principle mechanism for pathogenesis in hospital environments involves the formation of biofilms , primarily on implanted medical devices . In this study , we constructed a transposon mutant ...	Biofilms are surface-associated communities of microorganisms . Biofilm-associated bacteria are protected from host defenses and antibiotics and are the cause of many infections . Klebsiella pneumoniae is primarily a hospital-acquired bacterial pathogen that causes pneumonia , urinary tract infections and septicemia . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "medicine", "microbiology", "dna", "transcription", "bacterial", "diseases", "bacterial", "pathogens", "infectious", "diseases", "cell", "adhesion", "gene", "expression", "klebsiella", "pneumonia", "biology", "molecular", "biology", "bacterial", "biofilms", ...	2011	MrkH, a Novel c-di-GMP-Dependent Transcriptional Activator, Controls Klebsiella pneumoniae Biofilm Formation by Regulating Type 3 Fimbriae Expression
Influenza A viruses are major pathogens in humans and in animals , whose genome consists of eight single-stranded RNA segments of negative polarity . Viral mRNAs are synthesized by the viral RNA-dependent RNA polymerase in the nucleus of infected cells , in close association with the cellular transcriptional machinery ...	Influenza A viruses are major pathogens which pose continuous animal and public health challenges . Enhancing the knowledge of their life cycle , and especially the understanding of how viral components interact with the host cell , is essential to achieve better prevention and treatment of the disease . The polymerase...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "medicine", "and", "health", "sciences", "molecular", "cell", "biology", "protein", "interactions", "pathology", "and", "laboratory", "medicine", "cell", "biology", "host-pathogen", "interactions", "proteins", "virology", "gene", "expression", "genetics", ...	2014	Recruitment of RED-SMU1 Complex by Influenza A Virus RNA Polymerase to Control Viral mRNA Splicing
Chagasic cardiomyopathy is caused by Trypanosoma cruzi infection . Poly ( ADP-ribose ) polymerase 1 ( PARP1 ) is known for its function in nuclear DNA repair . In this study , we have employed genetic deletion and chemical inhibition approaches to determine the role of PARP1 in maintaining mtDNA dependent mitochondrial...	Chagasic cardiomyopathy is caused by Trypanosoma cruzi infection , and it affects ~7 million individuals on the American continent . Poly ( ADP-ribose ) polymerase 1 ( PARP1 ) is a nuclear DNA repair enzyme . In this study , we demonstrate that PARP1 tends to be localized to mitochondria in chagasic myocardium . The mt...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "respiratory", "infections", "mitochondrial", "dna", "cardiovascular", "anatomy", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "pulmonology", "protozoans", "heart", "forms", "of", "dna", "mitochondria...	2018	PARP1 depletion improves mitochondrial and heart function in Chagas disease: Effects on POLG dependent mtDNA maintenance
DNA repair and other chromatin-associated processes are carried out by enzymatic macromolecular complexes that assemble at specific sites on the chromatin fiber . How the rate of these molecular machineries is regulated by their constituent parts is poorly understood . Here we quantify nucleotide-excision DNA repair in...	The nucleotide-excision repair pathway removes mutagen-inflicted DNA lesions from the genome . Repair proteins recognize DNA lesions and form multi-protein complexes that catalyze the excision of the lesion and the re-synthesis of the excised part . Imaging the dynamics of fluorescently labeled repair proteins in livin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "biochemical", "simulations", "nucleic", "acids", "dna", "dna", "repair", "biology", "computational", "biology", "molecular", "cell", "biology" ]	2014	Robustness of DNA Repair through Collective Rate Control
The nervous and immune systems influence each other , allowing animals to rapidly protect themselves from changes in their internal and external environment . However , the complex nature of these systems in mammals makes it difficult to determine how neuronal signaling influences the immune response . Here we show tha...	The nervous and immune systems respond quickly and precisely to changes in the environment . Communication between these systems may underlie neurological disorders such as depression , and explain why environmental factors , such as psychological stress , increase infection susceptibility . What are the molecular mech...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Serotonergic Chemosensory Neurons Modify the C. elegans Immune Response by Regulating G-Protein Signaling in Epithelial Cells
We used molecular dynamics ( MD ) simulations to explore the transport of single cations through the channel of the muscle nicotinic acetylcholine receptor ( nAChR ) . Four MD simulations of 16 ns were performed at physiological and hyperpolarized membrane potentials , with and without restraints of the structure , but...	Communication between a cell and its environment relies on channel-forming proteins to provide a low energy pathway for ions to move in and out . Although channel-forming proteins are essential to all life forms , the atomic-scale mechanisms that enable ions to pass through the channel remain elusive due to the lack of...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "homo", "(human)", "computational", "biology" ]	2008	Control of Cation Permeation through the Nicotinic Receptor Channel
The evolution of postzygotic reproductive isolation is an important component of speciation . But before isolation is complete there is sometimes a phase of heterosis in which hybrid fitness exceeds that of the two parental species . The genetics and evolution of heterosis and postzygotic isolation have typically been ...	As populations diverge and ultimately evolve into distinct species , hybrids between them gradually become inviable and infertile . Before this happens , there can be a brief period in which hybrids are actually more fit than their parents , a condition called heterosis or hybrid vigor . This paper describes a model of...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "epistasis", "mutation", "substitution", "mutation", "heterosis", "fitness", "epistasis", "simulation", "and", "modeling", "natural", "selection", "heredity", "speciation", "genetics", "biology", "and", "life", "sciences", "evolutionary", "biology", "evolutionary", "proce...	2019	The evolution of hybrid fitness during speciation
Facioscapulohumeral muscular dystrophy ( FSHD ) is a common muscle disease whose molecular pathogenesis remains largely unknown . Over-expression of FSHD region gene 1 ( FRG1 ) in mice , frogs , and worms perturbs muscle development and causes FSHD–like phenotypes . FRG1 has been implicated in splicing , and we asked h...	Alternative splicing is a major contributor to the complexity of human cells , and its disruption can lead to a wide range of human disorders . FSHD is one of the most important muscle diseases . While muscle differentiation defects have been widely reported in the disease , the molecular mechanisms responsible are lar...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "gene", "regulation", "cell", "differentiation", "animal", "models", "developmental", "biology", "model", "organisms", "molecular", "genetics", "gene", "expression", "gene", "splicing", "muscular", "dystrophies", "biology", "mouse", "molecular", "biology", "...	2013	Rbfox1 Downregulation and Altered Calpain 3 Splicing by FRG1 in a Mouse Model of Facioscapulohumeral Muscular Dystrophy (FSHD)
Drosophila melanogaster is a well-studied model organism , especially in the field of neurophysiology and neural circuits . The brain of the Drosophila is small but complex , and the image of a single neuron in the brain can be acquired using confocal microscopy . Analyzing the Drosophila brain is an ideal start to und...	It is now possible to image a single neuron in the fruit fly brain . However , manually reconstructing neuronal structures is tremendously time consuming . The proposed method avoids user interventions by first automatically identifying the end points and detecting the appropriate representative point of the soma , and...	[ "Abstract", "Introduction", "Results", "Methods", "Discussion" ]	[ "computer", "science", "image", "processing", "signal", "processing", "software", "engineering", "software", "tools", "engineering" ]	2012	High-throughput Computer Method for 3D Neuronal Structure Reconstruction from the Image Stack of the Drosophila Brain and Its Applications
Recent analyses of human-associated bacterial diversity have categorized individuals into ‘enterotypes’ or clusters based on the abundances of key bacterial genera in the gut microbiota . There is a lack of consensus , however , on the analytical basis for enterotypes and on the interpretation of these results . We tes...	Recent work has suggested that individuals can be classified into ‘enterotypes’ based on the abundance of key bacterial taxa in gut microbial communities . However , the generality of enterotypes across populations , and the existence of similar cluster types for other body sites , remains to be evaluated . We combined...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[ "biology", "computational", "biology", "microbiology" ]	2013	A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets
Borrelia turicatae , an agent of tick-borne relapsing fever , is an example of a pathogen that can adapt to disparate conditions found when colonizing the mammalian host and arthropod vector . However , little is known about the genetic factors necessary during the tick-mammalian infectious cycle , therefore we develop...	Relapsing fever spirochetes are a global yet neglected pathogen causing recurrent febrile episodes , nausea , vomiting , and pregnancy complications including miscarriage . Most species of tick-borne relapsing fever spirochetes are maintained in enzootic cycles , and given an approximately 20 year life span , the arthr...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2013	Development of Genetic System to Inactivate a Borrelia turicatae Surface Protein Selectively Produced within the Salivary Glands of the Arthropod Vector
Epilepsy will affect nearly 3% of people at some point during their lifetime . Previous copy number variants ( CNVs ) studies of epilepsy have used array-based technology and were restricted to the detection of large or exonic events . In contrast , whole-genome sequencing ( WGS ) has the potential to more comprehensiv...	Epilepsy is a common neurological disorder affecting around 3% of the population . In some cases , epilepsy is caused by brain trauma or other brain anomalies but there are often no clear causes . Genetic factors have been associated with epilepsy in the past such as rare genetic variations found by linkage studies as ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "computer", "applications", "medicine", "and", "health", "sciences", "population", "genetics", "catalogs", "twins", "genomic", "databases", "developmental", "biology", "genome", "analysis", "population", "biology", "research", "and", "analysis", "methods", "epilepsy", "...	2018	Global characterization of copy number variants in epilepsy patients from whole genome sequencing
The basal ganglia ( BG ) , serving as an intermediate bridge between the cerebral cortex and thalamus , are believed to play crucial roles in controlling absence seizure activities generated by the pathological corticothalamic system . Inspired by recent experiments , here we systematically investigate the contribution...	One prevailing viewpoint on the genesis of absence seizures is suggested to involve the pathological interactions within the corticothalamic system . As intriguing deep nuclei of brain , the basal ganglia are reported to play crucial roles in controlling absence seizures through multiple nigro-thalamic pathways . Besid...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Critical Roles of the Direct GABAergic Pallido-cortical Pathway in Controlling Absence Seizures
The generation of a RecA filament on single-stranded DNA is a critical step in homologous recombination . Two main pathways leading to the formation of the nucleofilament have been identified in bacteria , based on the protein complexes mediating RecA loading: RecBCD ( AddAB ) and RecFOR . Many bacterial species seem t...	Homologous recombination plays an essential role in maintaining genomic integrity and in allowing genetic diversity within a population . In the case of bacteria , two main pathways for the initiation of recombination have been described . These pathways are defined by the protein complexes , present in the model syste...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "genetics", "and", "genomics/gene", "discovery", "microbiology", "genetics", "and", "genomics", "genetics", "and", "genomics/bioinformatics" ]	2008	Unveiling Novel RecO Distant Orthologues Involved in Homologous Recombination
The elimination of Triatoma infestans , the main Chagas disease vector in the Gran Chaco region , remains elusive . We implemented an intensified control strategy based on full-coverage pyrethroid spraying , followed by frequent vector surveillance and immediate selective insecticide treatment of detected foci in a wel...	Vector-borne transmission of Chagas disease has not been effectively controlled in large parts of Latin America , particularly in the Gran Chaco ecoregion . To better understand the challenges in this region , we assessed the effectiveness of an intensified insecticide-based spraying strategy in suppressing the major v...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "ecology", "epidemiology", "biology", "spatial", "epidemiology" ]	2013	Intensified Surveillance and Insecticide-based Control of the Chagas Disease Vector Triatoma infestans in the Argentinean Chaco
Neuropeptides play crucial roles in modulating neuronal networks , including changing intrinsic properties of neurons and synaptic efficacy . We previously reported a Caenorhabditis elegans mutant , acr-2 ( gf ) , that displays spontaneous convulsions as the result of a gain-of-function mutation in a neuronal nicotinic...	Imbalanced neuronal circuit activity is considered a major underlying cause in many neurological disorders , such as epilepsy and autism . Neuropeptides are small polypeptides that are released from neurons . They are widely known to provide neuromodulatory functions and have diverse roles in the nervous system . By in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2013	Neuropeptides Function in a Homeostatic Manner to Modulate Excitation-Inhibition Imbalance in C. elegans
While there has been significant progress in determining the transcriptional cascade involved in terminal adipocyte differentiation , less is known about early events leading to lineage commitment and cell fate choice . It has been recently discovered that zinc finger protein 423 ( Zfp423 ) is an early actor in adipose...	Adipocytes or fat cells derive from the same stem cells that give rise to bone , cartilage , and muscle . Understanding the switch between bone and fat is of particular medical importance , with implications for diseases like osteoporosis and obesity . Here , we have identified a transcription factor called Zfp521 whic...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "cell", "fate", "determination", "biology", "cell", "differentiation" ]	2012	Regulation of Early Adipose Commitment by Zfp521
Dengue is the most prevalent arboviral infection , affecting millions of people every year . Attempts to control such infection are being made , and the development of a vaccine is a World Health Organization priority . Among the proteins being tested as vaccine candidates in preclinical settings is the non-structural ...	Dengue is one of the most prevalent viral infections . It affects millions of people every year and can be life-threatening if left untreated . The development of a dengue vaccine is a public health priority . In the present study , we decided to use a dengue virus derived protein , named non-structural protein 1 ( NS1...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "immunizations", "viral", "vaccines", "adaptive", "immunity", "immune", "cells", "immunity", "virology", "antigen-presenting", "cells", "t", "cells", "immunology", "immunity", "to", "infections", "biology", "microbiology", "immune", "response", "immunoglobulins" ]	2013	Targeting the Non-structural Protein 1 from Dengue Virus to a Dendritic Cell Population Confers Protective Immunity to Lethal Virus Challenge
Alpha satellite domains that currently function as centromeres of human chromosomes are flanked by layers of older alpha satellite , thought to contain dead centromeres of primate progenitors , which lost their function and the ability to homogenize satellite repeats , upon appearance of a new centromere . Using cladis...	The primate centromere evolves by amplification of alpha satellite sequences in its inner core , which expands and moves the peripheral sequences sideways , forming layers of different age in the “pericentromeric” area . The expanding centromere model poses two main questions: ( 1 ) whether the succession of layers is ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology/human", "evolution", "molecular", "biology/molecular", "evolution", "molecular", "biology/centromeres", "molecular", "biology/chromosome", "structure", "genetics", "and", "genomics/chromosome", "biology", "evolutionary", "biology/genomics", "molecular", "...	2009	The Evolutionary Origin of Man Can Be Traced in the Layers of Defunct Ancestral Alpha Satellites Flanking the Active Centromeres of Human Chromosomes
Three different prenyltransferases attach isoprenyl anchors to C-terminal motifs in substrate proteins . These lipid anchors serve for membrane attachment or protein–protein interactions in many pathways . Although well-tolerated selective prenyltransferase inhibitors are clinically available , their mode of action rem...	Various cellular functions require reversible membrane localization of proteins . This is often facilitated by attaching lipids to the respective proteins , thus anchoring them to the membrane . For example , addition of prenyl lipid anchors ( prenylation ) is directed by a motif in the protein sequence that can be pre...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "oncology", "viruses", "biochemistry", "cell", "biology", "plant", "biology", "virology", "eukaryotes", "computational", "biology", "evolutionary", "biology" ]	2007	Towards Complete Sets of Farnesylated and Geranylgeranylated Proteins
The DREAM ( Dp/Retinoblastoma ( Rb ) -like/E2F/MuvB ) transcriptional repressor complex acts as a gatekeeper of the mammalian cell cycle by establishing and maintaining cellular quiescence . How DREAM’s three functional components , the E2F-DP heterodimer , the Rb-like pocket protein , and the MuvB subcomplex , form an...	The 8-subunit DREAM transcriptional repressor complex contains 3 functional components that together control expression of cell cycle and developmental genes . How the E2F-DP transcription factor heterodimer , the pocket protein , and the highly conserved MuvB complex coalesce on chromatin and repress DREAM target gene...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "rna", "interference", "caenorhabditis", "cell", "cycle", "and", "cell", "division", "cell", "processes", "animals", "dna", "transcription", "animal", "models", "developmental", "biology", "caenorhabditis", "elegans", "model", "organisms", "experimental",...	2017	Loss of the Caenorhabditis elegans pocket protein LIN-35 reveals MuvB's innate function as the repressor of DREAM target genes
Repeated adaptation to a new environment often leads to convergent phenotypic changes whose underlying genetic mechanisms are rarely known . Here , we study adaptation of color vision in threespine stickleback during the repeated postglacial colonization of clearwater and blackwater lakes in the Haida Gwaii archipelago...	When organisms colonize a new environment in replicate , natural selection often leads to similar phenotypic adaptations . Such “convergent evolution” is known from both distant relatives , e . g . , sea cows and whales adapting to an aquatic life , and from multiple populations within a species , but the causing genet...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "ecology", "and", "environmental", "sciences", "vertebrates", "light", "animals", "electromagnetic", "radiation", "genetic", "mapping", "osteichthyes", "aquatic", "environments", "fresh", "water", "bodies", "of", "water", "convergent", "evolution", "evolutionary", "adapta...	2017	Convergent evolution of SWS2 opsin facilitates adaptive radiation of threespine stickleback into different light environments
For the first time , differential attraction of pathogen vectors to vertebrate animals is investigated for novel repellents which when applied to preferred host animals turn them into non-hosts thereby providing a new paradigm for innovative vector control . For effectively controlling tsetse flies ( Glossina spp . ) ,...	We investigated the potential of non-host odors from un-preferred animals , i . e . not fed upon , related to cattle , the waterbuck ( Kobus ellipsiprymnus defassa ) which are common in tsetse habitats for their efficacy to protect cattle from tsetse flies that transmit nagana to cattle in Africa . The identified water...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Sampling", "Ethics", "statement", "Results", "Social-economic", "impact", "of", "tsetse", "repellent", "collars", "Discussion" ]	[ "invertebrates", "livestock", "medicine", "and", "health", "sciences", "parasitic", "protozoans", "animals", "parasitology", "glossina", "protozoans", "animal", "behavior", "tsetse", "fly", "infectious", "disease", "control", "insect", "vectors", "zoology", "veterinary", ...	2017	Protecting cows in small holder farms in East Africa from tsetse flies by mimicking the odor profile of a non-host bovid
Methadone maintenance treatment ( MMT ) is commonly used for controlling opioid dependence , preventing withdrawal symptoms , and improving the quality of life of heroin-dependent patients . A steady-state plasma concentration of methadone enantiomers , a measure of methadone metabolism , is an index of treatment respo...	Methadone maintenance treatment ( MMT ) , among the most effective therapies for heroin-dependent patients , reduces craving and withdrawal symptoms , increases treatment compliance , and improves the quality of life of patients . The plasma concentration of methadone is a primary index for quantifying and determining ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "medicine", "and", "health", "sciences", "engineering", "and", "technology", "replication", "studies", "population", "genetics", "quantitative", "traits", "research", "design", "industrial", "engineering", "quality", "control", "pharmacology", "population",...	2016	Genome-Wide Pharmacogenomic Study on Methadone Maintenance Treatment Identifies SNP rs17180299 and Multiple Haplotypes on CYP2B6, SPON1, and GSG1L Associated with Plasma Concentrations of Methadone R- and S-enantiomers in Heroin-Dependent Patients
The ecological context in which mosquitoes and malaria parasites interact has received little attention , compared to the genetic and molecular aspects of malaria transmission . Plant nectar and fruits are important for the nutritional ecology of malaria vectors , but how the natural diversity of plant-derived sugar so...	The Anopheles coluzzii mosquito is an effective vector of human Plasmodium falciparum malaria . Besides feeding on blood , females readily feed on natural sources of plant sugars; but how plant diversity affects their ability to transmit malaria parasites is currently unknown . Here we show that mosquito feeding on per...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "parasite", "groups", "plasmodium", "gametocytes", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "animals", "parasitology", "germ", "cells", "apicomplexa", "protozoans", "crops", "inse...	2016	Plant-Mediated Effects on Mosquito Capacity to Transmit Human Malaria
Pterosaurs were the first vertebrates to evolve powered flight and the largest animals to ever take wing . The pterosaurs persisted for over 150 million years before disappearing at the end of the Cretaceous , but the patterns of and processes driving their extinction remain unclear . Only a single family , Azhdarchida...	Pterosaurs were winged cousins of the dinosaurs and lived from around 200 million years ago to 66 million years ago , when the last pterosaurs disappeared during the Cretaceous-Paleogene extinction that wiped out the dinosaurs . The pterosaurs are thought to have declined in diversity before their final extinction , su...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "geologic", "time", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "vertebrate", "paleontology", "humerus", "vertebrates", "biodiversity", "animals", "animal", "anatomy", "geology", "paleontology", "skeleton", "amniotes", "zoology"...	2018	Late Maastrichtian pterosaurs from North Africa and mass extinction of Pterosauria at the Cretaceous-Paleogene boundary
There has been much recent excitement about the use of genetics to elucidate ancestral history and demography . Whole genome data from humans and other species are revealing complex stories of divergence and admixture that were left undiscovered by previous smaller data sets . A central challenge is to estimate the tim...	In this paper , we study the length distribution of tracts of identity by state ( IBS ) , which are the gaps between pairwise differences in an alignment of two DNA sequences . These tract lengths contain information about the amount of genetic diversity that existed at various times in the history of a species and can...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "algorithms", "computer", "science", "mathematics", "theoretical", "biology", "algebra", "calculus", "statistics", "genetics", "applied", "mathematics", "population", "biology", "biology", "genomics", "evolutionary", "biology", "computerized", "simulations", "computational", ...	2013	Inferring Demographic History from a Spectrum of Shared Haplotype Lengths
Plasmodium vivax can potentially lead to life-threatening episodes but the mechanisms underlying severe disease remain poorly defined . Cytoadhesion of infected erythrocytes may contribute to P . vivax sequestration and organ injury although its physiological impact is still unknown . Here , we aimed to describe clinic...	Despite being considered a relatively benign disease , Plasmodium vivax infection has been recently associated with fatal outcomes . The mechanisms contributing to severe disease in P . vivax malaria remain largely unknown , although scarce evidences suggests that similarly to P . falciparum , P . vivax may also adhere...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "plasmodium", "vivax", "malaria", "parasitic", "diseases" ]	2013	Rosetting in Plasmodium vivax: A Cytoadhesion Phenotype Associated with Anaemia
Rhinovirus infections are the major cause of asthma exacerbations . We hypothesised that IL-15 , a cytokine implicated in innate and acquired antiviral immunity , may be deficient in asthma and important in the pathogenesis of asthma exacerbations . We investigated regulation of IL-15 induction by rhinovirus in human m...	We previously reported deficiency in interferon production in asthma , which correlated with disease severity and viral load during experimental rhinovirus infection . Here we show that macrophages produce IL-15 upon rhinovirus infection and that IFN-β plays an important role in IL-15 production . In asthmatic subjects...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "clinical", "immunology", "immunity", "innate", "immunity", "rhinovirus", "infection", "immunology", "viral", "diseases", "respiratory", "medicine", "pulmonology", "asthma" ]	2011	The Role of IL-15 Deficiency in the Pathogenesis of Virus-Induced Asthma Exacerbations
Recent mathematical models have been developed to study the dynamics of chronic myelogenous leukemia ( CML ) under imatinib treatment . None of these models incorporates the anti-leukemia immune response . Recent experimental data show that imatinib treatment may promote the development of anti-leukemia immune response...	Recent mathematical models have been developed to study the dynamics of chronic myelogenous leukemia ( CML ) under imatinib treatment . None of these models incorporates the anti-leukemia immune response . Recent experimental data show that imatinib treatment may promote the development of anti-leukemia immune response...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "mathematics", "oncology/hematological", "malignancies" ]	2008	Dynamics and Potential Impact of the Immune Response to Chronic Myelogenous Leukemia
The obligate human pathogen Neisseria gonorrhoeae is the sole aetiologic agent of the sexually transmitted infection , gonorrhea . Required for gonococcal infection , Type IV pili ( Tfp ) mediate many functions including adherence , twitching motility , defense against neutrophil killing , and natural transformation . ...	Neisseria gonorrhoeae , the bacterium responsible for the disease gonorrhea , is capable of undergoing natural DNA transformation , a critical mechanism by which bacteria can take up DNA from the environment . Uptake of foreign DNA can lead to adaptation to a changing environment and allow the spread of antibiotic resi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "pathogens", "immunology", "antigenic", "variation", "microbiology", "neisseria", "gonorrhoeae", "cloning...	2016	The Pilin N-terminal Domain Maintains Neisseria gonorrhoeae Transformation Competence during Pilus Phase Variation
Blocking the PD-1/PD-L1 pathway has emerged as a potential therapy to restore impaired immune responses in human immunodeficiency virus ( HIV ) -infected individuals . Most reports have studied the impact of the PD-L1 blockade on effector cells and neglected possible effects on regulatory T cells ( Treg cells ) , which...	HIV infection causes a progressive impairment of effector immune responses , contributing to virus persistence . The restoration of these responses is essential to achieve a drug-free control over HIV . One strategy that could restore effector immune responses is the relief of the inhibitory signal displayed by the PD-...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	PD-L1 Blockade Differentially Impacts Regulatory T Cells from HIV-Infected Individuals Depending on Plasma Viremia
The globally important Zika , dengue and chikungunya viruses are primarily transmitted by the invasive mosquitoes , Aedes aegypti and Aedes albopictus . In Australia , there is an increasing risk that these species may invade highly urbanized regions and trigger outbreaks . We describe the development of a Rapid Survei...	Aedes ( Stegomyia ) vectors of dengue , Zika and chikungunya viruses utilize artificial and natural containers as larval habitats . Adults do not usually disperse far ( < 500 m ) from these larval habitats in urban and peri-urban environments . Highly heterogeneous distributions raise significant logistic challenges to...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "reverse", "transcriptase-polymerase", "chain", "reaction", "invertebrates", "species", "colonization", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "pathology", "and", "laboratory", "medicine", "togaviruses", "invasive", "species"...	2017	Rapid Surveillance for Vector Presence (RSVP): Development of a novel system for detecting Aedes aegypti and Aedes albopictus
Several studies have demonstrated the presence of pathogen-specific Foxp3+ CD4 regulatory T cells ( Treg ) in infected animals , but little is known about where and how these cells affect the effector T cell responses and whether they are more suppressive than bulk Treg populations . We recently showed the presence of ...	By repressing immune responses against pathogens , regulatory CD4 T cells are double edged swords . On one hand , they ameliorate immunopathological disease , diminishing morbidity but they also potentially contribute to pathogen persistence . Tregs have long been thought to be primarily directed at self-antigens , but...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immunity", "to", "infections", "immunology", "lymphocyte", "activation", "immunoregulation", "immunomodulation", "infectious", "diseases", "white", "blood", "cells", "animal", "cells", "t", "cells", "immune", ...	2014	Virus-Specific Regulatory T Cells Ameliorate Encephalitis by Repressing Effector T Cell Functions from Priming to Effector Stages
Critical to the pathogenesis of intestinal amebiasis , Entamoeba histolytica ( Eh ) induces mucus hypersecretion and degrades the colonic mucus layer at the site of invasion . The parasite component ( s ) responsible for hypersecretion are poorly defined , as are regulators of mucin secretion within the host . In this ...	An interesting facet to the protozoan parasite Entamoeba histolytica is the ability to cause disease in a very limited subset of individuals , subject to first overcoming the intestinal mucus barrier within the gastrointestinal tract . Mucins , which are the primary constituent of the mucus layer are secreted basally t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "phosphorylation", "flow", "cytometry", "medicine", "and", "health", "sciences", "body", "fluids", "enzymes", "cell", "processes", "enzymology", "physiological", "processes", "integrins", "cellular", "structures", "and", "organelles", "research", "and", "analysis", "met...	2016	Entamoeba histolytica Cysteine Proteinase 5 Evokes Mucin Exocytosis from Colonic Goblet Cells via αvβ3 Integrin
Retroviruses engage the ESCRT pathway through late assembly ( L ) domains in Gag to promote virus release . HIV-1 uses a PTAP motif as its primary L domain , which interacts with the ESCRT-I component Tsg101 . In contrast , certain other retroviruses primarily use PPxY-type L domains , which constitute ligands for NEDD...	To promote its escape from cells , HIV-1 hijacks cellular budding machinery through so-called L domains in its structural Gag protein . However , HIV-1 lacks a type of L domain that recruits NEDD4 ubiquitin ligases , a family of cellular enzymes that attach one or more copies of a small protein called ubiquitin to othe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/virion", "structure,", "assembly,", "and", "egress", "virology/immunodeficiency", "viruses" ]	2010	Rescue of HIV-1 Release by Targeting Widely Divergent NEDD4-Type Ubiquitin Ligases and Isolated Catalytic HECT Domains to Gag
In many rural areas at risk for enteric fever , there are few data on Salmonella enterica serotypes Typhi ( S . Typhi ) and Paratyphi ( S . Paratyphi ) incidence , due to limited laboratory capacity for microbiologic culture . Here , we describe an approach that permits recovery of the causative agents of enteric fever...	Every year , 20 million people worldwide suffer from typhoid , a bacterial infection spread by contaminated food and water , and over 200 , 000 die from the infection . However , few data are available on the prevalence and antimicrobial resistance profiles of the causative agents of typhoid , especially in settings wi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "bacterial", "diseases", "infectious", "diseases", "clinical", "laboratory", "sciences", "diagnostic", "medicine", "global", "health", "salmonella" ]	2013	Evaluation of an Electricity-free, Culture-based Approach for Detecting Typhoidal Salmonella Bacteremia during Enteric Fever in a High Burden, Resource-limited Setting
Coordination between cellular metabolism and DNA replication determines when cells initiate division . It has been assumed that metabolism only plays a permissive role in cell division . While blocking metabolism arrests cell division , it is not known whether an up-regulation of metabolic reactions accelerates cell cy...	How cells determine when to divide is critical for understanding biological processes where cell proliferation is manifest . Because cells need to accumulate precursors prior to duplication , cellular metabolism is expected to impact cell division . Mitochondrial processes are central to the control of overall cell met...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/microbial", "physiology", "and", "metabolism", "molecular", "biology/dna", "replication", "cell", "biology/cell", "growth", "and", "division", "molecular", "biology/histone", "modification" ]	2008	An Increase in Mitochondrial DNA Promotes Nuclear DNA Replication in Yeast
The nematodes Wuchereria bancrofti and Brugia spp . infect over 120 million people worldwide , causing lymphedema , elephantiasis and hydrocele , collectively known as lymphatic filariasis . Most infected individuals appear to be asymptomatic , but many exhibit sub-clinical manifestations including the lymphangiectasia...	Lymphatic filariasis is caused by parasitic worms with approximately 120 million people infected worldwide and over 1 billion people at risk . The adult worms reside in host lymphatic vessels ( LV ) but most infected individuals do not present with overt clinical symptoms . Individuals exhibiting lymphedema , a common ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "immunology", "microbiology", "parasitology", "emerging", "infectious", "diseases", "infectious", "diseases", "white", "blood", "cells", "animal",...	2014	Filarial Excretory-Secretory Products Induce Human Monocytes to Produce Lymphangiogenic Mediators
Predictive markers linking drug efficacy to clinical outcome are a key component in the drug discovery and development process . In HIV infection , two different measures , viral load decay and phenotypic assays , are used to assess drug efficacy in vivo and in vitro . For the newly introduced class of integrase inhibi...	To guide drug discovery and development , measures of drug efficacy that are linked to clinical outcome are of key importance . In HIV treatment , decay of plasma viral load is typically used as an in vivo measure of drug efficacy , whereas phenotypic assays are used to assess drug efficacy in vitro . The recent develo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "pharmacology/drug", "resistance", "virology/immunodeficiency", "viruses", "virology/new", "therapies,", "including", "antivirals", "and", "immunotherapy", "pharmacology/drug", "development", "virology/antivirals,", "including", "modes", "of", "action", "and", "resistance", "co...	2010	Drug-Class Specific Impact of Antivirals on the Reproductive Capacity of HIV
Giardia intestinalis is a common cause of diarrheal disease and it consists of eight genetically distinct genotypes or assemblages ( A-H ) . Only assemblages A and B infect humans and are suggested to represent two different Giardia species . Correlations exist between assemblage type and host-specificity and to some e...	Giardia is a single cell intestinal parasite and a common cause of diarrhea in humans and animals . Giardia is an unusual eukaryote by possessing two nuclei , a highly reduced genome and simple transcriptional apparatus . We have characterized the transcriptome of Giardia at single nucleotide resolution , which allowed...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results/Discussion" ]	[ "parastic", "protozoans", "giardia", "lamblia", "genome", "analysis", "tools", "genomics", "protozoology", "biology", "computational", "biology", "microbiology", "genetics", "and", "genomics", "transcriptomes" ]	2013	Transcriptome Profiling of Giardia intestinalis Using Strand-specific RNA-Seq
The availability of genomes of many closely related bacteria with diverse metabolic capabilities offers the possibility of tracing metabolic evolution on a phylogeny relating the genomes to understand the evolutionary processes and constraints that affect the evolution of metabolic networks . Using simple ( independent...	Metabolic networks correspond to one of the most complex cellular processes . Most organisms have a common set of reactions as a part of their metabolic networks that relate to essential processes such as generation of energy and the synthesis of important biological molecules , which are required for their survival . ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "computational", "biology/evolutionary", "modeling", "computational", "biology/metabolic", "networks", "computational", "biology/systems", "biology" ]	2010	A Bayesian Approach to the Evolution of Metabolic Networks on a Phylogeny
In April , 2004 , chikungunya virus ( CHIKV ) re-emerged in Kenya and eventually spread to the islands in the Indian Ocean basin , South-East Asia , and the Americas . The virus , which is often associated with high levels of viremia in humans , is mostly transmitted by the urban vector , Aedes aegypti . The expansion ...	A chikungunya epidemic recently occurred in Mandera , Northern Kenya , with over 1 , 700 cases reported . The disease epidemics are linked to the urban vector , Aedes aegypti . This mosquito species is rapidly expanding its range and it is currently abundant in and around the major urban cities of Kenya . In this study...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "legs", "pathology", "and", "laboratory", "medicine", "togaviruses", "chikungunya", "infection", "pathogens", "tropical", "diseases", "microbiology", "limbs", "(anatomy)", "geographical", "locatio...	2017	Vector competence of populations of Aedes aegypti from three distinct cities in Kenya for chikungunya virus
Synchronous spiking during cerebellar tasks has been observed across Purkinje cells: however , little is known about the intrinsic cellular mechanisms responsible for its initiation , cessation and stability . The Phase Response Curve ( PRC ) , a simple input-output characterization of single cells , can provide insigh...	The phase response curve ( PRC ) quantifies the effect of an infinitesimal perturbation on the phase of an oscillator , be it mechanical , electronic or biological . In the particular case of neurons , PRCs can be employed to infer several network properties that are influenced by intrinsic membrane mechanisms . It has...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	On the Firing Rate Dependency of the Phase Response Curve of Rat Purkinje Neurons In Vitro
HIV-1 release is mediated through two motifs in the p6 region of Gag , PTAP and LYPXnL , which recruit cellular proteins Tsg101 and Alix , respectively . The Nucleocapsid region of Gag ( NC ) , which binds the Bro1 domain of Alix , also plays an important role in HIV-1 release , but the underlying mechanism remains unc...	Human immunodeficiency virus type 1 ( HIV-1 ) assembles its structural protein Gag into a viral shell at the plasma membrane . Gag is divided into several regions , each with its own distinct function ( s ) . Within the p6 region of Gag , there are two short peptide sequences , called Late ( L ) domains , that serve to...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/virion", "structure,", "assembly,", "and", "egress", "virology/immunodeficiency", "viruses" ]	2009	The Nucleocapsid Region of HIV-1 Gag Cooperates with the PTAP and LYPXnL Late Domains to Recruit the Cellular Machinery Necessary for Viral Budding
Genomic instability associated with DNA replication stress is linked to cancer and genetic pathologies in humans . If not properly regulated , replication stress , such as fork stalling and collapse , can be induced at natural replication impediments present throughout the genome . The fork protection complex ( FPC ) i...	In every round of the cell cycle , cells must accurately replicate their full genetic information . This process is highly regulated , as defects during DNA replication cause genomic instability , leading to various genetic disorders including cancers . To thwart these problems , cells carry an array of complex mechani...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "chromosome", "structure", "and", "function", "molecular", "probe", "techniques", "dna", "damage", "telomeres", "fungi", "model", "organisms", "dna", "replication", "protein", "structure", "dna", "epigenetics", "molecular", "biology", "techniques", "gel", "electrophores...	2016	Swi1Timeless Prevents Repeat Instability at Fission Yeast Telomeres
The midgut microbial community in insect vectors of disease is crucial for an effective immune response against infection with various human and animal pathogens . Depending on the aspects of their development , insects can acquire microbes present in soil , water , and plants . Sand flies are major vectors of leishman...	Symbiotic microorganisms influence many aspects of the physiology of their hosts . In insects , symbiotic bacteria are able among other things to modulate the immune response and the development of the insect from larval stages to adult . Many bacteria first gain access to insect tissues , such as the gut , during larv...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Bacterial Infection and Immune Responses in Lutzomyia longipalpis Sand Fly Larvae Midgut
The West African Ebola epidemic has demonstrated that the existing range of medical and epidemiological responses to emerging disease outbreaks is insufficient , especially in post-conflict contexts with exceedingly poor healthcare infrastructures . In this context , community-based responses have proven vital for cont...	In this study the authors analyzed data from the 2014 Ebola outbreak in Monrovia and Montserrado County , Liberia . The data were collected for the purposes of program design and evaluation by the World Health Organization ( WHO ) and the Government of Liberia ( GOL ) , in order to identify: ( 1 ) local knowledge about...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Community-Centered Responses to Ebola in Urban Liberia: The View from Below
High affinity antigen-specific T cells play a critical role during protective immune responses . Epitope enhancement can elicit more potent T cell responses and can subsequently lead to a stronger memory pool; however , the molecular basis of such enhancement is unclear . We used the consensus peptide-binding motif for...	Enhancing the immune responses to pathogens is a chief goal of vaccine development . Here , we describe the development of an engineered CD8+ T cell epitope that elicits an immune response to the native epitope that is more potent than the one that occurs during the natural infection . We showed that this “improved” ( ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neurological", "disorders/infectious", "diseases", "of", "the", "nervous", "system", "immunology/immunity", "to", "infections", "virology/animal", "models", "of", "infection", "virology/immune", "evasion" ]	2008	Prevention of Cytotoxic T Cell Escape Using a Heteroclitic Subdominant Viral T Cell Determinant
Few studies have focused on the cognitive morbidity of neurocysticercosis ( NCC ) , one of the most common parasitic infections of the central nervous system . We longitudinally assessed the cognitive status and quality of life ( QoL ) of patients with incident symptomatic NCC cases and matched controls . The setting o...	Neurocysticercosis ( NCC ) is one of the most common parasitic infections of the central nervous system . Cognitive changes have been frequently reported with this disease but have not been well studied . Our study team recruited a group of new onset NCC cases and a matched set of healthy neighborhood controls and new ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "global", "health", "neurology", "neurological", "disorders" ]	2012	Cognitive Changes and Quality of Life in Neurocysticercosis: A Longitudinal Study
Nogo-A is a membrane protein of the central nervous system ( CNS ) restricting neurite growth and synaptic plasticity via two extracellular domains: Nogo-66 and Nogo-A-Δ20 . Receptors transducing Nogo-A-Δ20 signaling remained elusive so far . Here we identify the G protein-coupled receptor ( GPCR ) sphingosine 1-phosph...	Recent studies have demonstrated an important role of Nogo-A signaling in the repression of structural and synaptic plasticity in mature neuronal networks of the central nervous system . These insights extended our understanding of Nogo-A's inhibitory function far beyond its well-studied role as axonal-growth inhibitor...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "lipoprotein", "receptors", "developmental", "neuroscience", "synaptic", "plasticity", "neurochemistry", "neurobiology", "of", "disease", "and", "regeneration", "proteins", "lipoproteins", "biology", "neuroscience" ]	2014	The Sphingolipid Receptor S1PR2 Is a Receptor for Nogo-A Repressing Synaptic Plasticity
Follicular T helper cells ( Tfh ) , a subset of CD4 T lymphocytes , provide crucial help to B cells in the production of antigen-specific antibodies . Although several studies have analyzed the dynamics of Tfh cells in peripheral blood and lymph nodes ( LNs ) during Aids , none has yet addressed the impact of SIV infec...	Among CD4 T lymphocytes , follicular T helper cells ( Tfh ) are essential for B cell responses . Understanding the impact of viral infections on Tfh function , in particular in deep tissues such as the spleen , which is the main organ for B cell response , may be important for vaccine development . We used a non-human ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Early Loss of Splenic Tfh Cells in SIV-Infected Rhesus Macaques
Human brucellosis ( HB ) is a bacterial zoonosis that is more frequent in low income and middle-income countries; it is sometimes associated with outbreaks . The aim of this study was to describe the largest outbreak of HB in Brazil . A retrospective cohort study of patients suspected of having contracted HB in the sta...	Human brucellosis ( HB ) is a bacterial zoonosis more frequent in low income and middle-income countries . The number of cases has increased in Southern Brazil since 2014 . Considering the risk of dissemination of the disease , the authors evaluated the whole spectrum of the disease in the State of Paraná , where cases...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "milk", "body", "fluids", "pathology", "and", "laboratory", "medicine", "pathogens", "tropical", "diseases", "microbiology", "geographical", "locations", "diet", "brucellosis", "organisms", "bacterial", "diseases", "nutrition", "...	2018	Outbreak of human brucellosis in Southern Brazil and historical review of data from 2009 to 2018
The mechanisms leading to latency and reactivation of human tuberculosis are still unclear , mainly due to the lack of standardized animal models for latent mycobacterial infection . In this longitudinal study of the progression of a mycobacterial disease in adult zebrafish , we show that an experimental intraperitonea...	One third of the world's population has been estimated to be infected with Mycobacterium tuberculosis , which under the appropriate set of circumstances causes lethal lung disease . According to current understanding , mycobacteria can persist in their host without causing symptoms – a state referred to as latency or s...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "medicine", "bacterial", "diseases", "zebrafish", "infectious", "diseases", "model", "organisms", "immunology", "biology", "microbiology", "host-pathogen", "interaction", "infectious", "disease", "modeling", "bacterial", "pathogens", "immune", "response"...	2012	Mycobacterium marinum Causes a Latent Infection that Can Be Reactivated by Gamma Irradiation in Adult Zebrafish
Plasmacytoid dendritic cells ( pDCs ) express the I-type lectin receptor Siglec-H and produce interferon α ( IFNα ) , a critical anti-viral cytokine during the acute phase of murine cytomegalovirus ( MCMV ) infection . The ligands and biological functions of Siglec-H still remain incompletely defined in vivo . Thus , w...	Plasmacytoid dendritic cells ( pDCs ) represent a minor but functionally important subset of dendritic cells . Siglec-H , a surface receptor expressed on these cells , was shown to modulate IFNα production , which in turn could influence anti-viral functions in vivo . A potential role for Siglec-H as a pathogen uptake ...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[]	2013	Absence of Siglec-H in MCMV Infection Elevates Interferon Alpha Production but Does Not Enhance Viral Clearance
Hematopoietic stem cells are capable of self-renewal or differentiation along three main lineages: myeloid , erythroid , and lymphoid . One of the earliest lineage decisions for blood progenitor cells is whether to adopt the lymphoid or myeloid fate . Previous work had shown that myocyte enhancer factor 2C ( MEF2C ) is...	B cells comprise important defense systems against infections in animals . Generating B cells requires the interplay of signals received by a blood stem cell and the ability of this cell to turn on or off gene expression , the latter of which is regulated largely by transcription factors . Despite the characterization ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "luciferase", "immune", "cells", "gene", "regulation", "enzymes", "regulatory", "proteins", "immunology", "biological", "cultures", "dna-binding", "proteins", "enzymology", "293t", "cells", "cell", "differentiat...	2016	MEF2C and EBF1 Co-regulate B Cell-Specific Transcription
The HIV-1 envelope ( Env ) spike , which consists of a compact , heterodimeric trimer of the glycoproteins gp120 and gp41 , is the target of neutralizing antibodies . However , the high mutation rate of HIV-1 and plasticity of Env facilitates viral evasion from neutralizing antibodies through various mechanisms . Mutat...	The Env glycoproteins , gp120 and gp41 , are the viral targets of HIV neutralizing antibodies . Accordingly , vaccine studies have focused on eliciting broadly neutralizing antibodies against epitopes in these proteins . Sequence diversity and the conformational flexibility of Env have made vaccine design efforts diffi...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "physics", "theoretical", "biology", "biophysic", "al", "simulations", "immunology", "biology", "computational", "biology", "evolutionary", "biology", "biophysics", "simulations", "biophysics" ]	2013	A Mechanistic Understanding of Allosteric Immune Escape Pathways in the HIV-1 Envelope Glycoprotein
The presence of spliceosomal introns in eukaryotes raises a range of questions about genomic evolution . Along with the fundamental mysteries of introns' initial proliferation and persistence , the evolutionary forces acting on intron sequences remain largely mysterious . Intron number varies across species from a few ...	The spliceosomal introns that interrupt eukaryotic genes show great number and sequence variation across species , from the rare , highly uniform yeast introns to the ubiquitous and highly variable vertebrate intron sequences . The causes of these differences remain mysterious . We studied sequences of intron branch po...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/genomics", "genetics", "and", "genomics/comparative", "genomics", "evolutionary", "biology/genomics", "genetics", "and", "genomics", "genetics", "and", "genomics/bioinformatics" ]	2008	Evolutionary Convergence on Highly-Conserved 3′ Intron Structures in Intron-Poor Eukaryotes and Insights into the Ancestral Eukaryotic Genome
To gain insight into which parameters of neural activity are important in shaping the perception of odors , we combined a behavioral measure of odor perception with optical imaging of odor representations at the level of receptor neuron input to the rat olfactory bulb . Instead of the typical test of an animal's abilit...	Olfactory stimuli elicit temporally complex patterns of activity across groups of receptor neurons as well as across central neurons . It remains unclear which parameters among these complex activity patterns are important in shaping odor perception . To address this issue , we imaged from the olfactory bulb of awake r...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience" ]	2008	Rapid Encoding and Perception of Novel Odors in the Rat
The link between mechanics and biology in the generation and the adaptation of bone has been well studied in context of skeletal development and fracture healing . Yet , the prediction of tissue genesis within - and the spatiotemporal healing of - postnatal defects , necessitates a quantitative evaluation of mechano-bi...	Arising as a consequence of trauma , tumor resection , removal of necrotic or infected tissue , and congenital abnormalities , critical-sized defects are too large to heal spontaneously and therefore require surgical intervention . New surgical approaches harness the regenerative power of the periosteum , a tissue memb...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "materials", "science", "engineering", "and", "technology", "biology", "and", "life", "sciences", "physical", "sciences" ]	2014	Mechanistic, Mathematical Model to Predict the Dynamics of Tissue Genesis in Bone Defects via Mechanical Feedback and Mediation of Biochemical Factors
While multiple studies have reported the accelerated evolution of brain gene expression in the human lineage , the mechanisms underlying such changes are unknown . Here , we address this issue from a developmental perspective , by analyzing mRNA and microRNA ( miRNA ) expression in two brain regions within macaques , c...	Species evolution is often depicted as a slow and continuous process punctuated by rapid changes . One example of the latter is the evolution of human cognition–emergence of an exceedingly complex phenotype within a few million years . What genetic mechanisms might have driven this process ? Nearly 40 years ago , it wa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "expression", "analysis", "organismal", "evolution", "developmental", "neuroscience", "genomics", "genetics", "human", "evolution", "biology", "evolutionary", "biology", "neuroscience", "evolutionary", "genetics", "genetics", "and", "genomics", "evolutionary", "de...	2011	MicroRNA-Driven Developmental Remodeling in the Brain Distinguishes Humans from Other Primates
In invertebrates , small interfering RNAs are at the vanguard of cell-autonomous antiviral immunity . In contrast , antiviral mechanisms initiated by interferon ( IFN ) signaling predominate in mammals . Whilst mammalian IFN-induced miRNA are known to inhibit specific viruses , it is not known whether host-directed mic...	How infected cells respond to a virus during the first minutes to hours after infection can determine whether a disease develops and influences the host’s long-term survival . In mammals , unlike plants and flies that use small RNAs to fight viral infections , virus-induced interferon responses are a critical early eve...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gene", "regulation", "microbiology", "micrornas", "small", "interfering", "rnas", "lipids", "proteins", "gene", "expression", "metabolic", "pathways", "viral", "replication", "sterols", "cholesterol", "biochemistry", "rna", "nucleic", "acids", "virology", "genetics", "...	2016	An Interferon Regulated MicroRNA Provides Broad Cell-Intrinsic Antiviral Immunity through Multihit Host-Directed Targeting of the Sterol Pathway
Streptococcus pneumoniae ( pneumococcus ) is a leading cause of death and disease in children and elderly . Genetic variability among isolates from this species is high . These differences , often the product of gene loss or gene acquisition via horizontal gene transfer , can endow strains with new molecular pathways ,...	Streptococcus pneumoniae ( pneumococcus ) , an important human pathogen , exhibits a dual lifestyle featuring asymptomatic colonization of the host on the one hand as well as infliction of severe local and systemic disease on the other . In pneumococcal strains , differences in gene possession often lead to varied phen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "chinchillas", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pneumococcus", "ears", "gene", "regulation", "pathogens", "rna", "extraction", "microbiology", "vertebrates", "animals", "mammals", "middle", "ear", "regulator", "gene...	2017	Promiscuous signaling by a regulatory system unique to the pandemic PMEN1 pneumococcal lineage
Using geo-referenced case data , we present spatial and spatio-temporal cluster analyses of the early spread of the 2013–2015 chikungunya virus ( CHIKV ) in Dominica , an island in the Caribbean . Spatial coordinates of the locations of the first 417 reported cases observed between December 15th , 2013 and March 11th ,...	Chikungunya is a disease transmitted by mosquitoes . Currently , there is an epidemic of chikungunya in several islands and countries in the Americas . Despite efforts at understanding and predicting spread , there have been no studies assessing the spatio-temporal spread of chikungunya in any of the Caribbean islands ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Spatial and Temporal Clustering of Chikungunya Virus Transmission in Dominica
Memory is attributed to strengthened synaptic connections among particular brain neurons , yet synaptic membrane components are transient , whereas memories can endure . This suggests synaptic information is encoded and ‘hard-wired’ elsewhere , e . g . at molecular levels within the post-synaptic neuron . In long-term ...	Memory is understood as strengthened synaptic connections among neurons . Paradoxically components of synaptic membranes are relatively short-lived and frequently re-cycled while memories can last a lifetime . This suggests synaptic information is encoded at a deeper , finer-grained scale of molecular information withi...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "physics", "signal", "transduction", "cell", "motility", "theoretical", "biology", "molecular", "biology", "signaling", "pathways", "biology", "computational", "biology", "molecular", "cell", "biology", "biophysics", "neuroscience" ]	2012	Cytoskeletal Signaling: Is Memory Encoded in Microtubule Lattices by CaMKII Phosphorylation?
Human schistosomiasis , a debilitating and chronic disease , is among a set of 17 neglected tropical infectious diseases of poverty that is currently posing a threat to the wellbeing of 2 billion people in the world . The SHAWN/WASH and MAM programmes in the study area require epidemiological data to enhance their effe...	In 1851 , human schistosomiasis was discovered in Egypt by a German surgeon named Theodor Bilharz . Therefore , it is alternatively called ‘bilharziasis’ . Being a disease that is closely associated with poverty in the tropics , chiefly the sub-Saharan Africa , Urinary Schistosomiasis is transmitted to humans who sourc...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "education", "helminths", "sociology", "tropical", "diseases", "social", "sciences", "parasitic", "diseases", "animals", "health", "care", "urine", "gastropods", "neglected", "tro...	2018	The current epidemiological status of urogenital schistosomiasis among primary school pupils in Katsina State, Nigeria: An imperative for a scale up of water and sanitation initiative and mass administration of medicines with Praziquantel
Epilepsy is one of the most common neurological disorders affecting about 1% of the world population . For patients with focal seizures that cannot be treated with antiepileptic drugs , the common treatment is a surgical procedure for removal of the seizure onset zone ( SOZ ) . In this work we introduce an algorithm fo...	Epilepsy is a common neurological disorder characterized by abnormal electrical disturbances in the brain that result in transient occurrence of signs and/or symptoms , also known as seizures . In focal epilepsy , this electrical activity originates from a limited area in the brain , commonly referred to as the seizure...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "machine", "learning", "algorithms", "medicine", "and", "health", "sciences", "applied", "mathematics", "neuroscience", "surgical", "and", "invasive", "medical", "procedures", "health", "care", "simulation", "and", "modeling", "algorithms", "mathematics", "artificial", ...	2018	SozRank: A new approach for localizing the epileptic seizure onset zone
The brain exhibits complex spatio-temporal patterns of activity . This phenomenon is governed by an interplay between the internal neural dynamics of cortical areas and their connectivity . Uncovering this complex relationship has raised much interest , both for theory and the interpretation of experimental data ( e . ...	The study of interactions between different cortical regions at rest or during a task has considerably developed in the past decades thanks to progress in non-invasive imaging techniques , such as fMRI , EEG and MEG . These techniques have revealed that distant cortical areas exhibit specific correlated activity during...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "diagnostic", "radiology", "functional", "magnetic", "resonance", "imaging", "neural", "networks", "engineering", "and", "technology", "signal", "processing", "random", "variables", "neuroscience", "covariance", "signal", "filterin...	2016	Estimation of Directed Effective Connectivity from fMRI Functional Connectivity Hints at Asymmetries of Cortical Connectome
Up to 50% of patients with the multibacillary form of leprosy are expected to develop acute systemic inflammatory episodes known as type 2 reactions ( T2R ) , thus aggravating their clinical status . Thalidomide rapidly improves T2R symptoms . But , due to its restricted use worldwide , novel alternative therapies are ...	Leprosy is caused by a mycobacterium that has a predilection for skin and nerve cells . The chronic course of the disease may be interrupted by acute inflammatory episodes known as reactions , despite effective bacterial killing with antibiotics . Reactions aggravate the patient’s clinical status and may become a medic...	[ "Abstract", "Introduction", "Methods", "Results", "and", "discussion" ]	[ "blood", "cells", "inflammatory", "diseases", "mycobacterium", "leprae", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "immunology", "tropical", "diseases", "bacterial", "diseases", "signs", "and", "symptoms", ...	2019	Neutrophil extracellular traps contribute to the pathogenesis of leprosy type 2 reactions
CHIP ( carboxyl terminus of heat shock 70-interacting protein ) has long been recognized as an active member of the cellular protein quality control system given the ability of CHIP to function as both a co-chaperone and ubiquitin ligase . We discovered a genetic disease , now known as spinocerebellar autosomal recessi...	CHIP is a multi-functional protein that bridges two opposing cellular processes: protein refolding and protein degradation . Mutations in CHIP are drivers of a debilitating and fatal disease , called spinocerebellar ataxia autosomal recessive 16 ( SCAR16 ) . Patients with CHIP mutations suffer from pathologies in both ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cognitive", "neurology", "medicine", "and", "health", "sciences", "molecular", "probe", "techniques", "enzymes", "neurodegenerative", "diseases", "brain", "enzymology", "vertebrates", "mice", "ubiquitin", "ligases", "animals", "mammals", "neuroscience", "animal", "models...	2018	Disrupted structure and aberrant function of CHIP mediates the loss of motor and cognitive function in preclinical models of SCAR16
During language processing , humans form complex embedded representations from sequential inputs . Here , we ask whether a “geometrical language” with recursive embedding also underlies the human ability to encode sequences of spatial locations . We introduce a novel paradigm in which subjects are exposed to a sequence...	The child’s acquisition of language has been suggested to rely on the ability to build hierarchically structured representations from sequential inputs . Does a similar mechanism also underlie the acquisition of geometrical rules ? Here , we introduce a learning situation in which human participants had to grasp simple...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "learning", "children", "linguistics", "social", "sciences", "geometry", "neuroscience", "learning", "and", "memory", "age", "groups", "adults", "cognitive", "psychology", "mathematics", "cognition", "memory", "families", "language", "syntax", "behavior", "people", "and...	2017	The language of geometry: Fast comprehension of geometrical primitives and rules in human adults and preschoolers
The high prevalence of HIV-1/AIDS in areas endemic for schistosomiasis and other helminthic infections has led to the hypothesis that parasites increase host susceptibility to immunodeficiency virus infection . We previously showed that rhesus macaques ( RM ) with active schistosomiasis were significantly more likely t...	Parasitic infections have been postulated to increase host susceptibility to HIV-1 . We previously demonstrated that rhesus monkeys with active schistosomiasis were significantly more likely to become systemically infected after intrarectal exposure to an R5-tropic clade C simian-human immunodeficiency virus then were ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "viral", "diseases", "parasitic", "diseases" ]	2011	Schistosoma mansoni Enhances Host Susceptibility to Mucosal but Not Intravenous Challenge by R5 Clade C SHIV
Streptococcus pneumoniae produces the pore-forming toxin pneumolysin ( PLY ) , which is a member of the cholesterol-dependent cytolysin ( CDC ) family of toxins . The CDCs recognize and bind the 3β-hydroxyl group of cholesterol at the cell surface , which initiates membrane pore formation . The cholesterol transport li...	The pore-forming cholesterol-dependent cytolysins ( CDCs ) are one of the most widely disseminated virulence factors expressed by Gram-positive pathogens . Streptococcus pneumoniae is a major human pathogen and expresses a CDC termed pneumolysin ( PLY ) . PLY and most CDCs bind cholesterol as their cellular receptor , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "medicine", "and", "health", "sciences", "animal", "studies", "bioassays", "and", "physiological", "analysis", "biology", "and", "life", "sciences", "microbiology", "research", "and", "analysis", "methods" ]	2014	Mouse, but Not Human, ApoB-100 Lipoprotein Cholesterol Is a Potent Innate Inhibitor of Streptococcus pneumoniae Pneumolysin
Host-associated bacterial communities vary extensively between individuals , but it can be very difficult to determine the sources of this heterogeneity . Here , we demonstrate that stochastic bacterial community assembly in the Caenorhabditis elegans intestine is sufficient to produce strong interworm heterogeneity in...	Host-associated bacterial communities—also known as microbiomes—vary extensively between individuals , even among clones exposed to the same environment . The sources of this variation are not entirely understood and can be very difficult to determine . In this manuscript , we demonstrate experimentally how randomness ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "death", "rates", "invertebrates", "medicine", "and", "health", "sciences", "demography", "caenorhabditis", "animals", "animal", "models", "physiological", "processes", "caenorhabditis", "elegans", "luminescent", "proteins", "model", "organisms", "yellow", "fluorescent", ...	2017	Stochastic assembly produces heterogeneous communities in the Caenorhabditis elegans intestine
Smooth muscle is present in a wide variety of anatomical locations , such as blood vessels , various visceral organs , and hair follicles . Contraction of smooth muscle is central to functions as diverse as peristalsis , urination , respiration , and the maintenance of vascular tone . Despite the varied physiological r...	It has been estimated that the human body contains approximately 200–400 distinct cell types . These estimates are largely based on the morphological characteristics of cells and have yielded , among many others , the category of smooth muscle cells , which have a distinct appearance and are present in a wide variety o...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion", "Supporting", "Information" ]	[ "in", "vitro", "genetics", "and", "genomics", "homo", "(human)" ]	2007	Gene Expression Programs of Human Smooth Muscle Cells: Tissue-Specific Differentiation and Prognostic Significance in Breast Cancers

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