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Attachment to the host mucosa is a key step in bacterial pathogenesis . On the apical surface of epithelial cells , members of the human carcinoembryonic antigen ( CEA ) family are abundant glycoproteins involved in cell-cell adhesion and modulation of cell signaling . Interestingly , several gram-negative bacterial pa...	Mucous surfaces are a hallmark of the nasal cavity and the throat as well as the intestinal and urogenital tracts . These surfaces serve as primary entry portals for a large number of pathogenic bacteria . To get a foothold on the mucosa , bacteria not only need to tightly attach to this tissue , but also need to overc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "hek", "293", "cells", "pathogens", "biological", "cultures", "microbiology", "neisseria", "gonorrhoeae", "cloning", "epithelial", "cells", "bacterial", "diseases", "i...	2016	Uropathogenic E. coli Exploit CEA to Promote Colonization of the Urogenital Tract Mucosa
Trachoma control programs utilize mass azithromycin distributions to treat ocular Chlamydia trachomatis as part of an effort to eliminate this disease world-wide . But it remains unclear what the community-level risk factors are for infection . This cluster-randomized , controlled trial entered 48 randomly selected com...	Trachoma is one of the most important neglected tropical diseases because it is the leading cause of blindness from an infection in the world . There are about 1 . 3 million persons blind from the disease and many more at risk of blindness in the future . It is caused by the common bacterium Chlamydia trachomatis and c...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "ophthalmology", "neglected", "tropical", "diseases", "trachoma" ]	2012	Community Risk Factors for Ocular Chlamydia Infection in Niger: Pre-Treatment Results from a Cluster-Randomized Trachoma Trial
How neuronal diversity emerges from complex patterns of gene expression remains poorly understood . Here we present an approach to understand electrophysiological diversity through gene expression by integrating pooled- and single-cell transcriptomics with intracellular electrophysiology . Using neuroinformatics method...	Brain cell types have different electrical features , determined by the genes that each cell expresses . By combining data from hundreds of articles studying individual cell types in isolation , we developed a dataset that combines neuron gene expression patterns with their electrical characteristics . We asked if patt...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "action", "potentials", "membrane", "potential", "brain", "electrophysiology", "electrophysiological", "properties", "electrophysiology", "neuroscience", "ion", "channels", "genome", "analysis", "bioassays", "and", "physiological", "...	2017	Transcriptomic correlates of neuron electrophysiological diversity
The antagonistic actions of Polycomb and Trithorax are responsible for proper cell fate determination in mammalian tissues . In the epidermis , a self-renewing epithelium , previous work has shown that release from Polycomb repression only partially explains differentiation gene activation . We now show that Trithorax ...	Human epidermal keratinocyte differentiation provides a highly suitable system to understand how progenitor cells become specialized . Previous work has implicated resolution of repressive histone modifications in the activation of the terminal differentiation gene expression program . Our work shows that this mechanis...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microarrays", "developmental", "biology", "gene", "expression", "genetics", "epigenetics", "biology", "computational", "biology", "chromatin", "genetics", "and", "genomics", "cell", "differentiation", "dna", "transcription", "histone", "modification" ]	2012	GRHL3/GET1 and Trithorax Group Members Collaborate to Activate the Epidermal Progenitor Differentiation Program
Treatment for human African trypanosomiasis is dependent on the species of trypanosome causing the disease and the stage of the disease ( stage 1 defined by parasites being present in blood and lymphatics whilst for stage 2 , parasites are found beyond the blood-brain barrier in the cerebrospinal fluid ( CSF ) ) . Curr...	Human African trypanosomiasis , also known as sleeping sickness , is a parasitic disease that affects people in sub-Saharan Africa . There are two stages of the infection . The first stage involves parasites proliferating in the bloodstream following introduction via the bite of an infected tsetse fly . The second , mo...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "nervous", "system", "african", "trypanosomiasis", "tropical", "diseases", "biomarkers", "parasitic", "diseases", "urine", "metabolomics", "metabolites", "neglected", "tropical", "diseases", "infectious", "disease...	2016	Metabolomics Identifies Multiple Candidate Biomarkers to Diagnose and Stage Human African Trypanosomiasis
Domestic dog rabies is an endemic disease in large parts of the developing world and also epidemic in previously free regions . For example , it continues to spread in eastern Indonesia and currently threatens adjacent rabies-free regions with high densities of free-roaming dogs , including remote northern Australia . ...	Rabies in domestic dog populations still causes >50 , 000 human deaths worldwide each year . While its eradication by vaccination of the reservoir population ( dogs and wildlife ) was successful in many parts of the world , it is still present in the developing world and continues to spread to new regions . Theoretical...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Development of a Novel Rabies Simulation Model for Application in a Non-endemic Environment
Genome-wide gene expression profiles accumulate at an alarming rate , how to integrate these expression profiles generated by different laboratories to reverse engineer the cellular regulatory network has been a major challenge . To automatically infer gene regulatory pathways from genome-wide mRNA expression profiles ...	The complex functions of a living cell are carried out through hierarchically organized regulatory pathways composed of complex interactions between regulators themselves and between regulators and their targets . Here we developed a Bayesian network inference algorithm , Deletion Mutant Bayesian Network ( DM_BN ) to r...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	Functional Dissection of Regulatory Models Using Gene Expression Data of Deletion Mutants
African Americans have a disproportionate risk for developing nephropathy . This disparity has been attributed to coding variants ( G1 and G2 ) in apolipoprotein L1 ( APOL1 ) ; however , there is little functional evidence supporting the role of this protein in renal function . Here , we combined genetics and in vivo m...	African Americans have a disproportionate risk for developing chronic kidney disease compared to European Americans . Previous studies have identified a region on chromosome 22 containing two genes , MYH9 and APOL1 , which likely accounts for nearly all of this difference . Previous reports provided strong statistical ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	In vivo Modeling Implicates APOL1 in Nephropathy: Evidence for Dominant Negative Effects and Epistasis under Anemic Stress
Preventive vaccination is a highly promising strategy for interrupting leishmaniasis transmission that can , additionally , contribute to elimination . A vaccine formulation based on naturally excreted secreted ( ES ) antigens was prepared from L . infantum promastigote culture supernatant . This vaccine achieved succe...	Visceral leishmaniasis ( VL ) , a potentially fatal disease caused by L . infantum , represents perfectly the need for a “One Health” approach for disease control , since it affects both humans and dogs , with similar clinical outcome and T-cell mediated immunity commitment . The dog vaccine development is highly requi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "immunology", "microbiology", "vertebrates", "parasitic", "diseases", "dogs", "animals", "mammals", "protozoan", "life", "cycles", "parasitic", "protozoans", "vaccines", "preventive", "medicin...	2016	Recombinant Forms of Leishmania amazonensis Excreted/Secreted Promastigote Surface Antigen (PSA) Induce Protective Immune Responses in Dogs
The large polymerase subunit ( L ) of non-segmented negative strand RNA viruses transcribes viral mRNAs and replicates the viral genome . Studies with VSV have shown that conserved region V ( CRV ) of the L protein is part of the capping domain . However , CRV folds over and protrudes into the polymerization domain , s...	Respiratory syncytial virus ( RSV ) is a leading cause of respiratory illness in infants , elderly , and immunocompromised individuals , yet treatment is limited to supportive medical care . The large polymerase protein ( L ) of RSV is essential for transcribing viral mRNAs and replicating the genome , and is an attrac...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "nucleic", "acid", "synthesis", "molecular", "probe", "techniques", "gene", "regulation", "rna", "analysis", "messenger", "rna", "dna-binding", "proteins", "northern", "blot", "polymerases", "molecular", "biology", "techniques", "rna", "synthesis", "dna", "gel", "elec...	2017	RNA elongation by respiratory syncytial virus polymerase is calibrated by conserved region V
PRODH , encoding proline oxidase ( POX ) , has been associated with schizophrenia through linkage , association , and the 22q11 deletion syndrome ( Velo-Cardio-Facial syndrome ) . Here , we show in a family-based sample that functional polymorphisms in PRODH are associated with schizophrenia , with protective and risk ...	Schizophrenia is a major mental illness affecting 1% of the population . It is known that genetics plays a role in the disease susceptibility , and it is thought that the illness is a complex disorder involving multiple genes . We show that the schizophrenia susceptibility gene , PRODH , conveys its risk through a vari...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neurological", "disorders/neuroimaging", "neurological", "disorders/neurogenetics", "radiology", "and", "medical", "imaging/magnetic", "resonance", "imaging", "genetics", "and", "genomics/medical", "genetics" ]	2008	Functional Polymorphisms in PRODH Are Associated with Risk and Protection for Schizophrenia and Fronto-Striatal Structure and Function
Cellular electrophysiology experiments , important for understanding cardiac arrhythmia mechanisms , are usually performed with channels expressed in non myocytes , or with non-human myocytes . Differences between cell types and species affect results . Thus , an accurate model for the undiseased human ventricular acti...	Understanding and preventing irregular heart rhythms that can lead to sudden death begins with basic research regarding single cell electrical behavior . Most of these studies are performed using non-human cells . However , differences between human and non-human cell properties affect experimental results and invoke d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bioengineering", "biomedical", "engineering", "biochemistry", "medicine", "biotechnology", "ion", "channels", "arrhythmias", "proteins", "electrophysiology", "biology", "engineering", "cardiovascular" ]	2011	Simulation of the Undiseased Human Cardiac Ventricular Action Potential: Model Formulation and Experimental Validation
In response to replication stress cells activate the intra-S checkpoint , induce DNA repair pathways , increase nucleotide levels , and inhibit origin firing . Here , we report that Rrm3 associates with a subset of replication origins and controls DNA synthesis during replication stress . The N-terminal domain required...	When cells duplicate their genome , the replication machinery is constantly at risk of encountering obstacles , including unusual DNA structures , bound proteins , or transcribing polymerases and transcripts . Cells possess DNA helicases that facilitate movement of the replication fork through such obstacles . Here , w...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "nucleic", "acid", "synthesis", "enzymes", "cell", "cycle", "and", "cell", "division", "cell", "processes", "enzymology", "dna", "damage", "mutation", "dna", "replication", "dna", "epigenetics", "synthesis", "phase", "chromatin", "dna", "synthesis", "chemical", "syn...	2016	A Novel Rrm3 Function in Restricting DNA Replication via an Orc5-Binding Domain Is Genetically Separable from Rrm3 Function as an ATPase/Helicase in Facilitating Fork Progression
Myeloid dendritic cells ( mDC ) are lost from blood in individuals with human immunodeficiency virus ( HIV ) infection but the mechanism for this loss and its relationship to disease progression are not known . We studied the mDC response in blood and lymph nodes of simian immunodeficiency virus ( SIV ) -infected rhesu...	Myeloid dendritic cells ( mDC ) are essential innate immune system cells that are lost from blood in human immunodeficiency virus infection through an ill-defined mechanism . We studied the kinetics of the mDC response in blood and lymph nodes of rhesus macaques infected with the closely related simian immunodeficiency...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/immune", "response", "immunology/innate", "immunity", "infectious", "diseases/hiv", "infection", "and", "aids", "pathology/immunology" ]	2010	Early Myeloid Dendritic Cell Dysregulation is Predictive of Disease Progression in Simian Immunodeficiency Virus Infection
Two modes of plant immunity against biotrophic pathogens , Effector Triggered Immunity ( ETI ) and Pattern-Triggered Immunity ( PTI ) , are triggered by recognition of pathogen effectors and Microbe-Associated Molecular Patterns ( MAMPs ) , respectively . Although the jasmonic acid ( JA ) /ethylene ( ET ) and salicylic...	Plants sense molecules originating from pathogens and turn on a battery of immune responses . Activation of immune responses is controlled by a complex network of signaling mechanisms . A traditional approach , knocking out one mechanism at a time , has revealed little about major parts of the signaling network involve...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "biology/plant-biotic", "interactions", "mathematics/statistics", "genetics", "and", "genomics/plant", "genetics", "and", "gene", "expression" ]	2009	Network Properties of Robust Immunity in Plants
Strongyloidiasis is a much-neglected soil born helminthiasis caused by the nematode Strongyloides stercoralis . Human derived S . stercoralis can be maintained in dogs in the laboratory and this parasite has been reported to also occur in dogs in the wild . Some authors have considered strongyloidiasis a zoonotic disea...	Infections of humans with the nematode Strongyloides stercoralis can persist for a very long time , due to the capacity of this pathogen to undergo an autoinfective life cycle and re-infect the same host over and over again . Clinical manifestation , known as human stongyloidiasis , may be fatal and can arise many year...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion", "Conclusions", "and", "outlook" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "vertebrates", "dogs", "animals", "genetic", "mapping", "mammals", "invertebrate", "genomics", "energy-producing", "organelles", "mammalian", "genomics", "bioenergetics",...	2017	Different but overlapping populations of Strongyloides stercoralis in dogs and humans—Dogs as a possible source for zoonotic strongyloidiasis
Comprehensive information on the timing and location of gene expression is fundamental to our understanding of embryonic development and tissue formation . While high-throughput in situ hybridization projects provide invaluable information about developmental gene expression patterns for model organisms like Drosophila...	When and where a gene is expressed is fundamental information for understanding embryonic development . Current knowledge for such expression patterns is typically far from complete . Even for the long-standing model organism , Drosophila melanogaster , with large-scale in situ projects that have provided invaluable ex...	[ "Abstract", "Introduction", "Results", "Methods" ]	[ "invertebrates", "machine", "learning", "algorithms", "medicine", "and", "health", "sciences", "muscle", "tissue", "applied", "mathematics", "pharyngeal", "muscles", "animals", "simulation", "and", "modeling", "animal", "models", "algorithms", "developmental", "biology", ...	2019	Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development
Many daily situations require us to track multiple objects and people . This ability has traditionally been investigated in observers tracking objects in a plane . This simplification of reality does not address how observers track objects when targets move in three dimensions . Here , we study how observers track mult...	Many daily life situations require us to track objects that are in motion . In the laboratory , this multiple object tracking problem is classically studied with objects moving on a two-dimensional screen , but in the real world objects typically move in three dimensions . Here we show that , despite the complexity of ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "velocity", "classical", "mechanics", "applied", "mathematics", "social", "sciences", "neuroscience", "learning", "and", "memory", "simulation", "and", "modeling", "algorithms", "cognitive", "neuroscience", "mathematics", "cognition", "memory", "extrapolation", "vision", ...	2017	Effect of depth information on multiple-object tracking in three dimensions: A probabilistic perspective
Prions , the agents causing transmissible spongiform encephalopathies , colonize the brain of hosts after oral , parenteral , intralingual , or even transdermal uptake . However , prions are not generally considered to be airborne . Here we report that inbred and crossbred wild-type mice , as well as tga20 transgenic m...	Prions , which are the cause of fatal neurodegenerative disorders termed transmissible spongiform encephalopathies ( TSEs ) , can be experimentally or naturally transmitted via prion-contaminated food , blood , milk , saliva , feces and urine . Here we demonstrate that prions can be transmitted through aerosols in mice...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "neuroscience", "pathology/neuropathology" ]	2011	Aerosols Transmit Prions to Immunocompetent and Immunodeficient Mice
Tsetse ( Glossina sensu stricto ) are cyclical vectors of human and animal trypanosomoses , that are presently targeted by the Pan African Tsetse and Trypanosomiasis Eradication Campaign ( PATTEC ) coordinated by the African Union . In order to achieve effective control of tsetse , there is need to produce elaborate pl...	Tse-tse flies are vectors of human and animal trypanosomoses , that are presently targeted by the Pan African Tsetse and Trypanosomiasis Eradication Campaign ( PATTEC ) coordinated by the African Union . In Zimbabwe , the government has devoted a full section of the veterinary services to tsetse and trypanosomosis cont...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "livestock", "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "ecological", "niches", "geographical", "locations", "trees", "parasitic", "diseases", "animals", "glossina", "materials", "science", "habitats", "surface...	2017	A pilot study to delimit tsetse target populations in Zimbabwe
Although it has been known for 50 years that adenoviruses ( Ads ) interact with erythrocytes ex vivo , the molecular and structural basis for this interaction , which has been serendipitously exploited for diagnostic tests , is unknown . In this study , we characterized the interaction between erythrocytes and unrelate...	In most cases , adenoviruses are thought to initially enter the host via contact with epithelial cells and spread within the host via an unknown mechanism . Most adenovirus serotypes use a cell adhesion molecule dubbed “CAR” to attach to cells . To assess , predict and understand adenovirus biology and vectorology , ma...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry/molecular", "evolution", "virology/persistence", "and", "latency", "virology/virus", "evolution", "and", "symbiosis", "virology/virion", "structure,", "assembly,", "and", "egress", "infectious", "diseases/viral", "infections", "biochemistry/biomacromolecule-ligand", ...	2009	The Cell Adhesion Molecule “CAR” and Sialic Acid on Human Erythrocytes Influence Adenovirus In Vivo Biodistribution
Recently , the heterogeneity that arises from stochastic fate decisions has been reported for several types of cancer-derived cell lines and several types of clonal cells grown under constant environmental conditions . However , the relation between this stochasticity and the responsiveness to extracellular stimuli rem...	Elucidation of the mechanisms that regulate cell fate has become one of the primary goals of research in cell biology and regenerative medicine . Growth factors are often used to regulate cell fate . However , stochastic cellular responses to growth regulators have prevented precise control of cell fate . We report our...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[]	2013	Optimality Conditions for Cell-Fate Heterogeneity That Maximize the Effects of Growth Factors in PC12 Cells
Spermatogenesis is a key developmental process allowing for a formation of a mature male gamete . During its final phase , spermiogenesis , haploid round spermatids undergo cellular differentiation into spermatozoa , which involves extensive restructuring of cell morphology , DNA , and epigenome . Using mouse models wi...	The mammalian Y chromosome was once thought to be a genetic wasteland with testis determinant Sry being the only gene of importance . We now know that there are many genes on this chromosome crucial for male reproduction but their specific roles are often undefined . Here , we investigated the function of the Y chromos...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Mouse Y-Encoded Transcription Factor Zfy2 Is Essential for Sperm Formation and Function in Assisted Fertilization
Hepatitis C virus ( HCV ) assembly and envelopment are coordinated by a complex protein interaction network that includes most of the viral structural and nonstructural proteins . While the nonstructural protein 4A ( NS4A ) is known to be important for viral particle production , the specific function of NS4A in this p...	RNA viruses , which encompass both established and emerging pathogens , pose significant public health challenges . Viruses in the family Flaviviridae , including Dengue virus , Zika virus , and hepatitis C virus ( HCV ) , continue to cause morbidity and mortality worldwide . One HCV protein , NS4A , acts in several st...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "sequencing", "techniques", "medicine", "and", "health", "sciences", "microbial", "mutation", "pathology", "and", "laboratory", "medicine", "hepacivirus", "pathogens", "enzymes", "microbiology", "enzymology", "viral", "structure", "viruses", "rna", "viruses", "molecular",...	2019	The acidic domain of the hepatitis C virus NS4A protein is required for viral assembly and envelopment through interactions with the viral E1 glycoprotein
The human cytomegalovirus ( HCMV ) clinical strain Toledo and the attenuated strain AD169 exhibit a striking difference in pathogenic potential and cell tropism . The virulent Toledo genome contains a 15-kb segment , which is present in all virulent strains but is absent from the AD169 genome . The pathogenic differenc...	Unlike the attenuated HCMV strain AD169 , the clinical isolates of HCMV , including the Toledo strain , are virulent and can cause disease in healthy adults . Toledo differs from AD169 in that Toledo contains a 15-kb DNA segment , encoding at least 19 ORFs and a single microRNA known as miR-UL148D . This 15-kb segment ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology", "biology", "microbiology" ]	2012	Human Cytomegalovirus Clinical Strain-Specific microRNA miR-UL148D Targets the Human Chemokine RANTES during Infection
Human African trypanosomiasis ( HAT ) , a major parasitic disease spread in Africa , urgently needs novel targets and new efficacious chemotherapeutic agents . Recently , we discovered that 4-[5- ( 4-phenoxyphenyl ) -2H-pyrazol-3-yl]morpholine ( compound 1 ) exhibits specific antitrypanosomal activity with an IC50 of 1...	Human African trypanosomiasis ( HAT ) , a devastating and fatal parasitic disease endemic in sub-Saharan Africa , urgently needs novel targets and efficacious chemotherapeutic agents . Recently , we discovered that 4-[5- ( 4-phenoxyphenyl ) -2H-pyrazol-3-yl]morpholine exhibits specific antitrypanosomal activity toward ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "chemical", "biology", "pharmacology", "biochemistry/protein", "chemistry", "biochemistry/drug", "discovery" ]	2009	Adenosine Kinase of T. b. rhodesiense Identified as the Putative Target of 4-[5-(4-phenoxyphenyl)-2H-pyrazol-3-yl]morpholine Using Chemical Proteomics
Bothrops , Crotalus and Lachesis represent the most medically relevant genera of pitvipers in Central and South America . Similarity in venom phenotype and physiopathological profile of envenomings caused by the four nominal Lachesis species led us to hypothesize that an antivenom prepared against venom from any of the...	Snakebite envenoming is a neglected public health problem in many developing countries and antivenom administration constitutes the mainstay in the treatment of such envenomings . Therapeutic antivenoms contain animal-derived antibodies against venom toxins and are produced by immunizing animals with the venom from one...	[ "Abstract", "Introduction", "Methods", "Results", "and", "discussion" ]	[ "medicine", "and", "health", "sciences", "costa", "rica", "toxins", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "enzyme-linked", "immunoassays", "immunology", "geographical", "locations", "tropical", "diseases", "vertebrates", "animals", "toxicol...	2017	Cross-reactivity, antivenomics, and neutralization of toxic activities of Lachesis venoms by polyspecific and monospecific antivenoms
The complexity of the eukaryotic parasite Trypanosoma ( T . ) cruzi manifests in its highly dynamic genome , multi-host life cycle , progressive morphologies and immune-evasion mechanisms . Accurate determination of infection or Chagas’ disease activity and prognosis continues to challenge researchers . We hypothesized...	The most prevalent parasite infection in Latin America causes Chagas’ disease . Diagnosis is based on serologic tests because direct detection of T . cruzi is very difficult beyond its brief acute phase . The complexity of this parasite’s pathophysiology and the human immune system’s elaborate engagement with it makes ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "chemical", "characterization", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "pathogens", "tropical", "diseases", "microbiology", "parasitic", "diseases", "parasitic", "protozoans", "viruses", "proto...	2017	An ImmunoSignature test distinguishes Trypanosoma cruzi, hepatitis B, hepatitis C and West Nile virus seropositivity among asymptomatic blood donors
Pulmonary emphysema is a connective tissue disease characterized by the progressive destruction of alveolar walls leading to airspace enlargement and decreased elastic recoil of the lung . However , the relationship between microscopic tissue structure and decline in stiffness of the lung is not well understood . In th...	Current standards for characterizing microscopic structural changes in emphysema are based on estimating the amount of tissue loss using stereological techniques . However , several previous studies reported that , in emphysema , there is a lack of correlation between stereological indices of tissue structure and incre...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "physics", "respiratory", "medicine/copd", "and", "allied", "disorders", "physiology/respiratory", "physiology" ]	2011	Linking Microscopic Spatial Patterns of Tissue Destruction in Emphysema to Macroscopic Decline in Stiffness Using a 3D Computational Model
In vertebrate neurons , the axon initial segment ( AIS ) is specialized for action potential initiation . It is organized by a giant 480 Kd variant of ankyrin G ( AnkG ) that serves as an anchor for ion channels and is required for a plasma membrane diffusion barrier that excludes somatodendritic proteins from the axon...	The axon initial segment ( AIS ) is currently thought to be a distinguishing feature of vertebrate neurons that adapts them for rapid , precise signaling . It serves as a hub for the regulation of neuronal excitability as the site of action potential initiation and also acts as the boundary between the highly-specializ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "vertebrates", "neuroscience", "animals", "invertebrate", "genomics", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "genome", "analysis", "nerve", "fibers", "neuronal", "dendrites", "drosophila", "research", "and", "analysis", "m...	2016	Bilaterian Giant Ankyrins Have a Common Evolutionary Origin and Play a Conserved Role in Patterning the Axon Initial Segment
Accurate prediction of active sites is an important tool in bioinformatics . Here we present an improved structure based technique to expose active sites that is based on large changes of solvent accessibility accompanying normal mode dynamics . The technique which detects EXPOsure of active SITes through normal modEs ...	In this paper , we present an improved technique to predict active sites in enzymes . Our technique is based on changes of solvent accessibility that accompany normal mode dynamics . We assert the technique strength using several enzyme datasets with known catalytic residues . We show the technique successfully locates...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusion" ]	[ "chemical", "characterization", "classical", "mechanics", "molecular", "dynamics", "enzymes", "enzymology", "protein", "structure", "prediction", "damage", "mechanics", "protein", "structure", "research", "and", "analysis", "methods", "bioinformatics", "proteins", "deformat...	2016	Normal Modes Expose Active Sites in Enzymes
Hepatitis E virus ( HEV ) is a positive-strand RNA virus encoding 3 open reading frames ( ORF ) . HEV ORF3 protein is a small , hitherto poorly characterized protein involved in viral particle secretion and possibly other functions . Here , we show that HEV ORF3 protein forms membrane-associated oligomers . Immunoblot ...	Hepatitis E virus ( HEV ) infection is believed to be the most common cause of acute hepatitis and jaundice in the world . HEV is a positive-strand RNA virus found as a non-enveloped virion in bile and feces or as a quasi-enveloped virion in blood and in cell culture . The HEV ORF3 protein is involved in viral particle...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "molecular", "probe", "techniques", "pathogens", "microbiology", "organic", "compounds", "membrane", "proteins", "viruses", "amino", "acids", "molecular", "bi...	2018	Palmitoylation mediates membrane association of hepatitis E virus ORF3 protein and is required for infectious particle secretion
Eukaryotic mRNA transcription and turnover is controlled by an enzymatic machinery that includes RNA polymerase II and the 3′ to 5′ exosome . The activity of these protein complexes is modulated by additional factors , such as the nuclear RNA polymerase II-associated factor 1 ( Paf1c ) and the cytoplasmic Superkiller (...	The production and turnover of messenger RNAs ( mRNAs ) are conserved processes in eukaryotes , from single-cell organisms to plants and mammals . To some degree , this is also true for modulators of these processes , such as the Paf1 and SKI complexes . One particular protein , SKI8 , has been described to have a role...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "model", "organisms", "plant", "and", "algal", "models", "molecular", "cell", "biology", "plant", "biology", "gene", "expression", "genetics", "yeast", "and", "fungal", "models", "biology", "genomics", "evolutionary", "biology", "microbiolo...	2012	Context-Dependent Dual Role of SKI8 Homologs in mRNA Synthesis and Turnover
In bacteria the concurrence of DNA replication and transcription leads to potentially deleterious encounters between the two machineries , which can occur in either the head-on ( lagging strand genes ) or co-directional ( leading strand genes ) orientations . These conflicts lead to replication fork stalling and can de...	In bacteria the concurrence of DNA replication and transcription leads to potentially deleterious encounters between the two machineries . These encounters can destabilize the genome and lead to mutations . Both eukaryotic and prokaryotic cells possess conflict resolution factors that reduce the detrimental effects of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The B. subtilis Accessory Helicase PcrA Facilitates DNA Replication through Transcription Units
Aedes albopictus is a highly invasive disease vector with an expanding worldwide distribution . Genetic assays using low to medium resolution markers have found little evidence of spatial genetic structure even at broad geographic scales , suggesting frequent passive movement along human transportation networks . Here ...	Aedes albopictus , the Asian Tiger Mosquito , is a highly invasive disease vector with a growing global distribution . Designing strategies to prevent invasion and to control Ae . albopictus populations in invaded regions requires knowledge of how Ae . albopictus disperses . Studies comparing Ae . albopictus population...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "genetic", "networks", "ecology", "and", "environmental", "sciences", "rivers", "engineering", "and", "technology", "transportation", "population", "genetics", "animals", "wolbachia", "genetic", "mapping", "transpo...	2017	Genome-wide SNPs reveal the drivers of gene flow in an urban population of the Asian Tiger Mosquito, Aedes albopictus
Neuronal synapses transmit electrochemical signals between cells through the coordinated action of presynaptic vesicles , ion channels , scaffolding and adapter proteins , and membrane receptors . In situ structural characterization of numerous synaptic proteins simultaneously through multiplexed imaging facilitates a ...	Multiplexed fluorescence imaging of synaptic proteins facilitates high throughput investigations in neuroscience and drug discovery . Currently , there are several approaches to synapse detection using computational image processing . Unsupervised techniques rely on the a priori knowledge of synapse properties , such a...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "fluorescence", "imaging", "medicine", "and", "health", "sciences", "neural", "networks", "engineering", "and", "technology", "nervous", "system", "condensed", "matter", "physics", "light", "microscopy", "electrophysiology", "anisotropy", "neuroscience", "microscopy", "ma...	2019	DoGNet: A deep architecture for synapse detection in multiplexed fluorescence images
One of the main outcomes of quantitative genetics approaches to natural variation is to reveal the genetic architecture underlying the phenotypic space . Complex genetic architectures are described as including numerous loci ( or alleles ) with small-effect and/or low-frequency in the populations , interactions with th...	The question of the complexity of the genetic variants underlying diversity in plant size and shape is central in evolutionary biology to better understand the impacts of selection and adaptation . In this work , we have combined the high resolution of a robotized platform designed to grow Arabidopsis plants under stri...	[ "Abstract", "Introduction", "Results", "Materials", "and", "methods" ]	[]	2019	The complex genetic architecture of shoot growth natural variation in Arabidopsis thaliana
Viral replication efficiency is in large part governed by the ability of viruses to counteract pro-apoptotic signals induced by infection of host cells . For HHV-8 , viral interferon regulatory factor-1 ( vIRF-1 ) contributes to this process in part via inhibitory interactions with BH3-only protein ( BOP ) Bim , recent...	Viruses possess mechanisms of subverting host cell defenses against infection and virus replication; these mechanisms are essential to the virus life cycle . Here , we identify and characterize a novel mechanism of HHV-8 mediated inhibition of virus-induced programmed cell death ( apoptosis ) . This function is specifi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "death", "cellular", "stress", "responses", "molecular", "cell", "biology", "cell", "biology", "virology", "biology", "microbiology", "host-pathogen", "interaction" ]	2012	Human Herpesvirus 8 Interferon Regulatory Factor-Mediated BH3-Only Protein Inhibition via Bid BH3-B Mimicry
Mobile genetic elements either encode their own mobilization machineries or hijack them from other mobile elements . Multiple classes of mobile elements often coexist within genomes and it is unclear whether they have the capacity to functionally interact and even collaborate . We investigate the possibility that molec...	Mobile genetic elements are segments of DNA that capable of “jumping” within a single DNA molecule , between chromosomes or even between cells . They usually encode the enzymes that mediate their own transfer and integration into new DNA locus . The transfer of mobile genetic elements between cells is known as horizont...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "lactococcus", "lactis", "transfer", "rna", "horizontal", "gene", "transfer", "medicine", "and", "health", "sciences", "genome", "evolution", "pathology", "and", "laboratory", "medicine", "pathogens", "plasmids", "gene", "transfer", "genetic", "elements", "bacterial", ...	2014	Interaction between Conjugative and Retrotransposable Elements in Horizontal Gene Transfer
The mite Varroa destructor is an obligatory ectoparasite of the honey bee ( Apis mellifera ) and is one of the major threats to apiculture worldwide . We previously reported that honey bees fed on double-stranded RNA ( dsRNA ) with a sequence homologous to that of the Israeli acute paralysis virus are protected from th...	Acquisition of RNAi components ( dsRNA , siRNA ) by ingestion and their spread within the recipient organism has been previously reported by us and others . Here we extend such observations , demonstrating cross-species horizontal transmission of dsRNA which , upon transmission from one organism to another still retain...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "veterinary", "science", "agriculture" ]	2012	Bidirectional Transfer of RNAi between Honey Bee and Varroa destructor: Varroa Gene Silencing Reduces Varroa Population
Lysozymes are nearly omnipresent as the first line of immune defense against microbes in animals . They exert bactericidal action through antimicrobial peptide activity and peptidoglycan hydrolysis . Gram-negative bacteria developed several weapons to battle lysozymes , including inhibitors of c-type lysozymes in the M...	Neisseria gonorrhoeae , the etiologic agent of gonorrhea , is a clinically important pathogen due to the emergence of multi-drug resistance and the lack of a vaccine ( s ) . During host colonization , pathogenic and commensal Neisseria inevitably encounter lysozyme , a major host innate defense factor that is abundantl...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "serum", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "molecular", "probe", "techniques", "enzymes", "pathogens", "microbiology", "neisseria", "gonorrhoeae", "immunoblotting", "enzymology", "animal", "...	2018	SliC is a surface-displayed lipoprotein that is required for the anti-lysozyme strategy during Neisseria gonorrhoeae infection
Specific members of complex microbiota can influence host phenotypes , depending on both the abiotic environment and the presence of other microorganisms . Therefore , it is challenging to define bacterial combinations that have predictable host phenotypic outputs . We demonstrate that plant–bacterium binary-associatio...	Symbiotic microbes influence host development and health , but predicting which microbes or groups of microbes will have a helpful or harmful effect is a major challenge in microbiome research . In this article , we describe a new method to design and predict bacterial communities that alter the plant host response to ...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "chemical", "compounds", "phosphates", "plant", "growth", "and", "development", "brassica", "developmental", "biology", "plant", "science", "model", "organisms", "metabolites", "experimental", "organism", "systems", "genome", "analysis", "seedlings", "plants", "bacteria",...	2018	Design of synthetic bacterial communities for predictable plant phenotypes
Experimental evidence suggests that a tetramer of integrase ( IN ) is the protagonist of the concerted strand transfer reaction , whereby both ends of retroviral DNA are inserted into a host cell chromosome . Herein we present two crystal structures containing the N-terminal and the catalytic core domains of maedi-visn...	Integrase is the viral enzyme that orchestrates insertion of both ends of retroviral DNA into a host cell chromosome . This process , thought to require a tetramer of integrase , involves two concerted cutting/joining ( transesterification ) reactions that target a pair of phosphodiester bonds in chromosomal DNA , sepa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/immunodeficiency", "viruses", "molecular", "biology", "biochemistry/protein", "chemistry", "virology/viral", "replication", "and", "gene", "regulation" ]	2009	Structural Basis for Functional Tetramerization of Lentiviral Integrase
Phagocytosis by hemocytes , Drosophila macrophages , is essential for resistance to Streptococcus pneumoniae in adult flies . Activated macrophages require an increased supply of energy and we show here that a systemic metabolic switch , involving the release of glucose from glycogen , is required for effective resista...	The immune response is an energy-demanding process and a sufficient energy supply is important for resistance to pathogens . However , the systemic metabolism must be tightly regulated during an immune response since nutrients may also be exploited by the pathogen and host energy reserves are limited . Here we present ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "glycosylamines", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pneumococcus", "intracellular", "pathogens", "pathogens", "cell", "processes", "microbiology", "diet", "nutrition", "bacteria", "bacterial", "pathogens", "adenosine", ...	2018	Extracellular adenosine modulates host-pathogen interactions through regulation of systemic metabolism during immune response in Drosophila
The effects of disease mutations on protein structure and function have been extensively investigated , and many predictors of the functional impact of single amino acid substitutions are publicly available . The majority of these predictors are based on protein structure and evolutionary conservation , following the a...	Intrinsically unstructured or disordered proteins have been implicated in the etiology of a wide spectrum of diseases . However , the molecular mechanisms that relate mutations in intrinsically disordered regions ( IDRs ) to disease pathogenesis have not been investigated . Disordered proteins do not conform to the pre...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequence", "analysis", "protein", "folding", "biology", "computational", "biology", "biophysics" ]	2012	Disease-Associated Mutations Disrupt Functionally Important Regions of Intrinsic Protein Disorder
The homologous p10 fusion-associated small transmembrane ( FAST ) proteins of the avian ( ARV ) and Nelson Bay ( NBV ) reoviruses are the smallest known viral membrane fusion proteins , and are virulence determinants of the fusogenic reoviruses . The small size of FAST proteins is incompatible with the paradigmatic mem...	Natural infections by fusogenic orthoreoviruses can result in severe afflictions ranging from neuropathogenicity to pneumonia and death . The fusogenic capacity of these viruses , attributable to a unique family of fusion-associated small transmembrane ( FAST ) proteins , is a correlate of virulence . The FAST proteins...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "lipids", "transmembrane", "proteins", "protein", "interactions", "host", "cells", "proteins", "viral", "transmission", "and", "infection", "virology", "emerging", "viral", "diseases", "protein", "structure", "membranes", "and", "sorting", "host-pathogen",...	2014	A Compact, Multifunctional Fusion Module Directs Cholesterol-Dependent Homomultimerization and Syncytiogenic Efficiency of Reovirus p10 FAST Proteins
Israeli acute paralysis virus ( IAPV ) is a widespread RNA virus of honey bees that has been linked with colony losses . Here we describe the transmission , prevalence , and genetic traits of this virus , along with host transcriptional responses to infections . Further , we present RNAi-based strategies for limiting a...	The mysterious outbreak of honey bee Colony Collapse Disorder ( CCD ) in the US in 2006–2007 has attracted massive media attention and created great concerns over the effects of various risk factors on bee health . Understanding the factors that are linked to the honey bee colony declines may provide insights for manag...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences", "agriculture" ]	2014	Israeli Acute Paralysis Virus: Epidemiology, Pathogenesis and Implications for Honey Bee Health
Formalin-inactivated Japanese encephalitis virus ( JEV ) vaccines are widely available , but the effects of formalin inactivation on the antigenic structure of JEV and the profile of antibodies elicited after vaccination are not well understood . We used a panel of monoclonal antibodies ( MAbs ) to map the antigenic st...	We demonstrated that formalin inactivation of Japanese encephalitis virus ( JEV ) alters the antigenic structure of the JEV envelope glycoprotein ( E ) , in particular an epitope in domain III , and that this reduces the ability of the inactivated vaccine to elicit protective neutralizing antibodies . Ours and others’ ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Formalin Inactivation of Japanese Encephalitis Virus Vaccine Alters the Antigenicity and Immunogenicity of a Neutralization Epitope in Envelope Protein Domain III
The basidiomycete smut fungus Ustilago hordei was previously shown to comprise isolates that are avirulent on various barley host cultivars . Through genetic crosses we had revealed that a dominant avirulence locus UhAvr1 which triggers immunity in barley cultivar Hannchen harboring resistance gene Ruh1 , resided withi...	Upon host infection , plant pathogens secrete suites of virulence effectors to suppress defense responses and support their own development . In certain cases , hosts evolve resistance genes that recognize such effectors or their actions to initiate defense responses . By deleting candidate genes , we identified the im...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "genome", "evolution", "pathology", "and", "laboratory", "medicine", "microbiology", "gene", "function", "cereal", "crops", "mutation", "fungi", "crops", "molecular", "genetics", "mycology", "medical", "microbiology", "microbial"...	2014	An Immunity-Triggering Effector from the Barley Smut Fungus Ustilago hordei Resides in an Ustilaginaceae-Specific Cluster Bearing Signs of Transposable Element-Assisted Evolution
The increasing incidence of dengue among adults in Malaysia and other countries has important implications for health services . Before 2004 , in order to cope with the surge in adult dengue admissions , each of the six medical wards in a university hospital took turns daily to admit and manage patients with dengue . D...	The epidemiology of dengue disease in the tropical regions is characterized by a rapid increase in the number of reported cases , and in some Asian countries , a shift in the age range predominance from children toward adults . This has important implications for health services , resources , and training , provision o...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Cohorting Dengue Patients Improves the Quality of Care and Clinical Outcome
Plasmacytoid dendritic cells ( pDC ) produce type I interferons ( IFN-I ) and proinflammatory cytokines in response to viruses; however , their contribution to antiviral immunity in vivo is unclear . In this study , we investigated the impact of pDC depletion on local and systemic antiviral responses to herpes simplex ...	Herpes simplex viruses ( HSV ) cause a variety of diseases in human from the common cold sore to more severe illnesses such as pneumonia , herpes simplex keratitis , genital herpes and encephalitis . HSV are large double-stranded DNA viruses that infect epithelial or epidermal cells before establishing a latent infecti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Plasmacytoid Dendritic Cells Contribute to Systemic but Not Local Antiviral Responses to HSV Infections
Zika virus ( ZIKV ) is an important flavivirus infection . Although ZIKV infection is rarely fatal , risk for severe disease in adults is not well described . Our objective was to describe the spectrum of illness in U . S . Veterans with ZIKV infection . Case series study including patients with laboratory-confirmed or...	Zika virus ( ZIKV ) infection has become an important flavivirus infection that affected over a half of a million people in the Western Hemisphere by the end of 2016 . Here we show risk factors for hospitalizations and neurologic complications in a US Veteran population . Over 700 Veterans with confirmed or presumed po...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "reverse", "transcriptase-polymerase", "chain", "reaction", "dengue", "virus", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "togaviruses", "pathogens", "microbiology", "cancers", "and", "neoplasms", "alphaviruses", "viruses", "org...	2018	Zika virus infection in the Veterans Health Administration (VHA), 2015-2016
Lytic or lysogenic infections by bacteriophages drive the evolution of enteric bacteria . Enterohemorrhagic Escherichia coli ( EHEC ) have recently emerged as a significant zoonotic infection of humans with the main serotypes carried by ruminants . Typical EHEC strains are defined by the expression of a type III secret...	Many significant infectious diseases that impact human health evolve in animal hosts . Our work focuses on infections caused by strains of enterohemorrhagic Escherichia coli ( EHEC ) that cause bloody diarrhoea and life threatening kidney and brain damage in humans as an incidental host , while ruminants are a reservoi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "animal", "types", "infectious", "diseases", "zoonoses", "large", "animals", "veterinary", "microbiology", "genetics", "biology", "microbiology", "evolutionary", "biology", "gastrointestinal", "infections", "genetics", "and", "genomics", "veterinary", "science" ...	2012	Lysogeny with Shiga Toxin 2-Encoding Bacteriophages Represses Type III Secretion in Enterohemorrhagic Escherichia coli
Kaposi's sarcoma-associated herpesvirus ( KSHV ) stabilizes hypoxia-inducible factor α ( HIF-1α ) during latent infection , and HIF-1α reactivates lytic replication under hypoxic stress . However , the mechanism utilized by KSHV to block lytic reactivation with the accumulation of HIF-1α in latency remains unclear . He...	Hypoxia stress is a common feature of tumor microenvironment and is widely associated with pathogenesis linked to many oncogenic viruses . Kaposi's sarcoma-associated herpesvirus ( KSHV ) , the etiological cause of Kaposi's sarcoma and primary effusion lymphoma , has been reported to encode several proteins that usurp ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	A Unique SUMO-2-Interacting Motif within LANA Is Essential for KSHV Latency
Phlebotomine sand flies that transmit the protozoan parasite Leishmania differ greatly in their ability to support different parasite species or strains in the laboratory: while some show considerable selectivity , others are more permissive . In “selective” sand flies , Leishmania binding and survival in the fly midgu...	Phlebotomine sand flies are tiny blood-feeding insects that transmit Leishmania protozoan parasites , which cause diseases afflicting millions of people . The world-wide distribution of Leishmania is determined by the availability of transmission-competent vectors . In the laboratory , some vectors support many differe...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "evolutionary", "biology/microbial", "evolution", "and", "genomics", "infectious", "diseases/neglected", "tropical", "diseases", "microbiology/parasitology", "infectious", "diseases/protozoal", "infections", "cell", "biology/cell", "adhesion" ]	2010	Leishmania major Survival in Selective Phlebotomus papatasi Sand Fly Vector Requires a Specific SCG-Encoded Lipophosphoglycan Galactosylation Pattern
Ethnic diversity has been long considered as one of the factors explaining why the severe forms of dengue are more prevalent in Southeast Asia than anywhere else . Here we take advantage of the admixed profile of Southeast Asians to perform coupled association-admixture analyses in Thai cohorts . For dengue shock syndr...	Dengue fever is endemic in tropical and subtropical areas of East Asia and America , but globalization and climate changes are introducing vector and virus to the naïve regions of Europe and North America . In this work we conducted a statistically robust , coupled association-admixture test in two dengue cohorts from ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "xenobiotic", "metabolism", "tropical", "diseases", "geographical", "locations", "genetic", "mapping", "ethnicities", "genetic", "predisposition", "genome", "analysis", "neglected", "tropical", "diseases", "sequence", "motif", "ana...	2018	Joint ancestry and association test indicate two distinct pathogenic pathways involved in classical dengue fever and dengue shock syndrome
Bacteria regulate many phenotypes via quorum sensing systems . Quorum sensing is typically thought to evolve because the regulated cooperative phenotypes are only beneficial at certain cell densities . However , quorum sensing systems are also threatened by non-cooperative “cheaters” that may exploit quorum-sensing reg...	Bacteria secrete signal molecules into their environment and use these to regulate many of their key phenotypes . This is called quorum sensing and it is thought to evolve because it allows cells to sense their density . Here we propose a new function for quorum sensing that sheds light on its evolution . We develop a ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biofilms", "organismal", "evolution", "medicine", "and", "health", "sciences", "cell", "cycle", "and", "cell", "division", "cell", "processes", "microbiology", "cloning", "simulation", "and", "modeling", "physiological", "processes", "microbial", "evolution", "molecula...	2016	The Evolution of Quorum Sensing as a Mechanism to Infer Kinship
Global climate change , increasingly erratic weather and a burgeoning global population are significant threats to the sustainability of future crop production . There is an urgent need for the development of robust measures that enable crops to withstand the uncertainty of climate change whilst still producing maximum...	Over coming decades , climate change models suggest that droughts and other unpredictable weather patterns will appear more frequently . It is imperative that we develop crops that can survive future climates but continue to yield . Numerous studies have shown that stress tolerance is genetically encoded . Naturally to...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Trehalose Accumulation Triggers Autophagy during Plant Desiccation
Rats discriminate surface textures using their whiskers ( vibrissae ) , but how whiskers extract texture information , and how this information is encoded by the brain , are not known . In the resonance model , whisker motion across different textures excites mechanical resonance in distinct subsets of whiskers , due t...	A fundamental problem in neuroscience is understanding how behaviorally relevant information is collected by a sensory organ and subsequently encoded by the brain . By actively moving their whiskers , rats can discriminate fine differences in textures . Little is known , however , about how whisker dynamics reflect tex...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biophysics", "neuroscience" ]	2008	Texture Coding in the Rat Whisker System: Slip-Stick Versus Differential Resonance
Failure to properly establish the left–right ( L/R ) axis is a major cause of congenital heart defects in humans , but how L/R patterning of the embryo leads to asymmetric cardiac morphogenesis is still unclear . We find that asymmetric Nodal signaling on the left and Bmp signaling act in parallel to establish zebrafis...	Defects in left–right ( L/R ) patterning can lead to severe defects in the formation of the heart . In fact , three of the most common forms of congenital heart disease , transposition of the great arteries , chamber septation defects , and chamber isomerisms , can be caused by earlier defects in L/R asymmetry . The No...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "developmental", "biology", "zebrafish", "model", "organisms", "organism", "development", "signaling", "molecular", "development", "birth", "defects", "cell", "migration", "heart", "development", "biology", "organogenesis", "morphogenesis" ]	2013	Integration of Nodal and BMP Signals in the Heart Requires FoxH1 to Create Left–Right Differences in Cell Migration Rates That Direct Cardiac Asymmetry
Influenza A viruses are respiratory pathogens that cause seasonal epidemics with up to 500 , 000 deaths each year . Yet there are currently only two classes of antivirals licensed for treatment and drug-resistant strains are on the rise . A major challenge for the discovery of new anti-influenza agents is the identific...	Influenza A viruses are contagious pathogens that cause an infection of the respiratory tract in humans , commonly referred to as flu . Each year seasonal epidemics occur with three to five million cases of severe illness and occasionally new strains can create pandemics like the 1918 Spanish Flu with a high mortality ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	Multiscale Modeling of Influenza A Virus Infection Supports the Development of Direct-Acting Antivirals
The primary constituents of plaques ( Aβ42/Aβ40 ) and neurofibrillary tangles ( tau and phosphorylated forms of tau [ptau] ) are the current leading diagnostic and prognostic cerebrospinal fluid ( CSF ) biomarkers for AD . In this study , we performed deep sequencing of APP , PSEN1 , PSEN2 , GRN , APOE and MAPT genes i...	Alzheimer's disease ( AD ) is the most common neurodegenerative disease affecting more than 5 . 3 million people in the US . AD-causing mutations have been identified in APP , PSEN1 and PSEN2 genes . Heterozygous carriers of APOE-ε4 allele exhibit a 3-fold increased risk for developing AD , while homozygous carriers sh...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "neurobiology", "of", "disease", "and", "regeneration", "neurodegenerative", "diseases", "population", "genetics", "quantitative", "traits", "neuroscience", "epistasis", "mutation", "alzheimer", "disease", "genetic", "polymorphism", "biology", "dementia", "genet...	2013	The PSEN1, p.E318G Variant Increases the Risk of Alzheimer's Disease in APOE-ε4 Carriers
Helicobacter pylori infection causes chronic active gastritis that after many years of infection can develop into peptic ulceration or gastric adenocarcinoma . The bacterium is highly adapted to surviving in the gastric environment and a key adaptation is the virulence factor urease . Although widely postulated , the r...	Helicobacter pylori is a bacterial pathogen that chronically infects half the global population and is a major contributor to the development of peptic ulcers and stomach cancer . H . pylori has evolved to survive in the stomach and one important adaptation is the enzyme urease . The bacteria cannot establish an infect...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "antimicrobials", "medicine", "and", "health", "sciences", "urea", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "ureases", "enzymes", "pathogens", "drugs", "enzymology", "microbiology", "organic", "compounds", "bacterial", "diseases", "helicobact...	2017	Helicobacter pylori gene silencing in vivo demonstrates urease is essential for chronic infection
Fascioliasis ( or fasciolosis ) is a socioeconomically important parasitic disease caused by liver flukes of the genus Fasciola . Flukicide resistance has exposed the need for new drugs and/or a vaccine for liver fluke control . A rapidly improving ‘molecular toolbox’ for liver fluke encompasses quality genomic/transcr...	Parasitic worms require a host organism in order to survive and reproduce . As such , it is difficult to study them outside of a host . Some parasites can be maintained in vitro using cell culture methods; in the case of F . hepatica , previously-reported methods are unsatisfactory because they are difficult to reprodu...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "livestock", "medicine", "and", "health", "sciences", "nucleic", "acid", "synthesis", "rna", "interference", "helminths", "tropical", "diseases", "vertebrates", "fascioliasis", "light", "microscopy", "parasitic", "diseases", "animals", "cell", "differenti...	2016	Stimulating Neoblast-Like Cell Proliferation in Juvenile Fasciola hepatica Supports Growth and Progression towards the Adult Phenotype In Vitro
The protozoan parasite Trypanosoma cruzi , the causative agent of Chagas disease , causes severe morbidity and mortality in afflicted individuals . About 30% of T . cruzi-infected individuals present with cardiac , gastrointestinal tract , and/or neurological disorders . Megacolon , one of the major pathologies of Chag...	Trypanosoma cruzi is a hemoflagellate that is now considered a global health threat in all industrialized regions of the world . Some chagasic patients present with digestive , neurological , and/or cardiac disorders . The mechanisms of T . cruzi-induced pathology remain to be elucidated . In this study , we challenged...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "phosphorylation", "medicine", "and", "health", "sciences", "gene", "regulation", "regulatory", "proteins", "dna-binding", "proteins", "parasitic", "diseases", "parasitic", "protozoans", "epithelial", "cells", "megacolon", "protozoans", "gastroenterology", "and", "hepatolog...	2018	Phospho-proteomic analysis of primary human colon epithelial cells during the early Trypanosoma cruzi infection phase
Genome-wide association studies ( GWAS ) have uncovered numerous genetic variants ( SNPs ) that are associated with blood pressure ( BP ) . Genetic variants may lead to BP changes by acting on intermediate molecular phenotypes such as coded protein sequence or gene expression , which in turn affect BP variability . The...	The focus of blood pressure ( BP ) GWAS has been the identification of common DNA sequence variants associated with the phenotype; this approach provides only one dimension of molecular information about BP . While it is a critical dimension , analyzing DNA variation alone is not sufficient for achieving an understandi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	A Meta-analysis of Gene Expression Signatures of Blood Pressure and Hypertension
In this study , we evaluated the long-term efficacy of a two-component subunit vaccine against Trypanosoma cruzi infection . C57BL/6 mice were immunized with TcG2/TcG4 vaccine delivered by a DNA-prime/Protein-boost ( D/P ) approach and challenged with T . cruzi at 120 or 180 days post-vaccination ( dpv ) . We examined ...	Chagas disease , caused by Trypanosoma cruzi infection , represents the third greatest tropical disease burden in the world . No vaccine or suitable treatment is available for control of this infection . Based upon several studies we have conducted , we believe that TcG2 and TcG4 candidate antigens that are highly cons...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	A Two-Component DNA-Prime/Protein-Boost Vaccination Strategy for Eliciting Long-Term, Protective T Cell Immunity against Trypanosoma cruzi
Most statistical and mechanistic models used to predict mosquito-borne disease transmission incorporate climate drivers of disease transmission by utilizing environmental data collected at geographic scales that are potentially coarser than what mosquito populations may actually experience . Temperature and relative hu...	Environmental factors influence the dynamics of mosquito-borne disease transmission . Most models used to predict mosquito-borne disease transmission incorporate climate data collected at coarser scales than mosquitoes typically experience . Climate conditions can vary greatly between indoor and outdoor environments , ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "autumn", "weather", "stations", "atmospheric", "science", "social", "sciences", "animals", "seasons", "summer", "land", "use", "physiological", "parameters", "humidity", "insect", "vectors", "human", "geography"...	2017	Fine-scale variation in microclimate across an urban landscape shapes variation in mosquito population dynamics and the potential of Aedes albopictus to transmit arboviral disease
Explaining how interactions between genes and the environment influence social behavior is a fundamental research goal , yet there is limited relevant information for species exhibiting natural variation in social organization . The fire ant Solenopsis invicta is characterized by a remarkable form of social polymorphis...	Fundamental research goals for scientists interested in social evolution are to determine the numbers and types of genes that directly regulate individual social behaviors as well as to understand how the social environment indirectly influences the expression of socially relevant traits . The fire ant Solenopsis invic...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology", "genetics", "and", "genomics/complex", "traits", "ecology/behavioral", "ecology", "genetics", "and", "genomics/gene", "expression" ]	2008	Genome-Wide Expression Patterns and the Genetic Architecture of a Fundamental Social Trait
Sepsis , a manifestation of the body’s inflammatory response to injury and infection , has a mortality rate of between 28%-50% and affects approximately 1 million patients annually in the United States . Currently , there are no therapies targeting the cellular/molecular processes driving sepsis that have demonstrated ...	Sepsis , characterized by the body’s inflammatory response to injury and infection , has a mortality rate of between 28%-50% and affects approximately 1 million patients annually in the United States . Currently , there are no therapies targeting the cellular/molecular processes driving sepsis that have demonstrated th...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "death", "rates", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "applied", "mathematics", "endothelial", "cells", "immunology", "genetic", "algorithms", "epitheli...	2018	Examining the controllability of sepsis using genetic algorithms on an agent-based model of systemic inflammation
Cell-mediated immunity is essential in protection against rickettsial illnesses , but the role of neutrophils in these intracellular vasculotropic infections remains unclear . This study analyzed the plasma levels of nucleosomes , FSAP-activation ( nucleosome-releasing factor ) , and neutrophil activation , as evidence...	Tropical rickettsial illnesses , especially scrub typhus and murine typhus , are increasingly recognized as a leading cause of treatable undifferentiated febrile illness in Asia , but remain severely neglected and under appreciated diseases in many areas . In this study we investigated the relationship of markers of ne...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Increased Nucleosomes and Neutrophil Activation Link to Disease Progression in Patients with Scrub Typhus but Not Murine Typhus in Laos
KSHV is etiologically associated with Kaposi's sarcoma ( KS ) , an angioproliferative endothelial cell malignancy . Macropinocytosis is the predominant mode of in vitro entry of KSHV into its natural target cells , human dermal microvascular endothelial ( HMVEC-d ) cells . Although macropinocytosis is known to be a maj...	KSHV is etiologically associated with Kaposi's sarcoma ( KS ) , the most common AIDS related neoplasm . The first key step in KSHV infection is its initial contact with target cells and entry . While it is known that KSHV uses macropinocytosis for its infectious entry into its natural target cells , HMVEC-d cells , we ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/viral", "infections", "virology/host", "invasion", "and", "cell", "entry", "virology/viruses", "and", "cancer", "virology" ]	2010	Interaction of c-Cbl with Myosin IIA Regulates Bleb Associated Macropinocytosis of Kaposi's Sarcoma-Associated Herpesvirus
Single-cell RNA sequencing ( scRNA-seq ) technology allows researchers to profile the transcriptomes of thousands of cells simultaneously . Protocols that incorporate both designed and random barcodes have greatly increased the throughput of scRNA-seq , but give rise to a more complex data structure . There is a need f...	Biotechnologies that allow researchers to measure gene activity in individual cells are growing in popularity . This has resulted in an avalanche of custom analysis methods designed to deal with the complex data that arises from this technology . Although hundreds of analysis methods are available , relatively few deal...	[ "Abstract", "Introduction", "Design", "and", "implementation", "Availability", "and", "future", "directions" ]	[ "engineering", "and", "technology", "industrial", "engineering", "quality", "control", "molecular", "biology", "techniques", "information", "technology", "data", "processing", "research", "and", "analysis", "methods", "sequence", "analysis", "exon", "mapping", "computer",...	2018	scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data
A recent study of plasma neutralization breadth in HIV-1 infected individuals at nine International AIDS Vaccine Initiative ( IAVI ) sites reported that viral load , HLA-A*03 genotype , and subtype C infection were strongly associated with the development of neutralization breadth . Here , we refine the findings of tha...	HIV-1 has proven difficult to vaccinate against due to its ability to generate high levels of genetic diversity , particularly in the envelope glycoproteins . An ideal prophylactic vaccine would therefore elicit immune responses capable of blocking the full range of HIV-1 variants to which a population might be exposed...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "medicine", "and", "health", "sciences", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "retroviruses", "viruses", "immunodeficiency", "viruses", "amino", "acid", "sequence", "an...	2016	Diversification in the HIV-1 Envelope Hyper-variable Domains V2, V4, and V5 and Higher Probability of Transmitted/Founder Envelope Glycosylation Favor the Development of Heterologous Neutralization Breadth
Although DNA methylation patterns in somatic cells are thought to be relatively stable , they undergo dramatic changes during embryonic development , gametogenesis , and during malignant transformation . The enzymology of DNA methyltransferases is well understood , but the mechanism that removes methylated cytosines fr...	During mammalian development , genome-wide DNA demethylation occurs both in developing germ cells and in fertilized oocytes . This rapid DNA demethylation is an active process that occurs in the absence of DNA replication . The mechanism of active DNA demethylation represents a conundrum for researchers in this field ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/epigenetics", "genetics", "and", "genomics" ]	2008	GADD45A Does Not Promote DNA Demethylation
For Hepatitis C virus ( HCV ) , initiation of translation is cap-independently mediated by its internal ribosome entry site ( IRES ) . Unlike other IRES-containing viruses that shut off host cap-dependent translation , translation of HCV coexists with that of the host . How HCV IRES-mediated translation is regulated in...	Hepatitis C virus ( HCV ) infection causes chronic liver diseases that threaten ∼2% of the world population . There is no effective vaccine , and the current standard therapy , the combination of interferon and ribavirin , is effective to less than 50% of genotype-1 infected patients . While antivirals targeting at spe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "rna", "interference", "microbiology", "internal", "ribosome", "entry", "site", "biology", "viral", "replication", "molecular", "biology", "drug", "discovery", "biochemistry", "rna", "nucleic", "acids", "virology", "antivirals", "molecular", "cell", "biology" ]	2012	Attenuation of 40S Ribosomal Subunit Abundance Differentially Affects Host and HCV Translation and Suppresses HCV Replication
Paroxysmal nocturnal hemoglobinuria ( PNH ) is an acquired clonal blood disorder characterized by hemolysis and a high risk of thrombosis , that is due to a deficiency in several cell surface proteins that prevent complement activation . Its origin has been traced to a somatic mutation in the PIG-A gene within hematopo...	The mechanisms leading to expansion of HSC with mutations in the PIG-A gene that leads to the PNH phenotype remains unclear . Data so far suggests there is no intrinsic fitness advantage of the mutant cells compared to normal cells . Assuming neutral drift within the HSC compartment , we determined from first principle...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "united", "states", "medicine", "and", "health", "sciences", "markov", "models", "cell", "cycle", "and", "cell", "division", "population", "genetics", "cell", "processes", "geographical", "locations", "cloning", "gene", "pool", "cell", "differentiation", "north", "a...	2018	Evolutionary dynamics of paroxysmal nocturnal hemoglobinuria
Plants have varying abilities to tolerate chilling ( low but not freezing temperatures ) , and it is largely unknown how plants such as Arabidopsis thaliana achieve chilling tolerance . Here , we describe a genome-wide screen for genes important for chilling tolerance by their putative knockout mutants in Arabidopsis t...	Compared to cold acclimation ( enhancement of freezing tolerance by a prior exposure to low non-freezing temperature ) , the tolerance mechanism to non-freezing chilling temperatures is not well understood . Here , we performed a genome-wide mutant screen for chilling sensitive phenotype and identified 49 candidate gen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "anatomy", "rna-binding", "proteins", "plant", "cell", "biology", "rna", "extraction", "brassica", "chloroplasts", "plant", "science", "model", "organisms", "plants", "cellular", "structures", "and", "organelles", "extraction", "techniques", "research", "and", ...	2016	Chloroplast RNA-Binding Protein RBD1 Promotes Chilling Tolerance through 23S rRNA Processing in Arabidopsis
Mutualistic associations between symbiotic bacteria and their hosts are common within insect systems . However , viruses are often considered as pathogens even though some have been reported to be beneficial to their hosts . Herein , we report a novel densovirus , Helicoverpa armigera densovirus-1 ( HaDNV-1 ) that appe...	The old world cotton bollworm , Helicoverpa armigera , is one of the most significant pests of crops throughout Asia , Europe , Africa and Australia . Herein , we report a novel densovirus ( HaDNV-1 ) which was widely distributed in wild populations of H . armigera and was beneficial to its host by increasing larval an...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "ecology", "virology", "microbial", "control", "biology", "and", "life", "sciences", "microbiology", "microbial", "ecology", "agriculture" ]	2014	Densovirus Is a Mutualistic Symbiont of a Global Crop Pest (Helicoverpa armigera) and Protects against a Baculovirus and Bt Biopesticide
Centromeres are sites for assembly of the chromosomal structures that mediate faithful segregation at mitosis and meiosis . Plant and animal centromeres are typically located in megabase-sized arrays of tandem satellite repeats , making their precise mapping difficult . However , some rice centromeres are largely embed...	Before a cell divides , its chromosomes must be duplicated and then separated to provide each daughter cell with an identical genome copy . To accomplish this separation , the cell-division apparatus attaches to structures on the chromosomes called centromeres . Most plant and animal centromeres contain highly repetiti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "biology", "evolutionary", "biology", "molecular", "biology", "genetics", "and", "genomics" ]	2008	Intergenic Locations of Rice Centromeric Chromatin
Apolipoprotein B ( ApoB ) and ApoE have been shown to participate in the particle formation and the tissue tropism of hepatitis C virus ( HCV ) , but their precise roles remain uncertain . Here we show that amphipathic α-helices in the apolipoproteins participate in the HCV particle formation by using zinc finger nucle...	In vitro systems have been developed for the study of hepatitis C virus ( HCV ) infection and have revealed many details of the life cycle of HCV . Apolipoprotein B ( ApoB ) and ApoE have been shown to play crucial roles in the particle formation of HCV , based on data obtained by siRNA-mediated gene knockdown and over...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "hepatitis", "c", "infectious", "diseases", "infectious", "hepatitis", "medicine", "and", "health", "sciences", "hepatitis", "gastroenterology", "and", "hepatology", "viral", "diseases", "liver", "diseases" ]	2014	Amphipathic α-Helices in Apolipoproteins Are Crucial to the Formation of Infectious Hepatitis C Virus Particles
Acquisition of malaria immunity in low transmission areas usually occurs after relatively few exposures to the parasite . A recent Plasmodium vivax experimental challenge trial in malaria naïve and semi-immune volunteers from Colombia showed that all naïve individuals developed malaria symptoms , whereas semi-immune su...	Malaria remains an important public health problem worldwide , with 13 . 8 million cases caused by Plasmodium vivax , a parasite species that predominates in South-East Asia and the American continent . Despite the epidemiological importance of this species , studies of the immune response and their potential for vacci...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "parasite", "groups", "medicine", "and", "health", "sciences", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "plasmodium", "immunology", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "parasitology", "membrane", "protei...	2016	Antibody Profiling in Naïve and Semi-immune Individuals Experimentally Challenged with Plasmodium vivax Sporozoites
Decision making and learning in a real-world context require organisms to track not only the choices they make and the outcomes that follow but also other untaken , or counterfactual , choices and their outcomes . Although the neural system responsible for tracking the value of choices actually taken is increasingly we...	Reinforcement learning ( RL ) models , which formally describe how we learn from direct experience , can explain a diverse array of animal behavior . Considering alternative outcomes that could have been obtained but were not falls outside the purview of traditional RL models . However , such counterfactual thinking ca...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cognitive", "neuroscience", "decision", "making", "biology", "neuroscience", "learning", "and", "memory" ]	2011	Counterfactual Choice and Learning in a Neural Network Centered on Human Lateral Frontopolar Cortex
Molybdenum ( Mo ) is an essential micronutrient for plants , serving as a cofactor for enzymes involved in nitrate assimilation , sulfite detoxification , abscisic acid biosynthesis , and purine degradation . Here we show that natural variation in shoot Mo content across 92 Arabidopsis thaliana accessions is controlled...	Plants must acquire all the mineral nutrients they require for survival from the complex chemical and biological environment of the soil . A better understanding of the way plants do this would not only allow improvements in sustainable agricultural productivity , but could also improve human health through enhancement...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "biology/plant", "genetics", "and", "gene", "expression", "plant", "biology/plant", "biochemistry", "and", "physiology" ]	2008	Variation in Molybdenum Content Across Broadly Distributed Populations of Arabidopsis thaliana Is Controlled by a Mitochondrial Molybdenum Transporter (MOT1)
Heavy-ion therapy has an advantage over conventional radiotherapy due to its superb biological effectiveness and dose conformity in cancer therapy . It could be a potential alternate approach for hydatid cyst treatment . However , there is no information currently available on the cellular and molecular basis for heavy...	Surgical removal of cysts may be impractical in cases that cysts are in multiple organs or tissues , or in risky locations . In that case , alternative treatment should be employed . Heavy-ion radiation could be an effective way for treatment of hydatid cysts , taking its full advantage of well-defined range , small la...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2013	Suppression of E. multilocularis Hydatid Cysts after Ionizing Radiation Exposure
The innate immune response to viruses is initiated when specialized cellular sensors recognize viral danger signals . Here we show that truncated forms of viral genomes that accumulate in infected cells potently trigger the sustained activation of the transcription factors IRF3 and NF-κB and the production type I IFNs ...	In infections with viruses well adapted to the host virus-encoded proteins that delay the cellular response allow the virus to replicate to high titers prior to host intervention . The mechanisms overcoming viral evasion of the immune system and leading to the production of the primary antiviral cytokine IFNβ are not w...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Defective Viral Genomes Arising In Vivo Provide Critical Danger Signals for the Triggering of Lung Antiviral Immunity
Human β-defensin 3 ( hBD3 ) is a cationic host defence peptide and is part of the innate immune response . HBD3 is present on a highly copy number variable block of six β-defensin genes , and increased copy number is associated with the autoimmune disease psoriasis . It is not known how this increase influences disease...	Defensins are classically known as antimicrobial peptides due to their ability to rapidly kill pathogens including bacteria , viruses and fungi . They are produced in the presence of infectious agents at body surfaces exposed to the environment . Increasingly , their functional repertoire is expanding , and they have b...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Human β-D-3 Exacerbates MDA5 but Suppresses TLR3 Responses to the Viral Molecular Pattern Mimic Polyinosinic:Polycytidylic Acid
Vector-borne diseases remain a threat to public health , especially in tropical countries . The incompatible insect technique has been explored as a potential control strategy for several important insect vectors . However , this strategy has not been tested in Culex pipiens pallens , the most prevalent mosquito specie...	Population suppression is an important component of mosquito control measures . The incompatible insect technique exploits the monogamous mating behavior of female mosquitoes to decrease the percentage of females inseminated by compatible males and hence reduce overall fecundity . Previous studies used genetically engi...	[ "Abstract", "Introduction", "Materials", "And", "Methods", "Results", "Discussion" ]	[ "biology", "zoology", "parasitology" ]	2013	Naturally Occurring Incompatibilities between Different Culex pipiens pallens Populations as the Basis of Potential Mosquito Control Measures
The embryonic cuticle is necessary for normal seed development and seedling establishment in Arabidopsis . Although mutants with defective embryonic cuticles have been identified , neither the deposition of cuticle material , nor its regulation , has been described during embryogenesis . Here we use electron microscopy...	Plant embryogenesis occurs deep within the tissues of the developing seed , and leads to the production of the mature embryo . In Arabidopsis and many other plant species embryo-derive structure ( such as the cotyledons ) are suddenly exposed to environmental stresses such as low humidity . In these species the embryon...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[]	2019	A stress-response-related inter-compartmental signalling pathway regulates embryonic cuticle integrity in Arabidopsis
Weight control diets favorably affect parameters of the metabolic syndrome and delay the onset of diabetic complications . The adaptations occurring in adipose tissue ( AT ) are likely to have a profound impact on the whole body response as AT is a key target of dietary intervention . Identification of environmental an...	In obesity , an excess of adipose tissue is associated with dyslipidemia and diabetic complications . Gene expression is under the control of various genetic and environmental factors . As a central organ for the control of metabolic disturbances in conditions of both weight gain and loss , a comprehensive understandin...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome-wide", "association", "studies", "genome", "expression", "analysis", "medicine", "nutrition", "obesity", "gene", "expression", "regulatory", "networks", "biology", "molecular", "biology", "genetics", "genomics", "molecular", "cell", "biology", "computational", "bi...	2012	Determinants of Human Adipose Tissue Gene Expression: Impact of Diet, Sex, Metabolic Status, and Cis Genetic Regulation
We have developed the first computational model of solute and water transport from Bowman space to the papillary tip of the nephron of a human kidney . The nephron is represented as a tubule lined by a layer of epithelial cells , with apical and basolateral transporters that vary according to cell type . The model is f...	In addition to its well-known function of waste removal from the body , the kidney is also responsible for the critical regulation of the body’s salt , potassium , acid content , and blood pressure . The kidneys perform these life-sustaining task by filtering and returning to blood stream about 200 quarts of blood ever...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "classical", "mechanics", "chemical", "compounds", "fluid", "mechanics", "vertebrates", "carbohydrates", "plant", "physiology", "organic", "compounds", "glucose", "animals", "mammals", "urine", "animal", "models...	2019	A computational model of epithelial solute and water transport along a human nephron
Organisms are continuously exposed to a myriad of environmental stresses . Central to an organism's survival is the ability to mount a robust transcriptional response to the imposed stress . An emerging mechanism of transcriptional control involves dynamic changes in chromatin structure . Alterations in chromatin struc...	In eukaryotes , genomic DNA is organized into a complex DNA-protein structure termed chromatin . The organization of chromatin serves to compact DNA within the nucleus and plays a central role in regulating transcription by controlling the access of DNA to transcriptional machinery . Chromatin structure can be altered ...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "plant", "biology/plant-biotic", "interactions", "plant", "biology/plant", "genetics", "and", "gene", "expression", "molecular", "biology/chromatin", "structure" ]	2008	The Chromatin Remodeler SPLAYED Regulates Specific Stress Signaling Pathways
Both brucellosis and tuberculosis are chronic-debilitating systemic granulomatous diseases with a high incidence in many countries in Africa , Central and South America , the Middle East and the Indian subcontinent . Certain focal complications of brucellosis and extrapulmonary tuberculosis are very difficult to differ...	Both brucellosis and tuberculosis are systemic infections which may involve any organ . When they affect specific locations , extrapulmonary tuberculosis and brucellosis cause symptoms that are very difficult to differentiate clinically . Mycobacterium tuberculosis complex and Brucella spp are slow-growing microorganis...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2013	Comparative Clinical Study of Different Multiplex Real Time PCR Strategies for the Simultaneous Differential Diagnosis between Extrapulmonary Tuberculosis and Focal Complications of Brucellosis
Targeting of Toxoplasma gondii by autophagy is an effective mechanism by which host cells kill the protozoan . Thus , the parasite must avoid autophagic targeting to survive . Here we show that the mammalian cytoplasmic molecule Focal Adhesion Kinase ( FAK ) becomes activated during invasion of host cells . Activated F...	Toxoplasma gondii is a protozoan that resides within host cells . Avoiding lysosomal degradation including that mediated by autophagy is central to the ability of T . gondii to survive within these cells . We uncovered that during the process of active invasion of host cells , T . gondii activates in a broad range of m...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "cell", "death", "medicine", "and", "health", "sciences", "autophagic", "cell", "death", "parasite", "groups", "viral", "transmission", "and", "infection", "toxoplasma", "gondii", "gene", "regulation", "cell", "processes", "microbiology", "parasitic",...	2017	Toxoplasma gondii induces FAK-Src-STAT3 signaling during infection of host cells that prevents parasite targeting by autophagy
Adaptive immunity to Mycobacterium tuberculosis controls progressive bacterial growth and disease but does not eradicate infection . Among CD4+ T cells in the lungs of M . tuberculosis-infected mice , we observed that few produced IFN-γ without ex vivo restimulation . Therefore , we hypothesized that one mechanism wher...	Mycobacterium tuberculosis causes persistent infection even in human or animal hosts that develop antigen-specific CD4+ and CD8+ T cell responses . To understand this phenomenon , we tested the hypothesis that the CD4+ effector T cells that are generated in response to M . tuberculosis infection fail to encounter their...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "immune", "cells", "immune", "activation", "antigen-presenting", "cells", "immunity", "to", "infections", "immunology", "microbiology", "bacterial", "diseases", "adaptive", "immunity", "immune", "defense", "immunomodulation", "immunotherapy", "infectious", "dise...	2011	Suboptimal Activation of Antigen-Specific CD4+ Effector Cells Enables Persistence of M. tuberculosis In Vivo
The Philippines has a population of approximately 103 million people , of which 6 . 7 million live in schistosomiasis-endemic areas with 1 . 8 million people being at risk of infection with Schistosoma japonicum . Although the country-wide prevalence of schistosomiasis japonica in the Philippines is relatively low , th...	Schistosomiasis is caused by infection with trematode blood flukes of the genus Schistosoma . Schistosoma japonicum is the causative agent of schistosomiasis in the Philippines , China and parts of Indonesia . In the Philippines , 6 . 7 million people live in endemic areas and 1 . 8 million are at risk of infection whe...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion", "Conclusion" ]	[]	2015	Real-time PCR Demonstrates High Prevalence of Schistosoma japonicum in the Philippines: Implications for Surveillance and Control
Opportunistic infections caused by Pseudomonas aeruginosa can be acute or chronic . While acute infections often spread rapidly and can cause tissue damage and sepsis with high mortality rates , chronic infections can persist for weeks , months , or years in the face of intensive clinical intervention . Remarkably , th...	Soft tissue infections , such as those in burns , bed sores , and diabetic ulcers , are a significant healthcare and economic burden in the developed and developing world . The opportunistic pathogen P . aeruginosa can cause both acute and chronic infections , and the trajectory of these two types of infections is vast...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "gram", "negative", "bacteria", "genome", "expression", "analysis", "microbial", "metabolism", "microbiology", "animal", "models", "model", "organisms", "genome", "analysis", "bacterial", "pathogens", "research", "and", "analysis", "methods", "microbial", ...	2014	Requirements for Pseudomonas aeruginosa Acute Burn and Chronic Surgical Wound Infection
Trypanosoma cruzi , the causative agent of Chagas disease , has high affinity for lipoproteins and adipose tissue . Infection results in myocarditis , fat loss and alterations in lipid homeostasis . This study was aimed at analyzing the effect of high fat diet ( HFD ) on regulating acute T . cruzi infection-induced myo...	Infection with Trypanosoma cruzi , the etiologic agent in Chagas disease , may result in heart disease . There has been an increase in obesity , diabetes , hypertension and ischemic cardiovascular disease in endemic areas . Previously , we demonstrated that adipose tissue is an early target and a reservoir for T . cruz...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "dyslipidemia", "veterinary", "diseases", "zoonoses", "medicine", "and", "health", "sciences", "nutrition", "biology", "and", "life", "sciences", "vector-borne", "diseases", "diet", "metabolic", "disorders", "veterinary", "science" ]	2014	High Fat Diet Modulates Trypanosoma cruzi Infection Associated Myocarditis
Upon viral infection , retinoic acid–inducible gene I–like receptors ( RLRs ) recognize viral RNA and trigger a series of signaling events , leading to the induction of type I interferons ( IFNs ) . These processes are delicately regulated to prevent excessive and harmful immune responses . In this study , we identifie...	Virus infection triggers the host cells to produce type I IFNs and proinflammatory cytokines , which are secreted proteins important for the host to clear viruses . Previously , we identified VISA ( also named as MAVS , IPS-1 and Cardif ) as a critical adaptor of virus-triggered , RLR-mediated induction of innate antiv...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "transfection", "luciferase", "assay", "molecular", "probe", "techniques", "293t", "cells", "biological", "cultures", "immunoblotting", "plasmid", "construction", "biochemical", "analysis", "enzyme", "assays", "immunoprecipitation", "signalosomes", "mitochondria", "molecular"...	2017	GPATCH3 negatively regulates RLR-mediated innate antiviral responses by disrupting the assembly of VISA signalosome
Sexual dimorphism in common disease is pervasive , including a dramatic male preponderance in autism spectrum disorders ( ASDs ) . Potential genetic explanations include a liability threshold model requiring increased polymorphism risk in females , sex-limited X-chromosome contribution , gene-environment interaction dr...	Autism Spectrum Disorders ( ASDs ) make up a debilitating neurodevelopmental disorder class . It has been known for a long time that more males than females are affected , but despite much speculation there is no clear etiological reason for this sex bias . As ASDs are highly heritable , we examined evidence in single ...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "genome-wide", "association", "studies", "medicine", "and", "health", "sciences", "social", "sciences", "autism", "anthropology", "developmental", "psychology", "neuroscience", "developmental", "biology", "mathematics", "genome", "analysis", "autism", "spectrum", "disorder"...	2016	Pleiotropic Mechanisms Indicated for Sex Differences in Autism

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