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While most miRNA knockouts exhibit only subtle defects , a handful of miRNAs are profoundly required for development or physiology . A particularly compelling locus is Drosophila mir-279 , which was reported as essential to restrict the emergence of CO2-sensing neurons , to maintain circadian rhythm , and to regulate o...	Amongst the small number of miRNA knockouts that exhibit substantially overt phenotypes , mutants of Drosophila mir-279 are notable . Previous studies have uncovered its essential requirements in a range of developmental and behavioral assays . Surprisingly , we find that the phenotypes attributed to mir-279 deletions ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Multiple In Vivo Biological Processes Are Mediated by Functionally Redundant Activities of Drosophila mir-279 and mir-996
Bacterial resistance to β-lactams may rely on acquired β-lactamases encoded by class 1 integron-borne genes . Rearrangement of integron cassette arrays is mediated by the integrase IntI1 . It has been previously established that integrase expression can be activated by the SOS response in vitro , leading to speculation...	The bacterial SOS response is a conserved regulatory network that is induced in response to DNA damage . Its activation in vitro leads to the emergence of resistance to antibiotics , leading to speculation that this is an important clinical mechanism of acquiring resistance . We found evidence here that antibiotic-indu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "medicine", "bacterial", "diseases", "infectious", "diseases", "bacterial", "evolution", "biology", "evolutionary", "biology", "genomic", "evolution", "microbiology", "infectious", "disease", "control", "bacterial", "pathogens" ]	2012	Evidence for Induction of Integron-Based Antibiotic Resistance by the SOS Response in a Clinical Setting
Bacterial pathogens and their toxins target host receptors , leading to aberrant behavior or host death by changing signaling events through subversion of host intracellular cAMP level . This is an efficient and widespread mechanism of microbial pathogenesis . Previous studies describe toxins that increase cAMP in host...	Interference with regulation of host signaling by pathogens can alter gene expression , leading to functional disarray in the host cells that causes abnormal division or death . Here , we propose a previously undescribed model for how bacterial toxins subvert host processes via interaction with GRK2 that influences cAM...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "phosphorylation", "invertebrates", "cell", "death", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "cell", "processes", "microbiology", "animals", "developmental", "biology", "silkworms", "g", "protein", "coupled", "...	2016	Bacillus bombysepticus α-Toxin Binding to G Protein-Coupled Receptor Kinase 2 Regulates cAMP/PKA Signaling Pathway to Induce Host Death
We assessed the role of myeloid dendritic cells ( mDCs ) in the outcome of SIV infection by comparing and contrasting their frequency , mobilization , phenotype , cytokine production and apoptosis in pathogenic ( pigtailed macaques , PTMs ) , nonpathogenic ( African green monkeys , AGMs ) and controlled ( rhesus macaqu...	Myeloid dendritic cells ( mDCs ) are potent antigen-presenting cells that regulate both innate and adaptive immune responses and act as “watch-dogs” , sensing and controlling aberrant immune activation; as such , they may significantly impact the outcome of HIV/SIV infection . By comparing and contrasting the frequency...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	Kinetics of Myeloid Dendritic Cell Trafficking and Activation: Impact on Progressive, Nonprogressive and Controlled SIV Infections
Eumycetoma is a chronic granulomatous subcutaneous infectious disease , endemic in tropical and subtropical regions and most commonly caused by the fungus Madurella mycetomatis . Interestingly , although grain formation is key in mycetoma , its formation process and its susceptibility towards antifungal agents are not ...	Mycetoma is a chronic subcutaneous infectious disease affecting different parts of the body but commonly seen in the foot . It can be caused by bacteria and fungi . Especially for fungi , the treatment options are meagre and therapeutic failures are common . In order to develop better therapeutic strategies for this di...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	A Madurella mycetomatis Grain Model in Galleria mellonella Larvae
Cysticercosis ( CC ) is a tissue infection caused by the larval cysts of the pork tapeworm Taenia solium . It is usually acquired by eating contaminated food or drinking water . CC Cysts can develop in the muscles , the eyes , the brain , and/or the spinal cord . T . solium is found worldwide , but its prevalence has d...	Cysticercosis ( CC ) , caused by the larval cysts of the pork tapeworm Taenia solium , is a neglected tropical disease ( NTD ) . It is acquired when worm eggs are ingested and the developing larvae migrate through the body and form cysts in tissues . Frequent in pigs , it can also affect humans , usually when they swal...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "hospitalizations", "medicine", "and", "health", "sciences", "european", "union", "tropical", "diseases", "geographical", "locations", "parasitic", "diseases", "health", "care", "neglected", "tropical", "diseases", "epilepsy", "infectious", "diseases", "spain", "zoonoses"...	2018	Clinical Cysticercosis epidemiology in Spain based on the hospital discharge database: What's new?
Chronic immune activation ( IA ) is considered as the driving force of CD4+ T cell depletion and AIDS . Fundamental clues in the mechanisms that regulate IA could lie in natural hosts of SIV , such as African green monkeys ( AGMs ) . Here we investigated the role of innate immune cells and IFN-α in the control of IA in...	Chronic inflammation is considered as directly involved in AIDS pathogenesis . The role of IFN-α as a driving force of chronic inflammation is under debate . Natural hosts of SIV , such as African green monkeys ( AGMs ) , avoid chronic inflammation . We show for the first time that NK cells are strongly activated durin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "flow", "cytometry", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "cytokines", "pathology", "and", "laboratory", "medicine", "immune", "activation", "antigen-presenting", "cells", "immunity", "to", "infect...	2014	Innate Immune Responses and Rapid Control of Inflammation in African Green Monkeys Treated or Not with Interferon-Alpha during Primary SIVagm Infection
The emergence of Zika virus ( ZIKV ) in the New World has led to more than 200 , 000 human infections . Perinatal infection can cause severe neurological complications , including fetal and neonatal microcephaly , and in adults there is an association with Guillain-Barré syndrome ( GBS ) . ZIKV is transmitted to humans...	The rapid spread of Zika virus through a naïve population in the Americas resulted in novel and severe disease manifestations , including fetal and neonatal microcephaly , and GBS . These disease complications make understanding the pathology and ecology of ZIKV a priority . Captive Jamaican fruit bats were challenged ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "reproductive", "system", "body", "fluids", "pathology", "and", "laboratory", "medicine", "pathogens", "animal", "models", "of", "disease", "microbiology", "vertebrates", "animals", "mammals", "viruses", "urine", "rna", "viruse...	2019	Experimental Zika virus infection of Jamaican fruit bats (Artibeus jamaicensis) and possible entry of virus into brain via activated microglial cells
Horizontal transmission of cytomegaloviruses ( CMV ) occurs via prolonged excretion from mucosal surfaces . We used murine CMV ( MCMV ) infection to investigate the mechanisms of immune control in secretory organs . CD4 T cells were crucial to cease MCMV replication in the salivary gland ( SG ) via direct secretion of ...	Cytomegaloviruses ( CMVs ) infect 50 to 90 % of the world's population and cause severe clinical complication in immunosuppressed individuals . An important tissue for horizontal transmission is the salivary gland ( SG ) . CD4 T cells are crucial for viral control in this organ . However , how CD4 T cells control MCMV ...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "medicine", "immune", "cells", "immunity", "to", "infections", "immunology", "cytomegalovirus", "infection", "adaptive", "immunity", "immune", "defense", "infectious", "disease", "control", "infectious", "diseases", "t", "cells", "biology", "immune", "response", "antige...	2011	Absence of Cross-Presenting Cells in the Salivary Gland and Viral Immune Evasion Confine Cytomegalovirus Immune Control to Effector CD4 T Cells
A robust ( long and thick ) root system is characteristic of upland japonica rice adapted to drought conditions . Using deep sequencing and large scale phenotyping data of 795 rice accessions and an integrated strategy combining results from high resolution mapping by GWAS and linkage mapping , comprehensive analyses o...	Asian cultivated rice is well-known for its rich-within-species diversity with two major subspecies , indica and japonica and subpopulation differentiation . A robust ( long and thick ) root system that is characteristic of upland japonica rice represents a predominant ecotype grown under aerobic and rain-fed condition...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "genome-wide", "association", "studies", "quantitative", "trait", "loci", "population", "genetics", "alleles", "genetic", "mapping", "gene", "pool", "protein", "expression", "rice", "experimental", "organism", "systems", "genome", "analysis", "molecular", "biology", "te...	2018	Loci and natural alleles underlying robust roots and adaptive domestication of upland ecotype rice in aerobic conditions
It is presently unclear how much individual community members contribute to the overall metabolic output of a gut microbiota . To address this question , we used the honey bee , which harbors a relatively simple and remarkably conserved gut microbiota with striking parallels to the mammalian system and importance for b...	Honey bees are important pollinators that harbor a relatively simple gut microbiota with striking parallels to the mammalian system . This makes them relevant models to study gut microbiota functions and their impact on host health . We applied untargeted metabolomics to characterize metabolic changes induced by the gu...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]	[ "invertebrates", "plant", "anatomy", "gut", "bacteria", "microbiome", "honey", "bees", "microbiology", "animals", "pollen", "metabolomics", "plant", "science", "metabolites", "bacteria", "microbial", "genomics", "bees", "hymenoptera", "medical", "microbiology", "insects",...	2017	Disentangling metabolic functions of bacteria in the honey bee gut
Aedes aegypti , is the major dengue vector and a worldwide public health threat combated basically by chemical insecticides . In this study , the vectorial competence of Ae . aegypti co-infected with a mildly virulent Metarhizium anisopliae and fed with blood infected with the DENV-2 virus , was examined . The study en...	Dengue is a worldwide public health problem . There is not an effective vaccine yet; the chemical struggle against its transmitter , the mosquito Aedes aegypti , is onerous and erratic , and the community participation to eliminate vector breeding sites is unconfident . Here , we examined mosquitoes fed on human blood ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "biology" ]	2013	Vectorial Capacity of Aedes aegypti for Dengue Virus Type 2 Is Reduced with Co-infection of Metarhizium anisopliae
Crossing-over is a central feature of meiosis . Meiotic crossover ( CO ) sites are spatially patterned along chromosomes . CO-designation at one position disfavors subsequent CO-designation ( s ) nearby , as described by the classical phenomenon of CO interference . If multiple designations occur , COs tend to be evenl...	Spatial patterning is a common feature of biological systems at all length scales , from molecular to multi-organismic . Meiosis is the specialized cellular program in which a diploid cell gives rise to haploid gametes for sexual reproduction . Crossing-over between homologous maternal and paternal chromosomes ( homolo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2014	Crossover Patterning by the Beam-Film Model: Analysis and Implications
Histidine kinases ( HKs ) are dimeric receptors that participate in most adaptive responses to environmental changes in prokaryotes . Although it is well established that stimulus perception triggers autophosphorylation in many HKs , little is known on how the input signal propagates through the HAMP domain to control ...	Bacteria use two-component signal transduction systems ( TCSs ) , composed of a histidine kinase ( HK ) and a downstream response regulator ( RR ) , to perceive a broad range of external stimuli and trigger an appropriate response . Prototypical HKs are transmembrane homodimeric receptors with an external sensor region...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "proteins", "protein", "structure", "biology", "microbiology" ]	2014	Segmental Helical Motions and Dynamical Asymmetry Modulate Histidine Kinase Autophosphorylation
The normalization model of attention proposes that attention can affect performance by response- or contrast-gain changes , depending on the size of the stimulus and attention field . Here , we manipulated the attention field by emotional valence , negative faces versus positive faces , while holding stimulus size cons...	Attentional selection is the mechanism by which the subset of incoming information is preferentially processed at the expense of distractors . The normalization model of attention suggests that attention-triggered modulatory effects on sensory responses in the visual cortex depend on two factors: the stimulus size and ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "diagnostic", "radiology", "functional", "magnetic", "resonance", "imaging", "face", "brain", "social", "sciences", "neuroscience", "magnetic", "resonance", "imaging", "cognitive", "psychology", "mathematics", "statistics", "(mathe...	2016	A Normalization Framework for Emotional Attention
Trichomonas vaginalis is a common sexually transmitted parasite that colonizes the human urogential tract where it remains extracellular and adheres to epithelial cells . Infections range from asymptomatic to highly inflammatory , depending on the host and the parasite strain . Here , we use a combination of methodolog...	Trichomoniasis , the most common non-viral sexually transmitted disease worldwide , infects over 275 million people annually . Infection results from the colonization of the human urogenital tract by the parasite Trichomonas vaginalis . To establish and maintain infection the parasite adheres to host cells , a process ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "cell", "biology", "microbial", "pathogens", "host-pathogen", "interaction", "biology", "microbiology", "pathogenesis", "parasitology" ]	2013	Trichomonas vaginalis Exosomes Deliver Cargo to Host Cells and Mediate Host∶Parasite Interactions
Many cellular responses to surrounding cues require temporally concerted transcriptional regulation of multiple genes . In prokaryotic cells , a single-input-module motif with one transcription factor regulating multiple target genes can generate coordinated gene expression . In eukaryotic cells , transcriptional activ...	Cellular responses to environmental stimulation are often accompanied by changes in gene expression patterns . Genes are linearly arranged along chromosomal DNA , which folds into a three-dimensional structure . The chromosome structure affects gene expression activities and is regulated by multiple events such as hist...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "markov", "models", "chromosome", "structure", "and", "function", "gene", "regulation", "regulatory", "proteins", "dna-binding", "proteins", "histone", "modification", "regulator", "genes", "mathematics", "transcription", "factors", "gene", "types", "epigenetics", "chroma...	2019	Spatial clustering and common regulatory elements correlate with coordinated gene expression
Scientific and technological advances that enable the tuning of integrated regulatory components to match network and system requirements are critical to reliably control the function of biological systems . RNA provides a promising building block for the construction of tunable regulatory components based on its rich ...	Riboswitches are RNA-based components that integrate ligand binding and gene regulation to dynamically respond to molecular signals within cells . Natural riboswitches are employed to regulate metabolism and other cellular processes , while synthetic riboswitches have been constructed to expand the sensory and regulato...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/transcriptional", "regulation", "molecular", "biology/mrna", "stability", "molecular", "biology/transcription", "elongation", "biotechnology/bioengineering", "molecular", "biology/translational", "regulation" ]	2009	Design Principles for Riboswitch Function
The phytohormone abscisic acid ( ABA ) regulates plant growth , development and responses to biotic and abiotic stresses . The core ABA signaling pathway consists of three major components: ABA receptor ( PYR1/PYLs ) , type 2C Protein Phosphatase ( PP2C ) and SNF1-related protein kinase 2 ( SnRK2 ) . Nevertheless , the...	The phytohormone abscisic acid ( ABA ) regulates multiple developmental processes such as seed dormancy , germination , root/shoot growth , flowering and senescence in plants . Although the core ABA perception and signaling pathway has been elucidated , the complexity of the pathway remains to be exploited . In the pre...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "biotechnology", "phosphorylation", "luciferase", "plant", "growth", "and", "development", "enzymes", "enzymology", "phosphatases", "developmental", "biology", "plant", "science", "genetically", "modified", "plants", "seedlings", "molecular", "biology", "techniques", "plant...	2016	Type One Protein Phosphatase 1 and Its Regulatory Protein Inhibitor 2 Negatively Regulate ABA Signaling
MicroRNAs ( miRNAs ) play key roles in the initiation and progression of various cancers by regulating genes . Regulatory interactions between genes and miRNAs are complex , as multiple miRNAs can regulate multiple genes . In addtion , these interactions vary from patient to patient and even among patients with the sam...	A microRNA ( miRNA ) is a small RNA molecule that regulates the expression of mRNA genes . A miRNA can regulate multiple genes , and a gene can be regulated by multiple miRNAs . The regulation of genes by miRNAs may vary from patient to patient , even if they suffer from the same type of cancer . In this study , we ide...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	A Computational Approach to Identifying Gene-microRNA Modules in Cancer
A major challenge in ecology is forecasting the effects of species' extinctions , a pressing problem given current human impacts on the planet . Consequences of species losses such as secondary extinctions are difficult to forecast because species are not isolated , but interact instead in a complex network of ecologic...	Predicting the consequences of species' extinction is a crucial problem in ecology . Species are not isolated , but connected to each others in tangled networks of relationships known as food webs . In this work we want to determine which species are critical as they support many other species . The fact that species a...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "ecology/theoretical", "ecology", "ecology/community", "ecology", "and", "biodiversity", "ecology", "computational", "biology" ]	2009	Googling Food Webs: Can an Eigenvector Measure Species' Importance for Coextinctions?
Haploid high quality reference genomes are an important resource in genomic research projects . A consequence is that DNA fragments carrying the reference allele will be more likely to map successfully , or receive higher quality scores . This reference bias can have effects on downstream population genomic analysis wh...	Mapping next-generation sequencing reads to a single linear reference genomes comes with the inherent problem that alleles not found in the reference sequence will achieve lower mapping scores . This reference bias can cause heterozygous sites to be falsely called as homozygous which will have an effect on downstream a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "heterozygosity", "population", "genetics", "ancient", "dna", "alleles", "genome", "analysis", "paleontology", "dna", "paleogenetics", "molecular", "genetics", "population", "biology", "genomic", "libraries", "molecular", "biology", "genetic", "loci", "biochemistry", "nuc...	2019	The presence and impact of reference bias on population genomic studies of prehistoric human populations
Virus infections induce CD8+ T cell responses comprised of a large population of terminal effector cells and a smaller subset of long-lived memory cells . The transcription factors regulating the relative expansion versus the long-term survival potential of anti-viral CD8+ T cells are not completely understood . We ide...	CD8+ T lymphocytes are essential for immune protection against viruses . In response to an infection , these cells are activated , proliferate , and generate antiviral effector cells that eradicate the infection . Following this , the majority of these effector cells die , leaving a small subset of long-lived virus-spe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "cytokines", "gene", "regulation", "immunology", "developmental", "biology", "immunoprecipitation", "genome", "analysis", "molecular", "de...	2017	Transient expression of ZBTB32 in anti-viral CD8+ T cells limits the magnitude of the effector response and the generation of memory
The genetic diversity of pathogens , and interactions between genotypes , can strongly influence pathogen phenotypes such as transmissibility and virulence . For vector-borne pathogens , both mammalian hosts and arthropod vectors may limit pathogen genotypic diversity ( number of unique genotypes circulating in an area...	Co-infection , the presence of multiple genotypes of the same pathogen species within an infected individual , is common . Genotype diversity , defined as the number of unique genotypes , and the interaction between genotypes , can strongly influence virulence and pathogen transmission . Understanding how genotypic div...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "vector-borne", "diseases", "microbiology", "bacterial", "diseases", "population", "modeling", "bacterial", "pathogens", "veterinary", "science", "animal", "models", "of", "infection", "infectious", "diseases", "veterinary", "disea...	2014	Restriction of Francisella novicida Genetic Diversity during Infection of the Vector Midgut
Coxiella burnetii is an intracellular pathogen that causes human Q fever , a disease that normally presents as a severe flu-like illness . Due to high infectivity and disease severity , the pathogen is considered a risk group 3 organism . Full-length lipopolysaccharide ( LPS ) is required for full virulence and disease...	Coxiella burnetii is the causative agent of Q fever , an acute febrile illness that can develop into a persistent focalized infection , such as endocarditis or vascular disease . Currently , the only licensed vaccine against Q fever is Q-Vax , a formalin-inactivated whole-cell preparation of the virulent C . burnetii H...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "deletion", "mutation", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "molecular", "probe", "techniques", "pathogens", "microbiology", "immunoblotting", "bacterial", "diseases", "mutation", "molecular", "biology", "techniques", "fr...	2018	Genetic mechanisms of Coxiella burnetii lipopolysaccharide phase variation
Imatinib mesylate ( Gleevec ) inhibits Abl1 , c-Kit , and related protein tyrosine kinases ( PTKs ) and serves as a therapeutic for chronic myelogenous leukemia and gastrointestinal stromal tumors . Imatinib also has efficacy against various pathogens , including pathogenic mycobacteria , where it decreases bacterial l...	Host-directed therapeutics ( HDTs ) for infectious diseases target cellular mechanisms used by pathogens to move into , through , or out of cells . The Abl tyrosine kinase ( TK ) inhibitor and cancer therapeutic imatinib mesylate ( Gleevec ) , for example , has activity against bacterial and viral pathogens via effects...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Low Doses of Imatinib Induce Myelopoiesis and Enhance Host Anti-microbial Immunity
Mutation signatures in cancer genomes reflect endogenous and exogenous mutational processes , offering insights into tumour etiology , features for prognostic and biologic stratification and vulnerabilities to be exploited therapeutically . We present a novel machine learning formalism for improved signature inference ...	Over time DNA accumulates mutations from a variety of sources . Some mutations result from external mutagens , such as UV radiation , while others result from processes occurring within the cell itself . Each of these sources can impart characteristic patterns of mutations on the genome , known as mutation signatures ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cancer", "genomics", "medicine", "and", "health", "sciences", "breast", "tumors", "reproductive", "system", "cancer", "risk", "factors", "cancers", "and", "neoplasms", "basic", "cancer", "research", "oncology", "mutation", "substitution", "mutation", "medical", "risk...	2019	Integrated structural variation and point mutation signatures in cancer genomes using correlated topic models
Dengue is a major mosquito-borne viral disease and an important public health problem . Identifying which factors are important determinants in the risk of dengue infection is critical in supporting and guiding preventive measures . In South-East Asia , half of all reported fatal infections are recorded in Indonesia , ...	Dengue has been detected in Indonesia and transmission is progressively rising to account for half of all fatal dengue cases recorded in South-East Asia . However , little is known about the epidemiology of the virus , which may hamper the effectiveness of preventive strategies carried out in the country . Identifying ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "geographical", "locations", "animals", "indonesia", "java", "health", "care", "probability", "distribution", "mathematics", "infectious", "disease", "control", "insect", "vectors", "morbidity", "infectious", "dise...	2016	The Importance of Socio-Economic Versus Environmental Risk Factors for Reported Dengue Cases in Java, Indonesia
The appropriate development of conidia and appressoria is critical in the disease cycle of many fungal pathogens , including Magnaporthe oryzae . A total of eight genes ( MoHOX1 to MoHOX8 ) encoding putative homeobox transcription factors ( TFs ) were identified from the M . oryzae genome . Knockout mutants for each Mo...	Pathogens have evolved diverse strategies to cause disease . Magnaporthe oryzae is the fungal phytopathogen that causes rice blast and is considered an important model for understanding mechanisms in fungal development and pathogenicity . Asexual reproduction and infection-related development play key roles in M . oryz...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/morphogenesis", "and", "cell", "biology", "infectious", "diseases/fungal", "infections", "developmental", "biology/cell", "differentiation", "genetics", "and", "genomics/gene", "function", "microbiology/cellular", "microbiology", "and", "pathogenesis" ]	2009	Homeobox Transcription Factors Are Required for Conidiation and Appressorium Development in the Rice Blast Fungus Magnaporthe oryzae
Systems-level consolidation refers to the time-dependent reorganisation of memory traces in the neocortex , a process in which the ventromedial prefrontal cortex ( vmPFC ) has been implicated . Capturing the precise temporal evolution of this crucial process in humans has long proved elusive . Here , we used multivaria...	Our past experiences are captured in autobiographical memories that allow us to recollect events from our lives long after they originally occurred . A part of the brain’s frontal lobe , called the ventromedial prefrontal cortex ( vmPFC ) , is known to be important for supporting autobiographical memories , especially ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "diagnostic", "radiology", "functional", "magnetic", "resonance", "imaging", "prefrontal", "cortex", "brain", "social", "sciences", "neuroscience", "learning", "and", "memory", "magnetic", "resonance", "imaging", "cognition", "br...	2018	Nonmonotonic recruitment of ventromedial prefrontal cortex during remote memory recall
Molecular circadian clocks are interconnected via neural networks . In Drosophila , PIGMENT-DISPERSING FACTOR ( PDF ) acts as a master network regulator with dual functions in synchronizing molecular oscillations between disparate PDF ( + ) and PDF ( − ) circadian pacemaker neurons and controlling pacemaker neuron outp...	Circadian clocks provide a mechanism for predicting and adapting behavioral and physiological processes to 24-hour rhythms in the environment . In animal nervous systems , cell-autonomous molecular oscillators are coupled via neural networks that control daily patterns of activity . A major neuropeptide synchronizing n...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "molecular", "neuroscience", "neurochemistry", "neural", "networks", "neuroscience", "animals", "gene", "function", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "neurotransmitters", "drosophila", "neuroimaging", "research", "and", ...	2014	Dual PDF Signaling Pathways Reset Clocks Via TIMELESS and Acutely Excite Target Neurons to Control Circadian Behavior
Lung disease caused by nontuberculous mycobacteria ( NTM ) is an emerging infectious disease of global significance . Epidemiologic studies have shown the Hawaiian Islands have the highest prevalence of NTM lung infections in the United States . However , potential environmental reservoirs and species diversity have no...	In the U . S . , the Hawaiian Islands have the highest number of nontuberculous mycobacterial ( NTM ) lung disease cases per capita . The tropical climate , geographical isolation of the islands , and aquifer water sources may have influence such prevalence . Previous studies suggest that NTM thrive in water biofilms a...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biofilms", "sequencing", "techniques", "united", "states", "medicine", "and", "health", "sciences", "geographical", "locations", "microbiology", "hawaii", "pulmonology", "north", "america", "environmental", "and", "occupational", "lung", "diseases", "molecular", "biology...	2016	Environmental Nontuberculous Mycobacteria in the Hawaiian Islands
Since platelet intracellular calcium mobilization [Ca ( t ) ]i controls granule release , cyclooxygenase-1 and integrin activation , and phosphatidylserine exposure , blood clotting simulations require prediction of platelet [Ca ( t ) ]i in response to combinatorial agonists . Pairwise Agonist Scanning ( PAS ) deployed...	Platelets regulate clotting during injury to prevent blood loss . Hyperactive platelets may increase risk of thrombosis , whereas hypoactive platelets may increase risk of bleeding . Platelets are activated during a clotting event by agonists , through different signaling pathways , all of which converge on intracellul...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	A Human Platelet Calcium Calculator Trained by Pairwise Agonist Scanning
Wing patterning in Heliconius butterflies is a longstanding example of both Müllerian mimicry and phenotypic radiation under strong natural selection . The loci controlling such patterns are “hotspots” for adaptive evolution with great allelic diversity across different species in the genus . We characterise nucleotide...	The diversity of wing patterns in Heliconius butterflies is a longstanding example of both Müllerian mimicry and adaptive radiation . The genetic regions controlling such patterns are “hotspots” for adaptive evolution , with small regions of the genome controlling major changes in wing pattern . Across multiple hybrid ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "evolutionary", "biology/animal", "genetics", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics", "evolutionary", "biology/genomics", "evolutionary", "biology/bioinformatics", "evolutionary", "biology/pattern", "formation", "evolutionary", "biology", "evolutio...	2010	Genomic Hotspots for Adaptation: The Population Genetics of Müllerian Mimicry in the Heliconius melpomene Clade
Protein knots , mostly regarded as intriguing oddities , are gradually being recognized as significant structural motifs . Seven distinctly knotted folds have already been identified . It is by and large unclear how these exceptional structures actually fold , and only recently , experiments and simulations have begun ...	Knots are ubiquitous in many aspects of our life , but remain elusive in proteins . The multitude of protein structures archived in the Protein Data Bank can be grouped into several hundred patterns , but only a handful are folded into knots . Combing through the recently added structures we found several novel knotted...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/molecular", "dynamics", "computational", "biology/macromolecular", "structure", "analysis" ]	2010	A Stevedore's Protein Knot
Although fitness landscapes are central to evolutionary theory , so far no biologically realistic examples for large-scale fitness landscapes have been described . Most currently available biological examples are restricted to very few loci or alleles and therefore do not capture the high dimensionality characteristic ...	Evolutionary adaptation can be understood as populations moving uphill on landscapes , in which height corresponds to evolutionary fitness . Although such fitness landscapes are central to evolutionary theory , there is currently a lack of biologically realistic examples . Here we analyze large-scale fitness landscapes...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "biology", "population", "biology", "evolutionary", "biology" ]	2012	Exploring the Complexity of the HIV-1 Fitness Landscape
Epstein-Barr virus ( EBV ) is etiologically linked to infectious mononucleosis and several human cancers . EBV encodes a conserved protein kinase BGLF4 that plays a key role in the viral life cycle . To provide new insight into the host proteins regulated by BGLF4 , we utilized stable isotope labeling by amino acids in...	Epstein-Barr virus ( EBV ) is a herpesvirus that is associated with B cell and epithelial human cancers . Herpesviruses encode a protein kinase which is an important regulator of lytic virus replication and is consequently a target for anti-viral drug development . The EBV genome encodes for a serine/threonine protein ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Phosphoproteomic Profiling Reveals Epstein-Barr Virus Protein Kinase Integration of DNA Damage Response and Mitotic Signaling
Syphilis is a Sexually Transmitted Infection ( IST ) with significant importance to public health , due to its impact during pregnancy ( Gestational Syphilis—GS ) ; especially because syphilis can affect fetus and neonates’ development ( mother-to-child transmission—MTCT of syphilis ) , by increasing susceptibility to ...	Syphilis is a sexually transmitted infection that can be transmitted to child during pregnancy , or postpartum , by an infected mother . Syphilis in children can interfere in the development and , in some cases , may lead to death . We analyzed cases of syphilis during pregnancy and mother-to-child transmission of syph...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infographics", "urology", "medicine", "and", "health", "sciences", "infectious", "disease", "epidemiology", "tropical", "diseases", "geographical", "locations", "charts", "health", "care", "treponematoses", "bacterial", "diseases", "sexually", "transmitted", "diseases", ...	2019	Mother-to-child transmission and gestational syphilis: Spatial-temporal epidemiology and demographics in a Brazilian region
Although the importance of humoral immunity to malaria has been established , factors that control antibody production are poorly understood . Follicular helper T cells ( Tfh cells ) are pivotal for generating high-affinity , long-lived antibody responses . While it has been proposed that expansion of antigen-specific ...	Plasmodium vivax is the most widely spread malaria parasite species and represents a significant impediment to social and economic development in endemic countries . Our goal was to assess the importance of T follicular helper cells in the development of the immune response during malaria . We found that P . vivax infe...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "parasite", "groups", "immune", "cells", "immune", "physiology", "plasmodium", "immunology", "tropical", "diseases", "parasitic", "diseases", "neuroscience", "learning", "and", "memory", "parasitology", "apicomp...	2017	T follicular helper cells regulate the activation of B lymphocytes and antibody production during Plasmodium vivax infection
The replication of human polyomavirus JCV , which causes Progressive Multifocal Leukoencephalopathy , is initiated by the virally encoded T-antigen ( T-ag ) . The structure of the JC virus T-ag origin-binding domain ( OBD ) was recently solved by X-ray crystallography . This structure revealed that the OBD contains a C...	A conserved feature of Polyomavirus T-antigens is a phenylalanine situated at the C-termini of their origin-binding domains ( OBDs ) . Using the T-antigen encoded by JC virus , we have investigated why this residue is critical for viral DNA replication . The studies presented herein establish that the consequences of t...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2016	Structural Based Analyses of the JC Virus T-Antigen F258L Mutant Provides Evidence for DNA Dependent Conformational Changes in the C-Termini of Polyomavirus Origin Binding Domains
Mass drug administration ( MDA ) with ivermectin for onchocerciasis was provided in Guatemala’s Central Endemic Zone ( CEZ ) over a 24 year period ( 1988–2011 ) . Elimination of Onchocerca volvulus transmission was declared in 2015 after a three year post MDA surveillance period ( 2012–2014 ) showed no evidence of recr...	Human onchocerciasis ( also known as ‘River Blindness’ ) is a parasitic disease of the skin and eyes whose etiological agent ( Onchocerca volvulus ) is transmitted by black flies . Guatemala was the country in the Americas most afflicted by onchocerciasis , and the largest focus of onchocerciasis in Guatemala was the C...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "onchocerca", "volvulus", "pathology", "and", "laboratory", "medicine", "vomiting", "tropical", "diseases", "geographical", "locations", "parasitic", "diseases", "animals", "onchocerca", "parasitology", "health", "...	2016	A Knowledge, Attitudes and Practices Survey Conducted Three Years after Halting Ivermectin Mass Treatment for Onchocerciasis in Guatemala
Morphotype switch is a cellular response to external and internal cues . The Cryptococcus neoformans species complex can undergo morphological transitions between the yeast and the hypha form , and such morphological changes profoundly affect cryptococcal interaction with various hosts . Filamentation in Cryptococcus w...	Cryptococcal meningitis claims half a million lives each year . There is no clinically available vaccine and the current antifungal therapies have serious limitations . Thus identifying cryptococcal specific programs that can be targeted for antifungal or vaccine development is of great value . We have shown previously...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cryptococcus", "neoformans", "medicine", "and", "health", "sciences", "deletion", "mutation", "cryptococcus", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "pathogens", "regulatory", "proteins", "microbiology", "dna-binding", "proteins", "mutation", ...	2017	Glucosamine stimulates pheromone-independent dimorphic transition in Cryptococcus neoformans by promoting Crz1 nuclear translocation
Mammalian genomes are pervasively transcribed outside mapped protein-coding genes . One class of extragenic transcription products is represented by long non-coding RNAs ( lncRNAs ) , some of which result from Pol_II transcription of bona-fide RNA genes . Whether all lncRNAs described insofar are products of RNA genes ...	Mammalian genomes contain vast intergenic regions that are extensively transcribed and generate various types of short and long non-coding RNAs ( ncRNAs ) . Although in some cases specific functions have been assigned to intergenic transcripts , the functional significance of this transcriptional output remains largely...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/histone", "modification", "cell", "biology/leukocyte", "signaling", "and", "gene", "expression", "immunology/innate", "immunity", "genetics", "and", "genomics/epigenetics", "cell", "biology/gene", "expression" ]	2010	A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers
The presence of poor quality medicines in the market is a global threat on public health , especially in developing countries . Therefore , we assessed the quality of two commonly used anthelminthic drugs [mebendazole ( MEB ) and albendazole ( ALB ) ] and one antiprotozoal drug [tinidazole ( TNZ ) ] in Ethiopia . A mul...	Access to medicines of good quality improves the chances of successful treatment for individual patients and promotes better outcomes for public health in general . At present , the prevailing strategy for improving access to medicines for neglected tropical diseases ( NTDs ) is drug donation programs . However , the p...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biology", "and", "life", "sciences", "medicine", "and", "health", "sciences" ]	2014	Quality of Medicines Commonly Used in the Treatment of Soil Transmitted Helminths and Giardia in Ethiopia: A Nationwide Survey
The human and chimpanzee X chromosomes are less divergent than expected based on autosomal divergence . We study incomplete lineage sorting patterns between humans , chimpanzees and gorillas to show that this low divergence can be entirely explained by megabase-sized regions comprising one-third of the X chromosome , w...	Because the speciation events that led to human , chimpanzee and gorilla were close in time , the genetic relationship of these species varies along the genome . While human and chimpanzee are the closest related species , in 15% of the genome , human and gorilla are more closely related , and in another 15% of the gen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Strong Selective Sweeps on the X Chromosome in the Human-Chimpanzee Ancestor Explain Its Low Divergence
The global transcriptional regulator , CodY , binds strongly to the regulatory region of the braB gene , which encodes a Bacillus subtilis branched-chain amino acid ( BCAA ) permease . However , under conditions that maximize CodY activity , braB expression was similar in wild-type and codY null mutant cells . Nonethel...	Expression of Bacillus subtilis BraB , a branched-chain amino acid permease , is under both negative and positive control by a global transcriptional regulator CodY . The negative control is direct and the positive control is indirect and mediated by another B . subtilis pleiotropic transcriptional regulator , ScoC , w...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Intermediate Levels of Bacillus subtilis CodY Activity Are Required for Derepression of the Branched-Chain Amino Acid Permease, BraB
Environmental factors and host genetics interact to control the gut microbiota , which may have a role in the development of obesity and insulin resistance . TLR2-deficient mice , under germ-free conditions , are protected from diet-induced insulin resistance . It is possible that the presence of gut microbiota could r...	An intricate interaction between genetic and environmental factors influences the development of obesity and diabetes . Previous studies have shown that mice lacking an important receptor of the innate immune system , Toll-like Receptor 2 ( TLR2 ) , are protected from insulin resistance . Given that the innate immune s...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "model", "organisms", "endocrinology", "immunology", "biology", "microbiology", "diabetes", "and", "endocrinology", "genetics", "and", "genomics", "metabolic", "disorders" ]	2011	Gut Microbiota Is a Key Modulator of Insulin Resistance in TLR 2 Knockout Mice
Certain Major Histocompatibility-I ( MHC-I ) types are associated with superior immune containment of HIV-1 infection by CD8+ cytotoxic T lymphocytes ( CTLs ) , but the mechanisms mediating this containment are difficult to elucidate in vivo . Here we provide controlled assessments of fitness landscapes and CTL-imposed...	Certain MHC class I types are associated with superior immune containment of HIV-1 , underscoring the importance of CD8+ cytotoxic T lymphocytes ( CTLs ) . Epitope escape mutations for these types is limited , indicating reduced immune evasion . Two proposed mechanisms are: 1 ) CTL targeting of highly sequence-constrai...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "pathogens", "immunology", "microbiology", "cloning", "organic", "compounds", "retroviruses", "viruses", "immunodeficiency", "viruses", "mutation", "substitution"...	2017	HIV-1 epitopes presented by MHC class I types associated with superior immune containment of viremia have highly constrained fitness landscapes
Chromatin insulators block the action of transcriptional enhancers when interposed between an enhancer and a promoter . In this study , we examined the role of chromatin loops formed by two unrelated insulators , gypsy and Fab-7 , in their enhancer-blocking activity . To test for this activity , we selected the white r...	The mechanism underlying enhancer blocking by insulators is unclear . Current models suggest that insulator proteins block enhancers either by formation of chromatin loops or by direct interaction with protein complexes bound to the enhancers and promoters . Here , we tested the role of a chromatin loop in blocking the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gene", "expression", "genetics", "epigenetics", "biology", "molecular", "cell", "biology" ]	2013	Effective Blocking of the White Enhancer Requires Cooperation between Two Main Mechanisms Suggested for the Insulator Function
Human tuberculosis ( TB ) in West Africa is not only caused by M . tuberculosis but also by bacteria of the two lineages of M . africanum . For instance , in The Gambia , 40% of TB is due to infections with M . africanum West African 2 . This bacterial lineage is associated with HIV infection , reduced ESAT-6 immunogen...	Mycobacterium tuberculosis and Mycobacterium africanum are the two major lineages within the M . tuberculosis complex that cause human tuberculosis in West Africa . Despite being closely related , the outcome after infection differs between these two pathogens . Although M . africanum has not yet been studied to the sa...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "bacteriology", "microbial", "metabolism", "microbial", "mutation", "microbial", "physiology", "microbial", "pathogens", "biology", "microbiology", "bacterial", "biochemistry" ]	2013	Deciphering the Growth Behaviour of Mycobacterium africanum
Recent years have seen the greatest ecological disturbances of our times , with global human expansion , species and habitat loss , climate change , and the emergence of new and previously-known infectious diseases . Biodiversity loss affects infectious disease risk by disrupting normal relationships between hosts and ...	Biodiversity affects the long-term health of a community by virtue of the many interactions constituent organisms depend upon . Mosquito-borne diseases are particularly likely to respond to changes on multiple transmission levels that span mosquito and vertebrate host communities . We characterized mosquito communities...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2013	Mosquito Vector Diversity across Habitats in Central Thailand Endemic for Dengue and Other Arthropod-Borne Diseases
Entamoeba histolytica is the pathogenic amoeba responsible for amoebiasis , an infectious disease targeting human tissues . Amoebiasis arises when virulent trophozoites start to destroy the muco-epithelial barrier by first crossing the mucus , then killing host cells , triggering inflammation and subsequently causing d...	Entamoeba histolytica is an intestinal parasite which displays diverse phenotypes with respect to pathogenesis in the human colon . Trophozoites can remain as commensal , without causing evident intestinal damage , or they can destroy the colonic mucosa leading to amoebiasis . Using human colon explants and transcripto...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Identification of the Virulence Landscape Essential for Entamoeba histolytica Invasion of the Human Colon
Monkeypox ( MPX ) is a zoonotic disease endemic in Central and West Africa and is caused by Monkeypox virus ( MPXV ) , the most virulent Orthopoxvirus affecting humans since the eradication of Variola virus ( VARV ) . Many aspects of the MPXV transmission cycle , including the natural host of the virus , remain unknown...	Monkeypox virus ( MPXV ) is a virus closely related to Variola virus , the cause of smallpox , and it causes a similar , though less severe , disease in humans in Central and West Africa . This disease is particularly dangerous for children and people with compromised immune systems and the mortality rate is estimated ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "respiratory", "infections", "immunology", "microbiology", "vertebrates", "animals", "electromagnetic", "radiation", "pulmonology", ...	2017	Characterization of Monkeypox virus infection in African rope squirrels (Funisciurus sp.)
The canary pox vector and gp120 vaccine ( ALVAC-HIV and AIDSVAX B/E gp120 ) in the RV144 HIV-1 vaccine trial conferred an estimated 31% vaccine efficacy . Although the vaccine Env AE . A244 gp120 is antigenic for the unmutated common ancestor of V1V2 broadly neutralizing antibody ( bnAbs ) , no plasma bnAb activity was...	Developing a successful HIV-1 vaccine remains a high global health priority . Several HIV-1 vaccine trials have been performed with only the RV144 vaccine trial showing vaccine efficacy , albeit modest . No broadly neutralizing antibody activity was identified in RV144 and inducing sterilizing immunity against a comple...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "viral", "vaccines", "medicine", "and", "health", "sciences", "chemical", "characterization", "immune", "physiology", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "immune", "cells", "pathogens", "immunology", "microbiolo...	2017	Boosting of HIV envelope CD4 binding site antibodies with long variable heavy third complementarity determining region in the randomized double blind RV305 HIV-1 vaccine trial
Kaposi sarcoma-associated herpesvirus ( KSHV ) is linked with the development of Kaposi sarcoma and the B lymphocyte disorders primary effusion lymphoma ( PEL ) and multi-centric Castleman disease . T cell immunity limits KSHV infection and disease , however the virus employs multiple mechanisms to inhibit efficient co...	Kaposi sarcoma-associated herpesvirus ( KSHV ) can cause disease in humans in the form of B lymphocyte disorders such as primary effusion lymphoma ( PEL ) and multicentric Castleman disease . Where tested , these are highly resistant to immune control by KSHV-specific T cells . To investigate how such KSHV-infected cel...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "flow", "cytometry", "cell", "death", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "cell", "processes", "biological", "cultures", "microbiology", "organisms", "vi...	2016	Azidothymidine Sensitizes Primary Effusion Lymphoma Cells to Kaposi Sarcoma-Associated Herpesvirus-Specific CD4+ T Cell Control and Inhibits vIRF3 Function
Microorganisms exist almost exclusively in interactive multispecies communities , but genetic determinants of the fitness of interacting bacteria , and accessible adaptive pathways , remain uncharacterized . Here , using a two-species system , we studied the antagonism of Pseudomonas aeruginosa against Escherichia coli...	Bacteria commonly exist in nature as part of large multispecies communities , and their behavior is affected by the surrounding species via secreted molecules or physical contact . Such interactions are poorly understood , and the pathways that actually affect bacterial growth and behavior in any multispecies system ha...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Multifactorial Competition and Resistance in a Two-Species Bacterial System
Graded Sonic hedgehog ( Shh ) signaling governs vertebrate limb skeletal patterning along the anteroposterior ( AP ) axis by regulating the activity of bifunctional Gli transcriptional regulators . The genetic networks involved in this patterning are well defined , however , the epigenetic control of the process by chr...	Anteroposterior ( AP ) limb skeletal patterning is directed by morphogen Sonic hedgehog ( Shh ) signaling . Modulation of Shh responsiveness and repression of Shh pathway activity in distinct limb bud regions are essential for proper limb skeletal formation . Although the genetic networks involved in these processes ha...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gene", "regulation", "dna", "transcription", "developmental", "biology", "regulator", "genes", "gene", "types", "epigenetics", "chromatin", "embryology", "limb", "buds", "chromosome", "biology", "gene", "expression", "hedgehog", "signaling", "signal", "transduction", "...	2016	Anteroposterior Limb Skeletal Patterning Requires the Bifunctional Action of SWI/SNF Chromatin Remodeling Complex in Hedgehog Pathway
Coronary heart disease ( CHD ) is the leading cause of mortality in African Americans . To identify common genetic polymorphisms associated with CHD and its risk factors ( LDL- and HDL-cholesterol ( LDL-C and HDL-C ) , hypertension , smoking , and type-2 diabetes ) in individuals of African ancestry , we performed a ge...	To date , most large-scale genome-wide association studies ( GWAS ) carried out to identify risk factors for complex human diseases and traits have focused on population of European ancestry . It is currently unknown whether the same loci associated with complex diseases and traits in Caucasians will replicate in popul...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/complex", "traits", "cardiovascular", "disorders/hypertension", "genetics", "and", "genomics/population", "genetics", "cardiovascular", "disorders/coronary", "artery", "disease", "cardiovascular", "disorders/myocardial", "infarction", "diabetes", "and...	2011	Genome-Wide Association Study of Coronary Heart Disease and Its Risk Factors in 8,090 African Americans: The NHLBI CARe Project
Schistosomiasis has been reported in 78 endemic countries and affects 240 million people worldwide . The digenetic parasite Schistosoma mansoni needs fresh water to compete its life cycle . There , it is susceptible to soluble compounds that can affect directly and/or indirectly the parasite’s biology . The cercariae s...	Intestinal schistosomiasis is among the most important parasitic disease caused by helminthes , affecting 67 million people worldwide . Vector and intermediate host of the parasitic worm are fresh water snails . WHO recommends use of molluscicides for control of local transmission . Among those , natural plant extracts...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "emulsions", "schistosoma", "mansoni", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "helminths", "granulomas", "immunology", "tropical", "diseases", "colloids", "parasitic", "dise...	2017	Double impact: natural molluscicide for schistosomiasis vector control also impedes development of Schistosoma mansoni cercariae into adult parasites
The cytosol is the major environment in all bacterial cells . The true physical and dynamical nature of the cytosol solution is not fully understood and here a modeling approach is applied . Using recent and detailed data on metabolite concentrations , we have created a molecular mechanical model of the prokaryotic cyt...	The cytosol is the major cellular environment housing the majority of cellular activity . Although the cytosol is an aqueous environment , it contains high concentrations of ions , metabolites , and proteins , making it very different from dilute aqueous solution , which is frequently used for in vitro biochemistry . R...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "Acknowledgments" ]	[ "biomacromolecule-ligand", "interactions", "molecular", "mechanics", "biochemistry", "molecular", "dynamics", "biochemistry", "simulations", "chemical", "physics", "small", "molecules", "chemical", "biology", "biophysics", "theory", "chemistry", "biology", "computational", "c...	2011	A New View of the Bacterial Cytosol Environment
Surface recognition and penetration are among the most critical plant infection processes in foliar pathogens . In Magnaporthe oryzae , the Pmk1 MAP kinase regulates appressorium formation and penetration . Its orthologs also are known to be required for various plant infection processes in other phytopathogenic fungi ...	The rice blast fungus is a major pathogen of rice and a model for studying fungal-plant interactions . Like many other fungal pathogens , it can recognize physical and chemical signals present on the rice leaf surface and form a highly specialized infection structure known as appressorium . A well conserved signal tran...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/microbial", "growth", "and", "development", "microbiology/cellular", "microbiology", "and", "pathogenesis", "cell", "biology/cell", "signaling" ]	2011	Multiple Plant Surface Signals are Sensed by Different Mechanisms in the Rice Blast Fungus for Appressorium Formation
Metarhizium spp . are being used as environmentally friendly alternatives to chemical insecticides , as model systems for studying insect-fungus interactions , and as a resource of genes for biotechnology . We present a comparative analysis of the genome sequences of the broad-spectrum insect pathogen Metarhizium aniso...	Aside from playing a crucial role in natural ecosystems , entomopathogenic fungi are being developed as environmentally friendly alternatives for the control of insect pests . We conducted the first genomic study of two of the best characterized entomopathogens , Metarhizium anisopliae and M . acridum . M . anisopliae ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "genetics", "and", "genomics/functional", "genomics", "biotechnology/applied", "microbiology", "cell", "biology/cell", "growth", "and", "division", "microbiology/microbial", "evolution", "and", "genomics...	2011	Genome Sequencing and Comparative Transcriptomics of the Model Entomopathogenic Fungi Metarhizium anisopliae and M. acridum
Insulin/insulin-like growth factor signaling ( IIS ) plays a pivotal role in the regulation of growth at the cellular and the organismal level during animal development . Flies with impaired IIS are developmentally delayed and small due to fewer and smaller cells . In the search for new growth-promoting genes , we iden...	The regulation of growth is among the most fundamental processes during development of multicellular organisms . Research over the past years has established a key function of the insulin/insulin-like growth factor signaling ( IIS ) pathway in ensuring proper growth at the cellular and the organismal level . Impaired I...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/animal", "genetics", "genetics", "and", "genomics/gene", "discovery", "developmental", "biology/morphogenesis", "and", "cell", "biology", "physiology/cell", "signaling", "genetics", "and", "genomics/gene", "function", "developmental", "biology/mol...	2009	The Drosophila SH2B Family Adaptor Lnk Acts in Parallel to Chico in the Insulin Signaling Pathway
ELISA-based methods of detecting Fasciola cathepsins in feces are powerful techniques for diagnosing infections by F . hepatica and F . gigantica . In the last decade , the in-house MM3-COPRO ELISA and its commercial version BIO K 201 ( BIO X Diagnostics , Belgium ) have been recognized as useful tools for detecting ea...	We have previously reported how the combined use of mAb MM3 with polyclonal antibodies obtained from rabbit immunized with Fasciola hepatica excretory-secretory antigens led to the development of the in-house MM3-COPRO ELISA and its commercial version BIO K 201 ( BIO X Diagnostics , Belgium ) , which are widely used to...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "invertebrates", "livestock", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "immune", "physiology", "ruminants", "distillation", "immunology", "vertebrates", "parasitic", "diseases", "animals", "mammals", "nematode", "infections", "trematodes", "...	2016	Rapid Enhanced MM3-COPRO ELISA for Detection of Fasciola Coproantigens
Bronchodilator response ( BDR ) is an important asthma phenotype that measures reversibility of airway obstruction by comparing lung function ( i . e . FEV1 ) before and after the administration of a short-acting β2-agonist , the most common rescue medications used for the treatment of asthma . BDR also serves as a tes...	Bronchodilator response ( BDR ) is an important asthma phenotype that measures reversibility of airway obstruction by comparing lung function before and after the administration of short-acting β2-agonists , common medications used for asthma treatment . We performed a genome-wide association study of BDR with 1 , 644 ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "medicine", "genetic", "association", "studies", "genetics", "genetics", "and", "genomics", "biology", "human", "genetics", "respiratory", "medicine", "genetics", "of", "disease", "pulmonology", "asthma" ]	2012	Genome-Wide Association Analysis in Asthma Subjects Identifies SPATS2L as a Novel Bronchodilator Response Gene
Normal embryonic development and tissue homeostasis require precise levels of retinoic acid ( RA ) signaling . Despite the importance of appropriate embryonic RA signaling levels , the mechanisms underlying congenital defects due to perturbations of RA signaling are not completely understood . Here , we report that zeb...	Retinoic acid ( RA ) is the most active metabolic product of Vitamin A . Appropriate levels of RA are required for proper embryonic development and tissue maintenance in all vertebrates . Inappropriate levels of RA in human embryos can cause congenital defects that affect many organs , including the heart and limbs , a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "And", "Methods" ]	[ "teratology", "cell", "differentiation", "animal", "models", "developmental", "biology", "model", "organisms", "organism", "development", "molecular", "development", "molecular", "genetics", "pattern", "formation", "embryology", "gene", "expression", "nuclear", "receptor", ...	2013	Depletion of Retinoic Acid Receptors Initiates a Novel Positive Feedback Mechanism that Promotes Teratogenic Increases in Retinoic Acid
The role of long non-coding RNA ( lncRNA ) in the progression of Nasopharyngeal carcinoma ( NPC ) has not been fully elucidated . The study was designed to explore the functional role of NKILA , a newly identified lncRNA , in the progression of NPC . We performed a lncRNA expression profile microarray using four NPC an...	NF-κB is a pivotal link between NPC and inflammation . Importantly , NF-κB was found to be overexpressed in nearly all NPC tissues , and inflammatory cytokines have also been observed in NPC tissues . Inflammatory cytokines promote the susceptibility of NPC cells to metastasize via constant NF-κB activation . Here , we...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "phosphorylation", "cell", "death", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "carcinomas", "immunology", "cancers", "and", "neoplasms", "basic", "cancer", ...	2019	NKILA represses nasopharyngeal carcinoma carcinogenesis and metastasis by NF-κB pathway inhibition
Hybridization and gene flow between species appears to be common . Even though it is clear that hybridization is widespread across all surveyed taxonomic groups , the magnitude and consequences of introgression are still largely unknown . Thus it is crucial to develop the statistical machinery required to uncover which...	Understanding the extent to which species or diverged populations hybridize in nature is crucially important if we are to understand the speciation process . Accordingly numerous research groups have developed methodology for finding the genetic evidence of such introgression . In this report we develop a supervised ma...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "and", "discussion" ]	[ "invertebrates", "population", "genetics", "invertebrate", "genomics", "animals", "genetic", "mapping", "artificial", "intelligence", "population", "biology", "drosophila", "computer", "and", "information", "sciences", "introgression", "animal", "genomics", "insects", "arth...	2018	Supervised machine learning reveals introgressed loci in the genomes of Drosophila simulans and D. sechellia
Plague , caused by Yersinia pestis , was classified as a reemerging infectious disease by the World Health Organization . The five human pneumonic plague cases in Yulong County in 2005 gave rise to the discovery of a Yulong plague focus in Yunnan province , China . Thereafter , continuous wild rodent plague ( sylvatic ...	Plague is a type of zoonosis that is highly lethal to humans . The surveillance of animal hosts is critical for the prevention and control of plague . The Yulong plague focus is a newly discovered plague focus in China in recent years . The plague outbreak had attracted widespread attention because 5 people were infect...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "taxonomy", "medicine", "and", "health", "sciences", "plagues", "pathology", "and", "laboratory", "medicine", "china", "pathogens", "geographical", "locations", "microbiology", "vertebrates", "animals", "mammals", "animal", "phylogenetics", "bacterial", "diseases", "phylo...	2018	Ten years of surveillance of the Yulong plague focus in China and the molecular typing and source tracing of the isolates
Success rates for catheter ablation of persistent atrial fibrillation patients are currently low; however , there is a subset of patients for whom electrical isolation of the pulmonary veins alone is a successful treatment strategy . It is difficult to identify these patients because there are a multitude of factors af...	Atrial fibrillation is the most commonly encountered cardiac arrhythmia , affecting a significant portion of the population . Currently , ablation is the most effective treatment but success rates are less than optimal , being 70% one-year post-treatment . There is a large effort to find better ablation strategies to p...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "engineering", "and", "technology", "cardiovascular", "anatomy", "fibrosis", "electrophysiology", "endocardium", "simulation", "and", "modeling", "developmental", "biology", "epicardium", "research", "and", "analysis", "methods", "...	2018	Variability in pulmonary vein electrophysiology and fibrosis determines arrhythmia susceptibility and dynamics
In 2014 , a major epidemic of human Ebola virus disease emerged in West Africa , where human-to-human transmission has now been sustained for greater than 12 months . In the summer of 2014 , there was great uncertainty about the answers to several key policy questions concerning the path to containment . What is the re...	There is considerable uncertainty regarding the steps needed to contain the ongoing Ebola crisis in West Africa , the timeline required to achieve control , and the projected burden of mortality . To address these issues , we develop a branching process model for Ebola transmission that focuses on offspring distributio...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Ebola Cases and Health System Demand in Liberia
The pathogenesis of persistent infection is dictated by the balance between opposing immune activation and suppression signals . Herein , virulent Salmonella was used to explore the role and potential importance of Foxp3-expressing regulatory T cells in dictating the natural progression of persistent bacterial infectio...	The balance between immune activation and suppression is intricately controlled allowing optimal host defense against infection , while simultaneously minimizing collateral immune-mediated damage to host tissues . Although regulatory T cells have been implicated to play critical roles in sustaining this balance , their...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/cellular", "microbiology", "and", "pathogenesis", "immunology/immunity", "to", "infections", "infectious", "diseases/bacterial", "infections" ]	2010	Regulatory T Cell Suppressive Potency Dictates the Balance between Bacterial Proliferation and Clearance during Persistent Salmonella Infection
Single amino acid repeats are prevalent in eukaryote organisms , although the role of many such sequences is still poorly understood . We have performed a comprehensive analysis of the proteins containing homopolymeric histidine tracts in the human genome and identified 86 human proteins that contain stretches of five ...	Single amino acid repeats are common in eukaryotic proteins . Some of them are associated with developmental and neurodegenerative disorders in humans , suggesting that they play important functions . However , the role of many of these repeats is unknown . Here , we have studied histidine repeats from a bioinformatics...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/sequence", "motif", "analysis", "cell", "biology/nuclear", "structure", "and", "function", "genetics", "and", "genomics/functional", "genomics", "genetics", "and", "genomics/nuclear", "structure", "and", "function", "biochemistry/bioinformatics", "co...	2009	Genome-Wide Analysis of Histidine Repeats Reveals Their Role in the Localization of Human Proteins to the Nuclear Speckles Compartment
Dengue is an increasing public health concern in Brazil . There is a need for an updated evaluation of the economic impact of dengue within the country . We undertook this multicenter study to evaluate the economic burden of dengue in Brazil . We estimated the economic burden of dengue in Brazil for the years 2009 to 2...	The World Health Organization estimates that 50–100 million dengue infections occur annually . However , estimates based on cartographic modeling approaches suggest that up to 390 million dengue infections annually . Dengue has become an increasing public health concern in the Americas . A substantial number of cases i...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Economic Impact of Dengue: Multicenter Study across Four Brazilian Regions
Pairwise maximum-entropy models have been used in neuroscience to predict the activity of neuronal populations , given only the time-averaged correlations of the neuron activities . This paper provides evidence that the pairwise model , applied to experimental recordings , would produce a bimodal distribution for the p...	Networks of interacting units are ubiquitous in various fields of biology; e . g . gene regulatory networks , neuronal networks , social structures . If a limited set of observables is accessible , maximum-entropy models provide a way to construct a statistical model for such networks , under particular assumptions . T...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "statistical", "mechanics", "neural", "networks", "vertebrates", "neuroscience", "animals", "mammals", "primates", "probability", "distribution", "mathematics", "statistics", "(mathematics)", "thermodynamics", "old", "world", "monkeys", "computer", "and", "information", "sc...	2017	Bistability, non-ergodicity, and inhibition in pairwise maximum-entropy models
Mali is endemic for all five targeted major neglected tropical diseases ( NTDs ) . As one of the five ‘fast-track’ countries supported with the United States Agency for International Development ( USAID ) funds , Mali started to integrate the activities of existing disease-specific national control programs on these di...	Neglected tropical diseases ( NTDs ) are a group of chronic infections that affect the poorest group of the populations in the world . There are currently five major NTDs targeted through mass drug treatment in the affected communities . The drug delivery can be integrated to deliver different drug packages as these NT...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "neglected", "tropical", "diseases", "parasitic", "diseases" ]	2012	Implementing Preventive Chemotherapy through an Integrated National Neglected Tropical Disease Control Program in Mali
As the Global Programme to Eliminate Lymphatic Filariasis ( LF ) approaches its 2020 goal , an increasing number of districts will enter the endgame phase where drug coverage rates from mass drug administration ( MDA ) are used to assess whether MDA can be stopped . As reported , the gap between reported and actual dru...	This research describes the process used to assist two districts endemic for lymphatic filariasis ( LF ) in Indonesia to better understand the reasons why their LF elimination programs have had suboptimal results . A novel survey design was used to collect stories about people’s direct experiences with mass drug admini...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "geographical", "locations", "indonesia", "research", "design", "pharmaceutics", "surveys", "pharmacology", "research", "and", "analysis", "methods", "drug", "safety", "drug", "distribution", "drug", "delivery", "pharmacokinetics",...	2016	Improving Coverage and Compliance in Mass Drug Administration for the Elimination of LF in Two ‘Endgame’ Districts in Indonesia Using Micronarrative Surveys
The evolution of degenerate characteristics remains a poorly understood phenomenon . Only recently has the identification of mutations underlying regressive phenotypes become accessible through the use of genetic analyses . Focusing on the Mexican cave tetra Astyanax mexicanus , we describe , here , an analysis of the ...	As we approach the 150th year since publication of On the Origin of Species , understanding the genetic architecture underlying evolutionary change remains an important challenge . When an organism enters a completely new environment or ecological niche , certain traits are no longer necessary for survival , while othe...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "genetics", "and", "genomics", "evolutionary", "biology/animal", "genetics", "developmental", "biology/developmental", "evolution", "ecology/evolutionary", "ecology" ]	2009	A Novel Role for Mc1r in the Parallel Evolution of Depigmentation in Independent Populations of the Cavefish Astyanax mexicanus
The intracellular parasite Theileria is the only eukaryote known to transform its mammalian host cells . We investigated the host mechanisms involved in parasite-induced transformation phenotypes . Tumour progression is a multistep process , yet ‘oncogene addiction’ implies that cancer cell growth and survival can be i...	Theileria is the only intracellular eukaryotic parasite known to transform its host cell into a cancer-like state . Infection by the T . annulata parasite causes tropical theileriosis , killing large numbers of cattle in North Africa and Asia , and the related T . parva parasite causes East Coast Fever . We investigate...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "rna", "rna", "interference", "nucleic", "acids", "microbial", "pathogens", "biology", "microbiology", "molecular", "cell", "biology", "parasitology" ]	2013	OncomiR Addiction Is Generated by a miR-155 Feedback Loop in Theileria-Transformed Leukocytes
The protozoan parasite , Toxoplasma , like many intracellular pathogens , suppresses interferon gamma ( IFN-γ ) -induced signal transducer and activator of transcription 1 ( STAT1 ) activity . We exploited this well-defined host–pathogen interaction as the basis for a high-throughput screen , identifying nine transcrip...	Immune responses are orchestrated by a diverse array of secreted ligands , yet the downstream transcriptional responses are coordinated by a relatively small set of key transcription factors , including nuclear factor kappa B ( NF-κB ) and signal transducers and activators of transcription ( STATs ) . The molecular mec...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Orphan Nuclear Receptor TLX Is an Enhancer of STAT1-Mediated Transcription and Immunity to Toxoplasma gondii
Transcranial brain stimulation and evidence of ephaptic coupling have recently sparked strong interests in understanding the effects of weak electric fields on the dynamics of brain networks and of coupled populations of neurons . The collective dynamics of large neuronal populations can be efficiently studied using si...	How extracellular electric fields—as generated endogenously or through transcranial brain stimulation—affect the dynamics of neuronal populations is of great interest but not well understood . To study neuronal activity at the network level single-compartment neuron models have been proven very successful , because of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "action", "potentials", "medicine", "and", "health", "sciences", "membrane", "potential", "electricity", "voltage", "electrophysiology", "neuroscience", "membrane", "electrophysiology", "electric", "field", "bioassays", "and", "physiological", "analysis", "neuronal", "dendr...	2016	Extending Integrate-and-Fire Model Neurons to Account for the Effects of Weak Electric Fields and Input Filtering Mediated by the Dendrite
Almost one third of herpesvirus proteins are expressed with late kinetics . Many of these late proteins serve crucial structural functions such as formation of virus particles , attachment to host cells and internalization . Recently , we and others identified a group of Epstein-Barr virus early proteins that form a pr...	EBV is an oncogenic virus involved in the development of about 1 . 5% of human cancers worldwide . EBV infection has latent and lytic forms . Both forms of infection contribute to the oncogenic capacity of the virus . During the lytic cycle , a cascade of temporally regulated events takes place leading to release of ne...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "protein", "interactions", "chemical", "compounds", "gene", "regulation", "microbiology", "threonine", "organic", "compounds", "dna", "transcription", "regulator", "genes", "amino", "acids", "gene", "types", "microbial", "genetics", "proteins", "gene", ...	2019	A single phosphoacceptor residue in BGLF3 is essential for transcription of Epstein-Barr virus late genes
Genome-wide association studies have revealed that many low-penetrance breast cancer susceptibility loci are located in non-protein coding genomic regions; however , few have been characterized . In a comparative genetics approach to model such loci in a rat breast cancer model , we previously identified the mammary ca...	Most non-Mendelian disease variants identified through genome-wide association studies are low-penetrance , common in the population and located in non-protein coding genomic loci . It is currently unknown how these loci modulate disease risk . Insights in their mechanisms could lead to the development of novel prevent...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "medicine", "oncology", "developmental", "biology", "genetic", "causes", "of", "cancer", "cancer", "genetics", "model", "organisms", "gene", "regulation", "genetics", "molecular", "genetics", "cancer", "risk", "factors", "biology", "cancer", "preve...	2013	The Gene Desert Mammary Carcinoma Susceptibility Locus Mcs1a Regulates Nr2f1 Modifying Mammary Epithelial Cell Differentiation and Proliferation
The detection of Trypanosoma cruzi genetic material in clinical samples is considered an important diagnostic tool for Chagas disease . We have previously demonstrated that PCR using clot samples yields greater sensitivity than either buffy coat or whole blood samples . However , phenol-chloroform DNA extraction from c...	Detection of nucleic acid has become an important tool for the diagnosis of Chagas disease . Whole blood samples are usually the source of DNA and qPCR the preferred technique to demonstrate the presence of T . cruzi DNA . Although DNA extracted from clot samples has shown higher sensitivity than from whole blood , DNA...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "organisms", "protozoans", "neglected", "tropical", "diseases", "molecular", "biology", "...	2019	Improved DNA extraction technique from clot for the diagnosis of Chagas disease
Nuclear factor of activated T cells ( NFAT ) transcription factors are required for induction of T-cell cytokine production and effector function . Although it is known that activation via the T-cell antigen receptor ( TCR ) results in 2 critical steps , calcineurin-mediated NFAT1 dephosphorylation and NFAT2 up-regulat...	The p38 MAP kinase , which is required for a large number of important biological responses , is activated by an enzymatic cascade that results in its dual phosphorylation on p38T180Y182 . T cells have evolved a unique pathway in which T-cell antigen receptor ( TCR ) ligation results in phosphorylation of p38Y323 ( the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "phosphorylation", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "cytokines", "enzyme-linked", "immunoassays", "immunology", "cloning", "developmental", "biology", "molecular", "developm...	2018	Unique properties of TCR-activated p38 are necessary for NFAT-dependent T-cell activation
Sumoylation regulates a wide range of essential cellular functions through diverse mechanisms that remain to be fully understood . Using S . cerevisiae , a model organism with a single essential SUMO gene ( SMT3 ) , we developed a library of >250 mutant strains with single or multiple amino acid substitutions of surfac...	The Small ubiquitin-related modifier ( SUMO ) is a 100 amino acid protein that is attached to other proteins and thereby regulates nearly all essential cell functions . To explore how this small protein modifier functions to regulate so many different processes , we generated a library of >250 mutant alleles of the SUM...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "chemical", "compounds", "molecular", "mass", "organic", "compounds", "mutation", "fungi", "model", "organisms", "sumoylation", "experimental", "organism", "systems", "basic", "amino", "acids", "amino", "acids", "research", "and", "analysis", "methods...	2017	A high throughput mutagenic analysis of yeast sumo structure and function
Infection with human cytomegalovirus ( HCMV ) is a threat for pregnant women and immunocompromised hosts . Although limited drugs are available , development of new agents against HCMV is desired . Through screening of the LOPAC library , we identified emetine as HCMV inhibitor . Additional studies confirmed its anti-H...	Infection with human Cytomegalovirus ( HCMV ) is a growing and pressing problem , creating ongoing management and therapeutic challenges . Despite the availability of DNA polymerase inhibitors , development of new strategies for HCMV therapy is needed . We report for the first time on the efficacy of an old drug ( emet...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "luciferase", "pathology", "and", "laboratory", "medicine", "molecular", "probe", "techniques", "enzymes", "pathogens", "microbiology", "immunoblotting", "light", "microscopy", "cell", "disruption", "enzymology", "viruses", "immuno...	2016	Efficacy and Mechanism of Action of Low Dose Emetine against Human Cytomegalovirus
Infectious disease surveillance is key to limiting the consequences from infectious pathogens and maintaining animal and public health . Following the detection of a disease outbreak , a response in proportion to the severity of the outbreak is required . It is thus critical to obtain accurate information concerning th...	We have developed a Bayesian approach that can estimate the historic trend of incidence from cross-sectional samples , without relying on ongoing surveillance . This could be used to evaluate changing disease trends , or to inform outbreak responses . We combine two or more diagnostic tests to estimate the time since i...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "animal", "diseases", "pathology", "and", "laboratory", "medicine", "pathogens", "pertussis", "bacterial", "diseases", "infectious", "disease", "control", "zoology", "veterinary", "science", "infectious", "diseases", "veterinary", ...	2016	Using Combined Diagnostic Test Results to Hindcast Trends of Infection from Cross-Sectional Data
Parent-of-origin effects comprise a range of genetic and epigenetic mechanisms of inheritance . Recently , detection of such effects implicated epigenetic mechanisms in the etiology of multiple sclerosis ( MS ) , a chronic inflammatory disease of the central nervous system . We here sought to dissect the magnitude and ...	Even with recent progress in determining the genetic basis of complex diseases , the issue of ‘missing heritability’ remains and its potential sources are frequently speculated about but rarely explained . Parent-of-origin effects might contribute to the ‘missing heritability’ and involve genetic and epigenetic mechani...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "of", "disease", "animal", "genetics", "genetics", "of", "the", "immune", "system", "clinical", "immunology", "heredity", "genetics", "biology", "and", "life", "sciences", "epigenetics", "immunology", "genetic", "linkage", "autoimmunity" ]	2014	Parent-of-Origin Effects Implicate Epigenetic Regulation of Experimental Autoimmune Encephalomyelitis and Identify Imprinted Dlk1 as a Novel Risk Gene
While most of the world is thought to be on long-term economic growth paths , more than one-sixth of the world is roughly as poor today as their ancestors were hundreds of years ago . The majority of the extremely poor live in the tropics . The latitudinal gradient in income is highly suggestive of underlying biophysic...	While most of the world is thought to be growing economically , more than one-sixth of the world is roughly as poor today as their ancestors were hundreds of years ago . The extremely poor live largely in the tropics . This latitudinal gradient in income suggests that there are biophysical factors , such as the burden ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "social", "and", "behavioral", "sciences", "biology" ]	2012	Disease Ecology, Biodiversity, and the Latitudinal Gradient in Income
There remains a lack of epidemiological data on the geographical distribution of trachoma to support global mapping and scale up of interventions for the elimination of trachoma . The Global Atlas of Trachoma ( GAT ) was launched in 2011 to address these needs and provide standardised , updated and accessible maps . Th...	In order to target resources and drugs to reach trachoma elimination targets by the year 2020 , data on the burden of disease are required . Using prevalence data in African countries derived from the Global Atlas of Trachoma ( GAT ) , the distribution of trachoma continues to be focused in East and West Sub-Saharan Af...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "disease", "mapping", "global", "health", "epidemiology", "neglected", "tropical", "diseases", "trachoma", "public", "health" ]	2013	The Geographical Distribution and Burden of Trachoma in Africa
p53 can serve as a paradigm in studies aiming to figure out how allosteric perturbations in transcription factors ( TFs ) triggered by small changes in DNA response element ( RE ) sequences , can spell selectivity in co-factor recruitment . p53-REs are 20-base pair ( bp ) DNA segments specifying diverse functions . The...	p53-response elements ( p53-REs ) are 20 base pairs ( bps ) DNA segments recognized by the p53 transcription factor ( TF ) . They are found in promoters and enhancers across the genome and are associated with genes that have diverse functions . Because the DNA sequences of p53-REs can be very similar to each other , di...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/transcriptional", "regulation", "cell", "biology", "biochemistry/bioinformatics", "computational", "biology", "biophysics", "computational", "biology/molecular", "dynamics" ]	2010	Lysine120 Interactions with p53 Response Elements can Allosterically Direct p53 Organization
Commissural axons must cross the midline to establish reciprocal connections between the two sides of the body . This process is highly conserved between invertebrates and vertebrates and depends on guidance cues and their receptors to instruct axon trajectories . The DCC family receptor Frazzled ( Fra ) signals chemoa...	The establishment of neuronal connections that cross the midline of the animal is essential to generate neural circuits that coordinate the left and right sides of the body . Axons that cross the midline to form these connections are called commissural axons and the molecules and mechanisms that control midline axon cr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "microtubules", "vertebrates", "neuroscience", "animals", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "raptors", "model", "organisms", "experimental", "organism", "systems", "nerve", "fibers", "embryos", "cellular", "struct...	2018	Brain Tumor promotes axon growth across the midline through interactions with the microtubule stabilizing protein Apc2
We report the results of an investigation of a small outbreak of hantavirus pulmonary syndrome in 2002 in the Department of Santa Cruz , Bolivia , where the disease had not previously been reported . Two cases were initially reported . The first case was a physician infected with Laguna Negra virus during a weekend vis...	Hantaviruses can evoke a severe , acute disease in humans known as hantavirus pulmonary syndrome with case fatalities up to 70% . Pathogenic hantaviruses are carried by rodents , with each virus species usually carried by a specific species of rodent . Hantavirus-host reservoir pairs continue to be discovered and detai...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "epidemiology", "biology", "microbiology", "public", "health" ]	2012	Hantavirus Pulmonary Syndrome in Santa Cruz, Bolivia: Outbreak Investigation and Antibody Prevalence Study
Helical cell shape of the gastric pathogen Helicobacter pylori has been suggested to promote virulence through viscosity-dependent enhancement of swimming velocity . However , H . pylori csd1 mutants , which are curved but lack helical twist , show normal velocity in viscous polymer solutions and the reason for their d...	The only habitat of Helicobacter pylori is the human stomach , where it can promote stomach ulcers and cancer . Cells lining the stomach are protected from luminal acid by a thick layer of gastric mucus composed of polymerized gastric mucins . Gastric mucin undergoes a physical transition between a viscoelastic solutio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "gastroenterology", "and", "hepatology", "biology", "microbiology" ]	2012	Multiple Peptidoglycan Modification Networks Modulate Helicobacter pylori's Cell Shape, Motility, and Colonization Potential
Plasmodium falciparum–infected erythrocytes bind endothelial receptors to sequester in vascular beds , and binding to ICAM1 has been implicated in cerebral malaria . Binding to ICAM1 may be mediated by the variant surface antigen family PfEMP1: for example , 6 of 21 DBLβC2 domains from the IT4 strain PfEMP1 repertoire ...	Plasmodium falciparum exports the protein PfEMP1 to the surface of parasitized erythrocytes for roles in immunoevasion and adhesion . The size and structural complexity of this diverse protein family have limited earlier studies of PfEMP1 biology to low throughput and semi-quantitative approaches . We developed a high ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/tropical", "and", "travel-associated", "diseases", "biophysics/protein", "folding", "infectious", "diseases/neglected", "tropical", "diseases", "immunology/immune", "response", "biochemistry/biomacromolecule-ligand", "interactions", "microbiology/parasitology", ...	2009	High Throughput Functional Assays of the Variant Antigen PfEMP1 Reveal a Single Domain in the 3D7 Plasmodium falciparum Genome that Binds ICAM1 with High Affinity and Is Targeted by Naturally Acquired Neutralizing Antibodies
Object perception is inherently multidimensional: information about color , material , texture and shape all guide how we interact with objects . We developed a paradigm that quantifies how two object properties ( color and material ) combine in object selection . On each experimental trial , observers viewed three blo...	Much is known about how the visual system extracts information about individual object properties , such as color or material . Considerably less is known about how percepts of these properties interact to form a multidimensional object representation . We report the first quantitative analysis of how perceived color a...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "infographics", "physical", "mapping", "statistics", "social", "sciences", "neuroscience", "charts", "perception", "cognitive", "psychology", "mathematics", "materials", "science", "vision", "molecular", "biology", "techniques", "research", "and", "analysis", "methods", "...	2019	The relative contribution of color and material in object selection
Understanding the molecular pathways by which oncogenes drive cancerous cell growth , and how dependence on such pathways varies between tumors could be highly valuable for the design of anti-cancer treatment strategies . In this work we study how dependence upon the canonical PI3K and MAPK cascades varies across HER2+...	Biomarkers capable of accurately predicting patient responses to alternate therapies are critical to realizing the vision of precision medicine . Identifying such biomarkers is , however , challenging due to the inherent complexity of biological networks . Here we sought to identify molecular features that predict how ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "death", "medicine", "and", "health", "sciences", "breast", "tumors", "cancer", "treatment", "cell", "processes", "cancers", "and", "neoplasms", "biomarkers", "oncology", "protein", "expression", "cell", "growth", "molecular", "biology", "techniques", "mapk", ...	2016	HER2+ Cancer Cell Dependence on PI3K vs. MAPK Signaling Axes Is Determined by Expression of EGFR, ERBB3 and CDKN1B
The transition from vegetative to reproductive growth is a critical process in the life cycle of higher plants . Previously , we cloned Rice Indeterminate 1 ( RID1 ) , which acts as the master switch for the transition from the vegetative to reproductive phase in rice . Although the photoperiod pathway of RID1 inducing...	Transition from vegetative to reproductive phase is a critical developmental switch in the life cycle of higher plants . In rice , our previous work suggested Rice Indeterminate 1 ( RID1 ) acts as the master switch for the transition to flowering . Mutation in RID1 results in a never-flowering phenotype . In order to u...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "biotechnology", "plant", "anatomy", "dna-binding", "proteins", "plant", "science", "rice", "genetically", "modified", "plants", "experimental", "organism", "systems", "sequence", "motif", "analysis", "molecular", "biology", "techniques", "plants", "flowering", "plants", ...	2017	Suppressor of rid1 (SID1) shares common targets with RID1 on florigen genes to initiate floral transition in rice
With the goal to identify novel trypanothione reductase ( TR ) inhibitors , we performed a combination of in vitro and in silico screening approaches . Starting from a highly diverse compound set of 2 , 816 compounds , 21 novel TR inhibiting compounds could be identified in the initial in vitro screening campaign again...	Trypanosomatidae are responsible for approximately half a million human fatalities per annum and the situation is compounded by substantial economic losses due to affecting live stock as well . Trypanothione reductase ( TR ) is an essential key enzyme of the unique trypanothione-based thiol metabolism of the trypanosom...	[ "Abstract", "Introduction", "Material", "and", "Methods", "Results", "and", "Discussion" ]	[]	2015	Trypanothione Reductase: A Target Protein for a Combined In Vitro and In Silico Screening Approach

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