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Since its first detection in the Caribbean in late 2013 , chikungunya virus ( CHIKV ) has affected 51 countries in the Americas . The CHIKV epidemic in the Americas was caused by the CHIKV-Asian genotype . In August 2014 , local transmission of the CHIKV-Asian genotype was detected in the Brazilian Amazon region . Howe...	Until the end of 2017 , Brazil notified the highest number of infections caused by chikungunya virus ( CHIKV ) in the Americas . We investigated a large CHIKV outbreak in Boa vista municipality in the Brazilian Amazon region . Rapid portable genome sequencing of 20 novel isolates and subsequent genetic analysis reveale...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "sequencing", "techniques", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "togaviruses", "chikungunya", "infection", "pathogens", "geographical", "locations", "microbiology", "tropical", "diseases", "alphaviruses", "viruses", "genome...	2019	Genomic, epidemiological and digital surveillance of Chikungunya virus in the Brazilian Amazon
Cytomegaloviruses ( CMVs ) have a highly restricted host range as they replicate only in cells of their own or closely related species . To date , the molecular mechanisms underlying the CMV host restriction remain poorly understood . However , it has been shown that mouse cytomegalovirus ( MCMV ) can be adapted to hum...	Human CMV is an opportunistic pathogen causing morbidity and mortality in immunocompromised individuals . It is a highly species-specific virus that replicates only in cells from humans or chimpanzees , but not in cells from mice or other laboratory animals . Mouse cytomegalovirus ( MCMV ) , the most commonly used mode...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "pathogens", "regulatory", "proteins", "cell", "processes", "cell", "cycle", "and", "cell", "division", "microbiology", "dna-binding", "proteins", "dna", "tran...	2018	Activation of E2F-dependent transcription by the mouse cytomegalovirus M117 protein affects the viral host range
Antiretroviral therapy , antibody and CD8+ T cell-mediated responses targeting human immunodeficiency virus-1 ( HIV-1 ) exert selection pressure on the virus necessitating escape; however , the ability of CD4+ T cells to exert selective pressure remains unclear . Using a computational approach on HIV gag/pol/nef sequen...	In HIV , CD4+ T cells are best known as the primary targets of infection . Although emerging data has suggested a more active role in viral pathogenesis , the CD4+ T cell population remains relatively understudied . Using a novel computational approach , we predicted 29 different epitopes with mutations that potentiall...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	HLA Class-II Associated HIV Polymorphisms Predict Escape from CD4+ T Cell Responses
Rift Valley fever ( RVF ) is a severe mosquito-borne disease affecting humans and domestic ruminants . Mosquito saliva contains compounds that counteract the hemostatic , inflammatory , and immune responses of the host . Modulation of these defensive responses may facilitate virus infection . Indeed , Aedes mosquito sa...	Rift Valley fever is an endemic and epidemic zoonosis in Africa and the Arabic Peninsula . In humans , in the most severe cases the viral infection causes fulminant hepatitis associated with haemorrhagic fever , permanent blindness or severe encephalitis . Despite the importance of vector transmission in the spread of ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "clinical", "immunology" ]	2013	Aedes Mosquito Saliva Modulates Rift Valley Fever Virus Pathogenicity
We study inter-trial movement fluctuations exhibited by human participants during the repeated execution of a virtual shuffleboard task . Focusing on skilled performance , theoretical analysis of a previously-developed general model of inter-trial error correction is used to predict the temporal and geometric structure...	During the repeated execution of precision movement tasks , humans face two formidable challenges from the motor system itself: dimensionality and noise . Human motor performance involves biomechanical , neuromotor , and perceptual degrees of freedom far in excess of those theoretically needed to prescribe typical goal...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "velocity", "medicine", "and", "health", "sciences", "tangents", "classical", "mechanics", "engineering", "and", "technology", "signal", "processing", "condensed", "matter", "physics", "anisotropy", "geometry", "autocorrelation", "regression", "analysis", "mathematics", "...	2016	Error Correction and the Structure of Inter-Trial Fluctuations in a Redundant Movement Task
Studies have demonstrated cross-reactivity of anti-dengue virus ( DENV ) antibodies in human sera against Zika virus ( ZIKV ) , promoting increased ZIKV infection in vitro . However , the correlation between in vitro and in vivo findings is not well characterized . Thus , we evaluated the impact of heterotypic flavivir...	Zika virus ( ZIKV ) is a mosquito-borne , emerging flavivirus . In addition to asymptomatic or mild febrile manifestations , ZIKV infection in humans is associated with comparatively rare congenital and neurological abnormalities . Previous in vitro studies have demonstrated cross-reactivity of antibodies derived from ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "body", "fluids", "pathogens", "immunology", "microbiology", "vertebrates", "cloning", "animals", "mammals", "viruses", "primate...	2017	Impact of prior flavivirus immunity on Zika virus infection in rhesus macaques
The cardiac muscarinic receptor ( M2R ) regulates heart rate , in part , by modulating the acetylcholine ( ACh ) activated K+ current IK , ACh through dissociation of G-proteins , that in turn activate KACh channels . Recently , M2Rs were noted to exhibit intrinsic voltage sensitivity , i . e . their affinity for ligan...	Heart rate regulation is dependent upon a delicate interplay between parasympathetic and sympathetic nerve activity at the level of the sinus node . Acetylcholine slows the heart rate by activating the M2 muscarinic receptor ( M2R ) that , in turn , opens the acetylcholine-activated potassium channel ( IK , ACh ) to sl...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "ion", "channel", "gating", "medicine", "and", "health", "sciences", "action", "potentials", "markov", "models", "depolarization", "membrane", "potential", "electrophysiology", "neuroscience", "simulation", "and", "modeling", "ion", "channels", "mathematics", "cardiology"...	2018	Modeling effects of voltage dependent properties of the cardiac muscarinic receptor on human sinus node function
Lung disease is regularly reported in human filarial infections but the molecular pathogenesis of pulmonary filariasis is poorly understood . We used Litomosoides sigmodontis , a rodent filaria residing in the pleural cavity responsible for pleural inflammation , to model responses to human filarial infections and prob...	Filarial infections are tropical diseases caused by nematodes of the Onchocercidae family . Infections due to filariae regularly induce pulmonary manifestations , however lung pathogenesis of human filarial infections is poorly understood . Litomosoides sigmodontis is a rodent filaria living in the pleural cavity and r...	[ "Abstract", "Introduction", "Material", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "body", "fluids", "pathology", "and", "laboratory", "medicine", "diagnostic", "radiology", "immune", "physiology", "cytokines", "immunology", "pleurae", "develo...	2019	IL-4 receptor dependent expansion of lung CD169+ macrophages in microfilaria-driven inflammation
Mathematical and computer models of epidemics have contributed to our understanding of the spread of infectious disease and the measures needed to contain or mitigate them . To help prepare for future influenza seasonal epidemics or pandemics , we developed a new stochastic model of the spread of influenza across a lar...	Computer simulations can provide valuable information to communities preparing for epidemics . These simulations can be used to investigate the effectiveness of various intervention strategies in reducing or delaying the peak of an epidemic . We have made a detailed influenza epidemic simulator for the United States pu...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology/epidemiology", "public", "health", "and", "epidemiology/infectious", "diseases", "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases", "computational", "biology" ]	2010	FluTE, a Publicly Available Stochastic Influenza Epidemic Simulation Model
Arsenic is a well-established human carcinogen of poorly understood mechanism of genotoxicity . It is generally accepted that arsenic acts indirectly by generating oxidative DNA damage that can be converted to replication-dependent DNA double-strand breaks ( DSBs ) , as well as by interfering with DNA repair pathways a...	Arsenic is a highly toxic compound which causes several types of cancer in humans . However , precise mechanisms of arsenic carcinogenesis remain elusive and are still a matter of debate . For example , the oxidative stress theory of arsenic proposes that arsenic generates reactive oxygen species producing oxidative DN...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mutagenesis", "cellular", "stress", "responses", "cancer", "genetics", "genetic", "mutation", "model", "organisms", "mutation", "types", "genetics", "yeast", "and", "fungal", "models", "biology", "saccharomyces", "cerevisiae", "molecular", "cell", "biology" ]	2013	Oxidative Stress and Replication-Independent DNA Breakage Induced by Arsenic in Saccharomyces cerevisiae
Dengue is one of the most widespread mosquito-borne diseases in the world . The causative agent , dengue virus ( DENV ) , is primarily transmitted by the mosquito Aedes aegypti , a species that has proved difficult to control using conventional methods . The discovery that A . aegypti transinfected with the wMel strain...	Almost half of the world's population is at risk of contracting dengue virus , particularly in the tropics and sub-tropics . The virus is transmitted by the mosquito Aedes aegypti , a cosmopolitan species that has proved difficult to control using traditional methods . A new biocontrol strategy has been developed invol...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "dengue", "fever", "neglected", "tropical", "diseases", "arboviral", "infections", "infectious", "disease", "control", "vectors", "and", "hosts" ]	2014	Limited Dengue Virus Replication in Field-Collected Aedes aegypti Mosquitoes Infected with Wolbachia
The MRX complex together with Sae2 initiates resection of DNA double-strand breaks ( DSBs ) to generate single-stranded DNA ( ssDNA ) that triggers homologous recombination . The absence of Sae2 not only impairs DSB resection , but also causes prolonged MRX binding at the DSBs that leads to persistent Tel1- and Rad53-d...	Genome instability is one of the most pervasive characteristics of cancer cells and can be due to DNA repair defects and failure to arrest the cell cycle . Among the many types of DNA damage , the DNA double strand break ( DSB ) is one of the most severe , because it can cause mutations and chromosomal rearrangements ....	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Sae2 Function at DNA Double-Strand Breaks Is Bypassed by Dampening Tel1 or Rad53 Activity
Persistent human papillomavirus ( HPV ) infection is the leading cause of cervical cancer . Although the fundamental link between HPV infection and oncogenesis is established , the specific mechanisms of virus-mediated transformation are not fully understood . We previously demonstrated that the HPV encoded E6 protein ...	Persistent infection with HPV is the predominant cause of anogenital and oral cancers . Transformation requires the re-wiring of signalling pathways in infected cells by virus encoded oncoproteins . At this point , a comprehensive understanding of the full range of host pathways necessary for HPV-mediated carcinogenesi...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "and", "materials" ]	[ "phosphorylation", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "hela", "cells", "cervical", "cancer", "pathogens", "gene", "regulation", "biological", "cultures", "cancers", "and", "neoplasms", ...	2019	Autocrine STAT3 activation in HPV positive cervical cancer through a virus-driven Rac1—NFκB—IL-6 signalling axis
The genetic model plant Arabidopsis thaliana , like many plant species , experiences a range of edaphic conditions across its natural habitat . Such heterogeneity may drive local adaptation , though the molecular genetic basis remains elusive . Here , we describe a study in which we used genome-wide association mapping...	The unusual geographical distribution of certain animal and plant species has provided puzzling questions to the scientific community regarding the interrelationship of evolutionary and geographic histories for generations . With DNA sequencing , such puzzles have now extended to the geographical distribution of geneti...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/functional", "genomics", "plant", "biology/plant-environment", "interactions", "evolutionary", "biology/plant", "genetics", "and", "gene", "expression", "ecology/spatial", "and", "landscape", "ecology", "plant", "biology/plant", "genetics", "and",...	2010	A Coastal Cline in Sodium Accumulation in Arabidopsis thaliana Is Driven by Natural Variation of the Sodium Transporter AtHKT1;1
Genetic exchange is a powerful tool to study gene function in microorganisms . Here , we tested the feasibility of generating Leishmania hybrids by electroporating genomic DNA of donor cells into recipient Leishmania parasites . The donor DNA was marked with a drug resistance marker facilitating the selection of DNA tr...	Leishmania spp . are pathogenic protozoa characterized by a substantial diversity in pathogenesis and virulence despite their considerable synteny at the genome level . The existence of genetic exchange was recently proven experimentally in the sand fly vector where hybrid parasites were isolated and generated . Here ,...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "molecular", "cell", "biology", "leishmaniasis", "biology", "microbiology", "parasitic", "diseases", "parasitology" ]	2012	Generation of Leishmania Hybrids by Whole Genomic DNA Transformation
Confirmatory diagnosis of visceral leishmaniasis ( VL ) , as well as diagnosis of relapses and test of cure , usually requires examination by microscopy of samples collected by invasive means , such as splenic , bone marrow or lymph node aspirates . This causes discomfort to patients , with risks of bleeding and iatrog...	Tissue aspiration , either from spleen , bone marrow or lymph node , remains the Gold Standard for parasitological confirmation in patients suspected of visceral leishmaniasis ( VL ) , and is often used for detection of relapses , and as a test of cure . The procedure is invasive , with risks of severe complications , ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "kala-azar", "medicine", "and", "health", "sciences", "body", "fluids", "immune", "physiology", "immunology", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "lymph", "nodes", "protozoans", "leishmania", "lymphatic", "system", "neglected", "t...	2018	Sensitive and less invasive confirmatory diagnosis of visceral leishmaniasis in Sudan using loop-mediated isothermal amplification (LAMP)
Human cystic and alveolar echinococcosis are helmintic zoonotic diseases caused by infections with the larval stages of the cestode parasites Echinococcus granulosus and E . multilocularis , respectively . Both diseases are progressive and chronic , and often fatal if left unattended for E . multilocularis . As a treat...	Human cystic and alveolar echinococcosis ( CE and AE ) , caused by the larval stages of the helminths Echinococcus granulosus and E . multilocularis , respectively , are progressive and chronic diseases affecting more than 1 million people worldwide . Both are considered orphan and neglected diseases by the World Healt...	[ "Abstract", "Introduction" ]	[ "medicine", "and", "health", "sciences", "vesicles", "tropical", "diseases", "parasitic", "diseases", "animal", "models", "routes", "of", "administration", "model", "organisms", "pharmaceutics", "experimental", "organism", "systems", "drug", "administration", "neglected",...	2018	Progress in the pharmacological treatment of human cystic and alveolar echinococcosis: Compounds and therapeutic targets
Cryptosporidium parvum is a protozoan parasite that infects the gastrointestinal epithelium and causes diarrheal disease worldwide . Innate epithelial immune responses are key mediators of the host's defense to C . parvum . MicroRNAs ( miRNAs ) regulate gene expression at the posttranscriptional level and are involved ...	MicroRNAs ( miRNAs ) are newly identified small non-coding RNAs that regulate gene expression at the posttranscriptional level . While much of our understanding of the cellular processes modulated by miRNAs has come from studies on development and tumorigenesis , the role of miRNAs in immune responses is now being grad...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/cellular", "microbiology", "and", "pathogenesis", "immunology/immune", "response", "gastroenterology", "and", "hepatology/biliary", "tract", "immunology/innate", "immunity", "microbiology/innate", "immunity", "infectious", "diseases/protozoal", "infections", "immunology...	2009	NF-kappaB p65-Dependent Transactivation of miRNA Genes following Cryptosporidium parvum Infection Stimulates Epithelial Cell Immune Responses
During lytic Kaposi’s sarcoma-associated herpesvirus ( KSHV ) infection , the viral endonuclease SOX promotes widespread degradation of cytoplasmic messenger RNA ( mRNA ) . However , select mRNAs escape SOX-induced cleavage and remain robustly expressed . Prominent among these is interleukin-6 ( IL-6 ) , a growth facto...	During replication of Kaposi’s sarcoma-associated herpesvirus ( KSHV ) , the vast majority of mRNAs in the cytoplasm are cleaved and degraded by the viral nuclease SOX . However , some mRNAs escape this fate , including the transcript encoding the immunoregulatory cytokine IL-6 . Here , we discover that this escape is ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	A Ribonucleoprotein Complex Protects the Interleukin-6 mRNA from Degradation by Distinct Herpesviral Endonucleases
Epigenetic variation , such as heritable changes of DNA methylation , can affect gene expression and thus phenotypes , but examples of natural epimutations are few and little is known about their stability and frequency in nature . Here , we report that the gene Qua-Quine Starch ( QQS ) of Arabidopsis thaliana , which ...	Epigenetics is defined as the study of heritable changes in gene expression that are not linked to changes in the DNA sequence . In plants , these heritable variations are often associated with differences in DNA methylation . So far , very little is known about the extent and stability of epigenetic variation in natur...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "science", "plant", "evolution", "genetics", "plant", "genetics", "population", "genetics", "epigenetics", "biology", "dna", "modification", "evolutionary", "biology" ]	2013	Extensive Natural Epigenetic Variation at a De Novo Originated Gene
The detailed assessment of nematode activity and viability still remains a relatively undeveloped area of biological and medical research . Computer-based approaches to assessing the motility of larger nematode stages have been developed , yet these lack the capability to detect and analyze the more subtle and importan...	Assessment of the health and number of nematodes still relies heavily on subjective monitoring of their motion . Although less-subjective techniques exist that utilize the motility as the primary indicator , the current approaches tend to be designed for use with larger worms and not for early developmental stages . We...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Analysis of Nematode Motion Using an Improved Light-Scatter Based System
Although T cells are critical for host defense against respiratory fungal infections , they also contribute to the immunopathogenesis of Pneumocystis pneumonia ( PcP ) . However , the precise downstream effector mechanisms by which T cells mediate these diverse processes are undefined . In the current study the effects...	Pneumocystis is a fungal respiratory pathogen that causes life-threatening pneumonia ( PcP ) in immunosuppressed patients . PcP remains an infectious complication of AIDS and cancer , and is emerging in previously unrecognized clinical settings . Despite dramatic advances in health care and the availability of antibiot...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "physiology/immunity", "to", "infections", "microbiology/immunity", "to", "infections", "pathology/pathophysiology", "immunology/immunomodulation", "infectious", "diseases/fungal", "infections", "physiology/respiratory", "physiology", "respiratory", "medicine/respiratory", "infections"...	2010	Immune Modulation with Sulfasalazine Attenuates Immunopathogenesis but Enhances Macrophage-Mediated Fungal Clearance during Pneumocystis Pneumonia
Schistosoma japonicum causes major public health problems in China and the Philippines; this parasite , which is transmitted by freshwater snails of the species Oncomelania hupensis , causes the disease intestinal schistosomiasis in humans and cattle . Researchers working on Schistosoma in Africa have described the rel...	Schistosomiasis is a disease caused by a parasitic worm transmitted to humans by certain species of freshwater snails . In spite of several decades of intensive coordinated control schistosomiasis still infects around 1 million people in China . In order to understand the potential for spread of the disease into new ar...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Comparative Phylogenetic Studies on Schistosoma japonicum and Its Snail Intermediate Host Oncomelania hupensis: Origins, Dispersal and Coevolution
Clonorchis sinensis is a group-I bio-carcinogen for cholangiocarcinoma ( CCA ) . Although the epidemiological evidence links clonorchiasis and CCA , the underlying molecular mechanism involved in this process is poorly understood . In the present study , we investigated expression of oncogenes and tumor suppressors , i...	Clonorchis sinensis is a helminth parasite and a carcinogenic agent for cholangiocarcinoma ( CCA ) or bile duct cancer in humans . Though a large and compelling body of evidence suggests an association between C . sinensis and CCA , the mechanism underlying at the genetic/proteomic level is little known . To explore th...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Involvement of PSMD10, CDK4, and Tumor Suppressors in Development of Intrahepatic Cholangiocarcinoma of Syrian Golden Hamsters Induced by Clonorchis sinensis and N-Nitrosodimethylamine
Epistatic interactions among genes can give rise to rugged fitness landscapes , in which multiple “peaks” of high-fitness allele combinations are separated by “valleys” of low-fitness genotypes . How populations traverse rugged fitness landscapes is a long-standing question in evolutionary biology . Sexual reproduction...	For a novel genotype to establish in a population , it must ( 1 ) be created , and ( 2 ) not be subsequently lost . Recombination is a double-edged sword in this process , potentially fostering creation , but also hastening loss as the novel genotype is being recombined with other genotypes , especially when rare . In ...	[ "Abstract", "Introduction", "Model", "Results", "and", "Discussion" ]	[ "variant", "genotypes", "alleles", "genetic", "mapping", "epistasis", "mathematics", "statistics", "(mathematics)", "dna", "evolutionary", "adaptation", "discrete", "mathematics", "combinatorics", "fitness", "epistasis", "evolutionary", "genetics", "genetic", "loci", "bioch...	2016	Evolution at ‘Sutures’ and ‘Centers’: Recombination Can Aid Adaptation of Spatially Structured Populations on Rugged Fitness Landscapes
Repetitive sequences are a conserved feature of many bacterial genomes . While first reported almost thirty years ago , and frequently exploited for genotyping purposes , little is known about their origin , maintenance , or processes affecting the dynamics of within-genome evolution . Here , beginning with analysis of...	DNA sequences that copy themselves throughout genomes , and make no specific contribution to reproductive success , are by definition “selfish . ” Such DNA is a feature of the genomes of all organisms and evident by virtue of its repetitive nature . In bacteria the predominant repetitive sequences are short ( ∼20 bp ) ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome", "evolution", "genome", "sequencing", "coevolution", "genome", "complexity", "comparative", "genomics", "biology", "evolutionary", "genetics", "genetic", "drift", "adaptation", "natural", "selection", "genetics", "genomics", "evolutionary", "biology", "evolutionary...	2011	Within-Genome Evolution of REPINs: a New Family of Miniature Mobile DNA in Bacteria
Myeloid blood cells are largely resistant to infection with human immunodeficiency virus type 1 ( HIV-1 ) . Recently , it was reported that Vpx from HIV-2/SIVsm facilitates infection of these cells by counteracting the host restriction factor SAMHD1 . Here , we independently confirmed that Vpx interacts with SAMHD1 and...	Lentiviral accessory proteins play important roles in antagonizing host proteins aimed at suppressing HIV-1 replication at a cellular level . The SIV/HIV-2 protein Vpx counteracts SAMHD1 , a previously unknown antiviral factor within myeloid blood cells , rendering these cells permissive to primate immunodeficiency vir...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunodeficiency", "viruses", "host", "cells", "immunity", "virology", "innate", "immunity", "viral", "transmission", "and", "infection", "biology", "microbiology", "host-pathogen", "interaction" ]	2011	SAMHD1-Deficient CD14+ Cells from Individuals with Aicardi-Goutières Syndrome Are Highly Susceptible to HIV-1 Infection
Infection of mammalian cells with vesicular stomatitis virus ( VSV ) results in the inhibition of cellular translation while viral translation proceeds efficiently . VSV RNA synthesis occurs entirely within the cytoplasm , where during transcription the viral polymerase produces 5 mRNAs that are structurally indistinct...	Viruses co-opt the host translational machinery and frequently suppress host cell protein synthesis . Many positive-strand RNA viruses manipulate initiation factors while bypassing their need for viral protein production using internal ribosome entry sites . Negative-strand RNA viruses and DNA viruses produce mRNAs tha...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "vesicular", "stomatitis", "virus", "pathology", "and", "laboratory", "medicine", "hela", "cells", "gene", "regulation", "pathogens", "messenger", "rna", "biological", "cultures", "microbiology", "polyribosomes", "viruses", "viru...	2019	Global analysis of polysome-associated mRNA in vesicular stomatitis virus infected cells
Ascaris lumbricoides and Necator americanus are soil-transmitted parasites with global geographic distribution , and they represent some of the most common and neglected infections in the world . Periodic treatment with mass drug administration ( MDA ) in endemic areas is the recommended action put forth by the World H...	The soil-transmitted helminths Ascaris lumbricoides and the hookworms ( Necator americanus and Ancylostoma duodenale ) are the most prevalent intestinal helminths of humans . The standard approach for geohelminth control is large-scale preventive chemotherapy predominantly using benzimidazoles through mass drug adminis...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "chemical", "compounds", "helminths", "hookworms", "animals", "organic", "compounds", "necator", "americanus", "organisms", "mutation", "ascaris", "ascaris", "lumbricoides", "molecular", "biology", "techniques", "research", "and", "analysis", "methods", "...	2018	PCR-RFLP screening of polymorphisms associated with benzimidazole resistance in Necator americanus and Ascaris lumbricoides from different geographical regions in Brazil
Yellow fever ( YF ) is endemic in much of Brazil , where cases of the disease are reported every year . Since 2008 , outbreaks of the disease have occurred in regions of the country where no reports had been registered for decades , which has obligated public health authorities to redefine risk areas for the disease . ...	Yellow fever ( YF ) is an infectious disease , transmitted by mosquitoes , and very common in North and Middle East region of Brazil , where cases of the disease are reported every year . Since 2008 , outbreaks of the disease have occurred in regions of the country where no reports had been registered for decades , whi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "science", "policy", "biology", "veterinary", "science" ]	2012	Methodology for Definition of Yellow Fever Priority Areas, Based on Environmental Variables and Multiple Correspondence Analyses
West Nile virus ( WNV ) is an emerging flavivirus capable of infecting the central nervous system ( CNS ) and mediating neuronal cell death and tissue destruction . The processes that promote inflammation and encephalitis within the CNS are important for control of WNV disease but , how inflammatory signaling pathways ...	Since its introduction into North America in 1999 , West Nile virus ( WNV ) has emerged as a leading cause of viral encephalitic disease in the United States . While low level inflammation is important for clearance of WNV , high levels of inflammation are associated with increased disease . The goal of this study was ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "inflammation", "immunity", "virology", "immunology", "biology", "microbiology" ]	2012	IL-1β Signaling Promotes CNS-Intrinsic Immune Control of West Nile Virus Infection
Growth rate and yield are fundamental features of microbial growth . However , we lack a mechanistic and quantitative understanding of the rate-yield relationship . Studies pairing computational predictions with experiments have shown the importance of maintenance energy and proteome allocation in explaining rate-yield...	This study reconciles multiple existing microbial rate-yield tradeoff theories with experimental data . There is great interest in developing quantitative descriptions of the relationship between growth rate and growth yield [1] . However , some reported experiments [2–4] in the literature do not agree with existing th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "protons", "carbohydrate", "metabolism", "medicine", "and", "health", "sciences", "enzymes", "enzymology", "glucose", "metabolism", "physiological", "processes", "enzyme", "metabolism", "evolutionary", "adaptation", "enzyme", "chemistry", "proteins", "metabolic", "pathways"...	2019	Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism
Fusion and fission of mitochondria maintain the functional integrity of mitochondria and protect against neurodegeneration , but how mitochondrial dysfunctions trigger neuronal loss remains ill-defined . Prohibitins form large ring complexes in the inner membrane that are composed of PHB1 and PHB2 subunits and are thou...	Mitochondria are the major site of cellular ATP production and are essential for the survival of neurons . High ATP levels are required to sustain neuronal activities and axonal transport of macromolecules and organelles . The functional integrity of mitochondria depends on fusion and fission of their membranes , which...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biochemistry", "neurological", "disorders", "neurology", "genetics", "biology", "molecular", "cell", "biology", "neuroscience", "genetics", "and", "genomics" ]	2012	Loss of Prohibitin Membrane Scaffolds Impairs Mitochondrial Architecture and Leads to Tau Hyperphosphorylation and Neurodegeneration
The high mutation rate of hepatitis C virus allows it to rapidly evade the humoral immune response . However , certain epitopes in the envelope glycoproteins cannot vary without compromising virus viability . Antibodies targeting these epitopes are resistant to viral escape from neutralization and understanding their b...	We report here the crystal structures of two neutralization-escape-resistant human monoclonal antibodies in complex with their peptide epitope . Recognition of the hepatitis C virus ( HCV ) by the humoral immune response is hampered by the high variability of the envelope glycoproteins . However , the contact site anal...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "hepatitis", "c", "biomacromolecule-ligand", "interactions", "medicine", "biochemistry", "infectious", "diseases", "infectious", "hepatitis", "hepatitis", "gastroenterology", "and", "hepatology", "immunology", "biology", "viral", "diseases", "liver", "diseases", "immunoglobul...	2013	Structural Basis of HCV Neutralization by Human Monoclonal Antibodies Resistant to Viral Neutralization Escape
When deciding between alternative options , a rational agent chooses on the basis of the desirability of each outcome , including associated costs . As different options typically result in different actions , the effort associated with each action is an essential cost parameter . How do humans discount physical effort...	Economic choice in humans and animals can be understood as a weighing of benefits ( e . g . , reward ) against costs ( e . g . , effort , delay , risk ) , leading to a preference for the behavioral option with highest expected utility . The costs of the action associated with a choice can thereby affect its utility: fo...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "decision", "making", "experimental", "design", "social", "sciences", "limbs", "(anatomy)", "neuroscience", "biomechanics", "research", "design", "cognitive", "psychology", "cognition", "vision", "research", "and", "analysis", "m...	2017	What makes a reach movement effortful? Physical effort discounting supports common minimization principles in decision making and motor control
Effective response to emerging infectious disease ( EID ) threats relies on health care systems that can detect and contain localised outbreaks before they reach a national or international scale . The Asia-Pacific region contains low and middle income countries in which the risk of EID outbreaks is elevated and whose ...	Low and middle income countries face a serious challenge when confronting emerging infectious disease ( EID ) threats . Their risk of experiencing outbreaks can be greater than in many high income countries , while their capacity to respond effectively may be constrained by competing demands on limited health care syst...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "decision", "making", "infectious", "disease", "epidemiology", "geographical", "locations", "neuroscience", "simulation", "and", "modeling", "cognition", "global", "health", "infectious", "disease", "control", "mathematical", "mode...	2016	Model-Informed Risk Assessment and Decision Making for an Emerging Infectious Disease in the Asia-Pacific Region
We here report on the existence of Leber’s hereditary optic neuropathy ( LHON ) associated with peculiar combinations of individually non-pathogenic missense mitochondrial DNA ( mtDNA ) variants , affecting the MT-ND4 , MT-ND4L and MT-ND6 subunit genes of Complex I . The pathogenic potential of these mtDNA haplotypes i...	Leber’s hereditary optic neuropathy ( LHON ) is a common cause of maternally inherited vision loss . In the large majority of cases LHON is due to mitochondrial DNA ( mtDNA ) point mutations , clearly distinct from common polymorphisms normally found in the general population , affecting the mitochondrial function , th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "protons", "medicine", "and", "health", "sciences", "mitochondrial", "dna", "population", "genetics", "skeletal", "muscles", "vertebrates", "animals", "mammals", "primates", "mutation", "forms", "of", "dna", "mitochondria", "dna", "population", "biology", "bioenergetics...	2018	Peculiar combinations of individually non-pathogenic missense mitochondrial DNA variants cause low penetrance Leber’s hereditary optic neuropathy
NOD-like receptor protein 3 ( NLRP3 ) inflammasome activation triggers caspase-1 activation-induced maturation of interleukin ( IL ) -1β and IL-18 and therefore is important for the development of the host defense against various RNA viral diseases . However , the implication of this protein complex in human metapneumo...	Human metapneumovirus ( HMPV ) , a negative-stranded , enveloped RNA virus , is recognized as one of the leading causes of acute respiratory disease in children since its discovery in 2001 . Nevertheless , there is currently no licensed vaccine for the prevention of HMPV infection and treatment modalities are limited t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[]	2019	Human metapneumovirus activates NOD-like receptor protein 3 inflammasome via its small hydrophobic protein which plays a detrimental role during infection in mice
Translating a set of disease regions into insight about pathogenic mechanisms requires not only the ability to identify the key disease genes within them , but also the biological relationships among those key genes . Here we describe a statistical method , Gene Relationships Among Implicated Loci ( GRAIL ) , that take...	Modern genetic studies , including genome-wide surveys for disease-associated loci and copy number variation , provide a list of critical genomic regions that play an important role in predisposition to disease . Using these regions to understand disease pathogenesis requires the ability to first distinguish causal gen...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/literature", "analysis", "genetics", "and", "genomics/gene", "discovery", "genetics", "and", "genomics/complex", "traits", "genetics", "and", "genomics/bioinformatics", "genetics", "and", "genomics/genetics", "of", "disease", "computational", "biolog...	2009	Identifying Relationships among Genomic Disease Regions: Predicting Genes at Pathogenic SNP Associations and Rare Deletions
An understanding of the immunological footprint of Mycobacterium tuberculosis ( MTB ) CD4 T cell recognition is still incomplete . Here we report that human Th1 cells specific for MTB are largely contained in a CXCR3+CCR6+ memory subset and highly focused on three broadly immunodominant antigenic islands , all related ...	Mycobacterium tuberculosis is one of the most life-threatening pathogens of all time , having infected one-third of the present human population . There is an urgent need for both novel vaccines and diagnostic strategies . Here , we were able to identify the targets most dominantly recognized by latently infected indiv...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "immune", "cells", "immunity", "to", "infections", "immunology", "bacterial", "diseases", "adaptive", "immunity", "immune", "defense", "infectious", "diseases", "tuberculosis", "t", "cells", "biology", "immune", "response", "antigen", "processing", "and", ...	2013	Memory T Cells in Latent Mycobacterium tuberculosis Infection Are Directed against Three Antigenic Islands and Largely Contained in a CXCR3+CCR6+ Th1 Subset
Many species are able to share information about their environment by communicating through auditory , visual , and olfactory cues . In Drosophila melanogaster , exposure to parasitoid wasps leads to a decline in egg laying , and exposed females communicate this threat to naïve flies , which also depress egg laying . W...	In this study , we find that many different Drosophila species never having been exposed to parasitoid wasps can trigger caspase activation in the ovary and depress egg-laying when placed next to flies that had visual experience with wasps . Interestingly , when teacher flies of one species are placed with a student of...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "learning", "invertebrates", "cell", "physiology", "medicine", "and", "health", "sciences", "reproductive", "system", "social", "sciences", "teachers", "neuroscience", "animals", "learning", "and", "memory", "animal", "signaling", "and", "communication", "animal", "mode...	2018	Drosophila species learn dialects through communal living
The precise establishment of gene expression patterns is a crucial step in development . Formation of a sharp boundary between high and low spatial expression domains requires a genetic mechanism that exhibits sensitivity , yet is robust to fluctuations , a demand that may not be easily achieved by morphogens alone . R...	Early embryonic development depends on robust patterning along the axes of the embryo . At the cellular level , neighboring segments are often identified via the concentrations of several gene products: the expression of such a gene may , for example , be high in the cells of one segment , and negligible in those of an...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "Supporting", "Information" ]	[ "developmental", "biology", "zea", "computational", "biology", "biophysics", "drosophila" ]	2007	Small Regulatory RNAs May Sharpen Spatial Expression Patterns
A biofilm is a surface-associated population of microorganisms embedded in a matrix of extracellular polymeric substances . Biofilms are a major natural growth form of microorganisms and the cause of pervasive device-associated infection . This report focuses on the biofilm matrix of Candida albicans , the major fungal...	A biofilm is a surface-associated population of microbes that is embedded in a cement of extracellular compounds . This cement is known as matrix . The two main functions of matrix are to protect cells from their surrounding environment , preventing drugs and other stresses from penetrating the biofilm , and to maintai...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "infectious", "diseases/fungal", "infections", "genetics", "and", "genomics/gene", "function", "microbiology/microbial", "growth", "and", "development" ]	2009	Biofilm Matrix Regulation by Candida albicans Zap1
Forkhead box P3 ( Foxp3+ ) regulatory T ( Treg ) -cell function is controlled by environmental cues of which cytokine-mediated signaling is a dominant component . In vivo , interleukin-4 ( IL-4 ) -mediated signaling via IL-4 receptor alpha ( IL-4Rα ) mediates Treg cell transdifferentiation into ex-Foxp3 T helper 2 ( Th...	Host soluble mediators such as cytokines play a key role in the regulation of the immune response . Forkhead box P3 ( Foxp3+ ) regulatory T ( Treg ) cells , which are involved in maintaining self-tolerance and immune system homeostasis , are influenced by cytokines , including interleukin-4 ( IL-4 ) . However , opposin...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "blood", "cells", "flow", "cytometry", "inflammatory", "diseases", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "forkhead", "box", "immune", "physiology", "cytokines", "cd", "coreceptors", "immunology", "animal", "models", ...	2018	The Foxp3+ regulatory T-cell population requires IL-4Rα signaling to control inflammation during helminth infections
Cytomegalovirus ( CMV ) is a leading infectious cause of morbidity in immune-compromised patients . γδ T cells have been involved in the response to CMV but their role in protection has not been firmly established and their dependency on other lymphocytes has not been addressed . Using C57BL/6 αβ and/or γδ T cell-defic...	γδ T cells are unconventional T lymphocytes that play a unique role in host protection against pathogens . Human Cytomegalovirus ( HCMV ) is a widespread virus that can cause severe organ disease such as hepatitis and pneumonitis in immune-compromised patients . Our decade-long study conveys compelling evidence for the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	γδ T Cells Confer Protection against Murine Cytomegalovirus (MCMV)
In mammals , taste buds develop in different regions of the oral cavity . Small epithelial protrusions form fungiform papillae on the ectoderm-derived dorsum of the tongue and contain one or few taste buds , while taste buds in the soft palate develop without distinct papilla structures . In contrast , the endoderm-der...	Gustatory perception is an evolutionary ancient sense , and the ability to discriminate toxic and digestible substances is vitally important for all organisms . In mammals , taste perception occurs in taste buds , groups of sensory cells that are housed in various types of taste papillae in the oral cavity . Little is ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "growth", "control", "cell", "fate", "determination", "embryology", "mutation", "anatomy", "gene", "expression", "genetics", "biology", "and", "life", "sciences", "morphogenesis", "pattern", "formation", "cell", "differentiation", "digestive", ...	2014	The Formation of Endoderm-Derived Taste Sensory Organs Requires a Pax9-Dependent Expansion of Embryonic Taste Bud Progenitor Cells
Severe fever with thrombocytopenia syndrome ( SFTS ) is an emerging disease that is caused by a novel bunyavirus , referred to as SFTS virus . During January 2011 to December 2011 we conducted a case-control study in Henan , Hubei and Shandong Provinces of China to determine the risk factors for SFTS . Case-patients we...	Since 2009 , an emerging infectious disease which was identified as the severe fever with thrombocytopenia syndrome ( SFTS ) was reported in rural areas of Hubei , Shandong and Henan provinces in China . A novel bunyavirus designated severe fever with thrombocytopenia syndrome bunyavirus ( SFTSV ) had been identified t...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "research", "design", "medicine", "and", "health", "sciences", "plant", "science", "survey", "methods", "survey", "research", "infectious", "disease", "epidemiology", "epidemiology", "plant", "pathology", "biology", "and", "life", "sciences", "research", "and", "analy...	2014	Risk Factors for Bunyavirus-Associated Severe Fever with Thrombocytopenia Syndrome, China
Cholera is endemic in Bangladesh , with outbreaks reported annually . Currently , the majority of epidemic cholera reported globally is El Tor biotype Vibrio cholerae isolates of the serogroup O1 . However , in Bangladesh , outbreaks attributed to V . cholerae serogroup O139 isolates , which fall within the same phylog...	Vibrio cholerae serogroup O1 is thought to be the sole causative agent for cholera in Bangladesh and most of the high risk developing countries . Whilst historically Vibrio cholerae serogroup O139 has been seen to cause sporadic disease , the overall numbers of reported O139 clinical cases are low , with none reported ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Vibrio cholerae Serogroup O139: Isolation from Cholera Patients and Asymptomatic Household Family Members in Bangladesh between 2013 and 2014
Within hosts , RNA viruses form populations that are genetically and phenotypically complex . Heterogeneity in RNA virus genomes arises due to error-prone replication and is reduced by stochastic and selective mechanisms that are incompletely understood . Defining how natural selection shapes RNA virus populations is c...	Viruses are constantly emerging into new areas and pose significant challenges to public health . Chikungunya and West Nile viruses ( WNV ) , both mosquito-borne RNA viruses , are quintessential examples of how increased globalization has facilitated the expansion of viruses into new territories . Rapid evolution of bo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Experimental Evolution of an RNA Virus in Wild Birds: Evidence for Host-Dependent Impacts on Population Structure and Competitive Fitness
Leptospira interrogans is a bacterial zoonosis with a worldwide distribution for which rats ( Rattus spp . ) are the primary reservoir in urban settings . In order to assess , monitor , and mitigate the risk to humans , it is important to understand the ecology of this pathogen in rats . The objective of this study was...	Urban Norway rats are the source of a number of zoonotic pathogens responsible for significant human illness . Leptospira interrogans is one of these pathogens , and although infection in rats is asymptomatic , humans infected through exposure to the bacterium in rat urine can develop fever , renal failure , and pulmon...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "leptospirosis", "medicine", "bacterial", "diseases", "infectious", "diseases", "animal", "types", "urban", "ecology", "veterinary", "diseases", "veterinary", "epidemiology", "wildlife", "ecology", "zoonotic", "diseases", "biology", "veterinary", "science", "microbial", "...	2013	Ecology of Leptospira interrogans in Norway Rats (Rattus norvegicus) in an Inner-City Neighborhood of Vancouver, Canada
One of the most intriguing dynamics in biological systems is the emergence of clustering , in the sense that individuals self-organize into separate agglomerations in physical or behavioral space . Several theories have been developed to explain clustering in , for instance , multi-cellular organisms , ant colonies , b...	Modern societies are characterized by a large degree of pluralism in social , political and cultural opinions . In addition , there is evidence that humans tend to form distinct subgroups ( clusters ) , characterized by opinion consensus within the clusters and differences between them . So far , however , formal theor...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "computational", "biology" ]	2010	Individualization as Driving Force of Clustering Phenomena in Humans
Mycobacterium bovis ( M . bovis ) is the main causative agent for bovine tuberculosis ( BTB ) and can also be the cause of zoonotic tuberculosis in humans . In view of its zoonotic nature , slaughterhouse surveillance , potentially resulting in total or partial condemnation of the carcasses and organs , is conducted ro...	The livestock sector plays a major role in poverty and hunger reduction in the vast majority of Africa , as a source of food , cash income , manure , draught power , transportation , savings , insurance and social status . However , for livestock to play this vital role , the impact of diseases of economic and zoonotic...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "livestock", "evolutionary", "biology", "geographical", "locations", "eritrea", "molecular", "genetics", "molecular", "biology", "techniques", "genotyping", "bacteria", "africa", "research", "and", "analysis", "methods", "artificial", "gene", "amplification", "and", "exte...	2018	Genetic profiling of Mycobacterium bovis strains from slaughtered cattle in Eritrea
Nanotechnology offers great potential for molecular genetic investigations and potential control of medically important arthropods . Major advances have been made in mammalian systems to define nanoparticle ( NP ) characteristics that condition trafficking and biodistribution of NPs in the host . Such information is cr...	Emerging insecticide resistance in disease vectors is of great public health concern . Discovery of new targets and novel strategies for insecticidal interventions to control vector borne diseases is a public health imperative . Nanotechnology offers great potential for molecular genetic investigations and for delivery...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Biodistribution and Trafficking of Hydrogel Nanoparticles in Adult Mosquitoes
DNA double-strand breaks ( DSBs ) are a common form of cellular damage that can lead to cell death if not repaired promptly . Experimental systems have shown that DSB repair in eukaryotic cells is often imperfect and may result in the insertion of extra chromosomal DNA or the duplication of existing DNA at the breakpoi...	The repair of DNA double-strand breaks ( DSBs ) is essential for the maintenance of genome integrity . The mechanisms by which DSBs are repaired have been the subject of intense experimental investigations . It has emerged that several imperfect repair pathways exist in eukaryotes that have the potential to result in c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology/genomics", "genetics", "and", "genomics/comparative", "genomics", "molecular", "biology/dna", "repair", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics" ]	2009	Repair-Mediated Duplication by Capture of Proximal Chromosomal DNA Has Shaped Vertebrate Genome Evolution
Noroviruses ( NoV ) are the most common cause of non-bacterial acute gastroenteritis and cause local outbreaks of illness , especially in confined situations . Despite being identified four decades ago , the correlates of protection against norovirus gastroenteritis are still being elucidated . Recent studies have show...	Human noroviruses ( HuNoV ) have become the major etiologic agent of epidemic and sporadic acute gastroenteritis . There are currently no licensed vaccines or drugs to prevent or treat NoV infection . HuNoV infects people of all ages and , even though infection is characteristically acute and self-limiting , infection ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "immune", "physiology", "immunology", "biological", "cultures", "microbiology", "cloning", "gastroenterology", "and", "hepatology", "molecular", "biology", "techniques", "antibodies", "immunologic", "...	2016	Frequent Use of the IgA Isotype in Human B Cells Encoding Potent Norovirus-Specific Monoclonal Antibodies That Block HBGA Binding
A deficiency in glucose-6-phosphatase-α ( G6Pase-α ) in glycogen storage disease type Ia ( GSD-Ia ) leads to impaired glucose homeostasis and metabolic manifestations including hepatomegaly caused by increased glycogen and neutral fat accumulation . A recent report showed that G6Pase-α deficiency causes impairment in a...	GSD-Ia is an autosomal recessive metabolic disorder caused by a deficiency in G6Pase-α , a key enzyme in maintaining blood glucose levels between meals . Despite strong compliance to dietary therapies , GSD-Ia patients continue manifesting metabolic aberrations including excessive accumulation of glycogen and lipid in ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "death", "carbohydrate", "metabolism", "autophagic", "cell", "death", "medicine", "and", "health", "sciences", "liver", "vesicles", "enzyme-linked", "immunoassays", "cell", "processes", "glucose", "metabolism", "liver", "diseases", "immunoprecipitation", "gastroen...	2017	Downregulation of SIRT1 signaling underlies hepatic autophagy impairment in glycogen storage disease type Ia
Intravenous challenge with Trypanosoma cruzi can be used to investigate the process and consequences of blood parasite clearance in experimental Chagas disease . One hour after intravenous challenge of chronically infected mice with 5×106 trypomastigotes , the liver constituted a major site of parasite accumulation , a...	Chagas disease , a Latin American illness caused by the protozoan parasite Trypanosoma cruzi , has only rare spontaneous cure , and in most patients a small number of parasites persists for life in the blood and tissues , leading to chronic disorders such as cardiomyopathy . In a murine model of chronic T . cruzi infec...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/protozoal", "infections", "immunology/immunity", "to", "infections", "immunology/immune", "response", "immunology/leukocyte", "activation" ]	2010	The Liver Plays a Major Role in Clearance and Destruction of Blood Trypomastigotes in Trypanosoma cruzi Chronically Infected Mice
Shigella spp . are pathogenic bacteria that cause bacillary dysentery in humans by invading the colonic and rectal mucosa where they induce dramatic inflammation . Here , we have analyzed the role of the soluble PRR Pentraxin 3 ( PTX3 ) , a key component of the humoral arm of innate immunity . Mice that had been intran...	Soluble pattern recognition molecules , PRMs , are components of the humoral arm of innate immunity . The long pentraxin 3 , PTX3 , is a prototypic soluble PRM that is produced in response to primary inflammatory signals . Shigella spp . are human entero-pathogens which invade colonic and rectal mucosa where they cause...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "tropical", "diseases", "microbiology", "shigella", "epithelial", "cells", "bacterial", "diseases", "signs", "and", "...	2018	Role of a fluid-phase PRR in fighting an intracellular pathogen: PTX3 in Shigella infection
Chemokines and their receptors ( members of the GPCR super-family ) are involved in a wide variety of physiological processes and diseases; thus , understanding the specificity of the chemokine receptor family could help develop new receptor specific drugs . Here , we explore the evolutionary mechanisms that led to the...	The chemokine-receptor system is involved in a broad array of pathologies , including autoimmune and inflammatory diseases , allergies , cancer metastasis , and HIV infection . It is an attractive , but difficult , target for drug development and a deeper understanding of the structure-function relationships of the che...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "motility", "medicine", "and", "health", "sciences", "ccr5", "coreceptor", "molecular", "dynamics", "pathology", "and", "laboratory", "medicine", "immunology", "homeostatic", "mechanisms", "sodium", "physiological", "processes", "signs", "and", "symptoms", "home...	2018	Evolution of chemokine receptors is driven by mutations in the sodium binding site
The in utero environment profoundly impacts childhood neurodevelopment and behaviour . A substantial proportion of pregnancies in Africa are at risk of malaria in pregnancy ( MIP ) however the impact of in utero exposure to MIP on fetal neurodevelopment is unknown . Complement activation , in particular C5a , may contr...	A growing body of evidence has established the importance of the in utero environment on neurodevelopment and long-term cognitive and behavioral outcomes . These data suggest factors that disrupt the tightly regulated in utero environment can modify normal neurodevelopmental processes . Approximately 125 million pregna...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Experimental Malaria in Pregnancy Induces Neurocognitive Injury in Uninfected Offspring via a C5a-C5a Receptor Dependent Pathway
High-throughput mRNA sequencing ( RNA-Seq ) is widely used for transcript quantification of gene isoforms . Since RNA-Seq data alone is often not sufficient to accurately identify the read origins from the isoforms for quantification , we propose to explore protein domain-domain interactions as prior knowledge for inte...	New sequencing technologies for transcriptome-wide profiling of RNAs have greatly promoted the interest in isoform-based functional characterizations of a cellular system . Elucidation of gene expressions at the isoform resolution could lead to new molecular mechanisms such as gene-regulations and alternative splicings...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis
Clostridium botulinum is a dangerous pathogen that forms the highly potent botulinum toxin , which when ingested causes a deadly neuroparalytic disease . The closely related Clostridium sporogenes is occasionally pathogenic , frequently associated with food spoilage and regarded as the non-toxigenic equivalent of Group...	Clostridium botulinum is a dangerous pathogen that forms the deadly botulinum neurotoxin . Strains of C . botulinum are present in the environment as spores . Under suitable conditions , the dormancy of the bacterial spore is broken , and germination occurs . Germination is initiated following the recognition of small ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "bacteriology", "microbial", "mutation", "microbiology", "cloning", "complementary", "dna", "cloning", "molecular", "cloning", "molecular", "biology", "techniques", "mutagenesis", "and", "gene", "deletion", "techniques", "bacterial", "genes", "dna", "clon...	2014	Functional Characterisation of Germinant Receptors in Clostridium botulinum and Clostridium sporogenes Presents Novel Insights into Spore Germination Systems
miRNAs are small RNAs directing many developmental processes by posttranscriptional regulation of protein-coding genes . We uncovered a new role for miR-1-1/133a-2 and miR-1-2/133a-1 clusters in the specification of embryonic cardiomyocytes allowing transition from an immature state characterized by expression of smoot...	miRNAs are small non-coding RNAs involved in posttranscriptional regulation of protein-coding genes . In the mammalian genome , two distinct gene clusters code for miR-1 and miR-133a . Primary sequences of mature miR-1 or miR-133a are identical and both gene clusters show similar expression in the heart and skeletal mu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	miR-1/133a Clusters Cooperatively Specify the Cardiomyogenic Lineage by Adjustment of Myocardin Levels during Embryonic Heart Development
The differentiated cell types of the epithelial and mesenchymal tissue compartments of the mature ureter of the mouse arise in a precise temporal and spatial sequence from uncommitted precursor cells of the distal ureteric bud epithelium and its surrounding mesenchyme . Previous genetic efforts identified a member of t...	The mammalian ureter is a simple tube with a specialized multi-layered epithelium , the urothelium , and a surrounding coat of fibroblasts and peristaltically active smooth muscle cells . Besides its important function in urinary drainage , the ureter represents a simple model system to study epithelial and mesenchymal...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "forkhead", "box", "in", "situ", "hybridization", "molecular", "probe", "techniques", "cell", "differentiation", "developmental", "biology", "ureter", "bioassays", "and", "physiological", "analysis", "molecular", "biology", "tech...	2017	A SHH-FOXF1-BMP4 signaling axis regulating growth and differentiation of epithelial and mesenchymal tissues in ureter development
Disruption of gene regulation by sequence variation in non-coding regions of the genome is now recognised as a significant cause of human disease and disease susceptibility . Sequence variants in cis-regulatory elements ( CREs ) , the primary determinants of spatio-temporal gene regulation , can alter transcription fac...	Cis-regulatory elements ( CREs ) play a vital role in gene regulation by providing spatial and temporal specificity to the expression of their target genes . Understanding how these regions of the genome work is of vital importance for human health as it has been demonstrated that genetic changes in these regions can r...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Functional Assessment of Disease-Associated Regulatory Variants In Vivo Using a Versatile Dual Colour Transgenesis Strategy in Zebrafish
Rabies is a uniformly fatal disease , but preventable by timely and correct use of post exposure prophylaxis ( PEP ) . Unfortunately , many health care facilities in Pakistan do not carry modern life-saving vaccines and rabies immunoglobulin ( RIG ) , assuming them to be prohibitively expensive and unsafe . Consequentl...	Rabies is a killer disease caused by the rabies virus that is present in the saliva of rabid animals , mainly the dog . Once symptoms become apparent , death is inevitable . However , rabies can be prevented if correct post exposure prophylaxis ( PEP ) is instituted as soon as possible after a dog bite and before sympt...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "tropical", "diseases", "microbiology", "vertebrates", "biological", "cultures", "dogs", "animals", "mammals", "vaccines", "preventive", "medicine", "viruses"...	2016	Reducing Cost of Rabies Post Exposure Prophylaxis: Experience of a Tertiary Care Hospital in Pakistan
Chagas disease is a chronic parasitic infection that progresses to dilated cardiomyopathy in 30% of human cases . Public health efforts target diagnosing asymptomatic cases , as therapeutic efficacy diminishes as irreversible tissue damage progresses . Physician diagnosis of Chagas disease cases in the United States is...	Chagas disease is a parasitic infection , which in 30% of people results in chronic dilated organomegaly over the course of decades . This progressive disease typically advances subclinically until end stage heart failure is established , at which point treatment is no longer efficacious . Thus , current public health ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "united", "states", "medicine", "and", "health", "sciences", "physicians", "medical", "doctors", "medical", "personnel", "hispanic", "people", "tropical", "diseases", "geographical", "locations", "parasitic", "diseases", "health", "care", "ethnicities", "north", "americ...	2018	Continuing evidence of Chagas disease along the Texas-Mexico border
Cutaneous leishmaniasis caused by Leishmania major is an emergent , uncontrolled public health problem and there is no vaccine . A promising prophylactic approach has been immunotherapy with Toll-like receptor ( TLR ) agonists to enhance parasite-specific immune responses . We have previously reported that vaccination ...	Cutaneous leishmaniasis is a skin infection caused by a protozoan parasite Leishmania major ( L . major ) . The only available treatment option is chemotherapy , which is toxic and expensive . Currently , there is no vaccine . Although inoculation of virulent L . major ( leishmanization ) that provides effective protec...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Coinjection with TLR2 Agonist Pam3CSK4 Reduces the Pathology of Leishmanization in Mice
Massive activation of dopamine neurons is critical for natural reward and drug abuse . In contrast , the significance of their spontaneous activity remains elusive . In Drosophila melanogaster , depolarization of the protocerebral anterior medial ( PAM ) cluster dopamine neurons en masse signals reward to the mushroom ...	Dopamine neurons in the midbrain of mammals fire action potentials in response to rewarding stimuli , while punitive stimuli or omission of reward suppress their activity . Different signs in the activity of dopamine neurons thus can encode appetitive and aversive values; however , how these bidirectional activities di...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "learning", "invertebrates", "cognitive", "neurology", "medicine", "and", "health", "sciences", "neurochemistry", "chemical", "compounds", "social", "sciences", "neuroscience", "organic", "compounds", "learning", "and", "memory", "animals", "hormones", "animal", "models",...	2016	Suppression of Dopamine Neurons Mediates Reward
Mongolia is one of the endemic countries for cystic echinococcosis ( CE ) , a zoonotic disease caused by the larval stage of Echinococcus granulosus . The goal of this study is to describe the current clinical management of CE in Mongolia , to capture the distribution of cyst stages of patients treated , and to contras...	Cystic Echinococcosis ( CE ) is a zoonotic disease , commonly known as dog tapeworm . The disease is distributed globally and predominantly affects rural populations with limited access to health care . Following the expert consensus of the WHO-Informal Working Group on Echinococcosis ( WHO—IWGE ) patients with uncompl...	[ "Abstract", "Introduction", "Materials", "and", "method", "Results", "Discussion" ]	[ "cystic", "echinococcosis", "medicine", "and", "health", "sciences", "diagnostic", "radiology", "ultrasound", "imaging", "chemical", "compounds", "tropical", "diseases", "geographical", "locations", "parasitic", "diseases", "organic", "compounds", "surgical", "and", "inva...	2018	Patients with cystic echinococcosis in the three national referral centers of Mongolia: A model for CE management assessment
In some transmission foci of Leishmania infantum in Brazil , Lutzomyia cruzi could be considered the main vector of this pathogen . In addition , L . cruzi is a permissive vector of L . amazonensis . Its geographical distribution seems to be restricted and limited to Cerrado and Pantanal biomes , which includes some ar...	Leishmaniases are vector-borne diseases caused by Leishmania parasites which are transmitted to humans by the bites of infected female sand flies . The sand fly Lutzomyia cruzi is the vector of Leishmania infantum , the causative agent of visceral leishmaniasis ( VL ) , in some specific areas of Brazil . The transmissi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "ecological", "niches", "atmospheric", "science", "population", "dynamics", "geographical", "locations", "sand", "flies", "parasitic", "protozoans", "organisms", "protozoans", "leishma...	2018	Ecological niche modelling and predicted geographic distribution of Lutzomyia cruzi, vector of Leishmania infantum in South America
In Uganda , Rhodesian sleeping sickness , caused by Trypanosoma brucei rhodesiense , and animal trypanosomiasis caused by T . vivax and T . congolense , are being controlled by treating cattle with trypanocides and/or insecticides . We used a mathematical model to identify treatment coverages required to break transmis...	In Uganda , cattle are an important reservoir for Trypanosoma brucei rhodesiense , the causative agent of Rhodesian sleeping sickness ( human African trypanosomiasis ) , transmitted by tsetse flies Glossina fuscipes fuscipes , which feed on cattle , humans , and wild vertebrates , particularly monitor lizards . Trypano...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "veterinary", "diseases", "mathematics", "theoretical", "biology", "pest", "control", "applied", "mathematics", "animal", "management", "biology", "population", "biology", "veterinary", "science", "agriculture" ]	2012	Modeling the Control of Trypanosomiasis Using Trypanocides or Insecticide-Treated Livestock
In eukaryotes , intracellular cholesterol homeostasis and trafficking are tightly regulated . Certain bacteria , such as Anaplasma phagocytophilum , also require cholesterol; it is unknown , however , how this cholesterol-dependent obligatory intracellular bacterium of granulocytes interacts with the host cell choleste...	Maintenance of the cholesterol amount and transport within cells are essential for healthy human cell functions . Most bacteria do not need cholesterol , but certain bacteria that infect human cells are dependent on host cell cholesterol for their infection . How infected human cells deal with these cholesterol-robbing...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "biology/leukocyte", "signaling", "and", "gene", "expression", "cell", "biology/membranes", "and", "sorting", "public", "health", "and", "epidemiology/infectious", "diseases", "infectious", "diseases/bacterial", "infections", "microbiology/cellular", "microbiology", "...	2009	Cholesterol-Dependent Anaplasma phagocytophilum Exploits the Low-Density Lipoprotein Uptake Pathway
The Special Programme for Research and Training in Tropical Diseases ( TDR ) co-sponsored by UNICEF , UNDP , World Bank and WHO has been supporting research capacity strengthening in low- and middle-income countries for over 40 years . In order to assess and continuously optimize its capacity strengthening approaches ,...	The Special Programme for Research and Training in Tropical Diseases ( TDR ) co-sponsored by UNICEF , UNDP , World Bank and WHO has been providing training grants to strengthen research capacity in low- and middle-income countries for over 40 years . In order to assess to what extent TDR’s grants made a difference on t...	[ "Abstract", "Introduction", "Methodology", "Results", "Discussion" ]	[ "learning", "employment", "social", "sciences", "neuroscience", "learning", "and", "memory", "careers", "trainees", "research", "design", "scientists", "cognitive", "psychology", "surveys", "educational", "status", "science", "and", "technology", "workforce", "research", ...	2017	Tracking the career development of scientists in low- and middle-income countries trained through TDR’s research capacity strengthening programmes: Learning from monitoring and impact evaluation
Despite World Health Organization ( WHO ) prequalification of two safe and effective oral cholera vaccines ( OCV ) , concerns about the acceptability , potential diversion of resources , cost and feasibility of implementing timely campaigns has discouraged their use . In 2012 , the Ministry of Health of Guinea , with t...	Two safe and effective oral cholera vaccines are recommended by the World Health Organization for cholera prevention and control; however , concerns about the acceptability , potential diversion of resources , cost and feasibility of implementing timely campaigns has discouraged their use . In 2012 , the Ministry of He...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2013	First Outbreak Response Using an Oral Cholera Vaccine in Africa: Vaccine Coverage, Acceptability and Surveillance of Adverse Events, Guinea, 2012
Complex diseases and traits are likely influenced by many common and rare genetic variants and environmental factors . Detecting disease susceptibility variants is a challenging task , especially when their frequencies are low and/or their effects are small or moderate . We propose here a comprehensive hierarchical gen...	Complex diseases and traits are likely influenced by many common and rare genetic variants and environmental factors . Next-generation sequencing technologies have provided unparalleled tools to sequence a large number of individuals , allowing for comprehensive studies of both common and rare variants . However , dete...	[ "Abstract", "Introduction", "Methods", "Discussion" ]	[ "medicine", "computer", "science", "mathematics", "genetics", "biology", "genetics", "and", "genomics" ]	2011	Hierarchical Generalized Linear Models for Multiple Groups of Rare and Common Variants: Jointly Estimating Group and Individual-Variant Effects
Nigeria is one of the countries endemic for Buruli ulcer ( BU ) in West Africa but did not have a control programme until recently . As a result , BU patients often access treatment services in neighbouring Benin where dedicated health facilities have been established to provide treatment free of charge for BU patients...	Buruli ulcer ( BU ) is a neglected tropical disease that mainly affects the skin . The disease results from infection with Mycobacterium ulcerans , an environmental bacterium . In Benin , the BU treatment centres usually receive patients from Nigeria . In 2014 , a study from one of the treatment centres ( CDTUB , Pobe ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "tropical", "diseases", "geographical", "locations", "surgical", "and", "invasive", "medical", "procedures", "health", "care", "bacterial", "diseases", "signs", "and", "symptoms", "...	2018	Report of a series of 82 cases of Buruli ulcer from Nigeria treated in Benin, from 2006 to 2016
With relatively low efficiency , differentiated cells can be reprogrammed to a pluripotent state by ectopic expression of a few transcription factors . An understanding of the mechanisms that underlie data emerging from such experiments can help design optimal strategies for creating pluripotent cells for patient-speci...	Most cells in an organism have the same DNA . Yet , different cell types express different proteins and carry out different functions . These differences are reflected by cell epigenetics; i . e . , DNA in different cell types is packaged distinctly , making it hard to express certain genes while facilitating the expre...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biophysics/theory", "and", "simulation" ]	2010	A Model for Genetic and Epigenetic Regulatory Networks Identifies Rare Pathways for Transcription Factor Induced Pluripotency
Chagas Disease is the leading cause of heart failure in Latin America . Current drug therapy is limited by issues of both efficacy and severe side effects . Trypansoma cruzi , the protozoan agent of Chagas Disease , is closely related to two other major global pathogens , Leishmania spp . , responsible for leishmaniasi...	Chagas Disease is caused by kinetoplastid protozoa Trypanosoma cruzi , whose sterols resemble those of fungi , in both composition and biosynthetic pathway . Azole inhibitors of sterol 14α-demethylase ( CYP51 ) , such as fluconazole , itraconazole , voriconazole , and posaconazole , successfully treat fungal infections...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[ "biochemistry/structural", "genomics", "infectious", "diseases/neglected", "tropical", "diseases", "biochemistry/biomacromolecule-ligand", "interactions", "biochemistry/drug", "discovery" ]	2010	Structural Characterization of CYP51 from Trypanosoma cruzi and Trypanosoma brucei Bound to the Antifungal Drugs Posaconazole and Fluconazole
Many bacteria inhibit motility concomitant with the synthesis of an extracellular polysaccharide matrix and the formation of biofilm aggregates . In Bacillus subtilis biofilms , motility is inhibited by EpsE , which acts as a clutch on the flagella rotor to inhibit motility , and which is encoded within the 15 gene eps...	Bacteria form persistent and antibiotic-resistant cell aggregates known as biofilms . Biofilms can form in environmental settings on plant and animal tissues , in industrial settings on pipes and the hulls of ships , and in clinical settings on catheters and medical devices . Biofilms are characterized by two features:...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/environmental", "microbiology", "microbiology/microbial", "growth", "and", "development" ]	2010	The EpsE Flagellar Clutch Is Bifunctional and Synergizes with EPS Biosynthesis to Promote Bacillus subtilis Biofilm Formation
Innate immune responses are essential for controlling poxvirus infection . The threat of a bioterrorist attack using Variola major , the smallpox virus , or zoonotic transmission of other poxviruses has renewed interest in understanding interactions between these viruses and their hosts . We recently determined that TL...	Toll-like receptors are a class of transmembrane proteins that detect the presence of infectious organisms and activate host innate and adaptive immune responses . Vaccinia virus is the prototypic poxvirus , and it is used as both a model and a vaccine for the virus that causes smallpox . We recently reported that Toll...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "immunology/immunity", "to", "infections", "virology/animal", "models", "of", "infection" ]	2008	Protective Effect of Toll-like Receptor 4 in Pulmonary Vaccinia Infection
Morbidity due to Schistosoma haematobium and hookworm infections is marked in those with intense co-infections by these parasites . The development of a spatial predictive decision-support tool is crucial for targeting the delivery of integrated mass drug administration ( MDA ) to those most in need . We investigated t...	Urinary schistosomiasis and hookworm infections cause considerable morbidity in school age children in West Africa . Severe morbidity is predominantly observed in individuals infected with both parasite types and , in particular , with heavy infections . We investigated for the first time the distribution of S . haemat...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "disease", "mapping", "infectious", "diseases", "environmental", "health", "public", "health", "and", "epidemiology", "pediatric", "epidemiology", "child", "health", "epidemiology", "infectious", "disease", "epidemiology", "neglected", "tropical", "diseases", ...	2011	Mapping Helminth Co-Infection and Co-Intensity: Geostatistical Prediction in Ghana
Buruli Ulcer ( BU ) is a neglected infectious disease caused by Mycobacterium ulcerans that is responsible for severe necrotizing cutaneous lesions that may be associated with bone involvement . Clinical presentations of BU lesions are classically classified as papules , nodules , plaques and edematous infiltration , u...	Buruli Ulcer ( BU ) is a neglected disease caused by Mycobacterium ulcerans . Clinical presentations of BU lesions are classically classified as papules , nodules , plaques and edematous infiltration , ulcer or osteomyelitis . Within these different clinical forms , lesions can be further classified as severe forms bas...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Clinical Epidemiology of Buruli Ulcer from Benin (2005-2013): Effect of Time-Delay to Diagnosis on Clinical Forms and Severe Phenotypes
Trypanosoma vivax is one of the causative agents of Animal African Trypanosomosis in cattle , which is endemic in sub-Saharan Africa and transmitted primarily by the bite of the tsetse fly vector . The parasite can also be mechanically transmitted , and this has allowed its spread to South America . Diagnostics are lim...	African Animal Trypanosomosis presents a significant problem for agricultural development in sub-Saharan Africa and leads to large economic losses . One of the main parasites responsible is Trypanosoma vivax . Current diagnostic methods are either symptom-based or too costly and technologically demanding for use in end...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "livestock", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "ruminants", "engineering", "and", "technology", "vertebrates", "parasitic", "diseases", "animals", "mammals", "veterinary", "diagnostics", "immunologic", "techniques", "veterinary", "sci...	2016	Proteomic Identification of Immunodiagnostic Antigens for Trypanosoma vivax Infections in Cattle and Generation of a Proof-of-Concept Lateral Flow Test Diagnostic Device
We have identified a large expansion of an ATTCT repeat within intron 9 of ATXN10 on chromosome 22q13 . 31 as the genetic mutation of spinocerebellar ataxia type 10 ( SCA10 ) . Our subsequent studies indicated that neither a gain nor a loss of function of ataxin 10 is likely the major pathogenic mechanism of SCA10 . He...	In an earlier study , we showed that the mutation of spinocerebellar ataxia 10 ( SCA10 ) is an enormous expansion of a gene segment , which contains a tandemly repeated 5-base ( ATTCT ) unit . Since SCA10 is the only known human disease that is proven to be caused by 5-base repeat expansion , it is important to learn h...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genetics", "of", "disease", "neurological", "disorders/neurogenetics", "neurological", "disorders/movement", "disorders", "neuroscience/neurobiology", "of", "disease", "and", "regeneration" ]	2010	Inactivation of hnRNP K by Expanded Intronic AUUCU Repeat Induces Apoptosis Via Translocation of PKCδ to Mitochondria in Spinocerebellar Ataxia 10
In budding yeast meiosis , the formation of class I interference-sensitive crossovers requires the ZMM proteins . These ZMM proteins are essential in forming a mature synaptonemal complex , and a subset of these ( Zip2 , Zip3 , and Zip4 ) has been proposed to compose the core of synapsis initiation complexes ( SICs ) ....	During meiosis two successive chromosomal divisions follow a single S phase , resulting in the formation of four haploid cells , each with half of the parental genetic material . This ploidy reduction occurs during the first meiotic division , when homologous chromosomes ( paternal and maternal ) are separated from eac...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "cell", "biology", "genetics", "and", "genomics", "arabidopsis", "(thale", "cress)", "plant", "biology" ]	2007	Zip4/Spo22 Is Required for Class I CO Formation but Not for Synapsis Completion in Arabidopsis thaliana
It has come to light that Zika virus ( ZIKV ) infection during pregnancy can result in trans-placental transmission to the fetus along with fetal death , congenital microcephaly , and/or Central Nervous System ( CNS ) malformations . There are projected to be >9 , 200 , 000 births annually in countries with ongoing ZIK...	Scientific consensus has now been reached that intrauterine Zika virus ( ZIKV ) infection can result in infection of the fetus and subsequent fetal death , congenital microcephaly , and/or Central Nervous System ( CNS ) malformations . Preliminary data suggest miscarriage and congenital Zika syndrome ( CZS ) are most l...	[ "Abstract", "Zika", "Virus", "and", "Microcephaly", "Transmission", "Seasonality", "Seasonally", "Timing", "Pregnancy" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "microcephaly", "pathology", "and", "laboratory", "medicine", "maternal", "health", "obstetrics", "and", "gynecology", "pathogens", "geographical", "locations", "microbiology", "animals", "viruses", "north", "ameri...	2016	Preventing Zika Virus Infection during Pregnancy Using a Seasonal Window of Opportunity for Conception
Lethal mutagenesis is a promising new antiviral therapy that kills a virus by raising its mutation rate . One potential shortcoming of lethal mutagenesis is that viruses may resist the treatment by evolving genomes with increased robustness to mutations . Here , we investigate to what extent mutational robustness can i...	The high mutation rate of RNA viruses , such as HIV , allows them to rapidly evolve resistance to host defenses and antiviral drugs . A new approach to treating these viruses—lethal mutagenesis—turns the mutation rate of these viruses against them . It uses mutagens to increase the viruses' mutation rates so much that ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "virology/virus", "evolution", "and", "symbiosis", "virology/new", "therapies,", "including", "antivirals", "and", "immunotherapy" ]	2010	Does Mutational Robustness Inhibit Extinction by Lethal Mutagenesis in Viral Populations?
In mass vaccination campaigns , large volumes of data must be managed efficiently and accurately . In a reactive oral cholera vaccination ( OCV ) campaign in rural Haiti during an ongoing epidemic , we used a mobile health ( mHealth ) system to manage data on 50 , 000 participants in two isolated communities . Data wer...	The World Health Organization ( WHO ) recently endorsed the creation of a global oral cholera vaccine ( OCV ) stockpile as part of an integrated , strategic framework to address the re-emerging threat that cholera causes worldwide . In conjunction , the WHO also called for continued monitoring and evaluation around the...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "and", "occupational", "health", "bacterial", "diseases", "infectious", "diseases", "medicine", "and", "health", "sciences", "behavioral", "and", "social", "aspects", "of", "health", "global", "health", "biology", "and", "life", "sciences", "immunology", "...	2014	Using Mobile Health (mHealth) and Geospatial Mapping Technology in a Mass Campaign for Reactive Oral Cholera Vaccination in Rural Haiti
Replicative DNA polymerases are stalled by damaged DNA while the newly discovered Y-family DNA polymerases are recruited to rescue these stalled replication forks , thereby enhancing cell survival . The Y-family DNA polymerases , characterized by low fidelity and processivity , are able to bypass different classes of D...	Faithful replication of genomic DNA by DNA polymerases is crucial for maintaining the genetic integrity of an organism . If DNA becomes damaged , specialized lesion-bypass DNA polymerases are recruited to correct errors in the DNA . A variety of kinetic and structural studies have established a minimal kinetic mechanis...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "biochemistry/replication", "and", "repair" ]	2009	Global Conformational Dynamics of a Y-Family DNA Polymerase during Catalysis
The simian parasite Plasmodium knowlesi is a common cause of human malaria in Malaysian Borneo and threatens the prospect of malaria elimination . However , little is known about the emergence of P . knowlesi , particularly in Sabah . We reviewed Sabah Department of Health records to investigate the trend of each malar...	The simian parasite Plasmodium knowlesi is a common cause of malaria in Malaysian Borneo; however , little is known about its emergence over time , particularly in Sabah . We reviewed all available Sabah Department of health malaria notification records from 1992–2011 , and considered notifications of P . malariae and ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "tropical", "diseases", "(non-neglected)", "malaria", "parasitic", "diseases" ]	2013	Increasing Incidence of Plasmodium knowlesi Malaria following Control of P. falciparum and P. vivax Malaria in Sabah, Malaysia
Limited data is available on the current status of scrub typhus infection in the aboriginal population in Malaysia . This study was aimed to provide recent data on the degree of exposure of 280 individuals from seven aboriginal subgroups to Orientia tsutsugamushi ( causative agent of scrub typhus ) in West Malaysia . T...	Scrub typhus has been recognized as a public health problem in the rural areas of Southeast Asia . The aboriginal population , one of the most impoverished groups in the Malaysia , may be exposed to the bite of Leptotrombidium mites ( vector for scrub typhus ) due to their involvement in the agricultural activities , l...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "veterinary", "science", "biology" ]	2013	Antibody Prevalence and Factors Associated with Exposure to Orientia tsutsugamushi in Different Aboriginal Subgroups in West Malaysia
Expression levels of human genes vary extensively among individuals . This variation facilitates analyses of expression levels as quantitative phenotypes in genetic studies where the entire genome can be scanned for regulators without prior knowledge of the regulatory mechanisms , thus enabling the identification of un...	Cellular characteristics and functions are determined largely by gene expression and expression levels differ among individuals , however it is not clear how these levels are regulated . While many cis-acting DNA sequence variants in promoters and enhancers that influence gene expression have been identified , only a f...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "genetics", "and", "genomics/complex", "traits", "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/functional", "genomics" ]	2010	Polymorphic Cis- and Trans-Regulation of Human Gene Expression
We present a model for the self-organized formation of place cells , head-direction cells , and spatial-view cells in the hippocampal formation based on unsupervised learning on quasi-natural visual stimuli . The model comprises a hierarchy of Slow Feature Analysis ( SFA ) nodes , which were recently shown to reproduce...	Rats excel at navigating through complex environments . In order to find their way , they need to answer two basic questions . Where am I ? In which direction am I heading ? As the brain has no direct access to information about its position in space , it has to rely on sensory signals—from eyes and ears for example—to...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "primates", "neuroscience", "rattus", "(rat)", "computational", "biology" ]	2007	Slowness and Sparseness Lead to Place, Head-Direction, and Spatial-View Cells
Rhizobiaceas are bacteria that fix nitrogen during symbiosis with plants . This symbiotic relationship is crucial for the nitrogen cycle , and understanding symbiotic mechanisms is a scientific challenge with direct applications in agronomy and plant development . Rhizobium etli is a bacteria which provides legumes wit...	Nitrogen fixation is an important process for improving plant development in crops . Overall , it constitutes a central role in the nitrogen cycle which is essential to life . In this work we were interested in understanding nitrogen fixation in Rhizobium etli from a genome-scale perspective . Using the genome annotati...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "rhizobium", "none", "in", "vitro", "computational", "biology", "bacteria" ]	2007	Metabolic Reconstruction and Modeling of Nitrogen Fixation in Rhizobium etli
The early detection of disease epidemics reduces the chance of successful introductions into new locales , minimizes the number of infections , and reduces the financial impact . We develop a framework to determine the optimal sampling strategy for disease detection in zoonotic host-vector epidemiological systems when ...	Outbreaks of zoonoses can have large costs to society through public health and agricultural impacts . Because many zoonoses co-occur in multiple animal populations simultaneously , detection of zoonotic outbreaks can be especially difficult . We evaluated how to design sampling strategies for the early detection of di...	[ "Abstract", "Introduction", "Models", "Discussion" ]	[ "medicine", "and", "health", "sciences", "decision", "theory", "infectious", "disease", "epidemiology", "applied", "mathematics", "systems", "science", "mathematics", "statistics", "(mathematics)", "population", "modeling", "veterinary", "science", "infectious", "diseases",...	2014	Optimal Sampling Strategies for Detecting Zoonotic Disease Epidemics
T cell memory is a cornerstone of protective immunity , and is the key element in successful vaccination . Upon encountering the relevant pathogen , memory T cells are thought to initiate cell division much more rapidly than their naïve counterparts , and this is thought to confer a significant biological advantage upo...	Vaccines are the only medical products that should be administered to almost every human worldwide , and it is well-known that they act by inducing so-called “memory” cells that can protect against subsequent encounter with the related micro-organism . Surprisingly , we do not understand precisely how these memory cell...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/vaccines", "immunology/immunity", "to", "infections", "virology/animal", "models", "of", "infection", "virology/host", "antiviral", "responses" ]	2008	Tentative T Cells: Memory Cells Are Quick to Respond, but Slow to Divide
A defining characteristic of living cells is the ability to respond dynamically to external stimuli while maintaining homeostasis under resting conditions . Capturing both of these features in a single kinetic model is difficult because the model must be able to reproduce both behaviors using the same set of molecular ...	Cells respond to extracellular signals through a complex coordination of interacting molecular components . Computational models can serve as powerful tools for prediction and analysis of signaling systems , but constructing large models typically requires extensive experimental datasets and computation . To facilitate...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results/Discussion" ]	[ "computational", "biology/signaling", "networks", "computational", "biology/systems", "biology", "computational", "biology" ]	2009	Steady-State Kinetic Modeling Constrains Cellular Resting States and Dynamic Behavior
Proteases and protease inhibitors have been identified in the ejaculates of animal taxa ranging from invertebrates to mammals and form a major protein class among Drosophila melanogaster seminal fluid proteins ( SFPs ) . Other than a single protease cascade in mammals that regulates seminal clot liquefaction , no prote...	Proteases can destroy , activate , or otherwise modulate the function of other proteins . In seminal fluid , many proteins have to be activated or degraded after mating; proteolysis is an effective way to accomplish this because seminal fluid proteins act outside of the cell , where most other regulatory processes cann...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "drosophila", "melanogaster", "animal", "genetics", "model", "organisms", "animal", "behavior", "genetics", "biology", "evolutionary", "biology", "evolutionary", "genetics", "genetics", "and", "genomics", "evolutionary", "developmental", "biology", "ge...	2012	The Drosophila melanogaster Seminal Fluid Protease “Seminase” Regulates Proteolytic and Post-Mating Reproductive Processes
Spores are the major transmissive form of the nosocomial pathogen Clostridium difficile , a leading cause of healthcare-associated diarrhea worldwide . Successful transmission of C . difficile requires that its hardy , resistant spores germinate into vegetative cells in the gastrointestinal tract . A critical step duri...	Clostridium difficile is the leading cause of health-care associated diarrhea worldwide . C . difficile infections begin when its spores transform into vegetative cells during a process called germination . In Clostridium sp . , germination requires that the spore cortex , a thick , protective layer , be removed by the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "genetics", "biology", "microbiology", "genetics", "and", "genomics" ]	2013	Structural and Functional Analysis of the CspB Protease Required for Clostridium Spore Germination

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