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Acute Myeloid Leukemia ( AML ) is a fatal hematological cancer . The genetic abnormalities underlying AML are extremely heterogeneous among patients , making prognosis and treatment selection very difficult . While clinical proteomics data has the potential to improve prognosis accuracy , thus far , the quantitative me...	Acute Myeloid Leukemia ( AML ) is a hematological cancer with a very low 5-year survival rate . It is a very heterogeneous disease , meaning that the molecular underpinnings that cause AML vary greatly among patients , necessitating the use of precision medicine for treatment . While this personalized approach could be...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "acute", "myeloid", "leukemia", "leukemias", "medicine", "and", "health", "sciences", "myeloid", "leukemia", "cancer", "treatment", "cancers", "and", "neoplasms", "neuroscience", "oncology", "hematologic", "cancers", "and", "related", "disorders", "systems", "science", ...	2016	A Crowdsourcing Approach to Developing and Assessing Prediction Algorithms for AML Prognosis
Argonaute ( AGO ) proteins partner with microRNAs ( miRNAs ) to target specific genes for post-transcriptional regulation . During larval development in Caenorhabditis elegans , Argonaute-Like Gene 1 ( ALG-1 ) is the primary mediator of the miRNA pathway , while the related ALG-2 protein is largely dispensable . Here w...	Tiny non-coding RNAs called microRNAs ( miRNAs ) are broadly conserved across animal species and have established roles in regulating development , metabolism and behavior . In humans , aberrant expression or function of specific miRNAs has been associated with a wide variety of diseases , underscoring the critical rol...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "sequencing", "techniques", "invertebrates", "medicine", "and", "health", "sciences", "rna", "interference", "caenorhabditis", "gene", "regulation", "animals", "animal", "models", "caenorhabditis", "elegans", "micrornas", "model", "organisms", "experimental", "organism", ...	2018	Opposing roles of microRNA Argonautes during Caenorhabditis elegans aging
Although acute lung injury ( ALI ) is a common complication of severe malaria , little is known about the underlying molecular basis of lung dysfunction . Animal models have provided powerful insights into the pathogenesis of severe malaria syndromes such as cerebral malaria ( CM ) ; however , no model of malaria-induc...	Acute lung injury ( ALI ) and acute respiratory distress syndrome ( ARDS ) can occur in adult malaria infections with a case fatality rate of 70%–100% . ALI and ARDS are characterized by protein-rich fluid in the lungs , with reduced gas exchange , and in malaria , often accompany high parasite levels and severe or cer...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "infectious", "diseases", "genetics", "and", "genomics/gene", "expression", "microbiology/innate", "immunity", "pathology/histopathology", "immunology/genetics", "of", "the", "immune", "system", "microbiology/parasitology" ]	2008	Parasite Burden and CD36-Mediated Sequestration Are Determinants of Acute Lung Injury in an Experimental Malaria Model
Regulatory T cells ( Treg ) diminish immune responses to microbial infection , which may contribute to preventing inflammation-related local tissue damage and autoimmunity but may also contribute to chronicity of infection . Nasopharyngeal carriage of pneumococcus is common in young children and can persist for long pe...	Streptococcus pneumoniae ( pneumococcus ) is a bacterium that causes pneumonia , meningitis and blood poisoning . Colonization with pneumococcus is common in young children , which may be why they are prone to some common infections such as otitis media ( ear infection ) and pneumonia . As children age , most develop n...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine" ]	2011	Characterisation of Regulatory T Cells in Nasal Associated Lymphoid Tissue in Children: Relationships with Pneumococcal Colonization
The high-resolution crystal structure of the leucine transporter ( LeuT ) is frequently used as a template for homology models of the dopamine transporter ( DAT ) . Although similar in structure , DAT differs considerably from LeuT in a number of ways: ( i ) when compared to LeuT , DAT has very long intracellular amino...	The dopamine transporter ( DAT ) regulates dopaminergic neurotransmission in the brain and is implicated in numerous human disease states . DAT is unique among the monoamine neurotransmitter transporter family because its substrate transport is inhibited by extracellular zinc . DAT homology models rely upon the crystal...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "neuropharmacology", "drugs", "and", "devices", "drug", "dependence", "neuroscience", "behavioral", "pharmacology", "protein", "structure", "neurotransmitters", "pharmacology", "psychopharmacology", "biology", "biochemical", "simulations", "biophysic", "al", "simu...	2013	Mutational Analysis of the High-Affinity Zinc Binding Site Validates a Refined Human Dopamine Transporter Homology Model
We previously used a single nucleotide polymorphism ( SNP ) in the CHRNA5-A3-B4 gene cluster associated with heaviness of smoking within smokers to confirm the causal effect of smoking in reducing body mass index ( BMI ) in a Mendelian randomisation analysis . While seeking to extend these findings in a larger sample w...	We found that a single nucleotide polymorphism in the CHRNA5-A3-B4 gene cluster , which is known to influence smoking heaviness , is associated with lower body mass index ( BMI ) in current smokers , but higher BMI in never smokers . This difference in effects suggests that the variant influences BMI both via pathways ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "biology", "and", "life", "sciences", "human", "genetics" ]	2014	Stratification by Smoking Status Reveals an Association of CHRNA5-A3-B4 Genotype with Body Mass Index in Never Smokers
In plants , RNA silencing-based antiviral defense is mediated by Dicer-like ( DCL ) proteins producing short interfering ( si ) RNAs . In Arabidopsis infected with the bipartite circular DNA geminivirus Cabbage leaf curl virus ( CaLCuV ) , four distinct DCLs produce 21 , 22 and 24 nt viral siRNAs . Using deep sequencin...	RNA silencing directed by small RNAs ( sRNAs ) regulates gene expression and mediates defense against invasive nucleic acids such as transposons , transgenes and viruses . In plants and some animals , RNA-dependent RNA polymerase ( RDR ) generates precursors of secondary sRNAs that reinforce silencing . Most plant mRNA...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "plant", "science", "plant", "biology", "plant", "pathogens", "plant", "pathology", "biology" ]	2012	Primary and Secondary siRNAs in Geminivirus-induced Gene Silencing
Chagas disease results from infection with the diploid protozoan parasite Trypanosoma cruzi . T . cruzi is highly genetically diverse , and multiclonal infections in individual hosts are common , but little studied . In this study , we explore T . cruzi infection multiclonality in the context of age , sex and clinical ...	Trypanosoma cruzi , the causal agent of Chagas disease in Latin America , infects several million people in some of the most economically deprived regions of Latin America . T . cruzi infection is lifelong and has a variable prognosis: some patients never exhibit symptoms while others experience debilitating and fatal ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Deep Sequencing of the Trypanosoma cruzi GP63 Surface Proteases Reveals Diversity and Diversifying Selection among Chronic and Congenital Chagas Disease Patients
Glycosylphosphatidylinositol ( GPI ) is a post-translational modification resulting in the attachment of modified proteins to the outer leaflet of the plasma membrane . Tissue culture experiments have shown GPI-anchored proteins ( GPI-APs ) to be targeted to the apical membrane of epithelial cells . However , the in vi...	Cell surface proteins , such as receptors , either integrate into the plasma membrane through a transmembrane domain or are tethered to it by an accessory glycosylated phospholipid ( GPI ) anchor that is attached to them after they are made . The GPI-anchor biosynthesis pathway is highly conserved from yeast to humans ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Glycosyl Phosphatidylinositol Anchor Biosynthesis Is Essential for Maintaining Epithelial Integrity during Caenorhabditis elegans Embryogenesis
Rickettsia ( R . ) typhi is the causative agent of endemic typhus , an emerging febrile disease that is associated with complications such as pneumonia , encephalitis and liver dysfunction . To elucidate how innate immune mechanisms contribute to defense and pathology we here analyzed R . typhi infection of CB17 SCID m...	Rickettsia typhi causes a relatively mild disease in humans and in immunocompetent mice the bacterium does not cause clinical symptoms as it is easily controlled by the adaptive T cell response . To analyze the role of innate immune mechanisms we here infected mice deficient in T and B cells and find that these mice di...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "flow", "cytometry", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "spleen", "immunology", "animal", "models", "development...	2016	Liver Necrosis and Lethal Systemic Inflammation in a Murine Model of Rickettsia typhi Infection: Role of Neutrophils, Macrophages and NK Cells
Functional inactivation of the Retinoblastoma ( pRB ) pathway is an early and obligatory event in tumorigenesis . The importance of pRB is usually explained by its ability to promote cell cycle exit . Here , we demonstrate that , independently of cell cycle exit control , in cooperation with the Hippo tumor suppressor ...	The inability to respond to growth inhibitory cues is one acquired trait of a cancer cell . Almost all such signals are eventually routed through the Retinoblastoma ( pRB ) tumor suppressor pathway . Therefore , inactivation of the pRB pathway is considered to be an early and obligatory event during transformation of a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/cell", "differentiation", "cell", "biology/cell", "growth", "and", "division" ]	2010	Combined Inactivation of pRB and Hippo Pathways Induces Dedifferentiation in the Drosophila Retina
The Dobzhansky and Muller ( D-M ) model explains the evolution of hybrid incompatibility ( HI ) through the interaction between lineage-specific derived alleles at two or more loci . In agreement with the expectation that HI results from functional divergence , many protein-coding genes that contribute to incompatibili...	When two different species mate , the hybrid progeny are often sterile or lethal . Such hybrid incompatibilities cause reproductive isolation between species and are an important mechanism for maintaining species as separate units . A gene called Lethal hybrid rescue ( Lhr ) is part of the cause of hybrid lethality bet...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gene", "expression", "genetics", "population", "genetics", "biology", "evolutionary", "biology", "evolutionary", "processes", "genetics", "and", "genomics" ]	2012	Cis-by-Trans Regulatory Divergence Causes the Asymmetric Lethal Effects of an Ancestral Hybrid Incompatibility Gene
Axis specification and segment determination in dipteran insects are an excellent model system for comparative analyses of gene network evolution . Antero-posterior polarity of the embryo is established through systems of maternal morphogen gradients . In Drosophila melanogaster , the anterior system acts through oppos...	The basic head-to-tail polarity of an animal is established very early in development . In dipteran insects ( flies , midges , and mosquitoes ) , polarity is established with the help of so-called morphogen gradients . Morphogens are regulatory proteins that are distributed as a concentration gradient , often involving...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Methods" ]	[]	2015	Maternal Co-ordinate Gene Regulation and Axis Polarity in the Scuttle Fly Megaselia abdita
During quiet resting behavior , involuntary movements are suppressed . Such movement control is attributed to cortico-basal ganglia loops , yet population dynamics within these loops during resting and their relation to involuntary movements are not well characterized . Here , we show by recording cortical and striatal...	Even in the absence of apparent motor output , the brain produces a rich repertoire of neuronal activity patterns known as “resting state” activity . In the outer layer of the cortex , resting state patterns emerge as neuronal avalanches , precisely scale-invariant spatiotemporal bursts that often engage large populati...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "action", "potentials", "laboratory", "equipment", "engineering", "and", "technology", "electronics", "membrane", "potential", "brain", "electrophysiology", "neuroscience", "membrane", "electrophysiology", "bioassays", "and", "physio...	2016	A Low-Correlation Resting State of the Striatum during Cortical Avalanches and Its Role in Movement Suppression
Traditional genome-wide scans for positive selection have mainly uncovered selective sweeps associated with monogenic traits . While selection on quantitative traits is much more common , very few signals have been detected because of their polygenic nature . We searched for positive selection signals underlying corona...	How genetic variation contributes to disease is complex , especially for those such as coronary artery disease ( CAD ) that develop over the lifetime of individuals . One of the fundamental questions about CAD––whose progression begins in young adults with arterial plaque accumulation leading to life-threatening outcom...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "population", "genetics", "cell", "signaling", "coronary", "heart", "disease", "population", "biology", "cardiology", "genomic", "signal", "processing", "genetic", "polymorphism", "gene", "expression", "genetic", "loci", "signal"...	2017	Genetic loci associated with coronary artery disease harbor evidence of selection and antagonistic pleiotropy
Epileptic seizures are known to follow specific changes in brain dynamics . While some algorithms can nowadays robustly detect these changes , a clear understanding of the mechanism by which these alterations occur and generate seizures is still lacking . Here , we provide crossvalidated evidence that such changes are ...	Understanding and predicting the generation of seizures in epileptic patients is fundamental to improving the quality of life of the more than 1% of the world population who suffer from this illness . Although seizure prediction has made important advances over the last decade , there is a lack of understanding of the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "brain", "electrophysiology", "brain", "electrophysiology", "neuroscience", "surgical", "and", "invasive", "medical", "procedures", "clinical", "medicine", "mathematics", "algebra", "network", "analysis", "brain", "mapping", "bioas...	2018	Degenerate time-dependent network dynamics anticipate seizures in human epileptic brain
Clostridium difficile spores must germinate in vivo to become actively growing bacteria in order to produce the toxins that are necessary for disease . C . difficile spores germinate in vitro in response to certain bile acids and glycine . In other sporulating bacteria , proteins embedded within the inner membrane of t...	Clostridium difficile infections ( CDI ) are steadily increasing in the United States and other countries . C . difficile spores are the infectious agent and often contaminate environmental surfaces . However , to initiate infection , C . difficile spores must germinate in vivo to actively growing bacteria . Certain bi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "bacterial", "physiology", "microbial", "pathogens", "biology", "microbiology" ]	2013	Bile Acid Recognition by the Clostridium difficile Germinant Receptor, CspC, Is Important for Establishing Infection
Receptor Ser/Thr protein kinases are candidates for sensors that govern developmental changes and disease processes of Mycobacterium tuberculosis ( Mtb ) , but the functions of these kinases are not established . Here , we show that Mtb protein kinase ( Pkn ) D overexpression alters transcription of numerous bacterial ...	Many bacteria , including Mycobacterium tuberculosis ( Mtb ) , sense the environment using a family of signaling proteins called Ser/Thr protein kinases ( STPKs ) , but the functions of these sensors are not well understood . This study shows that the Mtb protein kinase ( Pkn ) D STPK attaches a phosphate group to one ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "biochemistry", "infectious", "diseases", "in", "vitro", "microbiology", "molecular", "biology", "genetics", "and", "genomics", "eubacteria" ]	2007	M. tuberculosis Ser/Thr Protein Kinase D Phosphorylates an Anti-Anti–Sigma Factor Homolog
Stress granules ( SGs ) contain stalled messenger ribonucleoprotein complexes and are related to the regulation of mRNA translation . Picornavirus infection can interfere with the formation of SGs . However , the detailed molecular mechanisms and functions of picornavirus-mediated regulation of SG formation are not cle...	When cellular translation initiation is stalled , translation initiation complexes aggregate in cytoplasm . We call these aggregations stress granules ( SGs ) , and they can be marked by components such as TIA-1 . SGs are always considered to be antiviral structures during viral infection , but viruses also regulate SG...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "hela", "cells", "enzymes", "messenger", "rna", "biological", "cultures", "enzymology", "viruses", "research", "design", "rna", "viruses", "cell", "cultures", "research", "and", "analysis", "methods", "specimen", "preparation", "and", "treatment", "...	2018	Picornavirus 2A protease regulates stress granule formation to facilitate viral translation
Cutaneous and mucosal leishmaniasis is widely distributed in Central and South America . Leishmania of the Viannia subgenus are the most frequent species infecting humans . L . ( V . ) braziliensis , L . ( V . ) panamensis are also responsible for metastatic mucosal leishmaniasis . Conventional or real time PCR is a mo...	Cutaneous leishmaniasis is a parasitic disease transmitted by the bite of sandflies that produces skin ulcers . The severe , disfiguring form of the disease is characterized by parasite dissemination to the mucosa of the nose and palate . Current diagnosis is based on microscopy which has low sensitivity in chronic cas...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "laboratory", "equipment", "engineering", "and", "technology", "tropical", "diseases", "geographical", "locations", "parasitic", "diseases", "parasitic", "protozoans", "peru", "organism...	2016	An Innovative Field-Applicable Molecular Test to Diagnose Cutaneous Leishmania Viannia spp. Infections
The Aspergillus fumigatus sterol regulatory element binding protein ( SREBP ) SrbA belongs to the basic Helix-Loop-Helix ( bHLH ) family of transcription factors and is crucial for antifungal drug resistance and virulence . The latter phenotype is especially striking , as loss of SrbA results in complete loss of virule...	Despite improvements in diagnostics and antifungal drug treatments , mortality rates from invasive mold infections remain high . Defining the fungal adaptation and growth mechanisms at the infection site microenvironment is one research focus that is expected to improve treatment of established invasive fungal infectio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "of", "infection", "mycology", "aspergillus", "fumigatus", "medical", "microbiology", "microbial", "pathogens", "biology", "and", "life", "sciences", "microbiology", "fungal", "pathogens" ]	2014	ChIP-seq and In Vivo Transcriptome Analyses of the Aspergillus fumigatus SREBP SrbA Reveals a New Regulator of the Fungal Hypoxia Response and Virulence
Coordinated surveillance , vaccination and public information efforts have brought the Chinese rabies epizootic under control , but significant numbers of fatalities are still reported annually with some cases occurring in previously rabies free regions . Tibet has remained virtually rabies free for 16 years , but sinc...	Until recently , Tibet , “the third pole” of the earth , has been relatively isolated from the outside world , and has stayed rabies free for almost two decades . However , from 2015 to 2017 , one human case has been reported each year . Investigation of the origins of these cases revealed each of the three human cases...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "epizootics", "medicine", "and", "health", "sciences", "animal", "diseases", "body", "fluids", "pathology", "and", "laboratory", "medicine", "china", "pathogens", "tropical", "diseases", "geographical", "locations", "vertebrates", "microbiology", "saliva", "animals", "m...	2019	The reemergence of human rabies and emergence of an Indian subcontinent lineage in Tibet, China
Global Program to Eliminate Lymphatic Filariasis ( GPELF ) launched by WHO aims to eliminate the disease by 2020 . To achieve the goal annual mass drug administration ( MDA ) with diethylcarbamazine ( DEC ) plus albendazole ( ABZ ) has been introduced in all endemic countries . The current policy however excludes pregn...	Lymphatic filariasis , commonly known as elephantiasis , is a painful and profoundly disfiguring disease . A massive global effort has been undertaken to eliminate this disease by 2020 using annual mass drug administration ( MDA ) . However the MDA excludes pregnant women and children below two years of age , which are...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Maternal Infection Is a Risk Factor for Early Childhood Infection in Filariasis
The nematode Caenorhabditis briggsae is an emerging model organism that allows evolutionary comparisons with C . elegans and exploration of its own unique biological attributes . To produce a high-resolution C . briggsae recombination map , recombinant inbred lines were generated from reciprocal crosses between two str...	The nematode Caenorhabditis briggsae is increasingly used for comparisons with its more famous relative , C . elegans . To improve genomic resources for C . briggsae , we created two sets of inbred lines derived from crosses between diverged C . briggsae strains . High-throughput genotyping of these has improved the re...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "biology", "genomics", "evolutionary", "biology", "population", "biology", "genetics", "and", "genomics" ]	2011	Caenorhabditis briggsae Recombinant Inbred Line Genotypes Reveal Inter-Strain Incompatibility and the Evolution of Recombination
Public health interventions based on distribution of anthelminthic drugs against lymphatic filariasis ( LF ) , onchocerciasis , soil-transmitted helminthiasis ( STH ) and schistosomiasis have been implemented separately to date . A better use of available resources might be facilitated by a more coordinated approach to...	This paper describes how the use of three drugs which are used separately in mass drug distribution programmes when given together appear safe for use in large populations which have been previously treated with the same drugs separately ( Mectizan [ivermectin] , albendazole and praziquantel ) . The target diseases—lym...	[ "Abstract", "Introduction", "Methods", "Results", "Results", "Discussion" ]	[]	2008	Triple Co-Administration of Ivermectin, Albendazole and Praziquantel in Zanzibar: A Safety Study
Heat stress commonly leads to inhibition of photosynthesis in higher plants . The transcriptional induction of heat stress-responsive genes represents the first line of inducible defense against imbalances in cellular homeostasis . Although heat stress transcription factor HsfA2 and its downstream target genes are well...	As a consequence of global warming , increasing temperature is a serious threat to crop production worldwide and may influence the objectives of breeding programs . As a universal cellular response to a shift up in temperature , the heat stress response represents the first line of inducible defense against imbalances ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "chloroplast", "plant", "science", "plant", "biology", "plant", "cell", "biology", "plant", "genetics", "biology", "plant", "physiology" ]	2012	Downregulation of Chloroplast RPS1 Negatively Modulates Nuclear Heat-Responsive Expression of HsfA2 and Its Target Genes in Arabidopsis
Heme oxygenase 1 ( HO-1 ) is an essential enzyme induced by heme and multiple stimuli associated with critical illness . In humans , polymorphisms in the HMOX1 gene promoter may influence the magnitude of HO-1 expression . In many diseases including murine malaria , HO-1 induction produces protective anti-inflammatory ...	HO-1 is an important anti-inflammatory enzyme induced by several stimuli associated with critical illness . In humans , the amount of HO-1 produced is influenced by a genetic polymorphism in the gene promoter region . Using Plasmodium falciparum malaria that can cause a sepsis-like syndrome as an example , we character...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "tropical", "diseases", "(non-neglected)", "parasitic", "diseases", "critical", "care", "and", "emergency", "medicine" ]	2012	HMOX1 Gene Promoter Alleles and High HO-1 Levels Are Associated with Severe Malaria in Gambian Children
Enterococcus faecium , an ubiquous colonizer of humans and animals , has evolved in the last 15 years from an avirulent commensal to the third most frequently isolated nosocomial pathogen among intensive care unit patients in the United States . E . faecium combines multidrug resistance with the potential of horizontal...	Whole-genome sequencing has become instrumental in investigating the genome contents of bacteria . However , there is enormous diversity within bacterial populations , and annotation of multiple genomes is costly and elaborate . For investigating diversity and phylogeny within bacterial species , comparative genomic hy...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "evolutionary", "biology", "molecular", "biology", "eubacteria", "microbiology" ]	2007	Insertion Sequence–Driven Diversification Creates a Globally Dispersed Emerging Multiresistant Subspecies of E. faecium
In 2005 , the Government of Senegal embarked on a campaign to eliminate a Glossina palpalis gambiensis population from the Niayes area ( ∼1000 km2 ) under the umbrella of the Pan African Tsetse and Trypanosomosis Eradication Campaign ( PATTEC ) . The project was considered an ecologically sound approach to intensify ca...	In 2005 , the Government of Senegal embarked on a campaign to eliminate a tsetse population from the Niayes area ( ∼1000 km2 ) around Dakar in order to intensify cattle production . Three main cattle farming systems are present in this area: a traditional system using trypanotolerant cattle and two “improved” systems u...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "african", "trypanosomiasis", "development", "economics", "tropical", "diseases", "social", "sciences", "agricultural", "economics", "animals", "integrated", "control", "glossina", "pest", "control", "neglected", "...	2014	Ex-ante Benefit-Cost Analysis of the Elimination of a Glossina palpalis gambiensis Population in the Niayes of Senegal
The Global Program to Eliminate Lymphatic Filariasis ( GPELF ) advocates for the treatment of entire endemic communities , in order to achieve its elimination targets . LF is predominantly a rural disease , and achieving the required treatment coverage in these areas is much easier compared to urban areas that are more...	The control of lymphatic filariasis depends on the treatment of entire endemic communities , ensuring that a greater proportion of the population is treated . In urban areas , this can be very difficult to achieve . In Ghana , parts of the Greater Accra Region , where the capital city is located , are also endemic for ...	[ "Abstract", "Introduction", "Method", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "tropical", "diseases", "sports", "and", "exercise", "medicine", "parasitic", "diseases", "physical", "activity", "health", "care", "research", "design", "filariasis", "pharmaceutics", "neglected", "tropical", "diseases", "pharma...	2017	Improving drug delivery strategies for lymphatic filariasis elimination in urban areas in Ghana
The human liver fluke , Opisthorchis viverrini , infects millions of people throughout south-east Asia and is a major cause of cholangiocarcinoma , or cancer of the bile ducts . The mechanisms by which chronic infection with O . viverrini results in cholangiocarcinogenesis are multi-factorial , but one such mechanism i...	The oriental liver fluke is endemic through South-East Asia and is the major cause of cause of liver cancer in north-eastern Thailand . The molecules that are secreted by the parasite cause cells to multiply quicker than they normally would , and excessive cell growth is a key stage in the initiation of many cancers . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/helminth", "infections", "microbiology/parasitology" ]	2009	A Granulin-Like Growth Factor Secreted by the Carcinogenic Liver Fluke, Opisthorchis viverrini, Promotes Proliferation of Host Cells
Population-wide oscillations are ubiquitously observed in mesoscopic signals of cortical activity . In these network states a global oscillatory cycle modulates the propensity of neurons to fire . Synchronous activation of neurons has been hypothesized to be a separate channel of signal processing information in the br...	In network theory , statistics are often considered to be stationary . While this assumption can be justified by experimental insights to some extent , it is often also made for reasons of simplicity . However , the time-dependence of statistical measures do matter in many cases . For example , time-dependent processes...	[ "Abstract", "Introduction", "Results", "Methods", "Discussion" ]	[ "resonance", "frequency", "perturbation", "theory", "neural", "networks", "random", "variables", "neuroscience", "covariance", "probability", "distribution", "mathematics", "algebra", "network", "analysis", "quantum", "mechanics", "computer", "and", "information", "sciences...	2017	Locking of correlated neural activity to ongoing oscillations
Vesicular stomatitis virus ( VSV ) suppresses antiviral responses in infected cells by inhibiting host gene expression at multiple levels , including transcription , nuclear cytoplasmic transport , and translation . The inhibition of host gene expression is due to the activity of the viral matrix ( M ) protein . Previo...	All viruses have mechanisms to suppress or evade host antiviral responses . These mechanisms are critical for viral pathogenicity . Vesicular stomatitis virus ( VSV ) suppresses antiviral responses by global inhibition of host gene expression mediated by the viral matrix ( M ) protein . M protein interacts with the hos...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "infectious", "diseases", "viral", "diseases" ]	2012	Complexes of Vesicular Stomatitis Virus Matrix Protein with Host Rae1 and Nup98 Involved in Inhibition of Host Transcription
Mitochondrial dysfunction underlies numerous age-related pathologies . In an effort to uncover how the detrimental effects of mitochondrial dysfunction might be alleviated , we examined how the nematode C . elegans not only adapts to disruption of the mitochondrial electron transport chain , but in many instances respo...	In humans , mitochondrial dysfunction contributes to numerous age-related diseases , and indeed even aging itself . Yet organisms also have an amazing capacity to compensate for mitochondrial impairment , paradoxically sometimes even living longer for it . This is exemplified in the roundworm Caenorhabditis elegans . I...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "rna", "interference", "caenorhabditis", "gene", "regulation", "regulatory", "proteins", "immunology", "dna-binding", "proteins", "animals", "animal", "models", "caenorhabditis", "elegans", "model", "organisms", "t...	2016	DLK-1, SEK-3 and PMK-3 Are Required for the Life Extension Induced by Mitochondrial Bioenergetic Disruption in C. elegans
Differentiation of one life-cycle stage to the next is critical for survival and transmission of apicomplexan parasites . A number of studies have shown that stage differentiation is a stochastic process and is associated with a point that commits the cell to a change over in the pattern of gene expression . Studies on...	The ability of vector-borne Apicomplexan parasites ( Babesia , Plasmodium and Theileria ) to change from one life-cycle stage to the next is critical for establishment of infection and transmission to new hosts . Stage differentiation steps of both Plasmodium and Theileria are known to involve stochastic transition thr...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	ApiAP2 Factors as Candidate Regulators of Stochastic Commitment to Merozoite Production in Theileria annulata
We investigated genomic diversity of a yeast species that is both an opportunistic pathogen and an important industrial yeast . Under the name Candida krusei , it is responsible for about 2% of yeast infections caused by Candida species in humans . Bloodstream infections with C . krusei are problematic because most iso...	Infections with yeasts resistant to antifungal drugs are an increasing cause of concern . One species , Candida krusei , has innate resistance to the widely-used drug fluconazole . It is one of the five most prevalent causes of clinical yeast infections , and is responsible for significant levels of morbidity and morta...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "taxonomy", "medicine", "and", "health", "sciences", "yeast", "infections", "pathology", "and", "laboratory", "medicine", "chromosome", "structure", "and", "function", "centromeres", "pathogens", "microbiology", "sequence", "assembly", "tools", "fungi", "phylogenetics", ...	2018	Population genomics shows no distinction between pathogenic Candida krusei and environmental Pichia kudriavzevii: One species, four names
Differential modulation of NF-κB during meningococcal infection is critical in innate immune response to meningococcal disease . Non-invasive isolates of Neisseria meningitidis provoke a sustained NF-κB activation in epithelial cells . However , the hyperinvasive isolates of the ST-11 clonal complex ( ST-11 ) only indu...	Strains of Neisseria meningitidis isolated from patients induce apoptotic cell death , whereas strains isolated from healthy carriage isolates do not . Part of the difference has been shown to arise from differential modulation of NF-κB during meningococcal infection . While non-invasive isolates of Neisseria meningiti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Hyperinvasive Meningococci Induce Intra-nuclear Cleavage of the NF-κB Protein p65/RelA by Meningococcal IgA Protease
Very solid evidence suggests that the core of full length PrPSc is a 4-rung β-solenoid , and that individual PrPSc subunits stack to form amyloid fibers . We recently used limited proteolysis to map the β-strands and connecting loops that make up the PrPSc solenoid . Using high resolution SDS-PAGE followed by epitope a...	PrPSc Prions propagate by inducing the refolding of the natively folded normal cellular prion protein ( PrPC ) into the prion conformation in brain and other mammalian tissues ( wild-type ) . Understanding the structure of PrPSc is essential to understanding how PrPSc prions propagate . The secondary structure of PrPC ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "animal", "diseases", "prions", "metabolic", "processes", "vertebrates", "animals", "mammals", "animal", "models", "animal", "prion", "diseases", "model", "organisms", "proteolysis", "experimental", "organism", "systems", "centri...	2018	Recombinant PrPSc shares structural features with brain-derived PrPSc: Insights from limited proteolysis
It has recently been appreciated that NK cells exhibit many features reminiscent of adaptive immune cells . Considerable heterogeneity exists with respect to the ligand specificity of individual NK cells and as such , a subset of NK cells can respond , expand , and differentiate into memory-like cells in a ligand-speci...	Natural killer ( NK ) cells are important cells of the immune system , because they kill abnormal cells such as those infected with viruses or have become cancerous . These abnormal cells can lose proteins known as MHC molecules , which are recognized by inhibitory receptors on NK cells . Thus , when an NK cell interac...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "gene", "regulation", "regulatory", "proteins", "immunology", "dna-binding", "proteins", "dna", "transcription", "immune", "receptor", "signaling", "signal", "inhibition", "clinical", "medicin...	2016	Activating Receptor Signals Drive Receptor Diversity in Developing Natural Killer Cells
An optimal HIV vaccine should induce broadly neutralizing antibodies ( bnAbs ) that neutralize diverse viral strains and subtypes . However , potent bnAbs develop in only a small fraction of HIV-infected individuals , all contain rare features such as extensive mutation , insertions , deletions , and/or long complement...	Many HIV vaccine design efforts aim to elicit so-called broadly neutralizing antibodies that bind and neutralize diverse strains and subtypes of the virus . However , these efforts are guided by very unusual antibodies isolated from HIV-infected individuals . These antibodies have rare features that limit their use as ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "deletion", "mutation", "medicine", "and", "health", "sciences", "microbial", "mutation", "immune", "physiology", "crystal", "structure", "pathology", "and", "laboratory", "medicine", "insertion", "mutation", "pathogens", "immunology", "condens...	2016	Minimally Mutated HIV-1 Broadly Neutralizing Antibodies to Guide Reductionist Vaccine Design
Bacterial communities are taxonomically highly diverse , yet the mechanisms that maintain this diversity remain poorly understood . We hypothesized that an obligate and mutual exchange of metabolites , as is very common among bacterial cells , could stabilize different genotypes within microbial communities . To test t...	Natural bacterial communities are usually very species-rich and bacterial cells within these communities often exchange metabolites with each other . Whether and to which extent obligate metabolic interactions can contribute to maintaining the observed bacterial diversity , however , is not known . In this study , we a...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "cell", "physiology", "ecology", "and", "environmental", "sciences", "population", "genetics", "cell", "metabolism", "metabolites", "molecular", "biology", "techniques", "population", "biology", "bacteria", "research", "and", "analysis", "methods", "amino", "acid", "ana...	2016	Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities
Dengue is endemic in more than 100 countries , mainly in tropical and subtropical regions , and the incidence has increased 30-fold in the past 50 years . The situation of dengue in China has become more and more severe , with an unprecedented dengue outbreak hitting south China in 2014 . Building a dengue early warnin...	Dengue has emerged as the most important mosquito-borne viral disease globally . With increasing global trade and population movement , the disease is transferred to regions which were previously dengue free . When dengue vector exists and weather factors are suitable , there is the possibility for dengue transmission ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Predicting Unprecedented Dengue Outbreak Using Imported Cases and Climatic Factors in Guangzhou, 2014
The essential and distinct functions of Protein Phosphatase type 1 ( PP1 ) catalytic subunit in eukaryotes are exclusively achieved through its interaction with a myriad of regulatory partners . In this work , we report the molecular and functional characterization of Gametocyte EXported Protein 15 ( GEXP15 ) , a Plasm...	In the absence of an effective vaccine and the emerging resistance to artemisinin combination therapy , malaria is still a significant threat to human health . Increasing our understanding of the specific mechanisms of the biology of Plasmodium is essential to propose new strategies to control this infection . Here , w...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "parasite", "groups", "medicine", "and", "health", "sciences", "plasmodium", "gene", "regulation", "enzymes", "gametocytes", "regulatory", "proteins", "dna-binding", "proteins", "enzymology", "parasitic", "diseases", "parasitology", "phosphatases", "germ"...	2019	Essential role of GEXP15, a specific Protein Phosphatase type 1 partner, in Plasmodium berghei in asexual erythrocytic proliferation and transmission
The relative female and male contributions to demography are of great importance to better understand the history and dynamics of populations . While earlier studies relied on uniparental markers to investigate sex-specific questions , the increasing amount of sequence data now enables us to take advantage of tens to h...	The history of populations and their social organization is often intricate due to breeding structures , migration patterns or population bottlenecks . Estimation of the female proportion of the effective population ( sex ratio ) is therefore important to better understand this underlying social structure and dynamics ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods", "Program", "availability" ]	[ "taxonomy", "medicine", "and", "health", "sciences", "ruminants", "vertebrates", "animals", "mammals", "alleles", "phylogenetics", "data", "management", "x-linked", "traits", "phylogenetic", "analysis", "amniotes", "molecular", "genetics", "population", "biology", "comput...	2018	Inferring sex-specific demographic history from SNP data
Protein contacts contain key information for the understanding of protein structure and function and thus , contact prediction from sequence is an important problem . Recently exciting progress has been made on this problem , but the predicted contacts for proteins without many sequence homologs is still of low quality...	Protein contact prediction and contact-assisted folding has made good progress due to direct evolutionary coupling analysis ( DCA ) . However , DCA is effective on only some proteins with a very large number of sequence homologs . To further improve contact prediction , we borrow ideas from deep learning , which has re...	[ "Abstract", "Introduction", "Results", "Conclusion", "and", "Discussion", "Method" ]	[ "neural", "networks", "split-decomposition", "method", "neuroscience", "membrane", "proteins", "multiple", "alignment", "calculation", "mathematics", "forecasting", "statistics", "(mathematics)", "protein", "structure", "prediction", "protein", "structure", "convolution", "pr...	2017	Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model
A possible role for Toxoplasma gondii in the etiopathogenesis of schizophrenia is supported by epidemiological studies and animal models of infection . However , recent studies attempting to link Toxoplasma to schizophrenia have yielded mixed results . We performed a nested case-control study measured serological evide...	The protozoan parasite Toxoplasma gondii has been previously associated with an increased risk of serious psychiatric disorders such as schizophrenia . However , this association has been found in some studies and not others . We examined whether the differences among previous studies might be explained by the timing o...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "psychoses", "medicine", "and", "health", "sciences", "toxoplasma", "gondii", "bipolar", "disorder", "parasitic", "protozoans", "protozoans", "mathematics", "toxoplasma", "statistics", "(mathematics)", "mood", "disorders", "research", "and", "analysis", "methods", "mathem...	2017	Evidence of increased exposure to Toxoplasma gondii in individuals with recent onset psychosis but not with established schizophrenia
An overwhelming neutrophil-driven response causes both acute symptoms and the lasting sequelae that result from infection with Neisseria gonorrhoeae . Neutrophils undergo an aggressive opsonin-independent response to N . gonorrhoeae , driven by the innate decoy receptor CEACAM3 . CEACAM3 is exclusively expressed by hum...	Gonorrhea is a sexually transmitted infection caused by the bacteria Neisseria gonorrhoeae . These bacteria have re-emerged as a public health priority due to its acquisition of resistance to multiple antibiotics , leading to fears of untreatable infection . The symptoms of gonorrhea include an intense inflammatory res...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacterial", "diseases", "infectious", "diseases", "gonorrhea", "medicine", "and", "health", "sciences", "sexually", "transmitted", "diseases", "population", "modeling", "biology", "and", "life", "sciences", "infectious", "disease", "modeling", "computational", "biology" ...	2014	Global Analysis of Neutrophil Responses to Neisseria gonorrhoeae Reveals a Self-Propagating Inflammatory Program
Chagas disease , caused by the protozoan parasite Trypanosoma cruzi , presents a variable clinical course , varying from asymptomatic to serious debilitating pathologies with cardiac , digestive or cardio-digestive impairment . Previous studies using two clonal T . cruzi populations , Col1 . 7G2 ( T . cruzi I ) and JG ...	Chagas disease , caused by the protozoan parasite Trypanosoma cruzi , presents a variable clinical course , varying from asymptomatic to serious debilitating pathologies with cardiac , digestive or cardio-digestive impairment . It has been suggested that parasite differential tissue tropism is responsible for the devel...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "respiratory", "infections", "oxidative", "stress", "enzymes", "microbiology", "enzymology", "parasitic", "diseases", "parasitic", "protozoans", "pulmonology", "protozoan", "life", "cycles", "developmental", "biology", "protozoans", ...	2017	Cardiomyocyte oxidants production may signal to T. cruzi intracellular development
The evolutionarily conserved family of AP-2 transcription factors ( TF ) regulates proliferation , differentiation , and apoptosis . Mutations in human AP-2 TF have been linked with bronchio-occular-facial syndrome and Char Syndrome , congenital birth defects characterized by craniofacial deformities and patent ductus ...	Mutations in the evolutionarily conserved family of AP-2 transcription factors are associated with multiple birth defects in Char syndrome and Brancio-oculo-facial syndrome . These DNA-binding proteins are known to regulate the proliferation , differentiation and death of specific cells during embryonic development but...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "caenorhabditis", "gene", "regulation", "cell", "cycle", "and", "cell", "division", "regulatory", "proteins", "cell", "processes", "dna-binding", "proteins", "animals", "animal", "models", "developmental", "biology", "caenorhabditis", "elegans", "mutation...	2016	The AP-2 Transcription Factor APTF-2 Is Required for Neuroblast and Epidermal Morphogenesis in Caenorhabditis elegans Embryogenesis
Algorithms to diagnose gambiense human African trypanosomiasis ( HAT , sleeping sickness ) are often complex due to the unsatisfactory sensitivity and/or specificity of available tests , and typically include a screening ( serological ) , confirmation ( parasitological ) and staging component . There is insufficient ev...	Gambiense human African trypanosomiasis ( HAT , sleeping sickness ) usually features low prevalence . The two stages of the disease require different treatments , and stage 2 is fatal if untreated . HAT diagnosis must therefore be highly sensitive ( i . e . , detect as many true cases as possible ) and specific ( i . e...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "neglected", "tropical", "diseases" ]	2011	Accuracy of Five Algorithms to Diagnose Gambiense Human African Trypanosomiasis
When malaria parasites infect host red blood cells ( RBC ) and proteolyze hemoglobin , a unique , albeit poorly understood parasite-specific mechanism , detoxifies released heme into hemozoin ( Hz ) . Here , we report the identification and characterization of a novel Plasmodium Heme Detoxification Protein ( HDP ) that...	Each year , more than one million people , most of them children under the age of 5 , succumb to malaria , a devastating disease caused by Plasmodium parasites . The parasite resides inside the red blood cells of the host , where , during its development , it proteolyzes vast amounts of host hemoglobin . This degradati...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/protozoal", "infections", "infectious", "diseases/tropical", "and", "travel-associated", "diseases" ]	2008	HDP—A Novel Heme Detoxification Protein from the Malaria Parasite
Leishmania mexicana can cause both localized ( LCL ) and diffuse ( DCL ) cutaneous leishmaniasis , yet little is known about factors regulating disease severity in these patients . We analyzed if the disease was associated with single nucleotide polymorphisms ( SNPs ) in IL-1β ( −511 ) , CXCL8 ( −251 ) and/or the inhib...	Leishmania mexicana is an intracellular parasite that causes two polarly opposed diseases: One is a self-limited disease , characterized by ulcerative lesions associated with a low infectious load , as found in patients with localized cutaneous leishmaniasis ( LCL ) . And the other pole is characterized by a progressiv...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "immunopathology", "infectious", "diseases", "inflammation", "clinical", "immunology", "immunity", "innate", "immunity", "leishmaniasis", "immunity", "to", "infections", "immunology", "parasitic", "diseases", "immune", "response" ]	2012	Disease Severity in Patients Infected with Leishmania mexicana Relates to IL-1β
Spatio-temporal dynamics of intracellular calcium , [Ca2+]i , regulate the contractile function of cardiac muscle cells . Measuring [Ca2+]i flux is central to the study of mechanisms that underlie both normal cardiac function and calcium-dependent etiologies in heart disease . However , current imaging techniques are l...	Calcium ( Ca2+ ) acts as a signal for many functions in the heart cell , from its primary role in triggering contractions during the heartbeat to acting as a signal for cell growth . Cellular function is tightly coupled to its ultra-structural organization . Spatially-realistic and biophysics-based computational models...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Examination of the Effects of Heterogeneous Organization of RyR Clusters, Myofibrils and Mitochondria on Ca2+ Release Patterns in Cardiomyocytes
Cytological and genetic evidence suggests that the Bacillus subtilis DNA uptake machinery localizes at a single cell pole and takes up single-stranded ( ss ) DNA . The integration of homologous donor DNA into the recipient chromosome requires RecA , while plasmid establishment , which is independent of RecA , requires ...	Many bacteria can actively acquire novel genetic material from their environment , which leads to the rapid spreading of , for example , antibiotic resistance genes . The bacterium Bacillus subtilis can differentiate into the state of competence , in which cells take up ssDNA through a DNA uptake complex that is specif...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "developmental", "biology/microbial", "growth", "and", "development", "cell", "biology/microbial", "growth", "and", "development", "biochemistry/replication", "and", "repair", "molecular", "biology/dna",...	2009	Evidence for Different Pathways during Horizontal Gene Transfer in Competent Bacillus subtilis Cells
Buruli ulcer , the third mycobacterial disease after tuberculosis and leprosy , is caused by the environmental mycobacterium M . ulcerans . Various modes of transmission have been suspected for this disease , with no general consensus acceptance for any of them up to now . Since laboratory models demonstrated the abili...	Buruli ulcer , caused by Mycobacterium ulcerans , is a devastating skin disease . Most cases of Buruli ulcer occur in poor rural communities . As a result , treatment is frequently sought too late and about 25% of those infected—particularly children—become permanently disabled . Outbreaks of Buruli ulcer have always b...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "ecology/community", "ecology", "and", "biodiversity", "microbiology/applied", "microbiology", "ecology/ecosystem", "ecology" ]	2010	Seasonal and Regional Dynamics of M. ulcerans Transmission in Environmental Context: Deciphering the Role of Water Bugs as Hosts and Vectors
Leprosy is a chronic infectious disease neglected , caused by Mycobacterium leprae , considered a public health problem because may cause permanent physical disabilities and deformities , leading to severe limitations . This review presents an overview of the results of epidemiological studies on leprosy occurrence in ...	Leprosy remains as a severe health problem in Brazil and its transmission in children under 15 years of age occurs mainly through intradomiciliary contacts . The number of leprosy cases in this age group is considered an important indicator for the surveillance of this disease . To understand how the epidemiological st...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "children", "medicine", "and", "health", "sciences", "disabilities", "tropical", "diseases", "geographical", "locations", "database", "searching", "bacterial", "diseases", "age", "groups", "neglected", "tropical", "diseases", "families", "research", "and", "analysis", "...	2018	Leprosy in children under 15 years of age in Brazil: A systematic review of the literature
The increased reliability and efficiency of the quantitative polymerase chain reaction ( qPCR ) makes it a promising tool for performing large-scale screening for infectious disease among high-risk individuals . To date , no study has evaluated the specificity and sensitivity of different qPCR assays for leprosy diagno...	Leprosy is a chronic infectious disease caused by Mycobacterium leprae an obligate intracellular pathogen that can infect cells in skin and nerves . Leprosy still affects 211 , 903 individuals per year worldwide and lead to permanent nerve injury that is generally associated with late diagnosis . The mechanisms of inte...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biotechnology", "biochemistry", "genomics", "mathematics", "nucleic", "acids", "statistics", "molecular", "genetics", "biology", "computational", "biology" ]	2011	Evaluation of qPCR-Based Assays for Leprosy Diagnosis Directly in Clinical Specimens
Boundary vector cells in entorhinal cortex fire when a rat is in locations at a specific distance from walls of an environment . This firing may originate from memory of the barrier location combined with path integration , or the firing may depend upon the apparent visual input image stream . The modeling work present...	Over the past few decades a variety of cells in hippocampal structures have been analyzed and their function has been identified . Head direction cells indicate the world-centered direction of the animals head like a compass . Place cells fire in locations associated with visual , auditory , or olfactory cues . Grid ce...	[ "Abstract", "Introduction", "Results", "Discussion", "Model" ]	[ "computer", "science", "computer", "modeling", "mathematics", "geometry", "neural", "networks", "computational", "neuroscience", "synthetic", "vision", "systems", "biology", "differential", "geometry", "neuroscience", "neurophysiology" ]	2012	Modeling Boundary Vector Cell Firing Given Optic Flow as a Cue
Differences in immune activation were identified as the most significant difference between AIDS-susceptible and resistant species . p38 MAPK , activated in HIV infection , is key to induction of interferon-stimulated genes and cytokine-mediated inflammation and is associated with some of the pathology produced by HIV ...	The hallmark of Human Immunodeficiency Virus and Simian Immunodeficiency Virus infection in disease-susceptible species is the progressive decline of the CD4+ T cell population and heightened immune activation , which by itself can contribute to CD4+ T-cell death . The cellular pathway regulated by p38 MAPK , which is ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "cytokines", "immune", "activation", "pathogens", "immunology", "microbiology", "vertebrates...	2018	Inhibition of p38 MAPK in combination with ART reduces SIV-induced immune activation and provides additional protection from immune system deterioration
The ability to control lentivirus replication may be determined , in part , by the extent to which individual viral proteins are targeted by the immune system . Consequently , defining the antigens that elicit the most protective immune responses may facilitate the design of effective HIV-1 vaccines . Here we vaccinate...	There is still some uncertainty as to which HIV-1 proteins should be targeted by vaccine-induced immune responses . Indeed , studies of primary HIV-1 and SIV infections have reported that T-cell responses against different viral proteins can influence viral replication levels . To understand which antigens elicit the a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "vertebrates", "animals", "mammals", "retroviruses", "primates", "immunodeficienc...	2017	Vaccine-induced immune responses against both Gag and Env improve control of simian immunodeficiency virus replication in rectally challenged rhesus macaques
Convergent adaptation occurs at the genome scale when independently evolving lineages use the same genes to respond to similar selection pressures . These patterns of genetic repeatability provide insights into the factors that facilitate or constrain the diversity of genetic responses that contribute to adaptive evolu...	How many ways can evolution solve the same adaptive problem ? While convergent adaptation is evident in many organisms at the phenotypic level , we are only beginning to understand how commonly this convergence extends to the genome scale . Quantifying the repeatability of adaptation at the genome scale is therefore cr...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "ecological", "metrics", "mutation", "ecology", "and", "environmental", "sciences", "species", "diversity", "quantitative", "trait", "loci", "ecology", "natural", "selection", "genetics", "biology", "and", "life", "sciences", "evolutionary", "adaptation", "convergent", ...	2018	Quantifying how constraints limit the diversity of viable routes to adaptation
Many biological systems perform computations on inputs that have very large dimensionality . Determining the relevant input combinations for a particular computation is often key to understanding its function . A common way to find the relevant input dimensions is to examine the difference in variance between the input...	In many areas of computational biology , including the analyses of genetic mutations , protein stability and neural coding , as well as in economics , one of the most basic and important steps of data analysis is to find the relevant input dimensions for a particular task . In neural coding problems , the spike-trigger...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Spike Triggered Covariance in Strongly Correlated Gaussian Stimuli
Traumatic brain injury often leads to epileptic seizures . Among other factors , homeostatic synaptic plasticity ( HSP ) mediates posttraumatic epileptogenesis through unbalanced synaptic scaling , partially compensating for the trauma-incurred loss of neural excitability . HSP is mediated in part by tumor necrosis fac...	Homeostatic plasticity refers to the ability of neurons and neuronal circuitry to adjust their properties in order to maintain physiologically relevant electrical activity notwithstanding perturbations in synaptic input . Synaptic input is often chronically reduced immediately following brain trauma , and previous stud...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biochemistry", "theoretical", "biology", "neurological", "disorders", "neurology", "biology", "computational", "biology", "neuroscience" ]	2013	Divide and Conquer: Functional Segregation of Synaptic Inputs by Astrocytic Microdomains Could Alleviate Paroxysmal Activity Following Brain Trauma
Acute Epstein-Barr virus ( EBV ) infection is the most common cause of Infectious Mononucleosis . Nearly all adult humans harbor life-long , persistent EBV infection which can lead to development of cancers including Hodgkin Lymphoma , Burkitt Lymphoma , nasopharyngeal carcinoma , gastric carcinoma , and lymphomas in i...	Epstein-Barr virus ( EBV ) is a herpesvirus that persistently infects nearly all humans by adulthood . Acute and persistent phases of EBV infection are associated with a variety of human diseases , including infectious mononucleosis and cancer . To investigate how EBV interacts with the host to successfully establish a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viruses", "and", "cancer", "animal", "models", "of", "infection", "viral", "immune", "evasion", "immunity", "virology", "innate", "immunity", "viral", "persistence", "and", "latency", "immunity", "to", "infections", "immunology", "biology", "microbiology", "viral", ...	2012	An Epstein-Barr Virus Encoded Inhibitor of Colony Stimulating Factor-1 Signaling Is an Important Determinant for Acute and Persistent EBV Infection
Melanin protects the skin and eyes from the harmful effects of UV irradiation , protects neural cells from toxic insults , and is required for sound conduction in the inner ear . Aberrant regulation of melanogenesis underlies skin disorders ( melasma and vitiligo ) , neurologic disorders ( Parkinson's disease ) , audit...	Aberrant pigment regulation correlates with skin disorders , opthalmologic disorders , and neurologic disorders . While extensive studies have identified regulators of mouse coat color , the regulation of human skin phenotypic variation is less well understood . To give a broader picture of the molecular regulators of ...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "genetics", "and", "genomics/functional", "genomics", "pharmacology/drug", "development", "cell", "biology/membranes", "and", "sorting", "dermatology/pigmentary", "disorders", "cell", "biology/gene", "expression" ]	2008	Genome-Wide siRNA-Based Functional Genomics of Pigmentation Identifies Novel Genes and Pathways That Impact Melanogenesis in Human Cells
Human schistosomiasis is a highly prevalent neglected tropical disease ( NTD ) caused by Schistosoma species . Research on the molecular mechanisms influencing the outcomes of bladder infection by Schistosoma haematobium is urgently needed to develop new diagnostics , therapeutics and infection prevention strategies . ...	The human microbiome comprises bacteria ( plus viruses , fungi and archeae ) inhabiting different sites of the body . They do not specifically cause diseases , but their presence , absence or population influence body functions . We therefore examined such organisms found along the urinary tract , in persons living in ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusion" ]	[ "fusobacterium", "infections", "medicine", "and", "health", "sciences", "body", "fluids", "microbiome", "acinetobacter", "infections", "enterococcus", "infections", "tropical", "diseases", "microbiology", "bladder", "parasitic", "diseases", "urine", "bacterial", "diseases",...	2017	The microbiome in urogenital schistosomiasis and induced bladder pathologies
MicroRNAs ( miRNAs ) , a large class of short noncoding RNAs found in many plants and animals , often act to post-transcriptionally inhibit gene expression . We report the generation of deletion mutations in 87 miRNA genes in Caenorhabditis elegans , expanding the number of mutated miRNA genes to 95 , or 83% of known C...	MicroRNAs ( miRNAs ) are tiny endogenous RNAs that regulate gene expression in plants and animals . Individual miRNAs have important roles in development , immunity , and cancer . Although the investigation of miRNA function is of great importance , to date few miRNAs have been studied in the intact organism because of...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "caenorhabditis", "genetics", "and", "genomics", "developmental", "biology", "molecular", "biology" ]	2007	Most Caenorhabditis elegans microRNAs Are Individually Not Essential for Development or Viability
HIV-1 envelope glycoprotein ( Env ) mediates virus attachment and entry into the host cells . Like other membrane-bound and secreted proteins , HIV-1 Env contains at its N terminus a signal peptide ( SP ) that directs the nascent Env to the endoplasmic reticulum ( ER ) where Env synthesis and post-translational modific...	HIV-1 envelope glycoprotein ( Env ) is indispensable for virus infection . HIV-1 Env contains at its N terminus a signal peptide ( SP ) that directs the protein to the endoplasmic reticulum . The SP sequences exhibits high variability among HIV-1 isolates , and the significance of such variability is unclear . We hypot...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "microbial", "mutation", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "293t", "cells", "pathogens", "biological", "cultures", "immunology", "microbiology", "viral", "structure", "...	2018	Alterations of HIV-1 envelope phenotype and antibody-mediated neutralization by signal peptide mutations
In mammals , the circadian clock allows them to anticipate and adapt physiology around the 24 hours . Conversely , metabolism and food consumption regulate the internal clock , pointing the existence of an intricate relationship between nutrient state and circadian homeostasis that is far from being understood . The St...	Circadian rhythmicity is part of our innate behavior and controls many physiological processes , such as sleeping and waking , activity , neurotransmitter production and a number of metabolic pathways . In mammals , the central circadian pacemaker in the hypothalamus is entrained on a daily basis by environmental cues ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2014	Genome-Wide Analysis of SREBP1 Activity around the Clock Reveals Its Combined Dependency on Nutrient and Circadian Signals
Manipulation of the mosquito gut microbiota can lay the foundations for novel methods for disease transmission control . Mosquito blood feeding triggers a significant , transient increase of the gut microbiota , but little is known about the mechanisms by which the mosquito controls this bacterial growth whilst limitin...	When a female mosquito takes a blood meal from a human , the bacteria residing within its gut grow significantly . Following a blood meal , female mosquitoes produce a barrier within their gut , known as the peritrophic matrix , which physically separates the blood meal from the cells of the epithelium . Here , we show...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "antimicrobials", "chitin", "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "microbiome", "gut", "bacteria", "drugs", "microbiology", "animals", "antibiotics", "enterobacteriaceae", "materials", "science", "pharmacology", "insect", "vectors", "...	2017	Microbiota-induced peritrophic matrix regulates midgut homeostasis and prevents systemic infection of malaria vector mosquitoes
The pathogenic yeast Cryptococcus neoformans causes cryptococcosis , a life-threatening fungal disease . C . neoformans has multiple virulence mechanisms that are non-host specific , induce damage and interfere with immune clearance . Microarray analysis of C . neoformans strains serially passaged in mice associated a ...	C . neoformans is a pathogenic yeast that is the causative agent of cryptococcal meningitis . This fungal pathogen causes disease in immune compromised hosts , primarily AIDS patients in developing countries , though it also afflicts organ transplant patients and patients undergoing chemotherapy . There are >600 , 000 ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cryptococcus", "neoformans", "medicine", "and", "health", "sciences", "cryptococcus", "protein", "metabolism", "pathology", "and", "laboratory", "medicine", "fungal", "genetics", "pathogens", "microbiology", "fungi", "bioassays", "and", "physiological", "analysis", "fung...	2016	A Small Protein Associated with Fungal Energy Metabolism Affects the Virulence of Cryptococcus neoformans in Mammals
Circadian clocks are biological timekeepers that allow living cells to time their activity in anticipation of predictable daily changes in light and other environmental factors . The complexity of the circadian clock in higher plants makes it difficult to understand the role of individual genes or molecular interaction...	Like most living organisms , plants are dependent on sunlight , and evolution has endowed them with an internal clock by which they can predict sunrise and sunset . The clock consists of many genes that control each other in a complex network , leading to daily oscillations in protein levels . The interactions between ...	[ "Abstract", "Introduction", "Results", "Methods", "Discussion" ]	[ "systems", "biology", "physiological", "processes", "computer", "and", "information", "sciences", "network", "analysis", "physiology", "chronobiology", "biology", "and", "life", "sciences", "regulatory", "networks", "computational", "biology", "computerized", "simulations" ...	2014	Rethinking Transcriptional Activation in the Arabidopsis Circadian Clock
Levels of certain circulating short-chain dicarboxylacylcarnitine ( SCDA ) , long-chain dicarboxylacylcarnitine ( LCDA ) and medium chain acylcarnitine ( MCA ) metabolites are heritable and predict cardiovascular disease ( CVD ) events . Little is known about the biological pathways that influence levels of most of the...	Cardiovascular disease is a strongly heritable trait . Despite application of the latest genomic technologies , the genetic architecture of disease risk remains poorly defined , and mechanisms underlying this susceptibility are incompletely understood . In this study , we performed genome-wide mapping of heart disease-...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Metabolomic Quantitative Trait Loci (mQTL) Mapping Implicates the Ubiquitin Proteasome System in Cardiovascular Disease Pathogenesis
In this study we show that incentives ( dog collars and owner wristbands ) are effective at increasing owner participation in mass dog rabies vaccination clinics and we conclude that household questionnaire surveys and the mark-re-sight ( transect survey ) method for estimating post-vaccination coverage are accurate wh...	It is estimated that 59 , 000 people die from canine-mediated rabies each year , over 99% in developing countries where rabies is endemic and nearly half of the victims are children . The annual global cost has been estimated at 8 . 6 billion dollars . Yet with highly effective vaccines and a single species of reservoi...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Incentives Increase Participation in Mass Dog Rabies Vaccination Clinics and Methods of Coverage Estimation Are Assessed to Be Accurate
Population bottlenecks followed by re-expansions have been common throughout history of many populations . The response of alleles under selection to such demographic perturbations has been a subject of great interest in population genetics . On the basis of theoretical analysis and computer simulations , we suggest th...	Dominance has played a central role in classical genetics since its inception . However , the effect of dominance introduces substantial technical complications into theoretical models describing dynamics of alleles in populations . As a result , dominance is often ignored in population genetic models . Statistical tes...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Dominance of Deleterious Alleles Controls the Response to a Population Bottleneck
The human papillomavirus DNA genome undergoes three distinct stages of replication: establishment , maintenance and amplification . We show that the HPV16 E6 protein is required for the maintenance of the HPV16 DNA genome as an extrachromosomal , nuclear plasmid in its natural host cell , the human keratinocyte . Based...	Human papillomaviruses ( HPVs ) infect epithelial tissues . HPVs that infect mucosal epithelia cause infectious lesions in the anogenital tract and oral cavity . HPV infections are normally cleared by the immune system; however , in rare cases , infections can persist for years . Persistent infections by certain HPVs p...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2013	Inactivation of p53 Rescues the Maintenance of High Risk HPV DNA Genomes Deficient in Expression of E6
Syndromes of hybrid dysgenesis ( HD ) have been critical for our understanding of the transgenerational maintenance of genome stability by piRNA . HD in D . virilis represents a special case of HD since it includes simultaneous mobilization of a set of TEs that belong to different classes . The standard explanation for...	Transposable elements ( TE ) can proliferate in genomes even if harmful . In response , mechanisms of small-RNA silencing have evolved to repress germline TE activity . Syndromes of hybrid dysgenesis in Drosophila—where unregulated TE activity in the germline causes sterility—have also revealed that maternal piRNAs pla...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Conclusions", "Materials", "and", "methods" ]	[ "sequencing", "techniques", "invertebrates", "medicine", "and", "health", "sciences", "reproductive", "system", "gene", "regulation", "invertebrate", "genomics", "animals", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "experimental", "organism", ...	2018	Spontaneous gain of susceptibility suggests a novel mechanism of resistance to hybrid dysgenesis in Drosophila virilis
Leptospirosis is an important zoonotic disease that causes considerable morbidity and mortality globally , primarily in residents of urban slums . While contact with contaminated water plays a critical role in the transmission of leptospirosis , little is known about the distribution and abundance of pathogenic Leptosp...	Leptospirosis is a globally distributed zoonotic disease that disproportionately affects vulnerable populations in urban slums . The disease is transmitted by direct contact with water , soil , or mud that has been contaminated with infected urine shed from chronically infected animals . Despite the critical role the e...	[ "Abstract", "Introduction", "Methods", "Results", "and", "discussion" ]	[ "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "animal", "pathogens", "leptospira", "zoonotic", "pathogens", "pathology", "and", "laboratory", "medicine", "engineering", "and", "technology", "sewage", "pathogens", "tropical", "di...	2018	Quantification of pathogenic Leptospira in the soils of a Brazilian urban slum
Mycetoma is a neglected , chronic , localized , progressively destructive , granulomatous infection caused either by fungi ( eumycetoma ) or by aerobic actinomycetes ( actinomycetoma ) . It is characterized by a triad of painless subcutaneous mass , multiple sinuses and discharge containing grains . Mycetoma commonly a...	Mycetoma is a neglected tropical disease caused either by fungi or aerobic actinomycetes . It predominantly affects poor people in remote communities , where access to health care is very limited and people usually rely on traditional treatment . The incidence of mycetoma in the Lao PDR is not known , although the firs...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Discussion", "Conclusion" ]	[]	2015	Case Report: Actinomycetoma Caused by Nocardia aobensis from Lao PDR with Favourable Outcome after Short-Term Antibiotic Treatment
Post-translational protein modifications such as phosphorylation and ubiquitinylation are common molecular targets of conflict between viruses and their hosts . However , the role of other post-translational modifications , such as ADP-ribosylation , in host-virus interactions is less well characterized . ADP-ribosylat...	The outcome of viral infections is determined by the repertoire and specificity of the antiviral genes in a particular animal species . The identification of candidate immunity genes and mechanisms is a key step in describing this repertoire . Despite advances in genome sequencing , identification of antiviral genes ha...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "innate", "immune", "system", "genetics", "of", "the", "immune", "system", "clinical", "immunology", "immunity", "biology", "and", "life", "sciences", "comparative", "genomics", "immunology", "computational", "biology", "evolutionary", "biology", "evolutionary", "geneti...	2014	Rapid Evolution of PARP Genes Suggests a Broad Role for ADP-Ribosylation in Host-Virus Conflicts
In resource-poor areas , infectious diseases may be important causes of morbidity among individuals infected with the Human T-Lymphotropic Virus type 1 ( HTLV-1 ) . We report the clinical associations of HTLV-1 infection among socially disadvantaged Indigenous adults in central Australia . HTLV-1 serological results fo...	The Human T-Lymphotropic Virus type 1 ( HTLV-1 ) infects at least 5–10 million people worldwide . In developed countries , the most frequently reported HTLV-1 associated diseases include a fatal hematological malignancy , Adult T-cell Leukemia/Lymphoma ( ATLL ) , and the neurological disorder , HTLV-1 associated myelop...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine" ]	2014	Clinical Associations of Human T-Lymphotropic Virus Type 1 Infection in an Indigenous Australian Population
The role of glia in modulating neuronal network activity is an important question . Oligodendrocyte precursor cells ( OPC ) characteristically express the transmembrane proteoglycan nerve-glia antigen 2 ( NG2 ) and are unique glial cells receiving synaptic input from neurons . The development of NG2+ OPC into myelinati...	Although glial cells substantially outnumber neurons in the mammalian brain , much remains to be discovered regarding their functions . Among glial cells , oligodendrocyte precursors differentiate into oligodendrocytes , whose function is to enwrap nerves with myelin to ensure proper impulse conduction . However , olig...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "specimen", "preparation", "and", "treatment", "molecular", "neuroscience", "mechanical", "treatment", "of", "specimens", "cellular", "neuroscience", "behavioral", "neuroscience", "specimen", "disruption", "neural", "networks", "biology", "and", "life", "sciences", "elect...	2014	Oligodendrocyte Precursor Cells Modulate the Neuronal Network by Activity-Dependent Ectodomain Cleavage of Glial NG2
The intricate interactions between viruses and hosts include an evolutionary arms race and adaptation that is facilitated by the ability of RNA viruses to evolve rapidly due to high frequency mutations and genetic RNA recombination . In this paper , we show evidence that the co-opted cellular DDX3-like Ded1 DEAD-box he...	A major force in virus evolution is the ability of viruses to recombine and change their genomes rapidly . Similar to viral replication that greatly depends on subverted cellular proteins , viral genetic recombination is also affected by host factors based on genome-wide screens with tomato bushy stunt virus ( TBSV ) i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Coordinated Function of Cellular DEAD-Box Helicases in Suppression of Viral RNA Recombination and Maintenance of Viral Genome Integrity
In preparation for dramatic morphogenetic events of gastrulation , rapid embryonic cell cycles slow at the mid-blastula transition ( MBT ) . In Drosophila melanogaster embryos , down-regulation of cyclin-dependent kinase 1 ( Cdk1 ) activity initiates this slowing by delaying replication of heterochromatic satellite seq...	Cells divide rapidly in the early embryos of most animals . However , during a conserved period of development known as the mid-blastula transition ( MBT ) , the cell cycle slows down dramatically . In Drosophila embryos , genome duplication abruptly slows to initiate this cell cycle prolongation . This is achieved thr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "cycle", "and", "cell", "division", "cell", "processes", "green", "fluorescent", "protein", "mitosis", "developmental", "biology", "luminescent", "proteins", "dna", "replication", "dna", "epigenetics", "synthesis", "phase", "embryos", "chromatin", "heterochromat...	2018	Rif1 prolongs the embryonic S phase at the Drosophila mid-blastula transition
The rise in dengue fever cases and the absence of dengue vaccines will likely cause governments to consider various types of effective means for controlling the disease . Given strong public interests in potential dengue vaccines , it is essential to understand the private economic benefits of dengue vaccines for accel...	Dengue is complicated . There are four serotypes of the dengue virus , and dengue infection occurs in almost all age groups . Infection with one serotype provides life-long immunity to that specific serotype but does not protect against the other three serotypes . Unlike other diseases which already have preventable va...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	A Multi-country Study of the Household Willingness-to-Pay for Dengue Vaccines: Household Surveys in Vietnam, Thailand, and Colombia
The corpus callosum ( CC ) is the main pathway responsible for interhemispheric communication . CC agenesis is associated with numerous human pathologies , suggesting that a range of developmental defects can result in abnormalities in this structure . Midline glial cells are known to play a role in CC development , bu...	The largest commissural tract in the human brain is the corpus callosum , with over 200 million callosal axons that channel information between the two cerebral hemispheres . Failure of the corpus callosum to form appropriately is observed in several human pathologies and can result from defects during different steps ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/neurodevelopment", "developmental", "biology/pattern", "formation" ]	2009	Transient Neuronal Populations Are Required to Guide Callosal Axons: A Role for Semaphorin 3C
The TOR ( Target of Rapamycin ) pathway is a highly-conserved signaling pathway in eukaryotes that regulates cellular growth and stress responses . The cellular response to amino acids or carbon sources such as glucose requires anchoring of the TOR kinase complex to the lysosomal/vacuolar membrane by the Ragulator ( ma...	Circadian clocks drive 24-hour rhythms in living things at all levels of organization , from single cells to whole organisms . In spite of the importance of daily clocks for organizing the activities and internal functions of organisms , there are still many unsolved problems concerning the molecular mechanisms . In eu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "vacuoles", "tor", "signaling", "fungi", "model", "organisms", "experimental", "organism", "systems", "chronobiology", "molecular", "biology", "techniques", "mutagenesis", "and", "gene", "deletion", "techniques", "cellular", "structures", "and", "organelles", "research", ...	2018	A component of the TOR (Target Of Rapamycin) nutrient-sensing pathway plays a role in circadian rhythmicity in Neurospora crassa
Francisella tularensis , the etiological agent of the inhalation tularemia , multiplies in a variety of cultured mammalian cells . Nevertheless , evidence for its in vivo intracellular residence is less conclusive . Dendritic cells ( DC ) that are adapted for engulfing bacteria and migration towards lymphatic organs co...	The high infectivity of Francisella tularensis via inhalation led to its classification as a Category-A bio-threat agent and renewed the interest in this pathogen . Here , we characterize early events in respiratory tularemia , which could be instrumental in designing new therapeutic approaches . We focus on the intera...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/cellular", "microbiology", "and", "pathogenesis", "microbiology/innate", "immunity", "immunology/leukocyte", "activation" ]	2008	Interrelationship between Dendritic Cell Trafficking and Francisella tularensis Dissemination following Airway Infection
Epstein-Barr virus ( EBV ) latently infects most of the human population and is strongly associated with lymphoproliferative disorders . EBV encodes several latency proteins affecting B cell proliferation and survival , including latent membrane protein 2A ( LMP2A ) and the EBV oncoprotein LMP1 . LMP1 and LMP2A signali...	As a ubiquitous human pathogen , Epstein-Barr virus ( EBV ) infection is associated with several human B cell diseases characterized by inappropriate B cell activation and function , including infectious mononucleosis and certain cancers . EBV latent membrane protein 1 ( LMP1 ) and 2A ( LMP2A ) hijack cell signaling pa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "genetics", "cancer", "genetics", "immune", "cells", "viruses", "and", "cancer", "immunology", "microbiology", "host-pathogen", "interaction", "gene", "function", "animal", "models", "histology", "adaptive", "immunity", "model", "organisms", "immunologic", "te...	2012	Epstein-Barr Virus LMP2A Reduces Hyperactivation Induced by LMP1 to Restore Normal B Cell Phenotype in Transgenic Mice
The Caenorhabditis elegans dosage compensation complex ( DCC ) equalizes X-chromosome gene dosage between XO males and XX hermaphrodites by two-fold repression of X-linked gene expression in hermaphrodites . The DCC localizes to the X chromosomes in hermaphrodites but not in males , and some subunits form a complex hom...	In many animals , males have one X chromosome and females have two . However , the same amount of gene expression from X chromosomes is needed in the two sexes . The process of dosage compensation ( DC ) globally regulates X-chromosome gene expression to make it equal between the sexes , and it occurs in different ways...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biology" ]	2012	H4K20me1 Contributes to Downregulation of X-Linked Genes for C. elegans Dosage Compensation
Dengue virus ( DENV ) causes more human infections than any other mosquito-borne virus . The current lack of antiviral strategies has prompted genome-wide screens for host genes that are required for DENV infectivity . Earlier transcriptomic studies that identified DENV host factors in the primary vector Aedes aegypti ...	Dengue virus ( DENV ) is transmitted among humans by mosquitoes , primarily Aedes aegypti . Despite their potential as targets to interrupt DENV transmission , mosquito genes that modulate infection in Ae . aegypti remain largely unknown . Using a field-derived Ae . aegypti population , we observed substantial variatio...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing", "techniques", "invertebrates", "dengue", "virus", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "animals", "viruses", "virus", "effects", "on", "host", "gene", "expre...	2017	Individual co-variation between viral RNA load and gene expression reveals novel host factors during early dengue virus infection of the Aedes aegypti midgut
During recent years , comparative genomic analysis has allowed the identification of Mycobacterium leprae-specific genes with potential application for the diagnosis of leprosy . In a previous study , 58 synthetic peptides derived from these sequences were tested for their ability to induce production of IFN-γ in PBMC ...	Despite the efforts to treat registered leprosy patients , the number of new cases reported globally remains stable and high ( about 200 , 000/year ) . As the treatment of multibacillary leprosy patients , the major recognized source for new infections , did not allow the expected reduction in new leprosy cases , addit...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "immunology", "biology", "microbiology" ]	2012	Pathogen-Specific Epitopes as Epidemiological Tools for Defining the Magnitude of Mycobacterium leprae Transmission in Areas Endemic for Leprosy
An important NK-cell inhibition with reduced TNF-α , IFN-γ and TLR2 expression had previously been identified in patients with diffuse cutaneous leishmaniasis ( DCL ) infected with Leishmania mexicana . In an attempt to pinpoint alterations in the signaling pathways responsible for the NK-cell dysfunction in patients w...	Leishmaniasis , caused by protozoan parasites is considered a neglected disease . Leishmania mexicana can cause localized or diffuse cutaneous leishmaniasis . Patients with localized cutaneous leishmaniasis contain the parasite within granulomas , whereas patients with diffuse cutaneous leishmaniasis show uncontrolled ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "cytokines", "immunology", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "immune", "receptor", "signaling", ...	2016	Down-Regulation of TLR and JAK/STAT Pathway Genes Is Associated with Diffuse Cutaneous Leishmaniasis: A Gene Expression Analysis in NK Cells from Patients Infected with Leishmania mexicana
For more than half a century , genotoxic agents have been used to induce mutations in the genome of model organisms to establish genotype-phenotype relationships . While inaccurate replication across damaged bases can explain the formation of single nucleotide variants , it remained unknown how DNA damage induces more ...	DNA damage poses a threat to cell survival as it impedes accurate and efficient copying of DNA that precedes mitotic division . If left unrepaired , DNA damage can give rise to DNA double-strand breaks ( DSBs ) , which is considered to be one of the most dangerous types of genomic insult . Repairing DSBs is vital to pr...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "caenorhabditis", "dna-binding", "proteins", "nucleotides", "animals", "invertebrate", "genomics", "thymine", "animal", "models", "dna", "damage", "caenorhabditis", "elegans", "model", "organisms", "polymerases", "dna", "replication", "dna", "research", "...	2016	Genomic Scars Generated by Polymerase Theta Reveal the Versatile Mechanism of Alternative End-Joining
Improved helminth control is required to alleviate the global burden of schistosomiasis and schistosome-associated pathologies . Current control efforts rely on the anti-helminthic drug praziquantel ( PZQ ) , which enhances immune responses to crude schistosome antigens but does not prevent re-infection . An anti-schis...	Schistosomiasis is caused by infection with Schistosoma spp . parasites , for which the main treatment is the drug praziquantel ( PZQ ) . Since PZQ does not prevent reinfection , an anti-schistosome vaccine based on the Schistosoma haematobium enzyme glutathione-S-transferase ( GST ) is being developed . In this study ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "helminth", "infections", "infectious", "diseases", "schistosomiasis", "medicine", "and", "health", "sciences", "neglected", "tropical", "diseases", "tropical", "diseases", "parasitic", "diseases" ]	2014	Cytokine Responses to the Anti-schistosome Vaccine Candidate Antigen Glutathione-S-transferase Vary with Host Age and Are Boosted by Praziquantel Treatment
Adeno-associated virus type 2 ( AAV ) is known to establish latency by preferential integration in human chromosome 19q13 . 42 . The AAV non-structural protein Rep appears to target a site called AAVS1 by simultaneously binding to Rep-binding sites ( RBS ) present on the AAV genome and within AAVS1 . In the absence of ...	This is the first unbiased genome-wide analysis of wildtype AAV integration combined with a thorough bioinformatic analysis of preferred genomic motifs and patterns in the neighbourhood of the integration sites identified . The preference of Rep-dependent AAV integration near multiple consensus Rep-binding sites was lo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/persistence", "and", "latency", "virology/virus", "evolution", "and", "symbiosis", "computational", "biology/sequence", "motif", "analysis", "computational", "biology/comparative", "sequence", "analysis", "virology" ]	2010	Integration Preferences of Wildtype AAV-2 for Consensus Rep-Binding Sites at Numerous Loci in the Human Genome
Drug development for neglected diseases has been historically hampered due to lack of market incentives . The advent of public domain resources containing chemical information from high throughput screenings is changing the landscape of drug discovery for these diseases . In this work we took advantage of data from ext...	Neglected tropical diseases are human infectious diseases that are often associated with poverty . Historically , lack of interest from the pharmaceutical industry resulted in the lack of good drugs to combat the majority of the pathogens that cause these diseases . Recently , the availability of open chemical informat...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2016	A Multilayer Network Approach for Guiding Drug Repositioning in Neglected Diseases
Regulatory T cells ( Tregs ) play a cardinal role in the immune system by suppressing detrimental autoimmune responses , but their role in acute , chronic infectious diseases and tumor microenvironment remains unclear . We recently demonstrated that IFN-α/β receptor ( IFNAR ) signaling promotes Treg function in autoimm...	Type I interferons ( IFNs ) play a predominant role in the immune response to infectious pathogens . The cellular targets of IFNs have been difficult to dissect because of the ubiquitous expression of the type I interferon receptor ( IFNAR ) . The immune response of mice to lymphocytic choriomeningitis virus ( LCMV ) i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "cytokines", "viral", "transmission", "and", "infection", "spleen", "immunology", "microbiology", "developmental", "biology", "molecular",...	2018	Type I interferon signaling attenuates regulatory T cell function in viral infection and in the tumor microenvironment
Brugia malayi , like most human filarial parasite species , harbors an endosymbiotic bacterium of the genus Wolbachia . Elimination of the endosymbiont leads to sterilization of the adult female . Previous biochemical and genetic studies have established that communication with its endobacterium is essential for surviv...	Filarial parasites afflict hundreds of millions of individuals worldwide , and cause significant public health problems in many of the poorest countries in the world . Most of the human filarial parasite species , including Brugia malayi , harbor endosymbiotic bacteria of the genus Wolbachia . Elimination of the endosy...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[ "genetics", "and", "genomics/genomics", "genetics", "and", "genomics/gene", "expression" ]	2009	Brugia malayi Gene Expression in Response to the Targeting of the Wolbachia Endosymbiont by Tetracycline Treatment
Leaves of Codiaeum variegatum ( “garden croton” ) are used against bloody diarrhoea by local populations in Cameroon . This study aims to search for the active components from C . variegatum against Entamoeba histolytica , and thereby initiate the study of their mechanism of action . A bioassay-guided screening of the ...	Amoebiasis is a disease caused by a protozoan parasite , Entamoeba histolytica , with or without clinical symptoms . Humans are the only relevant host of this parasite , which mainly targets the large intestine and the liver . The current drug , metronidazole , has been successfully used against this parasite for sever...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "parastic", "protozoans", "entamoeba", "histolytica", "microbial", "pathogens", "microbial", "control", "protozoology", "biology", "microbiology", "pathogenesis", "parasitology", "parasite", "physiology" ]	2014	Bioassay-Guided Fractionation of Extracts from Codiaeum variegatum against Entamoeba histolytica Discovers Compounds That Modify Expression of Ceramide Biosynthesis Related Genes

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