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Preventive chemotherapy and transmission control ( PCT ) by mass drug administration is the cornerstone of the World Health Organization ( WHO ) ’s policy to control soil-transmitted helminthiases ( STHs ) caused by Ascaris lumbricoides ( roundworm ) , Trichuris trichiura ( whipworm ) and hookworm species ( Necator ame...	Soil-transmitted helminthiases ( STHs ) caused by roundworm , whipworm or hookworm affect over one billion of the world’s poorest people mostly living in low and middle income countries , exerting a major health and economic toll . These infections are controlled by regular mass drug distribution to affected population...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusions" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "helminths", "tropical", "diseases", "hookworms", "database", "searching", "parasitic", "diseases", "animals", "pharmaceutics", "drug", "administration", "neglected", "tropical", "diseases", "ascariasis", "research",...	2017	Systematic review of studies generating individual participant data on the efficacy of drugs for treating soil-transmitted helminthiases and the case for data-sharing
By genetic manipulations , we study the roles played by insulin-producing cells ( IPCs ) in the brain and their target , the corpora allata ( CA ) , for reproductive dormancy in female Drosophila melanogaster , which is induced by exposing them to a combination of low temperature ( 11°C ) , short-day photoperiod ( 10L:...	In the temperate zone , winter is a challenging season for many animals because of the freezing temperature and shortage of foods , which are sustained over a period of several months . Wild mammals such as bears and squirrels have acquired the ability to hibernate , by reducing energy consumption to the minimum necess...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "reproductive", "system", "neuroscience", "animals", "circadian", "oscillators", "endocrine", "physiology", "animal", "models", "physiological", "processes", "developmental", "biology", "drosophila", "melanogaster", ...	2018	Genetic dissection of stress-induced reproductive arrest in Drosophila melanogaster females
Heterogeneities in contact networks have a major effect in determining whether a pathogen can become epidemic or persist at endemic levels . Epidemic models that determine which interventions can successfully prevent an outbreak need to account for social structure and mixing patterns . Contact patterns vary across age...	The risk of infectious disease transmission varies in different settings , for instance at home , at work or in the community , as a result of the different social structures and mixing patterns in those locations . These social structures vary across countries in different stages of development and with different demo...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "european", "union", "education", "infectious", "disease", "epidemiology", "sociology", "geographical", "locations", "social", "sciences", "age", "groups", "south", "africa", "africa", "infectious", "diseases", "south", "america"...	2017	Projecting social contact matrices in 152 countries using contact surveys and demographic data
In mice , experimental infection with Trypanosoma brucei causes decreased bone marrow B-cell development , abolished splenic B-cell maturation and loss of antibody mediated protection including vaccine induced memory responses . Nothing is known about this phenomenon in human African trypanosomiasis ( HAT ) , but if oc...	African trypanosomes are parasites that cause sleeping sickness in humans . In mice models , trypanosomiasis causes loss of the spleen memory B-cell precursors , of the host memory response and of protection against certain pathogens , built up by vaccination . The phenomenon has never been studied in human sleeping si...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "clinical", "immunology", "african", "trypanosomiasis", "neglected", "tropical", "diseases", "immune", "response" ]	2014	Gambiense Human African Trypanosomiasis and Immunological Memory: Effect on Phenotypic Lymphocyte Profiles and Humoral Immunity
Contact structure is believed to have a large impact on epidemic spreading and consequently using networks to model such contact structure continues to gain interest in epidemiology . However , detailed knowledge of the exact contact structure underlying real epidemics is limited . Here we address the question whether ...	One of the recent key innovations in the epidemiology of infectious diseases was the incorporation of explicit contact structure ( i . e . who can infect whom ) into epidemiological models . Theoretical studies have generated a broad consensus in the field that knowledge of the contact network may help to greatly impro...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "population", "modeling", "epidemiology", "biology", "computational", "biology", "population", "biology" ]	2012	Inferring Epidemic Contact Structure from Phylogenetic Trees
The exceptional toxicity of botulinum neurotoxins ( BoNTs ) is mediated by high avidity binding to complex polysialogangliosides and intraluminal segments of synaptic vesicle proteins embedded in the presynaptic membrane . One peculiarity is an exposed hydrophobic loop in the toxin’s cell binding domain HC , which is l...	Botulinum neurotoxins are Janus-faced molecules: due to their exquisite toxicity , botulinum neurotoxins are considered as biological weapons , but they are also highly effective medicines for numerous neurological indications . However , what mediates their exquisite toxicity ? The exclusive binding to neurons and the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "chemical", "characterization", "medicine", "and", "health", "sciences", "toxins", "protein", "interactions", "pathology", "and", "laboratory", "medicine", "affinity", "chromatography", "sphingolipids", "toxicology", "toxic", "agents", "toxicity", "glutathione", "chromatogr...	2018	A lipid-binding loop of botulinum neurotoxin serotypes B, DC and G is an essential feature to confer their exquisite potency
Dengue fever ( DF ) is an emerging infectious disease in the tropics and subtropics . Determinants of DF epidemiology and factors involved in severe cases—dengue haemorrhagic fever ( DHF ) and dengue shock syndrome ( DSS ) —remain imperfectly characterized . Since 2000 , serotype 1 ( DENV-1 ) has predominated in the So...	The molecular characterization of 181 serotype 1 Dengue fever ( DENV-1 ) viruses collected regularly during the 2001–2006 period in French Polynesia ( FP ) from patients experiencing various clinical presentations revealed that the virus responsible for the severe 2001 outbreak was introduced from South-East Asia , and...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/viral", "infections", "infectious", "diseases/tropical", "and", "travel-associated", "diseases" ]	2009	Dengue 1 Diversity and Microevolution, French Polynesia 2001–2006: Connection with Epidemiology and Clinics
HIV Dependency Factors ( HDFs ) are a class of human proteins that are essential for HIV replication , but are not lethal to the host cell when silenced . Three previous genome-wide RNAi experiments identified HDF sets with little overlap . We combine data from these three studies with a human protein interaction netwo...	Medicines to cure infectious diseases usually target proteins in the pathogens . Since pathogens have short life cycles , the targeted proteins can rapidly evolve and make the medicines ineffective , especially in viruses such as HIV . However , since viruses have very small genomes , they must exploit the cellular mac...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "systems", "biology", "immunodeficiency", "viruses", "data", "mining", "virology", "signal", "processing", "biology", "computational", "biology", "microbiology", "host-pathogen", "interaction", "genetics", "and", "genomics", "engineering" ]	2011	Network-Based Prediction and Analysis of HIV Dependency Factors
Neutrophils are classically defined as terminally differentiated , short-lived cells; however , neutrophils can be long-lived with phenotypic plasticity . During inflammation , a subset of neutrophils transdifferentiate into a population called neutrophil-DC hybrids ( PMN-DCs ) having properties of both neutrophils and...	Several patient populations including those with cancer or that receive organ-transplants are at risk of life-threatening invasive fungal infections , in part due to reduced function or numbers of white blood cells . Because of limitations in antifungal drug therapy , immune-based strategies to augment white blood cell...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "yeast", "infections", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "cell", "differentiation", "developmental", "biology", "fungi", "clinical", "med...	2018	An unappreciated role for neutrophil-DC hybrids in immunity to invasive fungal infections
Vertebrate development requires communication among cells of the embryo in order to define the body axis , and the Wnt-signaling network plays a key role in axis formation as well as in a vast array of other cellular processes . One arm of the Wnt-signaling network , the non-canonical Wnt pathway , mediates intracellul...	Vertebrate development requires communication among cells in order to define the body axis ( front/back , head/tail , or left/right ) . Secreted factors such as Wnts play key roles in a vast array of cellular processes , including patterning of the body axis . One arm of the Wnt-signaling network , the non-canonical pa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/cell", "differentiation", "developmental", "biology/developmental", "molecular", "mechanisms", "developmental", "biology/morphogenesis", "and", "cell", "biology", "cell", "biology/cell", "signaling" ]	2010	Regulator of G Protein Signaling 3 Modulates Wnt5b Calcium Dynamics and Somite Patterning
Target identification is one of the most critical steps following cell-based phenotypic chemical screens aimed at identifying compounds with potential uses in cell biology and for developing novel disease therapies . Current in silico target identification methods , including chemical similarity database searches , are...	Determining the targets of compounds identified in cell-based high-throughput chemical screens is a critical step for downstream drug development and understanding of compound mechanism of action . However , current computational target prediction approaches like chemical similarity database searches are limited to sin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Large-Scale Chemical Similarity Networks for Target Profiling of Compounds Identified in Cell-Based Chemical Screens
Uropathogenic Escherichia coli ( UPEC ) represent the predominant cause of urinary tract infections ( UTIs ) . A key UPEC molecular virulence mechanism is type 1 fimbriae , whose expression is controlled by the orientation of an invertible chromosomal DNA element—the fim switch . Temperature has been shown to act as a ...	Urinary tract infections ( UTIs ) represent a major growing threat to global public health . With over 15 million cases a year in the United States alone , UTIs are characterized by very high recurrence/reinfection rates , particularly among women and minority groups [1] . The predominant cause of UTIs is uropathogenic...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry", "computer", "science/applications", "infectious", "diseases/urological", "infections", "public", "health", "and", "epidemiology", "computational", "biology/transcriptional", "regulation", "urology/urological", "infections", "biophysics/theory", "and", "simulation", ...	2010	Temperature Control of Fimbriation Circuit Switch in Uropathogenic Escherichia coli: Quantitative Analysis via Automated Model Abstraction
Estrogen-related receptor α ( ERRα ) is a member of the nuclear receptor superfamily controlling energy homeostasis; however , its precise role in regulating antiviral innate immunity remains to be clarified . Here , we showed that ERRα deficiency conferred resistance to viral infection both in vivo and in vitro . Mech...	As a member of the nuclear receptor superfamily involved in metabolism signaling , the precise role of ERRα in antiviral innate immunity remains to be clarified . Here , we showed that ERRα deficiency led to increased interferon production , resulting in enhanced resistance to viral infection both in vivo and in vitro ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "luciferase", "assay", "medicine", "and", "health", "sciences", "luciferase", "vesicular", "stomatitis", "virus", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "molecular", "probe", "techniques", "293t", "c...	2017	ERRα negatively regulates type I interferon induction by inhibiting TBK1-IRF3 interaction
The bacterial cell wall , which is comprised of a mesh of polysaccharide strands crosslinked via peptide bridges ( peptidoglycan , PG ) , is critical for maintenance of cell shape and survival . PG assembly is mediated by a variety of Penicillin Binding Proteins ( PBP ) whose fundamental activities have been characteri...	Bacteria surround themselves with a mesh-like peptidoglycan ( PG ) cell wall , which is essential for maintenance of cell shape and survival . While the enzymes that catalyze the assembly of the cell wall ( aka penicillin-binding proteins ( PBPs ) ) have been extensively characterized , our understanding of the factors...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology", "biology", "and", "life", "sciences", "microbiology" ]	2014	A Novel Peptidoglycan Binding Protein Crucial for PBP1A-Mediated Cell Wall Biogenesis in Vibrio cholerae
Epidermal stratification of the mammalian skin requires proliferative basal progenitors to generate intermediate cells that separate from the basal layer and are replaced by post-mitotic cells . Although Wnt signaling has been implicated in this developmental process , the mechanism underlying Wnt-mediated regulation o...	Epidermis , a thin layer of stratified epithelium forming the outmost surface of the skin , provides the crucial function to protect animals from environmental insults , such as bacterial pathogens and water loss . This barrier function is established in embryogenesis , during which single layered epithelial cells diff...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences" ]	2014	BMP-FGF Signaling Axis Mediates Wnt-Induced Epidermal Stratification in Developing Mammalian Skin
The prevalence of previously undiagnosed leprosy ( PPUL ) in the general population was determined to estimate the background level of leprosy in the population and to compare this with registered prevalence and the known PPUL in different levels of contacts of leprosy patients . Multistage cluster sampling including 2...	In order to estimate the level of leprosy in an area with many leprosy patients , we determined the prevalence of previously undiagnosed leprosy in the general population and compared this with the registered ( or known ) number of leprosy patients . We also compared it with the known prevalence of leprosy in contacts ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/bacterial", "infections", "infectious", "diseases/neglected", "tropical", "diseases", "public", "health", "and", "epidemiology/infectious", "diseases", "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases" ]	2008	The Prevalence of Previously Undiagnosed Leprosy in the General Population of Northwest Bangladesh
One Health addresses complex challenges to promote the health of all species and the environment by integrating relevant sciences at systems level . Its application to zoonotic diseases is recommended , but few coherent frameworks exist that combine approaches from multiple disciplines . Rabies requires an interdiscipl...	Successful rabies control generates benefits in terms of improved human and animal health and well-being and safer environments . A key requirement of successful and sustainable rabies control is empowering policy makers to make decisions in an efficient manner; essential to this is the availability of evidence support...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "medicine", "and", "health", "sciences", "animal", "welfare", "veterinary", "epidemiology", "social", "sciences", "management", "engineering", "engineering", "and", "technology", "economic", "analysis", "biology", "and", "life", "sciences", "an...	2014	A One Health Framework for the Evaluation of Rabies Control Programmes: A Case Study from Colombo City, Sri Lanka
The malarial life cycle involves repeated rounds of intraerythrocytic replication interspersed by host cell rupture which releases merozoites that rapidly invade fresh erythrocytes . Apical membrane antigen-1 ( AMA1 ) is a merozoite protein that plays a critical role in invasion . Antibodies against AMA1 prevent invasi...	The malaria parasite invades red blood cells . During invasion several parasite proteins , including a vaccine candidate called PfAMA1 , are clipped from the parasite surface . Most of this clipping is performed by an enzyme called PfSUB2 , but some also occurs through intramembrane cleavage . The function of this shed...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "hydrolases", "enzyme", "classes", "enzymes", "microbial", "pathogens", "parasitology", "biology", "microbiology", "host-pathogen", "interaction" ]	2011	Juxtamembrane Shedding of Plasmodium falciparum AMA1 Is Sequence Independent and Essential, and Helps Evade Invasion-Inhibitory Antibodies
RNA-seq technologies have provided significant insight into the transcription networks of mycobacteria . However , such studies provide no definitive information on the translational landscape . Here , we use a combination of high-throughput transcriptome and proteome-profiling approaches to more rigorously understand ...	The current paradigm for bacterial translation is based on an mRNA that includes an untranslated leader sequence containing the ribosome-binding site upstream of the initiation codon . We applied genome-scale approaches to map the protein-coding regions in the genomes of Mycobacterium smegmatis and Mycobacterium tuberc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Leaderless Transcripts and Small Proteins Are Common Features of the Mycobacterial Translational Landscape
Mammalian common fragile sites are loci of frequent chromosome breakage and putative recombination hotspots . Here , we utilized Replication Slow Zones ( RSZs ) , a budding yeast homolog of the mammalian common fragile sites , to examine recombination activities at these loci . We found that rates of URA3 inactivation ...	Chromosome rearrangements are frequently associated with human cancers . Such rearrangement can result from a DNA break followed by an erroneous repair . Mammalian common fragile sites are one of the most extensively studied naturally occurring breakage prone regions of the genome . It has been proposed that fragile si...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Recombinogenic Conditions Influence Partner Choice in Spontaneous Mitotic Recombination
For almost 50 years sub-Saharan Africa , including Uganda , has experienced several outbreaks due to Vibrio cholerae . Our aim was to determine the genetic relatedness and spread of strains responsible for cholera outbreaks in Uganda . Sixty-three V . cholerae isolates collected from outbreaks in Uganda between 2014 an...	Cholera , an acute diarrheal disease , essentially was eliminated in the western world many decades ago , but has continued to cause many deaths in sub-Saharan Africa , South America and Asia . Cholera diagnosis in most countries in sub-Saharan Africa , including Uganda , is by stool culture , serology and biochemical ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "vibrio", "tropical", "diseases", "microbiology", "geographical", "locations", "uganda", "bacterial", "diseases", "vibrio", ...	2018	Molecular characterization of Vibrio cholerae responsible for cholera epidemics in Uganda by PCR, MLVA and WGS
Understanding of scabies immunopathology has been hampered by the inability to undertake longitudinal studies in humans . Pigs are a useful animal model for scabies , and show clinical and immunologic changes similar to those in humans . Crusted scabies can be readily established in pigs by treatment with the glucocort...	Scabies is a neglected tropical skin disease caused by the tiny parasitic mite Sarcoptes scabiei . Scabies is common in developing countries , and scabies outbreaks also occur in institutional settings worldwide . Scabies often underlies secondary bacterial skin infection and resulting complications , and is thus assoc...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Prospective Study in a Porcine Model of Sarcoptes scabiei Indicates the Association of Th2 and Th17 Pathways with the Clinical Severity of Scabies
The nuclear genomes of vertebrates show a highly organized program of DNA replication where GC-rich isochores are replicated early in S-phase , while AT-rich isochores are late replicating . GC-rich regions are gene dense and are enriched for active transcription , suggesting a connection between gene regulation and re...	All eukaryotic organisms must duplicate their genome precisely once before cell division . This occurs according to an established temporal program during S-phase ( when DNA synthesis takes place ) of the cell cycle . In vertebrates , this program is regulated at the level of large chromosomal domains ranging from 200 ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "genomics", "molecular", "cell", "biology", "genetics", "and", "genomics" ]	2012	USF Binding Sequences from the HS4 Insulator Element Impose Early Replication Timing on a Vertebrate Replicator
The first line treatment for Chagas disease , a neglected tropical disease caused by the protozoan parasite Trypanosoma cruzi , involves administration of benznidazole ( Bzn ) . Bzn is a 2-nitroimidazole pro-drug which requires nitroreduction to become active , although its mode of action is not fully understood . In t...	The unicellular parasite Trypanosoma cruzi infects humans , leading to Chagas disease , endemic in Central and South America and responsible for 13 , 000 annual deaths . Only two drugs have proven effective against Chagas , nifurtimox and benznidazole ( Bzn ) . Bzn has the best safety and efficacy profiles and is thus ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biotechnology", "medicine", "and", "health", "sciences", "medicinal", "chemistry", "small", "molecules", "tropical", "diseases", "chemical", "biology", "parasitic", "diseases", "neglected", "tropical", "diseases", "pharmacology", "infectious", "diseases", "metabolic", "p...	2014	Benznidazole Biotransformation and Multiple Targets in Trypanosoma cruzi Revealed by Metabolomics
Cells adjust to hypoxic stress within the tumor microenvironment by downregulating energy-consuming processes including translation . To delineate mechanisms of cellular adaptation to hypoxia , we performed RNA-Seq of normoxic and hypoxic head and neck cancer cells . These data revealed a significant down regulation of...	Tumor hypoxia is a negative prognostic factor for many solid cancers . Cellular adaptation to hypoxia is largely mediated by widespread changes in gene expression and enables cancer cells to adjust and survive . Recently , alternative splicing has been implicated in this process . To identify biologically impactful hyp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "molecular", "probe", "techniques", "gene", "regulation", "immunoblotting", "alternative", "splicing", "hypoxia", "molecular", "biology", "techniques", "research", "and", "analysis", "methods", "small", "interfering", "rnas", "genome", "complexity", "pr...	2017	Transcriptome analysis of hypoxic cancer cells uncovers intron retention in EIF2B5 as a mechanism to inhibit translation
As some of the most widely utilised intercellular signalling molecules , transforming growth factor β ( TGFβ ) superfamily members play critical roles in normal development and become disrupted in human disease . Establishing appropriate levels of TGFβ signalling involves positive and negative feedback , which are coup...	Cells depend on signals from their microenvironment to carry out their normal functions and coordinate responses . Once initiated , such signals often self-amplify via positive feedback to reach a sufficient level , when negative feedback can then be employed to dampen excess signalling . These feedback loops dynamical...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	A Novel TGFβ Modulator that Uncouples R-Smad/I-Smad-Mediated Negative Feedback from R-Smad/Ligand-Driven Positive Feedback
The unicellular eukaryote Tetrahymena thermophila has seven mating types . Cells can mate only when they recognize cells of a different mating type as non-self . As a ciliate , Tetrahymena separates its germline and soma into two nuclei . During growth the somatic nucleus is responsible for all gene transcription while...	Tetrahymena thermophila is a single-celled organism with seven sexes . After two cells of different sexes mate , the progeny cells can be of any one of the seven sexes . In this article we show how this sex decision is made . Every cell has two genomes , each contained within a separate nucleus . The germline genome is...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "model", "organisms", "molecular", "cell", "biology", "genetics", "biology", "genomics", "evolutionary", "biology", "microbiology", "genetics", "and", "genomics" ]	2013	Selecting One of Several Mating Types through Gene Segment Joining and Deletion in Tetrahymena thermophila
To mate , the fungal pathogen Candida albicans must undergo homozygosis at the mating-type locus and then switch from the white to opaque phenotype . Paradoxically , opaque cells were found to be unstable at physiological temperature , suggesting that mating had little chance of occurring in the host , the main niche o...	To mate , the human fungal pathogen Candida albicans must undergo a complex phenotypic change from a round “white” to large , elongated “opaque” cell . This involves the regulation of approximately 5% of the organism's genes . Surprisingly , this complex transition is not required for mating in other related yeast . Ev...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology" ]	2010	N-Acetylglucosamine Induces White to Opaque Switching, a Mating Prerequisite in Candida albicans
Transposable elements ( TEs ) are repetitive nucleotide sequences that make up a large portion of eukaryotic genomes . They can move and duplicate within a genome , increasing genome size and contributing to genetic diversity within and across species . Accurate identification and classification of TEs present in a gen...	Over the years , with the increase of the acquisition of biological data , the extraction of knowledge from this data is getting more important . To understand how biology works is very important to increase the quality of the products and services which use biological data . This directly influences companies and gove...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "retrotransposons", "engineering", "and", "technology", "brassica", "animals", "invertebrate", "genomics", "animal", "models", "decision", "analysis", "drosophila", "melanogaster", "model", "organisms", "management", "engineering", "artificial", "intelligence...	2018	A machine learning based framework to identify and classify long terminal repeat retrotransposons
Melioidosis is a severe disease caused by Burkholderia pseudomallei . Clinical manifestations are diverse and acute infections require immediate treatment with effective antibiotics . While culture is the current diagnostic standard , it is time-consuming and has low sensitivity . In endemic areas , inaccessibility to ...	Melioidosis , caused by Burkholderia pseudomallei , is a life-threatening infection endemic in tropical countries . Definitive diagnosis of melioidosis relies upon bacterial culture which requires suitable laboratory facilities and reliable antibody testing . To obtain an effective target antigen for use in a simple po...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "typhus", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "immune", "physiology", "melioidosis", "immunology", "tropical", "diseases", "ethnicities", "diabetes", "mellitus", "bacterial", "diseases", "endocrine", "disorders", "neglected", "tropical"...	2017	Comparison of O-polysaccharide and hemolysin co-regulated protein as target antigens for serodiagnosis of melioidosis
Trophic relationships , such as those between predator and prey or between pathogen and host , are key interactions linking species in ecological food webs . The structure of these links and their strengths have major consequences for the dynamics and stability of food webs . The existence and strength of particular tr...	The presence and strength of interactions between species has frequently been inferred from observational data on changes in species abundance . For example , correlated cycles in potential predator and prey species may be interpreted as evidence that the species interact , while the absence of such coupled oscillation...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viruses", "ecology", "evolutionary", "biology", "plants", "animals", "eubacteria" ]	2007	Cryptic Population Dynamics: Rapid Evolution Masks Trophic Interactions
In mid-2015 , Salvador , Brazil , reported an outbreak of Guillain-Barré syndrome ( GBS ) , coinciding with the introduction and spread of Zika virus ( ZIKV ) . We found that GBS incidence during April–July 2015 among those ≥12 years of age was 5 . 6 cases/100 , 000 population/year and increased markedly with increasin...	Shortly following the introduction of Zika virus ( ZIKV ) , a type of flavivirus transmitted by mosquitoes , into Brazil in early 2015 , the Brazil Ministry of Health began receiving increased reports of a paralyzing condition known as Guillain-Barré syndrome ( GBS ) . The areas with the greatest number of GBS cases ap...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "respiratory", "infections", "chikungunya", "infection", "pathogens", "immunology", "tropical", "diseases", "microbiology", "geographical", "locations", "pulmonolo...	2017	Increased rates of Guillain-Barré syndrome associated with Zika virus outbreak in the Salvador metropolitan area, Brazil
Ants are a highly successful family of insects that thrive in a variety of habitats across the world . Perhaps their best-known features are complex social organization and strict division of labor , separating reproduction from the day-to-day maintenance and care of the colony , as well as strict discrimination agains...	Chemical communication is an important factor in the regulation of social interaction in animals . The family of eusocial insects commonly known as ants offers an almost unique opportunity for examining the genetic basis for the chemosensory pathways that underlie ant sociality . In order to address this issue , we hav...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "analysis", "tools", "genomics", "gustatory", "system", "olfactory", "system", "biology", "evolutionary", "biology", "comparative", "genomics", "neuroscience", "sensory", "systems", "genetics", "and", "genomics", "transcriptomes" ]	2012	Phylogenetic and Transcriptomic Analysis of Chemosensory Receptors in a Pair of Divergent Ant Species Reveals Sex-Specific Signatures of Odor Coding
Between December 2015 and July 2016 , a yellow fever ( YF ) outbreak affected urban areas of Angola and the Democratic Republic of the Congo ( DRC ) . We described the outbreak in DRC and assessed the accuracy of the YF case definition , to facilitate early diagnosis of cases in future urban outbreaks . In DRC , suspec...	Yellow fever is a mosquito-borne viral infection characterized by fever , followed after several days by jaundice , liver or kidney failure , shock or bleeding in up to 25% of cases . Although the virus primarily circulates in forests among primates , it can also be transmitted from human to human by mosquitoes in urba...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "angola", "tropical", "diseases", "geographical", "locations", "parasitic", "diseases", "signs", "and", "symptoms", "infectious", "disease", "control", ...	2018	Urban yellow fever outbreak—Democratic Republic of the Congo, 2016: Towards more rapid case detection
Sirtuin genes have been associated with aging and are known to affect multiple cellular pathways . Sirtuin 2 was previously shown to modulate proteotoxicity associated with age-associated neurodegenerative disorders such as Alzheimer and Parkinson disease ( PD ) . However , the precise molecular mechanisms involved rem...	Parkinson disease is an age-associated neurodegenerative disorder characterized by the loss of dopamine-producing neurons from a region in the brain known as the substantia nigra and by the accumulation of the protein alpha-synuclein in intracellular clumps called inclusions . Whether these inclusions are the cause or ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "death", "medicine", "and", "health", "sciences", "autophagic", "cell", "death", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "neurodegenerative", "diseases", "cell", "processes", "neuroscience", "organic", "compounds", "toxicology", "t...	2017	The mechanism of sirtuin 2–mediated exacerbation of alpha-synuclein toxicity in models of Parkinson disease
Cholinergic agonists such as levamisole and pyrantel are widely used as anthelmintics to treat parasitic nematode infestations . These drugs elicit spastic paralysis by activating acetylcholine receptors ( AChRs ) expressed in nematode body wall muscles . In the model nematode Caenorhabditis elegans , genetic screens l...	Parasitic nematodes have global health and economic impacts . They infect animals , including livestock , humans , and plants including all major food crops . Their control in human and veterinary medicine is reliant on anthelmintic drugs but this is now challenged by resistant worms especially in livestock . Important...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "Materials" ]	[ "invertebrates", "neurochemistry", "caenorhabditis", "gene", "regulation", "vertebrates", "neuroscience", "animals", "xenopus", "animal", "models", "developmental", "biology", "caenorhabditis", "elegans", "model", "organisms", "amphibians", "experimental", "organism", "system...	2018	Deciphering the molecular determinants of cholinergic anthelmintic sensitivity in nematodes: When novel functional validation approaches highlight major differences between the model Caenorhabditis elegans and parasitic species
New mode-of-action insecticides are sought to provide continued control of pesticide resistant arthropod vectors of neglected tropical diseases ( NTDs ) . We previously identified antagonists of the AaDOP2 D1-like dopamine receptor ( DAR ) from the yellow fever mosquito , Aedes aegypti , with toxicity to Ae . aegypti l...	New mode-of-action insecticides are required to control arthropod vectors of neglected tropical diseases ( NTDs ) . Rational drug design approaches offer attractive methods to identify new insecticidal chemistries that are potent and selective for molecular targets of arthropod vectors . Previously identified antagonis...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Dopamine Receptor Antagonists as New Mode-of-Action Insecticide Leads for Control of Aedes and Culex Mosquito Vectors
The C-type lectin receptor DCIR , which has been shown very recently to act as an attachment factor for HIV-1 in dendritic cells , is expressed predominantly on antigen-presenting cells . However , this concept was recently challenged by the discovery that DCIR can also be detected in CD4+ T cells found in the synovial...	The type II transmembrane protein DCIR belongs to the C-type lectin domain family receptor and is predominantly expressed in cells of the myeloid lineage . However recent evidence suggests that it can also be induced in CD4+ T cells placed under an inflammatory condition . We assessed the capacity of HIV-1 to promote D...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/hiv", "infection", "and", "aids", "virology/immunodeficiency", "viruses", "microbiology/cellular", "microbiology", "and", "pathogenesis" ]	2010	HIV-1 Induces DCIR Expression in CD4+ T Cells
Some studies suggest that complex arm movements in humans and monkeys may optimize several objective functions , while others claim that arm movements satisfy geometric constraints and are composed of elementary components . However , the ability to unify different constraints has remained an open question . The criter...	Although our movements are flexible and versatile , they are nonetheless highly stereotypical . This versatility is similar to that of natural language sentences , which are composed of words which , in turn , are constructed from a small alphabet of elementary phonemes . Parabolic drawings are simple , smooth and rema...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "neuroscience/behavioral", "neuroscience", "neuroscience/cognitive", "neuroscience", "neuroscience/theoretical", "neuroscience", "neuroscience/motor", "systems" ]	2009	A Compact Representation of Drawing Movements with Sequences of Parabolic Primitives
Despite the crucial importance of Hox genes functions during animal development , the mechanisms that control their transcription in time and space are not yet fully understood . In this context , it was proposed that Hotair , a lncRNA transcribed from within the HoxC cluster regulates Hoxd gene expression in trans , t...	During mammalian embryonic development , Hox genes must be tightly regulated . It was proposed earlier that part of this regulation relies upon Hotair , a long non-coding RNA that recruits repressive protein complexes onto the HoxD gene cluster to keep these genes silent before they become activated . A genetic deletio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "gene", "regulation", "rna", "extraction", "long", "non-coding", "rnas", "fibroblasts", "dna", "transcription", "developmental", "biology", "connective", "tissue", "cells", "embryos", "extraction", "techniques", "research", "and"...	2016	Hotair Is Dispensible for Mouse Development
In 2006 , we reported a mariner ( Mos1 ) -transformed Aedes aegypti line , Carb77 , which was highly resistant to dengue-2 virus ( DENV2 ) . Carb77 mosquitoes expressed a DENV2-specific inverted-repeat ( IR ) RNA in midgut epithelial cells after ingesting an infectious bloodmeal . The IR-RNA formed double-stranded DENV...	Expression of a DENV2 sequence-derived IR RNA in the mosquito midgut initiates an antiviral intracellular RNAi response that efficiently blocks DENV2 infection and profoundly impairs vector competence for that virus in Aedes aegypti . DENV2-specific IR RNA expression in the Carb109M strain has maintained the RNAi-based...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "virology", "epidemiology", "vector", "biology", "genetics", "biology", "and", "life", "sciences", "microbiology", "disease", "vectors" ]	2014	Fitness Impact and Stability of a Transgene Conferring Resistance to Dengue-2 Virus following Introgression into a Genetically Diverse Aedes aegypti Strain
Vascular development is a complex process regulated by dynamic biological networks that vary in topology and state across different tissues and developmental stages . Signals regulating de novo blood vessel formation ( vasculogenesis ) and remodeling ( angiogenesis ) come from a variety of biological pathways linked to...	We built a novel computational model of vascular development that includes multiple cell types responding to growth factor signaling , inflammatory chemokine pathways and extracellular matrix interactions . This model represents the normal biology of capillary plexus formation , both in terms of morphology and emergent...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "systems", "biology", "biochemistry", "predictive", "toxicology", "biology", "genetics", "and", "genomics", "toxicology" ]	2013	A Computational Model Predicting Disruption of Blood Vessel Development
An elegantly simple and probably ancient molecular mechanism of allostery is described for the Escherichia coli arginine repressor ArgR , the master feedback regulator of transcription in L-arginine metabolism . Molecular dynamics simulations with ArgRC , the hexameric domain that binds L-arginine with negative coopera...	A controversial prediction of the famous allostery model of Monod , Wyman , and Changeux is that constraints imposed on protein subunits by multimerization are relaxed by ligand binding , but with conservation of symmetry in partially-liganded states . Interpretation of thermodynamic ligand-binding data through the len...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results/Discussion" ]	[ "computational", "biology/molecular", "dynamics", "biochemistry/biomacromolecule-ligand", "interactions", "biophysics/theory", "and", "simulation" ]	2010	Symmetric Allosteric Mechanism of Hexameric Escherichia coli Arginine Repressor Exploits Competition between L-Arginine Ligands and Resident Arginine Residues
Chronic parasitic infections are associated with active immunomodulation which may include by-stander effects on unrelated antigens . It has been suggested that pre-natal exposure to parasitic infections in the mother impacts immunological development in the fetus and hence the offspring’s response to vaccines , and th...	Parasitic infections , such as worms and malaria , have potent effects on the human immune system . These effects include modification of immune responses in the fetus and infant if a mother has a parasitic infection during pregnancy . These immunological changes can influence the way a child responds to the same infec...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "children", "medicine", "and", "health", "sciences", "immune", "physiology", "helminths", "immunology", "tropical", "diseases", "hookworms", "parasitic", "diseases", "animals", "vaccines", "preventive", "medicine", "age", "groups", "infants", "vaccination...	2017	The impact of prenatal exposure to parasitic infections and to anthelminthic treatment on antibody responses to routine immunisations given in infancy: Secondary analysis of a randomised controlled trial
Down Syndrome ( DS ) is caused by trisomy of chromosome 21 ( Hsa21 ) and results in a spectrum of phenotypes including learning and memory deficits , and motor dysfunction . It has been hypothesized that an additional copy of a few Hsa21 dosage-sensitive genes causes these phenotypes , but this has been challenged by o...	Down Syndrome is caused by an extra copy of chromosome 21 and results in many different phenotypes including learning difficulties , Alzheimer’s disease and problems with motor function such as abnormal gait and poor fine motor skills . These different phenotypes are thought to result from an increased copy of one more...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "nervous", "system", "brain", "vertebrates", "mice", "neuroscience", "biological", "locomotion", "animals", "mammals", "motor", "neurons", "animal", "models", "model", "organisms", "experimental", "organism", "systems", "cerebell...	2018	Analysis of motor dysfunction in Down Syndrome reveals motor neuron degeneration
Sensing viruses by pattern recognition receptors ( PRR ) triggers the innate immune system of the host cell and activates immune signaling cascades such as the RIG-I/IRF3 pathway . Mitochondrial antiviral-signaling protein ( MAVS , also known as IPS-1 , Cardif , and VISA ) is the crucial adaptor protein of this pathway...	Mammalian cells developed several defense mechanisms against viral infection . One major strategy involves pattern recognition receptors ( PRRs ) recognizing non-self motifs in viral RNA and triggering the production of type I and III interferon ( IFN ) that induce an antiviral state . One central signaling molecule in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Activation of Type I and III Interferon Response by Mitochondrial and Peroxisomal MAVS and Inhibition by Hepatitis C Virus
Several intracellular pathogens arrest the phagosome maturation in the host cells to avoid transport to lysosomes . In contrast , the Leishmania containing parasitophorous vacuole ( PV ) is shown to recruit lysosomal markers and thus Leishmania is postulated to be residing in the phagolysosomes in macrophages . Here , ...	Leishmania donovani causes visceral leishmaniasis in human . This parasite is thought to reside and replicate in a phagolysosomal compartment in macrophages . But , how Leishmania survives in such a detrimental compartment in macrophages is not known . In contrast , most of the intracellular pathogens avoid targeting t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "emulsions", "medicine", "and", "health", "sciences", "lysosomes", "immune", "cells", "hela", "cells", "gene", "regulation", "immunology", "biological", "cultures", "colloids", "parasitic", "diseases", "parasitic", "protozoans", "micrornas", "protozoan...	2017	Leishmania donovani resides in modified early endosomes by upregulating Rab5a expression via the downregulation of miR-494
It is well known that iron is an essential element for life but is toxic when in excess or in certain forms . Accordingly there are many diseases that result directly from either lack or excess of iron . Yet many molecular and physiological aspects of iron regulation have only been discovered recently and others are st...	Iron is an essential nutrient in almost all life forms . In humans and animals iron is used for respiration and for transporting oxygen inside red blood cells . But in excess iron can be toxic and therefore the body regulates its distribution and absortion through the action of hormones , which is not yet completely un...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "hemochromatosis", "medicine", "and", "health", "sciences", "immune", "physiology", "body", "fluids", "spleen", "genetic", "diseases", "diet", "anemia", "liver", "diseases", "animal", "models", "physiological", "processes", "model", "organisms", "nutrition", "gastroente...	2019	A computational model to understand mouse iron physiology and disease
Dengue is an arthropod-borne virus of great public health importance , and control of its mosquito vectors is currently the only available method for prevention . Previous research has suggested that insecticide treated curtains ( ITCs ) can lower dengue vector infestations in houses . This observational study investig...	Dengue is an arthropod-borne virus of great public health importance . Vector control is currently the only available method for dengue prevention . This cluster-randomized trial investigated individual and household-level socio-demographic factors associated with correct and consistent use of insecticide-treated curta...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "children", "medicine", "and", "health", "sciences", "education", "sociology", "geographical", "locations", "social", "sciences", "animals", "peru", "age", "groups", "infectious", "disease", "control", "insect", "vectors", "families", "public", "and", ...	2016	Factors Associated with Correct and Consistent Insecticide Treated Curtain Use in Iquitos, Peru
The eukaryotic cytoskeleton is essential for structural support and intracellular transport , and is therefore a common target of animal pathogens . However , no phytopathogenic effector has yet been demonstrated to specifically target the plant cytoskeleton . Here we show that the Pseudomonas syringae type III secrete...	Many bacterial pathogens disrupt key components of host physiology by injecting virulence proteins ( or “effectors” ) via a needle-like structure , called the type III secretion system , directly into eukaryotic cells . The YopJ / HopZ superfamily of type III secreted effector proteins is found in pathogens of both ani...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "science", "model", "organisms", "plant", "and", "algal", "models", "plant", "biology", "plant", "pathology", "biology", "microbiology", "bacterial", "pathogens" ]	2012	A Bacterial Acetyltransferase Destroys Plant Microtubule Networks and Blocks Secretion
The rapid invasion and spread of Aedes albopictus ( Skuse , 1894 ) within new continents and climatic ranges has created favorable conditions for the emergence of tropical arboviral diseases in the invaded areas . We used mosquito abundance data from 2014 collected across ten sites in northern Italy to calibrate a popu...	The tropical mosquito Aedes albopictus is a vector for several viruses that can be transmitted to human hosts through infectious bites . In the last 20 years , Aedes albopictus has rapidly expanded its habitat to temperate climates and it is now widespread in a large part of southern Europe and the United States . Here...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "chikungunya", "infection", "infectious", "disease", "epidemiology", "atmospheric", "science", "tropical", "diseases", "geographical", "locations", "animals", "neglected", "tropical", "diseases", "population", "biolo...	2016	Potential Risk of Dengue and Chikungunya Outbreaks in Northern Italy Based on a Population Model of Aedes albopictus (Diptera: Culicidae)
The treatment for leishmaniasis is currently based on pentavalent antimonials and amphotericin B; however , these drugs result in numerous adverse side effects . The lack of affordable therapy has necessitated the urgent development of new drugs that are efficacious , safe , and more accessible to patients . Natural pr...	Leishmaniasis is an important neglected disease caused by protozoa of the genus Leishmania and affects more than 12 million people worldwide . Pentavalent antimonials and amphotericin B have been used for decades to treat leishmaniasis; however , these drugs result in numerous adverse side effects , have variable effic...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[ "blood", "cells", "cell", "death", "medicine", "and", "health", "sciences", "autophagic", "cell", "death", "immune", "cells", "pathology", "and", "laboratory", "medicine", "immunology", "tropical", "diseases", "microbiology", "cell", "processes", "parasitic", "disease...	2016	Oral Efficacy of Apigenin against Cutaneous Leishmaniasis: Involvement of Reactive Oxygen Species and Autophagy as a Mechanism of Action
Infants born to dengue immune mothers acquire maternal antibodies to dengue . These antibodies , though initially protective , decline during the first year of life to levels thought to be disease enhancing , before reaching undetectable levels . Infants have long been studied to understand the interaction between infe...	Infants born to dengue immune mothers acquire maternal dengue antibodies . These antibodies , though initially protective , decline during the first year of life to levels thought to be disease enhancing , before reaching undetectable levels . We show that in this population , DENV-2 and DENV-4 almost exclusively cause...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Epidemiology of Infant Dengue Cases Illuminates Serotype-Specificity in the Interaction between Immunity and Disease, and Changes in Transmission Dynamics
Scabies is highly prevalent in socially disadvantaged communities such as indigenous populations and in developing countries . Generalized itching causes discomfort to the patient; however , serious complications can occur as a result of secondary bacterial pyoderma , commonly caused by Streptococcus pyogenes ( GAS ) o...	Australian Aborigines experience streptococcal invasive diseases at a five times greater rate than the general Australian population [1] , contributing to an estimated life expectancy gap of currently 13 years [2] with infectious diseases being the major cause in remote areas . Alternative approaches to control skin in...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "dermatology", "complement", "system", "immunology", "group", "a", "streptococcal", "infection", "parasitic", "diseases", "bacterial", "diseases", "skin", "infections", "impetigo", "neglected", "tropical", "diseases", "infectious", "diseases", "scabies", "stre...	2012	Complement Inhibitors from Scabies Mites Promote Streptococcal Growth – A Novel Mechanism in Infected Epidermis?
Leptospirosis , a spirochaetal zoonosis , occurs in diverse epidemiological settings and affects vulnerable populations , such as rural subsistence farmers and urban slum dwellers . Although leptospirosis is a life-threatening disease and recognized as an important cause of pulmonary haemorrhage syndrome , the lack of ...	Leptospirosis is a zoonotic bacterial disease that affects vulnerable populations such as rural subsistence farmers and urban slum dwellers . Although leptospirosis causes life-threatening clinical manifestations , such as pulmonary hemorrhage syndrome , and has a worldwide distribution , the key barrier to addressing ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Global Morbidity and Mortality of Leptospirosis: A Systematic Review
Over the last few years , momentum has gathered around the feasibility and opportunity of eliminating gambiense human African trypanosomiasis ( g-HAT ) . Under the leadership of the World Health Organization ( WHO ) , a large coalition of stakeholders is now committed to achieving this goal . A roadmap has been laid ou...	Control activities conducted over the last 15 years against gambiense human African trypanosomiasis ( g-HAT ) have had a tremendous impact on disease transmission , and the elimination of g-HAT now appears achievable . In this context , accurate monitoring is crucial . This paper analyzes g-HAT epidemiological trends b...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Monitoring the Progress towards the Elimination of Gambiense Human African Trypanosomiasis
There is currently no licensed antiviral drug for treatment of dengue . Chloroquine ( CQ ) inhibits the replication of dengue virus ( DENV ) in vitro . A double-blind , randomized , placebo-controlled trial of CQ in 307 adults hospitalized for suspected DENV infection was conducted at the Hospital for Tropical Diseases...	There is no available drug or vaccine against dengue , an acute viral disease that affects ∼50 million people annually in tropical and sub-tropical countries . Chloroquine ( CQ ) , a cheap and well-tolerated drug , inhibits the growth of dengue viruses in the laboratory with concentrations achievable in the body . To m...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "infectious", "diseases/tropical", "and", "travel-associated", "diseases", "infectious", "diseases/viral", "infections" ]	2010	A Randomized Controlled Trial of Chloroquine for the Treatment of Dengue in Vietnamese Adults
Murine gammaherpesvirus 68 ( MHV68 ) establishes long-term latency in memory B cells similar to the human gammaherpesvirus Epstein Barr Virus ( EBV ) . EBV encodes an interleukin-10 ( IL-10 ) homolog and modulates cellular IL-10 expression; however , the role of IL-10 in the establishment and/or maintenance of chronic ...	Gammaherpesviruses are able to maintain life-long , quiescent infections ( latency ) in lymphocytes characterized by intermittent production of infectious progeny virus ( reactivation ) . The murine gammaherpesvirus 68 ( MHV68 ) has extensive genetic and phenotypic similarities to the human gammaherpesviruses Epstein-B...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "virology/animal", "models", "of", "infection", "virology", "microbiology", "virology/immune", "evasion", "virology/effects", "of", "virus", "infection", "on", "host", "gene", "expression" ]	2008	The MHV68 M2 Protein Drives IL-10 Dependent B Cell Proliferation and Differentiation
Regulation of mitochondrial DNA ( mtDNA ) expression is critical for the control of oxidative phosphorylation in response to physiological demand , and this regulation is often impaired in disease and aging . We have previously shown that mitochondrial transcription termination factor 3 ( MTERF3 ) is a key regulator th...	One of the main functions of the mitochondrial network is to provide the energy currency ATP to drive a large array of cellular metabolic processes . The formation of the mitochondrial respiratory chain , which allows this energy supply , is under the control of two separate genetic systems , the nuclear and the mitoch...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "model", "organisms", "genetics", "biology", "genetics", "and", "genomics", "gene", "function" ]	2013	MTERF3 Regulates Mitochondrial Ribosome Biogenesis in Invertebrates and Mammals
Antibody ( Ab ) to the Wuchereria bancrofti ( Wb ) infective larval ( L3 ) antigen Wb123 , using a Luciferase Immunoprecipitation System ( LIPS ) assay , has been shown to be a species-specific , early marker of infection developed for potential use as a surveillance tool following transmission interruption post mass d...	Lymphatic filariasis ( LF ) causes an enormous disease burden throughout the tropics and subtropics . The Global Programme to Eliminate Lymphatic Filariasis was begun in 2000 following the advent of large donations from drug companies for treating LF and the development of a rapid antigen assay for detection of infecti...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "clinical", "immunology", "global", "health", "immunoassays", "neglected", "tropical", "diseases", "immunology", "immunologic", "techniques", "lymphatic", "filariasis" ]	2012	Antibody to the Filarial Antigen Wb123 Reflects Reduced Transmission and Decreased Exposure in Children Born following Single Mass Drug Administration (MDA)
The protein O-glucosyltransferase Rumi/POGLUT1 regulates Drosophila Notch signaling by adding O-glucose residues to the Notch extracellular domain . Rumi has other predicted targets including Crumbs ( Crb ) and Eyes shut ( Eys ) , both of which are involved in photoreceptor development . However , whether Rumi is requi...	Glycosylation ( addition of sugars to proteins and other organic molecules ) is important for protein function and animal development . Each form of glycosylation is usually present on multiple proteins . Therefore , a major challenge in understanding the role of sugars in animal development is to identify which protei...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "arthropoda", "biochemistry", "developmental", "biology", "invertebrates", "genetics", "biology", "and", "life", "sciences", "drosophila", "glycobiology", "animals", "organisms", "insects" ]	2014	The Protein O-glucosyltransferase Rumi Modifies Eyes Shut to Promote Rhabdomere Separation in Drosophila
Angelman syndrome ( AS ) is a severe neurodevelopmental disorder caused by maternal deficiency of the imprinted gene UBE3A . Individuals with AS suffer from intellectual disability , speech impairment , and motor dysfunction . Currently there is no cure for the disease . Here , we evaluated the phenotypic effect of act...	Angelman syndrome ( AS ) is a devastating neurodevelopmental disorder diagnosed in young children , currently with no effective treatments . It is characterized by absence of speech , ataxia , intellectual disability , epilepsy , and a characteristic behavior of frequent laughter and smiling . The disease is caused by ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Truncation of Ube3a-ATS Unsilences Paternal Ube3a and Ameliorates Behavioral Defects in the Angelman Syndrome Mouse Model
Dendritic spines are the main postsynaptic site of excitatory contacts between neurons in the central nervous system . On cortical neurons , spines undergo a continuous turnover regulated by development and sensory activity . However , the functional implications of this synaptic remodeling for network properties remai...	In the central nervous system , excitatory contacts between neurons occur mainly on postsynaptic protrusions called dendritic spines . For decades , these structures have been considered static , and the adaptive properties of neuronal networks were thought to be only due to changes in the strength of neuronal connecti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience", "cell", "biology" ]	2008	LTP Promotes a Selective Long-Term Stabilization and Clustering of Dendritic Spines
Previous studies have shown that exponentially growing Escherichia coli can detect mild acidity ( ~pH 5 . 5 ) and , in response , synthesize enzymes that protect against severe acid shock . This adaptation is controlled by the EvgS/EvgA phosphorelay , a signal transduction system present in virtually every E . coli iso...	Bacteria employ a class of proteins , sensor kinases , to sense environmental cues and initiate cellular responses through phosphorylation of partner response regulator proteins . Individual kinases are generally assumed to have the same sensory activity across members of a bacterial species . In this work , we report ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "bacteriology", "taxonomy", "medicine", "and", "health", "sciences", "gut", "bacteria", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "operons", "light", "microscopy", "plasmid", "construction", "escherichia", "coli", "prokaryotic", "models", ...	2017	Natural variation of a sensor kinase controlling a conserved stress response pathway in Escherichia coli
Cumulative evidence supports a role for neutralizing antibodies contributing to spontaneous viral clearance during acute hepatitis C virus ( HCV ) infection . Information on the timing and specificity of the B cell response associated with clearance is crucial to inform vaccine design . From an individual who cleared t...	Studies of hepatitis C virus ( HCV ) infected individuals spontaneously clearing acute infections provide an opportunity to characterize the specificities of associated protective antibody responses . In an individual who resolved three separate HCV infections with different HCV genotypes , the antibodies induced durin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "hepacivirus", "pathogens", "epitope", "mapping", "immunology", "microbiology", "vi...	2019	Broadly neutralizing antibodies from an individual that naturally cleared multiple hepatitis C virus infections uncover molecular determinants for E2 targeting and vaccine design
GC-biased gene conversion ( gBGC ) is a recombination-associated process that favors the fixation of G/C alleles over A/T alleles . In mammals , gBGC is hypothesized to contribute to variation in GC content , rapidly evolving sequences , and the fixation of deleterious mutations , but its prevalence and general functio...	Interpreting patterns of DNA sequence variation in the genomes of closely related species is critically important for understanding the causes and functional effects of nucleotide substitutions . Classical models describe patterns of substitution in terms of the fundamental forces of mutation , recombination , neutral ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "sequence", "analysis", "genome", "complexity", "genome", "evolution", "natural", "selection", "evolutionary", "processes", "evolutionary", "modeling", "genetics", "population", "genetics", "comparative", "genomics", "biology", "genomics", "evolutionary", "biology", "genomi...	2013	A Model-Based Analysis of GC-Biased Gene Conversion in the Human and Chimpanzee Genomes
Biological network figures are ubiquitous in the biology and medical literature . On the one hand , a good network figure can quickly provide information about the nature and degree of interactions between items and enable inferences about the reason for those interactions . On the other hand , good network figures are...	Biological network figures are ubiquitous in the biology and medical literature . In this paper , we outline 10 simple rules for creating biological network figures for communication , from choosing layouts , to applying color or other channels to show attributes , to the use of layering and separation .	[ "Abstract", "Introduction", "Rule", "1:", "First,", "determine", "the", "figure", "purpose", "and", "assess", "the", "network", "Rule", "2:", "Consider", "alternative", "layouts", "Rule", "3:", "Beware", "of", "unintended", "spatial", "interpretations", "Rule", "4...	[ "medicine", "and", "health", "sciences", "protein", "interactions", "protein", "interaction", "networks", "sociology", "blastomas", "cancers", "and", "neoplasms", "social", "sciences", "light", "electromagnetic", "radiation", "oncology", "neurological", "tumors", "luminan...	2019	Ten simple rules to create biological network figures for communication
Great strides have been made in understanding the evolutionary history of simian immunodeficiency virus ( SIV ) and the zoonoses that gave rise to HIV-1 and HIV-2 . What remains unknown is how long these SIVs had been circulating in non-human primates before the transmissions to humans . Here , we use relaxed molecular...	HIV/AIDS continues to be a major health problem worldwide . An understanding of the evolution of HIV in humans may be greatly improved by detailed knowledge of its predecessor , simian immunodeficiency virus ( SIV ) , in non-human primates . While HIV causes AIDS in humans , SIV generally produces a benign infection in...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "virology/immunodeficiency", "viruses", "evolutionary", "biology/microbial", "evolution", "and", "genomics", "virology/virus", "evolution", "and", "symbiosis" ]	2009	Dating the Age of the SIV Lineages That Gave Rise to HIV-1 and HIV-2
MicroRNAs ( miRNAs ) posttranscriptionally regulate targeted messenger RNAs ( mRNAs ) by inducing cleavage or otherwise repressing their translation . We address the problem of detecting m/miRNA targeting relationships in homo sapiens from microarray data by developing statistical models that are motivated by the biolo...	MicroRNAs are a family of small RNAs that play important roles in the development , physiological function and stress responses of a wide variety of organisms , and if abnormally expressed are associated with multiple types of cancer in humans . Rather than being translated into proteins , members of the family of micr...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "genetics", "and", "genomics/genomics", "computational", "biology/systems", "biology", "computational", "biology/transcriptional", "regulation", "molecular", "biology/mrna", "stability", "molecular", "biology/rna", "splicing", "molecular", "biology/bioinformatics", "computational",...	2009	Statistical Use of Argonaute Expression and RISC Assembly in microRNA Target Identification
TRAM is a conserved domain among RNA modification proteins that are widely distributed in various organisms . In Archaea , TRAM occurs frequently as a standalone protein with in vitro RNA chaperone activity; however , its biological significance and functional mechanism remain unknown . This work demonstrated that TRAM...	RNAs frequently misfold into stable but biologically inactive structures especially under stresses , while RNA chaperones interact with various RNAs to prevent the structures that may cause premature transcriptional termination or pausing , and affect mRNA decay and translation . This work for the first time reports th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "sequencing", "techniques", "rna-binding", "proteins", "messenger", "rna", "dna", "transcription", "rna", "stem-loop", "structure", "archaea", "molecular", "biology", "techniques", "rna", "sequencing", "research", "and", "analysis", "methods", "rna", "structure", "prote...	2019	The archaeal RNA chaperone TRAM0076 shapes the transcriptome and optimizes the growth of Methanococcus maripaludis
Across all kingdoms of biological life , protein-coding genes exhibit unequal usage of synonymous codons . Although alternative theories abound , translational selection has been accepted as an important mechanism that shapes the patterns of codon usage in prokaryotes and simple eukaryotes . Here we analyze patterns of...	Any protein can be encoded by multiple , synonymous spellings . But organisms typically prefer one spelling over another—a phenomenon known as codon bias . Codon bias is generally understood to result from selection for synonymous spellings that increase the rate and accuracy of protein translation . In this work , we ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/population", "genetics", "computational", "biology/sequence", "motif", "analysis", "computational", "biology/genomics" ]	2008	Genome Landscapes and Bacteriophage Codon Usage
The dominant phenotype of greying with age in horses , caused by a 4 . 6-kb duplication in intron 6 of STX17 , is associated with a high incidence of melanoma and vitiligo-like skin depigmentation . However , the progressive greying and the incidence of melanoma , vitiligo-like depigmentation , and amount of speckling ...	Clarifying the genetic architecture of complex traits is a problem with profound implications for agriculture , biology , and medicine . Using data from Lipizzan horses with the grey coat phenotype , we present an example of a single mutation ( intronic duplication in STX17 ) that explains 18%–55% of phenotypic variati...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biology", "veterinary", "science", "agriculture" ]	2013	Complex Inheritance of Melanoma and Pigmentation of Coat and Skin in Grey Horses
Next-generation sequencing technology provides novel opportunities for gathering genome-scale sequence data in natural populations , laying the empirical foundation for the evolving field of population genomics . Here we conducted a genome scan of nucleotide diversity and differentiation in natural populations of three...	Oceanic threespine stickleback have invaded and adapted to freshwater habitats countless times across the northern hemisphere . These freshwater populations have often evolved in similar ways from the ancestral marine stock from which they independently derived . With the exception of a few identified genes , the genet...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "evolutionary", "biology/genomics", "ecology/marine", "and", "freshwater", "ecology", "computational", "biology/genomics", "evolutionary", "biology/developmental", "evolution" ]	2010	Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags
Reduced antimicrobial susceptibility threatens treatment efficacy in sub-Saharan Africa , where data on the burden and correlates of antibiotic resistance among enteric pathogens are limited . Fecal samples from children aged 6 mos—15 yrs presenting with acute diarrhea in western Kenya were cultured for bacterial patho...	Children in Sub-Saharan Africa experience frequent enteric infections and antibiotics are often used to treat diarrheal disease . Some bacterial causes of diarrhea have developed resistance to commonly used antibiotics yet this information is rarely available to managing clinicians . We sought to identify which childre...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusion" ]	[ "antimicrobials", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "drugs", "tropical", "diseases", "microbiology", "shigella", "diarrhea", "bacterial", "diseases", "antibiotic", "resistance", "signs", "and", "symptoms", ...	2017	Correlates of multi-drug non-susceptibility in enteric bacteria isolated from Kenyan children with acute diarrhea
Understanding the factors underlying the spatio-temporal distribution of infectious diseases provides useful information regarding their prevention and control . Dengue fever spatio-temporal patterns result from complex interactions between the virus , the host , and the vector . These interactions can be influenced by...	Dengue fever is the most important viral arthropod-borne disease worldwide and its geographical expansion during the past decades has been of growing concern for scientists and public health authorities because of its heavy sanitary burden and economic impacts . In the absence of an effective vaccine , control is curre...	[ "Abstract", "Introduction", "Material", "and", "Methods", "Results", "Discussion" ]	[]	2015	Socio-economic and Climate Factors Associated with Dengue Fever Spatial Heterogeneity: A Worked Example in New Caledonia
Understanding the functional relationship between intracellular factors and extracellular signals is required for reconstructing gene regulatory networks ( GRN ) involved in complex biological processes . One of the best-studied bilaterian GRNs describes endomesoderm specification and predicts that both mesoderm and en...	Cnidarians ( anemones , corals , and “jellyfish” ) are an animal group whose adults possess derivatives of only two germ layers: ectoderm and a bifunctional ( absorptive and contractile ) gastrodermal ( gut ) layer . Cnidarians are the closest living relatives to bilaterally symmetrical animals that possess all three g...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "embryology", "dna", "transcription", "signaling", "molecular", "development", "genetics", "gene", "expression", "biology", "gene", "networks", "genetics", "and", "genomics", "cell", "fate", "determination", "evolutionary", "developmental", "bi...	2012	A Framework for the Establishment of a Cnidarian Gene Regulatory Network for “Endomesoderm” Specification: The Inputs of ß-Catenin/TCF Signaling
Phlebotomine sand flies transmit Leishmania , phlebo-viruses and Bartonella to humans . A prominent gap in our knowledge of sand fly biology remains the ecology of their immature stages . Sand flies , unlike mosquitoes do not breed in water and only small numbers of larvae have been recovered from diverse habitats that...	Sand flies are small blood sucking flies that transmit Leishmania , the etiologic agent of leishmaniasis - a prevalent disease over large areas of the World . Unlike mosquitoes , sand flies do not breed in water . Their larvae develop in humid habitats containing decaying organic matter ( e . g . habitats such as burro...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "ecology", "biology" ]	2012	Breeding Sites of Phlebotomus sergenti, the Sand Fly Vector of Cutaneous Leishmaniasis in the Judean Desert
Understanding buffering mechanisms for various perturbations is essential for understanding robustness in cellular systems . Protein-level dosage compensation , which arises when changes in gene copy number do not translate linearly into protein level , is one mechanism for buffering against genetic perturbations . Her...	Cells are exposed to environmental changes leading to fluctuations in biological processes . For example , changes in gene copy number are a source of such fluctuations . An increase in gene copy number generally leads to a linear increase in the amount of protein; however , a small number of genes do not show a propor...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "dosage", "compensation", "gene", "regulation", "messenger", "rna", "fungi", "protein", "expression", "molecular", "biology", "techniques", "cellular", "structures", "and", "organelles", "research", "and", "analysis", "methods", "chromosome", "biology", "gene", "express...	2017	Post-Translational Dosage Compensation Buffers Genetic Perturbations to Stoichiometry of Protein Complexes
The incidence of leptospirosis , a neglected zoonotic disease , is uncertain in Tanzania and much of sub-Saharan Africa , resulting in scarce data on which to prioritize resources for public health interventions and disease control . In this study , we estimate the incidence of leptospirosis in two districts in the Kil...	Leptospirosis is a zoonotic infection that occurs worldwide and is caused by a spirochete , Leptospira spp . The incidence of leptospirosis is unknown in most of sub-Saharan Africa , including Tanzania . Incidence estimates are important in prioritizing resources for disease prevention and control . In this study , we ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2013	Estimating Leptospirosis Incidence Using Hospital-Based Surveillance and a Population-Based Health Care Utilization Survey in Tanzania
Prion diseases are incurable neurodegenerative disorders in which the normal cellular prion protein ( PrPC ) converts into a misfolded isoform ( PrPSc ) with unique biochemical and structural properties that correlate with disease . In humans , prion disorders , such as Creutzfeldt-Jakob disease , present typically wit...	Creutzfeldt-Jakob disease is a type of dementia caused by the deposition of the prion protein in the brain . This disorder belongs to a unique class of degenerative diseases that includes mad-cow disease in bovine and scrapie in sheep . An abnormal form of the prion protein is not only responsible for the disease in se...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/disease", "models", "neurological", "disorders/prion", "diseases", "biochemistry/protein", "folding" ]	2009	In Vivo Generation of Neurotoxic Prion Protein: Role for Hsp70 in Accumulation of Misfolded Isoforms
Aphids are economically important pests that display exceptional variation in host range . The determinants of diverse aphid host ranges are not well understood , but it is likely that molecular interactions are involved . With significant progress being made towards understanding host responses upon aphid attack , the...	Aphids are phloem-feeding insects that cause feeding damage and transmit plant viruses to many crops . While most aphid species are restricted to one or few host plants , some aphids can infest a wide range of plant species . These insects spend a considerable time on non-hosts , where they probe the leaf tissue and se...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Characterization of Arabidopsis Transcriptional Responses to Different Aphid Species Reveals Genes that Contribute to Host Susceptibility and Non-host Resistance
Fluctuations in the temporal durations of sensory signals constitute a major source of variability within natural stimulus ensembles . The neuronal mechanisms through which sensory systems can stabilize perception against such fluctuations are largely unknown . An intriguing instantiation of such robustness occurs in h...	The brain has a robust ability to process sensory stimuli , even when those stimuli are warped in time . The most prominent example of such perceptual robustness occurs in speech communication . Rates of speech can be highly variable both within and across speakers , yet our perceptions of words remain stable . The neu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience/neuronal", "signaling", "mechanisms", "neuroscience/theoretical", "neuroscience", "neuroscience/sensory", "systems", "computational", "biology/computational", "neuroscience" ]	2009	Time-Warp–Invariant Neuronal Processing
Neuronal avalanches are a form of spontaneous activity widely observed in cortical slices and other types of nervous tissue , both in vivo and in vitro . They are characterized by irregular , isolated population bursts when many neurons fire together , where the number of spikes per burst obeys a power law distribution...	Networks of neurons display a broad variety of behavior that nonetheless can often be described in very simple statistical terms . Here we explain the basis of one particularly striking statistical rule: that in many systems , the likelihood that groups of neurons burst , or fire together , is linked to the number of n...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "mathematics", "neuroscience/theoretical", "neuroscience", "computational", "biology/computational", "neuroscience" ]	2010	Avalanches in a Stochastic Model of Spiking Neurons
Epigenomes commonly refer to the sequence of presence/absence of specific epigenetic marks along eukaryotic chromatin . Complete histone-borne epigenomes have now been described at single-nucleosome resolution from various organisms , tissues , developmental stages , or diseases , yet their intra-species natural variat...	Nucleosomes are the basic units of chromatin , with part of the long DNA molecule wrapped around a multiprotein core , which makes unpacked chromatin often portrayed as a string of pearls . This string can carry three types of sequences: DNA , methyl groups on cytosines , and , on every pearl , the presence-or-absence ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/population", "genetics", "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "genetics", "and", "genomics/comparative", "genomics", "computational", "biology/transcriptional", "regulation", "genetics", "and", "genomics/functional", ...	2010	Natural Single-Nucleosome Epi-Polymorphisms in Yeast
Metabolism , the conversion of nutrients into usable energy and biochemical building blocks , is an essential feature of all cells . The genetic factors responsible for inter-individual metabolic variability remain poorly understood . To investigate genetic causes of metabolome variation , we measured the concentration...	Many traits , from human height to E . coli growth rate , quantitatively vary across members of a species . Among the most medically and agriculturally important traits are levels of cellular metabolites , such as cholesterol levels in humans or starch in food crops . Metabolic variation in yeast also holds practical i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "biochemistry", "genetics", "biology", "metabolism" ]	2014	Genetic Basis of Metabolome Variation in Yeast
Kaposi's sarcoma ( KS ) is caused by infection with Kaposi's sarcoma-associated herpesvirus ( KSHV ) . The virus expresses unique microRNAs ( miRNAs ) , but the targets and functions of these miRNAs are not completely understood . In order to identify human targets of viral miRNAs , we measured protein expression chang...	Kaposi's sarcoma-associated herpesvirus is the virus associated with multiple proliferative disorders , including Kaposi's sarcoma , primary effusion lymphoma and multicentric Castleman's disease . This virus expresses small nucleic acids ( with sequences distinct from other organisms ) , called microRNAs , that can li...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "proteomic", "databases", "viral", "immune", "evasion", "viruses", "and", "cancer", "virology", "biology", "microbiology", "proteomics" ]	2013	Proteomic Screening of Human Targets of Viral microRNAs Reveals Functions Associated with Immune Evasion and Angiogenesis
Sub-Saharan Africa harbors the majority of the global burden of malaria and schistosomiasis infections . The co-endemicity of these two tropical diseases has prompted investigation into the mechanisms of coinfection , particularly the competing immunological responses associated with each disease . Epidemiological stud...	Malaria and Schistosoma mansoni are co-endemic in many regions of sub-Saharan Africa . Evidence from clinical and epidemiological studies support the hypothesis that concurrent infection with S . mansoni is associated with greater malaria incidence among school-age children . We use mathematical modeling to evaluate th...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "helminth", "infections", "medicine", "and", "health", "sciences", "schistosomiasis", "population", "modeling", "biology", "and", "life", "sciences", "infectious", "disease", "modeling", "computational", "biology", "infectious", "disease", "contr...	2014	Impact of Schistosoma mansoni on Malaria Transmission in Sub-Saharan Africa
The master regulators of the cell cycle are cyclin-dependent kinases ( Cdks ) , which influence the function of a myriad of proteins via phosphorylation . Mitotic Cdk1 is activated by A-type , as well as B1- and B2-type , cyclins . However , the role of a third , conserved cyclin B family member , cyclin B3 , is less w...	Every time a cell divides in two , the genetic material , DNA , is copied; each copied chromosome is referred to as a pair of sister chromatids . Each chromatid must be cleanly separated from its sister so that each daughter cell inherits the same DNA complement as the starting cell . The mitotic spindle is a cellular ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/cell", "growth", "and", "division" ]	2010	Caenorhabditis elegans Cyclin B3 Is Required for Multiple Mitotic Processes Including Alleviation of a Spindle Checkpoint–Dependent Block in Anaphase Chromosome Segregation
The Alliance for the Global Elimination of Trachoma has set the target for eliminating trachoma as a public health problem by 2020 . However , challenges remain , including socio-cultural issues . Districts in Northern Tanzania , predominantly inhabited by the Maasai ethnic group , remain endemic for trachoma . We expl...	While global efforts to control and ultimately eliminate trachoma have been successful in many contexts , it has proven to be more challenging in many societies . Due to social , political or economic vulnerabilities , the approach to delivering global health programmes to some marginalized communities requires a more ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "skin", "plant", "anatomy", "medicine", "and", "health", "sciences", "integumentary", "system", "face", "tropical", "diseases", "geographical", "locations", "bacterial", "diseases", "plant", "science", "tanzania", "eye", "diseases", "neglected", "tropical", "diseases", ...	2019	Knowledge, perceptions and experiences of trachoma among Maasai in Tanzania: Implications for prevention and control
Anti-leishmanial drug regimens that include a single dose AmBisome® could be suitable for eastern African patients with symptomatic visceral leishmaniasis ( VL ) but the appropriate single dose is unknown . A multi-centre , open-label , non-inferiority , randomized controlled trial with an adaptive design , was conduct...	Visceral leishmaniasis is a potentially fatal disease which affects 0 . 2–0 . 4 million people every year , principally in South-East Asia , Latin America or Eastern Africa . Currently the safest drug in use is AmBisome® , which cures 90% of patients in India at 5 mg/kg , and is even more effective at higher doses ( 10...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine" ]	2014	Safety and Efficacy of Single Dose versus Multiple Doses of AmBisome® for Treatment of Visceral Leishmaniasis in Eastern Africa: A Randomised Trial
Receptor tyrosine kinases ( RTKs ) typically contain multiple autophosphorylation sites in their cytoplasmic domains . Once activated , these autophosphorylation sites can recruit downstream signaling proteins containing Src homology 2 ( SH2 ) and phosphotyrosine-binding ( PTB ) domains , which recognize phosphotyrosin...	Cells rely on networks of interacting biomolecules to sense and respond to environmental perturbations and signals . However , it is unclear how information is processed to generate appropriate and specific responses to signals , especially given that these networks tend to share many components . For example , recepto...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "binding", "phosphorylation", "cell", "physiology", "chemical", "characterization", "chemical", "compounds", "organic", "compounds", "simulation", "and", "modeling", "tyrosine", "amino", "acids", "research", "and", "analysis", "methods", "aromatic", "amino", "ac...	2019	Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor
Human excreta is a low cost source of nutrients vital to plant growth , but also a source of pathogens transmissible to people and animals . We investigated the cost-savings and infection risk of soil transmitted helminths ( STHs ) in four scenarios where farmers used either inorganic fertilizer or fresh/composted huma...	Each year , hundreds of millions of people worldwide are infected with intestinal worms spread by contaminated soil , also known as soil transmitted helminths ( STHs ) . These worms are most common in tropical climates in areas lacking good hygiene and sanitation , and negatively impact child development , quality of l...	[ "Abstract", "Introduction", "Methods", "Discussion", "Conclusions" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "helminths", "tropical", "diseases", "parasitic", "diseases", "animals", "rice", "ascaris", "lumbricoides", "mathematics", "ascaris", "statistics", "(mathematics)", "experimental", "organism", "systems", "neglected",...	2017	Turning poop into profit: Cost-effectiveness and soil transmitted helminth infection risk associated with human excreta reuse in Vietnam
Corpus allatum ( CA ) ablation results in juvenile hormone ( JH ) deficiency and pupal lethality in Drosophila . The fly CA produces and releases three sesquiterpenoid hormones: JH III bisepoxide ( JHB3 ) , JH III , and methyl farnesoate ( MF ) . In the whole body extracts , MF is the most abundant sesquiterpenoid , fo...	Methyl farnesoate ( MF ) is the immediate precursor of juvenile hormone ( JH ) III in the JH biosynthetic pathway , and lacks the epoxide moiety characteristic of JHs . The potential role of MF as a JH in arthropods has been an issue of a long-standing debate . In this report , comprehensive molecular genetics studies ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Methyl Farnesoate Plays a Dual Role in Regulating Drosophila Metamorphosis
The genetic basis of most heritable traits is complex . Inhibitory compounds and their effects in model organisms have been used in many studies to gain insights into the genetic architecture underlying quantitative traits . However , the differential effect of compound concentration has not been studied in detail . In...	Variation in response to a drug can be determined by many factors . In the model organism baker's yeast , many studies of chemical resistance traits have uncovered a complex genetic basis of such resistance . However , an in-depth study of how drug dose alters the effects of underlying genetic factors is lacking . Here...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "biology", "and", "life", "sciences", "microbiology", "evolutionary", "biology", "molecular", "biology" ]	2014	Genetic Basis of Haloperidol Resistance in Saccharomyces cerevisiae Is Complex and Dose Dependent
Testosterone concentrations in men are associated with cardiovascular morbidity , osteoporosis , and mortality and are affected by age , smoking , and obesity . Because of serum testosterone's high heritability , we performed a meta-analysis of genome-wide association data in 8 , 938 men from seven cohorts and followed...	Testosterone is the most important testicular androgen in men . Low serum testosterone concentrations are associated with cardiovascular morbidity , metabolic syndrome , type 2 diabetes mellitus , atherosclerosis , osteoporosis , sarcopenia , and increased mortality risk . Thus , there is growing evidence that serum te...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "public", "health", "and", "epidemiology", "personalized", "medicine", "endocrinology", "reproductive", "endocrinology", "epidemiology", "endocrine", "physiology", "diabetes", "and", "endocrinology", "genetics", "and", "genomics", "genetic", "epidemiology", "cli...	2011	Genetic Determinants of Serum Testosterone Concentrations in Men
BAHD1 is a vertebrate protein that promotes heterochromatin formation and gene repression in association with several epigenetic regulators . However , its physiological roles remain unknown . Here , we demonstrate that ablation of the Bahd1 gene results in hypocholesterolemia , hypoglycemia and decreased body fat in m...	The importance of epigenetics in regulation and dysfunction of metabolic pathways is increasingly recognized but the underlying mechanisms and molecular actors involved remain incompletely characterized . Here , we provide evidence that the heterochromatinization factor BAHD1 cooperates with MIER proteins to assemble c...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "reproductive", "system", "gene", "regulation", "developmental", "biology", "immunoprecipitation", "genome", "analysis", "epigenetics", "dna", "chromatin", "dna", "methylation", "research", "and", "analysis", "methods", "small", ...	2016	Role of the BAHD1 Chromatin-Repressive Complex in Placental Development and Regulation of Steroid Metabolism
Toxoplasma gondii is a zoonotic protozoan with a worldwide occurrence , but the determinants of the current pattern in the geographical distribution of T . gondii lineages and strains remain poorly understood . To test the influence of human trade on T . gondii populations , we conducted a population genetic study of 7...	Toxoplasma gondii is a zoonotic protozoan with a worldwide distribution and which can infects virtually all warm-blooded species , including human . Clinical expression of human toxoplasmosis , as well as T . gondii strains diversity , exhibit contrasting patterns across geographic regions . The determinants of this ge...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "biogeography", "animal", "types", "ecology", "and", "environmental", "sciences", "toxoplasma", "gondii", "population", "dynamics", "population", "genetics", "geographical", "locations", "domestic", "animals", "parasitic", "protozoans", "animals", "protozoans", "toxoplasma"...	2019	The introduction of new hosts with human trade shapes the extant distribution of Toxoplasma gondii lineages
Odor perception requires that each olfactory sensory neuron ( OSN ) class continuously express a single odorant receptor ( OR ) regardless of changes in the environment . However , little is known about the control of the robust , class-specific OR expression involved . Here , we investigate the cis-regulatory mechanis...	Our neurons can become over a hundred years old . Even if neurons are restructured and remodeled by their constant work of receiving , storing and sending information , they stay devoted to one single task and retain their identity for their whole life . How a neuron keeps its identity is not well understood . In the o...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Cis-Regulatory Mechanisms for Robust Olfactory Sensory Neuron Class-restricted Odorant Receptor Gene Expression in Drosophila
Accumulation of unfolded proteins in the lumen of the endoplasmic reticulum ( ER ) causes ER stress . Snf1 , the Saccharomyces cerevisiae ortholog of AMP–activated protein kinase ( AMPK ) , plays a crucial role in the response to various environmental stresses . However , the role of Snf1 in ER stress response remains ...	All organisms are always exposed to several environmental stresses , including ultraviolet , heat , and chemical compounds . Therefore , every cell possesses defense mechanisms to maintain their survival under stressed conditions . Numerous studies have shown that a family of protein kinases plays a principal role in a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Saccharomyces cerevisiae AMPK, Snf1, Negatively Regulates the Hog1 MAPK Pathway in ER Stress Response
Low copy number plasmids in bacteria require segregation for stable inheritance through cell division . This is often achieved by a parABC locus , comprising an ATPase ParA , DNA-binding protein ParB and a parC region , encoding ParB-binding sites . These minimal components space plasmids equally over the nucleoid , ye...	How DNA is stably inherited through cell division is a fundamental question in cell biology . The most common system that mediates plasmid DNA inheritance in bacteria is through a parABC locus , encoding proteins ParA and ParB , and DNA sequence parC . These components can position plasmids at equally spaced positions ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences", "microbiology", "computational", "biology" ]	2014	Competing ParA Structures Space Bacterial Plasmids Equally over the Nucleoid

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