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headings list	keywords list	title stringlengths 20 281	id stringlengths 20 20	toc stringlengths 57 522 ⌀	sections list	abstract list	summary list	year stringclasses 13 values
[ "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 and analysis methods", "parasitic intestinal...	Systematic review of studies generating individual participant data on the efficacy of drugs for treating soil-transmitted helminthiases and the case for data-sharing	journal.pntd.0006053	null	[ [ "Soil-transmitted helminthiases ( STHs ) are a group of intestinal nematode infections of humans most commonly , though not exclusively , caused by the roundworm Ascaris lumbricoides , the whipworm Trichuris trichiura and the hookworm species ( Necator americanus or Ancylostoma duodenale ) .", "These infe...	[ "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 ( Necato...	[ "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 ...	2017
[ "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", "model organisms", "experimental organism system...	Genetic dissection of stress-induced reproductive arrest in Drosophila melanogaster females	journal.pgen.1007434	null	[ [ "To tolerate unfavorable environmental conditions such as extreme temperatures and desiccation , organisms , particularly insects , have evolved a powerful mechanism , in which the genetic program serves to arrest development and reproduction at a set developmental stage and confers resistance to environmenta...	[ "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 (...	[ "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 mini...	2018
[ "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", "epidemiology", "schools", "home education", "peop...	Projecting social contact matrices in 152 countries using contact surveys and demographic data	journal.pcbi.1005697	null	[ [ "Events over the last decade have highlighted the threat posed internationally by contact-transmissible infectious diseases such as hand , foot and mouth disease [1 , 2] , MERS-CoV [3] , Ebola [4] , influenza [5] , and Tuberculosis [6] , putting pressure on governments and public health institutes [6] to ensu...	[ "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 ...	[ "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 diff...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "clinical immunology", "african trypanosomiasis", "neglected tropical diseases", "immune response" ]	Gambiense Human African Trypanosomiasis and Immunological Memory: Effect on Phenotypic Lymphocyte Profiles and Humoral Immunity	journal.ppat.1003947	null	[ [ "Human African Trypanosomiasis ( HAT ) or sleeping sickness , is a vector-borne parasitic disease occurring in sub-Saharan Africa .", "About 70 million persons are at risk for infection and 30 000 persons are estimated to be infected [1] .", "The parasites concerned belong to the Trypanosoma genus and...	[ "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 ) ,...	[ "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 hu...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "public health and epidemiology", "population modeling", "epidemiology", "biology", "computational biology", "population biology" ]	Inferring Epidemic Contact Structure from Phylogenetic Trees	journal.pcbi.1002413	null	[ [ "Infectious disease epidemiology has a longstanding history of mathematical modeling .", "Simple population dynamical models assuming random-mixing between infected and susceptible individuals have yielded important insights into the dynamics and control of infectious diseases [1] .", "The assumption ...	[ "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 qu...	[ "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 gre...	2012
[ "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 chromatography", "thermodynamics", "research and analysis met...	A lipid-binding loop of botulinum neurotoxin serotypes B, DC and G is an essential feature to confer their exquisite potency	journal.ppat.1007048	null	[ [ "Botulinum neurotoxins ( BoNTs ) are the most toxic bacterial toxins known and are produced e . g . in food by the anaerobic , spore-forming bacteria Clostridium ( C . ) botulinum , C . butyricum , and C . baratii .", "When contaminated food is ingested , BoNTs specifically inhibit acetylcholine release a...	[ "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 , ...	[ "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 ...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases/viral infections", "infectious diseases/tropical and travel-associated diseases" ]	Dengue 1 Diversity and Microevolution, French Polynesia 2001–2006: Connection with Epidemiology and Clinics	journal.pntd.0000493	null	[ [ "Dengue fever is the most common vector-borne viral disease affecting humans and represents an archetypal emerging infectious disease whose epidemiological landscape has been substantially modified during the past century [1] , [2] .", "Each year , an estimated 100 million people contract dengue fever ( D...	[ "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 predomi...	[ "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 ...	2009
[ "Introduction", "Results/Discussion", "Methods" ]	[ "systems biology", "immunodeficiency viruses", "data mining", "virology", "signal processing", "biology", "computational biology", "microbiology", "host-pathogen interaction", "genetics and genomics", "engineering" ]	Network-Based Prediction and Analysis of HIV Dependency Factors	journal.pcbi.1002164	null	[ [ "Conventional high-throughput antiviral discovery often targets the activities of specific viral enzymes .", "These approaches have been ineffective in stemming the emergence of drug-resistant variants , especially in the face of rapidly-mutating RNA viruses .", "One powerful yet under-explored avenue...	[ "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 in...	[ "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 t...	2011
[ "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 medicine", "experimental organism systems", "fungal disease...	An unappreciated role for neutrophil-DC hybrids in immunity to invasive fungal infections	journal.ppat.1007073	null	[ [ "In the waging battles between host immunity and microbial invaders , polymorphonuclear cells ( PMN ) or neutrophils are the most numerous cellular soldiers under the host banner .", "Neutrophils ward off and eliminate many infections , particularly those caused by fungi .", "As the infantry of an inf...	[ "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 neutr...	[ "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 ...	2018
[ "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" ]	Regulator of G Protein Signaling 3 Modulates Wnt5b Calcium Dynamics and Somite Patterning	journal.pgen.1001020	null	[ [ "The Wnt signaling network is classified into β-catenin-dependent and β-catenin-independent pathways [1]–[3] .", "β-catenin-dependent Wnt signaling acts through the stabilization of β-catenin and subsequent transcriptional activation of β-catenin targets [4] , whereas β-catenin-independent Wnt signaling i...	[ "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 i...	[ "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 n...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Large-Scale Chemical Similarity Networks for Target Profiling of Compounds Identified in Cell-Based Chemical Screens	journal.pcbi.1004153	null	[ [ "The use of chemical screens to identify molecules for the treatment of proliferative diseases like cancer has relied on two major strategies , target-based screening and phenotypic screening [1 , 2] .", "Unbiased cell-based screens , including phenotypic screens , have successfully discovered numerous cy...	[ "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 sear...	[ "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 limi...	2015
[ "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", "physiology", "computer science/numerical analysis ...	Temperature Control of Fimbriation Circuit Switch in Uropathogenic Escherichia coli: Quantitative Analysis via Automated Model Abstraction	journal.pcbi.1000723	null	[ [ "Type 1 fimbriae ( pili ) represent the foremost virulence factor in lower urinary tract infections ( UTIs ) by uropathogenic Escherichia coli ( UPEC ) —the main causative agent that accounts for 80–90 percent of all community-acquired UTIs in the United States [1]–[4] .", "These adhesive surface organell...	[ "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 sho...	[ "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 i...	2010
[ "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 cells", "pathogens", "enzymes", "biological cultures", "microbiology...	ERRα negatively regulates type I interferon induction by inhibiting TBK1-IRF3 interaction	journal.ppat.1006347	null	[ [ "The innate immune system plays important roles in the detection and elimination of invading pathogens .", "The host senses viral and bacterial pathogen invasion via the recognition of pathogen-associated molecular patterns ( PAMPs ) by pattern recognition receptors ( PRRs ) , including membrane-bound Tol...	[ "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 vi...	[ "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...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular biology", "biology and life sciences", "microbiology" ]	A Novel Peptidoglycan Binding Protein Crucial for PBP1A-Mediated Cell Wall Biogenesis in Vibrio cholerae	journal.pgen.1004433	null	[ [ "The bacterial cell wall is a remarkably sturdy , web-like structure composed mainly of peptidoglycan ( PG ) , a polysaccharide mesh whose approximately parallel strands are crosslinked via peptide sidechains [1]–[3] .", "It forms a relatively thin layer between the inner and outer membranes of gram-negat...	[ "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 ...	[ "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 t...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology and life sciences" ]	BMP-FGF Signaling Axis Mediates Wnt-Induced Epidermal Stratification in Developing Mammalian Skin	journal.pgen.1004687	null	[ [ "Vertebrate epidermis , the outermost layer of skin , functions as a barrier for protection against environmental insult and dehydration .", "At approximately embryonic day 8 . 5 ( E8 . 5 ) during mouse embryogenesis , the single-layered surface ectoderm adopts an epidermal developmental fate by turning o...	[ "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 re...	[ "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 ...	2014
[ "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" ]	The Prevalence of Previously Undiagnosed Leprosy in the General Population of Northwest Bangladesh	journal.pntd.0000198	null	[ [ "For over 60 years it is known that contacts of leprosy patients have a higher risk of developing leprosy than people in the general population . [1]", "Besides the type of leprosy of the index patient , i . e . multibacillary ( MB ) leprosy , the physical distance is also an important factor determining ...	[ "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 i...	[ "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...	2008
[ "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", "animal management", "management planning and control", "program eval...	A One Health Framework for the Evaluation of Rabies Control Programmes: A Case Study from Colombo City, Sri Lanka	journal.pntd.0003270	null	[ [ "The One Health paradigm aims to effectively manage complex risks affecting human , animal , and environmental health by forging new interdisciplinary partnerships and collaborations .", "Rabies , an acute progressive encephalomyelitis with almost 100% case fatality rate caused by viruses in the genus Lys...	[ "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 ...	[ "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 eviden...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "hydrolases", "enzyme classes", "enzymes", "microbial pathogens", "parasitology", "biology", "microbiology", "host-pathogen interaction" ]	Juxtamembrane Shedding of Plasmodium falciparum AMA1 Is Sequence Independent and Essential, and Helps Evade Invasion-Inhibitory Antibodies	journal.ppat.1002448	null	[ [ "The phylum Apicomplexa contains several pathogens of major clinical and veterinary importance .", "These include the aetiological agents of coccidiosis in poultry , theileriosis and babesiosis in cattle , and toxoplasmosis , cryptosporidiosis and malaria in humans .", "In all cases , the causative ag...	[ "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...	[ "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 f...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Leaderless Transcripts and Small Proteins Are Common Features of the Mycobacterial Translational Landscape	journal.pgen.1005641	null	[ [ "The mechanism of bacterial translation initiation has been the subject of intensive study in the model organism , Escherichia coli .", "Canonical translation initiation in bacteria is a multistep process that begins with the binding of a small ( 30S ) ribosomal subunit to a Shine-Dalgarno element in the ...	[ "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 rigorou...	[ "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 Mycobacter...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Recombinogenic Conditions Influence Partner Choice in Spontaneous Mitotic Recombination	journal.pgen.1003931	null	[ [ "Accidental DNA double strand breaks ( DSBs ) arise during unperturbed proliferation .", "Such “endogenous” or “spontaneous” chromosome breakage does not occur randomly throughout the genome , but at specific loci , often referred to as fragile sites .", "Fragile sites have been observed in organisms ...	[ "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 URA...	[ "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 prop...	2013
[ "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 cholerae", "tanzania", "aquatic environments", "bodies of...	Molecular characterization of Vibrio cholerae responsible for cholera epidemics in Uganda by PCR, MLVA and WGS	journal.pntd.0006492	null	[ [ "Vibrio cholerae remains a major cause of morbidity and mortality globally [1] .", "There have been seven cholera pandemics since the disease was recognized as a global threat [2] .", "The English record of pandemics of cholera started in 1816 , but cholera as a disease goes back centuries in Indian l...	[ "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 ...	[ "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 bi...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Prospective Study in a Porcine Model of Sarcoptes scabiei Indicates the Association of Th2 and Th17 Pathways with the Clinical Severity of Scabies	journal.pntd.0003498	null	[ [ "Sarcoptes scabiei infestation is associated with considerable global morbidity [1] .", "The disease is prevalent in overcrowded living conditions , with the highest disease burdens seen in young children [2] .", "The link between scabies , secondary bacterial infection and sequleae such as post-strep...	[ "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 wit...	[ "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 , an...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology", "genomics", "molecular cell biology", "genetics and genomics" ]	USF Binding Sequences from the HS4 Insulator Element Impose Early Replication Timing on a Vertebrate Replicator	journal.pbio.1001277	A combination of cis-regulatory elements can impose the formation of an early replicating domain in a naturally late replicating region and might constitute the basic unit of early replicating domains.	[ [ "The nuclear genome of higher eukaryotes is replicated according to an established temporal program .", "Although replication timing has been precisely analyzed in many cell types from several organisms , the molecular mechanisms involved in its regulation are still poorly characterized [1] .", "It is...	[ "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 regulat...	[ "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 ra...	2012
[ "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 pathways", "chemistry", "protozoan infections", "drug d...	Benznidazole Biotransformation and Multiple Targets in Trypanosoma cruzi Revealed by Metabolomics	journal.pntd.0002844	null	[ [ "Ten million people worldwide are infected with Trypanosoma cruzi , the causative agent of Chagas disease , and 40 million are at risk of infection [1] , [2] .", "In spite of a substantial reduction in prevalence over the last few decades , the disease is considered among the world's 17 most neglected tro...	[ "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 underst...	[ "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 profil...	2014
[ "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", "proteins", "gene expression", "rna splicing", "molecular...	Transcriptome analysis of hypoxic cancer cells uncovers intron retention in EIF2B5 as a mechanism to inhibit translation	journal.pbio.2002623	null	[ [ "Reduced availability of oxygen , or hypoxia , is a major feature of solid tumors that contributes to metastasis and resistance to therapy [1] .", "Tumor hypoxia occurs due to several physiological factors , such as limited diffusion of oxygen and irregular vascular structure [2] .", "While oxygen lev...	[ "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 dow...	[ "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 biolog...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	A Novel TGFβ Modulator that Uncouples R-Smad/I-Smad-Mediated Negative Feedback from R-Smad/Ligand-Driven Positive Feedback	journal.pbio.1002051	A LIM domain binding protein mediates both positive and negative feedback to fine-tune the regulation of transcription in response to transforming growth factor β signalling during embryonic development.	[ [ "In vertebrates , the transforming growth factor β ( TGFβ ) superfamily comprises a large number of ligands , including TGFβs , Nodal , Activin , and bone morphogenetic proteins ( BMPs ) , each of which can direct lineage-specific transcriptional responses that regulate biological processes as diverse as cell...	[ "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 , whic...	[ "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 ...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "model organisms", "molecular cell biology", "genetics", "biology", "genomics", "evolutionary biology", "microbiology", "genetics and genomics" ]	Selecting One of Several Mating Types through Gene Segment Joining and Deletion in Tetrahymena thermophila	journal.pbio.1001518	In Tetrahymena, a multi-sexed single-celled organism, the sex of the progeny is randomly determined by site-specific recombination events that assemble one complete gene pair and delete all others.	[ [ "Unicellular eukaryotes reproduce asexually , but most also have a sexual stage to their life cycle that increases genotypic variability .", "Sexual partners are usually morphologically indistinguishable and mating types , as part of a self/non-self recognition system , foster outbreeding .", "Mating ...	[ "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...	[ "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 .", ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "microbiology" ]	N-Acetylglucosamine Induces White to Opaque Switching, a Mating Prerequisite in Candida albicans	journal.ppat.1000806	null	[ [ "The white-opaque transition in MTL-homozygous strains of Candida albicans affects cellular physiology , cell morphology , gene expression , virulence and biofilm formation [1]–[3] .", "It is repressed by the a1-α2 co-repressor in a/α cells and derepressed in cells that have undergone MTL-homozygosis to b...	[ "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 ma...	[ "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 rel...	2010
[ "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", "experimental organism systems", "gene...	A machine learning based framework to identify and classify long terminal repeat retrotransposons	journal.pcbi.1006097	null	[ [ "Transposable elements ( TEs ) are DNA sequences that can move and duplicate within a genome , autonomously or with the assistance of other elements .", "The field of TE annotation includes various steps such as the identification and classification of TE families .", "In this article , we focus on th...	[ "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 p...	[ "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 com...	2018
[ "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 diseases", "antibodies", "immunologic techniqu...	Comparison of O-polysaccharide and hemolysin co-regulated protein as target antigens for serodiagnosis of melioidosis	journal.pntd.0005499	null	[ [ "Melioidosis is a severe infectious disease caused by the Gram-negative environmental bacterium , Burkholderia pseudomallei .", "It is an under-recognized tropical disease that is a common cause of community-acquired infections in Southeast Asia and northern Australia .", "It is recognized that melioi...	[ "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 ,...	[ "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...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "viruses", "ecology", "evolutionary biology", "plants", "animals", "eubacteria" ]	Cryptic Population Dynamics: Rapid Evolution Masks Trophic Interactions	journal.pbio.0050235	Contemporary rapid evolution in prey and pathogen species masks strong tropic interactions with predators and hosts. These "cryptic dynamics" reveal a need for a new approach to measuring interaction strengths in food webs.	[ [ "Empirical and theoretical studies suggest that the structure and strength of trophic links have large influences on ecosystem attributes such as species diversity [1 , 2] , the abundance and productivity of different trophic levels [3 , 4] , and the stability and dynamical behavior of component populations (...	[ "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 o...	[ "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 o...	2007
[ "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", "pulmonology", "viruses", "clinical medicine", "rna viruses...	Increased rates of Guillain-Barré syndrome associated with Zika virus outbreak in the Salvador metropolitan area, Brazil	journal.pntd.0005869	null	[ [ "Guillain-Barré syndrome ( GBS ) is a peripheral polyneuropathy characterized by acute onset of bilateral , symmetric limb weakness with decreased or absent deep-tendon reflexes .", "GBS is a progressive illness with clinical nadir occurring generally within 2–4 weeks .", "The underlying disease mecha...	[ "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...	[ "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 GB...	2017
[ "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" ]	Phylogenetic and Transcriptomic Analysis of Chemosensory Receptors in a Pair of Divergent Ant Species Reveals Sex-Specific Signatures of Odor Coding	journal.pgen.1002930	null	[ [ "The family of insects commonly known as ants ( family Formicidae ) originated during the Cretaceous period , approximately 140 million years ago [1] .", "Since that time , they have established a global presence , with only the most remote locations lacking ant species [2] .", "Indeed , in some cases...	[ "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 discriminat...	[ "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...	2012
[ "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", "immunologic techniques", "africa", "research and analysis metho...	Urban yellow fever outbreak—Democratic Republic of the Congo, 2016: Towards more rapid case detection	journal.pntd.0007029	null	[ [ "Yellow fever ( YF ) is a mosquito-borne viral infection characterized by an initial non-specific flu-like phase that lasts for 3 to 6 days and includes fever , headaches and myalgia .", "In 15%–25% of cases , a toxic phase follows with mild or severe jaundice , liver and kidney failure , which might lead...	[ "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 .", "...	[ "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 mosquito...	2018
[ "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", "toxicity", "immunoprecipitation", "basic amino acids", "amin...	The mechanism of sirtuin 2–mediated exacerbation of alpha-synuclein toxicity in models of Parkinson disease	journal.pbio.2000374	null	[ [ "Sirtuins are NAD+-dependent deacylases and lifespan determinants in several model organisms .", "Sirtuin proteins have been implicated in neurodegenerative disorders , conditions that are strongly associated with aging [1 , 2] .", "In mammals , there are seven members of the sirtuin ( SIRT ) family: ...	[ "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 mechanis...	[ "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...	2017
[ "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 systems", "neurotransmitters", "resea...	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	journal.ppat.1006996	null	[ [ "In the absence of efficient alternative strategies , treatment and prophylaxis of parasitic nematode infections rely on anthelmintic compounds .", "However , resistance against these drugs compromises the sustainable control of highly pathogenic nematode species infecting humans , livestock and companion...	[ "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 , ge...	[ "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 livest...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Dopamine Receptor Antagonists as New Mode-of-Action Insecticide Leads for Control of Aedes and Culex Mosquito Vectors	journal.pntd.0003515	null	[ [ "Arthropod vectors transmit six of the 17 neglected tropical diseases ( NTDs ) currently recognized by the World Health Organization ( WHO ) .", "Of these , the causative agents of dengue virus and lymphatic filariasis are transmitted by mosquitoes in the subfamily Culicinae ( Phylum Arthropoda; Class Ins...	[ "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 ....	[ "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 ident...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/hiv infection and aids", "virology/immunodeficiency viruses", "microbiology/cellular microbiology and pathogenesis" ]	HIV-1 Induces DCIR Expression in CD4+ T Cells	journal.ppat.1001188	null	[ [ "The Dendritic Cell ImmunoReceptor ( DCIR ) is a recently described member of the C-type lectin family .", "It is mainly expressed in cells of the myeloid lineage ( i . e . neutrophils , dendritic cells , monocytes and macrophages ) and also in B cells [1] .", "Its precise role and function are not co...	[ "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 th...	[ "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...	2010
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "neuroscience/behavioral neuroscience", "neuroscience/cognitive neuroscience", "neuroscience/theoretical neuroscience", "neuroscience/motor systems" ]	A Compact Representation of Drawing Movements with Sequences of Parabolic Primitives	journal.pcbi.1000427	null	[ [ "Despite decades of research on the formation of human hand trajectories , the basic mechanisms of neuromotor control underlying the generation of even the simplest drawing movements remain poorly understood [1] .", "Various studies have proposed that human movement preparation aims at optimizing either k...	[ "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 ."...	[ "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 , ...	2009
[ "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 analysis methods", "embryology", "animal cells", "gene expr...	Hotair Is Dispensible for Mouse Development	journal.pgen.1006232	null	[ [ "Hox genes encode transcription factors with crucial roles in the specification of regional identities along the body axes during development .", "Mutations affecting specific Hox genes typically lead to homeotic transformations , whereby a particular body part is transformed into the identity of another ...	[ "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...	[ "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 ...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "virology", "epidemiology", "vector biology", "genetics", "biology and life sciences", "microbiology", "disease vectors" ]	Fitness Impact and Stability of a Transgene Conferring Resistance to Dengue-2 Virus following Introgression into a Genetically Diverse Aedes aegypti Strain	journal.pntd.0002833	null	[ [ "The four serotypes of dengue viruses ( DENV1-4; Flaviviridae; Flavivirus ) are considered the most important mosquito-transmitted arboviruses infecting humans .", "Epidemiologists have estimated 100–390 million people per year acquire DENV infections in tropical and subtropical regions of the world [1] ,...	[ "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 doubl...	[ "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 ...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "systems biology", "biochemistry", "predictive toxicology", "biology", "genetics and genomics", "toxicology" ]	A Computational Model Predicting Disruption of Blood Vessel Development	journal.pcbi.1002996	null	[ [ "Vascular development is a complex process regulated by biological networks that vary in topology and state across different tissues and gestational stages .", "Initial stages of blood vessel development in the embryo encompass a morphogenetic series of events from angioblast differentiation into a self-o...	[ "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...	[ "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 an...	2013
[ "Introduction", "Materials and Methods", "Results/Discussion" ]	[ "computational biology/molecular dynamics", "biochemistry/biomacromolecule-ligand interactions", "biophysics/theory and simulation" ]	Symmetric Allosteric Mechanism of Hexameric Escherichia coli Arginine Repressor Exploits Competition between L-Arginine Ligands and Resident Arginine Residues	journal.pcbi.1000801	null	[ [ "Arginine repressor ( ArgR ) is the master regulator of the arginine regulon in a wide variety of bacteria [1] , acting as direct sensor and transcriptional transducer of intracellular L-arginine ( L-arg ) concentrations to provide feedback control over biosynthesis and catabolism of L-arg .", "The co-eff...	[ "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 negati...	[ "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 throu...	2010
[ "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 and immunization", "antibodies", "f...	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	journal.pntd.0005213	null	[ [ "There is substantial evidence that pre-natal exposures are important in shaping immunological development [1] .", "This includes strong evidence that prenatal exposure and sensitisation to parasite antigens determines susceptibility to the same parasite in the offspring [1] and that immunisation during p...	[ "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 vaccine...	[ "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...	2017
[ "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", "cerebellum", "research and analysis methods", "granule...	Analysis of motor dysfunction in Down Syndrome reveals motor neuron degeneration	journal.pgen.1007383	null	[ [ "Down Syndrome ( DS ) , trisomy 21 , is characterized by a wide range of phenotypes including cognitive deficits , early-onset Alzheimer’s disease , locomotor dysfunction and congenital heart defects [1 , 2] .", "These diverse phenotypes could be caused by small numbers of dosage-sensitive genes on Hsa21 ...	[ "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 chall...	[ "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 o...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Activation of Type I and III Interferon Response by Mitochondrial and Peroxisomal MAVS and Inhibition by Hepatitis C Virus	journal.ppat.1005264	null	[ [ "Vertebrates developed several defense mechanisms against invading pathogens .", "Upon viral infection foreign RNA or DNA is introduced into the host cell where it is detected by highly conserved pattern recognition receptors ( PRRs ) sensing distinct non-self motifs [1–7] .", "Well known examples of ...	[ "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 th...	[ "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 signal...	2015
[ "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", "protozoans", "leishmania", "materials science", "cell...	Leishmania donovani resides in modified early endosomes by upregulating Rab5a expression via the downregulation of miR-494	journal.ppat.1006459	null	[ [ "Leishmania donovani ( Ld ) is an obligate intracellular parasite which causes visceral leishmaniasis in the mammalian hosts that affects annually about 12 million people worldwide [1] .", "This parasite is postulated to reside and replicate in a phagolysosomal compartment in mouse macrophages as the para...	[ "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...	[ "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 pathoge...	2017
[ "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", "gastroenterology and hepatology", "experimental organism s...	A computational model to understand mouse iron physiology and disease	journal.pcbi.1006680	null	[ [ "Iron is an essential metal in living organisms , which is required as a co-factor for many proteins with roles in electron transport and oxygen binding .", "In mammals the majority of the body’s iron is used for oxygen transport in the form of hemoglobin in red blood cells ( RBC ) .", "Anemia arises ...	[ "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 an...	[ "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 ye...	2019
[ "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 occupational health", "infectious diseases", "agr...	Factors Associated with Correct and Consistent Insecticide Treated Curtain Use in Iquitos, Peru	journal.pntd.0004409	null	[ [ "Dengue viruses , transmitted primarily by the diurnal-biting mosquito , Aedes aegypti , are the cause of more human morbidity and mortality than any other arthropod-borne virus , with an estimated 96 million apparent infections and an additional 294 million inapparent infections occurring globally in 2010 [1...	[ "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...	[ "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 insecticid...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "plant science", "model organisms", "plant and algal models", "plant biology", "plant pathology", "biology", "microbiology", "bacterial pathogens" ]	A Bacterial Acetyltransferase Destroys Plant Microtubule Networks and Blocks Secretion	journal.ppat.1002523	null	[ [ "The disruption of critical host cellular structures and processes is an important virulence tactic employed by bacterial pathogens of both plants and animals [1] , [2] .", "Many Gram-negative bacterial pathogens accomplish this goal using the type III secretion system ( T3SS ) to inject virulence protein...	[ "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 t...	[ "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 o...	2012
[ "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 biology", "insect vectors", "zoology", "infectious diseases...	Potential Risk of Dengue and Chikungunya Outbreaks in Northern Italy Based on a Population Model of Aedes albopictus (Diptera: Culicidae)	journal.pntd.0004762	null	[ [ "The invasive mosquito species Aedes ( Stegomyia ) albopictus ( Skuse , 1894 ) ( syn . Stegomyia albopicta ) has spread widely in Europe over the last twenty years , especially in the Mediterranean region [1 , 2] .", "Aedes albopictus is a highly competent vector for many arboviruses including chikungunya...	[ "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 calibr...	[ "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 Sta...	2016
[ "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 diseases", "protozoan life cycles", "toxicology", "parasitology", "pa...	Oral Efficacy of Apigenin against Cutaneous Leishmaniasis: Involvement of Reactive Oxygen Species and Autophagy as a Mechanism of Action	journal.pntd.0004442	null	[ [ "Leishmaniasis is a parasitic disease endemic in 98 countries , affecting more than 12 million people worldwide .", "Cutaneous leishmaniasis has an incidence of approximately 1 . 2 million cases per year [1] .", "Leishmania amazonensis is the etiological agent of cutaneous or diffuse cutaneous lesions...	[ "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 ."...	[ "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 vari...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Epidemiology of Infant Dengue Cases Illuminates Serotype-Specificity in the Interaction between Immunity and Disease, and Changes in Transmission Dynamics	journal.pntd.0004262	null	[ [ "DENV is a flavivirus that exists as four serotypes .", "Infection with one serotype leads to long-term immunity to that serotype .", "There is also a short-term period of cross-protection to other serotypes [1 , 2] followed by an indeterminate period during which infection by another serotype may lea...	[ "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 interacti...	[ "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 ex...	2015
[ "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", "streptococcal infections", "immune system", "clini...	Complement Inhibitors from Scabies Mites Promote Streptococcal Growth – A Novel Mechanism in Infected Epidermis?	journal.pntd.0001563	null	[ [ "The global prevalence of pyoderma from various bacterial infections has been estimated to exceed 111 million children , making it one of the most common skin afflictions along with scabies and tinea [5] .", "In tropical climates , scabies predisposes to secondary bacterial skin infections in particular b...	[ "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...	[ "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 contr...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Global Morbidity and Mortality of Leptospirosis: A Systematic Review	journal.pntd.0003898	null	[ [ "Leptospirosis is a zoonotic bacterial disease that occurs in diverse epidemiological settings but imparts its greatest burden on resource-poor populations [1–6] .", "The disease has a broad geographical distribution due to the large spectrum of mammalian hosts that harbour and excrete the spirochete agen...	[ "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 , th...	[ "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 a...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Monitoring the Progress towards the Elimination of Gambiense Human African Trypanosomiasis	journal.pntd.0003785	null	[ [ "Thanks to the efforts of a wide range of stakeholders , as well as to the commitment of countless field workers in affected countries , the elimination of gambiense human African trypanosomiasis ( g-HAT ) seems achievable .", "In 2001 , when the number of infected people was reaching alarming levels [1] ...	[ "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 h...	[ "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 epidemiol...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases/neglected tropical diseases", "infectious diseases/tropical and travel-associated diseases", "infectious diseases/viral infections" ]	A Randomized Controlled Trial of Chloroquine for the Treatment of Dengue in Vietnamese Adults	journal.pntd.0000785	null	[ [ "Dengue is a globally important public health problem .", "This mosquito-borne viral infection results in an estimated 50 million cases of symptomatic illness each year in over 100 affected countries [1] .", "There are no licensed vaccines to prevent dengue and no specific therapies to stop or limit v...	[ "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 Tr...	[ "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 b...	2010
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "virology/animal models of infection", "virology", "microbiology", "virology/immune evasion", "virology/effects of virus infection on host gene expression" ]	The MHV68 M2 Protein Drives IL-10 Dependent B Cell Proliferation and Differentiation	journal.ppat.1000039	null	[ [ "Herpesviruses establish life-long , latent infections characterized by episodic virus reactivation and subsequent virus shedding .", "Chronic infections with the lymphotropic gammaherpesviruses are associated with a variety of lymphomas and carcinomas which in humans includes Burkitt's lymphoma , nasopha...	[ "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 o...	[ "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...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "model organisms", "genetics", "biology", "genetics and genomics", "gene function" ]	MTERF3 Regulates Mitochondrial Ribosome Biogenesis in Invertebrates and Mammals	journal.pgen.1003178	null	[ [ "There is a growing interest in molecular mechanisms regulating oxidative phosphorylation capacity because of the increasing number of diseases associated with mitochondrial dysfunction [1] and as aging is associated with mitochondrial functional decline [2] , [3] .", "Regulation of mitochondrial gene exp...	[ "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 re...	[ "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 ...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "clinical immunology", "global health", "immunoassays", "neglected tropical diseases", "immunology", "immunologic techniques", "lymphatic filariasis" ]	Antibody to the Filarial Antigen Wb123 Reflects Reduced Transmission and Decreased Exposure in Children Born following Single Mass Drug Administration (MDA)	journal.pntd.0001940	null	[ [ "The Global Programme to Eliminate Lymphatic Filariasis ( GPELF ) was begun in 2000 [1] in response to a World Health Assembly Resolution to eliminate filarial disease caused by Wuchereria bancrofti , Brugia malayi and Brugia timori .", "The success of this mass drug administration ( MDA ) -based program ...	[ "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 m...	[ "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 ...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "arthropoda", "biochemistry", "developmental biology", "invertebrates", "genetics", "biology and life sciences", "drosophila", "glycobiology", "animals", "organisms", "insects" ]	The Protein O-glucosyltransferase Rumi Modifies Eyes Shut to Promote Rhabdomere Separation in Drosophila	journal.pgen.1004795	null	[ [ "Diurnal insects possess “apposition eyes” in which ommatidia are optically isolated from each other [1] , [2] .", "In most diurnal insects like honeybee and butterflies , the apical rhodopsin-housing structures of each ommatidium—the rhabdomeres—are fused at the center .", "This allows the group of p...	[ "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 , whethe...	[ "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 identi...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Truncation of Ube3a-ATS Unsilences Paternal Ube3a and Ameliorates Behavioral Defects in the Angelman Syndrome Mouse Model	journal.pgen.1004039	null	[ [ "Angelman syndrome ( AS ) is clinically manifested by features of intellectual and developmental disability , absence of speech , ataxic movement , epilepsy , and unique behaviors such as frequent laughter and fascination with water [1] , [2] .", "Despite absence of effective treatment currently , therape...	[ "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 phen...	[ "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 diseas...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "neuroscience", "cell biology" ]	LTP Promotes a Selective Long-Term Stabilization and Clustering of Dendritic Spines	journal.pbio.0060219	In hippocampal neurons, the induction of learning related patterns of activity leads to a selective stabilization of activated synapses. Moreover, new dendritic spines, which are functional, cluster in close proximity to activated synapses.	[ [ "Integration of synaptic signals during learning processes is critical to the function of cortical networks .", "This processing is achieved through various mechanisms that involve generation of coincident rhythmic activity , induction of properties of plasticity such as long-term potentiation ( LTP ) , b...	[ "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 p...	[ "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 neurona...	2008
[ "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", "phylogenetics", "model organisms", "data managem...	Natural variation of a sensor kinase controlling a conserved stress response pathway in Escherichia coli	journal.pgen.1007101	null	[ [ "The species Escherichia coli comprises a remarkably diverse collection of bacteria , reflecting their capacity to colonize and manipulate disparate in vivo and ex vivo niches .", "Most of the well-documented phenotypic differences between E . coli strains are associated with genes found in only a subset ...	[ "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 ...	[ "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 wo...	2017
[ "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", "viruses", "rna viruses", "molecular biology techniques", ...	Broadly neutralizing antibodies from an individual that naturally cleared multiple hepatitis C virus infections uncover molecular determinants for E2 targeting and vaccine design	journal.ppat.1007772	null	[ [ "Over 70 million people worldwide are infected with hepatitis C virus ( HCV ) , with an annual mortality of approximately 400 , 000 associated with liver failure and hepatocellular carcinoma [1 , 2] .", "Encouragingly for patients with chronic infections with HCV , advances in understanding of HCV virolog...	[ "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 individua...	[ "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 ind...	2019
[ "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", "genomic evolution", "computational biology", "e...	A Model-Based Analysis of GC-Biased Gene Conversion in the Human and Chimpanzee Genomes	journal.pgen.1003684	null	[ [ "Gene conversion is the nonreciprocal exchange of genetic information from a ‘donor’ to an ‘acceptor’ sequence , primarily resulting from the repair of mismatched bases in heteroduplex recombination intermediates during meiosis [1] .", "In many cases , the process of resolving mismatches between G/C ( gua...	[ "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 gener...	[ "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 ...	2013
[ "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: Provide readable labels and captions", "Rule 5: Choose the right level of detail", "Rule 6: Use color responsibly...	[ "medicine and health sciences", "protein interactions", "protein interaction networks", "sociology", "blastomas", "cancers and neoplasms", "social sciences", "light", "electromagnetic radiation", "oncology", "neurological tumors", "luminance", "network analysis", "protein structure", "vi...	Ten simple rules to create biological network figures for communication	journal.pcbi.1007244	null	[ [ "Biological networks are present in many areas of biology , including studies of cancer and other diseases , metagenomics , pathway analysis , proteomics , molecular interactions , cell–cell interactions , epidemiology , network rewiring due to perturbations or evolution , etc .", "Increasingly , publishe...	[ "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 netw...	[ "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 ." ]	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "virology/immunodeficiency viruses", "evolutionary biology/microbial evolution and genomics", "virology/virus evolution and symbiosis" ]	Dating the Age of the SIV Lineages That Gave Rise to HIV-1 and HIV-2	journal.pcbi.1000377	null	[ [ "HIV/AIDS is the result of at least eleven cross-species transmission events of simian immunodeficiency virus ( SIV ) from non-human African primates to humans .", "Three transmissions of SIVcpz from the central African chimpanzee subspecies ( Pan troglodytes troglodytes ) gave rise to HIV-1 groups M , N ...	[ "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 re...	[ "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 beni...	2009
[ "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 biology/genomics", "mathematics/statistics", "geneti...	Statistical Use of Argonaute Expression and RISC Assembly in microRNA Target Identification	journal.pcbi.1000516	null	[ [ "Micro RNAs ( miRNAs ) are small ( 20–22 bp ) RNAs transcribed by a wide variety of organisms , from viruses [1] , to plants [2] , [3] , to animals such as C . elegans , Drosophila and humans [4]–[6] .", "While most RNAs function in ribosomes or splicesomes , or are translated into proteins necessary for ...	[ "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...	[ "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 fami...	2009
[ "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", "proteins", "gene expression", "molecular biology", "biochemistry...	The archaeal RNA chaperone TRAM0076 shapes the transcriptome and optimizes the growth of Methanococcus maripaludis	journal.pgen.1008328	null	[ [ "RNA chaperones impact mRNA metabolism including transcript synthesis , processing and degradation as well as translation .", "They play an important role in controlling gene expression , especially in response to environmental perturbations such as cold shock [1] .", "The distinctive features of RNA ...	[ "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 demonst...	[ "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 ...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "computational biology/population genetics", "computational biology/sequence motif analysis", "computational biology/genomics" ]	Genome Landscapes and Bacteriophage Codon Usage	journal.pcbi.1000001	null	[ [ "The genomes of most organisms exhibit significant codon bias—that is , the unequal usage of synonymous codons .", "There are longstanding and contradictory theories to account for such biases .", "Variation in codon usage between taxa , particularly within mammals , is sometimes attributed to neutral...	[ "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 anal...	[ "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 .", ...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "biology", "veterinary science", "agriculture" ]	Complex Inheritance of Melanoma and Pigmentation of Coat and Skin in Grey Horses	journal.pgen.1003248	null	[ [ "Recent developments in molecular genetics have enabled molecular dissection of quantitative traits in humans [1] , model organisms [2] and domestic animals [3] .", "Genome-wide association ( GWA ) studies suggest that variability of complex traits is caused by many loci , most exerting tiny effects , whe...	[ "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 ...	[ "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 phenotyp...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "evolutionary biology/genomics", "ecology/marine and freshwater ecology", "computational biology/genomics", "evolutionary biology/developmental evolution" ]	Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags	journal.pgen.1000862	null	[ [ "Population genetics provides a rich and mathematically rigorous framework for understanding evolutionary processes in natural populations .", "This theory was built over the last hundred years by modeling the processes of selection , genetic drift , mutation and migration in spatially distributed populat...	[ "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 population...	[ "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 ge...	2010
[ "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", "tetracyclines", "antibiotics", "enterobacteriace...	Correlates of multi-drug non-susceptibility in enteric bacteria isolated from Kenyan children with acute diarrhea	journal.pntd.0005974	null	[ [ "Diarrheal diseases account for an estimated 10% of childhood deaths in Sub-Saharan Africa[1] .", "Bacterial enteric infections such as Shigella species ( spp . ) , Salmonella spp .", ", and pathogenic Escherichia coli ( E . coli ) are leading causes of diarrhea[2 , 3] and the attribution of diarrhea ...	[ "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 bacte...	[ "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 identif...	2017
[ "Introduction", "Material and Methods", "Results", "Discussion" ]	[]	Socio-economic and Climate Factors Associated with Dengue Fever Spatial Heterogeneity: A Worked Example in New Caledonia	journal.pntd.0004211	null	[ [ "Dengue fever is the most important mosquito-borne viral disease , with an estimated 50 million people being infected each year and 2 . 5 billion people living in areas at risk of dengue worldwide [1] .", "The true burden of clinically apparent dengue could be twice as high , and the total burden of dengu...	[ "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 b...	[ "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 , contro...	2015
[ "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 biology", "gene function" ]	A Framework for the Establishment of a Cnidarian Gene Regulatory Network for “Endomesoderm” Specification: The Inputs of ß-Catenin/TCF Signaling	journal.pgen.1003164	null	[ [ "During metazoan development one cell gives rise to thousands of daughter cells , each acquiring a particular fate depending on their temporal and spatial coordinates within the organism .", "The information required to assume a specific fate of a given cell is present in the genome of all cells , requiri...	[ "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 mesod...	[ "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 a...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "ecology", "biology" ]	Breeding Sites of Phlebotomus sergenti, the Sand Fly Vector of Cutaneous Leishmaniasis in the Judean Desert	journal.pntd.0001725	null	[ [ "The leishmaniases are a group of diseases endangering some 350 million people in 88 countries , most of them in the poorer regions of the globe .", "The two major clinical forms are cutaneous leishmaniasis ( CL ) and visceral leishmaniasis ( VL ) .", "CL manifests as a sore at the bite site of the in...	[ "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 divers...	[ "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 . habitat...	2012
[ "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 expression", "chemistry", "molecular biology", "molecular biology assay...	Post-Translational Dosage Compensation Buffers Genetic Perturbations to Stoichiometry of Protein Complexes	journal.pgen.1006554	null	[ [ "Robustness in biological systems is a general trait of living cells and a fundamental feature involving the maintenance of stability during perturbation [1–4] .", "It is a universal challenge to cope with perturbations leading to fluctuations in biological processes because cells are exposed to changes i...	[ "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 perturbat...	[ "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 no...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Estimating Leptospirosis Incidence Using Hospital-Based Surveillance and a Population-Based Health Care Utilization Survey in Tanzania	journal.pntd.0002589	null	[ [ "Incidence estimates of infectious diseases are crucial for determining burden of disease and prioritizing resources for disease control .", "However , these estimates are often unavailable in resource constrained settings , resulting in scarce data on which to base recommendations for public health inter...	[ "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 ...	[ "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 .", ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/disease models", "neurological disorders/prion diseases", "biochemistry/protein folding" ]	In Vivo Generation of Neurotoxic Prion Protein: Role for Hsp70 in Accumulation of Misfolded Isoforms	journal.pgen.1000507	null	[ [ "The prion protein ( PrP ) appears to be an essential element in the pathogenesis of an incurable class of neurological disorders called transmissible spongiform encephalopathies ( TSE ) or prion diseases .", "These protein deposition disorders can present with sporadic , inherited or infectious origins a...	[ "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 typ...	[ "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 th...	2009
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Characterization of Arabidopsis Transcriptional Responses to Different Aphid Species Reveals Genes that Contribute to Host Susceptibility and Non-host Resistance	journal.ppat.1004918	null	[ [ "Aphids are hemipteran insects that display exceptional variation in host range .", "While some aphid species , such as Myzus persicae ( green peach aphid ) , are able to infest plants in over 40 families , including many important crops , closely related Myzus cerasi ( black cherry aphid ) is only able t...	[ "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 aph...	[ "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 lea...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "neuroscience/neuronal signaling mechanisms", "neuroscience/theoretical neuroscience", "neuroscience/sensory systems", "computational biology/computational neuroscience" ]	Time-Warp–Invariant Neuronal Processing	journal.pbio.1000141	A biophysical mechanism acting in auditory neurons allows the brain to process the high variability of speaking rates in natural speech in a time-warp-invariant manner.	[ [ "Robustness of neuronal information processing to temporal warping of natural stimuli poses a difficult computational challenge to the brain [1]–[9] .", "This is particularly true for auditory stimuli , which often carry perceptually relevant information in fine differences between temporal cues [10] , [1...	[ "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 robustn...	[ "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 s...	2009
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "mathematics", "neuroscience/theoretical neuroscience", "computational biology/computational neuroscience" ]	Avalanches in a Stochastic Model of Spiking Neurons	journal.pcbi.1000846	null	[ [ "In what follows we provide a theory for the formation of avalances using a stochastic version of the sigmoid rate model originally introduced to represent individual neural activity [8] .", "We call this the stochastic rate model [9]–[11] .", "Each neuron spikes with a probability per unit time depen...	[ "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 di...	[ "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 n...	2010
[ "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 genomics", "genetics and genomics/gene expression", "genetics and gen...	Natural Single-Nucleosome Epi-Polymorphisms in Yeast	journal.pgen.1000913	null	[ [ "Divergence of DNA sequences between individuals has been the basis of genetics for half a century .", "More recently , epimutations were identified where inter-individual differences resided in DNA methylation patterns rather than in the DNA sequence itself , with notable consequences on imprinting and p...	[ "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 natu...	[ "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-o...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genome-wide association studies", "biochemistry", "genetics", "biology", "metabolism" ]	Genetic Basis of Metabolome Variation in Yeast	journal.pgen.1004142	null	[ [ "Inter-individual differences in metabolism are of substantial biological importance .", "In humans , they underlie susceptibility to type II diabetes [1] , obesity [2] and Crohn's disease [3] , while in yeast , they contribute to the flavor profile of wine [4] and to the efficiency of ethanol generation ...	[ "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 th...	[ "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 ho...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "proteomic databases", "viral immune evasion", "viruses and cancer", "virology", "biology", "microbiology", "proteomics" ]	Proteomic Screening of Human Targets of Viral microRNAs Reveals Functions Associated with Immune Evasion and Angiogenesis	journal.ppat.1003584	null	[ [ "At our current understanding , the herpesvirus family is the only viral family expressing multiple miRNAs .", "Kaposi's sarcoma-associated herpesvirus ( human herpesvirus 8 ) expresses 12 pre-miRNAs [1] , [2] , [3] , [4] .", "These miRNAs are encoded in the latency locus of the KSHV genome and all KS...	[ "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 e...	[ "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 , t...	2013
[ "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 control", "malaria", "parasitic diseases" ]	Impact of Schistosoma mansoni on Malaria Transmission in Sub-Saharan Africa	journal.pntd.0003234	null	[ [ "Malaria is highly endemic throughout sub-Saharan Africa in which 85% of global malaria cases and 90% of malaria deaths occur [1] .", "Schistosoma mansoni ( the causative agent of intestinal schistosomiasis ) is likewise prevalent in many sub-Saharan African countries [2] , [3] , accounting for approximat...	[ "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 .", "Epide...	[ "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...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology/cell growth and division" ]	Caenorhabditis elegans Cyclin B3 Is Required for Multiple Mitotic Processes Including Alleviation of a Spindle Checkpoint–Dependent Block in Anaphase Chromosome Segregation	journal.pgen.1001218	null	[ [ "The eukaryotic cell cycle is driven by the temporally controlled activation of cyclin-dependent kinases ( CDKs ) in association with their requisite cofactors , the cyclins [1] .", "The expression and stability of individual cyclins is coordinated with specific cell cycle stages .", "For instance , c...	[ "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...	[ "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...	2010
[ "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", "eyes", "africa", "blindness", "infectious diseases"...	Knowledge, perceptions and experiences of trachoma among Maasai in Tanzania: Implications for prevention and control	journal.pntd.0007508	null	[ [ "Trachoma is the commonest infectious cause of blindness worldwide , caused by chlamydia trachomatis and remains a significant public health concern .", "This neglected tropical disease ( NTD ) tends to mostly impact poor and underdeveloped areas .", "Current estimates indicate about 182 million peopl...	[ "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 tra...	[ "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 requir...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine" ]	Safety and Efficacy of Single Dose versus Multiple Doses of AmBisome® for Treatment of Visceral Leishmaniasis in Eastern Africa: A Randomised Trial	journal.pntd.0002613	null	[ [ "Visceral leishmaniasis ( VL ) is a life-threatening disease and a major health burden in developing countries [1] , [2] , [3] .", "WHO estimates there are approximately 0 . 2–0 . 4 million cases of VL annually; and more than 90% of global VL cases occur in six countries: India , Bangladesh , Sudan , Sout...	[ "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 , w...	[ "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 ...	2014
[ "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 acids", "proteins", "biological databases", "chemistry", "p...	Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor	journal.pcbi.1006706	null	[ [ "Cellular regulatory networks encompass conserved patterns of protein-protein interactions , which have been called network motifs [1 , 2] .", "One key network motif is the phosphotyrosine-based reader/writer/eraser motif [3 , 4] , which is found in many important human cell signaling systems , including ...	[ "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 phos...	[ "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 ex...	2019
[ "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 tropical diseases", "plants", "research an...	Turning poop into profit: Cost-effectiveness and soil transmitted helminth infection risk associated with human excreta reuse in Vietnam	journal.pntd.0006088	null	[ [ "Application of human excreta onto rice paddies as fertilizer is a common practice in northern Vietnam , where many farmers use single or double vault latrines , lack access to wastewater infrastructure , and have variable access to commercial inorganic fertilizers [1] .", "Using organic waste to fertiliz...	[ "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/comp...	[ "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 , qu...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Methyl Farnesoate Plays a Dual Role in Regulating Drosophila Metamorphosis	journal.pgen.1005038	null	[ [ "Juvenile hormones ( JHs ) are members of a family of sesquiterpenoid compounds synthesized primarily by the corpus allatum ( CA ) of insects .", "Several forms of JH have been identified , including JH 0 , JH I , 4-methyl JH I , JH II , JH III , JH bisepoxide ( JHB3 ) and JH skipped bisepoxide .", "J...	[ "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 sesqu...	[ "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 ge...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics", "biology and life sciences", "microbiology", "evolutionary biology", "molecular biology" ]	Genetic Basis of Haloperidol Resistance in Saccharomyces cerevisiae Is Complex and Dose Dependent	journal.pgen.1004894	null	[ [ "The budding yeast Saccharomyces cerevisiae has become a powerful model for elucidating fundamental principles and mechanisms of complex trait genetics [1] .", "Many quantitative trait loci ( QTL ) – and the causal genes underlying these loci – have been identified for diverse biological processes , inclu...	[ "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...	[ "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...	2014
[ "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", "clinical genetics" ]	Genetic Determinants of Serum Testosterone Concentrations in Men	journal.pgen.1002313	null	[ [ "Testosterone , the most important testicular androgen in men , is largely bound to two plasma proteins .", "Most of the circulating testosterone ( ∼50–60% ) is bound with high affinity to sex hormone-binding globulin ( SHBG ) , while a smaller fraction ( 40–50% ) is bound loosely to albumin , and 1–3% is...	[ "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 an...	[ "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 evidenc...	2011
[ "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 interfering rnas", "embryology", "genomics", "placent...	Role of the BAHD1 Chromatin-Repressive Complex in Placental Development and Regulation of Steroid Metabolism	journal.pgen.1005898	null	[ [ "Chromatin-based transcriptional repression is mediated by macromolecular complexes containing proteins involved in chromatin writing , reading , erasing and remodeling activities .", "The combinatorial assembly of subunits with transcription factors affects cell-specific gene expression in response to de...	[ "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 decrease...	[ "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 ...	2016
[ "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", "population biology", "zoology", "africa",...	The introduction of new hosts with human trade shapes the extant distribution of Toxoplasma gondii lineages	journal.pntd.0007435	null	[ [ "Toxoplasma gondii is a zoonotic protozoan with a worldwide distribution .", "Felids are the only final hosts and all other species of mammals and birds are intermediate hosts .", "Within the domestic cycle , infection can occur through the ingestion of few of the million oocysts shed in the environme...	[ "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 ...	[ "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 determin...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Cis-Regulatory Mechanisms for Robust Olfactory Sensory Neuron Class-restricted Odorant Receptor Gene Expression in Drosophila	journal.pgen.1005051	null	[ [ "The expression of developmental genes is regulated such that they are either on or off at the appropriate time and in the correct place .", "The expression patterns of these genes must be robust; they must be stable and resistant to changes in both external and internal environments [1] .", "Mechanis...	[ "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-regu...	[ "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 unders...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The Saccharomyces cerevisiae AMPK, Snf1, Negatively Regulates the Hog1 MAPK Pathway in ER Stress Response	journal.pgen.1005491	null	[ [ "The endoplasmic reticulum ( ER ) is the cellular organelle responsible for the folding and modification of newly synthesized secretory or membrane proteins .", "Environmental or developmental changes which perturb ER homeostasis , or genetic alterations causing production of irreversibly misfolded protei...	[ "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 re...	[ "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 prin...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology and life sciences", "microbiology", "computational biology" ]	Competing ParA Structures Space Bacterial Plasmids Equally over the Nucleoid	journal.pcbi.1004009	null	[ [ "parABC loci generate equally spaced positioning of many bacterial low copy number plasmids , thereby ensuring stable plasmid inheritance [1] .", "However , the underlying mechanism of action is not satisfactorily understood .", "In contrast , plasmid segregation mediated by actin homolog ParM is incr...	[ "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 th...	[ "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 sp...	2014

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