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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", "Results", "Discussion", "Materials and Methods" ]	[]	Multiple In Vivo Biological Processes Are Mediated by Functionally Redundant Activities of Drosophila mir-279 and mir-996	journal.pgen.1005245	null	[ [ "microRNAs ( miRNAs ) are ~22 nucleotide ( nt ) regulatory RNAs derived from hairpin precursors [1] , and there are 100s ~ 1000 miRNA loci in well-studied animal genomes [2] .", "As animal miRNAs regulate targets exhibiting as little as 7 nt of complementarity to their 5' regions ( principally nts 2–8 , k...	[ "While most miRNA knockouts exhibit only subtle defects , a handful of miRNAs are profoundly required for development or physiology .", "A particularly compelling locus is Drosophila mir-279 , which was reported as essential to restrict the emergence of CO2-sensing neurons , to maintain circadian rhythm , and to ...	[ "Amongst the small number of miRNA knockouts that exhibit substantially overt phenotypes , mutants of Drosophila mir-279 are notable .", "Previous studies have uncovered its essential requirements in a range of developmental and behavioral assays .", "Surprisingly , we find that the phenotypes attributed to mir...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "bacteriology", "medicine", "bacterial diseases", "infectious diseases", "bacterial evolution", "biology", "evolutionary biology", "genomic evolution", "microbiology", "infectious disease control", "bacterial pathogens" ]	Evidence for Induction of Integron-Based Antibiotic Resistance by the SOS Response in a Clinical Setting	journal.ppat.1002778	null	[ [ "Transferable genes encoding antibiotic resistance to major antibiotics ( e . g . β-lactams , aminoglycosides ) are often carried by class 1 integrons in Gram negative pathogens [1] .", "In these genetic elements the antibiotic resistance genes are carried inside mobile structures called gene cassettes , ...	[ "Bacterial resistance to β-lactams may rely on acquired β-lactamases encoded by class 1 integron-borne genes .", "Rearrangement of integron cassette arrays is mediated by the integrase IntI1 .", "It has been previously established that integrase expression can be activated by the SOS response in vitro , leading...	[ "The bacterial SOS response is a conserved regulatory network that is induced in response to DNA damage .", "Its activation in vitro leads to the emergence of resistance to antibiotics , leading to speculation that this is an important clinical mechanism of acquiring resistance .", "We found evidence here that ...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "phosphorylation", "invertebrates", "cell death", "medicine and health sciences", "pathology and laboratory medicine", "pathogens", "cell processes", "microbiology", "animals", "developmental biology", "silkworms", "g protein coupled receptors", "bacterial pathogens", "proteins", "medica...	Bacillus bombysepticus α-Toxin Binding to G Protein-Coupled Receptor Kinase 2 Regulates cAMP/PKA Signaling Pathway to Induce Host Death	journal.ppat.1005527	null	[ [ "Infectious diseases caused by pathogens result in deaths .", "Mechanisms of how infection of hosts leads to death have been studied in detail for many pathogens that involve destruction of the cell membrane , inhibition of protein synthesis , or activation of second messenger pathways .", "However , ...	[ "Bacterial pathogens and their toxins target host receptors , leading to aberrant behavior or host death by changing signaling events through subversion of host intracellular cAMP level .", "This is an efficient and widespread mechanism of microbial pathogenesis .", "Previous studies describe toxins that increa...	[ "Interference with regulation of host signaling by pathogens can alter gene expression , leading to functional disarray in the host cells that causes abnormal division or death .", "Here , we propose a previously undescribed model for how bacterial toxins subvert host processes via interaction with GRK2 that infl...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Kinetics of Myeloid Dendritic Cell Trafficking and Activation: Impact on Progressive, Nonprogressive and Controlled SIV Infections	journal.ppat.1003600	null	[ [ "Myeloid dendritic cells ( mDCs ) are potent antigen-presenting cells which are responsible for initiating both innate and adaptive immune responses .", "mDCs stimulate NK , B and T cells [1] , [2] , but can also act as “watch-dogs” to sense and regulate aberrant immune activation , induce tolerance and t...	[ "We assessed the role of myeloid dendritic cells ( mDCs ) in the outcome of SIV infection by comparing and contrasting their frequency , mobilization , phenotype , cytokine production and apoptosis in pathogenic ( pigtailed macaques , PTMs ) , nonpathogenic ( African green monkeys , AGMs ) and controlled ( rhesus m...	[ "Myeloid dendritic cells ( mDCs ) are potent antigen-presenting cells that regulate both innate and adaptive immune responses and act as “watch-dogs” , sensing and controlling aberrant immune activation; as such , they may significantly impact the outcome of HIV/SIV infection .", "By comparing and contrasting the...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	A Madurella mycetomatis Grain Model in Galleria mellonella Larvae	journal.pntd.0003926	null	[ [ "Mycetoma is a chronic granulomatous subcutaneous infectious disease , characterized by massive deformities and disabilities .", "It is endemic in tropical and subtropical regions .", "It can be caused by 56 different micro-organisms , including both bacteria ( actinomyctoma ) and fungi ( eumycetoma )...	[ "Eumycetoma is a chronic granulomatous subcutaneous infectious disease , endemic in tropical and subtropical regions and most commonly caused by the fungus Madurella mycetomatis .", "Interestingly , although grain formation is key in mycetoma , its formation process and its susceptibility towards antifungal agent...	[ "Mycetoma is a chronic subcutaneous infectious disease affecting different parts of the body but commonly seen in the foot .", "It can be caused by bacteria and fungi .", "Especially for fungi , the treatment options are meagre and therapeutic failures are common .", "In order to develop better therapeutic st...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "hospitalizations", "medicine and health sciences", "european union", "tropical diseases", "geographical locations", "parasitic diseases", "health care", "neglected tropical diseases", "epilepsy", "infectious diseases", "spain", "zoonoses", "epidemiology", "hospitals", "taeniasis", "pe...	Clinical Cysticercosis epidemiology in Spain based on the hospital discharge database: What's new?	journal.pntd.0006316	null	[ [ "Cysticercosis ( CC ) is a parasitic tissue infection caused by larval cysts of the pork tapeworm Taenia solium [1] .", "Pigs , the CC natural intermediate hosts , become infected by eating tapeworm eggs in the feces of a human infected with a tapeworm .", "Human acquire CC through faecal-oral contami...	[ "Cysticercosis ( CC ) is a tissue infection caused by the larval cysts of the pork tapeworm Taenia solium .", "It is usually acquired by eating contaminated food or drinking water .", "CC Cysts can develop in the muscles , the eyes , the brain , and/or the spinal cord .", "T . solium is found worldwide , but ...	[ "Cysticercosis ( CC ) , caused by the larval cysts of the pork tapeworm Taenia solium , is a neglected tropical disease ( NTD ) .", "It is acquired when worm eggs are ingested and the developing larvae migrate through the body and form cysts in tissues .", "Frequent in pigs , it can also affect humans , usually...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "flow cytometry", "innate immune system", "medicine and health sciences", "immune cells", "cytokines", "pathology and laboratory medicine", "immune activation", "antigen-presenting cells", "immunity to infections", "immunology", "microbiology", "lymphoid organs", "animal mod...	Innate Immune Responses and Rapid Control of Inflammation in African Green Monkeys Treated or Not with Interferon-Alpha during Primary SIVagm Infection	journal.ppat.1004241	null	[ [ "Chronic immune activation during HIV infection is considered as the main driver of CD4+ T cell depletion and AIDS , and early T cell activation is a better predictor of the outcome of the infection than viral load [1] .", "Recent observations suggest that inflammation is even more important than T cell a...	[ "Chronic immune activation ( IA ) is considered as the driving force of CD4+ T cell depletion and AIDS .", "Fundamental clues in the mechanisms that regulate IA could lie in natural hosts of SIV , such as African green monkeys ( AGMs ) .", "Here we investigated the role of innate immune cells and IFN-α in the c...	[ "Chronic inflammation is considered as directly involved in AIDS pathogenesis .", "The role of IFN-α as a driving force of chronic inflammation is under debate .", "Natural hosts of SIV , such as African green monkeys ( AGMs ) , avoid chronic inflammation .", "We show for the first time that NK cells are stro...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "reproductive system", "body fluids", "pathology and laboratory medicine", "pathogens", "animal models of disease", "microbiology", "vertebrates", "animals", "mammals", "viruses", "urine", "rna viruses", "immunologic techniques", "fruit bats", "digestive...	Experimental Zika virus infection of Jamaican fruit bats (Artibeus jamaicensis) and possible entry of virus into brain via activated microglial cells	journal.pntd.0007071	null	[ [ "Zika virus ( ZIKV ) was first isolated from a sentinel rhesus macaque in Uganda in 1947 and subsequently from Aedes africanus mosquitoes in the same location [1] .", "The first human cases were identified in 1954 in Nigeria and serosurveys found evidence of a broad geographic distribution for ZIKV throug...	[ "The emergence of Zika virus ( ZIKV ) in the New World has led to more than 200 , 000 human infections .", "Perinatal infection can cause severe neurological complications , including fetal and neonatal microcephaly , and in adults there is an association with Guillain-Barré syndrome ( GBS ) .", "ZIKV is transm...	[ "The rapid spread of Zika virus through a naïve population in the Americas resulted in novel and severe disease manifestations , including fetal and neonatal microcephaly , and GBS .", "These disease complications make understanding the pathology and ecology of ZIKV a priority .", "Captive Jamaican fruit bats w...	2019
[ "Introduction", "Results", "Discussion", "Material and Methods" ]	[ "medicine", "immune cells", "immunity to infections", "immunology", "cytomegalovirus infection", "adaptive immunity", "immune defense", "infectious disease control", "infectious diseases", "t cells", "biology", "immune response", "antigen processing and recognition", "immunity", "viral d...	Absence of Cross-Presenting Cells in the Salivary Gland and Viral Immune Evasion Confine Cytomegalovirus Immune Control to Effector CD4 T Cells	journal.ppat.1002214	null	[ [ "Cytomegaloviruses ( CMVs ) , members of the β-herpesvirus family , establish a latent persistent infection .", "Although primary infection in immune-competent individuals is in general clinically silent , severe complications caused by reactivation or primary infection are frequent in immune-compromised ...	[ "Horizontal transmission of cytomegaloviruses ( CMV ) occurs via prolonged excretion from mucosal surfaces .", "We used murine CMV ( MCMV ) infection to investigate the mechanisms of immune control in secretory organs .", "CD4 T cells were crucial to cease MCMV replication in the salivary gland ( SG ) via direc...	[ "Cytomegaloviruses ( CMVs ) infect 50 to 90 % of the world's population and cause severe clinical complication in immunosuppressed individuals .", "An important tissue for horizontal transmission is the salivary gland ( SG ) .", "CD4 T cells are crucial for viral control in this organ .", "However , how CD4 T...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "genome-wide association studies", "quantitative trait loci", "population genetics", "alleles", "genetic mapping", "gene pool", "protein expression", "rice", "experimental organism systems", "genome analysis", "molecular biology techniques", "population biology", "plants", "research and an...	Loci and natural alleles underlying robust roots and adaptive domestication of upland ecotype rice in aerobic conditions	journal.pgen.1007521	null	[ [ "Asian cultivated rice ( Oryza sativa L . , O . sativa ) is a staple food for half the world’s population .", "Grown in diverse environments worldwide , O . sativa is also well-known for its rich-within-species diversity with two major subspecies , indica ( also referred to as Xian ) and japonica ( also r...	[ "A robust ( long and thick ) root system is characteristic of upland japonica rice adapted to drought conditions .", "Using deep sequencing and large scale phenotyping data of 795 rice accessions and an integrated strategy combining results from high resolution mapping by GWAS and linkage mapping , comprehensive ...	[ "Asian cultivated rice is well-known for its rich-within-species diversity with two major subspecies , indica and japonica and subpopulation differentiation .", "A robust ( long and thick ) root system that is characteristic of upland japonica rice represents a predominant ecotype grown under aerobic and rain-fed...	2018
[ "Introduction", "Results and discussion", "Materials and methods" ]	[ "invertebrates", "plant anatomy", "gut bacteria", "microbiome", "honey bees", "microbiology", "animals", "pollen", "metabolomics", "plant science", "metabolites", "bacteria", "microbial genomics", "bees", "hymenoptera", "medical microbiology", "insects", "arthropoda", "biochemist...	Disentangling metabolic functions of bacteria in the honey bee gut	journal.pbio.2003467	null	[ [ "Metabolic activities of the microbiota are key for symbiotic interactions in the gut and impact health and disease of the host in manifold ways .", "Gut bacteria facilitate the breakdown of refractory or toxic dietary compounds [1–3] , produce metabolites that promote host growth and physiology [4–7] , a...	[ "It is presently unclear how much individual community members contribute to the overall metabolic output of a gut microbiota .", "To address this question , we used the honey bee , which harbors a relatively simple and remarkably conserved gut microbiota with striking parallels to the mammalian system and import...	[ "Honey bees are important pollinators that harbor a relatively simple gut microbiota with striking parallels to the mammalian system .", "This makes them relevant models to study gut microbiota functions and their impact on host health .", "We applied untargeted metabolomics to characterize metabolic changes in...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "biology" ]	Vectorial Capacity of Aedes aegypti for Dengue Virus Type 2 Is Reduced with Co-infection of Metarhizium anisopliae	journal.pntd.0002013	null	[ [ "The susceptibility of Aedes aegypti adults to infection with Beauveria bassiana was first reported in the late 1960s [1] .", "However the potential of entomopathogenic Ascomycetes ( Hypocreales ) as adulticides of vector mosquitoes was largely overlooked until Metarhizium anisopliae was demonstrated to i...	[ "Aedes aegypti , is the major dengue vector and a worldwide public health threat combated basically by chemical insecticides .", "In this study , the vectorial competence of Ae .", "aegypti co-infected with a mildly virulent Metarhizium anisopliae and fed with blood infected with the DENV-2 virus , was examined...	[ "Dengue is a worldwide public health problem .", "There is not an effective vaccine yet; the chemical struggle against its transmitter , the mosquito Aedes aegypti , is onerous and erratic , and the community participation to eliminate vector breeding sites is unconfident .", "Here , we examined mosquitoes fed ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology" ]	Crossover Patterning by the Beam-Film Model: Analysis and Implications	journal.pgen.1004042	null	[ [ "Crossover ( CO ) recombination interactions occur stochastically at different positions in different meiotic nuclei .", "Nonetheless , along a given chromosome , COs tend to be evenly spaced .", "This interesting phenomenon implies the existence of communication along chromosomes , the nature of whic...	[ "Crossing-over is a central feature of meiosis .", "Meiotic crossover ( CO ) sites are spatially patterned along chromosomes .", "CO-designation at one position disfavors subsequent CO-designation ( s ) nearby , as described by the classical phenomenon of CO interference .", "If multiple designations occur , ...	[ "Spatial patterning is a common feature of biological systems at all length scales , from molecular to multi-organismic .", "Meiosis is the specialized cellular program in which a diploid cell gives rise to haploid gametes for sexual reproduction .", "Crossing-over between homologous maternal and paternal chrom...	2014
[ "Introduction", "Results and Discussion", "Materials and Methods" ]	[ "biochemistry", "proteins", "protein structure", "biology", "microbiology" ]	Segmental Helical Motions and Dynamical Asymmetry Modulate Histidine Kinase Autophosphorylation	journal.pbio.1001776	Step-by-step structures of a prototypical E. coli histidine kinase reveal how external stimuli drive helical bending motions to control asymmetric movements of the catalytic domains.	[ [ "Bacteria commonly use two-component signal transduction pathways to couple environmental stimuli to adaptive responses [1] .", "Typically composed of a sensor histidine kinase ( HK ) and a response regulator ( RR ) , two-component systems ( TCSs ) are abundant in bacterial genomes , reflecting the divers...	[ "Histidine kinases ( HKs ) are dimeric receptors that participate in most adaptive responses to environmental changes in prokaryotes .", "Although it is well established that stimulus perception triggers autophosphorylation in many HKs , little is known on how the input signal propagates through the HAMP domain t...	[ "Bacteria use two-component signal transduction systems ( TCSs ) , composed of a histidine kinase ( HK ) and a downstream response regulator ( RR ) , to perceive a broad range of external stimuli and trigger an appropriate response .", "Prototypical HKs are transmembrane homodimeric receptors with an external sen...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "diagnostic radiology", "functional magnetic resonance imaging", "face", "brain", "social sciences", "neuroscience", "magnetic resonance imaging", "cognitive psychology", "mathematics", "statistics (mathematics)", "brain mapping", "neuroimaging", "research a...	A Normalization Framework for Emotional Attention	journal.pbio.1002578	Using a combination of psychophysics and functional MRI, this study reveals that emotional attention interacts with normalization processes depending on emotional valence (positive or negative faces), best explained by feedback modulation from the dorsolateral prefrontal cortex.	[ [ "Attentional selection is the mechanism by which the subset of incoming information is preferentially processed at the expense of distractors .", "Numerous studies have suggested that attentional selection modulates both visual performance and neuronal activity in striate and extrastriate visual cortices ...	[ "The normalization model of attention proposes that attention can affect performance by response- or contrast-gain changes , depending on the size of the stimulus and attention field .", "Here , we manipulated the attention field by emotional valence , negative faces versus positive faces , while holding stimulus...	[ "Attentional selection is the mechanism by which the subset of incoming information is preferentially processed at the expense of distractors .", "The normalization model of attention suggests that attention-triggered modulatory effects on sensory responses in the visual cortex depend on two factors: the stimulus...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular cell biology", "microbial pathogens", "host-pathogen interaction", "biology", "microbiology", "pathogenesis", "parasitology" ]	Trichomonas vaginalis Exosomes Deliver Cargo to Host Cells and Mediate Host∶Parasite Interactions	journal.ppat.1003482	null	[ [ "The parasite Trichomonas vaginalis causes the most common non-viral sexually transmitted infection , with an estimated 275 million people infected each year worldwide [1] .", "Disease manifestations may include vaginitis , cervicitis , urethritis , pelvic inflammatory disease , and adverse birth outcomes...	[ "Trichomonas vaginalis is a common sexually transmitted parasite that colonizes the human urogential tract where it remains extracellular and adheres to epithelial cells .", "Infections range from asymptomatic to highly inflammatory , depending on the host and the parasite strain .", "Here , we use a combinatio...	[ "Trichomoniasis , the most common non-viral sexually transmitted disease worldwide , infects over 275 million people annually .", "Infection results from the colonization of the human urogenital tract by the parasite Trichomonas vaginalis .", "To establish and maintain infection the parasite adheres to host cel...	2013
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "markov models", "chromosome structure and function", "gene regulation", "regulatory proteins", "dna-binding proteins", "histone modification", "regulator genes", "mathematics", "transcription factors", "gene types", "epigenetics", "chromatin", "transcriptional control", "chromosome biolog...	Spatial clustering and common regulatory elements correlate with coordinated gene expression	journal.pcbi.1006786	null	[ [ "A cell continuously receives signals from its local environment and accordingly adjusts cellular programs , such as cell proliferation , motility and metabolism [1] .", "Typically , regulation of a cellular process requires changes in the expression of a group of genes in a temporally coordinated manner ...	[ "Many cellular responses to surrounding cues require temporally concerted transcriptional regulation of multiple genes .", "In prokaryotic cells , a single-input-module motif with one transcription factor regulating multiple target genes can generate coordinated gene expression .", "In eukaryotic cells , transc...	[ "Cellular responses to environmental stimulation are often accompanied by changes in gene expression patterns .", "Genes are linearly arranged along chromosomal DNA , which folds into a three-dimensional structure .", "The chromosome structure affects gene expression activities and is regulated by multiple even...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "computational biology/transcriptional regulation", "molecular biology/mrna stability", "molecular biology/transcription elongation", "biotechnology/bioengineering", "molecular biology/translational regulation" ]	Design Principles for Riboswitch Function	journal.pcbi.1000363	null	[ [ "The breadth of function exhibited by biological systems provides a foundation from which to develop solutions to global challenges including sustainability , renewable energy production , material synthesis , and medical advancement .", "Underlying these systems-level functions are regulatory components ...	[ "Scientific and technological advances that enable the tuning of integrated regulatory components to match network and system requirements are critical to reliably control the function of biological systems .", "RNA provides a promising building block for the construction of tunable regulatory components based on...	[ "Riboswitches are RNA-based components that integrate ligand binding and gene regulation to dynamically respond to molecular signals within cells .", "Natural riboswitches are employed to regulate metabolism and other cellular processes , while synthetic riboswitches have been constructed to expand the sensory an...	2009
[ "Introduction", "Results", "Discussion", "Material and Methods" ]	[ "biotechnology", "phosphorylation", "luciferase", "plant growth and development", "enzymes", "enzymology", "phosphatases", "developmental biology", "plant science", "genetically modified plants", "seedlings", "molecular biology techniques", "plants", "genetic engineering", "research and ...	Type One Protein Phosphatase 1 and Its Regulatory Protein Inhibitor 2 Negatively Regulate ABA Signaling	journal.pgen.1005835	null	[ [ "The phytohormone abscisic acid ( ABA ) in plants controls a variety of developmental processes such as seed dormancy , germination , root/shoot growth , flowering and senescence [1–3] .", "When plants encounter stressful conditions , ABA can rapidly induce the reprogramming of gene expression and trigger...	[ "The phytohormone abscisic acid ( ABA ) regulates plant growth , development and responses to biotic and abiotic stresses .", "The core ABA signaling pathway consists of three major components: ABA receptor ( PYR1/PYLs ) , type 2C Protein Phosphatase ( PP2C ) and SNF1-related protein kinase 2 ( SnRK2 ) .", "Nev...	[ "The phytohormone abscisic acid ( ABA ) regulates multiple developmental processes such as seed dormancy , germination , root/shoot growth , flowering and senescence in plants .", "Although the core ABA perception and signaling pathway has been elucidated , the complexity of the pathway remains to be exploited ."...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	A Computational Approach to Identifying Gene-microRNA Modules in Cancer	journal.pcbi.1004042	null	[ [ "Cancer is one of the leading causes of death worldwide .", "Although remarkable progress has been achieved in cancer therapies , the molecular mechanisms of cancer have not yet been fully identified .", "Among various regulations of cancer-related genes and pathways in several stages , the regulation...	[ "MicroRNAs ( miRNAs ) play key roles in the initiation and progression of various cancers by regulating genes .", "Regulatory interactions between genes and miRNAs are complex , as multiple miRNAs can regulate multiple genes .", "In addtion , these interactions vary from patient to patient and even among patien...	[ "A microRNA ( miRNA ) is a small RNA molecule that regulates the expression of mRNA genes .", "A miRNA can regulate multiple genes , and a gene can be regulated by multiple miRNAs .", "The regulation of genes by miRNAs may vary from patient to patient , even if they suffer from the same type of cancer .", "In...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "ecology/theoretical ecology", "ecology/community ecology and biodiversity", "ecology", "computational biology" ]	Googling Food Webs: Can an Eigenvector Measure Species' Importance for Coextinctions?	journal.pcbi.1000494	null	[ [ "The robustness of ecosystems to species losses is a central question in ecology given the current pace of extinctions and the many species threatened by human impacts [1]–[3] .", "The loss of species in complex ecological networks can cascade into further extinctions because of the mutual dependence of s...	[ "A major challenge in ecology is forecasting the effects of species' extinctions , a pressing problem given current human impacts on the planet .", "Consequences of species losses such as secondary extinctions are difficult to forecast because species are not isolated , but interact instead in a complex network o...	[ "Predicting the consequences of species' extinction is a crucial problem in ecology .", "Species are not isolated , but connected to each others in tangled networks of relationships known as food webs .", "In this work we want to determine which species are critical as they support many other species .", "The...	2009
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "heterozygosity", "population genetics", "ancient dna", "alleles", "genome analysis", "paleontology", "dna", "paleogenetics", "molecular genetics", "population biology", "genomic libraries", "molecular biology", "genetic loci", "biochemistry", "nucleic acids", "heredity", "earth scie...	The presence and impact of reference bias on population genomic studies of prehistoric human populations	journal.pgen.1008302	null	[ [ "The possibility to sequence whole genomes in a cost-efficient way has revolutionized the way how we do genetic and population genetic research .", "Annotated , high-quality reference genomes are a cornerstone for resequencing surveys which aim to study the genetic variation and demographic history of an ...	[ "Haploid high quality reference genomes are an important resource in genomic research projects .", "A consequence is that DNA fragments carrying the reference allele will be more likely to map successfully , or receive higher quality scores .", "This reference bias can have effects on downstream population geno...	[ "Mapping next-generation sequencing reads to a single linear reference genomes comes with the inherent problem that alleles not found in the reference sequence will achieve lower mapping scores .", "This reference bias can cause heterozygous sites to be falsely called as homozygous which will have an effect on do...	2019
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "innate immune system", "medicine and health sciences", "immune cells", "immune physiology", "cytokines", "gene regulation", "immunology", "developmental biology", "immunoprecipitation", "genome analysis", "molecular development", "cytotoxic t cells", "research and analysis ...	Transient expression of ZBTB32 in anti-viral CD8+ T cells limits the magnitude of the effector response and the generation of memory	journal.ppat.1006544	null	[ [ "The anti-viral CD8+ T cell response has been the topic of intense investigation over recent years , beginning with early ground-breaking studies demonstrating that , at early times post-infection , effector cells destined to die could be distinguished from those destined to populate the long-lived memory poo...	[ "Virus infections induce CD8+ T cell responses comprised of a large population of terminal effector cells and a smaller subset of long-lived memory cells .", "The transcription factors regulating the relative expansion versus the long-term survival potential of anti-viral CD8+ T cells are not completely understoo...	[ "CD8+ T lymphocytes are essential for immune protection against viruses .", "In response to an infection , these cells are activated , proliferate , and generate antiviral effector cells that eradicate the infection .", "Following this , the majority of these effector cells die , leaving a small subset of long-...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "vector-borne diseases", "microbiology", "bacterial diseases", "population modeling", "bacterial pathogens", "veterinary science", "animal models of infection", "infectious diseases", "veterinary diseases", "zoonoses", "veterinary microbiology", "medical micro...	Restriction of Francisella novicida Genetic Diversity during Infection of the Vector Midgut	journal.ppat.1004499	null	[ [ "Genetic diversity within a single microbial species can lead to infection of hosts with mixtures of pathogen genotypes .", "Remarkably , studies across numerous systems have demonstrated that mixed-genotype infections are more common than infections with a single clonal variant [1]–[5] .", "The degre...	[ "The genetic diversity of pathogens , and interactions between genotypes , can strongly influence pathogen phenotypes such as transmissibility and virulence .", "For vector-borne pathogens , both mammalian hosts and arthropod vectors may limit pathogen genotypic diversity ( number of unique genotypes circulating ...	[ "Co-infection , the presence of multiple genotypes of the same pathogen species within an infected individual , is common .", "Genotype diversity , defined as the number of unique genotypes , and the interaction between genotypes , can strongly influence virulence and pathogen transmission .", "Understanding ho...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "deletion mutation", "medicine and health sciences", "pathology and laboratory medicine", "molecular probe techniques", "pathogens", "microbiology", "immunoblotting", "bacterial diseases", "mutation", "molecular biology techniques", "frameshift mutation", "gel electrophoresis", "bacterial pa...	Genetic mechanisms of Coxiella burnetii lipopolysaccharide phase variation	journal.ppat.1006922	null	[ [ "Coxiella burnetii is a gram-negative intracellular bacterial pathogen and the etiological agent of the zoonosis Q fever .", "Sheep , goats , and dairy cattle are considered relevant animal reservoirs for human infection .", "Infection generally results from inhalation of aerosols containing the highl...	[ "Coxiella burnetii is an intracellular pathogen that causes human Q fever , a disease that normally presents as a severe flu-like illness .", "Due to high infectivity and disease severity , the pathogen is considered a risk group 3 organism .", "Full-length lipopolysaccharide ( LPS ) is required for full virule...	[ "Coxiella burnetii is the causative agent of Q fever , an acute febrile illness that can develop into a persistent focalized infection , such as endocarditis or vascular disease .", "Currently , the only licensed vaccine against Q fever is Q-Vax , a formalin-inactivated whole-cell preparation of the virulent C . ...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Low Doses of Imatinib Induce Myelopoiesis and Enhance Host Anti-microbial Immunity	journal.ppat.1004770	null	[ [ "Signaling by protein tyrosine kinases ( PTKs ) mediates a variety of cellular processes including migration , morphogenesis , stress responses , and cytoskeletal reorganization [1 , 2] .", "Dysregulation of PTK activity causes a variety of diseases , including cancer .", "One such cancer , chronic my...	[ "Imatinib mesylate ( Gleevec ) inhibits Abl1 , c-Kit , and related protein tyrosine kinases ( PTKs ) and serves as a therapeutic for chronic myelogenous leukemia and gastrointestinal stromal tumors .", "Imatinib also has efficacy against various pathogens , including pathogenic mycobacteria , where it decreases b...	[ "Host-directed therapeutics ( HDTs ) for infectious diseases target cellular mechanisms used by pathogens to move into , through , or out of cells .", "The Abl tyrosine kinase ( TK ) inhibitor and cancer therapeutic imatinib mesylate ( Gleevec ) , for example , has activity against bacterial and viral pathogens v...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cancer genomics", "medicine and health sciences", "breast tumors", "reproductive system", "cancer risk factors", "cancers and neoplasms", "basic cancer research", "oncology", "mutation", "substitution mutation", "medical risk factors", "molecular biology techniques", "mutagenesis and gene d...	Integrated structural variation and point mutation signatures in cancer genomes using correlated topic models	journal.pcbi.1006799	null	[ [ "Patterns of mutation in cancer genomes reflect both endogenous and exogenous mutagenic processes [1] , allowing inference of causative mechanisms , prognostic associations [2] , and clinically actionable [3–6] vulnerabilities in tumors .", "Many mutational processes leave distinct genomic “footprints” , ...	[ "Mutation signatures in cancer genomes reflect endogenous and exogenous mutational processes , offering insights into tumour etiology , features for prognostic and biologic stratification and vulnerabilities to be exploited therapeutically .", "We present a novel machine learning formalism for improved signature ...	[ "Over time DNA accumulates mutations from a variety of sources .", "Some mutations result from external mutagens , such as UV radiation , while others result from processes occurring within the cell itself .", "Each of these sources can impart characteristic patterns of mutations on the genome , known as mutati...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "geographical locations", "animals", "indonesia", "java", "health care", "probability distribution", "mathematics", "infectious disease control", "insect vectors", "morbidity", "infectious diseases", "geography", "epidemiology", "disease...	The Importance of Socio-Economic Versus Environmental Risk Factors for Reported Dengue Cases in Java, Indonesia	journal.pntd.0004964	null	[ [ "Dengue virus ( DENV ) is a positive-strand RNA virus ( Flaviviridae ) that is spread by Aedes aegypti and also Ae .", "albopictus mosquitoes [1] .", "DENV infection rates worldwide may have been underestimated , with a recent study suggesting 390 million infections per year [2] .", "Dengue diseas...	[ "Dengue is a major mosquito-borne viral disease and an important public health problem .", "Identifying which factors are important determinants in the risk of dengue infection is critical in supporting and guiding preventive measures .", "In South-East Asia , half of all reported fatal infections are recorded ...	[ "Dengue has been detected in Indonesia and transmission is progressively rising to account for half of all fatal dengue cases recorded in South-East Asia .", "However , little is known about the epidemiology of the virus , which may hamper the effectiveness of preventive strategies carried out in the country .", ...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology/morphogenesis and cell biology", "infectious diseases/fungal infections", "developmental biology/cell differentiation", "genetics and genomics/gene function", "microbiology/cellular microbiology and pathogenesis" ]	Homeobox Transcription Factors Are Required for Conidiation and Appressorium Development in the Rice Blast Fungus Magnaporthe oryzae	journal.pgen.1000757	null	[ [ "Magnaporthe oryzae is an ascomycete fungus and the causal agent of rice blast , the most destructive disease of rice worldwide .", "The annual yield loss from rice blast is equivalent to rice that could feed about 60 million people [1] .", "Rice blast has served as an important model for studying mol...	[ "The appropriate development of conidia and appressoria is critical in the disease cycle of many fungal pathogens , including Magnaporthe oryzae .", "A total of eight genes ( MoHOX1 to MoHOX8 ) encoding putative homeobox transcription factors ( TFs ) were identified from the M . oryzae genome .", "Knockout muta...	[ "Pathogens have evolved diverse strategies to cause disease .", "Magnaporthe oryzae is the fungal phytopathogen that causes rice blast and is considered an important model for understanding mechanisms in fungal development and pathogenicity .", "Asexual reproduction and infection-related development play key ro...	2009
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "diagnostic radiology", "functional magnetic resonance imaging", "prefrontal cortex", "brain", "social sciences", "neuroscience", "learning and memory", "magnetic resonance imaging", "cognition", "brain mapping", "memory", "neuroimaging", "research and analy...	Nonmonotonic recruitment of ventromedial prefrontal cortex during remote memory recall	journal.pbio.2005479	null	[ [ "We possess a remarkable ability to retrieve , with ease , one single experience from a lifetime of memories .", "How these individual autobiographical memories are represented in the brain over time is a central question of memory neuroscience that remains unanswered .", "Consolidation takes place on...	[ "Systems-level consolidation refers to the time-dependent reorganisation of memory traces in the neocortex , a process in which the ventromedial prefrontal cortex ( vmPFC ) has been implicated .", "Capturing the precise temporal evolution of this crucial process in humans has long proved elusive .", "Here , we ...	[ "Our past experiences are captured in autobiographical memories that allow us to recollect events from our lives long after they originally occurred .", "A part of the brain’s frontal lobe , called the ventromedial prefrontal cortex ( vmPFC ) , is known to be important for supporting autobiographical memories , e...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "invertebrates", "molecular neuroscience", "neurochemistry", "neural networks", "neuroscience", "animals", "gene function", "animal models", "drosophila melanogaster", "model organisms", "neurotransmitters", "drosophila", "neuroimaging", "research and analysis methods", "specimen prepara...	Dual PDF Signaling Pathways Reset Clocks Via TIMELESS and Acutely Excite Target Neurons to Control Circadian Behavior	journal.pbio.1001810	Studies in Drosophila circadian neurons reveal a bifurcation in the Pigment Dispersing Factor (PDF) neuropeptide signaling pathway, independently synchronizing circadian clocks via PKA or acutely controlling neuronal excitability via cAMP.	[ [ "Circadian clocks endow organisms with the ability to predict and respond adaptively to daily changes in the environment .", "In many taxa , these clocks consist of cell-autonomous molecular feedback loops , producing ∼24-hour oscillations at the mRNA and protein levels .", "In insects and mammals the...	[ "Molecular circadian clocks are interconnected via neural networks .", "In Drosophila , PIGMENT-DISPERSING FACTOR ( PDF ) acts as a master network regulator with dual functions in synchronizing molecular oscillations between disparate PDF ( + ) and PDF ( − ) circadian pacemaker neurons and controlling pacemaker n...	[ "Circadian clocks provide a mechanism for predicting and adapting behavioral and physiological processes to 24-hour rhythms in the environment .", "In animal nervous systems , cell-autonomous molecular oscillators are coupled via neural networks that control daily patterns of activity .", "A major neuropeptide ...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "biofilms", "sequencing techniques", "united states", "medicine and health sciences", "geographical locations", "microbiology", "hawaii", "pulmonology", "north america", "environmental and occupational lung diseases", "molecular biology techniques", "bacteria", "research and analysis methods...	Environmental Nontuberculous Mycobacteria in the Hawaiian Islands	journal.pntd.0005068	null	[ [ "Nontuberculous mycobacteria ( NTM ) are ubiquitous inhabitants of natural and human-engineered environments .", "To date , there are over 175 species of NTM with standing in nomenclature [1] .", "They range in virulence from benign environmental microorganisms to difficult-to-treat human pathogens [2...	[ "Lung disease caused by nontuberculous mycobacteria ( NTM ) is an emerging infectious disease of global significance .", "Epidemiologic studies have shown the Hawaiian Islands have the highest prevalence of NTM lung infections in the United States .", "However , potential environmental reservoirs and species di...	[ "In the U . S . , the Hawaiian Islands have the highest number of nontuberculous mycobacterial ( NTM ) lung disease cases per capita .", "The tropical climate , geographical isolation of the islands , and aquifer water sources may have influence such prevalence .", "Previous studies suggest that NTM thrive in w...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	A Human Platelet Calcium Calculator Trained by Pairwise Agonist Scanning	journal.pcbi.1004118	null	[ [ "Platelet activation during heart attack and stroke occurs through combined signaling pathways involving various receptors responding to collagen , thrombin , ADP , and thromboxane .", "Endothelial production of prostacyclin is highly protective against thrombotic platelet activation as revealed by the kn...	[ "Since platelet intracellular calcium mobilization [Ca ( t ) ]i controls granule release , cyclooxygenase-1 and integrin activation , and phosphatidylserine exposure , blood clotting simulations require prediction of platelet [Ca ( t ) ]i in response to combinatorial agonists .", "Pairwise Agonist Scanning ( PAS ...	[ "Platelets regulate clotting during injury to prevent blood loss .", "Hyperactive platelets may increase risk of thrombosis , whereas hypoactive platelets may increase risk of bleeding .", "Platelets are activated during a clotting event by agonists , through different signaling pathways , all of which converge...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "evolutionary biology/animal genetics", "evolutionary biology/evolutionary and comparative genetics", "evolutionary biology/genomics", "evolutionary biology/bioinformatics", "evolutionary biology/pattern formation", "evolutionary biology", "evolutionary biology/developmental evolution" ]	Genomic Hotspots for Adaptation: The Population Genetics of Müllerian Mimicry in the Heliconius melpomene Clade	journal.pgen.1000794	null	[ [ "One of the central outstanding questions in evolutionary biology concerns the predictability of evolution .", "Specifically , can we predict the number and effect size of genes involved in evolution , and the types of genetic changes that underlie particular kinds of evolution ?", "Striking empirical...	[ "Wing patterning in Heliconius butterflies is a longstanding example of both Müllerian mimicry and phenotypic radiation under strong natural selection .", "The loci controlling such patterns are “hotspots” for adaptive evolution with great allelic diversity across different species in the genus .", "We characte...	[ "The diversity of wing patterns in Heliconius butterflies is a longstanding example of both Müllerian mimicry and adaptive radiation .", "The genetic regions controlling such patterns are “hotspots” for adaptive evolution , with small regions of the genome controlling major changes in wing pattern .", "Across m...	2010
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "computational biology/molecular dynamics", "computational biology/macromolecular structure analysis" ]	A Stevedore's Protein Knot	journal.pcbi.1000731	null	[ [ "In the last decade , our knowledge about structure and characteristics of proteins has considerably expanded .", "The ability of proteins of small and medium size to fold into native structures is attributed to a minimally frustrated free energy landscape , which allows for fast and robust folding [1] , ...	[ "Protein knots , mostly regarded as intriguing oddities , are gradually being recognized as significant structural motifs .", "Seven distinctly knotted folds have already been identified .", "It is by and large unclear how these exceptional structures actually fold , and only recently , experiments and simulati...	[ "Knots are ubiquitous in many aspects of our life , but remain elusive in proteins .", "The multitude of protein structures archived in the Protein Data Bank can be grouped into several hundred patterns , but only a handful are folded into knots .", "Combing through the recently added structures we found severa...	2010
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "biology", "population biology", "evolutionary biology" ]	Exploring the Complexity of the HIV-1 Fitness Landscape	journal.pgen.1002551	null	[ [ "The fitness landscape is one of the central concepts in evolutionary biology .", "Ever since Sewall Wright [1] , it has been used to study and conceptualize the process of long-term evolutionary adaptation .", "Fundamentally , knowledge of fitness landscapes is required to translate microevolutionary...	[ "Although fitness landscapes are central to evolutionary theory , so far no biologically realistic examples for large-scale fitness landscapes have been described .", "Most currently available biological examples are restricted to very few loci or alleles and therefore do not capture the high dimensionality chara...	[ "Evolutionary adaptation can be understood as populations moving uphill on landscapes , in which height corresponds to evolutionary fitness .", "Although such fitness landscapes are central to evolutionary theory , there is currently a lack of biologically realistic examples .", "Here we analyze large-scale fit...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Phosphoproteomic Profiling Reveals Epstein-Barr Virus Protein Kinase Integration of DNA Damage Response and Mitotic Signaling	journal.ppat.1005346	null	[ [ "Infection with Epstein-Barr virus ( EBV ) , a ubiquitous herpesvirus , is associated with malignant disease , including Burkitt lymphoma , nasopharyngeal carcinoma , gastric carcinoma , and post-transplant lymphoproliferative disease [1 , 2] .", "While EBV latency proteins drive proliferation , lytic EBV...	[ "Epstein-Barr virus ( EBV ) is etiologically linked to infectious mononucleosis and several human cancers .", "EBV encodes a conserved protein kinase BGLF4 that plays a key role in the viral life cycle .", "To provide new insight into the host proteins regulated by BGLF4 , we utilized stable isotope labeling by...	[ "Epstein-Barr virus ( EBV ) is a herpesvirus that is associated with B cell and epithelial human cancers .", "Herpesviruses encode a protein kinase which is an important regulator of lytic virus replication and is consequently a target for anti-viral drug development .", "The EBV genome encodes for a serine/thr...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infographics", "urology", "medicine and health sciences", "infectious disease epidemiology", "tropical diseases", "geographical locations", "charts", "health care", "treponematoses", "bacterial diseases", "sexually transmitted diseases", "neglected tropical diseases", "infectious disease co...	Mother-to-child transmission and gestational syphilis: Spatial-temporal epidemiology and demographics in a Brazilian region	journal.pntd.0007122	null	[ [ "Treponema pallidum is a spirochete bacterium that causes syphilis , a sexually transmitted infection ( STI ) transmitted due to contact with infected lesions .", "However , the transmission is not limited to this route since pregnant women infected with the microorganism can develop gestational syphilis ...	[ "Syphilis is a Sexually Transmitted Infection ( IST ) with significant importance to public health , due to its impact during pregnancy ( Gestational Syphilis—GS ) ; especially because syphilis can affect fetus and neonates’ development ( mother-to-child transmission—MTCT of syphilis ) , by increasing susceptibilit...	[ "Syphilis is a sexually transmitted infection that can be transmitted to child during pregnancy , or postpartum , by an infected mother .", "Syphilis in children can interfere in the development and , in some cases , may lead to death .", "We analyzed cases of syphilis during pregnancy and mother-to-child trans...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "blood cells", "medicine and health sciences", "parasite groups", "immune cells", "immune physiology", "plasmodium", "immunology", "tropical diseases", "parasitic diseases", "neuroscience", "learning and memory", "parasitology", "apicomplexa", "cognition", "memory", "memory b cells", ...	T follicular helper cells regulate the activation of B lymphocytes and antibody production during Plasmodium vivax infection	journal.ppat.1006484	null	[ [ "Malaria , caused by the protozoan parasite Plasmodium , remains one of the most widespread and mortality-causing infectious diseases worldwide .", "Plasmodium vivax is the most frequent cause of recurring malaria and infects 130–390 million people each year , representing approximately 50% of all malaria...	[ "Although the importance of humoral immunity to malaria has been established , factors that control antibody production are poorly understood .", "Follicular helper T cells ( Tfh cells ) are pivotal for generating high-affinity , long-lived antibody responses .", "While it has been proposed that expansion of an...	[ "Plasmodium vivax is the most widely spread malaria parasite species and represents a significant impediment to social and economic development in endemic countries .", "Our goal was to assess the importance of T follicular helper cells in the development of the immune response during malaria .", "We found that...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Structural Based Analyses of the JC Virus T-Antigen F258L Mutant Provides Evidence for DNA Dependent Conformational Changes in the C-Termini of Polyomavirus Origin Binding Domains	journal.ppat.1005362	null	[ [ "There are presently fourteen known human polyomavirus family members [1 , 2] .", "Reasons for interest in these viruses include the diseases they are associated with , particularly in immunocompromised individuals [3–5] .", "As examples , JC virus ( JCV ) causes the often fatal demyelinating disease ...	[ "The replication of human polyomavirus JCV , which causes Progressive Multifocal Leukoencephalopathy , is initiated by the virally encoded T-antigen ( T-ag ) .", "The structure of the JC virus T-ag origin-binding domain ( OBD ) was recently solved by X-ray crystallography .", "This structure revealed that the O...	[ "A conserved feature of Polyomavirus T-antigens is a phenylalanine situated at the C-termini of their origin-binding domains ( OBDs ) .", "Using the T-antigen encoded by JC virus , we have investigated why this residue is critical for viral DNA replication .", "The studies presented herein establish that the co...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "onchocerca volvulus", "pathology and laboratory medicine", "vomiting", "tropical diseases", "geographical locations", "parasitic diseases", "animals", "onchocerca", "parasitology", "health care", "north america", "diarrhea", "research des...	A Knowledge, Attitudes and Practices Survey Conducted Three Years after Halting Ivermectin Mass Treatment for Onchocerciasis in Guatemala	journal.pntd.0004777	null	[ [ "Human onchocerciasis ( River Blindness ) is caused by the filarial nematode Onchocerca volvulus that is transmitted by the bite of infected Simulium black flies that breed in rapid flowing rivers and streams .", "The adult worms of O . volvulus live mainly in subcutaneous nodules , which are often palpab...	[ "Mass drug administration ( MDA ) with ivermectin for onchocerciasis was provided in Guatemala’s Central Endemic Zone ( CEZ ) over a 24 year period ( 1988–2011 ) .", "Elimination of Onchocerca volvulus transmission was declared in 2015 after a three year post MDA surveillance period ( 2012–2014 ) showed no eviden...	[ "Human onchocerciasis ( also known as ‘River Blindness’ ) is a parasitic disease of the skin and eyes whose etiological agent ( Onchocerca volvulus ) is transmitted by black flies .", "Guatemala was the country in the Americas most afflicted by onchocerciasis , and the largest focus of onchocerciasis in Guatemala...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cryptococcus neoformans", "medicine and health sciences", "deletion mutation", "cryptococcus", "pathology and laboratory medicine", "gene regulation", "pathogens", "regulatory proteins", "microbiology", "dna-binding proteins", "mutation", "fungi", "transcription factors", "molecular biolo...	Glucosamine stimulates pheromone-independent dimorphic transition in Cryptococcus neoformans by promoting Crz1 nuclear translocation	journal.pgen.1006982	null	[ [ "The opportunistic environmental fungal pathogen , Cryptococcus neoformans , is a leading killer of HIV-infected patients worldwide [1 , 2] .", "It causes 1 million infections and more than half a million deaths each year worldwide [1] .", "C . neoformans is a species complex containing several seroty...	[ "Morphotype switch is a cellular response to external and internal cues .", "The Cryptococcus neoformans species complex can undergo morphological transitions between the yeast and the hypha form , and such morphological changes profoundly affect cryptococcal interaction with various hosts .", "Filamentation in...	[ "Cryptococcal meningitis claims half a million lives each year .", "There is no clinically available vaccine and the current antifungal therapies have serious limitations .", "Thus identifying cryptococcal specific programs that can be targeted for antifungal or vaccine development is of great value .", "We h...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular biology/histone modification", "cell biology/leukocyte signaling and gene expression", "immunology/innate immunity", "genetics and genomics/epigenetics", "cell biology/gene expression" ]	A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers	journal.pbio.1000384	A substantial fraction of extragenic Pol II transcription sites coincides with transcriptional enhancers, which may be relevant for functional annotation of mammalian genomes.	[ [ "A most striking finding of modern genomic biology has been the identification of a large amount of transcription that occurs outside mapped protein-coding genes and generates a heterogeneous spectrum of transcripts [1] , [2] , which may in principle exert broad regulatory or effector functions [3]–[5] .", ...	[ "Mammalian genomes are pervasively transcribed outside mapped protein-coding genes .", "One class of extragenic transcription products is represented by long non-coding RNAs ( lncRNAs ) , some of which result from Pol_II transcription of bona-fide RNA genes .", "Whether all lncRNAs described insofar are product...	[ "Mammalian genomes contain vast intergenic regions that are extensively transcribed and generate various types of short and long non-coding RNAs ( ncRNAs ) .", "Although in some cases specific functions have been assigned to intergenic transcripts , the functional significance of this transcriptional output remai...	2010
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "biology and life sciences", "medicine and health sciences" ]	Quality of Medicines Commonly Used in the Treatment of Soil Transmitted Helminths and Giardia in Ethiopia: A Nationwide Survey	journal.pntd.0003345	null	[ [ "Intestinal parasites are a diverse group of organisms that include single-celled protozoans and multi-cellular intestinal helminths that affect the gastro-intestinal tract of humans and other animals [1] .", "Soil-transmitted helminthiasis is caused primarily by four species of nematodes , i . e . Ascari...	[ "The presence of poor quality medicines in the market is a global threat on public health , especially in developing countries .", "Therefore , we assessed the quality of two commonly used anthelminthic drugs [mebendazole ( MEB ) and albendazole ( ALB ) ] and one antiprotozoal drug [tinidazole ( TNZ ) ] in Ethiop...	[ "Access to medicines of good quality improves the chances of successful treatment for individual patients and promotes better outcomes for public health in general .", "At present , the prevailing strategy for improving access to medicines for neglected tropical diseases ( NTDs ) is drug donation programs .", "...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Strong Selective Sweeps on the X Chromosome in the Human-Chimpanzee Ancestor Explain Its Low Divergence	journal.pgen.1005451	null	[ [ "Despite constituting only 5–6% of the human genome , the human X chromosome is important for elucidating evolutionary mechanisms .", "Because of its particular inheritance pattern and its cosegregation with the very different Y chromosome , evolutionary forces may act upon it in different ways than on th...	[ "The human and chimpanzee X chromosomes are less divergent than expected based on autosomal divergence .", "We study incomplete lineage sorting patterns between humans , chimpanzees and gorillas to show that this low divergence can be entirely explained by megabase-sized regions comprising one-third of the X chro...	[ "Because the speciation events that led to human , chimpanzee and gorilla were close in time , the genetic relationship of these species varies along the genome .", "While human and chimpanzee are the closest related species , in 15% of the genome , human and gorilla are more closely related , and in another 15% ...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Intermediate Levels of Bacillus subtilis CodY Activity Are Required for Derepression of the Branched-Chain Amino Acid Permease, BraB	journal.pgen.1005600	null	[ [ "BraB is one of three permeases demonstrated to be involved in the uptake of branched-chain amino acids ( BCAA ) in Bacillus subtilis [1] .", "Given the important role of BCAA in cell metabolism , it is not surprising that the synthesis of the permeases is strictly regulated and coordinated .", "The m...	[ "The global transcriptional regulator , CodY , binds strongly to the regulatory region of the braB gene , which encodes a Bacillus subtilis branched-chain amino acid ( BCAA ) permease .", "However , under conditions that maximize CodY activity , braB expression was similar in wild-type and codY null mutant cells ...	[ "Expression of Bacillus subtilis BraB , a branched-chain amino acid permease , is under both negative and positive control by a global transcriptional regulator CodY .", "The negative control is direct and the positive control is indirect and mediated by another B . subtilis pleiotropic transcriptional regulator ...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "model organisms", "endocrinology", "immunology", "biology", "microbiology", "diabetes and endocrinology", "genetics and genomics", "metabolic disorders" ]	Gut Microbiota Is a Key Modulator of Insulin Resistance in TLR 2 Knockout Mice	journal.pbio.1001212	A genetic and pharmacological approach reveals novel insights into how changes in gut microbiota can subvert genetically predetermined phenotypes from lean to obese.	[ [ "The recent epidemics of obesity and type 2 diabetes mellitus ( T2DM ) in the past 20 years have stimulated researchers to investigate the mechanisms that are responsible for the development of these diseases .", "The general view is that obesity and T2DM have a genetic background and are strongly influen...	[ "Environmental factors and host genetics interact to control the gut microbiota , which may have a role in the development of obesity and insulin resistance .", "TLR2-deficient mice , under germ-free conditions , are protected from diet-induced insulin resistance .", "It is possible that the presence of gut mic...	[ "An intricate interaction between genetic and environmental factors influences the development of obesity and diabetes .", "Previous studies have shown that mice lacking an important receptor of the innate immune system , Toll-like Receptor 2 ( TLR2 ) , are protected from insulin resistance .", "Given that the ...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "chemical compounds", "pathogens", "immunology", "microbiology", "cloning", "organic compounds", "retroviruses", "viruses", "immunodeficiency viruses", "mutation", "substitution mutation", "rna viruses", "amino acid sub...	HIV-1 epitopes presented by MHC class I types associated with superior immune containment of viremia have highly constrained fitness landscapes	journal.ppat.1006541	null	[ [ "HIV-1-specific CD8+ cytotoxic T-lymphocytes ( CTLs ) play a significant protective role in the pathogenesis of HIV-1 infection [1–3] , but ultimately fail to prevent disease progression in most persons .", "Myriad failure mechanisms have been proposed , but given the remarkable mutation rate and sequence...	[ "Certain Major Histocompatibility-I ( MHC-I ) types are associated with superior immune containment of HIV-1 infection by CD8+ cytotoxic T lymphocytes ( CTLs ) , but the mechanisms mediating this containment are difficult to elucidate in vivo .", "Here we provide controlled assessments of fitness landscapes and C...	[ "Certain MHC class I types are associated with superior immune containment of HIV-1 , underscoring the importance of CD8+ cytotoxic T lymphocytes ( CTLs ) .", "Epitope escape mutations for these types is limited , indicating reduced immune evasion .", "Two proposed mechanisms are:", "1 ) CTL targeting of high...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "gene expression", "genetics", "epigenetics", "biology", "molecular cell biology" ]	Effective Blocking of the White Enhancer Requires Cooperation between Two Main Mechanisms Suggested for the Insulator Function	journal.pgen.1003606	null	[ [ "The complexity of regulatory systems in higher eukaryotes , featuring many distantly located enhancers that nonetheless properly activate the target , has promoted the hypothesis that the action of enhancers should be restricted by elements called insulators .", "Initially , insulators were regarded as g...	[ "Chromatin insulators block the action of transcriptional enhancers when interposed between an enhancer and a promoter .", "In this study , we examined the role of chromatin loops formed by two unrelated insulators , gypsy and Fab-7 , in their enhancer-blocking activity .", "To test for this activity , we selec...	[ "The mechanism underlying enhancer blocking by insulators is unclear .", "Current models suggest that insulator proteins block enhancers either by formation of chromatin loops or by direct interaction with protein complexes bound to the enhancers and promoters .", "Here , we tested the role of a chromatin loop ...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "bacteriology", "microbial metabolism", "microbial mutation", "microbial physiology", "microbial pathogens", "biology", "microbiology", "bacterial biochemistry" ]	Deciphering the Growth Behaviour of Mycobacterium africanum	journal.pntd.0002220	null	[ [ "Mycobacterium africanum , a member of the Mycobacterium tuberculosis complex , was first described in 1968 in Dakar , Senegal [1] .", "Infections with M . africanum are generally geographically restricted to human populations in West Africa , and are not well understood [2] .", "Molecular techniques ...	[ "Human tuberculosis ( TB ) in West Africa is not only caused by M . tuberculosis but also by bacteria of the two lineages of M . africanum .", "For instance , in The Gambia , 40% of TB is due to infections with M . africanum West African 2 .", "This bacterial lineage is associated with HIV infection , reduced E...	[ "Mycobacterium tuberculosis and Mycobacterium africanum are the two major lineages within the M . tuberculosis complex that cause human tuberculosis in West Africa .", "Despite being closely related , the outcome after infection differs between these two pathogens .", "Although M . africanum has not yet been st...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Mosquito Vector Diversity across Habitats in Central Thailand Endemic for Dengue and Other Arthropod-Borne Diseases	journal.pntd.0002507	null	[ [ "Our expanding and increasingly globalized human population has seen the emergence of new infectious diseases such as SARS and the resurgence of familiar diseases such as dengue and influenza to epidemic proportions .", "At the same time , our environment has experienced substantial ecological disturbance...	[ "Recent years have seen the greatest ecological disturbances of our times , with global human expansion , species and habitat loss , climate change , and the emergence of new and previously-known infectious diseases .", "Biodiversity loss affects infectious disease risk by disrupting normal relationships between ...	[ "Biodiversity affects the long-term health of a community by virtue of the many interactions constituent organisms depend upon .", "Mosquito-borne diseases are particularly likely to respond to changes on multiple transmission levels that span mosquito and vertebrate host communities .", "We characterized mosqu...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Identification of the Virulence Landscape Essential for Entamoeba histolytica Invasion of the Human Colon	journal.ppat.1003824	null	[ [ "In the human colon , mucus acts as a lubricant facilitating the passage of digestive content , protects the underlying epithelium from mechanical stress , and provides a protective barrier against pathogens .", "Mucin 2 ( MUC2 ) is the major component of the mucus layer .", "MUC2 is a heavily glycosy...	[ "Entamoeba histolytica is the pathogenic amoeba responsible for amoebiasis , an infectious disease targeting human tissues .", "Amoebiasis arises when virulent trophozoites start to destroy the muco-epithelial barrier by first crossing the mucus , then killing host cells , triggering inflammation and subsequently...	[ "Entamoeba histolytica is an intestinal parasite which displays diverse phenotypes with respect to pathogenesis in the human colon .", "Trophozoites can remain as commensal , without causing evident intestinal damage , or they can destroy the colonic mucosa leading to amoebiasis .", "Using human colon explants ...	2013
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "enzyme-linked immunoassays", "immune physiology", "pathology and laboratory medicine", "respiratory infections", "immunology", "microbiology", "vertebrates", "animals", "electromagnetic radiation", "pulmonology", "mammals", "signs and symptoms", "antibodies...	Characterization of Monkeypox virus infection in African rope squirrels (Funisciurus sp.)	journal.pntd.0005809	null	[ [ "Monkeypox virus ( MPXV ) is a zoonotic Orthopoxvirus ( OPXV ) endemic to West and Central Africa .", "MPXV causes monkeypox disease ( MPX ) in humans , characterized by fever , maculopapular rash , and lymphadenopathy [3] , with a mortality rate of approximately 10% in the more pathogenic Central African...	[ "Monkeypox ( MPX ) is a zoonotic disease endemic in Central and West Africa and is caused by Monkeypox virus ( MPXV ) , the most virulent Orthopoxvirus affecting humans since the eradication of Variola virus ( VARV ) .", "Many aspects of the MPXV transmission cycle , including the natural host of the virus , rema...	[ "Monkeypox virus ( MPXV ) is a virus closely related to Variola virus , the cause of smallpox , and it causes a similar , though less severe , disease in humans in Central and West Africa .", "This disease is particularly dangerous for children and people with compromised immune systems and the mortality rate is ...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "viral vaccines", "medicine and health sciences", "chemical characterization", "immune physiology", "enzyme-linked immunoassays", "pathology and laboratory medicine", "immune cells", "pathogens", "immunology", "microbiology", "retroviruses", "viruses", "immunodeficiency viru...	Boosting of HIV envelope CD4 binding site antibodies with long variable heavy third complementarity determining region in the randomized double blind RV305 HIV-1 vaccine trial	journal.ppat.1006182	null	[ [ "Six HIV-1 vaccine efficacy trials have been performed [1–5] , of which only one , the ALVAC-HIV and AIDSVAX B/E prime-boost RV144 trial , showed vaccine protection , with estimated vaccine efficacies of 60% at 12 months [6] and 31% at 42 months [7] .", "Plasma IgG antibodies binding to HIV-1 envelope var...	[ "The canary pox vector and gp120 vaccine ( ALVAC-HIV and AIDSVAX B/E gp120 ) in the RV144 HIV-1 vaccine trial conferred an estimated 31% vaccine efficacy .", "Although the vaccine Env AE . A244 gp120 is antigenic for the unmutated common ancestor of V1V2 broadly neutralizing antibody ( bnAbs ) , no plasma bnAb ac...	[ "Developing a successful HIV-1 vaccine remains a high global health priority .", "Several HIV-1 vaccine trials have been performed with only the RV144 vaccine trial showing vaccine efficacy , albeit modest .", "No broadly neutralizing antibody activity was identified in RV144 and inducing sterilizing immunity a...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "flow cytometry", "cell death", "medicine and health sciences", "immune cells", "pathology and laboratory medicine", "pathogens", "immunology", "cell processes", "biological cultures", "microbiology", "organisms", "viruses", "dna viruses", "infectious disease control", "...	Azidothymidine Sensitizes Primary Effusion Lymphoma Cells to Kaposi Sarcoma-Associated Herpesvirus-Specific CD4+ T Cell Control and Inhibits vIRF3 Function	journal.ppat.1006042	null	[ [ "Kaposi sarcoma-associated herpesvirus ( KSHV ) is an oncogenic human γ-herpesvirus which infects endothelial cells and establishes a latent infection in B lymphocytes .", "It is associated with the endothelial cell malignancy Kaposi sarcoma ( KS ) and the B lymphocyte disorders primary effusion lymphoma ...	[ "Kaposi sarcoma-associated herpesvirus ( KSHV ) is linked with the development of Kaposi sarcoma and the B lymphocyte disorders primary effusion lymphoma ( PEL ) and multi-centric Castleman disease .", "T cell immunity limits KSHV infection and disease , however the virus employs multiple mechanisms to inhibit ef...	[ "Kaposi sarcoma-associated herpesvirus ( KSHV ) can cause disease in humans in the form of B lymphocyte disorders such as primary effusion lymphoma ( PEL ) and multicentric Castleman disease .", "Where tested , these are highly resistant to immune control by KSHV-specific T cells .", "To investigate how such KS...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Multifactorial Competition and Resistance in a Two-Species Bacterial System	journal.pgen.1005715	null	[ [ "Microorganisms are typically found in complex communities such as those in the soil , aquatic environments , and the microbiome [1] , and interactions between microbial species can critically impact their survival and evolutionary trajectories [1 , 2] .", "Current knowledge suggests that competition play...	[ "Microorganisms exist almost exclusively in interactive multispecies communities , but genetic determinants of the fitness of interacting bacteria , and accessible adaptive pathways , remain uncharacterized .", "Here , using a two-species system , we studied the antagonism of Pseudomonas aeruginosa against Escher...	[ "Bacteria commonly exist in nature as part of large multispecies communities , and their behavior is affected by the surrounding species via secreted molecules or physical contact .", "Such interactions are poorly understood , and the pathways that actually affect bacterial growth and behavior in any multispecies...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "gene regulation", "dna transcription", "developmental biology", "regulator genes", "gene types", "epigenetics", "chromatin", "embryology", "limb buds", "chromosome biology", "gene expression", "hedgehog signaling", "signal transduction", "cell biology", "genetics", "biology and life s...	Anteroposterior Limb Skeletal Patterning Requires the Bifunctional Action of SWI/SNF Chromatin Remodeling Complex in Hedgehog Pathway	journal.pgen.1005915	null	[ [ "Vertebrate limb anteroposterior ( AP ) patterning is controlled by a diffusible morphogen , Sonic hedgehog ( Shh ) , that is produced from the posteriorly located zone of polarizing activity ( ZPA ) [1] .", "Cell fate marking studies on mouse limb buds have revealed that Shh signaling regulates identitie...	[ "Graded Sonic hedgehog ( Shh ) signaling governs vertebrate limb skeletal patterning along the anteroposterior ( AP ) axis by regulating the activity of bifunctional Gli transcriptional regulators .", "The genetic networks involved in this patterning are well defined , however , the epigenetic control of the proc...	[ "Anteroposterior ( AP ) limb skeletal patterning is directed by morphogen Sonic hedgehog ( Shh ) signaling .", "Modulation of Shh responsiveness and repression of Shh pathway activity in distinct limb bud regions are essential for proper limb skeletal formation .", "Although the genetic networks involved in the...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/complex traits", "cardiovascular disorders/hypertension", "genetics and genomics/population genetics", "cardiovascular disorders/coronary artery disease", "cardiovascular disorders/myocardial infarction", "diabetes and endocrinology/type 2 diabetes" ]	Genome-Wide Association Study of Coronary Heart Disease and Its Risk Factors in 8,090 African Americans: The NHLBI CARe Project	journal.pgen.1001300	null	[ [ "Coronary heart disease ( CHD ) is the leading cause of mortality in African-American men and women [1] .", "The risk factors for CHD in African Americans are similar to those reported in Caucasians , but their relative impact varies between the two ethnic groups .", "Multiple studies have reported th...	[ "Coronary heart disease ( CHD ) is the leading cause of mortality in African Americans .", "To identify common genetic polymorphisms associated with CHD and its risk factors ( LDL- and HDL-cholesterol ( LDL-C and HDL-C ) , hypertension , smoking , and type-2 diabetes ) in individuals of African ancestry , we perf...	[ "To date , most large-scale genome-wide association studies ( GWAS ) carried out to identify risk factors for complex human diseases and traits have focused on population of European ancestry .", "It is currently unknown whether the same loci associated with complex diseases and traits in Caucasians will replicat...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "emulsions", "schistosoma mansoni", "medicine and health sciences", "immune cells", "pathology and laboratory medicine", "helminths", "granulomas", "immunology", "tropical diseases", "colloids", "parasitic diseases", "animals", "materials science", "negl...	Double impact: natural molluscicide for schistosomiasis vector control also impedes development of Schistosoma mansoni cercariae into adult parasites	journal.pntd.0005789	null	[ [ "Schistosomiasis is a chronic parasitic disease caused by trematodes of the Schistosoma genus .", "It has been reported in 78 endemic countries and affects more than 240 million people worldwide [1] .", "If left untreated , it is associated with fibrosis , abdominal pain , diarrhea and anemia , result...	[ "Schistosomiasis has been reported in 78 endemic countries and affects 240 million people worldwide .", "The digenetic parasite Schistosoma mansoni needs fresh water to compete its life cycle .", "There , it is susceptible to soluble compounds that can affect directly and/or indirectly the parasite’s biology ."...	[ "Intestinal schistosomiasis is among the most important parasitic disease caused by helminthes , affecting 67 million people worldwide .", "Vector and intermediate host of the parasitic worm are fresh water snails .", "WHO recommends use of molluscicides for control of local transmission .", "Among those , na...	2017
[ "Introduction", "Results", "Discussion", "Methods", "Acknowledgments" ]	[ "biomacromolecule-ligand interactions", "molecular mechanics", "biochemistry", "molecular dynamics", "biochemistry simulations", "chemical physics", "small molecules", "chemical biology", "biophysics theory", "chemistry", "biology", "computational chemistry", "biophysics simulations", "bio...	A New View of the Bacterial Cytosol Environment	journal.pcbi.1002066	null	[ [ "The composition of metabolites , ions and proteins , and processes such as metabolism and signalling which take place in the E . coli cytosol are largely well defined [1] , [2] .", "However , the structure and dynamical nature of the cytosol solution is less well understood whether on the local or cytoso...	[ "The cytosol is the major environment in all bacterial cells .", "The true physical and dynamical nature of the cytosol solution is not fully understood and here a modeling approach is applied .", "Using recent and detailed data on metabolite concentrations , we have created a molecular mechanical model of the ...	[ "The cytosol is the major cellular environment housing the majority of cellular activity .", "Although the cytosol is an aqueous environment , it contains high concentrations of ions , metabolites , and proteins , making it very different from dilute aqueous solution , which is frequently used for in vitro bioche...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "microbiology/microbial growth and development", "microbiology/cellular microbiology and pathogenesis", "cell biology/cell signaling" ]	Multiple Plant Surface Signals are Sensed by Different Mechanisms in the Rice Blast Fungus for Appressorium Formation	journal.ppat.1001261	null	[ [ "The heterothallic ascomycete Magnaporthe oryzae is an important pathogen of rice throughout the world .", "In the past two decades , the rice-M .", "oryzae pathosystem has been developed as a model to study fungal-plant interactions [1] , [2] , [3] .", "M . oryzae initiates infection of rice leav...	[ "Surface recognition and penetration are among the most critical plant infection processes in foliar pathogens .", "In Magnaporthe oryzae , the Pmk1 MAP kinase regulates appressorium formation and penetration .", "Its orthologs also are known to be required for various plant infection processes in other phytopa...	[ "The rice blast fungus is a major pathogen of rice and a model for studying fungal-plant interactions .", "Like many other fungal pathogens , it can recognize physical and chemical signals present on the rice leaf surface and form a highly specialized infection structure known as appressorium .", "A well conser...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/microbial evolution and genomics", "genetics and genomics/functional genomics", "biotechnology/applied microbiology", "cell biology/cell growth and division", "microbiology/microbial evolution and genomics", "microbiology/applied microbiology" ]	Genome Sequencing and Comparative Transcriptomics of the Model Entomopathogenic Fungi Metarhizium anisopliae and M. acridum	journal.pgen.1001264	null	[ [ "Most fungi with sequenced genomes are plants pathogens or saprophytes .", "However , there are also thousands of entomopathogenic fungal species that play a crucial role in controlling insect populations .", "The genus Metarhizium includes the best studied entomopathogenic fungi at the molecular and ...	[ "Metarhizium spp .", "are being used as environmentally friendly alternatives to chemical insecticides , as model systems for studying insect-fungus interactions , and as a resource of genes for biotechnology .", "We present a comparative analysis of the genome sequences of the broad-spectrum insect pathogen Me...	[ "Aside from playing a crucial role in natural ecosystems , entomopathogenic fungi are being developed as environmentally friendly alternatives for the control of insect pests .", "We conducted the first genomic study of two of the best characterized entomopathogens , Metarhizium anisopliae and M . acridum .", "...	2011
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "genetics and genomics/animal genetics", "genetics and genomics/gene discovery", "developmental biology/morphogenesis and cell biology", "physiology/cell signaling", "genetics and genomics/gene function", "developmental biology/molecular development" ]	The Drosophila SH2B Family Adaptor Lnk Acts in Parallel to Chico in the Insulin Signaling Pathway	journal.pgen.1000596	null	[ [ "The control of cell , organ and body size is tightly regulated to ensure proper development of multicellular organisms .", "A key pathway controlling growth , metabolism , reproduction and longevity is the insulin/insulin-like growth factor signaling ( IIS ) pathway [1] .", "The insulin receptor ( In...	[ "Insulin/insulin-like growth factor signaling ( IIS ) plays a pivotal role in the regulation of growth at the cellular and the organismal level during animal development .", "Flies with impaired IIS are developmentally delayed and small due to fewer and smaller cells .", "In the search for new growth-promoting ...	[ "The regulation of growth is among the most fundamental processes during development of multicellular organisms .", "Research over the past years has established a key function of the insulin/insulin-like growth factor signaling ( IIS ) pathway in ensuring proper growth at the cellular and the organismal level ."...	2009
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "invertebrates", "livestock", "medicine and health sciences", "enzyme-linked immunoassays", "immune physiology", "ruminants", "distillation", "immunology", "vertebrates", "parasitic diseases", "animals", "mammals", "nematode infections", "trematodes", "antibodies", "immunologic techniq...	Rapid Enhanced MM3-COPRO ELISA for Detection of Fasciola Coproantigens	journal.pntd.0004872	null	[ [ "Fascioliasis ( = fasciolosis ) is a worldwide emergent zoonotic disease produced by infection with trematodes of the genus Fasciola .", "The two main species of this genus , F . hepatica and F . gigantica , are pathogenic to humans and livestock [1] .", "Considering the worldwide distribution , F . g...	[ "ELISA-based methods of detecting Fasciola cathepsins in feces are powerful techniques for diagnosing infections by F . hepatica and F . gigantica .", "In the last decade , the in-house MM3-COPRO ELISA and its commercial version BIO K 201 ( BIO X Diagnostics , Belgium ) have been recognized as useful tools for de...	[ "We have previously reported how the combined use of mAb MM3 with polyclonal antibodies obtained from rabbit immunized with Fasciola hepatica excretory-secretory antigens led to the development of the in-house MM3-COPRO ELISA and its commercial version BIO K 201 ( BIO X Diagnostics , Belgium ) , which are widely us...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genome-wide association studies", "medicine", "genetic association studies", "genetics", "genetics and genomics", "biology", "human genetics", "respiratory medicine", "genetics of disease", "pulmonology", "asthma" ]	Genome-Wide Association Analysis in Asthma Subjects Identifies SPATS2L as a Novel Bronchodilator Response Gene	journal.pgen.1002824	null	[ [ "Asthma is a chronic respiratory disease that affects over 20 million Americans and 300 million people worldwide [1] , [2] .", "A hallmark characteristic of asthma is reversible airway obstruction , which is commonly measured via a bronchodilator response ( BDR ) test , in which the reduction of bronchoco...	[ "Bronchodilator response ( BDR ) is an important asthma phenotype that measures reversibility of airway obstruction by comparing lung function ( i . e . FEV1 ) before and after the administration of a short-acting β2-agonist , the most common rescue medications used for the treatment of asthma .", "BDR also serve...	[ "Bronchodilator response ( BDR ) is an important asthma phenotype that measures reversibility of airway obstruction by comparing lung function before and after the administration of short-acting β2-agonists , common medications used for asthma treatment .", "We performed a genome-wide association study of BDR wit...	2012
[ "Introduction", "Results", "Discussion", "Materials And Methods" ]	[ "teratology", "cell differentiation", "animal models", "developmental biology", "model organisms", "organism development", "molecular development", "molecular genetics", "pattern formation", "embryology", "gene expression", "nuclear receptor signaling", "biology", "morphogens", "zebrafis...	Depletion of Retinoic Acid Receptors Initiates a Novel Positive Feedback Mechanism that Promotes Teratogenic Increases in Retinoic Acid	journal.pgen.1003689	null	[ [ "Improper retinoic acid ( RA ) signaling during development can cause congenital malformations that affect the forelimbs , ocular , cardiovascular , respiratory , urogenital and nervous systems [1]–[4] .", "Despite almost a century of investigation , the mechanisms underlying many congenital defects due t...	[ "Normal embryonic development and tissue homeostasis require precise levels of retinoic acid ( RA ) signaling .", "Despite the importance of appropriate embryonic RA signaling levels , the mechanisms underlying congenital defects due to perturbations of RA signaling are not completely understood .", "Here , we ...	[ "Retinoic acid ( RA ) is the most active metabolic product of Vitamin A . Appropriate levels of RA are required for proper embryonic development and tissue maintenance in all vertebrates .", "Inappropriate levels of RA in human embryos can cause congenital defects that affect many organs , including the heart and...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "phosphorylation", "cell death", "innate immune system", "medicine and health sciences", "immune physiology", "cytokines", "pathology and laboratory medicine", "carcinomas", "immunology", "cancers and neoplasms", "basic cancer research", "cell processes", "long non-coding rnas", "oncology"...	NKILA represses nasopharyngeal carcinoma carcinogenesis and metastasis by NF-κB pathway inhibition	journal.pgen.1008325	null	[ [ "Nasopharyngeal carcinoma ( NPC ) , a metastasis-prone cancer , which is particularly common in southeast Asia and southern China [1–4] .", "Due to the high radiosensitivity , radiotherapy has become the main treatment for locoregional NPC .", "Radiation oncology has improved the locoregional control ...	[ "The role of long non-coding RNA ( lncRNA ) in the progression of Nasopharyngeal carcinoma ( NPC ) has not been fully elucidated .", "The study was designed to explore the functional role of NKILA , a newly identified lncRNA , in the progression of NPC .", "We performed a lncRNA expression profile microarray us...	[ "NF-κB is a pivotal link between NPC and inflammation .", "Importantly , NF-κB was found to be overexpressed in nearly all NPC tissues , and inflammatory cytokines have also been observed in NPC tissues .", "Inflammatory cytokines promote the susceptibility of NPC cells to metastasize via constant NF-κB activat...	2019
[ "Introduction", "Materials and methods", "Results and discussion" ]	[ "invertebrates", "population genetics", "invertebrate genomics", "animals", "genetic mapping", "artificial intelligence", "population biology", "drosophila", "computer and information sciences", "introgression", "animal genomics", "insects", "arthropoda", "machine learning", "haplotypes"...	Supervised machine learning reveals introgressed loci in the genomes of Drosophila simulans and D. sechellia	journal.pgen.1007341	null	[ [ "Up to 10% of animal [1] and plant [2] species have the ability to hybridize with other species .", "Our recent ability to collect large-scale genomic data has confirmed that hybridization is common in nature .", "Indeed the ubiquity of hybridization upon secondary contact raises the question of how l...	[ "Hybridization and gene flow between species appears to be common .", "Even though it is clear that hybridization is widespread across all surveyed taxonomic groups , the magnitude and consequences of introgression are still largely unknown .", "Thus it is crucial to develop the statistical machinery required t...	[ "Understanding the extent to which species or diverged populations hybridize in nature is crucially important if we are to understand the speciation process .", "Accordingly numerous research groups have developed methodology for finding the genetic evidence of such introgression .", "In this report we develop ...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "taxonomy", "medicine and health sciences", "plagues", "pathology and laboratory medicine", "china", "pathogens", "geographical locations", "microbiology", "vertebrates", "animals", "mammals", "animal phylogenetics", "bacterial diseases", "phylogenetics", "data management", "yersinia",...	Ten years of surveillance of the Yulong plague focus in China and the molecular typing and source tracing of the isolates	journal.pntd.0006352	null	[ [ "Plague is an acute infectious disease caused by Yersinia pestis ( Y . pestis ) .", "Four Y . pestis biovars have been recognized based on their biochemical properties , i . e . , Antiqua , Mediaevalis , Orientalis and Microtus .", "Each Y . pestis biovar has a different geographic distribution throug...	[ "Plague , caused by Yersinia pestis , was classified as a reemerging infectious disease by the World Health Organization .", "The five human pneumonic plague cases in Yulong County in 2005 gave rise to the discovery of a Yulong plague focus in Yunnan province , China .", "Thereafter , continuous wild rodent pla...	[ "Plague is a type of zoonosis that is highly lethal to humans .", "The surveillance of animal hosts is critical for the prevention and control of plague .", "The Yulong plague focus is a newly discovered plague focus in China in recent years .", "The plague outbreak had attracted widespread attention because ...	2018
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "engineering and technology", "cardiovascular anatomy", "fibrosis", "electrophysiology", "endocardium", "simulation and modeling", "developmental biology", "epicardium", "research and analysis methods", "cardiology", "arrhythmia", "atrial fibrillation", "rot...	Variability in pulmonary vein electrophysiology and fibrosis determines arrhythmia susceptibility and dynamics	journal.pcbi.1006166	null	[ [ "Success rates for catheter ablation of persistent atrial fibrillation ( AF ) patients are currently low; however , there is a subset of patients for whom pulmonary vein isolation ( PVI ) alone is a successful treatment strategy [1] .", "PVI ablation may work by preventing triggered beats from entering th...	[ "Success rates for catheter ablation of persistent atrial fibrillation patients are currently low; however , there is a subset of patients for whom electrical isolation of the pulmonary veins alone is a successful treatment strategy .", "It is difficult to identify these patients because there are a multitude of ...	[ "Atrial fibrillation is the most commonly encountered cardiac arrhythmia , affecting a significant portion of the population .", "Currently , ablation is the most effective treatment but success rates are less than optimal , being 70% one-year post-treatment .", "There is a large effort to find better ablation ...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Ebola Cases and Health System Demand in Liberia	journal.pbio.1002056	The authors develop a multi-type branching process model of the 2014 Liberian Ebola outbreak that incorporates the impacts of changes in behavior on potential transmission scenarios, thereby informing the path to containment of the epidemic.	[ [ "The 2014 epidemic of Ebola virus in West Africa is an emerging public health and humanitarian crisis of epic dimensions [1] .", "This epidemic originated in an outbreak in Guéckédou , Guinea in December 2013 .", "The Ministry of Health of Guinea and Médecins Sans Frontières ( MSF ) were alerted to cl...	[ "In 2014 , a major epidemic of human Ebola virus disease emerged in West Africa , where human-to-human transmission has now been sustained for greater than 12 months .", "In the summer of 2014 , there was great uncertainty about the answers to several key policy questions concerning the path to containment .", ...	[ "There is considerable uncertainty regarding the steps needed to contain the ongoing Ebola crisis in West Africa , the timeline required to achieve control , and the projected burden of mortality .", "To address these issues , we develop a branching process model for Ebola transmission that focuses on offspring d...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunology/cellular microbiology and pathogenesis", "immunology/immunity to infections", "infectious diseases/bacterial infections" ]	Regulatory T Cell Suppressive Potency Dictates the Balance between Bacterial Proliferation and Clearance during Persistent Salmonella Infection	journal.ppat.1001043	null	[ [ "Typhoid fever is a systemic , persistent infection caused by highly adapted host-specific strains of Salmonella [1] , [2] , [3] .", "Human typhoid is caused predominantly by S . enterica serotype Typhi [4] , while mice develop a typhoid-like disease following S . enterica serotype Typhimurium infection ....	[ "The pathogenesis of persistent infection is dictated by the balance between opposing immune activation and suppression signals .", "Herein , virulent Salmonella was used to explore the role and potential importance of Foxp3-expressing regulatory T cells in dictating the natural progression of persistent bacteria...	[ "The balance between immune activation and suppression is intricately controlled allowing optimal host defense against infection , while simultaneously minimizing collateral immune-mediated damage to host tissues .", "Although regulatory T cells have been implicated to play critical roles in sustaining this balan...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "computational biology/sequence motif analysis", "cell biology/nuclear structure and function", "genetics and genomics/functional genomics", "genetics and genomics/nuclear structure and function", "biochemistry/bioinformatics", "computational biology/genomics", "genetics and genomics/bioinformatics" ]	Genome-Wide Analysis of Histidine Repeats Reveals Their Role in the Localization of Human Proteins to the Nuclear Speckles Compartment	journal.pgen.1000397	null	[ [ "Single amino acid repeats ( SARs ) , also known as homopolymeric tracts , are very common in eukaryotes [1] and between 18–20% of proteins in the human genome contain such repetitive sequences [2] .", "Although most of them are thought to be functionally neutral , recent evidence suggests they may play i...	[ "Single amino acid repeats are prevalent in eukaryote organisms , although the role of many such sequences is still poorly understood .", "We have performed a comprehensive analysis of the proteins containing homopolymeric histidine tracts in the human genome and identified 86 human proteins that contain stretche...	[ "Single amino acid repeats are common in eukaryotic proteins .", "Some of them are associated with developmental and neurodegenerative disorders in humans , suggesting that they play important functions .", "However , the role of many of these repeats is unknown .", "Here , we have studied histidine repeats f...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Economic Impact of Dengue: Multicenter Study across Four Brazilian Regions	journal.pntd.0004042	null	[ [ "Dengue is a viral infection transmitted by Aedes mosquitoes , with global distribution , mainly in the tropical regions [1] .", "Infection with one of the four antigenically distinct dengue serotypes ( serotypes 1 , 2 , 3 , and 4 ) is often asymptomatic/inapparent or mildly symptomatic , but has the pote...	[ "Dengue is an increasing public health concern in Brazil .", "There is a need for an updated evaluation of the economic impact of dengue within the country .", "We undertook this multicenter study to evaluate the economic burden of dengue in Brazil .", "We estimated the economic burden of dengue in Brazil for...	[ "The World Health Organization estimates that 50–100 million dengue infections occur annually .", "However , estimates based on cartographic modeling approaches suggest that up to 390 million dengue infections annually .", "Dengue has become an increasing public health concern in the Americas .", "A substanti...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "statistical mechanics", "neural networks", "vertebrates", "neuroscience", "animals", "mammals", "primates", "probability distribution", "mathematics", "statistics (mathematics)", "thermodynamics", "old world monkeys", "computer and information sciences", "entropy", "monkeys", "animal ...	Bistability, non-ergodicity, and inhibition in pairwise maximum-entropy models	journal.pcbi.1005762	null	[ [ "Correlated activity between pairs of cells was observed early on in the history of neuroscience [1 , 2] .", "Immediately the question arose whether there is a functional interpretation of this observation [3] , and this question is still with us .", "Hypotheses range from synchronous activation of ne...	[ "Pairwise maximum-entropy models have been used in neuroscience to predict the activity of neuronal populations , given only the time-averaged correlations of the neuron activities .", "This paper provides evidence that the pairwise model , applied to experimental recordings , would produce a bimodal distribution...	[ "Networks of interacting units are ubiquitous in various fields of biology; e . g . gene regulatory networks , neuronal networks , social structures .", "If a limited set of observables is accessible , maximum-entropy models provide a way to construct a statistical model for such networks , under particular assum...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "public health", "medicine", "infectious diseases", "public health and epidemiology", "neglected tropical diseases", "parasitic diseases" ]	Implementing Preventive Chemotherapy through an Integrated National Neglected Tropical Disease Control Program in Mali	journal.pntd.0001574	null	[ [ "Neglected tropical diseases ( NTDs ) are a group of diseases that affect the most vulnerable and the poorest group of the populations in the world [1] , [2] .", "The World Health Organization ( WHO ) recommends five public health strategies for the prevention and control of the NTDs: preventive chemother...	[ "Mali is endemic for all five targeted major neglected tropical diseases ( NTDs ) .", "As one of the five ‘fast-track’ countries supported with the United States Agency for International Development ( USAID ) funds , Mali started to integrate the activities of existing disease-specific national control programs o...	[ "Neglected tropical diseases ( NTDs ) are a group of chronic infections that affect the poorest group of the populations in the world .", "There are currently five major NTDs targeted through mass drug treatment in the affected communities .", "The drug delivery can be integrated to deliver different drug packa...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "geographical locations", "indonesia", "research design", "pharmaceutics", "surveys", "pharmacology", "research and analysis methods", "drug safety", "drug distribution", "drug delivery", "pharmacokinetics", "people and places", "survey research", "drug re...	Improving Coverage and Compliance in Mass Drug Administration for the Elimination of LF in Two ‘Endgame’ Districts in Indonesia Using Micronarrative Surveys	journal.pntd.0005027	null	[ [ "More than fifteen years ago , the Global Programme to Eliminate Lympatic Filariasis ( GPELF ) was launched with the goal to interrupt transmission of the disease in endemic countries by 2020 [1] .", "Considerable progress in reducing transmission and burden of disease has been made since World Health Ass...	[ "As the Global Programme to Eliminate Lymphatic Filariasis ( LF ) approaches its 2020 goal , an increasing number of districts will enter the endgame phase where drug coverage rates from mass drug administration ( MDA ) are used to assess whether MDA can be stopped .", "As reported , the gap between reported and ...	[ "This research describes the process used to assist two districts endemic for lymphatic filariasis ( LF ) in Indonesia to better understand the reasons why their LF elimination programs have had suboptimal results .", "A novel survey design was used to collect stories about people’s direct experiences with mass d...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "genetics and genomics", "evolutionary biology/animal genetics", "developmental biology/developmental evolution", "ecology/evolutionary ecology" ]	A Novel Role for Mc1r in the Parallel Evolution of Depigmentation in Independent Populations of the Cavefish Astyanax mexicanus	journal.pgen.1000326	null	[ [ "The blind Mexican cave tetra , Astyanax mexicanus , is a troglobitic characin fish exhibiting a variety of cave-specialized traits .", "In general , the cave ecosystem supports the evolution of some traits that are enhanced or increased over time ( i . e . , “constructive” traits ) , as well as some trai...	[ "The evolution of degenerate characteristics remains a poorly understood phenomenon .", "Only recently has the identification of mutations underlying regressive phenotypes become accessible through the use of genetic analyses .", "Focusing on the Mexican cave tetra Astyanax mexicanus , we describe , here , an a...	[ "As we approach the 150th year since publication of On the Origin of Species , understanding the genetic architecture underlying evolutionary change remains an important challenge .", "When an organism enters a completely new environment or ecological niche , certain traits are no longer necessary for survival , ...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "rna", "rna interference", "nucleic acids", "microbial pathogens", "biology", "microbiology", "molecular cell biology", "parasitology" ]	OncomiR Addiction Is Generated by a miR-155 Feedback Loop in Theileria-Transformed Leukocytes	journal.ppat.1003222	null	[ [ "Both infection and cancer have been extensively linked to the induction of microRNAs ( miRs ) which can exert diverse effects on cellular phenotypes by targeting many genes [1] , [2] .", "microRNAs ( miRNAs ) are a class of small non-coding RNAs , 22 nt in length , that modulate post-transcriptional gene...	[ "The intracellular parasite Theileria is the only eukaryote known to transform its mammalian host cells .", "We investigated the host mechanisms involved in parasite-induced transformation phenotypes .", "Tumour progression is a multistep process , yet ‘oncogene addiction’ implies that cancer cell growth and su...	[ "Theileria is the only intracellular eukaryotic parasite known to transform its host cell into a cancer-like state .", "Infection by the T . annulata parasite causes tropical theileriosis , killing large numbers of cattle in North Africa and Asia , and the related T . parva parasite causes East Coast Fever .", ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The Orphan Nuclear Receptor TLX Is an Enhancer of STAT1-Mediated Transcription and Immunity to Toxoplasma gondii	journal.pbio.1002200	Exploitation of the parasite Toxoplasma gondii identifies the host orphan nuclear hormone receptor TLX as a key enhancer of STAT1-dependent immune signaling and host defense.	[ [ "Interferon gamma ( IFN-γ ) and STAT1 signaling play an essential role in cellular immunity , as indicated by extreme susceptibility to infection in mice and humans carrying mutant alleles for these genes and pathways [1–5] .", "The binding of IFN-γ to its cell surface receptor leads to phosphorylation , ...	[ "The protozoan parasite , Toxoplasma , like many intracellular pathogens , suppresses interferon gamma ( IFN-γ ) -induced signal transducer and activator of transcription 1 ( STAT1 ) activity .", "We exploited this well-defined host–pathogen interaction as the basis for a high-throughput screen , identifying nine...	[ "Immune responses are orchestrated by a diverse array of secreted ligands , yet the downstream transcriptional responses are coordinated by a relatively small set of key transcription factors , including nuclear factor kappa B ( NF-κB ) and signal transducers and activators of transcription ( STATs ) .", "The mol...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "action potentials", "medicine and health sciences", "membrane potential", "electricity", "voltage", "electrophysiology", "neuroscience", "membrane electrophysiology", "electric field", "bioassays and physiological analysis", "neuronal dendrites", "research and analysis methods", "animal cel...	Extending Integrate-and-Fire Model Neurons to Account for the Effects of Weak Electric Fields and Input Filtering Mediated by the Dendrite	journal.pcbi.1005206	null	[ [ "Extracellular electric fields in the brain and their impact on neural activity have gained a considerable amount of attention in neuroscience over the past decade .", "These electric fields can be generated endogenously [1–3] or through transcranial ( alternating ) current stimulation [4–6] , and can mod...	[ "Transcranial brain stimulation and evidence of ephaptic coupling have recently sparked strong interests in understanding the effects of weak electric fields on the dynamics of brain networks and of coupled populations of neurons .", "The collective dynamics of large neuronal populations can be efficiently studie...	[ "How extracellular electric fields—as generated endogenously or through transcranial brain stimulation—affect the dynamics of neuronal populations is of great interest but not well understood .", "To study neuronal activity at the network level single-compartment neuron models have been proven very successful , b...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "phosphorylation", "protein interactions", "chemical compounds", "gene regulation", "microbiology", "threonine", "organic compounds", "dna transcription", "regulator genes", "amino acids", "gene types", "microbial genetics", "proteins", "gene expression", "chemistry", "viral genetics",...	A single phosphoacceptor residue in BGLF3 is essential for transcription of Epstein-Barr virus late genes	journal.ppat.1007980	null	[ [ "Lytic infection is intrinsic to the pathogenesis of herpesviruses .", "Virus particles are synthesized and assembled exclusively during the lytic phase .", "The lytic phase of oncogenic gamma herpesviruses contributes to tumor development by expanding the population of latently infected cells that po...	[ "Almost one third of herpesvirus proteins are expressed with late kinetics .", "Many of these late proteins serve crucial structural functions such as formation of virus particles , attachment to host cells and internalization .", "Recently , we and others identified a group of Epstein-Barr virus early proteins...	[ "EBV is an oncogenic virus involved in the development of about 1 . 5% of human cancers worldwide .", "EBV infection has latent and lytic forms .", "Both forms of infection contribute to the oncogenic capacity of the virus .", "During the lytic cycle , a cascade of temporally regulated events takes place lead...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "animal models", "medicine", "oncology", "developmental biology", "genetic causes of cancer", "cancer genetics", "model organisms", "gene regulation", "genetics", "molecular genetics", "cancer risk factors", "biology", "cancer prevention", "mouse", "rat", "cell differentiation" ]	The Gene Desert Mammary Carcinoma Susceptibility Locus Mcs1a Regulates Nr2f1 Modifying Mammary Epithelial Cell Differentiation and Proliferation	journal.pgen.1003549	null	[ [ "An important indicator for breast cancer risk is the family history , suggesting a strong genetic component in breast cancer susceptibility [1] .", "The heritable portion of a woman's risk to breast cancer consists of numerous risk-increasing and risk-decreasing alleles .", "Through familial linkage ...	[ "Genome-wide association studies have revealed that many low-penetrance breast cancer susceptibility loci are located in non-protein coding genomic regions; however , few have been characterized .", "In a comparative genetics approach to model such loci in a rat breast cancer model , we previously identified the ...	[ "Most non-Mendelian disease variants identified through genome-wide association studies are low-penetrance , common in the population and located in non-protein coding genomic loci .", "It is currently unknown how these loci modulate disease risk .", "Insights in their mechanisms could lead to the development o...	2013
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "body fluids", "pathology and laboratory medicine", "tropical diseases", "parasitic diseases", "parasitic protozoans", "organisms", "protozoans", "neglected tropical diseases", "molecular biology techniques", "extraction techniques", "research and analysis metho...	Improved DNA extraction technique from clot for the diagnosis of Chagas disease	journal.pntd.0007024	null	[ [ "Chagas disease , caused by the protozoan parasite Trypanosoma cruzi , is endemic in many parts of the Americas [1 , 2] , where 6 to 7 million people are infected [3] .", "In the acute phase of the infection , serology by IgG may still be negative but positive for parasite by microscopic examination or by...	[ "The detection of Trypanosoma cruzi genetic material in clinical samples is considered an important diagnostic tool for Chagas disease .", "We have previously demonstrated that PCR using clot samples yields greater sensitivity than either buffy coat or whole blood samples .", "However , phenol-chloroform DNA ex...	[ "Detection of nucleic acid has become an important tool for the diagnosis of Chagas disease .", "Whole blood samples are usually the source of DNA and qPCR the preferred technique to demonstrate the presence of T . cruzi DNA .", "Although DNA extracted from clot samples has shown higher sensitivity than from wh...	2019
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "phosphorylation", "innate immune system", "medicine and health sciences", "immune cells", "immune physiology", "cytokines", "enzyme-linked immunoassays", "immunology", "cloning", "developmental biology", "molecular development", "tcr signaling cascade", "molecular biology t...	Unique properties of TCR-activated p38 are necessary for NFAT-dependent T-cell activation	journal.pbio.2004111	null	[ [ "Many activation events downstream of the T-cell antigen receptor ( TCR ) are up-regulated by the nuclear factor of activated T cells ( NFAT ) transcription factor family [1] .", "There are 5 NFAT family members: NFAT1 ( also known as NFATc2 or NFATp ) , NFAT2 ( NFATc1 or NFATc ) , NFAT3 ( NFATc4 ) , NFAT...	[ "Nuclear factor of activated T cells ( NFAT ) transcription factors are required for induction of T-cell cytokine production and effector function .", "Although it is known that activation via the T-cell antigen receptor ( TCR ) results in 2 critical steps , calcineurin-mediated NFAT1 dephosphorylation and NFAT2 ...	[ "The p38 MAP kinase , which is required for a large number of important biological responses , is activated by an enzymatic cascade that results in its dual phosphorylation on p38T180Y182 .", "T cells have evolved a unique pathway in which T-cell antigen receptor ( TCR ) ligation results in phosphorylation of p38...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "phosphorylation", "chemical compounds", "molecular mass", "organic compounds", "mutation", "fungi", "model organisms", "sumoylation", "experimental organism systems", "basic amino acids", "amino acids", "research and analysis methods", "saccharomyces", "chemical properties", "physical c...	A high throughput mutagenic analysis of yeast sumo structure and function	journal.pgen.1006612	null	[ [ "Small ubiquitin-related modifiers ( SUMOs ) are ~100 amino acid proteins that are covalently attached to other proteins and thereby function as reversible , posttranslational protein modifications .", "Hundreds of proteins are regulated through sumoylation , accounting for effects on nearly every aspect ...	[ "Sumoylation regulates a wide range of essential cellular functions through diverse mechanisms that remain to be fully understood .", "Using S . cerevisiae , a model organism with a single essential SUMO gene ( SMT3 ) , we developed a library of >250 mutant strains with single or multiple amino acid substitutions...	[ "The Small ubiquitin-related modifier ( SUMO ) is a 100 amino acid protein that is attached to other proteins and thereby regulates nearly all essential cell functions .", "To explore how this small protein modifier functions to regulate so many different processes , we generated a library of >250 mutant alleles ...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "luciferase", "pathology and laboratory medicine", "molecular probe techniques", "enzymes", "pathogens", "microbiology", "immunoblotting", "light microscopy", "cell disruption", "enzymology", "viruses", "immunoprecipitation", "microscopy", "dna viruses", ...	Efficacy and Mechanism of Action of Low Dose Emetine against Human Cytomegalovirus	journal.ppat.1005717	null	[ [ "Infection with Human Cytomegalovirus ( HCMV ) continues to be a major threat for transplant recipients and patients with AIDS [1–3] .", "It is also the most common congenital infection worldwide [4] .", "The systemic anti-HCMV drugs all target the viral DNA polymerase and effectively suppress HCMV re...	[ "Infection with human cytomegalovirus ( HCMV ) is a threat for pregnant women and immunocompromised hosts .", "Although limited drugs are available , development of new agents against HCMV is desired .", "Through screening of the LOPAC library , we identified emetine as HCMV inhibitor .", "Additional studies ...	[ "Infection with human Cytomegalovirus ( HCMV ) is a growing and pressing problem , creating ongoing management and therapeutic challenges .", "Despite the availability of DNA polymerase inhibitors , development of new strategies for HCMV therapy is needed .", "We report for the first time on the efficacy of an ...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "animal diseases", "pathology and laboratory medicine", "pathogens", "pertussis", "bacterial diseases", "infectious disease control", "zoology", "veterinary science", "infectious diseases", "veterinary diseases", "veterinary epidemiology", "epidemiology", "p...	Using Combined Diagnostic Test Results to Hindcast Trends of Infection from Cross-Sectional Data	journal.pcbi.1004901	null	[ [ "Infectious disease surveillance is the first line of detection and defence against infectious pathogens and therefore crucial to maintaining animal and public health .", "However , the current state of disease surveillance has been characterised as deficient in terms of both coverage and reporting speed ...	[ "Infectious disease surveillance is key to limiting the consequences from infectious pathogens and maintaining animal and public health .", "Following the detection of a disease outbreak , a response in proportion to the severity of the outbreak is required .", "It is thus critical to obtain accurate informatio...	[ "We have developed a Bayesian approach that can estimate the historic trend of incidence from cross-sectional samples , without relying on ongoing surveillance .", "This could be used to evaluate changing disease trends , or to inform outbreak responses .", "We combine two or more diagnostic tests to estimate t...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics of disease", "animal genetics", "genetics of the immune system", "clinical immunology", "heredity", "genetics", "biology and life sciences", "epigenetics", "immunology", "genetic linkage", "autoimmunity" ]	Parent-of-Origin Effects Implicate Epigenetic Regulation of Experimental Autoimmune Encephalomyelitis and Identify Imprinted Dlk1 as a Novel Risk Gene	journal.pgen.1004265	null	[ [ "Complex diseases , like common chronic inflammatory conditions , arise from an interplay between multiple risk genes and environmental factors .", "Etiology is often largely unknown with variable penetrance and expressivity making it difficult to identify contributing factors .", "Epigenetic mechanis...	[ "Parent-of-origin effects comprise a range of genetic and epigenetic mechanisms of inheritance .", "Recently , detection of such effects implicated epigenetic mechanisms in the etiology of multiple sclerosis ( MS ) , a chronic inflammatory disease of the central nervous system .", "We here sought to dissect the...	[ "Even with recent progress in determining the genetic basis of complex diseases , the issue of ‘missing heritability’ remains and its potential sources are frequently speculated about but rarely explained .", "Parent-of-origin effects might contribute to the ‘missing heritability’ and involve genetic and epigenet...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "social and behavioral sciences", "biology" ]	Disease Ecology, Biodiversity, and the Latitudinal Gradient in Income	journal.pbio.1001456	Vector-borne and parasitic diseases are drivers of the latitudinal gradient in income, and the burden of these diseases is predicted to rise as biodiversity falls.	[ [ "The primary challenge for understanding relationships between the ecology of human health and global patterns of economic development through statistical analysis of country-level indicators is the problem of endogeneity [38]: economic activity is hypothesized to be both a cause and a consequence of health ....	[ "While most of the world is thought to be on long-term economic growth paths , more than one-sixth of the world is roughly as poor today as their ancestors were hundreds of years ago .", "The majority of the extremely poor live in the tropics .", "The latitudinal gradient in income is highly suggestive of under...	[ "While most of the world is thought to be growing economically , more than one-sixth of the world is roughly as poor today as their ancestors were hundreds of years ago .", "The extremely poor live largely in the tropics .", "This latitudinal gradient in income suggests that there are biophysical factors , such...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "disease mapping", "global health", "epidemiology", "neglected tropical diseases", "trachoma", "public health" ]	The Geographical Distribution and Burden of Trachoma in Africa	journal.pntd.0002359	null	[ [ "The last decade has witnessed tremendous progress towards the global elimination of trachoma , the leading infectious cause of blindness worldwide .", "Since the establishment in 1998 of the Global Elimination of Trachoma by 2020 ( GET2020 ) initiative , an increasing number of endemic countries have imp...	[ "There remains a lack of epidemiological data on the geographical distribution of trachoma to support global mapping and scale up of interventions for the elimination of trachoma .", "The Global Atlas of Trachoma ( GAT ) was launched in 2011 to address these needs and provide standardised , updated and accessible...	[ "In order to target resources and drugs to reach trachoma elimination targets by the year 2020 , data on the burden of disease are required .", "Using prevalence data in African countries derived from the Global Atlas of Trachoma ( GAT ) , the distribution of trachoma continues to be focused in East and West Sub-...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "computational biology/transcriptional regulation", "cell biology", "biochemistry/bioinformatics", "computational biology", "biophysics", "computational biology/molecular dynamics" ]	Lysine120 Interactions with p53 Response Elements can Allosterically Direct p53 Organization	journal.pcbi.1000878	null	[ [ "p53-response elements ( p53-REs ) are two 10-bp palindromic DNA segments with the consensus sequence of 5′-Pu1Pu2Pu3C4 ( A/T ) 5 ( A/T ) 5′G4′Py3′Py2′Py1′-3′ for each of the two half sites , where Pu and Py stand for purine and pyrimidine bases , respectively [1] , [2] .", "The two half sites can be sepa...	[ "p53 can serve as a paradigm in studies aiming to figure out how allosteric perturbations in transcription factors ( TFs ) triggered by small changes in DNA response element ( RE ) sequences , can spell selectivity in co-factor recruitment .", "p53-REs are 20-base pair ( bp ) DNA segments specifying diverse funct...	[ "p53-response elements ( p53-REs ) are 20 base pairs ( bps ) DNA segments recognized by the p53 transcription factor ( TF ) .", "They are found in promoters and enhancers across the genome and are associated with genes that have diverse functions .", "Because the DNA sequences of p53-REs can be very similar to ...	2010
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "microtubules", "vertebrates", "neuroscience", "animals", "animal models", "developmental biology", "drosophila melanogaster", "raptors", "model organisms", "experimental organism systems", "nerve fibers", "embryos", "cellular structures and organelles", "drosophila", ...	Brain Tumor promotes axon growth across the midline through interactions with the microtubule stabilizing protein Apc2	journal.pgen.1007314	null	[ [ "Organisms with bilateral symmetry coordinate the left and right sides of their body by establishing reciprocal connections in the central nervous system .", "During development , commissural axons navigate across the midline to form contralateral connections by responding to attractant and repellant cues...	[ "Commissural axons must cross the midline to establish reciprocal connections between the two sides of the body .", "This process is highly conserved between invertebrates and vertebrates and depends on guidance cues and their receptors to instruct axon trajectories .", "The DCC family receptor Frazzled ( Fra )...	[ "The establishment of neuronal connections that cross the midline of the animal is essential to generate neural circuits that coordinate the left and right sides of the body .", "Axons that cross the midline to form these connections are called commissural axons and the molecules and mechanisms that control midli...	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "public health and epidemiology", "epidemiology", "biology", "microbiology", "public health" ]	Hantavirus Pulmonary Syndrome in Santa Cruz, Bolivia: Outbreak Investigation and Antibody Prevalence Study	journal.pntd.0001840	null	[ [ "Hantaviruses ( family Bunyaviridae , genus Hantavirus ) are enveloped , tripartite , single-stranded , negative-sense RNA viruses .", "On the American continents , these viruses can evoke a severe , acute disease in humans known as hantavirus pulmonary syndrome ( HPS ) [1] .", "Hantavirus pulmonary s...	[ "We report the results of an investigation of a small outbreak of hantavirus pulmonary syndrome in 2002 in the Department of Santa Cruz , Bolivia , where the disease had not previously been reported .", "Two cases were initially reported .", "The first case was a physician infected with Laguna Negra virus durin...	[ "Hantaviruses can evoke a severe , acute disease in humans known as hantavirus pulmonary syndrome with case fatalities up to 70% .", "Pathogenic hantaviruses are carried by rodents , with each virus species usually carried by a specific species of rodent .", "Hantavirus-host reservoir pairs continue to be disco...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "gastroenterology and hepatology", "biology", "microbiology" ]	Multiple Peptidoglycan Modification Networks Modulate Helicobacter pylori's Cell Shape, Motility, and Colonization Potential	journal.ppat.1002603	null	[ [ "Helicobacter pylori is a helical rod shaped Gram ( - ) Proteobacterium with only one known niche , the viscous epithelial mucus layer of the human stomach [1] .", "Infection with H . pylori generally occurs during infancy or childhood , persists through adulthood unless treated , and leads to serious cli...	[ "Helical cell shape of the gastric pathogen Helicobacter pylori has been suggested to promote virulence through viscosity-dependent enhancement of swimming velocity .", "However , H . pylori csd1 mutants , which are curved but lack helical twist , show normal velocity in viscous polymer solutions and the reason f...	[ "The only habitat of Helicobacter pylori is the human stomach , where it can promote stomach ulcers and cancer .", "Cells lining the stomach are protected from luminal acid by a thick layer of gastric mucus composed of polymerized gastric mucins .", "Gastric mucin undergoes a physical transition between a visco...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/tropical and travel-associated diseases", "biophysics/protein folding", "infectious diseases/neglected tropical diseases", "immunology/immune response", "biochemistry/biomacromolecule-ligand interactions", "microbiology/parasitology", "biotechnology/protein chemistry and proteomics"...	High Throughput Functional Assays of the Variant Antigen PfEMP1 Reveal a Single Domain in the 3D7 Plasmodium falciparum Genome that Binds ICAM1 with High Affinity and Is Targeted by Naturally Acquired Neutralizing Antibodies	journal.ppat.1000386	null	[ [ "The variant surface antigen Plasmodium falciparum erythrocyte membrane protein 1 ( PfEMP1 ) is a virulence factor of the human malaria parasite P . falciparum .", "PfEMP1 variants are encoded by about 60 var genes per parasite , and have been implicated in the cytoadhesion of P . falciparum-infected eryt...	[ "Plasmodium falciparum–infected erythrocytes bind endothelial receptors to sequester in vascular beds , and binding to ICAM1 has been implicated in cerebral malaria .", "Binding to ICAM1 may be mediated by the variant surface antigen family PfEMP1: for example , 6 of 21 DBLβC2 domains from the IT4 strain PfEMP1 r...	[ "Plasmodium falciparum exports the protein PfEMP1 to the surface of parasitized erythrocytes for roles in immunoevasion and adhesion .", "The size and structural complexity of this diverse protein family have limited earlier studies of PfEMP1 biology to low throughput and semi-quantitative approaches .", "We de...	2009
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "infographics", "physical mapping", "statistics", "social sciences", "neuroscience", "charts", "perception", "cognitive psychology", "mathematics", "materials science", "vision", "molecular biology techniques", "research and analysis methods", "computer and information sciences", "gene m...	The relative contribution of color and material in object selection	journal.pcbi.1006950	null	[ [ "In daily life , we rely on vision to select objects for a variety of goal-directed actions .", "For example , when we crave tomatoes , we use color to decide which tomato on the vine is the ripest ( Fig 1A ) ; when we sip coffee , we use glossiness to judge whether a cup is made of porcelain or paper , w...	[ "Object perception is inherently multidimensional: information about color , material , texture and shape all guide how we interact with objects .", "We developed a paradigm that quantifies how two object properties ( color and material ) combine in object selection .", "On each experimental trial , observers v...	[ "Much is known about how the visual system extracts information about individual object properties , such as color or material .", "Considerably less is known about how percepts of these properties interact to form a multidimensional object representation .", "We report the first quantitative analysis of how pe...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell death", "medicine and health sciences", "breast tumors", "cancer treatment", "cell processes", "cancers and neoplasms", "biomarkers", "oncology", "protein expression", "cell growth", "molecular biology techniques", "mapk signaling cascades", "research and analysis methods", "oncogeni...	HER2+ Cancer Cell Dependence on PI3K vs. MAPK Signaling Axes Is Determined by Expression of EGFR, ERBB3 and CDKN1B	journal.pcbi.1004827	null	[ [ "The elevated rate of proliferation and apoptotic-resistance characteristic of cancer cells depends on the activation of oncogenic signaling pathways .", "Such oncogenic pathway dependence creates molecular vulnerabilities , which can be exploited by targeted therapies .", "The effectiveness of such d...	[ "Understanding the molecular pathways by which oncogenes drive cancerous cell growth , and how dependence on such pathways varies between tumors could be highly valuable for the design of anti-cancer treatment strategies .", "In this work we study how dependence upon the canonical PI3K and MAPK cascades varies ac...	[ "Biomarkers capable of accurately predicting patient responses to alternate therapies are critical to realizing the vision of precision medicine .", "Identifying such biomarkers is , however , challenging due to the inherent complexity of biological networks .", "Here we sought to identify molecular features th...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "biotechnology", "plant anatomy", "dna-binding proteins", "plant science", "rice", "genetically modified plants", "experimental organism systems", "sequence motif analysis", "molecular biology techniques", "plants", "flowering plants", "genetic engineering", "research and analysis methods", ...	Suppressor of rid1 (SID1) shares common targets with RID1 on florigen genes to initiate floral transition in rice	journal.pgen.1006642	null	[ [ "The post-embryonic development of flowering plants can be divided into two major phases: the vegetative and reproductive growth stages .", "During vegetative development , shoot apical meristems continue to produce leaves for the generation of organic materials through photosynthesis .", "After a giv...	[ "The transition from vegetative to reproductive growth is a critical process in the life cycle of higher plants .", "Previously , we cloned Rice Indeterminate 1 ( RID1 ) , which acts as the master switch for the transition from the vegetative to reproductive phase in rice .", "Although the photoperiod pathway o...	[ "Transition from vegetative to reproductive phase is a critical developmental switch in the life cycle of higher plants .", "In rice , our previous work suggested Rice Indeterminate 1 ( RID1 ) acts as the master switch for the transition to flowering .", "Mutation in RID1 results in a never-flowering phenotype ...	2017
[ "Introduction", "Material and Methods", "Results and Discussion" ]	[]	Trypanothione Reductase: A Target Protein for a Combined In Vitro and In Silico Screening Approach	journal.pntd.0003773	null	[ [ "Trypanosomatidae are responsible for approximately half a million of human fatalities per annum in subtropical and tropical regions around the world [1] .", "Trypanosoma brucei rhodesiense and T . b .", "gambiense are the causative agents of African sleeping sickness [2] .", "T . cruzi is respons...	[ "With the goal to identify novel trypanothione reductase ( TR ) inhibitors , we performed a combination of in vitro and in silico screening approaches .", "Starting from a highly diverse compound set of 2 , 816 compounds , 21 novel TR inhibiting compounds could be identified in the initial in vitro screening camp...	[ "Trypanosomatidae are responsible for approximately half a million human fatalities per annum and the situation is compounded by substantial economic losses due to affecting live stock as well .", "Trypanothione reductase ( TR ) is an essential key enzyme of the unique trypanothione-based thiol metabolism of the ...	2015

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