Split (3)

train · 24.8k rows

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" ]	[ "cell death", "lysosomes", "medicine and health sciences", "autophagic cell death", "rna interference", "oxidative stress", "gene regulation", "regulatory proteins", "cell processes", "dna-binding proteins", "transcription factors", "epigenetics", "cellular structures and organelles", "dig...	Graded Proteasome Dysfunction in Caenorhabditis elegans Activates an Adaptive Response Involving the Conserved SKN-1 and ELT-2 Transcription Factors and the Autophagy-Lysosome Pathway	journal.pgen.1005823	null	[ [ "The content and quality of the cellular proteome reflects a balance between the synthesis , folding and refolding , and degradation of individual proteins [1] .", "Within this framework , the ubiquitin-proteasome system ( UPS ) plays a key role in maintaining the abundance of cellular proteins via the co...	[ "The maintenance of cellular proteins in a biologically active and structurally stable state is a vital endeavor involving multiple cellular pathways .", "One such pathway is the ubiquitin-proteasome system that represents a major route for protein degradation , and reductions in this pathway usually have adverse...	[ "Proteins are complex molecules assembled from individual amino acids that are linked head to tail in a linear chain .", "Once assembled , the proteins play vital roles in the structure and function of every cell in the body .", "However , for these proteins to work properly , they must be assembled correctly a...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases/tropical and travel-associated diseases", "hematology/coagulation disorders" ]	Severe Plasmodium falciparum Malaria Is Associated with Circulating Ultra-Large von Willebrand Multimers and ADAMTS13 Inhibition	journal.ppat.1000349	null	[ [ "In spite of the significant mortality associated with P . falciparum infection , the molecular mechanisms involved in its pathophysiology remain poorly understood .", "However , sequestration of P . falciparum-infected erythrocytes ( IE ) in the microvasculature of vital organs including the brain and pl...	[ "Plasmodium falciparum infection results in adhesion of infected erythrocytes to blood vessel endothelium , and acute endothelial cell activation , together with sequestration of platelets and leucocytes .", "We have previously shown that patients with severe infection or fulminant cerebral malaria have significa...	[ "Malaria is caused by infection of red blood cells ( erythrocytes ) with protozoan parasites of the genus Plasmodium .", "Infected erythrocytes adhere to and disrupt the inner lining , or endothelium , of small blood vessels , especially those of the brain , resulting in blockage and subsequent cerebral malaria ....	2009
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "invertebrates", "body weight", "ecology and environmental sciences", "medicine and health sciences", "ecological niches", "pathology and laboratory medicine", "geographical locations", "tropical diseases", "vertebrates", "parasitic diseases", "parasitic protozoans", "animals", "mammals", ...	Coarse-resolution Ecology of Etiological Agent, Vector, and Reservoirs of Zoonotic Cutaneous Leishmaniasis in Libya	journal.pntd.0004381	null	[ [ "Leishmaniasis remains one of the major public health problems in the Mediterranean Basin .", "In Libya , two forms of leishmaniasis occur: visceral leishmaniasis ( VL ) , and cutaneous leishmaniasis ( CL ) .", "VL has been reported in the country since 1904; however , little information is available ...	[ "Cutaneous leishmaniasis ranks among the tropical diseases least known and most neglected in Libya .", "World Health Organization reports recognized associations of Phlebotomus papatasi , Psammomys obesus , and Meriones spp .", ", with transmission of zoonotic cutaneous leishmaniasis ( ZCL; caused by Leishmania...	[ "Zoonotic cutaneous leishmaniasis ( ZCL ) represents a major public health problem in North Africa where Leishmania major is the potential etiological agent associated with all ZCL cases .", "In many countries across North Africa , L . major is transmitted by the sand fly Phlebotomus papatasi , with rodents as li...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "protein transport", "medicine and health sciences", "immune physiology", "pathology and laboratory medicine", "intracellular pathogens", "hepacivirus", "pathogens", "immunology", "cell processes", "microbiology", "viral structure", "viruses", "physiological processes", "rna viruses", "a...	The amino-terminus of the hepatitis C virus (HCV) p7 viroporin and its cleavage from glycoprotein E2-p7 precursor determine specific infectivity and secretion levels of HCV particle types	journal.ppat.1006774	null	[ [ "Hepatitis C virus ( HCV ) infection is a major cause of chronic liver diseases worldwide .", "With 180 million people persistently infected , chronic HCV infection induces liver diseases such as liver cirrhosis and hepatocellular carcinoma .", "Although new direct antiviral agents are now able to era...	[ "Viroporins are small transmembrane proteins with ion channel activities modulating properties of intracellular membranes that have diverse proviral functions .", "Hepatitis C virus ( HCV ) encodes a viroporin , p7 , acting during assembly , envelopment and secretion of viral particles ( VP ) .", "HCV p7 is rel...	[ "Viroporins are small transmembrane viral proteins with ion channel activities modulating properties of intracellular membranes , which impacts several fundamental biological processes such as trafficking , ion fluxes as well as connections and exchanges between organelles .", "Hepatitis C virus ( HCV ) encodes a...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Complete Firing-Rate Response of Neurons with Complex Intrinsic Dynamics	journal.pcbi.1004636	null	[ [ "Integration and resonance are two operational modes of the spiking dynamics of single neurons .", "These two modes can be distinguished from each other by observing the neuron’s signal transfer properties: how features in its input current transfer to features in its output spiking .", "The tradition...	[ "The response of a neuronal population over a space of inputs depends on the intrinsic properties of its constituent neurons .", "Two main modes of single neuron dynamics–integration and resonance–have been distinguished .", "While resonator cell types exist in a variety of brain areas , few models incorporate ...	[ "Dynamic gain , the amount by which features at specific frequencies in the input to a neuron are amplified or attenuated in its output spiking , is fundamental for the encoding of information by neural populations .", "Most studies of dynamic gain have focused on neurons without intrinsic degrees of freedom exhi...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "rna interference", "parasitic cell cycles", "cell cycle and cell division", "cell processes", "parasitic protozoans", "parasitology", "developmental biology", "protozoans", "dna replication", "cytokinesis", "dna", "epigenetics", "cellular structures and organelles", "research and analysis...	A leucine aminopeptidase is involved in kinetoplast DNA segregation in Trypanosoma brucei	journal.ppat.1006310	null	[ [ "Kinetoplast ( k ) DNA is one of the hallmarks of the family Kinetoplastea , and is a unique form of mitochondrial ( mt ) DNA .", "Kinetoplastids are a species-rich group , which includes numerous obligatory parasitic trypanosomatids , such as Trypanosoma brucei , T . cruzi and Leishmania spp .", ", c...	[ "The kinetoplast ( k ) , the uniquely packaged mitochondrial DNA of trypanosomatid protists is formed by a catenated network of minicircles and maxicircles that divide and segregate once each cell cycle .", "Although many proteins involved in kDNA replication and segregation are now known , several key steps in t...	[ "Trypanosomes bear a single mitochondrion with its genome ( kinetoplast , or kDNA ) arranged as a network of circular molecules .", "kDNA is essential for the Trypanosoma brucei life cycle , as it is required for proper functioning of the mitochondrion and progression through the insect vector .", "Division of ...	2017
[ "Introduction", "Results", "Materials and Methods", "Discussion" ]	[ "computer and information sciences", "computer vision", "computational neuroscience", "biology and life sciences", "computational biology", "neuroscience" ]	Deep Supervised, but Not Unsupervised, Models May Explain IT Cortical Representation	journal.pcbi.1003915	null	[ [ "Visual object recognition is thought to rely on a high-level representation in the inferior temporal ( IT ) cortex , which has been intensively studied in humans and monkeys [1]–[12] .", "Object images that are less distinct in the IT representation are perceived as more similar by humans [10] and are mo...	[ "Inferior temporal ( IT ) cortex in human and nonhuman primates serves visual object recognition .", "Computational object-vision models , although continually improving , do not yet reach human performance .", "It is unclear to what extent the internal representations of computational models can explain the IT...	[ "Computers cannot yet recognize objects as well as humans can .", "Computer vision might learn from biological vision .", "However , neuroscience has yet to explain how brains recognize objects and must draw from computer vision for initial computational models .", "To make progress with this chicken-and-egg ...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Recurrent Modification of a Conserved Cis-Regulatory Element Underlies Fruit Fly Pigmentation Diversity	journal.pgen.1003740	null	[ [ "Recurrence is a widespread phenomenon in evolutionary biology [1] , where similar derived traits have often been found to evolve in parallel .", "This theme of recurrence extends to the molecular level , as the same genes are often targeted by evolutionary change to generate convergent phenotypes [2] .",...	[ "The development of morphological traits occurs through the collective action of networks of genes connected at the level of gene expression .", "As any node in a network may be a target of evolutionary change , the recurrent targeting of the same node would indicate that the path of evolution is biased for the r...	[ "Trait development occurs through networks of genes that are connected by interactions between transcription factor proteins and binding site sequences within cis-regulatory element ( CRE ) DNA sequences .", "These interactions enable CREs to function as switches that control the expression of a gene ( s ) they r...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "biofilms", "blood cells", "bacteriology", "medicine and health sciences", "immune cells", "body fluids", "pathology and laboratory medicine", "pneumococcus", "cardiovascular anatomy", "pathogens", "immunology", "microbiology", "organisms", "bacteria", "neutrophils", "bacterial pathoge...	Streptococcus pneumoniae in the heart subvert the host response through biofilm-mediated resident macrophage killing	journal.ppat.1006582	null	[ [ "Hospitalization for community-acquired pneumonia ( CAP ) is an established risk factor for adverse cardiac events that includes heart failure , arrhythmia , and infarction; with as many as one-in-four adults hospitalized for CAP experiencing some form of pneumonia-associated adverse cardiac event ( PACE ) [1...	[ "For over 130 years , invasive pneumococcal disease has been associated with the presence of extracellular planktonic pneumococci , i . e . diplococci or short chains in affected tissues .", "Herein , we show that Streptococcus pneumoniae that invade the myocardium instead replicate within cellular vesicles and t...	[ "Since its discovery in 1881 , invasive disease caused by Streptococcus pneumoniae , the leading cause of community-acquired pneumonia and a prototypical extracellular pathogen , has been tied exclusively to the planktonic phenotype , i . e . individual diplococci or short chains .", "Herein , we report that hear...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "legs", "diagnostic radiology", "lymphoscintigraphy", "pathology and laboratory medicine", "geographical locations", "limbs (anatomy)", "india", "animals", "health care", "pediatrics", "brugia", "signs and symptoms", "pediatric infections"...	Lymphatic pathology in asymptomatic and symptomatic children with Wuchereria bancrofti infection in children from Odisha, India and its reversal with DEC and albendazole treatment	journal.pntd.0005631	null	[ [ "Treatment with albendazole and either ivermectin or diethylcarbamazine citrate ( DEC ) used in the Global Program for Elimination of Lymphatic Filariasis ( GPELF ) works on the basis of elimination of microfilaria that are infective to the mosquito vector .", "Transmission within communities is thereby r...	[ "Once interruption of transmission of lymphatic filariasis is achieved , morbidity prevention and management becomes more important .", "A study in Brugia malayi filariasis from India has shown sub-clinical lymphatic pathology with potential reversibility .", "We studied a Wuchereria bancrofti infected populati...	[ "Infection with lymphatic filarial parasites usually occurs early in childhood in endemic areas , but clinical signs appear much later .", "Reversal of lymphatic pathology has been shown with the much less common Brugia malayi infection using DEC and albendazole and there is scarce evidence whether the same occur...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "systems biology", "theoretical biology", "genetics", "biology", "genomics", "evolutionary biology", "microbiology", "population biology", "genetics and genomics" ]	Bet Hedging in Yeast by Heterogeneous, Age-Correlated Expression of a Stress Protectant	journal.pbio.1001325	A new experimental approach reveals a bet-hedging strategy in unstressed, clonal yeast cells, whereby they adopt a range of growth states that correlate with expression of a trehalose-synthesis regulator and predict resistance to future stress.	[ [ "Clonal populations of cells grown in a constant environment display a striking amount of cell-to-cell heterogeneity .", "For example , in bacteria , yeast , and mammalian cell lines , levels of some gene products vary widely between cells [1]–[5] .", "A crucial challenge is to understand how much of ...	[ "Genetically identical cells grown in the same culture display striking cell-to-cell heterogeneity in gene expression and other traits .", "A crucial challenge is to understand how much of this heterogeneity reflects the noise tolerance of a robust system and how much serves a biological function .", "In bacter...	[ "Genetically identical cells grown in the same environment can display heterogeneity in their morphology , behavior , and composition of their cellular components .", "In some microorganisms , such cellular heterogeneity can underlie a phenomenon known as bet hedging because it enables some cells to survive in ha...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "psychology", "social and behavioral sciences", "animal behavior", "ecology", "evolutionary biology", "behavior", "biology", "zoology", "neuroscience", "behavioral ecology" ]	Radar Tracking and Motion-Sensitive Cameras on Flowers Reveal the Development of Pollinator Multi-Destination Routes over Large Spatial Scales	journal.pbio.1001392	Automated tracking of bumblebees and computer simulations reveal how bees locate a series of flowers and optimize their routes to visit them all.	[ [ "Animals moving in familiar environments often follow habitual routes to navigate between important locations , such as the nest and feeding sites .", "Most knowledge on route following behaviours has been deduced from the stereotyped paths insects [1]–[4] and birds [5] develop when travelling between hom...	[ "Central place foragers , such as pollinating bees , typically develop circuits ( traplines ) to visit multiple foraging sites in a manner that minimizes overall travel distance .", "Despite being taxonomically widespread , these routing behaviours remain poorly understood due to the difficulty of tracking the fo...	[ "Many food resources , such as flowers refilling with nectar or fruits ripening on a tree , replenish over time , so animals that depend on them need to develop strategies to reduce the energy they use during foraging .", "Here we placed five artificial flowers in a field and set out to examine how bumblebees opt...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/chromosome biology" ]	Cohesin Is Limiting for the Suppression of DNA Damage–Induced Recombination between Homologous Chromosomes	journal.pgen.1001006	null	[ [ "Genome stability is maintained by a network of proteins that ensure faithful DNA replication and efficient response to DNA damage .", "Variation in levels of proteins across the cell cycle , between tissues and even through natural fluctuations are common [1] , [2] , [3] and could influence genome stabil...	[ "Double-strand break ( DSB ) repair through homologous recombination ( HR ) is an evolutionarily conserved process that is generally error-free .", "The risk to genome stability posed by nonallelic recombination or loss-of-heterozygosity could be reduced by confining HR to sister chromatids , thereby preventing r...	[ "The cellular concentrations of individual proteins are expected to be kept within an optimal range , but protein expression is often stochastic .", "Some proteins are known to be in limiting amounts , so that even modest reduction can lead to malfunction .", "Within the network of genes that determine genome s...	2010
[ "Introduction", "Results/Discussion", "Methods" ]	[ "immunology/cellular microbiology and pathogenesis", "nutrition", "microbiology/innate immunity" ]	The Role of Anorexia in Resistance and Tolerance to Infections in Drosophila	journal.pbio.1000150	Infections initiate a signaling loop in which sick animals become anorexic, and the resulting change in diet alters the body's ability to fight infections in good and bad ways.	[ [ "Infectious diseases are predicted to drive the natural selection of behaviors that increase fitness .", "Loss of appetite ( anorexia ) is a common behavior that sick animals exhibit when faced with an immune challenge [1]–[5] .", "Traditionally , anorexia was thought of as an adverse secondary respon...	[ "Most infections induce anorexia but its function , if any , remains unclear .", "Because this response is common among animals , we hypothesized that infection-induced diet restriction might be an adaptive trait that modulates the host's ability to fight infection .", "Two defense strategies protect hosts agai...	[ "Two routes to decreasing susceptibility to infection are resistance ( the ability to clear pathogens ) and tolerance ( the ability to limit damage in response to pathogens ) .", "Anorexia induced by sickness puts animals into a diet-restricted state , a state that is generally believed to extend lifespan .", "...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology/persistence and latency", "evolutionary biology/microbial evolution and genomics", "virology/virus evolution and symbiosis", "dermatology/skin cancers, including melanoma and lymphoma", "virology", "virology/emerging viral diseases", "dermatology/skin infections", "virology/viruses and cance...	Discovery of a New Human Polyomavirus Associated with Trichodysplasia Spinulosa in an Immunocompromized Patient	journal.ppat.1001024	null	[ [ "Members of the polyomavirus family ( Polyomaviridae ) infect mammals ( rodents , bovines , primates ) and birds ( fowl , psittacines ) , and can affect various organs .", "So far five human polyomaviruses have been described .", "Two of these , JC-polyomavirus ( JCPyV or JCV ) and BK-polyomavirus ( B...	[ "The Polyomaviridae constitute a family of small DNA viruses infecting a variety of hosts .", "In humans , polyomaviruses can cause infections of the central nervous system , urinary tract , skin , and possibly the respiratory tract .", "Here we report the identification of a new human polyomavirus in plucked f...	[ "Diseases that occur exclusively in immunocompromized patients are often of an infectious nature .", "Trichodysplasia spinulosa ( TS ) is such a disease characterized by development of papules , spines and alopecia in the face .", "Fortunately this disease is rare , because facial features can change dramatical...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biotechnology", "bioengineering", "gene expression", "synthetic biology", "biology", "molecular cell biology", "molecular biology", "engineering" ]	Broad-Specificity mRNA–rRNA Complementarity in Efficient Protein Translation	journal.pgen.1002598	null	[ [ "The ribosome is widely recognized as a broad-specificity ribozyme that is able to translate mRNA at different rates to maintain appropriate relative protein levels and thereby fulfill the dynamic needs of the cell [1]–[3] .", "Problems with increased or decreased translation of certain messages are known...	[ "Studies of synthetic , well-defined biomolecular systems can elucidate inherent capabilities that may be difficult to uncover in a native biological context .", "Here , we used a minimal , reconstituted translation system from Escherichia coli to identify efficient ribosome binding sites ( RBSs ) in an unbiased ...	[ "In order to maintain an appropriate balance of proteins in the cell , the protein factories ( ribosomes ) translate different messages ( mRNAs ) into protein at different rates .", "Many human diseases , including cancer and certain hereditary diseases , are caused by making too much or too little protein .", ...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "animal models", "drosophila melanogaster", "animal genetics", "model organisms", "behavioral neuroscience", "genetic screens", "genetics", "neurotransmitters", "biology", "neuroscience", "genetics and genomics" ]	Cul3 and the BTB Adaptor Insomniac Are Key Regulators of Sleep Homeostasis and a Dopamine Arousal Pathway in Drosophila	journal.pgen.1003003	null	[ [ "Sleep is a homeostatically regulated process , consuming roughly one-third of our lives , yet its function remains a mystery .", "To identify novel pathways governing sleep , we and others have employed a genetic approach in Drosophila .", "The fruit fly shares several core features of sleep with its...	[ "Sleep is homeostatically regulated , such that sleep drive reflects the duration of prior wakefulness .", "However , despite the discovery of genes important for sleep , a coherent molecular model for sleep homeostasis has yet to emerge .", "To better understand the function and regulation of sleep , we employ...	[ "Sleep is an essential behavior that encompasses roughly a third of our lives; however , the underlying function remains a mystery .", "The fruit fly has emerged as an important model system for understanding sleep behavior , exhibiting several behavioral and genetic similarities with mammalian sleep , including ...	2012
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "rna interference", "cloning", "neuroscience", "animals", "neurites", "animal models", "drosophila melanogaster", "model organisms", "experimental organism systems", "molecular biology techniques", "epigenetics", "neuroblasts", "neuronal dendrites", "drosophila", "rese...	Semaphorin-1a prevents Drosophila olfactory projection neuron dendrites from mis-targeting into select antennal lobe regions	journal.pgen.1006751	null	[ [ "In the olfactory system , odorant inputs are detected by olfactory sensory neurons ( OSNs ) in the periphery and converged into individual glomeruli of the primary olfactory center , termed the antennal lobe ( AL ) in Drosophila and the olfactory bulb in mice , where projection neurons ( PNs in Drosophila an...	[ "Elucidating how appropriate neurite patterns are generated in neurons of the olfactory system is crucial for comprehending the construction of the olfactory map .", "In the Drosophila olfactory system , projection neurons ( PNs ) , primarily derived from four neural stem cells ( called neuroblasts ) , populate t...	[ "In the Drosophila olfactory system , olfactory projection neurons ( PNs ) are derived from four neural stem cells ( called neuroblasts ) during the development .", "Intriguingly , these PNs generate complex dendritic patterns within the primary olfactory center of the brain , the antennal lobe ( AL ) , to relay ...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "plant immune system", "plant biology", "type iii effector", "arabidopsis", "microbiology" ]	Type III Effector Activation via Nucleotide Binding, Phosphorylation, and Host Target Interaction	journal.ppat.0030048	null	[ [ "Many Gram-negative bacterial pathogens of plants or animals employ type III secretion systems ( TTSSs ) to translocate type III effector proteins into host cells [1] .", "Type III effector proteins manipulate host cellular targets and signaling pathways to promote the infection process in genetically sus...	[ "The Pseudomonas syringae type III effector protein avirulence protein B ( AvrB ) is delivered into plant cells , where it targets the Arabidopsis RIN4 protein ( resistance to Pseudomonas maculicula protein 1 [RPM1]–interacting protein ) .", "RIN4 is a regulator of basal host defense responses .", "Targeting of...	[ "Many bacterial pathogens use a specialized protein “injection needle” called a type III secretion system to help colonize cells of higher organisms .", "The type III secretion needle attaches to a host cell and is the delivery conduit for a variety of bacterial proteins that act inside of the host cell .", "Th...	2007
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "biotechnology", "bioengineering", "systems biology", "biological systems engineering", "control engineering", "engineering and technology", "synthetic biology", "biology and life sciences", "computational biology" ]	In-Vivo Real-Time Control of Protein Expression from Endogenous and Synthetic Gene Networks	journal.pcbi.1003625	null	[ [ "A crucial feature of biological systems is their ability to maintain homeostasis in spite of ever-changing environmental and intracellular conditions .", "In man-made systems , this ability can be engineered in devices ranging from the simple thermostat to the complex autopilot of a modern plane using “c...	[ "We describe an innovative experimental and computational approach to control the expression of a protein in a population of yeast cells .", "We designed a simple control algorithm to automatically regulate the administration of inducer molecules to the cells by comparing the actual protein expression level in th...	[ "A crucial feature of biological systems is their ability to maintain homeostasis in spite of ever-changing conditions .", "In engineering , this ability can be embedded in devices ranging from the thermostat to the autopilot of a modern plane using control systems which operate via a negative feedback mechanism:...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "mosquitoes", "neglected tropical diseases", "vectors and hosts", "lymphatic filariasis" ]	No Evidence for Lymphatic Filariasis Transmission in Big Cities Affected by Conflict Related Rural-Urban Migration in Sierra Leone and Liberia	journal.pntd.0002700	null	[ [ "Lymphatic filariasis ( LF ) is a major cause of acute and chronic morbidity in humans in 73 countries in Asia , Africa , the Western Pacific and the Americas .", "Nearly 1 . 4 billion people are exposed to infection from three mosquito-borne filarial parasites ( Wuchereria bancrofti , Brugia malayi and B...	[ "In West Africa , the principal vectors of lymphatic filariasis ( LF ) are Anopheles species with Culex species playing only a minor role in transmission , if any .", "Being a predominantly rural disease , the question remains whether conflict-related migration of rural populations into urban areas would be suffi...	[ "There have been many arguments regarding the implementation of Mass Drug Administration ( MDA ) activities for elephantiasis control in urban areas , and especially in countries where the disease is mostly found in rural settings .", "Blanket MDA in implementation units in big cities , may be costly and unnecess...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "insertion mutation", "invertebrate genomics", "animals", "animal models", "mutation", "substitution mutation", "drosophila melanogaster", "model organisms", "dna recombination", "dna", "gene conversion", "drosophila", "research and analysis methods", "chromosome biology...	Low Genetic Quality Alters Key Dimensions of the Mutational Spectrum	journal.pbio.1002419	The genome sequences of Drosophila mutation accumulation lines suggest that low-quality genotypes repair genetic damage using more error-prone mechanisms; mutation rates vary with both individual condition and local sequence context.	[ [ "In the genomes of all organisms , there is an inescapable risk of spontaneous mutations , which are seldom beneficial .", "This risk is reduced by cellular mechanisms that correct replication errors and repair DNA damage .", "If the degree of damage or the efficacy of repair is influenced by local se...	[ "Mutations affect individual health , population persistence , adaptation , diversification , and genome evolution .", "There is evidence that the mutation rate varies among genotypes , but the causes of this variation are poorly understood .", "Here , we link differences in genetic quality with variation in sp...	[ "The replication and maintenance of genomes is essential to all organisms , and multiple cellular pathways serve to correct replication errors and repair DNA damage .", "The use of these repair pathways can vary among individuals , and we hypothesized that those in poor condition may be less capable of effectivel...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Integrated Modeling of Gene Regulatory and Metabolic Networks in Mycobacterium tuberculosis	journal.pcbi.1004543	null	[ [ "Tuberculosis ( TB ) remains a major global health challenge with a need for enhanced drug development efforts .", "The current standard treatment for drug-susceptible tuberculosis involves treating for 6 months with a cocktail of first-line drugs that have serious side-effects [1] .", "Antibiotic res...	[ "Mycobacterium tuberculosis ( MTB ) is the causative bacterium of tuberculosis , a disease responsible for over a million deaths worldwide annually with a growing number of strains resistant to antibiotics .", "The development of better therapeutics would greatly benefit from improved understanding of the mechani...	[ "Tuberculosis remains a major global health challenge with a need for enhanced drug development efforts .", "Drug development would be aided by understanding more about the bacteria that causes the disease , Mycobacterium tuberculosis ( MTB ) , and how it adapts to survive the broad range of conditions within hos...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology/mechanisms of resistance and susceptibility, including host genetics", "virology/immunodeficiency viruses", "virology/antivirals, including modes of action and resistance" ]	Gag Mutations Strongly Contribute to HIV-1 Resistance to Protease Inhibitors in Highly Drug-Experienced Patients besides Compensating for Fitness Loss	journal.ppat.1000345	null	[ [ "The Human Immunodeficiency virus type 1 ( HIV-1 ) protease ( PR ) is a key enzyme in viral replication and a major target for therapeutic intervention .", "Protease inhibitors ( PI ) are the backbone of some of the most active combinations of antiretroviral drugs used in the treatment of HIV-infected pat...	[ "Human immunodeficiency virus type 1 ( HIV-1 ) resistance to protease inhibitors ( PI ) results from mutations in the viral protease ( PR ) that reduce PI binding but also decrease viral replicative capacity ( RC ) .", "Additional mutations compensating for the RC loss subsequently accumulate within PR and in Gag...	[ "Protease inhibitors are among the most active antiviral drugs used in the treatment of Human immunodeficiency virus type 1 ( HIV-1 ) infection .", "The efficacy of these compounds , however , can be threatened by the emergence of viral resistance , the result of the gradual accumulation of specific mutations in ...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "chemical characterization", "cardiovascular physiology", "microbiology", "glycocalyx", "chemical biology", "opportunistic infections", "biochemical analysis", "bacterial diseases", "histochemistry and cytochemistry techniques", "bioassays and physiological analys...	Oral Streptococci Utilize a Siglec-Like Domain of Serine-Rich Repeat Adhesins to Preferentially Target Platelet Sialoglycans in Human Blood	journal.ppat.1004540	null	[ [ "Infective endocarditis ( IE ) remains a disease with considerable morbidity and mortality [1] , [2] .", "Of the numerous bacteria that have the opportunity to enter the bloodstream , three major genera of Gram-positive pathogens ( streptococci , staphylococci and enterococci ) dominate in IE .", "Str...	[ "Damaged cardiac valves attract blood-borne bacteria , and infective endocarditis is often caused by viridans group streptococci .", "While such bacteria use multiple adhesins to maintain their normal oral commensal state , recognition of platelet sialoglycans provides an intermediary for binding to damaged valvu...	[ "Bacterial infective endocarditis remains a disease with considerable morbidity and mortality .", "Of the numerous bacteria that can enter the bloodstream , certain oral commensal viridans group streptococci are among the major causative organisms of endocarditis .", "However , mechanisms underlying this select...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "immune cells", "immunity", "innate immunity", "immune defense", "immunology", "immune suppression", "biology", "immunity to infections", "microbiology", "immune tolerance", "immune response" ]	Persistently Active Microbial Molecules Prolong Innate Immune Tolerance In Vivo	journal.ppat.1003339	null	[ [ "A great deal is known about how animals kill bacteria but very little about what happens to the corpses .", "Most bacterial structures seem to be broken down by phagocytes [1] , [2] , yet much of the catabolic machinery is made by the bacteria themselves ( phospholipases [3] , peptidoglycan hydrolases [4...	[ "Measures that bolster the resolution phase of infectious diseases may offer new opportunities for improving outcome .", "Here we show that inactivation of microbial lipopolysaccharides ( LPS ) can be required for animals to recover from the innate immune tolerance that follows exposure to Gram-negative bacteria ...	[ "We showed previously that mice lacking acyloxyacyl hydrolase ( AOAH ) , the host enzyme that inactivates Gram-negative bacterial lipopolysaccharides ( LPS ) , are unable to regain normal immune responsiveness for many weeks/months after they are exposed in vivo to a small amount of LPS or Gram-negative bacteria ."...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Identification of a Single Strand Origin of Replication in the Integrative and Conjugative Element ICEBs1 of Bacillus subtilis	journal.pgen.1005556	null	[ [ "Horizontal gene transfer , the ability of cells to acquire DNA from exogenous sources , is a driving force in bacterial evolution , facilitating the movement of genes conferring antibiotic resistance , pathogenicity , and other traits [1] .", "Conjugation , a form of horizontal gene transfer , is the con...	[ "We identified a functional single strand origin of replication ( sso ) in the integrative and conjugative element ICEBs1 of Bacillus subtilis .", "Integrative and conjugative elements ( ICEs , also known as conjugative transposons ) are DNA elements typically found integrated into a bacterial chromosome where th...	[ "Mobile genetic elements facilitate movement of genes , including those conferring antibiotic resistance and other traits , between bacteria .", "Integrative and conjugative elements ( ICEs ) are a large family of mobile genetic elements that are typically found integrated in the chromosome of their host bacteriu...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Computing the Local Field Potential (LFP) from Integrate-and-Fire Network Models	journal.pcbi.1004584	null	[ [ "Models of recurrently connected networks of leaky integrate-and-fire ( LIF ) neurons are well established tools for studying brain function [1 , 2] .", "The equations describing the single LIF neuron are simple and can be easily adapted to generate complex dynamics [3 , 4] .", "Despite their simplici...	[ "Leaky integrate-and-fire ( LIF ) network models are commonly used to study how the spiking dynamics of neural networks changes with stimuli , tasks or dynamic network states .", "However , neurophysiological studies in vivo often rather measure the mass activity of neuronal microcircuits with the local field pot...	[ "Leaky integrate-and-fire ( LIF ) networks are often used to model neural network activity .", "The spike trains they produce , however , cannot be directly compared to the local field potentials ( LFPs ) that are measured by low-pass filtering the potential recorded from extracellular electrodes .", "This is b...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "bacteriology", "medicine and health sciences", "crystal structure", "pathology and laboratory medicine", "pathogens", "immunology", "condensed matter physics", "microbiology", "immune receptor signaling", "bacterial diseases", "mutation", "helicobacter", "membrane receptor signaling", "en...	The role of the C-terminal D0 domain of flagellin in activation of Toll like receptor 5	journal.ppat.1006574	null	[ [ "Toll-like receptors ( TLRs ) belong to a family of germ-line encoded innate immune receptors able to sense pathogen-associated molecular patterns ( PAMPs ) [1] .", "Upon ligand binding , TLRs dimerize , recruiting adaptor molecules that bind to the intracellular TIR domain dimer and induce downstream sig...	[ "Flagellin is a wide-spread bacterial virulence factor sensed by the membrane-bound Toll-like receptor 5 ( TLR5 ) and by the intracellular NAIP5/NLRC4 inflammasome receptor .", "TLR5 recognizes a conserved region within the D1 domain of flagellin , crucial for the interaction between subunits in the flagellum and...	[ "Receptors of the innate immune system typically recognize conserved microbial patterns , crucial for pathogen fitness and survival .", "Flagellin , the main structural protein of bacterial flagella , is recognized by two receptors of the innate immune system , the intracellular inflammasome receptor NAIP5/NLRC4 ...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	HANABA TARANU (HAN) Bridges Meristem and Organ Primordia Boundaries through PINHEAD, JAGGED, BLADE-ON-PETIOLE2 and CYTOKININ OXIDASE 3 during Flower Development in Arabidopsis	journal.pgen.1005479	null	[ [ "Leaves and flowers originate from the shoot apical meristem ( SAM ) , which contains pluripotent stem cells and resides at the tip of each stem .", "Primordia are initiated from the peripheral zone of the SAM in a predictable pattern , and develop into leaves during the vegetative stage , and into flower...	[ "Shoot organ primordia are initiated from the shoot apical meristem and develop into leaves during the vegetative stage , and into flowers during the reproductive phase .", "Between the meristem and the newly formed organ primordia , a boundary with specialized cells is formed that separates meristematic activity...	[ "The shoot apical meristem is the stem cell pool in plants that gives rise to all above-ground organs including leaves , flowers and fruits .", "Between the meristem and the newly formed organ primordia , a boundary with specialized cells is formed to separate them .", "Boundary genes are specifically expressed...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Drosophila Lipophorin Receptors Recruit the Lipoprotein LTP to the Plasma Membrane to Mediate Lipid Uptake	journal.pgen.1005356	null	[ [ "Lipids are continuously trafficked between tissues , from sites of absorption and synthesis to the organs that will utilize them .", "These transport routes must adapt to the changing metabolic status and developmental stage of the animal .", "Thus , during the feeding period of Drosophila larvae , a...	[ "Lipophorin , the main Drosophila lipoprotein , circulates in the hemolymph transporting lipids between organs following routes that must adapt to changing physiological requirements .", "Lipophorin receptors expressed in developmentally dynamic patterns in tissues such as imaginal discs , oenocytes and ovaries c...	[ "In multicellular animals , nutrients and metabolites required for cell growth are distributed throughout the body by the blood circulation or in insects , by hemolymph .", "The uptake of these molecules by cells is tightly controlled to ensure the necessary coordination between cellular requirements and organism...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Neto-Mediated Intracellular Interactions Shape Postsynaptic Composition at the Drosophila Neuromuscular Junction	journal.pgen.1005191	null	[ [ "Ionotropic glutamate receptors ( iGluRs ) play major roles in excitatory transmission in the vertebrate brain and at the insect neuromuscular junction ( NMJ ) .", "The synapse properties are primarily shaped by the subunit composition of the receptors , which could be further modified by RNA editing and ...	[ "The molecular mechanisms controlling the subunit composition of glutamate receptors are crucial for the formation of neural circuits and for the long-term plasticity underlying learning and memory .", "Here we use the Drosophila neuromuscular junction ( NMJ ) to examine how specific receptor subtypes are recruit...	[ "Ionotropic receptors assembled from different subunits have strikingly different properties and uses .", "In mammalian brain , the molecular mechanisms controlling the subunit composition of glutamate receptors are critical for the formation of neural circuits and for the long-term plasticity underlying learning...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "sequence analysis", "genome expression analysis", "genomics", "gene regulation", "genetics", "regulatory networks", "molecular genetics", "biology", "computational biology", "gene expression", "genetics and genomics", "dna transcription" ]	Validation of Skeletal Muscle cis-Regulatory Module Predictions Reveals Nucleotide Composition Bias in Functional Enhancers	journal.pcbi.1002256	null	[ [ "A regulatory network represents the complex interplay between regulatory proteins and biochemical processes that govern when and where genes are expressed .", "Two important components of a regulatory network are cis-regulatory modules ( CRM ) , composed of functionally interacting clusters of transcript...	[ "We performed a genome-wide scan for muscle-specific cis-regulatory modules ( CRMs ) using three computational prediction programs .", "Based on the predictions , 339 candidate CRMs were tested in cell culture with NIH3T3 fibroblasts and C2C12 myoblasts for capacity to direct selective reporter gene expression to...	[ "For efficient identification of genomic sequences responsible for regulating gene expression , a number of computer programs have been developed for automatic annotation of these regulatory regions .", "We searched for potential regulatory regions responsible for controlling the expression of skeletal muscle-spe...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "mutation", "genetic mutation", "mutation types", "natural selection", "gene identification and analysis", "genetics", "molecular genetics", "biology", "gene duplication", "population genetics", "genetics of disease", "genetics and genomics", "mutational hypotheses" ]	Fine Characterisation of a Recombination Hotspot at the DPY19L2 Locus and Resolution of the Paradoxical Excess of Duplications over Deletions in the General Population	journal.pgen.1003363	null	[ [ "Several mechanisms have been proposed to cause genomic rearrangements , notably: Non Allelic Homologous Recombination ( NAHR ) , Non Homologous End Joining ( NHEJ ) , Fork Stalling and Template Switching ( FoSTeS ) and Break-Induced Replication ( BIR ) [1] , [2] .", "NAHR takes place between duplicated s...	[ "We demonstrated previously that 75% of infertile men with round , acrosomeless spermatozoa ( globozoospermia ) had a homozygous 200-Kb deletion removing the totality of DPY19L2 .", "We showed that this deletion occurred by Non-Allelic Homologous Recombination ( NAHR ) between two homologous 28-Kb Low Copy Repeat...	[ "We demonstrated previously that most men with globozoospermia , who produce only round acrosomeless spermatozoa and are 100% infertile , had a homozygous deletion removing the totality of DPY19L2 .", "We also showed that this deletion occurred by Non-Allelic Homologous Recombination ( NAHR ) .", "NAHR results ...	2013
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "cancer genomics", "taxonomy", "medicine and health sciences", "breast tumors", "cancers and neoplasms", "basic cancer research", "oncology", "phylogenetics", "data management", "materials science", "copy number variation", "materials by structure", "genome complexity", "computer and infor...	Automated deconvolution of structured mixtures from heterogeneous tumor genomic data	journal.pcbi.1005815	null	[ [ "Tumor heterogeneity is now recognized as a pervasive feature of cancer biology with implications for every step of cancer development , progression , metastasis , and mortality .", "Most solid tumors exhibit some form of hypermutability phenotype [1] , leading to extensive genomic variability as tumor ce...	[ "With increasing appreciation for the extent and importance of intratumor heterogeneity , much attention in cancer research has focused on profiling heterogeneity on a single patient level .", "Although true single-cell genomic technologies are rapidly improving , they remain too noisy and costly at present for p...	[ "One of the major challenges in making sense of cancer genomics is high heterogeneity cell-to-cell , as a tumor is typically made up of multiple cell populations with distinct genomes and gene expression patterns .", "The difficulty of working with such data has led to interest in computationally inferring the co...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Common Cell Shape Evolution of Two Nasopharyngeal Pathogens	journal.pgen.1005338	null	[ [ "Some pathogenic bacteria like Neisseria meningitidis , Streptococcus pneumoniae , Haemophilus influenzae , and Moraxella catarrhalis are highly adapted to the ecological niche of the human nasopharynx ( NP ) .", "This one defines the upper part of the pharynx from the end of nasal cavities ( choanoe ) to...	[ "Respiratory infectious diseases are the third cause of worldwide death .", "The nasopharynx is the portal of entry and the ecological niche of many microorganisms , of which some are pathogenic to humans , such as Neisseria meningitidis and Moraxella catarrhalis .", "These microbes possess several surface stru...	[ "The nasopharynx hosts an important microbial community that comprises some well-known pathogens such as Neisseria meningitidis and Moraxella catarrhalis .", "In some circumstances , it also represents the portal of entry of systemic infections such as septicemia and meningitis , or infections of the respiratory ...	2015
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "ocean waves", "invertebrates", "medicine and health sciences", "atmospheric science", "population dynamics", "experimental design", "animals", "research design", "developmental biology", "physiological processes", "diapause", "population biology", "infectious disease control", "insect vec...	Potential effects of heat waves on the population dynamics of the dengue mosquito Aedes albopictus	journal.pntd.0007528	null	[ [ "Originated from Southeast Asia , Asian tiger mosquito ( Aedes albopictus ) is the most prevalent vector in all continents except the Antarctica [1 , 2 , 3 , 4 , 5] .", "The pathogens it transmits pose a severe threat to human health by global epidemics , including dengue and Zika arboviruses .", "For...	[ "Extreme weather events affect the development and survival of disease pathogens and vectors .", "Our aim was to investigate the potential effects of heat waves on the population dynamics of Asian tiger mosquito ( Aedes albopictus ) , which is a major vector of dengue and Zika viruses .", "We modeled the popula...	[ "Understanding the population dynamics of Asian Tiger mosquito ( Ae . albopictus ) –the most prevalent vector of global epidemics including West Nile virus , dengue fever , Zika–could shed lights on improving the understanding of vector transmission as well as developing effective disease control strategies .", "...	2019
[ "Introduction", "Models", "Results", "Discussion", "Conclusions" ]	[ "cell binding", "phosphorylation", "cell physiology", "cell cycle and cell division", "cell processes", "cloning", "developmental biology", "cell growth", "molecular development", "molecular biology techniques", "chemical dissociation", "research and analysis methods", "cell proliferation", ...	Expanding signaling-molecule wavefront model of cell polarization in the Drosophila wing primordium	journal.pcbi.1005610	null	[ [ "The growth and patterning of developing tissues are inextricably intertwined; epithelial cells typically become polarized along a body axis as they proliferate .", "This polarization is regarded as being dependent upon spatial variations in the concentration of morphogens .", "However , there are cas...	[ "In developing tissues , cell polarization and proliferation are regulated by morphogens and signaling pathways .", "Cells throughout the Drosophila wing primordium typically show subcellular localization of the unconventional myosin Dachs on the distal side of cells ( nearest the center of the disc ) .", "Dach...	[ "In the tissues of a developing organism , specialized proteins can control cell growth and give cells a sense of direction , e . g . , which way is the head or the tail , by having their concentration vary throughout the tissue .", "In cells of the developing fruit fly wing , a protein called Dachs localizes on ...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "public health and epidemiology/infectious diseases", "virology/animal models of infection", "genetics and genomics/population genetics" ]	Gene Flow, Subspecies Composition, and Dengue Virus-2 Susceptibility among Aedes aegypti Collections in Senegal	journal.pntd.0000408	null	[ [ "Aedes aegypti , the “yellow fever mosquito” , is the primary vector to humans of the four serotypes of dengue viruses ( DENV1-4 ) , yellow fever virus ( YFV ) and is a known vector of Chikungunya virus .", "Dengue is a major public health problem in tropical regions of the world , causing millions of den...	[ "Aedes aegypti , the “yellow fever mosquito” , is the primary vector to humans of the four serotypes of dengue viruses ( DENV1-4 ) and yellow fever virus ( YFV ) and is a known vector of Chikungunya virus .", "There are two recognized subspecies of Ae .", "aegypti sensu latu ( s . l . ) : the presumed ancestral...	[ "We conducted a population genetic study with 1 , 040 Aedes aegypti sensu latu ( s . l . ) collected from 19 sites distributed across the five phytogeographic regions of Senegal .", "Adult mosquitoes without pale scales on their first abdominal tergite were classified as Aedes aegypti formosus ( Aaf ) and those h...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Communication and Common Interest	journal.pcbi.1003282	null	[ [ "Many theorists have seen communication as a fundamentally cooperative phenomenon [1]–[4] .", "In an evolutionary context , however , cooperation cannot be taken for granted , because of problems of subversion and free-riding [5] .", "In the case of communication , these problems include both refusal ...	[ "Explaining the maintenance of communicative behavior in the face of incentives to deceive , conceal information , or exaggerate is an important problem in behavioral biology .", "When the interests of agents diverge , some form of signal cost is often seen as essential to maintaining honesty .", "Here , novel ...	[ "How can honest communication evolve , given the many incentives to deceive , conceal information , or exaggerate ?", "In recent work , it has often been supposed that either common interest between the sender and receiver of messages must be present , or special factors ( such as a special cost for dishonest pro...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Conformational Changes during Pore Formation by the Perforin-Related Protein Pleurotolysin	journal.pbio.1002049	A combination of structural methods reveals the complex process by which the perforin-like fungal toxin Pleurotolysin rearranges its structure to form a pore that punches a hole in target cell membranes.	[ [ "Membrane pore-forming proteins have the unique property of being expressed as metastable , water-soluble monomers that convert into a membrane inserted form .", "These proteins typically assemble into prepore oligomers on the target membrane surface .", "A dramatic conformational change then permits ...	[ "Membrane attack complex/perforin-like ( MACPF ) proteins comprise the largest superfamily of pore-forming proteins , playing crucial roles in immunity and pathogenesis .", "Soluble monomers assemble into large transmembrane pores via conformational transitions that remain to be structurally and mechanistically c...	[ "Animals , plants , fungi , and bacteria all use pore-forming proteins of the membrane attack complex-perforin ( MACPF ) family as lethal , cell-killing weapons .", "These proteins are able to insert into the plasma membranes of target cells , creating large pores that short circuit the natural separation between...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "public health and epidemiology", "epidemiology", "global health" ]	Global Distribution of Outbreaks of Water-Associated Infectious Diseases	journal.pntd.0001483	null	[ [ "Although substantial advances in biomedical sciences and public health measures have facilitated control of many infectious diseases in the past century , the world has witnessed an increasing incidence and geographical expansion of emerging and re-emerging infectious diseases [1] , which , together with som...	[ "Water plays an important role in the transmission of many infectious diseases , which pose a great burden on global public health .", "However , the global distribution of these water-associated infectious diseases and underlying factors remain largely unexplored .", "Based on the Global Infectious Disease and...	[ "Water is essential for maintaining life on Earth but can also serve as a media for many pathogenic organisms , causing a high disease burden globally .", "However , how the global distribution of water-associated infectious pathogens/diseases looks like and how such distribution is related to possible social and...	2012
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "cell motility", "medicine and health sciences", "mathematical models", "animal models", "developmental biology", "model organisms", "probability distribution", "mathematics", "experimental organism systems", "information technology", "data processing", "digestive system", "research and anal...	A hierarchical Bayesian model for understanding the spatiotemporal dynamics of the intestinal epithelium	journal.pcbi.1005688	null	[ [ "The intestinal epithelium provides crucial barrier , transport and homeostatic functions .", "These requirements lead it to undergo constant repair and regeneration , and dysfunctions can result in pathologies such as tumorigenesis [1–7] .", "Much work has been carried out on estimating the rate para...	[ "Our work addresses two key challenges , one biological and one methodological .", "First , we aim to understand how proliferation and cell migration rates in the intestinal epithelium are related under healthy , damaged ( Ara-C treated ) and recovering conditions , and how these relations can be used to identify...	[ "The intestinal epithelium is an important model system for studying the dynamics and regulation of multicellular populations .", "It is characterised by rapid rates of self-renewal and repair; dysregulation of these processes is thought to explain , in part , why many tumours form in the intestinal and similar e...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Ehrlichia chaffeensis Uses Its Surface Protein EtpE to Bind GPI-Anchored Protein DNase X and Trigger Entry into Mammalian Cells	journal.ppat.1003666	null	[ [ "Ehrlichia chaffeensis causes human monocytic ehrlichiosis ( HME ) , an emerging tick-borne zoonosis .", "From the site of infected tick bite on human skin , E . chaffeensis infects monocytes and spreads via the bloodstream to various tissues , causing a systemic febrile disease .", "HME is characteri...	[ "Ehrlichia chaffeensis , an obligatory intracellular rickettsial pathogen , enters and replicates in monocytes/macrophages and several non-phagocytic cells .", "E . chaffeensis entry into mammalian cells is essential not only for causing the emerging zoonosis , human monocytic ehrlichiosis , but also for its surv...	[ "Human monocytic ehrlichiosis ( HME ) , discovered in 1986 , was designated as a nationally notifiable disease by Centers for Disease Control and Prevention in 1998 .", "HME is one of the most prevalent , life-threatening emerging infectious diseases in the United States .", "HME is caused by a bacterium , Ehrl...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "bacteriology", "antimicrobials", "biofilms", "cell physiology", "medicine and health sciences", "neurochemistry", "pathology and laboratory medicine", "pathogens", "drugs", "microbiology", "cell metabolism", "neuroscience", "epithelial cells", "pseudomonas aeruginosa", "metabolites", ...	Host metabolites stimulate the bacterial proton motive force to enhance the activity of aminoglycoside antibiotics	journal.ppat.1007697	null	[ [ "While many biochemical substances that modulate antibiotic activity are known [1–10] , the influence of the local environment at the host-pathogen interface on bacterial responses to antibiotics is still poorly understood [4] .", "Supplementation of exogenous metabolites has been found to enhance the act...	[ "Antibiotic susceptibility of bacterial pathogens is typically evaluated using in vitro assays that do not consider the complex host microenvironment .", "This may help explaining a significant discrepancy between antibiotic efficacy in vitro and in vivo , with some antibiotics being effective in vitro but not in...	[ "There is a poor correlation between the activity of antibiotics in the laboratory and in patients , including in several infectious diseases of the respiratory tract .", "What may help explaining differences between antibiotic activity in vitro and in vivo is that current antibiotic susceptibility tests do not c...	2019
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "data acquisition", "neural networks", "social sciences", "neuroscience", "simulation and modeling", "systems science", "mathematics", "network analysis", "research and analysis methods", "computer and information sciences", "behavior", "dynamical systems", "research assessment", "psycholo...	Comparison of fluctuations in global network topology of modeled and empirical brain functional connectivity	journal.pcbi.1006497	null	[ [ "Neural elements in the brain are structurally connected and functionally coupled heterogeneously to form complex networks , in which neurons , neuronal populations , or brain regions can be viewed as nodes linked by edges of structural connectivity and functional connectivity [1 , 2] .", "Structural conn...	[ "Dynamic models of large-scale brain activity have been used for reproducing many empirical findings on human brain functional connectivity .", "Features that have been shown to be reproducible by comparing modeled to empirical data include functional connectivity measured over several minutes of resting-state fu...	[ "In human neuroscience , there is growing interest in temporal fluctuations in coactivation patterns of resting-state brain activity .", "To elucidate generative mechanisms of these fluctuations , theoretical studies try to reproduce their empirical properties by simulations using dynamic models of large-scale sp...	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Activity Profile of an FDA-Approved Compound Library against Schistosoma mansoni	journal.pntd.0003962	null	[ [ "Worldwide , schistosomiasis continues to affect the health and quality of life of millions , causing 3 . 3 million Disability-Adjusted Life-Years lost [1] .", "Most of the burden is contained in the tropics , mostly in Sub-Saharan Africa , where it disproportionally affects children in poor rural areas [...	[ "As plans to expand mass drug treatment campaigns to fight schistosomiasis form , worries about reliance on praziquantel as the sole available treatment motivate the investigation for novel antischistosomal compounds .", "Drug repurposing might be an inexpensive and effective source of novel antischistosomal lead...	[ "For a disease of large global health importance , schistosomiasis has a disproportionally small treatment tool box- only praziquantel is used to treat all 3 major forms of the disease .", "While drug discovery can be a long , laborious and expensive process , especially for an under-funded neglected disease such...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "genetics and genomics/complex traits", "nutrition/obesity" ]	NRXN3 Is a Novel Locus for Waist Circumference: A Genome-Wide Association Study from the CHARGE Consortium	journal.pgen.1000539	null	[ [ "Body mass index ( BMI ) is a commonly used measure of overall adiposity .", "However , specific fat depots may confer differential metabolic risk .", "In particular , central abdominal fat , as measured by waist circumference ( WC ) , may be more strongly associated with the development of metabolic ...	[ "Central abdominal fat is a strong risk factor for diabetes and cardiovascular disease .", "To identify common variants influencing central abdominal fat , we conducted a two-stage genome-wide association analysis for waist circumference ( WC ) .", "In total , three loci reached genome-wide significance .", "...	[ "Obesity is a major health concern worldwide .", "In the past two years , genome-wide association studies of DNA markers known as SNPs ( single nucleotide polymorphisms ) have identified two novel genetic factors that may help scientists better understand why some people may be more susceptible to obesity .", "...	2009
[ "Introduction", "Models", "Results", "Discussion" ]	[ "population modeling", "biology", "computational biology", "infectious disease modeling" ]	A Multi-scale Analysis of Influenza A Virus Fitness Trade-offs due to Temperature-dependent Virus Persistence	journal.pcbi.1002989	null	[ [ "Influenza A viruses infect both humans and animals , causing frequent outbreaks [1] , [2] .", "In humans , the infection can be life-threatening for individuals with weak immune systems , leading to an estimated annual worldwide mortality burden of [3] , [4] .", "Due to its zoonotic nature , and freq...	[ "Successful replication within an infected host and successful transmission between hosts are key to the continued spread of most pathogens .", "Competing selection pressures exerted at these different scales can lead to evolutionary trade-offs between the determinants of fitness within and between hosts .", "H...	[ "It has recently been suggested that for avian influenza viruses , prolonged persistence in the environment plays an important role in the transmission between birds .", "In such situations , influenza virus strains may face a trade-off: they need to persist well in the environment at low temperatures , but they ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "rna", "molecular cell biology", "rna interference", "cell biology", "nucleic acids", "cell growth", "gene expression", "regulatory networks", "biology", "computational biology", "signaling networks", "molecular biology" ]	Capture of MicroRNA–Bound mRNAs Identifies the Tumor Suppressor miR-34a as a Regulator of Growth Factor Signaling	journal.pgen.1002363	null	[ [ "microRNAs ( miRNAs ) that promote cell differentiation , inhibit cell proliferation , or enhance DNA damage or stress-induced cell cycle arrest or death , and whose expression is reduced in some cancers , are candidate tumor suppressor genes [1] .", "One of the most well studied tumor suppressor miRNAs i...	[ "A simple biochemical method to isolate mRNAs pulled down with a transfected , biotinylated microRNA was used to identify direct target genes of miR-34a , a tumor suppressor gene .", "The method reidentified most of the known miR-34a regulated genes expressed in K562 and HCT116 cancer cell lines .", "Transcript...	[ "microRNAs ( miRNAs ) are small RNAs that regulate gene expression by binding to mRNAs bearing a partially complementary sequence .", "miRNAs decrease the stability or translation of mRNA targets , leading to reduced protein expression .", "Understanding the biological function of a miRNA requires identifying i...	2011
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "microbiology/microbial evolution and genomics" ]	The Genome of a Pathogenic Rhodococcus: Cooptive Virulence Underpinned by Key Gene Acquisitions	journal.pgen.1001145	null	[ [ "Rhodococcus bacteria belong to the mycolic acid-containing group of actinomycetes together with other major genera such as Corynebacterium , Mycobacterium and Nocardia [1] .", "The genus Rhodococcus comprises more than 40 species widely distributed in the environment , many with biotechnological applicat...	[ "We report the genome of the facultative intracellular parasite Rhodococcus equi , the only animal pathogen within the biotechnologically important actinobacterial genus Rhodococcus .", "The 5 . 0-Mb R . equi 103S genome is significantly smaller than those of environmental rhodococci .", "This is due to genome ...	[ "Rhodococcus is a prototypic genus within the Actinobacteria , one of the largest microbial groups on Earth .", "Many of the ubiquitous rhodococcal species are biotechnologically useful due to their metabolic versatility and biodegradative properties .", "We have deciphered the genome of a facultatively parasit...	2010
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "biological cultures", "immunology", "cancers and neoplasms", "vertebrates", "animals", "dna transcription", "oncology", "epigenetics", "dna", "dna methylation", "chromatin", "research and analysis methods", "white blood ce...	Selection for avian leukosis virus integration sites determines the clonal progression of B-cell lymphomas	journal.ppat.1006708	null	[ [ "Avian leukosis virus ( ALV ) is a simple retrovirus that causes cancer , primarily B-cell lymphomas in chickens [1–3] .", "The ALV genome does not contain a viral oncogene and induces aberrant host gene expression via use of strong viral enhancer and promoter elements .", "Relative to other well stud...	[ "Avian leukosis virus ( ALV ) is a simple retrovirus that causes a wide range of tumors in chickens , the most common of which are B-cell lymphomas .", "The viral genome integrates into the host genome and uses its strong promoter and enhancer sequences to alter the expression of nearby genes , frequently inducin...	[ "The Avian Leukosis Virus ( ALV ) is a simple retrovirus that causes cancer in chickens .", "The virus integrates its genome into the host genome and induces changes in expression of nearby genes .", "Here , we determine the sites of viral integrations and their role in the progression of tumors .", "We repor...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "biology", "microbiology", "parasitology" ]	Longitudinal Monitoring of the Development of Antifilarial Antibodies and Acquisition of Wuchereria bancrofti in a Highly Endemic Area of Haiti	journal.pntd.0001941	null	[ [ "Lymphatic filariasis ( LF ) is a significant cause of global morbidity and is responsible for causing lymphedema , elephantiasis , and hydrocele .", "Research focusing on the pathogenesis of LF has historically neglected children , both because the onset of clinical disease tends to occur in adults and d...	[ "Antifilarial antibody testing has been established as a sensitive and specific method of diagnosing lymphatic filariasis .", "However , the development of serological responses to specific filarial antigens and their relationship to acquisition of infection is poorly understood .", "In order to evaluate whethe...	[ "Programs to eliminate lymphatic filariasis ( LF ) are designed to interrupt transmission of the parasite by treating the human reservoir of infection .", "As infection levels decline , assessing infection and transmission levels becomes more and more challenging .", "In principle , measuring the level of antib...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "schistosomiasis", "public health and epidemiology", "epidemiology", "infectious disease epidemiology", "global health", "neglected tropical diseases", "infectious disease control", "infectious disease modeling", "parasitic diseases" ]	Repeated Schistosoma japonicum Infection Following Treatment in Two Cohorts: Evidence for Host Susceptibility to Helminthiasis?	journal.pntd.0002098	null	[ [ "Recent multinational efforts to control and eliminate helminthiasis have the potential to dramatically reduce morbidity among the rural poor [1] , [2] .", "Approximately one billion people are infected with one or more helminthes and the health impacts of these infections , including impaired growth , co...	[ "In light of multinational efforts to reduce helminthiasis , we evaluated whether there exist high-risk subpopulations for helminth infection .", "Such individuals are not only at risk of morbidity , but may be important parasite reservoirs and appropriate targets for disease control interventions .", "We follo...	[ "Approximately 1 billion people are infected with one or more helminthes – a class of parasites that can impair physical , mental and economic development .", "We are interested in whether there exist groups who are repeatedly infected with helminthes over time in areas where treatment is ongoing .", "Such indi...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Onchocerciasis Transmission in Ghana: Persistence under Different Control Strategies and the Role of the Simuliid Vectors	journal.pntd.0003688	null	[ [ "The London Declaration on Neglected Tropical Diseases ( NTDs ) [1] and the World Health Organization’s ( WHO ) road map to accelerate progress for overcoming the impact of NTDs [2] have set goals for the elimination of human onchocerciasis by 2020 in selected African countries .", "Based on the results o...	[ "The World Health Organization ( WHO ) aims at eliminating onchocerciasis by 2020 in selected African countries .", "Current control focuses on community-directed treatment with ivermectin ( CDTI ) .", "In Ghana , persistent transmission has been reported despite long-term control .", "We present spatial and ...	[ "The World Health Organization ( WHO ) aims at eliminating onchocerciasis by 2020 in selected African countries .", "The success of elimination using ivermectin treatment alone will depend on several interacting factors including baseline endemicity , treatment coverage and vector species mix .", "In Ghana , tr...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "phosphorylation", "plant anatomy", "plant growth and development", "plant embryo anatomy", "brassica", "hormones", "developmental biology", "plant science", "model organisms", "signaling cascades", "plant hormones", "seedlings", "inflorescences", "plants", "mapk signaling cascades", "...	Mitogen-Activated Protein Kinase Cascade MKK7-MPK6 Plays Important Roles in Plant Development and Regulates Shoot Branching by Phosphorylating PIN1 in Arabidopsis	journal.pbio.1002550	The MKK7-MPK6 cascade plays a specific role in regulating auxin-related developmental events and phosphorylates PIN1, affecting its polarization and determining shoot branching in Arabidopsis.	[ [ "Mitogen-activated protein kinase ( MAPK/MPK ) cascades play important roles in a broad spectrum of signals , including biotic and abiotic stresses and hormone-mediated development in higher plants [1] .", "The basic MAPK module is composed of three sequentially activated kinases: MAPK kinase kinase ( MAP...	[ "Emerging evidences exhibit that mitogen-activated protein kinase ( MAPK/MPK ) signaling pathways are connected with many aspects of plant development .", "The complexity of MAPK cascades raises challenges not only to identify the MAPK module in planta but also to define the specific role of an individual module ...	[ "MAPK cascades play important roles in transducing environmental and developmental signals into adaptive and programmed responses .", "Because of the complexity of MAPK cascades , revealing the specificity of the MAPK modules is key to forming a functional and fully connected signal transduction system in higher ...	2016
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "biochemistry", "computational chemistry", "earth sciences", "chemistry", "biology", "computational biology", "biophysics", "geochemistry" ]	Energetic Selection of Topology in Ferredoxins	journal.pcbi.1002463	null	[ [ "Metals in proteins play important roles in stabilizing structure , promoting electron transfer and performing catalysis .", "Whole-genome analyses of phylogenetically diverse microorganisms suggest the earliest proteins incorporated metals and that metal usage over biological history evolved to match the...	[ "Models of early protein evolution posit the existence of short peptides that bound metals and ions and served as transporters , membranes or catalysts .", "The Cys-X-X-Cys-X-X-Cys heptapeptide located within bacterial ferredoxins , enclosing an Fe4S4 metal center , is an attractive candidate for such an early pe...	[ "The ferredoxin fold is one of the oldest structures capable of catalyzing electron transfer reactions .", "In nature , only a right-handed topology exists in the ferredoxin fold .", "To understand how a specific fold-handedness was selected , we analyzed the structural motif using the tools of de novo protein ...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics", "neuroscience", "biology and life sciences", "genomics" ]	Global Genetic Variations Predict Brain Response to Faces	journal.pgen.1004523	null	[ [ "Interactions with peers are of high relevance to our mental health .", "Patients with various psychological disorders show impairments in face perception and emotion recognition [1]–[4] .", "Similarly , differential neural responses to faces have been reported in various psychological disorders inclu...	[ "Face expressions are a rich source of social signals .", "Here we estimated the proportion of phenotypic variance in the brain response to facial expressions explained by common genetic variance captured by ∼500 , 000 single nucleotide polymorphisms .", "Using genomic-relationship-matrix restricted maximum lik...	[ "We measured brain response to facial expressions in a large sample of typically developing adolescents ( n = 1 , 620 ) and assessed “heritability” of the response using common genetic variations across the genome .", "In a subset of brain regions , we explained 40–50% of phenotypic variance by genetic variance ....	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "genome-wide association studies", "body weight", "medicine and health sciences", "cardiovascular anatomy", "variant genotypes", "chromosome 16", "genetic mapping", "physiological parameters", "heart", "genome analysis", "chromosome biology", "hypertension", "blood pressure", "chromosome p...	Rare variants in fox-1 homolog A (RBFOX1) are associated with lower blood pressure	journal.pgen.1006678	null	[ [ "High blood pressure ( BP ) is a common condition associated with multiple health outcomes , including heart , brain , and kidney diseases [1 , 2] .", "Previous studies have shown that BP is a genetically determined trait with estimated heritability of 30% to 60% [3 , 4] .", "Multiple large genome-wid...	[ "Many large genome-wide association studies ( GWAS ) have identified common blood pressure ( BP ) variants .", "However , most of the identified BP variants do not overlap with the linkage evidence observed from family studies .", "We thus hypothesize that multiple rare variants contribute to the observed linka...	[ "Hypertension is a risk factor for cardiovascular disease and the most important risk factor for stroke .", "Family studies suggest that hypertension related traits are heritable .", "Previous genome-wide association studies ( GWAS ) have identified multiple common blood pressure ( BP ) variants but these varia...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "neuroscience/behavioral neuroscience", "neuroscience/sensory systems", "neurological disorders/pain management", "immunology/immune response", "microbiology/innate immunity", "immunology/innate immunity", "microbiology/applied microbiology", "immunology/leukocyte signaling and gene expression", "im...	Mycobacteria Attenuate Nociceptive Responses by Formyl Peptide Receptor Triggered Opioid Peptide Release from Neutrophils	journal.ppat.1000362	null	[ [ "The four cardinal signs of inflammation are rubor ( redness ) , calor ( hyperthermia ) , dolor ( pain/hyperalgesia ) and functio laesa ( impaired function ) .", "Bacteria and their components play a critical role in eliciting pain since inflammatory pain is significantly decreased in animals raised under...	[ "In inflammation , pain is regulated by a balance of pro- and analgesic mediators .", "Analgesic mediators include opioid peptides which are secreted by neutrophils at the site of inflammation , leading to activation of opioid receptors on peripheral sensory neurons .", "In humans , local opioids and opioid pep...	[ "Inflammation of peripheral tissue can be caused by bacteria and is frequently accompanied by pain .", "Pain severity depends on the balance of enhancing ( proalgesic ) and decreasing ( analgesic ) mediators .", "Local endogenous pain control involves the release of opioid peptides from immune cells at the site...	2009
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "enzyme-linked immunoassays", "biopsy", "hela cells", "biological cultures", "surgical and invasive medical procedures", "bacterial diseases", "cell cultures", "immunologic techniques", "enterohaemorrhagic escherichia coli", "digestive system", "research and ana...	A nanobody targeting the translocated intimin receptor inhibits the attachment of enterohemorrhagic E. coli to human colonic mucosa	journal.ppat.1008031	null	[ [ "Enterohemorrhagic E . coli ( EHEC ) is a major public health concern in industrial countries with most severe infections linked to serotype O157:H7 .", "In addition to diarrhoea , EHEC can cause hemorrhagic colitis as well as life-threatening hemolytic uremic syndrome ( HUS ) damaging the kidneys and cen...	[ "Enterohemorrhagic E . coli ( EHEC ) is a human intestinal pathogen that causes hemorrhagic colitis and hemolytic uremic syndrome .", "No vaccines or specific therapies are currently available to prevent or treat these infections .", "EHEC tightly attaches to the intestinal epithelium by injecting the intimin r...	[ "Currently , there is no effective treatment or vaccine against enterohemorrhagic E . coli ( EHEC ) , a bacterial pathogen that infects human colon after the ingestion of contaminated food .", "It thrives in the colon thanks to its ability to attach intimately to the intestinal epithelium .", "Here , we have id...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	A Critical Role for CLSP2 in the Modulation of Antifungal Immune Response in Mosquitoes	journal.ppat.1004931	null	[ [ "Female mosquitoes require repeated blood feedings during their life cycle to satisfy their reproductive nutritional needs and , as a consequence , they serve as vectors of numerous human diseases [1] .", "Malaria , transmitted by the Anopheles genus , is the most devastating vector-borne human disease an...	[ "Entomopathogenic fungi represent a promising class of bio-insecticides for mosquito control .", "Thus , detailed knowledge of the molecular mechanisms governing anti-fungal immune response in mosquitoes is essential .", "In this study , we show that CLSP2 is a modulator of immune responses during anti-fungal i...	[ "Entomopathogenic fungi represent a promising class of bio-insecticides for mosquito control .", "Detailed knowledge of molecular mechanisms governing anti-fungal immune response in mosquitoes is essential .", "CLSP2 composed of serine protease and lectin domains functions as a modulator of the mosquito immune ...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "chemical bonding", "medicine and health sciences", "chemical characterization", "crystal structure", "pathology and laboratory medicine", "chemical compounds", "pathogens", "condensed matter physics", "microbiology", "organic compounds", "membrane proteins", "outer membrane proteins", "basi...	Lactoferrin binding protein B – a bi-functional bacterial receptor protein	journal.ppat.1006244	null	[ [ "Neisseria meningitidis is a diplococcal , Gram-negative bacteria that lives commensally in the nasopharyngeal tract of approximately 10–20% of humans [1] .", "N . meningitidis is an opportunistic pathogen that can cause serious invasive infections including meningitis and sepsis .", "This pathogen ac...	[ "Lactoferrin binding protein B ( LbpB ) is a bi-lobed outer membrane-bound lipoprotein that comprises part of the lactoferrin ( Lf ) receptor complex in Neisseria meningitidis and other Gram-negative pathogens .", "Recent studies have demonstrated that LbpB plays a role in protecting the bacteria from cationic an...	[ "Bacteria responsible for important infections in humans and food production animals survive and proliferate within their host by ‘hijacking’ iron from the host iron-binding proteins , transferrin and lactoferrin .", "The iron-hijacking process is mediated by a set of surface receptors that are specific for trans...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "animal models of infection", "mycology", "aspergillus fumigatus", "medical microbiology", "microbial pathogens", "biology and life sciences", "immunology", "microbiology", "fungal pathogens" ]	The pH-Responsive PacC Transcription Factor of Aspergillus fumigatus Governs Epithelial Entry and Tissue Invasion during Pulmonary Aspergillosis	journal.ppat.1004413	null	[ [ "Spores of the mould pathogen Aspergillus fumigatus are agents of multiple human diseases , most of which initiate with inhalation of fungal spores and , dependent upon host immune status , compromise pulmonary integrity .", "Amongst the resultant diseases , invasive aspergillosis ( IA ) exerts the highes...	[ "Destruction of the pulmonary epithelium is a major feature of lung diseases caused by the mould pathogen Aspergillus fumigatus .", "Although it is widely postulated that tissue invasion is governed by fungal proteases , A . fumigatus mutants lacking individual or multiple enzymes remain fully invasive , suggesti...	[ "Inhaled spores of the pathogenic mould Aspergillus fumigatus cause fungal lung infections in humans having immune defects .", "A . fumigatus spores germinate within the immunocompromised lung , producing invasively growing , elongated cells called hyphae .", "Hyphae degrade the surrounding pulmonary tissue , a...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Notes Added in Proof" ]	[ "histology", "biophysic al simulations", "biology", "computational biology" ]	A Two-Dimensional Model of the Colonic Crypt Accounting for the Role of the Basement Membrane and Pericryptal Fibroblast Sheath	journal.pcbi.1002515	null	[ [ "Colorectal cancer ( CRC ) is one of the leading causes of cancer-related death worldwide , demanding a response from scientists and clinicians to understand its aetiology and develop effective treatment .", "CRC is thought to originate via genetic alterations that cause disruption to the cellular dynamic...	[ "The role of the basement membrane is vital in maintaining the integrity and structure of an epithelial layer , acting as both a mechanical support and forming the physical interface between epithelial cells and the surrounding connective tissue .", "The function of this membrane is explored here in the context o...	[ "At the onset of colorectal carcinogenesis , marked changes can be observed in the structure and dynamics of the crypts of Lieberkühn .", "These test tube shaped glands regularly punctuate the surface of the gut and are lined with a monolayer of epithelial cells which divide and migrate upwards to renew the intes...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "animal models", "medicine", "model organisms", "gene expression", "genetics", "mouse", "molecular genetics", "atherosclerosis", "biology", "computational biology", "gene networks", "cardiovascular" ]	Plasma Cholesterol–Induced Lesion Networks Activated before Regression of Early, Mature, and Advanced Atherosclerosis	journal.pgen.1004201	null	[ [ "Atherosclerosis , primarily in coronary artery disease ( CAD ) or carotid stenosis , is the main cause of myocardial infarction ( MI ) and stroke , which together are responsible for more than 50% of deaths worldwide [1] .", "Although the extent of atherosclerosis in the arterial bed is an unreliable mar...	[ "Plasma cholesterol lowering ( PCL ) slows and sometimes prevents progression of atherosclerosis and may even lead to regression .", "Little is known about how molecular processes in the atherosclerotic arterial wall respond to PCL and modify responses to atherosclerosis regression .", "We studied atheroscleros...	[ "The main underlying cause of heart attacks and strokes is atherosclerosis .", "One strategy to prevent these often deadly clinical events is therefore either to slow atherosclerosis progression or better , induce regression of atherosclerotic plaques making them more stable .", "Plasma cholesterol lowering ( P...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biophysics", "cell biology", "developmental biology", "none" ]	Fundamental Limits to Position Determination by Concentration Gradients	journal.pcbi.0030078	null	[ [ "To determine position in a biological system , some component within the system must have a nonuniform spatial distribution .", "Often , this is achieved through the formation of gradients of protein concentration .", "Typically , a gradient forms when a protein is manufactured/injected within a smal...	[ "Position determination in biological systems is often achieved through protein concentration gradients .", "Measuring the local concentration of such a protein with a spatially varying distribution allows the measurement of position within the system .", "For these systems to work effectively , position determ...	[ "Many biological systems require precise positional information to function correctly .", "Examples include positioning of the site of cell division and determination of cell fate during embryonic development .", "This positional information often is encoded in concentration gradients .", "A specific protein ...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "histone modification", "cell biology", "post-translational modification", "proteins", "acetylation", "chromosome biology", "gene expression", "genetics", "biology and life sciences", "epigenetics", "histone acetylation", "molecular genetics", "euchromatin", "chromatin", ...	Multifaceted Genome Control by Set1 Dependent and Independent of H3K4 Methylation and the Set1C/COMPASS Complex	journal.pgen.1004740	null	[ [ "In eukaryotic cells , DNA-based processes operate within the context of a chromatin template [1] , [2] .", "Chromatin-modifying complexes targeting select residues of histones for posttranslational modifications exert various levels of genome control including chromatin assembly , transcription , DNA rep...	[ "Histone modifiers are critical regulators of chromatin-based processes in eukaryotes .", "The histone methyltransferase Set1 , a component of the Set1C/COMPASS complex , catalyzes the methylation at lysine 4 of histone H3 ( H3K4me ) , a hallmark of euchromatin .", "Here , we show that the fission yeast Schizos...	[ "Methylation of histone H3 at lysine 4 ( H3K4me ) is a well-documented mark associated with euchromatin .", "In this study , we investigate the contributions of the histone methyltransferase Set1 ( KMT2 ) and its associated Set1C/COMPASS complex in the fission yeast Schizosaccharomyces pombe to histone H3 lysine ...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "bacteriology", "medicine", "immunopathology", "infectious diseases", "bacterial diseases", "inflammation", "immune cells", "genetics of the immune system", "clinical immunology", "immunity", "bacterial taxonomy", "tuberculosis", "host-pathogen interaction", "biology", "microbiology", ...	Ethnic Variation in Inflammatory Profile in Tuberculosis	journal.ppat.1003468	null	[ [ "Mycobacterium tuberculosis ( MTB ) , the causative agent of tuberculosis ( TB ) , emerged as a pathogen in Africa and has co-evolved with humans following migration to Europe and Asia some 70 , 000 years ago [1] .", "Distinct phylogenetic lineages of MTB consistently associate with human populations of d...	[ "Distinct phylogenetic lineages of Mycobacterium tuberculosis ( MTB ) cause disease in patients of particular genetic ancestry , and elicit different patterns of cytokine and chemokine secretion when cultured with human macrophages in vitro .", "Circulating and antigen-stimulated concentrations of these inflammat...	[ "Mycobacterium tuberculosis ( MTB ) is the causative agent of tuberculosis .", "Genetically distinct strains of MTB cause disease in particular ethnic groups , and these strains vary in their ability to elicit inflammatory responses from antigen-presenting cells in vitro .", "Circulating and antigen-stimulated ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "adaptive immunity", "demyelinating disorders", "immunity", "multiple sclerosis", "neurology", "neurological disorders", "immunology", "biology", "microbiology", "immune response", "immunotherapy" ]	Changes in JC Virus-Specific T Cell Responses during Natalizumab Treatment and in Natalizumab-Associated Progressive Multifocal Leukoencephalopathy	journal.ppat.1003014	null	[ [ "Progressive Multifocal Leukoencephalopathy ( PML ) is a demyelinating disease of the central nervous system caused by JC virus ( JCV ) [1] .", "PML occurs most often in the setting of immunodeficiency , such as AIDS , leukemia , organ transplantation and idiopathic CD4 lymphopenia .", "However , case...	[ "Progressive multifocal leukoencephalopathy ( PML ) induced by JC virus ( JCV ) is a risk for natalizumab-treated multiple sclerosis ( MS ) patients .", "Here we characterize the JCV-specific T cell responses in healthy donors and natalizumab-treated MS patients to reveal functional differences that may account f...	[ "Progressive multifocal leukoencephalopathy ( PML ) is a complication of treatment with natalizumab in patients with multiple sclerosis ( MS ) and Crohn's disease .", "PML results from a failure of the immune system to control replication of JC virus ( JCV ) in the brain .", "We studied the T cell responses of ...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "pig models", "tropical diseases", "geographical locations", "vertebrates", "parasitic diseases", "animals", "mammals", "peru", "animal models", "physiological processes", "experimental organism systems", "neglected tropi...	Spatial relationship between Taenia solium tapeworm carriers and necropsy cyst burden in pigs	journal.pntd.0005536	null	[ [ "Taenia solium , the pork tapeworm , is a parasite that affects 50 million people worldwide [1] .", "When the parasite infects the human central nervous system , the result is a severe neurological condition called neurocysticercosis ( NCC ) , which may lead to seizures , headaches , and stroke .", "I...	[ "Taenia solium , a parasite that affects humans and pigs , is the leading cause of preventable epilepsy in the developing world .", "Geographic hotspots of pigs testing positive for serologic markers of T . solium exposure have been observed surrounding the locations of human tapeworm carriers .", "This cluster...	[ "Taenia solium , the pork tapeworm , is a parasite transmitted between humans and pigs .", "The disease is most common in developing countries where access to sanitation is limited and domestic pigs are allowed to roam freely .", "Humans infected with the intestinal tapeworm release T . solium eggs into the env...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular biology/centromeres", "molecular biology/chromatin structure", "genetics and genomics/chromosome biology" ]	LINE Retrotransposon RNA Is an Essential Structural and Functional Epigenetic Component of a Core Neocentromeric Chromatin	journal.pgen.1000354	null	[ [ "Despite the fact that the functional role of the centromere in mitotic and meiotic cell divisions is evolutionarily conserved , the underlying DNA sequences of the centromeres are highly variable across the phylogeny and show no obvious conservation [1] , [2] .", "Thus , a conundrum remains as to whether...	[ "We have previously identified and characterized the phenomenon of ectopic human centromeres , known as neocentromeres .", "Human neocentromeres form epigenetically at euchromatic chromosomal sites and are structurally and functionally similar to normal human centromeres .", "Recent studies have indicated that ...	[ "The centromere is an essential chromosomal structure for the correct segregation of chromosomes during cell division .", "Normal human centromeres comprise a 171-bp α-satellite DNA arranged into tandem and higher-order arrays .", "Neocentromeres are fully functional centromeres that form epigenetically on nonc...	2009
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "immunology", "microbiology", "parasitology", "veterinary science", "vaccination", "veterinary diseases", "veterinary parasitology", "cytochemistry", "proteins", "biology", "recombinant proteins", "biochemistry", "histochemistry", "clinical immunology", "immunity", "vacci...	The Sigma Class Glutathione Transferase from the Liver Fluke Fasciola hepatica	journal.pntd.0001666	null	[ [ "The liver flukes , Fasciola hepatica and Fasciola gigantica are the causative agents of fasciolosis , a foodborne zoonotic disease affecting grazing animals and humans worldwide [1] .", "Liver fluke causes economic losses of over US$ 3 billion worldwide per annum to livestock via mortality , reduction in...	[ "Liver fluke infection of livestock causes economic losses of over US$ 3 billion worldwide per annum .", "The disease is increasing in livestock worldwide and is a re-emerging human disease .", "There are currently no commercial vaccines , and only one drug with significant efficacy against adult worms and juve...	[ "Combating neglected parasitic diseases is of paramount importance to improve the health of human populations and/or their domestic animals .", "Uncovering key roles in host-parasite interactions may support the vaccine potential portfolio of a parasite protein .", "Fasciola hepatica causes global disease in hu...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "learning", "action potentials", "medicine and health sciences", "nervous system", "membrane potential", "social sciences", "electrophysiology", "neuroscience", "learning and memory", "synaptic plasticity", "cognitive psychology", "computational neuroscience", "neuronal dendrites", "neuron...	Prospective Coding by Spiking Neurons	journal.pcbi.1005003	null	[ [ "Animals can learn to predict upcoming stimuli .", "In delayed paired-associate tasks , animals learn to respond to pairs of stimuli ( e . g . images A1-B1 and A2-B2 ) separated by a delay .", "These tasks can be solved by either keeping a memory of the first stimulus ( A1 or A2 ) during the delay per...	[ "Animals learn to make predictions , such as associating the sound of a bell with upcoming feeding or predicting a movement that a motor command is eliciting .", "How predictions are realized on the neuronal level and what plasticity rule underlies their learning is not well understood .", "Here we propose a bi...	[ "Sensory inputs are often predictable .", "Lightning is followed by thunder , a falling object causes noise when hitting the ground , our skin gets wet when we jump into the water .", "Humans learn regularities like these without effort .", "Learned predictions allow to cover the ears in anticipation of thund...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "medicine and health sciences", "lysosomes", "immune cells", "bovine tuberculosis", "immunology", "tropical diseases", "diabetes mellitus", "bacterial diseases", "endocrine disorders", "cellular structures and organelles", "bacteria", "infectious diseases", "lipids", "whit...	Oxidized low-density lipoprotein (oxLDL) supports Mycobacterium tuberculosis survival in macrophages by inducing lysosomal dysfunction	journal.ppat.1007724	null	[ [ "Type 2 diabetes mellitus ( DM ) has been recognized as a major risk factor for tuberculosis ( TB ) for decades [1] .", "Recent epidemiological studies have demonstrated that DM triples the risk of developing active TB [2] , and approximately 15% of global TB cases can be attributed to DM comorbidity [3] ...	[ "Type 2 diabetes mellitus ( DM ) is a major risk factor for developing tuberculosis ( TB ) .", "TB-DM comorbidity is expected to pose a serious future health problem due to the alarming rise in global DM incidence .", "At present , the causal underlying mechanisms linking DM and TB remain unclear .", "DM is a...	[ "Tuberculosis ( TB ) is an infectious disease of the lungs caused by a bacterium , Mycobacterium tuberculosis ( Mtb ) , and is responsible for over a million deaths per year worldwide .", "Population studies have demonstrated that type 2 diabetes mellitus ( DM ) is a risk factor for TB as it triples the risk of d...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "geomorphology", "livestock", "medicine and health sciences", "leptospira", "pathology and laboratory medicine", "landforms", "ruminants", "pathogens", "topography", "tropical diseases", "microbiology", "vertebrates", "animals", "mammals", "dogs", "bacterial diseases", "neglected tro...	A systematic review of human and animal leptospirosis in the Pacific Islands reveals pathogen and reservoir diversity	journal.pntd.0006503	null	[ [ "Leptospira is a genus of bacteria belonging to the phylum of Spirochaetes causing leptospirosis in humans and other mammals [1] .", "Leptospirosis is the most widespread and potentially fatal bacterial zoonosis worldwide [2] , with an estimated 1 . 03 million human cases and 58 , 900 deaths worldwide eac...	[ "The Pacific Islands have environmental conditions highly favourable for transmission of leptospirosis , a neglected zoonosis with highest incidence in the tropics , and Oceania in particular .", "Recent reports confirm the emergence and outbreaks of leptospirosis in the Pacific Islands , but the epidemiology and...	[ "Leptospirosis is an important bacterial zoonosis that affects people and animals worldwide .", "It is common in tropical areas , especially in island ecosystems .", "Because islands are relatively small , isolated , and have limited health and diagnostic facilities , the disease burden is often underestimated ...	2018
[ "Introduction", "Materials and methods", "Results and discussion" ]	[ "medicine and health sciences", "body fluids", "cardiovascular physiology", "cardiovascular anatomy", "cancer treatment", "basic cancer research", "oncology", "angiogenesis", "developmental biology", "pharmaceutics", "tumor physiology", "drug administration", "tumor angiogenesis", "cellula...	In-silico dynamic analysis of cytotoxic drug administration to solid tumours: Effect of binding affinity and vessel permeability	journal.pcbi.1006460	null	[ [ "Inefficient delivery of drugs to solid tumours is one of the main reasons for chemotherapy failure .", "To reach cancer cells , blood borne therapeutic agents have to travel through the tumour vasculature to reach the tumour site , subsequently to extravasate into the tumour interstitial space and finall...	[ "The delivery of blood-borne therapeutic agents to solid tumours depends on a broad range of biophysical factors .", "We present a novel multiscale , multiphysics , in-silico modelling framework that encompasses dynamic tumour growth , angiogenesis and drug delivery , and use this model to simulate the intravenou...	[ "One of the main challenges in optimising cancer therapy is understanding the in-vivo cancer environment and how it changes over time .", "The efficacy of chemotherapeutic drugs is known to be strongly dependent on blood vessel wall properties and the architecture of the developing tumour vasculature , which in t...	2018
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "plant biology/plant growth and development", "plant biology/plant genetics and gene expression", "plant biology" ]	Signaling Role of Fructose Mediated by FINS1/FBP in Arabidopsis thaliana	journal.pgen.1001263	null	[ [ "Myriad metabolic pathways enable cells to sustain life with basic carbon and nitrogenous compounds .", "Thus , the integration of metabolite status , which reflects external and internal living conditions , into cellular activities ( e . g . , gene expression ) is a pivotal process that equips organisms ...	[ "Sugars are evolutionarily conserved signaling molecules that regulate the growth and development of both unicellular and multicellular organisms .", "As sugar-producing photosynthetic organisms , plants utilize glucose as one of their major signaling molecules .", "However , the details of other sugar signalin...	[ "Among the many plant sugar metabolites , glucose signaling has received the most attention .", "Although fructose is also an abundant hexose , its signaling role in plant growth and development has not been addressed clearly and systematically to date .", "We found that fructose functions as a regulatory sugar...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "reverse transcriptase-polymerase chain reaction", "dengue virus", "medicine and health sciences", "body fluids", "pathology and laboratory medicine", "respiratory infections", "pathogens", "tropical diseases", "microbiology", "pulmonology", "viruses", "throat", "rna viruses", "signs and s...	Isolation of dengue virus from the upper respiratory tract of four patients with dengue fever	journal.pntd.0005520	null	[ [ "Dengue fever is a mosquito-borne disease caused by dengue virus ( DENV ) .", "There are four serotypes–DENV-1 , DENV-2 , DENV-3 and DENV-4 .", "Dengue is widely distributed throughout tropical and sub-tropical areas around the world and imposes great economic burden .", "It is transmitted by Aede...	[ "Dengue fever is an important arboviral disease .", "The clinical manifestations vary from a mild non-specific febrile syndrome to severe life-threatening illness .", "The virus can usually be detected in the blood during the early stages of the disease .", "Dengue virus has also been found in isolated cases ...	[ "Dengue virus is rarely identified in respiratory specimens .", "We retrospectively identified four patients with dengue fever who had the virus isolated from their nose or throat .", "All the patients had respiratory signs or symptoms .", "Half had family members who also had respiratory symptoms .", "Furt...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public health and epidemiology", "rabies", "veterinary diseases", "zoonotic diseases", "animal management", "public health", "veterinary science", "agriculture" ]	Implementation of an Intersectoral Program to Eliminate Human and Canine Rabies: The Bohol Rabies Prevention and Elimination Project	journal.pntd.0001891	null	[ [ "More than 99% of all global human rabies deaths occur as a result of being exposed to infected dogs .", "In the Philippines , as in most Asian countries , canine rabies is endemic and poses a particularly perilous risk for persons living in rural areas [1] .", "The number of human deaths attributed t...	[ "The province of Bohol , located in the Visayas islands region in the Philippines has a human population of 1 . 13 million and was the 4th highest region for human rabies deaths in the country , averaging 10 per year , prior to the initiation of the Bohol Rabies Prevention and Elimination Project ( BRPEP ) .", "T...	[ "The Province of Bohol , Philippines has eliminated dog and human rabies in less than three years by empowering the community and implementing an intersectoral strategy .", "In 2006 , Bohol ranked 4th highest in the Philippines for human rabies , averaging 10 deaths per year .", "Launched in 2007 , the program ...	2012
[ "Introduction", "Materials and methods", "Results and discussion" ]	[ "fluorescence imaging", "medicine and health sciences", "classical mechanics", "diagnostic radiology", "neuroscience", "magnetic resonance imaging", "optimization", "histology", "mathematics", "brain mapping", "damage mechanics", "neuroimaging", "research and analysis methods", "specimen p...	On variational solutions for whole brain serial-section histology using a Sobolev prior in the computational anatomy random orbit model	journal.pcbi.1006610	null	[ [ "Recent advances in brain imaging [1 , 2] , methods to label neurons [3] , and computational methods have brought about a new era of neuroanatomical research , with a focus on comprehensively mapping brain circuits [4] .", "Mapping whole-brain circuitry is important for three distinct reasons: scientific ...	[ "This paper presents a variational framework for dense diffeomorphic atlas-mapping onto high-throughput histology stacks at the 20 μm meso-scale .", "The observed sections are modelled as Gaussian random fields conditioned on a sequence of unknown section by section rigid motions and unknown diffeomorphic transfo...	[ "New developments in neural tracing techniques have motivated the widespread use of histology as a modality for exploring the circuitry of the brain .", "Automated mapping of pre-labeled atlases onto modern large datasets of histological imagery is a critical step for elucidating the brain’s neural circuitry and ...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "carbohydrate metabolism", "cell death", "chemical compounds", "gene regulation", "metabolic processes", "cell processes", "carbohydrates", "glucose metabolism", "organic compounds", "glucose", "glycolysis", "oxidative phosphorylation", "micrornas", "molecular biology techniques", "resea...	An Oncogenic Virus Promotes Cell Survival and Cellular Transformation by Suppressing Glycolysis	journal.ppat.1005648	null	[ [ "It has been recognized that metabolic reprogramming is a core hallmark of cancer[1] .", "The Warburg effect describes the dependence of cancer cells on aerobic glycolysis for their growth and proliferation[2] .", "Increased glucose uptake and aerobic glycolysis are widely observed in cancer and clini...	[ "Aerobic glycolysis is essential for supporting the fast growth of a variety of cancers .", "However , its role in the survival of cancer cells under stress conditions is unclear .", "We have previously reported an efficient model of gammaherpesvirus Kaposi’s sarcoma-associated herpesvirus ( KSHV ) -induced cel...	[ "KSHV is causally associated with the development of Kaposi’s sarcoma and primary effusion lymphoma; however , the mechanism underlying KSHV-induced malignant transformation remains unclear .", "The recent development of an efficient KSHV-induced cellular transformation model of primary rat mesenchymal stem cells...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "leptospira", "pathology and laboratory medicine", "pathogens", "immunology", "tropical diseases", "microbiology", "vertebrates", "animals", "mammals", "membrane proteins", "animal models", "bacterial diseases", "signs and symptoms", "outer membrane protei...	Lp25 membrane protein from pathogenic Leptospira spp. is associated with rhabdomyolysis and oliguric acute kidney injury in a guinea pig model of leptospirosis	journal.pntd.0005615	null	[ [ "Leptospirosis is an emerging zoonosis that is caused by pathogenic spirochetes of the genus Leptospira .", "Approximately 1 . 03 million cases of the disease occur in humans worldwide , with approximately 60 , 000 deaths annually [1] .", "Many species of wild and domestic animals are leptospirosis re...	[ "Acute kidney injury ( AKI ) from leptospirosis is frequently nonoliguric with hypo- or normokalemia .", "Higher serum potassium levels are observed in non-survivor patients and may have been caused by more severe AKI , metabolic disarrangement , or rhabdomyolysis .", "An association between the creatine phosph...	[ "Rhabdomyolysis is a syndrome that results from the disruption of skeletal muscle integrity , leading to a massive release of the intracellular contents into the blood stream , including myoglobin , creatine phosphokinase , aspartate transaminase , lactate dehydrogenase , aldolase , and electrolytes .", "Complica...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Epstein Barr Virus-Induced 3 (EBI3) Together with IL-12 Negatively Regulates T Helper 17-Mediated Immunity to Listeria monocytogenes Infection	journal.ppat.1003628	null	[ [ "The generation of pathogen-specific T cell responses is essential for the clearance of infectious agents .", "This involves the differentiation of naïve T cells into distinct pathogen-specific helper T cell lineages in a process that largely depends on the cytokine milieu created by innate immune cells u...	[ "Although the protective functions by T helper 17 ( Th17 ) cytokines against extracellular bacterial and fungal infection have been well documented , their importance against intracellular bacterial infection remains unclear .", "Here , we investigated the contribution of Th17 responses to host defense against in...	[ "There is a considerable gap in our understanding of how pathogenic intracellular bacteria escape innate and adaptive host immunity .", "Production of IL-12 , and subsequently IFNγ , upon infection triggers host immunity that prevents early dissemination of pathogenic intracellular pathogens .", "This is eviden...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	MPV17 Loss Causes Deoxynucleotide Insufficiency and Slow DNA Replication in Mitochondria	journal.pgen.1005779	null	[ [ "Mitochondria contain their own DNA ( mtDNA ) , which encodes thirteen subunits of the oxidative phosphorylation ( OXPHOS ) complexes essential for cellular respiration and ATP production .", "The faithful synthesis and maintenance of mtDNA depends on nuclear-encoded genes which , when mutated , can cause...	[ "MPV17 is a mitochondrial inner membrane protein whose dysfunction causes mitochondrial DNA abnormalities and disease by an unknown mechanism .", "Perturbations of deoxynucleoside triphosphate ( dNTP ) pools are a recognized cause of mitochondrial genomic instability; therefore , we determined DNA copy number and...	[ "Mitochondrial DNA depletion syndrome ( MDS ) is a genetically heterogeneous condition characterized by a decrease of mitochondrial DNA ( mtDNA ) copy number and decreased activities of respiratory chain enzymes .", "Depletion of mtDNA has been associated with mutations in several genes , which encode either prot...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "public health and epidemiology", "diagnostic medicine", "epidemiology", "global health", "ophthalmology", "public health" ]	Diagnostic Accuracy of a Prototype Point-of-Care Test for Ocular Chlamydia trachomatis under Field Conditions in The Gambia and Senegal	journal.pntd.0001234	null	[ [ "Trachoma is caused by ocular infection with the bacterium Chlamydia trachomatis and is the leading infectious cause of blindness worldwide [1] .", "The World Health Organization ( WHO ) simplified grading system , designed for the simple and reliable grading of trachoma clinical signs by non-specialist s...	[ "The clinical signs of active trachoma are often present in the absence of ocular Chlamydia trachomatis infection in low prevalence and mass treated settings .", "Treatment decisions are currently based on the prevalence of clinical signs , and this may result in the unnecessary distribution of mass antibiotic tr...	[ "Trachoma , caused by infection of the eye with the bacterium Chlamydia trachomatis , is the leading infectious cause of blindness and is associated with poverty .", "Antibiotic treatment of all community members is one of the recommended control strategies for trachoma .", "However , in places where the preval...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Altered Ca2+ Kinetics Associated with α-Actinin-3 Deficiency May Explain Positive Selection for ACTN3 Null Allele in Human Evolution	journal.pgen.1004862	null	[ [ "The sarcomeric α-actinins , α-actinin-2 and -3 , are highly homologous actin-binding proteins localised to the Z-discs of skeletal muscle fibres , where they cross-link the actin filaments of adjoining sarcomeres and interact with a host of metabolic and signalling proteins .", "α-Actinin-2 is present in...	[ "Over 1 . 5 billion people lack the skeletal muscle fast-twitch fibre protein α-actinin-3 due to homozygosity for a common null polymorphism ( R577X ) in the ACTN3 gene .", "α-Actinin-3 deficiency is detrimental to sprint performance in elite athletes and beneficial to endurance activities .", "In the human gen...	[ "α-Actinin-3 is a protein found inside the muscles of most people around the world .", "It is encoded by a gene called ACTN3 , popularly known as “the gene for speed . ”", "In 1 . 5 billion people , a certain variation in the genetic sequence of their ACTN3 gene causes their muscles to produce no α-actinin-3 pr...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "immunology", "microbiology", "host-pathogen interaction", "bacterial diseases", "pseudomonas infections", "bacterial pathogens", "infectious diseases", "microbial pathogens", "biology", "immune response", "gram negative", "immunity", "innate immunity" ]	Step-Wise Loss of Bacterial Flagellar Torsion Confers Progressive Phagocytic Evasion	journal.ppat.1002253	null	[ [ "Pathogen recognition by the innate immune system is one of the first lines of defense in cellular immunity to infection [1] .", "However , how bacteria establish chronic infections , as observed in patients with cystic fibrosis ( CF ) , and the reasons that these infective agents cannot be eliminated by ...	[ "Phagocytosis of bacteria by innate immune cells is a primary method of bacterial clearance during infection .", "However , the mechanisms by which the host cell recognizes bacteria and consequentially initiates phagocytosis are largely unclear .", "Previous studies of the bacterium Pseudomonas aeruginosa have ...	[ "Flagella-driven bacterial motility , referred to as swimming , has been recognized for over 20 years to affect the ability of bacteria to infect and colonize a host .", "The common theme is that bacteria must be motile to colonize the host but must become non-motile to chronically persist; this has been observed...	2011
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Tunable Stochastic Pulsing in the Escherichia coli Multiple Antibiotic Resistance Network from Interlinked Positive and Negative Feedback Loops	journal.pcbi.1003229	null	[ [ "Antimicrobial drug resistance has been studied extensively due to its clinical importance .", "Traditionally , research has focused on heritable genetic mechanisms , but transient mechanisms , where only a subset of the population expresses resistance genes , are beginning to receive attention for their ...	[ "Cells live in uncertain , dynamic environments and have many mechanisms for sensing and responding to changes in their surroundings .", "However , sudden fluctuations in the environment can be catastrophic to a population if it relies solely on sensory responses , which have a delay associated with them .", "C...	[ "Cells can sense their environment and respond to changes , however the sudden appearance of a stressor can be catastrophic if the time it takes to sense and initiate a response is slow relative to the action of a stressor .", "A possible solution is to couple a sensory response with a stochastic , random approac...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "model organisms", "genetics", "immunology", "biology", "genomics", "molecular cell biology", "genetics and genomics" ]	A Conserved Role for Human Nup98 in Altering Chromatin Structure and Promoting Epigenetic Transcriptional Memory	journal.pbio.1001524	In yeast and humans, interaction of a nuclear pore protein with promoters alters chromatin structure and allows RNA polymerase II to bind, poising them for faster reactivation for several generations.	[ [ "The nuclear pore complex ( NPC ) is a conserved macromolecular structure that mediates the essential transport of molecules between the nucleus and the cytoplasm [1] .", "The NPC is an 8-fold symmetric channel derived from ∼30 proteins associated with cytoplasmic filaments and a nucleoplasmic “basket” [2...	[ "The interaction of nuclear pore proteins ( Nups ) with active genes can promote their transcription .", "In yeast , some inducible genes interact with the nuclear pore complex both when active and for several generations after being repressed , a phenomenon called epigenetic transcriptional memory .", "This in...	[ "Cells respond to changes in nutrients or signaling molecules by altering the expression of genes .", "The rate at which genes are turned on is not uniform; some genes are induced rapidly and others are induced slowly .", "In brewer's yeast , previous experience can enhance the rate at which genes are turned on...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "biotechnology", "plant anatomy", "plant growth and development", "plant cell biology", "plant embryo anatomy", "brassica", "chloroplasts", "developmental biology", "plant science", "model organisms", "genetically modified plants", "experimental organism systems", "seedlings", "embryos", ...	Functional divergence of chloroplast Cpn60α subunits during Arabidopsis embryo development	journal.pgen.1007036	null	[ [ "Chaperonins are a class of molecular chaperones that are characterized by a barrel-shaped architecture formed by two stacked oligomeric rings consisting of several subunits of approximately 60 kDa .", "Two types of chaperonins have been identified: type I chaperonins are found in eubacteria , chloroplast...	[ "Chaperonins are a class of molecular chaperones that assist in the folding and assembly of a wide range of substrates .", "In plants , chloroplast chaperonins are composed of two different types of subunits , Cpn60α and Cpn60β , and duplication of Cpn60α and Cpn60β genes occurs in a high proportion of plants .",...	[ "Chaperonins are large oligomeric complexes that are involved in the folding and assembly of numerous proteins in various species .", "In contrast to other types of chaperonins , chloroplast chaperonins are characterized by the hetero-oligomeric structure composed of two unique types of subunits , Cpn60α and Cpn6...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Mycobacterium Ulcerans Treatment – Can Antibiotic Duration Be Reduced in Selected Patients?	journal.pntd.0003503	null	[ [ "Mycobacterium ulcerans ( M . ulcerans ) infection , or Buruli ulcer , is a necrotizing infection of the skin and subcutaneous tissue and is the third most common mycobacterial infection in immunocompetant people after tuberculosis and leprosy .", "It has been reported in 33 predominantly subtropical and ...	[ "Mycobacterium ulcerans ( M . ulcerans ) is a necrotizing skin infection endemic to the Bellarine Peninsula , Australia .", "Current treatment recommendations include 8 weeks of combination antibiotics , with adjuvant surgery if necessary .", "However , antibiotic toxicity often results in early treatment cessa...	[ "Buruli ulcer is a necrotizing skin and subcutaneous tissue infection caused by Mycobacterium ulcerans and is the third most common mycobacterial infection , behind tuberculosis and leprosy , world-wide .", "In recent years , the World Health Organisation has modified its guidelines for M . ulcerans treatment , m...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "computational biology/evolutionary modeling", "genetics and genomics/gene expression", "developmental biology/stem cells", "computational biology/transcriptional regulation" ]	Modeling Co-Expression across Species for Complex Traits: Insights to the Difference of Human and Mouse Embryonic Stem Cells	journal.pcbi.1000707	null	[ [ "A major goal in biology is to understand the evolution of complex traits , such as the development of multicellular body plans or an organism's physical state as it ages [1] .", "To a certain extent , complex traits are governed by regulated gene expression , and considerable plasticity exists such that ...	[ "Complex interactions between genes or proteins contribute substantially to phenotypic evolution .", "We present a probabilistic model and a maximum likelihood approach for cross-species clustering analysis and for identification of conserved as well as species-specific co-expression modules .", "This model ena...	[ "A major goal in biology is to understand the evolution of complex traits , such as the development of multicellular body plans .", "To a certain extent , complex traits are governed by regulated gene expression .", "The comparison expression data between species requires extra considerations than sequence comp...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "plant science", "plant biology", "biology", "genomics", "microbiology", "genetics and genomics" ]	Genome-wide Transcriptional Profiling of Appressorium Development by the Rice Blast Fungus Magnaporthe oryzae	journal.ppat.1002514	null	[ [ "The ascomycete fungus Magnaporthe oryzae is the causal agent of rice-blast disease , which can destroy up to 18% of the annual rice harvest [1] .", "Because more than half of the global population depends on rice as a staple food crop , rice blast disease represents a significant factor that impacts upon...	[ "The rice blast fungus Magnaporthe oryzae is one of the most significant pathogens affecting global food security .", "To cause rice blast disease the fungus elaborates a specialised infection structure called an appressorium .", "Here , we report genome wide transcriptional profile analysis of appressorium dev...	[ "The fungus Magnaporthe oryzae causes a disease of rice , known as rice blast .", "Half the world's population depends on rice as a staple food source and rice blast disease destroys 18% of the rice harvest annually .", "It is therefore important to develop methods to control blast as a means of ensuring global...	2012
[ "Introduction", "Materials and methods", "Results" ]	[ "innate immune system", "medicine and health sciences", "immune physiology", "cytokines", "cancer treatment", "immunology", "parasitic diseases", "nematode infections", "oncology", "animal models", "developmental biology", "model organisms", "gastroenterology and hepatology", "experimental...	Chronic Trichuris muris infection causes neoplastic change in the intestine and exacerbates tumour formation in APC min/+ mice	journal.pntd.0005708	null	[ [ "Colon cancer is one of the leading causes of death within the western world and prevalence in developing countries has increased in the last decade [1] .", "There exists a strong link between inflammation and cancer [2] .", "This is emphasized in the colon where individuals with inflammatory bowel di...	[ "Incidences of infection-related cancers are on the rise in developing countries where the prevalence of intestinal nematode worm infections are also high .", "Trichuris muris ( T . muris ) is a murine gut-dwelling nematode that is the direct model for human T . trichiura , one of the major soil-transmitted helmi...	[ "It is estimated that now 2 billion people currently live with chronic parasitic worm infections .", "As the incidences of cancer increase worldwide , the importance of these chronic inflammatory conditions on the development of cancer becomes more important .", "Several bacterial , viral and parasitic infectio...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Immune Protection against Trypanosoma cruzi Induced by TcVac4 in a Canine Model	journal.pntd.0003625	null	[ [ "Trypanosoma cruzi ( T . cruzi ) is a pathogenic protozoan that belongs to the Trypanosomatidae family .", "It is the etiologic agent of Chagas disease [1] .", "Approximately , 5% of the infected humans develop a lethal acute infection , and 30–40% progress to a chronic debilitating illness of the car...	[ "Chagas disease , caused by Trypanosoma cruzi , is endemic in southern parts of the American continent .", "Herein , we have tested the protective efficacy of a DNA-prime/T .", "rangeli-boost ( TcVac4 ) vaccine in a dog ( Canis familiaris ) model .", "Dogs were immunized with two-doses of DNA vaccine ( pcDNA3...	[ "Chagas disease , is an illness caused by Trypanosoma cruzi , is endemic in southern parts of the American continent .", "We tested the protective efficacy of a DNA-prime/T .", "rangeli-boost ( TcVac4 ) vaccine in a dog ( Canis familiaris ) model .", "Dogs were immunized with two-doses of DNA vaccine followed...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "developmental biology", "biology", "cell differentiation" ]	RNA-seq Analysis of Host and Viral Gene Expression Highlights Interaction between Varicella Zoster Virus and Keratinocyte Differentiation	journal.ppat.1003896	null	[ [ "Replication in skin and mucosa is central to the pathogenesis of varicella zoster virus ( VZV ) , a member of the alphaherpesvirus subfamily that causes chickenpox ( varicella ) upon a primary infection and shingles ( herpes-zoster ) following reactivation from a neuronal latent state .", "In both diseas...	[ "Varicella zoster virus ( VZV ) is the etiological agent of chickenpox and shingles , diseases characterized by epidermal skin blistering .", "Using a calcium-induced keratinocyte differentiation model we investigated the interaction between epidermal differentiation and VZV infection .", "RNA-seq analysis show...	[ "Varicella zoster virus ( VZV ) causes chickenpox and shingles , which are characterised by the formation of fluid-filled skin lesions .", "Infectious viral particles present in these lesions are critical for airborne spread to cause chickenpox in non-immune contacts and for infection of nerve ganglia via nerve e...	2014
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "developmental biology/molecular development", "molecular biology/translational regulation", "genetics and genomics/gene expression" ]	Regulation of Ubx Expression by Epigenetic Enhancer Silencing in Response to Ubx Levels and Genetic Variation	journal.pgen.1000633	null	[ [ "The transcriptional control of gene expression in eukaryotes is governed by cis-regulatory elements , also known as enhancers , that integrate cell-type and temporal information by binding combinations of transcription factors .", "Genes that exhibit complex expression patterns are typically controlled b...	[ "For gene products that must be present in cells at defined concentrations , expression levels must be tightly controlled to ensure robustness against environmental , genetic , and developmental noise .", "By studying the regulation of the concentration-sensitive Drosophila melanogaster Hox gene Ultrabithorax ( U...	[ "Gene expression is generally governed by cis-regulatory elements , also called enhancers .", "For genes whose expression levels must be tightly controlled , enhancer activities must be tightly regulated .", "In this work , we show that enhancers that control the expression of the Hox gene Ultrabithorax ( Ubx )...	2009
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "microbiology/cellular microbiology and pathogenesis", "microbiology/immunity to infections" ]	Monoclonal Antibodies Against Peptidorhamnomannans of Scedosporium apiospermum Enhance the Pathogenicity of the Fungus	journal.pntd.0000853	null	[ [ "The filamentous and saprophytic fungus Scedosporium apiospermum is an emerging clinically important pathogen that causes localized as well as disseminated infections in both immunocompetent and immunocompromised hosts [1]–[2] .", "S . apiospermum is an important cause of mycetoma , acquired by traumatic ...	[ "Scedosporium apiospermum is part of the Pseudallescheria-Scedosporium complex .", "Peptidorhamnomannans ( PRMs ) are cell wall glycopeptides present in some fungi , and their structures have been characterized in S . apiospermum , S . prolificans and Sporothrix schenckii .", "Prior work shows that PRMs can int...	[ "The incidence of fungal infections has increased dramatically over the last 50 years , largely because of the increasing size of the population at risk , which especially includes immunocompromised hosts .", "Scedosporium apiospermum is a filamentous fungus that causes a variety of infections , ranging from loca...	2010
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "sequencing techniques", "medicine and health sciences", "immune physiology", "tissue proteins", "pathology and laboratory medicine", "pathogens", "immunology", "tropical diseases", "microbiology", "vertebrates", "animals", "mammals", "amino acid sequence analysis", "viruses", "rabies", ...	Novel mass spectrometry based detection and identification of variants of rabies virus nucleoprotein in infected brain tissues	journal.pntd.0006984	null	[ [ "Mass spectrometry ( MS ) based proteomics is a collection of rapidly evolving techniques being utilized as a diagnostic tool for infectious diseases .", "MALDI-TOF MS ( matrix-assisted laser desorption/ionization–time-of-flight ) is being used in clinical microbiology laboratories to identify an impressi...	[ "Human rabies is an encephalitic disease transmitted by animals infected with lyssaviruses .", "The most common lyssavirus that causes human infection is rabies virus ( RABV ) , the prototypic member of the genus .", "The incubation period of RABV in humans varies from few weeks to several months in some instan...	[ "Although rabies is almost always fatal after the symptom onset phase , it can be prevented by timely administration of post-exposure prophylaxis ( PEP ) , which involves passive antibody transfer and vaccination .", "One of the primary laboratory confirmatory tests for RABV infection is antigen detection , direc...	2018

Subsets and Splits

No community queries yet

The top public SQL queries from the community will appear here once available.