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headings list	keywords list	title stringlengths 20 281	id stringlengths 20 20	toc stringlengths 57 522 ⌀	sections list	abstract list	summary list	year stringclasses 13 values
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "text mining", "natural language processing", "social and behavioral sciences", "population modeling", "social networks", "sociology", "biology", "computational biology", "infectious disease modeling" ]	Assessing Vaccination Sentiments with Online Social Media: Implications for Infectious Disease Dynamics and Control	journal.pcbi.1002199	null	[ [ "Outbreaks of vaccine preventable diseases are a major public health issue .", "Outbreaks are more likely to occur if either overall vaccination rates decline [1] , or if communities with very low vaccination rates increase in frequency or size [2] , [3] .", "As individual health behaviors appear to b...	[ "There is great interest in the dynamics of health behaviors in social networks and how they affect collective public health outcomes , but measuring population health behaviors over time and space requires substantial resources .", "Here , we use publicly available data from 101 , 853 users of online social medi...	[ "Sentiments about vaccination can strongly affect individual vaccination decisions .", "Measuring such sentiments - and how they are distributed in a population - is typically a difficult and resource-intensive endeavor .", "We use publicly available data from Twitter , a popular online social media service , t...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology", "microbiology" ]	The Effect of Cell Growth Phase on the Regulatory Cross-Talk between Flagellar and Spi1 Virulence Gene Expression	journal.ppat.1003987	null	[ [ "Tens of millions of human cases of Salmonellosis , a foodborne gastroenteritis caused by Salmonella enterica , occur worldwide every year killing more than a hundred thousand people annually ( World Health Organization Fact sheet N°139 , August 2013 ) .", "Typhoid fever caused by Salmonella Typhi kills a...	[ "The flagellar regulon controls Salmonella biofilm formation , virulence gene expression and the production of the major surface antigen present on the cell surface: flagellin .", "At the top of a flagellar regulatory hierarchy is the master operon , flhDC , which encodes the FlhD4C2 transcriptional complex requi...	[ "Flagellar-mediated motility is fundamental to Salmonella pathogenesis , which takes the lives of hundreds of thousands of people each year .", "The genes of the Salmonella pathogenicity island 1 and those of the flagellar regulon are part of the same transcriptional hierarchy .", "We report the novel finding w...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/helminth infections" ]	Suppression of mRNAs Encoding Tegument Tetraspanins from Schistosoma mansoni Results in Impaired Tegument Turnover	journal.ppat.1000840	null	[ [ "Schistosomes are parasitic trematodes that cause chronic infection in over 207 million people in 76 developing tropical countries .", "Schistosomiasis is generally associated with poverty , poor water supply and inadequate sanitation [1] .", "Infection rates and intensities are high in early childhoo...	[ "Schistosomes express a family of integral membrane proteins , called tetraspanins ( TSPs ) , in the outer surface membranes of the tegument .", "Two of these tetraspanins , Sm-TSP-1 and Sm-TSP-2 , confer protection as vaccines in mice , and individuals who are naturally resistant to S . mansoni infection mount a...	[ "Schistosomes , or blood flukes , reside in the blood vessels surrounding the liver and bowel of their human hosts .", "They infect 200 million people and kill many thousands each year in developing countries .", "The parasites cover themselves in a unique series of cell membranes called the tegument .", "Mol...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Beyond Glycolysis: GAPDHs Are Multi-functional Enzymes Involved in Regulation of ROS, Autophagy, and Plant Immune Responses	journal.pgen.1005199	null	[ [ "Innate immunity is the most ancient and evolutionarily conserved system mediating pathogen perception in animals , fungi and plants [1] .", "Although plants lack an adaptive immune system , germ line encoded plant immune receptors recognize pathogen derived molecules or proteins and mount a successful de...	[ "Glyceraldehyde-3-phosphate dehydrogenase ( GAPDH ) is an important enzyme in energy metabolism with diverse cellular regulatory roles in vertebrates , but few reports have investigated the importance of plant GAPDH isoforms outside of their role in glycolysis .", "While animals possess one GAPDH isoform , plants...	[ "Plants can be infected by all pathogen classes , significantly impacting crop production and food security .", "Innate immune responses are critical to plant survival but must be tightly regulated in order to avoid negative impacts on growth and development .", "Here , we investigated the role of glyceraldehyd...	2015
[ "Introduction", "Results", "Methods", "Discussion" ]	[ "invertebrates", "traumatic injury", "medicine and health sciences", "cognitive neurology", "neural networks", "engineering and technology", "caenorhabditis", "nervous system", "neuroscience", "animals", "biomechanics", "biological locomotion", "animal models", "decision analysis", "caen...	Functionality and Robustness of Injured Connectomic Dynamics in C. elegans: Linking Behavioral Deficits to Neural Circuit Damage	journal.pcbi.1005261	null	[ [ "Understanding networked and dynamic systems is of growing importance across the engineering , physical and biological sciences .", "Such systems are often composed of a diverse set of dynamic elements whose connectivity are prescribed by sparse and/or dense connections that are local and/or long-range in...	[ "Using a model for the dynamics of the full somatic nervous system of the nematode C . elegans , we address how biological network architectures and their functionality are degraded in the presence of focal axonal swellings ( FAS ) arising from neurodegenerative disease and/or traumatic brain injury .", "Using bi...	[ "Neurodegenerative diseases such as Alzheimer’s disease , Creutzfeldt-Jakob’s disease , HIV dementia , Multiple Sclerosis and Parkinson’s disease are leading causes of cognitive impairment and death worldwide .", "Similarly , traumatic brain injury , the signature injury of the Iraq and Afghanistan wars , affects...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "innate immune system", "medicine and health sciences", "immune cells", "pathology and laboratory medicine", "immunology", "microbiology", "infectious disease immunology", "white blood cells", "animal cells", "viral immune evasion", "pathogenesis", "immune response", "immune...	Inhibition of the TRAIL Death Receptor by CMV Reveals Its Importance in NK Cell-Mediated Antiviral Defense	journal.ppat.1004268	null	[ [ "Tumor necrosis factor ( TNF ) -family cytokines regulate multiple aspects of host antiviral immunity , in part through their abilities to promote cell death and survival [1] .", "In many cases , this involves both the direct killing of virally infected cells , as well as assisting in terminating the host...	[ "TNF-related apoptosis inducing ligand ( TRAIL ) death receptors ( DR ) regulate apoptosis and inflammation , but their role in antiviral defense is poorly understood .", "Cytomegaloviruses ( CMV ) encode many immune-modulatory genes that shape host immunity , and they utilize multiple strategies to target the TN...	[ "TRAIL death receptors regulate apoptosis and inflammation , and growing evidence suggests their importance in promoting antiviral defenses .", "Many viruses encode strategies to modulate signaling by TNF family cytokines in order to shape host defenses .", "Cytomegaloviruses encode many immune modulatory genes...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology/cell signaling", "cell biology/cell growth and division", "computational biology/signaling networks", "computational biology/systems biology", "molecular biology/dna repair" ]	Minimum Criteria for DNA Damage-Induced Phase Advances in Circadian Rhythms	journal.pcbi.1000384	null	[ [ "Circadian rhythms are periodic physiological events that recur about every 24 hours .", "The importance of circadian rhythms is well recognized in many different organisms' survival as well as in human physiology .", "Misregulations in circadian rhythms may lead to different conditions such as depres...	[ "Robust oscillatory behaviors are common features of circadian and cell cycle rhythms .", "These cyclic processes , however , behave distinctively in terms of their periods and phases in response to external influences such as light , temperature , nutrients , etc .", "Nevertheless , several links have been fou...	[ "Molecular components and mechanisms that connect cell cycle and circadian rhythms are important for the well-being of an organism .", "Cell cycle machinery regulates the progress of cell growth and division while the circadian rhythm network generates an ∼24 h time-keeping mechanism that regulates the daily proc...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases/viral infections" ]	Subversion of Innate Defenses by the Interplay between DENV and Pre-Existing Enhancing Antibodies: TLRs Signaling Collapse	journal.pntd.0000924	null	[ [ "Dengue is the most prevalent vector-borne disease occurring in tropical and subtropical regions with an estimated 50 to 100 million people infected each year .", "This includes 500 , 000 cases of life-threatening disease which are dengue hemorrhagic fever ( DHF ) and dengue shock syndrome ( DSS ) [1] , [...	[ "The phenomenon of antibody dependent enhancement as a major determinant that exacerbates disease severity in DENV infections is well accepted .", "While the detailed mechanism of antibody enhanced disease severity is unclear , evidence suggests that it is associated with both increased DENV infectivity and suppr...	[ "Dengue is the most common vector-borne viral disease in humans , with 50–100 million infections per year .", "The severity of dengue ranges from an acute febrile illness , DF , to a life-threatening vascular leakage syndrome with or without shock , DHF/DSS .", "Determinants of these syndromes are mainly host f...	2010
[ "Introduction", "Results", "Discussion", "Material and Methods" ]	[ "computational biology/systems biology", "developmental biology/morphogenesis and cell biology" ]	The Role of Spatially Controlled Cell Proliferation in Limb Bud Morphogenesis	journal.pbio.1000420	Oriented cell behaviors likely have a more important role in limb bud elongation during development than previously suggested by the “growth-based morphogenesis” hypothesis.	[ [ "Vertebrate limb development is a classical model system which has contributed to some of the key concepts in the developmental field [1] , [2] .", "Over a period of 1–2 d a roughly homogeneous mass of undifferentiated mesenchymal cells develops into a complex collection of different cell types ( includin...	[ "Although the vertebrate limb bud has been studied for decades as a model system for spatial pattern formation and cell specification , the cellular basis of its distally oriented elongation has been a relatively neglected topic by comparison .", "The conventional view is that a gradient of isotropic proliferatio...	[ "Although the vertebrate limb bud has been studied for decades as a classical model system for the spatial control of cell fates , the question of how the limb bud physically elongates has been much less studied .", "One particular hypothesis has been dominant in the field , known either as the proliferation grad...	2010
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Seasonal and Spatial Dynamics of the Primary Vector of Plasmodium knowlesi within a Major Transmission Focus in Sabah, Malaysia	journal.pntd.0004135	null	[ [ "Significant progress has been made fighting malaria in the last decade , decreasing the incidence of cases and mortality by 30% and 47% respectively on a global scale [1] and reducing cases by 76% in Asia Pacific countries [2] .", "The development and use of better tools for diagnostics and treatment [3]...	[ "The simian malaria parasite Plasmodium knowlesi is emerging as a public health problem in Southeast Asia , particularly in Malaysian Borneo where it now accounts for the greatest burden of malaria cases and deaths .", "Control is hindered by limited understanding of the ecology of potential vector species .", ...	[ "The first natural infection of Plasmodium knowlesi was reported 40 years ago .", "At that time it was perceived that the infection would not affect humans .", "However , now P . knowlesi is the predominant malaria species ( 38% of the cases ) infecting people in Malaysia and is a notable obstacle to malaria el...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/gene expression", "genetics and genomics/nuclear structure and function", "genetics and genomics/chromosome biology", "genetics and genomics/gene function", "genetics and genomics/epigenetics" ]	SU(VAR)3-7 Links Heterochromatin and Dosage Compensation in Drosophila	journal.pgen.1000066	null	[ [ "Drosophila melanogaster uses two systems of whole chromosome regulation: dosage compensation mediating the two fold up-regulation of male X-linked genes and the Painting of Fourth , POF , regulating the mainly heterochromatic fourth chromosome .", "Binding of POF to the fourth chromosome is dependent on ...	[ "In Drosophila , dosage compensation augments X chromosome-linked transcription in males relative to females .", "This process is achieved by the Dosage Compensation Complex ( DCC ) , which associates specifically with the male X chromosome .", "We previously found that the morphology of this chromosome is sens...	[ "In Drosophila , females have two X chromosomes and males only one .", "The difference in the dose of X-associated genes is compensated by male-specific protein machinery , the Dosage Compensation Complex ( DCC ) , which augments the activity of genes of the single male X . We report that the specific targeting o...	2008
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "statistical noise", "engineering and technology", "nervous system", "signal processing", "ocular anatomy", "electrophysiology", "neuroscience", "mathematics", "statistics (mathematics)", "computational neuroscience", "coding mechanisms", "gaussian noise", "...	How Do Efficient Coding Strategies Depend on Origins of Noise in Neural Circuits?	journal.pcbi.1005150	null	[ [ "Our sensory systems encode information about the external environment and transmit this information to higher brain areas with remarkable fidelity , despite a number of sources of noise that corrupt the incoming signal .", "Noise—variability in neural responses that masks the relevant signal—can arise fr...	[ "Neural circuits reliably encode and transmit signals despite the presence of noise at multiple stages of processing .", "The efficient coding hypothesis , a guiding principle in computational neuroscience , suggests that a neuron or population of neurons allocates its limited range of responses as efficiently as...	[ "For decades the efficient coding hypothesis has been a guiding principle in determining how neural systems can most efficiently represent their inputs .", "However , conclusions about whether neural circuits are performing optimally depend on assumptions about the noise sources encountered by neural signals as t...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology and life sciences", "medicine and health sciences" ]	A HECT Ubiquitin-Protein Ligase as a Novel Candidate Gene for Altered Quinine and Quinidine Responses in Plasmodium falciparum	journal.pgen.1004382	null	[ [ "Quinine , an active ingredient of cinchona bark , is an important drug in the pharmacopoeia against malaria , an infectious disease that causes an estimated 219 million clinical cases and 0 . 66 million deaths annually [1] .", "Quinine is used , together with partner drugs , as a second line treatment of...	[ "The emerging resistance to quinine jeopardizes the efficacy of a drug that has been used in the treatment of malaria for several centuries .", "To identify factors contributing to differential quinine responses in the human malaria parasite Plasmodium falciparum , we have conducted comparative quantitative trait...	[ "Quinine , a natural product from cinchona bark , has been used in the treatment of malaria for centuries .", "Unfortunately , a progressive loss in responsiveness of the human malaria parasite Plasmodium falciparum to quinine has been observed , particularly in Southeast Asia , where cases of quinine treatment f...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "taste buds", "medicine and health sciences", "social sciences", "neuroscience", "epithelial cells", "tongue", "connective tissue cells", "nerve fibers", "digestive system", "animal cells", "taste", "stromal cells", "connective tissue", "biological tissue", "sensory receptors", "hedgeh...	Maintenance of Taste Organs Is Strictly Dependent on Epithelial Hedgehog/GLI Signaling	journal.pgen.1006442	null	[ [ "Hedgehog ( HH ) signaling plays complex regulatory roles in adult organ and tissue maintenance [1] .", "From regulation in epithelia that turn over slowly and normally are ‘quiescent’ [2] to skin that regularly renews [3] , roles for HH activity are temporally- and niche-specific , and rely on interactio...	[ "For homeostasis , lingual taste papilla organs require regulation of epithelial cell survival and renewal , with sustained innervation and stromal interactions .", "To investigate a role for Hedgehog/GLI signaling in adult taste organs we used a panel of conditional mouse models to manipulate GLI activity within...	[ "Taste papillae are small organs visible on the surface of the tongue that contain taste buds , which are connected to nerves that transmit signals for taste sensation to the brain .", "To function properly , taste papilla and taste bud cells need to be continuously replenished .", "We are studying how collecti...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "ecology and environmental sciences", "water resources", "face", "pathology and laboratory medicine", "immunology", "tropical diseases", "health care", "bacterial diseases", "signs and symptoms", "eye diseases", "sanitation", "neglected tropical diseases", "...	Sanitation and water supply coverage thresholds associated with active trachoma: Modeling cross-sectional data from 13 countries	journal.pntd.0006110	null	[ [ "Trachoma is the leading infectious cause of blindness [1] .", "An estimated 450 , 000 people suffer from trachoma-related blindness with another 1 . 4 million suffering from trachoma-related moderate to severe visual impairment globally [2] .", "Trachoma is a public health problem in 42 countries , w...	[ "Facial cleanliness and sanitation are postulated to reduce trachoma transmission , but there are no previous data on community-level herd protection thresholds .", "We characterize associations between active trachoma , access to improved sanitation facilities , and access to improved water sources for the purpo...	[ "Trachoma is the leading infectious cause of blindness .", "Previous association studies have primarily assessed household-level exposures , ignoring potential community-level protection from water and sanitation coverage in neighboring houses .", "There is biological plausibility that increased community-level...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "physiological processes", "behavioral neuroscience", "neurochemistry", "neuromodulation", "animal behavior", "neurochemicals", "physiology", "sleep", "hormones", "biology and life sciences", "neuropeptides", "evolutionary biology", "zoology", "neuroscience", "peptide h...	A Homeostatic Sleep-Stabilizing Pathway in Drosophila Composed of the Sex Peptide Receptor and Its Ligand, the Myoinhibitory Peptide	journal.pbio.1001974	A ligand of the sex peptide receptor maintains sleep stability and homeostasis by inhibiting wakefulness-promoting neurons in Drosophila.	[ [ "Sleep is an evolutionarily conserved physiological state marked by sustained and reversible quiescence during which animals display reduced responsiveness to external stimuli [1] .", "Sleep is important for diverse biological processes , such as immune responses , metabolism , obesity , longevity , and l...	[ "Sleep , a reversible quiescent state found in both invertebrate and vertebrate animals , disconnects animals from their environment and is highly regulated for coordination with wakeful activities , such as reproduction .", "The fruit fly , Drosophila melanogaster , has proven to be a valuable model for studying...	[ "Sleep is a common trait in animals , from insects to mammals , and it needs to be coordinated with other critical activities such as feeding and reproduction .", "However , the mechanisms by which this is achieved are not fully understood .", "The fruit fly Drosophila melanogaster has become a key model organi...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases/helminth infections", "immunology/immunity to infections", "immunology/immune response", "infectious diseases/neglected tropical diseases" ]	Immunisation with a Multivalent, Subunit Vaccine Reduces Patent Infection in a Natural Bovine Model of Onchocerciasis during Intense Field Exposure	journal.pntd.0000544	null	[ [ "Onchocerciasis ( ‘River Blindness’ ) is recognised as one of the world's most important neglected tropical diseases [1] .", "The first-stage larva ( microfilaria , Mf ) of the nematode Onchocerca volvulus causes debilitating lesions of the eyes and skin [2] , with >99% of the global burden confined to su...	[ "Human onchocerciasis , caused by the filarial nematode Onchocerca volvulus , is controlled almost exclusively by the drug ivermectin , which prevents pathology by targeting the microfilariae .", "However , this reliance on a single control tool has led to interest in vaccination as a potentially complementary st...	[ "River blindness , or onchocerciasis , is caused by a parasitic worm ( Onchocerca volvulus ) that is transmitted by blood-feeding blackflies , which breed in fast-flowing rivers .", "More than 37 million people are infected and may experience visual impairment and/or severe dermatitis .", "Control of onchocerci...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "mathematics", "physiology/muscle and connective tissue", "biophysics/theory and simulation", "physiology/motor systems", "computational biology/systems biology" ]	Interactions between Connected Half-Sarcomeres Produce Emergent Mechanical Behavior in a Mathematical Model of Muscle	journal.pcbi.1000560	null	[ [ "Many biological systems are irreducible meaning that they have more complicated properties than the structures of which they are composed .", "Detailed understanding of a complete system therefore requires knowledge both about how its individual components function and about how those components interact...	[ "Most reductionist theories of muscle attribute a fiber's mechanical properties to the scaled behavior of a single half-sarcomere .", "Mathematical models of this type can explain many of the known mechanical properties of muscle but have to incorporate a passive mechanical component that becomes ∼300% stiffer in...	[ "Quantitative muscle biophysics has been dominated for the last 60 years by reductionist theories that try to explain the mechanical properties of an entire muscle fiber as the scaled behavior of a single half-sarcomere ( typical muscle fibers contain ∼106 such structures ) .", "This work tests the hypothesis tha...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public health and epidemiology", "mathematical computing", "mathematics", "epidemiology", "infectious disease epidemiology" ]	Age-Specificity of Clinical Dengue during Primary and Secondary Infections	journal.pntd.0001180	null	[ [ "Dengue ranks among the most important infectious diseases with a major impact on public health in many countries in the tropics and subtropics .", "Estimates showed that approximately 3 . 5 billion people , ∼55% of the world's population live in countries at risk for dengue [1] .", "The global incide...	[ "This study aims to estimate the age-specific risks of clinical dengue attack ( i . e . , the risk of symptomatic dengue among the total number of dengue virus ( DENV ) infections ) during primary and secondary infections .", "We analyzed two pieces of epidemiological information in Binh Thuan province , southern...	[ "Although age at dengue virus ( DENV ) infection is recognized as playing a key role in characterizing the risks of clinical attack and disease severity , the contributions of age to disease development have yet to be quantified in detail .", "We estimated the age-specific risk of clinical attack ( i . e . , the ...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "horizontal gene transfer", "chemical compounds", "gene transfer", "nitrates", "fungal evolution", "hypoxia", "bacteria", "research and analysis methods", "sequence analysis", "mycology", "sequence alignment", "bioinformatics", "gene expression", "chemistry", "actinobacteria", "genetic...	Horizontal acquisition of a hypoxia-responsive molybdenum cofactor biosynthesis pathway contributed to Mycobacterium tuberculosis pathoadaptation	journal.ppat.1006752	null	[ [ "Mycobacterium tuberculosis ( Mtb ) is an obligate , strictly human-adapted pathogen of major public health importance [1] .", "One of the most striking features of this microorganism is its ability to persist in lung lesions , the granulomas , for years and even decades in a so-called “dormant” state , b...	[ "The unique ability of the tuberculosis ( TB ) bacillus , Mycobacterium tuberculosis , to persist for long periods of time in lung hypoxic lesions chiefly contributes to the global burden of latent TB .", "We and others previously reported that the M . tuberculosis ancestor underwent massive episodes of horizonta...	[ "Mycobacterium tuberculosis , the etiological agent of tuberculosis ( TB ) , can persist for years and even decades in the lungs of its human host .", "Here we report that a unique M . tuberculosis gene cluster involved in the synthesis of the molybdenum cofactor , a cofactor for several oxidoreductases including...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "infectious disease epidemiology", "immunology", "tropical diseases", "ebola hemorrhagic fever", "simulation and modeling", "vaccines", "preventive medicine", "clinical medicine", "mathematics", "statistics (mathematics)", "neglected tropical diseases", "pharm...	Using simulation to aid trial design: Ring-vaccination trials	journal.pntd.0005470	null	[ [ "The West African Ebola epidemic highlighted the need to identify a range of trial designs to evaluate vaccine effects rapidly , efficiently and rigorously during emerging disease outbreaks .", "The ring-vaccination trial approach employed in the Ebola ça suffit trial in Guinea is one innovative approach ...	[ "The 2014–6 West African Ebola epidemic highlights the need for rigorous , rapid clinical trial methods for vaccines .", "A challenge for trial design is making sample size calculations based on incidence within the trial , total vaccine effect , and intracluster correlation , when these parameters are uncertain ...	[ "The urgency , as well as the logistical and sometimes ethical challenges of clinical trials for interventions during epidemics of emerging diseases prompts the need for novel designs and analytic strategies .", "The successful use of a novel cluster-randomized ring-vaccination trial to test an Ebola vaccine in G...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "analytical chemistry", "molecular cell biology", "gene expression", "genetics", "chemical biology", "epigenetics", "biology", "chemistry", "molecular biology", "genetics and genomics", "histone modification" ]	Quantitative Analysis of Histone Modifications: Formaldehyde Is a Source of Pathological N6-Formyllysine That Is Refractory to Histone Deacetylases	journal.pgen.1003328	null	[ [ "In addition to physiological secondary modifications , proteins are subjected to reactions with endogenous electrophiles generated by oxidative stress , inflammation , and normal cell metabolic processes [1]–[5] .", "These adventitious or pathological modifications typically arise by reaction of the nucl...	[ "Aberrant protein modifications play an important role in the pathophysiology of many human diseases , in terms of both dysfunction of physiological modifications and the formation of pathological modifications by reaction of proteins with endogenous electrophiles .", "Recent studies have identified a chemical ho...	[ "Oxidative stress and inflammation lead to the generation of a multitude of electrophiles in cells that in turn react with nucleophilic macromolecules such as DNA , RNA , polyunsaturated fatty acids , and proteins , leading to progression of a variety of disorders and diseases .", "Emerging evidence points to wid...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "evolutionary biology", "parasite evolution", "plant cell biology", "microbiology", "marine biology", "parasitology", "chloroplast", "plant science", "plants", "divergent evolution", "forms of evolution", "phycology", "biology", "algae", "rna", "rna processing", "nucleic acids", "p...	Evolution of Chloroplast Transcript Processing in Plasmodium and Its Chromerid Algal Relatives	journal.pgen.1004008	null	[ [ "The transition from a photosynthetic to a parasitic lifestyle has occurred a multitude of times across the eukaryotes [1] .", "Parasitism , concomitant with either the complete loss or a severe reduction in dependence on photosynthesis , has been documented in members of the land plants and the green , r...	[ "It is well understood that apicomplexan parasites , such as the malaria pathogen Plasmodium , are descended from free-living algae , and maintain a vestigial chloroplast that has secondarily lost all genes of photosynthetic function .", "Recently , two fully photosynthetic relatives of parasitic apicomplexans ha...	[ "Chloroplasts contain their own genomes , containing two broad functional types of gene: genes encoding proteins directly involved in photosynthesis , and genes with a non-photosynthesis function , such as cofactor biosynthesis , assembly of protein complexes , or expression of the chloroplast genome .", "Thus fa...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "amorphous solids", "medicine and health sciences", "ocular system", "gene regulation", "regulatory proteins", "dna-binding proteins", "glass", "social sciences", "neuroscience", "animals", "animal models", "drosophila melanogaster", "model organisms", "materials science...	Multilevel regulation of the glass locus during Drosophila eye development	journal.pgen.1008269	null	[ [ "While genes of the retinal determination network ( RDN ) are necessary and sufficient for inducing eye tissue in the imaginal-disc , distinct transcription factors are subsequently involved in promoting the developmental program of cell fate determination as well as terminal differentiation .", "The zinc...	[ "Development of eye tissue is initiated by a conserved set of transcription factors termed retinal determination network ( RDN ) .", "In the fruit fly Drosophila melanogaster , the zinc-finger transcription factor Glass acts directly downstream of the RDN to control identity of photoreceptor as well as non-photor...	[ "Changes of the genomic context can have a profound influence on gene expression .", "Addition or deletion of transcription factor binding sites can influence when and where a gene is transcribed .", "Changes in exon/intron structure can affect protein length and composition .", "Stop codon readtrough results...	2019
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "taxonomy", "fish", "atlantic ocean", "japan", "population genetics", "geographical locations", "oceans", "vertebrates", "animals", "osteichthyes", "phylogenetics", "data management", "pacific ocean", "phylogenetic analysis", "speciation", "bodies of water", "population biology", "...	The genomic landscape at a late stage of stickleback speciation: High genomic divergence interspersed by small localized regions of introgression	journal.pgen.1007358	null	[ [ "Speciation is a continuous process through which reproductive isolation is established [1–3] .", "According to the genic view of speciation [4] , when populations are in contact , gene flow is initially restricted at barrier loci ( i . e . loci underlying reproductive isolation ) , leading to the emergen...	[ "Speciation is a continuous process and analysis of species pairs at different stages of divergence provides insight into how it unfolds .", "Previous genomic studies on young species pairs have revealed peaks of divergence and heterogeneous genomic differentiation .", "Yet less known is how localised peaks of ...	[ "When species evolve , reproductive isolation leads to a build-up of differentiation in the genome where genes involved in the process occur .", "Spanning the speciation continuum , stickleback species pairs are ideal for investigating how genomic divergence accumulates during speciation .", "However , much of ...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "enzyme-linked immunoassays", "immune physiology", "pathology and laboratory medicine", "togaviruses", "chikungunya infection", "pathogens", "immunology", "tropical diseases", "microbiology", "geographical locations", "alphaviruses", "pediatrics", "viruses",...	Seroprevalence of Anti-Chikungunya Virus Antibodies in Children and Adults in Managua, Nicaragua, After the First Chikungunya Epidemic, 2014-2015	journal.pntd.0004773	null	[ [ "Chikungunya virus ( CHIKV ) is an alphavirus belonging to the Togaviridae family and is primarily transmitted by Aedes ( Ae . ) aegypti and Ae .", "albopictus mosquitos [1] .", "The main epidemic cycle consists of human-mosquito-human transmission , although a natural reservoir of CHIKV in non-human ...	[ "Chikungunya is a viral disease transmitted by Aedes aegypti and Ae .", "albopictus mosquitoes .", "In late 2013 , chikungunya virus ( CHIKV ) was introduced into the Caribbean island of St . Martin .", "Since then , approximately 2 million chikungunya cases have been reported by the Pan American Health Organ...	[ "Chikungunya is a viral disease primarily characterized by high fever and joint pain .", "Chikungunya virus ( CHIKV ) is transmitted by infected Aedes aegypti and Ae .", "albopictus mosquitos .", "Although chikungunya was first described in 1952 and CHIKV has circulated in parts of Africa and Asia , since the...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	The Trypanosoma cruzi Vitamin C Dependent Peroxidase Confers Protection against Oxidative Stress but Is Not a Determinant of Virulence	journal.pntd.0003707	null	[ [ "The protozoan parasite Trypanosoma cruzi is the causative agent of Chagas disease .", "In Latin America , 8–10 million people are infected , with many more at risk .", "In addition , as a result of migration , the disease is becoming a public health issue in non-endemic regions , such as Europe and t...	[ "The neglected parasitic infection Chagas disease is rapidly becoming a globalised public health issue due to migration .", "There are only two anti-parasitic drugs available to treat this disease , benznidazole and nifurtimox .", "Thus it is important to identify and validate new drug targets in Trypanosoma cr...	[ "The single-cell parasite Trypanosoma cruzi causes Chagas disease , one of the major neglected tropical infections .", "Throughout Latin America , this disease is an important cause of premature death due to heart failure , and it is currently an emerging public health problem in the US , Europe and across the wo...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "medicine and health sciences", "caenorhabditis", "social sciences", "neuroscience", "animals", "animal models", "physiological processes", "developmental biology", "caenorhabditis elegans", "model organisms", "altmetrics", "experimental organism systems", "nerve fibers", ...	Diapause induces functional axonal regeneration after necrotic insult in C. elegans	journal.pgen.1007863	null	[ [ "Animals that enter diapause or hibernate not only survive for long periods of time without eating , but also preserve their nervous systems [1– 3] .", "This protection has been proposed to be a result of a high capacity for detoxification and maintenance of low oxidative stress [1– 4] .", "The bacter...	[ "Many neurons are unable to regenerate after damage .", "The ability to regenerate after an insult depends on life stage , neuronal subtype , intrinsic and extrinsic factors .", "C . elegans is a powerful model to test the genetic and environmental factors that affect axonal regeneration after damage , since it...	[ "Diapause entry and hibernation have the striking ability to protect the nervous system from diverse types of damage .", "Here we show that the diapausing dauer larvae of C . elegans regenerate broken mechanosensory neurons that were damaged by the hyperactivation of degenerins ( MEC-4d ) or by axotomy during dia...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "bacterial diseases", "infectious diseases", "zoonoses", "immune cells", "monocytes", "immunity", "t cells", "microbial control", "immunology", "host-pathogen interaction", "biology", "immunoregulation", "microbiology", "neglected tropical diseases", "bacterial pathogens", ...	CD4+ T Cell-derived IL-10 Promotes Brucella abortus Persistence via Modulation of Macrophage Function	journal.ppat.1003454	null	[ [ "Persistent bacterial infections have a significant impact on public health [1] .", "While evasion of host immune responses is a prerequisite for these chronic infections , the underlying mechanisms are not fully understood .", "Human brucellosis , caused by the intracellular gram-negative coccobacill...	[ "Evasion of host immune responses is a prerequisite for chronic bacterial diseases; however , the underlying mechanisms are not fully understood .", "Here , we show that the persistent intracellular pathogen Brucella abortus prevents immune activation of macrophages by inducing CD4+CD25+ T cells to produce the an...	[ "Brucella spp .", "are pathogens causing chronic intracellular infections that evade detection by pattern recognition receptors of the innate immune system .", "In this work , we tested the hypothesis that , in addition to eliciting a weak proinflammatory response during infection , induction of an immunoregula...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "antimicrobials", "medicine and health sciences", "chemical compounds", "parasitic cell cycles", "drugs", "microbiology", "antifungals", "protozoan life cycles", "parasitic protozoans", "parasitology", "organisms", "developmental biology", "protozoans", "leishmania", "energy-producing or...	In vitro activity and mode of action of phenolic compounds on Leishmania donovani	journal.pntd.0007206	null	[ [ "Leishmaniasis is caused by the parasitic , single-cell eukaryotic organism called Leishmania .", "It is transmitted to man and animals ( e . g . rodents , hydrax , canids ) via a blood meal feed of the female sand-fly [1] .", "Currently , there are about 18 different Leishmania species including Leis...	[ "Leishmaniasis is a disease caused by the protozoan parasite , Leishmania .", "The disease remains a global threat to public health requiring effective chemotherapy for control and treatment .", "In this study , the effect of some selected phenolic compounds on Leishmania donovani was investigated .", "The co...	[ "The available drugs used in treatment of leishmaniasis , a disease caused by the Leishmania parasite , include pentavalent antimonials and amphotericin B . The cost and associated toxicity of the drugs , side effects and the emergence of drug resistance parasites , as well as the discomfort in drug administration ...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Eye Selector Logic for a Coordinated Cell Cycle Exit	journal.pgen.1004981	null	[ [ "Selector genes are transcription factors that instruct the development of organs .", "The processes under the control of selector genes include the assignation of cell fates and their organ-specific responses to extracellular signals [1] .", "But organ development also requires the faithful execution...	[ "Organ-selector transcription factors control simultaneously cell differentiation and proliferation , ensuring the development of functional organs and their homeostasis .", "How this is achieved at the molecular level is still unclear .", "Here we have investigated how the transcriptional pulse of string/cdc25...	[ "Organs develop from groups of undifferentiated cells that proliferate and differentiate into specific cell types .", "During development , the coupling between proliferation and differentiation programs ensures that enough cells of the different cell types are generated .", "This is critical for proper organ f...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "physics", "biochemistry", "computer science", "computational chemistry", "classical mechanics", "statistical mechanics", "chemistry", "biology", "computational biology", "theoretical chemistry", "information technology", "biophysics" ]	Ab Initio Modeling and Experimental Assessment of Janus Kinase 2 (JAK2) Kinase-Pseudokinase Complex Structure	journal.pcbi.1003022	null	[ [ "Janus tyrosine kinase 2 ( JAK2 ) belongs to the JAK family of intracellular non-receptor tyrosine kinases , which mediates signaling from a plethora of cytokine receptors [1] .", "Like other JAK members , JAK2 is kept inactive in the basal state .", "Dimerization/oligomerization of cytokine receptors...	[ "The Janus Kinase 2 ( JAK2 ) plays essential roles in transmitting signals from multiple cytokine receptors , and constitutive activation of JAK2 results in hematopoietic disorders and oncogenesis .", "JAK2 kinase activity is negatively regulated by its pseudokinase domain ( JH2 ) , where the gain-of-function mut...	[ "Protein-protein interactions ( PPIs ) are essential to cellular signal transduction , and structural information about PPIs is crucial for understanding of how cellular machinery functions at the atomistic level .", "However , both experimental structural determination and computational prediction of PPI are cha...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Neuroblastoma Tyrosine Kinase Signaling Networks Involve FYN and LYN in Endosomes and Lipid Rafts	journal.pcbi.1004130	null	[ [ "Neuroblastoma arises from cells of the neural crest , a population of multipotent , migrating cells that differentiate into neurons in the peripheral nervous system , melanocytes , and structural cells [1] .", "Neuroblastoma represents 7–10% of childhood cancers and about half of all infant cancers .", ...	[ "Protein phosphorylation plays a central role in creating a highly dynamic network of interacting proteins that reads and responds to signals from growth factors in the cellular microenvironment .", "Cells of the neural crest employ multiple signaling mechanisms to control migration and differentiation during dev...	[ "Neuroblastoma is a childhood cancer for which therapeutic progress has been slow .", "We analyzed a large number phosphorylated proteins in neuroblastoma cells to discern patterns that indicate functional signal transduction pathways .", "To analyze the data , we developed novel techniques that resolve data st...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	A New Role of the Mosquito Complement-like Cascade in Male Fertility in Anopheles gambiae	journal.pbio.1002255	The complement-related protein TEP1, which helps kill malaria parasites, also labels damaged cells for removal during mosquito spermatogenesis and promotes male fertility in the malaria vector Anopheles gambiae.	[ [ "Anopheles gambiae mosquitoes are the most efficient vectors of human malaria .", "Mosquitoes actively respond to Plasmodium infections by mounting immune responses that destroy the majority of invading parasites .", "These responses are largely mediated by thioester-containing protein 1 ( TEP1 ) [1–4...	[ "Thioester-containing protein 1 ( TEP1 ) is a key immune factor that determines mosquito resistance to a wide range of pathogens , including malaria parasites .", "Here we report a new allele-specific function of TEP1 in male fertility .", "We demonstrate that during spermatogenesis TEP1 binds to and removes da...	[ "While Anopheline mosquitoes are the most efficient vectors of human malaria , they do have protective mechanisms directed against the causative parasite , Plasmodium falciparum .", "Their immune system targets the invading parasites through activation of the mosquito complement-like system .", "A central compo...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "animal models", "developmental biology", "mathematical computing", "model organisms", "mathematics", "biology" ]	Multi-Cellular Rosettes in the Mouse Visceral Endoderm Facilitate the Ordered Migration of Anterior Visceral Endoderm Cells	journal.pbio.1001256	Modeling and experimental results suggest a role for Planar Cell Polarity-dependent multi-cellular rosette structures in ensuring correct epithelial cell migration in the mouse visceral endoderm.	[ [ "Epithelia have structural and functional roles throughout embryonic development and adult life .", "Their organised , cohesive nature makes them ideal for lining structures and acting as selective barriers .", "Epithelia show distinct apical-basolateral polarity , with the apical domain characterised...	[ "The visceral endoderm ( VE ) is a simple epithelium that forms the outer layer of the egg-cylinder stage mouse embryo .", "The anterior visceral endoderm ( AVE ) , a specialised subset of VE cells , is responsible for specifying anterior pattern .", "AVE cells show a stereotypic migratory behaviour within the ...	[ "The mouse visceral endoderm ( VE ) is a simple epithelium in the egg cylinder stage mouse embryo .", "Many functions associated with epithelia require them to undergo extensive remodelling through changes in the shape and relative positions of constituent cells , a process about which we understand relatively li...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "evolutionary biology/plant genetics and gene expression", "evolutionary biology/evolutionary ecology" ]	Local-Scale Patterns of Genetic Variability, Outcrossing, and Spatial Structure in Natural Stands of Arabidopsis thaliana	journal.pgen.1000890	null	[ [ "Gaining a detailed understanding of Arabidopsis thaliana in its native context is becoming especially important as this species is increasingly employed as a model in studies of adaptation and evolution [1] , [2] .", "Arabidopsis thaliana is an annual herb that exists in the wild in fragmented population...	[ "As Arabidopsis thaliana is increasingly employed in evolutionary and ecological studies , it is essential to understand patterns of natural genetic variation and the forces that shape them .", "Previous work focusing mostly on global and regional scales has demonstrated the importance of historical events such a...	[ "The popular model plant Arabidopsis thaliana is increasingly used to investigate questions in evolution and ecology .", "Thus it is important to understand the dynamics of wild populations at a scale relevant to single plants .", "We analyzed over 1 , 000 individuals from 77 ecologically diverse stands near Tü...	2010
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "biotechnology", "medicine and health sciences", "body fluids", "pathology and laboratory medicine", "manganese", "enterococcus infections", "pathogens", "catheters", "bladder", "microbiology", "vertebrates", "rabbits", "animals", "mammals", "urine", "animal models", "bacterial disea...	Manganese acquisition is essential for virulence of Enterococcus faecalis	journal.ppat.1007102	null	[ [ "While normal residents of the gastrointestinal ( GI ) tract of animals and humans , enterococci are also the third most frequent cause of hospital-acquired infections and a major threat to public health due to the alarming rise of multidrug-resistant isolates [1] .", "Enterococcal infections in humans ar...	[ "Manganese ( Mn ) is an essential micronutrient that is not readily available to pathogens during infection due to an active host defense mechanism known as nutritional immunity .", "To overcome this nutrient restriction , bacteria utilize high-affinity transporters that allow them to compete with host metal-bind...	[ "Enterococcus faecalis is a leading cause of hospital-acquired infections that are often difficult to treat due to their exceptional multidrug resistance .", "Manganese ( Mn ) is an essential micronutrient for bacterial pathogens during infection .", "To prevent infection , the host limits Mn bioavailability to...	2018
[ "Introduction", "Materials and Methods", "Discussion" ]	[ "public and occupational health", "infectious diseases", "medicine and health sciences", "chagas disease", "social sciences", "behavioral and social aspects of health", "epidemiology", "global health", "neglected tropical diseases", "sociology", "tropical diseases", "infectious disease control...	Opportunities for Improved Chagas Disease Vector Control Based on Knowledge, Attitudes and Practices of Communities in the Yucatan Peninsula, Mexico	journal.pntd.0002763	null	[ [ "Chagas disease is a vector-borne parasitic disease endemic in the Americas , where it is of major public health importance , affecting up to 8–9 million people [1] .", "Recent estimates also illustrate the very high disease burden it causes [2] .", "Chagas disease is present in Mexico , but its impor...	[ "Chagas disease is a vector-borne parasitic disease of major public health importance .", "Current prevention efforts are based on triatomine vector control to reduce transmission to humans .", "Success of vector control interventions depends on their acceptability and value to affected communities .", "We ai...	[ "Chagas disease is an important parasitic disease transmitted by triatomine bugs .", "Current prevention efforts are based on eliminating triatomines from homes to reduce disease transmission to humans .", "However , the success of these control interventions depends on their acceptability and value to affected...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "chemical characterization", "gene regulation", "regulatory proteins", "dna-binding proteins", "dna transcription", "transcription factors", "sequence motif analysis", "research and analysis methods", "sequence analysis", "transcriptional control", "bioinformatics", "proteins", "gene express...	Mapping DNA sequence to transcription factor binding energy in vivo	journal.pcbi.1006226	null	[ [ "High-throughput sequencing allows us to sequence the genome of nearly any species at will .", "The amount of genomic data available is already enormous and will only continue to grow .", "However , this mass of data is largely uninformative without appropriate methods of analyzing it .", "Despite...	[ "Despite the central importance of transcriptional regulation in biology , it has proven difficult to determine the regulatory mechanisms of individual genes , let alone entire gene networks .", "It is particularly difficult to decipher the biophysical mechanisms of transcriptional regulation in living cells and ...	[ "It has been said that we live in the “genomic era , ” a time where we can readily sequence full genomes at will .", "However , it remains difficult to interpret much of the information within a genome .", "This is especially true of non-coding sequences such as promoters , which contain a number of features su...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "microbiology/immunity to infections", "neurological disorders/infectious diseases of the nervous system", "immunology/immune response", "virology/emerging viral diseases", "immunology/immunity to infections", "virology/host antiviral responses" ]	The First Human Epitope Map of the Alphaviral E1 and E2 Proteins Reveals a New E2 Epitope with Significant Virus Neutralizing Activity	journal.pntd.0000739	null	[ [ "Venezuelan equine encephalitis virus ( VEEV ) is a member of the Alphavirus genus in the family Togaviridae and is maintained in a natural enzootic cycle between mosquitoes and rodent hosts , although equines and humans may also be infected in an epizootic cycle [1] .", "While VEEV causes high-titered vi...	[ "Venezuelan equine encephalitis virus ( VEEV ) is responsible for VEE epidemics that occur in South and Central America and the U . S .", "The VEEV envelope contains two glycoproteins E1 ( mediates cell membrane fusion ) and E2 ( binds receptor and elicits virus neutralizing antibodies ) .", "Previously we cons...	[ "Although the murine immune response to Venezuelan equine encephalitis virus ( VEEV ) is well-characterized , little is known about the human antibody response to VEEV .", "In this study we used phage display technology to isolate a panel of 11 VEEV-specfic Fabs from two human donors .", "Seven E2-specific and ...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "microbiology/immunity to infections", "cell biology/cell signaling", "microbiology/innate immunity", "virology/animal models of infection", "immunology/innate immunity", "virology/new therapies, including antivirals and immunotherapy", "infectious diseases/viral infections", "infectious diseases/bact...	FimH Adhesin of Type 1 Fimbriae Is a Potent Inducer of Innate Antimicrobial Responses Which Requires TLR4 and Type 1 Interferon Signalling	journal.ppat.1000233	null	[ [ "The innate immune system plays a crucial role in the early defence against microbial infections [1] , [2] , [3] , [4] , [5] , [6] .", "A key aspect of the innate immune response is the synthesis and secretion of type I interferons ( IFN ) such as IFN-α and IFN-β .", "The innate immune system detects ...	[ "Components of bacteria have been shown to induce innate antiviral immunity via Toll-like receptors ( TLRs ) .", "We have recently shown that FimH , the adhesin portion of type 1 fimbria , can induce the innate immune system via TLR4 .", "Here we report that FimH induces potent in vitro and in vivo innate antim...	[ "The innate immune system is an evolutionarily conserved defence mechanism that protects the host from infection by microbes such as viruses , bacteria and fungi .", "Incoming pathogens are recognized by a set of evolutionary conserved receptors , including the Toll-like receptors ( TLRs ) , that can be found on ...	2008
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "medicine and health sciences", "pathology and laboratory medicine", "caenorhabditis", "gene regulation", "pathogens", "immunology", "microbiology", "animals", "dna transcription", "pseudomonas aeruginosa", "animal models", "caenorhabditis elegans", "model organisms", "e...	The nuclear hormone receptor NHR-86 controls anti-pathogen responses in C. elegans	journal.pgen.1007935	null	[ [ "Nuclear hormone receptors ( NHRs ) are transcription factors that regulate a number of key biological processes following recognition of specific exogenous or endogenous ligands .", "Interestingly , the genomes of Caenorhabditis species contain a large number of NHRs compared to other metazoans [1] .", ...	[ "Nuclear hormone receptors ( NHRs ) are ligand-gated transcription factors that control adaptive host responses following recognition of specific endogenous or exogenous ligands .", "Although NHRs have expanded dramatically in C . elegans compared to other metazoans , the biological function of only a few of thes...	[ "The family of nuclear hormone receptors ( NHRs ) has expanded in the nematode C . elegans .", "NHRs are intracellular sensors that control adaptive host responses following recognition of specific endogenous or exogenous ligands .", "These proteins are therefore well positioned to function in pathogen sensing ...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "viral diseases", "rotavirus infection" ]	Recombinant Monovalent Llama-Derived Antibody Fragments (VHH) to Rotavirus VP6 Protect Neonatal Gnotobiotic Piglets against Human Rotavirus-Induced Diarrhea	journal.ppat.1003334	null	[ [ "Diarrhea is the second most common cause of childhood mortality worldwide , causing 1 . 3 million deaths among children younger than 5 years of age [1] .", "Group A rotavirus ( RVA ) is the leading cause of severe diarrhea in children worldwide and is responsible for approximately 29% of all diarrheal de...	[ "Group A Rotavirus ( RVA ) is the leading cause of severe diarrhea in children .", "The aims of the present study were to determine the neutralizing activity of VP6-specific llama-derived single domain nanoantibodies ( VHH nanoAbs ) against different RVA strains in vitro and to evaluate the ability of G6P[1] VP6-...	[ "Group A rotavirus ( RVA ) is the most common cause of severe diarrhea in human infants worldwide .", "Live-attenuated rotavirus vaccines are available to prevent rotavirus diarrhea in children , although their efficacy in impoverished areas has been questioned , in addition to not being suitable for children suf...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "biochemistry", "spectrometric identification of proteins", "proteome", "proteins", "immunity", "gene expression", "immunity to infections", "immunology", "recombinant proteins", "biology", "molecular cell biology", "proteomics" ]	Serological Screening of the Schistosoma mansoni Adult Worm Proteome	journal.pntd.0002745	null	[ [ "Schistosomiasis is one of the most important parasitic diseases , being prevalent in 76 countries [1] .", "Despite many control efforts , mainly after the introduction of a chemotherapeutic treatment in 1980s , the disease is still highly prevalent [2] .", "The control of the main medically important...	[ "New interventions tools are a priority for schistosomiasis control and elimination , as the disease is still highly prevalent .", "The identification of proteins associated with active infection and protective immune response may constitute the basis for the development of a successful vaccine and could also ind...	[ "Despite intensive efforts towards disease control , schistosomiasis is still highly prevalent in most endemic countries .", "Although effective treatment is available and widely used , it does not prevent reinfection , as it could be achieved with the use of a vaccine .", "Efforts to control and eradicate schi...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology" ]	Evidence for Two Different Regulatory Mechanisms Linking Replication and Segregation of Vibrio cholerae Chromosome II	journal.pgen.1003579	null	[ [ "Studies in bacteria as well as in eukaryotes have shown that processes that maintain chromosomes , such as replication , recombination and repair , although able to occur independently of each other , often influence each other .", "Chromosome segregation is a major maintenance process but our knowledge ...	[ "Understanding the mechanisms that coordinate replication initiation with subsequent segregation of chromosomes is an important biological problem .", "Here we report two replication-control mechanisms mediated by a chromosome segregation protein , ParB2 , encoded by chromosome II of the model multichromosome bac...	[ "Replication and segregation are the two main processes that maintain chromosomes in growing cells .", "In eukaryotes , the two processes are restricted to distinct phases of the cell cycle .", "In bacteria , segregation follows replication initiation with a modest lag .", "Influences of one process on the ot...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma mansoni", "medicine and health sciences", "biomphalaria", "helminths", "immunology", "parasitic diseases", "animals", "invertebrate genomics", "physiological processes", "gastropods", "genome analysis", "snails", "immune system proteins", "g...	Transcriptomic responses of Biomphalaria pfeifferi to Schistosoma mansoni: Investigation of a neglected African snail that supports more S. mansoni transmission than any other snail species	journal.pntd.0005984	null	[ [ "Schistosomiasis is one of the world’s most prevalent neglected tropical diseases with over 218 million people worldwide requiring preventive chemotherapy in 2015 , 92% of those occurring in 41 countries in Africa [1] .", "Human schistosomiasis has a greater public health impact than usually appreciated [...	[ "Biomphalaria pfeifferi is highly compatible with the widespread human-infecting blood fluke Schistosoma mansoni and transmits more cases of this parasite to people than any other snail species .", "For these reasons , B . pfeifferi is the world’s most important vector snail for S . mansoni , yet we know relative...	[ "Biomphalaria pfeifferi is the world’s most important snail vector for the widespread human-infecting blood fluke Schistosoma mansoni .", "Despite this , we know relatively little about the biology of this highly compatible African snail host of S . mansoni , especially for specimens from the field .", "Using a...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "molecular cell biology", "biology", "genomics", "microbiology", "genetics and genomics" ]	In Vivo Expression of Salmonella enterica Serotype Typhi Genes in the Blood of Patients with Typhoid Fever in Bangladesh	journal.pntd.0001419	null	[ [ "Salmonella enterica serotype Typhi is a Gram-negative bacterium and the cause of typhoid fever .", "Typhoid fever affects over 21 million people each year , killing 200 , 000 [1] .", "S . Typhi is a human-restricted pathogen and this has greatly limited studies of S . Typhi pathogenesis .", "Our ...	[ "Salmonella enterica serotype Typhi is the cause of typhoid fever .", "It is a human-restricted pathogen , and few data exist on S . Typhi gene expression in humans .", "We applied an RNA capture and amplification technique , Selective Capture of Transcribed Sequences ( SCOTS ) , and microarray hybridization to...	[ "Salmonella enterica serotype Typhi is the cause of typhoid fever and infects over 21 million cases and causes 200 , 000 deaths each year .", "S . Typhi only infects humans and this has greatly limited studies of S . Typhi pathogenesis .", "To study bacterial gene expression in human hosts , we used Selective C...	2011
[ "Introduction", "Results/Discussion", "Methods" ]	[ "developmental biology", "genomics", "biology", "computational biology", "evolutionary biology", "genetics and genomics" ]	Divergence of Mammalian Higher Order Chromatin Structure Is Associated with Developmental Loci	journal.pcbi.1003017	null	[ [ "Chromatin structure plays critical roles in genome functions such as transcription , replication and repair , it can mediate human disease processes [1] and is implicated in ageing [2] .", "The primary level of eukaryotic chromatin structure involves the DNA sequence wrapped around nucleosomes and the co...	[ "Several recent studies have examined different aspects of mammalian higher order chromatin structure – replication timing , lamina association and Hi-C inter-locus interactions — and have suggested that most of these features of genome organisation are conserved over evolution .", "However , the extent of evolut...	[ "The mammalian genome is organised into large multi-megabase domains defined by their physical structure , or higher order chromatin structure .", "Although these structures are believed to be well conserved between species , there have been few studies attempting to quantify such conservation , or identify diver...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "signal transduction", "infectious diseases", "medicine and health sciences", "helminth infections", "schistosomiasis", "cell biology", "biology and life sciences", "molecular cell biology", "parasitic diseases" ]	Regulation of Schistosoma mansoni Development and Reproduction by the Mitogen-Activated Protein Kinase Signaling Pathway	journal.pntd.0002949	null	[ [ "Schistosomes are parasitic flatworms ( Phylum Platyhelminths ) that can survive for years or decades in the mammalian host [1] , [2] .", "Besides strategies to inhibit or modulate host immune responses , the maintenance of homeostasis and complex cellular adaptations , Schistosoma integrates specific ext...	[ "Protein kinases are proven targets for drug development with an increasing number of eukaryotic Protein Kinase ( ePK ) inhibitors now approved as drugs .", "Mitogen-activated protein kinase ( MAPK ) family members connect cell-surface receptors to regulatory targets within cells and influence a number of tissue-...	[ "Enzymes known as mitogen-activated protein kinases ( MAP kinases/MAPKs ) influence a number of essential biological activities , such as cell proliferation , differentiation and survival .", "However , for the Schistosoma mansoni flatworm parasite , very little is known about these enzymes .", "We used RNA int...	2014
[ "Introduction", "Results/Discussion", "Methods" ]	[ "systems biology", "medicine", "clinical research design", "biophysic al simulations", "atherosclerosis", "biology", "computational biology", "anatomy and physiology", "cardiovascular system", "modeling", "cardiovascular" ]	An In-Silico Model of Lipoprotein Metabolism and Kinetics for the Evaluation of Targets and Biomarkers in the Reverse Cholesterol Transport Pathway	journal.pcbi.1003509	null	[ [ "Epidemiological studies have shown that high levels of low-density lipoprotein cholesterol ( LDL-C ) as well as low levels of high-density lipoprotein cholesterol ( HDL-C ) are associated with increased cardiovascular disease ( CVD ) risk [1] , [2] .", "While LDL-C lowering therapies have been shown cons...	[ "High-density lipoprotein ( HDL ) is believed to play an important role in lowering cardiovascular disease ( CVD ) risk by mediating the process of reverse cholesterol transport ( RCT ) .", "Via RCT , excess cholesterol from peripheral tissues is carried back to the liver and hence should lead to the reduction of...	[ "Epidemiological studies have shown a strong inverse association between HDL-C and cardiovascular risk and led to the formulation of the “HDL cholesterol hypothesis”: under this hypothesis , interventions raising HDL-C should decrease risk .", "However , the recent failures of HDL-C raising therapies in improving...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "public health and epidemiology", "global health", "dengue fever", "travel-associated diseases", "neglected tropical diseases", "dengue", "viral diseases", "public health" ]	Utilities and Limitations of the World Health Organization 2009 Warning Signs for Adult Dengue Severity	journal.pntd.0002023	null	[ [ "Dengue is an acute febrile disease with a wide range of clinical presentations .", "The disease has been known for more than a century in the tropical areas of South East Asia and the Western Pacific regions [1] .", "Epidemics of dengue have now become a regular occurrence worldwide [2] .", "Alth...	[ "In 2009 , the World Health Organization ( WHO ) proposed seven warning signs ( WS ) as criteria for hospitalization and predictors of severe dengue ( SD ) .", "We assessed their performance for predicting dengue hemorrhagic fever ( DHF ) and SD in adult dengue .", "DHF , WS and SD were defined according to the...	[ "Dengue is a mosquito-borne infection with significant public health burden in tropical and subtropical regions .", "Clinical presentations may vary from self-limiting fever to severe dengue including death .", "The World Health Organization 2009 dengue guidelines classified dengue into dengue with and without ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "bacterial gastroenteritis", "bacterial diseases", "developmental biology", "innate immune system", "medicine and health sciences", "inflammation", "infectious diseases", "cytokines", "immunity", "gastroenterology and hepatology", "gastroenteritis", "molecular development", "biology and life...	The Cofilin Phosphatase Slingshot Homolog 1 (SSH1) Links NOD1 Signaling to Actin Remodeling	journal.ppat.1004351	null	[ [ "Effective immune defense in mammals relies on the detection of conserved pathogen structures by pattern recognition receptors ( PRRs ) of the innate immune system to prime immune responses [1] .", "Several PRRs have been identified and extensively studied in the last decade .", "In particular , membe...	[ "NOD1 is an intracellular pathogen recognition receptor that contributes to anti-bacterial innate immune responses , adaptive immunity and tissue homeostasis .", "NOD1-induced signaling relies on actin remodeling , however , the details of the connection of NOD1 and the actin cytoskeleton remained elusive .", "...	[ "NOD1 was one of the first NLR-family members shown to act as an important intracellular pattern-recognition molecule mediating antimicrobial activities in mammals .", "It has been demonstrated that perturbation of F-actin and RhoGTPase activity affects NOD1 and NOD2 signaling , however , the effectors of this pr...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "biotechnology", "invertebrates", "cell motility", "medicine and health sciences", "neurochemistry", "pathology and laboratory medicine", "caenorhabditis", "pathogens", "bacillus", "microbiology", "neuroscience", "parasitic diseases", "animals", "hormones", "nematode infections", "anim...	Nematode neuropeptides as transgenic nematicides	journal.ppat.1006237	null	[ [ "Plant parasitic nematodes ( PPNs ) are responsible for an estimated 12 . 3% reduction in crop yield each year , which equates to losses of around $US80 billion worldwide [1 , 2] .", "Traditionally PPNs have been controlled through the use of fumigant , carbamate and organophosphate nematicides which are ...	[ "Plant parasitic nematodes ( PPNs ) seriously threaten global food security .", "Conventionally an integrated approach to PPN management has relied heavily on carbamate , organophosphate and fumigant nematicides which are now being withdrawn over environmental health and safety concerns .", "This progressive wi...	[ "Plant parasitic nematodes ( PPN ) reduce crop plant yield globally , undermining food security .", "Many of the chemicals used to kill these parasites are non-specific and highly toxic , and are being phased out of general use through governmental and EU regulation .", "The withdrawal of these chemicals is ben...	2017
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "inflammatory diseases", "medicine and health sciences", "respiratory infections", "cardiovascular anatomy", "enzymes", "tropical diseases", "enzymology", "dismutases", "parasitic diseases", "parasitic protozoans", "pulmonology", "organisms", "protozoans", "mitochondria", "neglected trop...	Manganese superoxide dismutase deficiency exacerbates the mitochondrial ROS production and oxidative damage in Chagas disease	journal.pntd.0006687	null	[ [ "Chagasic cardiomyopathy is caused by the protozoan Trypanosoma cruzi ( Tc or T . cruzi ) [1] .", "Infected individuals exhibit an acute phase of peak blood parasitemia that is resolved in 2-3-months .", "Approximately , 30–40% of infected individuals progress to present ventricular fibrillation , thr...	[ "In this study , we have investigated the effects of manganese superoxide dismutase ( SOD2 or MnSOD ) deficiency on mitochondrial function and oxidative stress during Chagas disease .", "For this , C57BL/6 wild type ( WT ) and MnSOD+/- mice were infected with Trypanosoma cruzi ( Tc ) , and evaluated at 150 days’ ...	[ "Infection by Trypanosoma cruzi parasitic protozoan remains endemic in Latin America .", "After acute parasitemia phase is controlled by host immune system , infected individuals remain clinically silent but manifest a number of micro and macro cardiac injuries for several years .", "Eventually many of the infe...	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases/helminth infections", "public health and epidemiology/global health", "public health and epidemiology/infectious diseases", "public health and epidemiology/screening" ]	Evaluation of Urine CCA Assays for Detection of Schistosoma mansoni Infection in Western Kenya	journal.pntd.0000951	null	[ [ "Recently , there has been increased interest in the development and assessment of control and elimination programs for schistosomiasis [1] .", "For design of effective control programs , it is important to determine an accurate estimate of infection prevalence in the program area .", "The method most...	[ "Although accurate assessment of the prevalence of Schistosoma mansoni is important for the design and evaluation of control programs , the most widely used tools for diagnosis are limited by suboptimal sensitivity , slow turn-around-time , or inability to distinguish current from former infections .", "Recently ...	[ "Control efforts for schistosomiasis have in part been hampered by the lack of a sensitive and accurate test that can be utilized to rapidly map the prevalence of the disease in different areas .", "Recently , new tests have become commercially available that may address this problem .", "This study was designe...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "phosphorylation", "meiosis", "medicine and health sciences", "enzymes", "cell cycle and cell division", "cell processes", "enzymology", "microhomology-mediated end joining", "surgical and invasive medical procedures", "dna damage", "fungi", "model organisms", "dna", "ligases", "saccharo...	The MRX Complex Ensures NHEJ Fidelity through Multiple Pathways Including Xrs2-FHA–Dependent Tel1 Activation	journal.pgen.1005942	null	[ [ "The DNA double-strand break ( DSB ) is one of the most severe types of DNA damage and is most often repaired by homologous recombination ( HR ) or canonical non-homologous end joining ( C-NHEJ ) which is known as precise NHEJ .", "There are , however , several other minor pathways for DSB repair , some o...	[ "Because DNA double-strand breaks ( DSBs ) are one of the most cytotoxic DNA lesions and often cause genomic instability , precise repair of DSBs is vital for the maintenance of genomic stability .", "Xrs2/Nbs1 is a multi-functional regulatory subunit of the Mre11-Rad50-Xrs2/Nbs1 ( MRX/N ) complex , and its funct...	[ "Genomic DNA provides the essential blueprint for life , and therefore living organisms have several mechanisms for maintaining the stability of their own genomes .", "DNA double-strand breaks ( DSBs ) are one of the most severe forms of DNA damage , which , without precise repair , can provoke a loss of genetic ...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	RNA Polymerase III Output Is Functionally Linked to tRNA Dimethyl-G26 Modification	journal.pgen.1005671	null	[ [ "Apart from their role in translation , tRNAs can regulate gene expression [1 , 2] and serve as metabolic sensors [3] , and their over-expression is associated with cell proliferation and transformation [4 , 5] .", "RNAP III is activated by oncogenes [6 , 7] whereas its repression reduces transformation a...	[ "Control of the differential abundance or activity of tRNAs can be important determinants of gene regulation .", "RNA polymerase ( RNAP ) III synthesizes all tRNAs in eukaryotes and it derepression is associated with cancer .", "Maf1 is a conserved general repressor of RNAP III under the control of the target o...	[ "Transfer RNAs ( tRNAs ) are molecular adapters necessary for translation of the genetic code from DNA to messenger RNA ( mRNA ) to synthesis of the proteins that constitute the energy producing enzymes and structural components of all cells and organisms on earth .", "In eukaryotic cells , tRNAs are synthesized ...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology/neurodevelopment", "developmental biology/stem cells", "genetics and genomics/functional genomics" ]	The Level of the Transcription Factor Pax6 Is Essential for Controlling the Balance between Neural Stem Cell Self-Renewal and Neurogenesis	journal.pgen.1000511	null	[ [ "A fundamental feature of neural development is the production of defined types of neurons in a temporal order from multipotent , regionally-specified neural stem and progenitor cells [1] .", "During nervous system development , maintaining the balance between stem cell self-renewal and neurogenesis is es...	[ "Neural stem cell self-renewal , neurogenesis , and cell fate determination are processes that control the generation of specific classes of neurons at the correct place and time .", "The transcription factor Pax6 is essential for neural stem cell proliferation , multipotency , and neurogenesis in many regions of...	[ "Neural stem cells make all of the neurons in the brain .", "A key feature of these cells is the ability to regulate the balance between making more neural stem cells , the process of self-renewal , and making nerve cells , the process of neurogenesis .", "Too much self-renewal would result in a brain with too ...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "oncology", "biochemistry", "medicine and health sciences", "genetics", "biology and life sciences", "hematology", "clinical genetics" ]	ATRA-Induced Cellular Differentiation and CD38 Expression Inhibits Acquisition of BCR-ABL Mutations for CML Acquired Resistance	journal.pgen.1004414	null	[ [ "Chronic myeloid leukemia ( CML ) is a myeloproliferative disease resulting from the clonal hematopoietic stem cell disorder that is caused by the transformation of oncogenic breakpoint cluster region-Abelson ( BCR-ABL ) fusion gene [1] .", "Typically , CML progresses from chronic phase ( CP ) to accelera...	[ "Acquired resistance through genetic mutations is a major obstacle in targeted cancer therapy , but the underlying mechanisms are poorly understood .", "Here we studied mechanisms of acquired resistance of chronic myeloid leukemia ( CML ) to tyrosine kinase inhibitors ( TKIs ) by examining genome-wide gene expres...	[ "Acquired resistance through genetic mutations is a major mechanism for cancer drug resistance and accounts for the short life of targeted therapy in several types of human cancer .", "Mechanistically , however , very little is understood about how resistant mutations are actually acquired during cancer therapy ....	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "immune physiology", "enzyme-linked immunoassays", "chemical compounds", "particle physics", "epitope mapping", "immunology", "deuterium", "organic compounds", "atoms", "amino acid substitution", "amino acids", "molecular biology techniques", "antibodies", ...	High Resolution Mapping of Bactericidal Monoclonal Antibody Binding Epitopes on Staphylococcus aureus Antigen MntC	journal.ppat.1005908	null	[ [ "Staphylococcus aureus protein MntC is the ligand-binding component of the ABC-type manganese transporter MntABC , which is at least partially responsible for the organism’s resistance to the oxidative stress [1 , 2] .", "The protein is expressed during early stages of infection [3] and binds manganese wi...	[ "The Staphylococcus aureus manganese transporter protein MntC is under investigation as a component of a prophylactic S . aureus vaccine .", "Passive immunization with monoclonal antibodies mAB 305-78-7 and mAB 305-101-8 produced using MntC was shown to significantly reduce S . aureus burden in an infant rat mode...	[ "Staphylococcus aureus protein MntC is a metal-binding protein of the ABC-type transporter involved in the acquisition of an essential nutrient , Mn2+ , by the pathogen .", "An earlier study demonstrated that use of MntC as an antigen in experimental vaccine can provide protection against staphylococcal infection...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biomacromolecule-ligand interactions", "biology", "computational biology", "signaling networks", "biophysics" ]	Quantifying Intramolecular Binding in Multivalent Interactions: A Structure-Based Synergistic Study on Grb2-Sos1 Complex	journal.pcbi.1002192	null	[ [ "Grb2 contains one SH2 domain flanked on each side by an SH3 domain [1] , [2] , each of which forms complexes with multiple polyproline motifs on Sos1 .", "The activation of the Ras signaling pathway requires the recruitment of Sos1 from the cytosol to the plasma membrane where it activates Ras by inducin...	[ "Numerous signaling proteins use multivalent binding to increase the specificity and affinity of their interactions within the cell .", "Enhancement arises because the effective binding constant for multivalent binding is larger than the binding constants for each individual interaction .", "We seek to gain bot...	[ "Many biochemical interactions are mediated by multivalent binding where signaling proteins use relatively weak promiscuous interactions to increase the strength and specificity of complex formation .", "For a bivalent adaptor protein binding to a multivalent ligand , the tethering of one of the adaptors binding ...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "invertebrates", "rna interference", "molecular probe techniques", "metaphase", "cell cycle and cell division", "cell processes", "chromatids", "animals", "animal models", "mitosis", "drosophila melanogaster", "model organisms", "epigenetics", "molecular biology techniques", "drosophila"...	Investigating the Interplay between Sister Chromatid Cohesion and Homolog Pairing in Drosophila Nuclei	journal.pgen.1006169	null	[ [ "It is well recognized that the three-dimensional organization of interphase nuclei is non-random and can affect gene expression , development , and numerous other processes [1–4] .", "In addition to cell-type specific interactions between and within chromosomes [5 , 6] , nuclear organization is shaped by...	[ "Following DNA replication , sister chromatids must stay connected for the remainder of the cell cycle in order to ensure accurate segregation in the subsequent cell division .", "This important function involves an evolutionarily conserved protein complex known as cohesin; any loss of cohesin causes premature si...	[ "As cells grow , they replicate their DNA to give rise to two copies of each chromosome , known as sister chromatids , which separate from each other once the cell divides .", "To ensure that sister chromatids end up in different daughter cells , they are kept together from DNA replication until mitosis via a con...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases", "medicine and health sciences", "radiology and imaging", "gastroenterology and hepatology", "biology and life sciences", "immunology", "microbiology", "surgical and invasive medical procedures" ]	Long-term Sonographic and Serological Follow-up of Inactive Echinococcal Cysts of the Liver: Hints for a “Watch-and-Wait” Approach	journal.pntd.0003057	null	[ [ "Cystic echinococcosis ( CE ) is a chronic , complex and neglected infection caused by Echinococcus granulosus , a cestode with a worldwide distribution affecting an estimated 1 . 2 million people , mainly in pastoral communities [1] , [2] , [3] .", "Its life cycle develops between the dog and other canid...	[ "Human cystic echinococcosis is a chronic , complex and neglected infection .", "Its clinical management has evolved over decades without adequate evaluation of efficacy .", "Recent expert opinion recommends that uncomplicated inactive cysts of the liver should be left untreated and solely monitored over time (...	[ "Human cystic echinococcosis ( CE ) is a chronic , complex and neglected parasitic infection presenting mostly as hepatic cysts , which are staged by ultrasound .", "Recent expert opinion recommends that uncomplicated inactive cysts should be left untreated and solely monitored over time , using the so-called “wa...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry", "cancer genetics", "dna replication", "nucleic acids", "genetics", "dna", "biology", "dna recombination", "dna repair", "genetics of disease", "molecular genetics", "genetics and genomics" ]	A Genetic and Structural Study of Genome Rearrangements Mediated by High Copy Repeat Ty1 Elements	journal.pgen.1002089	null	[ [ "Gross chromosomal rearrangements ( GCRs ) are associated with many different diseases .", "Disease-causing GCRs include translocations , deletions , and inversions that can inactivate genes , form chimeric genes encoding proteins with altered activity , or change gene copy numbers or gene expression .", ...	[ "Ty elements are high copy number , dispersed repeated sequences in the Saccharomyces cerevisiae genome known to mediate gross chromosomal rearrangements ( GCRs ) .", "Here we found that introduction of Ty912 , a previously identified Ty1 element , onto the non-essential terminal region of the left arm of chromos...	[ "In this study , we developed a Saccharomyces cerevisiae gross chromosomal rearrangement ( GCR ) assay that measures the rate of GCRs mediated by high copy , dispersed repeat sequences in the S . cerevisiae genome known as Ty elements .", "Like LINE and Alu elements found in the human genome , Ty elements are rep...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology/neuronal signaling mechanisms", "genetics and genomics/disease models", "neuroscience/neurodevelopment", "developmental biology/neurodevelopment", "neurological disorders/epilepsy" ]	A Missense Mutation in a Highly Conserved Alternate Exon of Dynamin-1 Causes Epilepsy in Fitful Mice	journal.pgen.1001046	null	[ [ "Epilepsy affects about 1% of the population and approximately 30% of cases are idiopathic , with no obvious explanation such as head injury , stroke , lesions or tumors [1] .", "Genetic factors are thought to lie behind idiopathic epilepsy [1] .", "Several human epilepsy genes have been identified [2...	[ "Dynamin-1 ( Dnm1 ) encodes a large multimeric GTPase necessary for activity-dependent membrane recycling in neurons , including synaptic vesicle endocytosis .", "Mice heterozygous for a novel spontaneous Dnm1 mutation—fitful—experience recurrent seizures , and homozygotes have more debilitating , often lethal se...	[ "Epilepsy , a group of chronic disorders characterized by recurrent seizures , results from abnormal , synchronized neuronal activity in the brain .", "The mouse represents a powerful system to study novel mutations that model neurological disease , including epilepsy .", "Here we describe a new mouse mutation ...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Caspase-1 Promotes Epstein-Barr Virus Replication by Targeting the Large Tegument Protein Deneddylase to the Nucleus of Productively Infected Cells	journal.ppat.1003664	null	[ [ "Post-translational modification of proteins by covalent linkage of ubiquitin ( Ub ) or ubiquitin-like proteins ( UbLs ) , such as SUMO , NEDD8 , ISG15 , regulates diverse cellular processes , including cell cycle progression , DNA repair , transcription , signal transduction and immune responses [1] , [2] ."...	[ "The large tegument proteins of herpesviruses contain N-terminal cysteine proteases with potent ubiquitin and NEDD8-specific deconjugase activities , but the function of the enzymes during virus replication remains largely unknown .", "Using as model BPLF1 , the homologue encoded by Epstein-Barr virus ( EBV ) , w...	[ "Viruses rely on the host cell for replication and have evolved sophisticated strategies to manipulate and harness the cellular metabolic pathways and defense responses .", "A better knowledge of these viral strategies will provide new targets for antiviral therapies .", "The N-terminus of the large tegument pr...	2013
[ "Introduction", "Results", "Discussion", "Material and Methods" ]	[ "genetics and genomics/epigenetics", "genetics and genomics/gene function", "plant biology/plant genetics and gene expression", "genetics and genomics/plant genetics and gene expression" ]	SRA-Domain Proteins Required for DRM2-Mediated De Novo DNA Methylation	journal.pgen.1000280	null	[ [ "Cytosine methylation is found in the genomes of most eukaryotes and plays a critical role in repression of transposable elements as well as in the epigenetic regulation of select genes [1]–[4] .", "In Arabidopsis thaliana cytosine methylation occurs in all sequence contexts , with the highest frequency o...	[ "De novo DNA methylation and the maintenance of DNA methylation in asymmetrical sequence contexts is catalyzed by homologous proteins in plants ( DRM2 ) and animals ( DNMT3a/b ) .", "In plants , targeting of DRM2 depends on small interfering RNAs ( siRNAs ) , although the molecular details are still unclear .", ...	[ "Our genetic heritage plays an important role in determining who we are and the characteristics we possess .", "However , in the past decade it has become increasingly clear that in addition to the genes we inherit , a second level of information is critical for expression of these genes .", "This information t...	2008
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "chemical compounds", "phosphates", "enzymes", "enzymology", "organic compounds", "plasmid construction", "dna construction", "molecular biology techniques", "cellular structures and organelles", "research and analysis methods", "imidazole", "artificial gene amplification and extension", "pr...	The T-cell leukemia related rpl10-R98S mutant traps the 60S export adapter Nmd3 in the ribosomal P site in yeast	journal.pgen.1006894	null	[ [ "The eukaryotic ribosome is composed of 4 ribosomal RNA molecules and roughly 80 ribosomal proteins that come together to form the large ( 60S ) and small ( 40S ) subunits that make up mature 80S ribosomes .", "Eukaryotic ribosome biogenesis is an intricate assembly pathway that requires the assistance of...	[ "Mutations in the ribosomal protein Rpl10 ( uL16 ) can be drivers of T-cell acute lymphoblastic leukemia ( T-ALL ) .", "We previously showed that these T-ALL mutations disrupt late cytoplasmic maturation of the 60S ribosomal subunit , blocking the release of the trans-acting factors Nmd3 and Tif6 in S . cerevisia...	[ "The ribosome is a large and structurally complex macromolecular machine , responsible for synthesizing proteins in all living cells , across all domains of life .", "The correct assembly of ribosomes is important for their ability to faithfully decode messenger RNAs and synthesize proteins .", "The insertion o...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Conserved Streptococcus pneumoniae Spirosomes Suggest a Single Type of Transformation Pilus in Competence	journal.ppat.1004835	null	[ [ "Despite medical advances and vaccination campaigns , respiratory tract invasion by Streptococcus pneumoniae remains a leading mortality cause worldwide [1–3] .", "A particular challenge in the prevention and treatment of pneumococcal infections lies in the bacterium’s striking genomic plasticity , as it ...	[ "The success of S . pneumoniae as a major human pathogen is largely due to its remarkable genomic plasticity , allowing efficient escape from antimicrobials action and host immune response .", "Natural transformation , or the active uptake and chromosomal integration of exogenous DNA during the transitory differe...	[ "Streptococcus pneumoniae often escapes prevention and treatment through rapid horizontal gene transfer via natural transformation .", "Uptake of exogenous DNA requires expression of a transformation pilus but two markedly different models for pilus assembly and function have been proposed .", "We previously re...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell binding", "cell physiology", "gene regulation", "regulatory proteins", "messenger rna", "population genetics", "dna-binding proteins", "gene pool", "dna transcription", "transcription factors", "population biology", "proteins", "gene expression", "biochemistry", "rna", "cell biol...	Effect of transcription factor resource sharing on gene expression noise	journal.pcbi.1005491	null	[ [ "Every living organism regulates gene expression through the action of transcription factors ( TFs ) , enabling the cell to respond to intra-cellular and environmental cues [1] .", "The binding and unbinding of both RNAP molecules and the TFs ( DNA binding proteins that abet or hinder RNAP binding ) to th...	[ "Gene expression is intrinsically a stochastic ( noisy ) process with important implications for cellular functions .", "Deciphering the underlying mechanisms of gene expression noise remains one of the key challenges of regulatory biology .", "Theoretical models of transcription often incorporate the kinetics ...	[ "Genetically identical cells , even when they are exposed to the same environmental conditions , display incredible diversity .", "Gene expression noise is attributed to be a key source of this phenotypic diversity .", "Transcriptional dynamics is a dominant source of expression noise .", "Although scores of ...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology", "virology", "gene expression", "genetics", "biology and life sciences", "microbiology", "molecular cell biology", "dna transcription" ]	Human Cytomegalovirus pUL79 Is an Elongation Factor of RNA Polymerase II for Viral Gene Transcription	journal.ppat.1004350	null	[ [ "HCMV is a prototypical beta-herpesvirus and a ubiquitous pathogen in the human population .", "Upon primary infection , HCMV establishes a lifelong persistent and latent/recurrent infection in a host [1] .", "Even though HCMV infection is usually asymptomatic , it acts as an opportunistic pathogen an...	[ "In this study , we have identified a unique mechanism in which human cytomegalovirus ( HCMV ) protein pUL79 acts as an elongation factor to direct cellular RNA polymerase II for viral transcription during late times of infection .", "We and others previously reported that pUL79 and its homologues are required fo...	[ "In this study , we report a novel mechanism used by human cytomegalovirus ( HCMV ) to regulate the elongation rate of RNA polymerase II ( RNAP II ) to facilitate viral transcription during late stages of infection .", "Recently , we and others have identified several viral factors that regulate gene expression d...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "public and occupational health", "medicine and health sciences", "global health" ]	Does Mass Azithromycin Distribution Impact Child Growth and Nutrition in Niger? A Cluster-Randomized Trial	journal.pntd.0003128	null	[ [ "Non-specific antibiotic use has been employed to enhance weight gain in livestock since the 1950s [1] .", "Previous studies have examined the association between antibiotics and livestock [1]–[6] .", "These studies have identified benefits of using antimicrobials to improve animal growth , prevent an...	[ "Antibiotic use on animals demonstrates improved growth regardless of whether or not there is clinical evidence of infectious disease .", "Antibiotics used for trachoma control may play an unintended benefit of improving child growth .", "In this sub-study of a larger randomized controlled trial , we assess ant...	[ "Recent studies suggest that antibiotic use could have an effect on growth in humans .", "Azithromycin is an antibiotic used for trachoma control , and hence , may have an unintended benefit of improving child growth .", "Niger is a trachoma-endemic country where mass antibiotic distributions for trachoma take ...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases/helminth infections", "public health and epidemiology/global health", "infectious diseases/epidemiology and control of infectious diseases", "infectious diseases/neglected tropical diseases" ]	Decision-Model Estimation of the Age-Specific Disability Weight for Schistosomiasis Japonica: A Systematic Review of the Literature	journal.pntd.0000158	null	[ [ "Schistosomiasis is one of the most prevalent parasitic infections worldwide .", "An estimated 779 million people are at risk for schistosomiasis , with 207 million infected in 76 countries and territories [1] , [2] .", "Approximately 120 million people are symptomatic and 20 million have severe and d...	[ "Schistosomiasis is among the most prevalent parasitic infections worldwide .", "However , current Global Burden of Disease ( GBD ) disability-adjusted life year estimates indicate that its population-level impact is negligible .", "Recent studies suggest that GBD methodologies may significantly underestimate t...	[ "Schistosomiasis is a parasitic infection caused by a flatworm that disproportionately affects the world's poorest populations .", "Schistosomiasis is one of the most common infections worldwide , affecting over 207 million people in 76 countries .", "Current international estimates indicate that schistosomiasi...	2008
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "leptospira", "body fluids", "pathology and laboratory medicine", "ruminants", "infectious disease epidemiology", "pathogens", "tropical diseases", "microbiology", "vertebrates", "animals", "mammals", "urine", "bacterial diseases", "neglected tropical dise...	Isolation of pathogenic Leptospira strains from naturally infected cattle in Uruguay reveals high serovar diversity, and uncovers a relevant risk for human leptospirosis	journal.pntd.0006694	null	[ [ "Leptospirosis is a zoonotic disease of worldwide importance caused by pathogenic spirochetes belonging to the genus Leptospira [1] .", "It affects humans and a broad range of domestic animals and wildlife .", "In cattle , leptospirosis is an important cause of reproductive failure , including abortio...	[ "Leptospirosis is a neglected zoonosis with worldwide distribution .", "The causative agents are spirochete bacteria of the Leptospira genus , displaying huge diversity of serovars , the identity of which is critical for effective diagnosis and vaccination purposes .", "Among many other mammalian species , Lept...	[ "Several species of the genus Leptospira cause leptospirosis , a disease that is transmitted from animals to humans ( zoonosis ) .", "Leptospirosis is the most extended zoonosis worldwide , with over a million human cases each year .", "Leptospira spp .", "infect a broad range of wildlife and domestic animals...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "organismal evolution", "public health and epidemiology", "evolutionary ecology", "infectious disease epidemiology", "parasite evolution", "population dynamics", "population genetics", "microbiology", "host-pathogen interaction", "parasitology", "escherichia coli", "prokaryotic models", "mod...	Evolution of Virulence in Emerging Epidemics	journal.ppat.1003209	null	[ [ "Understanding and predicting the conditions under which pathogens evolve towards higher levels of virulence ( pathogen induced host mortality ) is a major challenge in the control of infectious diseases [1] , [2] .", "Nevertheless , the theoretical understanding of virulence evolution is often based on s...	[ "Theory predicts that selection for pathogen virulence and horizontal transmission is highest at the onset of an epidemic but decreases thereafter , as the epidemic depletes the pool of susceptible hosts .", "We tested this prediction by tracking the competition between the latent bacteriophage λ and its virulent...	[ "Why are some pathogens more virulent than others ?", "Theory predicts that pathogens that ‘keep their host alive’ can sometimes outcompete virulent pathogens in times when transmission to new susceptible hosts is unlikely .", "Yet , this prospect of finding a new susceptible host changes itself throughout an e...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology", "genetics", "biology and life sciences", "microbiology", "genomics", "molecular cell biology" ]	Essential Genetic Interactors of SIR2 Required for Spatial Sequestration and Asymmetrical Inheritance of Protein Aggregates	journal.pgen.1004539	null	[ [ "Cell division in budding yeast , Saccharomyces cerevisiae , and specific adult stem/progenitor cells includes asymmetrical inheritance of oxidized proteins , ensuring low levels of cytosolic damage in a specific cell lineage [1]–[3] .", "In both yeast and adult precursor cells , the lineage inheriting le...	[ "Sir2 is a central regulator of yeast aging and its deficiency increases daughter cell inheritance of stress- and aging-induced misfolded proteins deposited in aggregates and inclusion bodies .", "Here , by quantifying traits predicted to affect aggregate inheritance in a passive manner , we found that a passive ...	[ "Asymmetric cell division is key to cellular rejuvenation and budding yeast exploits this mode of cytokinesis to generate a young daughter cell from a mother cell that with each division grows progressively older .", "Thus , age physiognomies are reset in the progeny during division , a phenomenon that requires a...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry/replication and repair", "microbiology/microbial evolution and genomics", "genetics and genomics/chromosome biology" ]	DNA Adenine Methylation Is Required to Replicate Both Vibrio cholerae Chromosomes Once per Cell Cycle	journal.pgen.1000939	null	[ [ "The regulatory potential of canonical DNA sequences can be greatly expanded by epigenetic modifications .", "Methylation is the most common modification of DNA and is widely used to control many cellular processes [1] .", "In bacteria , DNA methylation is restricted to adenine and cytosine residues [...	[ "DNA adenine methylation is widely used to control many DNA transactions , including replication .", "In Escherichia coli , methylation serves to silence newly synthesized ( hemimethylated ) sister origins .", "SeqA , a protein that binds to hemimethylated DNA , mediates the silencing , and this is necessary to...	[ "Bacteria usually have one chromosome but can have extrachromosomal replicons , called plasmids .", "Although normally dispensable , plasmids can confer adaptive advantage to cells in stressful environments .", "Bacteria can also have multiple chromosomes , each carrying essential genes , as in eukaryotes .", ...	2010
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "biochemistry", "proteins", "protein structure", "biology and life sciences", "computational biology", "biophysics" ]	Stability Curve Prediction of Homologous Proteins Using Temperature-Dependent Statistical Potentials	journal.pcbi.1003689	null	[ [ "The understanding of the mechanisms used by nature to stabilize proteins against thermal inactivation is still an open issue of primary importance .", "From a theoretical perspective , such comprehension is fundamental in the study of the adaptive strategies used by the organisms to inhabit extreme envir...	[ "The unraveling and control of protein stability at different temperatures is a fundamental problem in biophysics that is substantially far from being quantitatively and accurately solved , as it requires a precise knowledge of the temperature dependence of amino acid interactions .", "In this paper we attempt to...	[ "The prediction of protein stability remains one of the key goals of protein science .", "Despite the significant efforts of the last decades , faster and more accurate stability predictors on the proteomic-wide scale are currently demanded .", "The determination and control of protein stability are indeed fund...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biotechnology", "genome-wide association studies", "medicine and health sciences", "neurodegenerative diseases", "genetic diseases", "geographical locations", "genetic mapping", "genome analysis", "molecular genetics", "autosomal dominant diseases", "huntington disease", "genetic engineering"...	Population-specific genetic modification of Huntington's disease in Venezuela	journal.pgen.1007274	null	[ [ "Huntington's disease ( HD; MIM 143100 ) , a familial neurodegenerative disorder characterized by progressive movement disorder , cognitive decline , and psychiatric disturbances , is caused by an expanded CAG glutamine codon repeat in HTT , which encodes huntingtin [1–3] .", "This genetic defect was orig...	[ "Modifiers of Mendelian disorders can provide insights into disease mechanisms and guide therapeutic strategies .", "A recent genome-wide association ( GWA ) study discovered genetic modifiers of Huntington's disease ( HD ) onset in Europeans .", "Here , we performed whole genome sequencing and GWA analysis of ...	[ "Huntington’s disease ( HD ) is a dominantly inherited neurodegenerative disorder caused by a CAG trinucleotide expansion in HTT , which encodes huntingtin .", "HD involves various neurological manifestations such as involuntary movements , cognitive decline , and personality change; age at onset of diagnostic si...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "africans", "medicine and health sciences", "pathology and laboratory medicine", "in situ hybridization", "molecular probe techniques", "pathogens", "microbiology", "ethnicities", "membrane proteins", "helicobacter", "outer membrane proteins", "phylogenetic analysis", "genome analysis", "m...	Rapid evolution of distinct Helicobacter pylori subpopulations in the Americas	journal.pgen.1006546	null	[ [ "In 1492 , Christopher Columbus initiated a rapid colonization of the New World , principally by European migrants and Africans brought as slaves that had catastrophic consequences for the indigenous population .", "The new migrants brought unfamiliar weapons and pathogens [1] , including new populations ...	[ "For the last 500 years , the Americas have been a melting pot both for genetically diverse humans and for the pathogenic and commensal organisms associated with them .", "One such organism is the stomach-dwelling bacterium Helicobacter pylori , which is highly prevalent in Latin America where it is a major curre...	[ "Helicobacter pylori is one of the best studied examples of an intimate association between bacteria and humans , due to its ability to colonize the stomach for decades and to transmit from generation to generation .", "A number of studies have sought to link diversity in H . pylori to human migrations but there ...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "inflammation", "immune cells", "cytokines", "genetics of the immune system", "immunity", "innate immunity", "allergy and hypersensitivity", "immunology", "biology", "autoimmunity", "immune system" ]	A20-Deficient Mast Cells Exacerbate Inflammatory Responses In Vivo	journal.pbio.1001762	Mast cells, best known as effector cells in pathogenic immunoglobulin-mediated responses, can sense a variety of “danger” signals; if manipulated to enhance their resulting inflammatory responses, they also exacerbate inflammatory diseases such as arthritis and lung inflammation.	[ [ "Mast cells are innate immune cells that localize preferentially to vascularized tissues at the host-environment barrier .", "Through their high-affinity IgE receptor ( FcεRI ) they can capture circulating IgE and are hence primed to degranulate and produce cytokines upon antigen encounter .", "Mast c...	[ "Mast cells are implicated in the pathogenesis of inflammatory and autoimmune diseases .", "However , this notion based on studies in mast cell-deficient mice is controversial .", "We therefore established an in vivo model for hyperactive mast cells by specifically ablating the NF-κB negative feedback regulator...	[ "Mast cells mediate allergic and anaphylactic immune reactions .", "They are also equipped with innate pattern recognition , cytokine , and alarmin receptors , which induce inflammatory responses .", "Correlative studies in human patients hinted at roles for mast cells in autoimmune and inflammatory diseases ."...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "biology" ]	Viperin Regulates Cellular Lipid Metabolism during Human Cytomegalovirus Infection	journal.ppat.1003497	null	[ [ "Human cytomegalovirus ( HCMV ) is associated with acute and chronic disease in both healthy and immunocompromised populations [1] , [2] , [3] .", "A characteristic of HCMV is that it modulates the metabolism of an infected cell in ways that favor viral replication [4] , [5] , [6] .", "HCMV infection ...	[ "Human cytomegalovirus ( HCMV ) has been shown to induce increased lipogenesis in infected cells , and this is believed to be required for proper virion envelopment .", "We show here that this increase is a consequence of the virus-induced redistribution of the host protein viperin to mitochondria and its capacit...	[ "Virus infection induces the production of interferons , which in turn stimulate the production of a set of proteins that often have antiviral functions .", "One of these interferon-inducible proteins is viperin , the product of the human Rsad2 gene .", "Human cytomegalovirus ( HCMV ) paradoxically induces expr...	2013
[ "Introduction", "Method", "Results", "Discussion" ]	[ "death rates", "medicine and health sciences", "pathology and laboratory medicine", "antiviral therapy", "pathogens", "immunology", "geographical locations", "microbiology", "drug screening", "health care", "retroviruses", "viruses", "preventive medicine", "immunodeficiency viruses", "so...	Bridging the gap between HIV epidemiology and antiretroviral resistance evolution: Modelling the spread of resistance in South Africa	journal.pcbi.1007083	null	[ [ "Since ART has been introduced in Southern Africa in 2004 , ART coverage has continuously increased .", "In 2016 , 55% of individuals living with HIV were receiving ART in the region , the great majority being treated with a standard first-line regimen consisting of two nucleoside reverse transcriptase in...	[ "The scale-up of antiretroviral therapy ( ART ) in South Africa substantially reduced AIDS-related deaths and new HIV infections .", "However , its success is threatened by the emergence of resistance to non-nucleoside reverse-transcriptase inhibitors ( NNRTI ) .", "The MARISA ( Modelling Antiretroviral drug Re...	[ "Resistance to non-nucleoside reverse transcriptase inhibitors ( NNRTI ) threatens the long-term success of antiretroviral therapy ( ART ) roll-out in South Africa .", "We developed a compartmental model integrating the local HIV epidemiology with biological mechanisms of drug resistance .", "A first dimension ...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "phosphorylation", "anaphase", "cell cycle and cell division", "cell processes", "biochemical analysis", "mitosis", "fungi", "in vitro kinase assay", "model organisms", "enzyme assays", "immunoprecipitation", "bioassays and physiological analysis", "schizosaccharomyces", "research and anal...	Mps1Mph1 Kinase Phosphorylates Mad3 to Inhibit Cdc20Slp1-APC/C and Maintain Spindle Checkpoint Arrests	journal.pgen.1005834	null	[ [ "Defects in chromosome segregation result in aneuploidy , which can lead to disease or cell death [1 , 2 , 3] .", "Mitosis is an extremely complicated and well orchestrated stage of the cell cycle , and many controls are employed to ensure its high fidelity .", "One of the major controls is the spindl...	[ "The spindle checkpoint is a mitotic surveillance system which ensures equal segregation of sister chromatids .", "It delays anaphase onset by inhibiting the action of the E3 ubiquitin ligase known as the anaphase promoting complex or cyclosome ( APC/C ) .", "Mad3/BubR1 is a key component of the mitotic checkpo...	[ "When cells divide they need to ensure that a complete copy of their genetic material is transmitted to both daughter cells .", "Cells have evolved many controls to ensure that every division is carried out with very high fidelity .", "The spindle checkpoint is one such control , which acts as a surveillance sy...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "crystal structure", "nucleases", "enzymes", "condensed matter physics", "dna-binding proteins", "enzymology", "dna damage", "dna structure", "dna", "crystallography", "solid state physics", "proteins", "ribonucleases", "chemistry", "molecular biology", "physics", "biochemistry", "...	Structural basis for overhang excision and terminal unwinding of DNA duplexes by TREX1	journal.pbio.2005653	null	[ [ "Three prime repair exonuclease 1 ( TREX1 ) is a member of the DEDDh family of exonucleases and accounts for most of the 3′–5′ exonuclease activity in mammalian cells [1 , 2] .", "Anchored in the plasma membrane of the endoplasmic reticulum ( ER ) through the C-terminal domain , TREX1 degrades a variety o...	[ "Three prime repair exonuclease 1 ( TREX1 ) is an essential exonuclease in mammalian cells , and numerous in vivo and in vitro data evidenced its participation in immunity regulation and in genotoxicity remediation .", "In these very complicated cellular functions , the molecular mechanisms by which duplex DNA su...	[ "Three prime repair exonuclease 1 ( TREX1 ) was shown to participate in various cellular events such as DNA repair , immunity regulation , and viral infection .", "In addition to relating to autoimmune diseases , this exonuclease also acts as a potential protein target for anticancer or antiviral therapies .", ...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "uterus", "medicine and health sciences", "reproductive system", "body fluids", "enzymes", "enzymology", "collagens", "epithelial cells", "germ cells", "enzyme inhibitors", "sperm", "semen", "animal cells", "proteins", "gene expression", "biological tissue", "biochemistry", "anatom...	Crucial role of estrogen for the mammalian female in regulating semen coagulation and liquefaction in vivo	journal.pgen.1006743	null	[ [ "In the United States , approximately 46% of women are unable to conceive within the first 12 months of trying to get pregnant [1] .", "Infertile couples may experience psychological distresses , including low self-esteem , isolation , and depression .", "Cumulatively , the infertile couples in the Un...	[ "Semen liquefaction changes semen from a gel-like to watery consistency and is required for sperm to gain mobility and swim to the fertilization site in the Fallopian tubes .", "Kallikrein-related peptidases 3 ( KLK3 ) and other kallikrein-related peptidases from male prostate glands are responsible for semen liq...	[ "Semen liquefaction has been considered to be solely modulated by prostate-derived kallikrein-related peptidases ( KLKs ) , especially KLK3 ( or prostate specific antigen ) .", "However , our research demonstrated that female mice lacking estrogen receptor alpha ( ERα ) in the uterine epithelial cells had a drast...	2017
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "death rates", "organismal evolution", "medicine and health sciences", "pathology and laboratory medicine", "demography", "pathogens", "microbiology", "epidemiological methods and statistics", "retroviruses", "viruses", "immunodeficiency viruses", "rna viruses", "sexually transmitted disease...	Effects of contact structure on the transient evolution of HIV virulence	journal.pcbi.1005453	null	[ [ "The evolution of pathogen virulence ( the harm done to the pathogen’s host ) has both theoretical and , potentially , practical importance .", "Evolutionary theory suggests that pathogens with higher reproduction numbers ( R 0 ) —the number of secondary infections caused by a single infected host over th...	[ "Early in an epidemic , high densities of susceptible hosts select for relatively high parasite virulence; later in the epidemic , lower susceptible densities select for lower virulence .", "Thus over the course of a typical epidemic the average virulence of parasite strains increases initially , peaks partway th...	[ "Pathogens such as HIV can evolve rapidly when the environment changes .", "One important aspect of a pathogen’s environment is the probability that an infectious contact ( a sneeze for a respiratory disease , or an unprotected sex act for a sexually transmitted disease ) encounters an uninfected person and thus ...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "learning", "medicine and health sciences", "classical mechanics", "sociology", "tropical diseases", "social sciences", "neuroscience", "learning and memory", "health care", "bacterial diseases", "human families", "cognitive psychology", "reflection", "neglected tropical diseases", "soci...	The Impact of a Rights-Based Counselling Intervention to Reduce Stigma in People Affected by Leprosy in Indonesia	journal.pntd.0005088	null	[ [ "In the past , stigma was primarily considered an attribute; a legacy of Goffman’s seminal work [21] , or of its interpretation .", "The current emphasis lies much more on stigma as a social process and thus goes beyond the individual body [22] .", "A well-known definition of health-related stigma tha...	[ "This paper assesses the impact of a counselling intervention on reducing leprosy-related stigma in Cirebon District , Indonesia .", "The unique features of this intervention are its rights-based approach , the underlying Cognitive Behavioural Therapy ( CBT ) model , the three types of counselling and the lay and...	[ "Can building knowledge , increasing the awareness of rights and developing confidence through counselling empower people affected by leprosy and reduce the stigma that surrounds them ?", "In this paper the authors describe the impact of a counselling module designed to address the widespread issue of stigma in C...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "neglected tropical diseases", "immunology", "biology", "parasitic diseases" ]	Cytokine Responses to Novel Antigens in an Indian Population Living in an Area Endemic for Visceral Leishmaniasis	journal.pntd.0001874	null	[ [ "Visceral leishmaniasis ( VL ) , also known as kala-azar , is a potentially fatal disease caused by obligate intracellular parasites of the Leishmania donovani species complex .", "VL is a serious public health problem in indigenous and rural populations in India , accounting for enormous morbidity and mo...	[ "There are no effective vaccines for visceral leishmaniasis ( VL ) , a neglected parasitic disease second only to malaria in global mortality .", "We previously identified 14 protective candidates in a screen of 100 Leishmania antigens as DNA vaccines in mice .", "Here we employ whole blood assays to evaluate h...	[ "Visceral leishmaniasis is a parasitic infection that results in death in susceptible people unless they are treated .", "Current drugs are expensive and toxic , and there are no vaccines in use in humans .", "We know that it is possible to become immune to infection with this parasite because people who have b...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "cell biology", "caenorhabditis", "eukaryotes", "animals", "molecular biology", "genetics and genomics", "nematodes" ]	C. elegans Germ Cells Switch between Distinct Modes of Double-Strand Break Repair During Meiotic Prophase Progression	journal.pgen.0030191	null	[ [ "Faithful inheritance of chromosomes during meiosis relies on crossover ( CO ) recombination events between the DNA molecules of homologous chromosomes .", "Interhomolog COs underpin the formation of chiasmata that temporarily link homologs and allow them to orient and segregate toward opposite poles of t...	[ "Chromosome inheritance during sexual reproduction relies on deliberate induction of double-strand DNA breaks ( DSBs ) and repair of a subset of these breaks as interhomolog crossovers ( COs ) .", "Here we provide a direct demonstration , based on our analysis of rad-50 mutants , that the meiotic program in Caeno...	[ "Faithful inheritance of chromosomes during sexual reproduction depends on the deliberate formation of double-strand DNA breaks ( DSBs ) and subsequent repair of a subset of these breaks by a mechanism that leads to crossovers between homologous chromosome pairs .", "The requirement for crossovers to ensure chrom...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "neuroscience/behavioral neuroscience", "neuroscience/cognitive neuroscience", "neuroscience", "neuroscience/experimental psychology", "neuroscience/theoretical neuroscience" ]	The Brain's Router: A Cortical Network Model of Serial Processing in the Primate Brain	journal.pcbi.1000765	null	[ [ "A ubiquitous aspect of brain function is its modular organization , with a large number of processors ( neurons , columns , or entire areas ) operating simultaneously and in parallel .", "Human cognition relies , to a large extent , on the ability to perform an arbitrarily large set of tasks by flexibly ...	[ "The human brain efficiently solves certain operations such as object recognition and categorization through a massively parallel network of dedicated processors .", "However , human cognition also relies on the ability to perform an arbitrarily large set of tasks by flexibly recombining different processors into...	[ "A ubiquitous aspect of brain function is its quasi-modular and massively parallel organization .", "The paradox is that this extraordinary parallel machine is incapable of performing a single large arithmetic calculation .", "How come it is so easy to recognize moving objects , but so difficult to multiply 357...	2010
[ "Introduction", "Results", "Methods" ]	[ "genome-wide association studies", "medicine and health sciences", "genetic networks", "pulmonology", "chronic obstructive pulmonary disease", "mathematics", "statistics (mathematics)", "test statistics", "genome analysis", "network analysis", "discrete mathematics", "combinatorics", "resear...	Bipartite Community Structure of eQTLs	journal.pcbi.1005033	null	[ [ "Genome Wide Association Studies ( GWAS ) have created new opportunities to understand the genetic factors that influence complex traits .", "Excepting highly-penetrant Mendelian disorders , the majority of genetic associations seem to be driven by many factors , each of which has a relatively small effec...	[ "Genome Wide Association Studies ( GWAS ) and expression quantitative trait locus ( eQTL ) analyses have identified genetic associations with a wide range of human phenotypes .", "However , many of these variants have weak effects and understanding their combined effect remains a challenge .", "One hypothesis i...	[ "Large-scale studies have identified thousands of genetic variants associated with different phenotypes without explaining their function .", "Expression quantitative trait locus analysis associates the compendium of genetic variants with expression levels of individual genes , providing the opportunity to link t...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "infectious diseases", "molecular biology", "infectious diseases/epidemiology and control of infectious\n diseases", "infectious diseases/tropical and travel-associated diseases" ]	Antigenic Variation in Plasmodium falciparum Malaria Involves a Highly Structured Switching Pattern	journal.ppat.1001306	null	[ [ "During blood-stage of infection with P . falciparum , members of the", "var gene encoded Erythrocyte Membrane Protein 1 ( PfEMP1 ) family", "are exposed on the surface of infected red blood cells .", "Here they act as important", "virulence factors by mediating adherence to a variety of host ...	[ "Many pathogenic bacteria , fungi , and protozoa achieve chronic infection through", "an immune evasion strategy known as antigenic variation .", "In the human malaria", "parasite Plasmodium falciparum , this involves transcriptional", "switching among members of the var gene family , causing", "parasites...	[ "The malaria parasite Plasmodium falciparum avoids recognition", "and clearance by the immune system by sequentially switching between members of", "the var multi-gene family which encode the immunodominant", "surface proteins PfEMP1 .", "However , some mechanism must exist to prevent rapid", "exposure of...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "microbiology/innate immunity", "immunology/innate immunity" ]	Identification of Host Cytosolic Sensors and Bacterial Factors Regulating the Type I Interferon Response to Legionella pneumophila	journal.ppat.1000665	null	[ [ "The intracellular bacterium Legionella pneumophila has become a valuable model for the study of immunosurveillance pathways .", "L . pneumophila is a motile gram-negative bacterium that is the cause of a severe pneumonia called Legionnaires' Disease [1] .", "In the environment , L . pneumophila is be...	[ "Legionella pneumophila is a gram-negative bacterial pathogen that replicates in host macrophages and causes a severe pneumonia called Legionnaires' Disease .", "The innate immune response to L . pneumophila remains poorly understood .", "Here we focused on identifying host and bacterial factors involved in the...	[ "Initial detection of invading microorganisms is one of the primary tasks of the innate immune system .", "However , the molecular mechanisms by which pathogens are recognized remain incompletely understood .", "Here , we provide evidence that an immunosurveillance pathway ( called the RIG-I/MDA5 pathway ) , th...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "urology", "cognitive neurology", "medicine and health sciences", "bladder and ureteric disorders", "pathology and laboratory medicine", "nervous system", "neurodegenerative diseases", "pathogens", "amyotrophic lateral sclerosis", "bladder", "microbiology", "neuroscience", "retroviruses", ...	Detection of clinical and neurological signs in apparently asymptomatic HTLV-1 infected carriers: Association with high proviral load	journal.pntd.0006967	null	[ [ "HTLV-1 , a human retrovirus , is the causative agent of Adult T Leukemia/Lymphoma ( ATLL ) and HTLV-1-associated myelopathy ( HAM/TSP ) [1] , at least 5–10 million people infected worldwide , almost 5–10% of them in Brazil [2] .", "However high , such numbers may be an underestimate since only 2/3 of the...	[ "Several studies suggest that HTLV-1 infection may be associated with a wider spectrum of neurologic manifestations that do not meet diagnostic criteria for HAM/TSP .", "These conditions may later progress to HAM/TSP or constitute an intermediate clinical form , between asymptomatic HTLV-1 carriers and those with...	[ "At least 5–10 million people live with the Human T-Cell Lymphotropic Virus type 1 ( HTLV-1 ) worldwide , and around 0 . 25–5% of them may develop HTLV-1-associated myelopathy/Tropical spastic paraparesis ( HAM/TSP ) , which is associated with chronic inflammation .", "In this study , involving 175 HTLV-1-infecte...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biophysics/theory and simulation", "computational biology" ]	Poisson-Nernst-Planck Models of Nonequilibrium Ion Electrodiffusion through a Protegrin Transmembrane Pore	journal.pcbi.1000277	null	[ [ "Antimicrobial peptides ( AMPs ) are small proteins produced by the innate immune system of many plants and animals as a first line of defense against bacterial infections [1] , [2] .", "Due to their persistence in nature as well as their nonspecific mechanism of action , there has been significant resear...	[ "Protegrin peptides are potent antimicrobial agents believed to act against a variety of pathogens by forming nonselective transmembrane pores in the bacterial cell membrane .", "We have employed 3D Poisson-Nernst-Planck ( PNP ) calculations to determine the steady-state ion conduction characteristics of such por...	[ "Protegrins are small peptides with strong antimicrobial properties , believed to kill bacteria primarily by forming nonselective pores in the bacterial membrane .", "This nonspecific and highly effective mechanism of action has created significant excitement about the use of protegrins as therapeutic antibiotics...	2009
[ "Introduction", "Results and Discussion", "Methods" ]	[ "physics", "biochemistry", "developmental biology", "cytokines", "proteins", "protein folding", "molecular development", "protein structure", "biology and life sciences", "physical sciences", "computational biology", "biophysics", "molecular biology", "macromolecular structure analysis" ]	Pierced Lasso Bundles Are a New Class of Knot-like Motifs	journal.pcbi.1003613	null	[ [ "The four-helix bundle is a common motif in nature [1] , [2] , [3] , [4] often used as a target for designed pharmaceutical and nutritional biomolecules [5] , [6] , [7] .", "The cytokine subfamily is a family of four-helix bundles that are soluble proteins secreted from different organs/tissues .", "C...	[ "A four-helix bundle is a well-characterized motif often used as a target for designed pharmaceutical therapeutics and nutritional supplements .", "Recently , we discovered a new structural complexity within this motif created by a disulphide bridge in the long-chain helical bundle cytokine leptin .", "When oxi...	[ "We discovered a new class of helical bundle proteins with knot-like structures where part of the polypeptide chain is threaded through a covalently bound loop .", "We call this unique structural motif a Pierced Lasso Bundle .", "We discovered 12 structurally homologous proteins in the PDB .", "Our results in...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "systems biology", "biochemistry", "biochemical simulations", "physiological processes", "biomineralization", "physiology", "earth sciences", "marine and aquatic sciences", "biology and life sciences", "computational biology", "marine biology" ]	Understanding the Sub-Cellular Dynamics of Silicon Transportation and Synthesis in Diatoms Using Population-Level Data and Computational Optimization	journal.pcbi.1003687	null	[ [ "Diatoms are the eukaryotic unicellular organisms , living in marine and fresh water environments .", "Diatoms are producers in the food chain .", "They generate around 40% of all organic carbon in the sea [9] .", "They contribute to the global carbon cycle , by photosynthetic carbon fixation as m...	[ "Controlled synthesis of silicon is a major challenge in nanotechnology and material science .", "Diatoms , the unicellular algae , are an inspiring example of silica biosynthesis , producing complex and delicate nano-structures .", "This happens in several cell compartments , including cytoplasm and silica dep...	[ "Understanding complex biological systems , especially at intracellular scales , has always been a big challenge , owing to the difficulties in measuring and manipulating such small quantities .", "Computational modeling brings promising possibilities to this area .", "The model organism we have studied here is...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "biology", "microbiology", "molecular cell biology" ]	SARS Coronavirus nsp1 Protein Induces Template-Dependent Endonucleolytic Cleavage of mRNAs: Viral mRNAs Are Resistant to nsp1-Induced RNA Cleavage	journal.ppat.1002433	null	[ [ "Severe acute respiratory syndrome ( SARS ) coronavirus ( SCoV ) is the causative agent of SARS , which was first recognized in southern China in 2002 and spread to different areas of the world in a 2002-2003 epidemic [1]-[3] .", "It is believed that the bat-derived SCoV-like CoV [4] , [5] underwent sever...	[ "SARS coronavirus ( SCoV ) nonstructural protein ( nsp ) 1 , a potent inhibitor of host gene expression , possesses a unique mode of action: it binds to 40S ribosomes to inactivate their translation functions and induces host mRNA degradation .", "Our previous study demonstrated that nsp1 induces RNA modification...	[ "Severe acute respiratory syndrome ( SARS ) coronavirus ( SCoV ) is the causative agent of SARS .", "The nsp1 protein of SCoV blocks host protein synthesis , including type I interferon , a general inhibitor of virus replication , in infected cells .", "This finding suggests that SCoV nsp1 protein plays a key r...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "sequencing techniques", "split-decomposition method", "messenger rna", "vertebrates", "animals", "mammals", "plasmid construction", "viruses", "multiple alignment calculation", "rna viruses", "bornaviruses", "dna construction", "molecular biology techniques", "research and analysis method...	Exaptation of Bornavirus-Like Nucleoprotein Elements in Afrotherians	journal.ppat.1005785	null	[ [ "Many eukaryotic genomes contain endogenous viral elements ( EVEs ) , which are derived from viruses [1 , 2] .", "Retroviruses are known as a major source of EVEs , such that approximately 8% of the human genome consists of endogenous retroviruses ( ERVs ) [3] .", "These EVEs not only serve as molecul...	[ "Endogenous bornavirus-like nucleoprotein elements ( EBLNs ) , the nucleotide sequence elements derived from the nucleoprotein gene of ancient bornavirus-like viruses , have been identified in many animal genomes .", "Here we show evidence that EBLNs encode functional proteins in their host .", "Some afrotheria...	[ "Endogenous retroviruses are representative of endogenous viral elements ( EVEs ) , which are known to have occasionally served as the source of evolutionary innovations of the host .", "Endogenous bornavirus-like nucleoprotein element ( EBLN ) was the first EVE identified in mammalian genomes to have been derive...	2016

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