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headings list	keywords list	title stringlengths 20 281	id stringlengths 20 20	toc stringlengths 57 522 ⌀	sections list	abstract list	summary list	year stringclasses 13 values
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "mathematics/statistics", "computational biology/comparative sequence analysis", "computational biology/transcriptional regulation", "computational biology" ]	High Resolution Models of Transcription Factor-DNA Affinities Improve In Vitro and In Vivo Binding Predictions	journal.pcbi.1000916	null	[ [ "Gene regulatory programs are orchestrated by transcription factors ( TFs ) , proteins that coordinate expression of target genes both through direct interaction with DNA and with non-DNA-binding accessory proteins ( cofactors ) .", "A recent catalog of human and mouse TFs documented almost 900 likely TFs...	[ "Accurately modeling the DNA sequence preferences of transcription factors ( TFs ) , and using these models to predict in vivo genomic binding sites for TFs , are key pieces in deciphering the regulatory code .", "These efforts have been frustrated by the limited availability and accuracy of TF binding site motif...	[ "Transcription factors ( TFs ) are proteins that bind sites in the non-coding DNA and regulate the expression of targeted genes .", "Being able to predict the genome-wide binding locations of TFs is an important step in deciphering gene regulatory networks .", "Historically , there was very limited experimental...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "parasite groups", "body fluids", "pathology and laboratory medicine", "parasite replication", "plasmodium", "tropical diseases", "parasitic diseases", "parasitic protozoans", "parasitology", "apicomplexa", "protozoans", "malarial parasites", "gene expressio...	Mosquito Passage Dramatically Changes var Gene Expression in Controlled Human Plasmodium falciparum Infections	journal.ppat.1005538	null	[ [ "Malaria is one of the most frequently occurring parasitic diseases worldwide with an estimated 198 million clinical cases in 2013 and a death toll of more than 0 . 5 million [1] .", "The virulence of the most deadly species of human malaria parasites , Plasmodium falciparum , is directly linked to the va...	[ "Virulence of the most deadly malaria parasite Plasmodium falciparum is linked to the variant surface antigen PfEMP1 , which is encoded by about 60 var genes per parasite genome .", "Although the expression of particular variants has been associated with different clinical outcomes , little is known about var gen...	[ "Parasites of the species Plasmodium falciparum , which are responsible for the most severe forms of malaria , escape from the human immune response by antigenic variation .", "A repertoire of 60 var genes codes for a broad range of different variant antigens presented on the surface of infected erythrocytes .", ...	2016
[ "Introduction", "Results/Discussion", "Material and Methods" ]	[ "marine and aquatic sciences/microbiology", "genetics and genomics/microbial evolution and genomics", "biochemistry/membrane proteins and energy transduction" ]	Proteorhodopsin Phototrophy Promotes Survival of Marine Bacteria during Starvation	journal.pbio.1000358	Mutational analysis provides direct evidence for the link between proteorhodopsin light-harvesting and enhanced survival of marine bacteria.	[ [ "Proteorhodopsins ( PRs ) are membrane-embedded , light-driven proton pumps , which generate a chemiosmotic potential by translocating protons across an energy-transducing membrane [1]–[3] .", "This proton gradient can subsequently be used for production of biologically available energy in the form of ade...	[ "Proteorhodopsins are globally abundant photoproteins found in bacteria in the photic zone of the ocean .", "Although their function as proton pumps with energy-yielding potential has been demonstrated , the ecological role of proteorhodopsins remains largely unexplored .", "Here , we report the presence and fu...	[ "It is estimated that marine microscopic algae—phytoplankton—are responsible for half of the Earth's photosynthesis .", "As much as half of the surface ocean bacteria have proteorhodopsins , which are membrane proteins that allow harvesting of energy from sunlight , implying a potentially significant role of non–...	2010
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "haplotypes", "genetic polymorphism", "effective population size", "molecular systematics", "population genetics", "biology", "evolutionary biology", "evolutionary systematics", "evolutionary genetics" ]	Molecular Evidence of Demographic Expansion of the Chagas Disease Vector Triatoma dimidiata (Hemiptera, Reduviidae, Triatominae) in Colombia	journal.pntd.0002734	null	[ [ "A population's demographic history as well as phylogeographic inferences are usually accessed by studying the reconstructed genealogical histories of individual genes ( gene trees ) sampled from different populations [1]–[3]: Studying patterns of genetic variation in a geographical context via gene trees can...	[ "Triatoma dimidiata is one of the most significant vectors of Chagas disease in Central America and Colombia , and , as in most species , its pattern of genetic variation within and among populations is strongly affected by its phylogeographic history .", "A putative origin from Central America has been proposed ...	[ "The Chagas disease vector Triatoma dimidiata is one of the most important vectors in America , owing to its wide genetic and epidemiological heterogeneity .", "Colombian T . dimidiata populations occupy eclectic sylvatic ecotopes , but have also been found in dwellings infected with Trypanosoma cruzi , and there...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "learning", "medicine and health sciences", "ellipses", "engineering and technology", "statistics", "social sciences", "geometry", "neuroscience", "learning and memory", "multivariate analysis", "age groups", "adults", "cognitive psychology", "mathematics", "body limbs", "research and ...	Goal-related feedback guides motor exploration and redundancy resolution in human motor skill acquisition	journal.pcbi.1006676	null	[ [ "The paradigmatic example of motor acquisition is infant motor development .", "Humans are born without a complete innate knowledge of how their bodies are configured .", "They lack motor coordination and have to learn how to control their hands , heads , feet , etc . , by exploratory activity .", ...	[ "The plasticity of the human nervous system allows us to acquire an open-ended repository of sensorimotor skills in adulthood , such as the mastery of tools , musical instruments or sports .", "How novel sensorimotor skills are learned from scratch is yet largely unknown .", "In particular , the so-called inver...	[ "Even in adulthood , humans can learn to master new motor skills with unfamiliar mappings between desired goals or sensations and corresponding movements , such as playing tennis or musical instruments .", "To master a new skill involves the resolution of motor redundancy; that is a selection from many possible m...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biotechnology", "plant anatomy", "microbiology", "plant science", "rhizobium", "genetically modified plants", "plant genomics", "molecular biology techniques", "plants", "bacteria", "genetic engineering", "agrobacteria", "research and analysis methods", "genetically modified organisms", ...	A Functional Bacterium-to-Plant DNA Transfer Machinery of Rhizobium etli	journal.ppat.1005502	null	[ [ "The Rhizobiales order contains many species of plant-associated bacteria , such as the related genera Agrobacterium and Rhizobium .", "Phylogenetic analyses based on 16S rDNA sequences led to the idea that Agrobacterium and Rhizobium could be regrouped into one genus [1] .", "Yet their lifestyles are...	[ "Different strains and species of the soil phytopathogen Agrobacterium possess the ability to transfer and integrate a segment of DNA ( T-DNA ) into the genome of their eukaryotic hosts , which is mainly mediated by a set of virulence ( vir ) genes located on the bacterial Ti-plasmid that also contains the T-DNA ."...	[ "Since the discovery of gene transfer from Agrobacterium to host plants in the late 1970s , this bacterial pathogen has been widely used in research and biotechnology to generate transgenic plants .", "Agrobacterium’s infection process relies on a set of virulence proteins that mediate the transfer of a segment o...	2016
[ "Introduction", "Results", "Discussion", "Material and Methods" ]	[]	A Zinc Finger Motif-Containing Protein Is Essential for Chloroplast RNA Editing	journal.pgen.1005028	null	[ [ "In vascular plants , specific cytidines are converted to uridines by RNA editing in the chloroplast transcripts [1–3] .", "A typical land plant modifies 30 to 40 C targets in chloroplasts , usually changing the encoded amino acid , and also acts upon hundreds of Cs in plant mitochondria [4 , 5] .", "...	[ "C-to-U editing of transcripts in plant organelles is carried out by small ( <400 kD ) protein complexes called editosomes .", "Recognition of the proper C target for editing is mediated by pentatricopeptide repeat ( PPR ) containing proteins that recognize cis-elements .", "Members of two additional gene famil...	[ "Transcripts encoding chloroplast and mitochondrial proteins of flowering plants are profoundly affected by RNA editing .", "In Arabidopsis , over 600 genomically-encoded Cs are modified to Us in organelle transcripts , altering the encoded amino acids and creating stop and start codons .", "Pentatricopeptide p...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "dermatology", "infectious diseases", "medicine and health sciences", "biology and life sciences", "immunology", "microbiology" ]	Strain-Specific Properties and T Cells Regulate the Susceptibility to Papilloma Induction by Mus musculus Papillomavirus 1	journal.ppat.1004314	null	[ [ "Papillomaviruses ( PV ) are DNA tumor viruses that infect stratified squamous epithelia of the skin and mucous membranes of humans and many other vertebrate species [1] .", "PV infections are species-restricted and region-restricted , in that only part of the skin and mucous membranes of the host species...	[ "The immunocytes that regulate papillomavirus infection and lesion development in humans and animals remain largely undefined .", "We found that immunocompetent mice with varying H-2 haplotypes displayed asymptomatic skin infection that produced L1 when challenged with 6×1010 MusPV1 virions , the recently identif...	[ "Infection with papillomaviruses can cause benign warts ( papillomas ) on skin and mucosae of humans and animals but also malignancies , especially anogenital carcinomas and , in genetically predisposed or immunocompromised individuals , cutaneous squamous cell cancers .", "Control and clearance of these viruses ...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Sharing and Specificity of Co-expression Networks across 35 Human Tissues	journal.pcbi.1004220	null	[ [ "Tissue-specificity , in which cells perform different functions despite possessing identical DNA , is achieved partially through tissue-dependent mechanisms of gene regulation , including epigenetic modification and transcriptional and post-transcriptional regulation [1–3] .", "These complex programs of ...	[ "To understand the regulation of tissue-specific gene expression , the GTEx Consortium generated RNA-seq expression data for more than thirty distinct human tissues .", "This data provides an opportunity for deriving shared and tissue specific gene regulatory networks on the basis of co-expression between genes ....	[ "Cells in different tissues perform very different functions with the same DNA .", "This requires tissue-specific gene expression and regulation; understanding this tissue-specificity is often instrumental to understanding complex diseases .", "Here , we use tissue-specific gene expression data to learn tissue-...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "immunity", "immunology", "biology", "microbiology", "zoology", "parasitology" ]	Induction of CD4+CD25+FOXP3+ Regulatory T Cells during Human Hookworm Infection Modulates Antigen-Mediated Lymphocyte Proliferation	journal.pntd.0001383	null	[ [ "Human hookworm infection is mainly caused by the blood-feeding nematodes Ancylostoma duodenale and Necator americanus , which infects 576 to 740 million people worldwide , especially in the tropics and subtropics [1] , [2] , [3] .", "Hookworm is considered one of the thirteen poverty-promoting neglected ...	[ "Hookworm infection is considered one of the most important poverty-promoting neglected tropical diseases , infecting 576 to 740 million people worldwide , especially in the tropics and subtropics .", "These blood-feeding nematodes have a remarkable ability to downmodulate the host immune response , protecting th...	[ "The hookworm infection is characterized by the long-term survival of the parasite and the concomitant modulation of the host immunity .", "Among several mechanisms that may account for the suppression of T cell response , we here described the presence and role of T regulatory cells ( also known as Tregs ) in th...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biotechnology", "applied microbiology", "biochemistry", "enzymes", "biology and life sciences", "enzymology", "microbiology" ]	VIB1, a Link between Glucose Signaling and Carbon Catabolite Repression, Is Essential for Plant Cell Wall Degradation by Neurospora crassa	journal.pgen.1004500	null	[ [ "Bioconversion of lignocellulosic biomass to simple sugars holds great promise in next-generation biofuel production and relies on a complex repertoire of proteins for enzymatic deconstruction of plant cell walls [1] .", "Many filamentous fungi have evolved to utilize cellulosic materials and are capable ...	[ "Filamentous fungi that thrive on plant biomass are the major producers of hydrolytic enzymes used to decompose lignocellulose for biofuel production .", "Although induction of cellulases is regulated at the transcriptional level , how filamentous fungi sense and signal carbon-limited conditions to coordinate cel...	[ "Many filamentous fungi that grow on plant biomass are capable of producing lignocellulase enzymes to break down plant cell walls into utilizable sugars , thus holding great potential in reducing the cost of the next-generation biofuels .", "Cellulase production is subject to induction by the presence of plant bi...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "cell biology", "immunology" ]	TSCOT + Thymic Epithelial Cell-Mediated Sensitive CD4 Tolerance by Direct Presentation	journal.pbio.0060191	A new study shows that antigen-specific negative selection of developing thymocytes is a property of thymic cortical epithelial cells, challenging the view that this process requires contact with specialized antigen-presenting cells found in the thymic medulla.	[ [ "T cell tolerance is established mainly in the thymus where the T cell population develops and learns by a process called negative selection to avoid harmful reactivity against self-antigens expressed in that thymus ( reviewed in [1 , 2] ) .", "In the periphery , organ-specific tolerance can be establishe...	[ "Although much effort has been directed at dissecting the mechanisms of central tolerance , the role of thymic stromal cells remains elusive .", "In order to further characterize this event , we developed a mouse model restricting LacZ to thymic stromal cotransporter ( TSCOT ) -expressing thymic stromal cells ( T...	[ "T cells play critical roles in the immune response .", "While developing in the thymus ( from whence T cells and their precursors , thymocytes , derive their name ) , thymocytes are selected for the ability to recognize harmful antigen ( positive selection ) , while those that respond to antigens present in thei...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The Role of piRNA-Mediated Epigenetic Silencing in the Population Dynamics of Transposable Elements in Drosophila melanogaster	journal.pgen.1005269	null	[ [ "Transposable elements ( TEs ) are genetic elements that increase their copy number in the host genome by copying themselves to new genomic locations .", "Despite reported incidences of potentially adaptive TEs [1–6] , the majority of TEs are considered deleterious to their host and widely viewed as “geno...	[ "The piwi-interacting RNAs ( piRNA ) are small RNAs that target selfish transposable elements ( TEs ) in many animal genomes .", "Until now , piRNAs’ role in TE population dynamics has only been discussed in the context of their suppression of TE transposition , which alone is not sufficient to account for the sk...	[ "The piwi-interacting RNAs ( piRNAs ) are small RNAs that can suppress the expression of selfish transposable elements ( TEs ) in many animal genomes .", "One mechanism by which piRNAs silence TEs is through the formation of heterochromatin , which is condensed chromatin and generally associated with repressed ge...	2015
[ "Introduction", "Results", "Discussion", "Material and methods" ]	[ "blood cells", "medicine and health sciences", "reproductive system", "immune cells", "immune physiology", "body fluids", "spleen", "immunology", "microbiology", "cytotoxic t cells", "research and analysis methods", "specimen preparation and treatment", "staining", "white blood cells", "...	Early primed KLRG1- CMV-specific T cells determine the size of the inflationary T cell pool	journal.ppat.1007785	null	[ [ "A hallmark of immunological memory is the ability of the adaptive immune system to generate long-lived antigen-specific memory T or B cells .", "Upon pathogen clearance , most virus-specific T cells undergo apoptosis and few of them form a stable pool of memory T cells , which is maintained lifelong in c...	[ "Memory T cell inflation is a process in which a subset of cytomegalovirus ( CMV ) specific CD8 T cells continuously expands mainly during latent infection and establishes a large and stable population of effector memory cells in peripheral tissues .", "Here we set out to identify in vivo parameters that promote ...	[ "Cytomegalovirus induces a lifelong infection in the majority of the world's population , due to the ability of the virus to establish latency .", "Upon CMV infection , large numbers of effector memory T cells are induced in peripheral tissues , a process that is termed memory inflation .", "As inflationary T c...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Dual Regulation of the Mitotic Exit Network (MEN) by PP2A-Cdc55 Phosphatase	journal.pgen.1003966	null	[ [ "During most of the cell cycle , Cdc14 is kept inactive and sequestered in the nucleolus through binding to its inhibitor Net1 [1] , [2] .", "Two pathways , FEAR ( Cdc14 early anaphase release ) and MEN ( mitotic exit network ) , activate Cdc14 , thereby promoting its release from the nucleolus in early a...	[ "Exit from mitosis in budding yeast is triggered by activation of the key mitotic phosphatase Cdc14 .", "At anaphase onset , the protease separase and Zds1 promote the downregulation of PP2ACdc55 phosphatase , which facilitates Cdk1-dependent phosphorylation of Net1 and provides the first wave of Cdc14 activity ....	[ "Cell cycle studies over the years have tried to elucidate the molecular mechanisms behind cell division , one of the most highly regulated of all cell processes , which ensures life in all organisms .", "Protein phosphorylation emerged as a key regulatory mechanism in the cell cycle .", "The highly conserved f...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genome-wide association studies", "population genetics", "quantitative traits", "anatomy and physiology", "microbiology", "physiological processes", "model organisms", "dna replication", "dna", "genetic polymorphism", "biology", "molecular biology", "aging", "trait locus", "nucleic acid...	A Natural Polymorphism in rDNA Replication Origins Links Origin Activation with Calorie Restriction and Lifespan	journal.pgen.1003329	null	[ [ "The budding yeast Saccharomyces cerevisiae has become a favorite model for studying the genetic and molecular basis for variation in lifespan [1] .", "In particular , the unequal division of mother and daughter cells in this species makes it especially amenable for analysis of replicative lifespan ( RLS ...	[ "Aging and longevity are complex traits influenced by genetic and environmental factors .", "To identify quantitative trait loci ( QTLs ) that control replicative lifespan , we employed an outbred Saccharomyces cerevisiae model , generated by crossing a vineyard and a laboratory strain .", "The predominant QTL ...	[ "Although many aging regulators have been discovered , we are still uncovering how each contributes to the basic biology underlying cell lifespan and how certain longevity-promoting regimens , such as calorie restriction , manipulate the aging process across species .", "Since many cellular aging processes betwee...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "plant science", "plant growth and development", "genetics", "plant genetics", "epigenetics", "biology and life sciences", "histone modification" ]	Regulation of Arabidopsis Flowering by the Histone Mark Readers MRG1/2 via Interaction with CONSTANS to Modulate FT Expression	journal.pgen.1004617	null	[ [ "The timing of floral transition from vegetative to reproductive development is a critical event in the plant life cycle and is coordinated by internal and environmental cues [1]–[3] .", "In Arabidopsis , the photoperiodic flowering pathway is regulated by the transcription factor CONSTANS ( CO ) and the ...	[ "Day-length is important for regulating the transition to reproductive development ( flowering ) in plants .", "In the model plant Arabidopsis thaliana , the transcription factor CONSTANS ( CO ) promotes expression of the florigen FLOWERING LOCUS T ( FT ) , constituting a key flowering pathway under long-day phot...	[ "The photoperiodic flowering in Arabidopsis requires the key regulator CO and its target gene FT .", "However , how CO regulates FT expression in the context of chromatin remains largely obscure .", "In this work , we present Arabidopsis MRG1/2 as novel chromatin effectors directly involved in the CO-FT photope...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "gastrointestinal infections" ]	Common Coinfections of Giardia intestinalis and Helicobacter pylori in Non-Symptomatic Ugandan Children	journal.pntd.0001780	null	[ [ "In low-income countries co-infections involving several different pathogens commonly ocurr [1] .", "Several recent , cross-sectional studies from different locations , have reported a potential association between G . intestinalis and H . pylori [2] , [3] , [4] .", "Both organisms colonize the gastro...	[ "The protozoan parasite Giardia intestinalis and the pathogenic bacterium Helicobacter pylori are well known for their high prevalences in human hosts worldwide .", "The prevalence of both organisms is known to peak in densely populated , low resource settings and children are infected early in life .", "Differ...	[ "G . intestinalis and H . pylori are known to infect the gastrointestinal tract of humans early in life and to be very prevalent in endemic areas throughout life .", "H . pylori colonizes the gastric mucosa and may give rise to peptic ulcers , chronic gastritis and gastric cancer whereas Giardia causes diarrhea ,...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "cell biology", "virology", "biology and life sciences", "microbiology", "molecular cell biology" ]	Structural Correlates of Rotavirus Cell Entry	journal.ppat.1004355	null	[ [ "Non-enveloped viruses must breach a membrane to enter and infect a cell .", "Various groups of viruses have evolved distinct molecular mechanisms to carry out this penetration step , which leads to translocation of the infecting particle from an endocytic vesicle or other intracellular compartment to the...	[ "Cell entry by non-enveloped viruses requires translocation into the cytosol of a macromolecular complex—for double-strand RNA viruses , a complete subviral particle .", "We have used live-cell fluorescence imaging to follow rotavirus entry and penetration into the cytosol of its ∼700 Å inner capsid particle ( “d...	[ "Non-enveloped viruses ( viruses lacking a lipid-bilayer membrane ) require local disruption of a cellular membrane to gain access to the cell interior and thereby initiate infection .", "Most double-strand RNA viruses have an outer protein layer that mediates this entry step and an inner-capsid particle that tra...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Mosquito-Parasite Interactions Can Shape Filariasis Transmission Dynamics and Impact Elimination Programs	journal.pntd.0002433	null	[ [ "Human lymphatic filariasis ( LF ) is a mosquito-borne disease that is a leading cause of morbidity worldwide .", "1 . 4 billion people in 81 countries are at risk of infection with the nematode parasites Wuchereria bancrofti , Brugia malayi or B . timori .", "Clinical manifestations , including acute...	[ "The relationship between mosquito vectors and lymphatic filariasis ( LF ) parasites can result in a range of transmission outcomes .", "Anophelines are generally characterized as poor vectors due to an inability to support development at low densities .", "However , it is important to understand the potential ...	[ "Lymphatic filariasis ( LF ) elimination requires interrupting transmission of microfilaria ( mf ) from humans to mosquitoes for 5–7 years , the average life span of adult worms .", "Current mf prevalence thresholds , below which transmission cannot be sustained , are unknown .", "Anopheline-transmitted LF is t...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The ATM Signaling Cascade Promotes Recombination-Dependent Pachytene Arrest in Mouse Spermatocytes	journal.pgen.1005017	null	[ [ "Meiosis generates haploid cells from a diploid progenitor by coupling one round of genome replication to two rounds of chromosome segregation .", "During prophase of the first division , SPO11 protein forms double-strand breaks ( DSBs ) , whose repair enables homologous chromosomes to pair , synapse and ...	[ "Most mutations that compromise meiotic recombination or synapsis in mouse spermatocytes result in arrest and apoptosis at the pachytene stage of the first meiotic prophase .", "Two main mechanisms are thought to trigger arrest: one independent of the double-strand breaks ( DSBs ) that initiate meiotic recombinat...	[ "Meiosis is the specialized cell division by which haploid cells are produced .", "As germ cells enter the first meiotic prophase , programmed double-stranded breaks ( DSBs ) are formed throughout the genome .", "Repair of these DSBs by homologous recombination is crucial for proper segregation of homologous ch...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "immune cells", "immunity to infections", "immunology", "microbiology", "liver diseases", "adaptive immunity", "infectious hepatitis", "hepatitis", "gastroenterology and hepatology", "infectious diseases", "t cells", "biology", "immune response", "immunopathology", "hepatit...	Kupffer Cells Hasten Resolution of Liver Immunopathology in Mouse Models of Viral Hepatitis	journal.ppat.1002061	null	[ [ "Kupffer cells ( KCs ) are non-parenchymal cells that account for approximately 15% of the total liver cell population and constitute 80%–90% of the tissue-resident macrophages in the whole body [1] .", "Due to their intravascular ( sinusoidal ) localization , KCs have long been studied as scavenger cells...	[ "Kupffer cells ( KCs ) are widely considered important contributors to liver injury during viral hepatitis due to their pro-inflammatory activity .", "Herein we utilized hepatitis B virus ( HBV ) -replication competent transgenic mice and wild-type mice infected with a hepatotropic adenovirus to demonstrate that ...	[ "Kupffer cells ( KCs ) , the resident macrophages of the liver , are considered important contributors to liver injury during viral hepatitis due to their pro-inflammatory activity .", "Herein we utilized two different mouse models of viral hepatitis ( where liver damage is triggered , as during viral hepatitis i...	2011
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Biodistribution and Toxicity Studies of PRINT Hydrogel Nanoparticles in Mosquito Larvae and Cells	journal.pntd.0003735	null	[ [ "Vector-borne diseases continue to be major causes of morbidity and mortality worldwide [1] .", "Malaria remains a major burden on humankind; more than 3 billion people are at risk for infection and more than 200 million people per year are infected , resulting in more than 600 , 000 reported deaths annua...	[ "Mosquito-borne diseases continue to remain major threats to human and animal health and impediments to socioeconomic development .", "Increasing mosquito resistance to chemical insecticides is a great public health concern , and new strategies/technologies are necessary to develop the next-generation of vector c...	[ "There is an urgent need for new interventions and novel insecticides to control mosquito vectors of human disease agents .", "Nanoparticle-based strategies have been explored extensively as means to deliver a molecule of interest for medical applications ( e . g . , antigens , drugs , nucleic acids , etc . ) to ...	2015
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "immunology", "vertebrates", "mice", "animals", "mammals", "simulation and modeling", "histology", "signs and symptoms", "materials science", "surfactants", "elastin", "research and analysis methods", "respiratory physi...	Histologic and biochemical alterations predict pulmonary mechanical dysfunction in aging mice with chronic lung inflammation	journal.pcbi.1005570	null	[ [ "The lung has a stylized architecture that is crucial for the efficient exchange of gases between the vasculature and the airways .", "Organ level mechanical function and the distribution of ventilation during health and disease are dependent upon the complex interactions between heterogeneous airway and ...	[ "Both aging and chronic inflammation produce complex structural and biochemical alterations to the lung known to impact work of breathing .", "Mice deficient in surfactant protein D ( Sftpd ) develop progressive age-related lung pathology characterized by tissue destruction/remodeling , accumulation of foamy macr...	[ "Aging and chronic inflammation produce complex changes to the structure of the lung including accumulation of cells and debris , thinning and destruction of air sacs , altered airway size and increased tendency for airway collapse .", "As these structural changes are observed concurrently , their individual cont...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "biology and life sciences", "viral vaccines", "microbiology", "virology" ]	Comparison of Safety and Immunogenicity of PVRV and PCECV Immunized in Patients with WHO Category II Animal Exposure: A Study Based on Different Age Groups	journal.pntd.0003412	null	[ [ "Rabies , caused by rabies virus infection , remains a global health threat , and became the leading cause of infectious disease mortality in May 2006 in China [1] .", "In the world , Rabies is estimated to cause more than 55000 deaths every year , and is considered to be endemic in more than 150 countrie...	[ "The aim of this study was to compare the safety and immunogenicity between purified vero cell rabies vaccine ( PVRV ) and purified chick embryo cell vaccine ( PCECV ) in patients with WHO category II animal exposure , especially in different age groups .", "In one-year clinical observation after vaccination with...	[ "Nowadays , many approved vaccines with different components ( such as purified vero cell rabies vaccine [PVRV] , purified chick embryo cell vaccine [PCECV] , and Human diploid cell vaccine [HDCV] ) and many regimens with different vaccination schedules ( Zagreb , Essen ) are being used in the world .", "Thus , w...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "hiv infections", "organoids", "medicine and health sciences", "innate immune system", "immune physiology", "cytokines", "pathology and laboratory medicine", "biopsy", "pathogens", "biological cultures", "immunology", "microbiology", "surgical and invasive medical procedures", "retroviruse...	A20 upregulation during treated HIV disease is associated with intestinal epithelial cell recovery and function	journal.ppat.1006806	null	[ [ "Infection with Human Immunodeficiency Virus ( HIV ) results in widespread inflammation in infected individuals with key changes in the immune system that have important clinical implications .", "Untreated HIV disease is characterized by high levels of systemic and tissue-localized proinflammatory cytoki...	[ "ClinicalTrials . gov Clinical Trial NCT00594880" ]	[ "Though the advent of antiretroviral therapy ( ART ) has significantly improved the lives of individuals infected with the Human Immunodeficiency Virus ( HIV ) , those on therapy still suffer from an enhanced risk of morbidities and mortalities that is caused , at least in part by , overactivation of the immune sys...	2018
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "arthropods", "eukaryotes", "evolutionary biology", "drosophila", "animals", "genetics and genomics", "insects" ]	Genome Organization and Gene Expression Shape the Transposable Element Distribution in the Drosophila melanogaster Euchromatin	journal.pgen.0030210	null	[ [ "Transposable elements ( TEs ) are selfish genomic elements on the order of one to several kilobases in length .", "They spread by replication and insertion across the host's genome , either with the help of enzymes they encode or by parasitizing the transposition machinery provided by other elements .", ...	[ "The distribution of transposable elements ( TEs ) in a genome reflects a balance between insertion rate and selection against new insertions .", "Understanding the distribution of TEs therefore provides insights into the forces shaping the organization of genomes .", "Past research has shown that TEs tend to a...	[ "Transposable elements ( TEs ) are parasitic DNA segments that can move within a host genome .", "These selfish mobile elements are present in virtually all eukaryote species and can contribute significantly to their DNA .", "TEs multiply by copying themselves within the genome .", "Depending on where they la...	2007
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "learning", "medicine and health sciences", "exponential functions", "social sciences", "neuroscience", "learning and memory", "simulation and modeling", "cognitive psychology", "mathematics", "probability distribution", "body limbs", "research and analysis methods", "musculoskeletal system"...	The gradient of the reinforcement landscape influences sensorimotor learning	journal.pcbi.1006839	null	[ [ "Whether a previous action is successful or unsuccessful is an important contributor to sensorimotor learning .", "Indeed , binary reinforcement feedback ( e . g . , reward ) is sufficient to cause adaptation of hand aim during a reaching task , independent from error feedback [1 , 2 , 3 , 4 , 5 , 6 , 7] ...	[ "Consideration of previous successes and failures is essential to mastering a motor skill .", "Much of what we know about how humans and animals learn from such reinforcement feedback comes from experiments that involve sampling from a small number of discrete actions .", "Yet , it is less understood how we lea...	[ "In recent years it has been shown that reinforcement feedback may also subserve our ability to acquire new motor skills .", "Here we address how the reinforcement gradient influences motor learning .", "We found that a steeper gradient increased both the rate and likelihood of learning .", "Moreover , while ...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "animal types", "viral classification", "microbiology", "rabies", "rna viruses", "veterinary science", "emergence", "veterinary diseases", "zoonotic diseases", "biology", "behavioral ecology", "wildlife", "ecology", "virology", "evolutionary biology", "evolutionary processes" ]	Rates of Viral Evolution Are Linked to Host Geography in Bat Rabies	journal.ppat.1002720	null	[ [ "RNA viruses display exceptionally variable rates of molecular evolution , with up to 6 orders of magnitude in nucleotide substitution rates observed among viral species [1] .", "Because of the importance of genetic and phenotypic evolution for infecting new host species , evading immune responses and obs...	[ "Rates of evolution span orders of magnitude among RNA viruses with important implications for viral transmission and emergence .", "Although the tempo of viral evolution is often ascribed to viral features such as mutation rates and transmission mode , these factors alone cannot explain variation among closely r...	[ "Rapid evolution of RNA viruses is intimately linked to their success in overcoming the defenses of their hosts .", "Several studies have shown that rates of viral evolution can vary dramatically among distantly related viral families .", "Variability in the speed of evolution among closely related viruses has ...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "virology/mechanisms of resistance and susceptibility, including host genetics", "infectious diseases/hiv infection and aids", "virology/immunodeficiency viruses" ]	Elite Suppressor–Derived HIV-1 Envelope Glycoproteins Exhibit Reduced Entry Efficiency and Kinetics	journal.ppat.1000377	null	[ [ "A minor subset of HIV-1–infected individuals maintains stable CD4+ T cell counts in the absence of antiretroviral therapy .", "A small proportion of these long-term nonprogressors ( LTNPs ) , termed elite suppressors ( ES ) , control plasma viral loads to <50 copies/ml [1] .", "Mechanism ( s ) respon...	[ "Elite suppressors ( ES ) are a rare subset of HIV-1–infected individuals who are able to maintain HIV-1 viral loads below the limit of detection by ultra-sensitive clinical assays in the absence of antiretroviral therapy .", "Mechanism ( s ) responsible for this elite control are poorly understood but likely inv...	[ "The majority of HIV-1–infected individuals experience high plasma viral loads and CD4+ T cells loss in the absence of antiretroviral therapy .", "However , a very rare and important subset of individuals termed elite suppressors is able to maintain HIV-1 plasma viral loads below the limit of viral detection in t...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The Toxoplasma gondii Cyst Wall Protein CST1 Is Critical for Cyst Wall Integrity and Promotes Bradyzoite Persistence	journal.ppat.1003823	null	[ [ "Toxoplasma gondii , an Apicomplexan , is an obligate intracellular protozoan parasite that can cause severe human disease .", "It is estimated that a third of the human population is chronically infected with T . gondii [1] , with prevalence rates ranging from a few percent to nearly 80% depending on the...	[ "Toxoplasma gondii infects up to one third of the world's population .", "A key to the success of T . gondii as a parasite is its ability to persist for the life of its host as bradyzoites within tissue cysts .", "The glycosylated cyst wall is the key structural feature that facilitates persistence and oral tra...	[ "Toxoplasma gondii causes severe encephalitis in immune compromised hosts after reactivation of brain cysts that persist for the life span of the host .", "The biological mechanisms of bradyzoite persistence within cysts are not fully understood .", "The glycosylated cyst wall is thought to play a crucial role ...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "immune cells", "rna viruses", "immunity", "virology", "immune activation", "antigen-presenting cells", "immunity to infections", "immunology", "biology", "microbiology", "viral classification" ]	Low CCR7-Mediated Migration of Human Monocyte Derived Dendritic Cells in Response to Human Respiratory Syncytial Virus and Human Metapneumovirus	journal.ppat.1002105	null	[ [ "The paramyxoviruses human respiratory syncytial virus ( HRSV ) , human metapneumovirus ( HMPV ) and human parainfluenza virus type 3 ( HPIV3 ) are common respiratory pathogens .", "HRSV is the most important viral agent of severe pediatric respiratory tract disease worldwide [1] , [2] , followed by HPIV3...	[ "Human respiratory syncytial virus ( HRSV ) and , to a lesser extent , human metapneumovirus ( HMPV ) and human parainfluenza virus type 3 ( HPIV3 ) , can re-infect symptomatically throughout life without significant antigenic change , suggestive of incomplete or short-lived immunity .", "In contrast , re-infecti...	[ "The respiratory viruses human respiratory syncytial virus ( HRSV ) and , to a lesser extent , human metapneumovirus virus ( HMPV ) and human parainfluenza virus ( HPIV3 ) , can re-infect humans throughout life without significant antigenic change , suggesting that immunity to these viruses is incomplete .", "In ...	2011
[ "Introduction", "Materials and Methods", "Discussion" ]	[ "cellular structures", "enzymes", "microbiology", "parastic protozoans", "nucleolus", "metabolic pathways", "biology", "biochemistry", "rna", "trypanosoma", "rna processing", "cell biology", "nucleic acids", "protozoology", "molecular cell biology", "metabolism" ]	Molecular and Functional Characterization of a Trypanosoma cruzi Nuclear Adenylate Kinase Isoform	journal.pntd.0002044	null	[ [ "Trypanosoma cruzi , the causative agent of Chagas' disease , is a protozoan parasite with a complex life cycle which involves two intermediary hosts , triatomine insects and mammals and three main parasite stages , epimastigotes and amastigotes which replicate in the insect vector and mammalian host respecti...	[ "Trypanosoma cruzi , the etiological agent of Chagas' disease , is an early divergent eukaryote in which control of gene expression relies mainly in post-transcriptional mechanisms .", "Transcription levels are globally up and down regulated during the transition between proliferating and non-proliferating life-c...	[ "Infection with Trypanosoma cruzi produces a condition known as Chagas disease which affects at least 17 million people .", "Adenylate kinases , so called myokinases , are involved in a wide variety of processes , mainly related to their role in nucleotide interconversion and energy management .", "Recently , n...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "population genetics", "microbiology", "epistasis", "mutation", "fungi", "population biology", "mycology", "evolutionary modeling", "biology", "evolutionary theory", "adaptation", "heredity", "genetics", "computational biology", "evolutionary biology", "evolutionary processes", "gene...	Evolutionary Accessibility of Mutational Pathways	journal.pcbi.1002134	null	[ [ "The dynamics of adaptation of a haploid asexual population on a given fitness landscape is governed by population size , selection strength and mutation rate , and different regimes for these parameters have been identified [22]–[24] .", "Here we assume a ‘strong-selection/weak mutation’ ( SSWM ) regime ...	[ "Functional effects of different mutations are known to combine to the total effect in highly nontrivial ways .", "For the trait under evolutionary selection ( ‘fitness’ ) , measured values over all possible combinations of a set of mutations yield a fitness landscape that determines which mutational states can b...	[ "Fitness landscapes describe the fitness of related genotypes in a given environment , and can be used to identify which mutational steps lead towards higher fitness under particular evolutionary scenarios .", "The structure of a fitness landscape results from the way mutations interact in determining fitness , a...	2011
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "artificial intelligence", "genome analysis", "pharmacology", "molecular biology techniques", "drug metabolism", "digestive system", "research and analysis methods", "cell labeling", "computer and information sciences", "genomics", "drug marketing", "gene expr...	Predicting gastrointestinal drug effects using contextualized metabolic models	journal.pcbi.1007100	null	[ [ "Side effects are unintended effects of administered drugs that lead to a decrease in the efficacy of treatment , lower patient compliance , and eventually the cessation of treatment with the development of adverse physiological consequences .", "Additionally , up to 25% of drug development programs fail ...	[ "Gastrointestinal side effects are among the most common classes of adverse reactions associated with orally absorbed drugs .", "These effects decrease patient compliance with the treatment and induce undesirable physiological effects .", "The prediction of drug action on the gut wall based on in vitro data sol...	[ "The gut wall is the first barrier that encounters orally absorbed drugs , and it substantially modulates the bioavailability of drugs and supports several classes of side effects .", "We developed context-specific metabolic models of the enterocyte constrained by drug-induced gene expression and trained a machin...	2019
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "animal types", "medicine and health sciences", "infectious disease epidemiology", "japan", "immunology", "tropical diseases", "geographical locations", "vertebrates", "pets and companion animals", "dogs", "animals", "mammals", "preventive medicine", "rabies", "neglected tropical disease...	The rise and fall of rabies in Japan: A quantitative history of rabies epidemics in Osaka Prefecture, 1914–1933	journal.pntd.0005435	null	[ [ "Rabies has been one of the most feared diseases throughout human history and has the highest known case-fatality rate [1] .", "This zoonosis is mainly maintained in domestic dog populations , and continues to cause approximately 59 , 000 human deaths every year globally [2] .", "More than 99% of thes...	[ "Japan has been free from rabies since the 1950s .", "However , during the early 1900s several large-scale epidemics spread throughout the country .", "Here we investigate the dynamics of these epidemics between 1914 and 1933 in Osaka Prefecture , using archival data including newspapers .", "The association ...	[ "Rabies is a lethal zoonosis mostly transmitted through bites by dogs infected with rabies virus .", "Japan has been free from rabies since the 1950s .", "However , there were several large-scale epidemics before its elimination .", "These past epidemics occurred both before and after dog rabies vaccine becam...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "pathology and laboratory medicine", "gene regulation", "pathogens", "immunology", "microbiology", "cytomegalovirus infection", "viruses", "bone marrow cells", "non-coding rna", "dna viruses", "herpesviruses", "human cytomega...	cGAS Senses Human Cytomegalovirus and Induces Type I Interferon Responses in Human Monocyte-Derived Cells	journal.ppat.1005546	null	[ [ "Human cytomegalovirus ( HCMV ) is a highly host-adapted , opportunistic β-herpesvirus that copes amazingly well with the host’s immune response due to a plethora of different evasion mechanisms [1 , 2] .", "These strategies allow HCMV to establish latency and to silently spread to naïve individuals .", ...	[ "Human cytomegalovirus ( HCMV ) infections of healthy individuals are mostly unnoticed and result in viral latency .", "However , HCMV can also cause devastating disease , e . g . , upon reactivation in immunocompromised patients .", "Yet , little is known about human immune cell sensing of DNA-encoded HCMV .",...	[ "Human cytomegalovirus ( HCMV ) has been shown to induce type I interferon ( IFN-I ) responses in myeloid cells such as plasmacytoid dendritic cells ( pDC ) .", "Although these cells were reported to sense the viral DNA genome in a Toll-like receptor ( TLR ) -dependent manner , previous studies showed that indivi...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "helminth infections", "medicine and health sciences", "filariasis", "neglected tropical diseases", "tropical diseases", "parasitic diseases", "lymphatic filariasis" ]	Assessing Progress in Reducing the At-Risk Population after 13 Years of the Global Programme to Eliminate Lymphatic Filariasis	journal.pntd.0003333	null	[ [ "Lymphatic filariasis ( LF ) is a Neglected Tropical Disease ( NTD ) endemic in 73 tropical and sub-tropical countries [1] .", "It is caused by three species of filarial worms – Wuchereria bancrofti , Brugia malayi and Brugia timori – and is transmitted by multiple species of mosquitoes .", "The disea...	[ "In 1997 , the World Health Assembly adopted Resolution 50 . 29 , committing to the elimination of lymphatic filariasis ( LF ) as a public health problem , subsequently targeted for 2020 .", "The initial estimates were that 1 . 2 billion people were at-risk for LF infection globally .", "Now , 13 years after th...	[ "Lymphatic filariasis ( LF ) is a widespread neglected tropical disease most frequently recognized as elephantiasis that is caused by parasitic worms and spread by mosquitoes .", "To overcome this public health problem , the World Health Organization created the Global Programme to Eliminate Lymphatic Filariasis ...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Comparing Algorithms That Reconstruct Cell Lineage Trees Utilizing Information on Microsatellite Mutations	journal.pcbi.1003297	null	[ [ "A multi-cellular organism develops from a single cell – the zygote , through cell division and cell death , and displays an astonishing complexity of trillions of cells of different types , residing in different tissues and expressing different genes .", "The development of an organism from a single cell...	[ "Organism cells proliferate and die to build , maintain , renew and repair it .", "The cellular history of an organism up to any point in time can be captured by a cell lineage tree in which vertices represent all organism cells , past and present , and directed edges represent progeny relations among them .", ...	[ "The history of an organism's cells , from a single cell until any particular moment in time , can be captured by a cell lineage tree .", "Many fundamental open questions in biology and medicine , such as which cells give rise to metastases , whether oocytes and beta cells renew , and what is the role of stem cel...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "evolutionary biology", "infectious diseases/helminth infections", "ecology" ]	Interactions between Natural Populations of Human and Rodent Schistosomes in the Lake Victoria Region of Kenya: A Molecular Epidemiological Approach	journal.pntd.0000222	null	[ [ "One of the world's most prevalent neglected diseases is schistosomiasis , which is caused by flatworms of the genus Schistosoma .", "It is estimated that 200 million people world wide are infected [1] .", "Schistosomiasis is notable for its chronic nature , for being difficult to control on a sustain...	[ "Schistosoma mansoni exists in a complex environmental milieu that may select for significant evolutionary changes in this species .", "In Kenya , the sympatric distribution of S . mansoni with S . rodhaini potentially influences the epidemiology , ecology , and evolutionary biology of both species , because they...	[ "One of the world's most prevalent neglected diseases is schistosomiasis , which infects approximately 200 million people worldwide .", "Schistosoma mansoni is transmitted to humans by skin penetration by free-living larvae that develop in freshwater snails .", "The origin of this species is East Africa , where...	2008
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "animal types", "medicine and health sciences", "body fluids", "enzyme-linked immunoassays", "pathology and laboratory medicine", "vertebrates", "parasitic diseases", "animals", "mammals", "urine", "primates", "veterinary diagnostics", "immunologic techniques", "zoology", "veterinary sci...	Identifying wildlife reservoirs of neglected taeniid tapeworms: Non-invasive diagnosis of endemic Taenia serialis infection in a wild primate population	journal.pntd.0005709	null	[ [ "Singular among cyclophyllidean tapeworms , taeniid species parasitize mammals in both their adult and larval stages [1] .", "Taeniid adult stages infect humans and carnivorous species that include canids , felids , hyaenids , mustelids , and viverrids [1 , 3] and cause few severe symptoms in healthy host...	[ "Despite the global distribution and public health consequences of Taenia tapeworms , the life cycles of taeniids infecting wildlife hosts remain largely undescribed .", "The larval stage of Taenia serialis commonly parasitizes rodents and lagomorphs , but has been reported in a wide range of hosts that includes ...	[ "Although tapeworm parasites of the genus Taenia are globally distributed and inflict enormous socioeconomic and health costs on their hosts , which include humans , little is known about taeniid tapeworms that infect wildlife .", "This gap in knowledge prevents an assessment of the potential for these parasites ...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "immune physiology", "pathology and laboratory medicine", "spleen", "pathogens", "immunology", "microbiology", "bone marrow cells", "animal models", "model organisms", "signs and symptoms", "experimental organism systems", "b...	Down regulation of macrophage IFNGR1 exacerbates systemic L. monocytogenes infection	journal.ppat.1006388	null	[ [ "Interferons ( IFN ) are critical mediators of host immunity .", "These cytokines are classified into two major groups: type I and type II .", "Type I IFNs are a family of homologous proteins including various IFNα subtypes and a single IFNβ [1 , 2] .", "They are synthesized and secreted in respon...	[ "Interferons ( IFNs ) target macrophages to regulate inflammation and resistance to microbial infections .", "The type II IFN ( IFNγ ) acts on a cell surface receptor ( IFNGR ) to promote gene expression that enhance macrophage inflammatory and anti-microbial activity .", "Type I IFNs can dampen macrophage resp...	[ "Interferon ( IFN ) γ promotes host resistance to invasive bacterial infections , but type I IFNs suppress macrophage activation and increase susceptibility to L . monocytogenes and other pathogenic bacteria .", "IFNγ promotes resistance by potently activating macrophages to become pro-inflammatory and antimicrob...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "reverse transcriptase-polymerase chain reaction", "medicine and health sciences", "pathology and laboratory medicine", "pathogens", "tropical diseases", "microbiology", "vertebrates", "rna extraction", "animals", "mammals", "dogs", "viruses", "rabies", "rna viruses", "neglected tropical...	Evaluation of Six Commercially Available Rapid Immunochromatographic Tests for the Diagnosis of Rabies in Brain Material	journal.pntd.0004776	null	[ [ "Rabies is an important zoonotic disease and exhibits the highest case fatality rate of any infectious disease in humans .", "Infection is usually transmitted by bites via saliva and it is invariably fatal once clinical signs develop .", "The etiological agents of the disease are the different lyssavi...	[ "Rabies is a neglected zoonotic disease that causes an estimated 60 , 000 human deaths annually .", "The main burden lies on developing countries in Asia and Africa , where surveillance and disease detection is hampered by absence of adequate laboratory facilities and/or the difficulties of submitting samples fro...	[ "Despite being preventable with adequate biologicals , rabies still causes an estimated 60 , 000 human deaths annually .", "The main burden lies on developing countries in Asia and Africa , where dog rabies surveillance is hampered by laboratory confirmation of disease due to a number of reasons , including labor...	2016
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "dengue virus", "medicine and health sciences", "immune physiology", "enzyme-linked immunoassays", "pathology and laboratory medicine", "pathogens", "epitope mapping", "immunology", "tropical diseases", "microbiology", "alternative splicing", "viruses", "rna viruses", "neglected tropical d...	Dengue virus specific IgY provides protection following lethal dengue virus challenge and is neutralizing in the absence of inducing antibody dependent enhancement	journal.pntd.0005721	null	[ [ "Almost half of the world is at risk for dengue virus ( DENV ) infections with up to 390 million infections occurring in nearly 100 endemic countries annually [1] .", "Dengue is a rapidly emerging disease with a 30-fold increase in disease incidence reported in the past 50 years [2] .", "Dengue has es...	[ "Dengue hemorrhagic fever ( DHF ) and dengue shock syndrome ( DSS ) are severe disease manifestations that can occur following sequential infection with different dengue virus serotypes ( DENV1-4 ) .", "At present , there are no licensed therapies to treat DENV-induced disease .", "DHF and DSS are thought to be...	[ "Dengue hemorrhagic fever ( DHF ) and dengue shock syndrome ( DSS ) are severe disease manifestations following secondary heterotypic dengue virus ( DENV ) infections .", "DENV infects almost 400 million people annually and there are currently no licensed therapies to treat DENV-induced disease .", "DHF and DSS...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "chemical compounds", "pathology and laboratory medicine", "enzymes", "enzymology", "neuroscience", "organic compounds", "serine proteases", "physiological processes", "serine", "amino acids", "enzyme inhibitors", "chymotrypsin", "animal cells", "proteins"...	Functional diversity of secreted cestode Kunitz proteins: Inhibition of serine peptidases and blockade of cation channels	journal.ppat.1006169	null	[ [ "Cestodes are a neglected group of platyhelminth parasites , despite causing chronic infections to humans and domestic animals worldwide [1] .", "Together with other researchers around the world [2] , we have been using Echinococcus granulosus as a model to study the molecular basis of the host-parasite c...	[ "We previously reported a multigene family of monodomain Kunitz proteins from Echinococcus granulosus ( EgKU-1-EgKU-8 ) , and provided evidence that some EgKUs are secreted by larval worms to the host interface .", "In addition , functional studies and homology modeling suggested that , similar to monodomain Kuni...	[ "Parasite secretions are key players at host-parasite interfaces: parasite establishment and persistence rely , to a great extent , on interactions between these molecules and their host counterparts .", "We present the functional characterization of a multigene family of secreted Kunitz proteins from the cestode...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/viral infections", "immunology/immunity to infections", "immunology/innate immunity" ]	MDA-5 Recognition of a Murine Norovirus	journal.ppat.1000108	null	[ [ "Norwalk virus and other human noroviruses are common human pathogens responsible for most of the nonbacterial epidemic gastroenteritis in both developed and developing countries [1] , [2] , [3] , [4] , [5] .", "In humans , norovirus infection can result in vomiting , diarrhea , fever , malaise , and abdo...	[ "Noroviruses are important human pathogens responsible for most cases of viral epidemic gastroenteritis worldwide .", "Murine norovirus-1 ( MNV-1 ) is one of several murine noroviruses isolated from research mouse facilities and has been used as a model of human norovirus infection .", "MNV-1 infection has been...	[ "Gastroenteritis is a common disease in both developed and developing countries .", "The two main causes of this affliction are bacteria and viruses .", "The primary viruses implicated in gastroenteritis have been shown to be noroviruses , which include Norwalk virus , notorious for numerous recent outbreaks on...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "computational biology/sequence motif analysis", "genetics and genomics/functional genomics", "molecular biology/bioinformatics", "molecular biology/mrna transport and localization", "computational biology/genomics", "genetics and genomics/bioinformatics" ]	Genome Analysis Reveals Interplay between 5′UTR Introns and Nuclear mRNA Export for Secretory and Mitochondrial Genes	journal.pgen.1001366	null	[ [ "In humans , ∼35% of all genes have introns in their 5′ untranslated regions ( UTRs ) [1]–[3] .", "These introns differ from those in coding regions , for example , in typical length and nucleotide composition [1]–[3] .", "Previously , 5′UTR introns ( 5UIs ) were suggested to be evolving under a neutr...	[ "In higher eukaryotes , messenger RNAs ( mRNAs ) are exported from the nucleus to the cytoplasm via factors deposited near the 5′ end of the transcript during splicing .", "The signal sequence coding region ( SSCR ) can support an alternative mRNA export ( ALREX ) pathway that does not require splicing .", "How...	[ "The function and evolution of introns have been topics of great interest since introns were discovered in the 1970s .", "Introns that interrupt protein-coding regions have the most obvious potential to affect coding sequences and their evolution , and they have therefore been studied most intensively .", "Howe...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "immunology", "biology", "microbiology" ]	Dengue Virus Targets the Adaptor Protein MITA to Subvert Host Innate Immunity	journal.ppat.1002780	null	[ [ "Dengue has emerged as a rapidly spreading vector-borne disease annually affecting 50 to 100 million people living in tropical and subtropical areas [1] , [2] .", "Dengue virus ( DEN ) infection of humans causes a spectrum of illnesses ranging from mild classical dengue fever to severe dengue hemorrhagic ...	[ "Dengue is one of the most important arboviral diseases caused by infection of four serotypes of dengue virus ( DEN ) .", "We found that activation of interferon regulatory factor 3 ( IRF3 ) triggered by viral infection and by foreign DNA and RNA stimulation was blocked by DEN-encoded NS2B3 through a protease-dep...	[ "The pathogenesis of severe dengue diseases remains unclear , but magnitude of dengue virus ( DEN ) replication is believed to be one of the major determining factors .", "Thus , revealing how DEN evades the host defense mechanism such as type I interferon ( IFN ) system is important for better understanding this...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Reversible and Rapid Transfer-RNA Deactivation as a Mechanism of Translational Repression in Stress	journal.pgen.1003767	null	[ [ "Environmental stress or suboptimal growth conditions reduce cell viability and put cells at risk .", "Cells maintain their internal homeostasis by adequate reprogramming of metabolic activities at all levels of gene expression , including chromatin remodeling , mRNA expression and degradation , translati...	[ "Stress-induced changes of gene expression are crucial for survival of eukaryotic cells .", "Regulation at the level of translation provides the necessary plasticity for immediate changes of cellular activities and protein levels .", "In this study , we demonstrate that exposure to oxidative stress results in a...	[ "Adequate reprogramming of metabolic activities by environmental stress or suboptimal growth conditions is crucial for cell survival .", "Cells employ a remarkable diversity of processes to maintain its homeostasis at all levels of gene expression , including chromatin remodeling , mRNA expression and degradation...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Involvement of the Cellular Phosphatase DUSP1 in Vaccinia Virus Infection	journal.ppat.1003719	null	[ [ "Poxviruses have evolved to efficiently counteract host immune responses through the modulation of extracellular and intracellular environment of the infected cell .", "Thereby , the ability of a poxvirus to produce a permissive infection in a specific cell type depends on the antiviral mechanisms that th...	[ "Poxviruses encode a large variety of proteins that mimic , block or enhance host cell signaling pathways on their own benefit .", "It has been reported that mitogen-activated protein kinases ( MAPKs ) are specifically upregulated during vaccinia virus ( VACV ) infection .", "Here , we have evaluated the role o...	[ "Phosphorylation is a post-translational modification that is highly conserved throughout the animal kingdom .", "Viruses have evolved to acquire their own kinases and phosphatases and to be able to modulate host phosphorylation mechanisms on their benefit .", "DUSP1 is an early induced gene that belongs to the...	2013
[ "Introduction", "Results", "Discussion", "Conclusion" ]	[ "medicine and health sciences", "genetic diseases", "alleles", "genetic mapping", "developmental biology", "population biology", "morphogenesis", "autosomal recessive diseases", "inherited metabolic disorders", "glycogen storage diseases", "sex chromosomes", "chromosome biology", "genetic lo...	Haploid selection, sex ratio bias, and transitions between sex-determining systems	journal.pbio.2005609	null	[ [ "We consider transitions between ancestral and novel sex-determining systems using a three-locus model , each locus having two alleles ( Fig 1 ) .", "A full description of our model , including recursion equations , is given in S1 Text .", "Locus X is the ancestral sex-determining region , with allele...	[ "Sex determination is remarkably dynamic; many taxa display shifts in the location of sex-determining loci or the evolution of entirely new sex-determining systems .", "Predominant theories for why we observe such transitions generally conclude that novel sex-determining systems are favoured by selection if they ...	[ "Systems of sex determination are strikingly diverse and labile in many clades .", "This poses the question: what drives transitions between sex-determining systems ?", "Here , we use models to derive conditions under which new sex-determining systems spread .", "Prevailing views suggest that new sex-determin...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "action potentials", "medicine and health sciences", "neural networks", "membrane potential", "electrophysiology", "neuroscience", "mathematics", "statistics (mathematics)", "network analysis", "computational neuroscience", "coding mechanisms", "research and analysis methods", "computer and ...	When do correlations increase with firing rates in recurrent networks?	journal.pcbi.1005506	null	[ [ "One prominent goal of modern theoretical neuroscience is to understand how the features of cortical neural networks lead to modulation of spiking statistics [1–3] .", "This understanding is essential to the larger question of how sensory information is encoded and transmitted , because such statistics ar...	[ "A central question in neuroscience is to understand how noisy firing patterns are used to transmit information .", "Because neural spiking is noisy , spiking patterns are often quantified via pairwise correlations , or the probability that two cells will spike coincidentally , above and beyond their baseline fir...	[ "A central question in neuroscience is to understand how noisy firing patterns are used to transmit information .", "We quantify spiking patterns by using pairwise correlations , or the probability that two cells will spike coincidentally , above and beyond their baseline firing rate .", "One observation freque...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "fungal genetics", "computational biology", "parasitic diseases", "nematode infections", "fungi", "plant science", "phylogenetic analysis", "genome analysis", "plant pathology", "molecular biology techniques", "research and analysis methods", "mycology", "bi...	Biosynthesis of Antibiotic Leucinostatins in Bio-control Fungus Purpureocillium lilacinum and Their Inhibition on Phytophthora Revealed by Genome Mining	journal.ppat.1005685	null	[ [ "Plant parasitic nematodes with wide host ranges cause enormous crop and economic losses amounting to $157 billion annually worldwide [1 , 2] .", "Biological control by fungi has become increasingly popular due to nematicides’ risks of environmental toxicity and adverse effects on human health [3] .", ...	[ "Purpureocillium lilacinum of Ophiocordycipitaceae is one of the most promising and commercialized agents for controlling plant parasitic nematodes , as well as other insects and plant pathogens .", "However , how the fungus functions at the molecular level remains unknown .", "Here , we sequenced two isolates ...	[ "Purpureocillium lilacinum , a well-known bio-control agent against various plant pathogens in agriculture , can produce antibiotic leucinostatins—peptaibiotic with extensive biological activities , including antimalarial , antiviral , antibacterial , antifungal , and antitumor activities , as well as phytotoxic ."...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "ecology/conservation and restoration ecology", "ecology/community ecology and biodiversity", "ecology/spatial and landscape ecology", "ecology/theoretical ecology", "ecology/population ecology", "ecology/ecosystem ecology" ]	Optimizing Metapopulation Sustainability through a Checkerboard Strategy	journal.pcbi.1000643	null	[ [ "In recent years , many studies in the field of biodiversity maintenance were focused on spatially structured populations [1]–[14] .", "Of particular importance are Levins type metapopulations [1] , [2] , [15] , where distinct subpopulations occupy spatially segregated patches of habitats connected by mig...	[ "The persistence of a spatially structured population is determined by the rate of dispersal among habitat patches .", "If the local dynamic at the subpopulation level is extinction-prone , the system viability is maximal at intermediate connectivity where recolonization is allowed , but full synchronization that...	[ "No one can produce all his needs by himself .", "Personal autarky poses a serious danger of collapse in cases of illness , drought , etc .", "Trade reduces the impact of local catastrophes , thus increasing economic stability .", "However , the recent series of econo-crises revealed that globalization induce...	2010
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "circuit models", "computational neuroscience", "biology", "computational biology", "sensory systems", "neuroscience" ]	The Laminar Cortex Model: A New Continuum Cortex Model Incorporating Laminar Architecture	journal.pcbi.1002733	null	[ [ "Neuronal activity changes the distribution of electric potentials in the brain [1] , [2] .", "Local field potentials ( LFPs ) are the low-frequency ( <100 Hz ) fluctuations in electric potentials in the extracellular space of the brain [2] , [3] .", "They represent a weighted average of the potential...	[ "Local field potentials ( LFPs ) are widely used to study the function of local networks in the brain .", "They are also closely correlated with the blood-oxygen-level-dependent signal , the predominant contrast mechanism in functional magnetic resonance imaging .", "We developed a new laminar cortex model ( LC...	[ "Local field potentials ( LFPs ) are low-frequency fluctuations of the electric fields produced by the brain .", "They have been widely studied to understand brain function and activity .", "LFPs reflect the activity of neurons within a few square millimeters of the cerebral cortex , an area containing more tha...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "humoral immunity", "immune cells", "cytokines", "immune activation", "antigen-presenting cells", "immunity to infections", "immunology", "microbiology", "host-pathogen interaction", "adaptive immunity", "immunomodulation", "bacterial pathogens", "immunizations", "t cells", "biology", ...	Brucella β 1,2 Cyclic Glucan Is an Activator of Human and Mouse Dendritic Cells	journal.ppat.1002983	null	[ [ "Cyclic glucans are intrinsic components of the envelopes of Gram negative bacteria such as Agrobacterium , Rhizobium , Ralstonia solanacearum , Xanthomonas campestris , Rhodobacter sphaeroides and Brucella spp .", "[1] .", "Brucellae are intracellular pathogens of mammals , including humans [2] .", ...	[ "Bacterial cyclic glucans are glucose polymers that concentrate within the periplasm of alpha-proteobacteria .", "These molecules are necessary to maintain the homeostasis of the cell envelope by contributing to the osmolarity of Gram negative bacteria .", "Here , we demonstrate that Brucella β 1 , 2 cyclic glu...	[ "Vaccination is one of the key strategies to fight against infectious diseases though numerous diseases remain without appropriate vaccines .", "The challenge is to generate potent vaccines capable of inducing long-lasting immunity in humans .", "Successful vaccines include adjuvants that enhance and appropriat...	2012
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "vesicles", "immune physiology", "pathology and laboratory medicine", "viral transmission and infection", "hela cells", "enzymes", "pathogens", "cell processes", "biological cultures", "microbiology", "immunology", "enzymology", "fluorophotometry", "cell c...	Lipopolysaccharide structure impacts the entry kinetics of bacterial outer membrane vesicles into host cells	journal.ppat.1006760	null	[ [ "Outer membrane vesicles ( OMVs ) are nano-sized proteoliposomes released from the bacterial cell envelope [1] .", "OMV release is a highly conserved process , occurring in all growth phases and environmental conditions [2] .", "OMVs contain and deliver a broad range of cargos , from large hydrophobic...	[ "Outer membrane vesicles are nano-sized microvesicles shed from the outer membrane of Gram-negative bacteria and play important roles in immune priming and disease pathogenesis .", "However , our current mechanistic understanding of vesicle-host cell interactions is limited by a lack of methods to study the rapid...	[ "All Gram negative species of bacteria , including those that cause significant disease , release small vesicles from their cell membrane .", "These vesicles deliver toxins and other virulence factors to host cells during infection .", "Current methods for studying host cell entry are limited due to the nanomet...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "medicine and health sciences", "helminths", "vertebrates", "rabbits", "parasitic diseases", "animals", "mammals", "animal models", "physiological processes", "developmental biology", "experimental organism systems", "population biology", "fecundity", "research and analy...	Changes in parasite traits, rather than intensity, affect the dynamics of infection under external perturbation	journal.pcbi.1006167	null	[ [ "The large variation in disease severity and transmission often observed among individuals infected with helminths is strongly determined by the local conditions that incoming and established parasites encounter within the host , in addition to variation in the exposure of hosts to infective stages [1–3] .", ...	[ "Understanding the mechanisms that generate complex host-parasite interactions , and how they contribute to variation between and within hosts , is important for predicting risk of infection and transmission , and for developing more effective interventions based on parasite properties .", "We used the T . retort...	[ "Host-parasite interactions frequently lead to complex dynamics of infection that can be difficult to explain when parasite data are not accurate or complete , which is often the case in natural systems .", "We used the helminth-rabbit study case and developed a state-space mathematical model to capture the varia...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunology/antigen processing and recognition", "virology/immunodeficiency viruses", "infectious diseases/hiv infection and aids", "immunology/immunity to infections", "virology/host antiviral responses" ]	HIV Controller CD4+ T Cells Respond to Minimal Amounts of Gag Antigen Due to High TCR Avidity	journal.ppat.1000780	null	[ [ "HIV controllers are rare individuals who spontaneously control HIV replication in the absence of antiretroviral treatment [1] , [2] .", "HIV controllers harbor plasma viral loads that remain undetectable by conventional assays and cell-associated HIV DNA loads that are in the very low range , close to on...	[ "HIV controllers are rare individuals who spontaneously control HIV replication in the absence of antiretroviral treatment .", "Emerging evidence indicates that HIV control is mediated through very active cellular immune responses , though how such responses can persist over time without immune exhaustion is not ...	[ "HIV infection , if left untreated , leads to the progressive disruption of the immune system , the destruction of the CD4+ T cell population , and the occurrence of multiple opportunistic infections .", "However , a small fraction of HIV-infected individuals ( less than 1% ) avoid these deleterious effects by sp...	2010
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell death", "neurobiology of disease and regeneration", "medicine and health sciences", "fish", "cell processes", "ocular anatomy", "social sciences", "vertebrates", "neuroscience", "animals", "cell differentiation", "animal models", "osteichthyes", "developmental biology", "model orga...	Regeneration of the zebrafish retinal pigment epithelium after widespread genetic ablation	journal.pgen.1007939	null	[ [ "The RPE is a polarized monolayer of pigment-containing cells that separates the retina from the choroid and performs many critical functions for vision .", "Microvilli extend from the apical RPE surface and interdigitate with photoreceptor outer segments , enabling the RPE to support photoreceptor health...	[ "The retinal pigment epithelium ( RPE ) is a specialized monolayer of pigmented cells within the eye that is critical for maintaining visual system function .", "Diseases affecting the RPE have dire consequences for vision , and the most prevalent of these is atrophic ( dry ) age-related macular degeneration ( AM...	[ "Diseases resulting in retinal pigment epithelium ( RPE ) degeneration are among the leading causes of blindness worldwide , and no therapy exists that can replace RPE or restore lost vision .", "One intriguing possibility is the development of therapies focused on stimulating endogenous RPE regeneration .", "F...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "signal transduction", "transcriptional signaling", "transcription activators", "cell biology", "proteins", "mechanisms of signal transduction", "transcription factors", "gene expression", "genetics", "regulatory proteins", "biology and life sciences", "gene regulation", "d...	Response Regulator Heterodimer Formation Controls a Key Stage in Streptomyces Development	journal.pgen.1004554	null	[ [ "Two-component signal transduction systems are of central importance in regulating gene expression in bacteria .", "Canonically they consist of a response regulator , which functions as a homodimer , and a cognate sensor histidine kinase ( which may also function as a cognate phosphatase ) .", "The ac...	[ "The orphan , atypical response regulators BldM and WhiI each play critical roles in Streptomyces differentiation .", "BldM is required for the formation of aerial hyphae , and WhiI is required for the differentiation of these reproductive structures into mature spores .", "To gain insight into BldM function , ...	[ "Two-component signal transduction systems are a primary means of regulating gene expression in bacteria .", "Recognizing the diversity of mechanisms associated with these systems is therefore critical to understanding the full signaling potential of bacterial cells .", "We have analyzed the behavior of two orp...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Structure-Bioactivity Relationship for Benzimidazole Thiophene Inhibitors of Polo-Like Kinase 1 (PLK1), a Potential Drug Target in Schistosoma mansoni	journal.pntd.0004356	null	[ [ "Flatworm parasites of the Schistosoma genus are responsible for schistosomiasis , a chronic and often painful disease of poverty that affects more than 200 million people worldwide [1–3] .", "For over 35 years , treatment and control of this disease has relied on a single drug , praziquantel ( PZQ ) [4–6...	[ "Schistosoma flatworm parasites cause schistosomiasis , a chronic and debilitating disease of poverty in developing countries .", "Praziquantel is employed for treatment and disease control .", "However , its efficacy spectrum is incomplete ( less active or inactive against immature stages of the parasite ) and...	[ "Just one drug is available to treat schistosomiasis , a parasitic disease that affects hundreds of millions of people in developing countries .", "In the search for new drugs and drug targets , therefore , we have been interested in the schistosome version of human polo-like kinase ( huPLK ) 1 , an enzyme with c...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases", "medicine and health sciences", "biology and life sciences", "tropical diseases", "parasitic diseases", "parasitology" ]	Formation of Linear Amplicons with Inverted Duplications in Leishmania Requires the MRE11 Nuclease	journal.pgen.1004805	null	[ [ "The protozoan parasite Leishmania is responsible for a group of diseases named leishmaniasis , affecting approximately 12 million people worldwide .", "No vaccine is currently available against Leishmania and treatments mainly rely on chemotherapy [1] , [2] .", "Pentavalent antimony is the main anti-...	[ "Extrachromosomal DNA amplification is frequent in the protozoan parasite Leishmania selected for drug resistance .", "The extrachromosomal amplified DNA is either circular or linear , and is formed at the level of direct or inverted homologous repeated sequences that abound in the Leishmania genome .", "The RA...	[ "Extrachromosomal DNA amplification is frequent in the human protozoan parasite Leishmania when challenged with drug or other stressful conditions .", "DNA amplicons , either circular or linear , are formed by recombination between direct or inverted repeats spread throughout the genome of the parasite .", "The...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "hookworm infection", "parasitic diseases", "helminth infection" ]	The Association of Parasitic Infections in Pregnancy and Maternal and Fetal Anemia: A Cohort Study in Coastal Kenya	journal.pntd.0002724	null	[ [ "Anemia affects nearly 25% of all pregnancies worldwide and more than 40% of those in Sub-Saharan Africa [1] .", "Associated with poor pregnancy outcomes including increased risk of fetal death and preterm birth , maternal anemia also increases risk of maternal mortality associated with obstetric hemorrha...	[ "Relative contribution of these infections on anemia in pregnancy is not certain .", "While measures to protect pregnant women against malaria have been scaling up , interventions against helminthes have received much less attention .", "In this study , we determine the relative impact of helminthes and malaria...	[ "International guidelines recommend routine prevention and treatments which are safe and effective during pregnancy to reduce hookworm , malaria and other infections among pregnant women living in geographic areas where these infections are prevalent .", "Despite their effectiveness , programs to address common i...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "ecology and environmental sciences", "medicine and health sciences", "water resources", "gut bacteria", "microbiome", "surface water", "microbiology", "social sciences", "diet", "ethnicities", "animal behavior", "nutrition", "zoology", "bacteria", "microbial genomics", "hydrology", ...	Gut microbiome transition across a lifestyle gradient in Himalaya	journal.pbio.2005396	null	[ [ "The human gut is comprised of a diverse community of bacteria , the microbiome or microbiota , that influences several aspects of human physiology , including nutrient metabolism , immune responses , and resistance to infectious pathogens [1–3] .", "This highly malleable microbial component of human biol...	[ "The composition of the gut microbiome in industrialized populations differs from those living traditional lifestyles .", "However , it has been difficult to separate the contributions of human genetic and geographic factors from lifestyle .", "Whether shifts away from the foraging lifestyle that characterize m...	[ "Although much of humanity’s history has been spent foraging in the forests , the advent of agriculture approximately 10 , 000 years ago and industrialization approximately 250 years ago mark major shifts in human lifestyle .", "Several studies have investigated the effect of industrialization on the human gut mi...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Bud-Localization of CLB2 mRNA Can Constitute a Growth Rate Dependent Daughter Sizer	journal.pcbi.1004223	null	[ [ "Cell size is a fundamental systems level property of life .", "It emerges as a combination of the cell cycle , controlling the orderly orchestration of duplication and division , and the individual growth rate , reflecting extra- and intracellular physiological conditions .", "The cell cycle and the ...	[ "Maintenance of cellular size is a fundamental systems level process that requires balancing of cell growth with proliferation .", "This is achieved via the cell division cycle , which is driven by the sequential accumulation and destruction of cyclins .", "The regulatory network around these cyclins , particul...	[ "The size between different organisms ranges considerably , yet , the size of the individuals and even the same types of cells within the individuals are remarkably constant .", "Cell size emerges from the balance between how fast the cell grows and the frequency with which it divides .", "This system level coo...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "biochemistry", "hydrolases", "enzymes", "biology and life sciences", "enzymology", "microbiology", "parasitology" ]	Trypsin- and Chymotrypsin-Like Serine Proteases in Schistosoma mansoni – ‘The Undiscovered Country’	journal.pntd.0002766	null	[ [ "Schistosomiasis caused by Schistosoma blood flukes is a chronic disease with more than 200 million people infected [1] .", "Schistosome larvae ( cercariae ) , released into an aquatic environment from snail intermediate hosts , penetrate human skin and subsequently develop into adult worms .", "Adult...	[ "Blood flukes ( Schistosoma spp . ) are parasites that can survive for years or decades in the vasculature of permissive mammalian hosts , including humans .", "Proteolytic enzymes ( proteases ) are crucial for successful parasitism , including aspects of invasion , maturation and reproduction .", "Most attenti...	[ "Schistosomes are blood flukes that live in the blood system and cause chronic and debilitating infection in hundreds of millions of people .", "Proteolytic enzymes ( proteases ) produced by the parasite allow it to survive and reproduce .", "We focused on understanding the repertoire of trypsin- and chymotryps...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "ecology and environmental sciences", "statistics", "tropical diseases", "geographical locations", "health care", "bacterial diseases", "chi square tests", "mathematics", "aquatic environments", "bodies of water", "neglected tropical diseases", "medical risk f...	The spatial epidemiology of leprosy in Kenya: A retrospective study	journal.pntd.0007329	null	[ [ "In 1991 , the World Health Assembly passed a resolution to “eliminate” leprosy as a public health problem by the year 2000 .", "Elimination , defined as a registered prevalence rate of less than 1 case per 10 000 persons , was realized globally in the year 2000 and in most countries by 2005 [1] .", "...	[ "Leprosy elimination defined as a registered prevalence rate of less than 1 case per 10 , 000 persons was achieved in Kenya at the national level in 1989 .", "However , there are still pockets of leprosy in some counties where late diagnosis and consequent physical disability persist .", "The epidemiology of le...	[ "Leprosy is a chronic bacterial disease that mainly affects the nerves .", "If untreated , it may cause progressive and permanent damage to the skin , nerves , limbs , and eyes leading to physical disability .", "Through use of a combination of drugs , Kenya was able to declare the disease as eliminated in the ...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "microbiology", "neuroscience", "protein expression", "eye diseases", "molecular biology techniques", "mammalian genomics", "eyes", "research and analysis methods", "animal cells", "biological tissue", "head", "viral replication", "molecular biology", "ani...	De Novo Herpes Simplex Virus VP16 Expression Gates a Dynamic Programmatic Transition and Sets the Latent/Lytic Balance during Acute Infection in Trigeminal Ganglia	journal.ppat.1005877	null	[ [ "Herpes simplex virus ( HSV ) remains a significant human pathogen associated with extensive acute and chronic disease in humans worldwide .", "Despite safe and effective antiviral treatment for limiting viral replication , the numbers of infected individuals continues to increase .", "The expansive r...	[ "The life long relationship between herpes simplex virus and its host hinges on the ability of the virus to aggressively replicate in epithelial cells at the site of infection and transport into the nervous system through axons innervating the infection site .", "Interaction between the virus and the sensory neur...	[ "Herpes simplex virus remains a significant human pathogen associated with extensive acute and chronic disease in humans worldwide .", "The virus invades the peripheral and central nervous systems where it replicates but also establishes life-long latent infections in neurons .", "Two distinct viral transcripti...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "population metrics", "genetic load", "heredity", "genetics", "biology and life sciences", "population genetics", "population biology", "evolutionary adaptation", "evolutionary biology", "gene flow", "evolutionary processes", "genetic loci", "genetic drift", "evolutionary genetics", "pop...	Is the sky the limit? On the expansion threshold of a species’ range	journal.pbio.2005372	null	[ [ "Species’ borders are not just determined by the limits of their ecological niche [1 , 2] .", "A species’ edge is typically sharper than would be implied by continuous change in the species’ environment ( reviewed in [3 , Table 2] ) .", "Moreover , although species’ ranges are inherently dynamic , it ...	[ "More than 100 years after Grigg’s influential analysis of species’ borders , the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity .", "The topic has become especially important recently as many scientists have become interested in the potential for species’...	[ "The flow of genetic diversity across environments has conflicting effects .", "On the beneficial side , it increases the genetic variation that is necessary for adaptation and counters the loss of genetic diversity due to genetic drift .", "However , it may also swamp adaptation to local conditions .", "This...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	A Pyranose-2-Phosphate Motif Is Responsible for Both Antibiotic Import and Quorum-Sensing Regulation in Agrobacterium tumefaciens	journal.ppat.1005071	null	[ [ "In bacteria , periplasmic binding proteins ( PBPs ) are involved in the import into the cell of a wide variety of extracellular compounds .", "PBPs recognize and bind chemical compounds in order to bring them to ABC transporters which transport them into cells [1] .", "PBPs are also potential vehicle...	[ "Periplasmic binding proteins ( PBPs ) in association with ABC transporters select and import a wide variety of ligands into bacterial cytoplasm .", "They can also take up toxic molecules , as observed in the case of the phytopathogen Agrobacterium tumefaciens strain C58 .", "This organism contains a PBP called...	[ "We succeeded in understanding how the periplasmic protein AccA from the pathogen A . tumefaciens can bind both the plant compound agrocinopine and the antibiotic agrocin 84 .", "Whereas agrocinopine acts as a nutrient and regulatory signal in A . tumefaciens , agrocin 84 is lethal once degraded by the enzyme Acc...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Phospholipase D1 Couples CD4+ T Cell Activation to c-Myc-Dependent Deoxyribonucleotide Pool Expansion and HIV-1 Replication	journal.ppat.1004864	null	[ [ "HIV-1 replication in resting CD4+ T cells is restricted post-entry , but prior to integration [1] .", "Several groups have reported that suboptimal dNTP pools in these metabolically quiescent cells support only inefficient reverse transcription and subsequent integration [2 , 3] .", "Cellular activat...	[ "Quiescent CD4+ T cells restrict human immunodeficiency virus type 1 ( HIV-1 ) infection at early steps of virus replication .", "Low levels of both deoxyribonucleotide triphosphates ( dNTPs ) and the biosynthetic enzymes required for their de novo synthesis provide one barrier to infection .", "CD4+ T cell act...	[ "Replication of all human viruses depends on building blocks derived from the metabolic pathways of the infected host cell .", "The production of progeny virions requires synthesis of viral nucleic acids from deoxyribonucleotide triphosphates ( dNTPs ) .", "HIV-1 infection in resting T cells is limited , at lea...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Improved Statistical Methods Enable Greater Sensitivity in Rhythm Detection for Genome-Wide Data	journal.pcbi.1004094	null	[ [ "Rhythmic behavior is ubiquitous across the spectrum of life [1–4] .", "Diverse fundamental biological functions such as cell division , energy metabolism , and sleep are periodic , and a growing body of evidence implicates temporal dysregulation as a contributing factor to depression , neurodegeneration ...	[ "Robust methods for identifying patterns of expression in genome-wide data are important for generating hypotheses regarding gene function .", "To this end , several analytic methods have been developed for detecting periodic patterns .", "We improve one such method , JTK_CYCLE , by explicitly calculating the n...	[ "Much biomedical research focuses on how the expression of genes changes over time .", "Many genes’ activities vary periodically .", "For example , circadian rhythms repeat daily with the light-dark cycle .", "Understanding how such rhythms couple to biological processes requires statistical methods that can ...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Widespread Recombination, Reassortment, and Transmission of Unbalanced Compound Viral Genotypes in Natural Arenavirus Infections	journal.ppat.1004900	null	[ [ "Several mechanisms generate viral genetic diversity [1–3] .", "All work by producing populations of viral genomes , a small fraction of which may exhibit an adaptive advantage in a new host species , different tissue , or in the face of drug or immune pressure .", "Replication of RNA viral genomes by...	[ "Arenaviruses are one of the largest families of human hemorrhagic fever viruses and are known to infect both mammals and snakes .", "Arenaviruses package a large ( L ) and small ( S ) genome segment in their virions .", "For segmented RNA viruses like these , novel genotypes can be generated through mutation ,...	[ "The facility with which viruses evolve underlies many of the problems they cause .", "Virus evolution is the reason we need a new flu vaccine each year .", "It’s how HIV and other viruses develop drug resistance .", "And it enables viruses to occasionally jump from animals to humans and cause new diseases ."...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "invertebrates", "microinjection", "enzymes", "enzymology", "neuroscience", "learning and memory", "animals", "animal models", "drosophila melanogaster", "model organisms", "immunoprecipitation", "materials science", "cognition", "memory", "molecular biology techniques", "oligomers", ...	Molecular Basis of Orb2 Amyloidogenesis and Blockade of Memory Consolidation	journal.pbio.1002361	Although amyloids are usually associated with abnormality and disease, some are functional. A study of the functional amyloid Orb2, which is needed for memory consolidation in flies, shows that despite structural similarities, key features of the kinetics of amyloid formation may underlie this crucial difference.	[ [ "Amyloids , whose cross-β fold has been postulated as the ancestral protein fold [1 , 2] , were initially associated with fatal neurodegenerative disorders [3 , 4] .", "However , more than a century after the identification of these “pathological amyloids , ” a growing list of so-called “functional amyloi...	[ "Amyloids are ordered protein aggregates that are typically associated with neurodegenerative diseases and cognitive impairment .", "By contrast , the amyloid-like state of the neuronal RNA binding protein Orb2 in Drosophila was recently implicated in memory consolidation , but it remains unclear what features of...	[ "Amyloids are ordered protein aggregates typically associated with neurodegenerative diseases , such as Alzheimer disease and Parkinson disease , which usually result in cognitive impairment .", "However , the amyloid state of the neuronal RNA binding protein Orb2 shows a quite opposite behaviour: instead of impa...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "medicine and health sciences", "reproductive system", "enzymes", "annealing (genetics)", "enzymology", "precursor cells", "animals", "animal models", "drosophila melanogaster", "model organisms", "immunoprecipitation", "rna helicases", "experimental organism systems", "...	Recruitment of Armitage and Yb to a transcript triggers its phased processing into primary piRNAs in Drosophila ovaries	journal.pgen.1006956	null	[ [ "Bulk of the eukaryotic genomes are composed of genetic material derived from mobile genetic elements called transposons .", "Their mobility within the genome can cause mutations or deletions , impacting genome integrity [1] .", "Given the diversity of transposable elements within any genome , small R...	[ "Small RNAs called PIWI -interacting RNAs ( piRNAs ) are essential for transposon control and fertility in animals .", "Primary processing is the small RNA biogenesis pathway that uses long single-stranded RNA precursors to generate millions of individual piRNAs , but the molecular mechanisms that identify a tran...	[ "PIWI-interacting RNAs ( piRNAs ) are 24–30 nucleotide ( nt ) small RNAs that are exclusively expressed in animal germlines and are essential for suppression of transposable elements or ‘jumping genes’ .", "Millions of piRNAs are produced from single-stranded transcripts that arise from large RNA polymerase II tr...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "genome-wide association studies", "statistics", "applied mathematics", "brassica", "random variables", "mathematical models", "covariance", "simulation and modeling", "algorithms", "model organisms", "mathematics", "test statistics", "genome analysis", "experimental organism systems", "...	Fast and flexible linear mixed models for genome-wide genetics	journal.pgen.1007978	null	[ [ "Population stratification , genetic relatedness , ascertainment , and other sources of heterogeneity lead to spurious signals and reduced power in genetic association studies [1–5] .", "When not properly taken into account , non-additive genetic effects and environmental variation can also bias estimates...	[ "Linear mixed effect models are powerful tools used to account for population structure in genome-wide association studies ( GWASs ) and estimate the genetic architecture of complex traits .", "However , fully-specified models are computationally demanding and common simplifications often lead to reduced power or...	[ "The goal of quantitative genetics is to characterize the relationship between genetic variation and variation in quantitative traits such as height , productivity , or disease susceptibility .", "A statistical method known as the linear mixed effect model has been critical to the development of quantitative gene...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "parasite groups", "medicine and health sciences", "body fluids", "plasmodium", "tropical diseases", "plasmodium falciparum", "parasitic diseases", "parasitic protozoans", "parasitology", "apicomplexa", "protozoans", "infectious disease control", "infectious diseases", "malarial parasites"...	Defining the next generation of Plasmodium vivax diagnostic tests for control and elimination: Target product profiles	journal.pntd.0005516	null	[ [ "The concerted international efforts initiated near the turn of this century to move from malaria control to malaria elimination and ultimately eradication show remarkable progress during the last decade [1] .", "Financial , political and scientific commitment to solve the malaria problem led so far to an...	[ "The global prevalence of malaria has decreased over the past fifteen years , but similar gains have not been realized against Plasmodium vivax because this species is less responsive to conventional malaria control interventions aimed principally at P . falciparum .", "Approximately half of all malaria cases out...	[ "Plasmodium vivax is the second most prevalent Plasmodium species amongst the five that can infect humans and cause malaria .", "The control and elimination of P . vivax is complicated by its specific biology , such as hard-to-detect low densities of blood-circulating parasites in infected individuals , the exist...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "model organisms", "genetics", "biology", "molecular cell biology", "genetics and genomics" ]	Septation of Infectious Hyphae Is Critical for Appressoria Formation and Virulence in the Smut Fungus Ustilago Maydis	journal.ppat.1002044	null	[ [ "Penetration of the plant cuticle is a prerequisite for the establishment of many plant-fungal interactions and involves the formation of specialized infection structures , called appressoria .", "These structures mediate plant penetration in parasitic as well as in symbiotic fungi [1] , [2] .", "Appr...	[ "Differentiation of hyphae into specialized infection structures , known as appressoria , is a common feature of plant pathogenic fungi that penetrate the plant cuticle .", "Appressorium formation in U . maydis is triggered by environmental signals but the molecular mechanism of this hyphal differentiation is lar...	[ "Pathogens exhibit various developmental stages during the process of infection and proliferation .", "The basidiomycete Ustilago maydis is a model organism for plant pathogenic fungi .", "On the plant surface U . maydis grows as a cell-cycle arrested filament .", "Growth of infectious hyphae involves regular...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Burden Analysis of Rare Microdeletions Suggests a Strong Impact of Neurodevelopmental Genes in Genetic Generalised Epilepsies	journal.pgen.1005226	null	[ [ "The epilepsies comprise a clinically heterogeneous group of neurological disorders defined by recurrent spontaneous seizures due to paroxysmal excessive and synchronous neuronal activity in the brain [1] .", "Epilepsy affects about 4% of the general population during their lifetime [2] and about 40% of a...	[ "Genetic generalised epilepsy ( GGE ) is the most common form of genetic epilepsy , accounting for 20% of all epilepsies .", "Genomic copy number variations ( CNVs ) constitute important genetic risk factors of common GGE syndromes .", "In our present genome-wide burden analysis , large ( ≥ 400 kb ) and rare ( ...	[ "Epilepsy affects about 4% of the general population during lifetime .", "The genetic generalised epilepsies ( GGEs ) represent the most common group of epilepsies with predominant genetic aetiology , accounting for 20% of all epilepsies .", "Despite their strong heritability , the genetic basis of the majority...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "sequencing techniques", "rna-binding proteins", "cellular stress responses", "medicine and health sciences", "messenger rna", "cell processes", "polyribosomes", "chaperone proteins", "sequence motif analysis", "molecular biology techniques", "cellular structures and organelles", "digestive sy...	Translation Regulation and RNA Granule Formation after Heat Shock of Procyclic Form Trypanosoma brucei: Many Heat-Induced mRNAs Are also Increased during Differentiation to Mammalian-Infective Forms	journal.pntd.0004982	null	[ [ "African trypanosomes , like all other organisms investigated so far , respond to heat shock by repressing general protein synthesis , while enhancing or retaining synthesis of proteins that are required to survive or recover from heat stress [1] .", "Unlike other organisms , however , trypanosomes lack t...	[ "African trypanosome procyclic forms multiply in the midgut of tsetse flies , and are routinely cultured at 27°C .", "Heat shocks of 37°C and above result in general inhibition of translation , and severe heat shock ( 41°C ) results in sequestration of mRNA in granules .", "The mRNAs that are bound by the zinc-...	[ "When trypanosomes are inside tsetse flies , they have to cope with temperature variations from below 20°C up to 37°C , due to diurnal variations and periodic intake of warm blood .", "In the laboratory , procyclic forms ( the form that multiplies in the midgut ) , are routinely cultured at 27°C .", "When procy...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Phosphoproteomic Analyses Reveal Signaling Pathways That Facilitate Lytic Gammaherpesvirus Replication	journal.ppat.1003583	null	[ [ "Post-translational modification of proteins by phosphorylation and dephosphorylation regulates numerous functional properties , including activation status [1] , stability [2] , protein-protein interactions [3] , and subcellular localization [4] .", "Such signals regulate the majority of cellular process...	[ "Lytic gammaherpesvirus ( GHV ) replication facilitates the establishment of lifelong latent infection , which places the infected host at risk for numerous cancers .", "As obligate intracellular parasites , GHVs must control and usurp cellular signaling pathways in order to successfully replicate , disseminate t...	[ "Systems-level evaluations of infection-related changes to host phosphoprotein networks are not currently available for any gammaherpesvirus ( GHV ) .", "Here we describe a quantitative phosphoproteomic analysis of productive GHV replication that demonstrates alterations in the phosphorylation status of more than...	2013
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "physicians", "medical doctors", "pathology and laboratory medicine", "togaviruses", "chikungunya infection", "behavioral and social aspects of health", "medical personnel", "pathogens", "tropical diseases", "microbiology", "social sciences", "alphaviruses", ...	Health-related impact on quality of life and coping strategies for chikungunya: A qualitative study in Curaçao	journal.pntd.0005987	null	[ [ "Chikungunya is an arboviral disease mainly transmitted by the mosquito species Aedes aegypti and Aedes albopictus [1] .", "Chikungunya has ( re- ) emerged in the Americas in 2013 [2] , when it rapidly spread from the islands of the Caribbean to the Latin-American mainland [2–4] .", "Since then , the ...	[ "Chikungunya is an emerging public health problem in tropical and subtropical regions , due to ongoing transmission and its incapacitating acute disease phase , and chronic sequelae .", "The disease is responsible for a major impact on Health Related Quality of Life ( HRQoL ) , which may last several years .", ...	[ "Chikungunya is a disease caused by a virus , which is transmitted by mosquitoes .", "During the past years , major outbreaks of chikungunya have occurred in the Americas .", "Normally , chikungunya presents with an acute , fever-like disease .", "After acute disease , many people develop chronic disease mani...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "computational biology/sequence motif analysis", "molecular biology/bioinformatics", "computational biology/macromolecular sequence analysis", "evolutionary biology/bioinformatics", "biophysics/membrane proteins and energy transduction" ]	Integration of Evolutionary Features for the Identification of Functionally Important Residues in Major Facilitator Superfamily Transporters	journal.pcbi.1000522	null	[ [ "The identification of functionally important cooperative residue is important for understanding the allosteric pathways of proteins .", "Cooperative residues are responsible for long-range allosteric communication from the substrate binding sites to the translocation pathways of membrane protein transpor...	[ "The identification of functionally important residues is an important challenge for understanding the molecular mechanisms of proteins .", "Membrane protein transporters operate two-state allosteric conformational changes using functionally important cooperative residues that mediate long-range communication fro...	[ "Major Facilitator Superfamily ( MFS ) transporters are one of the largest families of membrane protein transporters and are ubiquitous to all three kingdoms of life .", "Structural studies of MFS transporters have revealed that the members of this superfamily share structural homology; however , due to weak sequ...	2009
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Lutzomyia longipalpis Presence and Abundance Distribution at Different Micro-spatial Scales in an Urban Scenario	journal.pntd.0003951	null	[ [ "Visceral leishmaniasis ( VL ) in America is caused by Leishmania infantum ( syn . chagasi ) .", "The sandfly Lutzomyia longipalpis was incriminated as the most important vector [1] and the domestic dog was involved as the main reservoir , both in urban areas [2–5] .", "Although Lu .", "longipalpi...	[ "The principal objective of this study was to assess a modeling approach to Lu .", "longipalpis distribution in an urban scenario , discriminating micro-scale landscape variables at microhabitat and macrohabitat scales and the presence from the abundance of the vector .", "For this objective , we studied vector...	[ "Visceral leishmaniasis in America is caused by an unicellular organism , Leishmania infantum ( syn . chagasi ) that is transmitted by insects belonging to Diptera:Phlebotominae , Lutzomyia longipalpis being the principal vector in urban areas .", "Therefore , the prevention and control of this vector is a sound ...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "cardiovascular disorders/congenital heart disease", "diabetes and endocrinology/obesity", "genetics and genomics/genetics of disease", "diabetes and endocrinology/type 2 diabetes" ]	A Genome-Wide Association Study Reveals Variants in ARL15 that Influence Adiponectin Levels	journal.pgen.1000768	null	[ [ "Adiponectin is an adipocyte-secreted protein that increases insulin sensitivity [1] , [2] , [3] , and has anti-diabetic [4] , [5] , [6] and anti-atherogenic effects [7] .", "Several features render adiponectin an attractive and tractable biomarker for large epidemiologic studies , such as its long half-l...	[ "The adipocyte-derived protein adiponectin is highly heritable and inversely associated with risk of type 2 diabetes mellitus ( T2D ) and coronary heart disease ( CHD ) .", "We meta-analyzed 3 genome-wide association studies for circulating adiponectin levels ( n = 8 , 531 ) and sought validation of the lead sing...	[ "Through a meta-analysis of genome-wide association studies of 14 , 733 individuals , we identified common base-pair variants in the genome which influence circulating adiponectin levels .", "Since adiponectin is an adipocyte-derived circulating protein which has been inversely associated with risk of obesity-rel...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "drosophila", "genetics and genomics", "developmental biology", "molecular biology" ]	The Essential Role of Drosophila HIRA for De Novo Assembly of Paternal Chromatin at Fertilization	journal.pgen.0030182	null	[ [ "The assembly of nucleosome particles on nuclear DNA is the initial step for the formation of chromatin .", "Nucleosome assembly initiates with the formation of a H3-H4 histone tetramer on DNA followed by the addition of two H2A-H2B dimers to form the octameric particle [1 , 2] .", "Although this orga...	[ "In many animal species , the sperm DNA is packaged with male germ line–specific chromosomal proteins , including protamines .", "At fertilization , these non-histone proteins are removed from the decondensing sperm nucleus and replaced with maternally provided histones to form the DNA replication competent male ...	[ "Chromatin is composed of basic units called nucleosomes , in which DNA wraps around a core of histone proteins .", "HIRA is a histone chaperone that is specifically involved in the assembly of nucleosomes containing H3 . 3 , a universally conserved type of histone 3 .", "To understand the function of HIRA in v...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "population modeling", "evolutionary modeling", "biology and life sciences", "infectious disease modeling", "computational biology" ]	The Route of HIV Escape from Immune Response Targeting Multiple Sites Is Determined by the Cost-Benefit Tradeoff of Escape Mutations	journal.pcbi.1003878	null	[ [ "HIV replication continues for years despite a highly active immune response .", "Depletion of cytotoxic CD8+ T cells ( CTL ) in SIV infected animals causes rapid increase in viremia [1] , [2] showing that CTL control HIV/SIV replication; that this response is antigen-specific is evident from rapid geneti...	[ "Cytotoxic T lymphocytes ( CTL ) are a major factor in the control of HIV replication .", "CTL arise in acute infection , causing escape mutations to spread rapidly through the population of infected cells .", "As a result , the virus develops partial resistance to the immune response .", "The factors control...	[ "Like many viruses , HIV has evolved mechanisms to evade the host immune response .", "As early as a few weeks after infection is initiated , mutations appear in the viral genome that reduce the ability of cytotoxic T lymphocytes ( CTL ) to control virus replication .", "However , of the many mutations in the v...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "public health and epidemiology", "diagnostic radiology", "clinical research design", "drugs and devices", "immunology", "parasitic diseases", "pharmacodynamics", "neglected tropical diseases", "pharmacology", "radiology", "ultrasonography", "echinococcosis", "infectious diseas...	Post-Treatment Follow-Up Study of Abdominal Cystic Echinococcosis in Tibetan Communities of Northwest Sichuan Province, China	journal.pntd.0001364	null	[ [ "Human cystic echinococcosis ( CE ) , caused by the metacestode stage of Echinococcus granulosus , is a complex , chronic disease with a cosmopolitan distribution , and the liver is the most frequently affected organ [1] .", "Clinical manifestation of this disease ranges from asymptomatic infection to sev...	[ "Human cystic echinococcosis ( CE ) , caused by the larval stage of Echinococcus granulosus , with the liver as the most frequently affected organ , is known to be highly endemic in Tibetan communities of northwest Sichuan Province .", "Antiparasitic treatment with albendazole remains the primary choice for the g...	[ "Cystic echinococcosis is a serious public health problem in Tibetan communities of northwest Sichuan Province , China .", "Antiparasitic treatment with albendazole remains the only choice in most cases , due to the poor socio-economy and inadequate hospital facilities in this area .", "A post-treatment follow-...	2011
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "taxonomy", "invertebrates", "heterozygosity", "helminths", "hookworms", "animals", "genetic mapping", "parasitology", "necator americanus", "developmental biology", "phylogenetics", "data management", "phylogenetic analysis", "strongyloides stercoralis", "research and analysis methods",...	Characterization of a non-sexual population of Strongyloides stercoralis with hybrid 18S rDNA haplotypes in Guangxi, Southern China	journal.pntd.0007396	null	[ [ "Soil-transmitted helminths ( STHs ) are parasitic worms that infect hosts by transmitting their eggs or larvae through contaminated soil .", "Among them are parasitic nematodes like giant roundworms ( Ascaris lumbricoides ) , hookworms ( Necator americanus and Ancylostoma spp . ) , whipworms ( Trichuris ...	[ "Strongyloidiasis is a much-neglected but sometimes fatal soil born helminthiasis .", "The causing agent , the small intestinal parasitic nematode Strongyloides stercoralis can reproduce sexually through the indirect/heterogonic life cycle , or asexually through the auto-infective or the direct/homogonic life cyc...	[ "The vast majority of multicellular organisms reproduce sexually .", "Sexual reproduction is believed to be advantageous because meiotic recombination separates beneficial and deleterious mutations and generates new , possibly better allele combinations .", "However , sexual reproduction comes at a cost .", "...	2019
[ "Introduction", "Model", "Results", "Discussion" ]	[ "biology" ]	Cell Patterns Emerge from Coupled Chemical and Physical Fields with Cell Proliferation Dynamics: The Arabidopsis thaliana Root as a Study System	journal.pcbi.1003026	null	[ [ "The study of stem-cell niche patterns , and specifically how stem cells can maintain their totipotent state while simultaneously giving rise to daughter cells that obtain distinct fates to form differentiated tissues and organs , is fundamental to understanding the development of multicellular organisms [1] ...	[ "A central issue in developmental biology is to uncover the mechanisms by which stem cells maintain their capacity to regenerate , yet at the same time produce daughter cells that differentiate and attain their ultimate fate as a functional part of a tissue or an organ .", "In this paper we propose that , during ...	[ "The emergence of tumors results from altered cell differentiation and proliferation during organ and tissue development .", "Understanding how such altered or normal patterns are established is still a challenge .", "Molecular genetic approaches to understanding pattern formation have searched for key central ...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases/neglected tropical diseases" ]	Improved Protective Efficacy of a Species-Specific DNA Vaccine Encoding Mycolyl-Transferase Ag85A from Mycobacterium ulcerans by Homologous Protein Boosting	journal.pntd.0000199	null	[ [ "Buruli ulcer ( BU ) , also known as Bairnsdale ulcer , is an infectious , necrotizing skin disease caused by Mycobacterium ulcerans ( M . ulcerans ) occurring mostly in tropical and subtropical areas .", "Cases have been reported in several countries in West and Central Africa , in Central and South Amer...	[ "Vaccination with plasmid DNA encoding Ag85A from M . bovis BCG can partially protect C57BL/6 mice against a subsequent footpad challenge with M . ulcerans .", "Unfortunately , this cross-reactive protection is insufficient to completely control the infection .", "Although genes encoding Ag85A from M . bovis BC...	[ "Buruli ulcer ( BU ) is an infectious disease characterized by deep , ulcerating skin lesions , particularly on arms and legs , that are provoked by a toxin .", "BU is caused by a microbe belonging to the same family that also causes tuberculosis and leprosy .", "The disease is emerging as a serious health prob...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "systems biology", "biology", "microbiology", "genetics and genomics" ]	The Thermoanaerobacter Glycobiome Reveals Mechanisms of Pentose and Hexose Co-Utilization in Bacteria	journal.pgen.1002318	null	[ [ "Renewable liquid fuels derived from lignocellulose , the most abundant biological polymer on earth , could alleviate global energy shortages and climate change .", "Consolidated bioprocessing ( CBP ) , which is one proposed scheme of lignocellulosic ethanol production , combines cellulase production , ce...	[ "Thermoanaerobic bacteria are of interest in cellulosic-biofuel production , due to their simultaneous pentose and hexose utilization ( co-utilization ) and thermophilic nature .", "In this study , we experimentally reconstructed the structure and dynamics of the first genome-wide carbon utilization network of th...	[ "Renewable liquid fuels derived from lignocellulosic biomass could alleviate global energy shortage and climate change .", "Cellulose and hemicellulose are the main components of lignocellulosic biomass .", "Therefore , the ability to simultaneously utilize pentose and hexose ( i . e . , co-utilization ) has be...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genome expression analysis", "functional genomics", "dna transcription", "gene function", "developmental biology", "genome analysis tools", "embryology", "gene expression", "regulatory networks", "biology", "transcriptomes", "computer science", "computer modeling", "genetics", "genomics...	Automatic Annotation of Spatial Expression Patterns via Sparse Bayesian Factor Models	journal.pcbi.1002098	null	[ [ "Detailed knowledge of the precise location and time span of gene expression is mandatory to deciphering dynamic cellular mechanisms .", "The application of microarray technology has led to genome-wide quantitative overviews of the relative changes of transcript levels in many organisms ( such as Drosophi...	[ "Advances in reporters for gene expression have made it possible to document and quantify expression patterns in 2D–4D .", "In contrast to microarrays , which provide data for many genes but averaged and/or at low resolution , images reveal the high spatial dynamics of gene expression .", "Developing computatio...	[ "High throughput image acquisition is a quickly increasing new source of data for problems in computational biology , such as phenotypic screens .", "Given the very diverse nature of imaging technology , samples , and biological questions , approaches are oftentimes very tailored and ad hoc to a specific data set...	2011
[ "Introduction", "TF beyond DR", "What do we mean by the term “drug resistance”?", "Molecular mechanisms of DR to antimonials", "Molecular epidemiology of DR in", "", "Molecular mechanisms of DR to MIL", "The molecular basis of AmB resistance in", "Resistance to drug combination therapy in", "Gener...	[ "medicine and health sciences", "tropical diseases", "microbiology", "parasitic diseases", "parasitic protozoans", "review", "protozoans", "leishmania", "pharmaceutics", "antimony", "neglected tropical diseases", "pharmacology", "infectious diseases", "antimicrobial resistance", "zoonose...	Drug resistance and treatment failure in leishmaniasis: A 21st century challenge	journal.pntd.0006052	null	[ [ "The leishmaniases are complex diseases of ( sub ) tropical regions of the world caused by Leishmania spp .", "( Protozoa , Kinetoplastida , Trypanosomatidae ) and spread by sand flies .", "The World Health Organization ( WHO ) considers the leishmaniases to be prominent among the global causes of dea...	[ "Reevaluation of treatment guidelines for Old and New World leishmaniasis is urgently needed on a global basis because treatment failure is an increasing problem .", "Drug resistance is a fundamental determinant of treatment failure , although other factors also contribute to this phenomenon , including the globa...	[ "Chemotherapy is central to the control and management of leishmaniasis .", "Antimonials remain the primary drugs against different forms of leishmaniasis in several regions .", "However , resistance to antimony has necessitated the use of alternative medications , especially in the Indian subcontinent ( ISC ) ...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular biology/post-translational regulation of gene expression", "molecular biology/rna-protein interactions", "genetics and genomics", "molecular biology/translational regulation" ]	Concordant Regulation of Translation and mRNA Abundance for Hundreds of Targets of a Human microRNA	journal.pbio.1000238	A specific microRNA reduces the synthesis of hundreds of proteins via concordant effects on the abundance and translation of the mRNAs that encode them.	[ [ "MicroRNAs ( miRNAs ) are small noncoding RNAs whose complementary pairing to target mRNAs potentially regulates expression of more than 60% of genes in many and perhaps all metazoans [1]–[6] .", "Destabilization of mRNA and translational repression have been suggested as the mechanisms of action for miRN...	[ "MicroRNAs ( miRNAs ) regulate gene expression posttranscriptionally by interfering with a target mRNA's translation , stability , or both .", "We sought to dissect the respective contributions of translational inhibition and mRNA decay to microRNA regulation .", "We identified direct targets of a specific miRN...	[ "The human genome contains directions to regulate the timing and magnitude of expression of its thousands of genes .", "MicroRNAs are important regulatory RNAs that tune the expression levels of tens to hundreds of specific genes by pairing to complimentary stretches in the messenger RNAs from these genes , there...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "animal models", "biochemistry", "developmental biology", "cellular structures", "drosophila melanogaster", "model organisms", "molecular development", "macromolecular assemblies", "genetics", "molecular genetics", "cellular types", "biology", "muscle fibers", "molecular cell biology", "...	DAAM Is Required for Thin Filament Formation and Sarcomerogenesis during Muscle Development in Drosophila	journal.pgen.1004166	null	[ [ "Striated muscles contain cylindrical structures , myofibrils , composed of repeating elements called sarcomeres , the basic contractile units of muscle .", "A sarcomere , defined as the region between neighboring Z-discs , contains two filament systems , the actin-containing thin filaments and the myosin...	[ "During muscle development , myosin and actin containing filaments assemble into the highly organized sarcomeric structure critical for muscle function .", "Although sarcomerogenesis clearly involves the de novo formation of actin filaments , this process remained poorly understood .", "Here we show that mouse ...	[ "Sarcomeres , the smallest contractile units of muscle , are formed by two major filament systems , the myosin containing thick and the actin containing thin filaments .", "Although it is well established that sarcomerogenesis involves the formation of novel actin filaments , so far it remained largely unclear ho...	2014
[ "Introduction", "Materials and Methods", "Discussion", "Conclusion" ]	[ "biogeography", "dengue virus", "medicine and health sciences", "ecology and environmental sciences", "pathology and laboratory medicine", "infectious disease epidemiology", "pathogens", "population genetics", "geographical locations", "microbiology", "north america", "viruses", "rna viruses...	Dengue in Latin America: Systematic Review of Molecular Epidemiological Trends	journal.pntd.0005224	null	[ [ "Dengue disease , caused by a dengue virus ( DENV ) , is the predominant arthropod-borne viral disease affecting humans .", "The primary vector is the Aedes aegypti ( A . aegypti ) ( Linnaeus ) mosquito .", "Dengue is caused by one of four distinct serotypes ( DENV-1 , -2 , -3 or -4 ) that are members...	[ "Dengue , the predominant arthropod-borne viral disease affecting humans , is caused by one of four distinct serotypes ( DENV-1 , -2 , -3 or -4 ) .", "A literature analysis and review was undertaken to describe the molecular epidemiological trends in dengue disease and the knowledge generated in specific molecula...	[ "The wide distribution of the mosquito vector and the co-circulation of multiple dengue virus serotypes has led to increases in the incidence of dengue in the Americas , where it is a major public health concern .", "Identifying molecular epidemiological trends may help to identify the reasons for the re-emergenc...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "enzyme-linked immunoassays", "immune physiology", "pathology and laboratory medicine", "pathogens", "immunology", "tropical diseases", "microbiology", "viruses", "vaccines", "preventive medicine", "rabies", "immunologic adjuvants", "rna viruses", "dna vir...	A simian-adenovirus-vectored rabies vaccine suitable for thermostabilisation and clinical development for low-cost single-dose pre-exposure prophylaxis	journal.pntd.0006870	null	[ [ "Despite the development of an efficacious rabies vaccine by Pasteur in 1885 , estimates of current global annual human rabies mortality range from 24 , 000 to 59 , 000 [1–3] .", "Among the neglected tropical diseases , the burden of mortality due to rabies is exceeded only by that due to leishmaniasis [1...	[ "Estimates of current global rabies mortality range from 26 , 000 to 59 , 000 deaths per annum .", "Although pre-exposure prophylaxis using inactivated rabies virus vaccines ( IRVs ) is effective , it requires two to three doses and is regarded as being too expensive and impractical for inclusion in routine child...	[ "Rabies was , after smallpox , the second human disease for which an efficacious vaccine was developed , by Pasteur in 1885 .", "Although it is eminently preventable , with highly efficacious vaccines available for both humans and animals , it still causes considerable mortality in low and middle-income countries...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biophysics/macromolecular assemblies and machines", "microbiology", "biophysics" ]	Structural Insight into the Rotational Switching Mechanism of the Bacterial Flagellar Motor	journal.pbio.1000616	Structural analysis of a clockwise-biased rotation mutant of the bacterial flagellar rotor protein FliG provides a new model for the arrangement of FliG subunits in the motor, and novel insights into rotation switching.	[ [ "Bacteria such as Escherichia coli and Salmonella", "enterica swim by rotating multiple flagella , which arise randomly over", "the cell surface .", "Each flagellum is a huge protein complex made up of about 30", "different proteins and can be divided into three distinct parts: the basal body ...	[ "The bacterial flagellar motor can rotate either clockwise ( CW ) or", "counterclockwise ( CCW ) .", "Three flagellar proteins , FliG , FliM , and FliN , are", "required for rapid switching between the CW and CCW directions .", "Switching is", "achieved by a conformational change in FliG induced by the bi...	[ "The bacterial flagellum is a rotating organelle that governs cell motility .", "At", "the base of each flagellum is a motor powered by the electrochemical potential", "difference of specific ions across the cytoplasmic membrane .", "In response to", "environmental stimuli , rotation of the motor switches...	2011

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