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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" ]	[ "immunology/cellular microbiology and pathogenesis", "virology/immunodeficiency viruses", "virology/animal models of infection", "infectious diseases/hiv infection and aids", "immunology/leukocyte activation" ]	Inadequate Clearance of Translocated Bacterial Products in HIV-Infected Humanized Mice	journal.ppat.1000867	null	[ [ "The clinical course of HIV infection varies considerably among patients , and the variability is even greater in simian models .", "Asian monkeys infected with simian immunodeficiency virus ( SIV ) rapidly progress to AIDS , but African monkeys do not get sick [1] .", "In general , a pathogenic cours...	[ "Bacterial translocation from the gut and subsequent immune activation are hallmarks of HIV infection and are thought to determine disease progression .", "Intestinal barrier integrity is impaired early in acute retroviral infection , but levels of plasma lipopolysaccharide ( LPS ) , a marker of bacterial translo...	[ "HIV infection leads to continuous destruction of the body's immune defenses .", "Furthermore , disease progression is linked to heightened levels of immune activation .", "However , the underlying activating factors and their relationships to HIV pathogenesis are controversial .", "In patients with chronic H...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "vertebrates", "social sciences", "autism", "developmental psychology", "neuroscience", "mammals", "animals", "primates", "mathematics", "bioassays and physiological analysis", "autism spectrum disorder", "neuronal dendrites", "discrete mathematics", "comb...	Disruption of an Evolutionarily Novel Synaptic Expression Pattern in Autism	journal.pbio.1002558	A comparative transcriptome study draws a connection between the gene expression alterations in autism and molecular features of cortical development that are unique to humans.	[ [ "Autism spectrum disorder ( ASD ) is a common neurodevelopmental condition characterized by the disruption of cognitive functions involved in socialization and communication and inclination toward restricted interests and repetitive behaviors [1–4] .", "The global median prevalence of ASD is estimated at ...	[ "Cognitive defects in autism spectrum disorder ( ASD ) include socialization and communication: key behavioral capacities that separate humans from other species .", "Here , we analyze gene expression in the prefrontal cortex of 63 autism patients and control individuals , as well as 62 chimpanzees and macaques ,...	[ "Autism spectrum disorder ( ASD ) involves disruptions in cognitive functions related to socialization and communication , which are also among the key behavioral capacities that separate humans from other species .", "This suggests that ASD may involve alterations in evolutionarily novel , human-specific develop...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases", "virology", "immunology", "microbiology", "molecular biology" ]	Vaccination and Timing Influence SIV Immune Escape Viral Dynamics In Vivo	journal.ppat.0040012	null	[ [ "CD8+ cytotoxic T lymphocyte ( CTL ) responses during acute HIV-1 and simian immunodeficiency virus ( SIV ) infection in humans and macaques , respectively , correlate with effective control of acute viremia [1–4] .", "CTL responses to both HIV-1 and SIV are , however , partially undermined by the evoluti...	[ "CD8+ cytotoxic T lymphocytes ( CTL ) can be effective at controlling HIV-1 in humans and SIV in macaques , but their utility is partly offset by mutational escape .", "The kinetics of CTL escape and reversion of escape mutant viruses upon transmission to MHC-mismatched hosts can help us understand CTL-mediated v...	[ "Immune escape from AIDS virus–specific cellular immunity is common .", "The driving forces behind how quickly cellular immunity forces escape are poorly understood .", "We developed a novel assay for a common immune escape variant of SIV in macaques .", "This allowed us to sensitively track the rates of immu...	2008
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Machine Learning Models and Pathway Genome Data Base for Trypanosoma cruzi Drug Discovery	journal.pntd.0003878	null	[ [ "In the 1980’s the pharmaceutical industry took advantage of advances in molecular biology/genetic engineering and began replacing phenotypic , whole-cell HTS with target-based screening assays [1] .", "Target-based screens using simple recombinant protein enzymatic assays offer advantages in terms of cos...	[ "Chagas disease is a neglected tropical disease ( NTD ) caused by the eukaryotic parasite Trypanosoma cruzi .", "The current clinical and preclinical pipeline for T . cruzi is extremely sparse and lacks drug target diversity .", "In the present study we developed a computational approach that utilized data from...	[ "Chagas disease is a neglected tropical disease ( NTD ) caused by the eukaryotic parasite Trypanosoma cruzi .", "The disease is endemic to Latin America but is increasingly found in North America and Europe , primarily through immigration , and the spread of this disease is bringing new attention to the need for ...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "biotechnology", "heterozygosity", "italian people", "variant genotypes", "genetic mapping", "ethnicities", "plant science", "model organisms", "experimental organism systems", "plant genomics", "plants", "research and analysis methods", "geography", "grasses", "maize", "plant genetics...	Independent introductions and admixtures have contributed to adaptation of European maize and its American counterparts	journal.pgen.1006666	null	[ [ "Expansion of species to conditions that differ from their native range depends on their abilities to adapt to new environments .", "Depletion of genetic diversity of introduced—founder—populations may however alter this ability .", "Despite loss of diversity associated with population bottlenecks dur...	[ "Through the local selection of landraces , humans have guided the adaptation of crops to a vast range of climatic and ecological conditions .", "This is particularly true of maize , which was domesticated in a restricted area of Mexico but now displays one of the broadest cultivated ranges worldwide .", "Here ...	[ "The spread of a species outside its native range depends on its ability to face new environmental challenges .", "Despite a loss of diversity associated with recurrent introductions , domesticated species offer excellent examples of rapid expansion and adaptation to new climatic and ecological conditions .", "...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Impact of Six Rounds of Mass Drug Administration on Brugian Filariasis and Soil-Transmitted Helminth Infections in Eastern Indonesia	journal.pntd.0002586	null	[ [ "Lymphatic filariasis ( LF ) has been targeted by the World Health Organization for global elimination by the year 2020 [1] .", "During the years 2000 to 2009 the Global Program to Eliminate Lymphatic Filariasis ( GPELF ) has provided >2 . 8 billion treatments with anti-filarial drugs to a minimum of 885 ...	[ "The lymphatic filarial parasite Brugia timori occurs only in eastern Indonesia where it causes high morbidity .", "The absence of an animal reservoir , the inefficient transmission by Anopheles mosquitoes and the high sensitivity to DEC/albendazole treatment make this species a prime candidate for elimination by...	[ "The impact of six annual rounds of mass drug administration ( MDA ) using DEC combined with albendazole on brugian filariasis and soil-transmitted helminths ( STH ) was evaluated .", "Microfilaria rates of B . timori dropped quickly after MDA and were below 1% for 34 months after stopping intervention when the s...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "mathematics", "statistics (mathematics)", "population modeling", "biology and life sciences", "physical sciences", "infectious disease modeling", "biostatistics", "computational biology" ]	Mathematical Modeling of Bacterial Kinetics to Predict the Impact of Antibiotic Colonic Exposure and Treatment Duration on the Amount of Resistant Enterobacteria Excreted	journal.pcbi.1003840	null	[ [ "Antibiotics are widely used in animal farming for curative , prophylaxis and metaphylaxis purposes .", "This results in massive excretion of antibiotics [1] , [2] and resistant bacteria with the feces of the animals during treatments [3] .", "It impacts the ecology of the environment and ultimately c...	[ "Fecal excretion of antibiotics and resistant bacteria in the environment are major public health threats associated with extensive farming and modern medical care .", "Innovative strategies that can reduce the intestinal antibiotic concentrations during treatments are in development .", "However , the effect o...	[ "Fecal excretion of antibiotics and resistant bacteria in the environment are major public health threats associated with extensive farming .", "Innovative strategies that reduce the intestinal antibiotic concentrations during treatment are in development and could help prevent the dissemination of resistance .",...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "sequence analysis", "biophysic al simulations", "evolutionary modeling", "biology", "computational biology", "macromolecular structure analysis" ]	Prediction of Mutational Tolerance in HIV-1 Protease and Reverse Transcriptase Using Flexible Backbone Protein Design	journal.pcbi.1002639	null	[ [ "The relationship between protein sequence and structure is fundamental for protein function , evolution and design [1] , [2] .", "Many sequences are compatible with a given structure and function and thus proteins are often robust to point mutation [3] , [4] , [5] .", "The concept of “tolerated seque...	[ "Predicting which mutations proteins tolerate while maintaining their structure and function has important applications for modeling fundamental properties of proteins and their evolution; it also drives progress in protein design .", "Here we develop a computational model to predict the tolerated sequence space ...	[ "Many related protein sequences can be consistent with the structure and function of a given protein , suggesting that proteins may be quite robust to mutations .", "This tolerance to mutations is frequently exploited by pathogens .", "In particular , pathogens can rapidly evolve mutated proteins that have a ne...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "mammals", "computational biology", "eukaryotes", "vertebrates", "mus (mouse)", "molecular biology", "animals" ]	Construction, Visualisation, and Clustering of Transcription Networks from Microarray Expression Data	journal.pcbi.0030206	null	[ [ "Complete genome sequencing of hundreds of pathogenic and model organisms has provided the parts list required for large-scale studies of gene function [1] .", "Enormous amounts of data pertaining to the nature of genes and proteins and their interactions in the cell have now been generated by techniques ...	[ "Network analysis transcends conventional pairwise approaches to data analysis as the context of components in a network graph can be taken into account .", "Such approaches are increasingly being applied to genomics data , where functional linkages are used to connect genes or proteins .", "However , while mic...	[ "This paper describes a novel approach for analysis of gene expression data .", "In this approach , normalized gene expression data is transformed into a graph where nodes in the graph represent transcripts connected to each other by virtue of their coexpression across multiple tissues or samples .", "The graph...	2007
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Population Structure of the Chagas Disease Vector Triatoma infestans in an Urban Environment	journal.pntd.0003425	null	[ [ "Chagas disease is a vector-borne disease endemic in Latin America that poses important public health risks [1] .", "Triatoma infestans , a true bug that commonly harbors the etiologic agent of Chagas disease , Trypanosoma cruzi , has historically occurred throughout southern South America [2 , 3] .", ...	[ "Chagas disease is a vector-borne disease endemic in Latin America .", "Triatoma infestans , a common vector of this disease , has recently expanded its range into rapidly developing cities of Latin America .", "We aim to identify the environmental features that affect the colonization and dispersal of T . infe...	[ "The colonization and dispersal of disease vectors in new and expanding urban areas pose important health risks .", "The population and demographic dynamics of these vectors are often unclear , and their temporal and spatial associations with urbanization are unknown .", "Here , we use molecular markers to desc...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "mathematics", "statistics", "genetics", "biology", "genetics and genomics" ]	The Empirical Power of Rare Variant Association Methods: Results from Sanger Sequencing in 1,998 Individuals	journal.pgen.1002496	null	[ [ "There is growing evidence that rare variants contribute to the etiology of complex diseases [1] , [2] , [3] , [4] .", "A striking difference in the distributions of the odds ratios ( ORs ) for common and rare variants has been illustrated in a wide range of recent publications , favoring higher ORs for s...	[ "The role of rare genetic variation in the etiology of complex disease remains unclear .", "However , the development of next-generation sequencing technologies offers the experimental opportunity to address this question .", "Several novel statistical methodologies have been recently proposed to assess the con...	[ "There is now evidence that rare variants can contribute to the etiology of complex disease .", "Next generation sequencing technologies have enabled their detection in large cohorts , and new statistical methods have been proposed to ascertain their association with complex diseases and traits in order to improv...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases/neglected tropical diseases", "infectious diseases/helminth infections", "infectious diseases/hiv infection and aids", "public health and epidemiology/infectious diseases", "infectious diseases/protozoal infections", "infectious diseases/tropical and travel-associated diseases", "in...	High Prevalence of Persistent Parasitic Infections in Foreign-Born, HIV-Infected Persons in the United States	journal.pntd.0001034	null	[ [ "Human immunodeficiency virus ( HIV ) co-infection with parasitic diseases is an issue not only in parasite-endemic countries but also for persons who have migrated to more developed countries such as the United States .", "HIV surveillance systems in the United States do not routinely assess country of b...	[ "Foreign-born , HIV-infected persons are at risk for sub-clinical parasitic infections acquired in their countries of origin .", "The long-term consequences of co-infections can be severe , yet few data exist on parasitic infection prevalence in this population .", "This cross-sectional study evaluated 128 fore...	[ "Undiagnosed and untreated parasitic infections can have severe consequences for human immunodeficiency virus ( HIV ) -infected persons .", "An estimated 2 billion people worldwide are infected with soil-transmitted helminths and schistosomiasis , yet there are few data on the prevalence in HIV-infected immigrant...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "immune cells", "clinical immunology", "immunity", "immunity to infections", "immunology", "immunoregulation", "immune response" ]	Tim-3-Expressing CD4+ and CD8+ T Cells in Human Tuberculosis (TB) Exhibit Polarized Effector Memory Phenotypes and Stronger Anti-TB Effector Functions	journal.ppat.1002984	null	[ [ "Tuberculosis ( TB ) , an infectious disease caused by Mycobacterium tuberculosis ( Mtb ) infection , remains a leading cause of morbidity and mortality worldwide [1] .", "CD4+ and CD8+ T cells may be important for host immune resistance to TB in humans [2] , [3] , [4] , [5] .", "In mouse models of Mt...	[ "T-cell immune responses modulated by T-cell immunoglobulin and mucin domain-containing molecule 3 ( Tim-3 ) during Mycobacterium tuberculosis ( Mtb ) infection in humans remain poorly understood .", "Here , we found that active TB patients exhibited increases in numbers of Tim-3-expressing CD4+ and CD8+ T cells ...	[ "Tuberculosis ( TB ) , an infectious disease caused by Mycobacterium tuberculosis ( Mtb ) infection , remains a leading cause of morbidity and mortality worldwide .", "While CD4+ and CD8+ T-cell effector functions producing Th1 or cytotoxic cytokines are required to mount anti-mycobacterial immunity , insufficien...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "helminths", "population genetics", "geographical locations", "vertebrates", "parasitic diseases", "animals", "dracunculus", "genetic mapping", "mammals", "dogs", "mitochondria", "bioenergetics", "dracunculus medinensis", "population bio...	Population genetic analysis of Chadian Guinea worms reveals that human and non-human hosts share common parasite populations	journal.pntd.0006747	null	[ [ "The international campaign to eradicate Guinea worm ( Dracunculus medinensis ) has made remarkable progress , reducing the annual number of cases from an estimated 3 . 5 million in the mid-1980s to 30 cases in 2017 [1 , 2] .", "Of the 21 countries that had endemic transmission at the eradication campaign...	[ "Following almost 10 years of no reported cases , Guinea worm disease ( GWD or dracunculiasis ) reemerged in Chad in 2010 with peculiar epidemiological patterns and unprecedented prevalence of infection among non-human hosts , particularly domestic dogs .", "Since 2014 , animal infections with Guinea worms have a...	[ "Since the mid-1980’s , when Guinea worm ( Dracunculus medinensis ) was formally targeted for eradication , the associated national and international efforts to control and eliminate the parasite have been remarkably successful .", "As of 2017 , 16 of the 21 countries with endemic transmission have been certified...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/epigenetics", "genetics and genomics/gene function", "genetics and genomics/genetics of disease", "genetics and genomics/gene expression" ]	CHD7 Targets Active Gene Enhancer Elements to Modulate ES Cell-Specific Gene Expression	journal.pgen.1001023	null	[ [ "CHD7 ( NM_017780 ) is a member of the chromodomain helicase DNA binding domain family of ATP-dependent chromatin remodeling enzymes .", "De novo mutation of CHD7 is a major cause of CHARGE syndrome ( OMIM 214800 ) , a genetic condition characterized by multiple congenital anomalies [1] .", "CHD7 muta...	[ "CHD7 is one of nine members of the chromodomain helicase DNA–binding domain family of ATP–dependent chromatin remodeling enzymes found in mammalian cells .", "De novo mutation of CHD7 is a major cause of CHARGE syndrome , a genetic condition characterized by multiple congenital anomalies .", "To gain insights ...	[ "The gene encoding chromodomain helicase DNA–binding protein 7 ( CHD7 ) is required for normal mammalian development .", "In humans , genetic mutations in CHD7 lead to CHARGE syndrome , a disorder characterized by multiple birth defects .", "In previous studies , CHD7 was shown to localize to the cell nucleus a...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "microbiology", "molecular biology", "genetics and genomics", "eubacteria" ]	A Novel Linear Plasmid Mediates Flagellar Variation in Salmonella Typhi	journal.ppat.0030059	null	[ [ "Flagella play a critical role in the lifestyle of many bacteria , and the flagellin subunit is an important target for pathogen recognition by the mammalian innate immune system through Toll-like receptor ( TLR ) 5 [1] .", "Antiserum against flagella ( H antigen ) and lipopolysaccharide ( O antigen ) are...	[ "Unlike the majority of Salmonella enterica serovars , Salmonella Typhi ( S . Typhi ) , the etiological agent of human typhoid , is monophasic .", "S . Typhi normally harbours only the phase 1 flagellin gene ( fliC ) , which encodes the H:d antigen .", "However , some S . Typhi strains found in Indonesia expres...	[ "Flagella are whip-like structures found on the surface of bacterial cells that mediate swimming .", "Flagella contain a protein called flagellin , which is recognised as a danger signal by the immune system .", "Salmonella Typhi , the bacteria that causes typhoid fever , normally have flagella called H:d , but...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "oncology", "medicine", "biochemistry", "infectious diseases", "molecular cell biology", "women's health", "proteins", "virology", "biology", "microbiology", "viral diseases" ]	The HPV16 E6 Oncoprotein Causes Prolonged Receptor Protein Tyrosine Kinase Signaling and Enhances Internalization of Phosphorylated Receptor Species	journal.ppat.1003237	null	[ [ "Human papillomaviruses ( HPVs ) are small viruses with double stranded DNA genomes that infect squamous epithelial tissue .", "Approximately 200 HPV types have been identified and categorized based on the type of host epithelial tissue they infect .", "A subset of HPVs infects the mucosal epithelium ...	[ "The high-risk human papillomavirus ( HPV ) E6 proteins are consistently expressed in HPV-associated lesions and cancers .", "HPV16 E6 sustains the activity of the mTORC1 and mTORC2 signaling cascades under conditions of growth factor deprivation .", "Here we report that HPV16 E6 activated mTORC1 by enhanced si...	[ "High-risk human papillomavirus infections are associated with nearly all cases of cervical cancer .", "HPVs infect basal epithelial cells but virion production is restricted to the outer , terminally differentiated layers of the infected epithelia where supply of nutrients and growth factors may be limited .", ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "phosphorylation", "medicine and health sciences", "vesicles", "pathology and laboratory medicine", "pathogens", "microbiology", "egfr signaling", "fibroblasts", "viruses", "immunoprecipitation", "dna viruses", "connective tissue cells", "cellular structures and organelles", "herpesviruses...	Opposing Regulation of the EGF Receptor: A Molecular Switch Controlling Cytomegalovirus Latency and Replication	journal.ppat.1005655	null	[ [ "Human cytomegalovirus ( CMV ) , a β-herpesvirus ubiquitous in the world’s population , has adapted many trade-offs for its persistence .", "CMV replicates to low titers and causes minimal cytopathology , such that the primary infection is typically unapparent .", "CMV , like all herpesviruses , persi...	[ "Herpesviruses persist indefinitely in their host through complex and poorly defined interactions that mediate latent , chronic or productive states of infection .", "Human cytomegalovirus ( CMV or HCMV ) , a ubiquitous β-herpesvirus , coordinates the expression of two viral genes , UL135 and UL138 , which have o...	[ "Cytomegalovirus , a herpesvirus , persists in its host through complex interactions that mediate latent , chronic or productive states of infection .", "Defining the mechanistic basis viral persistence is important for defining the costs and possible benefits of viral persistence and to mitigate pathologies asso...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "evidence-based healthcare/clinical decision-making", "microbiology/immunity to infections", "virology/vaccines", "virology/diagnosis", "infectious diseases/neglected tropical diseases", "virology/emerging viral diseases", "evidence-based healthcare/methods for diagnostic and therapeutic studies", "in...	Evaluation of Serological Diagnostic Test Systems Assessing the Immune Response to Japanese Encephalitis Vaccination	journal.pntd.0000883	null	[ [ "Japanese encephalitis virus ( JEV ) , a mosquito-borne pathogen of the genus Flavivirus , family Flaviviridae , is the main cause of viral encephalitis in Asia .", "Three billion people live in the endemic areas and at least 50 , 000 clinical Japanese encephalitis ( JE ) cases occur each year , which are...	[ "A new commercial anti-Japanese encephalitis virus IgM and IgG indirect immunofluorescence test ( IIFT ) was evaluated for the detection of the humoral immune response after Japanese encephalitis vaccination .", "The IgM IIFT was compared to two IgM capture ELISAs and the IgG IIFT was analysed in comparison to a ...	[ "Japanese encephalitis , caused by the Japanese encephalitis virus , is the most prominent viral encephalitis in Asia .", "Three billion people live in endemic areas and at least 50 , 000 clinical cases occur each year , although reliable vaccines are available .", "Concerning the burden caused by this disease ...	2010
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "health promotion", "medicine and health sciences", "population dynamics", "geographical locations", "tropical diseases", "ebola hemorrhagic fever", "health care", "simulation and modeling", "health services administration and management", "neglected tropical diseases", "population biology", "...	Successful Control of Ebola Virus Disease: Analysis of Service Based Data from Rural Sierra Leone	journal.pntd.0004498	null	[ [ "Ebola Virus Disease ( EVD ) is a severe viral illness of humans , with recorded case fatality rates of up to 90% in past outbreaks [1] .", "The current EVD outbreak , caused by the Zaire strain of Ebolavirus , is the first recorded in West Africa .", "It commenced in Guinea in December 2013 , then sp...	[ "The scale and geographical distribution of the current outbreak in West Africa raised doubts as to the effectiveness of established methods of control .", "Ebola Virus Disease ( EVD ) was first detected in Sierra Leone in May 2014 in Kailahun district .", "Despite high case numbers elsewhere in the country , t...	[ "Ebola Virus Disease ( EVD ) is a severe illness that is usually spread from person to person through caring for someone who is sick , or if they die , contact with their body during their funeral .", "The recent EVD outbreak in West Africa caused illness and death in many thousands in Guinea , Sierra Leone and L...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "inflammatory diseases", "infectious diseases", "medicine and health sciences", "biology and life sciences", "immunology" ]	Mycobacterial Antigen Driven Activation of CD14++CD16− Monocytes Is a Predictor of Tuberculosis-Associated Immune Reconstitution Inflammatory Syndrome	journal.ppat.1004433	null	[ [ "Implementation of antiretroviral therapy ( ART ) in patients co-infected with HIV and tuberculosis ( TB ) has greatly improved life expectancy [1]–[5] .", "Anti-retroviral therapy reconstitutes the number and function of CD4+ T-cells and most patients manifest clinical improvement of signs and symptoms o...	[ "Paradoxical tuberculosis-associated immune reconstitution inflammatory syndrome ( TB-IRIS ) is an aberrant inflammatory response occurring in a subset of TB-HIV co-infected patients initiating anti-retroviral therapy ( ART ) .", "Here , we examined monocyte activation by prospectively quantitating pro-inflammato...	[ "Tuberculosis and HIV majorly impact host immune responses , resulting in immune deregulation and inflammation-driven tissue damage .", "Initiation of anti-retroviral therapy in patients with HIV-TB co-infection may result in immune reconstitution inflammatory syndrome ( TB-IRIS ) , a disorder associated with inc...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "skeletal muscles", "fibrosis", "animal models", "developmental biology", "muscle proteins", "model organisms", "immunoprecipitation", "co-immunoprecipitation", "molecular biology techniques", "research and analysis methods", "musculoskeletal system", "protein...	Overexpression of Latent TGFβ Binding Protein 4 in Muscle Ameliorates Muscular Dystrophy through Myostatin and TGFβ	journal.pgen.1006019	null	[ [ "Latent TGFβ binding proteins ( LTBPs ) are extracellular matrix ( ECM ) proteins that bind and sequester the small latent complex of TGFβ .", "There are more than 30 TGFβ family members , and the primary TGFβ family members 1 , 2 and 3 are known to coordinate cell growth during development and regulate r...	[ "Latent TGFβ binding proteins ( LTBPs ) regulate the extracellular availability of latent TGFβ .", "LTBP4 was identified as a genetic modifier of muscular dystrophy in mice and humans .", "An in-frame insertion polymorphism in the murine Ltbp4 gene associates with partial protection against muscular dystrophy ....	[ "Muscular dystrophy is a genetic disease with muscle weakness , replacement of muscle tissue with fibrosis , and premature death .", "The gene for latent TGFβ binding protein 4 ( LTBP4 ) was previously found to modify muscular dystrophy in both mice and humans with variants that confer protection from disease .",...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "signal transduction", "infectious diseases", "molecular cell biology", "cell biology", "virology", "membranes and sorting", "cellular types", "biology", "microbiology", "molecular biology" ]	Entry of Human Papillomavirus Type 16 by Actin-Dependent, Clathrin- and Lipid Raft-Independent Endocytosis	journal.ppat.1002657	null	[ [ "Human Papillomaviruses ( HPVs ) are a family of small non-enveloped viruses that induce mostly benign papillomas .", "However , several high risk HPV types , most prominently HPV-16 , cause cervical cancer and other epithelial tumors .", "While the molecular biology of transformation has been studied...	[ "Infectious endocytosis of incoming human papillomavirus type 16 ( HPV-16 ) , the main etiological agent of cervical cancer , is poorly characterized in terms of cellular requirements and pathways .", "Conflicting reports attribute HPV-16 entry to clathrin-dependent and -independent mechanisms .", "To comprehen...	[ "Human papillomavirus type 16 is the main etiological agent of cervical cancer .", "Despite advances in our understanding of transformation and cancer progression , as well as preventative vaccination strategies , the early events in papillomavirus infections are incompletely understood .", "Here , we investiga...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular biology", "genetics and genomics" ]	Genome-Wide Control of the Distribution of Meiotic Recombination	journal.pbio.1000035	Dsbc1 is a novel locus involved in controlling the localization of meiotic recombination events in the mouse genome.	[ [ "During the first meiotic prophase , chromosomes undergo a series of unique events that lead to the formation of stable connections between homologous chromosomes ( homologs ) , which are required for the reductional segregation at the first meiotic division .", "In most species , these connections result...	[ "Meiotic recombination events are not randomly distributed in the genome but occur in specific regions called recombination hotspots .", "Hotspots are predicted to be preferred sites for the initiation of meiotic recombination and their positions and activities are regulated by yet-unknown controls .", "The act...	[ "In many organisms , an essential feature of meiosis is genetic recombination , which creates diversity in the gametes by mixing the genetic information from each parent into new combinations .", "Reciprocal recombination , or crossovers , also play a mechanical role during meiosis and are required for the proper...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "biophysics/theory and simulation", "immunology/immune response" ]	Optimality of Mutation and Selection in Germinal Centers	journal.pcbi.1000800	null	[ [ "As one of the adaptive immune responses [1] , [2] , [3] , [4] , Affinity Maturation ( AM ) is the procedure in germinal centers ( GC ) to develop Immunoglobulins ( Ig ) , i . e . , antibodies , with increased affinities to a new antigen .", "Understanding the basic functional and physical principles of G...	[ "The population dynamics theory of B cells in a typical germinal center could play an important role in revealing how affinity maturation is achieved .", "However , the existing models encountered some conflicts with experiments .", "To resolve these conflicts , we present a coarse-grained model to calculate th...	[ "The antibodies in our immune system could efficiently improve their abilities in recognizing new antigens .", "This is done with the help of proliferation , mutation and selection of B cells which carry antibodies , but we have difficulties in developing a quantitative description of this adaptation process whic...	2010
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "transfection", "herpes simplex virus", "phosphorylation", "medicine and health sciences", "pathology and laboratory medicine", "molecular probe techniques", "gene regulation", "pathogens", "immunoblotting", "microbiology", "viruses", "immunoprecipitation", "dna viruses", "molecular biolog...	The deubiquitinase CYLD is a specific checkpoint of the STING antiviral signaling pathway	journal.ppat.1007435	null	[ [ "The innate immune system represents the first line of host defense against invading pathogens and employs germline-encoded pattern-recognition receptors ( PRRs ) to detect conserved microbial molecules known as pathogen-associated molecular patterns ( PAMPs ) .", "Upon sensing their corresponding PAMPs ,...	[ "Stimulator of interferon genes ( STING ) is critical for cytosolic DNA-triggered innate immunity .", "STING is modified by several types of polyubiquitin chains .", "Here , we report that the deubiquitinase CYLD sustains STING signaling by stabilizing the STING protein .", "CYLD deficiency promoted the K48-l...	[ "STING is critical for mediating the production of type I interferons and other proinflammatory cytokines .", "The appropriate activation of STING signaling is precisely modulated to maintain immune homeostasis .", "It is well established that covalent modification of STING by different types of polyubiquitin c...	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "haplotypes", "genetics", "population genetics", "biology", "zoology", "genetics and genomics", "parasitology" ]	Genetic Diversity within Schistosoma haematobium: DNA Barcoding Reveals Two Distinct Groups	journal.pntd.0001882	null	[ [ "Ethical approval was obtained from Imperial College Research Ethics Committee ( ICREC ) , Imperial College London in the UK , in combination with the ongoing Schistosomiasis Control Initiative ( SCI ) activities .", "In Senegal , ethical approval was obtained from the ethical committees of the Ministry o...	[ "Schistosomiasis in one of the most prevalent parasitic diseases , affecting millions of people and animals in developing countries .", "Amongst the human-infective species S . haematobium is one of the most widespread causing urogenital schistosomiasis , a major human health problem across Africa , however in te...	[ "Schistosomiasis is a disease caused by parasitic blood flukes of the genus Schistosoma .", "Species that infect humans are prevalent in developing countries , having a major impact on public health and well-being as well as an impediment to socioeconomic development .", "More people are infected with Schistoso...	2012
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "genomics", "biology", "computational biology", "evolutionary biology", "genetics and genomics" ]	Network Evolution: Rewiring and Signatures of Conservation in Signaling	journal.pcbi.1002411	null	[ [ "Peptide recognition modules ( PRMs ) and kinase domains bind short linear peptide motifs on their protein binding partners and are integral members of many signaling pathways [1]–[3] .", "PRM members include the SH3 ( Src homology 3 ) , SH2 ( Src homology 2 ) , and PDZ ( PSD-95/Discs-large/ZO-1 ) domains...	[ "The analysis of network evolution has been hampered by limited availability of protein interaction data for different organisms .", "In this study , we investigate evolutionary mechanisms in Src Homology 3 ( SH3 ) domain and kinase interaction networks using high-resolution specificity profiles .", "We constru...	[ "Protein interaction networks control virtually all cellular processes .", "The rules governing their evolution have remained elusive , as comprehensive protein interaction data is available for only a small number of very distant species , making evolutionary network studies difficult .", "Here we attempt to o...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "viruses", "organismal evolution", "infectious diseases", "medicine and health sciences", "microbial evolution", "genetics", "parasitology", "biology and life sciences", "microbiology", "evolutionary biology", "bacteria", "animals", "organisms" ]	Symbionts Commonly Provide Broad Spectrum Resistance to Viruses in Insects: A Comparative Analysis of Wolbachia Strains	journal.ppat.1004369	null	[ [ "Heritable symbionts are major players in arthropod evolution owing to their high incidence and the diversity of effects they have on their host's phenotype [1]–[3] .", "Primary ( obligate ) symbionts are mutualists that play some essential role — typically synthesizing nutrients missing from the insect's...	[ "In the last decade , bacterial symbionts have been shown to play an important role in protecting hosts against pathogens .", "Wolbachia , a widespread symbiont in arthropods , can protect Drosophila and mosquito species against viral infections .", "We have investigated antiviral protection in 19 Wolbachia str...	[ "In recent years it has been discovered that many organisms are infected with bacterial symbionts that protect them against pathogens .", "Wolbachia is a bacterial symbiont that is found in many species of insects , and several strains are known to protect the insects against viral infection .", "We took 19 str...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/protozoal infections" ]	Malaria Parasite Invasion of the Mosquito Salivary Gland Requires Interaction between the Plasmodium TRAP and the Anopheles Saglin Proteins	journal.ppat.1000265	null	[ [ "Plasmodium spp .", ", the causative agent of malaria , is responsible for about 500 million clinical cases and about 2 million deaths every year , mostly of African children [1] .", "Furthermore , the number of cases is increasing [2] indicating that the available means to fight the disease are insuf...	[ "SM1 is a twelve-amino-acid peptide that binds tightly to the Anopheles salivary gland and inhibits its invasion by Plasmodium sporozoites .", "By use of UV-crosslinking experiments between the peptide and its salivary gland target protein , we have identified the Anopheles salivary protein , saglin , as the rece...	[ "Transmission of Plasmodium , the causative agent of malaria , requires the completion of a complex life cycle in the mosquito , which includes invasion of the salivary glands .", "This invasion depends on the recognition of mosquito salivary gland surface components by the parasite .", "This work demonstrates ...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "chagas disease", "neglected tropical diseases", "parasitic diseases" ]	IL-17RA Signaling Reduces Inflammation and Mortality during Trypanosoma cruzi Infection by Recruiting Suppressive IL-10-Producing Neutrophils	journal.ppat.1002658	null	[ [ "The IL-17 cytokine family is formed by six members: IL-17A ( also called IL-17 ) , IL-17B , IL-17C , IL-17D , IL-17E ( also called IL-25 ) and IL-17F [1] .", "The IL-17A and IL-17F are the best characterized members of the IL-17 family .", "These cytokines share the highest homology , are co-ordinate...	[ "Members of the IL-17 cytokine family play an important role in protection against pathogens through the induction of different effector mechanisms .", "We determined that IL-17A , IL-17E and IL-17F are produced during the acute phase of T . cruzi infection .", "Using IL-17RA knockout ( KO ) mice , we demonstra...	[ "IL-17 family is comprised for six members ( IL-17A to F ) that have been reported to play protective effects in bacterial and fungal infections and contradictory roles in parasite infections .", "Using mice deficient in IL-17RA , the common receptor subunit for many IL-17 family members , we determined that thes...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "knee joints", "medicine and health sciences", "limbs (anatomy)", "biomechanics", "developmental biology", "embryos", "elbow", "ankle joints", "embryology", "musculoskeletal system", "gene expression", "joints (anatomy)", "arms", "anatomy", "bone and joint mechanics", "genetics", "bi...	Heads, Shoulders, Elbows, Knees, and Toes: Modular Gdf5 Enhancers Control Different Joints in the Vertebrate Skeleton	journal.pgen.1006454	null	[ [ "Synovial joints are the key articulations that connect bones and allow movement in vertebrate skeletons .", "A typical synovial joint consists of the ends of two long bones , thin layers of articular cartilage covering the bones , a joint cavity filled with synovial fluid , and ligaments and a fibrous ca...	[ "Synovial joints are crucial for support and locomotion in vertebrates , and are the frequent site of serious skeletal defects and degenerative diseases in humans .", "Growth and differentiation factor 5 ( Gdf5 ) is one of the earliest markers of joint formation , is required for normal joint development in both ...	[ "Joints , such as the hip and knee , are crucial for support and locomotion in animals , and are the frequent sites of serious human diseases such as arthritis .", "The Growth and differentiation factor 5 ( Gdf5 ) gene is required for normal joint formation , and has been linked to risk of common arthritis in Eur...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Metabolic Needs and Capabilities of Toxoplasma gondii through Combined Computational and Experimental Analysis	journal.pcbi.1004261	null	[ [ "The phylum of Apicomplexa comprises a large number of obligate intracellular parasites that can infect organisms across the whole animal kingdom .", "An important member of this phylum , Toxoplasma gondii , is a ubiquitous opportunistic pathogen responsible for one of the most common parasitic infections...	[ "Toxoplasma gondii is a human pathogen prevalent worldwide that poses a challenging and unmet need for novel treatment of toxoplasmosis .", "Using a semi-automated reconstruction algorithm , we reconstructed a genome-scale metabolic model , ToxoNet1 .", "The reconstruction process and flux-balance analysis of t...	[ "Understanding the metabolism of disease-causing microorganisms can guide drug design through the identification of metabolic enzymes whose activity is indispensable for important cellular functions .", "Such understanding can come from the reconstruction and computational analysis of metabolic networks .", "In...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	β-HPV 5 and 8 E6 Disrupt Homology Dependent Double Strand Break Repair by Attenuating BRCA1 and BRCA2 Expression and Foci Formation	journal.ppat.1004687	null	[ [ "Human papillomaviruses ( HPVs ) are a large family of small double stranded DNA viruses that infect the mucosal and cutaneous epithelia of humans .", "Based on sequence homology , HPVs are divided into five genera [1] .", "Members of two of these genera , high risk α-HPV ( HR-α HPVs ) and some β-HPVs...	[ "Recent work has explored a putative role for the E6 protein from some β-human papillomavirus genus ( β-HPVs ) in the development of non-melanoma skin cancers , specifically β-HPV 5 and 8 E6 .", "Because these viruses are not required for tumor maintenance , they are hypothesized to act as co-factors that enhance...	[ "Human Papillomaviruses are a family of viruses with over 100 different members that infect mucous membranes and skin .", "Infections with some of these viruses are linked to cancers of the cervix and oropharynx .", "In this work , we explore the question of whether other members of this virus family may also c...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunopathology", "clinical immunology", "biology and life sciences", "immunology", "immune response" ]	Pulmonary Infection with Hypervirulent Mycobacteria Reveals a Crucial Role for the P2X7 Receptor in Aggressive Forms of Tuberculosis	journal.ppat.1004188	null	[ [ "Tuberculosis ( TB ) is a serious public health issue , with nearly 9 million new annual cases of the disease worldwide and 1 . 3 million deaths per year [1] .", "A third of the global population is infected with bacteria of the Mycobacterium tuberculosis complex ( Mycobacterium tuberculosis – Mtb and Myc...	[ "The purinergic P2X7 receptor ( P2X7R ) is a sensor of extracellular ATP , a damage-associated molecule that is released from necrotic cells and that induces pro-inflammatory cytokine production and cell death .", "To investigate whether the innate immune response to damage signals could contribute to the develop...	[ "Nearly 9 million new cases of tuberculosis and 1 . 3 million deaths are reported yearly worldwide .", "Most individuals infected with tubercle bacilli remain asymptomatic; however , some develop active tuberculosis due to the reactivation of latent infections .", "Progressive primary tuberculosis is an alterna...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "molecular biology/transcription initiation and activation", "genetics and genomics/gene expression", "genetics and genomics/functional genomics", "genetics and genomics/gene function", "cell biology/gene expression" ]	Molecular Characterization of the Schistosoma mansoni Zinc Finger Protein SmZF1 as a Transcription Factor	journal.pntd.0000547	null	[ [ "Schistosomiasis is a disease caused by trematode worms , mainly Schistosoma mansoni , S . haematobium and S . japonicum .", "According to World Health Organization , this parasitic disease affects 200 million people throughout the world [1] .", "Although the level of schistosome-associated morbidity ...	[ "During its development , the parasite Schistosoma mansoni is exposed to different environments and undergoes many morphological and physiological transformations as a result of profound changes in gene expression .", "Characterization of proteins involved in the regulation of these processes is of importance for...	[ "Schistosomes are parasites that exhibit a complex life cycle during which they progress through many morphological and physiological transformations .", "These transformations are likely accompanied by alterations in gene expression , making genetic regulation important for parasite development .", "Here we de...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "sequencing techniques", "genome-wide association studies", "neutral theory", "population genetics", "genome sequencing", "mutation", "effective population size", "genome analysis", "molecular biology techniques", "ecological metrics", "genomics", "genetic polymorphism", "molecular biology",...	The Impact of Population Demography and Selection on the Genetic Architecture of Complex Traits	journal.pgen.1004379	null	[ [ "Genome-wide association studies ( GWAS ) have successfully detected associations between hundreds of common single nucleotide polymorphisms ( SNPs ) and complex traits in humans [1] , [2] .", "While this catalog of genes has revealed important biological insights , for most traits the discovered associat...	[ "Population genetic studies have found evidence for dramatic population growth in recent human history .", "It is unclear how this recent population growth , combined with the effects of negative natural selection , has affected patterns of deleterious variation , as well as the number , frequency , and effect si...	[ "Many human populations have dramatically expanded over the last several thousand years .", "I use population genetic models to investigate how recent population expansions affect patterns of mutations that reduce reproductive fitness and contribute to the genetic basis of complex traits ( including common diseas...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "cell physiology", "hiv infections", "medicine and health sciences", "immune cells", "body fluids", "pathology and laboratory medicine", "nervous system", "pathogens", "immunology", "microbiology", "cloning", "electrophysiology", "neuroscience", "retroviruses", "viruses"...	Limited immune surveillance in lymphoid tissue by cytolytic CD4+ T cells during health and HIV disease	journal.ppat.1006973	null	[ [ "CD4+ T cells are classically known to orchestrate immunity by providing helper functions to other arms of the immune system .", "However , CD4+ T cells can also exercise direct cell-to-cell mediated effector functions to control pathogens and tumors .", "Effector CD4+ T cells with cytolytic activity ...	[ "CD4+ T cells subsets have a wide range of important helper and regulatory functions in the immune system .", "Several studies have specifically suggested that circulating effector CD4+ T cells may play a direct role in control of HIV replication through cytolytic activity or autocrine β-chemokine production .", ...	[ "CD4+ T cells have classically been divided into different subsets based on their different abilities to help and regulate specific parts of the immune system .", "Recent work in the HIV field has demonstrated that HIV-specific CD4+ T cells with unique effector functions , such as cytolytic activity and β-chemoki...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "cell biology", "ophthalmology", "drosophila", "genetics and genomics" ]	The Molecular Mechanisms of OPA1-Mediated Optic Atrophy in Drosophila Model and Prospects for Antioxidant Treatment	journal.pgen.0040006	null	[ [ "Autosomal dominant optic atrophy ( DOA ) is the most common hereditary optic atrophy with an incidence rate as high as 1:10 , 000–1:50 , 000 [1 , 2] .", "It is characterized by central vision loss , color vision abnormalities [1 , 3–5] , and degeneration of the retinal ganglion cells [6] .", "The ons...	[ "Mutations in optic atrophy 1 ( OPA1 ) , a nuclear gene encoding a mitochondrial protein , is the most common cause for autosomal dominant optic atrophy ( DOA ) .", "The condition is characterized by gradual loss of vision , color vision defects , and temporal optic pallor .", "To understand the molecular mecha...	[ "Optic atrophies are a group of neurodegenerative disorders characterized by a gradual loss of vision , color vision defects , and temporal optic pallor .", "Autosomal dominant optic atrophy ( DOA ) , a type of optic atrophy , contributes to a large portion of optic atrophy cases .", "Mutations of the optic atr...	2008
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "deletion mutation", "ecology and environmental sciences", "population genetics", "simulation and modeling", "mutation", "effective population size", "population biology", "research and analysis methods", "conservation biology", "ecological metrics", "conservation science", "population metrics...	Mutation load dynamics during environmentally-driven range shifts	journal.pgen.1007450	null	[ [ "The rate of environmental change experienced by organisms plays a major role in driving evolution and determining species survival .", "Global climate change is just one example of a force driving environmental change .", "The rate of climate warming is unprecedented in recent history [1] and is pred...	[ "The fitness of spatially expanding species has been shown to decrease over time and space , but specialist species tracking their changing environment and shifting their range accordingly have been little studied .", "We use individual-based simulations and analytical modeling to compare the impact of range expa...	[ "As environments change through time across the globe , species must adapt or relocate to survive .", "Specialized species must track the specific moving environments to which they are adapted , as compared to generalists which can spread widely .", "During colonization of new habitat , individuals can accumula...	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "infectious disease epidemiology", "population genetics", "spatial epidemiology", "bacterial diseases", "phylogenetics", "molecular biology techniques", "infectious disease control", "genetic epidemiology", "infectious diseases", "cholera", "genetic polymorphism...	Deciphering the Origin of the 2012 Cholera Epidemic in Guinea by Integrating Epidemiological and Molecular Analyses	journal.pntd.0002898	null	[ [ "Cholera is generally considered endemic in West Africa [1] , especially in countries such as Nigeria , Benin , Togo , Ghana , Liberia and the Republic of Guinea [2] .", "In 2004–2008 , Guinea was struck by a succession of regional cholera outbreaks responsible for 17 , 638 reported cases and 786 deaths [...	[ "Cholera is typically considered endemic in West Africa , especially in the Republic of Guinea .", "However , a three-year lull period was observed from 2009 to 2011 , before a new epidemic struck the country in 2012 , which was officially responsible for 7 , 350 suspected cases and 133 deaths .", "To determine...	[ "Cholera is a potentially deadly diarrheic disease caused by the toxin-secreting bacterium Vibrio cholerae .", "In many poor countries , this prototypical waterborne disease is considered endemic and linked to the climate-driven proliferation of environmental reservoirs of the pathogen .", "Although such a stat...	2014
[ "Introduction", "Methods", "Results", "Discussion", "Results" ]	[ "people and places", "infectious diseases", "computer and information sciences", "medicine and health sciences", "research funding", "south america", "science policy", "network analysis", "bibliometrics", "research grants", "geographical locations", "health care policy", "research assessment...	The catalytic role of a research university and international partnerships in building research capacity in Peru: A bibliometric analysis	journal.pntd.0007483	null	[ [ "In the 1960s , a group of Peruvian physician-scientists who trained abroad returned home with the vision that research should be a fundamental component of medical education .", "They founded the Universidad Peruana Cayetano Heredia ( UPCH ) in 1961 and worked with their international collaborators to se...	[ "In Peru , the past three decades have witnessed impressive growth in biomedical research catalyzed from a single research university and its investigators who secured international partnerships and funding .", "We conducted a bibliometric analysis of publications by Peruvian authors to understand the roots of th...	[ "One measure of a country’s productivity in biomedical research is through an analysis of the publications in the peer reviewed literature .", "We have searched the Web of Science database of English language biomedical publications with a Peruvian author to examine the growth in the number of publications over t...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biomacromolecule-ligand interactions", "protein interactions", "molecular dynamics", "density functional theory", "biophysics simulations", "quantum mechanics", "proteins", "chemistry", "biology", "biophysics", "physics", "biochemistry", "interdisciplinary physics", "computational chemist...	Interrogation of the Protein-Protein Interactions between Human BRCA2 BRC Repeats and RAD51 Reveals Atomistic Determinants of Affinity	journal.pcbi.1002096	null	[ [ "The human breast cancer suppressor protein BRCA2 controls the functions of the RAD51 recombinase , an enzyme conserved in all kingdoms of life , which carries out the strand exchange reaction central to homologous DNA recombination ( HDR ) [1] .", "This essential cellular pathway is responsible for the e...	[ "The breast cancer suppressor BRCA2 controls the recombinase RAD51 in the reactions that mediate homologous DNA recombination , an essential cellular process required for the error-free repair of DNA double-stranded breaks .", "The primary mode of interaction between BRCA2 and RAD51 is through the BRC repeats , w...	[ "The atomic scale interactions that occur at the interfaces between proteins are fundamental to all biological processes .", "One such critical interface is formed between the proteins , human BRCA2 and RAD51 .", "BRCA2 binds to and delivers RAD51 to sites of DNA damage , where RAD51 mediates the error-free rep...	2011
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Optimal Population-Level Infection Detection Strategies for Malaria Control and Elimination in a Spatial Model of Malaria Transmission	journal.pcbi.1004707	null	[ [ "Malaria is a widespread infectious disease caused by Plasmodium parasites and leads to over half a million deaths each year , mostly in children under five years of age [1] .", "As global burden has decreased dramatically over the past decade , local elimination of malaria is within sight for more and mo...	[ "Mass campaigns with antimalarial drugs are potentially a powerful tool for local elimination of malaria , yet current diagnostic technologies are insufficiently sensitive to identify all individuals who harbor infections .", "At the same time , overtreatment of uninfected individuals increases the risk of accele...	[ "Millions of people worldwide live at risk for malaria , a parasitic infectious disease transmitted by mosquitoes .", "Great progress has been made in reducing malaria burden in recent years , and many regions are now devising strategies for elimination .", "One way to eliminate malaria is to deplete the reserv...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "statistics", "random variables", "mathematics", "population modeling", "population biology", "genetic testing", "personalized medicine", "biology", "probability theory", "genetics", "human genetics", "genetics of disease", "statistical methods", "genetics and genomics" ]	Comparison of Family History and SNPs for Predicting Risk of Complex Disease	journal.pgen.1002973	null	[ [ "Over the last half decade , genome-wide association studies ( GWASs ) have revolutionized the conduct of human genetic research .", "Today , numerous companies offer consumers the opportunity to access their genetic data and provide individuals with personalized interpretations of their data based on gen...	[ "The clinical utility of family history and genetic tests is generally well understood for simple Mendelian disorders and rare subforms of complex diseases that are directly attributable to highly penetrant genetic variants .", "However , little is presently known regarding the performance of these methods in sit...	[ "In clinical practice , obtaining a detailed family history is often considered the standard-of-care for characterizing the inherited component of an individual's disease risk .", "Recently , genetic risk assessments based on the cumulative effect of known single nucleotide polymorphism ( SNP ) disease associatio...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "inflammation", "immunity", "virology", "immunity to infections", "biology and life sciences", "immunology", "microbiology", "immune response" ]	Suppressor of Cytokine Signaling 4 (SOCS4) Protects against Severe Cytokine Storm and Enhances Viral Clearance during Influenza Infection	journal.ppat.1004134	null	[ [ "Influenza is a highly infectious , acute respiratory disease that causes profound morbidity and mortality .", "Annual seasonal influenza epidemics result in ∼500 , 000 deaths worldwide and substantial losses to global economies [1] .", "The development of a “cytokine storm” coupled with damage to pul...	[ "Suppressor of cytokine signaling ( SOCS ) proteins are key regulators of innate and adaptive immunity .", "There is no described biological role for SOCS4 , despite broad expression in the hematopoietic system .", "We demonstrate that mice lacking functional SOCS4 protein rapidly succumb to infection with a pa...	[ "The suppressor of cytokine signaling proteins are key regulators of immunity .", "As yet there is no described biological role for SOCS4 , despite its broad expression in cells of the immune system .", "Given the important role of other SOCS proteins in controlling the immune response , we have generated SOCS4...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "ecology and environmental sciences", "rivers", "melioidosis", "geographical locations", "india", "australia", "diabetes mellitus", "bacterial diseases", "cereal crops", "farms", "endocrine disorders", "rice", "model organisms", "aquatic environments", "...	Seroprevalence of Burkholderia pseudomallei among Adults in Coastal Areas in Southwestern India	journal.pntd.0004610	null	[ [ "Burkholderia pseudomallei , the etiological agent of melioidosis , is known to inhabit the soil and water in endemic areas in countries such as northeast Thailand , Singapore , Malaysia and the top end of Northern territory of Australia [1] .", "In these areas , the rural population involved in agricultu...	[ "Although melioidosis , is an important disease in many Southeast Asian countries and Australia , there is limited data on its prevalence and disease burden in India .", "However , an increase in case reports of melioidosis in recent years indicates its endemicity in India .", "A population-based cross-sectiona...	[ "Melioidosis is an underdiagnosed and underreported disease in India with protean clinical manifestation and high fatality .", "Causative agent B . pseudomallei , after environmental exposure , may cause disease or survive unnoticed for a long time in human and animal hosts .", "Individuals with diabetes and re...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "haloferax volcanii", "archaea", "halobacterium salinarum", "microbiology", "molecular biology", "genetics and genomics" ]	Experimental Characterization of Cis-Acting Elements Important for Translation and Transcription in Halophilic Archaea	journal.pgen.0030229	null	[ [ "Determination of the 5′- and 3′-ends of transcripts is used to identify the points of transcription initiation and termination in order to gain important information about both processes .", "In fact , determination of transcript 5′-ends led to the conclusion that archaea have basal promoter elements tha...	[ "The basal transcription apparatus of archaea is well characterized .", "However , much less is known about the mechanisms of transcription termination and translation initation .", "Recently , experimental determination of the 5′-ends of ten transcripts from Pyrobaculum aerophilum revealed that these are devoi...	[ "Expression of the information encoded in the genome of an organism into its phenotype involves transcription of the DNA into messenger RNAs and translation of mRNAs into proteins .", "The textbook view is that an mRNA consists of an untranslated region ( 5′-UTR ) , an open reading frame encoding the protein , an...	2007
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing techniques", "variant genotypes", "genetic mapping", "simulation and modeling", "genome sequencing", "gene sequencing", "genome analysis", "molecular biology techniques", "research and analysis methods", "sequence analysis", "genomic libraries", "chromosome biology", "bioinformat...	Optimal sequencing strategies for identifying disease-associated singletons	journal.pgen.1006811	null	[ [ "New sequencing technologies are shifting the focus of genetic association studies to rare variants .", "Rare variants may explain much of the heritability of common , complex diseases [1 , 2] .", "Importantly , trait-associated rare variants are more likely to severely disrupt gene function [1 , 3] ,...	[ "With the increasing focus of genetic association on the identification of trait-associated rare variants through sequencing , it is important to identify the most cost-effective sequencing strategies for these studies .", "Deep sequencing will accurately detect and genotype the most rare variants per individual ...	[ "Genetic studies of rare variants can help us understand the biology of human disease .", "With modern techniques and sufficient effort , it is possible to very accurately resolve any human genome , identifying most of its unique features .", "When funding is limited , applying these techniques to study human d...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "squamous cell lung carcinoma", "clinical research design", "neural networks", "nephrology", "carcinomas", "cancers and neoplasms", "renal cancer", "neuroscience", "endocrine physiology", "artificial neural networks", "oncology", "research design", "mathemat...	Cox-nnet: An artificial neural network method for prognosis prediction of high-throughput omics data	journal.pcbi.1006076	null	[ [ "With the wide application of genomics technologies , gene expression data of patients are often used as inputs to predict patients’ survival .", "Computationally , survival prediction is usually framed as a regression problem to model patients’ survival time ( or other event time ) .", "The most comm...	[ "Artificial neural networks ( ANN ) are computing architectures with many interconnections of simple neural-inspired computing elements , and have been applied to biomedical fields such as imaging analysis and diagnosis .", "We have developed a new ANN framework called Cox-nnet to predict patient prognosis from h...	[ "The increasing application of high-througput transcriptomics data to predict patient prognosis demands modern computational methods .", "With the re-gaining popularity of artificial neural networks , we asked if a refined neural network model could be used to predict patient survival , as an alternative to the c...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "evolutionary biology", "systems biology", "biology and life sciences", "computational biology" ]	Estimating HIV-1 Fitness Characteristics from Cross-Sectional Genotype Data	journal.pcbi.1003886	null	[ [ "The emergence of drug resistant mutants remains a major obstacle to long-term treatment success of highly active antiretroviral therapy ( HAART ) against HIV-1 [1] , [2] .", "Mathematical models of in vivo viral infection dynamics have provided critical insights into HIV-1 disease and therapy by disentan...	[ "Despite the success of highly active antiretroviral therapy ( HAART ) in the management of human immunodeficiency virus ( HIV ) -1 infection , virological failure due to drug resistance development remains a major challenge .", "Resistant mutants display reduced drug susceptibilities , but in the absence of drug...	[ "Mutations conferring drug resistance represent major threats to the therapeutic success of highly active antiretroviral therapy ( HAART ) against human immunodeficiency virus ( HIV ) -1 infection .", "Viral mutants differ in their fitness and assessing viral fitness is a challenging task .", "In this article ,...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biophysics/theory and simulation", "computational biology/systems biology", "physics/interdisciplinary physics", "computational biology/signaling networks" ]	The Role of Incoherent MicroRNA-Mediated Feedforward Loops in Noise Buffering	journal.pcbi.1001101	null	[ [ "MicroRNAs ( miRNAs ) are endogenous small non-coding RNAs which negatively regulate the protein production of their targets in metazoans and plants .", "They are expected to target a substantial portion of the human genome [1] and have been shown to play key roles in several biological processes ranging ...	[ "MicroRNAs are endogenous non-coding RNAs which negatively regulate the expression of protein-coding genes in plants and animals .", "They are known to play an important role in several biological processes and , together with transcription factors , form a complex and highly interconnected regulatory network .",...	[ "The expression of protein-coding genes is controlled by a complex network of regulatory interactions .", "It is becoming increasingly appreciated that the post-transcriptional repression by microRNAs , a class of small non-coding RNAs , is a key layer of regulation in several biological processes .", "Since ge...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "microbiome", "metabolic networks", "microbiology", "metagenomics", "mathematics", "metabolites", "statistics (mathematics)", "network analysis", "gastroenterology and hepatology", "inflammatory bowel disease", "microbial genomics", "statistical inference", ...	BiomeNet: A Bayesian Model for Inference of Metabolic Divergence among Microbial Communities	journal.pcbi.1003918	null	[ [ "Microorganisms comprise up to one-third of the Earths' biomass , and those living on a human can outnumber their cells by a factor of ten [1] .", "These microbes are believed to form metabolically integrated communities [2] playing a critical role at many levels , from globally significant nutrient cycli...	[ "Metagenomics yields enormous numbers of microbial sequences that can be assigned a metabolic function .", "Using such data to infer community-level metabolic divergence is hindered by the lack of a suitable statistical framework .", "Here , we describe a novel hierarchical Bayesian model , called BiomeNet ( Ba...	[ "Metagenomic studies of microbial communities yield enormous numbers of gene sequences that have a known enzymatic function , and thus have potential to contribute to community-level metabolic activities .", "Ecologically divergent microbial communities are presumed to differ in metabolic repertoire and function ...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/neglected tropical diseases", "cell biology/extra-cellular matrix", "biochemistry/biomacromolecule-ligand interactions", "microbiology/parasitology", "microbiology/cellular microbiology and pathogenesis" ]	Giardia Cyst Wall Protein 1 Is a Lectin That Binds to Curled Fibrils of the GalNAc Homopolymer	journal.ppat.1001059	null	[ [ "Giardia lamblia , which is a deeply divergent protist , causes diarrhea in the developing world where hygiene is inadequate to block its transmission by the fecal-oral route [1]–[3] .", "In addition , some two million Americans are infected each year with Giardia , which is present in streams and lakes o...	[ "The infectious and diagnostic stage of Giardia lamblia ( also known as G . intestinalis or G . duodenalis ) is the cyst .", "The Giardia cyst wall contains fibrils of a unique β-1 , 3-linked N-acetylgalactosamine ( GalNAc ) homopolymer and at least three cyst wall proteins ( CWPs ) composed of Leu-rich repeats (...	[ "While the walls of plants and fungi contain numerous sugar homopolymers ( cellulose , chitin , and β-1 , 3-glucans ) and dozens of proteins , the cyst wall of Giardia is relatively simple .", "The Giardia wall contains a unique homopolymer of β-1 , 3-linked N-acetylgalactosamine ( GalNAc ) and at least three cys...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology/persistence and latency", "virology/virulence factors and mechanisms", "virology/viral replication and gene regulation", "cell biology/nuclear structure and function", "virology/viruses and cancer", "virology/host antiviral responses" ]	Genome-Wide Screen of Three Herpesviruses for Protein Subcellular Localization and Alteration of PML Nuclear Bodies	journal.ppat.1000100	null	[ [ "Herpesviruses are large DNA viruses that each encode between 80 and >200 proteins .", "This complex network of proteins results in a variety of effects on the host cell and ensures efficient proliferation of the virus .", "While the functions of a subset of these proteins are reasonably well understo...	[ "Herpesviruses are large , ubiquitous DNA viruses with complex host interactions , yet many of the proteins encoded by these viruses have not been functionally characterized .", "As a first step in functional characterization , we determined the subcellular localization of 234 epitope-tagged proteins from herpes ...	[ "Herpes simplex virus , Epstein–Barr virus , and cytomegalovirus are three types of human herpesviruses that infect most people for their entire life and , under some circumstances , cause significant diseases .", "Each virus encodes a large number of proteins that function to manipulate the host cell to the best...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "hepatitis c", "medicine", "infectious diseases", "hepatitis", "viral diseases" ]	Elucidation of Hepatitis C Virus Transmission and Early Diversification by Single Genome Sequencing	journal.ppat.1002880	null	[ [ "Hepatitis C virus ( HCV ) infects as many as 170 million people or nearly 3% of the world's population .", "The virus causes a wide variety of pathologic outcomes , the most significant being chronic liver disease , cirrhosis and hepatocellular carcinoma , which is nearly always fatal .", "HCV infect...	[ "A precise molecular identification of transmitted hepatitis C virus ( HCV ) genomes could illuminate key aspects of transmission biology , immunopathogenesis and natural history .", "We used single genome sequencing of 2 , 922 half or quarter genomes from plasma viral RNA to identify transmitted/founder ( T/F ) ...	[ "Hepatitis C virus infects as many as 170 million people worldwide .", "Globally , there are seven major genotypes of HCV that differ by approximately 30% in nucleotide sequence .", "Importantly , the natural history of HCV infection is variable , ranging from spontaneous resolution to persistent viremia and ch...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "geomorphology", "schistosoma", "invertebrates", "schistosoma mansoni", "medicine and health sciences", "ecology and environmental sciences", "landforms", "helminths", "topography", "parasitic diseases", "animals", "farms", "aquatic environments", "materials science", "wetlands", "mate...	Risk of Intestinal Parasitic Infections in People with Different Exposures to Wastewater and Fecal Sludge in Kampala, Uganda: A Cross-Sectional Study	journal.pntd.0004469	null	[ [ "Africa and Asia are urbanizing faster than any other region of the world and an increase of 16% of the urban population is predicted for 2050 [1] .", "With such a demographic expansion , safe wastewater and fecal sludge management and use strategies are of pivotal importance for a healthy life in urban s...	[ "There are health risks associated with wastewater and fecal sludge management and use , but little is known about the magnitude , particularly in rapidly growing urban settings of low- and middle-income countries .", "We assessed the point-prevalence and risk factors of intestinal parasite infections in people w...	[ "Urban wastewater and fecal sludge use is of growing importance all over the world .", "However , unsafe management and inappropriate use might exacerbate the transmission of infectious diseases , including those caused by intestinal protozoa ( e . g . , amebiasis and giardiasis ) and parasitic worms ( e . g . , ...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "microbiome", "pathology and laboratory medicine", "vibrio", "pathogens", "microbiology", "vertebrates", "animals", "animal models", "osteichthyes", "model organisms", "aeromonas", "gastroenterology and hepatology", "bacteria", "microbial genomics", "dig...	Host Gut Motility Promotes Competitive Exclusion within a Model Intestinal Microbiota	journal.pbio.1002517	Live imaging of a model intestinal microbiota reveals that enteric neural function and peristalsis, combined with the spatial structure of microbial communities, can drive competition between bacterial species.	[ [ "Trillions of microbial cells representing hundreds of species make up the human intestinal microbiota .", "This multispecies symbiont supports activities as diverse as host development , nutrient acquisition , immune system education , neural function , and defense against pathogens [1–5] .", "Change...	[ "The gut microbiota is a complex consortium of microorganisms with the ability to influence important aspects of host health and development .", "Harnessing this “microbial organ” for biomedical applications requires clarifying the degree to which host and bacterial factors act alone or in combination to govern t...	[ "Hundreds of microbial species thrive within the gut of humans and other animals , where they can influence the health of their host in profound ways .", "The factors that shape the composition of the resident gut microbiota are not well understood , but identifying them represents an important step toward develo...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma mansoni", "innate immune system", "medicine and health sciences", "immune physiology", "cytokines", "helminths", "immunology", "tropical diseases", "parasitic diseases", "animals", "regression analysis", "age groups", "developmental biology", ...	Multivariable Regression Analysis in Schistosoma mansoni-Infected Individuals in the Sudan Reveals Unique Immunoepidemiological Profiles in Uninfected, egg+ and Non-egg+ Infected Individuals	journal.pntd.0004629	null	[ [ "Schistosomiasis is elicited by parasitic trematodes and can lead to a chronic disease state .", "It remains one of the most prevalent neglected tropical diseases with an estimated 800 million people at risk and currently more than 230 million infected individuals [1–3] .", "The disease is widespread ...	[ "In the Sudan , Schistosoma mansoni infections are a major cause of morbidity in school-aged children and infection rates are associated with available clean water sources .", "During infection , immune responses pass through a Th1 followed by Th2 and Treg phases and patterns can relate to different stages of inf...	[ "Schistosome infections are a major public health problem and currently 230 million people are infected with these blood-dwelling parasitic helminths .", "Schistosomiasis remains the most prevalent parasitic disease in the Sudan and control of the infection relies on large-scale administration of praziquantel .",...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "action potentials", "medicine and health sciences", "perturbation theory", "neural networks", "membrane potential", "electrophysiology", "neuroscience", "mathematics", "algebra", "quantum mechanics", "research and analysis methods", "computer and information sciences", "transfer functions",...	Coherent chaos in a recurrent neural network with structured connectivity	journal.pcbi.1006309	null	[ [ "Firing-rate fluctuations and irregular spiking are ubiquitous in the neocortex [1 , 2] .", "Furthermore this temporal variability is often observed to be correlated across spatial scales ranging from local cortical circuits to the entire brain: in local cortical circuits both in membrane potential fluctu...	[ "We present a simple model for coherent , spatially correlated chaos in a recurrent neural network .", "Networks of randomly connected neurons exhibit chaotic fluctuations and have been studied as a model for capturing the temporal variability of cortical activity .", "The dynamics generated by such networks , ...	[ "Neural activity observed in the neocortex is temporally variable , displaying irregular temporal fluctuations at every accessible level of measurement .", "Furthermore , these temporal fluctuations are often found to be spatially correlated whether at the scale of local measurements such as membrane potentials a...	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "blood cells", "inflammatory diseases", "innate immune system", "medicine and health sciences", "cardiomyopathies", "immune cells", "immune physiology", "cytokines", "pathology and laboratory medicine", "immunology", "tropical diseases", "parasitic diseases", "parasitic protozoans", "devel...	Differential Expression of Matrix Metalloproteinases 2, 9 and Cytokines by Neutrophils and Monocytes in the Clinical Forms of Chagas Disease	journal.pntd.0005284	null	[ [ "Chagas disease , a disease caused by the infection with Trypanosoma cruzi , was described by Carlos Chagas [1] over a century ago and is still a major public health problem in Latin America .", "There is a potential threat to other non-endemic countries , mainly in the United States , Europe and the West...	[ "Dilated cardiomyopathy , the most severe manifestation in chronic phase of Chagas disease , affects about 30% of patients and is characterized by myocardial dysfunction and interstitial fibrosis due to extracellular matrix ( ECM ) remodeling .", "ECM remodeling is regulated by proteolytic enzymes such as matrix ...	[ "Chagas disease , also known as American trypanosomiasis , is a neglected parasitic disease caused by the protozoan Trypanosoma cruzi .", "After the acute phase , a chronic debilitating disease is established and different clinical forms may develop .", "Dilated cardiomyopathy is the most severe alteration , af...	2017
[ "Introduction", "Model", "Results", "Discussion" ]	[ "somatosensory system", "linguistics", "medicine and health sciences", "social sciences", "neuroscience", "auditory pathway", "probability distribution", "mathematics", "geology", "sensory physiology", "vowels", "phonemes", "speech", "probability theory", "phonetics", "grammar", "aud...	What drives the perceptual change resulting from speech motor adaptation? Evaluation of hypotheses in a Bayesian modeling framework	journal.pcbi.1005942	null	[ [ "The influence of speech motor learning on speech perception was first reported by Shiller et al . [2] ( this study is called “S-09” henceforth ) .", "Motor learning was implemented by perturbing the auditory feedback of subjects when they were producing the fricative /s/: it consisted in shifting down th...	[ "Shifts in perceptual boundaries resulting from speech motor learning induced by perturbations of the auditory feedback were taken as evidence for the involvement of motor functions in auditory speech perception .", "Beyond this general statement , the precise mechanisms underlying this involvement are not yet fu...	[ "Experimental evidence suggest that motor learning influences categories in speech perception .", "These observations are consistent with studies of arm motor control showing that motor learning alters the perception of the arm location in the space , and that these perceptual changes are associated with increase...	2018
[ "Introduction", "Results", "Discussion", "Material and methods" ]	[ "medicine and health sciences", "action potentials", "neural networks", "membrane potential", "brain", "social sciences", "electrophysiology", "vertebrates", "neuroscience", "animals", "mammals", "primates", "network analysis", "vision", "sensory physiology", "computer and information ...	Microsaccade-rhythmic modulation of neural synchronization and coding within and across cortical areas V1 and V2	journal.pbio.2004132	null	[ [ "Perception is an active process [1–3] in which animals explore their environment through specific movements of their sensory organs .", "For most animals that rely on visual perception , particularly for primates , large and small saccadic eye movements play a critical role in visual exploration [4–6] ."...	[ "Primates sample their visual environment actively through saccades and microsaccades ( MSs ) .", "Saccadic eye movements not only modulate neural spike rates but might also affect temporal correlations ( synchrony ) among neurons .", "Neural synchrony plays a role in neural coding and modulates information tra...	[ "During visual exploration , we continuously move our eyes in a quick , coordinated manner several times a second to scan our environment .", "These movements are called saccades .", "Even while we fixate on a visual object , we unconsciously execute small saccades that are termed microsaccades ( MSs ) .", "D...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "computational biology/systems biology", "computational biology/genomics", "computational biology" ]	Decomposition of Gene Expression State Space Trajectories	journal.pcbi.1000626	null	[ [ "Our understanding of the molecular basis of a wide range of biological processes , including development , differentiation , and disease , has evolved significantly in recent years .", "Increasingly , we are coming to recognize that it is not single genes , but rather complex networks of genes , gene pro...	[ "Representing and analyzing complex networks remains a roadblock to creating dynamic network models of biological processes and pathways .", "The study of cell fate transitions can reveal much about the transcriptional regulatory programs that underlie these phenotypic changes and give rise to the coordinated pat...	[ "Understanding how cells differentiate from one state to another is a fundamental problem in biology with implications for better understanding evolution , the development of complex organisms from a single fertilized egg , and the etiology of human disease .", "One way to view these processes is to examine cells...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cytokines", "immunity", "bone marrow", "innate immunity", "immunology", "biology", "immune system" ]	Extramedullary Myelopoiesis in Malaria Depends on Mobilization of Myeloid-Restricted Progenitors by IFN-γ Induced Chemokines	journal.ppat.1003406	null	[ [ "Myeloid cells play essential roles in the control of infection such as that caused by malaria parasite , Plasmodium .", "Although the ultimate control of blood-stage malaria in mice depends on an adaptive immune system [1] , the removal of parasite-infected red blood cells requires an efficient early res...	[ "Resolution of a variety of acute bacterial and parasitic infections critically relies on the stimulation of myelopoiesis leading in cases to extramedullary hematopoiesis .", "Here , we report the isolation of the earliest myeloid-restricted progenitors in acute infection with the rodent malaria parasite , Plasmo...	[ "Malaria in man and in most animal models is accompanied by splenomegaly .", "At the same time , the spleen is the main organ for the control resolution of the parasitemia .", "This process initially depends mostly on the innate immune system and requires increased production of myeloid cells .", "We investig...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "biotechnology", "public health and epidemiology", "cell biology", "computational biology", "mus (mouse)", "rattus (rat)" ]	PPARα siRNA–Treated Expression Profiles Uncover the Causal Sufficiency Network for Compound-Induced Liver Hypertrophy	journal.pcbi.0030030	null	[ [ "Determining the pathways underlying drug-induced toxicity from genome-wide expression profiles is essential for drug development .", "Knowledge of the components of the identified pathways and their sufficiency order for toxicity is crucial for selecting mechanism-based biomarkers to assess the safety of...	[ "Uncovering pathways underlying drug-induced toxicity is a fundamental objective in the field of toxicogenomics .", "Developing mechanism-based toxicity biomarkers requires the identification of such novel pathways and the order of their sufficiency in causing a phenotypic response .", "Genome-wide RNA interfer...	[ "Approaches for discovering mechanisms of action and for identifying molecular biomarkers in biomedical research are evolving today , as the growing symbiosis with computational sciences becomes more widely appreciated .", "In fact , the combination of various new technologies has been pushing forward both fronti...	2007
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Immucillins ImmA and ImmH Are Effective and Non-toxic in the Treatment of Experimental Visceral Leishmaniasis	journal.pntd.0004297	null	[ [ "Visceral leishmaniasis ( VL ) is a neglected tropical disease [1] caused by Leishmania ( L . ) donovani in India and Central Africa , by Leishmania ( L . ) infantum in the Middle East , Central Asia , China and Mediterranean and by Leishmania ( L . ) infantum chagasi in America .", "Approximately 0 . 2–0...	[ "Immucillins ImmA ( IA ) , ImmH ( IH ) and SerMe-ImmH ( SMIH ) are synthetic deazapurine nucleoside analogues that inhibit Leishmania ( L . ) infantum chagasi and Leishmania ( L . ) amazonensis multiplication in vitro without macrophage toxicity .", "Immucillins are compared to the Glucantime standard drug in the...	[ "The IA , IH , and SMIH immucillins are known to impair the replication of promastigotes of L . ( L . ) infantum chagasi and L . ( L . ) amazonensis imucillins in vitro and impair the replication of intracellular amastigotes of L . ( L . ) infantum chagasi in vitro with no toxicity for macrophages .", "IA and IH ...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "biotechnology", "biochemistry", "biochemical simulations", "medicine", "infectious diseases", "viral hemorrhagic fevers", "drug research and development", "drugs and devices", "dengue fever", "neglected tropical diseases", "dengue", "biology", "computational biology", "viral diseases", ...	Sulfated Polysaccharide, Curdlan Sulfate, Efficiently Prevents Entry/Fusion and Restricts Antibody-Dependent Enhancement of Dengue Virus Infection In Vitro: A Possible Candidate for Clinical Application	journal.pntd.0002188	null	[ [ "Globally , an estimated 50–100 million people are infected with DENV each year [1] .", "Dengue is the most important mosquito-transmitted viral disease in the world , particularly in the tropical and subtropical countries [2] , [3] .", "The virus is transmitted to humans via the mosquito vectors , Ae...	[ "Curdlan sulfate ( CRDS ) , a sulfated 1→3-β-D glucan , previously shown to be a potent HIV entry inhibitor , is characterized in this study as a potent inhibitor of the Dengue virus ( DENV ) .", "CRDS was identified by in silico blind docking studies to exhibit binding potential to the envelope ( E ) protein of ...	[ "There is no specific approved antiviral and vaccine for treatment or prevention of dengue , an acute mosquito-transmitted viral disease that affects more than 50 million people each year .", "Dengue virus ( DENV ) entry is a critical step that establishes the infection and enables virus replication .", "Curdla...	2013
[ "Introduction", "Results", "Discussion", "Material and Methods" ]	[ "molecular cell biology", "biology", "radiobiology" ]	ATM Release at Resected Double-Strand Breaks Provides Heterochromatin Reconstitution to Facilitate Homologous Recombination	journal.pgen.1003667	null	[ [ "DNA double-strand breaks ( DSBs ) are among the most deleterious cellular lesions since they threaten genomic integrity and cell viability .", "To counteract cell degeneration and to preserve genomic integrity , a complex network of DSB repair and signaling processes has evolved [1]–[4] .", "Two main...	[ "Non-homologous end-joining ( NHEJ ) and homologous recombination ( HR ) represent the two main pathways for repairing DNA double-strand breaks ( DSBs ) .", "During the G2 phase of the mammalian cell cycle , both processes can operate and chromatin structure is one important factor which determines DSB repair pat...	[ "Double-strand breaks ( DSBs ) are critical DNA lesions because they can lead to cell death or , which is even more devastating , the formation of genomic rearrangements .", "Cells are equipped with two main pathways to repair such lesions , homologous recombination ( HR ) and non-homologous end-joining ( NHEJ ) ...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "epizootics", "taxonomy", "organismal evolution", "medicine and health sciences", "animal diseases", "pathology and laboratory medicine", "pathogens", "split-decomposition method", "immunology", "geographical locations", "microbiology", "viruses", "preventive medicine", "multiple alignment...	Persistence of Yellow fever virus outside the Amazon Basin, causing epidemics in Southeast Brazil, from 2016 to 2018	journal.pntd.0006538	null	[ [ "Yellow fever virus ( YFV ) ( family Flaviviridae , genus Flavivirus ) is the etiologic agent of yellow fever ( YF ) .", "In Brazil , the urban cycle has not occured since 1942 , but sylvatic yellow fever ( SYF ) occurs in the Amazon Basin ( S1A Fig ) in an enzootic cycle involving non-human primates ( NH...	[ "Yellow fever ( YF ) is endemic in the Brazilian Amazon Basin , and sporadic outbreaks take place outside the endemic area in Brazil .", "Since 2016 , YF epidemics have been occurring in Southeast Brazil , with more than 1 , 900 human cases and more than 1 , 600 epizooties of non-human primates ( NHPs ) reported ...	[ "Yellow fever ( YF ) is endemic in the Brazilian Amazon Basin , but sporadic outbreaks may take place outside this region .", "At the end of 2016 , YF epidemics have been occurring in Southeast Brazil , with thousands of human cases ( more than 1 , 900 ) and deaths of non-human primates ( NHPs ) reported so far ....	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious disease epidemiology", "spatial epidemiology", "microbiology", "bacterial diseases", "skin infections", "emerging infectious diseases", "clinical epidemiology", "neglected tropical diseases", "disease mapping", "infectious diseases", "buruli ulcer", "disease ecology",...	Geographic Distribution, Age Pattern and Sites of Lesions in a Cohort of Buruli Ulcer Patients from the Mapé Basin of Cameroon	journal.pntd.0002252	null	[ [ "Buruli ulcer ( BU ) , a neglected tropical disease ( NTD ) of the skin , is caused by Mycobacterium ulcerans [1] and if untreated , can lead to disability .", "Worldwide , local BU incidence rates are highest in West Africa and Australia , where the classical lineage of M . ulcerans is found [2]–[4] and ...	[ "Buruli ulcer ( BU ) , a neglected tropical disease of the skin , caused by Mycobacterium ulcerans , occurs most frequently in children in West Africa .", "Risk factors for BU include proximity to slow flowing water , poor wound care and not wearing protective clothing .", "Man-made alterations of the environme...	[ "Buruli ulcer ( BU ) is an infectious disease caused by Mycobacterium ulcerans that is affecting mostly children in endemic areas of West Africa .", "Proximity to slow flowing water is a risk factor , but the exact mode of transmission of BU remains unclear .", "Man-made environmental changes , such as sand min...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "engineering and technology", "enzymes", "signal processing", "signaling networks", "enzymology", "phosphatases", "systems science", "mathematics", "network analysis", "protein kinase signaling cascade", "computer and information sciences", "proteins", "dynamic response", "molecular evolut...	Enzyme Sequestration as a Tuning Point in Controlling Response Dynamics of Signalling Networks	journal.pcbi.1004918	null	[ [ "Molecular signalling networks enable cells to generate appropriate dynamical responses to external signals including pulsed , oscillatory , ultrasensitive , and adaptive dynamics [1 , 2] [3] .", "Such response dynamics are also implemented in human-engineered systems , motivating the use engineering prin...	[ "Signalling networks result from combinatorial interactions among many enzymes and scaffolding proteins .", "These complex systems generate response dynamics that are often essential for correct decision-making in cells .", "Uncovering biochemical design principles that underpin such response dynamics is a prer...	[ "Biological systems utilise signalling networks that are composed of multiple interacting proteins to process environmental information .", "The function of these networks is critical for cells to respond and adapt to their environment by converting environmental signals to appropriate cellular response dynamics ...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "molecular cell biology", "rna viruses", "viruslike particles", "sars", "virology", "viral classification", "biology", "microbiology", "viral diseases" ]	A Single Polar Residue and Distinct Membrane Topologies Impact the Function of the Infectious Bronchitis Coronavirus E Protein	journal.ppat.1002674	null	[ [ "Coronaviruses ( CoVs ) are enveloped , positive strand RNA viruses that infect a variety of mammalian and avian species .", "In humans , CoVs are responsible for nearly 20% of common cold cases .", "CoVs can also lead to more serious disease as seen during the outbreak of the severe acute respiratory...	[ "The coronavirus E protein is a small membrane protein with a single predicted hydrophobic domain ( HD ) , and has a poorly defined role in infection .", "The E protein is thought to promote virion assembly , which occurs in the Golgi region of infected cells .", "It has also been implicated in the release of i...	[ "Coronaviruses are enveloped viruses that bud and assemble intracellularly , and therefore must use the host secretory pathway for release .", "Coronavirus E is a small protein that contains a single predicted hydrophobic domain and is targeted to the Golgi region .", "The E protein has been implicated in the a...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Genetic Architecture of Abdominal Pigmentation in Drosophila melanogaster	journal.pgen.1005163	null	[ [ "Body pigmentation is a conspicuous trait that is variable within species , giving rise to natural variation , polyphenism and sexual dimorphism [1–4] .", "It also varies between species , contributing to species recognition , mate choice , thermoregulation , protection ( warning signals ) , mimicry , and...	[ "Pigmentation varies within and between species and is often adaptive .", "The amount of pigmentation on the abdomen of Drosophila melanogaster is a relatively simple morphological trait , which serves as a model for mapping the genetic basis of variation in complex phenotypes .", "Here , we assessed natural va...	[ "Body pigmentation contributes to the spectacular biodiversity present in nature and mediates mate choice , mimicry , and physiological functions such as thermoregulation and UV resistance .", "Thus , pigmentation is a significant contributor to fitness .", "In order to understand how complex traits such as pig...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "public health and epidemiology", "epidemiology", "protozoology", "biology", "microbiology", "population biology" ]	Molecular Mechanisms of Drug Resistance in Natural Leishmania Populations Vary with Genetic Background	journal.pntd.0001514	null	[ [ "Leishmania , a protozoan parasite transmitted by phlebotomine sand flies , causes a neglected infectious disease commonly referred to as leishmaniasis .", "The species Leishmania ( Leishmania ) donovani is the causative agent of visceral leishmaniasis ( VL ) or kala-azar , the most severe form of leishma...	[ "The evolution of drug-resistance in pathogens is a major global health threat .", "Elucidating the molecular basis of pathogen drug-resistance has been the focus of many studies but rarely is it known whether a drug-resistance mechanism identified is universal for the studied pathogen; it has seldom been clarifi...	[ "Drug resistance is a serious problem that strikes at the core of infectious disease control .", "The mechanisms developed by pathogens to become resistant against existing drug treatments have been studied for many years but these studies have frequently scrutinized a few lines of the pathogen and rarely is it k...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "behavioral neuroscience", "cognitive neuroscience", "computational neuroscience", "biology and life sciences", "computational biology", "neuroscience", "learning and memory" ]	Estimating Location without External Cues	journal.pcbi.1003927	null	[ [ "Accurate spatial navigation is crucial to animal survival .", "Localization is the process of determining current location , critical for many navigation behaviours .", "Starting from an unknown location and direction ( jointly called “pose” ) , the ability to localize is thought to depend on the det...	[ "The ability to determine one's location is fundamental to spatial navigation .", "Here , it is shown that localization is theoretically possible without the use of external cues , and without knowledge of initial position or orientation .", "With only error-prone self-motion estimates as input , a fully disori...	[ "Spatial navigation is one of the most important functions of animal brains .", "Multiple regions and cell types encode the current location in mammalian brains , but the underlying interactions between sensory and memory information remain unclear .", "Recent experimental and theoretical evidence have been fou...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	SAMHD1 Inhibits LINE-1 Retrotransposition by Promoting Stress Granule Formation	journal.pgen.1005367	null	[ [ "SAM domain and HD domain containing protein 1 ( SAMHD1 ) was first identified as an interferonγ-induced protein in macrophages and dendritic cells , and was regarded as a negative regulator of cellular innate immunity [1] .", "Mutations in SAMHD1 were later found to associate with the Aicardi-Goutieres s...	[ "The SAM domain and HD domain containing protein 1 ( SAMHD1 ) inhibits retroviruses , DNA viruses and long interspersed element 1 ( LINE-1 ) .", "Given that in dividing cells , SAMHD1 loses its antiviral function yet still potently restricts LINE-1 , we propose that , instead of blocking viral DNA synthesis by vi...	[ "Long interspersed element 1 ( LINE-1 or L1 ) comprises 17% of human genome , and has played a major role in shaping the evolution of human genome .", "Approximately 100 copies of LINE-1 are still active in an average individual genome .", "Movement of these LINE-1 sequences to new loci in the genome has the po...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "invertebrates", "medicine and health sciences", "rna interference", "cell cycle and cell division", "tor signaling", "cell processes", "animals", "endocrine physiology", "animal models", "developmental biology", "drosophila melanogaster", "model organisms", "experimental organism systems", ...	Nutrient-Dependent Endocycling in Steroidogenic Tissue Dictates Timing of Metamorphosis in Drosophila melanogaster	journal.pgen.1006583	null	[ [ "Animals are heterotrophic and need to ingest nutrients from the environment during postembryonic development .", "Both availability and quality of food therefore are critical for timing animal growth and maturation .", "Since differentiation and functional maturation of each tissue are coordinated by...	[ "Many animals have an intrinsic growth checkpoint during juvenile development , after which an irreversible decision is made to upregulate steroidogenesis , triggering the metamorphic juvenile-to-adult transition .", "However , a molecular process underlying such a critical developmental decision remains obscure ...	[ "Onset of sexual maturation constitutes a point of no return in animals; once this life-changing decision is made , upregulation of steroidogenesis leads to irreversible juvenile-to-adult transition in humans and insects alike .", "While nutrient signals contributing to this decision-making process have been well...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "medicine and health sciences", "chemical compounds", "pathology and laboratory medicine", "aliphatic amino acids", "caenorhabditis", "atrophy", "neuroscience", "organic compounds", "animals", "parasitic diseases", "motor neurons", "nematode infections", "animal models", ...	Immobility in the sedentary plant-parasitic nematode H. glycines is associated with remodeling of neuromuscular tissue	journal.ppat.1007198	null	[ [ "The sedentary plant-parasitic nematodes are among the most damaging pathogens to agricultural crop production [1] .", "For example , the soybean cyst nematode , Heterodera glycines , accounts for over a billion dollars in yield loss yearly [2] .", "H . glycines hatches as an infective , mobile second...	[ "The sedentary plant-parasitic nematodes are considered among the most economically damaging pathogens of plants .", "Following infection and the establishment of a feeding site , sedentary nematodes become immobile .", "Loss of mobility is reversed in adult males while females never regain mobility .", "The ...	[ "The sedentary plant-parasitic nematodes are an economically devastating group of pathogens .", "They are capable of modifying their host’s metabolism by establishing a permanent feeding site within the plant roots .", "Following infection , sedentary nematodes remain at their feeding site where they are only c...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "organismal evolution", "haplotypes", "animal genetics", "genetic polymorphism", "animal evolution", "genetics", "population genetics", "biology", "evolutionary biology", "zoology", "evolutionary genetics", "genetics and genomics", "animal phylogenetics" ]	Ever-Young Sex Chromosomes in European Tree Frogs	journal.pbio.1001062	null	[ [ "Here we use European tree frogs to test contrasting predictions from these two", "models .", "All Eurasian tree frogs have homomorphic sex chromosomes [27] .", "Male", "heterogamety was first evidenced in Hyla arborea by sex", "differences in the allelic distribution of microsatellite mar...	[ "Non-recombining sex chromosomes are expected to undergo evolutionary decay ,", "ending up genetically degenerated , as has happened in birds and mammals .", "Why are", "then sex chromosomes so often homomorphic in cold-blooded vertebrates ?", "One", "possible explanation is a high rate of turnover events...	[ "Non-recombining sex chromosomes , such as the Y chromosome , are expected to", "degenerate over evolutionary times because they accumulate deleterious mutations", "that cannot be corrected by recombination with a pristine copy .", "In most", "cold-blooded vertebrates , such as frogs , however , sex chromos...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "social influence", "learning", "decision making", "experimental design", "social sciences", "neuroscience", "learning and memory", "research design", "cognitive psychology", "mathematics", "forecasting", "statistics (mathematics)", "cognition", "research and analysis methods", "human le...	Learning about and from others' prudence, impatience or laziness: The computational bases of attitude alignment	journal.pcbi.1005422	null	[ [ "Subjective traits or attitudes such as \"prudence\" , \"impatience\" or \"laziness\" are key determinants of goal-directed behaviour .", "This is because they determine how people arbitrate between canonical but conflicting decision dimensions , e . g . , the prospect of reward and costs such as risk , d...	[ "Peoples' subjective attitude towards costs such as , e . g . , risk , delay or effort are key determinants of inter-individual differences in goal-directed behaviour .", "Thus , the ability to learn about others' prudent , impatient or lazy attitudes is likely to be critical for social interactions .", "Conver...	[ "What do people learn from observing others' attitudes , such as \"prudence\" , \"impatience\" or \"laziness\" ?", "Rather than viewing these attitudes as examples of highly subjective personality traits , we assume that they derive from uncertain ( and mostly implicit ) beliefs about how to best weigh risks , de...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology/persistence and latency", "cell biology/cell signaling", "cell biology/developmental molecular mechanisms", "cell biology/microbial growth and development", "infectious diseases/viral infections", "virology/viruses and cancer", "oncology/hematological malignancies", "molecular biology/transl...	Activation of Host Translational Control Pathways by a Viral Developmental Switch	journal.ppat.1000334	null	[ [ "Regulation of gene expression at the level of mRNA translation is important for the control of numerous biological processes including cell growth , differentiation , development and the response to environmental stress [1] , [2] .", "Unlike prokaryotes , the vast majority of eukaryotic mRNAs are unable ...	[ "In response to numerous signals , latent herpesvirus genomes abruptly switch their developmental program , aborting stable host–cell colonization in favor of productive viral replication that ultimately destroys the cell .", "To achieve a rapid gene expression transition , newly minted capped , polyadenylated vi...	[ "Kaposi's sarcoma-associated herpesvirus ( KSHV ) is an important human pathogen and , like all herpesviruses , establishes a state of permanent residency in the infected host called latency .", "Major sites of KSHV latency are cells of the immune system and cells lining blood vessels .", "In individuals with w...	2009
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "bac cloning", "pathogens", "cloning", "vector cloning", "plant science", "rice", "experimental organism systems", "plant pathology", "molecular genetics", "molecular biology techniques", "plants", "research and analysis ...	Components of Brachypodium distachyon resistance to nonadapted wheat stripe rust pathogens are simply inherited	journal.pgen.1007636	null	[ [ "Only a limited number of phytopathogen species are adapted to paracitise a given plant species .", "The numerous phyopathogens unable of colonising a plant species ( nonadapted ) are often suppressed by an active plant resistance response upon challenge [1 , 2 , 3 , 4] .", "Plant resistance against n...	[ "Phytopathogens have a limited range of host plant species that they can successfully parasitise ie .", "that they are adapted for .", "Infection of plants by nonadapted pathogens often results in an active resistance response that is relatively poorly characterised because phenotypic variation in this response...	[ "Plant pathogens are specialists and can colonise only a limited number of plant species ( hosts ) .", "Pathogen infection of a plant that is not a host of the disease often results in an active plant defense response .", "This poorly characterised defense response is durable as phytopathogens rarely successful...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "skin", "plant anatomy", "medicine and health sciences", "integumentary system", "cell cycle and cell division", "cell processes", "cell differentiation", "membrane proteins", "pollen", "developmental biology", "plant science", "epidermis", "cellular structures and organelles", "flower ana...	Control of Anther Cell Differentiation by the Small Protein Ligand TPD1 and Its Receptor EMS1 in Arabidopsis	journal.pgen.1006147	null	[ [ "Successful sexual reproduction depends on the specification of different types of somatic and reproductive cells that give rise to eggs and sperm in both plants and animals .", "The anther is where male gametophytes ( pollen ) are produced in seed plants; it typically has four lobes ( microsporangia ) or...	[ "A fundamental feature of sexual reproduction in plants and animals is the specification of reproductive cells that conduct meiosis to form gametes , and the associated somatic cells that provide nutrition and developmental cues to ensure successful gamete production .", "The anther , which is the male reproducti...	[ "The differentiation of distinct somatic and reproductive cells in flowers is required for the successful sexual reproduction of plants .", "The anther produces reproductive microsporocytes ( pollen mother cells ) that give rise to pollen ( male gametophytes ) , as well as surrounding somatic cells ( particularly...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/animal genetics", "developmental biology/stem cells", "developmental biology/morphogenesis and cell biology", "developmental biology/cell differentiation", "genetics and genomics/gene function", "genetics and genomics/pharmacogenomics", "developmental biology/developmental molecul...	Defects in ErbB-Dependent Establishment of Adult Melanocyte Stem Cells Reveal Independent Origins for Embryonic and Regeneration Melanocytes	journal.pgen.1000544	null	[ [ "As with other teleosts , the zebrafish has a remarkable ability to regenerate a wide range of tissues and organs including fins [1] , heart [2] , and retina [3]–[5] .", "Epimorphic regeneration , involving the cell division and differentiation of undifferentiated post-embryonic precursors , or adult stem...	[ "Adult stem cells are responsible for maintaining and repairing tissues during the life of an organism .", "Tissue repair in humans , however , is limited compared to the regenerative capabilities of other vertebrates , such as the zebrafish ( Danio rerio ) .", "An understanding of stem cell mechanisms , such a...	[ "The promise of regenerative medicine lies in the ability to find or create stem cells that can be manipulated to replace damaged tissues and organs .", "Such ability requires an understanding of how adult stem cells are established and then later recruited to regenerate different tissues .", "Here , we study t...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "pathology and laboratory medicine", "immunology", "microbiology", "parasitology", "white blood cells", "inflammation", "animal cells", "pathogenesis", "immune response", "immune system", "cell biology", "monocytes", "immun...	Ly6Chi Monocyte Recruitment Is Responsible for Th2 Associated Host-Protective Macrophage Accumulation in Liver Inflammation due to Schistosomiasis	journal.ppat.1004282	null	[ [ "Schistosomiasis is a complex multiorgan disease caused by infection with helminth parasites of the genus Schistosoma , and characterized by the development of granulomatous lesions around parasite eggs trapped within organs such as the liver and intestine .", "Granulomas are , by definition , macrophage-...	[ "Accumulation of M2 macrophages in the liver , within the context of a strong Th2 response , is a hallmark of infection with the parasitic helminth , Schistosoma mansoni , but the origin of these cells is unclear .", "To explore this , we examined the relatedness of macrophages to monocytes in this setting .", ...	[ "Schistosomiasis is an important neglected tropical disease caused by parasitic worms of the genus Schistosoma .", "During infection with S . mansoni , parasite eggs become trapped in the liver and elicit granulomatous inflammation characterized by accumulations of immune cells intermixed with liver cells around ...	2014
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "neuroscience" ]	Circadian Remodeling of Neuronal Circuits Involved in Rhythmic Behavior	journal.pbio.0060069	The circadian clock controls a wide array of biological phenomena ranging from basal transcription to overt behavior. Now, new evidence shows that the clock affects a striking remodeling of the circuit controlling rest-activity cycles inDrosophila.	[ [ "Many organisms display daily rest–activity cycles , which are reminiscent of the sleep–wake cycles observed in humans .", "This rhythmic activity is sustained even in the absence of environmental light-dark cues , revealing its endogenous origin .", "Along the years , many of the components of the ci...	[ "Clock output pathways are central to convey timing information from the circadian clock to a diversity of physiological systems , ranging from cell-autonomous processes to behavior .", "While the molecular mechanisms that generate and sustain rhythmicity at the cellular level are well understood , it is unclear ...	[ "Circadian systems evolved as a mechanism that allows organisms to adapt to the environmental changes in light and dark which occur as a consequence of the rotation of Earth .", "Because of its unique repertoire of genetic tools , Drosophila is a well established model for the study of the circadian clock .", "...	2008
[ "Introduction", "Materials and Methods", "Results and Discussion" ]	[ "infectious diseases/neglected tropical diseases", "infectious diseases/tropical and travel-associated diseases", "microbiology/parasitology" ]	Stage-Specific Adhesion of Leishmania Promastigotes to Sand Fly Midguts Assessed Using an Improved Comparative Binding Assay	journal.pntd.0000816	null	[ [ "Medically important protozoan parasites of the genus Leishmania have a two host life-cycle , alternating between various mammalian hosts and female haematophagous phlebotomine sand flies .", "The life-cycle within the sand fly gut is complex , varies between subgenera Leishmania and Viannia , and include...	[ "The binding of Leishmania promastigotes to the midgut epithelium is regarded as an essential part of the life-cycle in the sand fly vector , enabling the parasites to persist beyond the initial blood meal phase and establish the infection .", "However , the precise nature of the promastigote stage ( s ) that med...	[ "Many infectious diseases such as leishmaniasis are transmitted to people by biting insects , in this case by female sand flies .", "To control this and similar diseases we need to understand why particular species of sand fly transmit particular species of Leishmania .", "One important feature of the Leishmani...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cancer genetics", "genetics", "biology", "genetics and genomics" ]	Synergistic Interaction of Rnf8 and p53 in the Protection against Genomic Instability and Tumorigenesis	journal.pgen.1003259	null	[ [ "DNA double strand breaks ( DSBs ) are among the most deleterious type of DNA lesions .", "They can be generated either by extrinsic factors such as ionizing radiation ( IR ) or during normal physiological processes such as class switch recombination ( CSR ) and meiosis [1] , [2] .", "DSBs are highly ...	[ "Rnf8 is an E3 ubiquitin ligase that plays a key role in the DNA damage response as well as in the maintenance of telomeres and chromatin remodeling .", "Rnf8−/− mice exhibit developmental defects and increased susceptibility to tumorigenesis .", "We observed that levels of p53 , a central regulator of the cell...	[ "DNA double-strand breaks are the most dangerous type of DNA lesions that can occur in cells .", "Failure to repair these breaks quickly and efficiently can result in either cell death or genomic instability and eventually malignant transformation .", "Rnf8 and p53 are key proteins in the DNA damage response ."...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "cell biology/nuclear structure and function", "cell biology/cell growth and division", "cell biology/developmental molecular mechanisms", "molecular biology" ]	Direct Binding of pRb/E2F-2 to GATA-1 Regulates Maturation and Terminal Cell Division during Erythropoiesis	journal.pbio.1000123	Cell differentiation is often coupled with cell cycle arrest. Here, we show that direct binding of the erythroid transcription factor GATA-1 to the retinoblastoma protein and the pRb/E2F transcription factor complex is critical for red blood cell formation.	[ [ "With more than 100 billion red blood cells generated every day , the erythroid lineage has the largest quantitative output of cell production in adult mammals .", "This impressive capability requires a pattern of cell proliferation closely related to that of embryonic cells followed by ultimate inhibitio...	[ "How cell proliferation subsides as cells terminally differentiate remains largely enigmatic , although this phenomenon is central to the existence of multicellular organisms .", "Here , we show that GATA-1 , the master transcription factor of erythropoiesis , forms a tricomplex with the retinoblastoma protein ( ...	[ "Red blood cell production , or erythropoiesis , proceeds by a tight coupling of proliferation and differentiation .", "The earliest erythroid progenitor identifiable possesses remnant stem cell characteristics as it both self-renews and differentiates .", "Each progenitor gives rise to more than 10 , 000 cells...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology", "sensory systems", "neuroscience", "neurophysiology" ]	Strength of Gamma Rhythm Depends on Normalization	journal.pbio.1001477	Manipulating a divisive normalization mechanism independently of attention in monkeys suggests that gamma power reflects excitation-inhibition interactions rather than plays a functional role in attentional processing.	[ [ "Modulations in gamma rhythms have consistently been observed during high-level cognitive processes such as attention [1]–[5] , memory [6] , feature-binding [7] , [8] , or conscious perception [9] , leading to the suggestion that these rhythms play a functional role in high-level cognitive processing [7] , [1...	[ "Neuronal assemblies often exhibit stimulus-induced rhythmic activity in the gamma range ( 30–80 Hz ) , whose magnitude depends on the attentional load .", "This has led to the suggestion that gamma rhythms form dynamic communication channels across cortical areas processing the features of behaviorally relevant ...	[ "Brain signals often show a stimulus-induced rhythm in the “gamma” band ( 30–80 Hz ) whose magnitude depends on attentional load , leading to suggestions that gamma rhythm plays a functional role in routing signals across cortical areas .", "However , gamma power also depends on simple stimulus features such as s...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Mycobacterium tuberculosis Type VII Secreted Effector EsxH Targets Host ESCRT to Impair Trafficking	journal.ppat.1003734	null	[ [ "An important virulence property of Mycobacterium tuberculosis ( Mtb ) - the causative agent of the disease tuberculosis- is its ability to avoid delivery to the lysosome .", "It has long been appreciated that Mtb alters phagosome maturation , such that internalized bacteria are not transported to the lys...	[ "Mycobacterium tuberculosis ( Mtb ) disrupts anti-microbial pathways of macrophages , cells that normally kill bacteria .", "Over 40 years ago , D'Arcy Hart showed that Mtb avoids delivery to lysosomes , but the molecular mechanisms that allow Mtb to elude lysosomal degradation are poorly understood .", "Specia...	[ "Mycobacterium tuberculosis ( Mtb ) causes the disease tuberculosis , one of the world's most deadly infections .", "The host immune system can't eradicate Mtb because it grows within macrophages , cells that normally kill bacteria .", "One of the intracellular survival strategies of Mtb is to avoid delivery to...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "rabies", "veterinary diseases", "veterinary epidemiology", "zoonotic diseases", "veterinary science" ]	Dog Bites in Humans and Estimating Human Rabies Mortality in Rabies Endemic Areas of Bhutan	journal.pntd.0001391	null	[ [ "Dog bites in human are a serious public health problem and have been well documented worldwide [1] , [2] .", "In the United States , 4 . 7 million people were estimated to have been bitten by dogs in 1994 ( an incidence rate of 16 . 1/1000 in adults and 24 . 5/1000 in children ) , of whom 800 , 000 requi...	[ "Dog bites in humans are a public health problem worldwide .", "The issues of increasing stray dog populations , rabies outbreaks , and the risk of dogs biting humans have been frequently reported by the media in Bhutan .", "This study aimed to estimate the bite incidence and identify the risk factors for dog b...	[ "Dog bites in humans are a public health problem worldwide .", "We conducted a hospital based questionnaire survey and described the incidence and risk factors for human dog bites in Bhutan .", "We also estimated the human death rate attributable to rabies in two rabies endemic areas of south Bhutan .", "Our ...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	CXCR3-Dependent CD4+ T Cells Are Required to Activate Inflammatory Monocytes for Defense against Intestinal Infection	journal.ppat.1003706	null	[ [ "The intestinal mucosa is a critical effector site for elimination of enteric pathogens .", "Toxoplasma gondii , a ubiquitous protozoan parasite , is a prime example of such a pathogen .", "Mammals are infected with T . gondii primarily by the ingestion of tissue cysts from undercooked meat or oocysts...	[ "Chemokines and their receptors play a critical role in orchestrating immunity to microbial pathogens , including the orally acquired Th1-inducing protozoan parasite Toxoplasma gondii .", "Chemokine receptor CXCR3 is associated with Th1 responses , and here we use bicistronic CXCR3-eGFP knock-in reporter mice to ...	[ "Inflammatory monocytes have recently emerged as important effectors in intestinal defense against enteric pathogens , but requirements for their activation are poorly defined .", "Here we use the protozoan Toxoplasma gondii , an orally acquired Th1-inducing pathogen , to study the requirements for inflammatory m...	2013
[ "Introduction", "Results", "Discussion", "Material and Methods" ]	[ "chemical biology", "ribozymes", "metagenomics", "structural genomics", "sequence analysis", "rna structure", "comparative genomics", "biology", "biophysics", "biochemistry", "rna", "rna processing", "nucleic acids", "genomics", "computational biology", "macromolecular structure analys...	Identification of Hammerhead Ribozymes in All Domains of Life Reveals Novel Structural Variations	journal.pcbi.1002031	null	[ [ "Hammerhead ribozymes [1] represent one of five distinct structural classes of natural self-cleaving RNAs identified to date [2] .", "The first hammerheads were discovered in viroids and plant satellite RNA viruses where they process RNA transcripts containing multimeric genomes to yield individual genomi...	[ "Hammerhead ribozymes are small self-cleaving RNAs that promote strand scission by internal phosphoester transfer .", "Comparative sequence analysis was used to identify numerous additional representatives of this ribozyme class than were previously known , including the first representatives in fungi and archaea...	[ "The expanding diversity of noncoding RNA discoveries is revealing a broader spectrum of roles RNA plays in cellular signaling and in biochemical functions .", "These discoveries in part are being facilitated by the expanding collection of genomic sequence data and by computational methods used to search for nove...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "machine learning algorithms", "applied mathematics", "neuroscience", "simulation and modeling", "membrane proteins", "algorithms", "mathematics", "stem cells", "artificial intelligence", "genome analysis", "cellular structures and organelles", "research and analysis methods", "computer and ...	Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics	journal.pcbi.1004920	null	[ [ "Cell biology is currently undergoing a data-driven paradigm shift [1] .", "Molecular biology tools , imaging , biochemical analyses and omics technologies , enable cell biologists to track the complexity of many fundamental processes such as signal transduction , gene regulation , protein interactions an...	[ "Sub-cellular localisation of proteins is an essential post-translational regulatory mechanism that can be assayed using high-throughput mass spectrometry ( MS ) .", "These MS-based spatial proteomics experiments enable us to pinpoint the sub-cellular distribution of thousands of proteins in a specific system und...	[ "Sub-cellular localisation of proteins is critical to their function in all cellular processes; proteins localising to their intended micro-environment , e . g organelles , vesicles or macro-molecular complexes , will meet the interaction partners and biochemical conditions suitable to pursue their molecular functi...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "immunology/immunomodulation", "immunology/leukocyte signaling and gene expression", "immunology/immune response" ]	Functional Impairment of Human Myeloid Dendritic Cells during Schistosoma haematobium Infection	journal.pntd.0000667	null	[ [ "Chronic parasitic helminth infections are generally associated with a T helper 2 ( Th2 ) -like immunological profile as well as immune hyporesponsiveness [1] , [2] .", "The latter characteristic is probably the result of immune evasion strategies that these pathogens have developed to ensure long term su...	[ "Chronic Schistosoma infection is often characterized by a state of T cell hyporesponsiveness of the host .", "Suppression of dendritic cell ( DC ) function could be one of the mechanisms underlying this phenomenon , since Schistosoma antigens are potent modulators of dendritic cell function in vitro .", "Yet ,...	[ "A key feature of schistosomiasis , as well as of other systemic helminth infections , is their chronic nature .", "This reflects the successful evasion and suppression of host immune responses by the parasites .", "One of the mechanisms that could underlie this phenomenon is modulation of the dendritic cells (...	2010
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "trachoma", "public health and epidemiology", "epidemiology", "infectious disease epidemiology", "ophthalmology", "neglected tropical diseases", "biology", "population biology" ]	Definitions and Standardization of a New Grading Scheme for Eyelid Contour Abnormalities after Trichiasis Surgery	journal.pntd.0001713	null	[ [ "Trichiasis surgery is a critical component of the “SAFE” strategy , which is promoted by the World Health Organization ( WHO ) to eliminate blinding trachoma worldwide .", "Trachomatous trichiasis ( TT ) is a late-stage result of trachoma , a disease caused by ocular infection with Chlamydia trachomatis ...	[ "Clear definitions of outcomes following trichiasis surgery are critical for planning program evaluations and for identifying ways to improve trichiasis surgery .", "Eyelid contour abnormality is an important adverse outcome of surgery; however , no standard method has been described to categorize eyelid contour ...	[ "Approximately 8 million individuals worldwide suffer from trichiasis , a condition characterized by in-turned lashes that rub against the eye .", "Trichiasis is caused by repeated or prolonged ocular infection with Chlamydia trachomatis .", "Surgery is available to correct in-turned lashes .", "In most progr...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "parasite groups", "medicine and health sciences", "vesicles", "plasmodium", "gametocytes", "parasitic diseases", "parasitology", "germ cells", "membrane proteins", "developmental biology", "apicomplexa", "cellular structures and organelles", "animal cells", "life cycles", "cell membrane...	A Putative Small Solute Transporter Is Responsible for the Secretion of G377 and TRAP-Containing Secretory Vesicles during Plasmodium Gamete Egress and Sporozoite Motility	journal.ppat.1005734	null	[ [ "Malaria is a vector-borne disease caused by parasitic protozoans from the genus Plasmodium .", "Although infection and mortality rates are decreasing , 2015 still showed more than 200 million infections and over 400 , 000 deaths , often children ( World Malaria Report 2015 , WHO ) .", "With approxima...	[ "Regulated protein secretion is required for malaria parasite life cycle progression and transmission between the mammalian host and mosquito vector .", "During transmission from the host to the vector , exocytosis of highly specialised secretory vesicles , such as osmiophilic bodies , is key to the dissolution o...	[ "Transmission of the malaria parasite between mosquito and host requires two different life cycle stages—the gametocyte and the sporozoite .", "In both parasite forms , transmission is dependent on exocytosis of stage-specific vesicles .", "In gametocytes these vesicles release proteins allowing egress from red...	2016
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "pathology and laboratory medicine", "fungal genetics", "pathogens", "immunology", "microbiology", "animals", "fungi", "fungal diseases", "insect vectors", "fungal pathogens", "infectious diseases", "lipids", "mycology", "fats", "medic...	Entomopathogenic fungal infection leads to temporospatial modulation of the mosquito immune system	journal.pntd.0006433	null	[ [ "The global increase in new and re-emergent vector-borne diseases has put into perspective once more the need for effective methods of vector control .", "Although insecticide-based interventions to manage mosquito populations remain important components of vector control programs , the use of biological ...	[ "Alternative methods of mosquito control are needed to tackle the rising burden of mosquito-borne diseases while minimizing the use of synthetic insecticides , which are threatened by the rapid increase in insecticide resistance in mosquito populations .", "Fungal biopesticides show great promise as potential alt...	[ "Fungal biopesticides constitute potential alternative methods of vector control to tackle the rising burden of mosquito-borne diseases and the development of insecticide resistance in mosquitoes .", "Insect-fungi interactions represent an intricate co-evolutionary arms race between the invading pathogen and its ...	2018

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