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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" ]	[]	CDK8-Cyclin C Mediates Nutritional Regulation of Developmental Transitions through the Ecdysone Receptor in Drosophila	journal.pbio.1002207	During the larval-pupal transition in Drosophila, CDK8-CycC helps to link nutrient intake to development by activating ecdysone receptor-dependent transcription and to fat metabolism by inhibiting SREBP-activated gene expression.	[ [ "In animals , the amount of juvenile growth is controlled by the coordinated timing of maturation and growth rate , which are strongly influenced by the environmental factors such as nutrient availability [1 , 2] .", "This is particularly evident in arthropods , such as insects , arachnids and crustaceans...	[ "The steroid hormone ecdysone and its receptor ( EcR ) play critical roles in orchestrating developmental transitions in arthropods .", "However , the mechanism by which EcR integrates nutritional and developmental cues to correctly activate transcription remains poorly understood .", "Here , we show that EcR-d...	[ "Arthropods are estimated to account for over 80% of animal species on earth .", "Characterized by their rigid exoskeletons , juvenile arthropods must periodically shed their thick outer cuticles by molting in order to grow .", "The steroid hormone ecdysone plays an essential role in regulating the timing of de...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "exopolysaccharides", "medicine and health sciences", "pathology and laboratory medicine", "pathogens", "microbiology", "epithelial cells", "materials science", "enterococcus", "macromolecules", "bacteria", "cellular structures and organelles", "bacterial pathogens", "digestive system", "p...	PolyGlcNAc-containing exopolymers enable surface penetration by non-motile Enterococcus faecalis	journal.ppat.1007571	null	[ [ "Microbes use a variety of strategies to obtain nutrients and ensure survival .", "While motility could be used as a means for accessing nutrient sources , non-motile bacterial species require unconventional mechanisms to accomplish this goal .", "Enterococcus faecalis is a non-motile , facultative an...	[ "Bacterial pathogens have evolved strategies that enable them to invade tissues and spread within the host .", "Enterococcus faecalis is a leading cause of local and disseminated multidrug-resistant hospital infections , but the molecular mechanisms used by this non-motile bacterium to penetrate surfaces and tran...	[ "Enterococcus faecalis is a microbial inhabitant of the human gastrointestinal tract that can cause lethal infections .", "Typically classified as a non-motile bacterium , E . faecalis can readily migrate and translocate across epithelial barriers to invade distant organs .", "Nevertheless , the molecular pathw...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases/protozoal infections", "infectious diseases/neglected tropical diseases", "infectious diseases/tropical and travel-associated diseases", "infectious diseases/epidemiology and control of infectious diseases" ]	Prevalence, Clinical Staging and Risk for Blood-Borne Transmission of Chagas Disease among Latin American Migrants in Geneva, Switzerland	journal.pntd.0000592	null	[ [ "Chagas disease is a zoonosis caused by Trypanosoma cruzi ( T . cruzi ) , a flagellated protozoa transmitted to humans by the faeces of blood-sucking triatomine bugs .", "The parasite can also be acquired by blood transfusion , organ transplant , ingestion of food contaminated with triatomines or their fe...	[ "Migration of Latin Americans to the USA , Canada and Europe has modified Chagas disease distribution , but data on imported cases and on risks of local transmission remain scarce .", "We assessed the prevalence and risk factors for Chagas disease , staged the disease and evaluated attitudes towards blood transfu...	[ "Chagas disease , a parasitic disease caused by Trypanosoma cruzi , is a leading cause of cardiac and digestive tract disorders in Mexico , Central and South America .", "An increasing number of cases have recently been reported in North America and Europe due to international human migration , but data outside L...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/bacterial infections", "microbiology/cellular microbiology and pathogenesis", "microbiology/innate immunity" ]	Staphylococcus epidermidis Strategies to Avoid Killing by Human Neutrophils	journal.ppat.1001133	null	[ [ "Staphylococcus epidermidis colonizes the epithelial surfaces of every human being .", "Furthermore , it is one of the most frequent causes of nosocomial infections .", "In addition to the abundant prevalence of S . epidermidis on the human skin , this high incidence is mainly due to the exceptional c...	[ "Staphylococcus epidermidis is a leading nosocomial pathogen .", "In contrast to its more aggressive relative S . aureus , it causes chronic rather than acute infections .", "In highly virulent S . aureus , phenol-soluble modulins ( PSMs ) contribute significantly to immune evasion and aggressive virulence by t...	[ "Staphylococcus epidermidis frequently causes chronic infections , indicating pronounced capacity to evade host defenses .", "However , S . epidermidis is in general much less aggressive than its close relative , S . aureus .", "Here we identify molecular underpinnings of that discrepancy by showing that S . ep...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "dna metabolism", "chemical compounds", "oxidative stress", "organic compounds", "sulfur", "plasmid construction", "organisms", "physiological processes", "amino acids", "dna construction", "dna", "molecular biology techniques", "bacteria", "cysteine", "...	Mycobacterium tuberculosis Thioredoxin Reductase Is Essential for Thiol Redox Homeostasis but Plays a Minor Role in Antioxidant Defense	journal.ppat.1005675	null	[ [ "Endogenous oxidative stress represents an inevitable challenge for microbes adapted to an aerobic lifestyle [1] .", "In addition , pathogens like Mycobacterium tuberculosis ( Mtb ) are confronted with exogenous oxidative stress imposed by the host [2] .", "The production of antimicrobial oxidants is ...	[ "Mycobacterium tuberculosis ( Mtb ) must cope with exogenous oxidative stress imposed by the host .", "Unlike other antioxidant enzymes , Mtb’s thioredoxin reductase TrxB2 has been predicted to be essential not only to fight host defenses but also for in vitro growth .", "However , the specific physiological ro...	[ "Mycobacterium tuberculosis ( Mtb ) antioxidant systems represent attractive targets for developing novel tuberculosis therapies .", "We demonstrate that targeting thioredoxin reductase TrxB2 eradicates Mtb during acute and chronic mouse infections .", "TrxB2 inactivation caused thiol-specific oxidizing stress ...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Molecular Basis for Oligomeric-DNA Binding and Episome Maintenance by KSHV LANA	journal.ppat.1003672	null	[ [ "Kaposi's sarcoma-associated herpesvirus ( KSHV ) is a human gammaherpesvirus that was first identified as the etiological agent of Kaposi's sarcoma and is also associated with pleural effusion lymphomas and multicentric Castleman's disease [1]–[3] .", "KSHV-associated tumors harbor latent viral genomes t...	[ "LANA is the KSHV-encoded terminal repeat binding protein essential for viral replication and episome maintenance during latency .", "We have determined the X-ray crystal structure of LANA C-terminal DNA binding domain ( LANADBD ) to reveal its capacity to form a decameric ring with an exterior DNA binding surfac...	[ "Kaposi's sarcoma-associated herpesvirus ( KSHV ) establishes latent infections that are associated with several cancers including Kaposi's sarcoma , pleural effusion lymphoma , and multicentric Caslteman's disease .", "One of the major viral proteins required for establishment and maintenance of the latent state...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular biology/post-translational regulation of gene expression", "cell biology/cell signaling", "biochemistry/protein chemistry", "virology", "cell biology/membranes and sorting", "biochemistry/cell signaling and trafficking structures", "virology/effects of virus infection on host gene expression"...	Enhanced Fusion Pore Expansion Mediated by the Trans-Acting Endodomain of the Reovirus FAST Proteins	journal.ppat.1000331	null	[ [ "The formation of multi-nucleated syncytia is an essential feature of a diverse range of biological processes [1] .", "Syncytiogenesis is contingent upon regulated cell–cell membrane fusion , which requires the involvement of protein catalysts to overcome the thermodynamic barriers that prevent spontaneou...	[ "The reovirus fusion-associated small transmembrane ( FAST ) proteins are virus-encoded membrane fusion proteins that function as dedicated cell–cell fusogens .", "The topology of these small , single-pass membrane proteins orients the majority of the protein on the distal side of the membrane ( i . e . , inside ...	[ "The reovirus FAST proteins are the only known examples of nonenveloped virus membrane fusion proteins .", "Functioning as virus-encoded cellular fusogens , they mediate cell–cell membrane fusion and syncytium formation rather than virus–cell fusion .", "The FAST proteins are also the smallest protein fusogens ...	2009
[ "Introduction", "Materials and Methods", "Results", "Discussion", "Supporting Information" ]	[ "viruses", "mammals", "virology", "microbiology", "evolutionary biology", "genetics and genomics", "mus (mouse)" ]	Role of APOBEC3 in Genetic Diversity among Endogenous Murine Leukemia Viruses	journal.pgen.0030183	null	[ [ "Retroviruses that integrate into the germ line may be inherited vertically as endogenous retroviral sequences ( ERVs ) [1] .", "A considerable fraction of mammalian genomes consists of ERVs [2–4] , most with numerous inactivating mutations , thus presenting the only known viral “fossil” record .", "O...	[ "The ability of human and murine APOBECs ( specifically , APOBEC3 ) to inhibit infecting retroviruses and retrotransposition of some mobile elements is becoming established .", "Less clear is the effect that they have had on the establishment of the endogenous proviruses resident in the human and mouse genomes ."...	[ "Vertebrate genomes are littered with remnants from earlier retroviral infections , in the form of endogenous retroviruses ( ERVs ) .", "Cellular host defenses against retroviruses , including the APOBEC3 family of cytidine deaminases , have been described previously .", "APOBEC3 proteins have been shown to edi...	2007
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "immunodeficiency viruses", "biochemical simulations", "viral latency", "systems biology", "genetic screens", "virology", "gene expression", "genetics", "biology", "computational biology", "microbiology", "viral replication", "gene networks" ]	Genetic Selection for Context-Dependent Stochastic Phenotypes: Sp1 and TATA Mutations Increase Phenotypic Noise in HIV-1 Gene Expression	journal.pcbi.1003135	null	[ [ "Non-genetic heterogeneity is a ubiquitous feature of cellular gene expression that can significantly impact the genotype–phenotype relationship .", "Even under highly controlled culture conditions , a clonal population of cells may demonstrate a broad range of expression levels for a given gene [1]–[4] ....	[ "The sequence of a promoter within a genome does not uniquely determine gene expression levels and their variability; rather , promoter sequence can additionally interact with its location in the genome , or genomic context , to shape eukaryotic gene expression .", "Retroviruses , such as human immunodeficiency v...	[ "The sequence of a gene within a cellular genome does not uniquely determine its expression level , even for a single type of cell under fixed conditions .", "Numerous other factors , including gene location on the chromosome and random gene-expression “noise , ” can alter expression patterns and cause difference...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "molecular complexes", "pathology and laboratory medicine", "enzymes", "viral enzymes", "regulatory proteins", "enzymology", "microbiology", "biocatalysis", "protein structure", "enzyme kinetics", "enzyme chemistry", "bacterial pathogens", "proteins", "med...	The CD27L and CTP1L Endolysins Targeting Clostridia Contain a Built-in Trigger and Release Factor	journal.ppat.1004228	null	[ [ "The increasing emergence of antibiotic resistance has led to a renaissance in the use of bacteriophage therapy as an alternative to eradicate pathogenic bacteria [1] .", "These bacterial viruses are potentially effective bactericides , with the additional advantage that they only affect a small portion o...	[ "The bacteriophage ΦCD27 is capable of lysing Clostridium difficile , a pathogenic bacterium that is a major cause for nosocomial infection .", "A recombinant CD27L endolysin lyses C . difficile in vitro , and represents a promising alternative as a bactericide .", "To better understand the lysis mechanism , we...	[ "Clostridium difficile infection is a common cause of hospital-acquired diarrhea , following broad-spectrum antibiotic treatment particularly in elderly patients .", "Bacteriophage therapy could provide an alternative treatment , but a better understanding of the viral components that lyse the bacterial cell is n...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "biotechnology", "plant anatomy", "medicine and health sciences", "senescence", "chemical compounds", "engineering and technology", "ethylene", "organic compounds", "dna transcription", "hormones", "physiological processes", "developmental biology", "plant science", "organism development",...	The H3K27me3 demethylase REF6 promotes leaf senescence through directly activating major senescence regulatory and functional genes in Arabidopsis	journal.pgen.1008068	null	[ [ "Histone methylation plays an essential role in diverse biological processes , ranging from transcriptional regulation to heterochromatin formation .", "Histone lysine methyltransferases ( “writers” ) and demethylases ( “eraser” ) dynamically regulate methylation levels , and in Arabidopsis , methylations...	[ "The roles of histone demethylation in the regulation of plant flowering , disease resistance , rhythmical response , and seed germination have been elucidated recently; however , how histone demethylation affects leaf senescence remains largely unclear .", "In this study , we exploited yeast one-hybrid ( Y1H ) t...	[ "Leaves of higher plants start yellowing and subsequently die ( senescence ) at particular developmental stages as a result of both internal and external regulations .", "Leaf senescence is evolved to facilitate nutrient remobilization to young/important organs to meet their rapid development , and a large number...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "genetics of the immune system", "clinical immunology", "genetics", "population genetics", "biology", "computational biology", "immunology", "genetics of disease", "genetics and genomics", "clinical genetics" ]	Meta-Analysis of Genome-Wide Association Studies in Celiac Disease and Rheumatoid Arthritis Identifies Fourteen Non-HLA Shared Loci	journal.pgen.1002004	null	[ [ "Autoimmune disorders , including rheumatoid arthritis ( RA ) and celiac disease ( CD ) , affect about 5% of the population and have a complex genetic background .", "Family-based epidemiology studies suggest that there is a shared genetic basis between the two autoimmune diseases [1] .", "Recent geno...	[ "Epidemiology and candidate gene studies indicate a shared genetic basis for celiac disease ( CD ) and rheumatoid arthritis ( RA ) , but the extent of this sharing has not been systematically explored .", "Previous studies demonstrate that 6 of the established non-HLA CD and RA risk loci ( out of 26 loci for each...	[ "Celiac disease ( CD ) and rheumatoid arthritis ( RA ) are two autoimmune diseases characterized by distinct clinical features but increased co-occurrence in families and individuals .", "Genome-wide association studies ( GWAS ) performed in CD and RA have identified the HLA region and 26 non-HLA genetic risk loc...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "public and occupational health", "medicine and health sciences", "disease ecology", "chagas disease", "mathematics", "statistics (mathematics)", "neglected tropical diseases", "tropical diseases", "physical sciences", "protozoan infections", "parasitic diseases", "statistical methods", "max...	All That Glisters Is Not Gold: Sampling-Process Uncertainty in Disease-Vector Surveys with False-Negative and False-Positive Detections	journal.pntd.0003187	null	[ [ "The primary prevention of most vector-borne diseases depends on averting contact between humans and pathogen vectors [1] .", "In turn , vector control often relies on the detection and elimination of infestation foci , particularly when the vectors occur in or around human residences .", "This is the...	[ "Vector-borne diseases are major public health concerns worldwide .", "For many of them , vector control is still key to primary prevention , with control actions planned and evaluated using vector occurrence records .", "Yet vectors can be difficult to detect , and vector occurrence indices will be biased when...	[ "Vector-borne disease prevention often relies on health agents inspecting dwellings and eliminating the vector infestation foci they detect .", "The effectiveness of prevention programs thus depends on vector-detection performance .", "Unfortunately , detection failures can be common , particularly when infesta...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[]	Satellite DNA-containing gigantic introns in a unique gene expression program during Drosophila spermatogenesis	journal.pgen.1008028	null	[ [ "Introns , non-coding elements of eukaryotic genes , often contain important regulatory sequences and allow for the production of diverse proteins from a single gene , adding critical regulatory layers to gene expression [1] .", "Curiously , some genes contain introns so large that more than 99% of the ge...	[ "Intron gigantism , where genes contain megabase-sized introns , is observed across species , yet little is known about its purpose or regulation .", "Here we identify a unique gene expression program utilized for the proper expression of genes with intron gigantism .", "We find that two Drosophila genes with i...	[ "Introns are non-coding elements of eukaryotic genes , often containing important regulatory sequences .", "Curiously , some genes contain introns so large that more than 99% of the gene locus is non-coding .", "One of the best-studied large genes , Dystrophin , a causative gene for Duchenne Muscular Dystrophy ...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "computer science", "mosquitoes", "dengue fever", "software engineering", "neglected tropical diseases", "malaria", "information technology", "software tools", "parasitic diseases", "vectors and hosts", "infectious disease control" ]	Multi-Disease Data Management System Platform for Vector-Borne Diseases	journal.pntd.0001016	null	[ [ "Emerging information technologies are improving our capacity to predict , prevent and control vector-borne and other infectious diseases [1]–[7] .", "In North America , for example , the United States Centers for Disease Control and Prevention has implemented a National Electronic Disease Surveillance Sy...	[ "Emerging information technologies present new opportunities to reduce the burden of malaria , dengue and other infectious diseases .", "For example , use of a data management system software package can help disease control programs to better manage and analyze their data , and thus enhances their ability to car...	[ "Emerging information technologies , such as data management system software packages , can help disease control programs to better manage and analyze their data , and thus make it easier to carry out continuous surveillance , monitor interventions and evaluate control program performance .", "This will lead to b...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cancer detection and diagnosis", "cell death", "genome expression analysis", "medicine and health sciences", "cancer genetics", "cell processes", "oncogenes", "oncology", "mutation", "genome analysis", "mutation databases", "research and analysis methods", "genomics", "necrotic cell death...	BRAF and AXL oncogenes drive RIPK3 expression loss in cancer	journal.pbio.2005756	null	[ [ "Necroptosis is a necrotic programmed cell death pathway mediated by the RIPK1-RIPK3-MLKL signaling cascade [1–4] .", "Receptor-interacting serine/threonine-protein kinase 1 ( RIPK1 ) can be activated when cells are stimulated by Tumor necrosis factor alpha ( TNFα ) , Fas , or TRAIL ligands as well as dow...	[ "Necroptosis is a lytic programmed cell death mediated by the RIPK1-RIPK3-MLKL pathway .", "The loss of Receptor-interacting serine/threonine-protein kinase 3 ( RIPK3 ) expression and necroptotic potential have been previously reported in several cancer cell lines; however , the extent of this loss across cancer ...	[ "Necroptosis is a regulated process that triggers cell death , resulting in necrosis and inflammation .", "Cancer cells have been shown to lose their ability to die via necroptosis , but the genetic factors that drive this resistance remain unknown .", "Here , we have analyzed 941 different cancer cell types an...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunology/genetics of the immune system", "mathematics", "computational biology/systems biology" ]	Combining Network Modeling and Gene Expression Microarray Analysis to Explore the Dynamics of Th1 and Th2 Cell Regulation	journal.pcbi.1001032	null	[ [ "The immune system is composed of diverse cell populations , for example antigen-presenting cells , T and B lymphocytes as well as effector cells like eosinophils , mast cells and neutrophils .", "One type of T lymphocytes , called T helper ( Th ) , has an important role in regulating this cellular networ...	[ "Two T helper ( Th ) cell subsets , namely Th1 and Th2 cells , play an important role in inflammatory diseases .", "The two subsets are thought to counter-regulate each other , and alterations in their balance result in different diseases .", "This paradigm has been challenged by recent clinical and experimenta...	[ "Different T helper ( Th ) cell subsets have an important role in regulating the immune response in inflammatory diseases .", "Th1 and Th2 cells are thought to counter-regulate each other , and alterations in their balance result in different diseases . This paradigm has been challenged by recent clinical and exp...	2010
[ "Introduction", "Results/Discussion", "Methods" ]	[ "physics", "computational chemistry", "molecular dynamics", "biophysic al simulations", "chemistry", "biology", "computational biology", "biophysics simulations", "biophysics" ]	Probing the Energy Landscape of Activation Gating of the Bacterial Potassium Channel KcsA	journal.pcbi.1003058	null	[ [ "K+ channels play a crucial role in a wide variety of physiological and pathophysiological processes including action potential modeling [1] , cancer cell proliferation [2] , and metabolic pathways mediation [3] .", "In the last few decades , the understanding of ion channels has increased tremendously ."...	[ "The bacterial potassium channel KcsA , which has been crystallized in several conformations , offers an ideal model to investigate activation gating of ion channels .", "In this study , essential dynamics simulations are applied to obtain insights into the transition pathways and the energy profile of KcsA pore ...	[ "Voltage gated ion channels are membrane embedded proteins that initiate electrical signaling upon changes in membrane potential .", "These channels are involved in biological key processes such as generation and propagation of nerve impulses .", "Mutations may lead to serious diseases such as cardiac arrhythmi...	2013
[ "Introduction", "Methods", "Results/Discussion" ]	[ "mathematics", "biochemistry/chemical biology of the cell", "computational biology/metabolic networks", "biochemistry/theory and simulation", "physiology/integrative physiology", "computational biology/systems biology" ]	A Model of Brain Circulation and Metabolism: NIRS Signal Changes during Physiological Challenges	journal.pcbi.1000212	null	[ [ "In recent years there has been widespread use of near infrared spectroscopy ( NIRS ) to", "monitor brain oxygenation , haemodynamics and metabolism [1] , [2] .", "Initially the primary", "chromophores of interest were oxy- and deoxy-haemoglobin , with changes ( termed", "ΔHbO2 and ΔHHb , resp...	[ "We construct a model of brain circulation and energy metabolism .", "The model is", "designed to explain experimental data and predict the response of the", "circulation and metabolism to a variety of stimuli , in particular , changes in", "arterial blood pressure , CO2 levels , O2 levels , and", "functi...	[ "Monitoring the brain noninvasively is key to solving various biological and", "clinical problems .", "Near-infrared spectroscopy ( NIRS ) is a technique that can", "measure changes in the colour of the brain .", "The brain has an absolute", "requirement for oxygen; the spectroscopically observed colour c...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "genetics", "biology", "microbiology", "molecular cell biology", "genetics and genomics" ]	A Unique Protein Phosphatase with Kelch-Like Domains (PPKL) in Plasmodium Modulates Ookinete Differentiation, Motility and Invasion	journal.ppat.1002948	null	[ [ "Reversible protein phosphorylation is a ubiquitous regulatory process for a variety of eukaryotic and prokaryotic pathways , including cell-cycle regulation , cell to cell signalling , cell proliferation and differentiation [1] .", "In humans , aberrant regulation of protein phosphorylation has been impl...	[ "Protein phosphorylation and dephosphorylation ( catalysed by kinases and phosphatases , respectively ) are post-translational modifications that play key roles in many eukaryotic signalling pathways , and are often deregulated in a number of pathological conditions in humans .", "In the malaria parasite Plasmodi...	[ "Malaria parasites are single-celled organisms , which alternate their life-cycle between vertebrate and mosquito hosts .", "In the mosquito , the malaria parasite undergoes sexual development , whereby a male and female gamete fuse to form a zygote .", "This zygote then elongates into an invasive stage , terme...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "bacterial diseases", "infectious diseases", "buruli ulcer", "neglected tropical diseases" ]	Implementation of a National Reference Laboratory for Buruli Ulcer Disease in Togo	journal.pntd.0002011	null	[ [ "Buruli ulcer disease ( BUD ) , caused by Mycobacterium ulcerans , is an infectious disease affecting skin , soft tissue and bones .", "If left untreated , extensive destruction of tissue followed by fibrous scarring and contractures may lead to severe functional limitations [1]–[6] .", "BUD is treate...	[ "In a previous study PCR analysis of clinical samples from suspected cases of Buruli ulcer disease ( BUD ) from Togo and external quality assurance ( EQA ) for local microscopy were conducted at an external reference laboratory in Germany .", "The relatively poor performance of local microscopy as well as effort ...	[ "Buruli ulcer disease ( BUD ) , the third most common mycobacterial disease worldwide , is treated with standardized antimycobacterial therapy .", "According to WHO recommendations at least 50% of cases should be laboratory confirmed by polymerase chain reaction ( PCR ) .", "In a previous study PCR analysis of ...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "immunology", "biology", "microbiology", "population biology" ]	Sero-Epidemiology as a Tool to Screen Populations for Exposure to Mycobacterium ulcerans	journal.pntd.0001460	null	[ [ "Buruli ulcer ( BU ) , a severe necrotizing skin disease , is caused by the environmental pathogen Mycobacterium ulcerans ( M . ulcerans ) .", "Globally , it is the third most prevalent mycobacterial disease that affects immunocompetent individuals after tuberculosis and leprosy [1] .", "Currently mor...	[ "Previous analyses of sera from a limited number of Ghanaian Buruli ulcer ( BU ) patients , their household contacts , individuals living in BU non-endemic regions as well as European controls have indicated that antibody responses to the M . ulcerans 18 kDa small heat shock protein ( shsp ) reflect exposure to thi...	[ "Sero-epidemiological analyses revealed that a higher proportion of sera from individuals living in the Buruli ulcer ( BU ) endemic Densu River Valley of Ghana contain Mycobacterium ulcerans 18 kDa small heat shock protein ( shsp ) -specific IgG than sera from inhabitants of the Volta Region , which was regarded so...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "blood cells", "medicine and health sciences", "immune cells", "immune physiology", "pathology and laboratory medicine", "fungal genetics", "spleen", "pathogens", "pichia pastoris", "immunology", "animal models", "fungi", "model organisms", "research and analysis methods", "mycology", ...	Mp1p Is a Virulence Factor in Talaromyces (Penicillium) marneffei	journal.pntd.0004907	null	[ [ "Talaromyces ( Penicillium ) marneffei is an opportunistic thermal dimorphic fungus most prevalent in Southeast Asia [1–6] .", "Bamboo rats and the soil of their burrows are known to be important sources of T . marneffei .", "Since the 1980s , a marked increase in the number of infections caused by T ...	[ "Talaromyces marneffei is an opportunistic dimorphic fungus prevalent in Southeast Asia .", "We previously demonstrated that Mp1p is an immunogenic surface and secretory mannoprotein of T . marneffei .", "Since Mp1p is a surface protein that can generate protective immunity , we hypothesized that Mp1p and/or it...	[ "Talaromyces ( Penicillium ) marneffei is an opportunistic thermal dimorphic fungus most prevalent in Southeast Asia .", "Our team has previously shown that Mp1p , a protein encoded by the MP1 gene , is an immunogenic surface and secretory protein of T . marneffei .", "In this study , we showed that mice challe...	2016
[ "Introduction", "Results", "Discussion", "Methods", "Supporting Information" ]	[ "biophysics", "biochemistry", "eukaryotes", "computational biology" ]	Operating Regimes of Signaling Cycles: Statics, Dynamics, and Noise Filtering	journal.pcbi.0030246	null	[ [ "Cells rely on chemical interactions to sense , transmit , and process time-varying signals originating in their environment .", "Because of the inherent stochasticity of chemical reactions , the signals transmitted in cell-signaling pathways are buried in noise .", "How can cells then differentiate t...	[ "A ubiquitous building block of signaling pathways is a cycle of covalent modification ( e . g . , phosphorylation and dephosphorylation in MAPK cascades ) .", "Our paper explores the kind of information processing and filtering that can be accomplished by this simple biochemical circuit .", "Signaling cycles a...	[ "A cell is subjected to constantly changing environments and time-varying stimuli .", "Signals sensed at the cell surface are transmitted inside the cell by signaling pathways .", "Such pathways can transform signals in diverse ways and perform some preliminary information processing .", "A ubiquitous buildin...	2007
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public health and epidemiology", "infectious disease epidemiology", "veterinary diagnostics", "veterinary science", "veterinary medicine", "veterinary diseases", "veterinary epidemiology", "veterinary parasitology", "molecular epidemiology", "zoonotic diseases", "epidemiology", ...	Prevalence and Factors Associated with Leishmania infantum Infection of Dogs from an Urban Area of Brazil as Identified by Molecular Methods	journal.pntd.0001291	null	[ [ "Human visceral leishmaniasis ( HVL ) constitutes a public health problem that affects millions of people throughout the world [1] .", "Over the past decade , there has been an average of 3379 cases of HVL per year in Brazil , with an incidence of 1 . 9 cases per 100 , 000 inhabitants [2] .", "During ...	[ "Various factors contribute to the urbanization of the visceral leishmaniasis ( VL ) , including the difficulties of implementing control measures relating to the domestic reservoir .", "The aim of this study was to determine the prevalence of canine visceral leishmaniasis in an urban endemic area in Brazil and t...	[ "Visceral leishmaniasis ( VL ) is a disease caused by the parasite Leishmania infantum , and dogs are the most important domestic reservoirs of the agent .", "During recent decades , VL has expanded to large Brazilian urban centers .", "In the present work , we have demonstrated by using molecular techniques th...	2011
[ "Introduction", "Results", "Materials and methods", "Discussion" ]	[ "blood cells", "medicine and health sciences", "immune cells", "enzyme-linked immunoassays", "immunology", "cloning", "sequence motif analysis", "cytotoxic t cells", "molecular biology techniques", "immunologic techniques", "research and analysis methods", "sequence analysis", "specimen prep...	Cross-sectional analysis of CD8 T cell immunity to human herpesvirus 6B	journal.ppat.1006991	null	[ [ "Human herpesvirus 6 ( HHV-6 ) may be among the most prevalent persistent viruses in the human population .", "Antibodies to HHV-6 are present in 95–100% of healthy adults [1 , 2] .", "Like other herpesviruses , HHV-6 establishes a lifelong infection .", "HHV-6 is a group of two virus species know...	[ "Human herpesvirus 6 ( HHV-6 ) is prevalent in healthy persons , causes disease in immunosuppressed carriers , and may be involved in autoimmune disease .", "Cytotoxic CD8 T cells are probably important for effective control of infection .", "However , the HHV-6-specific CD8 T cell repertoire is largely unchara...	[ "This paper deals with the immune response to a very common virus , called human herpesvirus 6 ( HHV-6 ) .", "Most people catch HHV-6 in early childhood , which often leads to a disease known as three-day fever .", "Later in life , the virus stays in the body , and an active immune response is needed to prevent...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "immune physiology", "pathology and laboratory medicine", "togaviruses", "chikungunya infection", "pathogens", "immunology", "tropical diseases", "microbiology", "geographical locations", "alphaviruses", "viruses", "north america", "chikungunya virus", "rn...	Seroprevalence of Chikungunya Virus in a Rural Community in Brazil	journal.pntd.0005319	null	[ [ "The Chikungunya virus ( CHIKV ) belongs to the genus Alphavirus of the family Togaviridae and has a single-stranded RNA genome and positive polarity [1] .", "The virus was first isolated in blood samples obtained during an epidemic of a \"dengue-like\" disease that occurred between 1952–1953 in Tanzania ...	[ "The emergence of the Chikungunya virus ( CHIKV ) is currently expanding .", "In 2015 , 38 , 332 cases of Chikungunya were reported to the Brazilian epidemiological surveillance system .", "Eighteen months after notification of the first case in the city of Feira de Santana , we conducted the first serosurvey t...	[ "The Chikungunya virus ( CHIKV ) epidemic is currently expanding .", "In 2015 , 38 , 332 cases of Chikungunya were reported to the Brazilian epidemiological surveillance system .", "To date , no serosurvey has described the impact of the disease on rural communities in Brazil .", "We conducted a survey in whi...	2017
[ "Introduction", "Models", "Results", "Discussion" ]	[ "cell physiology", "organismal evolution", "symbiosis", "cell cycle and cell division", "cell processes", "cell metabolism", "cell differentiation", "developmental biology", "animal behavior", "chemical composition", "zoology", "animal sociality", "reaction dynamics", "physical chemistry",...	Symbiotic Cell Differentiation and Cooperative Growth in Multicellular Aggregates	journal.pcbi.1005042	null	[ [ "As unicellular organisms grow and divide , they often form a crowded aggregate .", "As exemplified by bacterial biofilms [1–3] and slime molds [4 , 5] , these aggregates are not merely crowded passively , but sometimes form a functional cell aggregate , in which cells strongly interact with each other by...	[ "As cells grow and divide under a given environment , they become crowded and resources are limited , as seen in bacterial biofilms and multicellular aggregates .", "These cells often show strong interactions through exchanging chemicals , as evident in quorum sensing , to achieve mutualism and division of labor ...	[ "Unicellular organisms , when aggregated under limited resources , often exhibit behaviors akin to multicellular organisms , possibly without advanced regulation mechanisms , as observed in biofilms and bacterial colonies .", "Cells in an aggregate have to differentiate into several types that are specialized for...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases/helminth infections", "infectious diseases/antimicrobials and drug resistance" ]	The New Anthelmintic Tribendimidine is an L-type (Levamisole and Pyrantel) Nicotinic Acetylcholine Receptor Agonist	journal.pntd.0000499	null	[ [ "Thirteen neglected tropical diseases have tremendous impact on the lives of billions of the poorest peoples in the world with an estimated total disease burden of 56 . 6 million disability-adjusted life years , exceeding that of malaria ( 46 . 5 million ) and tuberculosis ( 34 . 7 million ) [1] , [2] .", ...	[ "Intestinal parasitic nematodes such as hookworms , Ascaris lumbricoides , and Trichuris trichiura are amongst most prevalent tropical parasites in the world today .", "Although these parasites cause a tremendous disease burden , we have very few anthelmintic drugs with which to treat them .", "In the past thre...	[ "Intestinal parasitic nematodes or roundworms infect over 1 billion people in tropical countries .", "Overall , they are a huge source of morbidity in infected people , including children and pregnant women , and are increasingly being recognized as key poverty-promoting parasites .", "Despite their importance ...	2009
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Locally Confined Clonal Complexes of Mycobacterium ulcerans in Two Buruli Ulcer Endemic Regions of Cameroon	journal.pntd.0003802	null	[ [ "Buruli ulcer ( BU ) , the third most common mycobacterial disease affecting humans after tuberculosis and leprosy , is caused by Mycobacterium ulcerans [1] .", "The disease is characterized by progressive necrosis of the skin and subcutaneous tissue , leading to sometimes extensive ulcerations .", "E...	[ "Mycobacterium ulcerans is the causative agent of the necrotizing skin disease Buruli ulcer ( BU ) , which has been reported from over 30 countries worldwide .", "The majority of notified patients come from West African countries , such as Côte d’Ivoire , Ghana , Benin and Cameroon .", "All clinical isolates of...	[ "Buruli ulcer ( BU ) is a progressively necrotizing disease of the skin , caused by infection with Mycobacterium ulcerans .", "BU occurs very focally with highest incidence in West Africa .", "The mode of transmission and the nature and role of potential environmental reservoirs are currently not entirely under...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "luciferase", "enzymes", "gene regulation", "population genetics", "carcinomas", "cancers and neoplasms", "enzymology", "cell processes", "gastrointestinal tumors", "liver diseases", "oncology", "gastroenterology and hepatology", "gene types", "dna", "po...	Selective Retention of an Inactive Allele of the DKK2 Tumor Suppressor Gene in Hepatocellular Carcinoma	journal.pgen.1006051	null	[ [ "Hepatocellular carcinoma ( HCC ) is the fifth most common cancer worldwide , and the third leading cause of cancer-related mortality , contributing to over 660 , 000 annual deaths worldwide [1 , 2] .", "HCC exhibits a distinct geographic distribution of over 80% of HCC cases occurring in Southeast Asia a...	[ "In an effort to identify the functional alleles associated with hepatocellular carcinoma ( HCC ) , we investigated 152 genes found in the 4q21-25 region that exhibited loss of heterozygosity ( LOH ) .", "A total of 2 , 293 pairs of primers were designed for 1 , 449 exonic and upstream promoter regions to amplify...	[ "Liver cancer is one of the most lethal human cancers .", "Identifying functional alleles associated with liver cancer can provide new insights into the disease’s pathogenesis and help to advance the development of new therapeutic approaches .", "We conducted re-sequencing of the 4q21-25 region that frequently ...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "antimicrobials", "cell physiology", "medicine and health sciences", "caulobacter", "drugs", "enzymology", "microbiology", "cell metabolism", "prokaryotic models", "metabolites", "antibiotics", "membrane metabolism", "enzyme metabolism", "experimental organism systems", "pharmacology", ...	Crosstalk between the tricarboxylic acid cycle and peptidoglycan synthesis in Caulobacter crescentus through the homeostatic control of α-ketoglutarate	journal.pgen.1006978	null	[ [ "Central metabolism is crucial for generating energy and biosynthetic precursors during cell growth and proliferation .", "In bacteria , cellular replication also requires the synthesis of peptidoglycan ( PG ) , a major component of the bacterial cell wall that determines the shape and size of the cell ."...	[ "To achieve robust replication , bacteria must integrate cellular metabolism and cell wall growth .", "While these two processes have been well characterized , the nature and extent of cross-regulation between them is not well understood .", "Here , using classical genetics , CRISPRi , metabolomics , transcript...	[ "Bacteria are well-known for their remarkable ability to multiply , a property that we often aim to control .", "To successfully self-replicate , bacterial cells must generate energy and building blocks through central metabolism and synthesize cell wall material to reproduce their shape and size .", "How cellu...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "microbiology", "biophysics", "neuroscience" ]	The Desensitization Gating of the MthK K+ Channel Is Governed by Its Cytoplasmic Amino Terminus	journal.pbio.0060223	The N terminus of the ion channel MthK functions as a structurally independent domain and is entirely responsible for the desensitization gating process required for neuron-to-neuron communication.	[ [ "K+ channels are found in almost every free-living organism , with a universally conserved architecture .", "Typically , a functional K+ channel is composed of four copies of a pore-forming subunit of two or six transmembrane ( TM ) helices with the amino ( N ) - and carboxyl ( C ) -termini usually residi...	[ "The RCK-containing MthK channel undergoes two inactivation processes: activation-coupled desensitization and acid-induced inactivation .", "The acid inactivation is mediated by the C-terminal RCK domain assembly .", "Here , we report that the desensitization gating is governed by a desensitization domain ( DD ...	[ "Nerve cells use ion channels , pores in the cell membrane , to send messages in the form of electrical signals between cells .", "Most ion channels have evolved several elaborate mechanisms that allow the channels to close quickly after opening to prevent wasteful leakage of the electrochemical potential—the cur...	2008
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing techniques", "luciferase", "hela cells", "gene regulation", "enzymes", "biological cultures", "enzymology", "marker genes", "cloning", "genetic elements", "cell cultures", "sequence motif analysis", "molecular biology techniques", "epigenetics", "chromatin", "research and a...	Mariner Transposons Contain a Silencer: Possible Role of the Polycomb Repressive Complex 2	journal.pgen.1005902	null	[ [ "Almost all eukaryotic genomes contain transposable elements ( TEs ) .", "Some of these , known as DNA transposons , move by a simple ‘cut-and-paste’ mechanism removing DNA from one site and inserting it into a new target site .", "Others , called retrotransposons , move via an RNA intermediate that i...	[ "Transposable elements are driving forces for establishing genetic innovations such as transcriptional regulatory networks in eukaryotic genomes .", "Here , we describe a silencer situated in the last 300 bp of the Mos1 transposase open reading frame ( ORF ) which functions in vertebrate and arthropod cells .", ...	[ "Transposons are mobile DNA sequences that have long co-evolved with the genome of their hosts .", "Consequently , they are involved in the generation of mutations , as well as the creation of genes and regulatory networks .", "Controlling the transposon activity , and consequently its negative effects on both ...	2016
[ "Introduction", "Materials & methods", "Result", "Discussion" ]	[ "blood cells", "cell motility", "innate immune system", "medicine and health sciences", "immune physiology", "cytokines", "pathology and laboratory medicine", "immune cells", "nervous system", "immunology", "microglial cells", "developmental biology", "signs and symptoms", "molecular devel...	Nitrosporeusine analogue ameliorates Chandipura virus induced inflammatory response in CNS via NFκb inactivation in microglia	journal.pntd.0006648	null	[ [ "Microglia , the developmental and functional equivalents of macrophages in somatic tissues [1] , exert a central role in a host defence and immune surveillance against infectious agents in the central nervous system ( CNS ) [2] .", "Microglia being multitasking act as scavengers and antigen-presenting ce...	[ "Chandipura Virus ( CHPV ) , a negative-stranded RNA virus belonging to the Rhabdoviridae family , has been previously reported to bring neuronal apoptosis by activating several factors leading to neurodegeneration .", "Following virus infection of the central nervous system , microglia , the ontogenetic and func...	[ "Chandipura virus is a negatively stranded single RNA virus , which has claimed many lives in several outbreaks in India and Indian subcontinent .", "Our previous study shows CNS inflammation plays a vital role in inducing neurodegeneration post infection .", "In continuation to that our present study systemati...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genomics", "plant biology", "crops", "genetics", "biology", "computational biology", "genetics and genomics", "agriculture" ]	Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens	journal.pgen.1003233	null	[ [ "The filamentous ascomycete genus Cochliobolus ( anamorph Bipolaris/Curvularia ) is comprised of more than forty closely related , often highly aggressive , pathogenic species with particular specificity to their host plants .", "All members of the genus known to cause serious crop diseases fall in a tigh...	[ "The genomes of five Cochliobolus heterostrophus strains , two Cochliobolus sativus strains , three additional Cochliobolus species ( Cochliobolus victoriae , Cochliobolus carbonum , Cochliobolus miyabeanus ) , and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute ( JGI ) .", "The ...	[ "The filamentous ascomycete genus Cochliobolus includes highly aggressive necrotrophic and hemibiotrophic pathogens with particular specificity to their host plants , often associated with production of host selective toxins ( HST ) that allow necrotrophs to trigger host cell death .", "Hemibiotrophs must keep th...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/microbial evolution and genomics", "evolutionary biology/microbial evolution and genomics", "cell biology/gene expression", "genetics and genomics/functional genomics", "infectious diseases/neglected tropical diseases", "microbiology/microbial evolution and genomics", "cell biolog...	A Genetically Hard-Wired Metabolic Transcriptome in Plasmodium falciparum Fails to Mount Protective Responses to Lethal Antifolates	journal.ppat.1000214	null	[ [ "Malaria parasites infect over 300 million people around the world and the most virulent species , Plasmodium falciparum , kills 1–2 million individuals per year [1]–[3] .", "The availability of genome-wide DNA microarrays for P . falciparum , has facilitated insights into many complex biological problems...	[ "Genome sequences of Plasmodium falciparum allow for global analysis of drug responses to antimalarial agents .", "It was of interest to learn how DNA microarrays may be used to study drug action in malaria parasites .", "In one large , tightly controlled study involving 123 microarray hybridizations between cD...	[ "Traditional knowledge of gene regulation , learned largely from non-pathogenic model organisms such as E . coli , yeast , and mice , suggests that RNA for metabolic pathways are regulated in large part by DNA-binding transcriptional factors that are responsive to cellular metabolic needs .", "We demonstrate that...	2008
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "viral hemorrhagic fevers", "infectious diseases", "public health and epidemiology", "clinical epidemiology", "clinical research design", "epidemiology", "infectious disease epidemiology", "dengue fever", "neglected tropical diseases", "retrospective studies", "arboviral infections...	Clinical Relevance and Discriminatory Value of Elevated Liver Aminotransferase Levels for Dengue Severity	journal.pntd.0001676	null	[ [ "Dengue is a mosquito-borne arboviral infection endemic to most tropical and subtropical countries [1] .", "Elevation of the liver enzymes aspartate aminotransferase ( AST ) and alanine aminotransferase ( ALT ) is common in acute dengue illness , occurring in 65–97% [2] , [3] , [4] , [5] of dengue patient...	[ "Elevation of aspartate aminotransferase ( AST ) and alanine aminotransferase ( ALT ) is prominent in acute dengue illness .", "The World Health Organization ( WHO ) 2009 dengue guidelines defined AST or ALT≥1000 units/liter ( U/L ) as a criterion for severe dengue .", "We aimed to assess the clinical relevance...	[ "Dengue is a global public health problem , as the incidence of the disease has reached hyperendemic proportions in recent decades .", "Infection with dengue can cause acute , febrile illness or severe disease , which can lead to plasma leakage , bleeding , and organ impairment .", "One of the most prominent cl...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics and genomics/bioinformatics", "genetics and genomics/gene expression" ]	Removal of AU Bias from Microarray mRNA Expression Data Enhances Computational Identification of Active MicroRNAs	journal.pcbi.1000189	null	[ [ "MicroRNAs ( miRs ) are a growing class of non-coding RNAs that is now recognized as a major tier of gene control , predicted to target more than 30% of all human protein-coding genes [1] , [2] .", "miRs suppress gene expression via binding to regulatory sites usually embedded in the 3′-UTRs of their targ...	[ "Elucidation of regulatory roles played by microRNAs ( miRs ) in various biological networks is one of the greatest challenges of present molecular and computational biology .", "The integrated analysis of gene expression data and 3′-UTR sequences holds great promise for being an effective means to systematically...	[ "MicroRNAs are a novel class of genes that encodes for short RNA molecules recognized to play key roles in the regulation of many biological networks .", "MicroRNAs , predicted to collectively target more than 30% of all human protein-coding genes , suppress gene expression by binding to regulatory elements usual...	2008
[ "Introduction", "Materials and Methods", "Results/Discussion" ]	[ "genetics and genomics/gene expression", "genetics and genomics/functional genomics", "infectious diseases/neglected tropical diseases", "infectious diseases/helminth infections", "genetics and genomics/gene function", "biochemistry/transcription and translation", "cell biology/gene expression" ]	Development of Functional Genomic Tools in Trematodes: RNA Interference and Luciferase Reporter Gene Activity in Fasciola hepatica	journal.pntd.0000260	null	[ [ "Parasitic diseases are a major problem worldwide being not only a health issue but also , when affecting productive species , an important factor in the economy .", "Advances in biochemistry and molecular biology of parasites have made possible to identify at the molecular level several candidate mediato...	[ "The growing availability of sequence information from diverse parasites through genomic and transcriptomic projects offer new opportunities for the identification of key mediators in the parasite–host interaction .", "Functional genomics approaches and methods for the manipulation of genes are essential tools fo...	[ "Reverse genetics tools allow assessing the function of unknown genes .", "Their application for the study of neglected infectious diseases could lead eventually to the identification of relevant gene products to be used in diagnosis , or as drug targets or immunization candidates .", "Being technically more si...	2008
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "genome expression analysis", "genetic mutation", "gene regulation", "gene function", "genome analysis tools", "pest control", "molecular genetics", "sequence analysis", "biology", "gene ontologies", "agriculture", "transcriptomes", "pesticides", "microarrays", "adaptation", "evolution...	Identification of Carboxylesterase Genes Implicated in Temephos Resistance in the Dengue Vector Aedes aegypti	journal.pntd.0002743	null	[ [ "Aedes aegypti is a major vector of dengue fever and yellow fever viruses .", "Despite an effective vaccine , there are over 200 , 000 cases of yellow fever each year ( WHO source , 2012 ) .", "With no vaccine currently available for dengue , and no specific drug treatment , approximately 40% of the w...	[ "Thailand is currently experiencing one of its worst dengue outbreaks in decades .", "As in most countries where this disease is endemic , dengue control in Thailand is largely reliant on the use of insecticides targeting both immature and adult stages of the Aedes mosquito , with the organophosphate insecticide ...	[ "Temephos is the most important insecticide used in larviciding campaigns to reduce the risk of dengue transmission .", "This organophosphate insecticide has been in use for over 50 years and resistance to this chemical has been reported in Aedes aegypti populations from Latin America , the Caribbean and from Asi...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics", "biology", "microbiology", "evolutionary biology", "population biology", "genetics and genomics" ]	A Trade-off between the Fitness Cost of Functional Integrases and Long-term Stability of Integrons	journal.ppat.1003043	null	[ [ "Horizontal gene transfer ( HGT ) enables bacteria to obtain alien genes and genetic elements from prokaryotic , archaeal , and eukaryotic organisms .", "This capacity for genetic exchange plays an important role in bacterial adaptive evolution , as exemplified by the rapid spread of antibiotic resistance...	[ "Horizontal gene transfer ( HGT ) plays a major role in bacterial microevolution as evident from the rapid emergence and spread of antimicrobial drug resistance .", "Few studies have however addressed the population dynamics of newly imported genetic elements after HGT .", "Here , we show that newly acquired cl...	[ "Horizontal acquisition of mobile and mobilizable genetic elements plays a major role in the development of antimicrobial drug resistance in bacteria .", "Despite their causal role in drug treatment failure , there is only limited understanding of how horizontal acquisitions of these elements affect bacterial fit...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "biophysics/theory and simulation", "cell biology/membranes and sorting", "computational biology", "biophysics", "physics/interdisciplinary physics" ]	Minimal Mesoscale Model for Protein-Mediated Vesiculation in Clathrin-Dependent Endocytosis	journal.pcbi.1000926	null	[ [ "The cellular process of endocytosis is important in the biological regulation of trafficking in cells , as well as impacts the technology of targeted drug delivery in nanomedicine [1] , [2] , [3] , [4] , [5] , [6] , [7] .", "In eukaryotic cells , the internalization of extracellular cargo via the endocyt...	[ "In eukaryotic cells , the internalization of extracellular cargo via the endocytic machinery is an important regulatory process required for many essential cellular functions .", "The role of cooperative protein-protein and protein-membrane interactions in the ubiquitous endocytic pathway in mammalian cells , na...	[ "Cell membranes and membrane-based organelles actively mediate several intracellular signaling and trafficking decisions .", "A growing number of applications rely on cooperative interactions between molecular assemblies and membranes .", "Yet , the studies of membrane-based and membrane-mediated signaling are ...	2010
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "immune cells", "pathology and laboratory medicine", "gene regulation", "endothelial cells", "pathogens", "antigen-presenting cells", "immunology", "microbiology", "cardiovascular medicine", "thrombosis", "epithelial cells", "bacterial diseases", "physiologi...	An ADAM-10 dependent EPCR shedding links meningococcal interaction with endothelial cells to purpura fulminans	journal.ppat.1006981	null	[ [ "Neisseria meningitidis is a natural host of the human nasopharynx .", "For still unknown reasons , it can invade the bloodstream , causing a severe disease with an annual incidence of about 1 case per 100 000 inhabitants in developed countries .", "During meningococcemia , patients usually present cu...	[ "Purpura fulminans is a deadly complication of Neisseria meningitidis infections due to extensive thrombosis of microvessels .", "Although a Disseminated Intra-vascular Coagulation syndrome ( DIC ) is frequently observed during Gram negative sepsis , it is rarely associated with extensive thrombosis like those ob...	[ "Neisseria meningitidis ( meningococcus ) is responsible for a severe syndrome called purpura fulminans in which the coagulation system is totally dysregulated , leading to an extensive occlusion of blood microvessels .", "The pathogenesis of this syndrome is still not understood .", "Here we show that the meni...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "mathematics/statistics", "computational biology/protein homology detection" ]	A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation	journal.pcbi.1000069	null	[ [ "Sequence similarity searching was advanced by the introduction of probabilistic modeling methods , such as profile hidden Markov models ( profile HMMs ) and pair-HMMs [1] .", "When parameters are probabilities rather than arbitrary scores , they are more readily optimized by objective mathematical criter...	[ "Sequence database searches require accurate estimation of the statistical significance of scores .", "Optimal local sequence alignment scores follow Gumbel distributions , but determining an important parameter of the distribution ( λ ) requires time-consuming computational simulation .", "Moreover , optimal a...	[ "Sequence database searches are a fundamental tool of molecular biology , enabling researchers to identify related sequences in other organisms , which often provides invaluable clues to the function and evolutionary history of genes .", "The power of database searches to detect more and more remote evolutionary ...	2008
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "biology", "genomics", "evolutionary biology", "genetics and genomics" ]	Contrasted Patterns of Molecular Evolution in Dominant and Recessive Self-Incompatibility Haplotypes in Arabidopsis	journal.pgen.1002495	null	[ [ "Sexual reproduction entails the combination of genetic material from different individuals to produce offspring .", "Yet in many species mating is not entirely random , being only possible between individuals with either distinct sexes or distinct mating-types [1] .", "Sexes or mating-types are typic...	[ "Self-incompatibility has been considered by geneticists a model system for reproductive biology and balancing selection , but our understanding of the genetic basis and evolution of this molecular lock-and-key system has remained limited by the extreme level of sequence divergence among haplotypes , resulting in a...	[ "Self-incompatibility is a common genetic system preventing selfing through recognition and rejection of self-pollen in hermaphroditic flowering plants .", "In the Brassicaceae family , this system is controlled by a single genomic region , called the S-locus , where many distinct specificities segregate in natur...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "taxonomy", "biogeography", "united states", "ecology and environmental sciences", "population genetics", "geographical locations", "north america", "phylogenetics", "data management", "fungi", "model organisms", "phylogenetic analysis", "molecular biology techniques", "population biology"...	Complex Ancestries of Lager-Brewing Hybrids Were Shaped by Standing Variation in the Wild Yeast Saccharomyces eubayanus	journal.pgen.1006155	null	[ [ "Humans changed from living in hunter-gatherer societies to agricultural societies in part through the domestication of animals and plants [1 , 2] .", "At the same time , humans began unwittingly domesticating microorganisms for the production of fermented beverages and foods , but the underlying source p...	[ "Lager-style beers constitute the vast majority of the beer market , and yet , the genetic origin of the yeast strains that brew them has been shrouded in mystery and controversy .", "Unlike ale-style beers , which are generally brewed with Saccharomyces cerevisiae , lagers are brewed at colder temperatures with ...	[ "Yeasts are key industrial microbes , most notably Saccharomyces cerevisiae , which is used to make a variety of products , including bread , wine , and ale-style beers .", "However , lager-style beers are brewed with interspecies hybrids of S . cerevisiae x Saccharomyces eubayanus .", "After its discovery in S...	2016
[ "Introduction", "Results", "Discussion", "Material and Methods" ]	[]	Correlations and Functional Connections in a Population of Grid Cells	journal.pcbi.1004052	null	[ [ "Grid cells are neurons in the medial entorhinal cortex ( MEC ) , one synapse away from the hippocampus , that show a strikingly regular spatial selectivity [1] .", "Each grid cell has several firing fields that spread out in a hexagonal pattern , tessellating the environment in which the animal navigates...	[ "We study the statistics of spike trains of simultaneously recorded grid cells in freely behaving rats .", "We evaluate pairwise correlations between these cells and , using a maximum entropy kinetic pairwise model ( kinetic Ising model ) , study their functional connectivity .", "Even when we account for the c...	[ "The way mammals navigate in space is hypothesized to depend on neural structures in the temporal lobe including the hippocampus and medial entorhinal cortex ( MEC ) .", "In particular , grid cells , neurons whose firing is mostly restricted to regions of space that form a hexagonal pattern , are believed to be a...	2015
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "blood cells", "cell death", "medicine and health sciences", "immune cells", "cell processes", "immunology", "microbiology", "tropical diseases", "parasitic diseases", "protozoan life cycles", "parasitic protozoans", "developmental biology", "protozoans", "leishmania", "mitochondria", ...	Mitochondria and lipid raft-located FOF1-ATP synthase as major therapeutic targets in the antileishmanial and anticancer activities of ether lipid edelfosine	journal.pntd.0005805	null	[ [ "Leishmaniasis , caused by several species of the protozoan Leishmania parasite , is one of the world’s most neglected diseases in terms of drug research and development , and for which current therapy is not satisfactory [1] .", "At present , about 350 million people in 98 countries worldwide are at risk...	[ "Leishmaniasis is the world’s second deadliest parasitic disease after malaria , and current treatment of the different forms of this disease is far from satisfactory .", "Alkylphospholipid analogs ( APLs ) are a family of anticancer drugs that show antileishmanial activity , including the first oral drug ( milte...	[ "Leishmaniasis is a major health problem worldwide , and can result in loss of human life or a lifelong stigma because of bodily scars .", "According to World Health Organization , leishmaniasis is considered as an emerging and uncontrolled disease , and its current treatment is far from ideal , with only a few d...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "viral attachment", "medicine and health sciences", "viral envelope", "viral entry", "protein interactions", "pathology and laboratory medicine", "molecular complexes", "host-pathogen interactions", "proteins", "virology", "viral transmission and infection", "biology and life...	Assembly and Architecture of the EBV B Cell Entry Triggering Complex	journal.ppat.1004309	null	[ [ "Epstein Barr Virus ( EBV ) or Human Herpesvirus 4 ( HHV-4 ) is a gammaherpesvirus that is ubiquitous in humans and predominantly infects host epithelial and B cells , in which it establishes long-term latency .", "It is an oncogenic virus associated with a wide array of human tumors including epithelial ...	[ "Epstein-Barr Virus ( EBV ) is an enveloped double-stranded DNA virus of the gammaherpesvirinae sub-family that predominantly infects humans through epithelial cells and B cells .", "Three EBV glycoproteins , gH , gL and gp42 , form a complex that targets EBV infection of B cells .", "Human leukocyte antigen ( ...	[ "The various steps by which lipid-enveloped viruses enter or ‘fuse’ with a host cell require the coordination of receptor recognition , viral protein activation and large protein conformational changes that can drive membrane bilayer fusion .", "Here we report biochemical , structural and functional experiments o...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "immune physiology", "pathology and laboratory medicine", "cardiovascular anatomy", "spleen", "pathogens", "animal models of disease", "microbiology", "animal models", "viruses", "histology", "model organisms", "heart", "rna viruses", "experimental organis...	Lineage-dependent differences in the disease progression of Zika virus infection in type-I interferon receptor knockout (A129) mice	journal.pntd.0005704	null	[ [ "Zika virus ( ZIKV ) is a flavivirus which was first isolated from a sentinel rhesus macaque placed in the Zika forest in Uganda in 1947 [1] and later from African mosquitoes collected in the same forest in the early 1960’s [2] .", "The virus remained a local curiosity of the East African Virus Research I...	[ "Zika virus ( ZIKV ) falls into two lineages: African ( ZIKVAF ) and Asian ( ZIKVAS ) .", "These lineages have not been tested comprehensively in parallel for disease progression using an animal model system .", "Here , using the established type-I interferon receptor knockout ( A129 ) mouse model , it is first...	[ "Since first being recognised in 1947 , Zika virus ( ZIKV ) has mainly been associated with a mild illness with symptoms including a limited fever and rash .", "In 2007 the virus spread from Africa and Asia into Micronesia , then in 2013 into French Polynesia and then onwards across Pacific regions and into South...	2017
[ "Introduction", "Discussion", "Material and methods" ]	[ "medicine and health sciences", "immune physiology", "pathology and laboratory medicine", "viral transmission and infection", "pathogens", "immunology", "microbiology", "vertebrates", "orthomyxoviruses", "animals", "viruses", "rna viruses", "viral release", "antibodies", "waterfowl", "...	Competition between influenza A virus subtypes through heterosubtypic immunity modulates re-infection and antibody dynamics in the mallard duck	journal.ppat.1006419	null	[ [ "Diversification is a common feature in pathogen populations and this often involves the evolution of antigenic variants [1] .", "Examples of this exist in various pathogen systems: viruses ( influenza A virus , Dengue virus , Bluetongue virus , and rotaviruses ) , bacteria ( Borrelia spp , Neisseria meni...	[ "Our overall hypothesis is that host population immunity directed at multiple antigens will influence the prevalence , diversity and evolution of influenza A virus ( IAV ) in avian populations where the vast subtype diversity is maintained .", "To investigate how initial infection influences the outcome of later ...	[ "Many features of pathogen diversification remain poorly explored although host immunity is recognized as a major driver of pathogen evolution .", "Influenza A viruses ( IAVs ) can infect many avian and mammalian hosts , but while few IAV subtypes circulate in human populations , subtype diversity is extensive in...	2017
[ "Introduction", "Materials and Methods", "Results and Discussion" ]	[ "diagnostic medicine", "infectious diseases", "tropical diseases", "medicine and health sciences" ]	Serological Diagnosis of Paracoccidioidomycosis: High Rate of Inter-laboratorial Variability among Medical Mycology Reference Centers	journal.pntd.0003174	null	[ [ "Paracoccidioidomycosis ( PCM ) is a neglected systemic fungal infection prevalent mostly in South America .", "Despite the significant progress in several areas of knowledge since it was described by Adolpho Lutz , in 1908 , it still shows high rates of morbidity and mortality and low visibility [1] .", ...	[ "Serological tests have long been established as rapid , simple and inexpensive tools for the diagnosis and follow-up of PCM .", "However , different protocols and antigen preparations are used and the few attempts to standardize the routine serological methods have not succeeded .", "We compared the performanc...	[ "Paracoccidioidomycosis ( PCM ) is a neglected systemic fungal infection prevalent mostly in South America .", "Serological tests have long been established as rapid , simple and inexpensive tools for the diagnosis and follow-up of PCM .", "However , different protocols and reagents are used .", "We compared ...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "organismal evolution", "deletion mutation", "insertion mutation", "population genetics", "microbiology", "operons", "cloning", "mutation", "nonsense mutation", "microbial evolution", "molecular biology techniques", "population biology", "dna", "evolutionary adaptation", "research and an...	A Mutational Hotspot and Strong Selection Contribute to the Order of Mutations Selected for during Escherichia coli Adaptation to the Gut	journal.pgen.1006420	null	[ [ "The composition of the gut microbiota can exert a strong influence on host physiology , behavior and health .", "Time series data have shown that the gut microbiota typically comprises a diverse community of species and that reduction of such diversity is frequently associated with illness [1] .", "L...	[ "The relative role of drift versus selection underlying the evolution of bacterial species within the gut microbiota remains poorly understood .", "The large sizes of bacterial populations in this environment suggest that even adaptive mutations with weak effects , thought to be the most frequently occurring , co...	[ "The relative contribution of random loss and migration versus de novo mutation to the overall diversity of the gut microbiota is far from understood .", "Population sizes of bacterial communities inhabiting the gut can be very large and therefore , both weak and strong effect beneficial mutations theoretically h...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases", "medicine and health sciences", "women's health", "obstetrics and gynecology", "gynecologic infections", "parasitic diseases" ]	A New Mouse Model for Female Genital Schistosomiasis	journal.pntd.0002825	null	[ [ "An estimated 240 million humans worldwide have schistosomiasis , an infection by Schistosoma worms of various species [1] .", "Human infection begins when aquatic cercariae found in contaminated water penetrate intact skin .", "Once in the human host , these cercariae migrate into the circulation as ...	[ "Over 112 million people worldwide are infected with Schistosoma haematobium , one of the most prevalent schistosome species affecting humans .", "Female genital schistosomiasis ( FGS ) occurs when S . haematobium eggs are deposited into the female reproductive tract by adult worms , which can lead to pelvic pain...	[ "Over 112 million people worldwide are infected with Schistosoma haematobium worms .", "S . haematobium eggs tend to be deposited in the tissue of pelvic organs such as the urinary bladder , lower ureters , cervix and vagina .", "Key sequelae include hematuria , dysuria , urinary frequency , and an increased ri...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "signal transduction", "developmental biology", "dna transcription", "rna interference", "cell biology", "molecular development", "gene expression", "genetics", "gene regulation", "biology and life sciences", "epigenetics", "molecular genetics", "molecular cell biology", "cell signaling", ...	The Homeodomain Protein Ladybird Late Regulates Synthesis of Milk Proteins during Pregnancy in the Tsetse Fly (Glossina morsitans)	journal.pntd.0002645	null	[ [ "Tsetse flies ( Glossina sp . ) are the exclusive vectors of Human African Trypanosomiasis ( HAT ) and nagana in Sub-Saharan Africa .", "HAT transmission can be prevented through tsetse population control by baited targets and trapping [1] .", "These control methods are effective due to the unusual na...	[ "Regulation of tissue and development specific gene expression patterns underlies the functional specialization of organs in multi-cellular organisms .", "In the viviparous tsetse fly ( Glossina ) , the female accessory gland is specialized to generate nutrients in the form of a milk-like secretion to support gro...	[ "Female tsetse flies ( Diptera: Glossina ) harbor and give birth to live young .", "To do this , they nourish their intrauterine larvae with milk secretions .", "This work focuses upon understanding the regulation of tsetse milk proteins , which are essential for fecundity and are expressed in a temporally and ...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases/protozoal infections", "infectious diseases/neglected tropical diseases", "public health and epidemiology/infectious diseases", "pediatrics and child health" ]	Risk Factors for Death in Children with Visceral Leishmaniasis	journal.pntd.0000877	null	[ [ "In Latin America , visceral leishmaniasis ( VL ) cases occur from Mexico to Argentina , but around 90% of reported cases come from Brazil [1] .", "Despite substantial underreporting in several different parts of the world [1] , Brazil's national surveillance system has informed estimates of disease burde...	[ "Despite the major public health importance of visceral leishmaniasis ( VL ) in Latin America , well-designed studies to inform diagnosis , treatment and control interventions are scarce .", "Few observational studies address prognostic assessment in patients with VL .", "This study aimed to identify risk facto...	[ "Visceral leishmaniasis ( VL ) is a deadly disease caused by a protozoan called Leishmania .", "It is transmitted to humans from infected animals by a sandfly bite .", "Most people actually manage to control the infection and do not get sick , while others develop a range of symptoms .", "VL impairs the produ...	2010
[ "Introduction", "Results", "Discussion", "Methods and models" ]	[ "meiosis", "parasite groups", "medicine and health sciences", "liver", "oocysts", "cell cycle and cell division", "gametocytes", "cell processes", "social sciences", "parasitic diseases", "parasitology", "health care", "germ cells", "apicomplexa", "infectious diseases", "health economi...	Modeling the genetic relatedness of Plasmodium falciparum parasites following meiotic recombination and cotransmission	journal.pcbi.1005923	null	[ [ "Unlike most bacterial and viral pathogens , the malaria parasite P . falciparum , while predominantly haploid , must sexually reproduce in a mosquito vector before infecting a new human host .", "Sexual recombination has a significant impact on the population genomics of the parasite , and its effects de...	[ "Unlike in most pathogens , multiple-strain ( polygenomic ) infections of P . falciparum are frequently composed of genetic siblings .", "These genetic siblings are the result of sexual reproduction and can coinfect the same host when cotransmitted by the same mosquito .", "The degree with which coinfecting str...	[ "Genomic studies of P . falciparum reveal that multi-strain infections can include genetically related strains .", "P . falciparum must reproduce sexually in the mosquito vector .", "One consequence of sexual reproduction is that parasites cotransmitted by the same mosquito are related to one another .", "The...	2018
[ "Introduction", "Model", "Results", "Discussion" ]	[ "computational biology/synthetic biology", "computer science/applications", "cell biology/cell signaling", "biophysics/theory and simulation", "cell biology/microbial growth and development", "microbiology/microbial growth and development", "computational biology/systems biology" ]	Spatial Simulations of Myxobacterial Development	journal.pcbi.1000686	null	[ [ "Bacteria are able to sense their surroundings in order to adapt to environmental change .", "Most bacteria live in dense populations , therefore other cells constitute a major part of their physical and chemical environment allowing regulatory interactions between cells to be established .", "The ben...	[ "Many bacteria exhibit multicellular behaviour , with individuals within a colony coordinating their actions for communal benefit .", "One example of complex multicellular phenotypes is myxobacterial fruiting body formation , where thousands of cells aggregate into large three-dimensional structures , within whic...	[ "Understanding how relatively simple , single cell bacteria can communicate and coordinate their actions is important for explaining how complex multicellular behaviour can emerge without a central controller .", "Myxobacteria are particularly interesting in this respect because cells undergo multiple phases of c...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell death", "signal transduction", "signaling in cellular processes", "molecular cell biology", "immune cells", "cell biology", "membrane receptor signaling", "t cells", "immunology", "biology", "autoimmunity", "molecular biology" ]	The Naturally Processed CD95L Elicits a c-Yes/Calcium/PI3K-Driven Cell Migration Pathway	journal.pbio.1001090	null	[ [ "Screening for death inducers led to the discovery of the receptor CD95 , which was initially cloned and described as a death receptor belonging to the TNF-R family [1] , [2] .", "Since CD95 is devoid of enzymatic activity , both aggregation [3] and conformational modification [4] of the receptor are cruc...	[ "Patients affected by chronic inflammatory disorders display high amounts of soluble CD95L .", "This homotrimeric ligand arises from the cleavage by metalloproteases of its membrane-bound counterpart , a strong apoptotic inducer .", "In contrast , the naturally processed CD95L is viewed as an apoptotic antagoni...	[ "The “death receptor” CD95 ( also known as Fas ) plays an essential role in ensuring immune tolerance of self antigens as well as in the elimination of the body's cells that have been infected or transformed .", "This receptor is engaged by the membrane-bound ligand CD95L , which can be released into blood circul...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods", "Data deposition" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "pathogens", "microbiology", "cytomegalovirus infection", "viral structure", "viruses", "materials science", "dna viruses", "protein structure", "oligomers", "herpesviruses", "human cytomegalovirus", "polymer chemistry", ...	Atomic structures and deletion mutant reveal different capsid-binding patterns and functional significance of tegument protein pp150 in murine and human cytomegaloviruses with implications for therapeutic development	journal.ppat.1007615	null	[ [ "Cytomegalovirus ( CMV ) is a member of the β-herpesvirus subfamily of the herpesvirus family and can establish lifelong subclinical ( latent ) infection among the majority of the human population .", "Active human CMV ( HCMV ) infection is the leading viral cause of birth defects ( in utero and in neonat...	[ "Cytomegalovirus ( CMV ) infection causes birth defects and life-threatening complications in immunosuppressed patients .", "Lack of vaccine and need for more effective drugs have driven widespread ongoing therapeutic development efforts against human CMV ( HCMV ) , mostly using murine CMV ( MCMV ) as the model s...	[ "Cytomegalovirus ( CMV ) infection is a leading viral cause of birth defects and could be deadly to AIDS patients and organ transplant recipients .", "Absence of effective vaccines and potent drugs against human CMV ( HCMV ) infections has motivated animal-based studies , mostly based on the mouse model with muri...	2019
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	A Dynamic Gene Regulatory Network Model That Recovers the Cyclic Behavior of Arabidopsis thaliana Cell Cycle	journal.pcbi.1004486	null	[ [ "The eukaryotic cell cycle ( CC ) in multicellular organisms is regulated spatio-temporally to yield normal morphogenetic patterns .", "In plants , organogenesis occurs over the entire lifespan , thus CC arrest , reactivation , and cell differentiation , as well as endoreduplication should be dynamically ...	[ "Cell cycle control is fundamental in eukaryotic development .", "Several modeling efforts have been used to integrate the complex network of interacting molecular components involved in cell cycle dynamics .", "In this paper , we aimed at recovering the regulatory logic upstream of previously known components ...	[ "In multicellular organisms , cells undergo a cyclic behavior of DNA duplication and delivery of a copy to daughter cells during cell division .", "In each of the main cell-cycle ( CC ) stages different sets of proteins are active and genes are expressed .", "Understanding how such cycling cellular behavior eme...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genome expression analysis", "animal genetics", "functional genomics", "gene function", "animal models", "developmental biology", "model organisms", "molecular genetics", "gene expression", "gene splicing", "biology", "molecular biology", "systems biology", "biochemistry", "nucleic acid...	Identification of Evolutionarily Conserved Exons as Regulated Targets for the Splicing Activator Tra2β in Development	journal.pgen.1002390	null	[ [ "Almost all transcripts from genes encoding multiple exons are alternatively spliced , and correct patterns of alternative splicing are important for health and normal development [1] , [2] , [3] .", "Alternative splicing introduces new coding information into mRNAs , thereby increasing genome capacity to...	[ "Alternative splicing amplifies the information content of the genome , creating multiple mRNA isoforms from single genes .", "The evolutionarily conserved splicing activator Tra2β ( Sfrs10 ) is essential for mouse embryogenesis and implicated in spermatogenesis .", "Here we find that Tra2β is up-regulated as t...	[ "Alternative splicing amplifies the informational content of the genome , making multiple mRNA isoforms from single genes .", "Tra2 proteins bind and activate alternative exons , and in mice Tra2β is essential for embryonic development through unknown target RNAs .", "Here we report the first target exons that ...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell physiology", "medicine and health sciences", "pathology and laboratory medicine", "pathogens", "microbiology", "viruses", "dna viruses", "viral genome", "genome analysis", "microbial genomics", "research and analysis methods", "sequence analysis", "genomic signal processing", "viral ...	HPV integration hijacks and multimerizes a cellular enhancer to generate a viral-cellular super-enhancer that drives high viral oncogene expression	journal.pgen.1007179	null	[ [ "High oncogenic-risk human papillomaviruses ( HPVs ) are the etiological agent responsible for virtually all cervical cancers [1] , and a growing number of other anogenital and oropharyngeal cancers [2] .", "During the normal viral life cycle , HPVs are maintained as extrachromosomal elements within the c...	[ "Integration of human papillomavirus ( HPV ) genomes into cellular chromatin is common in HPV-associated cancers .", "Integration is random , and each site is unique depending on how and where the virus integrates .", "We recently showed that tandemly integrated HPV16 could result in the formation of a super-en...	[ "Oncogenic human papillomavirus ( HPV ) infection is responsible for ~5% human cancers .", "A key event in the development of many of these cancers is integration of the viral genome into host chromatin .", "Integration results in dysregulated expression of the viral oncogenes , which promotes unregulated cellu...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics of the immune system", "genetic polymorphism", "zoology", "immunity", "entomology", "innate immunity", "immunity to infections", "immunology", "host-pathogen interaction", "biology", "microbiology", "population biology", "population genetics", "immune response" ]	Genetic Dissection of Anopheles gambiae Gut Epithelial Responses to Serratia marcescens	journal.ppat.1003897	null	[ [ "Genetic variation within populations of the An .", "gambiae mosquito , especially with regard to genes encoding immune factors , is believed to play an important role in the mosquito susceptibility to infection by the malaria parasite Plasmodium falciparum [1]–[3] .", "Many immune factors exhibit bot...	[ "Genetic variation in the mosquito Anopheles gambiae profoundly influences its ability to transmit malaria .", "Mosquito gut bacteria are shown to influence the outcome of infections with Plasmodium parasites and are also thought to exert a strong drive on genetic variation through natural selection; however , a ...	[ "In malaria vector mosquitoes , the presence of bacteria and malaria parasites is tightly linked .", "Bacteria that are part of the mosquito gut ecosystem are critical modulators of the immune response elicited during infection with malaria parasites .", "Furthermore , responses against oral bacterial infection...	2014
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "evolutionary biology/microbial evolution and genomics", "virology/virus evolution and symbiosis", "evolutionary biology/bioinformatics", "evolutionary biology/evolutionary ecology" ]	The Evolutionary Genetics and Emergence of Avian Influenza Viruses in Wild Birds	journal.ppat.1000076	null	[ [ "Low pathogenic ( LP ) , antigenically diverse influenza A viruses are widely distributed in wild avian species around the world .", "They are maintained by asymptomatic infections , most frequently documented in aquatic birds of the orders Anseriformes and Charadriformes .", "As such , wild birds rep...	[ "We surveyed the genetic diversity among avian influenza virus ( AIV ) in wild birds , comprising 167 complete viral genomes from 14 bird species sampled in four locations across the United States .", "These isolates represented 29 type A influenza virus hemagglutinin ( HA ) and neuraminidase ( NA ) subtype combi...	[ "Influenza A viruses are an extremely divergent group of RNA viruses that infect in a variety of warm-blooded animals , including birds , horses , pigs , and humans .", "Since they contain a segmented RNA genome , mixed infection can lead to genetic reassortment .", "It is thought that the natural reservoir of ...	2008
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "antimicrobials", "pharmacologic analysis", "deletion mutation", "medicine and health sciences", "pathology and laboratory medicine", "antibiotic susceptibility testing", "pathogens", "drugs", "bacillus", "microbiology", "operons", "mutation", "prokaryotic models", "antibiotics", "materi...	A metabolic checkpoint protein GlmR is important for diverting carbon into peptidoglycan biosynthesis in Bacillus subtilis	journal.pgen.1007689	null	[ [ "Bacillus subtilis provides a powerful model system for understanding cell wall homeostasis in Gram positive bacteria .", "Disruption of pathways for the synthesis of peptidoglycan ( PG ) and other cell envelope components elicits complex adaptive responses often controlled by alternative σ factors or two...	[ "The Bacillus subtilis GlmR ( formerly YvcK ) protein is essential for growth on gluconeogenic carbon sources .", "Mutants lacking GlmR display a variety of phenotypes suggestive of impaired cell wall synthesis including antibiotic sensitivity , aberrant cell morphology and lysis .", "To define the role of GlmR...	[ "Bacterial cells are surrounded by a peptidoglycan cell wall that is , under most conditions , required for viability .", "Synthesis of the cell wall requires a considerable diversion of resources from central carbon metabolism into a lipid-linked precursor ( lipid II ) that is exported from the cell for wall ass...	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "dengue", "viral diseases" ]	The Early Clinical Features of Dengue in Adults: Challenges for Early Clinical Diagnosis	journal.pntd.0001191	null	[ [ "The mosquito-borne dengue virus ( DENV ) has emerged in the latter half of the 20th century to become an important cause of morbidity and mortality .", "Over half of the world's population live at risk of infection annually [1] .", "Infection with any of the four antigenically distinct virus serotype...	[ "The emergence of dengue throughout the tropical world is affecting an increasing proportion of adult cases .", "The clinical features of dengue in different age groups have not been well examined , especially in the context of early clinical diagnosis .", "We structured a prospective study of adults ( ≥18 year...	[ "Dengue infection in adults has become increasingly common throughout the world .", "As most of the clinical features of dengue have been described in children , we undertook a prospective study to determine the early symptoms and signs of dengue in adults .", "We show here that , overall , dengue cases present...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "ecology/evolutionary ecology", "evolutionary biology/evolutionary ecology" ]	Aging in a Long-Lived Clonal Tree	journal.pbio.1000454	Using genetic estimates of clone age in trembling aspen, this study demonstrates a significant decline in male sexual fitness with increasing age, showing that long-lived clonal organisms are vulnerable to aging.	[ [ "Many species of animals , and even bacteria , demonstrate a decline in survivorship or reproductive performance with increasing age ( “senescence” ) [1] , [2] .", "Evidence for senescence in perennial plants , however , is scant [3] , [4] , [7] .", "One feature that distinguishes plants from many ani...	[ "From bacteria to multicellular animals , most organisms exhibit declines in survivorship or reproductive performance with increasing age ( “senescence” ) [1] , [2] .", "Evidence for senescence in clonal plants , however , is scant [3] , [4] .", "During asexual growth , we expect that somatic mutations , which ...	[ "Aging has been demonstrated in many animals and even in bacteria , but there is little empirical work showing that clonal plants age .", "Evidence for aging in long-lived perennials is scarce because it typically requires survivorship or fecundity schedules from long-term demographic data .", "Given the extrem...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "drosophila", "genetics and genomics" ]	Evidence for Transgenerational Transmission of Epigenetic Tumor Susceptibility in Drosophila	journal.pgen.0030151	null	[ [ "Epigenetic regulation of gene expression refers to repression or activation of gene expression via covalent modifications of DNA or histones , such as methylation or acetylation , without changing the DNA sequence of the gene [1–3] .", "Epigenetic modifications are usually stably heritable through subseq...	[ "Transgenerational epigenetic inheritance results from incomplete erasure of parental epigenetic marks during epigenetic reprogramming at fertilization .", "The significance of this phenomenon , and the mechanism by which it occurs , remains obscure .", "Here , we show that genetic mutations in Drosophila may c...	[ "It is well known that many genetic mutations in oncogenes or tumor suppressors can cause or greatly increase a person's susceptibility to cancer .", "It is generally assumed that persons should feel relieved if they have not inherited the particular “cancer-causing” mutation carried by their parents .", "Howev...	2007
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "bacterial diseases", "infectious diseases", "molecular epidemiology", "infectious disease epidemiology", "environmental epidemiology", "epidemiology", "neglected tropical diseases", "leptospirosis" ]	Regional Differences of Leptospirosis in Sri Lanka: Observations from a Flood-Associated Outbreak in 2011	journal.pntd.0002626	null	[ [ "Sri Lanka is a tropical island located southeast of India .", "Annual rainfall varies from <1 , 500 mm in “dry” zones , where water reservoirs may dry to completeness , to 5 , 000 mm in the “wet” zones with a mean annual temperature between 26 . 5°C to 28 . 5°C .", "Based on Ministry of Health notifi...	[ "Leptospirosis is known to be an important cause of weather disaster-related infectious disease epidemics .", "In 2011 , an outbreak of leptospirosis occurred in the relatively dry district of Anuradhapura , Sri Lanka where diagnosis was resisted by local practitioners because leptospirosis was not known in the a...	[ "Leptospirosis outbreaks occur predictably in Sri Lanka after seasonal rains and flooding in the endemic wet zone .", "Molecular investigations with quantification of a post-flood leptospirosis outbreak in the non-endemic dry zone of Sri Lanka in 2011 suggest variation of biological , clinical , and molecular cha...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases/bacterial infections", "infectious diseases/neglected tropical diseases", "infectious diseases/tropical and travel-associated diseases", "microbiology/cellular microbiology and pathogenesis" ]	Cross-Reactivity of Antibodies against Leptospiral Recurrent Uveitis-Associated Proteins A and B (LruA and LruB) with Eye Proteins	journal.pntd.0000778	null	[ [ "Infectious disease caused by spirochetes of the genus Leptospira is a veterinary and public health problem of global proportions [1] , [2] .", "Humans and other mammals are exposed to the organism when they contact groundwater contaminated with urine from carrier animals .", "The disease in humans va...	[ "Infection by Leptospira interrogans has been causally associated with human and equine uveitis .", "Studies in our laboratories have demonstrated that leptospiral lipoprotein LruA and LruB are expressed in the eyes of uveitic horses , and that antibodies directed against LruA and LruB react with equine lenticula...	[ "Leptospira is the most common infectious cause of uveitis , a potentially debilitating inflammation of the eye .", "In our earlier work , we discovered that eye fluids of uveitic horses contain high levels of antibodies directed against novel leptospiral proteins , which we named LruA and LruB ( Leptospiral recu...	2010
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "evolutionary biology", "computational biology/genomics", "evolutionary biology/evolutionary and comparative genetics" ]	Tracking Marsupial Evolution Using Archaic Genomic Retroposon Insertions	journal.pbio.1000436	Genome-wide comparisons of shared retroposon insertion patterns resolve the phylogeny of marsupials, clearly distinguishing South American and Australian species and lending support to Didelphimorphia as the basal split.	[ [ "The phylogenetic relationships among the four Australasian and three South American marsupial orders have been intensively debated ever since the small species Dromiciops was taxonomically moved from Didelphimorphia into the new order Microbiotheria and the cohort Australidelphia was erected based on ankle j...	[ "The Australasian and South American marsupial mammals , such as kangaroos and opossums , are the closest living relatives to placental mammals , having shared a common ancestor around 130 million years ago .", "The evolutionary relationships among the seven marsupial orders have , however , so far eluded resolut...	[ "Ever since the first Europeans reached the Australian shores and were fascinated by the curious marsupials they found , the evolutionary relationships between the living Australian and South American marsupial orders have been intensively investigated .", "However , neither the morphological nor the more recent ...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "organismal evolution", "genetic mutation", "genome evolution", "gene classes", "microbiology", "sequence assembly tools", "genome sequencing", "genome analysis tools", "genome databases", "mutation types", "microbial evolution", "molecular genetics", "tsetse fly", "sequence analysis", "...	A Novel Human-Infection-Derived Bacterium Provides Insights into the Evolutionary Origins of Mutualistic Insect–Bacterial Symbioses	journal.pgen.1002990	null	[ [ "Obligate host-associated bacteria often have reduced genome sizes in comparison to related bacteria that are known to engage in free-living or opportunistic lifestyles [1] .", "This is exemplified by inspection of the genome sequences of mutualistic , maternally transmitted , bacterial endosymbionts of i...	[ "Despite extensive study , little is known about the origins of the mutualistic bacterial endosymbionts that inhabit approximately 10% of the world's insects .", "In this study , we characterized a novel opportunistic human pathogen , designated “strain HS , ” and found that it is a close relative of the insect e...	[ "Many insects harbor symbiotic bacteria that perform diverse functions within their hosts .", "However , the origins of these associations have been difficult to define .", "In this study we isolate a novel bacterium from a human infection and show that this bacterium is a close relative of the Sodalis-allied c...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "neonatology", "insulin-like growth factor", "immune physiology", "cytokines", "growth retardation", "enzymes", "regulatory proteins", "integrative physiology", "anatomy and physiology", "rna stability", "pediatrics", "endocrine physiology", "gene function", "animal models", ...	Zcchc11 Uridylates Mature miRNAs to Enhance Neonatal IGF-1 Expression, Growth, and Survival	journal.pgen.1003105	null	[ [ "Non-canonical poly ( A ) polymerases ( PAPs ) comprise a family of enzymes highly conserved across Eukaryota and capable of catalyzing the template-independent transfer of uridines and adenines onto single-stranded RNA substrates [1] , [2] .", "Several non-canonical PAPs , including the uridyltransferase...	[ "The Zcchc11 enzyme is implicated in microRNA ( miRNA ) regulation .", "It can uridylate let-7 precursors to decrease quantities of the mature miRNA in embryonic stem cell lines , suggested to mediate stem cell maintenance .", "It can uridylate mature miR-26 to relieve silencing activity without impacting miRNA...	[ "MicroRNAs ( miRNAs ) are molecules that regulate gene expression , usually serving silencing functions .", "Mechanisms regulating miRNAs are poorly understood .", "In test tube experiments , the enzyme Zcchc11 adds uridines to the ends of miRNAs and their precursors , with uridyation of miRNA precursors decrea...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "phosphorylation", "cell death", "cell viability testing", "chemical compounds", "gene regulation", "cell processes", "biological cultures", "organic compounds", "animal signaling and communication", "tyrosine", "animal behavior", "amino acids", "bioassays and physiological analysis", "zoo...	An Evolution-Guided Analysis Reveals a Multi-Signaling Regulation of Fas by Tyrosine Phosphorylation and its Implication in Human Cancers	journal.pbio.1002401	Signalling by the tumor necrosis factor receptor (TNFR) superfamily member Fas can promote either survival or death of a cell, but the mechanism underlying this choice is unclear. This study reveals that the outcome of Fas signalling (death versus survival) is determined by the tyrosine phosphorylation status of its de...	[ [ "Fas ( CD95/APO-1/TNFRSF6 ) , a tumor necrosis factor ( TNF ) receptor superfamily member , is a well-known apoptosis activator .", "The binding with Fas ligand ( FasL ) can lead to the recruitment of Fas-associated protein with death domain ( FADD ) and procaspase-8 , forming the death-inducing signaling...	[ "Demonstrations of both pro-apoptotic and pro-survival abilities of Fas ( TNFRSF6/CD95/APO-1 ) have led to a shift from the exclusive “Fas apoptosis” to “Fas multisignals” paradigm and the acceptance that Fas-related therapies face a major challenge , as it remains unclear what determines the mode of Fas signaling ...	[ "The versatility of the tumor necrosis factor receptor superfamily members in cell fate regulation is well illustrated by the dual signaling generated by one of the most extensively studied members of the family , Fas ( CD95/TNFSFR6 ) .", "Upon binding its ligand , Fas is able to elicit both pro-death and pro-sur...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/fungal infections", "immunology/immunity to infections", "immunology/innate immunity" ]	Neutrophil Extracellular Traps Contain Calprotectin, a Cytosolic Protein Complex Involved in Host Defense against Candida albicans	journal.ppat.1000639	null	[ [ "Neutrophils are an essential component of the innate immune response since neutropenia or impairment of neutrophil function results in microbial infections that are often fatal [1] .", "Microbes engulfed by neutrophils are efficiently killed by reactive oxygen species ( ROS ) and antimicrobial proteins w...	[ "Neutrophils are the first line of defense at the site of an infection .", "They encounter and kill microbes intracellularly upon phagocytosis or extracellularly by degranulation of antimicrobial proteins and the release of Neutrophil Extracellular Traps ( NETs ) .", "NETs were shown to ensnare and kill microbe...	[ "Neutrophils are phagocytes that disarm and kill microbes by engulfing them .", "Less well characterized than their phagocytic killing mechanisms is how neutrophils cope with microbes that are too large to be internalized .", "Notably , neutrophils may also kill or inhibit extracellularly by releasing Neutrophi...	2009
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "organismal evolution", "medicine and health sciences", "microbiology", "mutation", "fungal evolution", "microbial evolution", "evolutionary adaptation", "pharmacology", "mycology", "antimicrobial resistance", "gene expression", "evolutionary genetics", "phenotypes", "genetics", "microbi...	Phenotypic heterogeneity promotes adaptive evolution	journal.pbio.2000644	null	[ [ "According to classical evolutionary theory , genetic variation provides the major source of heritable variation on which natural selection acts .", "However , many scholars argue that phenotypic heterogeneity can accelerate adaptive evolution [1–3] .", "Phenotypic heterogeneity can take many forms , ...	[ "Genetically identical cells frequently display substantial heterogeneity in gene expression , cellular morphology and physiology .", "It has been suggested that by rapidly generating a subpopulation with novel phenotypic traits , phenotypic heterogeneity ( or plasticity ) accelerates the rate of adaptive evoluti...	[ "Phenotypic heterogeneity of genetically identical cells can generate nonheritable variation in a population .", "Is this heterogeneity favorable for microbes ?", "In a changing environment , the answer is a definite yes .", "While scholars have argued that stochastically generated variation precedes genetic ...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	FGFR3 Deficiency Causes Multiple Chondroma-like Lesions by Upregulating Hedgehog Signaling	journal.pgen.1005214	null	[ [ "Enchondromas and osteochondromas are the most frequently occurring benign cartilaginous tumors affecting the skeleton [1 , 2] .", "The former develop as ectopic cartilaginous tissue within the bone marrow , while the latter manifest as cartilage-covered bony lesions arising on the bone surface [3] .", ...	[ "Most cartilaginous tumors are formed during skeletal development in locations adjacent to growth plates , suggesting that they arise from disordered endochondral bone growth .", "Fibroblast growth factor receptor ( FGFR ) 3 signaling plays essential roles in this process; however , the role of FGFR3 in cartilagi...	[ "Benign cartilaginous tumors , especially osteochondromas and enchondromas , are the most common primary bone tumors in humans .", "Several hereditary diseases are characterized by the development of cartilaginous tumors , including hereditary multiple exostoses , metachondromatosis , and enchondromatosis , which...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry/protein folding", "biochemistry/protein chemistry", "microbiology", "infectious diseases/bacterial infections", "biochemistry/structural genomics" ]	The Subtilisin-Like Protease AprV2 Is Required for Virulence and Uses a Novel Disulphide-Tethered Exosite to Bind Substrates	journal.ppat.1001210	null	[ [ "Dichelobacter nodosus is a Gram negative , anaerobic rod that is the principal causative agent of ovine footrot , a debilitating disease of the hoof of ruminants .", "The disease results in significant costs to the worldwide sheep industry due to a reduction in meat and wool production and the expenditur...	[ "Many bacterial pathogens produce extracellular proteases that degrade the extracellular matrix of the host and therefore are involved in disease pathogenesis .", "Dichelobacter nodosus is the causative agent of ovine footrot , a highly contagious disease that is characterized by the separation of the hoof from t...	[ "Extracellular proteases are produced by many bacterial pathogens and are commonly involved in the degradation of the host extracellular matrix , facilitating invasion and colonization .", "One such pathogen is Dichelobacter nodosus , the causative agent of ovine footrot , a disease of major economic significance...	2010
[ "Introduction", "Results and Discussion", "Materials and Methods" ]	[]	Release of Small RNA-containing Exosome-like Vesicles from the Human Filarial Parasite Brugia malayi	journal.pntd.0004069	null	[ [ "The parasitic filarial nematodes Wuchereria bancrofti , Brugia malayi and B . timori are etiological agents of Lymphatic filariasis ( LF ) , a chronic and debilitating disease infecting over 120 million people in 73 endemic countries [1] .", "Adult parasites reside in the lymphatic vasculature of infecte...	[ "Lymphatic filariasis ( LF ) is a socio-economically devastating mosquito-borne Neglected Tropical Disease caused by parasitic filarial nematodes .", "The interaction between the parasite and host , both mosquito and human , during infection , development and persistence is dynamic and delicately balanced .", "...	[ "Lymphatic filariasis is caused by parasitic nematodes that invade and occupy the host lymphatic system .", "The extent of lymphatic filariasis is staggering , with over 120 million people infected in 73 endemic countries and an estimated 40 million people suffering from a range of disfiguring and debilitating cl...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "antimicrobials", "medicine and health sciences", "drugs", "microbiology", "operons", "antibiotic resistance", "fungi", "plant science", "antibiotics", "plant pathology", "pharmacology", "dna", "molecular biology techniques", "cellular structures and organelles", "research and analysis m...	A Chemical-Genomic Screen of Neglected Antibiotics Reveals Illicit Transport of Kasugamycin and Blasticidin S	journal.pgen.1006124	null	[ [ "The emerging threat of antibiotic resistance [1] necessitates new efforts and ideas to control bacterial pathogens .", "Mapping the determinants of antibiotic resistance in bacteria will be critical for evaluating new antibiotics .", "In addition to the direct target of the antibiotic , drug efflux ,...	[ "Fighting antibiotic resistance requires a deeper understanding of the genetic factors that determine the antibiotic susceptibility of bacteria .", "Here we describe a chemical-genomic screen in Escherichia coli K-12 that was designed to discover new aspects of antibiotic resistance by focusing on a set of 26 ant...	[ "Bacterial species differ in their susceptibility to antibiotics but the reason for these differences remains an open question .", "Understanding the genetic basis of antibiotic susceptibility will be critical for predicting the efficacy of new antibiotics and possibly finding new antibiotic targets .", "Here w...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "hematologic cancers and related disorders", "medicine", "genome expression analysis", "leukemias", "genomics", "biology", "computational biology", "epigenomics", "hematology" ]	Base-Pair Resolution DNA Methylation Sequencing Reveals Profoundly Divergent Epigenetic Landscapes in Acute Myeloid Leukemia	journal.pgen.1002781	null	[ [ "Acute myeloid leukemia ( AML ) is considered to be a genetically heterogeneous group of diseases , featuring functionally distinct somatic mutations and chromosomal translocations [1] .", "Many of these mutations involve aberrant transcriptional and epigenetic regulators , such as translocations involvin...	[ "We have developed an enhanced form of reduced representation bisulfite sequencing with extended genomic coverage , which resulted in greater capture of DNA methylation information of regions lying outside of traditional CpG islands .", "Applying this method to primary human bone marrow specimens from patients wi...	[ "Acute myeloid leukemias ( AML ) are a group of malignancies that originate in the bone marrow .", "While many different genetic lesions have been linked to the different forms of this disease , it is also clear that these genetic lesions are not always sufficient to cause AML .", "DNA methylation plays a role ...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "taxonomy", "invertebrates", "organismal evolution", "medicine and health sciences", "microbiome", "microbiology", "vertebrates", "animals", "mammals", "animal phylogenetics", "animal models", "phylogenetics", "drosophila melanogaster", "model organisms", "data management", "phylogenet...	Phylosymbiosis: Relationships and Functional Effects of Microbial Communities across Host Evolutionary History	journal.pbio.2000225	null	[ [ "A large body of literature has documented genetic and environmental influences on the composition of host-associated microbial communities [1–10] .", "Although environmental factors are considered to play a much larger role than host genetics and evolutionary history [11] , host influences and their func...	[ "Phylosymbiosis was recently proposed to describe the eco-evolutionary pattern , whereby the ecological relatedness of host-associated microbial communities parallels the phylogeny of related host species .", "Here , we test the prevalence of phylosymbiosis and its functional significance under highly controlled ...	[ "Studies on the assembly and function of host-microbiota symbioses are inherently complicated by the diverse effects of diet , age , sex , host genetics , and endosymbionts .", "Central to unraveling one effect from the other is an experimental framework that reduces confounders .", "Using common rearing condit...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genome complexity", "genomics", "genome evolution", "genetics", "population genetics", "biology", "evolutionary biology", "genetics and genomics", "human genetics" ]	Complex Patterns of Genomic Admixture within Southern Africa	journal.pgen.1003309	null	[ [ "Southern Africa is home to populations carrying significant human genomic variation .", "The analysis of patterns of DNA variation , have placed modern human origins within Africa [1] , with the most divergent contemporary lineages found in the indigenous Khoesan inhabitants of southern Africa [2]–[6] ."...	[ "Within-population genetic diversity is greatest within Africa , while between-population genetic diversity is directly proportional to geographic distance .", "The most divergent contemporary human populations include the click-speaking forager peoples of southern Africa , broadly defined as Khoesan .", "Both ...	[ "The Khoesan have received recent attention , as they are the most genetically diverse contemporary human populations .", "However , Khoesan populations are poorly defined , while archeological evidence suggests a once broader dispersal of click-speaking southern African foragers .", "Migrations into the region...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "chile (country)", "vector-borne diseases", "geographical locations", "vertebrates", "parasitic diseases", "parasitic protozoans", "animals", "mammals", "organisms", "seasons", "protozoans", "infectious diseases", "south america", "winter", "protozoan in...	Spatio-temporal characterization of Trypanosoma cruzi infection and discrete typing units infecting hosts and vectors from non-domestic foci of Chile	journal.pntd.0007170	null	[ [ "Chagas disease is a zoonotic parasitic disease , endemic in 22 countries of America , caused by the flagellated protozoa Trypanosoma cruzi .", "This disease affects approximately 7 million people in the world and represents the third parasitic disease of major world impact [1] .", "The parasite is tr...	[ "Trypanosoma cruzi is a protozoan parasite that is transmitted by triatomine vectors to mammals .", "It is classified in six discrete typing units ( DTUs ) .", "In Chile , domestic vectorial transmission has been interrupted; however , the parasite is maintained in non-domestic foci .", "The aim of this study...	[ "Trypanosoma cruzi is a parasite that infects mammals , transmitted by triatomine insect vectors in America , causing Chagas disease in humans .", "There are six T . cruzi discrete typing units ( DTUs ) .", "Our goal was to estimate T . cruzi infection rates and describe the DTUs present in mammals and triatomi...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/genetics of disease", "oncology/prostate cancer", "genetics and genomics/gene expression" ]	Analysis of the 10q11 Cancer Risk Locus Implicates MSMB and NCOA4 in Human Prostate Tumorigenesis	journal.pgen.1001204	null	[ [ "Variation at rs10993994 on chromosome 10q11 is associated with prostate cancer risk [1]–[5] .", "The risk polymorphism is located at the telomeric end of a 50 kilobase ( kb ) linkage disequilibrium block and is within 60 base pairs ( bp ) of the transcription start site of beta-microseminoprotein ( MSMB ...	[ "Genome-wide association studies ( GWAS ) have established a variant , rs10993994 , on chromosome 10q11 as being associated with prostate cancer risk .", "Since the variant is located outside of a protein-coding region , the target genes driving tumorigenesis are not readily apparent .", "Two genes nearest to t...	[ "Family history has long been recognized as an important risk factor for prostate cancer .", "Beginning in 2006 , researchers have identified several genetic variants that are associated with prostate cancer risk .", "Intriguingly , the majority of prostate cancer risk variants do not reside in genes .", "Det...	2010
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "ecology and environmental sciences", "water resources", "cross-sectional studies", "tropical diseases", "geographical locations", "health care", "bacterial diseases", "research design", "mathematics", "statistics (mathematics)", "neglected tropical diseases", ...	Socioeconomic risk markers of leprosy in high-burden countries: A systematic review and meta-analysis	journal.pntd.0006622	null	[ [ "Leprosy , a chronic infectious disease caused by Mycobacterium leprae , remains endemic in 13 low and middle-income countries worldwide [1] .", "While effective and affordable multidrug therapies have the potential to cure infections , failures in detection and treatment can lead to the development of st...	[ "Over 200 , 000 new cases of leprosy are detected each year , of which approximately 7% are associated with grade-2 disabilities ( G2Ds ) .", "For achieving leprosy elimination , one of the main challenges will be targeting higher risk groups within endemic communities .", "Nevertheless , the socioeconomic risk...	[ "Many cases of leprosy still occur in low and middle-income countries , with a considerable proportion of them leading to permanent nerve damage and visible physical deformities .", "Disease elimination can be achieved with a better understanding of the sociodemographic characteristics of those most affected by t...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "gonorrhea", "gram negative", "sexually transmitted diseases", "microbial pathogens", "host-pathogen interaction", "biology", "microbiology", "bacterial pathogens" ]	Pilus Phase Variation Switches Gonococcal Adherence to Invasion by Caveolin-1-Dependent Host Cell Signaling	journal.ppat.1003373	null	[ [ "The human-specific Gram-negative bacterium Neisseria gonorrhoeae is the cause of the sexually-transmitted disease gonorrhea .", "With more than 106 million infections per year ( source: WHO ) it presents a serious threat to world health .", "Moreover , the current global dramatic spread of multi-resi...	[ "Many pathogenic bacteria cause local infections but occasionally invade into the blood stream , often with fatal outcome .", "Very little is known about the mechanism underlying the switch from local to invasive infection .", "In the case of Neisseria gonorrhoeae , phase variable type 4 pili ( T4P ) stabilize ...	[ "Neisseria gonorrhoeae is a human-specific bacterial pathogen causing gonorrhea .", "With over 100 million infections per year it is among the most prevalent sexually-transmitted diseases worldwide .", "Whereas most infections are localized , occasionally N . gonorrhoeae invades the blood stream .", "The resu...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "enzyme-linked immunoassays", "tropical diseases", "geographical locations", "health care", "north america", "bacterial diseases", "neglected tropical diseases", "caribbean", "immunologic techniques", "research and analysis methods", "guadeloupe", "public and ...	Underestimation of Leptospirosis Incidence in the French West Indies	journal.pntd.0004668	null	[ [ "Leptospirosis is a zoonotic bacterial disease which is particularly widespread in tropical and subtropical regions .", "It produces a wide array of clinical symptoms , ranging from an undifferentiated mild fever to severe multi-organ failure [1] .", "None of these symptoms is specific to the disease ...	[ "Leptospirosis is a neglected zoonosis affecting mainly tropical and subtropical regions worldwide , particularly South America and the Caribbean .", "As in many other countries , under-reporting of cases was suspected in the French West Indies because of inadequate access to diagnostic tests for the general popu...	[ "Leptospirosis is a common disease in tropical regions around the world .", "It is caused by a bacteria excreted in environmental waters by mammals , especially rodents , through their urine .", "Leptospirosis has symptoms similar to other tropical diseases , including dengue fever , and early laboratory diagno...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	NatB Domain-Containing CRA-1 Antagonizes Hydrolase ACER-1 Linking Acetyl-CoA Metabolism to the Initiation of Recombination during C. elegans Meiosis	journal.pgen.1005029	null	[ [ "Achieving accurate chromosome segregation is a critical outcome for any cell division process .", "This is strikingly evident during the meiotic cell divisions leading to the formation of haploid gametes ( i . e . oocytes and sperm ) , where errors in chromosome segregation result in aneuploidy and there...	[ "The formation of DNA double-strand breaks ( DSBs ) must take place during meiosis to ensure the formation of crossovers , which are required for accurate chromosome segregation , therefore avoiding aneuploidy .", "However , DSB formation must be tightly regulated to maintain genomic integrity .", "How this reg...	[ "Achieving accurate chromosome segregation is a critical outcome for any cell division process .", "Programmed DNA double-strand break formation is a central mechanism set in place to promote faithful chromosome segregation during meiosis .", "A subset of these DSBs is repaired as crossovers via reciprocal exch...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "urology/renal cancer", "genetics and genomics/cancer genetics", "genetics and genomics/bioinformatics", "cell biology/cell signaling" ]	Somatic Pairing of Chromosome 19 in Renal Oncocytoma Is Associated with Deregulated ELGN2-Mediated Oxygen-Sensing Response	journal.pgen.1000176	null	[ [ "Cellular adaptation to changes in oxygen tension is vital for the integrity , maintenance and survival of cells .", "Hypoxia-inducible factor ( HIF ) , the major transcription factor of the ubiquitous oxygen-sensing pathway , is a heterodimer composed of α and β subunits [1] .", "While HIFβ is consti...	[ "Chromosomal abnormalities , such as structural and numerical abnormalities , are a common occurrence in cancer .", "The close association of homologous chromosomes during interphase , a phenomenon termed somatic chromosome pairing , has been observed in cancerous cells , but the functional consequences of somati...	[ "Together , renal oncocytoma and chromophobe renal cell carcinoma ( RCC ) account for approximately 10% of masses that are resected from the kidney .", "However , the molecular defects that are associated with the development of these neoplasias are not clear .", "Here , we take advantage of recent advances in ...	2008
[ "Introduction", "Results and Discussion", "Materials and Methods" ]	[]	Somatic mtDNA Mutation Spectra in the Aging Human Putamen	journal.pgen.1003990	null	[ [ "The accumulation of heteroplasmic mitochondrial DNA ( mtDNA ) mutations is a well-accepted facet of the biology of aging [1] .", "Heteroplasmic single nucleotide variants ( SNVs ) which are predominately transitions have been identified in all regions of mtDNA in aged tissues .", "Heteroplasmic delet...	[ "The accumulation of heteroplasmic mitochondrial DNA ( mtDNA ) deletions and single nucleotide variants ( SNVs ) is a well-accepted facet of the biology of aging , yet comprehensive mutation spectra have not been described .", "To address this , we have used next generation sequencing of mtDNA-enriched libraries ...	[ "Mitochondria are unique among animal organelles in that they contain their own multi-copy genome ( mtDNA ) .", "For the past 20 years it has been known that tissues like brain and muscle accumulate somatic mtDNA mutations with age .", "Because individual mtDNA mutations are present at very low levels , few det...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "rna interference", "protein interactions", "parasitic protozoans", "trypanosoma brucei", "fungi", "trypanosoma brucei gambiense", "model organisms", "protozoans", "experimental organism systems", "mitochondria", "epigenetics", "bioenergetics", "cellular structures and organelles", "resear...	Branched late-steps of the cytosolic iron-sulphur cluster assembly machinery of Trypanosoma brucei	journal.ppat.1007326	null	[ [ "Iron-sulphur ( Fe-S ) clusters are simple and versatile cofactors involved in a plethora of cellular processes from bacteria to humans and theorised to have formed the ancient surfaces upon which prebiotic chemical reactions took place , laying the ground for the origin of life itself [1 , 2] .", "Biogen...	[ "Fe-S clusters are ubiquitous cofactors of proteins involved in a variety of essential cellular processes .", "The biogenesis of Fe-S clusters in the cytosol and their insertion into proteins is accomplished through the cytosolic iron-sulphur protein assembly ( CIA ) machinery .", "The early- and middle-acting ...	[ "Cytosolic and nuclear proteins containing iron-sulphur clusters ( Fe-S ) are essential for the survival of every extant eukaryotic cell .", "The biogenesis of Fe-S clusters and their insertion into proteins is accomplished through the cytosolic iron-sulphur protein assembly ( CIA ) machinery .", "Recently , th...	2018
[ "Introduction", "Results and Discussion", "Materials and Methods" ]	[ "plant science", "gene expression", "plant genomics", "plant genetics", "biology", "molecular cell biology" ]	Transcriptomics and Functional Genomics of ROS-Induced Cell Death Regulation by RADICAL-INDUCED CELL DEATH1	journal.pgen.1004112	null	[ [ "Plants live in a world of change - fluctuating light , temperature , water availability and pathogen attack are among the conditions that require an appropriate response from the plant .", "Stress responses are energetically costly [1]–[3] , hence environmental and growth signals must be integrated and b...	[ "Plant responses to changes in environmental conditions are mediated by a network of signaling events leading to downstream responses , including changes in gene expression and activation of cell death programs .", "Arabidopsis thaliana RADICAL-INDUCED CELL DEATH1 ( RCD1 ) has been proposed to regulate plant stre...	[ "Reactive oxygen species ( ROS ) are utilized in plants as signaling molecules to regulate development , stress responses and cell death .", "One extreme form of defense uses programmed cell death ( PCD ) in a scorched earth strategy to deliberately kill off cells invaded by a pathogen .", "Compared to animals ...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "functional genomics", "biology", "genomics", "proteomics", "genetics and genomics" ]	Proteome-Wide Analysis of Disease-Associated SNPs That Show Allele-Specific Transcription Factor Binding	journal.pgen.1002982	null	[ [ "Genome-wide association studies ( GWAS ) of common diseases typically result in the identification of genomic susceptibility loci , in which several single nucleotide polymorphisms ( SNPs ) showing strong inter-marker linkage disequilibrium ( LD ) are equally associated with disease predisposition .", "F...	[ "A causative role for single nucleotide polymorphisms ( SNPs ) in many genetic disorders has become evident through numerous genome-wide association studies .", "However , identification of these common causal variants and the molecular mechanisms underlying these associations remains a major challenge .", "Dif...	[ "Genome-wide association studies ( GWAS ) are a powerful approach to identifying genes contributing to risk of disease .", "However , individual mapped single nucleotide polymorphisms ( SNPs ) may not map close to a gene , and it can be difficult to distinguish marker SNPs from causal SNPs .", "Furthermore , th...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Fine Mapping of the Interaction between C4b-Binding Protein and Outer Membrane Proteins LigA and LigB of Pathogenic Leptospira interrogans	journal.pntd.0004192	null	[ [ "Leptospirosis is a worldwide zoonosis caused by spirochetes from the genus Leptospira [1] .", "Rodents are the main reservoir of Leptospira , which can be excreted in animal urine [2] .", "The disease is transmitted by contact of abraded skin or mucosal membranes with water contaminated with infected...	[ "The complement system consists of more than 40 proteins that participate in the inflammatory response and in pathogen killing .", "Complement inhibitors are necessary to avoid the excessive consumption and activation of this system on host cells .", "Leptospirosis is a worldwide zoonosis caused by spirochetes ...	[ "Leptospirosis is a neglected infectious disease of public health significance .", "It is one of the most important zoonosis worldwide , affecting at least 500 , 000 people each year of which approximately 10–20% of cases are fatal .", "Most of the cases occur in tropical developing countries which lack proper ...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "virulence factors and mechanisms", "viral immune evasion", "virology", "biology", "microbiology", "host-pathogen interaction", "pathogenesis" ]	The Influenza Virus Protein PB1-F2 Inhibits the Induction of Type I Interferon at the Level of the MAVS Adaptor Protein	journal.ppat.1002067	null	[ [ "Influenza viruses cause annual epidemics and occasional pandemics which may result in up to 50 million excess deaths as seen during the outbreak in 1918 [1] .", "The virus strains causing the influenza pandemics that occurred in the years of 1918 , 1957 and 1968 , all have been found to express the virul...	[ "PB1-F2 is a 90 amino acid protein that is expressed from the +1 open reading frame in the PB1 gene of some influenza A viruses and has been shown to contribute to viral pathogenicity .", "Notably , a serine at position 66 ( 66S ) in PB1-F2 is known to increase virulence compared to an isogenic virus with an aspa...	[ "Influenza viruses can cause global pandemics and are thus a major health concern .", "The novel H1N1 pandemic virus infected a large number of people , but resulted in relatively mild symptoms in the majority of cases .", "In contrast , the avian H5N1 viruses are associated with a high mortality rate , but are...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "neuroglial development", "molecular neuroscience", "developmental neuroscience", "cellular neuroscience", "neural homeostasis", "biology and life sciences", "neuroscience" ]	PI3K Signaling and Stat92E Converge to Modulate Glial Responsiveness to Axonal Injury	journal.pbio.1001985	Activation of glial cells following axon injury is mediated by a positive feedback loop downstream of the glial phagocytic receptor Draper, allowing the strength of the response to match the severity of injury.	[ [ "Glial cells are extraordinarily sensitive to disruptions in central nervous system ( CNS ) homeostasis and exhibit an impressive ability to respond to a diversity of neural injuries including hypoxia , chemical insults , and mechanical injury ( e . g . , axotomy or traumatic brain injury ) [1]–[3] .", "D...	[ "Glial cells are exquisitely sensitive to neuronal injury but mechanisms by which glia establish competence to respond to injury , continuously gauge neuronal health , and rapidly activate reactive responses remain poorly defined .", "Here , we show glial PI3K signaling in the uninjured brain regulates baseline l...	[ "Acute injuries of the central nervous system ( CNS ) trigger a robust reaction from glial cells—a non-neuronal population of cells that regulate and support neural development and physiology .", "Although this process occurs after all types of CNS trauma in mammals , how it is activated and its precise role in r...	2014
[ "Introduction", "Models", "Results/Discussion" ]	[ "ecology and environmental sciences", "statistical mechanics", "applied mathematics", "simulation and modeling", "systems science", "mathematics", "adaptive systems", "population modeling", "altruistic behavior", "stochastic processes", "evolutionary emergence", "research and analysis methods"...	Evolution of All-or-None Strategies in Repeated Public Goods Dilemmas	journal.pcbi.1003945	null	[ [ "The emergence and sustainability of cooperation constitutes one of the most important problems in social and biological sciences [1] .", "It revolves around the clash between individual and collective interest , which becomes particularly clear when one considers the evolution of collective action involv...	[ "Many problems of cooperation involve repeated interactions among the same groups of individuals .", "When collective action is at stake , groups often engage in Public Goods Games ( PGG ) , where individuals contribute ( or not ) to a common pool , subsequently sharing the resources .", "Such scenarios of repe...	[ "The problem of cooperation has been a target of many studies , and some of the most complex dilemmas arise when we deal with groups repeatedly interacting by means of a Public Goods Game ( PGG ) , where individuals may contribute to a common pool , subsequently sharing the resources .", "Here we study generalize...	2014

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