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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", "Methods", "Results", "Discussion" ]	[ "epidemiology", "biology and life sciences", "medicine and health sciences", "computational biology" ]	Strategies for Controlling Non-Transmissible Infection Outbreaks Using a Large Human Movement Data Set	journal.pcbi.1003809	null	[ [ "The development of epidemiological models to inform public health strategies for infectious disease control has been greatly aided by incorporating an understanding of human movement behaviour , drawing on the increasing availability of data describing human movement patterns [1]–[5] .", "Recent studies ...	[ "Prediction and control of the spread of infectious disease in human populations benefits greatly from our growing capacity to quantify human movement behavior .", "Here we develop a mathematical model for non-transmissible infections contracted from a localized environmental source , informed by a detailed descr...	[ "Public health strategies for infectious disease control can benefit greatly from our growing capacity to predict human movement behaviour .", "This is facilitated by modern methods of electronic data generation and storage that allow us to track detailed human movement patterns .", "Here we develop a mathemati...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "children", "medicine and health sciences", "leptospira", "pathology and laboratory medicine", "japan", "pathogens", "tropical diseases", "geographical locations", "microbiology", "pediatrics", "bacterial diseases", "age groups", "signs and symptoms", "neglected tropical diseases", "pedi...	Childhood leptospirosis in an industrialized country: Population-based study in Okinawa, Japan	journal.pntd.0006294	null	[ [ "Leptospirosis is a neglected zoonotic disease with global distribution that is caused by infection of spirochetes from the genus Leptospira .", "Although leptospirosis usually presents as mild , self-limiting symptoms , severe cases with high mortality and morbidity might occur [1] .", "Therefore , e...	[ "Leptospirosis is considered underdiagnosed because of its nonspecific presentation and lack of proper understanding of its epidemiology .", "Early diagnosis and treatment are crucial .", "However , few data are available on confirmed leptospirosis cases in children in industrialized countries .", "We therefo...	[ "Leptospirosis is a bacterial disease that affects humans and animals .", "It is caused by Leptospira .", "Leptospira is a spiral-shaped Gram-negative spirochete with internal flagella , which enters the host through mucosa and broken skin .", "Leptospirosis is a worldwide zoonosis , but it is considered unde...	2018
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "african trypanosomiasis", "variant genotypes", "tropical diseases", "geographical locations", "uganda", "parasitic diseases", "parasitic protozoans", "malawi", "genetic mapping", "trypanosoma brucei", "protozoans", "neglected tropical diseases", "molecular ...	Association of APOL1 renal disease risk alleles with Trypanosoma brucei rhodesiense infection outcomes in the northern part of Malawi	journal.pntd.0007603	null	[ [ "Human African trypanosomiasis ( HAT ) , also known as sleeping sickness , is one of the major neglected infectious diseases .", "Sleeping sickness is endemic in 36 African countries and over 60 million people are at risk of being infected [1] .", "HAT is more prevalent in rural areas where health car...	[ "Trypanosoma brucei ( T . b . ) rhodesiense is the cause of the acute form of human African trypanosomiasis ( HAT ) in eastern and southern African countries .", "There is some evidence that there is diversity in the disease progression of T . b . rhodesiense in different countries .", "HAT in Malawi is associa...	[ "Though some work has been done on the genetics of trypanosome infections in animals , relatively little is known about the genetics of human African trypanosomiasis ( HAT ) infections .", "To test whether any variants are associated with reduced or increased risk of trypanosomiasis , 96 variants in 17 genes were...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing techniques", "organismal evolution", "vertebrates", "animals", "membrane proteins", "fungi", "phylogenetic analysis", "fungal evolution", "eukaryotic evolution", "molecular biology techniques", "cellular structures and organelles", "research and analysis methods", "sequence analy...	Interactome Mapping Reveals the Evolutionary History of the Nuclear Pore Complex	journal.pbio.1002365	Dissection of the nuclear pore complex—an ancient eukaryotic molecular machine—exposes a fundamental divergence in structure and function between yeast and humans versus trypanosomes and provides insights into the evolution of the nucleus.	[ [ "In order to uncover the origins of eukaryotes , we must understand how their defining organelle , the nucleus , and its delineating nuclear envelope ( NE ) arose .", "The NE provides a barrier that defines the nucleoplasm and cytoplasm , and this discrimination represents a major evolutionary transition ...	[ "The nuclear pore complex ( NPC ) is responsible for nucleocytoplasmic transport and constitutes a hub for control of gene expression .", "The components of NPCs from several eukaryotic lineages have been determined , but only the yeast and vertebrate NPCs have been extensively characterized at the quaternary lev...	[ "Much of the core architecture of the eukaryotic cell was established over one billion years ago .", "Significantly , many cellular systems possess lineage-specific features , and architectural and compositional variation of complexes and pathways that are likely keyed to specific functional adaptations .", "Th...	2016
[ "Introduction", "Results", "Materials and methods" ]	[ "medicine and health sciences", "liver", "pathology and laboratory medicine", "gene regulation", "hepacivirus", "pathogens", "biological cultures", "microbiology", "hepatoma cells", "viruses", "rna viruses", "immunoprecipitation", "cell cultures", "co-immunoprecipitation", "research and ...	Infection with hepatitis C virus depends on TACSTD2, a regulator of claudin-1 and occludin highly downregulated in hepatocellular carcinoma	journal.ppat.1006916	null	[ [ "Infection with hepatitis C virus ( HCV ) is a major public health problem worldwide because it is a primary cause of chronic hepatitis , cirrhosis and hepatocellular carcinoma ( HCC ) [1] .", "Although there have been remarkable advances in our knowledge of HCV and its related disease manifestations , se...	[ "Entry of hepatitis C virus ( HCV ) into hepatocytes is a complex process that involves numerous cellular factors , including the scavenger receptor class B type 1 ( SR-B1 ) , the tetraspanin CD81 , and the tight junction ( TJ ) proteins claudin-1 ( CLDN1 ) and occludin ( OCLN ) .", "Despite expression of all kno...	[ "Infection with hepatitis C virus ( HCV ) is associated with a high risk of developing hepatocellular carcinoma ( HCC ) .", "However , it is unknown whether HCV promotes HCC indirectly , through chronic inflammation , fibrosis and liver regeneration , or directly , in a manner similar to other oncogenic viruses ....	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "bartonella", "medicine", "infectious diseases", "neglected tropical diseases" ]	Bartonella bacilliformis: A Systematic Review of the Literature to Guide the Research Agenda for Elimination	journal.pntd.0001819	null	[ [ "Bartonella bacilliformis is a gram negative , facultative intracellular , aerobic coccobacillus which is a member of the alpha-proteobacteria group along with Rickettsia and Brucella [1] .", "It is responsible for a spectrum of disease which , despite its limited distribution , has been given a multitude...	[ "Carrion's disease affects small Andean communities in Peru , Colombia and Ecuador and is characterized by two distinct disease manifestations: an abrupt acute bacteraemic illness ( Oroya fever ) and an indolent cutaneous eruptive condition ( verruga Peruana ) .", "Case fatality rates of untreated acute disease c...	[ "Carrion's disease is one of the truly neglected tropical diseases .", "It affects children predominantly in small Andean communities in Peru , Colombia and Ecuador .", "Case fatality rates of untreated acute disease can exceed 80% during outbreaks .", "Diagnostic and treatment guidelines are based on very lo...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "antimicrobials", "invertebrates", "dengue virus", "medicine and health sciences", "microbiome", "pathology and laboratory medicine", "pathogens", "drugs", "microbiology", "enterobacter infections", "animals", "wolbachia", "viruses", "bacterial diseases", "rna viruses", "antibiotics", ...	The microbiome composition of Aedes aegypti is not critical for Wolbachia-mediated inhibition of dengue virus	journal.pntd.0005426	null	[ [ "Dengue virus ( DENV ) is an RNA arbovirus and the causative agent of dengue fever and the more severe dengue haemorrhagic fever .", "There are four serotypes of DENV ( DENV1-4 ) , which together are estimated to infect 390 million people per year [1] .", "Currently there are no specific antiviral the...	[ "Dengue virus ( DENV ) is primarily vectored by the mosquito Aedes aegypti , and is estimated to cause 390 million human infections annually .", "A novel method for DENV control involves stable transinfection of Ae .", "aegypti with the common insect endosymbiont Wolbachia , which mediates an antiviral effect ....	[ "Dengue virus is transmitted by the mosquito Aedes aegypti and can cause dengue fever and dengue haemorrhagic fever in humans .", "The World Health Organization currently considers it as the most important mosquito-borne virus globally .", "One method to control dengue infection of Ae .", "aegypti is to infec...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "enzyme-linked immunoassays", "pathology and laboratory medicine", "immunology", "cell-mediated immunity", "parasitic diseases", "infectious disease immunology", "clinical medicine", "immunologic techniques", "research and analysis...	Surfactant Protein-D Is Essential for Immunity to Helminth Infection	journal.ppat.1005461	null	[ [ "Surfactant Protein ( SP ) -D is a constitutively expressed C-type lectin , which has a well recognized role in innate pulmonary immunity against viruses , bacteria and fungi , as well as in maintaining pulmonary homeostasis [1] .", "Direct SP-D interactions with immune ( such as alveolar macrophages [2] ...	[ "Pulmonary epithelial cell responses can enhance type 2 immunity and contribute to control of nematode infections .", "An important epithelial product is the collectin Surfactant Protein D ( SP-D ) .", "We found that SP-D concentrations increased in the lung following Nippostrongylus brasiliensis infection; thi...	[ "Infections by parasitic worms are very common , and controlling them is a major medical and veterinary challenge .", "Very few drugs exist to treat them , and the parasites can develop resistance to these .", "In order to find new ways to control worm infections , understanding how our immune system responds t...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "virology", "biology", "microbiology" ]	G Protein-Coupled Receptor Kinase 2 Promotes Flaviviridae Entry and Replication	journal.pntd.0001820	null	[ [ "Although a century has passed since yellow fever virus ( YFV ) , which gave flaviviruses their name , was shown to cause a human disease , flaviviral epidemics still represent a serious threat worldwide .", "Viruses such as dengue virus ( DENV ) and YFV have undergone a major geographic expansion in the ...	[ "Flaviviruses cause a wide range of severe diseases ranging from encephalitis to hemorrhagic fever .", "Discovery of host factors that regulate the fate of flaviviruses in infected cells could provide insight into the molecular mechanisms of infection and therefore facilitate the development of anti-flaviviral dr...	[ "The Flavivirus genus includes several emergent and reemergent viruses , such as dengue and yellow fever viruses , which cause severe diseases in humans for which there is no approved treatment .", "Flaviviruses are transmitted to humans by arthropods and they rely on scores of vertebrate and invertebrate factors...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "social and behavioral sciences", "biology", "computational biology" ]	Traffic Instabilities in Self-Organized Pedestrian Crowds	journal.pcbi.1002442	null	[ [ "In many biological and social systems , such as fish schools , ant colonies , or human crowds , repeated local interactions among individuals support the emergence of a variety of collective patterns of motion [1]–[4] .", "Under certain conditions , the emerging organization allows the group to solve eff...	[ "In human crowds as well as in many animal societies , local interactions among individuals often give rise to self-organized collective organizations that offer functional benefits to the group .", "For instance , flows of pedestrians moving in opposite directions spontaneously segregate into lanes of uniform wa...	[ "A crowd of pedestrians is a complex system that exhibits a rich variety of self-organized collective behaviours .", "For instance , when two flows of people are walking in opposite directions in a crowded street , pedestrians spontaneously share the available space by forming lanes of uniform walking directions ...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Bacterial Factors Associated with Lethal Outcome of Enteropathogenic Escherichia coli Infection: Genomic Case-Control Studies	journal.pntd.0003791	null	[ [ "Nearly 70 years ago , bacterial strains now known as enteropathogenic Escherichia coli ( EPEC ) were first reported to cause neonatal and infant diarrhea with high case-fatality rates [1 , 2] .", "During the ensuing years , investigators made great strides in elucidating the molecular mechanisms and cell...	[ "Typical enteropathogenic Escherichia coli ( tEPEC ) strains were associated with mortality in the Global Enteric Multicenter Study ( GEMS ) .", "Genetic differences in tEPEC strains could underlie some of the variability in clinical outcome .", "We produced draft genome sequences of all available tEPEC strains...	[ "Typical enteropathogenic E . coli ( tEPEC ) strains are associated with high mortality among infants with moderate-to-severe diarrhea , but most infants infected with tEPEC strains survive , and some have no symptoms .", "To investigate the bacterial factors associated with severe outcome , we determined the gen...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases/helminth infections", "infectious diseases", "infectious diseases/antimicrobials and drug resistance", "infectious diseases/neglected tropical diseases" ]	Phenotypic Evidence of Emerging Ivermectin Resistance in Onchocerca volvulus	journal.pntd.0000998	null	[ [ "Ivermectin ( Mectizan ) has been in operational use for the control of human onchocerciasis in the former Onchocerciasis Control Programme in West Africa ( OCP ) areas since 1987 and is still the drug of choice for the African Programme for Onchocerciasis Control ( APOC ) and the Onchocerciasis Elimination P...	[ "Ivermectin ( IVM ) has been used in Ghana for over two decades for onchocerciasis control .", "In recent years there have been reports of persistent microfilaridermias despite multiple treatments .", "This has necessitated a reexamination of its microfilaricidal and suppressive effects on reproduction in the a...	[ "Onchocerciasis , commonly known as river blindness , is caused by the filarial nematode Onchocerca volvulus and is transmitted by a blackfly vector .", "Over 37 million people are thought to be infected , with over 90 million at risk .", "Infection predominantly occurs in sub-Saharan Africa .", "Foci also ex...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cellular structures", "viral classification", "microbiology", "rna viruses", "emerging infectious diseases", "cell nucleus", "viral nucleic acid", "biology", "viral packaging", "viral replication complex", "viral replication", "cell biology", "virology", "molecular cell biology" ]	Influenza Virus Ribonucleoprotein Complexes Gain Preferential Access to Cellular Export Machinery through Chromatin Targeting	journal.ppat.1002187	null	[ [ "Influenza viruses are nearly unique among RNA viruses , in that they perform all of their viral RNA synthesis in the nucleus of infected cells .", "While this exceptional attribute provides some advantages to the virus , such as access to capped cellular pre-mRNAs and the host splicing machinery , it als...	[ "In contrast to most RNA viruses , influenza viruses replicate their genome in the nucleus of infected cells .", "As a result , newly-synthesized vRNA genomes , in the form of viral ribonucleoprotein complexes ( vRNPs ) , must be exported to the cytoplasm for productive infection .", "To characterize the compos...	[ "Influenza viruses replicate their single-stranded RNA genomes in the nucleus of infected cells .", "Since new virus particles are formed at the plasma membrane , these genomes must be exported in the form of a viral ribonucleoprotein complex ( vRNP ) from the nucleus to the cytoplasm at a late point during infec...	2011
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "bacteriology", "genome sequencing", "bacterial physiology", "microbial metabolism", "microbial physiology", "biology", "genomics", "microbiology", "bacterial biochemistry", "genetics and genomics" ]	Genome of Herbaspirillum seropedicae Strain SmR1, a Specialized Diazotrophic Endophyte of Tropical Grasses	journal.pgen.1002064	null	[ [ "Soil bacteria can interact in many ways with plant partners ranging from beneficial to pathogenic .", "Among beneficial interactions the rhizobia play a central role , forming symbioses with legume species to produce nitrogen-fixing nodules , which supply most of the required fixed nitrogen to many agric...	[ "The molecular mechanisms of plant recognition , colonization , and nutrient exchange between diazotrophic endophytes and plants are scarcely known .", "Herbaspirillum seropedicae is an endophytic bacterium capable of colonizing intercellular spaces of grasses such as rice and sugar cane .", "The genome of H . ...	[ "In this work we describe the genome of H . seropedicae SmR1 , a bacterium capable of fixing nitrogen and promoting the growth of important plant crops such as maize , rice , and sugar cane .", "Several investigations have shown that H . seropedicae supplies fixed nitrogen to the associated plant and increases gr...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "viral transmission and infection", "microbiology", "host-pathogen interaction", "mutation", "hepatitis", "hepatitis c", "sequence analysis", "infectious diseases", "biology", "pathogenesis", "viral evolution", "genetic drift", "natural selection", "virology", "viral diseas...	Sequential Bottlenecks Drive Viral Evolution in Early Acute Hepatitis C Virus Infection	journal.ppat.1002243	null	[ [ "Hepatitis C virus ( HCV ) infection is a major cause of chronic liver disease , resulting in substantial morbidity and mortality worldwide , with between 123 and 170 million persons infected [1] .", "Transmission is predominantly via blood-to-blood contact associated with contaminated injection devices ....	[ "Hepatitis C is a pandemic human RNA virus , which commonly causes chronic infection and liver disease .", "The characterization of viral populations that successfully initiate infection , and also those that drive progression to chronicity is instrumental for understanding pathogenesis and vaccine design .", "...	[ "Primary hepatitis C ( HCV ) infection is typically asymptomatic and commonly results in persistent infection .", "The characteristics of early infection remain undefined .", "Four subjects were studied longitudinally from within a few weeks of transmission until resolution of outcome , via a full genome analys...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "neuroscience", "evolutionary biology" ]	Basic Math in Monkeys and College Students	journal.pbio.0050328	Monkeys have an ability to represent numerical values even though they lack linguistic abilities. The authors show that monkeys can also perform addition on numerical values and that they perform similarly to college students who are asked to add without counting.	[ [ "The fact that humans and nonhuman animals represent numerical values nonverbally using a common cognitive process is well established [1–7] .", "Both human and nonhuman animals can nonverbally estimate the numerical values of arrays of dots or sequences of tones [8–12] and determine which of two sets is ...	[ "Adult humans possess a sophisticated repertoire of mathematical faculties .", "Many of these capacities are rooted in symbolic language and are therefore unlikely to be shared with nonhuman animals .", "However , a subset of these skills is shared with other animals , and this set is considered a cognitive ves...	[ "Adult humans possess mathematical abilities that are unmatched by any other member of the animal kingdom .", "Yet , there is increasing evidence that the ability to enumerate sets of objects nonverbally is a capacity that humans share with other animal species .", "That is , like humans , nonhuman animals poss...	2007
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell binding", "cell physiology", "medicine and health sciences", "chemical characterization", "crystal structure", "chemical compounds", "pathology and laboratory medicine", "viral transmission and infection", "pathogens", "condensed matter physics", "microbiology", "organic compounds", "v...	Mapping of the Lassa virus LAMP1 binding site reveals unique determinants not shared by other old world arenaviruses	journal.ppat.1006337	null	[ [ "Receptor switching is a newly discovered event in the cell entry process of Lassa virus ( LASV ) [1] , a zoonotic , enveloped , negative-strand RNA virus that belongs to the Arenaviridae family [2] .", "LASV is a devastating pathogen that causes severe hemorrhagic fevers with significant mortality in Wes...	[ "Cell entry of many enveloped viruses occurs by engagement with cellular receptors , followed by internalization into endocytic compartments and pH-induced membrane fusion .", "A previously unnoticed step of receptor switching was found to be critical during cell entry of two devastating human pathogens: Ebola an...	[ "To infect , enveloped viruses need to fuse their membrane with the host membrane .", "Fusion is mediated by special glycoprotein machineries that must be triggered only at the right time and at the right place .", "A major cue that viruses utilize for triggering is acidic pH . Until recently , such pH-induced ...	2017
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "bacteriology", "sequencing techniques", "applied mathematics", "microbiology", "human genomics", "invertebrate genomics", "simulation and modeling", "algorithms", "mathematics", "algebra", "bacterial genetics", "molecular biology techniques", "directed graphs", "microbial genetics", "po...	Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing	journal.pcbi.1005777	null	[ [ "Throughout this paper , k denotes the length of a k-mer word , while L denotes the length of the long sequences .", "Definition 1 ( de Bruijn Graph ) .", "A de Bruijn graph of order k over alphabet Σ is a directed graph in which every vertex has an associated label ( a string over Σ ) of length k ( k...	[ "With the rapidly increasing volume of deep sequencing data , more efficient algorithms and data structures are needed .", "Minimizers are a central recent paradigm that has improved various sequence analysis tasks , including hashing for faster read overlap detection , sparse suffix arrays for creating smaller i...	[ "High-throughput sequencing data has been accumulating at an extreme pace .", "The need to efficiently analyze and process it has become a critical challenge of the field .", "Many of the data structures and algorithms for this task rely on k-mer sets ( DNA words of length k ) to represent the sequences in a da...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious disease surveillance", "bacterial diseases", "infectious diseases", "buruli ulcer", "plant science", "medicine and health sciences", "public and occupational health", "disease ecology", "infectious disease epidemiology", "epidemiology", "disease dynamics", "global health", "disea...	Spatio-temporal Patterns and Landscape-Associated Risk of Buruli Ulcer in Akonolinga, Cameroon	journal.pntd.0003123	null	[ [ "Buruli ulcer ( BU ) disease is an extensively damaging skin infection caused by Mycobacterium ulcerans ( MU ) , a pathogen distantly related to Mycobacterium tuberculosis and M . leprae [1] , [2] .", "BU presents as a necrotising infection of the skin , causing debility and crippling deformity if left un...	[ "Buruli ulcer ( BU ) is an extensively damaging skin infection caused by Mycobacterium ulcerans , whose transmission mode is still unknown .", "The focal distribution of BU and the absence of interpersonal transmission suggest a major role of environmental factors , which remain unidentified .", "This study pro...	[ "Buruli ulcer ( BU ) remains a mysterious disease without efficient prevention since the mode of transmission of its agent , Mycobacterium ulcerans , is still unknown .", "The disease is highly localised within countries and even at the village scale within endemic regions , but environmental factors explaining t...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology and life sciences", "microbiology" ]	Inactivation of Genes for Antigenic Variation in the Relapsing Fever Spirochete Borrelia hermsii Reduces Infectivity in Mice and Transmission by Ticks	journal.ppat.1004056	null	[ [ "Borrelia hermsii is one of many human pathogens that escapes the host’s adaptive immune response by changing its outer surface proteins through antigenic variation [1]–[3] .", "This mechanism of immune evasion involves a large repertoire of genes that encode dominant outer surface proteins , the variable...	[ "Borrelia hermsii , a causative agent of relapsing fever of humans in western North America , is maintained in enzootic cycles that include small mammals and the tick vector Ornithodoros hermsi .", "In mammals , the spirochetes repeatedly evade the host’s acquired immune response by undergoing antigenic variation...	[ "Borrelia hermsii , an agent of tick-borne relapsing fever when infecting humans , employs antigenic variation of the variable major proteins ( Vmps ) to escape the host immune response .", "This mechanism allows the bacteria to persist in the blood of a mammal , which increases their potential for acquisition by...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "blood cells", "innate immune system", "medicine and health sciences", "cytokines", "hiv immunopathogenesis", "immunology", "microbiology", "liver diseases", "immunodeficiency viruses", "developmental biology", "infectious hepatitis", "hepatitis", "gastroenterology and hepatology", "molecu...	HIV and HCV Activate the Inflammasome in Monocytes and Macrophages via Endosomal Toll-Like Receptors without Induction of Type 1 Interferon	journal.ppat.1004082	null	[ [ "Human immunodeficiency virus ( HIV ) and hepatitis C virus ( HCV ) are RNA viruses capable of causing chronic infection , with an estimated 35 million [1] and 170 million [2] people infected worldwide , respectively .", "The innate immune response to these viruses generates an antiviral state that alters...	[ "Innate immune sensing of viral infection results in type I interferon ( IFN ) production and inflammasome activation .", "Type I IFNs , primarily IFN-α and IFN-β , are produced by all cell types upon virus infection and promote an antiviral state in surrounding cells by inducing the expression of IFN-stimulated ...	[ "Pathogens are detected by the immune system in multiple ways that initiate responses to control infection .", "Two systems of first line defense against viruses are", "1 ) the production of Type I interferons and", "2 ) production of the cytokines IL-1β and IL-18 by the inflammasome .", "Type I interferons...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell binding", "cell physiology", "medicine and health sciences", "immune physiology", "pathology and laboratory medicine", "pathogens", "immunology", "microbiology", "cloning", "retroviruses", "viruses", "immunodeficiency viruses", "mutation", "substitution mutation", "rna viruses", ...	Broadly resistant HIV-1 against CD4-binding site neutralizing antibodies	journal.ppat.1007819	null	[ [ "Recent scientific advances have identified a growing number of broadly neutralizing antibodies ( bnAbs ) against human immunodeficiency virus type I ( HIV-1 ) , providing promising candidates for HIV-1 prevention and treatment [1–5] .", "Compared with bnAbs isolated in earlier studies , these bnAbs demon...	[ "Recently identified broadly neutralizing antibodies ( bnAbs ) show great potential for clinical interventions against HIV-1 infection .", "However , resistant strains may impose substantial challenges .", "Here , we report on the identification and characterization of a panel of HIV-1 strains with broad and po...	[ "Recently identified broadly neutralizing antibodies ( bnAbs ) show great potential for clinical interventions against HIV-1 infection .", "Among the bnAbs isolated to date , those targeting the CD4bs are the most abundant and thoroughly studied as they disrupt the crucial step of viral interaction with the cellu...	2019
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "computational biology/macromolecular structure analysis", "biophysics/theory and simulation", "computational biology", "computational biology/molecular dynamics" ]	Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL	journal.pcbi.1000360	null	[ [ "Several computational methods have been developed in the last two decades for", "exploring the structural transition pathways of biomolecules ( for reviews see", "[21] , [22] ) .", "These include", "methods based on minimizing path-dependent functionals [23] , [24] , stochastic path integrati...	[ "Identification of pathways involved in the structural transitions of biomolecular", "systems is often complicated by the transient nature of the conformations", "visited across energy barriers and the multiplicity of paths accessible in the", "multidimensional energy landscape .", "This task becomes even m...	[ "Most proteins are biomolecular machines .", "They perform their function by", "undergoing changes between different structures .", "Understanding the mechanism of", "transition between these structures is of major importance to design methods for", "controlling such transitions , and thereby modulating p...	2009
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "bacteriology", "organismal evolution", "ecology and environmental sciences", "astrobiology", "archaeal physiology", "microbiology", "extremophiles", "archaeal evolution", "microbial evolution", "microbial genomics", "bacterial genomics", "microbial physiology", "molecular evolution", "com...	Phylogenetically Driven Sequencing of Extremely Halophilic Archaea Reveals Strategies for Static and Dynamic Osmo-response	journal.pgen.1004784	null	[ [ "Organisms across the tree of life routinely experience changes in osmotic conditions .", "The ability to adjust physiological responses to these osmotic fluxes plays a role in processes ranging from desiccation tolerance and virulence of pathogenic bacteria [1] , [2] , to drought resistance in food crops...	[ "Organisms across the tree of life use a variety of mechanisms to respond to stress-inducing fluctuations in osmotic conditions .", "Cellular response mechanisms and phenotypes associated with osmoadaptation also play important roles in bacterial virulence , human health , agricultural production and many other b...	[ "The ability to adjust to changing osmotic conditions ( osmoadaptation ) is crucial to the survival of organisms across the tree of life .", "However , significant gaps still exist in our understanding of this important phenomenon .", "To help fill some of these gaps , we have produced high-quality draft genome...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "variant genotypes", "alleles", "genetic mapping", "genome analysis", "research and analysis methods", "sequence analysis", "epilepsy", "bioinformatics", "genetic loci", "dna sequence analysis", "heredity", "database and informatics methods", "neurology", ...	De novo and inherited private variants in MAP1B in periventricular nodular heterotopia	journal.pgen.1007281	null	[ [ "Malformations of cortical development are phenotypically heterogeneous and frequently associated with epilepsy , intellectual disability and congenital neurological deficits [1] .", "Periventricular nodular heterotopia ( PVNH ) is one such malformation where a population of neurons fails to migrate to th...	[ "Periventricular nodular heterotopia ( PVNH ) is a malformation of cortical development commonly associated with epilepsy .", "We exome sequenced 202 individuals with sporadic PVNH to identify novel genetic risk loci .", "We first performed a trio-based analysis and identified 219 de novo variants .", "Althou...	[ "Almost 20 years ago the first gene responsible for periventricular nodular heterotopia ( PVNH ) , a disorder that leads to abnormal migration of neurons during fetal brain development , was discovered .", "Since that time additional genes have been identified , but collectively they only explain a minority of ca...	2018
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "chemical compounds", "pathology and laboratory medicine", "intracellular pathogens", "metabolic processes", "ketones", "pathogens", "parasitic diseases", "animals", "pyruvate", "glycolysis", "wolbachia", "brugia", "pharmacology", "bacte...	Pyruvate produced by Brugia spp. via glycolysis is essential for maintaining the mutualistic association between the parasite and its endosymbiont, Wolbachia	journal.ppat.1008085	null	[ [ "Human parasitic nematodes such as Wuchereria bancrofti , Brugia malayi , B . timori , and Onchocerca volvulus are responsible for lymphatic filariasis ( LF , elephantiasis ) and onchocerciasis ( river blindness ) in more than 80 countries .", "In 2016 , the global prevalence of LF was in the range of 24 ...	[ "Human parasitic nematodes are the causative agents of lymphatic filariasis ( elephantiasis ) and onchocerciasis ( river blindness ) , diseases that are endemic to more than 80 countries and that consistently rank in the top ten for the highest number of years lived with disability .", "These filarial nematodes h...	[ "Wuchereria bancrofti , Brugia malayi , Brugia timori , and Onchocerca volvulus are human parasitic nematodes and causative agents of lymphatic filariasis ( LF , elephantiasis ) and onchocerciasis ( river blindness ) .", "These neglected tropical diseases are ranked in the top ten for the highest years lived with...	2019
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "immune physiology", "viral transmission and infection", "spleen", "immunology", "microbiology", "cytotoxic t cells", "antibodies", "research and analysis methods", "immune system proteins", "specimen preparation and treatment", ...	NK cell–intrinsic FcεRIγ limits CD8+ T-cell expansion and thereby turns an acute into a chronic viral infection	journal.ppat.1007797	null	[ [ "CD8+ T cells are key antiviral effector cells during infection with persistence-prone viruses , such as hepatitis B virus ( HBV ) , hepatitis C virus ( HCV ) , and human immunodeficiency virus ( HIV ) [1] .", "Several host factors promote tight regulation of CD8+ T-cell functions , thereby modulating the...	[ "During viral infection , tight regulation of CD8+ T-cell functions determines the outcome of the disease .", "Recently , others and we determined that the natural killer ( NK ) cells kill hyperproliferative CD8+ T cells in the context of viral infection , but molecules that are involved in shaping the regulatory...	[ "FcRγ is a signaling molecule for Fc receptors and NK cell killer activating receptor ( KAR ) complex .", "FcRγ is highly expressed by NK cells and involved in NK cell activity .", "NK cells are widely defined to regulate the expansion of T cells .", "Here using chronic LCMV model , we described the role of F...	2019
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "sequencing techniques", "medicine and health sciences", "gene regulation", "chickens", "vertebrates", "animals", "developmental biology", "mammalian genomics", "molecular biology techniques", "rna sequencing", "body limbs", "research and analysis methods", "sequence analysis", "embryology...	Similarities and differences in the regulation of HoxD genes during chick and mouse limb development	journal.pbio.3000004	A comparison of Hox gene regulation during the development of limbs in birds and mammals reveals that whereas the characteristic bimodal regulatory system, based on large chromatin domains, is largely conserved between these morphologically distinct structures, some differences are revealed in the way this is implement...	[ [ "Tetrapod limbs are organized into three parts bearing skeletal elements—the stylopodium ( humerus/femur ) , the zeugopodium ( radius/fibula , ulna/tibia ) , and the autopodium , the latter including the acropod ( phalanges , metacarpals/metatarsals ) and the mesopodium ( carpals and tarsals ) [1] .", "Li...	[ "In all tetrapods examined thus far , the development and patterning of limbs require the activation of gene members of the HoxD cluster .", "In mammals , they are regulated by a complex bimodal process that controls first the proximal patterning and then the distal structure .", "During the shift from the form...	[ "The shapes of limbs vary greatly among tetrapod species , even between the forelimbs and hindlimbs of the same animal .", "Hox genes regulate the proper growth and patterning of tetrapod limbs .", "In order to evaluate whether variations in the complex regulation of a cluster of Hox genes—the Hoxd genes—during...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "adaptive immunity", "immune cells", "viral immune evasion", "immunity", "viral persistence and latency", "virology", "innate immunity", "antigen-presenting cells", "t cells", "immunology", "immune suppression", "biology", "immune tolerance", "immunity to infections", "microbiology", "...	Negative Regulation of Type I IFN Expression by OASL1 Permits Chronic Viral Infection and CD8+ T-Cell Exhaustion	journal.ppat.1003478	null	[ [ "Pattern-recognition receptors ( PRRs ) displayed on innate immune cells such as dendritic cells ( DCs ) and macrophages ( Macs ) sense pathogens by recognizing conserved pathogen-associated molecular patterns ( PAMPs ) [1] , [2] .", "Major trans-membrane PRRs that sense viruses are the Toll-like receptor...	[ "The type I interferons ( IFN-Is ) are critical not only in early viral control but also in prolonged T-cell immune responses .", "However , chronic viral infections such as those of human immunodeficiency virus ( HIV ) and hepatitis C virus ( HCV ) in humans and lymphocytic choriomeningitis virus ( LCMV ) in mic...	[ "Chronic viral infections , such as those of human immunodeficiency virus ( HIV ) and hepatitis C virus ( HCV ) in humans , remain serious health problems worldwide , necessitating alternative targets/reagents for better treatment .", "Although the production of and/or response to type I interferon ( IFN-I ) , a ...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell cycle and cell division", "cell processes", "dna-binding proteins", "dna replication", "epigenetics", "dna", "synthesis phase", "chromatin", "heterochromatin", "chromosome biology", "proteins", "gene expression", "histones", "genetic loci", "nucleosomes", "biochemistry", "cell ...	Replication stress affects the fidelity of nucleosome-mediated epigenetic inheritance	journal.pgen.1006900	null	[ [ "In eukaryotic cells , genomic DNA are packaged into arrays of nucleosomes [1] , each comprised of a 147bp DNA fragment wrapped around a histone octamer core .", "The combination of histone variants and the large repertoire of covalent modifications on histones result in a highly complex biochemical signa...	[ "The fidelity of epigenetic inheritance or , the precision by which epigenetic information is passed along , is an essential parameter for measuring the effectiveness of the process .", "How the precision of the process is achieved or modulated , however , remains largely elusive .", "We have performed quantita...	[ "In this study , we found replication stresses reduce the fidelity of nucleosome-mediated epigenetic inheritance .", "Using Position Effect Variegation ( PEV ) in centromere as an indicator of chromatin epigenetic stability , we quantified the precision of nucleosomal inheritance and found replication stresses re...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell physiology", "invertebrates", "medicine and health sciences", "diabetic endocrinology", "nervous system", "junctional complexes", "electrophysiology", "neuroscience", "animals", "hormones", "endocrine physiology", "animal models", "gap junctions", "physiological processes", "develo...	Reduced insulin signaling maintains electrical transmission in a neural circuit in aging flies	journal.pbio.2001655	null	[ [ "Synapses undergo age-associated morphological and functional changes in a number of model organisms [1–3] and in humans [4–6] .", "In the fruit fly Drosophila melanogaster and the worm Caenorhabditis elegans , synaptic changes were seen during normal aging in both central and peripheral parts of the nerv...	[ "Lowered insulin/insulin-like growth factor ( IGF ) signaling ( IIS ) can extend healthy lifespan in worms , flies , and mice , but it can also have adverse effects ( the “insulin paradox” ) .", "Chronic , moderately lowered IIS rescues age-related decline in neurotransmission through the Drosophila giant fiber s...	[ "Insulin and insulin-like growth factors play an important role in the nervous system development and function .", "Reduced insulin signaling , however , can improve symptoms of neurodegenerative diseases in different model organisms and protect against age-associated decline in neuronal function extending lifesp...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Invasive Non-Typhoidal Salmonella Typhimurium ST313 Are Not Host-Restricted and Have an Invasive Phenotype in Experimentally Infected Chickens	journal.pntd.0002487	null	[ [ "Invasive non-typhoidal salmonellosis ( iNTS ) has emerged as the most common bloodstream infection in sub-Saharan Africa , frequently as a co-infection with HIV or malaria , leading to mortality events of up to 25% [1] .", "The predominant Salmonella serovar associated with in iNTS is Salmonella enterica...	[ "Salmonella enterica serovar Typhimurium Sequence Type ( ST ) 313 is a major cause of invasive non-Typhoidal salmonellosis in sub-Saharan Africa .", "No animal reservoir has been identified , and it has been suggested that ST313 is adapted to humans and transmission may occur via person-to-person spread .", "He...	[ "Salmonella enterica serovar Typhimurium usually causes foodborne diarrheal infections in humans .", "Recently variants of S . Typhimurium have emerged in Africa associated with invasive and often fatal disease , especially in adults infected by HIV and children with malaria or malnutrition .", "Analysis of the...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry/molecular evolution", "genetics and genomics/microbial evolution and genomics", "evolutionary biology/microbial evolution and genomics", "cell biology/cell signaling", "molecular biology/molecular evolution", "microbiology/microbial evolution and genomics", "cell biology/microbial growth a...	Systematic Dissection and Trajectory-Scanning Mutagenesis of the Molecular Interface That Ensures Specificity of Two-Component Signaling Pathways	journal.pgen.1001220	null	[ [ "Protein-protein interactions are crucial to virtually every cellular process .", "Within the crowded confines of the cell , proteins must distinguish between their cognate partners and non-cognate partners , in order to avoid unproductive and potentially deleterious interactions .", "The problem of i...	[ "Two-component signal transduction systems enable bacteria to sense and respond to a wide range of environmental stimuli .", "Sensor histidine kinases transmit signals to their cognate response regulators via phosphorylation .", "The faithful transmission of information through two-component pathways and the av...	[ "Maintaining the specificity of signal transduction pathways is critical to the ability of cells to process information , make decisions , and regulate their behavior .", "Preventing cross-talk often relies predominantly on molecular recognition and a set of specificity-determining residues in cognate proteins ."...	2010
[ "Introduction", "Results", "Discussion", "Material and methods" ]	[ "invertebrates", "medicine and health sciences", "gut bacteria", "microbiome", "pathology and laboratory medicine", "pathogens", "cell processes", "microbiology", "animals", "animal models", "drosophila melanogaster", "model organisms", "helicobacter", "experimental organism systems", "b...	The bacterial virulence factor CagA induces microbial dysbiosis that contributes to excessive epithelial cell proliferation in the Drosophila gut	journal.ppat.1006631	null	[ [ "Gut microbiota , a complex consortium of bacteria , archaea , viruses and eukaryotes found in the gut , play critical roles in human health .", "The microbiota is known to facilitate nutrient acquisition , confer resistance to pathogens , and contribute to developmental processes [1] .", "Pathologic ...	[ "Gut microbiota facilitate many aspects of human health and development , but dysbiotic microbiota can promote hyperplasia and inflammation and contribute to human diseases such as cancer .", "Human patients infected with the gastric cancer-causing bacterium Helicobacter pylori have altered microbiota; however , ...	[ "Microbial communities in the gut , termed microbiota are important for human health , and when altered can sometimes promote disease .", "Infections , such as with the cancer-causing bacterium Helicobacter pylori , can cause altered gut microbiota , but why these alterations occur and whether the altered communi...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "children", "medicine and health sciences", "pathology and laboratory medicine", "pathogens", "immunology", "microbiology", "social sciences", "neuroscience", "reoviruses", "vaccines", "viruses", "age groups", "developmental biology", "cognitive psychology", "signs and symptoms", "rna ...	Role of maternal health and infant inflammation in nutritional and neurodevelopmental outcomes of two-year-old Bangladeshi children	journal.pntd.0006363	null	[ [ "159 million children under five years old , or 23 . 8% of the world’s population in this age range , are stunted ( length-for-age Z score [LAZ] < -2 standard deviations [SD] ) [1] .", "In a pooled analysis , stunting conferred a hazard ratio of 2 . 28 for mortality prior to five years of age with severe ...	[ "Previous studies have shown maternal , inflammatory , and socioeconomic variables to be associated with growth and neurodevelopment in children from low-income countries .", "However , these outcomes are multifactorial and work describing which predictors most strongly influence them is lacking .", "We conduct...	[ "Children from low-income settings experience linear growth faltering and neurodevelopmental delay that have been associated with maternal , socioeconomic , and infectious/inflammatory variables .", "Given the interdependent nature of these associations , understanding which variables are the best predictors of p...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "skin", "invertebrates", "medicine and health sciences", "rna interference", "integumentary system", "engineering and technology", "light microscopy", "cloning", "animals", "animal models", "drosophila melanogaster", "model organisms", "microscopy", "experimental organism systems", "epid...	Allocation of distinct organ fates from a precursor field requires a shift in expression and function of gene regulatory networks	journal.pgen.1007185	null	[ [ "In organisms as diverse as flies and humans , it is common for multiple adult tissues/organs to originate from adjacent territories within a uniform precursor field .", "For example , the developing anterior forebrain in vertebrates gives rise to the eyes , hypothalamus , diencephalon , and telencephalon...	[ "A common occurrence in metazoan development is the rise of multiple tissues/organs from a single uniform precursor field .", "One example is the anterior forebrain of vertebrates , which produces the eyes , hypothalamus , diencephalon , and telencephalon .", "Another instance is the Drosophila wing disc , whic...	[ "A battery of transcription factors collectively called the retinal determination ( RD ) network controls the earliest steps in the specification of the fruit fly compound eye .", "Loss-of-function mutations lead to the loss of the compound eyes while over-expression of RD network members in non-retinal tissues i...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "transfection", "cell physiology", "medicine and health sciences", "pathology and laboratory medicine", "viral transmission and infection", "pathogens", "microbiology", "cell metabolism", "physiological processes", "helicobacter", "molecular biology techniques", "bacteria", "bacterial pathog...	Helicobacter pylori modulates host cell responses by CagT4SS-dependent translocation of an intermediate metabolite of LPS inner core heptose biosynthesis	journal.ppat.1006514	null	[ [ "The successful bacterial gastric colonizer and human pathogen Helicobacter pylori has conquered a largely uninhabitable niche , the human stomach mucosa , where it persists in about 50% of the world’s population .", "Navigation systems guide the bacteria closely to the gastric mucosa , where they dwell i...	[ "Highly virulent Helicobacter pylori cause proinflammatory signaling inducing the transcriptional activation and secretion of cytokines such as IL-8 in epithelial cells .", "Responsible in part for this signaling is the cag pathogenicity island ( cagPAI ) that codetermines the risk for pathological sequelae of an...	[ "The Cag Type IV secretion system , which contributes to inflammation and cancerogenesis during chronic infection , is one of the major virulence and fitness factors of the bacterial gastric pathogen Helicobacter pylori .", "Up to now , the mechanisms leading to cagPAI-dependent signal transduction and cytokine s...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "physicians", "medical doctors", "pathology and laboratory medicine", "education", "medical personnel", "sociology", "tropical diseases", "diet", "social sciences", "vertebrates", "parasitic diseases", "migraine", "animals", "mammals", "animal products",...	Estimating the association between being seropositive for cysticercosis and the prevalence of epilepsy and severe chronic headaches in 60 villages of rural Burkina Faso	journal.pntd.0007101	null	[ [ "Epilepsy is reported to disproportionately affect rural low income countries [1] , with lifetime epilepsy estimated to being nearly three times higher in rural developing countries compared to developed countries [1] .", "The prevalence of epilepsy is also reported to vary within sub-Saharan Africa ( SSA...	[ "Individuals diagnosed with neurocysticercosis often present with epilepsy and sometimes with progressively worsening severe chronic headaches ( WSCH ) .", "While cross-sectional associations between seropositivity to cysticercal antigens and epilepsy have been reported , few large scale studies have been conduct...	[ "Taenia solium is a parasite that can be transmitted between humans and pigs in areas with poor sanitation and pig management practices .", "When this parasite infects the human brain , it can cause epilepsy or severe headaches .", "Our study aimed to measure the association between being seropositive to cystic...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "game theory", "mathematics", "theoretical biology", "evolutionary modeling", "applied mathematics", "biology and life sciences", "physical sciences", "evolutionary theory", "evolutionary biology", "computational biology" ]	Evolutionary Game Dynamics in Populations with Heterogenous Structures	journal.pcbi.1003567	null	[ [ "Population structure has long been known to affect the outcome of an evolutionary process [1]–[4] .", "Evolutionary graph theory has emerged as a convenient framework for modelling structured populations [4] , [5] .", "Individuals reside on vertices of the graph and the edges define the interaction n...	[ "Evolutionary graph theory is a well established framework for modelling the evolution of social behaviours in structured populations .", "An emerging consensus in this field is that graphs that exhibit heterogeneity in the number of connections between individuals are more conducive to the spread of cooperative ...	[ "Understanding the evolution of cooperation is a persistent challenge to evolutionary theorists .", "A contemporary take on this subject is to model populations with interactions structured as close as possible to actual social networks .", "These networks are heterogeneous in the number and type of contact eac...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/disease models", "genetics and genomics/animal genetics" ]	Genomic Instability, Defective Spermatogenesis, Immunodeficiency, and Cancer in a Mouse Model of the RIDDLE Syndrome	journal.pgen.1001381	null	[ [ "DNA damage checkpoint signaling and DNA repair pathways are key elements of the DNA damage response ( DDR ) and are critical for the maintenance of genomic integrity [1]–[3] .", "Mammalian cells constantly experience DNA damage as a result of exogenous exposure to ionizing radiation ( IR ) , ultraviolet ...	[ "Eukaryotic cells have evolved to use complex pathways for DNA damage signaling and repair to maintain genomic integrity .", "RNF168 is a novel E3 ligase that functions downstream of ATM , γ-H2A . X , MDC1 , and RNF8 .", "It has been shown to ubiquitylate histone H2A and to facilitate the recruitment of other D...	[ "The repair of DNA damage is fundamental as illustrated by the many human syndromes , immunodeficiencies , and cancers associated with defects in DNA damage signaling and repair .", "RIDDLE syndrome , caused by mutations of the human RNF168 , is a novel hereditary disease clinically characterized by radiosensitiv...	2011
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "neuroscience", "fibroblasts", "connective tissue cells", "genome analysis", "epigenetics", "chromatin", "heterochromatin", "genomics", "animal cells", "chromosome biology", "gene expression", "connective tissue", "biological tissue", "gene ontologies", ...	β-actin regulates a heterochromatin landscape essential for optimal induction of neuronal programs during direct reprograming	journal.pgen.1007846	null	[ [ "In mammals , six functional actin genes expressed in a tissue-specific manner form the actin cytoskeleton , a basic physical and organizational intracellular structure that dynamically regulates cell polarity , membrane properties and cell behavior [1 , 2] .", "Actin-containing structures are involved in...	[ "During neuronal development , β-actin serves an important role in growth cone mediated axon guidance .", "Consistent with this notion , in vivo ablation of the β-actin gene leads to abnormalities in the nervous system .", "However , whether β-actin is involved in the regulation of neuronal gene programs is not...	[ "Although β-actin plays an important role in growth cone mediated axon guidance in neurons , the potential role of β-actin in controlling neuron differentiation remains unknown .", "Here , we converted β-actin+/+ WT , β-actin+/- HET and β-actin-/- KO mouse embryonic fibroblast ( MEFs ) into chemically induced neu...	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "viral diseases", "calicivirus infection" ]	Crystallography of a Lewis-Binding Norovirus, Elucidation of Strain-Specificity to the Polymorphic Human Histo-Blood Group Antigens	journal.ppat.1002152	null	[ [ "Noroviruses , a genus in the family Caliciviridae , are a group of small-round structured , nonenveloped RNA viruses causing epidemic acute gastroenteritis in all age in both developing and developed countries [1] , [2] , [3] .", "Structurally , norovirus possesses an outer protein capsid that encapsulat...	[ "Noroviruses , an important cause of acute gastroenteritis in humans , recognize the histo-blood group antigens ( HBGAs ) as host susceptible factors in a strain-specific manner .", "The crystal structures of the HBGA-binding interfaces of two A/B/H-binding noroviruses , the prototype Norwalk virus ( GI . 1 ) and...	[ "The interactions of noroviruses with histo-blood group antigens ( HBGAs ) are diverse , in which strains in both genogroups I and II ( GI and GII ) recognizing either the secretor or the non-secretor ( Lewis ) HBGAs have been reported .", "The crystal structures of the HBGA binding interfaces of two secretor bin...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "cell biology", "yeast and fungi", "eukaryotes" ]	The Spindle Pole Bodies Facilitate Nuclear Envelope Division during Closed Mitosis in Fission Yeast	journal.pbio.0050170	Spindle pole bodies allow nuclear division during mitosis, when there is no nuclear envelope breakdown in fission yeast.	[ [ "The nuclear envelope ( NE ) delineates the boundary of the nucleus in eukaryotic cells and is composed of two membranes enclosing a luminal space .", "Because chromosomes are located in the nucleus , cells must enable the access of spindle microtubules to the nucleoplasm in order to segregate the daughte...	[ "Many organisms divide chromosomes within the confines of the nuclear envelope ( NE ) in a process known as closed mitosis .", "Thus , they must ensure coordination between segregation of the genetic material and division of the NE itself .", "Although many years of work have led to a reasonably clear understan...	[ "Chromosomes replicate in the nucleus , which is surrounded by the double-layered nuclear envelope ( NE ) .", "During so-called open mitosis , the NE breaks down to allow spindle microtubules ( which do the work of pulling the replicated chromosomes apart ) access to the nuclear interior .", "Alternatively , in...	2007
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "drug absorption", "body fluids", "classical mechanics", "fluid mechanics", "biological cultures", "cell cultures", "damage mechanics", "pharmacology", "cellular structures and organelles", "research and analysis methods", "mucus", "deformation", "fluid dyna...	Modeling and Simulation of Mucus Flow in Human Bronchial Epithelial Cell Cultures – Part I: Idealized Axisymmetric Swirling Flow	journal.pcbi.1004872	null	[ [ "The propulsion of mucus in human airways to the trachea by the collective , coordinated action of cilia , known as mucociliary clearance ( MCC ) , remains an outstanding modeling and computational challenge .", "In the lungs , the airway surface liquid ( ASL ) protects the airway epithelium from inhaled ...	[ "A multi-mode nonlinear constitutive model for mucus is constructed directly from micro- and macro-rheology experimental data on cell culture mucus , and a numerical algorithm is developed for the culture geometry and idealized cilia driving conditions .", "This study investigates the roles that mucus rheology , ...	[ "In the lungs , the airway surface liquid protects the airway epithelium from inhaled pathogens and particulates .", "It is well known that failure to properly clear mucus from the airways leads to chronic , even fatal , lung infections .", "To date , there is no validated constitutive model capable of recapitu...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases/bacterial infections", "infectious diseases/epidemiology and control of infectious diseases" ]	Estimating the Duration of Pertussis Immunity Using Epidemiological Signatures	journal.ppat.1000647	null	[ [ "Pertussis has been an important cause of morbidity and mortality for centuries [1] and remains a significant cause of infant mortality worldwide [2] .", "During the 1940s and 1950s , many industrialized countries implemented widespread pertussis immunization programmes , which resulted in dramatic declin...	[ "Case notifications of pertussis have shown an increase in a number of countries with high rates of routine pediatric immunization .", "This has led to significant public health concerns over a possible pertussis re-emergence .", "A leading proposed explanation for the observed increase in incidence is the loss...	[ "The eradication of vaccine-preventable infectious diseases remains an important public health priority .", "To achieve this goal , the level of immunity afforded needs to be high and long-lasting .", "For pertussis , one of the leading causes of mortality in infants , immunity has been shown to wane in some in...	2009
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience", "neuroscience/cognitive neuroscience", "neuroscience/theoretical neuroscience" ]	The Statistical Neuroanatomy of Frontal Networks in the Macaque	journal.pcbi.1000050	null	[ [ "The advent and application of modern anatomical tract tracing methods has led to extensive mapping of connections between architectonically defined areas of the macaque brain , resulting in the generation of a massive amount of information on connectivity .", "Given the complexity of the cortex , however...	[ "We were interested in gaining insight into the functional properties of frontal networks based upon their anatomical inputs .", "We took a neuroinformatics approach , carrying out maximum likelihood hierarchical cluster analysis on 25 frontal cortical areas based upon their anatomical connections , with 68 input...	[ "The anatomical input to a cortical area defines , to a large extent , the functions that the area can perform .", "For example , if an area has no visual inputs , it cannot carry out computations on visual information .", "Therefore , understanding the inputs to a patch of cortex can provide fundamental insigh...	2008
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "fourier analysis", "medicine and health sciences", "neural networks", "social sciences", "neuroscience", "human performance", "vision", "research and analysis methods", "sensory physiology", "computer and information sciences", "animal cells", "genetic interference", "behavior", "mathemat...	Beyond Bouma's window: How to explain global aspects of crowding?	journal.pcbi.1006580	null	[ [ "Organisation: Feed-forward ( features at a given level are only affected by lower level features ) vs . recurrent processing ( features at a given level can be affected by lower or higher level features ) .", "Grouping component: Does the model incorporate a grouping component ?", "Certain models exp...	[ "In crowding , perception of an object deteriorates in the presence of nearby elements .", "Although crowding is a ubiquitous phenomenon , since elements are rarely seen in isolation , to date there exists no consensus on how to model it .", "Previous experiments showed that the global configuration of the enti...	[ "Visual crowding highlights interactions between elements in the visual field .", "For example , an object is more difficult to recognize if it is presented in clutter .", "Crowding is one of the most fundamental aspects of vision , playing crucial roles in object recognition , reading and visual perception in ...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genome-wide association studies", "genome expression analysis", "immune cells", "population genetics", "quantitative traits", "immunology", "gene expression", "biology", "haplotypes", "monocytes", "heredity", "genetics", "genomics", "genetics and genomics", "complex traits" ]	Genome-Wide Haplotype Analysis of Cis Expression Quantitative Trait Loci in Monocytes	journal.pgen.1003240	null	[ [ "The development of high throughput technologies has stimulated comprehensive surveys on genome-wide expression and DNA variability data for disentangling the genetic architecture of human diseases [1]–[3] .", "The genetics of transcript abundance has been extensively investigated through genome-wide expr...	[ "In order to assess whether gene expression variability could be influenced by several SNPs acting in cis , either through additive or more complex haplotype effects , a systematic genome-wide search for cis haplotype expression quantitative trait loci ( eQTL ) was conducted in a sample of 758 individuals , part of...	[ "In order to assess whether gene expression variability could be influenced by the presence of more than one cis-acting SNP , we have conducted a systematic genome-wide search for haplotypic cis eQTL effects in a sample of 758 individuals and replicated the findings in an independent sample of 1 , 374 subjects .", ...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "pathology and laboratory medicine", "parasitic diseases", "animals", "parasitology", "organisms", "molecular biology techniques", "strongyloides stercoralis", "cellular structures and organelles", "extraction techniques", "research and analysis...	Accuracy of molecular biology techniques for the diagnosis of Strongyloides stercoralis infection—A systematic review and meta-analysis	journal.pntd.0006229	null	[ [ "Strongyloides stercoralis is a soil-transmitted helminth ( STH ) affecting around 370 million people worldwide , particularly in remote rural areas[1] .", "Chronic strongyloidiasis is characterized by non-specific , mostly mild symptoms involving the gastrointestinal tract ( abdominal pain , diarrhea ) ,...	[ "Strongyloides stercoralis infection is a neglected tropical disease which can lead to severe symptoms and even death in immunosuppressed people .", "Unfortunately , its diagnosis is hampered by the lack of a gold standard , as the sensitivity of traditional parasitological tests ( including microscopic examinati...	[ "Strongyloides stercoralis is a worm that can potentially kill affected immunosuppressed individuals .", "The parasite is not easily detected with stool microscopy , hence novel tests have been implemented , such as polymerase chain reaction ( PCR ) , that can detect the DNA of the parasite .", "This work aims ...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "death rates", "medicine and health sciences", "ecology and environmental sciences", "demography", "geographical locations", "tropical diseases", "india", "sand flies", "parasitic diseases", "neglected tropical diseases", "population biology", "insect vectors", "bangladesh", "nepal", "ag...	Efficacy, Safety and Cost of Insecticide Treated Wall Lining, Insecticide Treated Bed Nets and Indoor Wall Wash with Lime for Visceral Leishmaniasis Vector Control in the Indian Sub-continent: A Multi-country Cluster Randomized Controlled Trial	journal.pntd.0004932	null	[ [ "Visceral leishmaniasis ( VL ) , also known as kala-azar , is a neglected vector-borne disease caused by the protozoan parasite Leishmania donovani and is transmitted by the female Phlebotomus argentipes sand fly .", "The poorest of the rural areas of Bangladesh , India , Nepal and East Africa are the vic...	[ "We investigated the efficacy , safety and cost of lime wash of household walls plus treatment of sand fly breeding places with bleach ( i . e . environmental management or EM ) , insecticide impregnated durable wall lining ( DWL ) , and bed net impregnation with slow release insecticide ( ITN ) for sand fly contro...	[ "Sand fly control is one of the main priorities of the Visceral Leishmaniasis ( VL ) Elimination Program in Bangladesh , India and Nepal .", "Currently , indoor residual spraying with insecticides ( IRS ) is the most effective method available for sand fly control .", "The efficacy of other methods of vector co...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "oncology", "medicine", "gynecological tumors", "viruses and cancer", "virology", "cervical cancer", "biology", "microbiology", "cancers and neoplasms" ]	Oncogenic Human Papillomaviruses Activate the Tumor-Associated Lens Epithelial-Derived Growth Factor (LEDGF) Gene	journal.ppat.1003957	null	[ [ "Oncogenic types of human papillomaviruses ( HPVs ) , such as HPV16 and HPV18 , are major human carcinogens .", "They cause cervical carcinoma , the second most common cancer in females worldwide and are closely linked to the development of other malignancies , including a subset of additional anogenital ...	[ "The expression of the human papillomavirus ( HPV ) E6/E7 oncogenes is crucial for HPV-induced malignant cell transformation .", "The identification of cellular targets attacked by the HPV oncogenes is critical for our understanding of the molecular mechanisms of HPV-associated carcinogenesis and may open novel t...	[ "Specific types of human papillomaviruses ( HPVs ) are closely linked to the development of malignant tumors , such as cervical cancer .", "Virtually all cervical cancers contain HPV DNA and the tumorigenic growth behavior of cervical cancer cells is dependent on the activity of two viral oncogenes , called E6 an...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "carbohydrate metabolism", "chemical compounds", "monomers", "metabolic processes", "carbohydrates", "glucose metabolism", "parasitic protozoans", "organic compounds", "glucose", "glycolysis", "trypanosoma brucei", "protozoans", "molecular biology techniques", "research and analysis method...	Gluconeogenesis using glycerol as a substrate in bloodstream-form Trypanosoma brucei	journal.ppat.1007475	null	[ [ "T . brucei is the causative agent of human and animal African trypanosomiases , devastating but neglected tropical diseases .", "The mammalian-infective form of the parasite , typically referred to as the bloodstream form ( BSF ) , lives in blood of mammalian hosts and enters the central nervous system (...	[ "Bloodstream form African trypanosomes are thought to rely exclusively upon glycolysis , using glucose as a substrate , for ATP production .", "Indeed , the pathway has long been considered a potential therapeutic target to tackle the devastating and neglected tropical diseases caused by these parasites .", "Ho...	[ "Trypanosomes are the etiological agents of human sleeping sickness and animal African trypanosomiases , a range of diseases in cattle , other livestock and horses caused by several Trypanosoma subspecies .", "The mammalian stage of the parasite circulates in the bloodstream , a nutrient-rich environment with con...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "mycology", "fungi", "sexual differentiation", "genetics", "biology and life sciences", "molecular genetics", "microbial growth and development", "microbiology", "fungal reproduction", "morphogenesis", "fungal structure", "organisms", "gene function" ]	Morphotype Transition and Sexual Reproduction Are Genetically Associated in a Ubiquitous Environmental Pathogen	journal.ppat.1004185	null	[ [ "Selective pressures from the environment shape microbial evolution .", "To cope with the challenges presented by both predictable and erratic environmental fluctuations , microbes employ various adaptation and bet-hedging strategies , like coordinated community behaviors and morphotype transition [1] , [...	[ "Sexual reproduction in an environmental pathogen helps maximize its lineage fitness to changing environment and the host .", "For the fungal pathogen Cryptococcus neoformans , sexual reproduction is proposed to have yielded hyper virulent and drug resistant variants .", "The life cycle of this pathogen commenc...	[ "Sex , despite its cost , is an important means to maximize species fitness in coping with unpredictable environmental challenges .", "In the human fungal pathogen Cryptococcus neoformans , sexual reproduction has yielded hyper virulent and drug resistant variants , and produces airborne infectious spores .", "...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunology/cellular microbiology and pathogenesis", "microbiology/innate immunity", "immunology/innate immunity", "infectious diseases/bacterial infections", "cardiovascular disorders", "immunology/leukocyte activation" ]	The Urokinase Receptor (uPAR) Facilitates Clearance of Borrelia burgdorferi	journal.ppat.1000447	null	[ [ "Lyme borreliosis , an emerging tick-borne disease in both the New and Old world , is", "caused by spirochetes belonging to the Borrelia burgdorferi sensu", "lato group and is predominantly transmitted by Ixodes ticks [1] .", "In", "the United States Borrelia burgdorferi sensu stricto , from h...	[ "The causative agent of Lyme borreliosis , the spirochete Borrelia", "burgdorferi , has been shown to induce expression of the urokinase", "receptor ( uPAR ) ; however , the role of uPAR in the immune response against", "Borrelia has never been investigated .", "uPAR not only acts as", "a proteinase recep...	[ "Lyme borreliosis is caused by the spirochete Borrelia", "burgdorferi and is transmitted through ticks .", "Since its discovery", "approximately 30 years ago it has become the most important vector-borne disease", "in the Western world .", "The pathogenesis of this complex zoonosis is still not", "entir...	2009
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "meiosis", "medicine and health sciences", "reproductive system", "spermatocytes", "anaphase", "chromosome structure and function", "metaphase", "centromeres", "cell cycle and cell division", "cell processes", "animals", "germ cells", "mitosis", "animal models", "droso...	Dynamics and control of sister kinetochore behavior during the meiotic divisions in Drosophila spermatocytes	journal.pgen.1007372	null	[ [ "The success of meiosis depends on regulation of sister kinetochore ( KT ) behavior during the two meiotic divisions .", "At the beginning of the first meiotic division , the two sister KTs function as a single unit .", "As a result , each of the two chromosomes in a bivalent , which results from pair...	[ "Sister kinetochores are connected to the same spindle pole during meiosis I and to opposite poles during meiosis II .", "The molecular mechanisms controlling the distinct behavior of sister kinetochores during the two meiotic divisions are poorly understood .", "To study kinetochore behavior during meiosis , w...	[ "For production of oocytes and sperm , cells have to complete meiosis which includes two successive divisions .", "These divisions convert diploid cells with a maternal and a paternal copy of each chromosome into haploid cells with only one copy of each chromosome .", "Chromosome copy reduction requires regulat...	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "computational neuroscience", "biology", "neuroscience", "neurophysiology" ]	Membrane Properties and the Balance between Excitation and Inhibition Control Gamma-Frequency Oscillations Arising from Feedback Inhibition	journal.pcbi.1002354	null	[ [ "The 30–80 Hz gamma rhythm is among the most prominent and ubiquitous forms of rhythmic activity in the brain [1]–[5] .", "Since its discovery , a multitude of functions and mechanisms have been ascribed to this form of oscillatory behavior .", "The gamma rhythm has been proposed as a requirement for ...	[ "Computational studies as well as in vivo and in vitro results have shown that many cortical neurons fire in a highly irregular manner and at low average firing rates .", "These patterns seem to persist even when highly rhythmic signals are recorded by local field potential electrodes or other methods that quanti...	[ "The gamma rhythm is a prominent , 30–80-Hz EEG signal that is associated with cognition .", "Several classes of computational models have been posited to explain the gamma rhythm mechanistically .", "We study a particular class in which the gamma rhythm arises from delayed negative feedback .", "Our study is...	2012
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "genome evolution", "applied mathematics", "histone modification", "algorithms", "simulation and modeling", "mathematics", "genetic elements", "sequence motif analysis", "epigenetics", "epigenomics", "chromatin", "research and analysis methods", "sequence analysis", "mobile genetic element...	A likelihood approach to testing hypotheses on the co-evolution of epigenome and genome	journal.pcbi.1006673	null	[ [ "Milestones of mathematical modeling of DNA evolution were marked by base substitution models in early 1980s [1–3] , extension to incorporation of sequence insertions and deletions ( indels ) in early 1990s [4] , and differential treatments of cis-regulatory sequences in the 2000-2010s [5–12] .", "The ris...	[ "Central questions to epigenome evolution include whether interspecies changes of histone modifications are independent of evolutionary changes of DNA , and if there is dependence whether they depend on any specific types of DNA sequence changes .", "Here , we present a likelihood approach for testing hypotheses ...	[ "Epigenetic modifications play a significant role in gene regulations and thus heavily influence phenotypic outcomes .", "Whereas cross-species epigenomic comparisons have been fruitful in revealing the function of epigenetic modifications , it still remains unclear how the epigenome changes across species .", ...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "model organisms", "genetics", "biology", "molecular cell biology", "genetics and genomics" ]	S Phase–Coupled E2f1 Destruction Ensures Homeostasis in Proliferating Tissues	journal.pgen.1002831	null	[ [ "During development , cells continually integrate extrinsic and intrinsic signals that control cell growth , proliferation and apoptosis .", "Mitogenic signals that drive growth and cell proliferation are balanced with apoptotic signals that eliminate damaged or unneeded cells .", "Genetic changes tha...	[ "Precise control of cell cycle regulators is critical for normal development and tissue homeostasis .", "E2F transcription factors are activated during G1 to drive the G1-S transition and are then inhibited during S phase by a variety of mechanisms .", "Here , we genetically manipulate the single Drosophila act...	[ "Rapidly growing tissues provide an excellent opportunity to study the careful balance between cell proliferation and apoptosis needed for normal organ structure and function in developing organisms .", "We present evidence that a transcription factor critical for regulating progression of the Drosophila melanoga...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "body fluids", "education", "population dynamics", "sociology", "geographical locations", "tropical diseases", "social sciences", "parasitic diseases", "animals", "filariasis", "pharmaceutics", "drug administration", "neglected tropical di...	The significant scale up and success of Transmission Assessment Surveys 'TAS' for endgame surveillance of lymphatic filariasis in Bangladesh: One step closer to the elimination goal of 2020	journal.pntd.0005340	null	[ [ "Bangladesh is a remarkable example in terms of the progress it has made in the elimination of lymphatic filariasis ( LF ) , following the launch of the Global Programme to Eliminate LF ( GPELF ) by the World Health Organization ( WHO ) in 2000 [1] .", "Bangladesh was one of the first countries in the Sou...	[ "Bangladesh had one of the highest burdens of lymphatic filariasis ( LF ) at the start of the Global Programme to Eliminate Lymphatic Filariasis ( GPELF ) with an estimated 70 million people at risk of infection across 34 districts .", "In total 19 districts required mass drug administration ( MDA ) to interrupt ...	[ "Lymphatic filariasis ( LF ) was highly endemic in Bangladesh at the start of the Global Programme to Eliminate Lymphatic Filariasis ( GPELF ) in 2000 , with approximately 70 million people at risk .", "To address this burden , the National LF Programme implemented mass drug administration ( MDA ) in 19 highly en...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell physiology", "organismal evolution", "medicine and health sciences", "luciferase", "immune physiology", "pathology and laboratory medicine", "evolutionary biology", "viral transmission and infection", "enzymes", "pathogens", "immunology", "microbiology", "enzymology", "retroviruses",...	Phenotypic deficits in the HIV-1 envelope are associated with the maturation of a V2-directed broadly neutralizing antibody lineage	journal.ppat.1006825	null	[ [ "Broadly neutralizing antibodies ( bnAbs ) are a focus of HIV-1 vaccine development and passive immunization strategies [1–7] .", "Owing to the exceptionally potent and broad bnAbs that have been isolated over recent years [8–12] , a wealth of information on their function has become available .", "Ho...	[ "Broadly neutralizing antibodies ( bnAbs ) to HIV-1 can evolve after years of an iterative process of virus escape and antibody adaptation that HIV-1 vaccine design seeks to mimic .", "To enable this , properties that render HIV-1 envelopes ( Env ) capable of eliciting bnAb responses need to be defined .", "Her...	[ "HIV-1 infected individuals rarely develop broadly neutralizing antibodies ( bnAbs ) that inhibit diverse HIV-1 subtypes .", "As activity against the majority of HIV-1 isolates is necessary for effective immunization against HIV-1 , current vaccine development seeks to generate regimens that evoke bnAb responses ...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "pathology and laboratory medicine", "chemical compounds", "pathogens", "immunology", "microbiology", "organic compounds", "dna transcription", "animal models", "bacterial diseases", "model organisms", "immunoprecipitation", ...	Acetylation of Lysine 201 Inhibits the DNA-Binding Ability of PhoP to Regulate Salmonella Virulence	journal.ppat.1005458	null	[ [ "As Gram-negative bacteria , salmonellae can cause enteric diseases in a wide range of animals .", "Salmonella Typhimurium , non-typhoidal Salmonella ( NTS ) , is usually used as a model organism to understand bacterial interactions with host cells .", "Salmonella can survive and multiply inside sever...	[ "The two-component system PhoP-PhoQ is highly conserved in bacteria and regulates virulence in response to various signals for bacteria within the mammalian host .", "Here , we demonstrate that PhoP could be acetylated by Pat and deacetylated by deacetylase CobB enzymatically in vitro and in vivo in Salmonella Ty...	[ "Salmonella Typhimurium is a facultative intracellular pathogen capable of survival within host phagocytic cells .", "The crucial two-component system regulator PhoP-PhoQ is involved in response to different stresses and essential for the virulence of S . Typhimurium .", "In this study , we show that PhoP can b...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Co-chaperone p23 Regulates C. elegans Lifespan in Response to Temperature	journal.pgen.1005023	null	[ [ "Temperature dramatically impacts the lifespan of ectotherms , with lower temperatures typically extending and higher temperatures shortening life [1–3] .", "The conventional view is that temperature passively affects the rate of chemical reactions and metabolism , thereby influencing species longevity ."...	[ "Temperature potently modulates various physiologic processes including organismal motility , growth rate , reproduction , and ageing .", "In ectotherms , longevity varies inversely with temperature , with animals living shorter at higher temperatures .", "Thermal effects on lifespan and other processes are asc...	[ "Temperature is a critical environmental factor that affects ageing in both cold-blooded and warm-blooded species .", "In invertebrate animals , lifespan varies inversely with temperature , with higher temperature resulting in faster development but shorter lifespan .", "This phenomenon has been usually attribu...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "death rates", "hiv infections", "medicine and health sciences", "european union", "evolutionary biology", "histoplasmosis", "geographical locations", "tropical diseases", "paracoccidioidomycosis", "neglected tropical diseases", "fungal diseases", "population biology", "infectious diseases",...	Imported endemic mycoses in Spain: Evolution of hospitalized cases, clinical characteristics and correlation with migratory movements, 1997-2014	journal.pntd.0006245	null	[ [ "Endemic mycoses are systemic fungal infections caused by pathogens that are endemic in temperate areas of the world .", "These infections are classified according to the infectivity of the fungus into two groups: produced by primary pathogens and by opportunistic pathogens [1] .", "The genus Histopla...	[ "Endemic mycoses are systemic fungal infections .", "Histoplasmosis is endemic in all temperate areas of the world; coccidioidomycosis and paracoccidioidomycosis are only present in the American continent .", "These pathogens are not present in Spain , but in the last years there has been an increase of reporte...	[ "Histoplasmosis , coccidioidomycosis and paracoccidioidomycosis are infections produced by environmental fungi .", "Despite the fact that these pathogens are not found in Spain , these diseases are an important health problem in many countries of the world , especially in Latin America .", "Due to the increased...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell motility", "medicine and health sciences", "neurochemistry", "chemical compounds", "optogenetics", "aliphatic amino acids", "brain", "neuroscience", "organic compounds", "developmental biology", "hindbrain", "brain mapping", "amino acids", "bioassays and physiological analysis", "n...	Neurotransmitter-mediated activity spatially controls neuronal migration in the zebrafish cerebellum	journal.pbio.2002226	null	[ [ "The brain is the most complex organ in the body .", "It carries out its tasks by networks of neurons that form separate spatial entities , which are often organized into layers or nuclei .", "During embryonic development , many neurons that arise in various progenitor zones migrate in order to build ...	[ "Neuronal migration during embryonic development contributes to functional brain circuitry .", "Many neurons migrate in morphologically distinct stages that coincide with differentiation , requiring tight spatial regulation .", "It had been proposed that neurotransmitter-mediated activity could exert this contr...	[ "Postmitotic neurons migrate from their site of origin to their final destination in the developing brain to form functional structures .", "These neurons typically follow defined routes through the tissue .", "Previous studies investigating progress along such route have identified neurotransmitters—chemicals ...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "social and behavioral sciences", "experimental psychology", "psychophysics", "psychology" ]	Testing Whether Humans Have an Accurate Model of Their Own Motor Uncertainty in a Speeded Reaching Task	journal.pcbi.1003080	null	[ [ "Human movement is prone to error .", "This error may be reduced after extensive practice or under careful control , but can never be entirely eliminated .", "It can have severe consequences when , for example , the outcome of a surgical procedure hangs on the accuracy of the surgeon's movements .", ...	[ "In many motor tasks , optimal performance presupposes that human movement planning is based on an accurate internal model of the subject's own motor error .", "We developed a motor choice task that allowed us to test whether the internal model implicit in a subject's choices differed from the actual in isotropy ...	[ "When you play darts , which part of the dartboard do you aim at ?", "The tiny bull's eye is worth 50 points .", "The 20-point section is much larger .", "If you're not very good at dart throwing you may want to take that into account .", "Your choice of target depends not on how good you are but on how goo...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "mitosis", "developmental biology", "chromosome biology", "chromosome structure and function", "birth defects", "gene expression", "genetics", "biology", "genomics", "molecular cell biology", "morphogenesis", "genetics of disease", "chromatin", "dna transcription" ]	A Cohesin-Independent Role for NIPBL at Promoters Provides Insights in CdLS	journal.pgen.1004153	null	[ [ "Genomes need to be stably inherited over numerous cell generations .", "For each cell division the genetic information has to be replicated , the copies identified and then equally distributed between daughter cells .", "This process crucially depends on the cohesin complex , consisting of the core s...	[ "The cohesin complex is crucial for chromosome segregation during mitosis and has recently also been implicated in transcriptional regulation and chromatin architecture .", "The NIPBL protein is required for the loading of cohesin onto chromatin , but how and where cohesin is loaded in vertebrate cells is unclear...	[ "The cohesin complex is crucial for chromosome segregation during cell divisions but was recently also implicated in transcriptional regulation and chromatin architecture .", "Cohesin's binding to chromatin depends on NIPBL , a factor that was found to be mutated in 50% of the cases of the human developmental dis...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "protein interactions", "microbiology", "light microscopy", "membrane proteins", "fungi", "confocal laser microscopy", "microscopy", "confocal microscopy", "peroxisomes", "cellular structures and organelles", "research and analysis methods", "lipids", "proteins", "viral replication", "st...	Assembly-hub function of ER-localized SNARE proteins in biogenesis of tombusvirus replication compartment	journal.ppat.1007028	null	[ [ "Positive-strand ( + ) RNA viruses assemble numerous membrane-bound viral replicase complexes ( VRCs ) within large replication compartments/organelles to support their replication in infected cells [1 , 2 , 3 , 4 , 5] .", "In addition to the viral-coded replication proteins and the viral RNA ( s ) , the ...	[ "Positive-strand RNA viruses assemble numerous membrane-bound viral replicase complexes within large replication compartments to support their replication in infected cells .", "Yet the detailed mechanism of how given subcellular compartments are subverted by viruses is incompletely understood .", "Although , T...	[ "Viral replication organelles are formed in subcellular compartments during positive-strand RNA virus infections to support robust virus replication .", "TBSV induces multivesicular body-like structures consisting of aggregated peroxisomes .", "However , endoplasmic reticulum ( ER ) and early endosomal proteins...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "chemical bonding", "crystal structure", "condensed matter physics", "simulation and modeling", "protein structure prediction", "protein structure", "crystallography", "thermodynamics", "hydrogen bonding", "physical chemistry", "research and analysis methods", "solid state physics", "protein...	Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours	journal.pcbi.1006578	null	[ [ "Since Anfinsen’s original demonstration that a protein’s sequence determines its structure , multiple computational strategies have been developed to predict a protein’s structure from its sequence .", "An additional facet of this challenge is to replicate the energy landscape that defines both the foldi...	[ "An ongoing challenge in protein chemistry is to identify the underlying interaction energies that capture protein dynamics .", "The traditional trade-off in biomolecular simulation between accuracy and computational efficiency is predicated on the assumption that detailed force fields are typically well-paramete...	[ "All-atom biomolecular simulations are useful but often take months to simulate biologically relevant reactions .", "Coarse-grain folding simulations reduce the computational requirements; however , they typically have reduced accuracy and knowledge of the native state is required .", "Here , we show that a pro...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Taenia solium Human Cysticercosis: A Systematic Review of Sero-epidemiological Data from Endemic Zones around the World	journal.pntd.0003919	null	[ [ "Taenia solium human cysticercosis ( HCC ) is a zoonotic parasitic disease causing severe health and economic problems in endemic areas in Latin America , Africa and Asia [1–4] .", "The disease is related to poor sanitary conditions , inadequate hygiene , open defecation , presence of free roaming pigs an...	[ "Taenia solium cysticercosis is a zoonotic neglected disease responsible for severe health disorders such as seizures and death .", "Understanding the epidemiology of human cysticercosis ( HCC ) in endemic regions will help to expose critical information about the transmission of the disease , which could be used...	[ "Human cysticercosis is a neglected zoonotic disease caused by the larval stage of the parasite Taenia solium .", "This disease is responsible for severe health disorders such as seizures , and in some cases even death .", "T . solium cysticercosis is endemic in countries in Africa , Latin America and Asia wher...	2015
[ "Introduction", "Materials and Methods", "Results/Discussion" ]	[ "computational biology/population genetics", "computer science/numerical analysis and theoretical computing", "genetics and genomics/bioinformatics", "genetics and genomics/population genetics" ]	Efficient and Accurate Construction of Genetic Linkage Maps from the Minimum Spanning Tree of a Graph	journal.pgen.1000212	null	[ [ "Genetic linkage mapping dates back to the early 20th century when scientists began to understand the recombinational nature and cellular behavior of chromosomes .", "In 1913 Sturtevant studied the first genetic linkage map of chromosome X of Drosophila melanogaster [1] .", "Genetic linkage maps began...	[ "Genetic linkage maps are cornerstones of a wide spectrum of biotechnology applications , including map-assisted breeding , association genetics , and map-assisted gene cloning .", "During the past several years , the adoption of high-throughput genotyping technologies has been paralleled by a substantial increas...	[ "Genetic linkage maps are cornerstones of a wide spectrum of biotechnology applications .", "In recent years , new high-throughput genotyping technologies have substantially increased the density and diversity of genetic markers , creating new algorithmic challenges for computational biologists .", "In this pap...	2008
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "neural networks", "nervous system", "population dynamics", "electrophysiology", "neuroscience", "learning and memory", "cognitive neuroscience", "cognition", "network analysis", "memory", "population biology", "computer and information sciences", "animal ce...	Oscillations in working memory and neural binding: A mechanism for multiple memories and their interactions	journal.pcbi.1006517	null	[ [ "The neuronal substrate of working memory is thought to be persistent elevated firing rates of neurons that have been found in numerous physiological and imaging studies across widely-varying scales , from single neurons up to neuronal populations and networks [1–6] .", "Moreover , for working memory to f...	[ "Neural oscillations have been recorded and implicated in many different basic brain and cognitive processes .", "For example , oscillatory neural activity has been suggested to play a role in binding and in the maintenance of information in working memory .", "With respect to the latter , the majority of work ...	[ "Working memory is a form of limited-capacity short term memory that is relevant to cognition .", "Various studies have shown that ensembles of neurons oscillate during working memory retention , and cross-frequency coupling ( between , e . g . , theta and gamma frequencies ) has been conjectured as underlying th...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biofilms", "antimicrobials", "medicine and health sciences", "toxins", "microbiome", "pathology and laboratory medicine", "drugs", "microbiology", "toxicology", "toxic agents", "antibiotic resistance", "nutrition", "antibiotics", "pharmacology", "microbial genomics", "antimicrobial re...	Community interactions and spatial structure shape selection on antibiotic resistant lineages	journal.pcbi.1006179	null	[ [ "The human body is home to extraordinarily diverse microbial communities , or microbiomes [1] .", "Metabolic interactions among microbial members are now known to play a critical role in host health , including beneficial effects such as protection against pathogens [2] , but also detrimental effects such...	[ "Polymicrobial interactions play an important role in shaping the outcome of antibiotic treatment , yet how multispecies communities respond to antibiotic assault is still little understood .", "Here we use an individual-based simulation model of microbial biofilms to investigate how competitive and mutualistic i...	[ "Pathogens -microorganisms that make us sick- often live within dynamic and complex multispecies communities , where they may not only compete for limiting resources but also exchange beneficial resources or services with other resident species .", "While antibiotics are commonly used to get rid of such harmful m...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "chicken", "homo (human)", "danio (zebrafish)", "vertebrates", "evolutionary biology", "molecular biology", "mus (mouse)" ]	Evolution of Nova-Dependent Splicing Regulation in the Brain	journal.pgen.0030173	null	[ [ "Alternative splicing is believed to be one of the major mechanisms by which proteome diversity is generated in multicelullar organisms [1 , 2] .", "Initial estimates that 5% of human genes are alternatively spliced [3] have recently been revised , such that it is now believed that 40%–60% of human genes ...	[ "A large number of alternative exons are spliced with tissue-specific patterns , but little is known about how such patterns have evolved .", "Here , we study the conservation of the neuron-specific splicing factors Nova1 and Nova2 and of the alternatively spliced exons they regulate in mouse brain .", "Whereas...	[ "Alternative splicing generates different mRNA isoforms from a single gene and thus increases the number of proteins a cell can produce .", "This is particularly important in the brain , which possesses a number of brain-specific splicing factors .", "In this study , we have looked at evolution of brain-specifi...	2007
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing techniques", "sequence analysis", "biochemistry", "proteins", "chaperone proteins", "biology and life sciences", "molecular biology techniques", "computational biology", "molecular biology" ]	ATPase Subdomain IA Is a Mediator of Interdomain Allostery in Hsp70 Molecular Chaperones	journal.pcbi.1003624	null	[ [ "The heat shock protein 70 ( Hsp70 ) family of molecular chaperones plays a key role in the quality control of protein folding , as well as in regulation of intracellular trafficking [1]–[3] .", "Hsp70 dysfunction has been implicated in a broad range of conditions/disorders including tumor growth and Alzh...	[ "The versatile functions of the heat shock protein 70 ( Hsp70 ) family of molecular chaperones rely on allosteric interactions between their nucleotide-binding and substrate-binding domains , NBD and SBD .", "Understanding the mechanism of interdomain allostery is essential to rational design of Hsp70 modulators ...	[ "The Hsp70 family of molecular chaperones assists in protein folding , degradation , assembly/disassembly of some complexes , and intracellular trafficking .", "These activities in the cell are accomplished by coupled conformational switches/signals between their nucleotide-binding and substrate-binding domains (...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "biology and life sciences" ]	Wolbachia Transcription Elongation Factor “Wol GreA” Interacts with α2ββ′σ Subunits of RNA Polymerase through Its Dimeric C-Terminal Domain	journal.pntd.0002930	null	[ [ "Lymphatic filariasis ( LF ) , recognized as the world's most disabling and disfiguring disease , is a huge and costly problem in developing nations .", "LF caused by the mosquito-borne , thread-like nematodes belonging to the genera Wuchereria and Brugia affects around 120 million people worldwide .", ...	[ "Wolbachia , an endosymbiont of filarial nematode , is considered a promising target for therapy against lymphatic filariasis .", "Transcription elongation factor GreA is an essential factor that mediates transcriptional transition from abortive initiation to productive elongation by stimulating the escape of RNA...	[ "Diethylcarbamazine and ivermectin , the conventional antifilarial drugs , exert poor activity on adult filarial worms .", "Brugia malayi , a causative agent of human lymphatic filariasis , harbors an obligate alpha-proteobacterium , Wolbachia .", "Because the endosymbiont is required for the development , viab...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "meiosis", "medicine and health sciences", "reproductive system", "cell cycle and cell division", "cell processes", "reproductive physiology", "germ cells", "developmental biology", "oocytes", "epididymis", "embryos", "cellular structures and organelles", "sperm", "acrosomes", "embryolog...	Complementary Critical Functions of Zfy1 and Zfy2 in Mouse Spermatogenesis and Reproduction	journal.pgen.1006578	null	[ [ "The Y chromosome plays an important role in spermatogenesis and sex determination [1 , 2] .", "However , specific Y chromosome genes responsible for spermatogenesis and sex determination have not been determined in mice using gene-targeting approaches because of challenges associated with genome recombin...	[ "The mammalian Y chromosome plays a critical role in spermatogenesis .", "However , the exact functions of each gene in the Y chromosome have not been completely elucidated , partly owing to difficulties in gene targeting analysis of the Y chromosome .", "Zfy was first proposed to be a sex determination factor ...	[ "The Y chromosome is known to play a critical role in spermatogenesis based on human genetic evidence .", "However , specific Y chromosome genes responsible for spermatogenesis have not been fully elucidated yet , because the targeted deletion of Y chromosome genes is difficult owing to its unique structure .", ...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "kala-azar", "medicine and health sciences", "body fluids", "enzyme-linked immunoassays", "tropical diseases", "parasitic diseases", "parasitic protozoans", "urine", "protozoans", "leishmania", "neglected tropical diseases", "immunologic techniques", "research and analysis methods", "infec...	Noninvasive Diagnosis of Visceral Leishmaniasis: Development and Evaluation of Two Urine-Based Immunoassays for Detection of Leishmania donovani Infection in India	journal.pntd.0005035	null	[ [ "Visceral Leishmaniasis ( VL ) is a vector-borne fatal infectious disease disseminated in 88 countries of the world , particularly in remote areas of India , Bangladesh , Sudan , Brazil , Ethiopia and South Sudan where 90% of the cases occur [1] .", "Around 200 to 400 thousands of new VL cases are reporte...	[ "Visceral Leishmaniasis ( VL ) , a severe parasitic disease , could be fatal if diagnosis and treatment is delayed .", "Post kala-azar dermal leishmaniasis ( PKDL ) , a skin related outcome , is a potential reservoir for the spread of VL .", "Diagnostic tests available for VL such as tissue aspiration are invas...	[ "Visceral leishmaniasis ( VL ) , one of the most prevalent parasitic diseases in the developing world causes serious health concerns .", "Post kala-azar dermal leishmaniasis ( PKDL ) is a skin disease which occurs after treatment as a sequel to VL .", "Parasitological diagnosis involves invasive tissue aspirati...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "genetic mutation", "immunology", "gene function", "bacterial diseases", "global health", "infectious disease control", "immunizations", "infectious diseases", "tuberculosis", "biology", "immune response", "immunity", "genetic association studies", "innate immunity", "genet...	Association of Human TLR1 and TLR6 Deficiency with Altered Immune Responses to BCG Vaccination in South African Infants	journal.ppat.1002174	null	[ [ "Tuberculosis ( TB ) is one of the leading causes of mortality worldwide , with 1 . 7 million deaths occurring annually [1] .", "Although murine studies have uncovered numerous genes and pathways which are critical for effective immune responses to Mycobacterium tuberculosis ( Mtb ) , the mechanisms of im...	[ "The development of effective immunoprophylaxis against tuberculosis ( TB ) remains a global priority , but is hampered by a partially protective Bacillus Calmette-Guérin ( BCG ) vaccine and an incomplete understanding of the mechanisms of immunity to Mycobacterium tuberculosis .", "Although host genetic factors ...	[ "Tuberculosis ( TB ) is one of the leading infectious causes of death worldwide .", "The current vaccine for TB , BCG , is widely used but it is not highly effective in preventing disease .", "We investigated the role of host genetics in the immune response to BCG vaccination .", "We found that variants of in...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "transfection", "medicine and health sciences", "pathology and laboratory medicine", "hek 293 cells", "pathogens", "biological cultures", "microbiology", "plasmid construction", "viruses", "dna replication", "dna viruses", "dna construction", "dna", "molecular biology techniques", "herpe...	An Epstein-Barr Virus-Encoded Protein Complex Requires an Origin of Lytic Replication In Cis to Mediate Late Gene Transcription	journal.ppat.1005718	null	[ [ "Epstein-Barr virus ( EBV ) is a γ-herpesvirus that infects more than 95% of the human adult population .", "Primary infection is usually asymptomatic if acquired early in life , but often results in infectious mononucleosis in adolescence [1 , 2] .", "EBV is associated with several B-cell and epithel...	[ "Epstein-Barr virus lytic replication is accomplished by an intricate cascade of gene expression that integrates viral DNA replication and structural protein synthesis .", "Most genes encoding structural proteins exhibit “true” late kinetics–their expression is strictly dependent on lytic DNA replication .", "R...	[ "A strict linkage between viral DNA replication and the onset of late gene expression is commonly found in DNA viruses .", "In herpesviruses , the precise mechanism for this requirement remains elusive .", "Competing models are titration of putative repressors as a result of increase in template copy number and...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The Homeodomain Iroquois Proteins Control Cell Cycle Progression and Regulate the Size of Developmental Fields	journal.pgen.1005463	null	[ [ "Development of the different body parts in multicellular organisms is a stepwise process that entails the specification within developmental fields of territories with the ability to acquire different fates .", "Morphogens , which orchestrate such territorial specification , are also able to regulate ter...	[ "During development , proper differentiation and final organ size rely on the control of territorial specification and cell proliferation .", "Although many regulators of these processes have been identified , how both are coordinated remains largely unknown .", "The homeodomain Iroquois/Irx proteins play a key...	[ "The correct development of body organs , with their characteristic size and shape , requires the coordination of cell division and cell differentiation .", "Here we show that the Iroquois proteins ( Irx in vertebrates ) slow down cell division in the Drosophila imaginal discs , in addition to their well-known ro...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "bacteriology", "antimicrobials", "gram negative bacteria", "medicine and health sciences", "pathology and laboratory medicine", "pathogens", "drugs", "geographical locations", "microbiology", "salmonella typhi", "bacterial diseases", "signs and symptoms", "enterobacteriaceae", "pharmacolo...	A systematic review of antimicrobial resistance in Salmonella enterica serovar Typhi, the etiological agent of typhoid	journal.pntd.0006779	null	[ [ "Enteric fever is a systemic infection , caused by the Gram-negative bacteria Salmonella enterica subspecies enterica serovars Typhi and Paratyphi A , that continues to be a significant cause of morbidity and mortality in endemic regions .", "Annually , it is estimated that over 26 million people are cult...	[ "The temporal and spatial change in trends of antimicrobial resistance ( AMR ) in typhoid have not been systematically studied , and such information will be critical for defining intervention , as well as planning sustainable prevention strategies .", "To identify the phenotypic trends in AMR , 13 , 833 individu...	[ "Typhoid is an invasive bacterial disease causing 26 million illness episodes globally , each year particularly in South Asia and sub-Saharan Africa afflicting children and poorer sections of society disproportionally .", "AMR is increasingly recognized among S . Typhi lineages spreading from South Asia to Africa...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "cellular structures", "subcellular organelles", "viral classification", "drugs and devices", "microbiology", "host-pathogen interaction", "viral structure", "hepatitis", "rna viruses", "pharmacology", "hepatitis c", "infectious diseases", "viral core", "virulence factors and...	Human Subtilase SKI-1/S1P Is a Master Regulator of the HCV Lifecycle and a Potential Host Cell Target for Developing Indirect-Acting Antiviral Agents	journal.ppat.1002468	null	[ [ "Hijacking of host lipids and their biosynthetic pathways is a common strategy for microbial infection .", "Human enveloped viruses including hepatitis C virus ( HCV ) and human immunodeficiency virus ( HIV ) -1 use cholesterol-rich lipid rafts for entry [1] , [2] , assembly [3] , and/or replication [2] ,...	[ "HCV infection is a major risk factor for liver cancer and liver transplantation worldwide .", "Overstimulation of host lipid metabolism in the liver by HCV-encoded proteins during viral infection creates a favorable environment for virus propagation and pathogenesis .", "In this study , we hypothesize that tar...	[ "Chronic hepatitis C virus ( HCV ) infection is one of the leading causes of liver cancer and liver transplantation worldwide .", "No vaccine is available for preventing the spread of HCV , and the current therapeutic regimen is only moderately effective and causes serious side effects .", "New antiviral agents...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "genomics", "functional genomics", "molecular cell biology", "gene expression", "genetics", "epigenetics", "biology", "microbial growth and development", "microbiology", "gene networks", "molecular biology", "genetics and genomics" ]	A Histone Deacetylase Adjusts Transcription Kinetics at Coding Sequences during Candida albicans Morphogenesis	journal.pgen.1003118	null	[ [ "Cells with identical genomes can adopt various phenotypes , which is a central feature during differentiation of multicellular organisms .", "During differentiation , the outside stimuli and the cellular machineries that process them are thought to determine the resulting cell types .", "Often , both...	[ "Despite their classical role as transcriptional repressors , several histone deacetylases , including the baker's yeast Set3/Hos2 complex ( Set3C ) , facilitate gene expression .", "In the dimorphic human pathogen Candida albicans , the homologue of the Set3C inhibits the yeast-to-filament transition , but the p...	[ "Many human pathogenic fungi are able to change their morphological properties , including their size and shape , in response to their outside environment .", "This ability , which is key for infection , is not completely understood on the molecular level .", "We have previously shown that not just DNA–binding ...	2012
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "animal models", "histology", "pathogenesis", "neurobiology of disease and regeneration", "model organisms", "immune cells", "virology", "immunology", "host-pathogen interaction", "biology", "anatomy and physiology", "immunologic techniques", "microbiology", "neuroscience", "immune syste...	T-Cell Tropism of Simian Varicella Virus during Primary Infection	journal.ppat.1003368	null	[ [ "Varicella-zoster virus ( VZV ) is a ubiquitous human neurotropic alphaherpesvirus that causes varicella ( chickenpox ) as a primary infection and herpes zoster ( shingles ) upon reactivation of latent virus [1] .", "Primary VZV infection is acquired via the respiratory route and varicella occurs 2–3 week...	[ "Varicella-zoster virus ( VZV ) causes varicella , establishes a life-long latent infection of ganglia and reactivates to cause herpes zoster .", "The cell types that transport VZV from the respiratory tract to skin and ganglia during primary infection are unknown .", "Clinical , pathological , virological and ...	[ "Varicella-zoster virus ( VZV ) causes varicella , establishes life-long latent infection in ganglia and reactivates later in life to cause zoster .", "VZV is acquired via the respiratory route , with skin rash occurring up to 3 weeks after exposure .", "The cell types that transport VZV to skin and ganglia dur...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "learning", "decision making", "applied mathematics", "social sciences", "neuroscience", "learning and memory", "simulation and modeling", "algorithms", "cognitive psychology", "systems science", "mathematics", "cognition", "research and analysis methods", "computer and information science...	Improving the reliability of model-based decision-making estimates in the two-stage decision task with reaction-times and drift-diffusion modeling	journal.pcbi.1006803	null	[ [ "While the w-parameter serves as a process-based measurement of model-based/free trade-off ( and thus has a clear interpretation ) , the literature makes use of model-agnostic measures that map directly to changes in the w-parameter .", "Model-agnostic measures can be beneficial as they are straightforwar...	[ "A well-established notion in cognitive neuroscience proposes that multiple brain systems contribute to choice behaviour .", "These include: ( 1 ) a model-free system that uses values cached from the outcome history of alternative actions , and ( 2 ) a model-based system that considers action outcomes and the tra...	[ "In this paper , we report a reliability analysis for the estimation of “model basedness”—a psychological construct that informs a wealth of studies in animal , human and clinical research .", "We consider an exemplar paradigm , the two-step task , widely used in the recent literature .", "We report low reliabi...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Type VI Secretion System Transports Zn2+ to Combat Multiple Stresses and Host Immunity	journal.ppat.1005020	null	[ [ "Specialized protein secretion systems are essential for many bacteria to survive in interactions with their hosts or within specific environmental niches .", "Among these , type VI secretion system ( T6SS ) is a complex macromolecular apparatus found in more than 25% of sequenced Gram-negative bacteria g...	[ "Type VI secretion systems ( T6SSs ) are widespread multi-component machineries that translocate effectors into either eukaryotic or prokaryotic cells , for virulence or for interbacterial competition .", "Herein , we report that the T6SS-4 from Yersinia pseudotuberculosis displays an unexpected function in the t...	[ "One unique feature of type VI secretion system is the presence of multiple distinct systems in certain bacterial species .", "It is well established that some of these systems function to compete for their living niches among diverse bacterial species , whilst the activity of many such transporters remains unkno...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "microbiology/environmental microbiology", "biophysics", "biochemistry/protein chemistry", "chemistry/biochemistry" ]	Structural Basis for the Aminoacid Composition of Proteins from Halophilic Archea	journal.pbio.1000257	In order to survive in highly saline environments, proteins from halophilic archea have evolved with biased amino acid compositions that have the capacity to reduce contacts with the solvent.	[ [ "Halophilic archea are extremophiles that thrive in highly saline environments such as natural salt lakes [1] .", "To maintain positive turgor pressure , salt concentration in the cytoplasm can reach 4 M [2] .", "Proteins from these organisms have evolved to maximize stability and activity at high sal...	[ "Proteins from halophilic organisms , which live in extreme saline conditions , have evolved to remain folded at very high ionic strengths .", "The surfaces of halophilic proteins show a biased amino acid composition with a high prevalence of aspartic and glutamic acids , a low frequency of lysine , and a high oc...	[ "Life on earth exhibits an enormous adaptive capacity and living organisms can be found even in extreme environments .", "The halophilic archea are a group of microorganisms that grow best in highly salted lakes ( with KCl concentrations between 2 and 6 molar ) .", "To avoid osmotic shock , halophilic archea ha...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "computational biology/macromolecular structure analysis", "biochemistry/biocatalysis", "cell biology/cellular death and stress responses", "computational biology/transcriptional regulation", "computational biology/comparative sequence analysis", "biochemistry/theory and simulation", "computational biol...	How Cations Can Assist DNase I in DNA Binding and Hydrolysis	journal.pcbi.1001000	null	[ [ "DNase I is a ubiquitous endonuclease that cleaves the phosphodiester backbone of the DNA double helix in the presence of divalent cations , introducing single-stranded nicks through hydrolysis of the P-O3′-bond and yielding 5′-phosphorylated fragments [1] , [2] .", "This enzyme plays a major role in dige...	[ "DNase I requires Ca2+ and Mg2+ for hydrolyzing double-stranded DNA .", "However , the number and the location of DNase I ion-binding sites remain unclear , as well as the role of these counter-ions .", "Using molecular dynamics simulations , we show that bovine pancreatic ( bp ) DNase I contains four ion-bindi...	[ "DNase I requires Ca2+ and Mg2+ for hydrolyzing double-stranded DNA .", "Here , we show that bovine pancreatic ( bp ) DNase I contains four ion-binding pockets .", "Two of them , previously observed in the crystallographic structure of free bpDNase I , strongly bind Ca2+ .", "The other two sites bind Mg2+ and...	2010
[ "Introduction", "Models", "Results", "Discussion" ]	[ "gene regulation", "signaling networks", "dna transcription", "mathematics", "molecular genetics", "stochastic processes", "biophysics simulations", "theoretical biology", "gene expression", "biophysics theory", "regulatory networks", "biology", "nonlinear dynamics", "biophysics", "proba...	Speed, Sensitivity, and Bistability in Auto-activating Signaling Circuits	journal.pcbi.1002265	null	[ [ "Biological organisms employ a variety of signaling networks to respond to changes in environmental conditions .", "An interesting class of examples is given by the two-component signaling ( TCS ) systems , which are ubiquitous in bacteria and plants [1] .", "TCS systems typically consist of two prote...	[ "Cells employ a myriad of signaling circuits to detect environmental signals and drive specific gene expression responses .", "A common motif in these circuits is inducible auto-activation: a transcription factor that activates its own transcription upon activation by a ligand or by post-transcriptional modificat...	[ "Different times call for different measures .", "Therefore , cells adjust their protein levels depending on their environment .", "Upon the detection of certain environmental signals , transcription factors are activated , which activate or inhibit the production of specific sets of proteins .", "As it turns...	2011
[ "Introduction", "Models", "Results", "Discussion" ]	[ "learning", "medicine and health sciences", "decision making", "brain", "social sciences", "neuroscience", "learning and memory", "simulation and modeling", "cognitive psychology", "systems science", "mathematics", "probability distribution", "cognition", "thermodynamics", "research and ...	Locus Coeruleus tracking of prediction errors optimises cognitive flexibility: An Active Inference model	journal.pcbi.1006267	null	[ [ "The locus coeruleus ( LC ) is the major source of noradrenaline ( NA ) in the brain , projecting to most territories from the frontal cortex to the distal spinal cord .", "Changes in LC firing have been associated with behavioural changes , most notably the switch from ‘exploiting’ to ‘exploring’ the env...	[ "The locus coeruleus ( LC ) in the pons is the major source of noradrenaline ( NA ) in the brain .", "Two modes of LC firing have been associated with distinct cognitive states: changes in tonic rates of firing are correlated with global levels of arousal and behavioural flexibility , whilst phasic LC responses a...	[ "The brain uses sensory information to build internal models and make predictions about the world .", "When errors of prediction occur , models must be updated to ensure desired outcomes are still achieved .", "Neuromodulator chemicals provide a possible pathway for triggering such changes in brain state .", ...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology and life sciences" ]	FHIT Suppresses Epithelial-Mesenchymal Transition (EMT) and Metastasis in Lung Cancer through Modulation of MicroRNAs	journal.pgen.1004652	null	[ [ "Metastasis , the spread of cells from the site of a primary tumor followed by growth of a secondary tumor in distant organs , is frequently a final and fatal step in tumor progression .", "This process consists of a series of steps , including angiogenesis , intravasation , survival in circulation , extr...	[ "Metastasis is the principal cause of cancer death and occurs through multiple , complex processes that involve the concerted action of many genes .", "A number of studies have indicated that the Fragile Histidine Triad ( FHIT ) gene product , FHIT , functions as a tumor suppressor in a variety of common human ca...	[ "Although Fragile Histidine Triad ( FHIT ) is known as a potential tumor suppressor gene in terms of tumor initiation and progression , the role of FHIT in the metastatic process is not well characterized .", "Here it is shown that FHIT reduces the motility and invasiveness of lung cancer cells in vitro and abili...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genome-wide association studies", "animal genetics", "functional genomics", "gene function", "genome analysis tools", "molecular genetics", "structural genomics", "gene expression", "gene splicing", "comparative genomics", "biology", "genetic screens", "genetics", "genomics", "genetics ...	Genome-Wide Association Study Implicates Testis-Sperm Specific FKBP6 as a Susceptibility Locus for Impaired Acrosome Reaction in Stallions	journal.pgen.1003139	null	[ [ "Acrosome is a large , membrane bound secretory vesicle in the head of mammalian sperm which releases its contents when sperm contacts the egg for fertilization .", "The process is known as regulated acrosomal exocytosis or acrosomal reaction ( AR ) and is triggered by egg's zona pellucida proteins which ...	[ "Impaired acrosomal reaction ( IAR ) of sperm causes male subfertility in humans and animals .", "Despite compelling evidence about the genetic control over acrosome biogenesis and function , the genomics of IAR is as yet poorly understood , providing no molecular tools for diagnostics .", "Here we conducted Eq...	[ "Impaired acrosomal reaction ( IAR ) of sperm causes male subfertility in humans and animals , and currently the molecular causes of the condition are not known .", "Here we report the mapping , identification , and functional analysis of a susceptibility locus for IAR in stallions .", "The candidate region was...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "inflammatory diseases", "medicine and health sciences", "respiratory infections", "pathology and laboratory medicine", "mitochondrial dna", "cardiovascular anatomy", "immunology", "parasitic protozoans", "pulmonology", "protozoans", "heart", "signs and symptoms", "forms of dna", "mitochon...	SIRT1-PGC1α-NFκB Pathway of Oxidative and Inflammatory Stress during Trypanosoma cruzi Infection: Benefits of SIRT1-Targeted Therapy in Improving Heart Function in Chagas Disease	journal.ppat.1005954	null	[ [ "Trypanosoma cruzi ( T . cruzi or Tc ) is the etiological agent of Chagas disease that is endemic in Latin America [1] .", "After an exposure to parasite , infected individuals develop mild-to-no overt clinical symptoms .", "However , several decades later , ~30% of the infected individuals progress t...	[ "Chronic chagasic cardiomyopathy ( CCM ) is presented by increased oxidative/inflammatory stress and decreased mitochondrial bioenergetics .", "SIRT1 senses the redox changes and integrates mitochondrial metabolism and inflammation; and SIRT1 deficiency may be a major determinant in CCM .", "To test this , C57B...	[ "In this study , we determined whether enhancing the activity of sirtuin 1 ( SIRT1 ) would be beneficial in maintaining heart health in Chagas disease .", "SIRT1 senses the redox shifts and integrates mitochondrial metabolism and inflammation .", "We found that treatment with SIRT1 agonists , given in a therape...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology" ]	Interplay between Structure-Specific Endonucleases for Crossover Control during Caenorhabditis elegans Meiosis	journal.pgen.1003586	null	[ [ "Structure-specific endonucleases are required for several kinds of DNA repair processes such as nucleotide excision repair ( NER ) , DNA interstrand crosslink repair ( ICL ) and double-strand break repair ( DSBR ) .", "Homologous recombination is an error free repair pathway because the broken DNA ends a...	[ "The number and distribution of crossover events are tightly regulated at prophase of meiosis I .", "The resolution of Holliday junctions by structure-specific endonucleases , including MUS-81 , SLX-1 , XPF-1 and GEN-1 , is one of the main mechanisms proposed for crossover formation .", "However , how these nuc...	[ "Abnormalities in the number and/or structure of the chromosomes can result in cancer , birth defects , miscarriages and infertility .", "In particular , the exchange of genetic material ( crossover formation ) between maternal and paternal chromosomes during the cell division program of meiosis is essential to p...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Epidemiological Interactions between Urogenital and Intestinal Human Schistosomiasis in the Context of Praziquantel Treatment across Three West African Countries	journal.pntd.0004019	null	[ [ "Globally , at least 230 million people are estimated to have schistosomiasis [1] .", "In sub-Saharan Africa where the disease burden is highest , Schistosoma haematobium and S . mansoni , causing urogenital and intestinal schistosomiasis respectively , frequently overlap in their geographic distribution ...	[ "In many parts of sub-Saharan Africa , urogenital and intestinal schistosomiasis co-occur , and mixed species infections containing both Schistosoma haematobium and S . mansoni can be common .", "During co-infection , interactions between these two species are possible , yet the extent to which such interactions ...	[ "In many parts of Africa both urinary and intestinal schistosomiasis are endemic , and mixed species infections can be common .", "However , little is known about potential within-host interactions between the causative parasites , S . haematobium and S . mansoni , and how these might influence treatment success ...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/gene discovery", "genetics and genomics/comparative genomics", "genetics and genomics/gene expression", "evolutionary biology", "evolutionary biology/developmental molecular mechanisms" ]	Evolution of a Core Gene Network for Skeletogenesis in Chordates	journal.pgen.1000025	null	[ [ "The skeleton is a hallmark of vertebrates and has been widely used over the past decades for phylogenetic analyses [1] .", "However , little is known about its molecular evolution .", "Descriptive data are available for the matrix proteins produced by the cells that constitute the skeleton in jawless...	[ "The skeleton is one of the most important features for the reconstruction of vertebrate phylogeny but few data are available to understand its molecular origin .", "In mammals the Runt genes are central regulators of skeletogenesis .", "Runx2 was shown to be essential for osteoblast differentiation , tooth dev...	[ "Important molecular mechanisms underlying mammalian skeletogenesis have been described but knowledge about the evolutionary origin of these gene networks is limited .", "The Runt gene family ( Runx1–3 ) is of extraordinary importance for skeletogenesis .", "Runx2 deficient mice completely lack bone .", "Runx...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "phosphorylation", "innate immune system", "medicine and health sciences", "immune physiology", "cytokines", "pathology and laboratory medicine", "immune cells", "pathogens", "immunology", "microbiology", "viruses", "physiological processes", "developmental biology", "rna ...	Zika Virus Antagonizes Type I Interferon Responses during Infection of Human Dendritic Cells	journal.ppat.1006164	null	[ [ "Zika virus ( ZIKV ) is an emerging mosquito-borne flavivirus that is causally linked to severe neonatal birth defects upon congenital infection , including microcephaly and spontaneous abortion [1–5] , and is associated with Guillain-Barre syndrome [6] and severe thrombocytopenia [7] in adults .", "ZIKV ...	[ "Zika virus ( ZIKV ) is an emerging mosquito-borne flavivirus that is causally linked to severe neonatal birth defects , including microcephaly , and is associated with Guillain-Barre syndrome in adults .", "Dendritic cells ( DCs ) are an important cell type during infection by multiple mosquito-borne flaviviruse...	[ "Zika virus ( ZIKV ) is an emerging mosquito-borne flavivirus that , upon congenital infection , can cause severe neonatal birth defects .", "To better understand the early innate immune response to ZIKV , we compared infection of human dendritic cells ( DCs ) between a contemporary Puerto Rican isolate and histo...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "molecular neuroscience", "clinical research design", "cgmp signaling", "animal models of disease", "anatomy and physiology", "signaling in selected disciplines", "neuroscience", "animal models", "developmental biology", "caenorhabditis elegans", "model organisms", "developmental...	Mutations in a Guanylate Cyclase GCY-35/GCY-36 Modify Bardet-Biedl Syndrome–Associated Phenotypes in Caenorhabditis elegans	journal.pgen.1002335	null	[ [ "The cilium plays diverse cellular functions in metazoans which include imparting motility , enabling sensory processes and regulating the activity of cell signalling pathways during development [1] .", "The biogenesis and maintenance of this evolutionarily conserved organelle relies on intraflagellar tra...	[ "Ciliopathies are pleiotropic and genetically heterogeneous disorders caused by defective development and function of the primary cilium .", "Bardet-Biedl syndrome ( BBS ) proteins localize to the base of cilia and undergo intraflagellar transport , and the loss of their functions leads to a multisystemic ciliopa...	[ "Bardet-Biedl syndrome ( BBS ) is a genetically heterogeneous , multisystemic disorder .", "Defects to the cilium , an evolutionarily conserved organelle , cause ciliopathies , a growing class of diseases that includes BBS .", "BBS proteins are involved in the vesicular transport of proteins to the cilium and i...	2011
[ "Introduction", "Results", "Discussion", "Software Availability", "Materials and Methods" ]	[ "taxonomy", "organismal evolution", "medicine and health sciences", "pathology and laboratory medicine", "pathogens", "spatial epidemiology", "microbiology", "simulation and modeling", "phylogenetics", "data management", "phylogenetic analysis", "microbial evolution", "molecular biology tech...	SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent	journal.pcbi.1005130	null	[ [ "Understanding the dynamics of transmission is fundamental for devising effective policies and practical measures that limit the spread of infectious diseases .", "In recent years , the introduction of affordable whole genome sequencing has provided unprecedented detail on the relatedness of pathogen samp...	[ "Exploiting pathogen genomes to reconstruct transmission represents a powerful tool in the fight against infectious disease .", "However , their interpretation rests on a number of simplifying assumptions that regularly ignore important complexities of real data , in particular within-host evolution and non-sampl...	[ "We present a new tool , SCOTTI , to efficiently reconstruct transmission events within outbreaks .", "Our approach combines genetic information from infection samples with epidemiological information of patient exposure to infection .", "While epidemiological information has been traditionally used to understa...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "clinical immunology", "immunology" ]	A TNF-Regulated Recombinatorial Macrophage Immune Receptor Implicated in Granuloma Formation in Tuberculosis	journal.ppat.1002375	null	[ [ "Macrophages are key players in major chronic inflammatory diseases including tuberculosis , atherosclerosis and rheumatoid arthritis .", "Based on their myeloid origin and professional phagocytic activity they are traditionally regarded as a pillar of innate immunity [1] .", "Tuberculosis is an infec...	[ "Macrophages play a central role in host defense against mycobacterial infection and anti- TNF therapy is associated with granuloma disorganization and reactivation of tuberculosis in humans .", "Here , we provide evidence for the presence of a T cell receptor ( TCR ) αβ based recombinatorial immune receptor in s...	[ "Infection with mycobacteria results in a host response which results in the formation of granulomas , highly organized structures characterized by the presence of macrophages , which are considered to rely solely on invariant immune receptors .", "On the other hand , the presence of variable immune receptors is ...	2011

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