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"
] | [
"invertebrates",
"heterozygosity",
"medicine and health sciences",
"pathology and laboratory medicine",
"geographical locations",
"parasitic diseases",
"animals",
"invertebrate genomics",
"parasitology",
"developmental biology",
"phylogenetic analysis",
"myanmar",
"molecular biology techniqu... | Genome-Wide Analyses of Individual Strongyloides stercoralis (Nematoda: Rhabditoidea) Provide Insights into Population Structure and Reproductive Life Cycles | journal.pntd.0005253 | null | [
[
"The helminth Strongyloides stercoralis , which is one of the most common and globally distributed human pathogens of clinical importance , infects 30–100 million people worldwide [1 , 2] .",
"This parasite most often resides in areas with tropical or subtropical climates and less frequently in areas with... | [
"The helminth Strongyloides stercoralis , which is transmitted through soil , infects 30–100 million people worldwide .",
"S . stercoralis reproduces sexually outside the host as well as asexually within the host , which causes a life-long infection .",
"To understand the population structure and transmission p... | [
"Strongyloides stercoralis , one of the most neglected helminths causes strongyloidiasis mainly in tropical and subtropical regions worldwide .",
"The parasite’s complex lifecycle includes sexual and asexual reproduction outside and inside the host , respectively .",
"The parasite can also asexually complete a ... | 2016 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"biology and life sciences",
"medicine and health sciences"
] | Pyrethroid-Resistance and Presence of Two Knockdown Resistance (kdr) Mutations, F1534C and a Novel Mutation T1520I, in Indian Aedes aegypti | journal.pntd.0003332 | null | [
[
"Aedes aegypti is globally distributed throughout the tropics and subtropics and highly adapted to humans and urban environments .",
"It acts as a primary vector for various arboviral infections including yellow fever virus , dengue virus ( DENV ) and chikungunya virus ( CHIKV ) [1]–[5] .",
"Dengue ha... | [
"Control of Aedes aegypti , the mosquito vector of dengue , chikungunya and yellow fever , is a challenging task .",
"Pyrethroid insecticides have emerged as a preferred choice for vector control but are threatened by the emergence of resistance .",
"The present study reports a focus of pyrethroid resistance an... | [
"Dengue and chikungunya are the two important human arboviral infections in India transmitted mainly by Aedes aegypti .",
"In absence of any specific drug or vaccine for these infections , vector control and personal protection are the only control options available .",
"The success of insecticide-based vector ... | 2015 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"public and occupational health",
"infectious diseases",
"medicine and health sciences",
"disease ecology",
"chagas disease",
"infectious disease epidemiology",
"epidemiology",
"neglected tropical diseases",
"tropical diseases",
"protozoan infections",
"parasitic diseases"
] | Chagas Disease Vector Control in a Hyperendemic Setting: The First 11 Years of Intervention in Cochabamba, Bolivia | journal.pntd.0002782 | null | [
[
"Chagas disease , caused by infection with the parasite Trypanosoma cruzi , is among the most serious public health problems in Bolivia [1]–[9] .",
"In particular , the disease has historically been hyperendemic in some areas of the country in which Triatoma infestans , the main vector of human Chagas dis... | [
"Chagas disease has historically been hyperendemic in the Bolivian Department of Cochabamba .",
"In the early 2000s , an extensive vector control program was implemented; 1 . 34 million dwelling inspections were conducted to ascertain infestation ( 2000–2001/2003–2011 ) , with blanket insecticide spraying in 2003... | [
"Chagas disease is among the most serious public health problems in Latin America; the highest prevalence of infection by its causative agent , the parasite Trypanosoma cruzi , has historically been recorded in some parts of Bolivia .",
"In the early 2000s , a massive insecticide-spraying program was set up to co... | 2014 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"nervous system",
"enzymes",
"messenger rna",
"cell processes",
"enzymology",
"electrophysiology",
"neuroscience",
"learning and memory",
"protein synthesis",
"cognition",
"memory",
"enzyme inhibitors",
"chemical synthesis",
"research and analysis methods"... | Coupled feedback loops maintain synaptic long-term potentiation: A computational model of PKMzeta synthesis and AMPA receptor trafficking | journal.pcbi.1006147 | null | [
[
"In his address to the Royal Society in 1894 , Santiago Ramon y Cajal hypothesized that the brain stores information by adjusting the strengths of associations between neurons , as well as by growing new connections [1] .",
"In the years since , the existence of both of these mechanisms , now known as syn... | [
"In long-term potentiation ( LTP ) , one of the most studied types of neural plasticity , synaptic strength is persistently increased in response to stimulation .",
"Although a number of different proteins have been implicated in the sub-cellular molecular processes underlying induction and maintenance of LTP , t... | [
"The brain stores memories by adjusting the strengths of connections between neurons , a phenomenon known as synaptic plasticity .",
"Different types of plasticity mechanisms have either a strengthening or a weakening effect and produce synaptic modifications that last from milliseconds to months or more .",
"O... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"viruses",
"virology"
] | HIV-1 gp120 Mannoses Induce Immunosuppressive Responses from Dendritic Cells | journal.ppat.0030169 | null | [
[
"One approach to a vaccine against HIV-1 is the use of the viral envelope glycoproteins ( Env ) as immunogens to induce neutralizing antibodies ( NAbs ) [1–3] .",
"Usually , the Env glycoproteins are presented as adjuvanted , soluble proteins after production in vitro as recombinant proteins , but they ca... | [
"The human immunodeficiency virus type 1 ( HIV-1 ) envelope glycoprotein gp120 is a vaccine immunogen that can signal via several cell surface receptors .",
"To investigate whether receptor biology could influence immune responses to gp120 , we studied its interaction with human , monocyte-derived dendritic cells... | [
"Dendritic cells ( DCs ) initiate immune responses to pathogens or vaccine antigens .",
"The HIV-1 gp120 envelope glycoprotein is an antigen that is a focus of vaccine design strategies .",
"We have studied how gp120 proteins interact with DCs in cell culture .",
"Certain gp120s stimulate DCs from some , but ... | 2007 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"infectious diseases/urological infections",
"urology/urological infections",
"cell biology/cell signaling",
"cell biology/membranes and sorting",
"infectious diseases/bacterial infections",
"microbiology/cellular microbiology and pathogenesis"
] | Bacteria-Induced Uroplakin Signaling Mediates Bladder Response to Infection | journal.ppat.1000415 | null | [
[
"Urinary tract infections ( UTIs ) are the second most common infectious disease in humans , following respiratory tract infections .",
"Approximately 90% of community-acquired UTIs are caused by uropathogenic E . coli ( UPEC ) [1] .",
"The type 1 pilus is the most common UPEC virulence factor; presen... | [
"Urinary tract infections are the second most common infectious disease in humans and are predominantly caused by uropathogenic E . coli ( UPEC ) .",
"A majority of UPEC isolates express the type 1 pilus adhesin , FimH , and cell culture and murine studies demonstrate that FimH is involved in invasion and apoptos... | [
"Urinary tract infections ( UTI ) are the second most common infectious disease in humans and are predominantly caused by uropathogenic E . coli ( UPEC ) .",
"In vitro and in vivo studies have demonstrated that UPEC induce several responses in the bladder , including inflammation , rapid onset of bladder cell dea... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"invertebrates",
"chemical characterization",
"gene regulation",
"regulatory proteins",
"dna-binding proteins",
"animals",
"animal models",
"developmental biology",
"mutation",
"drosophila melanogaster",
"model organisms",
"experimental organism systems",
"transcription factors",
"sequence... | A new mode of DNA binding distinguishes Capicua from other HMG-box factors and explains its mutation patterns in cancer | journal.pgen.1006622 | null | [
[
"HMG-box factors are abundant nuclear proteins with highly diverse functions in the cell .",
"They contain one or more HMG-box domains that bind the minor groove of DNA , bending the duplex away from the interaction site .",
"Proteins with tandem HMG-box domains usually function as architectural and c... | [
"HMG-box proteins , including Sox/SRY ( Sox ) and TCF/LEF1 ( TCF ) family members , bind DNA via their HMG-box .",
"This binding , however , is relatively weak and both Sox and TCF factors employ distinct mechanisms for enhancing their affinity and specificity for DNA .",
"Here we report that Capicua ( CIC ) , ... | [
"Transcription factors bind specific sites in the genome via discrete protein domains that recognize their target DNA sequences .",
"One such domain is the HMG-box , which is found in many chromatin and transcriptional regulators across species .",
"Two salient groups of HMG-box proteins are the Sox/SRY and TCF... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"systems biology",
"computer science",
"biology",
"computational biology",
"computerized simulations",
"genetics and genomics"
] | Analyzing the Functional Properties of the Creatine Kinase System with Multiscale ‘Sloppy’ Modeling | journal.pcbi.1002130 | null | [
[
"It is well established that creatine kinase ( CK ) catalyzes the reversible transfer of phosphate from ATP to creatine ( Cr ) : ( 1 ) However , how this biochemical function plays a role in cell functioning has been the subject of intense controversy [1] .",
"It is remarkable that two distinct isoforms o... | [
"In this study the function of the two isoforms of creatine kinase ( CK; EC 2 . 7 . 3 . 2 ) in myocardium is investigated .",
"The ‘phosphocreatine shuttle’ hypothesis states that mitochondrial and cytosolic CK plays a pivotal role in the transport of high-energy phosphate ( HEP ) groups from mitochondria to myof... | [
"Creatine kinase ( CK ) has several functions in cellular energy metabolism .",
"It catalyzes the reversible transfer of high-energy phosphate from ATP to creatine , facilitating storage of energy in the form of phosphocreatine .",
"In muscle cells , this extra energy buffer plays a pivotal role in maintaining ... | 2011 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine",
"histology",
"infectious diseases",
"drugs and devices",
"biology"
] | Fexinidazole: A Potential New Drug Candidate for Chagas Disease | journal.pntd.0001870 | null | [
[
"One century after its discovery , American trypanosomiasis , or Chagas disease , remains a serious health problem in Latin America , where it affects 8–10 million people with 100 million at risk of acquiring the disease [1] .",
"Chemotherapy , together with vector and transfusion control , is one of the ... | [
"New safe and effective treatments for Chagas disease ( CD ) are urgently needed .",
"Current chemotherapy options for CD have significant limitations , including failure to uniformly achieve parasitological cure or prevent the chronic phase of CD , and safety and tolerability concerns .",
"Fexinidazole , a 2-s... | [
"This study describes the in vivo activity of fexinidazole against Trypanosoma cruzi , the protozoan parasite causing Chagas disease , using mice infected with parasite strains with varying susceptibility to benznidazole , the standard treatment for Chagas .",
"Fexinidazole and benznidazole were shown to have sim... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods",
"Supporting Information"
] | [
"infectious diseases",
"arthropods",
"microbiology",
"mus (mouse)",
"eubacteria"
] | Outer Surface Protein B Is Critical for Borrelia burgdorferi Adherence and Survival within Ixodes Ticks | journal.ppat.0030033 | null | [
[
"Lyme disease is the most common tick-borne disease in the United States [1] .",
"The causative organism , Borrelia burgdorferi , is a microaerophilic spirochete that contains a 910-kb linear chromosome and at least 21 linear and circular plasmids [2] .",
"B . burgdorferi is composed of several genosp... | [
"Survival of Borrelia burgdorferi in ticks and mammals is facilitated , at least in part , by the selective expression of lipoproteins .",
"Outer surface protein ( Osp ) A participates in spirochete adherence to the tick gut .",
"As ospB is expressed on a bicistronic operon with ospA , we have now investigated ... | [
"Lyme disease is the most common vector-borne disease in North America and Europe .",
"The causative agent Borrelia burgdorferi is a bacterium that is maintained in an enzoonotic cycle between Ixodes ticks and a large range of mammals .",
"Accidental encounters of infected Ixodes ticks with humans results in th... | 2007 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"microbiology/innate immunity",
"microbiology/immunity to infections"
] | Tsetse Immune System Maturation Requires the Presence of Obligate
Symbionts in Larvae | journal.pbio.1000619 | Tsetse harbors an obligate symbiont, Wigglesworthia glossinidia,
that must be present during larval maturation for the fly's immune system to
develop and function properly during adulthood. | [
[
"Bacteria comprise the most abundant and diverse life form on earth .",
"The ubiquity of",
"bacteria means they have colonized virtually every ecological niche , including",
"habitation within more evolutionarily sophisticated multi-cellular animals .",
"Co-evolution",
"over millions of ye... | [
"Beneficial microbial symbionts serve important functions within their hosts ,",
"including dietary supplementation and maintenance of immune system homeostasis .",
"Little is known about the mechanisms that enable these bacteria to induce specific",
"host phenotypes during development and into adulthood .",
... | [
"Beneficial bacterial symbionts , which are ubiquitous in nature , are often",
"characterized by the extent to which they interact with the host .",
"In the case of",
"mutualistic symbioses , both partners benefit so that each one can inhabit diverse",
"ecological niches where neither could survive on its o... | 2011 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"antimicrobials",
"medicine and health sciences",
"pathology and laboratory medicine",
"clinical research design",
"drugs",
"tropical diseases",
"microbiology",
"antifungals",
"parasitic diseases",
"parasitic protozoans",
"physiological processes",
"research design",
"protozoans",
"signs a... | Liposomal amphotericin B in travelers with cutaneous and muco-cutaneous leishmaniasis: Not a panacea | journal.pntd.0006094 | null | [
[
"Tegumentary leishmaniasis ( TL ) occurs when one of the 20 Leishmania species that can infect humans causes lesions of the skin or mucosae .",
"Because TL is observed in patients of all ages , either immunocompetent or immunocompromised , the result is a wide continuum of clinical forms and medical situa... | [
"Complex cutaneous and muco-cutaneous leishmaniasis ( CL and MCL ) often requires systemic therapy .",
"Liposomal amphotericin B ( L-AmB ) has a strong potential for a solid clinical benefit in this indication .",
"We conducted a retrospective analysis of data from a French centralized referral treatment progra... | [
"Cutaneous and muco-cutaneous leishmaniasis ( CL/MCL ) are disfiguring diseases caused by a worldwide distributed parasite called Leishmania and its 20 species .",
"Clinical manifestations span a wide continuum from single nodular lesion to disseminated form with mucosal involvement .",
"Though local treatment ... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"medicine and health sciences",
"diagnostic radiology",
"functional magnetic resonance imaging",
"neural networks",
"reaction time",
"social sciences",
"neuroscience",
"magnetic resonance imaging",
"perception",
"cognitive neuroscience",
"cognitive psychology",
"cognition",
"brain mapping",
... | Subgraphs of functional brain networks identify dynamical constraints of cognitive control | journal.pcbi.1006234 | null | [
[
"In human cognition , internally-generated cognitive control processes modulate attention , facilitate task switching , and inhibit prepotent behavior [1] .",
"One avenue by which the brain may rapidly traverse a cognitive state-space is through its functional interactions—coherent fluctuations in brain a... | [
"Brain anatomy and physiology support the human ability to navigate a complex space of perceptions and actions .",
"To maneuver across an ever-changing landscape of mental states , the brain invokes cognitive control—a set of dynamic processes that engage and disengage different groups of brain regions to modulat... | [
"Brain networks support the human ability to navigate a complex space of perceptions and actions through cognitive control .",
"Here we ask , “How do brain networks coordinate task-relevant information as individuals adapt to cognitive demands imposed by a task ? ”",
"We study the fMRI BOLD signal of twenty-eig... | 2018 |
[
"Introduction",
"Results/Discussion",
"Materials and Methods"
] | [
"genetics and genomics/genomics",
"oncology",
"oncology/breast cancer",
"genetics and genomics/gene expression",
"genetics and genomics/chromosome biology",
"biochemistry/bioinformatics",
"biochemistry/macromolecular assemblies and machines",
"computational biology/genomics",
"biochemistry/transcrip... | Proteomic Changes Resulting from Gene Copy Number Variations in Cancer Cells | journal.pgen.1001090 | null | [
[
"Chromosomal aberrations are a hallmark of cancer cells .",
"During transformation cells lose cell-cycle control and fidelity of DNA replication causing multiple changes in DNA copy numbers [1] , [2] .",
"Although chromosomal aberrations are associated with transformation , changes in DNA copy number ... | [
"Along the transformation process , cells accumulate DNA aberrations , including mutations , translocations , amplifications , and deletions .",
"Despite numerous studies , the overall effects of amplifications and deletions on the end point of gene expression—the level of proteins—is generally unknown .",
"Her... | [
"In the course of cancer development , cells lose regulation of the cell cycle and quality control of DNA replication .",
"As a result , many genomic alterations accumulate , among them amplifications and deletions of chromosomal regions of varying sizes .",
"Oncogenes that drive transformation often reside in ... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"gene networks",
"rna interference",
"histone modification",
"gene function",
"stem cells",
"epigenetics",
"cell potency",
"embryonic stem cells",
"gene expression",
"biology",
"dna modification",
"rna",
"signal transduction",
"rna processing",
"nucleic acids",
"neurons",
"genetics",... | Wnt Signaling Regulates the Lineage Differentiation Potential of Mouse Embryonic Stem Cells through Tcf3 Down-Regulation | journal.pgen.1003424 | null | [
[
"Embryonic stem cells ( ESCs ) are in vitro cultured cells derived from the preimplantation-stage embryo , which possess unconfined capacity for self-renewal and multi-lineage differentiation towards different embryonic germ layers .",
"Pluripotency and self-renewal are two essential features of ESCs , wh... | [
"Canonical Wnt signaling plays a rate-limiting role in regulating self-renewal and differentiation in mouse embryonic stem cells ( ESCs ) .",
"We have previously shown that mutation in the Apc ( adenomatous polyposis coli ) tumor suppressor gene constitutively activates Wnt signaling in ESCs and inhibits their ca... | [
"The future successes of regenerative medicine largely rely on our knowledge of , and our capacity to manipulate , the cellular and molecular mechanisms governing stem cell differentiation .",
"A growing body of evidence suggests that , in mouse embryonic stem cells , canonical Wnt/β-catenin signaling not only en... | 2013 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"sequencing techniques",
"organismal evolution",
"microbiology",
"invertebrate genomics",
"viruses",
"rna viruses",
"genome analysis",
"microbial evolution",
"molecular biology techniques",
"nucleotide mapping",
"rna sequencing",
"microbial genomics",
"research and analysis methods",
"geno... | Parallel ClickSeq and Nanopore sequencing elucidates the rapid evolution of defective-interfering RNAs in Flock House virus | journal.ppat.1006365 | null | [
[
"RNA viruses are extremely diverse and rapidly evolving .",
"Their RNA-dependent RNA polymerases ( RdRps ) readily generate single-nucleotide variants whilst lacking proof-reading capabilities[1] .",
"RdRps are also highly prone to RNA recombination[2]; either through template-switching[3] or through ... | [
"Defective-Interfering RNAs ( DI-RNAs ) have long been known to play an important role in virus replication and transmission .",
"DI-RNAs emerge during virus passaging in both cell-culture and their hosts as a result of non-homologous RNA recombination .",
"However , the principles of DI-RNA emergence and their... | [
"Defective RNAs are versions of a viral genome that arise naturally during viral infections but have been truncated or rearranged by non-homologous recombination .",
"While not encoding for functional viruses , they can be amplified and co-passaged with the wild-type virus , effectively parasitizing the normal vi... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"mathematics/statistics",
"genetics and genomics/bioinformatics",
"computational biology/genomics"
] | Incorporating Biological Pathways via a Markov Random Field Model in Genome-Wide Association Studies | journal.pgen.1001353 | null | [
[
"In genome-wide association studies ( GWAS ) researchers examine a large number of markers across the genome in many individuals to identify associations between genetic variants and disease , or to prioritize markers for follow up studies .",
"However , most of the times the signals from individual marke... | [
"Genome-wide association studies ( GWAS ) examine a large number of markers across the genome to identify associations between genetic variants and disease .",
"Most published studies examine only single markers , which may be less informative than considering multiple markers and multiple genes jointly because g... | [
"Statistical methods used in most GWAS are based on the analysis of single markers .",
"Prior biological information about markers , genes , and pathways is not commonly incorporated in the detection of associated disease loci .",
"Recently a number of methods have been developed to incorporate such information... | 2011 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"leptospira",
"pathology and laboratory medicine",
"pathogens",
"geographical locations",
"microbiology",
"vertebrates",
"tropical diseases",
"animals",
"mammals",
"bacterial diseases",
"neglected tropical diseases",
"molecular biology techniques",
"bacteria... | Prevalence and Genotype Allocation of Pathogenic Leptospira Species in Small Mammals from Various Habitat Types in Germany | journal.pntd.0004501 | null | [
[
"Leptospira spp .",
"are helical-shaped bacteria and form a particular group of causative agents for the zoonotic disease Leptospirosis .",
"Leptospira spp .",
"are transmitted through infected urine of small mammals or contaminated water via the direct contact to skin lesions or conjunctivae [1] ... | [
"Small mammals serve as most important reservoirs for Leptospira spp .",
", the causative agents of Leptospirosis , which is one of the most neglected and widespread zoonotic diseases worldwide .",
"The knowledge about Leptospira spp .",
"occurring in small mammals from Germany is scarce .",
"Thus , this st... | [
"Leptospirosis is one of the most widespread zoonotic diseases and is caused by Leptospira spp .",
"Small mammals often serve as maintenance hosts .",
"We evaluated host-pathogen relations for Leptospira species and sequence types in different small mammal species captured at three German study sites .",
"Lep... | 2016 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [] | Distribution and Risk Factors for Plasmodium and Helminth Co-infections: A Cross-Sectional Survey among Children in Bagamoyo District, Coastal Region of Tanzania | journal.pntd.0003660 | null | [
[
"Parasitic infections such as Plasmodium present a major public health problem among children in Africa [1 , 2] and its coexistence with Soil Transmitted Helminth ( STH ) infections is common [3 , 4] .",
"Multipasitism is a norm among children in developing countries including United Republic of Tanzania ... | [
"Plasmodium and soil transmitted helminth infections ( STH ) are a major public health problem , particularly among children .",
"There are conflicting findings on potential association between these two parasites .",
"This study investigated the Plasmodium and helminth co-infections among children aged 2 month... | [
"Parasitic infectious agents rarely occur in isolation and multiparasitism is a norm specifically in children living in endemic areas of Tanzania .",
"We studied the pattern and predictors of Plasmodium and STH co-infections in rural Bagamoyo district , coastal region of Tanzania .",
"Parents/guardians of healt... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine and health sciences",
"pathology and laboratory medicine",
"molecular probe techniques",
"enzymes",
"pathogens",
"vibrio",
"biological cultures",
"microbiology",
"immunoblotting",
"enzymology",
"neisseria gonorrhoeae",
"pili and fimbriae",
"phosphatases",
"hormones",
"physiolog... | The Vibrio cholerae Minor Pilin TcpB Initiates Assembly and Retraction of the Toxin-Coregulated Pilus | journal.ppat.1006109 | null | [
[
"Vibrio cholerae is a Gram-negative bacterial pathogen that causes the human diarrheal disease cholera , which afflicts millions of people each year [1] .",
"Cholera is marked by copious watery diarrhea that can lead to dehydration , shock , organ failure and death as little as 24 hours after infection [2... | [
"Type IV pilus ( T4P ) systems are complex molecular machines that polymerize major pilin proteins into thin filaments displayed on bacterial surfaces .",
"Pilus functions require rapid extension and depolymerization of the pilus , powered by the assembly and retraction ATPases , respectively .",
"A set of low ... | [
"Bacterial pathogens utilize a number of highly complex and sophisticated molecular systems to colonize their hosts and alter them , creating customized niches in which to reproduce .",
"One such system is the Type IV pilus system , made up of dozens of proteins that form a macromolecular machine to polymerize sm... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | The Eukaryotic-Like Ser/Thr Kinase PrkC Regulates the Essential WalRK Two-Component System in Bacillus subtilis | journal.pgen.1005275 | null | [
[
"Regulatory Ser/Thr phosphorylation has been assumed to be largely absent from prokaryotes .",
"However , recently , phosphoproteomic analysis has identified numerous ( ~50 ) proteins phosphorylated on Ser or Thr residues in both Gram-positive and Gram-negative bacteria [1] .",
"Likely candidates for ... | [
"Most bacteria contain both eukaryotic-like Ser/Thr kinases ( eSTKs ) and eukaryotic-like Ser/Thr phosphatases ( eSTPs ) .",
"Their role in bacterial physiology is not currently well understood in large part because the conditions where the eSTKs are active are generally not known .",
"However , all sequenced G... | [
"A central question in bacterial physiology is how bacteria sense and respond to their environment .",
"The archetype of bacterial signaling systems is the two-component signaling system composed of a sensor protein histidine kinase that activates a transcription factor response regulator in response to a specifi... | 2015 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine",
"molecular epidemiology",
"infectious disease epidemiology",
"microbial evolution",
"epidemiology",
"microbial pathogens",
"biology",
"microbiology"
] | Molecular Epidemiology and Genetic Variation of Pathogenic Vibrio parahaemolyticus in Peru | journal.pntd.0002210 | null | [
[
"Vibrio parahaemolyticus is a Gram-negative halophilic bacterium that naturally inhabits marine and estuarine environments throughout the world .",
"While many strains of V . parahaemolyticus are strictly environmental , some groups are pathogenic and may cause gastroenteritis in human [1] .",
"V . pa... | [
"Vibrio parahaemolyticus is a foodborne pathogen that has become a public health concern at the global scale .",
"The epidemiological significance of V . parahaemolyticus infections in Latin America received little attention until the winter of 1997 when cases related to the pandemic clone were detected in the re... | [
"Infections caused by Vibrio parahaemolyticus have increased significantly over the last two decades , with cases now regularly reported globally .",
"The emergence of cholera at global scale has brought the attention toward other Vibrio diseases in developing countries .",
"This was the situation in Peru , whe... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genetics and genomics/comparative genomics",
"genetics and genomics/population genetics"
] | Duplication and Gene Conversion in the Drosophila melanogaster Genome | journal.pgen.1000305 | null | [
[
"As proposed almost four decades ago , gene duplication is one of the major sources to create genetic novelty [1] .",
"Gene duplication followed by the fixation of a mutation providing a slightly different function should be a possible scenario of the evolution of new gene function via duplication ( i . e... | [
"Using the genomic sequences of Drosophila melanogaster subgroup , the pattern of gene duplications was investigated with special attention to interlocus gene conversion .",
"Our fine-scale analysis with careful visual inspections enabled accurate identification of a number of duplicated blocks ( genomic regions ... | [
"Eukaryote genomes have a number of duplicated genes , which could potentially coevolve by exchanging DNA sequences by interlocus gene conversion .",
"However , the extent of gene conversion on a genomic scale is not well understood , except that an extensive role of gene conversion was reported in yeast .",
"H... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"gastroenterology and hepatology/gastrointestinal infections",
"biochemistry/macromolecular assemblies and machines",
"microbiology",
"infectious diseases/bacterial infections",
"microbiology/cellular microbiology and pathogenesis",
"infectious diseases/gastrointestinal infections"
] | Helicobacter pylori Lipopolysaccharide Is Synthesized via a Novel Pathway with an Evolutionary Connection to Protein N-Glycosylation | journal.ppat.1000819 | null | [
[
"Lipopolysaccharide ( LPS ) is a prevalent macromolecule in the outer membrane of Gram negative bacteria and represents an important virulence factor .",
"LPS is composed of three parts: lipid A which is embedded in the outer membrane , the core oligosaccharide , and the O antigen [1] .",
"Lipid A is ... | [
"Lipopolysaccharide ( LPS ) is a major component on the surface of Gram negative bacteria and is composed of lipid A-core and the O antigen polysaccharide .",
"O polysaccharides of the gastric pathogen Helicobacter pylori contain Lewis antigens , mimicking glycan structures produced by human cells .",
"The inte... | [
"Bacterial surfaces are decorated with glycans .",
"The human stomach pathogen Helicobacter pylori exposes lipopolysaccharide ( LPS ) containing Lewis antigens that mimic human glycan structures .",
"H . pylori alters its Lewis antigen display in adaptation to the individual host .",
"Lewis antigens can inter... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"invertebrates",
"borrelia infection",
"rheumatology",
"medicine and health sciences",
"immune physiology",
"ixodes",
"pathology and laboratory medicine",
"body fluids",
"enzyme-linked immunoassays",
"pathogens",
"immunology",
"microbiology",
"animals",
"bacterial diseases",
"development... | Infection history of the blood-meal host dictates pathogenic potential of the Lyme disease spirochete within the feeding tick vector | journal.ppat.1006959 | null | [
[
"Borrelia burgdorferi sensu lato ( s . l . ) , the spirochetal agents of Lyme disease , comprise several closely related genospecies of pathogenic bacteria that are maintained in nature in an enzootic cycle involving Ixodes ticks and a wide range of vertebrate hosts .",
"While these spirochetes can cause ... | [
"Lyme disease in humans is caused by several genospecies of the Borrelia burgdorferi sensu lato ( s . l . ) complex of spirochetal bacteria , including B . burgdorferi , B . afzelii and B . garinii .",
"These bacteria exist in nature as obligate parasites in an enzootic cycle between small vertebrate hosts and Ix... | [
"Lyme disease is a tick-borne infection of humans that is caused by a spirochetal bacterium called Borrelia burgdorferi .",
"It is a zoonosis , which means that these bacteria exist in nature outside of people .",
"Many different strains of B . burgdorferi are stably maintained in the same local population of i... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods",
"Supporting Information"
] | [
"homo (human)",
"genetics and genomics"
] | Identification of Common Genetic Variation That Modulates Alternative Splicing | journal.pgen.0030099 | null | [
[
"The sequencing of the human genome [1 , 2] and subsequent work describing sequence variation amongst human populations [3] has provided the necessary resources for large-scale studies of the effects of genetic variation on human gene expression .",
"Identifying functionally important variation has the po... | [
"Alternative splicing of genes is an efficient means of generating variation in protein function .",
"Several disease states have been associated with rare genetic variants that affect splicing patterns .",
"Conversely , splicing efficiency of some genes is known to vary between individuals without apparent ill... | [
"Genetic variation , through its effects on gene expression , influences many aspects of the human phenotype .",
"Understanding the impact of genetic variation on human disease risk has become a major goal for biomedical research and has the potential of revealing both novel disease mechanisms and novel functiona... | 2007 |
[
"Introduction",
"Results and Discussion",
"Materials and Methods"
] | [] | Essential Role for Endogenous siRNAs during Meiosis in Mouse Oocytes | journal.pgen.1005013 | null | [
[
"The RNase III enzyme DICER is responsible for biosynthesis of short-interfering RNAs ( siRNAs ) and microRNAs ( miRNAs ) .",
"DICER processes long double-stranded RNA ( dsRNA ) precursors into 21–23 bp-long duplexes known as siRNAs [1] .",
"miRNAs are encoded by specific genomic loci and are processe... | [
"The RNase III enzyme DICER generates both microRNAs ( miRNAs ) and endogenous short interfering RNAs ( endo-siRNAs ) .",
"Both small RNA species silence gene expression post-transcriptionally in association with the ARGONAUTE ( AGO ) family of proteins .",
"In mammals , there are four AGO proteins ( AGO1-4 ) ,... | [
"In animals , the three main classes of small RNAs are microRNAs , short interfering RNAs , and PIWI-interacting RNAs .",
"All three RNA species silence gene expression post-transcriptionally through interaction with the ARGONAUTE family of proteins .",
"In mammals in particular , microRNAs are ubiquitously exp... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"molecular biology/dna replication",
"virology/viral replication and gene regulation",
"virology/effects of virus infection on host gene expression",
"virology"
] | Human Cytomegalovirus Protein pUL117 Targets the Mini-Chromosome Maintenance Complex and Suppresses Cellular DNA Synthesis | journal.ppat.1000814 | null | [
[
"The manipulation of host DNA synthesis is a critical step for many DNA viruses , including human cytomegalovirus ( HCMV ) , to establish productive infection leading to disease [1] , [2] , [3] .",
"HCMV is a prototypical β-herpesvirus , a ubiquitous pathogen , and one of the most common causes of birth d... | [
"Modulation of host DNA synthesis is essential for many viruses to establish productive infections and contributes to viral diseases .",
"Human cytomegalovirus ( HCMV ) , a large DNA virus , blocks host DNA synthesis and deregulates cell cycle progression .",
"We report that pUL117 , a viral protein that we rec... | [
"Inhibition of host DNA synthesis is pivotal for many viruses to establish productive infection and cause disease .",
"Human cytomegalovirus ( HCMV ) is the top viral cause of birth defects in newborns and leads to life-threatening diseases in individuals with compromised immunity .",
"HCMV blocks host DNA synt... | 2010 |
[
"Introduction",
"Materials and Methods",
"Results and Discussion"
] | [
"taxonomy",
"medicine and health sciences",
"pathology and laboratory medicine",
"evolutionary biology",
"pathogens",
"bacillus",
"microbiology",
"phylogenetics",
"data management",
"phylogenetic analysis",
"genome analysis",
"molecular biology techniques",
"bacteria",
"bacterial pathogens... | Improving Phylogeny Reconstruction at the Strain Level Using Peptidome Datasets | journal.pcbi.1005271 | null | [
[
"The most common techniques for bacterial classification and identification are conventional DNA:DNA hybridization ( DDH ) [1] , comparison of 16S or 23S rRNA gene sequences or 16S–23S rRNA spacer regions [2] , multi-locus sequence typing ( MLST ) [3] and rep-PCR fingerprinting [4] , among others [5] .",
... | [
"Typical bacterial strain differentiation methods are often challenged by high genetic similarity between strains .",
"To address this problem , we introduce a novel in silico peptide fingerprinting method based on conventional wet-lab protocols that enables the identification of potential strain-specific peptide... | [
"Molecular based differentiation of bacterial species is important in phylogenetic studies , diagnostics and epidemiological surveillance , particularly where unusual phenotype makes the classical phenotypic identification of bacteria difficult .",
"Typical bacterial differentiation methods are often challenged b... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"molecular biology/post-translational regulation of gene expression",
"developmental biology/stem cells",
"molecular biology",
"genetics and genomics",
"cell biology/gene expression"
] | Genome-Wide Identification of Targets and Function of Individual MicroRNAs in Mouse Embryonic Stem Cells | journal.pgen.1001163 | null | [
[
"Embryonic stem cells , which are derived from the inner cell mass of the blastocyst , hold great clinical promise because of their unique capacity to both self-renew and differentiate into potentially any cell type .",
"Understanding the molecular controls of pluripotency is key to realising their therap... | [
"Mouse Embryonic Stem ( ES ) cells express a unique set of microRNAs ( miRNAs ) , the miR-290-295 cluster .",
"To elucidate the role of these miRNAs and how they integrate into the ES cell regulatory network requires identification of their direct regulatory targets .",
"The difficulty , however , arises from t... | [
"Stem cells in plants and animals contain many small RNAs , which help to regulate differentiation into diverse cell types .",
"Mutation in a gene necessary for the maturation of small RNAs in plants causes the stem cells ( called meristem cells ) to remain in an indeterminate , overproliferating state .",
"Sim... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"molecular biology/dna replication",
"molecular biology/recombination",
"molecular biology/chromosome structure",
"molecular biology/dna repair"
] | Fission Yeast Tel1ATM and Rad3ATR Promote Telomere Protection and Telomerase Recruitment | journal.pgen.1000622 | null | [
[
"Telomeres , the nucleoprotein protective structures at ends of eukaryotic chromosomes , are essential for stable maintenance of eukaryotic genomes [1] .",
"In most eukaryotic species , telomeric DNA is made up of short repetitive G-rich sequences that can be extended by the specialized reverse transcript... | [
"The checkpoint kinases ATM and ATR are redundantly required for maintenance of stable telomeres in diverse organisms , including budding and fission yeasts , Arabidopsis , Drosophila , and mammals .",
"However , the molecular basis for telomere instability in cells lacking ATM and ATR has not yet been elucidated... | [
"Stable maintenance of telomeres is critical to preserve genomic integrity and to prevent accumulation of undesired mutations that might lead to formation of tumor cells .",
"Fission yeast cells serve as a particularly attractive model system to study telomere maintenance mechanisms , since proteins critical for ... | 2009 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | A Systematic Review of the Mortality from Untreated Leptospirosis | journal.pntd.0003866 | null | [
[
"Leptospirosis is a bacterial zoonosis caused by pathogenic Leptospira species which are transmitted to humans by exposure to water containing the urine of infected mammals , predominantly rodents [1] .",
"The disease occurs worldwide and over 853 , 000 cases and 48 , 000 deaths are estimated to occur eac... | [
"Leptospirosis occurs worldwide , but the global incidence of human disease and its mortality are not well understood .",
"Many patients are undiagnosed and untreated due to its non-specific symptoms and a lack of access to diagnostics .",
"This study systematically reviews the literature to clarify the mortali... | [
"Leptospirosis is a common cause of fever in the developing world but often goes undiagnosed and untreated due to its non-specific clinical features and the limited availability of point-of-care diagnostics .",
"This review systematically evaluated available literature to clarify the mortality from untreated lept... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"animal genetics",
"immunity to infections",
"population genetics",
"immunology",
"gene function",
"animal models",
"drosophila melanogaster",
"model organisms",
"coevolution",
"immune defense",
"molecular genetics",
"forms of evolution",
"genetic polymorphism",
"biology",
"evolutionary ... | Successive Increases in the Resistance of Drosophila to Viral Infection through a Transposon Insertion Followed by a Duplication | journal.pgen.1002337 | null | [
[
"The presence of a parasite elicits strong selection pressures for the host to evolve increased resistance and the parasite to overcome host defences .",
"This can drive rapid changes in allele frequencies in both organisms and result in “Red Queen” evolution , where both species must constantly evolve ju... | [
"To understand the molecular basis of how hosts evolve resistance to their parasites , we have investigated the genes that cause variation in the susceptibility of Drosophila melanogaster to viral infection .",
"Using a host-specific pathogen of D . melanogaster called the sigma virus ( Rhabdoviridae ) , we mappe... | [
"Though much is known about host–parasite coevolution in plants , relatively little is understood in animals .",
"Most studies using animal systems have focused on either generalist parasites or those that do not naturally occur in the host .",
"The sigma virus is specific to Drosophila melanogaster , which pro... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine and health sciences",
"nucleic acid synthesis",
"crystal structure",
"condensed matter physics",
"microbiology",
"dna-binding proteins",
"viral structure",
"limbs (anatomy)",
"thumbs",
"crystals",
"polymerases",
"materials science",
"rna synthesis",
"crystallography",
"material... | Dengue Virus Nonstructural Protein 5 (NS5) Assembles into a Dimer with a Unique Methyltransferase and Polymerase Interface | journal.ppat.1005451 | null | [
[
"Flaviviridae includes at least 70 mosquito- and tick-borne viral species , some of which act as the etiological agents of human diseases such as dengue virus ( DENV ) , West Nile virus ( WNV ) , Japanese encephalitis virus ( JEV ) , and yellow fever virus ( YFV ) .",
"Dengue is the most prevalent mosquit... | [
"Flavivirus nonstructural protein 5 ( NS5 ) consists of methyltransferase ( MTase ) and RNA-dependent RNA polymerase ( RdRp ) domains , which catalyze 5’-RNA capping/methylation and RNA synthesis , respectively , during viral genome replication .",
"Although the crystal structure of flavivirus NS5 is known , no d... | [
"Many plus-strand RNA viruses encode a viral RNA polymerase and capping enzymes to synthesize a 5’-capped RNA genome .",
"However , how these two activities are coordinated during viral replication is not understood .",
"In flaviviruses , polymerase and capping enzymes are encoded in a single multifunctional pr... | 2016 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"biochemistry",
"immunity",
"immune defense",
"immunology",
"biology",
"immunity to infections"
] | Serine Protease(s) Secreted by the Nematode Trichuris muris Degrade the Mucus Barrier | journal.pntd.0001856 | null | [
[
"Immune mediated elimination of gastrointestinal ( GI ) parasitic nematodes has been a subject of considerable investigation [1] .",
"Hyperplasia of goblet cells that produce the secreted mucosal barrier is one of the most prominent features of the TH2-type immune response necessary for the expulsion of t... | [
"The polymeric mucin component of the intestinal mucus barrier changes during nematode infection to provide not only physical protection but also to directly affect pathogenic nematodes and aid expulsion .",
"Despite this , the direct interaction of the nematodes with the mucins and the mucus barrier has not prev... | [
"Gastrointestinal parasitic worm infections cause significant morbidity , affecting up to a third of the world's populationand their domestic pets and livestock .",
"Mucus , the gel-like material that blankets the surface of the intestine , forms a protective barrier that is an important part of our innate immune... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine and health sciences",
"action potentials",
"optogenetics",
"nervous system",
"membrane potential",
"electrophysiology",
"neuroscience",
"simulation and modeling",
"brain mapping",
"bioassays and physiological analysis",
"neuronal dendrites",
"research and analysis methods",
"animal... | Visual physiology of the layer 4 cortical circuit in silico | journal.pcbi.1006535 | null | [
[
"Although our knowledge of the cortex has been improving dramatically thanks to the ongoing revolution in experimental neuroscience methods , the field is still far from an overall understanding of cortical circuits and their specific function .",
"One essential component necessary to address this problem... | [
"Despite advances in experimental techniques and accumulation of large datasets concerning the composition and properties of the cortex , quantitative modeling of cortical circuits under in-vivo-like conditions remains challenging .",
"Here we report and publicly release a biophysically detailed circuit model of ... | [
"How can we capture the incredible complexity of brain circuits in quantitative models , and what can such models teach us about mechanisms underlying brain activity ?",
"To answer these questions , we set out to build extensive , bio-realistic models of brain circuitry by employing systematic datasets on brain s... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"blood cells",
"flow cytometry",
"medicine and health sciences",
"immune cells",
"pathology and laboratory medicine",
"pathogens",
"cell cycle and cell division",
"immunology",
"cell processes",
"microbiology",
"cloning",
"orthomyxoviruses",
"epithelial cells",
"viruses",
"rna viruses",
... | Long-term surviving influenza infected cells evade CD8+ T cell mediated clearance | journal.ppat.1008077 | null | [
[
"Influenza A virus ( IAV ) is a negative sense segmented RNA virus causing significant morbidity and mortality annually .",
"IAV has a broad tropism in the respiratory tract infecting club cells , ciliated cells , type I and type II alveolar cells among others [1] .",
"IAV drives destruction of infect... | [
"Influenza A virus ( IAV ) is a seasonal pathogen with the potential to cause devastating pandemics .",
"IAV infects multiple epithelial cell subsets in the respiratory tract , eliciting damage to the lungs .",
"Clearance of IAV is primarily dependent on CD8+ T cells , which must balance control of the infectio... | [
"Influenza A virus is a seasonal respiratory pathogen that can cause severe lung damage and death .",
"We previously made the discovery that cells infected with influenza virus do not have a death sentence .",
"An infected cell can survive both influenza virus infection and the immune response to eliminate the ... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"biochemistry",
"hematopoiesis",
"gene expression",
"genetics",
"epigenetics",
"biology",
"hematology",
"gene function"
] | USF1 and hSET1A Mediated Epigenetic Modifications Regulate Lineage Differentiation and HoxB4 Transcription | journal.pgen.1003524 | null | [
[
"Embryonic stem cells ( ESCs ) have the ability to differentiate into any cell type of the body and therefore offer a great tool for studying processes involved in cellular differentiation .",
"ESCs also provide a great potential for application of regenerative medicine that is based on two key properties... | [
"The interplay between polycomb and trithorax complexes has been implicated in embryonic stem cell ( ESC ) self-renewal and differentiation .",
"It has been shown recently that WRD5 and Dpy-30 , specific components of the SET1/MLL protein complexes , play important roles during ESC self-renewal and differentiatio... | [
"Embryonic stem cells ( ESCs ) are capable of differentiating into any type of cell or tissue of the body .",
"It is important to understand how developmental genes are controlled during differentiation of ESCs into specific cell types .",
"The hSET1/MLL histone modifying protein complexes add methyl groups to ... | 2013 |
[
"Introduction",
"Results/Discussion",
"Materials and Methods"
] | [
"homo (human)",
"computational biology"
] | A Macaque's-Eye View of Human Insertions and Deletions: Differences in Mechanisms | journal.pcbi.0030176 | null | [
[
"Despite the significance of insertions and deletions ( indels ) for human genetic disease [1] and genome evolution [2–5] , the mechanisms of their mutagenesis are not completely understood .",
"Both replication and recombination have been proposed as potential contributors; however , their relative roles... | [
"Insertions and deletions ( indels ) cause numerous genetic diseases and lead to pronounced evolutionary differences among genomes .",
"The macaque sequences provide an opportunity to gain insights into the mechanisms generating these mutations on a genome-wide scale by establishing the polarity of indels occurri... | [
"Insertions and deletions ( indels ) represent a significant source of evolutionary change .",
"In this manuscript , the authors investigate the patterns of genome-wide rate variation for indels that occurred in the human lineage since its divergence from chimpanzee .",
"Earlier work suggested that insertion an... | 2007 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biology"
] | Polyglutamine Toxicity Is Controlled by Prion Composition and Gene Dosage in Yeast | journal.pgen.1002634 | null | [
[
"A variety of human neurodegenerative disorders are associated with expansions of polyglutamine ( poly-Q ) repeats in certain proteins [1] , [2] .",
"One well known example is Huntington's disease ( HD ) , which is caused by an expansion of the poly-Q stretch , located within the N-terminal stretch of the... | [
"Polyglutamine expansion causes diseases in humans and other mammals .",
"One example is Huntington's disease .",
"Fragments of human huntingtin protein having an expanded polyglutamine stretch form aggregates and cause cytotoxicity in yeast cells bearing endogenous QN-rich proteins in the aggregated ( prion ) ... | [
"Polyglutamine diseases , including Huntington disease , are associated with expansions of polyglutamine tracts , resulting in aggregation of respective proteins .",
"The severity of Huntington disease is controlled by both DNA and non–DNA factors .",
"Mechanisms of such a control are poorly understood .",
"P... | 2012 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | Human Immunodeficiency Virus, Antiretroviral Therapy and Markers of Lymphatic Filariasis Infection: A Cross-sectional Study in Rural Northern Malawi | journal.pntd.0003825 | null | [
[
"Human immunodeficiency virus ( HIV ) and parasitic infections affect widely overlapping populations in sub-Saharan Africa .",
"Of the estimated 35 million people infected with HIV worldwide at the end of 2013 , about 70% were from sub-Saharan Africa [1] .",
"Parasitic infections , including lymphatic... | [
"Lymphatic filariasis ( LF ) and human immunodeficiency virus ( HIV ) are major public health problems .",
"Individuals may be co-infected , raising the possibility of important interactions between these two pathogens with consequences for LF elimination through annual mass drug administration ( MDA ) .",
"We ... | [
"Lymphatic filariasis ( LF ) and HIV are both major public health problems worldwide and where they co-exist have the potential to interact .",
"The main strategy for LF elimination is annual mass drug administration ( MDA ) .",
"A particular concern is whether HIV , through its impact on the immune system , wi... | 2015 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine and health sciences",
"organ transplantation",
"pathology and laboratory medicine",
"tropical diseases",
"social sciences",
"parasitic diseases",
"animals",
"surgical and invasive medical procedures",
"health care",
"liver transplantation",
"screening guidelines",
... | High seroprevalence of Strongyloides stercoralis among individuals from endemic areas considered for solid organ transplant donation: A retrospective serum-bank based study | journal.pntd.0007010 | null | [
[
"Strongyloides stercoralis is a parasitic infection which is endemic in large parts of Latin America , Asia and Africa with an estimated prevalence of more than 400 million infected [1] .",
"Due to its characteristic life cycle , individuals can carry the infection lifelong with mild or no symptoms , unle... | [
"Strongyloides stercoralis is a worldwide disseminated parasitic disease that can be transmitted from solid organ transplant ( SOT ) donors to recipients .",
"We determined the serological prevalence of S . stercoralis among deceased individuals from endemic areas considered for SOT donation , using our instituti... | [
"Strongyloidiasis is a neglected tropical disease caused by a parasite which is endemic in most parts of the world .",
"It can cause a life-threatening disease among immunosuppressed individuals and can be transmitted from solid organ transplant donors to recipients .",
"We retrospectively investigated the prev... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"virology/host antiviral responses",
"immunology/innate immunity"
] | An RIG-I-Like RNA Helicase Mediates Antiviral RNAi Downstream of Viral siRNA Biogenesis in Caenorhabditis elegans | journal.ppat.1000286 | null | [
[
"Innate immunity is active immediately upon pathogen attack and represents an ancient defense mechanism conserved in diverse multicellular organisms .",
"Innate immunity is initiated by pattern recognition receptors ( PRRs ) that recognize conserved molecular patterns associated with microbes .",
"Wel... | [
"Dicer ribonucleases of plants and invertebrate animals including Caenorhabditis elegans recognize and process a viral RNA trigger into virus-derived small interfering RNAs ( siRNAs ) to guide specific viral immunity by Argonaute-dependent RNA interference ( RNAi ) .",
"C . elegans also encodes three Dicer-relate... | [
"The genome of Caenorhabditis elegans encodes three Dicer-related helicases ( DRHs ) highly homologous to the DExD/H box helicase domain found in two distinct families of virus sensors , Dicer ribonucleases and RIG-I-like helicases ( RLRs ) .",
"Dicer initiates the specific , RNAi-mediated viral immunity in plant... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"infectious diseases",
"mathematics",
"epidemiology",
"statistics",
"statistical methods",
"biostatistics",
"biology",
"computational biology"
] | Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data | journal.pcbi.1003457 | null | [
[
"Statistical methods for analyzing detailed epidemiological data collected during infectious disease outbreaks have seen rapid development in recent years [1] , [2] , [3] , [4] , [5] , [6] , [7] , [8] .",
"These methods probabilistically reconstruct likely transmission links between cases using data on th... | [
"Recent years have seen progress in the development of statistically rigorous frameworks to infer outbreak transmission trees ( “who infected whom” ) from epidemiological and genetic data .",
"Making use of pathogen genome sequences in such analyses remains a challenge , however , with a variety of heuristic appr... | [
"Understanding how infectious diseases are transmitted from one individual to another is essential for designing containment strategies and epidemic prevention .",
"Recently , the reconstruction of transmission trees ( “who infected whom” ) has been revolutionized by the availability of pathogen genome sequences ... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"meiosis",
"chromosome biology",
"nucleic acids",
"gene expression",
"dna",
"dna repair",
"biology",
"genomics",
"molecular cell biology",
"dna transcription"
] | SPO11-Independent DNA Repair Foci and Their Role in Meiotic Silencing | journal.pgen.1003538 | null | [
[
"During meiotic prophase in yeast and mammals , the induction of DNA double-strand breaks ( DSBs ) by the transesterase SPO11 precedes stable pairing and synapsis of homologous chromosomes [1] , [2] .",
"Synapsis between chromosomes is achieved by the formation of a specific protein complex , consisting o... | [
"In mammalian meiotic prophase , the initial steps in repair of SPO11-induced DNA double-strand breaks ( DSBs ) are required to obtain stable homologous chromosome pairing and synapsis .",
"The X and Y chromosomes pair and synapse only in the short pseudo-autosomal regions .",
"The rest of the chromatin of the ... | [
"Meiosis is a special cell division that generates genetically divergent haploid germ cells .",
"At the very beginning of this process , during meiotic prophase , the enzyme SPO11 generates hundreds of DNA double-strand breaks ( DSBs ) .",
"Meiotic DSBs are repaired via a mechanism that requires the presence of... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"blood cells",
"organismal evolution",
"medicine and health sciences",
"chemical characterization",
"immune physiology",
"immune cells",
"pathology and laboratory medicine",
"pathogens",
"immunology",
"population genetics",
"microbiology",
"retroviruses",
"viruses",
"immunodeficiency virus... | Host-Pathogen Coevolution and the Emergence of Broadly Neutralizing Antibodies in Chronic Infections | journal.pgen.1006171 | null | [
[
"It takes decades for humans to reproduce , but our pathogens can reproduce in less than a day .",
"How can we coexist with pathogens whose potential to evolve is 104-times faster than our own ?",
"In vertebrates , the answer lies in their adaptive immune system , which uses recombination , mutation ,... | [
"The vertebrate adaptive immune system provides a flexible and diverse set of molecules to neutralize pathogens .",
"Yet , viruses such as HIV can cause chronic infections by evolving as quickly as the adaptive immune system , forming an evolutionary arms race .",
"Here we introduce a mathematical framework to ... | [
"We normally think of evolution occurring in a population of organisms , in response to their external environment .",
"Rapid evolution of cellular populations also occurs within our bodies when the adaptive immune system works to eliminate infections .",
"Some viruses , such as HIV , are able to evolve as quic... | 2016 |
[
"Introduction",
"Results and Discussion",
"Materials and Methods"
] | [
"flow cytometry",
"cell physiology",
"medicine and health sciences",
"pathology and laboratory medicine",
"pathogens",
"microbiology",
"light microscopy",
"plasmid construction",
"microscopy",
"yersinia",
"lymphatic system",
"dna construction",
"molecular biology techniques",
"yersinia pse... | A Precise Temperature-Responsive Bistable Switch Controlling Yersinia Virulence | journal.ppat.1006091 | null | [
[
"Temperature is a prominent signal used by pathogens to adjust their virulence and host survival programs during infection .",
"Different biomolecules can act as thermosensors , including DNA , RNA and regulatory proteins .",
"They all detect changes in temperature through thermally induced conformati... | [
"Different biomolecules have been identified in bacterial pathogens that sense changes in temperature and trigger expression of virulence programs upon host entry .",
"However , the dynamics and quantitative outcome of this response in individual cells of a population , and how this influences pathogenicity are u... | [
"The ability of pathogens to sense temperature changes when they enter their mammalian hosts from the environment is crucial to optimize their fitness and adjust expression of their virulence programs .",
"Until now it has been assumed that all cells within a population participate in the thermo-triggered adaptiv... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"virology/viruses and cancer",
"infectious diseases/epidemiology and control of infectious diseases",
"virology"
] | Seroepidemiology of Human Polyomaviruses | journal.ppat.1000363 | null | [
[
"Polyomaviruses are small , non-enveloped dsDNA viruses that occupy replicative niches in a variety of vertebrates , and have been extensively studied as oncogenic agents in experimental systems .",
"Five human polyomaviruses have now been identified: BKV [1] , JCV [2] , KIV [3] , WUV [4] , and most recen... | [
"In addition to the previously characterized viruses BK and JC , three new human polyomaviruses ( Pys ) have been recently identified: KIV , WUV , and Merkel Cell Py ( MCV ) .",
"Using an ELISA employing recombinant VP1 capsid proteins , we have determined the seroprevalence of KIV , WUV , and MCV , along with BK... | [
"Polyomaviruses occupy a replicative niche in animals from birds to humans .",
"Two human polyomaviruses , BKV and JCV , were discovered in 1971 and within the last two years , three new polyomaviruses have been found in humans: KI ( KIV ) , WU ( WUV ) , and Merkel Cell ( MCV ) polyomavirus .",
"MCV was identif... | 2009 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"community ecology",
"evolutionary ecology",
"coevolution",
"ecology",
"evolutionary biology",
"theoretical biology",
"evolutionary modeling",
"evolutionary immunology",
"biology",
"computational biology",
"species interactions",
"evolutionary processes",
"evolutionary theory"
] | On Genetic Specificity in Symbiont-Mediated Host-Parasite Coevolution | journal.pcbi.1002633 | null | [
[
"Parasitism is one of the main lifestyles in nature and a major source of evolutionary pressure .",
"Despite its central place in evolutionary ecology , however , the details of the genetic architecture underlying resistance and infectivity are not known for most host-parasite associations .",
"Mathem... | [
"Existing theory of host-parasite interactions has identified the genetic specificity of interaction as a key variable affecting the outcome of coevolution .",
"The Matching Alleles ( MA ) and Gene For Gene ( GFG ) models have been extensively studied as the canonical examples of specific and non-specific interac... | [
"Coevolution between hosts and parasites is believed to be central to a number of biological phenomena , most notably the observed patterns of biodiversity and the origins of sexual reproduction .",
"However , classical mathematical models of host-parasite coevolution account neither for the hosts' use of bacteri... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"deletion mutation",
"nucleic acid synthesis",
"retrotransposons",
"chemical compounds",
"carbohydrates",
"organic compounds",
"glucose",
"dna transcription",
"mutation",
"fungi",
"model organisms",
"experimental organism systems",
"genetic elements",
"molecular biology techniques",
"rna... | The Mediator co-activator complex regulates Ty1 retromobility by controlling the balance between Ty1i and Ty1 promoters | journal.pgen.1007232 | null | [
[
"Retrotransposons have been extensively characterized as catalysts of evolutionary change and agents of genome instability [1–6] .",
"In humans , retrotransposons have been shown to be upregulated in cancerous cells [7] , and have been implicated in tumorigenesis [8] .",
"Long terminal repeat ( LTR ) ... | [
"The Ty1 retrotransposons present in the genome of Saccharomyces cerevisiae belong to the large class of mobile genetic elements that replicate via an RNA intermediary and constitute a significant portion of most eukaryotic genomes .",
"The retromobility of Ty1 is regulated by numerous host factors , including se... | [
"Retrotransposons are mobile genetic elements that copy their RNA genomes into DNA and insert the DNA copies into the host genome .",
"These elements contribute to genome instability , control of host gene expression and adaptation to changing environments .",
"Retrotransposons depend on numerous host factors f... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biology"
] | Host Cell Entry of Respiratory Syncytial Virus Involves Macropinocytosis Followed by Proteolytic Activation of the F Protein | journal.ppat.1003309 | null | [
[
"Human respiratory syncytial virus ( RSV ) belongs to the Paramyxoviridae , a family of enveloped viruses with a negative-stranded RNA genome .",
"It is a ubiquitous human pathogen that causes severe respiratory tract infections affecting mainly children and the elderly worldwide .",
"Despite ongoing ... | [
"Respiratory Syncytial Virus ( RSV ) is a highly pathogenic member of the Paramyxoviridae that causes severe respiratory tract infections .",
"Reports in the literature have indicated that to infect cells the incoming viruses either fuse their envelope directly with the plasma membrane or exploit clathrin-mediate... | [
"Respiratory Syncytial Virus ( RSV ) is a highly pathogenic paramyxovirus .",
"We developed assays for RSV endocytosis , intracellular trafficking , membrane fusion , and infection .",
"The results showed that RSV was rapidly and efficiently internalized , and that acid-independent membrane fusion occurred intr... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"infectious diseases",
"immune cells",
"major histocompatibility complex",
"antigen processing and recognition",
"clinical immunology",
"immunity",
"antigen-presenting cells",
"t cells",
"immunology",
"immunity to infections",
"biology",
"microbiology",
"host-pathogen interacti... | Location of the CD8 T Cell Epitope within the Antigenic Precursor Determines Immunogenicity and Protection against the Toxoplasma gondii Parasite | journal.ppat.1003449 | null | [
[
"CD8 T cells play a critical role in immune-mediated protection against intracellular apicomplexan parasites .",
"Antigenic determinants recognized by CD8 T cells are short peptides of 8 to 10 amino acids presented by class I molecules of the major histocompatibility complex ( MHC I ) .",
"Antigenic p... | [
"CD8 T cells protect the host from disease caused by intracellular pathogens , such as the Toxoplasma gondii ( T . gondii ) protozoan parasite .",
"Despite the complexity of the T . gondii proteome , CD8 T cell responses are restricted to only a small number of peptide epitopes derived from a limited set of antig... | [
"Toxoplasma gondii is a widespread intracellular parasite that can cause severe disease in immunocompromised individuals and lead to fetal abnormalities if contracted during pregnancy .",
"Establishment of protective immunity relies on CD8 T cells , which recognize antigenic peptides presented by MHC class I mole... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"blood cells",
"medicine and health sciences",
"immune cells",
"pathology and laboratory medicine",
"pathogens",
"immunology",
"microbiology",
"vertebrates",
"cloning",
"animals",
"mammals",
"retroviruses",
"primates",
"immunodeficiency viruses",
"viruses",
"animal models",
"clinical... | KIR3DL01 upregulation on gut natural killer cells in response to SIV infection of KIR- and MHC class I-defined rhesus macaques | journal.ppat.1006506 | null | [
[
"Natural killer cells provide a critical early defense against viral pathogens by directly responding to infected cells without prior antigenic stimulation .",
"This is accomplished through the integration of signals from activating and inhibitory receptors , which in primates include the highly polymorph... | [
"Natural killer cells provide an important early defense against viral pathogens and are regulated in part by interactions between highly polymorphic killer-cell immunoglobulin-like receptors ( KIRs ) on NK cells and their MHC class I ligands on target cells .",
"We previously identified MHC class I ligands for t... | [
"Natural killer ( NK ) cells are an important cellular defense against viral pathogens , and are regulated in part by interactions between killer-cell immunoglobulin-like receptors ( KIRs ) on NK cells and MHC class I ligands on target cells .",
"Using multi-parameter flow cytometry , we report the first longitud... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"sequencing techniques",
"antimicrobials",
"medicine and health sciences",
"pathology and laboratory medicine",
"gene regulation",
"pathogens",
"drugs",
"microbiology",
"operons",
"pseudomonas aeruginosa",
"antibiotic resistance",
"regulator genes",
"antibiotics",
"gene types",
"sequence... | CpxR Activates MexAB-OprM Efflux Pump Expression and Enhances Antibiotic Resistance in Both Laboratory and Clinical nalB-Type Isolates of Pseudomonas aeruginosa | journal.ppat.1005932 | null | [
[
"Pseudomonas aeruginosa , a major pathogen associated with cystic fibrosis , is known for its intrinsic resistance to a wide range of antimicrobial agents and its ability to develop multidrug resistance following antibiotic therapy [1] .",
"Resistance-Nodulation-Division ( RND ) efflux systems are largely... | [
"Resistance-Nodulation-Division ( RND ) efflux pumps are responsible for multidrug resistance in Pseudomonas aeruginosa .",
"In this study , we demonstrate that CpxR , previously identified as a regulator of the cell envelope stress response in Escherichia coli , is directly involved in activation of expression o... | [
"Pseudomonas aeruginosa is one of the major pathogens associated with cystic fibrosis and multidrug resistant P . aeruginosa has been listed as the Top 10 antibiotic resistance threats in the US CDC report ( http://www . cdc . gov/drugresistance/biggest_threats . html ) .",
"Drug efflux systems play a major role ... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Conclusion",
"Materials and Methods"
] | [
"traumatic injury",
"medicine and health sciences",
"nervous system",
"brain",
"neuroscience",
"biological locomotion",
"biomechanics",
"surgical and invasive medical procedures",
"macroglial cells",
"mathematics",
"statistics (mathematics)",
"schwann cells",
"research and analysis methods",... | Olfactory Ensheathing Cell Transplantation in Experimental Spinal Cord Injury: Effect size and Reporting Bias of 62 Experimental Treatments: A Systematic Review and Meta-Analysis | journal.pbio.1002468 | This meta-analysis study examines the effects of transplanting olfactory ensheathing cells in rodents with experimental spinal cord injury, finding evidence for significant recovery and identifying aspects of the procedure that influence the effect size. | [
[
"Cellular transplantation strategies applying different cellular sources have been tested in experimental spinal cord injury ( SCI ) models as a possible treatment to propagate functional recovery [1–3] .",
"Restoration of function after SCI remains one of the most formidable challenges in regenerative me... | [
"Olfactory ensheathing cell ( OEC ) transplantation is a candidate cellular treatment approach for human spinal cord injury ( SCI ) due to their unique regenerative potential and autologous origin .",
"The objective of this study was , through a meta-epidemiologic approach ,",
"( i ) to assess the efficacy of O... | [
"Spinal cord injury converts into a debilitating disease affecting millions of chronic patients worldwide .",
"Despite increased molecular knowledge over the last decades , no causal pharmacological or cellular therapy has proven effective so far .",
"Due to their unique regenerative capabilities and their auto... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"gene networks",
"genetic mutation",
"protein interactions",
"mechanisms of signal transduction",
"gene regulation",
"immunology",
"dna-binding proteins",
"anatomy and physiology",
"signaling in selected disciplines",
"cytogenetic analysis",
"hormones",
"endocrine physiology",
"dna transcrip... | Regulation of Drosophila Metamorphosis by Xenobiotic Response Regulators | journal.pgen.1003263 | null | [
[
"Cellular responses to many xenobiotic compounds , including various toxins and pharmacological agents , are controlled by mammalian Nrf2 and Keap1 , and by the homologous Drosophila CncC and dKeap1 proteins [1] , [2] , [3] .",
"The Nrf2-Keap1 complex has multiple effects on carcinogenesis .",
"Nrf2-d... | [
"Mammalian Nrf2-Keap1 and the homologous Drosophila CncC-dKeap1 protein complexes regulate both transcriptional responses to xenobiotic compounds as well as native cellular and developmental processes .",
"The relationships between the functions of these proteins in xenobiotic responses and in development were un... | [
"Human Nrf2-Keap1 and the fruit fly CncC-dKeap1 protein complexes function both in response to foreign chemicals and in development .",
"We found that CncC and dKeap1 control fruit fly development by regulating the production and actions of the principal hormone that controls the transformation of larvae into pup... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | A Voltage-Based STDP Rule Combined with Fast BCM-Like Metaplasticity Accounts for LTP and Concurrent “Heterosynaptic” LTD in the Dentate Gyrus In Vivo | journal.pcbi.1004588 | null | [
[
"Synaptic plasticity , i . e . long-lasting activity-dependent changes in synaptic transmission , is widely considered to be a critical neural mechanism for memory storage .",
"Computational models are being increasingly used to understand the precise activity rules that govern the induction and persisten... | [
"Long-term potentiation ( LTP ) and long-term depression ( LTD ) are widely accepted to be synaptic mechanisms involved in learning and memory .",
"It remains uncertain , however , which particular activity rules are utilized by hippocampal neurons to induce LTP and LTD in behaving animals .",
"Recent experimen... | [
"The vast majority of computational studies that model synaptic plasticity neglect the fact that in vivo neurons exhibit an ongoing spontaneous spiking which affects the dynamics of synaptic changes .",
"Here we study how key components of learning mechanisms in the brain , namely spike timing-dependent plasticit... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"molecular biology",
"genetics and genomics"
] | Dynamic Remodeling of Individual Nucleosomes Across a Eukaryotic Genome in Response to Transcriptional Perturbation | journal.pbio.0060065 | Ultra-high-throughput sequencing is used to show that distinct, localized patterns of nucleosome repositioning at promoters underlie the genome-wide transcriptional response to a physiological stimulus. | [
[
"The eukaryotic genome is compacted into nucleosomal arrays composed of 146-bp DNA wrapped around a core histone octamer complex [1] .",
"The location of nucleosomes affects nearly every cellular process requiring access to genomic DNA , but it is not well understood how nucleosomes are positioned and rem... | [
"The eukaryotic genome is packaged as chromatin with nucleosomes comprising its basic structural unit , but the detailed structure of chromatin and its dynamic remodeling in terms of individual nucleosome positions has not been completely defined experimentally for any genome .",
"We used ultra-high–throughput se... | [
"The eukaryotic genome is packed in a systematic hierarchy to accommodate it within the confines of the cell's nucleus .",
"This packing , however , presents an impediment to the transcription machinery when it must access genomic DNA to regulate gene expression .",
"A fundamental aspect of genome packing is th... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biotechnology",
"biology and life sciences",
"pharmacogenomics",
"computational biology"
] | Analysis of Individual Protein Regions Provides Novel Insights on Cancer Pharmacogenomics | journal.pcbi.1004024 | null | [
[
"With the body of genomic and pharmacologic data on cancer growing exponentially , the main bottleneck to translate such information into meaningful and clinically relevant hypothesis is data analysis [1]–[3] .",
"While numerous methods have been recently applied to the analysis of such datasets [4] most ... | [
"The promise of personalized cancer medicine cannot be fulfilled until we gain better understanding of the connections between the genomic makeup of a patient's tumor and its response to anticancer drugs .",
"Several datasets that include both pharmacologic profiles of cancer cell lines as well as their genomic a... | [
"There is increasing evidence that altering different functional regions within the same protein can lead to dramatically distinct phenotypes .",
"Here we show how , by focusing on individual regions instead of whole proteins , we are able to identify novel correlations that predict the activity of anticancer dru... | 2015 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious diseases",
"global health",
"neglected tropical diseases",
"vectors and hosts"
] | A Wolbachia wMel Transinfection in Aedes albopictus Is Not Detrimental to Host Fitness and Inhibits Chikungunya Virus | journal.pntd.0002152 | null | [
[
"Aedes albopictus is a medically important invasive mosquito that has expanded from Asia into many new regions of the tropics and also into temperate regions of the Americas and Europe; it transmits a number of arboviruses including dengue and chikungunya [1] .",
"All known wild populations of Ae .",
... | [
"Wolbachia inherited intracellular bacteria can manipulate the reproduction of their insect hosts through cytoplasmic incompatibility ( CI ) , and certain strains have also been shown to inhibit the replication or dissemination of viruses .",
"Wolbachia strains also vary in their relative fitness effects on their... | [
"The tiger mosquito Aedes albopictus is an invasive disease vector whose range has expanded throughout the tropics , and some temperate regions , in recent decades from its native South East Asia .",
"It is an important vector of human viruses including dengue and chikungunya; in recent years a mutation has been ... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"blood cells",
"medicine and health sciences",
"parasite groups",
"immune physiology",
"immune cells",
"enzyme-linked immunoassays",
"plasmodium",
"immunology",
"cloning",
"parasitology",
"apicomplexa",
"molecular biology techniques",
"antibodies",
"immunologic techniques",
"antibody res... | T-dependent B cell responses to Plasmodium induce antibodies that form a high-avidity multivalent complex with the circumsporozoite protein | journal.ppat.1006469 | null | [
[
"Malaria caused by Plasmodium falciparum causes the deaths of around 430 , 000 people each year [1] .",
"The most advanced vaccine candidate for malaria is the RTS , S/AS01 vaccine which consists of a truncated version of the sporozoite-surface circumsporozoite protein ( CSP ) , packaged in a Hepatitis C ... | [
"The repeat region of the Plasmodium falciparum circumsporozoite protein ( CSP ) is a major vaccine antigen because it can be targeted by parasite neutralizing antibodies; however , little is known about this interaction .",
"We used isothermal titration calorimetry , X-ray crystallography and mutagenesis-validat... | [
"Vaccines aim to protect by inducing the immune system to make molecules called antibodies that can recognize molecules on the surface of invading pathogens .",
"In the case of malaria , our most advanced vaccine candidates aim to promote the production of antibodies that recognize the circumsporozoite protein ( ... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"cell biology",
"computational biology",
"molecular biology",
"genetics and genomics",
"hematology"
] | Expression Quantitative Trait Loci Are Highly Sensitive to Cellular Differentiation State | journal.pgen.1000692 | null | [
[
"Genetical genomics uses quantitative genetics on a panel of densely genotyped individuals to map genomic loci that modulate gene expression [1] .",
"The quantitative trait loci identified in this manner are referred to as expression quantitative trait loci , or eQTLs [2] .",
"Most genetical genomics ... | [
"Genetical genomics is a strategy for mapping gene expression variation to expression quantitative trait loci ( eQTLs ) .",
"We performed a genetical genomics experiment in four functionally distinct but developmentally closely related hematopoietic cell populations isolated from the BXD panel of recombinant inbr... | [
"Blood cell development from multipotent hematopoietic stem cells to specialized blood cells is accompanied by drastic changes in gene expression for which the triggers remain mostly unknown .",
"Genetical genomics is an approach linking natural genetic variation to gene expression variation , thereby allowing th... | 2009 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine and health sciences",
"pathology and laboratory medicine",
"togaviruses",
"viral transmission and infection",
"pathogens",
"geographical locations",
"microbiology",
"australia",
"animals",
"alphaviruses",
"viral vectors",
"viruses",
"developmental biology",
"ch... | Holding back the tiger: Successful control program protects Australia from Aedes albopictus expansion | journal.pntd.0005286 | null | [
[
"The Asian tiger mosquito , Aedes albopictus , is a major public health concern .",
"It is a vector of dengue , chikungunya and Zika viruses , and a potential vector of a wide range of other arboviruses [1–6] .",
"Furthermore , Ae .",
"albopictus is also considered one of the most significant nuis... | [
"The Asian tiger mosquito , Aedes albopictus , is an important vector of dengue , chikungunya and Zika viruses and is a highly invasive and aggressive biter .",
"Established populations of this species were first recognised in Australia in 2005 when they were discovered on islands in the Torres Strait , between m... | [
"Aedes albopictus is a disease vector and biting nuisance of major public health concern .",
"Established populations of Ae .",
"albopictus were first recognised in Australia in 2005 after they were discovered on islands in the Torres Strait .",
"Consequently , a control program was established in the same ye... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"infectious diseases/protozoal infections"
] | Extreme CD8 T Cell Requirements for Anti-Malarial Liver-Stage Immunity following Immunization with Radiation Attenuated Sporozoites | journal.ppat.1000998 | null | [
[
"Plasmodium infections are a global health crisis resulting in ∼300 million cases of malaria each year and ∼1 million deaths [1] , [2] , [3] , [4] , [5] .",
"At present , there are no effective licensed anti-malarial vaccines .",
"Most vaccines under clinical evaluation are only partially protective a... | [
"Radiation-attenuated Plasmodium sporozoites ( RAS ) are the only vaccine shown to induce sterilizing protection against malaria in both humans and rodents .",
"Importantly , these “whole-parasite” vaccines are currently under evaluation in human clinical trials .",
"Studies with inbred mice reveal that RAS-ind... | [
"Plasmodium infections are a global health crisis resulting in ∼300 million cases of malaria each year and ∼1 million deaths .",
"Radiation-attenuated Plasmodium sporozoites ( RAS ) are the only vaccines that induce sterilizing anti-malarial immunity in humans .",
"Importantly , “whole parasite” anti-malarial R... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Small Regulatory RNA-Induced Growth Rate Heterogeneity of Bacillus subtilis | journal.pgen.1005046 | null | [
[
"In their natural habitats , bacteria constantly adapt to changing environmental conditions while simultaneously anticipating further disturbances .",
"To efficiently cope with these changes , intricate interlinked metabolic and genetic regulation has evolved [1] .",
"This complex regulatory network i... | [
"Isogenic bacterial populations can consist of cells displaying heterogeneous physiological traits .",
"Small regulatory RNAs ( sRNAs ) could affect this heterogeneity since they act by fine-tuning mRNA or protein levels to coordinate the appropriate cellular behavior .",
"Here we show that the sRNA RnaC/S1022 ... | [
"Bacterial cells that share the same genetic information can display very different phenotypes , even if they grow under identical conditions .",
"Despite the relevance of this population heterogeneity for processes like drug resistance and development , the molecular players that induce heterogenic phenotypes ar... | 2015 |
[
"Introduction",
"Results and discussion",
"Methods"
] | [
"genome-wide association studies",
"medicine and health sciences",
"breast tumors",
"cancers and neoplasms",
"hormones",
"oncology",
"mathematics",
"genome analysis",
"genetic interactions",
"discrete mathematics",
"steroid hormones",
"combinatorics",
"glutathione",
"breast cancer",
"gen... | Pathway-based discovery of genetic interactions in breast cancer | journal.pgen.1006973 | null | [
[
"Cancer , like many common diseases , is influenced by a variety of genetic and environmental factors .",
"With the rise of inexpensive genotyping technologies , the portion of risk due to inherited genetic variants has been measured with unprecedented resolution .",
"A recent comprehensive study repo... | [
"Breast cancer is the second largest cause of cancer death among U . S . women and the leading cause of cancer death among women worldwide .",
"Genome-wide association studies ( GWAS ) have identified several genetic variants associated with susceptibility to breast cancer , but these still explain less than half... | [
"Susceptibility to breast cancer is partially encoded in our genomes , but despite the development of new genomic technologies over the past decade , we are still not able to accurately predict disease susceptibility from genome sequences .",
"One reason for this gap is that we lack methods for finding combinatio... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biotechnology",
"phosphorylation",
"plant anatomy",
"cereal crops",
"regulator genes",
"plant science",
"rice",
"model organisms",
"genetically modified plants",
"crops",
"gene types",
"plant genomics",
"molecular biology techniques",
"plants",
"flowering plants",
"genetic engineering... | The Oryza sativa Regulator HDR1 Associates with the Kinase OsK4 to Control Photoperiodic Flowering | journal.pgen.1005927 | null | [
[
"The ability of plants to reproduce during the appropriate season enables them to adapt to environmental changes in day length and temperature and requires precise monitoring of environmental and endogenous signals [1–5] .",
"These external and internal signals comprise a complex regulatory network that i... | [
"Rice is a facultative short-day plant ( SDP ) , and the regulatory pathways for flowering time are conserved , but functionally modified , in Arabidopsis and rice .",
"Heading date 1 ( Hd1 ) , an ortholog of Arabidopsis CONSTANS ( CO ) , is a key regulator that suppresses flowering under long-day conditions ( LD... | [
"In rice , flowering time affects the potential yield , the growing season and regional adaptability .",
"Change in day length is a key seasonal cue for regulating flowering time in rice , a facultative short-day ( SD ) plant .",
"The photoperiodic pathway of rice contains the evolutionarily conserved Hd1-Hd3a ... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biology"
] | Role of Pirh2 in Mediating the Regulation of p53 and c-Myc | journal.pgen.1002360 | null | [
[
"Protein ubiquitylation is essential for a broad spectrum of cellular processes including nuclear export , endocytosis , transcriptional regulation , DNA damage repair and proteasomal degradation [1] .",
"Impairment of the ubiquitylation process has been associated with a variety of human diseases includi... | [
"Ubiquitylation is fundamental for the regulation of the stability and function of p53 and c-Myc .",
"The E3 ligase Pirh2 has been reported to polyubiquitylate p53 and to mediate its proteasomal degradation .",
"Here , using Pirh2 deficient mice , we report that Pirh2 is important for the in vivo regulation of ... | [
"Tumor suppressors and oncogenes play critical roles in cancer development .",
"The tumor suppressor p53 and the oncogene c-MYC are among the most frequently deregulated genes in human cancer , and their ubiquitylation mediated by several E3 ligases is critical for their turnover and their functions .",
"P53 ha... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"cell biology/cell growth and division",
"cell biology",
"microbiology/parasitology",
"infectious diseases/protozoal infections",
"cell biology/cytoskeleton"
] | The Transforming Parasite Theileria Co-opts Host Cell Mitotic and Central Spindles to Persist in Continuously Dividing Cells | journal.pbio.1000499 | The transforming protozoan Theileria recruits Plk1, a host kinase that regulates mitosis, to its surface and engages spindle microtubules to secure its division and inheritance into both daughter cells. | [
[
"The apicomplexan parasites Theileria annulata and T . parva are transmitted by ticks and cause severe lymphoproliferative disease in cattle in large areas of Africa , the Middle East , and Asia .",
"The pronounced pathology and high mortality are linked to the ability of Theileria to stimulate the uncont... | [
"The protozoan parasite Theileria inhabits the host cell cytoplasm and possesses the unique capacity to transform the cells it infects , inducing continuous proliferation and protection against apoptosis .",
"The transforming schizont is a multinucleated syncytium that resides free in the host cell cytoplasm and ... | [
"As part of their survival tactics , intracellular parasites often resort to cunning mechanisms to manipulate the cells they inhabit .",
"Theileria , an important and particularly artful parasite of cattle in the tropics , transforms parasitized cells ( that is , it induces continuous proliferation and protection... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Interferon-γ Promotes Inflammation and Development of T-Cell Lymphoma in HTLV-1 bZIP Factor Transgenic Mice | journal.ppat.1005120 | null | [
[
"Human T-cell leukemia virus type 1 ( HTLV-1 ) infects to mainly CD4+ T cells [1] , and the provirus is known to exist in effector/memory T cell and regulatory T cell ( Treg ) subsets [2 , 3] .",
"HTLV-1 induces clonal expansion of infected cells and consequently causes a malignancy of CD4+CD25+ T cells ,... | [
"Human T-cell leukemia virus type 1 ( HTLV-1 ) is an etiological agent of several inflammatory diseases and a T-cell malignancy , adult T-cell leukemia ( ATL ) .",
"HTLV-1 bZIP factor ( HBZ ) is the only viral gene that is constitutively expressed in HTLV-1-infected cells , and it has multiple functions on T-cell... | [
"HTLV-1 is a retrovirus which causes a cancer , ATL , and inflammatory diseases of several tissues , such as the spinal cord , eye , skin , and lung .",
"Although these HTLV-1-mediated malignant and inflammatory diseases are recognized as distinct pathological entities , an increased number of HTLV-1 infected cel... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | A Boolean Function for Neural Induction Reveals a Critical Role of Direct Intercellular Interactions in Patterning the Ectoderm of the Ascidian Embryo | journal.pcbi.1004687 | null | [
[
"In animal embryos , cell-cell interactions directed by secreted and membrane-bound signaling ligands play an important role in establishing specific gene expression patterns .",
"There are 16 ectodermal cells in the animal hemisphere of the 32-cell embryo of the ascidian , Ciona intestinalis , and all 16... | [
"A complex system of multiple signaling molecules often produce differential gene expression patterns in animal embryos .",
"In the ascidian embryo , four signaling ligands , Ephrin-A . d ( Efna . d ) , Fgf9/16/20 , Admp , and Gdf1/3-r , coordinately induce Otx expression in the neural lineage at the 32-cell stag... | [
"It is often difficult to understand a complex system of multiple signaling molecules in animal embryos only with experimental procedures .",
"Although theoretical analysis might solve this problem , it is often difficult to precisely determine parameters for signaling gradients and kinetics of signaling molecule... | 2015 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"sequencing techniques",
"condensed matter physics",
"parasitic protozoans",
"organisms",
"protozoans",
"leishmania",
"molecular biology techniques",
"research and analysis methods",
"sequence analysis",
"artificial gene amplification and extension",
"sequence alignment",
"melting",
"leishma... | High Resolution Melting Analysis Targeting hsp70 as a Fast and Efficient Method for the Discrimination of Leishmania Species | journal.pntd.0004485 | null | [
[
"Leishmaniases are a major worldwide public health problem and manifest themselves as a spectrum of diseases that may be exacerbated by other infections , such as human immunodeficiency virus .",
"According to the World Health Organization , these diseases are endemic in 98 countries on 5 continents , wit... | [
"Protozoan parasites of the genus Leishmania cause a large spectrum of clinical manifestations known as Leishmaniases .",
"These diseases are increasingly important public health problems in many countries both within and outside endemic regions .",
"Thus , an accurate differential diagnosis is extremely releva... | [
"The different clinical forms of the Leishmaniases range from cutaneous to visceral infections and are caused by organisms belonging to the genus Leishmania .",
"Controversy over the validity of different molecular methods to correctly identify a species hinders the association of a given species with different c... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Postnatal Loss of Hap1 Reduces Hippocampal Neurogenesis and Causes Adult Depressive-Like Behavior in Mice | journal.pgen.1005175 | null | [
[
"Depression is the most common mental disorder and a leading cause of disability around the world [1 , 2] .",
"In the US , the lifetime prevalence for major depression is estimated to be as high as 16 . 2% [3] .",
"There are a variety of symptoms associated with depression , including anhedonia , depr... | [
"Depression is a serious mental disorder that affects a person’s mood , thoughts , behavior , physical health , and life in general .",
"Despite our continuous efforts to understand the disease , the etiology of depressive behavior remains perplexing .",
"Recently , aberrant early life or postnatal neurogenesis... | [
"Although the majority of the neurons in the brain are generated during embryonic stage , new neurons are continuously being produced postnatally , and at a much lower rate in adulthood .",
"As postnatal neurogenesis is a key component of the brain maturation process that creates dynamic ‘wirings’ in the brain ne... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine and health sciences",
"enzymes",
"metabolic processes",
"293t cells",
"immunology",
"biological cultures",
"enzymology",
"vertebrates",
"animals",
"mammals",
"plasmid construction",
"primates",
"inflammasomes",
"amniotes",
"dna construction",
"molecular biology techniques",
... | Functional and Evolutionary Analyses Identify Proteolysis as a General Mechanism for NLRP1 Inflammasome Activation | journal.ppat.1006052 | null | [
[
"Mammals have evolved multiple mechanisms to detect microbes in order to initiate immune responses during infection .",
"While both harmless and pathogenic microbes are detected , pathogens generally induce robust responses sufficient to mediate their elimination , whereas commensals trigger milder respon... | [
"Inflammasomes are cytosolic multi-protein complexes that initiate immune responses to infection by recruiting and activating the Caspase-1 protease .",
"Human NLRP1 was the first protein shown to form an inflammasome , but its physiological mechanism of activation remains unknown .",
"Recently , specific varia... | [
"Hosts and their pathogens often engage in evolutionary ‘arms races’ , iterative cycles of adaptation , in which each opponent evolves strategies to overcome the other .",
"For example , the anthrax bacterium overcomes the host immune response by producing lethal factor , a proteolytic enzyme that specifically cl... | 2016 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"blood cells",
"mhc class i genes",
"innate immune system",
"medicine and health sciences",
"antigen presentation",
"immune cells",
"immune physiology",
"statistics",
"immunology",
"neuroscience",
"artificial neural networks",
"clinical medicine",
"mathematics",
"forecasting",
"artificia... | Systematically benchmarking peptide-MHC binding predictors: From synthetic to naturally processed epitopes | journal.pcbi.1006457 | null | [
[
"The increasing wealth of immunogenomic information generated by next-generation sequencing ( NGS ) technologies is boosting the application of cancer immunotherapy that takes full advantage of individual’s adaptive immunity by administrating personalized cancer vaccines .",
"[1–3] An essential step in pr... | [
"A number of machine learning-based predictors have been developed for identifying immunogenic T-cell epitopes based on major histocompatibility complex ( MHC ) class I and II binding affinities .",
"Rationally selecting the most appropriate tool has been complicated by the evolving training data and machine lear... | [
"Computationally predicting antigen peptide sequences that elicit T-cell immune response has broad and significant impact on vaccine design .",
"The most widely accepted approach is to rely on machine learning classifier , trained on large-scale major-histocompatibility complex ( MHC ) -binding peptide dataset ."... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"medicine and health sciences",
"diagnostic radiology",
"functional magnetic resonance imaging",
"neural networks",
"brain electrophysiology",
"social sciences",
"electrophysiology",
"neuroscience",
"magnetic resonance imaging",
"perception",
"clinical medicine",
"cognitive psychology",
"bra... | Perceptual inference employs intrinsic alpha frequency to resolve perceptual ambiguity | journal.pbio.3000025 | Electroencephalography, intracranial recording, and fMRI measurements of the human brain reveal how perceptual inference employs intrinsic brain activity to bias the perception of ambiguous sensory information towards predicted percepts. | [
[
"The brain is increasingly being understood as engaged in probabilistic unconscious perceptual inference to actively predict and explain observed sensory inputs , which helps to resolve ambiguity in sensory signals [1–6] .",
"Therefore , our perception of the world is not simply based on our sensory input... | [
"The brain uses its intrinsic dynamics to actively predict observed sensory inputs , especially under perceptual ambiguity .",
"However , it remains unclear how this inference process is neurally implemented in biasing perception of ambiguous inputs towards the predicted percepts .",
"The process of perceptual ... | [
"Our subjective perception of the external world is constantly shaped not only by sensory inputs but also by the real-time internal status of our own brain .",
"Upon facing an ambiguous sensory input , our brain employs its intrinsic dynamics to bias perception towards the predicted percept , resolving in this ma... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genome-wide association studies",
"urology",
"medicine and health sciences",
"pathology and laboratory medicine",
"cervical cancer",
"pathogens",
"immunology",
"cancers and neoplasms",
"microbiology",
"genetic mapping",
"oncology",
"viruses",
"clinical medicine",
"linkage disequilibrium",... | Defining the genetic susceptibility to cervical neoplasia—A genome-wide association study | journal.pgen.1006866 | null | [
[
"Cervical cancer remains a major cause of female mortality worldwide , particularly in developing countries that have limited screening programs [1] .",
"Only a small fraction ( ~1% ) of women with cervical human papillomavirus ( HPV ) infection go on to develop cervical neoplasia [2] , and the factors de... | [
"A small percentage of women with cervical HPV infection progress to cervical neoplasia , and the risk factors determining progression are incompletely understood .",
"We sought to define the genetic loci involved in cervical neoplasia and to assess its heritability using unbiased unrelated case/control statistic... | [
"Around 1% of women with cervical human papillomavirus ( HPV ) infection progress to cervical cancer .",
"Previous studies had indicated that a person’s genetic makeup could predispose to HPV-associated cervical cancer , and that some of the genes likely to be involved include the immune-related human leukocyte a... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genome expression analysis",
"organismal evolution",
"botany",
"crop genetics",
"plant science",
"crops",
"plant genomics",
"fibers",
"gene expression",
"plant genetics",
"ethnobotany",
"comparative genomics",
"biology",
"evolutionary genetics",
"cotton",
"agriculture",
"plant evolu... | Comparative Evolutionary and Developmental Dynamics of the Cotton (Gossypium hirsutum) Fiber Transcriptome | journal.pgen.1004073 | null | [
[
"Ever since Darwin's time , biologists have recognized that human domestication of wild plants and animals offers promising opportunities for enhancing our understanding of the evolutionary process .",
"As highlighted in recent reviews [1] , [2] , comparisons among wild and domesticated forms of crop plan... | [
"The single-celled cotton ( Gossypium hirsutum ) fiber provides an excellent model to investigate how human selection affects phenotypic evolution .",
"To gain insight into the evolutionary genomics of cotton domestication , we conducted comparative transcriptome profiling of developing cotton fibers using RNA-Se... | [
"Ever since Darwin biologists have recognized that comparative study of crop plants and their wild relatives offers a powerful framework for generating insights into the mechanisms that underlie evolutionary change .",
"Here , we study the domestication process in cotton , Gossypium hirsutum , an allopolyploid sp... | 2014 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [] | Functional Activity Limitation and Quality of Life of Leprosy Cases in an Endemic Area in Northeastern Brazil | journal.pntd.0003900 | null | [
[
"Leprosy is still a neglected public health problem with at least 200 , 000 new cases diagnosed annually worldwide .",
"The highest prevalence occurs in low and middle income countries such as India , Brazil , Myanmar , Madagascar , Nepal , and Mozambique [1] .",
"This chronic and insidious infection ... | [
"Few studies have evaluated the association between quality of life ( QoL ) and functional activity limitations ( FAL ) of leprosy patients as determined by the Screening of Activity Limitation and Safety Awareness scale ( SALSA ) .",
"To identify the association between FALs and the QoL of patients during and po... | [
"Leprosy is still a neglected public health problem .",
"Leprosy causes disability and functional limitations ( FALs ) if not treated early .",
"We describe the functional activity and quality of life ( QoL ) of adults with leprosy attending two reference centres in Sergipe , Brazil .",
"Patients with leprosy... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"medicine and health sciences",
"peroxidases",
"body fluids",
"pathology and laboratory medicine",
"molecular probe techniques",
"enzymes",
"pathogens",
"microbiology",
"enzymology",
"immunoblotting",
"pseudomonas aeruginosa",
"animal models",
"model organisms",
"experimental organism syst... | Peroxidasin contributes to lung host defense by direct binding and killing of gram-negative bacteria | journal.ppat.1007026 | null | [
[
"The lung is exposed to a constant barrage of inhaled harmful agents and microorganisms .",
"Several layers of defense in the normal lung help prevent infection from inhaled or aspirated microorganisms .",
"These include the mechanical filtering of particles that occur in the nasal airway , the trappi... | [
"Innate immune recognition is classically mediated by the interaction of host pattern-recognition receptors and pathogen-associated molecular patterns; this triggers a series of downstream signaling events that facilitate killing and elimination of invading pathogens .",
"In this report , we provide the first evi... | [
"Multicellular organisms have evolved diversified host defense mechanisms for survival against invading pathogens .",
"Of the mechanisms , the recognition of pathogens is classically mediated by the interaction of host and pathogen , which triggers a series of downstream responses to eliminate pathogens .",
"Pr... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"biofilms",
"blood cells",
"medicine and health sciences",
"immune cells",
"pathology and laboratory medicine",
"gene regulation",
"pathogens",
"immunology",
"microbiology",
"fungi",
"experimental organism systems",
"fungal pathogens",
"research and analysis methods",
"mycology",
"white ... | Functional diversification accompanies gene family expansion of MED2 homologs in Candida albicans | journal.pgen.1007326 | null | [
[
"Changes in gene copy number provide a rapid mechanism of adaptation to new or different environments by utilizing available functional sequences to cope with altered conditions .",
"Gene duplication commonly arises through errors in DNA replication or sister chromatid recombination to produce a second id... | [
"Gene duplication facilitates functional diversification and provides greater phenotypic flexibility to an organism .",
"Expanded gene families arise through repeated gene duplication but the extent of functional divergence that accompanies each paralogous gene is generally unexplored because of the difficulty in... | [
"Gene duplication is a rapid mechanism to generate additional sequences for natural selection to act upon and confer greater organismal fitness .",
"If additional copies of the gene are beneficial , this process may be repeated to produce an expanded gene family containing many copies of related sequences .",
"... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"deletion mutation",
"genetic networks",
"chromosome structure and function",
"telomeres",
"mutation",
"fungi",
"model organisms",
"network analysis",
"experimental organism systems",
"research and analysis methods",
"saccharomyces",
"telomere length",
"computer and information sciences",
... | Cdc73 suppresses genome instability by mediating telomere homeostasis | journal.pgen.1007170 | null | [
[
"Gross chromosomal rearrangements ( GCRs ) , such as translocations and deletions , are common in many cancers [1] .",
"DNA repair and DNA damage signaling defects that cause increased rates of accumulating GCRs in model systems like Saccharomyces cerevisiae have been identified in sporadic tumors and in ... | [
"Defects in the genes encoding the Paf1 complex can cause increased genome instability .",
"Loss of Paf1 , Cdc73 , and Ctr9 , but not Rtf1 or Leo1 , caused increased accumulation of gross chromosomal rearrangements ( GCRs ) .",
"Combining the cdc73Δ mutation with individual deletions of 43 other genes , includi... | [
"Maintaining a stable genome is crucial for all organisms , and loss of genome stability has been linked to multiple human diseases , including many cancers .",
"Previously we found that defects in Cdc73 , a component of the Paf1 transcriptional elongation complex , give rise to increased genome instability .",
... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"immunology",
"biology"
] | Memory Phenotype CD4 T Cells Undergoing Rapid, Nonburst-Like, Cytokine-Driven Proliferation Can Be Distinguished from Antigen-Experienced Memory Cells | journal.pbio.1001171 | Contrary to the current paradigm that nearly all memory T cells proliferate in response to antigenic stimulation, this paper shows that an important population of CD4 T lymphocytes achieves memory/effector status independent of antigenic stimulation. | [
[
"Peripheral non-Treg CD4+ T cells are often divided into two major subpopulations that can be designated naïve-phenotype ( NP ) and memory-phenotype ( MP ) cells , respectively [1] .",
"In the mouse , MP cells are characterized by the expression of high levels of CD44 and low levels of CD45RB; they lack F... | [
"Memory phenotype ( CD44bright , CD25negative ) CD4 spleen and lymph node T cells ( MP cells ) proliferate rapidly in normal or germ-free donors , with BrdU uptake rates of 6% to 10% per day and Ki-67 positivity of 18% to 35% .",
"The rapid proliferation of MP cells stands in contrast to the much slower prolifera... | [
"The class of immune cells called CD4 T lymphocytes consists of two major cell types: naïve cells that have not yet participated in an immune response and memory cells , which are cells that have responded to antigen , expanded in number , and acquired new characteristics .",
"These two cell types can be distingu... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"learning",
"neural networks",
"engineering and technology",
"signal processing",
"social sciences",
"vertebrates",
"neuroscience",
"learning and memory",
"animals",
"mammals",
"simulation and modeling",
"primates",
"cognitive psychology",
"cognition",
"network analysis",
"research and... | Learning to synchronize: How biological agents can couple neural task modules for dealing with the stability-plasticity dilemma | journal.pcbi.1006604 | null | [
[
"Humans and other primates are remarkably flexible in adapting to constantly changing environments .",
"Additionally , they excel at integrating information in the long run to detect regularities in the environment and generalize across contexts .",
"In contrast , artificial neural networks ( ANN ) , ... | [
"We provide a novel computational framework on how biological and artificial agents can learn to flexibly couple and decouple neural task modules for cognitive processing .",
"In this way , they can address the stability-plasticity dilemma .",
"For this purpose , we combine two prominent computational neuroscie... | [
"Artificial and biological agents alike face a critical trade-off between being sufficiently adaptive to acquiring novel information ( plasticity ) and retaining older information ( stability ) ; this is known as the stability-plasticity dilemma .",
"Previous work on this dilemma has focused either on computation... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"biology"
] | A Natural System of Chromosome Transfer in Yersinia pseudotuberculosis | journal.pgen.1002529 | null | [
[
"Horizontal gene transfer ( HGT ) is a driving force for bacterial evolution , as it allows the dispersion of adaptive loci between closely related and also phylogenetically distant bacterial species .",
"Well-characterized mobile genetic elements such as conjugative plasmids , transposons , Integrative c... | [
"The High Pathogenicity Island of Yersinia pseudotuberculosis IP32637 was previously shown to be horizontally transferable as part of a large chromosomal segment .",
"We demonstrate here that at low temperature other chromosomal loci , as well as a non-mobilizable plasmid ( pUC4K ) , are also transferable .",
"... | [
"All living species have the capacity to evolve in order to adapt to new and often hostile conditions .",
"Horizontal gene transfer is a major route for rapid bacterial evolution .",
"Some clearly identified mobile genetic elements ( plasmids , phages , etc . ) are by essence exchanged between bacteria .",
"H... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biomacromolecule-ligand interactions",
"medicine",
"streptococci",
"microbiology",
"bacterial diseases",
"protein structure",
"bacterial pathogens",
"animal models of infection",
"infectious diseases",
"virulence factors and mechanisms",
"proteins",
"biology",
"biophysics",
"streptococcal... | A Structural Model for Binding of the Serine-Rich Repeat Adhesin GspB to Host Carbohydrate Receptors | journal.ppat.1002112 | null | [
[
"The serine-rich repeat ( SRR ) glycoproteins of Gram-positive bacteria are an expanding family of microbial adhesins and virulence factors [1]–[6] .",
"These proteins consist of a distinctive signal sequence and export-targeting region at the N-terminus , a short SRR region ( ∼50–170 amino acids ) , a li... | [
"GspB is a serine-rich repeat ( SRR ) adhesin of Streptococcus gordonii that mediates binding of this organism to human platelets via its interaction with sialyl-T antigen on the receptor GPIbα .",
"This interaction appears to be a major virulence determinant in the pathogenesis of infective endocarditis .",
"T... | [
"The binding of bacteria to human platelets is thought to be important for development of infective endocarditis , a life-threatening infection of the cardiovascular system .",
"Streptococcus gordonii is a leading cause of endocarditis .",
"This pathogen uses a protein called GspB to attach to carbohydrates on ... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"infectious diseases",
"cell biology/cell signaling",
"cell biology",
"cell biology/membranes and sorting",
"infectious diseases/bacterial infections",
"cell biology/cell adhesion",
"infectious diseases/gastrointestinal infections"
] | Listeria monocytogenes Internalin B Activates Junctional Endocytosis to Accelerate Intestinal Invasion | journal.ppat.1000900 | null | [
[
"Listeria monocytogenes ( Lm ) is a potentially deadly food-borne pathogen that colonizes the gastrointestinal tract of several mammalian species , and can also cause invasive disease and systemic spread if it crosses the intestinal epithelial barrier [1] .",
"Lm evolved two major molecular invasion prote... | [
"Listeria monocytogenes ( Lm ) uses InlA to invade the tips of the intestinal villi , a location at which cell extrusion generates a transient defect in epithelial polarity that exposes the receptor for InlA , E-cadherin , on the cell surface .",
"As the dying cell is removed from the epithelium , the surrounding... | [
"The anatomical context in which attachment and invasion factors find host receptors determines when and where microbes can colonize and invade .",
"For example , Listeria monocytogenes ( Lm ) , a cause of human and animal food-borne disease , invades the villous epithelium only at the intestinal villus tips wher... | 2010 |
[
"Introduction",
"Methods"
] | [
"medicine and health sciences",
"cost-effectiveness analysis",
"economic analysis",
"tropical diseases",
"social sciences",
"parasitic diseases",
"health care",
"research design",
"global health",
"neglected tropical diseases",
"research and analysis methods",
"public and occupational health",... | Evaluating the sustainability, scalability, and replicability of an STH transmission interruption intervention: The DeWorm3 implementation science protocol | journal.pntd.0005988 | null | [
[
"DeWorm3 is a series of cluster randomized trials evaluating the feasibility of interrupting transmission of STH using biannual ( twice annually ) community-wide MDA targeting eligible community members of all ages .",
"Additionally , DeWorm3 aims to assess the relative influence of community-wide MDA on ... | [
"Hybrid trials that include both clinical and implementation science outcomes are increasingly relevant for public health researchers that aim to rapidly translate study findings into evidence-based practice .",
"The DeWorm3 Project is a series of hybrid trials testing the feasibility of interrupting the transmis... | [
"The DeWorm3 Project is a series of randomized clinical trials testing the feasibility of interrupting the transmission of soil-transmitted helminths .",
"We have integrated implementation science research questions into the trials in order to optimize delivery of trial interventions as well as to speed the trans... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"meiosis",
"developmental biology",
"embryology",
"aneuploidy",
"genomics",
"telomeres",
"chromosomal disorders",
"chromosome biology",
"genetics",
"biology",
"human genetics",
"genetics and genomics"
] | Telomere DNA Deficiency Is Associated with Development of Human Embryonic Aneuploidy | journal.pgen.1002161 | null | [
[
"Gain or loss of an entire chromosome ( aneuploidy ) is the most common genetic cause of miscarriage and developmental delay in humans .",
"Advanced maternal age is a well known risk factor and a reflection of the observation that aneuploidy primarily arises during meiosis of the maternal gamete , the ooc... | [
"Aneuploidy represents the most prevalent form of genetic instability found in human embryos and is the leading genetic cause of miscarriage and developmental delay in newborns .",
"Telomere DNA deficiency is associated with genomic instability in somatic cells and may play a role in development of aneuploidy com... | [
"Human eggs ( oocytes ) are exceptionally prone to the erroneous acquisition of too few ( monosomy ) or too many ( trisomy ) chromosomes during development ( meiosis ) .",
"In fact , this type of instability , termed aneuploidy , represents the most common genetic cause of miscarriage in pregnant women ( i . e . ... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Synergistic and Dose-Controlled Regulation of Cellulase Gene Expression in Penicillium oxalicum | journal.pgen.1005509 | null | [
[
"Cellulolytic fungi have an inherent characteristic of cellulose deconstruction and can be used for bioconversion of insoluble plant cell wall polysaccharides into fermentable sugars [1–3] .",
"The highly efficient production of their extracellular hydrolytic enzymes and other synergistic proteins [2 , 4]... | [
"Filamentous fungus Penicillium oxalicum produces diverse lignocellulolytic enzymes , which are regulated by the combinations of many transcription factors .",
"Here , a single-gene disruptant library for 470 transcription factors was constructed and systematically screened for cellulase production .",
"Twenty ... | [
"Cellulolytic fungi have evolved into sophisticated lignocellulolytic systems to adapt to their natural habitat .",
"This trait is important for filamentous fungi , which are the main source of cellulases utilized to degrade lignocellulose to fermentable sugars .",
"Penicillium oxalicum , which produces lignoce... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"viral entry",
"transposons",
"molecular cell biology",
"retrotransposons",
"viral transmission and infection",
"virology",
"biology",
"microbiology",
"host-pathogen interaction",
"molecular biology"
] | The Mouse IAPE Endogenous Retrovirus Can Infect Cells through Any of the Five GPI-Anchored EphrinA Proteins | journal.ppat.1002309 | null | [
[
"Mammalian genomes are filled with numerous copies of mobile genetic elements .",
"Among them , endogenous retroviruses are the remnants of infectious retroviruses that once infected the germline of their host and have since then been transmitted from one generation to the other following a mendelian patt... | [
"The IAPE ( Intracisternal A-type Particles elements with an Envelope ) family of murine endogenous retroelements is present at more than 200 copies in the mouse genome .",
"We had previously identified a single copy that proved to be fully functional , i . e . which can generate viral particles budding out of th... | [
"In mammals , nearly half the genome is composed of reiterated scattered sequences .",
"Some of them , called endogenous retroviruses , have a structure similar to that observed for the integrated form of infectious retroviruses .",
"The current theory to account for their presence is that an infectious retrovi... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Methods and Models"
] | [] | On the Adjacency Matrix of RyR2 Cluster Structures | journal.pcbi.1004521 | null | [
[
"Mechanical contraction of the heart occurs as a result of intracellular Ca2+ release in cardiac myocytes .",
"L-type Ca2+ channels ( LCCs ) and a packed cluster of up to 100 Ca2+-sensitive Ca2+-release channels [1 , 2] , known as ryanodine receptors ( RyR2s ) , are co-located at discrete subcellular junc... | [
"In the heart , electrical stimulation of cardiac myocytes increases the open probability of sarcolemmal voltage-sensitive Ca2+ channels and flux of Ca2+ into the cells .",
"This increases Ca2+ binding to ligand-gated channels known as ryanodine receptors ( RyR2 ) .",
"Their openings cause cell-wide release of ... | [
"Many transmembrane receptors have been shown to aggregate into supramolecular clusters that enhance sensitivity to external stimuli in a variety of cell types .",
"Advances in super-resolution microscopy have enabled researchers to study these structures with sufficient detail to distinguish the precise location... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"cell death",
"medicine and health sciences",
"immune physiology",
"pathology and laboratory medicine",
"nervous system",
"astrocytes",
"pathogens",
"cell processes",
"immunology",
"microbiology",
"neuroscience",
"macroglial cells",
"viruses",
"rna viruses",
"antibodies",
"immune syste... | Deleterious effect of Usutu virus on human neural cells | journal.pntd.0005913 | null | [
[
"The recent Zika virus ( ZIKV ) outbreak has reminded us that the emergence of new viruses depends on multiple factors and is therefore extremely difficult to predict .",
"Among potential emerging viruses , Usutu virus ( USUV ) has recently focused attention .",
"USUV is an African mosquito-borne viru... | [
"In the last decade , the number of emerging Flaviviruses described worldwide has increased considerably .",
"Among them Zika virus ( ZIKV ) and Usutu virus ( USUV ) are African mosquito-borne viruses that recently emerged .",
"Recently , ZIKV has been intensely studied due to major outbreaks associated with ne... | [
"Usutu virus ( USUV ) is an African mosquito-borne virus closely related to West Nile virus and belongs to the Japanese encephalitis virus serogroup in the Flavivirus genus .",
"Recently several neurological disorders such as encephalitis , meningitis and meningoencephalitis were associated with USUV-infection in... | 2017 |
[
"Introduction",
"Methods"
] | [
"medicine and health sciences",
"ocular anatomy",
"alleles",
"cell differentiation",
"animal models",
"developmental biology",
"model organisms",
"experimental organism systems",
"biometrics",
"eyes",
"research and analysis methods",
"myopia",
"mouse models",
"head",
"genetic loci",
"v... | Müller glia-derived PRSS56 is required to sustain ocular axial growth and prevent refractive error | journal.pgen.1007244 | null | [
[
"The molecular and cellular mechanisms involved in ocular size regulation and refractive development are poorly understood .",
"Here , we have used a combination of genetic mouse models to elucidate the role of PRSS56 in ocular axial growth .",
"We show that loss of PRSS56 function causes ocular axial... | [
"A mismatch between optical power and ocular axial length results in refractive errors .",
"Uncorrected refractive errors constitute the most common cause of vision loss and second leading cause of blindness worldwide .",
"Although the retina is known to play a critical role in regulating ocular growth and refr... | [
"Refractive errors mainly occur when changes in ocular size ( ocular axial length ) prevent light from focusing directly on the retina .",
"Myopia ( nearsightedness ) is the most common form of refractive errors in which the focused image falls in front of the retina .",
"The recent unprecedented rise in the in... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | The Relationship between Gene Network Structure and Expression Variation among Individuals and Species | journal.pgen.1005398 | null | [
[
"Phenotypic variation within populations is a prerequisite of evolution by natural selection , and in theory has the potential to bias the trajectory and rate of evolutionary change [1–6] .",
"As such , identifying the processes that shape phenotypic variation has long been a fundamental pursuit of evolut... | [
"Variation among individuals is a prerequisite of evolution by natural selection .",
"As such , identifying the origins of variation is a fundamental goal of biology .",
"We investigated the link between gene interactions and variation in gene expression among individuals and species using the mammalian limb as... | [
"The variation generating mechanisms of development interact with the variation sorting mechanism of natural selection to produce organismal diversity .",
"While the impacts of natural selection on existing variation have received much study , those of development on the generation of this variation remain less u... | 2015 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"antiviral immune response",
"protein interactions",
"molecular probe techniques",
"immunology",
"immunoblotting",
"microbiology",
"chaperone proteins",
"mitochondria",
"molecular biology techniques",
"bioenergetics",
"microbial genetics",
"cellular structures... | The 14-3-3η chaperone protein promotes antiviral innate immunity via facilitating MDA5 oligomerization and intracellular redistribution | journal.ppat.1007582 | null | [
[
"Among the RIG-I-like Receptor ( RLR ) family , RIG-I and MDA5 share a number of structural similarities , and both of them include three distinct domains .",
"The N-terminus caspase activation and recruitment domains ( CARDs ) function as the activation domain to directly interact with the CARD of downst... | [
"MDA5 belongs to the RIG-I-like receptor family and plays a non-redundant role in recognizing cytoplasmic viral RNA to induce the production of type I IFNs .",
"Upon RNA ligand stimulation , we observed the redistribution of MDA5 from the cytosol to mitochondrial membrane fractions .",
"However , the molecular ... | [
"In this study , we utilized biochemistry and molecular biology approaches to defines the molecular mechanisms by which melanoma differentiation-associated protein 5 ( MDA5 ) , a cytoplasmic RNA helicase and pattern recognition receptor molecule , is regulated by 14-3-3η to govern its innate immune signaling activi... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"genetics of the immune system",
"clinical immunology",
"chronic kidney disease",
"autoimmune diseases",
"immunology",
"nephrology"
] | Geographic Differences in Genetic Susceptibility to IgA Nephropathy: GWAS Replication Study and Geospatial Risk Analysis | journal.pgen.1002765 | null | [
[
"IgA nephropathy ( IgAN ) is a common kidney disease with a complex genetic determination .",
"This disorder is diagnosed based on detection of mesangial proliferation and glomerular deposits of IgA1 .",
"Most frequently , IgAN has a progressing course and 20–50% of cases develop end-stage renal disea... | [
"IgA nephropathy ( IgAN ) , major cause of kidney failure worldwide , is common in Asians , moderately prevalent in Europeans , and rare in Africans .",
"It is not known if these differences represent variation in genes , environment , or ascertainment .",
"In a recent GWAS , we localized five IgAN susceptibili... | [
"IgA nephropathy ( IgAN ) is the most common cause of kidney failure in Asia , has lower prevalence in Europe , and is very infrequent among populations of African ancestry .",
"A long-standing question in the field is whether these differences represent variation in genes , environment , or ascertainment .",
"... | 2012 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"blood cells",
"sequencing techniques",
"medicine and health sciences",
"immune cells",
"immune physiology",
"chemical compounds",
"statistics",
"immunology",
"organic compounds",
"mutation",
"substitution mutation",
"mathematics",
"forecasting",
"amino acid substitution",
"amino acids",... | Predicting B cell receptor substitution profiles using public repertoire data | journal.pcbi.1006388 | null | [
[
"In the therapeutic antibody discovery and engineering field , researchers commonly isolate antibodies from animal or human immunizations and screen for functional properties such as binding to a target protein .",
"Following the initial screening process , a small number of well-behaving antibodies ( hit... | [
"B cells develop high affinity receptors during the course of affinity maturation , a cyclic process of mutation and selection .",
"At the end of affinity maturation , a number of cells sharing the same ancestor ( i . e . in the same “clonal family” ) are released from the germinal center; their amino acid freque... | [
"Antibody engineering can be greatly informed by knowledge about the underlying affinity maturation process .",
"As such this can be probed by sequencing , but unfortunately , in practice often only one member of the clonal family is sequenced , making it difficult to determine a set of possible amino acid mutati... | 2018 |
[
"Introduction",
"Results/Discussion",
"Materials and Methods"
] | [
"medicine",
"influenza",
"immunity to infections",
"immunology",
"immunoregulation",
"immunomodulation",
"infectious diseases",
"inflammation",
"biology",
"immune response",
"clinical immunology",
"immunity",
"sars",
"viral diseases"
] | CD200 Receptor Controls Sex-Specific TLR7 Responses to Viral Infection | journal.ppat.1002710 | null | [
[
"To generate an appropriately controlled response during infections , the immune system is balanced by the action of activating and inhibitory receptors .",
"Lack of inhibition leads to excessive inflammation and autoimmunity and other severe disease symptoms .",
"One of the receptors regulating this ... | [
"Immunological checkpoints , such as the inhibitory CD200 receptor ( CD200R ) , play a dual role in balancing the immune system during microbial infection .",
"On the one hand these inhibitory signals prevent excessive immune mediated pathology but on the other hand they may impair clearance of the pathogen .",
... | [
"Immune responses need to be carefully orchestrated to prevent disease due to an overactive immune system .",
"Immunological checkpoints are provided by immune inhibitory receptors , which set a threshold for activation and dampen the immune system .",
"In the case of a viral infection , this prevents pathology... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"developmental biology/stem cells",
"developmental biology/developmental evolution",
"developmental biology/pattern formation",
"neuroscience/neurodevelopment",
"developmental biology/neurodevelopment",
"developmental biology/molecular development",
"developmental biology/organogenesis"
] | Prox1 Is Required for Granule Cell Maturation and Intermediate Progenitor Maintenance During Brain Neurogenesis | journal.pbio.1000460 | The transcription factor Prox1 plays a crucial role in intermediate progenitor maintenance and hippocampal neuron differentiation during adult neurogenesis in the dentate gyrus region of the hippocampus. | [
[
"In the brain , the dentate gyrus ( DG ) is the primary afferent pathway into the hippocampus .",
"The DG has a crucial role in learning and memory [1] , [2] , [3] .",
"In mammals , neurogenesis occurs in the subgranular zone ( SGZ ) of the DG throughout adulthood [4] , [5] , [6] , [7]; this activity ... | [
"The dentate gyrus has an important role in learning and memory , and adult neurogenesis in the subgranular zone of the dentate gyrus may play a role in the acquisition of new memories .",
"The homeobox gene Prox1 is expressed in the dentate gyrus during embryonic development and adult neurogenesis .",
"Here we... | [
"In the brain , the hippocampus has a crucial role in learning and memory .",
"In mammals , neurogenesis ( the birth of new neurons ) occurs in the dentate gyrus region of the hippocampus throughout adulthood , and this activity is thought to be the basis for the acquisition of new memories .",
"In this study w... | 2010 |
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