headings list | keywords list | title stringlengths 20 281 | id stringlengths 20 20 | toc stringlengths 57 522 ⌀ | sections list | abstract list | summary list | year stringclasses 13
values |
|---|---|---|---|---|---|---|---|---|
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"blood cells",
"medicine and health sciences",
"neurochemistry",
"immune cells",
"pathology and laboratory medicine",
"intracellular pathogens",
"pathogens",
"immunology",
"microbiology",
"neuroscience",
"salmonellosis",
"bacterial diseases",
"enterobacteriaceae",
"cytotoxic t cells",
"b... | Salmonella escapes adaptive immune response via SIRT2 mediated modulation of innate immune response in dendritic cells | journal.ppat.1007437 | null | [
[
"Sirtuins are a family of proteins originally discovered in yeast as a homolog to silent information regulator 2 gene ( Sir2 ) .",
"Pioneering studies on Sir2 in Saccharomyces cerevisiae demonstrate its deacetylase function which is essential for silencing transcription at silent mating loci , telomeres a... | [
"Salmonella being a successful pathogen , employs a plethora of immune evasion mechanisms .",
"This contributes to pathogenesis , persistence and also limits the efficacy of available treatment .",
"All these contributing factors call upon for new drug targets against Salmonella .",
"For the first time , we h... | [
"Salmonella enterica is the cause of infectious diseases which ranges from self-limiting diarrhoea to fatal systemic illness like typhoid .",
"During its pathogenesis , Salmonella survives inside dendritic cells ( DCs ) by suppressing antigen presentation , thereby successfully evading host response .",
"Althou... | 2018 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"molecular biology/bioinformatics",
"infectious diseases/helminth infections",
"microbiology/parasitology"
] | Gene Atlasing of Digestive and Reproductive Tissues in
Schistosoma mansoni | journal.pntd.0001043 | null | [
[
"The last decade has seen an exponential growth in the availability of genomic and",
"proteomic data for Schistosoma mansoni and S .",
"japonicum through genomic sequencing projects [1] , [2] and numerous transcriptomic",
"and proteomic studies [3] , [4] , [5] , [6] , [7] , [8] , [9] .",
"Howe... | [
"While considerable genomic and transcriptomic data are available for",
"Schistosoma mansoni , many of its genes lack significant",
"annotation .",
"A transcriptomic study of individual tissues and organs of",
"schistosomes could play an important role in functional annotation of the",
"unknown genes , pa... | [
"There is currently only one drug available for treatment of",
"schistosomiasis mansoni and no vaccine .",
"The searches for",
"possible new drug and vaccine candidates remain two major areas of current",
"research in schistosomiasis .",
"There are considerable amounts of data available on",
"the genomi... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Model"
] | [
"computational biology/population genetics",
"computational biology/macromolecular structure analysis",
"biophysics/theory and simulation",
"computational biology/evolutionary modeling",
"evolutionary biology",
"computational biology/systems biology"
] | Interplay between Pleiotropy and Secondary Selection Determines Rise and Fall of Mutators in Stress Response | journal.pcbi.1000710 | null | [
[
"Bacterial populations often respond to various stresses by inducing mutagenesis whereby mutator clones rise to fixation , at least transiently , during adaptation to stressful environments [1]–[5] .",
"The rise of mutator clones has been observed as a universal response regardless of the nature of stress... | [
"Mutators are clones whose mutation rate is about two to three orders of magnitude higher than the rate of wild-type clones and their roles in adaptive evolution of asexual populations have been controversial .",
"Here we address this problem by using an ab initio microscopic model of living cells , which combine... | [
"The dramatic rise of mutators has been found to accompany adaptation of bacteria in response to many kinds of stress .",
"Two views on the evolutionary origin of this phenomenon emerged: the pleiotropic hypothesis positing that it is a byproduct of environmental stress or other specific stress response mechanism... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biotechnology",
"developmental biology",
"plant science",
"cell biology",
"genetics",
"biology and life sciences",
"molecular cell biology",
"agricultural biotechnology",
"agricultural production",
"agriculture"
] | Interaction between Two Timing MicroRNAs Controls Trichome Distribution in Arabidopsis | journal.pgen.1004266 | null | [
[
"MicroRNA ( miRNA ) was first identified as the regulator of the juvenile-to-adult transition in Caenorhabditis elegans [1] , and a similar function was later assigned to plant miRNA: miR156 and its target SQUAMOSA PROMOTER BINDING PROTEIN LIKE ( SPL ) genes define an endogenous aging and flowering pathway [2... | [
"The miR156-targeted SQUAMOSA PROMOTER BINDING PROTEIN LIKE ( SPL ) transcription factors function as an endogenous age cue in regulating plant phase transition and phase-dependent morphogenesis , but the control of SPL output remains poorly understood .",
"In Arabidopsis thaliana the spatial pattern of trichome ... | [
"MicroRNAs are important aging regulators in many organisms .",
"In Arabidopsis the miR156-targeted SQUAMOSA PROMOTER BINDING PROTEIN LIKE ( SPL ) transcription factors play important roles as an endogenous age cue in programming phase transition and phase-dependent morphogenesis , including trichome patterning .... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Inactivation of Intergenic Enhancers by EBNA3A Initiates and Maintains Polycomb Signatures across a Chromatin Domain Encoding CXCL10 and CXCL9 | journal.ppat.1003638 | null | [
[
"Epstein Barr virus ( EBV ) is a ubiquitous human herpesvirus that establishes a persistent latent infection in more than 90% of the adult human population .",
"EBV can cause infectious mononucleosis and is associated with the pathogenesis of endemic Burkitt's lymphoma , Hodgkin lymphoma , lymphoprolifera... | [
"Epstein-Barr virus ( EBV ) causes a persistent infection in human B cells by establishing specific transcription programs to control B cell activation and differentiation .",
"Transcriptional reprogramming of EBV infected B cells is predominantly driven by the action of EBV nuclear antigens , among them the tran... | [
"Epstein-Barr virus ( EBV ) is a γ-herpesvirus which establishes a latent infection in human B cells and is associated with the pathogenesis of several types of cancer .",
"Here , we report that cellular genes repressed by the EBV nuclear antigen 3A ( EBNA3A ) in EBV infected B cells frequently form contiguous cl... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"blood cells",
"trypanosoma cruzi",
"white blood cells",
"trypanosoma",
"immune cells",
"protozoans",
"cell biology",
"animal cells",
"t cells",
"cellular types",
"biology and life sciences",
"cell processes",
"macrophages",
"parasitic protozoans",
"phagocytosis",
"organisms"
] | P47phox−/− Mice Are Compromised in Expansion and Activation of CD8+ T Cells and Susceptible to Trypanosoma cruzi Infection | journal.ppat.1004516 | null | [
[
"Chagas disease is caused by the protozoan Trypanosoma cruzi [1] , [2] .",
"During acute phase of infection , parasites can be found in the circulating blood , and host may develop fever or swelling around the site of inoculation , and rarely , severe inflammation in heart muscle or brain .",
"Several... | [
"Macrophage activation of NAD ( P ) H oxidase ( NOX2 ) and reactive oxygen species ( ROS ) is suggested to kill Trypanosoma cruzi that causes Chagas disease .",
"However , the role of NOX2 in generation of protective immunity and whether these mechanisms are deregulated in the event of NOX2 deficiency are not kno... | [
"Macrophage activation of NADPH oxidase NOX2 ) and reactive oxygen species ( ROS ) is suggested to mediate control of Trypanosoma cruzi infection that is the causative agent of Chagas disease .",
"However , how NOX2/ROS deficiency affects parasite persistence and chronic disease is not known .",
"In this study ... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Models"
] | [
"biology and life sciences",
"evolutionary adaptation",
"population genetics",
"evolutionary theory",
"evolutionary biology",
"evolutionary processes"
] | Multidimensional Epistasis and the Transitory Advantage of Sex | journal.pcbi.1003836 | null | [
[
"Sexual reproduction is a phenomenon that has existed for more than one billion years [1] .",
"It is widespread in nature , which means that it must be advantageous compared to asexual reproduction , at least under certain conditions .",
"Nevertheless , it is not well understood why this should be the... | [
"Identifying and quantifying the benefits of sex and recombination is a long-standing problem in evolutionary theory .",
"In particular , contradictory claims have been made about the existence of a benefit of recombination on high dimensional fitness landscapes in the presence of sign epistasis .",
"Here we pr... | [
"Sexual reproduction is costly and often dangerous for the mating individuals , but nevertheless it is widespread in all higher organisms .",
"To resolve this paradox , evolutionary theory searches for fundamental benefits in the recombination of genes that balance the cost of sex .",
"Although many possible be... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genome-wide association studies",
"gene regulation",
"population genetics",
"microbiology",
"protein abundance",
"model organisms",
"molecular genetics",
"genetic polymorphism",
"gene expression",
"biology",
"proteomics",
"systems biology",
"biochemistry",
"protein translation",
"geneti... | Genetic Variation Shapes Protein Networks Mainly through Non-transcriptional Mechanisms | journal.pbio.1001144 | Variation in the levels of co-regulated proteins that function within networks in an outbred yeast population is not driven by variation in the corresponding transcripts. | [
[
"Genetic variation leads to networks of co-regulated transcripts .",
"The implications of these network structures have been discussed extensively , generally with the assumption that such transcriptional networks give rise to corresponding protein networks [1]–[6] .",
"However , due to limitations in... | [
"Networks of co-regulated transcripts in genetically diverse populations have been studied extensively , but little is known about the degree to which these networks cause similar co-variation at the protein level .",
"We quantified 354 proteins in a genetically diverse population of yeast segregants , which allo... | [
"The level of protein produced by each gene corresponds approximately to the level of mRNA transcript produced by that gene: so high-abundance proteins , like those involved in protein synthesis , are represented by high-abundance transcripts , whereas low-abundance proteins , like those involved in signaling pathw... | 2011 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"africans",
"innate immune system",
"medicine and health sciences",
"immune physiology",
"cytokines",
"body fluids",
"immunology",
"tropical diseases",
"ethnicities",
"bacterial diseases",
"developmental biology",
"molecular development",
"bacteria",
"infectious diseases",
"tuberculosis"... | Host Immune Responses Differ between M. africanum- and M. tuberculosis-Infected Patients following Standard Anti-tuberculosis Treatment | journal.pntd.0004701 | null | [
[
"Mycobacterium africanum ( Maf ) is an ancient lineage of the Mycobacterium tuberculosis ( Mtb ) Complex ( MTBC ) , mostly found in West Africa where it causes up to half of all tuberculosis ( TB ) cases [1] .",
"Apart from descriptions of the epidemiological differences between Maf and Mtb infection in t... | [
"Epidemiological differences exist between Mycobacterium africanum ( Maf ) - and Mycobacterium tuberculosis ( Mtb ) -infected patients , but to date , contributing host factors have not been characterised .",
"We analysed clinical outcomes , as well as soluble markers and gene expression profiles in unstimulated ... | [
"In the Gambia tuberculosis is caused my two major lineages within the Mycobacterium tuberculosis complex ( MTBC ) , M . tuberculosis lineages 4 and M . africanum lineage 6 .",
"Our analysis of 26 M . africanum- and 49 M . tuberculosis -HIV-negative tuberculosis patients’ clinic parameters and antigen-stimulated ... | 2016 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"infectious diseases",
"medicine and health sciences"
] | Recombinant Modified Vaccinia Virus Ankara Expressing Glycoprotein E2 of Chikungunya Virus Protects AG129 Mice against Lethal Challenge | journal.pntd.0003101 | null | [
[
"Chikungunya virus ( CHIKV ) belongs to the family Togaviridae , genus Alphavirus .",
"The virus was first isolated in 1952 during an epidemic of arthralgic disease in Tanzania , and CHIKV is now known as a mosquito-borne virus endemic in many parts of Sub-Saharan Africa as well as in Asia [1] .",
"Ep... | [
"Chikungunya virus ( CHIKV ) infection is characterized by rash , acute high fever , chills , headache , nausea , photophobia , vomiting , and severe polyarthralgia .",
"There is evidence that arthralgia can persist for years and result in long-term discomfort .",
"Neurologic disease with fatal outcome has been... | [
"The Chikungunya virus ( CHIKV ) represents a threat to Europe .",
"This is supported by its recent introduction and autochthonous transmission in Italy and France in 2007 and 2010 respectively .",
"CHIKV causes an acute febrile illness and severe joint pains that may last for several months in some patients ."... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Active Transport and Diffusion Barriers Restrict Joubert Syndrome-Associated ARL13B/ARL-13 to an Inv-like Ciliary Membrane Subdomain | journal.pgen.1003977 | null | [
[
"Primary cilia are organized into specific subcompartments , defined by distinct ultrastructure , protein and lipid compositions , and include the basal body ( BB ) , the adjacent transition zone ( TZ ) , and axonemal regions consisting of doublet and singlet microtubules [1] .",
"Ciliary subcompartments ... | [
"Cilia are microtubule-based cell appendages , serving motility , chemo-/mechano-/photo- sensation , and developmental signaling functions .",
"Cilia are comprised of distinct structural and functional subregions including the basal body , transition zone ( TZ ) and inversin ( Inv ) compartments , and defects in ... | [
"Protruding from most cells surfaces is a hair-like extension called the primary cilium .",
"This organelle functions as a cellular antenna , receiving physical and chemical signals such as light , odorants , and molecules that coordinate cell growth , differentiation and migration .",
"Underscoring their impor... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"computational chemistry",
"molecular dynamics",
"protein structure",
"chemistry",
"biology",
"computational biology",
"macromolecular structure analysis"
] | Phosphorylation of the Retinoic Acid Receptor Alpha Induces a Mechanical Allosteric Regulation and Changes in Internal Dynamics | journal.pcbi.1003012 | null | [
[
"Nuclear receptors are ligand-dependent transcription factors that participate in many cellular signaling networks involved in various physiological phenomena , such as embryogenesis , cell differentiation , cell growth , reproduction and apoptosis [1] .",
"Disruption or abrogation of these signaling path... | [
"Nuclear receptor proteins constitute a superfamily of proteins that function as ligand dependent transcription factors .",
"They are implicated in the transcriptional cascades underlying many physiological phenomena , such as embryogenesis , cell growth and differentiation , and apoptosis , making them one of th... | [
"Allosteric regulation of proteins is critically important in many biological processes .",
"Here we focused on the allosteric pathway of communication within a ligand-regulated transcription factor , the Retinoic Acid Receptor ( RAR ) .",
"Recent experimental studies performed with the RARα subtype have shown ... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Inhibition of Telomere Recombination by Inactivation of KEOPS Subunit Cgi121 Promotes Cell Longevity | journal.pgen.1005071 | null | [
[
"Aging is generally defined as the time-dependent functional decline and increased mortality in most living organisms .",
"Although aging appears to be a natural process , increasing evidence indicates that aging is genetically controlled .",
"In order to elucidate how aging is influenced by intrinsic... | [
"DNA double strand break ( DSB ) is one of the major damages that cause genome instability and cellular aging .",
"The homologous recombination ( HR ) -mediated repair of DSBs plays an essential role in assurance of genome stability and cell longevity .",
"Telomeres resemble DSBs and are competent for HR .",
... | [
"Aging is a general biological process among the living organisms which is affected by environmental stimuli but also genetically controlled .",
"Genome instability is one of the aging hallmarks and has long been implicated as one of the main causal factors in aging .",
"DNA double strand breaks ( DSBs ) are th... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"microbiology",
"viral structure",
"viruses",
"rna viruses",
"microbial genomics",
"chemical properties",
"physical chemistry",
"viral genomics",
"lipids",
"dimerization",
"viral core",
"proteins",
"chemistry",
"viral replication",
"biochemistry",
"virology",
"genetics",
"protein d... | A role for domain I of the hepatitis C virus NS5A protein in virus assembly | journal.ppat.1006834 | null | [
[
"Hepatitis C virus ( HCV ) is a member of the Flaviviridae family of enveloped , positive-strand RNA viruses [1] .",
"It is estimated to infect up to 170 million individuals globally [2] .",
"HCV causes inflammation and fibrosis in the liver via damage to hepatocytes .",
"Over time , chronic infec... | [
"The NS5A protein of hepatitis C virus ( HCV ) plays roles in both virus genome replication and assembly .",
"NS5A comprises three domains , of these domain I is believed to be involved exclusively in genome replication .",
"In contrast , domains II and III are required for the production of infectious virus pa... | [
"Hepatitis C virus infects 170 million people worldwide , causing long term liver disease .",
"Recently new therapies comprising direct-acting antivirals ( DAAs ) , small molecule inhibitors of virus proteins , have revolutionised treatment for infected patients .",
"Despite this , we have a limited understandi... | 2018 |
[
"Introduction",
"Results/Discussion",
"Materials and Methods"
] | [
"haplotypes",
"effective population size",
"genetic drift",
"genetics",
"population genetics",
"biology",
"gene flow",
"genetics and genomics",
"gene pool"
] | Genome-Wide Diversity in the Levant Reveals Recent Structuring by Culture | journal.pgen.1003316 | null | [
[
"The Levant is a geographical area in the eastern Mediterranean region bounded by Anatolia , Egypt , and the Arabian Desert .",
"It includes Lebanon , Syria , Jordan , Israel , Palestine , and often Cyprus and historical Armenia .",
"The region has been central to human cultural development , embracin... | [
"The Levant is a region in the Near East with an impressive record of continuous human existence and major cultural developments since the Paleolithic period .",
"Genetic and archeological studies present solid evidence placing the Middle East and the Arabian Peninsula as the first stepping-stone outside Africa .... | [
"Population stratification caused by nonrandom mating between groups of the same species is often due to geographical distances leading to physical separation followed by genetic drift of allele frequencies in each group .",
"In humans , population structures are also often driven by geographical barriers or dist... | 2013 |
[
"Introduction",
"Materials and methods",
"Results/Discussion",
"Conclusions"
] | [
"taxonomy",
"animal types",
"medicine and health sciences",
"canada",
"pathology and laboratory medicine",
"chemical compounds",
"pathogens",
"geographical locations",
"microbiology",
"tropical diseases",
"vertebrates",
"animals",
"mammals",
"organic compounds",
"viruses",
"north ameri... | Origins of the arctic fox variant rabies viruses responsible for recent cases of the disease in southern Ontario | journal.pntd.0007699 | null | [
[
"Rabies virus ( RABV ) , the type species of the Lyssavirus genus , is the most commonly encountered etiological agent of rabies , a serious zoonosis considered virtually 100% lethal once clinical signs are apparent [1] .",
"This neurotropic agent propagates in the central nervous system of its victim and... | [
"A subpopulation of the arctic fox lineage of rabies virus has circulated extensively in red fox populations of Ontario , Canada , between the 1960s and 1990s .",
"An intensive wildlife rabies control program , in which field operations were initiated in 1989 , resulted in elimination of the disease in eastern On... | [
"Rabies , a serious disease which almost invariably results in death once clinical signs appear , is caused by the rabies virus .",
"The arctic fox lineage of rabies virus persists in fox populations in northern Canada and from the 1960s onwards a sub-population of this virus has circulated in red foxes in the pr... | 2019 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious diseases",
"medicine and health sciences",
"biology and life sciences",
"immunology",
"vaccination and immunization",
"parasitology"
] | Schistosome Syntenin Partially Protects Vaccinated Mice against Schistosoma mansoni Infection | journal.pntd.0003107 | null | [
[
"Schistosomiasis , which is caused by trematode worms of the genus Schistosoma , is considered the most important human helminth infection in terms of global mortality and occurs primarily in developing countries .",
"In sub-Saharan Africa , higher mortality rates , such as 280 , 000 deaths per year , hav... | [
"Schistosomiasis is a neglected tropical disease caused by several species of trematode of the genus Schistosoma .",
"The disease affects more than 200 million people in the world and causes up to 280 , 000 deaths per year , besides having high morbidity due to chronic illness that damages internal organs .",
"... | [
"Schistosomiasis affects more than 200 million people worldwide and causes up to 280 , 000 deaths per year .",
"In terms of global mortality and morbidity , this disease is the most important human helminth infection .",
"Current control strategies are based on chemotherapy , but recurrent re-infection of peopl... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"immunology/antigen processing and recognition",
"immunology/immunomodulation",
"immunology/innate immunity",
"infectious diseases/hiv infection and aids",
"infectious diseases/viral infections",
"immunology/immunity to infections"
] | Complement as an Endogenous Adjuvant for Dendritic Cell-Mediated Induction of Retrovirus-Specific CTLs | journal.ppat.1000891 | null | [
[
"During the acute phase of HIV-1 infection the immune system responds with a massive , oligoclonal expansion of CD8+ T cells [1] .",
"The appearance of virus-specific CTLs correlates with declining viremia during this acute phase of infection , but CTLs are not associated with control of the virus during ... | [
"Previous studies have demonstrated the involvement of complement ( C ) in induction of efficient CTL responses against different viral infections , but the exact role of complement in this process has not been determined .",
"We now show that C opsonization of retroviral particles enhances the ability of dendrit... | [
"Upon entering the body , HIV initiates immediate responses of the immune system .",
"The complement system constitutes a first line of defense against HIV and bridges innate and adaptive immunity .",
"Thus , in the acute phase of infection , HIV is coated with complement fragments .",
"Following seroconversi... | 2010 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine",
"biology"
] | Identification of a Novel Antimicrobial Peptide from Human Hepatitis B Virus Core Protein Arginine-Rich Domain (ARD) | journal.ppat.1003425 | null | [
[
"The increase of drug-resistant pathogens caused by the extensive use of traditional antibiotics is a serious concern worldwide .",
"There is an urgent need to develop more effective treatment to overcome the drug-resistance problem .",
"Antimicrobial peptides ( AMP ) are a new class of antibiotics wi... | [
"The rise of multidrug-resistant ( MDR ) pathogens causes an increasing challenge to public health .",
"Antimicrobial peptides are considered a possible solution to this problem .",
"HBV core protein ( HBc ) contains an arginine-rich domain ( ARD ) at its C-terminus , which consists of 16 arginine residues sepa... | [
"Antibiotics-resistant pathogens have been a major problem to our public health .",
"Recently , in our studies of human hepatitis B virus ( HBV ) , we accidentally discovered potent and broad spectrum antimicrobial peptides from HBV core protein ( HBc ) arginine-rich domain ( ARD ) .",
"The peptides are mainly ... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"infectious diseases",
"biology",
"microbiology",
"evolutionary biology"
] | TRIM5 alpha Drives SIVsmm Evolution in Rhesus Macaques | journal.ppat.1003577 | null | [
[
"The epidemic of human immunodeficiency virus ( HIV ) , including both HIV-1 and HIV-2 , is a consequence of cross-species transmission of lentiviruses from non-human primates ( NHP ) to humans 1 , 2 .",
"HIV-1 is derived from cross-species infection of simian immunodeficiency virus in chimpanzees ( SIVcp... | [
"The antagonistic interaction with host restriction proteins is a major driver of evolutionary change for viruses .",
"We previously reported that polymorphisms of the TRIM5α B30 . 2/SPRY domain impacted the level of SIVsmm viremia in rhesus macaques .",
"Viremia in macaques homozygous for the non-restrictive T... | [
"Human immunodeficiency virus ( HIV ) resulted from the transmission of simian immunodeficiency viruses ( SIV ) from nonhuman primates followed by adaptation and expansion as a pandemic in humans .",
"This required the virus to overcome a variety of intrinsic host restriction factors in humans in order to replica... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"physics",
"statistical mechanics",
"neural networks",
"computational neuroscience",
"sensory systems",
"biology",
"neuroscience"
] | Searching for Collective Behavior in a Large Network of Sensory Neurons | journal.pcbi.1003408 | null | [
[
"The idea of maximizing entropy has its origin in thermodynamics and statistical mechanics .",
"The idea that we can use this principle to build models of systems that are not in thermal equilibrium is more recent , but still more than fifty years old [41]; in the past few years , there has been a new sur... | [
"Maximum entropy models are the least structured probability distributions that exactly reproduce a chosen set of statistics measured in an interacting network .",
"Here we use this principle to construct probabilistic models which describe the correlated spiking activity of populations of up to 120 neurons in th... | [
"Sensory neurons encode information about the world into sequences of spiking and silence .",
"Multi-electrode array recordings have enabled us to move from single units to measuring the responses of many neurons simultaneously , and thus to ask questions about how populations of neurons as a whole represent thei... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"cell biology/cell growth and division"
] | Context-Dependent Requirement for dE2F during Oncogenic Proliferation | journal.pgen.1000205 | null | [
[
"The Retinoblastoma tumor suppressor protein ( pRB ) and the related proteins p107 and p130 negatively regulate cell proliferation .",
"In a textbook model , the role of pRB family members in cell cycle regulation is explained by their ability to attenuate the activity of E2F transcription factors .",
... | [
"The Hippo pathway negatively regulates the cell number in epithelial tissue .",
"Upon its inactivation , an excess of cells is produced .",
"These additional cells are generated from an increased rate of cell division , followed by inappropriate proliferation of cells that have failed to exit the cell cycle ."... | [
"The E2F transcription factor family is considered to be the best-characterized downstream target of the retinoblastoma protein ( pRB ) .",
"The pRB pathway is functionally inactivated in most tumor cells , and it is thought that unrestrained activity of E2F drives inappropriate proliferation in tumors .",
"We ... | 2008 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine",
"public health and epidemiology",
"pathology",
"infectious disease epidemiology",
"microbiology",
"microsporidiosis",
"population biology",
"fungal diseases",
"animal management",
"zoology",
"veterinary science",
"veterinary medicine",
"infectious diseases",
"veterinary disease... | Nosema ceranae Escapes Fumagillin Control in Honey Bees | journal.ppat.1003185 | null | [
[
"Bicyclohexylammonium fumagillin , an antibiotic isolated from the fungus Aspergillus fumigatus , has been the only widely used treatment for nosemosis , or “nosema disease” , in western honey bees , Apis mellifera , [1] , [2] for nearly 60 years [2] .",
"The antibiotic ( hereafter “fumagillin” ) , in the... | [
"Fumagillin is the only antibiotic approved for control of nosema disease in honey bees and has been extensively used in United States apiculture for more than 50 years for control of Nosema apis .",
"It is toxic to mammals and must be applied seasonally and with caution to avoid residues in honey .",
"Fumagill... | [
"Nosema ceranae , a microsporidian pathogen described from Asian honey bees , was discovered infecting European honey bees coincident with early reports of Colony Collapse Disorder ( CCD ) and has been suggested to be a factor in honey bee declines .",
"Use of fumagillin , the only known reliable treatment for th... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"neuroscience",
"songbird"
] | Spike Correlations in a Songbird Agree with a Simple Markov Population Model | journal.pcbi.0030249 | null | [
[
"Spontaneous neural activity in the absence of sensory stimulation ( e . g . , during sleep ) often exhibits stereotyped sequences that can resemble sensory or motor sequences [1–5] .",
"A central question pertaining to such observations is the extent to which spike sequences in single neurons reflect seq... | [
"The relationships between neural activity at the single-cell and the population levels are of central importance for understanding neural codes .",
"In many sensory systems , collective behaviors in large cell groups can be described by pairwise spike correlations .",
"Here , we test whether in a highly specia... | [
"To deal with the vast complexity of the brain and its many degrees of freedom , many reductionist methods have been designed that can be used to simplify neural interactions to just a few key underlying macroscopic variables .",
"Despite these theoretical advances , even today relatively few population models ha... | 2007 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods",
"Supporting Information"
] | [
"plants",
"genetics and genomics",
"arabidopsis",
"plant biology"
] | Genetic Basis for Dosage Sensitivity in Arabidopsis thaliana | journal.pgen.0030070 | null | [
[
"Most eukaryotic genomes maintain genes in a one-to-one relationship by their syntenic organization on chromosomes .",
"This normal stoichiometry between chromosomes of a set can sometimes be disrupted , resulting in altered dosage of both genes and their encoded products .",
"Such disruptions can ari... | [
"Aneuploidy , the relative excess or deficiency of specific chromosome types , results in gene dosage imbalance .",
"Plants can produce viable and fertile aneuploid individuals , while most animal aneuploids are inviable or developmentally abnormal .",
"The swarms of aneuploid progeny produced by Arabidopsis tr... | [
"Each eukaryotic genome is subdivided into a specific number of chromosome types , which in turn are present in a characteristic number of copies , usually the same for all chromosomes .",
"In the condition called aneuploidy , copy number differs among chromosome types , disrupting their balance and that of their... | 2007 |
[
"Introduction",
"Results",
"Discussion",
"Material and methods"
] | [
"inflammatory diseases",
"medicine and health sciences",
"body fluids",
"pathology and laboratory medicine",
"pneumococcus",
"nervous system",
"pathogens",
"microbiology",
"bacterial diseases",
"bacteria",
"bacterial pathogens",
"infectious diseases",
"infectious diseases of the nervous syst... | In vivo proteomics identifies the competence regulon and AliB oligopeptide transporter as pathogenic factors in pneumococcal meningitis | journal.ppat.1007987 | null | [
[
"Bacterial meningitis accounts for approximately 0 . 5% of all deaths worldwide [1] and this catapults bacterial meningitis into the list of the top ten infectious burdens around the world [2] .",
"Streptococcus pneumoniae ( the pneumococcus ) is one of the most common and most aggressive pathogen causing... | [
"Streptococcus pneumoniae ( pneumococci ) is a leading cause of severe bacterial meningitis in many countries worldwide .",
"To characterize the repertoire of fitness and virulence factors predominantly expressed during meningitis we performed niche-specific analysis of the in vivo proteome in a mouse meningitis ... | [
"Pneumococci are one of the most common and aggressive meningitis pathogens associated with mortality rates between 10% and 30% .",
"Due to severe complications during therapeutic intervention , prevention strategies to combat pneumococcal meningitis ( PM ) are preferred .",
"The vaccines available are so far s... | 2019 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | Ecological Drivers of Mansonella perstans Infection in Uganda and Patterns of Co-endemicity with Lymphatic Filariasis and Malaria | journal.pntd.0004319 | null | [
[
"The human filarial parasite Mansonella perstans has been considered as one of the most prevalent human parasites in Africa [1] .",
"Despite the wide distribution , only very few studies have addressed its epidemiology and associated health consequences , and currently no effective drug therapy for treatm... | [
"Mansonella perstans is a widespread , but relatively unknown human filarial parasite transmitted by Culicoides biting midges .",
"Although it is found in many parts of sub-Saharan Africa , only few studies have been carried out to deepen the understanding of its ecology , epidemiology , and health consequences .... | [
"Mansonella perstans is a widespread , but relatively unknown human filarial parasite that occurs in many parts of Africa .",
"In a nationwide survey carried out in Uganda in 2000–2003 , the distribution of M . perstans was assessed by screening school children .",
"Here , we studied the underlying environmenta... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | A Cullin1-Based SCF E3 Ubiquitin Ligase Targets the InR/PI3K/TOR Pathway to Regulate Neuronal Pruning | journal.pbio.1001657 | null | [
[
"The selective removal of unnecessary or exuberant neuronal processes without loss of neurons , referred to as pruning , is a central theme in the maturation of the nervous system during animal development [1] .",
"Pruning occurs widely in a variety of neurons of invertebrates [2] , [3] and vertebrates [4... | [
"Pruning that selectively eliminates unnecessary axons/dendrites is crucial for sculpting the nervous system during development .",
"During Drosophila metamorphosis , dendrite arborization neurons , ddaCs , selectively prune their larval dendrites in response to the steroid hormone ecdysone , whereas mushroom bod... | [
"Neurons have the ability to engage in selective pruning that eliminates unnecessary axons/dendrites .",
"This process is crucial for sculpting the nervous system during development .",
"During Drosophila development , dendrite arborization sensory neurons ( ddaCs ) selectively prune their larval dendrites in r... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods",
"Supporting Information"
] | [
"molecular biology",
"genetics and genomics",
"microbiology",
"eubacteria"
] | The Unconventional Xer Recombination Machinery of Streptococci/Lactococci | journal.pgen.0030117 | null | [
[
"Chromosome replication is a key function in living cells , and any factor that impedes progression of replication forks can result in mutagenesis and genome instability .",
"Several strategies have evolved to rescue replication forks stalled by DNA damage .",
"Most of these depend on homologous recom... | [
"Homologous recombination between circular sister chromosomes during DNA replication in bacteria can generate chromosome dimers that must be resolved into monomers prior to cell division .",
"In Escherichia coli , dimer resolution is achieved by site-specific recombination , Xer recombination , involving two para... | [
"In bacteria , genetic information is mainly carried by a single circular chromosome .",
"The replication of this circular molecule sometimes leads to the formation of a chromosome dimer unable to segregate in the daughter cells during the division process .",
"In the bacterial model E . coli , chromosome dimer... | 2007 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"blood cells",
"innate immune system",
"medicine and health sciences",
"immune cells",
"immune physiology",
"cytokines",
"statistics",
"immunology",
"regression analysis",
"developmental biology",
"mathematics",
"molecular development",
"cytotoxic t cells",
"antibodies",
"research and an... | Peripheral immune response in the African green monkey model following Nipah-Malaysia virus exposure by intermediate-size particle aerosol | journal.pntd.0007454 | null | [
[
"A comprehensive understanding of disease processes requires the use of a model that accurately recapitulates significant components of human disease .",
"In this study , we continue efforts to develop the African green monkey ( AGM ) model of Nipah virus ( NiV ) infection .",
"This work focused on ex... | [
"The ability to appropriately mimic human disease is critical for using animal models as a tool for understanding virus pathogenesis .",
"In the case of Nipah virus ( NiV ) , infection of humans appears to occur either through inhalation , contact with or consumption of infected material .",
"In two of these ci... | [
"Nipah virus ( NiV ) infection in Malaysia , Bangladesh and India has been correlated with severe respiratory and neurological disease that led to death in over 50% of known cases .",
"In this study , we used a nonhuman primate model for NiV infection to evaluate the peripheral immune response to virus infection ... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | A Next-Generation Cleaved, Soluble HIV-1 Env Trimer, BG505 SOSIP.664 gp140, Expresses Multiple Epitopes for Broadly Neutralizing but Not Non-Neutralizing Antibodies | journal.ppat.1003618 | null | [
[
"One approach to creating a preventative vaccine against human immunodeficiency virus type 1 ( HIV-1 ) infection is to design an immunogen capable of inducing adequate titers of broadly neutralizing antibodies ( bNAbs ) [1] .",
"NAbs prevent HIV-1 from infecting target cells by binding to the viral envelo... | [
"A desirable but as yet unachieved property of a human immunodeficiency virus type 1 ( HIV-1 ) vaccine candidate is the ability to induce broadly neutralizing antibodies ( bNAbs ) .",
"One approach to the problem is to create trimeric mimics of the native envelope glycoprotein ( Env ) spike that expose as many bN... | [
"A protective HIV-1 vaccine is badly needed , but no candidate has yet provided an adequate level of protection against infection .",
"Most existing vaccines provide immune protection by inducing neutralizing antibodies , also a goal of many HIV-1 immunogen design projects .",
"The trimeric envelope protein com... | 2013 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"antimicrobials",
"urology",
"typhus",
"medicine and health sciences",
"pathology and laboratory medicine",
"maternal health",
"obstetrics and gynecology",
"drugs",
"tropical diseases",
"microbiology",
"parasitic diseases",
"bacterial diseases",
"women's health",
"signs and symptoms",
"a... | The Aetiologies and Impact of Fever in Pregnant Inpatients in Vientiane, Laos | journal.pntd.0004577 | null | [
[
"Maternal death and poor birth outcomes remain significant public health problems in much of the world [1 , 2] .",
"Most of the mortality and morbidity burden around delivery are related to direct obstetrical problems such as bleeding .",
"However , there is relatively little information on the import... | [
"Laos has the highest maternal mortality ratio in mainland Southeast Asia and a high incidence of infectious diseases .",
"Globally , malaria has been the pathogen most intensively investigated in relation to impact on pregnancy , but there has been relatively little research on the aetiology and impact of other ... | [
"Laos has a high incidence of infectious diseases and high prevalence of poverty .",
"Malaria in pregnancy if of great public health interest .",
"However , malaria has not been reported in Vientiane City for decades , but others diseases such as dengue fever , rickettsioses , typhoid fever , leptospirosis and ... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genome sequencing",
"genome expression analysis",
"developmental biology",
"systems biology",
"functional genomics",
"stem cells",
"embryonic stem cells",
"gene expression",
"biology",
"genomics",
"molecular cell biology",
"cell fate determination"
] | Zfp322a Regulates Mouse ES Cell Pluripotency and Enhances Reprogramming Efficiency | journal.pgen.1004038 | null | [
[
"Embryonic stem ( ES ) cells , which are derived from the inner cell mass ( ICM ) of mammalian blastocysts , are characterised by their ability to self-renew and by their potential to differentiate into many different cell types [1] , [2] .",
"ES cells provide a prime platform for biomedical research sinc... | [
"Embryonic stem ( ES ) cells derived from the inner cell mass ( ICM ) of blastocysts are characterised by their ability to self-renew and their potential to differentiate into many different cell types .",
"Recent studies have shown that zinc finger proteins are crucial for maintaining pluripotent ES cells .",
... | [
"Embryonic stem ( ES ) cells are featured by their ability to self-renew and by their potential to differentiate into many different cell types .",
"Recent studies have revealed that the unique properties of mouse ES cells are governed by a specific transcription regulatory network , including master regulators O... | 2014 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine and health sciences",
"viral transmission and infection",
"geographical locations",
"tropical diseases",
"microbiology",
"animals",
"indonesia",
"viral vectors",
"developmental biology",
"neglected tropical diseases",
"infectious disease control",
"insect vectors",... | Integrated vector management with additional pre-transmission season thermal fogging is associated with a reduction in dengue incidence in Makassar, Indonesia: Results of an 8-year observational study | journal.pntd.0007606 | null | [
[
"Dengue is the most common vector-borne viral disease in the world , infecting as many as 400 million people per year [1] .",
"The disease is caused by four serotypes [dengue-1 , -2 , -3 and -4] transmitted by Aedes mosquitoes [2–5] .",
"Aedes aegypti and Ae .",
"albopictus differ in both their mo... | [
"Dengue virus transmission is endemic in Makassar , Indonesia , with the majority of cases reported soon after the start of the annual rainy season .",
"Before 2006 , larval source reduction , larvaciding , and reactive routine , outdoor , insecticide fogging campaigns did not result in a reduction in seasonal de... | [
"Dengue is the most common mosquito-borne viral disease in the world , infecting as many as 400 million people per year .",
"While comprehensive , rigorous vector control can reduce transmission , in practice inadequate coverage , improper application , insecticide resistance , high labor costs , and community in... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"blood cells",
"transfection",
"medicine and health sciences",
"immune cells",
"immune physiology",
"pathology and laboratory medicine",
"spleen",
"pathogens",
"immunology",
"microbiology",
"viruses",
"dna replication",
"dna viruses",
"molecular biology techniques",
"dna",
"herpesvirus... | Cross-species conservation of episome maintenance provides a basis for in vivo investigation of Kaposi's sarcoma herpesvirus LANA | journal.ppat.1006555 | null | [
[
"Kaposi’s sarcoma-associated herpesvirus ( KSHV ) , a gamma-2 herpesvirus , is the etiologic agent of Kaposi’s sarcoma , primary effusion lymphoma , and multicentric Castleman’s disease[1–5] .",
"KSHV infection of tumor cells is predominantly latent .",
"During latent infection , KSHV persists as a nu... | [
"Many pathogens , including Kaposi’s sarcoma herpesvirus ( KSHV ) , lack tractable small animal models .",
"KSHV persists as a multi-copy , nuclear episome in latently infected cells .",
"KSHV latency-associated nuclear antigen ( kLANA ) binds viral terminal repeat ( kTR ) DNA to mediate episome persistence .",... | [
"KSHV latently infects cells and persists as a multi-copy , nuclear episome .",
"KSHV LANA ( kLANA ) maintains episomes by acting on viral terminal repeat ( kTR ) elements .",
"Model pathogen MHV68 mLANA acts analogously on mTR DNA .",
"To date , KSHV investigation has been limited by lack of a tractable , sm... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED | journal.pcbi.1004557 | null | [
[
"Quantifying proteins of interest from metagenomic sequencing data in a fast and accurate manner is a central challenge in microbial community analysis .",
"Whole metagenome shotgun ( WMS ) sequencing provides millions of short nucleotide sequences ( often 100–250 bases long ) from the DNA of organisms in... | [
"Profiling microbial community function from metagenomic sequencing data remains a computationally challenging problem .",
"Mapping millions of DNA reads from such samples to reference protein databases requires long run-times , and short read lengths can result in spurious hits to unrelated proteins ( loss of sp... | [
"High throughput DNA sequencing of the human microbiome presents a tremendous resource for researchers interested in studying microbial community functions such as antibiotic resistance .",
"However , assigning DNA reads to protein families remains a challenging problem , as reads derived from a given protein-cod... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"cell biology/cellular death and stress responses",
"cell biology",
"molecular biology/rna splicing",
"oncology/lung cancer",
"cell biology/gene expression"
] | Cancer-Associated Splicing Variant of Tumor Suppressor AIMP2/p38: Pathological Implication in Tumorigenesis | journal.pgen.1001351 | null | [
[
"Alternative splicing is implicated in the regulation of gene function and diversification [1]–[3] .",
"Although this process can provide another level of flexibility in gene regulation , the disruption in the balance between splicing variants or the generation of aberrant alternative splicing variants ca... | [
"Although ARS-interacting multifunctional protein 2 ( AIMP2 , also named as MSC p38 ) was first found as a component for a macromolecular tRNA synthetase complex , it was recently discovered to dissociate from the complex and work as a potent tumor suppressor .",
"Upon DNA damage , AIMP2 promotes apoptosis throug... | [
"Lung cancer is one of the most common cancers and a leading cause of death resulting from cancer .",
"Despite intensive investigation , effective therapeutic targets and reliable biomarkers are still limited .",
"Here we found that a tumor suppressor , AIMP2 ( MSC p38 ) , produces a variant lacking a part of i... | 2011 |
[
"Introduction",
"Model",
"Results",
"Discussion"
] | [
"infectious diseases/viral infections",
"computational biology/ecosystem modeling"
] | The Role of Environmental Transmission in Recurrent Avian Influenza
Epidemics | journal.pcbi.1000346 | null | [
[
"Many important infectious diseases persist on a knife-edge: rapid rates of",
"transmission coupled with brief infectious periods generate boom-and-bust epidemics",
"that court extinction .",
"Such violent epidemic behavior has been observed in measles",
"[1]–[4] , plague [5] ,",
"cholera ... | [
"Avian influenza virus ( AIV ) persists in North American wild waterfowl , exhibiting",
"major outbreaks every 2–4 years .",
"Attempts to explain the patterns of",
"periodicity and persistence using simple direct transmission models are",
"unsuccessful .",
"Motivated by empirical evidence , we examine the... | [
"Avian influenza viruses ( AIVs ) in wild waterfowl constitute the historic source",
"of human influenza viruses , having a rich pool of genetic and antigenic",
"diversity that often leads to cross-species transmission .",
"Although the emergence",
"of H5N1 avian influenza virus onto the international scene... | 2009 |
[
"Introduction",
"Models",
"Results",
"Discussion"
] | [
"antimicrobials",
"medicine and health sciences",
"pathology and laboratory medicine",
"infectious disease epidemiology",
"pathogens",
"drugs",
"immunology",
"vector-borne diseases",
"microbiology",
"vector construction",
"preventive medicine",
"dna construction",
"pharmacology",
"molecula... | Integrating Transgenic Vector Manipulation with Clinical Interventions to Manage Vector-Borne Diseases | journal.pcbi.1004695 | null | [
[
"Vector-borne diseases account for a significant share of the global infectious disease burden ( [1] ) , comprising as much as 17% of this burden according to some studies ( [2] ) .",
"They are typically managed by two broad approaches:",
"( i ) clinical interventions ( such as vaccines or drug treatm... | [
"Many vector-borne diseases lack effective vaccines and medications , and the limitations of traditional vector control have inspired novel approaches based on using genetic engineering to manipulate vector populations and thereby reduce transmission .",
"Yet both the short- and long-term epidemiological effects ... | [
"Despite decades of attempted vector control , several vector-borne diseases remain endemic .",
"Recent high-profile studies suggest that candidate vaccines , particularly for dengue , may be less than completely effective as public health interventions .",
"Nevertheless , the epidemiological consequences of us... | 2016 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"infographics",
"medicine and health sciences",
"clinical laboratory sciences",
"pathology and laboratory medicine",
"pathogens",
"microbiology",
"charts",
"health care",
"diarrhea",
"regression analysis",
"sepsis",
"nutrition",
"signs and symptoms",
"mathematics",
"statistics (mathemati... | Ileus in children presenting with diarrhea and severe acute malnutrition: A chart review | journal.pntd.0005603 | null | [
[
"Globally , diarrhea accounted for 9% of an estimated 5 . 9 million deaths in children under five years old in 2015 [1] .",
"Most of the deaths occurred in lower and middle-income countries including Bangladesh [2] .",
"The case-fatality rate ( CFR ) from diarrhea in Bangladesh was 6% among an estimat... | [
"Severely malnourished children aged under five years requiring hospital admission for diarrheal illness frequently develop ileus during hospitalization with often fatal outcomes .",
"However , there is no data on risk factors and outcome of ileus in such children .",
"We intended to evaluate predictive factors... | [
"Childhood malnutrition and diarrhea are important problems in lower and middle-income countries , including Bangladesh .",
"Severe acute malnutrition ( SAM ) and diarrhea are responsible for more than one third of all deaths in children below five years old globally .",
"Most of these deaths occur because of c... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biochemistry/replication and repair",
"genetics and genomics/chromosome biology"
] | Methylated H3K4, a Transcription-Associated Histone Modification, Is Involved in the DNA Damage Response Pathway | journal.pgen.1001082 | null | [
[
"Genomes of living organisms are continuously exposed to DNA damaging agents such as ultraviolet light , ionizing radiation , reactive oxygen intermediates or other chemical mutagens .",
"These agents can cause mutations and ultimately genome instability .",
"For mammalian cells , it has been estimate... | [
"Eukaryotic genomes are associated with a number of proteins such as histones that constitute chromatin .",
"Post-translational histone modifications are associated with regulatory aspects executed by chromatin and all transactions on genomic DNA are dependent on them .",
"Thus , it will be relevant to understa... | [
"Over the last years , it has become evident that chromatin plays a crucial role in a variety of cellular processes .",
"Insights into the tight regulation of chromatin opening and closing via chromatin remodelers , as well as post-translational modifications of proteins making up chromatin , have revealed new fa... | 2010 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"pathology and laboratory medicine",
"pathogens",
"microbiology",
"vertebrates",
"mice",
"animals",
"mammals",
"viruses",
"amino acid sequence analysis",
"rna viruses",
"research and analysis methods",
"rabies virus",
"sequence analysis",
"bioinformatics",... | Comparative analysis of European bat lyssavirus 1 pathogenicity in the mouse model | journal.pntd.0005668 | null | [
[
"Rabies is an acute , progressive and incurable viral encephalitis , caused by negative strand RNA viruses of the Lyssavirus genus belonging to the order Mononegavirales , family Rhabdoviridae , which is transmitted by bites of infected mammals .",
"Taxonomically , the etiological agents are classified in... | [
"European bat lyssavirus 1 is responsible for most bat rabies cases in Europe .",
"Although EBLV-1 isolates display a high degree of sequence identity , different sublineages exist .",
"In individual isolates various insertions and deletions have been identified , with unknown impact on viral replication and pa... | [
"European bat lyssavirus 1 ( EBLV-1 ) is one of fourteen officially recognized lyssavirus species causing rabies , a zoonosis resulting inevitably in death once clinical signs appear .",
"EBLV-1 is responsible for most bat rabies cases detected in Europe , and spill-over infections in humans highlight its zoonoti... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"medicine and health sciences",
"nucleic acid synthesis",
"immune physiology",
"gene regulation",
"293t cells",
"immunology",
"biological cultures",
"microbiology",
"immunoprecipitation",
"rna synthesis",
"antibodies",
"microbial genomics",
"chemical synthesis",
"research and analysis meth... | The R2TP complex regulates paramyxovirus RNA synthesis | journal.ppat.1007749 | null | [
[
"Many human and animal pathogens are members of the family Paramyxoviridae [1] , including mumps rubulavirus ( MuV ) and measles morbillivirus ( MeV ) .",
"Mumps is a common childhood illness characterized by painful swelling of the parotid glands , and is often accompanied by severe complications such as... | [
"The regulation of paramyxovirus RNA synthesis by host proteins is poorly understood .",
"Here , we identified a novel regulation mechanism of paramyxovirus RNA synthesis by the Hsp90 co-chaperone R2TP complex .",
"We showed that the R2TP complex interacted with the paramyxovirus polymerase L protein and that s... | [
"The family Paramyxoviridae includes several important human and animal pathogens such as mumps virus ( MuV ) and measles virus ( MeV ) .",
"Paramyxovirus RNA synthesis is strictly regulated by both viral and host proteins .",
"In this study , we identified the R2TP complex as a novel host factor regulating par... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Base Pairing Interaction between 5′- and 3′-UTRs Controls icaR mRNA Translation in Staphylococcus aureus | journal.pgen.1004001 | null | [
[
"Regulation of translation is used to modulate gene expression in a wide range of biological situations in all living organisms .",
"Compared to transcriptional regulation , mRNA translational control provides several advantages such as a more rapid response , reversibility , fine-tuning of protein amount... | [
"The presence of regulatory sequences in the 3′ untranslated region ( 3′-UTR ) of eukaryotic mRNAs controlling RNA stability and translation efficiency is widely recognized .",
"In contrast , the relevance of 3′-UTRs in bacterial mRNA functionality has been disregarded .",
"Here , we report evidences showing th... | [
"At both sides of the protein-coding region , the mRNA molecule contains sequences that are not translated to protein .",
"In eukaryotes , the untranslated 3′ region ( 3′-UTR ) , which comprises from the last codon used in translation to the 3′ end of the mRNA , controls mRNA stability , location and translation ... | 2013 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | Population Genetics of Plasmodium vivax in the Peruvian Amazon | journal.pntd.0004376 | null | [
[
"According to the World Health Organization ( WHO ) , Plasmodium vivax caused about 14 . 2 million malaria cases outside sub-Saharan Africa in 2013 [1] .",
"Despite considerable efforts , Asian and South American countries are still far from achieving malaria elimination [2] .",
"In Peru , the vast ma... | [
"Characterizing the parasite dynamics and population structure provides useful information to understand the dynamic of transmission and to better target control interventions .",
"Despite considerable efforts for its control , vivax malaria remains a major health problem in Peru .",
"In this study , we have ex... | [
"We present the population genetics of malaria vivax parasites in a large area of the Peruvian Amazon .",
"Our results showed that the parasite population had a predominant clonal propagation , reproducing themselves with identically or closely related parasites; therefore , the same genetic characteristics are m... | 2016 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"rna-binding proteins",
"cellular stress responses",
"rna interference",
"chemical compounds",
"messenger rna",
"cell processes",
"parasitic protozoans",
"organic compounds",
"protozoans",
"genome analysis",
"sequence motif analysis",
"epigenetics",
"alcohols",
"research and analysis metho... | Stress susceptibility in Trypanosoma brucei lacking the RNA-binding protein ZC3H30 | journal.pntd.0006835 | null | [
[
"The African trypanosomes Trypanosoma brucei , T . congolense and T . vivax infect mammals and Tsetse flies .",
"Their major impact is on domestic livestock , for which it was recently estimated that trypanosomiasis elimination could bring a benefit of 2 . 5 billion US dollars [1] .",
"The human disea... | [
"Trypanosomes rely on post-transcriptional mechanisms and mRNA-binding proteins for control of gene expression .",
"Trypanosoma brucei ZC3H30 is an mRNA-binding protein that is expressed in both the bloodstream form ( which grows in mammals ) and the procyclic form ( which grows in the tsetse fly midgut ) .",
"... | [
"RNA-binding proteins are essential for control of gene expression in trypanosomes and leishmanias .",
"ZC3H30 is a protein which was shown to bind to mRNAs; when it is attached to an mRNA , that mRNA is degraded .",
"Procyclic-form trypanosomes that lack ZC3H30 grow normally under standard conditions , but wer... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"animal models",
"drosophila melanogaster",
"model organisms",
"genetic mutation",
"nucleic acids",
"genetics",
"dna",
"biology",
"molecular cell biology"
] | Oxidative Stress Is Not a Major Contributor to Somatic Mitochondrial DNA Mutations | journal.pgen.1003974 | null | [
[
"Mitochondria play crucial cellular roles in energy production , Ca2+ buffering , metabolite synthesis , and programmed cell death in metazoans [1]–[3] .",
"While most mitochondrial proteins are encoded in the nuclear genome , mitochondria also contain a compact genome that generally encodes 37 genes [4] ... | [
"The accumulation of somatic mitochondrial DNA ( mtDNA ) mutations is implicated in aging and common diseases of the elderly , including cancer and neurodegenerative disease .",
"However , the mechanisms that influence the frequency of somatic mtDNA mutations are poorly understood .",
"To develop a simple inver... | [
"Mitochondria are the evolutionary remnants of bacteria that were acquired by the cells of our ancestors more than a billion years ago and now produce virtually all of the cellular energy .",
"Due to their bacterial ancestry , mitochondria have their own genomes , which encode some of the machinery responsible fo... | 2014 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"arthropoda",
"invertebrates",
"disease vectors",
"mosquitoes",
"medicine and health sciences",
"epidemiology",
"arthropod vectors",
"biology and life sciences",
"insect vectors",
"parasitic diseases",
"animals",
"insects",
"organisms"
] | The Effect of Virus-Blocking Wolbachia on Male Competitiveness of the Dengue Vector Mosquito, Aedes aegypti | journal.pntd.0003294 | null | [
[
"Vector-borne diseases are infections transmitted by the bite of arthropod species , primarily mosquitoes .",
"These diseases ( e . g . , malaria , dengue , Chagas disease and filariasis ) are major contributors to human mortality and morbidity , especially in developing tropical countries .",
"Tradit... | [
"The bacterial endosymbiont Wolbachia blocks the transmission of dengue virus by its vector mosquito Aedes aegypti , and is currently being evaluated for control of dengue outbreaks .",
"Wolbachia induces cytoplasmic incompatibility ( CI ) that results in the developmental failure of offspring in the cross betwee... | [
"Dengue is a tropical , potentially lethal disease transmitted by mosquitoes .",
"A new control method involves the release of mosquitoes infected by the bacterium Wolbachia that blocks the transmission of the dengue virus to humans .",
"However , possible negative effects of Wolbachia on mosquito reproductive ... | 2014 |
[
"Introduction",
"Results/Discussion",
"Materials and Methods",
"Supporting Information"
] | [
"arabidopsis",
"plants",
"genetics and genomics"
] | Whole-Genome Analysis of Histone H3 Lysine 27 Trimethylation in Arabidopsis | journal.pbio.0050129 | This paper demonstrates that histone H3 lysine 27 methylation is a major gene-silencing histone modification in plants. | [
[
"Trimethylation of histone H3 lysine 27 ( H3K27me3 ) is critically important for the normal development of animals .",
"The Polycomb-group ( PcG ) protein complexes PhoRC , PRC1 , and PRC2 collectively establish and maintain H3K27me3 at ~400 and ~2 , 000 genes in Drosophila and mammals , respectively [1–4... | [
"Trimethylation of histone H3 lysine 27 ( H3K27me3 ) plays critical roles in regulating animal development , and in several cases , H3K27me3 is also required for the proper expression of developmentally important genes in plants .",
"However , the extent to which H3K27me3 regulates plant genes on a genome-wide sc... | [
"During plant and animal development , genes must be activated or repressed according to a strict temporal and spatial schedule .",
"Histones , which are DNA-packaging proteins , play a key role in this process .",
"For development to proceed normally , an amino acid residue ( lysine 27 ) in histone H3 must und... | 2007 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"invertebrates",
"medicine and health sciences",
"reproductive system",
"animals",
"animal models",
"drosophila melanogaster",
"integrins",
"model organisms",
"stem cells",
"cellular structures and organelles",
"drosophila",
"research and analysis methods",
"specimen preparation and treatmen... | Maintenance of Stem Cell Niche Integrity by a Novel Activator of Integrin Signaling | journal.pgen.1006043 | null | [
[
"Adult stem cells have the unique capacity to undergo self-renewal for extended periods of time and to generate differentiating daughter cells with the potential for tissue repair and regeneration .",
"Such features of adult stem cells depend critically on the microenvironment , or niche [1] .",
"The ... | [
"Stem cells depend critically on the surrounding microenvironment , or niche , for their maintenance and self-renewal .",
"While much is known about how the niche regulates stem cell self-renewal and differentiation , mechanisms for how the niche is maintained over time are not well understood .",
"At the apica... | [
"Stem cells are vital for development and for regeneration and repair of tissues in an organism .",
"The ability of adult stem cells to maintain their “stemness” depends critically on the localized microenvironment , or niche .",
"While much is known about how the niche regulates stem cell self-renewal and diff... | 2016 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious diseases/neglected tropical diseases",
"microbiology/medical microbiology",
"infectious diseases/skin infections",
"dermatology/skin infections"
] | Therapeutic Effect of a Novel Oxazolidinone, DA-7867, in BALB/c Mice Infected with Nocardia brasiliensis | journal.pntd.0000289 | null | [
[
"Mycetoma is a multi-etiological subcutaneous infection caused by true fungi and aerobic actinomycetes observed in many tropical and sub-tropical countries .",
"In Mexico , 98% of the total cases are produced by actinomycetes and about 86% are produced by N . brasiliensis [1] .",
"Many antimicrobials ... | [
"Mycetoma is a chronic infectious disease of tropical and subtropical countries .",
"It is produced by true fungi and actinobacteria .",
"In México , Nocardia brasiliensis is the main causative agent of mycetoma , producing about 86% of the cases; the gold standard for the therapy of mycetoma by N . brasiliensi... | [
"Actinomycetoma is an infectious disease of tropical and subtropical regions produced by actinobacteria of the genera Nocardia , Streptomyces , and Actinomadura .",
"Therapeutic alternatives are scarce and include trimethoprim-sulfamethoxazole , diaminodiphenylsulfone , amoxicillin-clavulanate , imipenem , and am... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"immunology/antigen processing and recognition",
"immunology/immunity to infections",
"immunology/immune response"
] | Direct Presentation Is Sufficient for an Efficient Anti-Viral CD8+ T Cell Response | journal.ppat.1000768 | null | [
[
"Activated CD8+ T lymphocytes ( TCD8+ ) kill virus infected cells that display virus-derived peptides presented on cell surface MHC I molecules .",
"Hence , TCD8+ play an essential role in the clearance of many primary viral infections .",
"Moreover , the memory TCD8+ that remain after a primary infec... | [
"The extent to which direct- and cross-presentation ( DP and CP ) contribute to the priming of CD8+ T cell ( TCD8+ ) responses to viruses is unclear mainly because of the difficulty in separating the two processes .",
"Hence , while CP in the absence of DP has been clearly demonstrated , induction of an anti-vira... | [
"Professional antigen presenting cells fragment viral proteins and display some of the resulting peptides bound to MHC molecules at the cell surface .",
"When virus-specific CD8+ T cells recognize these viral peptides they become activated , proliferate , and kill virus-infected cells to help rid the body of the ... | 2010 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [] | Changes in Rodent Abundance and Weather Conditions Potentially Drive Hemorrhagic Fever with Renal Syndrome Outbreaks in Xi’an, China, 2005–2012 | journal.pntd.0003530 | null | [
[
"Hantaviruses ( family Bunyaviridae , genus Hantavirus ) are negative-stranded , trisegmented viruses that cause approximately 200 , 000 hospitalized cases annually , with case fatality rates of 0 . 5%–40% , depending on the virus [1 , 2] .",
"In Eurasia , hemorrhagic fever with renal syndrome ( HFRS ) , ... | [
"Increased risks for hemorrhagic fever with renal syndrome ( HFRS ) caused by Hantaan virus have been observed since 2005 , in Xi’an , China .",
"Despite increased vigilance and preparedness , HFRS outbreaks in 2010 , 2011 , and 2012 were larger than ever , with a total of 3 , 938 confirmed HFRS cases and 88 deat... | [
"Hemorrhagic fever with renal syndrome ( HFRS , caused by hantavirus ) is a zoonotic infectious disease reservoired in rodent populations worldwide , but with 90% of the total cases occurring in China .",
"Xi’an is one of the most endemic areas in China , with a total of 7 , 748 confirmed HFRS cases from 2005 to ... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"medicine and health sciences",
"neurochemistry",
"vesicles",
"chemical compounds",
"nervous system",
"electrophysiology",
"neuroscience",
"organic compounds",
"motor neurons",
"synaptic vesicles",
"serotonin",
"physiological processes",
"neurotransmitters",
"cellular structures and organe... | Local neuropeptide signaling modulates serotonergic transmission to shape the temporal organization of C. elegans egg-laying behavior | journal.pgen.1006697 | null | [
[
"Animals have robust mechanisms in place to shape their behavior in a manner that is beneficial both for their survival and for the survival of their progeny .",
"In many cases behaviors are composed from discrete , opposing behavioral states .",
"Examples of behaviors that are organized in this manne... | [
"Animal behaviors are often composed of distinct alternating behavioral states .",
"Neuromodulatory signals are thought to be critical for establishing stable behavioral states and for orchestrating transitions between them .",
"However , we have only a limited understanding of how neuromodulatory systems act i... | [
"Animals have robust mechanisms in place to shape their behavior in a manner that is beneficial both for their survival and for the survival of their progeny .",
"A class of signaling molecules known as neuropeptides have been implicated in driving transitions between behavioral states but we have only a limited ... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine and health sciences",
"pathology and laboratory medicine",
"pathogens",
"messenger rna",
"immunology",
"microbiology",
"cloning",
"plasmid construction",
"vaccines",
"preventive medicine",
"physiological parameters",
"body temperature",
"dna construction",
"molecular biology tech... | Thermoregulation of Meningococcal fHbp, an Important Virulence Factor and Vaccine Antigen, Is Mediated by Anti-ribosomal Binding Site Sequences in the Open Reading Frame | journal.ppat.1005794 | null | [
[
"Neisseria meningitidis is a harmless member of the human nasopharyngeal flora in a significant proportion of healthy individuals [1] .",
"However in some instances , the bacterium spreads from the upper airway into the systemic circulation , where it can replicate and spread to the rest of the body [2] ,... | [
"During colonisation of the upper respiratory tract , bacteria are exposed to gradients of temperatures .",
"Neisseria meningitidis is often present in the nasopharynx of healthy individuals , yet can occasionally cause severe disseminated disease .",
"The meningococcus can evade the human complement system usi... | [
"The bacterium Neisseria meningitidis is exquisitely adapted to survive in the human host , and possesses several mechanisms to interact with host cells in the upper airway and to circumvent immune responses .",
"However , the mechanisms that govern the expression of factors that contribute to colonisation and di... | 2016 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious diseases",
"schistosomiasis",
"immune cells",
"monocytes",
"antigen processing and recognition",
"t cells",
"immunology",
"biology",
"parasitic diseases",
"infectious disease modeling",
"immunomodulation",
"immune response"
] | Modulation of Innate Antigen-Presenting Cell Function by Pre-patent Schistosome Infection | journal.pntd.0002136 | null | [
[
"Schistosomes are intravascular helminths affecting approximately 200 million people throughout the tropics and subtropics [1] , [2] , with more than 90% of cases occurring in sub-Saharan Africa [3] .",
"Upon infection , a variety of host responses are induced .",
"Exposure of antigen-presenting cells... | [
"Schistosomes are intravascular helminths that infect over 200 million people worldwide .",
"Deposition of eggs by adult schistosomes stimulates Th2 responses to egg antigens and induces granulomatous pathology that is a hallmark of schistosome infection .",
"Paradoxically , schistosomes require host immune fun... | [
"The disease schistosomiasis is caused by a parasitic blood fluke found mainly in the tropics and subtropics and affects over 200 million people worldwide .",
"Using mice to model human schistosome infection , our previous studies showed that schistosome development in the infected host is linked to host immune f... | 2013 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"developmental biology/pattern formation",
"developmental biology/developmental molecular mechanisms"
] | Bmp4 Is Essential for the Formation of the Vestibular Apparatus that Detects Angular Head Movements | journal.pgen.1000050 | null | [
[
"The ability to detect angular head movements in vertebrates lies within the vestibular apparatus of the inner ear [1]–[3] .",
"This portion of the apparatus consists of three fluid-filled semicircular canals ( anterior , lateral and posterior ) that are oriented in nearly orthogonal planes ( Figure 1A ) ... | [
"Angular head movements in vertebrates are detected by the three semicircular canals of the inner ear and their associated sensory tissues , the cristae .",
"Bone morphogenetic protein 4 ( Bmp4 ) , a member of the Transforming growth factor family ( TGF-β ) , is conservatively expressed in the developing cristae ... | [
"Disruption of the sense of balance is highly debilitating , causing vertigo and nausea .",
"Maintenance of proper balance requires sensory inputs from many body parts , including the inner ears and the eyes .",
"Within the inner ear , the vestibular apparatus plays a key role in the sense of balance and is res... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"biology"
] | Nonsex Genes in the Mating Type Locus of Candida albicans Play Roles in a/α Biofilm Formation, Including Impermeability and Fluconazole Resistance | journal.ppat.1002476 | null | [
[
"The a and α copies of the mating type locus ( MTL ) of Candida albicans contain several genes that play highly specialized roles in the mating process , MATa1 and MATa2 in the a copy , and MATα1 and MATα2 in the α copy [1] .",
"This locus also contains three genes apparently unrelated to mating , the non... | [
"The mating type locus ( MTL ) of Candida albicans contains the mating type genes and has , therefore , been assumed to play an exclusive role in the mating process .",
"In mating-incompetent a/α cells , two of the mating type genes , MTLa1 and MTLα2 , encode components of the a1-α2 corepressor that suppresses ma... | [
"Most natural strains of the yeast pathogen Candida albicans are diploid and heterozygous ( a/α ) at the mating type locus ( MTL ) .",
"The MTL locus contains mating type genes and has been assumed to play roles exclusively in the mating process of a/a and α/α cells .",
"In C . albicans , however , the MTL locu... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine and health sciences",
"neurochemistry",
"action potentials",
"vesicles",
"nervous system",
"astrocytes",
"membrane potential",
"electrophysiology",
"neuroscience",
"macroglial cells",
"sodium",
"neurotransmitters",
"cellular structures and organelles",
"animal cells",
"chemistr... | A computational study of astrocytic glutamate influence on post-synaptic neuronal excitability | journal.pcbi.1006040 | null | [
[
"Glutamate is the most abundant excitatory neurotransmitter in the brain [1] and due to its neurotoxic effects [2] glutamate homeostasis must be tightly regulated .",
"This requires that glutamate must , for the most part , be contained intracellularly and that the release of glutamate from both neuronal ... | [
"The ability of astrocytes to rapidly clear synaptic glutamate and purposefully release the excitatory transmitter is critical in the functioning of synapses and neuronal circuits .",
"Dysfunctions of these homeostatic functions have been implicated in the pathology of brain disorders such as mesial temporal lobe... | [
"The role of astrocytes in the excitability and hyperexcitability of neurons is a subject which has gained a lot of attention , particularly in the pathology of neurological disorders including epilepsy .",
"Although not completely understood , the control of glutamate homeostasis is believed to play a role in pa... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Roles of XRCC2, RAD51B and RAD51D in RAD51-Independent SSA Recombination | journal.pgen.1003971 | null | [
[
"DNA double-strand breaks ( DSB ) are produced by ionizing radiation , free radicals derived from metabolism , DNA crosslinking reagents and during DNA replication [1] , [2] .",
"DSB can lead to mutations and rearrangements and/or loss of chromosomes , causing tumorigenesis or cell death .",
"DSB must... | [
"The repair of DNA double-strand breaks by recombination is key to the maintenance of genome integrity in all living organisms .",
"Recombination can however generate mutations and chromosomal rearrangements , making the regulation and the choice of specific pathways of great importance .",
"In addition to end-... | [
"The repair of DNA double-strand breaks by recombination is key to the maintenance of genome integrity in all living organisms .",
"Recombination can however generate mutations and chromosomal rearrangements , making the regulation and the choice of specific pathways of great importance .",
"Through modulation ... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"blood cells",
"fluorescence imaging",
"medicine and health sciences",
"immune cells",
"pathology and laboratory medicine",
"pathogens",
"immunology",
"microbiology",
"vertebrates",
"animals",
"animal models",
"osteichthyes",
"developmental biology",
"routes of administration",
"model or... | Macrophages, but not neutrophils, are critical for proliferation of Burkholderia cenocepacia and ensuing host-damaging inflammation | journal.ppat.1006437 | null | [
[
"Bacteria belonging to the Burkholderia cepacia complex ( Bcc ) are ubiquitously found in the natural environment , specifically the rhizosphere of plants , and were first identified as the cause of onion rot; however , they are important opportunistic pathogens of individuals with cystic fibrosis ( CF ) and ... | [
"Bacteria of the Burkholderia cepacia complex ( Bcc ) can cause devastating pulmonary infections in cystic fibrosis ( CF ) patients , yet the precise mechanisms underlying inflammation , recurrent exacerbations and transition from chronic stages to acute infection and septicemia are not known .",
"Bcc bacteria ar... | [
"Burkholderia cenocepacia is a bacterial pathogen that increases morbidity and mortality in cystic fibrosis patients , but can also cause serious hospital-acquired infections .",
"In this work we demonstrate that macrophages , but not neutrophils , critically contribute to the development of a rapidly fatal infla... | 2017 |
[
"Introduction",
"Results/Discussion",
"Materials and Methods"
] | [
"biochemistry",
"prokaryotes",
"eukaryotes",
"evolutionary biology",
"molecular biology",
"genetics and genomics"
] | Predicting Protein Function with Hierarchical Phylogenetic Profiles: The Gene3D Phylo-Tuner Method Applied to Eukaryotic Genomes | journal.pcbi.0030237 | null | [
[
"Comparison of the phylogenetic profiles of orthologous proteins in different species is a well-known and powerful method for detecting functionally related proteins .",
"The approach assumes that two functionally related proteins will have been inherited or eliminated in a codependent fashion through spe... | [
"“Phylogenetic profiling” is based on the hypothesis that during evolution functionally or physically interacting genes are likely to be inherited or eliminated in a codependent manner .",
"Creating presence–absence profiles of orthologous genes is now a common and powerful way of identifying functionally associa... | [
"The vast number of protein sequences being determined by the international genomics projects means that it is not possible to functionally characterise all the proteins through direct experimentation .",
"One of the more successful electronic methods for detecting functionally associated genes has been through t... | 2007 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Complement-Opsonized HIV-1 Overcomes Restriction in Dendritic Cells | journal.ppat.1005005 | null | [
[
"Dendritic cells ( DCs ) are key regulators of immunity given their pivotal role in initiating and shaping adaptive immune responses against a vast array of pathogens and cancers [1–3] .",
"HIV-1 has evolved strategies to evade DC-mediated antiviral immunity , i . e . inefficient replication .",
"When... | [
"DCs express intrinsic cellular defense mechanisms to specifically inhibit HIV-1 replication .",
"Thus , DCs are productively infected only at very low levels with HIV-1 , and this non-permissiveness of DCs is suggested to go along with viral evasion .",
"We now illustrate that complement-opsonized HIV-1 ( HIV-... | [
"We here give insight into a substantial novel way of dendritic cell modulation at least during acute HIV-1 infection by triggering integrin receptor signaling .",
"We found that complement-opsonization of the virus is able to relieve SAMHD1 restriction in DCs , thereby initiating strong maturation and co-stimula... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | Structural and Functional Analysis of Murine Polyomavirus Capsid Proteins Establish the Determinants of Ligand Recognition and Pathogenicity | journal.ppat.1005104 | null | [
[
"The engagement of one or several host cell receptors is the first step in the infectious cycle of a virus .",
"A large number of viruses , including many human pathogens , depend on carbohydrate recognition for initial attachment to the cell surface .",
"Viral tropism and the internalization pathway ... | [
"Murine polyomavirus ( MuPyV ) causes tumors of various origins in newborn mice and hamsters .",
"Infection is initiated by attachment of the virus to ganglioside receptors at the cell surface .",
"Single amino acid exchanges in the receptor-binding pocket of the major capsid protein VP1 are known to drasticall... | [
"Viruses are obligate intracellular pathogens , and all of them share one crucial step in their life cycle—the attachment to their host cell via cellular receptors , which are usually proteins or carbohydrates .",
"This step is decisive for the selection of target cells and virus entry .",
"In this study , we i... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"systems biology",
"developmental biology",
"biology",
"computational biology",
"molecular cell biology"
] | Changes in Oscillatory Dynamics in the Cell Cycle of Early Xenopus laevis Embryos | journal.pbio.1001788 | A quantitative study of the Xenopus laevis embryonic cell cycle reveals a transition in the first few cycles between two types of oscillator dynamics to meet two different developmental requirements that increase embryo viability. | [
[
"The early embryonic cell cycles mark the beginning of the life of an organism .",
"Across different phyla , including worms [1] , flies [2] , sea urchins [3] , zebrafish [4] , and frogs [5] , these cycles have a characteristic temporal pattern , with the first cycle being longer and the subsequent cycles... | [
"During the early development of Xenopus laevis embryos , the first mitotic cell cycle is long ( ∼85 min ) and the subsequent 11 cycles are short ( ∼30 min ) and clock-like .",
"Here we address the question of how the Cdk1 cell cycle oscillator changes between these two modes of operation .",
"We found that the... | [
"The early embryonic cell cycles , which initiate cell division , mark the beginning of the life of an organism .",
"Across different phyla , these cycles have a characteristic temporal pattern , with the first cycle being long and the subsequent cycles shorter , leading to rapid increase in cell numbers .",
"H... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"medicine and health sciences",
"chemical compounds",
"parasite evolution",
"tropical diseases",
"sequence tagged site analysis",
"parasitic diseases",
"organic compounds",
"parasitic protozoans",
"parasitology",
"protozoans",
"sequence motif analysis",
"dna",
"homologous recombination",
"... | Identifying functional groups among the diverse, recombining antigenic var genes of the malaria parasite Plasmodium falciparum from a local community in Ghana | journal.pcbi.1006174 | null | [
[
"To address the functional variation present within variable gene families , phylogenetic analyses can typically identify structural and/or functional divergence occurring on a simple , tree-like evolutionary history ( e . g . , [1 , 2] ) .",
"However , this approach is not possible for protein families t... | [
"A challenge in studying diverse multi-copy gene families is deciphering distinct functional types within immense sequence variation .",
"Functional changes can in some cases be tracked through the evolutionary history of a gene family; however phylogenetic approaches are not possible in cases where gene families... | [
"Many disease-causing microbes vary their surface proteins to escape their host’s adaptive immune response—a phenomenon called antigenic variation .",
"Some such systems rely on large , hyper-variable multi-copy gene families that encode functionally diverse protein variants .",
"Because these gene families typ... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"biotechnology",
"phosphorylation",
"plant anatomy",
"cell cycle and cell division",
"cell processes",
"brassica",
"cloning",
"vector cloning",
"membrane proteins",
"plant science",
"model organisms",
"genetically modified plants",
"experimental organism systems",
"molecular biology techni... | Tomato leaf curl Yunnan virus-encoded C4 induces cell division through enhancing stability of Cyclin D 1.1 via impairing NbSKη -mediated phosphorylation in Nicotiana benthamiana | journal.ppat.1006789 | null | [
[
"Geminiviruses cause devastating diseases in fields and economic losses in agriculture in the world [1–7] .",
"They have a single-stranded DNA genome , 2 . 5~3 . 0 kb , encoding 6~7 genes .",
"Some of the viruses are associated with satellites [5] .",
"Many geminiviruses replicate in differentiate... | [
"The whitefly-transmitted geminiviruses induce severe developmental abnormalities in plants .",
"Geminivirus-encoded C4 protein functions as one of viral symptom determinants that could induce abnormal cell division .",
"However , the molecular mechanism by which C4 contributes to cell division induction remain... | [
"Induction of cell division is essential for DNA virus replication in differentiated plant cells .",
"To achieve efficient replication , DNA viruses encode C4 protein to induce cell division .",
"However , the mechanism of C4-induced cell division is still largely unknown .",
"This study demonstrates that tom... | 2018 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | Multilocus Analysis of Divergence and Introgression in Sympatric and Allopatric Sibling Species of the Lutzomyia longipalpis Complex in Brazil | journal.pntd.0002495 | null | [
[
"Speciation events are the result of a complex array of interesting and dynamic biological processes that remain only partially understood [1] .",
"The intricate balance among mutation , recombination , gene flow , genetic drift and natural selection can either unify or differentiate genetic variation , a... | [
"Lutzomyia longipalpis , the main vector of visceral leishmaniasis in Latin America , is a complex of sibling species .",
"In Brazil , a number of very closely related sibling species have been revealed by the analyses of copulation songs , sex pheromones and molecular markers .",
"However , the level of diverg... | [
"The sand fly Lutzomyia longipalpis , the most important vector of visceral leishmaniasis in the Americas , is a complex of cryptic species distributed from Argentina to Mexico .",
"There is evidence for the existence of a number of closely related sibling species of this complex in Brazil that differ in their ma... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"neural networks",
"computational neuroscience",
"psychophysics",
"biology",
"sensory perception",
"sensory systems",
"neuroscience",
"coding mechanisms"
] | Optimality of Human Contour Integration | journal.pcbi.1002520 | null | [
[
"The human's analysis and perception of complex natural scenes under greatly varying environmental conditions is robust and rapid .",
"This remarkable ability of our brain relies on various interacting processes which can be assumed to build representations of visual objects from the information contained... | [
"For processing and segmenting visual scenes , the brain is required to combine a multitude of features and sensory channels .",
"It is neither known if these complex tasks involve optimal integration of information , nor according to which objectives computations might be performed .",
"Here , we investigate i... | [
"Since Helmholtz put forward his concept that the brain performs inference on its sensory input for building an internal representation of the outside world , it is a puzzle for neuroscientific research whether visual perception can indeed be understood from first principles .",
"An important part of vision is th... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"blood cells",
"parasite groups",
"plasmodium",
"viral transmission and infection",
"microbiology",
"parasitic protozoans",
"parasitology",
"developmental biology",
"apicomplexa",
"protozoans",
"red blood cells",
"immunoprecipitation",
"molecular biology techniques",
"research and analysis... | Divergent roles for the RH5 complex components, CyRPA and RIPR in human-infective malaria parasites | journal.ppat.1007809 | null | [
[
"Malaria , caused by Plasmodium parasites , remains a major world health problem with 219 million annual malaria cases and 435 , 000 deaths reported in 2017 [1] .",
"While P . falciparum is responsible for most deaths , predominantly in sub-Saharan Africa , P . vivax is responsible for 34% of all cases ou... | [
"Malaria is caused by Plasmodium parasites , which invade and replicate in erythrocytes .",
"For Plasmodium falciparum , the major cause of severe malaria in humans , a heterotrimeric complex comprised of the secreted parasite proteins , PfCyRPA , PfRIPR and PfRH5 is essential for erythrocyte invasion , mediated ... | [
"Malaria is one of the most devastating infectious diseases , causing significant human suffering and death .",
"It is caused by parasites of the genus Plasmodium proliferating in the bloodstream .",
"Understanding the mechanism of erythrocyte invasion is key for developing novel intervention strategies .",
"... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"oncology",
"genetics and genomics"
] | The Atonal Proneural Transcription Factor Links Differentiation and Tumor Formation in Drosophila | journal.pbio.1000040 | We establish a direct genetic link between cancer and the initiation of differentiation in theDrosophila eye. | [
[
"Cell fate commitment in neural and neuroendocrine lineages of the peripheral nervous system ( PNS ) as well as secretory epithelia is controlled by genes of the basic helix-loop-helix ( bHLH ) superfamily of transcription factors .",
"One of the most structurally and functionally conserved groups within ... | [
"The acquisition of terminal cell fate and onset of differentiation are instructed by cell type–specific master control genes .",
"Loss of differentiation is frequently observed during cancer progression , but the underlying causes and mechanisms remain poorly understood .",
"We tested the hypothesis that maste... | [
"During embryonic development , cells become more and more specialized , and this process is referred to as differentiation .",
"In contrast to normal adult cells , cancer cells—like embryonic cells—display fewer differentiated properties .",
"It has been postulated that the acquisition of terminal differentiat... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"public health and epidemiology",
"plant biology",
"statistics",
"spatial epidemiology",
"plant science",
"mathematics",
"plant pathology",
"population biology",
"biostatistics",
"epidemiological methods",
"infectious diseases",
"theoretical biology",
"epidemiology",
"biology... | The Effect of Heterogeneity on Invasion in Spatial Epidemics: From Theory to Experimental Evidence in a Model System | journal.pcbi.1002174 | null | [
[
"Host heterogeneity is receiving increasing attention as one of the factors affecting the dynamics of epidemic spread .",
"The properties of individual hosts , such as contact rate , susceptibility , or infectiousness , can vary across a population as a result of environmental [1] , [2] , genetic [3] and ... | [
"Heterogeneity in host populations is an important factor affecting the ability of a pathogen to invade , yet the quantitative investigation of its effects on epidemic spread is still an open problem .",
"In this paper , we test recent theoretical results , which extend the established “percolation paradigm” to t... | [
"Pathogen spread and epidemic invasion in plant , animal and human populations depend on host properties ( infectivity , susceptibility ) that can vary amongst hosts within the same population .",
"However , such host variability ( or heterogeneity ) is typically difficult to control experimentally , and little e... | 2011 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine",
"dermatology",
"infectious diseases",
"bacterial diseases",
"public health and epidemiology",
"non-clinical medicine",
"clinical research design",
"drugs and devices",
"epidemiology",
"biology",
"microbiology",
"vectors and hosts",
"health care policy"
] | Comparison of Real-Time Quantitative PCR and Culture for the Diagnosis of Emerging Rickettsioses | journal.pntd.0001540 | null | [
[
"Rickettsial diseases are zoonoses caused by obligate intracellular bacteria found in the order Rickettsiales [1] .",
"In the past , only research laboratories were able to isolate rickettsiae from clinical specimens [2] .",
"However , in recent years , the development of cell culture systems for vira... | [
"Isolation of Rickettsia species from skin biopsies may be replaced by PCR .",
"We evaluated culture sensitivity compared to PCR based on sampling delay and previous antibiotic treatment .",
"Skin biopsies and ticks from patients with suspected Rickettsia infection were screened for Rickettsia spp .",
"using ... | [
"Diagnosis of Rickettsia infection would benefit by use of the more rapid and sensitive method of quantitative real-time PCR than the time-intensive and less sensitive method of culturing Rickettsia species from skin biopsies .",
"We evaluated culture sensitivity compared to PCR according to sampling delay and pr... | 2012 |
[
"Introduction",
"Results/Discussion",
"Materials and Methods"
] | [
"medicine",
"cell motility",
"statistics",
"african trypanosomiasis",
"microbiology",
"host-pathogen interaction",
"parasitic diseases",
"parasitology",
"model organisms",
"mathematics",
"biophysics simulations",
"infectious diseases",
"protozoan models",
"biology",
"biophysics",
"phys... | Impact of Microscopic Motility on the Swimming Behavior of Parasites: Straighter Trypanosomes are More Directional | journal.pcbi.1002058 | null | [
[
"Eukaryotic cell motility plays a key role in many physiological functions including cell division , development , survival , as well as disease pathogenesis [1]–[4] .",
"Studies of single cell motility have not only uncovered different aspects of these functions , but also provide great biophysical insig... | [
"Microorganisms , particularly parasites , have developed sophisticated swimming mechanisms to cope with a varied range of environments .",
"African Trypanosomes , causative agents of fatal illness in humans and animals , use an insect vector ( the Tsetse fly ) to infect mammals , involving many developmental cha... | [
"Single cell motility is essential for many physiological functions .",
"We seek to further our understanding of the swimming mechanism of trypanosomes - parasites responsible for deadly disease in humans and cattle .",
"Trypanosomes are found both in the blood stream and invading tissue spaces .",
"The swimm... | 2011 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"global health"
] | Estimating Diarrheal Illness and Deaths Attributable to Shigellae and Enterotoxigenic Escherichia coli among Older Children, Adolescents, and Adults in South Asia and Africa | journal.pntd.0002705 | null | [
[
"Although frequently underappreciated as a significant health problem , recent publications have highlighted the potential importance of diarrhea as a continuing cause of morbidity and mortality among older children , adolescents and adults living in low- and middle-income countries [1] , [2] .",
"Similar... | [
"While Shigellae and strains of enterotoxigenic Escherichia coli ( ETEC ) are important causes of diarrhea-associated morbidity and mortality among infants and young children ( <5 years of age ) , their health impact in older age groups is unclear .",
"We sought to quantify the overall burden of shigellosis and E... | [
"We aimed to estimate the burden of diarrhea due to Shigellae and ETEC among persons ≥5 years of age in Africa and South Asia using two methodological approaches .",
"Method 1 employed diarrhea proportionate mortality and published estimates of pathogen-specific hospitalization .",
"Method 2 utilized published ... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biochemistry",
"virology",
"computational biology"
] | A Specificity Map for the PDZ Domain Family | journal.pbio.0060239 | A genome-scale specificity map for PDZ domains reveals how family members recognize ligands to assemble signaling complexes and also reveals how viruses target these domains to subvert host cell function. | [
[
"Modular protein–protein recognition domains are involved in the assembly of numerous intracellular complexes that mediate diverse cellular functions .",
"Thousands of recognition domains are contained within the human proteome , and these have been classified into over 70 distinct families [1] .",
"T... | [
"PDZ domains are protein–protein interaction modules that recognize specific C-terminal sequences to assemble protein complexes in multicellular organisms .",
"By scanning billions of random peptides , we accurately map binding specificity for approximately half of the over 330 PDZ domains in the human and Caenor... | [
"The PDZ domain is a structural domain that functions as a protein–protein interaction module that recognizes specific C-terminal peptide sequences to assemble intracellular complexes important in signaling pathways of multicellular organisms .",
"These modules are associated with human disease and are targets of... | 2008 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine and health sciences",
"enzyme-linked immunoassays",
"pathology and laboratory medicine",
"togaviruses",
"chikungunya infection",
"pathogens",
"tropical diseases",
"microbiology",
"geographical locations",
"sudan",
"animals",
"alphaviruses",
"viruses",
"chikungu... | Urban Chikungunya in the Middle East and North Africa: A systematic review | journal.pntd.0005707 | null | [
[
"The objective of this study was to characterize the epidemiology of urban CHIKV in the MENA region through a systematic review of published human prevalence and incidence studies , human outbreaks and reported cases , and studies reporting CHIKV detections and prevalence/infection rates in Aedes mosquitoes .... | [
"The epidemiology of Chikungunya virus ( CHIKV ) in the Middle East and North Africa ( MENA ) is not well characterized despite increasing recognition of its expanding infection and disease burden in recent years .",
"Following Cochrane Collaboration guidelines and reporting our findings following PRISMA guidelin... | [
"Chikungunya virus ( CHIKV ) is an alphavirus whose principal vectors are the Aedes aegypti and Aedes albopictus mosquitoes .",
"Though long endemic to Asia and Africa , detection of CHIKV has recently been reported throughout the Western Hemisphere , including much of South America and the Caribbean .",
"In th... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"molecular biology/recombination",
"microbiology/microbial evolution and genomics",
"infectious diseases/antimicrobials and drug resistance"
] | Structural Features of Single-Stranded Integron Cassette attC Sites and Their Role in Strand Selection | journal.pgen.1000632 | null | [
[
"Integrons are DNA elements that acquire open-reading frames through site-specific recombination and convert them to functional genes by ensuring their correct expression .",
"Integrons were first identified , in the 1980′s , as a device used by Gram negative bacteria to acquire and disseminate antibiotic... | [
"We recently showed that cassette integration and deletion in integron platforms were occurring through unconventional site-specific recombination reactions involving only the bottom strand of attC sites .",
"The lack of sequence conservation among attC sites led us to hypothesize that sequence-independent struct... | [
"Integrons play a preponderant role in the development of multiple antibiotic resistances among Gram-negative bacteria .",
"Their success is rooted in their unique aptitude to assemble genes through a site-specific recombination process .",
"They have recently been shown to use an unconventional recombination p... | 2009 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"blood cells",
"medicine and health sciences",
"immune physiology",
"enzyme-linked immunoassays",
"immune cells",
"immunology",
"microbiology",
"parasitic diseases",
"protozoan life cycles",
"parasitic protozoans",
"vaccines",
"animal models",
"developmental biology",
"model organisms",
... | An α-Gal-containing neoglycoprotein-based vaccine partially protects against murine cutaneous leishmaniasis caused by Leishmania major | journal.pntd.0006039 | null | [
[
"Cutaneous leishmaniasis ( CL ) is a neglected , vector-borne disease caused by several species of the protozoan parasite , Leishmania .",
"CL currently affects up to 1 . 2 million people worldwide annually [1] , although due to stigma and psychological burden post-infection , its prevalence has been rece... | [
"Protozoan parasites from the genus Leishmania cause broad clinical manifestations known as leishmaniases , which affect millions of people worldwide .",
"Cutaneous leishmaniasis ( CL ) , caused by L . major , is one the most common forms of the disease in the Old World .",
"There is no preventive or therapeuti... | [
"Despite a worldwide prevalence , cutaneous leishmaniasis ( CL ) remains largely neglected , with no prophylactic or therapeutic vaccine available .",
"In the Old World , CL is mainly caused by either Leishmania major or L . tropica parasites , which produce localized cutaneous ulcers , often leading to scarring ... | 2017 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"epidemiology"
] | Epidemiologic Features and Environmental Risk Factors of Severe Fever with Thrombocytopenia Syndrome, Xinyang, China | journal.pntd.0002820 | null | [
[
"Severe fever with thrombocytopenia syndrome ( SFTS ) is an emerging infectious disease discovered in middle-eastern China [1] .",
"The disease usually presents as fever , thrombocytopenia , and leukocytopenia , with case-fatality rates ranging from 2 . 5% to 30% .",
"In 2009 , the causative agent was... | [
"Severe fever with thrombocytopenia syndrome ( SFTS ) is an emerging infectious disease discovered in rural areas of Central China in 2009 , caused by a novel bunyavirus , SFTS virus ( SFTSV ) .",
"The disease usually presents as fever , thrombocytopenia , and leukocytopenia , with case-fatality rates ranging fro... | [
"Severe fever with thrombocytopenia syndrome ( SFTS ) is an emerging infectious disease discovered in rural areas of Central China in 2009 , caused by a novel bunyavirus , SFTS virus ( SFTSV ) .",
"The disease usually presents as fever , thrombocytopenia , and leukocytopenia , with case-fatality rates ranging fro... | 2014 |
[
"Introduction",
"Materials and Methods",
"Results and Discussion"
] | [
"developmental biology",
"biology",
"zoology",
"parasitology",
"helminthology"
] | Transcriptional Analysis of a Unique Set of Genes Involved in Schistosoma mansoni Female Reproductive Biology | journal.pntd.0001907 | null | [
[
"Schistosomiasis , caused by infections with trematode parasites from the genus Schistosoma , affects more than 200 million people worldwide [1] .",
"Cercariae released by intermediate host snails penetrate the skin of the mammalian definitive host where they develop into schistosomula .",
"Schistosom... | [
"Schistosomiasis affects more than 200 million people globally .",
"The pathology of schistosome infections is due to chronic tissue inflammation and damage from immune generated granulomas surrounding parasite eggs trapped in host tissues .",
"Schistosoma species are unique among trematode parasites because th... | [
"Schistosomiasis is a chronic , debilitating disease that affects over 200 million people globally .",
"The pathology associated with schistosomiasis is caused by host immune responses to parasite eggs .",
"Therefore , it is imperative to identify pathways responsible for controlling worm reproductive biology .... | 2012 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious diseases",
"emerging infectious diseases",
"vector biology",
"virology",
"leishmaniasis",
"co-infections",
"biology",
"microbiology",
"parasitic diseases",
"parasitology",
"viral vectors"
] | Epidemiologic Relationship between Toscana Virus Infection and Leishmania infantum Due to Common Exposure to Phlebotomus perniciosus Sandfly Vector | journal.pntd.0001328 | null | [
[
"Sand flies are tiny insects living in periurban or rural environments , often close to domestic animals and humans; they fly silently and only on short distances .",
"Sand flies are widely distributed in peri-Mediterranean countries where their activity peaks during summertime .",
"Their bite ( only ... | [
"Sand flies are recognised vectors of parasites in the genus Leishmania and a number of arthropod-borne viruses , in particular viruses within the genus Phlebovirus , family Bunyaviridae .",
"In southern France , Toscana phlebovirus ( TOSV ) is recognized as a prominent cause of summer meningitis .",
"Since Lei... | [
"Sand flies are tiny insects widely distributed in peri-Mediterranean countries where they can transmit Leishmania parasite and Toscana virus ( TOSV ) .",
"Since those microorganisms have a common vector , an epidemiologic link has been assumed for a long time .",
"However , there is no scientific evidence of s... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"medicine and health sciences",
"linguistics",
"neural networks",
"linguistic morphology",
"transcranial magnetic stimulation",
"brain",
"social sciences",
"brain electrophysiology",
"electrophysiology",
"neuroscience",
"cognitive psychology",
"network analysis",
"brain mapping",
"bioassay... | Data-driven brain network models differentiate variability across language tasks | journal.pcbi.1006487 | null | [
[
"Cognitive responses and human behavior have been hypothesized to be the outcome of complex interactions between regional populations of neurons [1 , 2] and show significant variability across individuals .",
"While certain patterns of brain activity are robust [3] , many patterns change with learning and... | [
"The relationship between brain structure and function has been probed using a variety of approaches , but how the underlying structural connectivity of the human brain drives behavior is far from understood .",
"To investigate the effect of anatomical brain organization on human task performance , we use a data-... | [
"How the organization of the brain drives human behavior is an important but open question in neuroscience .",
"Recent advances in non-invasive imaging techniques and analytical tools allow one to build personalized brain network models that simulate an individual’s brain activity based on the underlying anatomic... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"blood cells",
"medicine and health sciences",
"immune cells",
"vesicles",
"pathology and laboratory medicine",
"viral transmission and infection",
"pathogens",
"immunology",
"microbiology",
"parasitic diseases",
"protozoan life cycles",
"parasitic protozoans",
"developmental biology",
"pr... | The host cell secretory pathway mediates the export of Leishmania virulence factors out of the parasitophorous vacuole | journal.ppat.1007982 | null | [
[
"The protozoan parasite Leishmania causes a spectrum of human diseases known as the leishmaniases [1] .",
"Infectious insect-stage promastigotes are inoculated in mammals upon the blood meal of the vector and are internalized by phagocytes where they differentiate into mammalian-stage amastigotes [2] .",
... | [
"To colonize phagocytes , Leishmania subverts microbicidal processes through components of its surface coat that include lipophosphoglycan and the GP63 metalloprotease .",
"How these virulence glycoconjugates are shed , exit the parasitophorous vacuole ( PV ) , and traffic within host cells is poorly understood .... | [
"Leishmania promastigotes are internalized by phagocytes into a highly modified phagosome that promotes parasite growth and differentiation into the amastigote form .",
"To survive in the phagosome , Leishmania employs surface-bound glycoconjugates such as the GP63 metalloprotease and lipophosphoglycan to subvert... | 2019 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"schistosoma",
"invertebrates",
"schistosoma mansoni",
"medicine and health sciences",
"education",
"helminths",
"sociology",
"social sciences",
"parasitic diseases",
"animals",
"health care",
"ascaris",
"ascaris lumbricoides",
"sanitation",
"public and occupational health",
"schools",... | School Water, Sanitation, and Hygiene, Soil-Transmitted Helminths, and Schistosomes: National Mapping in Ethiopia | journal.pntd.0004515 | null | [
[
"Improvements in child health and education are key targets in many international development programs , but relatively little is known about the multiple health and educational benefits of integrating different school-based health interventions .",
"Preventive chemotherapy ( PC ) can reduce morbidity cau... | [
"It is thought that improving water , sanitation , and hygiene ( WASH ) might reduce the transmission of schistosomes and soil-transmitted helminths , owing to their life cycles .",
"However , few large-scale studies have yet assessed the real extent of associations between WASH and these parasites .",
"In the ... | [
"Water , sanitation , and hygiene ( WASH ) are potentially important control measures for parasitic worms , but few large-scale and well-designed research studies have aimed to quantify the relationships between WASH and infections with these parasites , or demonstrated the practicality of integrating WASH assessme... | 2016 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"cell death",
"medicine and health sciences",
"radiation therapy",
"oxygen",
"cell cycle and cell division",
"cancer treatment",
"cell processes",
"pulmonology",
"oncology",
"physiological processes",
"radiation effects",
"pharmacology",
"oxygen consumption",
"medical hypoxia",
"respirat... | Spatial Metrics of Tumour Vascular Organisation Predict Radiation Efficacy in a Computational Model | journal.pcbi.1004712 | null | [
[
"It is increasingly recognised that an important aspect of cancers is their heterogeneity [1] .",
"This heterogeneity exists between patients , between different tumours within a single patient [2] , within the differing cellular populations in a single tumour and even at the genetic scale between cancer ... | [
"Intratumoural heterogeneity is known to contribute to poor therapeutic response .",
"Variations in oxygen tension in particular have been correlated with changes in radiation response in vitro and at the clinical scale with overall survival .",
"Heterogeneity at the microscopic scale in tumour blood vessel arc... | [
"In this paper we use a mathematical model , called a hybrid cellular automaton , to study the effect of different vessel distributions on radiation therapy outcomes at the cellular level .",
"We show that the correlation between radiation outcome and spatial organization of vessels changes signs between relative... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"dosage compensation",
"invertebrates",
"genetic networks",
"gene regulation",
"animals",
"invertebrate genomics",
"dna transcription",
"animal models",
"drosophila melanogaster",
"model organisms",
"network analysis",
"genome analysis",
"epigenetics",
"drosophila",
"chromatin",
"resea... | Effects of Gene Dose, Chromatin, and Network Topology on Expression in Drosophila melanogaster | journal.pgen.1006295 | null | [
[
"Deficiency ( Df ) is a genetic definition for mutations that affect contiguous loci on a chromosome [1] .",
"They are now known to be a result of DNA deletion [2] and have many important uses in genetic analysis .",
"Dfs are part of an important series of tests for defining the nature of mutant allel... | [
"Deletions , commonly referred to as deficiencies by Drosophila geneticists , are valuable tools for mapping genes and for genetic pathway discovery via dose-dependent suppressor and enhancer screens .",
"More recently , it has become clear that deviations from normal gene dosage are associated with multiple diso... | [
"Deletions alter gene dose in heterozygotes and bring distant regions of the genome into juxtaposition .",
"We find that the transcriptional dose response is generally varied , gene-specific and coherently propagates into gene expression regulatory networks .",
"Analysis of expression profiles of deletion heter... | 2016 |
[
"Introduction",
"Results",
"Motif dynamics",
"Discussion",
"Methods"
] | [] | Self-Organization of Microcircuits in Networks of Spiking Neurons with Plastic Synapses | journal.pcbi.1004458 | null | [
[
"The wiring of neuronal networks exhibits structure across a broad range of spatial scales [1] .",
"For example , patterns of connectivity among small groups of cortical neurons are over- or under-represented compared to random networks [2–5] .",
"The prevalence of these motifs is related to neurons’ ... | [
"The synaptic connectivity of cortical networks features an overrepresentation of certain wiring motifs compared to simple random-network models .",
"This structure is shaped , in part , by synaptic plasticity that promotes or suppresses connections between neurons depending on their joint spiking activity .",
... | [
"The connectivity of mammalian brains exhibits structure at a wide variety of spatial scales , from the broad ( which brain areas connect to which ) to the extremely fine ( where synapses form on the morphology of individual neurons ) .",
"Recent experimental work in the neocortex has highlighted structure at the... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine and health sciences",
"crystal structure",
"pathology and laboratory medicine",
"pneumococcus",
"chemical compounds",
"nucleases",
"enzymes",
"pathogens",
"condensed matter physics",
"microbiology",
"dna-binding proteins",
"enzymology",
"carbohydrates",
"organic compounds",
"an... | Molecular Characterization of N-glycan Degradation and Transport in Streptococcus pneumoniae and Its Contribution to Virulence | journal.ppat.1006090 | null | [
[
"The covalent attachment of carbohydrates to macromolecules , such as proteins and lipids , to form glycoconjugates is one of the most abundant modifications of molecules in nature .",
"In the human body , the glycans displayed on glycoproteins and glycolipids in and on the outer surface of cells help to ... | [
"The carbohydrate-rich coating of human tissues and cells provide a first point of contact for colonizing and invading bacteria .",
"Commensurate with N-glycosylation being an abundant form of protein glycosylation that has critical functional roles in the host , some host-adapted bacteria possess the machinery t... | [
"Streptococcus pneumoniae ( pneumococcus ) is a bacterium that causes extensive morbidity and mortality in humans .",
"Vaccines and antibiotics are effective forms of prevention and treatment , respectively , but present challenges as it is a constant race to vaccinate against the enormous and ever evolving pool ... | 2017 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"cell biology",
"animal cells",
"computational neuroscience",
"astrocytes",
"biology and life sciences",
"cellular types",
"computational biology",
"glial cells",
"biophysics",
"macroglial cells",
"biophysical simulations"
] | Glutamate Mediated Astrocytic Filtering of Neuronal Activity | journal.pcbi.1003964 | null | [
[
"Evidence obtained during the last few years inaugurated the notion that astrocytes may play a role in information processing in the brain .",
"The \"tripartite synapse\" concept ( presynaptic , postsynaptic , astrocyte ) [1] , [2] is gaining acceptance , and is progressively replacing the historical bipa... | [
"Neuron-astrocyte communication is an important regulatory mechanism in various brain functions but its complexity and role are yet to be fully understood .",
"In particular , the temporal pattern of astrocyte response to neuronal firing has not been fully characterized .",
"Here , we used neuron-astrocyte cult... | [
"Over the past 20 years , astrocytes , a type of brain cells that were considerably disregarded , have gradually been found to actually display remarkable properties .",
"In contrast with neurons , which communicate through changes in their membrane potential , astrocytes communicate as networks through propagate... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"blood cells",
"medicine and health sciences",
"immune cells",
"body fluids",
"pathology and laboratory medicine",
"immune physiology",
"viral transmission and infection",
"spleen",
"pathogens",
"immunology",
"microbiology",
"viruses",
"dna viruses",
"cytotoxic t cells",
"herpesviruses",... | EBV persistence without its EBNA3A and 3C oncogenes in vivo | journal.ppat.1007039 | null | [
[
"Epstein Barr virus ( EBV ) was discovered as the first human candidate tumor virus in Burkitt lymphoma 54 years ago [1 , 2] .",
"EBV is probably the most potent of all the human tumor viruses , because it can readily transform human B cells in vitro [3] .",
"In the resulting lymphoblastoid cell lines... | [
"The oncogenic Epstein Barr virus ( EBV ) infects the majority of the human population and usually persists within its host for life without symptoms .",
"The EBV oncoproteins nuclear antigen 3A ( EBNA3A ) and 3C ( EBNA3C ) are required for B cell transformation in vitro and are expressed in EBV associated immuno... | [
"Epstein Barr virus ( EBV ) was discovered 54 years ago as the first human candidate tumor virus .",
"In vitro , EBV can readily transform human B cells into indefinitely growing cell lines .",
"In this transformation process , multiple EBV proteins play an important role , such as the two oncogenes EBNA3A and ... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"blood cells",
"flow cytometry",
"vero cells",
"medicine and health sciences",
"immune cells",
"pathology and laboratory medicine",
"togaviruses",
"viral transmission and infection",
"chikungunya infection",
"pathogens",
"immunology",
"biological cultures",
"skeletal muscles",
"microbiolog... | Inflammatory monocytes mediate control of acute alphavirus infection in mice | journal.ppat.1006748 | null | [
[
"Chikungunya ( CHIKV ) , Ross River ( RRV ) , Mayaro , and o’nyong-nyong viruses are mosquito-transmitted positive-sense , enveloped RNA viruses in the Alphavirus genus of the family Togaviridae .",
"These viruses cause both endemic and explosive epidemics of debilitating acute and chronic musculoskeletal... | [
"Chikungunya virus ( CHIKV ) and Ross River virus ( RRV ) are mosquito-transmitted alphaviruses that cause debilitating acute and chronic musculoskeletal disease .",
"Monocytes are implicated in the pathogenesis of these infections; however , their specific roles are not well defined .",
"To investigate the rol... | [
"Mosquito-transmitted arthritogenic alphaviruses , such as chikungunya virus ( CHIKV ) , Mayaro virus , and Ross River virus ( RRV ) , cause large disease outbreaks .",
"Infection with these viruses results in severe pain and inflammation in joints , tendons , and muscles , likely due to direct viral infection of... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"invertebrates",
"meiosis",
"medicine and health sciences",
"reproductive system",
"cell cycle and cell division",
"cell processes",
"animals",
"reproductive physiology",
"germ cells",
"animal models",
"drosophila melanogaster",
"model organisms",
"experimental organism systems",
"mitochon... | Sperm-Leucylaminopeptidases are required for male fertility as structural components of mitochondrial paracrystalline material in Drosophila melanogaster sperm | journal.pgen.1007987 | null | [
[
"Insects are the record-holders for the sperm size; they have the smallest and the biggest flagellated sperm among the animals .",
"Insect sperm contain the same structural elements as mammalian sperm , such as the plasma membrane , the acrosome , the elongated nucleus , the axoneme and the mitochondria .... | [
"Drosophila melanogaster sperm reach an extraordinary long size , 1 . 8 mm , by the end of spermatogenesis .",
"The mitochondrial derivatives run along the entire flagellum and provide structural rigidity for flagellar movement , but its precise function and organization is incompletely understood .",
"The two ... | [
"Mitochondria are essential organelles of developing spermatids , but many of the factors that necessary to mitochondrial differentiation , elongation and structural composition during spermatogenesis need to be identified .",
"In almost all insect species there are two mitochondrial derivatives in mature sperm .... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"medicine and health sciences",
"cancer treatment",
"immunology",
"cancers and neoplasms",
"enzymology",
"cancer immunotherapy",
"oncology",
"hematologic cancers and related disorders",
"clinical medicine",
"artificial intelligence",
"pharmacology",
"lymphomas",
"enzyme inhibitors",
"immun... | Rational discovery of dual-indication multi-target PDE/Kinase inhibitor for precision anti-cancer therapy using structural systems pharmacology | journal.pcbi.1006619 | null | [
[
"Multi-factorial , multi-genic complex diseases such as cancer and Alzheimer’s disease are associated with multiple pathological manifestations .",
"For example , hypertension , inflammation , and herpes virus infection could all be related to the tau and amyloid beta pathologies of Alzheimer’s disease [1... | [
"Many complex diseases such as cancer are associated with multiple pathological manifestations .",
"Moreover , the therapeutics for their treatments often lead to serious side effects .",
"Thus , it is needed to develop multi-indication therapeutics that can simultaneously target multiple clinical indications o... | [
"Polypharmacology has emerged as a new strategy for discovering novel therapeutics .",
"Existing efforts in the rational design of polypharmacology have three limitations: focus on a single clinical indication , difficulties in target selection and lead identification/optimization , and ignorance of genome-wide d... | 2019 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"hepatitis c",
"medicine",
"infectious diseases",
"hepatitis",
"theoretical biology",
"sexually transmitted diseases",
"population dynamics",
"biology",
"population biology",
"viral diseases",
"infectious disease modeling"
] | Analysis of Hepatitis C Virus Decline during Treatment with the Protease Inhibitor Danoprevir Using a Multiscale Model | journal.pcbi.1002959 | null | [
[
"Hepatitis C virus ( HCV ) infection is a major cause of chronic liver disease and a leading reason of liver transplant in the world .",
"About 130–170 million people are chronically infected with HCV [1] .",
"Achieving a long-term sustained virologic response ( SVR ) , defined as an undetectable HCV ... | [
"The current paradigm for studying hepatitis C virus ( HCV ) dynamics in patients utilizes a standard viral dynamic model that keeps track of uninfected ( target ) cells , infected cells , and virus .",
"The model does not account for the dynamics of intracellular viral replication , which is the major target of ... | [
"Chronic infection with hepatitis C virus ( HCV ) remains an important health-care problem worldwide despite significant progress in the development of HCV therapy since the discovery of the virus in 1989 .",
"Current treatment options are focused on direct-acting antiviral agents ( DAAs ) that target specific st... | 2013 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"infectious diseases/neglected tropical diseases",
"evolutionary biology/morphogenesis and cell biology"
] | Multi-host Model-Based Identification of Armillifer agkistrodontis (Pentastomida), a New Zoonotic Parasite from China | journal.pntd.0000647 | null | [
[
"Human pentastomiasis is a food- or water-borne parasitic zoonosis caused by pentastomids or “tongue worms” [1] .",
"Pentastomida are dioecious obligate parasites commonly placed into a separate sub-class of the subphylum Crustacea , phylum Arthropoda , despite their worm-like appearance .",
"However ... | [
"Pentastomiasis is a rare parasitic infection of humans .",
"Pentastomids are dioecious obligate parasites requiring multiple hosts to complete their lifecycle .",
"Despite their worm-like appearance , they are commonly placed into a separate sub-class of the subphylum Crustacea , phylum Arthropoda .",
"Howev... | [
"Little information is currently available on the lifecycle and morphology of pentastomids , a new zoonotic parasite in China .",
"The lifecycle of Armillifer agkistrodontis was established in multiple hosts , i . e . , an intermediate host and a definitive host , and the parasite examined in terms of morphology ... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"vero cells",
"chemical bonding",
"chemical compounds",
"molecular probe techniques",
"293t cells",
"biological cultures",
"immunoblotting",
"esters",
"immunoprecipitation",
"molecular biology techniques",
"research and analysis methods",
"physical chemistry",
"lipids",
"chemistry",
"cro... | Critical role for cholesterol in Lassa fever virus entry identified by a novel small molecule inhibitor targeting the viral receptor LAMP1 | journal.ppat.1007322 | null | [
[
"Lassa fever virus ( LASV ) is a highly pathogenic enveloped RNA virus that is endemic in western Africa [1 , 2] .",
"In early studies of LASV infection , the surface membrane protein α-dystroglycan ( α-DG ) was identified as a glycoprotein ( GP ) attachment factor and a key determinant of tissue tropism ... | [
"Lassa fever virus ( LASV ) is endemic in West Africa and causes severe hemorrhagic fever and sensorineural hearing loss .",
"We identified a small molecule inhibitor of LASV and used it to analyze the mechanism of entry .",
"Using a photo-reactive analog that retains antiviral activity as a probe , we identifi... | [
"Lassa fever virus ( LASV ) is endemic in West Africa and can cause fatal infection .",
"Currently , there is no vaccine or effective post-exposure treatment .",
"Here we identify 3 . 3 , a small molecule that inhibits LASV infection by targeting lysosome-associated membrane protein 1 ( LAMP1 ) , which binds to... | 2018 |
[
"Introduction",
"Materials and Methods",
"Results and Discussion"
] | [
"malacology",
"gene expression",
"biology",
"molecular cell biology",
"zoology",
"molecular biology",
"parasitology",
"helminthology"
] | Polyethyleneimine (PEI) Mediated siRNA Gene Silencing in the Schistosoma mansoni Snail Host, Biomphalaria glabrata | journal.pntd.0001212 | null | [
[
"Biomphalaria glabrata is an intermediate snail host that transmits the digenean platyhelminth parasite , Schistosoma mansoni , in the Western Hemisphere .",
"This snail host is easily maintained in the laboratory outside of its natural environment and , therefore , serves as a useful model organism for c... | [
"An in vivo , non-invasive technique for gene silencing by RNA interference ( RNAi ) in the snail , Biomphalaria glabrata , has been developed using cationic polymer polyethyleneimine ( PEI ) mediated delivery of long double-stranded ( ds ) and small interfering ( si ) RNA .",
"Cellular delivery was evaluated and... | [
"Freshwater snails are important in the transmission of schistosomiasis .",
"As part of an integral control effort to combat the spread of schistosomiasis new intervention tools are being sought .",
"One method is to interrupt the transmission of the causative schistosome parasite during the intra-molluscan pha... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Natural Killer Cell Sensing of Infected Cells Compensates for MyD88 Deficiency but Not IFN-I Activity in Resistance to Mouse Cytomegalovirus | journal.ppat.1004897 | null | [
[
"Type I interferons ( IFN-I ) orchestrate vertebrate antiviral defenses through two complementary mechanisms [1] .",
"These cytokines induce multiple Interferon Stimulated Genes ( ISG ) coding for effector molecules of cell-intrinsic antiviral immunity .",
"IFN-I instruct antiviral innate and adaptive... | [
"In mice , plasmacytoid dendritic cells ( pDC ) and natural killer ( NK ) cells both contribute to resistance to systemic infections with herpes viruses including mouse Cytomegalovirus ( MCMV ) .",
"pDCs are the major source of type I IFN ( IFN-I ) during MCMV infection .",
"This response requires pDC-intrinsic... | [
"Type I interferons ( IFN-I ) are innate cytokines crucial for vertebrate antiviral defenses .",
"IFN-I exert antiviral effector functions and orchestrate antiviral immunity .",
"IFN-I are induced early after infection , upon sensing of viral particles or infected cells by immune receptors .",
"Intracellular ... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | New Strains Intended for the Production of Inactivated Polio Vaccine at Low-Containment After Eradication | journal.ppat.1005316 | null | [
[
"The Global Polio Eradication Initiative ( GPEI ) is the biggest and most ambitious health programme aimed at a single disease in history and is very close to eliminating naturally occurring wild poliovirus from the planet [1] .",
"It has involved the extensive use of both the live attenuated vaccines tha... | [
"Poliomyelitis has nearly been eradicated through the efforts of the World Health Organization’s Global Eradication Initiative raising questions on containment of the virus after it has been eliminated in the wild .",
"Most manufacture of inactivated polio vaccines currently requires the growth of large amounts o... | [
"New polio vaccines will be needed to safeguard global eradication: Sabin strains are known to evolve to fill the niche left by wild-strains so their long-term use is incompatible with eradication; most current inactivated vaccine is made from wild polioviruses so that production presents a significant biosecurity ... | 2015 |
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