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"
] | [] | Vpu Exploits the Cross-Talk between BST2 and the ILT7 Receptor to Suppress Anti-HIV-1 Responses by Plasmacytoid Dendritic Cells | journal.ppat.1005024 | null | [
[
"Plasmacytoid dendritic cells ( pDCs ) are a distinct subset of DCs that exhibit a unique ability to secrete high amounts of interferons and other cytokines in response to viruses .",
"Even though they constitute less than 1% of the total cell content of peripheral blood in humans , they are considered a ... | [
"Plasmacytoid dendritic cells ( pDCs ) constitute a major source of type-I interferon ( IFN-I ) production during acute HIV infection .",
"Their activation results primarily from TLR7-mediated sensing of HIV-infected cells .",
"However , the interactions between HIV-infected T cells and pDCs that modulate this ... | [
"Plasmacytoid dendritic cells ( pDCs ) produce large quantities of type I interferon ( IFN-I ) upon stimulation by many viruses , including HIV .",
"Their activation is very effective following cell contacts with HIV-1-infected CD4+ T cells .",
"We investigated whether HIV-1 could regulate the antiviral respons... | 2015 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"radiology and medical imaging",
"radiology and medical imaging/pet and spect imaging"
] | In Vivo Imaging of Schistosomes to Assess Disease Burden Using Positron Emission Tomography (PET) | journal.pntd.0000827 | null | [
[
"Schistosomiasis is a disease of chronic morbidity affecting the liver , mesentery , and urogenital tract of infected individuals , caused by the parasitic trematode worms , schistosomes .",
"In certain endemic regions like China , the increasing focus on antischistosomal chemotherapy over the past 30 yea... | [
"Schistosomes are chronic intravascular helminth parasites of humans causing a heavy burden of disease worldwide .",
"Diagnosis of schistosomiasis currently requires the detection of schistosome eggs in the feces and urine of infected individuals .",
"This method unreliably measures disease burden due to poor s... | [
"Schistosomiasis is a well studied parasitic disease that is far from eradication despite the development of an effective treatment .",
"The lack of an efficacious vaccine and high re-infection rates after treatment are major factors in its intractable worldwide prevalence .",
"A non-invasive imaging technique ... | 2010 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"geomorphology",
"invertebrates",
"medicine and health sciences",
"landforms",
"helminths",
"topography",
"tropical diseases",
"hookworms",
"parasitic diseases",
"anemia",
"animals",
"health care",
"ascaris",
"ascaris lumbricoides",
"neglected tropical diseases",
"strongyloides stercor... | Clinical evaluation for morbidity associated with soil-transmitted helminth infection in school-age children on Pemba Island, Tanzania | journal.pntd.0007581 | null | [
[
"Soil-transmitted helminths ( Ascaris lumbricoides , hookworm , Strongyloides stercoralis , and Trichuris trichiura ) affect more than 1 . 5 billion people worldwide with the highest prevalence and intensity of infection often observed in school-age children in low- and middle-income countries [1 , 2] .",
... | [
"More than 1 . 5 billion people are infected with soil-transmitted helminths ( Ascaris lumbricoides , hookworm , Strongyloides stercoralis , and Trichuris trichiura ) , causing an estimated global burden in excess of 3 million disability-adjusted life years .",
"However , the relationship between soil-transmitted... | [
"Soil-transmitted helminth infections frequently affect children and impoverished individuals in low-resource settings and are associated with negative health effects .",
"We attempted to measure morbidity in school-age children from Pemba Island , Tanzania who are infected with soil-transmitted helminths but wit... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genome-wide association studies",
"mathematics",
"gene expression",
"genetics",
"statistics",
"biology",
"biostatistics",
"statistical methods",
"genetics and genomics"
] | Joint Modelling of Confounding Factors and Prominent Genetic Regulators Provides Increased Accuracy in Genetical Genomics Studies | journal.pcbi.1002330 | null | [
[
"Genome-wide analysis of the regulatory role of polymorphic loci on gene expression has been carried out in a range of different study designs and biological systems .",
"For example , association mapping in human has uncovered an abundance of cis associations that contribute to the variation of a third o... | [
"Expression quantitative trait loci ( eQTL ) studies are an integral tool to investigate the genetic component of gene expression variation .",
"A major challenge in the analysis of such studies are hidden confounding factors , such as unobserved covariates or unknown subtle environmental perturbations .",
"The... | [
"The computational analysis of genetical genomics studies is challenged by confounding variation that is unrelated to the genetic factors of interest .",
"Several approaches to account for these confounding factors have been proposed , greatly increasing the sensitivity in recovering direct genetic ( cis ) associ... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"sequencing techniques",
"medicine and health sciences",
"infectious disease epidemiology",
"population genetics",
"quantitative traits",
"genomic databases",
"genome analysis",
"molecular biology techniques",
"population biology",
"sequence analysis",
"epidemiology",
"molecular biology",
"s... | The Contribution of Viral Genotype to Plasma Viral Set-Point in HIV Infection | journal.ppat.1004112 | null | [
[
"Plasma viral load has long been considered one of the most important clinical measures in HIV-positive patients .",
"The progression time from infection to AIDS or death varies enormously from a few years to decades , and ‘set-point’ viral load , taken early in the asymptomatic phase of the disease , is ... | [
"Disease progression in HIV-infected individuals varies greatly , and while the environmental and host factors influencing this variation have been widely investigated , the viral contribution to variation in set-point viral load , a predictor of disease progression , is less clear .",
"Previous studies , using t... | [
"HIV viral load , the amount of virus in the blood , is an important predictor of rate of CD4+ cell decline , time to AIDS and onwards transmission .",
"Plasma viral load is influenced by many environmental and host factors , but the contribution of the viral genome is not yet clear .",
"We have adapted a metho... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"invertebrates",
"medicine and health sciences",
"rna interference",
"nervous system",
"neuroscience",
"animals",
"animal models",
"developmental biology",
"drosophila melanogaster",
"model organisms",
"physiological parameters",
"experimental organism systems",
"epigenetics",
"morphogenes... | The sex of specific neurons controls female body growth in Drosophila | journal.pbio.2002252 | null | [
[
"The sex of an organism has profound effects on its morphology , physiology , and behaviour .",
"It also influences the risk of developing diseases of growth and metabolism such as obesity , metabolic syndrome , cardiovascular disease , and cancer [1 , 2] .",
"One important feature of sexual dimorphis... | [
"Sexual dimorphisms in body size are widespread throughout the animal kingdom but their underlying mechanisms are not well characterized .",
"Most models for how sex chromosome genes specify size dimorphism have emphasized the importance of gonadal hormones and cell-autonomous influences in mammals versus strictl... | [
"Males and females differ in size in many animal species .",
"This reflects differences in body growth during development that are under the control of sex chromosome genes .",
"In mammals , sex chromosome genes act in the gonads to instruct them to produce secreted hormones that regulate male-female difference... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biology"
] | Regulating Repression: Roles for the Sir4 N-Terminus in Linker DNA Protection and Stabilization of Epigenetic States | journal.pgen.1002727 | null | [
[
"The eukaryotic genome is organized into euchromatic and heterochromatic domains that generally reflect their potential for gene expression .",
"Chromatin repressed by the Silent information regulator ( SIR ) complex in the budding yeast Saccharomyces cerevisiae shares many key features with heterochromat... | [
"Silent information regulator proteins Sir2 , Sir3 , and Sir4 form a heterotrimeric complex that represses transcription at subtelomeric regions and homothallic mating type ( HM ) loci in budding yeast .",
"We have performed a detailed biochemical and genetic analysis of the largest Sir protein , Sir4 .",
"The ... | [
"Three Silent Information Regulator ( SIR ) proteins Sir2 , Sir3 , and Sir4 are involved in the epigenetic gene silencing of the homothallic mating ( HM ) loci and of telomere-proximal genes in budding yeast .",
"They bind as a heterotrimeric complex to chromatin , repressing the underlying genes .",
"Sir2 has ... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"virology"
] | Identification of Amino Acids in HA and PB2 Critical for the Transmission of H5N1 Avian Influenza Viruses in a Mammalian Host | journal.ppat.1000709 | null | [
[
"The H5N1 avian influenza viruses ( AIVs ) have attracted extensive attention for their deadly impact on both animals and humans .",
"The number of people who have been subclinically infected with H5N1 viruses is very limited [1] , and H5N1 AIVs have a 60% fatality rate in humans ( World Health Organizati... | [
"Since 2003 , H5N1 influenza viruses have caused over 400 known cases of human infection with a mortality rate greater than 60% .",
"Most of these cases resulted from direct contact with virus-contaminated poultry or poultry products .",
"Although only limited human-to-human transmission has been reported to da... | [
"H5N1 influenza viruses have caused over 400 human infections in 15 countries and continue to circulate in poultry and wild birds .",
"Most human infections resulted from direct contact with virus-contaminated poultry or poultry products .",
"It would be disastrous if H5N1 viruses acquired the ability to effici... | 2009 |
[
"Introduction",
"Methods and Materials",
"Results",
"Discussion"
] | [
"medicine",
"infectious diseases",
"clinical immunology",
"immunology",
"parasitic diseases"
] | Characterising the Mucosal and Systemic Immune Responses to Experimental Human Hookworm Infection | journal.ppat.1002520 | null | [
[
"The hookworms Necator americanus and Ancylostoma duodenale infect an estimated 740 million people , mostly in tropical regions of the world , causing significant burden of disease [1] .",
"As for most Neglected Tropical Diseases ( NTDs ) , there is currently no prophylactic or therapeutic vaccine against... | [
"The mucosal cytokine response of healthy humans to parasitic helminths has never been reported .",
"We investigated the systemic and mucosal cytokine responses to hookworm infection in experimentally infected , previously hookworm naive individuals from non-endemic areas .",
"We collected both peripheral blood... | [
"Parasitic worms reside in the gastrointestinal tracts of billions of humans in developing countries .",
"Despite the enormous disease burdens associated with these infections , very little is known about the immune response in the gut tissue of humans to these parasites .",
"We conducted a clinical trial where... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"humoral immunity",
"invertebrates",
"innate immune system",
"mucosal immunity",
"immune activation",
"immunology",
"microbiology",
"animals",
"viruses",
"infectious disease immunology",
"rna viruses",
"immunoregulation",
"gene disruption",
"insects",
"immune response",
"immune system"... | The Toll-Dorsal Pathway Is Required for Resistance to Viral Oral Infection in Drosophila | journal.ppat.1004507 | null | [
[
"Pathogens can infect their hosts through many different routes .",
"In humans , for instance , microbes can directly enter the host through skin lesions or mediated by insect vectors .",
"However , most of human infections start at mucosal surfaces of the respiratory , digestive or genital tracts .",... | [
"Pathogen entry route can have a strong impact on the result of microbial infections in different hosts , including insects .",
"Drosophila melanogaster has been a successful model system to study the immune response to systemic viral infection .",
"Here we investigate the role of the Toll pathway in resistance... | [
"Pathogenic microbes can enter their hosts through different routes .",
"This can have a strong impact on which host defensive mechanisms are elicited and in disease outcome .",
"We used the model organism Drosophila melanogaster to understand how resistance to viruses differs between infection by direct virus ... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"humoral immunity",
"medicine",
"infectious diseases",
"tropical diseases (non-neglected)",
"immunity",
"flavivirus",
"biology",
"microbiology",
"host-pathogen interaction"
] | A Dynamic Landscape for Antibody Binding Modulates Antibody-Mediated Neutralization of West Nile Virus | journal.ppat.1002111 | null | [
[
"Flaviviruses are a group of ∼70 RNA viruses that cause morbidity and mortality on a global scale , with greater than 100 million human infections annually [1] .",
"Viruses within this genus of medical concern include yellow fever virus , tick-borne encephalitis virus , Japanese encephalitis virus , dengu... | [
"Neutralizing antibodies are a significant component of the host's protective response against flavivirus infection .",
"Neutralization of flaviviruses occurs when individual virions are engaged by antibodies with a stoichiometry that exceeds a required threshold .",
"From this “multiple-hit” perspective , the ... | [
"Neutralizing antibodies are a critical aspect of protection from flavivirus infection .",
"The primary targets of neutralizing antibodies are the envelope ( E ) proteins incorporated into virions .",
"The neutralizing activity of antibodies is determined by the affinity with which they interact with the virion... | 2011 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"socioeconomic aspects of health",
"geography",
"public health and epidemiology",
"disease ecology",
"social and behavioral sciences",
"epidemiology",
"infectious disease epidemiology",
"global health",
"public health",
"human geography"
] | The Role of Socioeconomic Status in Longitudinal Trends of Cholera in Matlab, Bangladesh, 1993–2007 | journal.pntd.0001997 | null | [
[
"Despite global efforts to improve drinking water quality and sanitation in developing countries , cholera continues to pose a serious public health problem .",
"In 2010 , 317 , 534 cases were reported from 48 countries , an increase of 130% from just 10 years earlier [1] .",
"Many of the cases in 201... | [
"There has been little evidence of a decline in the global burden of cholera in recent years as the number of cholera cases reported to WHO continues to rise .",
"Cholera remains a global threat to public health and a key indicator of lack of socioeconomic development .",
"Overall socioeconomic development is t... | [
"Cholera is a bacterial disease usually spread through contaminated water that causes severe diarrhea and dehydration .",
"Modern sewage and water treatment have virtually eliminated cholera in industrialized countries but cholera is still present throughout much of SE Asia , Latin America and sub-Saharan Africa ... | 2013 |
[
"Introduction",
"Methods",
"Data analysis",
"Results",
"Discussion"
] | [
"invertebrates",
"dengue virus",
"medicine and health sciences",
"pathology and laboratory medicine",
"pathogens",
"microbiology",
"animals",
"wolbachia",
"viruses",
"organisms",
"age groups",
"rna viruses",
"infectious disease control",
"insect vectors",
"bacteria",
"near-infrared spe... | Near-Infrared Spectroscopy, a Rapid Method for Predicting the Age of Male and Female Wild-Type and Wolbachia Infected Aedes aegypti | journal.pntd.0005040 | null | [
[
"The mosquito Aedes aegypti is the primary vector for dengue , Zika and chikungunya viruses .",
"Up to 100 million dengue cases occur annually [5 , 6] and an estimated 440 , 000–1 , 300 , 000 Zika cases were reported in early 2016 .",
"Notably , 3893 babies born to Zika infected mothers have been diag... | [
"Estimating the age distribution of mosquito populations is crucial for assessing their capacity to transmit disease and for evaluating the efficacy of available vector control programs .",
"This study reports on the capacity of the near-infrared spectroscopy ( NIRS ) technique to rapidly predict the ages of the ... | [
"Aedes aegypti is the principal vector for dengue , chikungunya and Zika viruses .",
"These viruses require a period of development inside the mosquito before they can be transmitted to humans .",
"Depending on environmental factors , dengue and Zika viruses take an average of 8–10 days to replicate inside the ... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"computational neuroscience",
"olfactory system",
"biology and life sciences",
"sensory systems",
"computational biology",
"neuroscience",
"coding mechanisms"
] | Heterogeneity and Convergence of Olfactory First-Order Neurons Account for the High Speed and Sensitivity of Second-Order Neurons | journal.pcbi.1003975 | null | [
[
"In insects and vertebrates the first two neuronal layers of the olfactory system present the same organization where many ORNs in the first layer converge to a small number of output neurons in the second layer – PNs in insects and mitral cells in vertebrates [1] , [2] .",
"The ORNs that project onto a s... | [
"In the olfactory system of male moths , a specialized subset of neurons detects and processes the main component of the sex pheromone emitted by females .",
"It is composed of several thousand first-order olfactory receptor neurons ( ORNs ) , all expressing the same pheromone receptor , that contact synaptically... | [
"Understanding how sensory signals are optimally encoded by nervous systems is of strong interest to neuroscientists , and also to engineers as it may lead to more efficient artificial detection systems .",
"This is particularly relevant to olfaction , because the current electronic noses are far outperformed by ... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"cytokines",
"respiratory infections",
"immunology",
"host-pathogen interaction",
"microbiology",
"staphylococcus aureus",
"pulmonology",
"bacterial diseases",
"skin infections",
"staphylococci",
"bacterial pathogens",
"infectious diseases",
"microbial pathogens",
"biology",
... | Induction of Type I Interferon Signaling Determines the Relative Pathogenicity of Staphylococcus aureus Strains | journal.ppat.1003951 | null | [
[
"Staphylococcus aureus is an important pathogen causing skin and soft tissue infections as well as pneumonia and superinfection post influenza [1] .",
"The development of antibiotic resistance , in particular methicillin resistant S . aureus ( MRSA ) and the highly transmissible clone USA300 are of signif... | [
"The tremendous success of S . aureus as a human pathogen has been explained primarily by its array of virulence factors that enable the organism to evade host immunity .",
"Perhaps equally important , but less well understood , is the importance of the intensity of the host response in determining the extent of ... | [
"The virulence of the S . aureus , and especially that associated with the epidemic MRSA USA300 strains , has been primarily explained by its expression of a specific set of virulence factors .",
"We postulated that that intensity of the host innate immune response activated by specific staphylococcal strains is ... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | A Temporal Gate for Viral Enhancers to Co-opt Toll-Like-Receptor Transcriptional Activation Pathways upon Acute Infection | journal.ppat.1004737 | null | [
[
"Infection by pathogens is detected by the host innate immune system through interaction of Pathogen-Associated Molecular Patterns ( PAMPs ) using a range of extra and intra-cellular host Pathogen-Recognitions-Receptors ( PRRs ) [1–3] .",
"The major group of PRRs is represented by the family of Toll-Like-... | [
"Viral engagement with macrophages activates Toll-Like-Receptors ( TLRs ) and viruses must contend with the ensuing inflammatory responses to successfully complete their replication cycle .",
"To date , known counter-strategies involve the use of viral-encoded proteins that often employ mimicry mechanisms to bloc... | [
"Here we discover how inflammatory signalling may unintentionally promote infection , as a result of viruses evolving DNA sequences , known as enhancers , which act as a bait to prey on the infected cell transcription factors induced by inflammation .",
"The major inflammatory transcription factors activated are ... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"developmental biology",
"plant science",
"plant growth and development",
"plant cell biology",
"plant genetics",
"biology",
"morphogenesis",
"pattern formation"
] | Cell Polarity and Patterning by PIN Trafficking through Early Endosomal Compartments in Arabidopsis thaliana | journal.pgen.1003540 | null | [
[
"Plant hormone auxin locally accumulates in plant tissues and regulates multiple processes of plant growth and development [1] , [2] .",
"Directional intercellular transport of auxin underlies most of known auxin-dependent control of development , including embryogenesis , root and shoot organogenesis , v... | [
"PIN-FORMED ( PIN ) proteins localize asymmetrically at the plasma membrane and mediate intercellular polar transport of the plant hormone auxin that is crucial for a multitude of developmental processes in plants .",
"PIN localization is under extensive control by environmental or developmental cues , but mechan... | [
"Auxin is a unique plant hormone , which is actively and directionally transported in plant tissues .",
"Transported auxin locally accumulates in the plant body and triggers a multitude of responses , including organ formation and patterning .",
"Therefore , regulation of the directional auxin transport is very... | 2013 |
[
"Introduction",
"Models and methods",
"Results",
"Discussion"
] | [
"phosphorylation",
"cell motility",
"vesicles",
"enzymes",
"enzymology",
"chemical equilibrium",
"membrane receptor signaling",
"network analysis",
"cellular structures and organelles",
"enzyme chemistry",
"physical chemistry",
"computer and information sciences",
"proteins",
"enzyme regul... | A dual regulation mechanism of histidine kinase CheA identified by combining network-dynamics modeling and system-level input-output data | journal.pcbi.1006305 | null | [
[
"Living systems sense environmental signals and respond by altered behaviors .",
"Control of behavior is achieved by a myriad of biochemical reactions forming a reaction network , in which some reactions are directly regulated by the sensed signals .",
"However , exactly which reactions are controlled... | [
"It is challenging to decipher molecular mechanisms in biological systems from system-level input-output data , especially for complex processes that involve interactions among multiple components .",
"We addressed this general problem for the bacterial histidine kinase CheA , the activity of which is regulated i... | [
"In complex biological systems , it is often difficult to determine which steps in the underlying biochemical network are regulated by the signal by using direct experimental measurements alone .",
"In this paper , we tackled this general problem in the case of the kinase activity of the multi-domain histidine ki... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genetics and genomics/disease models",
"genetics and genomics/animal genetics",
"oncology/prostate cancer",
"genetics and genomics/cancer genetics"
] | Interactions between Cells with Distinct Mutations in c-MYC and Pten in Prostate Cancer | journal.pgen.1000542 | null | [
[
"Prevailing models of multistep carcinogenesis posit that oncogenic mutations arise in isolated cells in situ followed by clonal expansion .",
"This implies that important competitive interactions occur between mutant and normal cells as well as between cells with distinct oncogenic mutations during tumor... | [
"In human somatic tumorigenesis , mutations are thought to arise sporadically in individual cells surrounded by unaffected cells .",
"This contrasts with most current transgenic models where mutations are induced synchronously in entire cell populations .",
"Here we have modeled sporadic oncogene activation usi... | [
"In most human cancers , mutations are thought to arise in a single cell or few cells surrounded by their unaffected neighbors .",
"Expansion of mutant cells can then allow the accumulation of additional mutations .",
"The cell–cell interactions that may occur between mutant and unaffected cells or between cell... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"neuroscience/motor systems",
"computer science/systems and control theory",
"neuroscience/theoretical neuroscience",
"computational biology/computational neuroscience"
] | Optimal Control Predicts Human Performance on Objects with Internal Degrees of Freedom | journal.pcbi.1000419 | null | [
[
"Humans regularly interact with objects with internal degrees of freedom from carrying a glass of water to using a cloth to polish a table .",
"While objects with no internal degrees of freedom can be regarded as a fixed extension of our limbs [1] , [2] non-rigid objects pose a more complex control proble... | [
"On a daily basis , humans interact with a vast range of objects and tools .",
"A class of tasks , which can pose a serious challenge to our motor skills , are those that involve manipulating objects with internal degrees of freedom , such as when folding laundry or using a lasso .",
"Here , we use the framewor... | [
"Humans are highly skilled at tool use .",
"Simple tools have no internal degrees of freedom .",
"For example , knowing the position and orientation of a hammer allows us to , in theory , predict the forces it will generate on our hand when we wield it and the consequences our actions will have on the hammer ."... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Material and methods"
] | [
"blood cells",
"phosphorylation",
"bacteriology",
"medicine and health sciences",
"immune cells",
"respiratory infections",
"pathology and laboratory medicine",
"pathogens",
"immunology",
"cell processes",
"microbiology",
"pulmonology",
"physiological processes",
"secretion systems",
"ne... | The Citrobacter rodentium type III secretion system effector EspO affects mucosal damage repair and antimicrobial responses | journal.ppat.1007406 | null | [
[
"Citrobacter rodentium is an extracellular , mouse specific , intestinal pathogen used to model mechanisms of virulence employed by the human pathogens enteropathogenic and enterohemorrhagic Escherichia coli ( EPEC and EHEC ) and inflammatory bowel diseases [1] .",
"In C57BL/6 mice , shedding of C . roden... | [
"Infection with Citrobacter rodentium triggers robust tissue damage repair responses , manifested by secretion of IL-22 , in the absence of which mice succumbed to the infection .",
"Of the main hallmarks of C . rodentium infection are colonic crypt hyperplasia ( CCH ) and dysbiosis .",
"In order to colonize th... | [
"Citrobacter rodentium is a gold standard model to study pathogen-host-microbiome interactions .",
"Two of the hallmarks of C . rodentium infection are colonic damage repair responses and colitis; symptoms that are shared with inflammatory bowel diseases in humans .",
"The processes leading to tissue damage rep... | 2018 |
[
"Introduction",
"Results/Discussion",
"Materials and Methods"
] | [
"genetic association studies",
"gene expression",
"genetics",
"biology",
"human genetics",
"genetics of disease",
"genetics and genomics"
] | Insertion/Deletion Polymorphisms in the ΔNp63 Promoter Are a Risk Factor for Bladder Exstrophy Epispadias Complex | journal.pgen.1003070 | null | [
[
"Bladder exstrophy epispadias complex ( BEEC; MIM600057 ) is a serious congenital anomaly present in 1 in 36 , 000 live births [1] .",
"BEEC is manifested as a cluster of ventral midline defects including:",
"1 ) ventral bladder and abdominal wall defects ,",
"2 ) epispadias ( split external genit... | [
"Bladder exstrophy epispadias complex ( BEEC ) is a severe congenital anomaly; however , the genetic and molecular mechanisms underlying the formation of BEEC remain unclear .",
"TP63 , a member of TP53 tumor suppressor gene family , is expressed in bladder urothelium and skin over the external genitalia during m... | [
"Bladder exstrophy epispadias complex is a severe congenital abnormality .",
"The affected babies' bladders are born open , leaking urine constantly .",
"Treatment involves multiple major reconstructive surgeries and the need for lifelong care for the complications of the disease .",
"Although a number of stu... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"plant biology/plant-biotic interactions",
"plant biology",
"molecular biology"
] | The Lectin Receptor Kinase LecRK-I.9 Is a Novel Phytophthora Resistance Component and a Potential Host Target for a RXLR Effector | journal.ppat.1001327 | null | [
[
"Plants deploy multiple strategies to defend themselves against pathogen attack .",
"A key step is the perception of pathogen molecules in order to activate various defense responses .",
"During infection pathogens produce microbe-associated molecular patterns ( MAMPs ) or elicit the production of hos... | [
"In plants , an active defense against biotrophic pathogens is dependent on a functional continuum between the cell wall ( CW ) and the plasma membrane ( PM ) .",
"It is thus anticipated that proteins maintaining this continuum also function in defense .",
"The legume-like lectin receptor kinase LecRK-I . 9 is ... | [
"Phytophthora species are notorious plant pathogens which cause a variety of devastating crop diseases .",
"Phytophthora pathogens secrete a plethora of effector proteins , several of which are known to interact with receptors in the host cell thereby either activating or suppressing defense responses .",
"Unli... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Surface-Associated Lipoproteins Link Enterococcus faecalis Virulence to Colitogenic Activity in IL-10-Deficient Mice Independent of Their Expression Levels | journal.ppat.1004911 | null | [
[
"The Gram-positive commensal Enterococcus faecalis is a member of the human intestinal core microbiota [1] , but is also known for harboring several putative virulence genes mediating its pathogenicity [2] .",
"The ability to acquire antibiotic resistance genes [3] and the emerging importance in nosocomia... | [
"The commensal Enterococcus faecalis is among the most common causes of nosocomial infections .",
"Recent findings regarding increased abundance of enterococci in the intestinal microbiota of patients with inflammatory bowel diseases and induction of colitis in IL-10-deficient ( IL-10-/- ) mice put a new perspect... | [
"Enterococcus faecalis is a commensal of the human intestinal core microbiota harboring several putative virulence factors , which highlight its role as opportunistic pathogen .",
"This dualistic character is supported by recent evidence linking Enterococcus spp .",
"to the pathogenesis of inflammatory bowel di... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"invertebrates",
"medicine and health sciences",
"reproductive system",
"gonads",
"vertebrates",
"animals",
"invertebrate genomics",
"alternative splicing",
"animal models",
"drosophila melanogaster",
"model organisms",
"genome analysis",
"drosophila",
"research and analysis methods",
"g... | Alternative Splicing within and between Drosophila Species, Sexes, Tissues, and Developmental Stages | journal.pgen.1006464 | null | [
[
"Alternative pre-mRNA splicing ( “AS” ) greatly expands the proteome diversity within species by creating different combinations of exons from the same genomic loci [1] .",
"The resulting mRNA isoforms are usually expressed in a tissue or developmental-stage specific manner and underlie numerous essential... | [
"Alternative pre-mRNA splicing ( “AS” ) greatly expands proteome diversity , but little is known about the evolutionary landscape of AS in Drosophila and how it differs between embryonic and adult stages or males and females .",
"Here we study the transcriptomes from several tissues and developmental stages in ma... | [
"Alternative pre-mRNA splicing ( “AS” ) greatly expands the proteome diversity within and between species by creating different combinations of exons from the same genomic loci .",
"Recent comparisons of transcriptomes of equivalent adult organs in several vertebrate species revealed that AS differs significantly... | 2016 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [] | Pathogenomic Inference of Virulence-Associated Genes in Leptospira interrogans | journal.pntd.0002468 | null | [
[
"Leptospirosis , caused by spirochete bacteria of the genus Leptospira , is a zoonotic disease of high public health impact [1] .",
"Globally , nearly 900 , 000 people are infected annually through contact with contaminated water , infected tissue or urine of mammalian reservoir hosts [2] .",
"Phyloge... | [
"Leptospirosis is a globally important , neglected zoonotic infection caused by spirochetes of the genus Leptospira .",
"Since genetic transformation remains technically limited for pathogenic Leptospira , a systems biology pathogenomic approach was used to infer leptospiral virulence genes by whole genome compar... | [
"Leptospirosis is one of the most common diseases transmitted by animals worldwide .",
"It is important because it causes an often lethal febrile illnesses in tropical and subtropical areas associated with poor sanitation and agriculture .",
"Leptospirosis may be epidemic , associated with natural disasters and... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"blood cells",
"medicine and health sciences",
"immune cells",
"enzymes",
"metalloproteases",
"immunology",
"enzymology",
"microbiology",
"silver staining",
"parasitic diseases",
"protozoan life cycles",
"parasitic protozoans",
"developmental biology",
"protozoans",
"leishmania",
"prom... | Leishmania major degrades murine CXCL1 – An immune evasion strategy | journal.pntd.0007533 | null | [
[
"Leishmania spp .",
"are unicellular eukaryotic protozoan parasites that are transmitted to mammalian hosts by sandfly ( Phlebotomine and Lutzomyia spp . ) bites [1] .",
"Upon transmission of L . major promastigotes ( the infectious stage for mammalian hosts with a long slender body and an anterior fl... | [
"Leishmaniasis is a global health problem with an estimated report of 2 million new cases every year and more than 1 billion people at risk of contracting this disease in endemic areas .",
"The innate immune system plays a central role in controlling L . major infection by initiating a signaling cascade that resu... | [
"Our study discovered a highly specific role for L . major metalloprotease in cleaving and degrading murine CXCL1 .",
"Indeed , L . major metalloprotease did not cleave murine CXCL2 or human CXCL1 , CXCL2 and CXCL8 .",
"CXCL1 is a critical chemokine required for neutrophil recruitment to the site of infection; ... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | Extremely High Mutation Rate of HIV-1 In Vivo | journal.pbio.1002251 | The rate of spontaneous mutation of the HIV-1 genome within its human host is exceptionally high, is mostly driven by host cytidine deaminases, and probably plays a role in disease progression. | [
[
"RNA viruses exist as extremely diverse populations , with every possible spontaneous mutation along the genome appearing within each patient every day [1] .",
"This diversity plays a fundamental role in HIV-1 biology , enabling the virus to successfully evade the immune system , rapidly modify cell tropi... | [
"Rates of spontaneous mutation critically determine the genetic diversity and evolution of RNA viruses .",
"Although these rates have been characterized in vitro and in cell culture models , they have seldom been determined in vivo for human viruses .",
"Here , we use the intrapatient frequency of premature sto... | [
"The high levels of genetic diversity of the HIV-1 virus grant it the ability to escape the immune system , to rapidly evolve drug resistance , and to circumvent vaccination strategies .",
"However , our knowledge of HIV-1 mutation rates has been largely restricted to in vitro and cell culture studies because of ... | 2015 |
[
"Introduction",
"Methods",
"Results",
"Discussion",
"Supporting Information"
] | [
"mathematics",
"homo (human)",
"genetics and genomics"
] | Imputation-Based Analysis of Association Studies: Candidate Regions and Quantitative Traits | journal.pgen.0030114 | null | [
[
"Although the development of cheap high-throughput genotyping assays have made large-scale association studies a reality , most ongoing association studies genotype only a small proportion of SNPs in the region of study ( be that the whole genome , or a set of candidate regions ) .",
"Because of correlati... | [
"We introduce a new framework for the analysis of association studies , designed to allow untyped variants to be more effectively and directly tested for association with a phenotype .",
"The idea is to combine knowledge on patterns of correlation among SNPs ( e . g . , from the International HapMap project or re... | [
"Ongoing association studies are evaluating the influence of genetic variation on phenotypes of interest ( hereditary traits and susceptibility to disease ) in large patient samples .",
"However , although genotyping is relatively cheap , most association studies genotype only a small proportion of SNPs in the re... | 2007 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods",
"Supporting Information"
] | [
"cell biology",
"plant biology",
"plants"
] | The Mother Centriole Plays an Instructive Role in Defining Cell Geometry | journal.pbio.0050149 | Six genes required for centriole positioning are identified inChlamydomonas. Analysis of cells with mutations in these genes reveals a crucial role for the centriole in positioning other organelles. | [
[
"A fundamental question in cell biology is how cell geometry is established and maintained [1–4] .",
"Cell geometry refers to the characteristic positioning of organelles within the cell body in order for a cell to be able to carry out its specified function .",
"Despite the importance of cell geometr... | [
"Centriole positioning is a key step in establishment and propagation of cell geometry , but the mechanism of this positioning is unknown .",
"The ability of pre-existing centrioles to induce formation of new centrioles at a defined angle relative to themselves suggests they may have the capacity to transmit spat... | [
"Cells are not just homogenous bags of enzymes , but instead have a precise and complex internal architecture .",
"However , the mechanisms that define this architecture remain unclear .",
"How do different organelles find their proper location within the cell ?",
"We have begun to address this question for o... | 2007 |
[
"Introduction",
"Results",
"Discussion",
"Methods",
"Supporting Information"
] | [
"drosophila",
"genetics and genomics",
"homo (human)",
"neurological disorders"
] | dAtaxin-2 Mediates Expanded Ataxin-1-Induced Neurodegeneration in a Drosophila Model of SCA1 | journal.pgen.0030234 | null | [
[
"Inherited ataxias are a genetically heterogeneous group of neurodegenerative diseases characterized by loss of motor coordination and balance .",
"They can be caused by loss-of-function or gain-of-function mechanisms; some ataxias are triggered by missense mutations , while others by triplet repeat expan... | [
"Spinocerebellar ataxias ( SCAs ) are a genetically heterogeneous group of neurodegenerative disorders sharing atrophy of the cerebellum as a common feature .",
"SCA1 and SCA2 are two ataxias caused by expansion of polyglutamine tracts in Ataxin-1 ( ATXN1 ) and Ataxin-2 ( ATXN2 ) , respectively , two proteins tha... | [
"The spinocerebellar ataxias ( SCAs ) are a group of ∼30 neurodegenerative disorders caused by different types of mutations in a variety of unrelated genes .",
"For example , SCA1 and SCA2 are caused by mutations in Ataxin-1 and Ataxin-2 , two proteins related in name only .",
"Despite these differences , most ... | 2007 |
[
"Introduction",
"Results and discussion",
"Materials and methods"
] | [
"cancer detection and diagnosis",
"cancer genomics",
"medicine and health sciences",
"carcinomas",
"cancers and neoplasms",
"basic cancer research",
"mathematical models",
"oncology",
"mutation",
"probability distribution",
"mathematics",
"adenocarcinomas",
"discrete mathematics",
"combina... | Estimating the number of genetic mutations (hits) required for carcinogenesis based on the distribution of somatic mutations | journal.pcbi.1006881 | null | [
[
"Cancer is known to result primarily from genetic mutations [1–3] .",
"Moreover , models of carcinogenesis–the multi-stage and multi-hit models–suggest that cancer results from a small number of ( two–seven ) mutations [4–11] .",
"Yet the availability of extensive genomic data [12 , 13] and decades of... | [
"Individual instances of cancer are primarily a result of a combination of a small number of genetic mutations ( hits ) .",
"Knowing the number of such mutations is a prerequisite for identifying specific combinations of carcinogenic mutations and understanding the etiology of cancer .",
"We present a mathemati... | [
"Cancer is primarily a result of genetic mutations .",
"Each individual instance of cancer is initiated by a specific combination of a small number of mutations ( hits ) .",
"In trying to identify these combinations of mutations , it is important to know how many hits to look for .",
"However , there are conf... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biology"
] | Exquisite Light Sensitivity of Drosophila melanogaster Cryptochrome | journal.pgen.1003615 | null | [
[
"Nearly all plants and animals use daily patterns of day and night to entrain their endogenous circadian oscillators .",
"These responses utilize photic input from both visual photoreceptors , as well as from non-visual circadian photopigments ( reviewed in [1]–[3] ) .",
"Both visual photopigments and... | [
"Drosophila melanogaster shows exquisite light sensitivity for modulation of circadian functions in vivo , yet the activities of the Drosophila circadian photopigment cryptochrome ( CRY ) have only been observed at high light levels .",
"We studied intensity/duration parameters for light pulse induced circadian p... | [
"We investigate the paradox that fruit flies show exquisite light sensitivity for day/night circadian clock functions , yet the circadian photoreceptor cryptochrome ( CRY ) responds only to very high light levels in assays requiring immediate responses .",
"Our in vivo behavioral assays are unique in that we expo... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"functional genomics",
"genome evolution",
"population genetics",
"microbiology",
"fungal evolution",
"microbial evolution",
"mycology",
"genetic polymorphism",
"comparative genomics",
"biology",
"genetic drift",
"yeast",
"natural selection",
"genetics",
"genomics",
"genetics and genom... | Trait Variation in Yeast Is Defined by Population History | journal.pgen.1002111 | null | [
[
"An overall aim in modern biology is to achieve an in-depth understanding of how selection for certain traits in the context of an organism's ecology favors specific mechanistic changes in the cell machinery and establish distinct genetic variants within populations .",
"The budding yeast Saccharomyces ce... | [
"A fundamental goal in biology is to achieve a mechanistic understanding of how and to what extent ecological variation imposes selection for distinct traits and favors the fixation of specific genetic variants .",
"Key to such an understanding is the detailed mapping of the natural genomic and phenomic space and... | [
"An overall aim in modern biology is to achieve an in-depth understanding of an organism's physiology in the context of its ecology and historic selective pressures that have been acting on its genome .",
"The baker's yeast , Saccharomyces cerevisiae , has a peculiar life history completely dominated by clonal re... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"taxonomy",
"genome evolution",
"phylogenetics",
"data management",
"phylogenetic analysis",
"genome analysis",
"computer and information sciences",
"proteins",
"molecular evolution",
"gene prediction",
"evolutionary systematics",
"biochemistry",
"eukaryota",
"proteomes",
"protein domain... | Measuring the impact of gene prediction on gene loss estimates in Eukaryotes by quantifying falsely inferred absences | journal.pcbi.1007301 | null | [
[
"During the evolution of eukaryotic genomes , the number of gene loss events is estimated to be higher than gene gains [1–4] and this high loss gives rise to patchy phylogenetic patterns of gene occurrence .",
"A high level of gene loss suggests a gene rich ancestor of eukaryotes .",
"Alternatively , ... | [
"In recent years it became clear that in eukaryotic genome evolution gene loss is prevalent over gene gain .",
"However , the absence of genes in an annotated genome is not always equivalent to the loss of genes .",
"Due to sequencing issues , or incorrect gene prediction , genes can be falsely inferred as abse... | [
"To understand the evolution of eukaryotic species , we can look at the differences and similarities in their genomes .",
"Since the first genomes were sequenced , scientists have , among other things , been studying these differences and similarities by evaluating the presences and absences of genes , and they h... | 2019 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine and health sciences",
"ixodes",
"pathology and laboratory medicine",
"ruminants",
"pathogens",
"microbiology",
"vertebrates",
"rickettsia",
"mammals",
"animals",
"dogs",
"metagenomics",
"mammalian genomics",
"ticks",
"rickettsiales",
"bacteria",
"bacteria... | Metagenomic profiling of ticks: Identification of novel rickettsial genomes and detection of tick-borne canine parvovirus | journal.pntd.0006805 | null | [
[
"Ticks are ectoparasitic arthropods that feed exclusively on the blood of their vertebrate hosts .",
"Across the world , ticks act as vectors of human and animal pathogens ( including viruses , bacteria and protozoa ) , often mediating transfer of infection from one host species to another , including zoo... | [
"Across the world , ticks act as vectors of human and animal pathogens .",
"Ticks rely on bacterial endosymbionts , which often share close and complex evolutionary links with tick-borne pathogens .",
"As the prevalence , diversity and virulence potential of tick-borne agents remain poorly understood , there is... | [
"We have shown how DNA sequencing can be used to detect and characterise potentially pathogenic microorganisms carried by ticks .",
"We surveyed hard ticks collected from domesticated animals across the West Bank territory of Palestine .",
"All the ticks came from species that are also capable of feeding on hum... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"developmental biology",
"model organisms",
"genetics",
"biology",
"molecular cell biology"
] | Chromosome Movements Promoted by the Mitochondrial Protein SPD-3 Are Required for Homology Search during Caenorhabditis elegans Meiosis | journal.pgen.1003497 | null | [
[
"Accurate chromosome segregation during meiosis requires the formation of physical attachments between homologous chromosomes ( homologs ) .",
"To achieve this , a series of events unfold during meiotic prophase to promote the formation of inter-homolog crossover events during meiotic recombination [1] ."... | [
"Pairing of homologous chromosomes during early meiosis is essential to prevent the formation of aneuploid gametes .",
"Chromosome pairing includes a step of homology search followed by the stabilization of homolog interactions by the synaptonemal complex ( SC ) .",
"These events coincide with dramatic changes ... | [
"Sexually reproducing organisms carry two copies of each chromosome ( homologs ) , which must be separated during gamete formation to prevent chromosome duplication in each generation .",
"This chromosome halving is achieved during meiosis , a type of cell division in which the homologs recognize and pair with on... | 2013 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [] | Recombinant NAD-dependent SIR-2 Protein of Leishmania donovani: Immunobiochemical Characterization as a Potential Vaccine against Visceral Leishmaniasis | journal.pntd.0003557 | null | [
[
"Leishmaniases ( cutaneous , mucocutaneous , and visceral ) is caused by an intracellular protozoan parasite complex by the invasion of the reticuloendothelial system .",
"Among the three types of clinical manifestations visceral leishmaniasis ( VL ) disease is the most severe one and remains a major conc... | [
"The development of a vaccine conferring long-lasting immunity remains a challenge against visceral leishmaniasis ( VL ) .",
"Immunoproteomic characterization of Leishmania donovani proteins led to the identification of a novel protein NAD+-dependent Silent Information regulatory-2 ( SIR2 family or sirtuin ) prot... | [
"Visceral Leishmaniasis ( VL ) is the most fatal form of leishmaniasis disease in Indian subcontinent .",
"Through proteomic approaches , NAD-dependent Silent information regulator-2 was identified as one of the potent immunostimulatory proteins .",
"Herein , it was first reported the cloning , expression , pur... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"blood cells",
"t helper cells",
"medicine and health sciences",
"immune cells",
"immunology",
"cytomegalovirus infection",
"connective tissue cells",
"cytotoxic t cells",
"infectious diseases",
"white blood cells",
"animal cells",
"stromal cells",
"t cells",
"connective tissue",
"biolog... | Control of primary mouse cytomegalovirus infection in lung nodular inflammatory foci by cooperation of interferon-gamma expressing CD4 and CD8 T cells | journal.ppat.1007252 | null | [
[
"The immune response against CMV infection in humans and murine cytomegalovirus ( MCMV ) in mice has been studied for decades [1] .",
"Understanding immune-cell mediated control of CMV infection is of essential interest since immunocompromised patients are particularly susceptible to CMV-disease [2] .",
... | [
"Human cytomegalovirus ( CMV ) and mouse cytomegalovirus ( MCMV ) infection share many characteristics .",
"Therefore infection of mice with MCMV is an important tool to understand immune responses and to design vaccines and therapies for patients at the risk of severe CMV disease .",
"In this study , we invest... | [
"Cytomegalovirus ( CMV ) is worldwide a highly prevalent β-herpesvirus .",
"While the primary infection in healthy individuals does not cause disease , infection of immunocompromised patients can lead to multiple organ disease and can sometimes be lethal .",
"CMV becomes latent and uses a series of mechanisms t... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"developmental biology",
"biology"
] | Maternal xNorrin, a Canonical Wnt Signaling Agonist and TGF-β Antagonist, Controls Early Neuroectoderm Specification in Xenopus | journal.pbio.1001286 | Xenopus maternal Norrin, which activates Wnt signaling but inhibits TGF-β family molecules, is essential for neuroectoderm formation. Loss of TGF-β inhibition in Norrin may contribute to the development of Norrie disease. | [
[
"Dorsal–ventral axis specification is one of the earliest patterning events in the embryo .",
"In vertebrates , early dorsal ectoderm gives rise to the neural plate , which in turn develops into the central nervous system ( CNS ) .",
"Previous studies have found that dorsal axis formation in amphibian... | [
"Dorsal–ventral specification in the amphibian embryo is controlled by β-catenin , whose activation in all dorsal cells is dependent on maternal Wnt11 .",
"However , it remains unknown whether other maternally secreted factors contribute to β-catenin activation in the dorsal ectoderm .",
"Here , we show that ma... | [
"A key step during early embryogenesis is the generation of neural precursors , which later form the central nervous system .",
"In vertebrates , this process requires proper dorsal–ventral axis specification , and we know that the canonical Wnt and BMP signaling pathways help pattern the dorsal ectoderm .",
"I... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"evolutionary biology",
"plants",
"eukaryotes"
] | The Evolution of Spinnable Cotton Fiber Entailed Prolonged Development and a Novel Metabolism | journal.pgen.0040025 | null | [
[
"One of the central questions in evolutionary biology concerns the developmental and genetic processes by which new phenotypes arise .",
"The recent merger of genomic technologies with phylogenetics has generated important insights into the evolution of developmental transformations in maize [1 , 2] , ric... | [
"A central question in evolutionary biology concerns the developmental processes by which new phenotypes arise .",
"An exceptional example of evolutionary innovation is the single-celled seed trichome in Gossypium ( “cotton fiber” ) .",
"We have used fiber development in Gossypium as a system to understand how ... | [
"Human domestication of plants has resulted in dramatic changes in mature structures , often over relatively short time frames .",
"The availability of both wild and domesticated forms of domesticated species provides an opportunity to understand the genetic and developmental steps involved in domestication , the... | 2008 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine",
"public health and epidemiology",
"clinical laboratory sciences",
"infectious disease epidemiology",
"hantavirus pulmonary syndrome",
"emerging viral diseases",
"puumala virus",
"immunology",
"microbiology",
"hemorrhagic fever with renal syndrome",
"test evaluation",
"viral pneumon... | Indirect Immunofluorescence Assay for the Simultaneous Detection of Antibodies against Clinically Important Old and New World Hantaviruses | journal.pntd.0002157 | null | [
[
"Hantaviruses are enveloped and negative-sense single-stranded RNA viruses of the Bunyaviridae family .",
"The hantavirus genome consists of three segments ( L , M , and S ) , coding for the viral RNA polymerase ( L protein ) , glycoproteins ( Gn and Gc ) and the nucleocapsid ( N ) protein , respectively ... | [
"In order to detect serum antibodies against clinically important Old and New World hantaviruses simultaneously , multiparametric indirect immunofluorescence assays ( IFAs ) based on biochip mosaics were developed .",
"Each of the mosaic substrates consisted of cells infected with one of the virus types Hantaan (... | [
"Hantaviruses are the causative agents of hemorrhagic fever with renal syndrome ( HFRS ) and hantavirus cardiopulmonary syndrome ( HCPS ) — serious emerging diseases , with case-fatality rates of up to 15% and about 35% , respectively .",
"So far , over 21 human pathogenic serotypes have been described , which ar... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Inactivation of Retinoblastoma Protein (Rb1) in the Oocyte: Evidence That Dysregulated Follicle Growth Drives Ovarian Teratoma Formation in Mice | journal.pgen.1005355 | null | [
[
"Ovarian tumors are a major source of cancer in women of all ages and can arise from both germ cells and somatic cells .",
"Germ cell tumors account for approximately 5 to 20% of ovarian cancers and mainly affect young women [1 , 2] .",
"These neoplasias are classified in many ways including dysgermin... | [
"The origin of most ovarian tumors is undefined .",
"Here , we report development of a novel mouse model in which conditional inactivation of the tumor suppressor gene Rb1 in oocytes leads to the formation of ovarian teratomas ( OTs ) .",
"While parthenogenetically activated ooctyes are a known source of OT in ... | [
"Ovarian teratomas ( OTs ) are the most frequent germ cell tumors in adult women , but their origin and molecular etiology remains poorly defined .",
"We found that conditional deletion of the tumor suppressor Rb1 in the oocyte leads to OT development in young adult female mice .",
"Further analysis revealed di... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"calcium imaging",
"smell",
"behavioral neuroscience",
"olfactory system",
"biology and life sciences",
"sensory systems",
"sensory perception",
"neuroscience",
"neuroimaging"
] | Perception of Odors Linked to Precise Timing in the Olfactory System | journal.pbio.1002021 | The temporal dynamics of glomeruli activity can be behaviorally discerned by mice down to 13 milliseconds. | [
[
"Different odor stimuli are represented by different spatial patterns of activated olfactory glomeruli in the olfactory bulb ( OB ) , as first shown by activity markers [1]–[3] and supported by the projection patterns of olfactory receptor cells [3]–[5] .",
"Subsequent studies have suggested that these od... | [
"While the timing of neuronal activity in the olfactory bulb ( OB ) relative to sniffing has been the object of many studies , the behavioral relevance of timing information generated by patterned activation within the bulbar response has not been explored .",
"Here we show , using sniff-triggered , dynamic , 2-D... | [
"Olfactory receptor neurons respond to odors in the olfactory epithelium located in the nasal cavity in mammals .",
"Each olfactory receptor neuron expresses only one olfactory receptor , out of several hundred encoded in the mammalian genome .",
"Olfactory receptor neurons expressing the same olfactory recepto... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"medicine and health sciences",
"chemical compounds",
"pneumococcus",
"pathology and laboratory medicine",
"oxides",
"gene regulation",
"pathogens",
"regulatory proteins",
"oxygen",
"microbiology",
"dna-binding proteins",
"organic compounds",
"transcription factors",
"amino acids",
"sequ... | RitR is an archetype for a novel family of redox sensors in the streptococci that has evolved from two-component response regulators and is required for pneumococcal colonization | journal.ppat.1007052 | null | [
[
"2 . 5 billion years ago when cyanobacteria introduced oxygenic photosynthesis the atmosphere became dominated by oxygen .",
"In response , life on earth had to drastically change its chemistry to avoid the toxic effects of this new abundant gas and its byproducts from reacting with iron , an element whic... | [
"To survive diverse host environments , the human pathogen Streptococcus pneumoniae must prevent its self-produced , extremely high levels of peroxide from reacting with intracellular iron .",
"However , the regulatory mechanism ( s ) by which the pneumococcus accomplishes this balance remains largely enigmatic ,... | [
"Most life requires elemental iron for survival .",
"Bacterial pathogens are no exception , where within the host environment iron availability can “make or break” a successful infection .",
"However , with healthy intracellular iron levels come great risks , as microbes must then strive to keep the needed iron... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"developmental biology/cell differentiation",
"computational biology/molecular dynamics",
"cell biology"
] | Regulated Fluctuations in Nanog Expression Mediate Cell Fate Decisions in Embryonic Stem Cells | journal.pbio.1000149 | The notion that the differentiated state of a cell population is determined simply by expression of specific marker genes is changing. In this work, the authors reveal that a pluripotent cell population comprises cells with temporal fluctuations in the expression of Nanog. | [
[
"Embryonic stem ( ES ) cells are cultured pluripotent cell populations derived from the epiblast of mammalian embryos , which can be induced to differentiate into a variety of cell types under controlled conditions [1]–[4] .",
"Most studies with ES cells have been performed on mouse cells , and their plur... | [
"There is evidence that pluripotency of mouse embryonic stem ( ES ) cells is associated with the activity of a network of transcription factors with Sox2 , Oct4 , and Nanog at the core .",
"Using fluorescent reporters for the expression of Nanog , we observed that a population of ES cells is best described by a d... | [
"Embryonic stem ( ES ) cells are a pluripotent cell population derived from early mammalian embryos .",
"An intrinsic feature of ES cells is their phenotypic heterogeneity: they display promiscuous activation of lineage-specific genes and exhibit a fluctuating flow of differentiating cells .",
"A gene regulator... | 2009 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion",
"Conclusion"
] | [
"viral vaccines",
"medicine and health sciences",
"immune physiology",
"enzyme-linked immunoassays",
"pathology and laboratory medicine",
"pathogens",
"immunology",
"microbiology",
"vaccines",
"viruses",
"bacterial diseases",
"rna viruses",
"infectious disease control",
"antibodies",
"im... | Heterogeneity and longevity of antibody memory to viruses and vaccines | journal.pbio.2006601 | null | [
[
"Immune memory is a cardinal feature of the adaptive immune response of vertebrates and is the principle that underlies vaccination [1–3] .",
"Immunological memory arises as a consequence of the increase in the magnitude of the antigen-specific response , augmented by increases in the quality of the respo... | [
"Determining the duration of protective immunity requires quantifying the magnitude and rate of loss of antibodies to different virus and vaccine antigens .",
"A key complication is heterogeneity in both the magnitude and decay rate of responses of different individuals to a given vaccine , as well as of a given ... | [
"Immunological memory , mediated by antibodies , is a hallmark of immunity .",
"A key problem for determining the longevity of protective immunity is heterogeneity in the responses of different individuals .",
"We characterize the extent of this heterogeneity and determine how it affects the longevity of protec... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"blood cells",
"medicine and health sciences",
"immune cells",
"enzyme-linked immunoassays",
"endothelial cells",
"immunology",
"tropical diseases",
"permeability",
"glycocalyx",
"epithelial cells",
"physiological processes",
"materials science",
"neglected tropical diseases",
"immunologic... | Macrophage migration inhibitory factor is critical for dengue NS1-induced endothelial glycocalyx degradation and hyperpermeability | journal.ppat.1007033 | null | [
[
"Dengue virus ( DENV ) is a flavivirus that infects approximately 390 million people and causes 500 , 000 infections requiring hospitalization every year , with an associated mortality rate of 2 . 5% [1] .",
"DENV infection usually causes a flu-like illness , known as dengue fever ( DF ) , which is associ... | [
"Vascular leakage is one of the salient characteristics of severe dengue .",
"Nonstructural protein 1 ( NS1 ) of dengue virus ( DENV ) can stimulate endothelial cells to secrete endothelial hyperpermeability factor , macrophage migration inhibitory factor ( MIF ) , and the glycocalyx degradation factor heparanase... | [
"DENV NS1 induces endothelial glycocalyx degradation and hyperpermeability via HPA-1 and MMP-9 activation in an MIF-dependent manner ."
] | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | A Unique Virulence Gene Occupies a Principal Position in Immune Evasion by the Malaria Parasite Plasmodium falciparum | journal.pgen.1005234 | null | [
[
"Mutually exclusive gene expression , whether selective expression of either the maternal or paternal allele in a diploid organism , the inactivation of an entire sex chromosome during dosage compensation , or the expression of a single gene while silencing all others within a multi-copy gene family , remains... | [
"Mutually exclusive gene expression , whereby only one member of a multi-gene family is selected for activation , is used by the malaria parasite Plasmodium falciparum to escape the human immune system and perpetuate long-term , chronic infections .",
"A family of genes called var encodes the chief antigenic and ... | [
"Many eukaryotic pathogens avoid the immune system of their hosts by switching expression between genes encoding their exposed surface antigens .",
"This process , called antigenic variation , is key to the ability of these organisms to cause long-term , chronic infections and represents a major virulence determi... | 2015 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"signal transduction",
"calcineurin signaling cascade",
"signaling in selected disciplines",
"oncogenic signaling",
"mechanisms of signal transduction",
"biology",
"molecular cell biology",
"signaling cascades"
] | Kaposi's Sarcoma Herpesvirus K15 Protein Contributes to Virus-Induced Angiogenesis by Recruiting PLCγ1 and Activating NFAT1-dependent RCAN1 Expression | journal.ppat.1002927 | null | [
[
"Kaposi's Sarcoma Herpesvirus ( KSHV ) or Human Herpesvirus 8 ( HHV8 ) is a gammaherpesvirus first identified in Kaposi's Sarcoma ( KS ) biopsies [1] .",
"Apart from being the etiological agent of the classic , AIDS-associated , endemic ( African ) and iatrogenic forms of Kaposi's sarcoma , it is also ass... | [
"Kaposi's Sarcoma ( KS ) , caused by Kaposi's Sarcoma Herpesvirus ( KSHV ) , is a highly vascularised angiogenic tumor of endothelial cells , characterized by latently KSHV-infected spindle cells and a pronounced inflammatory infiltrate .",
"Several KSHV proteins , including LANA-1 ( ORF73 ) , vCyclin ( ORF72 ) ,... | [
"Kaposi's Sarcoma Herpesvirus ( KSHV ) causes a multifocal angio-proliferative neoplasm , Kaposi's Sarcoma ( KS ) , whose development involves angiogenic growth factors and cytokines .",
"The K15 protein of KSHV upregulates the host factor RCAN1/DSCR1 .",
"RCAN1/DSCR1 has been implicated in angiogenesis but its... | 2012 |
[
"Introduction",
"Results/Discussion",
"Methods"
] | [
"computational biology/genomics"
] | SHRiMP: Accurate Mapping of Short Color-space Reads | journal.pcbi.1000386 | null | [
[
"Next generation sequencing ( NGS ) technologies are revolutionizing the study of variation among individuals in a population .",
"The ability of sequencing platforms such as AB SOLiD and Illumina ( Solexa ) to sequence one billion basepairs ( gigabase ) or more in a few days has enabled the cheap re-sequ... | [
"The development of Next Generation Sequencing technologies , capable of sequencing hundreds of millions of short reads ( 25–70 bp each ) in a single run , is opening the door to population genomic studies of non-model species .",
"In this paper we present SHRiMP - the SHort Read Mapping Package: a set of algorit... | [
"Next Generation Sequencing ( NGS ) technologies are revolutionizing the way biologists acquire and analyze genomic data .",
"NGS machines , such as Illumina/Solexa and AB SOLiD , are able to sequence genomes more cheaply by 200-fold than previous methods .",
"One of the main application areas of NGS technologi... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"cell death",
"leukemias",
"medicine and health sciences",
"protein interactions",
"pathology and laboratory medicine",
"protein interaction networks",
"cell processes",
"immunology",
"cancers and neoplasms",
"oncology",
"hematologic cancers and related disorders",
"signs and symptoms",
"sum... | Insight into glucocorticoid receptor signalling through interactome model analysis | journal.pcbi.1005825 | null | [
[
"Glucocorticoids ( GCs ) steroid hormones released from the adrenal cortex as part of the stress response play an important role in a variety of bodily processes such as inflammation , immunity , and numerous metabolic processes [1–3] .",
"Their varied effects allow for their clinical application in numer... | [
"Glucocorticoid hormones ( GCs ) are used to treat a variety of diseases because of their potent anti-inflammatory effect and their ability to induce apoptosis in lymphoid malignancies through the glucocorticoid receptor ( GR ) .",
"Despite ongoing research , high glucocorticoid efficacy and widespread usage in m... | [
"Here we present modelling of the glucocorticoid receptor ( GR ) signalling network .",
"The GR is the effector for a class of drugs known as corticosteroids , which are widely used in medicine for their anti-inflammatory effects and ability to induce apoptosis in leukaemic cells .",
"However , side effects , t... | 2017 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"united states",
"invertebrates",
"heterozygosity",
"biogeography",
"medicine and health sciences",
"ecology and environmental sciences",
"california",
"population genetics",
"geographical locations",
"animals",
"north america",
"molecular biology techniques",
"population biology",
"infect... | Multiple introductions of the dengue vector, Aedes aegypti, into California | journal.pntd.0005718 | null | [
[
"Dengue , Zika , and chikungunya are severe mosquito-borne infectious diseases that are of growing concern in tropical and sub-tropical regions , and yellow fever is re-emerging in many regions [1] .",
"The viruses causing these diseases are primarily transmitted by the mosquito vector Aedes aegypti .",
... | [
"The yellow fever mosquito Aedes aegypti inhabits much of the tropical and subtropical world and is a primary vector of dengue , Zika , and chikungunya viruses .",
"Breeding populations of A . aegypti were first reported in California ( CA ) in 2013 .",
"Initial genetic analyses using 12 microsatellites on coll... | [
"Infectious diseases transmitted by Aedes aegypti , also known as the yellow fever mosquito , are of growing concern in tropical and subtropical regions .",
"Dengue and Zika incidences are increasing , and no vaccines are currently available .",
"Here we investigate the origin of California A . aegypti and find... | 2017 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"antimicrobials",
"medicine and health sciences",
"immune physiology",
"pathology and laboratory medicine",
"engineering and technology",
"electronics",
"spleen",
"drugs",
"tropical diseases",
"microbiology",
"geographical locations",
"antifungals",
"parasitic diseases",
"toxicology",
"t... | Efficacy and safety of available treatments for visceral leishmaniasis in Brazil: A multicenter, randomized, open label trial | journal.pntd.0005706 | null | [
[
"Visceral leishmaniasis ( VL ) is a public health problem in developing countries .",
"The overall annual incidence is estimated at approximately 200 , 000 to 400 , 000 cases [1] , with a case-fatality rate of 10% per year ( i . e . 20 , 000 to 40 , 000 deaths per year ) [2] .",
"In Latin America , VL... | [
"There is insufficient evidence to support visceral leishmaniasis ( VL ) treatment recommendations in Brazil and an urgent need to improve current treatments .",
"Drug combinations may be an option .",
"A multicenter , randomized , open label , controlled trial was conducted in five sites in Brazil to evaluate ... | [
"Visceral leishmaniasis remains a worldwide public health concern with high mortality even when proper treatment is instituted .",
"There is a need to develop efficacious , safer and shorter treatment alternatives as the current options suffer from high toxicity and long treatment duration .",
"Combination ther... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genome expression analysis",
"gene networks",
"animal genetics",
"neuroscience",
"homeostatic mechanisms",
"ion channels",
"molecular genetics",
"gene expression",
"biology",
"cellular neuroscience",
"central nervous system",
"synapses",
"neural homeostasis",
"genetics",
"genomics",
"... | CELF4 Regulates Translation and Local Abundance of a Vast Set of mRNAs, Including Genes Associated with Regulation of Synaptic Function | journal.pgen.1003067 | null | [
[
"Idiopathic epilepsies ( IE ) have an unknown etiology , but are generally accepted to be genetic in origin .",
"Although ion channel defects have been identified as primary causal agents in some rare monogenic forms of IE , the genetic underpinnings of the vast majority of more common IE cases , which ar... | [
"RNA–binding proteins have emerged as causal agents of complex neurological diseases .",
"Mice deficient for neuronal RNA–binding protein CELF4 have a complex neurological disorder with epilepsy as a prominent feature .",
"Human CELF4 has recently been associated with clinical features similar to those seen in ... | [
"Epilepsy is a devastating brain disorder whereby a loss of regulation of electrochemical signals between neurons causes too much excitation and ultimately results in an “electrical storm” known as a seizure .",
"Epilepsy can be heritable , but it is usually genetically complex , resulting from a collaboration of... | 2012 |
[
"Introduction",
"Methods",
"Results and Discussion"
] | [] | DynaFace: Discrimination between Obligatory and Non-obligatory Protein-Protein Interactions Based on the Complex’s Dynamics | journal.pcbi.1004461 | null | [
[
"Inter-protein interactions mediate a wide range of cellular and biochemical processes [1 , 2] .",
"The Protein Data Bank ( PDB; [3] ) includes a wealth of information on these important interactions , observed in X-ray crystal , NMR , and cryo-electron microscopy structures .",
"Indeed , this large r... | [
"Protein-protein interfaces have been evolutionarily-designed to enable transduction between the interacting proteins .",
"Thus , we hypothesize that analysis of the dynamics of the complex can reveal details about the nature of the interaction , and in particular whether it is obligatory , i . e . , persists thr... | [
"Protein-protein interactions mediate , in essence , all inter- and intra-cellular processes .",
"Thus , understanding their molecular mechanism is of utmost importance .",
"Here we focus on one mechanistic aspect: differentiation between obligatory interactions , which persist throughout the entire lifetime of... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"beer",
"animal types",
"medicine and health sciences",
"alcoholic beverages",
"domestic animals",
"geographical locations",
"diet",
"departures from diploidy",
"alleles",
"animals",
"genetic mapping",
"fungi",
"model organisms",
"nutrition",
"experimental organism systems",
"zoology",... | A polyploid admixed origin of beer yeasts derived from European and Asian wine populations | journal.pbio.3000147 | Brewer's yeast has been used to make fermented beverages for millennia. A genome analysis of beer and other yeast strains shows that beer yeast have a polyploid admixed origin derived from European and Asian wine populations. | [
[
"The brewer's yeast Saccharomyces cerevisiae is known for its strong fermentative characteristics .",
"The preference for fermentation in the presence of oxygen arose as a multistep evolutionary process around the time of an ancient genome duplication , endowing numerous species with the ability to produc... | [
"Strains of Saccharomyces cerevisiae used to make beer , bread , and wine are genetically and phenotypically distinct from wild populations associated with trees .",
"The origins of these domesticated populations are not always clear; human-associated migration and admixture with wild populations have had a stron... | [
"The budding yeast Saccharomyces cerevisiae has long been used to make beer .",
"Yeast strains used to make ales are known to differ genetically and phenotypically from strains used to make wine and from strains isolated from nature , such as oak isolates .",
"Beer strains are also known to be polyploid , havin... | 2019 |
[
"Introduction",
"Results and Discussion",
"Materials and Methods"
] | [
"infectious diseases",
"evolutionary ecology",
"avian influenza a viruses",
"veterinary diseases",
"zoonoses",
"medicine and health sciences",
"ecology",
"influenza viruses",
"medical microbiology",
"viral pathogens",
"influenza",
"microbial pathogens",
"biology and life sciences",
"microb... | Adaptive Evolution and Environmental Durability Jointly Structure Phylodynamic Patterns in Avian Influenza Viruses | journal.pbio.1001931 | Avian influenza viruses show high genetic diversity, but give rise to pandemic human influenza strains which are much less diverse; we show that these contrasting degrees of viral diversity can be explained by both host (demography) and viral (environmental durability and mutability) factors. | [
[
"Seasonal epidemics of influenza viruses are responsible for significant human morbidity and mortality [1] .",
"Owing to their RNA makeup , evolution of influenza A viruses occurs rapidly [2] , [3] and is an important driver of their epidemiology [4] , [5] .",
"Over the past decade , there has been an... | [
"Avian influenza viruses ( AIVs ) have been pivotal to the origination of human pandemic strains .",
"Despite their scientific and public health significance , however , there remains much to be understood about the ecology and evolution of AIVs in wild birds , where major pools of genetic diversity are generated... | [
"Human populations have experienced several pandemics involving new subtypes of influenza virus over the past century .",
"All of these pandemic strains contained gene segments that originated in wild birds , a host pool that supports a very large and genetically diverse array of influenza viruses .",
"However ... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"infectious diseases/fungal infections",
"microbiology/innate immunity",
"cell biology/cytoskeleton"
] | The Human Fungal Pathogen Cryptococcus neoformans Escapes Macrophages by a Phagosome Emptying Mechanism That Is Inhibited by Arp2/3 Complex-Mediated Actin Polymerisation | journal.ppat.1001041 | null | [
[
"The ingestion and destruction of pathogens by phagocytes is essential to our innate immune response .",
"Macrophages provide a front-line defence at the site of infection and , because of this , many pathogens have evolved elaborate mechanisms to subvert macrophage behaviour [1] , [2] , [3] .",
"Non-... | [
"The lysis of infected cells by disease-causing microorganisms is an efficient but risky strategy for disseminated infection , as it exposes the pathogen to the full repertoire of the host's immune system .",
"Cryptococcus neoformans is a widespread fungal pathogen that causes a fatal meningitis in HIV and other ... | [
"Cryptococcus neoformans is fatal fungal pathogen of HIV-positive and other immunocompromised patients that causes an estimated 650 000 deaths per annum .",
"Cryptococcus is able to undermine our immune system by growing within and escaping from immune cells called macrophages .",
"In this study we describe how... | 2010 |
[
"Introduction",
"Materials and Methods",
"Results/Discussion"
] | [] | Case Report: No Response to Liposomal Daunorubicin in a Patient with Drug-Resistant HIV-Associated Visceral Leishmaniasis | journal.pntd.0003983 | null | [
[
"Visceral leishmaniasis ( VL ) is a relatively common AIDS illness in regions where Leishmania donovani , L . infantum or other Leishmania species are endemic , e . g . South Asia , Brazil , Southern Europe [1] and especially East Africa .",
"[2] Between 1986 and 1997 , VL occurred in ~ 2% of patients wit... | [
"Visceral leishmaniasis ( VL ) in patients with HIV co-infection presents a significant therapeutic challenge due to the lessened chance of achieving long-term cure .",
"We report a case of VL in a 60-year-old man with HIV infection who became refractory to anti-leishmania treatment due to multi-drug resistance .... | [
"In areas where leishmaniasis is endemic , visceral leishmaniasis ( VL ) is a potentially incurable AIDS illness in HIV infected people .",
"Co-infection with HIV and any of the Leishmania species that cause VL can result in failure of the CD4 lymphocyte count to rise above 200 cells/mm3 despite sustained , effec... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Material and methods"
] | [
"blood cells",
"dimers (chemical physics)",
"crystal structure",
"condensed matter physics",
"membrane proteins",
"red blood cells",
"crystallography",
"cellular structures and organelles",
"lipids",
"solid state physics",
"animal cells",
"chemistry",
"cell membranes",
"cholesterol",
"ph... | Interaction of the human erythrocyte Band 3 anion exchanger 1 (AE1, SLC4A1) with lipids and glycophorin A: Molecular organization of the Wright (Wr) blood group antigen | journal.pcbi.1006284 | null | [
[
"Band 3 , the human erythrocyte anion exchanger 1 ( AE1 , SLC4A1 ) is responsible for the rapid electro-neutral exchange of chloride and bicarbonate across the plasma membrane; a process that increases the blood’s capacity to carry carbon dioxide as plasma bicarbonate [1] .",
"Human Band 3 is a 911 amino ... | [
"The Band 3 ( AE1 , SLC4A1 ) membrane protein is found in red blood cells and in kidney where it functions as an electro-neutral chloride/bicarbonate exchanger .",
"In this study , we have used molecular dynamics simulations to provide the first realistic model of the dimeric membrane domain of human Band 3 in an... | [
"Human Band 3 ( AE1 , SLC4A1 ) , an abundant 911 amino acid glycoprotein , catalyzes the exchange of bicarbonate and chloride across the red blood cell membrane , a process necessary for efficient respiration .",
"Malfunction of Band 3 leads to inherited diseases such as Southeast Asian Ovalocytosis , hereditary ... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biology",
"microbiology",
"evolutionary biology"
] | Point Mutations in FimH Adhesin of Crohn's Disease-Associated Adherent-Invasive Escherichia coli Enhance Intestinal Inflammatory Response | journal.ppat.1003141 | null | [
[
"The molecular pathogenesis of inflammatory bowel disease ( IBD ) , a chronic inflammation of the digestive tract , remains poorly understood .",
"However , current evidence suggests that Crohn's disease ( CD ) pathogenesis involves interactions between the intestinal microbiome and the immune system , in... | [
"Adherent-invasive Escherichia coli ( AIEC ) are abnormally predominant on Crohn's disease ( CD ) ileal mucosa .",
"AIEC reference strain LF82 adheres to ileal enterocytes via the common type 1 pili adhesin FimH and recognizes CEACAM6 receptors abnormally expressed on CD ileal epithelial cells .",
"The fimH gen... | [
"The etiology of inflammatory bowel diseases , in particular Crohn's disease ( CD ) , involves disorders in host genetic factors and intestinal microbiota .",
"Adherent-invasive Escherichia coli ( AIEC ) are receiving increasing attention because they have been reported worldwide to be more prevalent in CD patien... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"medicine and health sciences",
"notch signaling",
"cell differentiation",
"epithelial cells",
"endocrine physiology",
"developmental biology",
"growth factors",
"embryos",
"mapk signaling cascades",
"fibroblast growth factor",
"erk signaling cascade",
"embryology",
"animal cells",
"endocr... | Lens differentiation is controlled by the balance between PDGF and FGF signaling | journal.pbio.3000133 | null | [
[
"Receptor Tyrosine Kinases ( RTKs ) are a large family of membrane proteins that can activate a common set of downstream pathways , but they are also known to elicit distinct biological responses .",
"This raises the question of how the signaling specificities of these receptors are generated .",
"The... | [
"How multiple receptor tyrosine kinases coordinate cell fate determination is yet to be elucidated .",
"We show here that the receptor for platelet-derived growth factor ( PDGF ) signaling recruits the p85 subunit of Phosphoinositide 3-kinase ( PI3K ) to regulate mammalian lens development .",
"Activation of PI... | [
"A central aim in understanding cell signaling is to decode the cellular logic that underlies the functional specificity of growth factors .",
"Although these factors are known to activate a common set of intracellular pathways , they nevertheless play specific roles in development and physiology .",
"Using len... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"plant biology/plant-biotic interactions",
"virology/virus evolution and symbiosis",
"evolutionary biology/evolutionary ecology",
"virology",
"ecology/population ecology"
] | Differential Tolerance to Direct and Indirect Density-Dependent Costs of Viral Infection in Arabidopsis thaliana | journal.ppat.1000531 | null | [
[
"Competition is one of the major selection factors in nature , acting at all phases of development [1] .",
"The key role of competition in shaping evolution is one of the bases of the Darwinian Theory , underlying the colonization success , expansion and suppression of genotypes and species .",
"The r... | [
"Population density and costs of parasite infection may condition the capacity of organisms to grow , survive and reproduce , i . e . their competitive ability .",
"In host–parasite systems there are different competitive interactions: among uninfected hosts , among infected hosts , and between uninfected and inf... | [
"Parasites are a potent selective force , as they reduce the fitness of their hosts through a direct cost of infection , due to parasitism itself , and an indirect cost , due to modification of the competitive ability of the infected host .",
"Theory predicts that fitness reduction will be higher under the combin... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods",
"Supporting Information"
] | [
"viruses",
"infectious diseases",
"cell biology",
"virology",
"microbiology",
"eukaryotes",
"mammals"
] | A SAP30 Complex Inhibits IFN-β Expression in Rift Valley Fever Virus Infected Cells | journal.ppat.0040013 | null | [
[
"It is now well established that in eukaryotic cells , transcriptional activation of finely regulated inducible genes requires disruption of chromatin structure in order to allow the access of RNA polymerase to DNA ( for recent reviews see [1–3] ) .",
"The nucleosome is the basic unit of chromatin , consi... | [
"Rift Valley fever virus ( RVFV ) nonstructural protein NSs acts as the major determinant of virulence by antagonizing interferon β ( IFN-β ) gene expression .",
"We demonstrate here that NSs interacts with the host protein SAP30 , which belongs to Sin3A/NCoR/HDACs repressor complexes and interacts with the trans... | [
"Rift Valley fever is a viral mosquito-borne disease affecting ruminants and humans .",
"The disease occurs in Africa and recently it spread to the Arabian Peninsula .",
"In humans , infection can progress to fatal hemorrhagic fever and in ruminants it leads to hepatitis , abortions , or deaths of young lambs .... | 2008 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | Global Burden of Leptospirosis: Estimated in Terms of Disability Adjusted Life Years | journal.pntd.0004122 | null | [
[
"Leptospirosis is a neglected emerging zoonotic disease that has an important public health impact worldwide , especially within economically vulnerable populations such as urban slums and rural subsistence farmers [1] .",
"Although it can have high fatality and is recognised as the most common and widesp... | [
"Leptospirosis , a spirochaetal zoonosis , occurs in diverse epidemiological settings and affects vulnerable populations , such as rural subsistence farmers and urban slum dwellers .",
"Although leptospirosis can cause life-threatening disease , there is no global burden of disease estimate in terms of Disability... | [
"Leptospirosis is a zoonotic bacterial disease that affects vulnerable populations such as rural subsistence farmers and urban slum dwellers .",
"Although leptospirosis can cause life-threatening clinical manifestations such as pulmonary hemorrhage syndrome and has a worldwide distribution , to date , the global ... | 2015 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"microbiology",
"mathematical models",
"simulation and modeling",
"population modeling",
"population biology",
"lassa fever",
"veterinary science",
"mathematical modeling",
"research and analysis methods",
"infectious diseases",
"veterinary diseases",
"zoonose... | Using Modelling to Disentangle the Relative Contributions of Zoonotic and Anthroponotic Transmission: The Case of Lassa Fever | journal.pntd.0003398 | null | [
[
"Diseases at the animal-human interface are in general subjected to different modes of cross-species transmission: animal-to-animal , animal-to-human , human-to-human and even human-to-animal .",
"Estimating the relative contribution of each is of fundamental importance for the planning and implementation... | [
"Zoonotic infections , which transmit from animals to humans , form the majority of new human pathogens .",
"Following zoonotic transmission , the pathogen may already have , or may acquire , the ability to transmit from human to human .",
"With infections such as Lassa fever ( LF ) , an often fatal , rodent-bo... | [
"Many pathogens have the ability to infect different species .",
"Lassa fever virus is an important example; this virus infects a species of rodent in West Africa , and can cause a severe disease in people .",
"Lassa fever virus is transmitted from rodent-to-rodent , rodent-to-human , human-to-human and perhaps... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"antimicrobials",
"invertebrates",
"medicine and health sciences",
"rna interference",
"pathology and laboratory medicine",
"caenorhabditis",
"gene regulation",
"pathogens",
"regulatory proteins",
"drugs",
"microbiology",
"dna-binding proteins",
"animals",
"dna transcription",
"pseudomon... | Non-proteolytic activity of 19S proteasome subunit RPT-6 regulates GATA transcription during response to infection | journal.pgen.1007693 | null | [
[
"The regulation of gene transcription plays crucial roles in the control of an array of critical biological processes , including immune responses against microbial infections [1 , 2] .",
"At the heart of immune activation are transcription factors , which directly bind to specific DNA motifs in promoter ... | [
"GATA transcription factors play a crucial role in the regulation of immune functions across metazoans .",
"In Caenorhabditis elegans , the GATA transcription factor ELT-2 is involved in the control of not only infections but also recovery after an infection .",
"We identified RPT-6 , part of the 19S proteasome... | [
"The conserved GATA transcription factor ELT-2 plays an important role in the control of genes required for both defense and recovery from infection .",
"We show that RPT-6 , a component of the 19S subunit , physically interacts with ELT-2 in vivo , controlling the expression of ELT-2-dependent genes and the resp... | 2018 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [] | Immunization of Knock-Out α/β Interferon Receptor Mice against High Lethal Dose of Crimean-Congo Hemorrhagic Fever Virus with a Cell Culture Based Vaccine | journal.pntd.0003579 | null | [
[
"Causative agent is Crimean Congo hemorrhagic fever ( CCHF ) virus which belongs to the Nairovirus genus in the family Bunyaviridae which are enveloped viruses containing tripartite , negative polarity , single-stranded RNA [1–3] .",
"CCHF is the most widely distributed tick-borne disease .",
"To date... | [
"Crimean-Congo hemorrhagic fever ( CCHF ) is an acute tick-borne zoonotic disease .",
"The disease has been reported in many countries of Africa , Asia , the Middle East , and in Eurasia .",
"During the past decade , new foci of CCHF have emerged in the Balkan Peninsula , southwest Russia , the Middle East , we... | [
"The CCHF virus is one of the most geographically widespread tick-borne viruses , and has been reported in many countries of Africa , Asia , the Middle East , and in Eurasia .",
"Since 2002 , there have been more than 8000 cases in Turkey , with mortality rate around 5% , making CCHF a public health concern .",
... | 2015 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"computational biology/systems biology",
"computational biology/transcriptional regulation",
"computational biology/genomics",
"genetics and genomics/epigenetics",
"genetics and genomics/bioinformatics"
] | ChromaSig: A Probabilistic Approach to Finding Common Chromatin Signatures in the Human Genome | journal.pcbi.1000201 | null | [
[
"In eukaryotes , DNA is packaged into nucleosomes , each consisting of an octamer of histone proteins [1]–[3] .",
"Histones are subject to an assortment of post-translational modifications including phosphorylation , acetylation , and methylation [4]–[6] .",
"Many of these modifications have been link... | [
"Computational methods to identify functional genomic elements using genetic information have been very successful in determining gene structure and in identifying a handful of cis-regulatory elements .",
"But the vast majority of regulatory elements have yet to be discovered , and it has become increasingly appa... | [
"The DNA in eukaryotes is packaged by histones .",
"Interestingly , histones can be marked by a variety of posttranslational modifications , and it has been hypothesized that distinct combinations of histone modifications mark at distinct functional regions of the genome .",
"The study of histone modifications ... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"small intestine",
"cell death",
"organoids",
"medicine and health sciences",
"biological cultures",
"cell processes",
"physiological processes",
"homeostasis",
"organ cultures",
"digestive system",
"research and analysis methods",
"biological tissue",
"gastrointestinal tract",
"signal tra... | Tankyrases maintain homeostasis of intestinal epithelium by preventing cell death | journal.pgen.1007697 | null | [
[
"The intestinal epithelium carries out many physiological functions including absorbing nutrients and providing barrier function [1 , 2] .",
"The intestinal epithelium is one of the most rapidly renewing tissues in adult mammals with renewal time of about every 5 days [3 , 4] .",
"This continual renew... | [
"Lgr5+ intestinal stem cells are crucial for fast homeostatic renewal of intestinal epithelium and Wnt/β-catenin signaling plays an essential role in this process by sustaining stem cell self-renewal .",
"The poly ( ADP-ribose ) polymerases tankyrases ( TNKSs ) mediate protein poly-ADP-ribosylation and are involv... | [
"Although tankyrases have been indicated to play important roles in telomere maintenance , mitosis and Wnt signaling regulation , little is known about their physiological function in intestinal epithelium .",
"Using Villin-creERT2;Tnks1-/-;Tnks2fl/fl mice , which harbored conventional Tnks1 deletion and inducibl... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | TURAN and EVAN Mediate Pollen Tube Reception in Arabidopsis Synergids through Protein Glycosylation | journal.pbio.1002139 | Protein glycosylation is essential for gametophyte interactions between the male pollen tube and the female ovule in plants, reminiscent of gamete interactions during fertilization in mammals. | [
[
"In flowering plants , male and female gametes are constituents of the male ( pollen ) and female gametophytes ( FG , embryo sac ) .",
"A complex series of communication events between the male gametophyte and the female tissues of the flower is required for the pollen tube ( PT ) to deliver the two immot... | [
"Pollen tube ( PT ) reception in flowering plants describes the crosstalk between the male and female gametophytes upon PT arrival at the synergid cells of the ovule .",
"It leads to PT growth arrest , rupture , and sperm cell release , and is thus essential to ensure double fertilization .",
"Here , we describ... | [
"In flowering plants , gametes are produced by the haploid , multicellular male ( pollen ) , and female ( embryo sac ) gametophytes , which develop within the reproductive organs of the flower .",
"Successful fertilization depends on delivery of the sperm cells to the embryo sac , which is embedded in the ovule ,... | 2015 |
[
"Introduction",
"Material and Methods",
"Results",
"Discussion"
] | [
"veterinary science"
] | Latent-Class Methods to Evaluate Diagnostics Tests for Echinococcus Infections in Dogs | journal.pntd.0002068 | null | [
[
"An efficient and adequate diagnosis is at the core of effective surveillance , control and elimination programmes .",
"For the effectiveness of such programmes , knowledge about test accuracies is indispensable , since even very accurate diagnostic tests might occasionally provide false positive and fals... | [
"The diagnosis of canine echinococcosis can be a challenge in surveillance studies because there is no perfect gold standard that can be used routinely .",
"However , unknown test specificities and sensitivities can be overcome using latent-class analysis with appropriate data .",
"We utilised a set of faecal a... | [
"Dogs are a key definitive host of Echinococcus spp; hence , accurate diagnosis in dogs is important for the surveillance and control of echinococcosis .",
"A perfect diagnostic test would detect every infected dog ( 100% sensitivity ) whilst never giving a false positive reaction in non-infected dogs ( 100% spec... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Dealing with the Evolutionary Downside of CRISPR Immunity: Bacteria and Beneficial Plasmids | journal.pgen.1003844 | null | [
[
"Clustered , Regularly Interspaced Short Palindromic Repeat ( CRISPR ) loci and their associated proteins ( Cas ) have been found in the genomes of about 90% of archaea and about 50% of eubacteria [1] , [2] , [3] .",
"In these loci , repeats are separated by short sequences of DNA ( 25–70 base pair-long )... | [
"The immune systems that protect organisms from infectious agents invariably have a cost for the host .",
"In bacteria and archaea CRISPR-Cas loci can serve as adaptive immune systems that protect these microbes from infectiously transmitted DNAs .",
"When those DNAs are borne by lytic viruses ( phages ) , this... | [
"In addition to the virtue of protecting archaea and bacteria from the ravages of lethal viruses ( phage ) , the immunity generated by the CRISPR-Cas systems have an evolutionary downside; they can prevent the acquisition of genes and genetic elements required for the adaptation and even the survival of these micro... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | A New Method for Detecting Associations with Rare Copy-Number Variants | journal.pgen.1005403 | null | [
[
"Copy-number variants ( CNVs ) , such as deletions and duplications , are changes in the number of DNA copies ( in comparison to the reference ) and are a major source of genetic variation in the human genome [1–3] .",
"While a sequence variant ( e . g . , a SNP ) affects a single nucleotide , a CNV affec... | [
"Copy number variants ( CNVs ) play an important role in the etiology of many diseases such as cancers and psychiatric disorders .",
"Due to a modest marginal effect size or the rarity of the CNVs , collapsing rare CNVs together and collectively evaluating their effect serves as a key approach to evaluating the c... | [
"Copy number variants ( CNVs ) are the gain or loss of DNA segments in the genome that can vary in dosage , length and details of gene disruptions .",
"Rare CNVs have been shown to be associated with neuropsychiatric disorders both collectively and at specific loci .",
"To evaluate the collective effects of rar... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | P-TEFb, the Super Elongation Complex and Mediator Regulate a Subset of Non-paused Genes during Early Drosophila Embryo Development | journal.pgen.1004971 | null | [
[
"RNA Polymerase II ( Pol II ) is responsible for the transcription of protein-coding genes in eukaryotes , and differs from all other RNA Polymerases in that its largest subunit contains a C-terminal domain ( CTD ) consisting of a heptapeptide repeat with the consensus YSPTSPS [reviewed in 1] .",
"Phospho... | [
"Positive Transcription Elongation Factor b ( P-TEFb ) is a kinase consisting of Cdk9 and Cyclin T that releases RNA Polymerase II ( Pol II ) into active elongation .",
"It can assemble into a larger Super Elongation Complex ( SEC ) consisting of additional elongation factors .",
"Here , we use a miRNA-based ap... | [
"Embryo development involves formation of various cell types through the regulation of gene transcription , resulting in expression of cell type specific RNAs and proteins .",
"A key regulatory step in transcription of animal genes involves the transition of RNA polymerase II ( Pol II ) into active elongation .",... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"transfection",
"medicine and health sciences",
"immune physiology",
"pathology and laboratory medicine",
"293t cells",
"pathogens",
"immunology",
"biological cultures",
"microbiology",
"electron cryo-microscopy",
"health care",
"retroviruses",
"viruses",
"immunodeficiency viruses",
"mut... | Neutralization-guided design of HIV-1 envelope trimers with high affinity for the unmutated common ancestor of CH235 lineage CD4bs broadly neutralizing antibodies | journal.ppat.1008026 | null | [
[
"The trimeric HIV-1 envelope glycoprotein ( Env ) spikes that mediate virus entry into cells are vulnerable to at least six distinct epitope classes of broadly neutralizing antibodies ( bnAbs ) , where each bnAb class is a major focus for vaccine design [1] .",
"These bnAbs arise during chronic HIV-1 infe... | [
"The CD4 binding site ( CD4bs ) of the HIV-1 envelope glycoprotein is susceptible to multiple lineages of broadly neutralizing antibodies ( bnAbs ) that are attractive to elicit with vaccines .",
"The CH235 lineage ( VH1-46 ) of CD4bs bnAbs is particularly attractive because the most mature members neutralize 90%... | [
"Despite a wealth of information on the epitopes , ontogeny , structure and maturation pathways of multiple epitope classes of HIV-1 broadly neutralizing antibodies ( bnAbs ) , there has been little progress eliciting similar antibodies by vaccination .",
"One major contributing factor is the failure of many cand... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"invertebrates",
"enzyme-linked immunoassays",
"onchocerca volvulus",
"helminths",
"animals",
"onchocerca",
"sequence motif analysis",
"bioassays and physiological analysis",
"immunologic techniques",
"chemical synthesis",
"research and analysis methods",
"sequence analysis",
"peptide synthe... | Identification of three immunodominant motifs with atypical isotype profile scattered over the Onchocerca volvulus proteome | journal.pntd.0005330 | null | [
[
"On the World Health Organization ( WHO ) list of Neglected Tropical Diseases ( NTD ) , 17 infectious diseases are listed [1] , eight of them caused by a helminth infection [2] .",
"Onchocerciasis ( or river blindness ) is caused by infection with the filarial nematode Onchocerca volvulus .",
"More th... | [
"Understanding the immune response upon infection with the filarial nematode Onchocerca volvulus and the mechanisms that evolved in this parasite to evade immune mediated elimination is essential to expand the toolbox available for diagnostics , therapeutics and vaccines development .",
"Using high-density peptid... | [
"Infection with the filarial parasite Onchocerca volvulus is the cause of river blindness .",
"We analyzed the immune response against this parasite in infected individuals in order to identify linear epitopes .",
"Using high-density peptide microarrays we discovered three immunodominant motifs in the Onchocerc... | 2017 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"biotechnology",
"medicine",
"infectious diseases",
"genetically modified organisms",
"entomology",
"dengue fever",
"neglected tropical diseases",
"biology",
"zoology",
"genetic engineering"
] | Field Cage Studies and Progressive Evaluation of Genetically-Engineered Mosquitoes | journal.pntd.0002001 | null | [
[
"The recent worldwide increase in dengue [1] , [2] has made urgent the development and assessment of new tools for controlling the disease [3] .",
"Because no vaccines or drugs are commercially available [4] , [5] , mosquito vector control by insecticides , insect growth regulators and larval development ... | [
"A genetically-engineered strain of the dengue mosquito vector Aedes aegypti , designated OX3604C , was evaluated in large outdoor cage trials for its potential to improve dengue prevention efforts by inducing population suppression .",
"OX3604C is engineered with a repressible genetic construct that causes a fem... | [
"The absence of a commercially-available dengue vaccine or anti-viral drug makes control of Aedes aegypti , the principal dengue mosquito vector , the only available method to prevent this disease .",
"Sustained , effective application of vector control , however , has been difficult and this led to the call for ... | 2013 |
[
"Introduction",
"Results/Discussion",
"Materials and Methods"
] | [
"organismal evolution",
"animal phylogenetics",
"animal models",
"developmental biology",
"phylogenetics",
"model organisms",
"zoology",
"pattern formation",
"gene expression",
"biology",
"evolutionary systematics",
"entomology",
"animal evolution",
"genetics",
"evolutionary biology",
... | A Single Origin for Nymphalid Butterfly Eyespots Followed by Widespread Loss of Associated Gene Expression | journal.pgen.1002893 | null | [
[
"One of the most conspicuous novelties in the animal world , the eyespot , has received considerable attention regarding its underlying developmental gene regulatory network [1]–[8] , but the origin of this “novel” complex trait remains unknown [9] .",
"At least twelve genes are known to be expressed in t... | [
"Understanding how novel complex traits originate involves investigating the time of origin of the trait , as well as the origin of its underlying gene regulatory network in a broad comparative phylogenetic framework .",
"The eyespot of nymphalid butterflies has served as an example of a novel complex trait , as ... | [
"Butterfly eyespots play an essential role in natural and sexual selection , yet the evolutionary origins of eyespots and of their underlying gene regulatory network remain unknown .",
"By scoring phenotypes and wing expression of five genes in 399 and 21 nymphalid species , respectively , we tested when eyespots... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"infectious disease immunology",
"innate immune system",
"inflammation",
"clinical immunology",
"immunity",
"biology and life sciences",
"immunology",
"immune response",
"immune system"
] | Neutrophil Elastase Causes Tissue Damage That Decreases Host Tolerance to Lung Infection with Burkholderia Species | journal.ppat.1004327 | null | [
[
"Although the inflammatory response elicited by infection is highly effective against microbes , it is also greatly pathogenic and , in extreme cases , the damage caused to host tissues becomes the main source of morbidity and mortality associated with the disease [1] .",
"After infection has occurred , t... | [
"Two distinct defense strategies can protect the host from infection: resistance is the ability to destroy the infectious agent , and tolerance is the ability to withstand infection by minimizing the negative impact it has on the host's health without directly affecting pathogen burden .",
"Burkholderia pseudomal... | [
"Two distinct defense strategies can protect the host from infection: resistance is the ability to destroy the infectious agent , and tolerance is the ability to withstand infection by minimizing the negative impact it has on the host's health without directly affecting pathogen burden .",
"Burkholderia pseudomal... | 2014 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"schistosoma",
"invertebrates",
"schistosoma mansoni",
"medicine and health sciences",
"body fluids",
"pathology and laboratory medicine",
"helminths",
"antiviral therapy",
"pathogens",
"immunology",
"bile",
"microbiology",
"animals",
"liver diseases",
"retroviruses",
"viruses",
"pre... | Increased hepatotoxicity among HIV-infected adults co-infected with Schistosoma mansoni in Tanzania: A cross-sectional study | journal.pntd.0005867 | null | [
[
"Hepatotoxicity increases mortality and morbidity among HIV-infected patients on antiretroviral therapy ( ART ) , especially those with high CD4+ T-lymphocyte ( CD4 ) counts at initiation of ART [1] .",
"The prevalence of hepatotoxicity due to ART is expected to increase in sub-Saharan Africa as ART becom... | [
"Little is known about hepatotoxicity in patients with schistosome and HIV co-infections .",
"Several studies have reported increased liver enzymes and bilirubin levels associated with schistosome infection .",
"We investigated whether HIV-infected adults on antiretroviral therapy who had S . mansoni co-infecti... | [
"Schistosoma sp .",
"are parasitic worms that infect at least 218 million people worldwide .",
"Over 90% of these individuals live in Africa , where HIV infection is also endemic .",
"Schistosome worms lay eggs that damage the gastrointestinal and genitourinary tracts , causing extensive morbidity and mortali... | 2017 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"bacteriology",
"gram negative",
"medicine and health sciences",
"pathology and laboratory medicine",
"host-pathogen interactions",
"medical microbiology",
"microbial pathogens",
"biology and life sciences",
"immunology",
"microbiology",
"pathogenesis",
"bacterial pathogens",
"immune respons... | A Thrombomodulin Mutation that Impairs Active Protein C Generation Is Detrimental in Severe Pneumonia-Derived Gram-Negative Sepsis (Melioidosis) | journal.pntd.0002819 | null | [
[
"Thrombomodulin ( TM , CD141 ) is a multifunctional transmembrane glycoprotein receptor expressed on the surface of all vascular cells and various hematopoietic cells involved in activation of various parameters of inflammation and coagulation including protein C ( PC ) , thrombin-activatable fibrinolysis inh... | [
"During severe ( pneumo ) sepsis inflammatory and coagulation pathways become activated as part of the host immune response .",
"Thrombomodulin ( TM ) is involved in a range of host defense mechanisms during infection and plays a pivotal role in activation of protein C ( PC ) into active protein C ( APC ) .",
"... | [
"Pneumonia and sepsis are conditions in which a procoagulant state is observed , with activation of coagulation and downregulation of anticoagulant pathways , both closely interrelated with inflammation .",
"The protein C ( PC ) system is an important anticoagulant pathway implicated in the pathogenesis of sepsis... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"bacteriology",
"bacterial physiology",
"microbial physiology",
"staphylococci",
"microbial pathogens",
"biology",
"microbiology",
"bacterial pathogens"
] | Expression of a Cryptic Secondary Sigma Factor Gene Unveils Natural Competence for DNA Transformation in Staphylococcus aureus | journal.ppat.1003003 | null | [
[
"Staphylococcus aureus , first discovered and described over 130 years ago [1] , [2] , belongs to the low G+C % Gram-positive Bacilli class of Firmicutes that also includes Bacillus subtilis and Listeria monocytogenes .",
"A commensal bacterium , often colonizing mammalian nasal cavities [3] , S . aureus ... | [
"It has long been a question whether Staphylococcus aureus , a major human pathogen , is able to develop natural competence for transformation by DNA .",
"We previously showed that a novel staphylococcal secondary sigma factor , SigH , was a likely key component for competence development , but the corresponding ... | [
"Staphylococcus aureus is a major human pathogen responsible for a broad spectrum of infections , emphasized by the emergence of multiple antibiotic-resistant strains with up to 60% of strains worldwide resistant to methicillin ( Methicillin Resistant Staphylococcus aureus or MRSA ) .",
"Indeed , MRSA-related inf... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"neuroscience/animal cognition",
"neuroscience/theoretical neuroscience"
] | How Informative Are Spatial CA3 Representations Established by the Dentate Gyrus? | journal.pcbi.1000759 | null | [
[
"The complete model considers the firing rate of a CA3 pyramidal cell , , to be determined by the firing rates of other cells in CA3 , which influence it through RC connections; by the firing rates of DG granule cells , which feed into it through MF connections; by the firing rates of layer II pyramidal cells... | [
"In the mammalian hippocampus , the dentate gyrus ( DG ) is characterized by sparse and powerful unidirectional projections to CA3 pyramidal cells , the so-called mossy fibers .",
"Mossy fiber synapses appear to duplicate , in terms of the information they convey , what CA3 cells already receive from entorhinal c... | [
"The CA3 region at the core of the hippocampus , a structure crucial to memory formation , presents one striking anatomical feature .",
"Its neurons receive many thousands of weak inputs from other sources , but only a few tens of very strong inputs from the neurons in the directly preceding region , the dentate ... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"blood cells",
"flow cytometry",
"t helper cells",
"hiv infections",
"medicine and health sciences",
"immune cells",
"pathology and laboratory medicine",
"pathogens",
"immunology",
"microbiology",
"retroviruses",
"viruses",
"immunodeficiency viruses",
"rna viruses",
"research and analysi... | Single-cell characterization and quantification of translation-competent viral reservoirs in treated and untreated HIV infection | journal.ppat.1007619 | null | [
[
"The persistence of a small pool of infected CD4+ T cells displaying a memory phenotype is one of the major hurdles to HIV eradication [1–4] .",
"This persistent viral reservoir is established during the early phase of infection and decays slowly over time [5–7]: more than 70 years of continuous ART would... | [
"The phenotypic characterization of the cells in which HIV persists during antiretroviral therapy ( ART ) remains technically challenging .",
"We developed a simple flow cytometry-based assay to quantify and characterize infected cells producing HIV proteins during untreated and treated HIV infection .",
"By co... | [
"HIV persists in a small pool of infected CD4+ T cells during ART .",
"A better characterization of these cells is a pre-requisite to the development of HIV eradication strategies .",
"We developed a novel assay , named HIV-Flow , to simultaneously quantify and characterize reservoir cells in individuals receiv... | 2019 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"action potentials",
"medicine and health sciences",
"membrane potential",
"vertebrates",
"electrophysiology",
"neuroscience",
"animals",
"mammals",
"auditory pathway",
"computational neuroscience",
"neuronal tuning",
"coding mechanisms",
"research and analysis methods",
"crystallographic ... | Roles for Coincidence Detection in Coding Amplitude-Modulated Sounds | journal.pcbi.1004997 | null | [
[
"Sound source localization , or the ability to determine the direction of a sound source , is a fundamental function of the auditory system .",
"The interaural level difference ( ILD ) , which is the difference of the sound levels between the two ears , is one of the primary cues of azimuthal sound locali... | [
"Many sensory neurons encode temporal information by detecting coincident arrivals of synaptic inputs .",
"In the mammalian auditory brainstem , binaural neurons of the medial superior olive ( MSO ) are known to act as coincidence detectors , whereas in the lateral superior olive ( LSO ) roles of coincidence dete... | [
"Detecting coincident arrivals of synaptic inputs is a shared fundamental property of many sensory neurons .",
"Such 'coincidence detection' usually refers to the detection of synchronized excitatory inputs only .",
"Experimental evidence , however , indicated that some auditory neurons are also sensitive to th... | 2016 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"pathology and laboratory medicine",
"fungal genetics",
"pathogens",
"tropical diseases",
"microbiology",
"vertebrates",
"animals",
"mammals",
"bacterial diseases",
"fungi",
"neglected tropical diseases",
"bioassays and physiological analysis",
"plants",
"... | High-Throughput Carbon Substrate Profiling of Mycobacterium ulcerans Suggests Potential Environmental Reservoirs | journal.pntd.0005303 | null | [
[
"Mycobacterium ulcerans is the etiologic agent of Buruli ulcer , a disabling infection of the cutaneous and subcutaneous tissues [1–3] .",
"M . ulcerans has been discovered in Bairnsdale , Australia , where Buruli ulcer was initially described [4 , 5] .",
"Buruli ulcer is a World Health Organization n... | [
"Mycobacterium ulcerans is a close derivative of Mycobacterium marinum and the agent of Buruli ulcer in some tropical countries .",
"Epidemiological and environmental studies pointed towards stagnant water ecosystems as potential sources of M . ulcerans , yet the ultimate reservoirs remain elusive .",
"We hypot... | [
"Buruli ulcer is a neglected tropical disease which has been reported in over 33 countries , mainly located in tropical and subtropical regions .",
"It is caused by Mycobacterium ulcerans , an environmental pathogen associated to slow-moving water .",
"The sources and reservoirs of M . ulcerans remain elusive a... | 2017 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"biogeography",
"medicine and health sciences",
"ecology and environmental sciences",
"pathology and laboratory medicine",
"population genetics",
"diarrhea",
"non-coding rna",
"signs and symptoms",
"gastroenterology and hepatology",
"molecular biology techniques",
"population biology",
"medica... | First survey of Enterocytozoon bieneusi and dominant genotype Peru6 among ethnic minority groups in southwestern China’s Yunnan Province and assessment of risk factors | journal.pntd.0007356 | null | [
[
"Microsporidia are a group of unicellular , obligate intracellular parasitic eukaryotes which are composed of approximately 1 , 300 to 1500 formally described species in more than 200 genera [1] .",
"Seventeen species belonging to nine genera have been identified in humans [2] .",
"Among them , Entero... | [
"Enterocytozoon bieneusi is the most common microsporidian species causing diarrhea and other intestinal disorders in humans and animals .",
"Like other infectious diseases , microsporidiosis usually disproportionately affects poor populations .",
"In China , some ethnic minority areas remain poor .",
"Curren... | [
"Enterocytozoon bieneusi is the most prevalent opportunistic microsporidian species causing diarrhea in humans and animals worldwide .",
"Due to frequent occurrence of chronic or life-threatening diarrhea mainly in HIV/AIDS patients and others patients such as elderly people , transplant recipients and cancer pat... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"statistical noise",
"decision making",
"social sciences",
"neuroscience",
"simulation and modeling",
"cognitive psychology",
"mathematics",
"statistics (mathematics)",
"cognition",
"computational neuroscience",
"neuronal tuning",
"coding mechanisms",
"research and analysis methods",
"gaus... | Robust averaging protects decisions from noise in neural computations | journal.pcbi.1005723 | null | [
[
"Decisions about the visual world often require observers to integrate information from multiple sources .",
"An ideal observer will give each source a weight that is proportional to its reliability .",
"Thus , where all sources are equally trustworthy , the best policy is simply to average the availa... | [
"An ideal observer will give equivalent weight to sources of information that are equally reliable .",
"However , when averaging visual information , human observers tend to downweight or discount features that are relatively outlying or deviant ( ‘robust averaging’ ) .",
"Why humans adopt an integration policy... | [
"Humans often make decisions by averaging information from multiple sources .",
"When all the sources are equally reliable , they should all have equivalent impact ( or weight ) on the decisions of an “ideal” observer , i . e . one with perfect memory .",
"However , recent experiments have suggested that humans... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"infectious diseases",
"global health",
"malaria",
"plasmodium falciparum",
"parasitic diseases"
] | PPARγ Agonists Improve Survival and Neurocognitive Outcomes in Experimental Cerebral Malaria and Induce Neuroprotective Pathways in Human Malaria | journal.ppat.1003980 | null | [
[
"Cerebral malaria ( CM ) is a severe complication of Plasmodium falciparum infection that is associated with high mortality rates despite potent anti-anti-malarial therapy [1]–[2] .",
"Adjunctive therapies , aimed at modifying the pathophysiological processes of malaria infection have been pursued as a wa... | [
"Cerebral malaria ( CM ) is associated with a high mortality rate , and long-term neurocognitive impairment in approximately one third of survivors .",
"Adjunctive therapies that modify the pathophysiological processes involved in CM may improve outcome over anti-malarial therapy alone .",
"PPARγ agonists have ... | [
"Cerebral malaria ( CM ) is a severe complication of Plasmodium falciparum infection that is associated with long-term neurocognitive impairment in about a third of survivors even when optimal anti-malarial therapy is used .",
"Since both the parasite and the host immune response to infection play a role in the d... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Nanoformulations of Rilpivirine for Topical Pericoital and Systemic Coitus-Independent Administration Efficiently Prevent HIV Transmission | journal.ppat.1005075 | null | [
[
"Although the annual number of new HIV infections continues to decline , the global HIV-1 pandemic remains an unprecedented public health problem , with 2 . 1 million new infections in 2013 and an estimated 35 million people already infected [1] .",
"This highlights the urgent need for effective and safe ... | [
"Vaginal HIV transmission accounts for the majority of new infections worldwide .",
"Currently , multiple efforts to prevent HIV transmission are based on pre-exposure prophylaxis with various antiretroviral drugs .",
"Here , we describe two novel nanoformulations of the reverse transcriptase inhibitor rilpivir... | [
"When taken consistently , PrEP has been shown to reduce the risk of HIV infection by up to 92% in people who are at high risk .",
"However , PrEP is much less effective if it is not taken consistently .",
"To improve adherence to the drug regimen , several new drug delivery systems , that include novel gel for... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"blood cells",
"innate immune system",
"medicine and health sciences",
"immune cells",
"immune physiology",
"cytokines",
"spleen",
"immunology",
"cloning",
"parasitic diseases",
"nematode infections",
"animal models",
"developmental biology",
"model organisms",
"experimental organism sys... | IRF-8 regulates expansion of myeloid-derived suppressor cells and Foxp3+ regulatory T cells and modulates Th2 immune responses to gastrointestinal nematode infection | journal.ppat.1006647 | null | [
[
"Interferon regulatory factor ( IRF ) -8 is a member of the IRF family of transcription factors and plays an important role in regulating proinflammatory cytokines especially IL-12p40 , which is critical for Th1 cell differentiation [1] .",
"IRF-8 is essential for the development of various myeloid-derive... | [
"Interferon regulatory factor-8 ( IRF-8 ) is critical for Th1 cell differentiation and negatively regulates myeloid cell development including myeloid-derived suppressor cells ( MDSC ) .",
"MDSC expand during infection with various pathogens including the gastrointestinal ( GI ) nematode Heligmosomoides polygyrus... | [
"We investigated if IRF-8 , which is critical for Th1 immunity and negatively regulates myeloid cell development including MDSC , contributes to Th2 immunity to the gastrointestinal nematode Heligmosomoides polygyrus bakeri ( Hpb ) .",
"Irf8 expression was down-regulated in MDSC from infected C57BL/6 ( B6 ) mice ... | 2017 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"blood cells",
"mycobacterium leprae",
"complement system",
"medicine and health sciences",
"immune cells",
"immune physiology",
"enzyme-linked immunoassays",
"pathology and laboratory medicine",
"body fluids",
"immunology",
"tropical diseases",
"bacterial diseases",
"signs and symptoms",
... | Differential immunoglobulin and complement levels in leprosy prior to development of reversal reaction and erythema nodosum leprosum | journal.pntd.0007089 | null | [
[
"Leprosy , a chronic infectious disease caused by Mycobacterium leprae , is still a public health challenge for many countries , including Brazil [1] .",
"There is a spectrum of leprosy that corresponds to the type of immune response elicited to M . leprae .",
"Clinical , histopathologic , and mycobac... | [
"Leprosy is a treatable infectious disease caused by Mycobacterium leprae .",
"However , there is additional morbidity from leprosy-associated pathologic immune reactions , reversal reaction ( RR ) and erythema nodosum leprosum ( ENL ) , which occur in 1 in 3 people with leprosy , even with effective treatment of... | [
"One in three people with leprosy develop an immune reaction , which worsen quality of life .",
"Reactions occur despite effective treatment of the causative bacteria of leprosy , Mycobacterium leprae , with antibiotics .",
"These reactions cause worsening skin lesions and additional nerve damage .",
"Reactio... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biology"
] | Down-Regulation of Rad51 Activity during Meiosis in Yeast Prevents Competition with Dmc1 for Repair of Double-Strand Breaks | journal.pgen.1004005 | null | [
[
"Meiotic recombination is a highly conserved process that is critical for the accurate segregation of homologous chromosomes to opposite poles at the first meiotic division .",
"Crossovers between non-sister chromatids , in combination with sister chromatid cohesion , physically connect homologous chromos... | [
"Interhomolog recombination plays a critical role in promoting proper meiotic chromosome segregation but a mechanistic understanding of this process is far from complete .",
"In vegetative cells , Rad51 is a highly conserved recombinase that exhibits a preference for repairing double strand breaks ( DSBs ) using ... | [
"Sexual reproduction involves the generation of chromosomally balanced gametes through the specialized cell division of meiosis .",
"A critical component of meiosis is the physical connection of homologous chromosomes through a combination of recombination and sister chromatid cohesion that is necessary for prope... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"microbiology",
"host-pathogen interaction",
"liver diseases",
"infectious hepatitis",
"gastroenterology and hepatology",
"hepatitis c",
"infectious diseases",
"biology",
"biochemistry",
"virology",
"molecular cell biology",
"metabolism"
] | Hepatitis C Virus Induces the Mitochondrial Translocation of Parkin and Subsequent Mitophagy | journal.ppat.1003285 | null | [
[
"Hepatitis C virus ( HCV ) infection most often leads to chronic hepatitis , which can progress to steatosis , fibrosis , cirrhosis , and hepatocellular carcinoma [1] .",
"HCV RNA genome encodes a polyprotein , which includes; core , E1 , E2 , p7 , NS2 , NS3 , NS4A , NS4B , NS5A , and NS5B [2] .",
"Vi... | [
"Hepatitis C Virus ( HCV ) induces intracellular events that trigger mitochondrial dysfunction and promote host metabolic alterations .",
"Here , we investigated selective autophagic degradation of mitochondria ( mitophagy ) in HCV-infected cells .",
"HCV infection stimulated Parkin and PINK1 gene expression , ... | [
"Hepatitis C virus ( HCV ) infection alters host lipid metabolism .",
"HCV-induced mitochondrial dysfunction may promote the metabolic alterations by affecting mitochondrial β-oxidation and oxidative phosphorylation .",
"Dysfunctional mitochondria are detrimental to cell survival and require rapid clearance to ... | 2013 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious diseases",
"biology",
"population biology",
"evolutionary biology"
] | Genetic Characterization of Trypanosoma cruzi DTUs in Wild Triatoma infestans from Bolivia: Predominance of TcI | journal.pntd.0001650 | null | [
[
"Trypanosoma cruzi , the agent of Chagas disease , is a serious threat to health in the Americas , accounting for the highest disease burden in Latin American , with eight to nine million people infected and 25–90 million at risk [1]–[3] .",
"This parasite , which belongs to the order Kinetoplastida , is ... | [
"The current persistence of Triatoma infestans ( one of the main vectors of Chagas disease ) in some domestic areas could be related to re-colonization by wild populations which are increasingly reported .",
"However , the infection rate and the genetic characterization of the Trypanosoma cruzi strains infecting ... | [
"Chagas disease is a neglected parasitic disease transmitted by bugs ( vectors ) and represents a serious health problem in the Americas .",
"Although the transmission generally occurs in the houses where the bugs are living , wild populations of vectors are now considered a problem because these populations migh... | 2012 |
[
"Results",
"Discussion",
"Methods"
] | [
"bacteriology",
"viral transmission and infection",
"microbiology",
"genetic elements",
"bacterial genetics",
"dna recombination",
"dna",
"microbial genetics",
"genomics",
"chromosome biology",
"gene disruption",
"genetic loci",
"biochemistry",
"biochemical simulations",
"host cells",
... | Horizontal DNA Transfer Mechanisms of Bacteria as Weapons of Intragenomic Conflict | journal.pbio.1002394 | Modelling and high-resolution genomic data demonstrate the evolutionary significance of an ongoing arms race between bacterial uptake of environmental DNA ("transformation") and horizontal DNA transfer driven by mobile genetic elements. | [
[
"To explore potential benefits of different evolutionary strategies to bacterial cells , a stochastic compartmental model was developed to simulate genetic exchange through HDT ( see Methods ) .",
"The first simulations investigated scenarios in which transformation might facilitate the import of benefici... | [
"Horizontal DNA transfer ( HDT ) is a pervasive mechanism of diversification in many microbial species , but its primary evolutionary role remains controversial .",
"Much recent research has emphasised the adaptive benefit of acquiring novel DNA , but here we argue instead that intragenomic conflict provides a co... | [
"Bacteria are able to rapidly change their characteristics , such as antibiotic resistance , by acquiring genes from surrounding cells .",
"Some sets of genes , called mobile genetic elements ( MGEs ) , drive their own movement between bacterial cells by transmitting in viral or viral-like manners .",
"These se... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genetics and genomics/bioinformatics",
"nephrology/dialysis and renal transplantation",
"cardiovascular disorders/cardiac surgery and transplantations",
"genetics and genomics/gene expression"
] | Differentially Expressed RNA from Public Microarray Data Identifies Serum Protein Biomarkers for Cross-Organ Transplant Rejection and Other Conditions | journal.pcbi.1000940 | null | [
[
"The utility of serum and plasma proteomic techniques to find diagnostic biomarkers has received considerable attention and investment in recent years .",
"However , the limited sensitivity of mass spectrometers , the dynamic range of protein concentrations , and the presence of high abundance proteins in... | [
"Serum proteins are routinely used to diagnose diseases , but are hard to find due to low sensitivity in screening the serum proteome .",
"Public repositories of microarray data , such as the Gene Expression Omnibus ( GEO ) , contain RNA expression profiles for more than 16 , 000 biological conditions , covering ... | [
"Protein biomarkers in the blood are urgently needed for the diagnosis of a wide variety of diseases to improve health care .",
"We aim to find a fast and cost-effective strategy to discover diagnostic protein biomarkers .",
"Hundreds of diseases have already been investigated using microarray technology , meas... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"growth control",
"animal genetics",
"gene regulation",
"cell differentiation",
"gene function",
"mitosis",
"developmental biology",
"cell division",
"organism development",
"molecular development",
"molecular genetics",
"signaling pathways",
"morphogenesis",
"pattern formation",
"embryo... | Tbx2 Controls Lung Growth by Direct Repression of the Cell Cycle Inhibitor Genes Cdkn1a and Cdkn1b | journal.pgen.1003189 | null | [
[
"The development of organs and organisms depends on the precise control of the progression through and the exit from the cell cycle to achieve appropriate patterns of proliferation and differentiation in time and space .",
"Progression through the cell cycle is regulated predominantly by a series of serin... | [
"Vertebrate organ development relies on the precise spatiotemporal orchestration of proliferation rates and differentiation patterns in adjacent tissue compartments .",
"The underlying integration of patterning and cell cycle control during organogenesis is insufficiently understood .",
"Here , we have investig... | [
"During organ formation , proliferation rates and differentiation patterns vary widely between different stages and tissue compartments .",
"It is poorly understood how cell cycle progression is locally controlled and integrated with patterning processes in these developmental programs .",
"Here , we used the m... | 2013 |
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