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 and Discussion",
"Discussion",
"Materials and Methods"
] | [
"cell physiology",
"ecology and environmental sciences",
"medicine and health sciences",
"aeromonas hydrophila",
"pathology and laboratory medicine",
"pathogens",
"microbiology",
"cell metabolism",
"mathematics",
"aeromonas",
"statistics (mathematics)",
"forecasting",
"network analysis",
"... | The Contribution of High-Order Metabolic Interactions to the Global Activity of a Four-Species Microbial Community | journal.pcbi.1005079 | null | [
[
"We are surrounded by complex communities of microbes , many that play a fundamental role in our everyday lives .",
"Microbial ecosystems in nature are typically composed of hundreds or thousands of microbial species , heterogeneously distributed in space and time .",
"Working together , these network... | [
"The activity of a biological community is the outcome of complex processes involving interactions between community members .",
"It is often unclear how to accurately incorporate these interactions into predictive models .",
"Previous work has shown a range of positive and negative metabolic pairwise interacti... | [
"Many wild microbial ecosystems contain hundreds to thousands of species , suggesting that interactions between species likely play an important role in regulating the behavior of such complex cellular networks .",
"Predicting how these interactions impact the overall activity of microbial communities remains a c... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | The Actin Nucleator Cobl Is Controlled by Calcium and Calmodulin | journal.pbio.1002233 | The calcium sensor calmodulin directly regulates the actin filament-promoting factor Cobl to help shape the complex architecture of neurons underlying neuronal network formation. | [
[
"Metazoan life critically relies on the formation , organization , and dynamics of actin filaments , which are , for example , crucial for shaping and movement of membranes and entire cells .",
"The polar and extremely arborized morphologies that neurons develop during pre- and postnatal brain development... | [
"Actin nucleation triggers the formation of new actin filaments and has the power to shape cells but requires tight control in order to bring about proper morphologies .",
"The regulation of the members of the novel class of WASP Homology 2 ( WH2 ) domain-based actin nucleators , however , thus far has largely re... | [
"The organization and the formation of new actin filaments by polymerization of actin monomers has the power to shape cells .",
"The rate-limiting step in actin polymerization is “nucleation”—a process during which the first actin monomers are assembled with the help of actin nucleators .",
"This nucleation ste... | 2015 |
[
"Introduction",
"Methods",
"Results/Discussion"
] | [
"biochemistry/structural genomics",
"computational biology/protein structure prediction",
"computational biology/macromolecular structure analysis"
] | Pushing Structural Information into the Yeast Interactome by High-Throughput Protein Docking Experiments | journal.pcbi.1000490 | null | [
[
"In the last decade , many genome-sequencing projects started delivering nearly complete lists of the macromolecules present in several model organisms .",
"However , taken individually , knowing the components reveal relatively little about how complex systems , such as a eukaryotic cell , assemble and c... | [
"The last several years have seen the consolidation of high-throughput proteomics initiatives to identify and characterize protein interactions and macromolecular complexes in model organisms .",
"In particular , more that 10 , 000 high-confidence protein-protein interactions have been described between the rough... | [
"Proteins are the main perpetrators of most biological processes .",
"However , they seldom act alone , and most cellular functions are , in fact , carried out by large macromolecular complexes and regulated through intricate protein-protein interaction networks .",
"Consequently , large efforts have been devot... | 2009 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine",
"bacterial diseases",
"infectious diseases",
"mycobacterium",
"biology",
"microbiology"
] | Emergence of Clinically Relevant Non-Tuberculous Mycobacterial Infections in Saudi Arabia | journal.pntd.0002234 | null | [
[
"Globally humans are exposed extensively to environmental sources ( soil , water , plant and animal materials ) of mycobacteria .",
"Predominantly Non-Tuberculous Mycobacterial ( NTM ) disease develops among immuno-compromised individuals although recently they emerge among immuno-competent personals also... | [
"Non-Tuberculous Mycobacteria ( NTM ) are emerging around the world due to a higher prevalence of immunosuppressive illness and therapy .",
"Saudi Arabia is not an exception as there have been novel mycobacterial species also identified .",
"In addition , several published case reports from different parts of t... | [
"Non-Tuberculous Mycobacteria ( NTM ) are opportunistic human pathogens .",
"Global reports show an emergence of various NTM diseases among immuno-suppressed as well as immuno-competent individuals .",
"In Saudi Arabia , data are scarce on the prevalence of NTM and their genetic diversity .",
"Currently , NTM... | 2013 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"antimicrobials",
"medicine and health sciences",
"body fluids",
"pathology and laboratory medicine",
"pathogens",
"drugs",
"geographical locations",
"microbiology",
"salmonellosis",
"retroviruses",
"viruses",
"immunodeficiency viruses",
"bacterial diseases",
"antibiotic resistance",
"rn... | Epidemiology and antimicrobial resistance of invasive non-typhoidal Salmonellosis in rural Thailand from 2006-2014 | journal.pntd.0006718 | null | [
[
"Invasive non-typhoidal Salmonella ( iNTS ) disease , frequently associated with extremes of age , clinical malaria , HIV infections and malnutrition can be fatal in up to 20–25% of patients [1 , 2] .",
"The vast majority of reported iNTS infections and related deaths occur in Africa [3] , where iNTS anti... | [
"Invasive salmonellosis is a common cause of bloodstream infection in Southeast Asia .",
"Limited epidemiologic and antimicrobial resistance data are available from the region .",
"Blood cultures performed in all 20 hospitals in the northeastern province of Nakhon Phanom ( NP ) and eastern province of Sa Kaeo (... | [
"Invasive strains of non-typhoidal salmonella ( iNTS ) are a common cause of bloodstream infection in Southeast Asia , however limited epidemiologic and antimicrobial resistance data are available and no population-based studies have been published from the region .",
"We use nine years of bloodstream infections ... | 2018 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [] | Pathogenesis of Progressive Scarring Trachoma in Ethiopia and Tanzania and Its Implications for Disease Control: Two Cohort Studies | journal.pntd.0003763 | null | [
[
"Blinding trachoma is the end result of the scarring sequelae of recurrent ocular Chlamydia trachomatis infection .",
"This obligate intracellular bacterium triggers prolonged inflammatory episodes in the conjunctival mucosa , which are believed to be central to the development of scarring [1] .",
"Ho... | [
"Trachoma causes blindness through a conjunctival scarring process initiated by ocular Chlamydia trachomatis infection; however , the rates , drivers and pathophysiological determinants are poorly understood .",
"We investigated progressive scarring and its relationship to conjunctival infection , inflammation an... | [
"Blinding trachoma is believed to be the end result of a long-term progressive scarring process that is initiated by recurrent infection by the bacterium Chlamydia trachomatis starting in childhood .",
"Scar tissue predominantly develops on the inner surface of the upper eyelids ( conjunctiva ) .",
"However , t... | 2015 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"neuroscience/motor systems",
"neuroscience/theoretical neuroscience",
"computational biology/computational neuroscience"
] | Coordinate Dependence of Variability Analysis | journal.pcbi.1000751 | null | [
[
"A study of multivariable behavior naturally raises the question of which reference frames the central nervous system ( CNS ) may use to coordinate its actions .",
"For example , Morasso [1] studied planar reaching movements and showed that translation and rotation of the start and target positions evoked... | [
"Analysis of motor performance variability in tasks with redundancy affords insight about synergies underlying central nervous system ( CNS ) control .",
"Preferential distribution of variability in ways that minimally affect task performance suggests sophisticated neural control .",
"Unfortunately , in the ana... | [
"Over the past decade the identification of synergies has become a prominent theme in motor neuroscience .",
"Like other aspects of neural organization ( e . g . , vision ) the control of coordinated movement is almost certainly hierarchical with synergies a key feature of this hypothesis .",
"In pursuit of ide... | 2010 |
[
"Introduction",
"Methods",
"Statistical analyses",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"pathology and laboratory medicine",
"maternal health",
"obstetrics and gynecology",
"education",
"pathogens",
"sociology",
"geographical locations",
"microbiology",
"social sciences",
"tropical diseases",
"ebola hemorrhagic fever",
"retroviruses",
"viruses"... | Ebola virus disease-related stigma among survivors declined in Liberia over an 18-month, post-outbreak period: An observational cohort study | journal.pntd.0007185 | null | [
[
"Ebola virus disease ( EVD ) -related stigma was a recognized but poorly understood consequence of Ebola outbreaks prior to the 2013 index case of EVD in Guinea .",
"[1–3] The 2013–2016 West Africa EVD outbreak was unprecedented in magnitude; of the 28 , 646 reported cases , 17 , 323 individuals survived ... | [
"While qualitative assessments of Ebola virus disease ( EVD ) -related stigma have been undertaken among survivors and the general public , quantitative tools and assessment targeting survivors have been lacking .",
"Beginning in June 2015 , EVD survivors from seven Liberian counties , where most of the country’s... | [
"Survivors of Ebola virus disease ( EVD ) experienced stigma throughout the 2013–2016 West African outbreak , but post-outbreak experiences of EVD-related stigma have been limited to qualitative studies .",
"We adapted a 7-item EVD-related stigma index from the HIV literature , which was administered to EVD survi... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"wavelet transforms",
"invertebrates",
"phytoplankton",
"animals",
"seasons",
"developmental biology",
"ocean temperature",
"echinoderms",
"plants",
"research and analysis methods",
"mathematical functions",
"oceanography",
"mathematical and statistical techniques",
"marine and aquatic sci... | Synchrony is more than its top-down and climatic parts: interacting Moran effects on phytoplankton in British seas | journal.pcbi.1006744 | null | [
[
"Many ecosystems are subject to large spatially synchronous fluctuations , with serious consequences for ecosystem services and stability across space and time .",
"Spatial synchrony is the tendency for spatially separated populations to undergo correlated fluctuations .",
"Spatial synchrony is a fund... | [
"Large-scale spatial synchrony is ubiquitous in ecology .",
"We examined 56 years of data representing chlorophyll density in 26 areas in British seas monitored by the Continuous Plankton Recorder survey .",
"We used wavelet methods to disaggregate synchronous fluctuations by timescale and determine that driver... | [
"The size of the annual bloom in phytoplankton can vary similarly from year to year in different parts of the same oceanic region , a phenomenon called spatial synchrony .",
"The growth of phytoplankton near the ocean surface is the foundation of marine food webs , which include numerous commercially exploited sp... | 2019 |
[
"Introduction",
"Methods",
"Discussion"
] | [
"infectious diseases/helminth infections",
"public health and epidemiology/infectious diseases",
"nutrition/malnutrition",
"nutrition/deficiencies"
] | Anemia of Inflammation Is Related to Cognitive Impairment among Children in Leyte, The Philippines | journal.pntd.0000533 | null | [
[
"Anemia of inflammation ( AI ) , is the second most prevalent type of anemia following iron deficiency anemia ( IDA ) [1] , [2] .",
"The most common conditions associated with AI include bacterial , viral , and parasitic infections , cancers , and autoimmune diseases [1] .",
"AI leads to alterations i... | [
"Many studies have addressed the relationship between iron deficiency anemia ( IDA ) and cognitive impairment , but none have evaluated the role of non-iron deficiency anemia ( NIDA ) .",
"One of the main causes of NIDA in developing countries is AI , largely due to infectious diseases , whereby iron is shunted a... | [
"Past studies have demonstrated that iron deficiency anemia is related to deficits in cognitive fucntioning in children , and treating iron deficiency anemia with iron supplementation can improve cognition .",
"Anemia of inflammation is another type of anemia caused by many diseases of lesser-developed countries ... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"evolutionary ecology",
"cytokines",
"immunity to infections",
"population genetics",
"immunology",
"microbiology",
"host-pathogen interaction",
"genetic polymorphism",
"biology",
"evolutionary genetics",
"immune system",
"genetics of the immune system",
"ecology",
"immunity",
"evolution... | Genetic Diversity in Cytokines Associated with Immune Variation and Resistance to Multiple Pathogens in a Natural Rodent Population | journal.pgen.1002343 | null | [
[
"Individuals vary in their resistance to infectious disease .",
"Much of this variation is genetic and , in natural populations , considerable attention has focussed on the potential for pathogens to act as a selective force on genetic diversity [1] , [2] .",
"However , studies into the role of host g... | [
"Pathogens are believed to drive genetic diversity at host loci involved in immunity to infectious disease .",
"To date , studies exploring the genetic basis of pathogen resistance in the wild have focussed almost exclusively on genes of the Major Histocompatibility Complex ( MHC ) ; the role of genetic variation... | [
"Much of what we know about the genetic basis of immunity to infection has come from studies of laboratory animals .",
"However , these animals are kept in conditions very different from those experienced in the natural environment .",
"In order to improve our understanding of the genetic determinants of diseas... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods",
"Supporting Information"
] | [
"biochemistry",
"infectious diseases",
"eukaryotes",
"microbiology",
"molecular biology"
] | A Function for a Specific Zinc Metalloprotease of African Trypanosomes | journal.ppat.0030150 | null | [
[
"Trypanosoma brucei is a protozoan parasite that causes African sleeping sickness .",
"Its life cycle consists of several developmental stages in its tsetse fly vector and mammalian host .",
"In the midgut of the tsetse fly , the parasites proliferate as an extracellular procyclic ( PRO ) form , which... | [
"The Trypanosoma brucei genome encodes three groups of zinc metalloproteases , each of which contains ∼30% amino acid identity with the major surface protease ( MSP , also called GP63 ) of Leishmania .",
"One of these proteases , TbMSP-B , is encoded by four nearly identical , tandem genes transcribed in both blo... | [
"African trypanosomes cause sleeping sickness , a fatal disease of humans and livestock in Africa .",
"During their life cycle , these protozoan parasites cycle between the bloodstream of mammals and tsetse flies .",
"Their two main developmental stages are the bloodstream form and the procyclic form in the tse... | 2007 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"rna interference",
"enzymes",
"immunology",
"microbiology",
"host-pathogen interaction",
"parasitology",
"parasite physiology",
"gene function",
"enzyme metabolism",
"dna",
"immunomodulation",
"proteins",
"metabolic pathways",
"gene expression",
"hemoproteins",
"biology",
"molecular... | Characterization of Schistosome Tegumental Alkaline Phosphatase (SmAP) | journal.pntd.0001011 | null | [
[
"Schistosomes are parasitic platyhelminths that constitute an important public health problem globally .",
"Infection can lead to a chronic , often debilitating disease that afflicts more than 200 million people in over 70 countries worldwide [1] , [2] .",
"Mortality is estimated at over a quarter of ... | [
"Schistosomes are parasitic platyhelminths that currently infect over 200 million people globally .",
"The parasites can live for years in a putatively hostile environment - the blood of vertebrates .",
"We have hypothesized that the unusual schistosome tegument ( outer-covering ) plays a role in protecting par... | [
"Schistosomes are parasitic worms that live for many years in the blood stream of ∼200 million people globally .",
"How they manage to avoid getting killed by host immune mechanisms is a puzzle .",
"We hypothesize that molecules in their skin ( tegument ) , e . g . the enzyme alkaline phosphatase ( SmAP ) , hel... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"animal models",
"motor systems",
"neurobiology of disease and regeneration",
"animal genetics",
"genetic mutation",
"model organisms",
"molecular cell biology",
"genetics",
"molecular genetics",
"biology",
"genetics of disease",
"neuroscience",
"genetics and genomics",
"gene function"
] | Mutations in a P-Type ATPase Gene Cause Axonal Degeneration | journal.pgen.1002853 | null | [
[
"Neuronal loss and axonal degeneration are important pathological features of neurodegenerative diseases , such as Alzheimer disease , Parkinson's disease , amyotrophic lateral sclerosis and glaucoma .",
"Axonopathies , conditions in which axon injury occurs first during disease progression , have been ex... | [
"Neuronal loss and axonal degeneration are important pathological features of many neurodegenerative diseases .",
"The molecular mechanisms underlying the majority of axonal degeneration conditions remain unknown .",
"To better understand axonal degeneration , we studied a mouse mutant wabbler-lethal ( wl ) .",... | [
"Axonal degeneration is an important pathological feature of many neurodegenerative diseases , such as Alzheimer disease , Parkinson's disease , and amyotrophic lateral sclerosis .",
"In most of these disease conditions , molecular mechanisms of axonal degeneration remain largely unknown .",
"Spontaneous mouse ... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"plant science",
"model organisms",
"genetics",
"biology",
"genomics",
"molecular cell biology"
] | Comprehensive High-Resolution Analysis of the Role of an Arabidopsis Gene Family in RNA Editing | journal.pgen.1003584 | null | [
[
"RNA editing alters the genetic information at specific sites on RNA molecules .",
"Editing has been described in a wide range of organisms from viruses to animals and plants .",
"Several systems involving unrelated mechanisms seem to have arisen separately during evolution [1] .",
"In flowering p... | [
"In flowering plants , mitochondrial and chloroplast mRNAs are edited by C-to-U base modification .",
"In plant organelles , RNA editing appears to be generally a correcting mechanism that restores the proper function of the encoded product .",
"Members of the Arabidopsis RNA editing-Interacting Protein ( RIP )... | [
"RNA editing is a co- or post-transcriptional RNA processing reaction that changes the nucleotide sequence of the RNA substrate .",
"In flowering plants , mRNA editing is confined to organelle transcripts , altering cytidine to uridine .",
"Recently , some members of a small Arabidopsis gene family were found t... | 2013 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"immune physiology",
"pathology and laboratory medicine",
"viral transmission and infection",
"spleen",
"pathogens",
"microbiology",
"vertebrates",
"animals",
"mammals",
"primates",
"viruses",
"filoviruses",
"rna viruses",
"immunologic techniques",
"vira... | Delayed Time-to-Treatment of an Antisense Morpholino Oligomer Is Effective against Lethal Marburg Virus Infection in Cynomolgus Macaques | journal.pntd.0004456 | null | [
[
"Marburg virus ( MARV ) is a member of the family Filoviridae that is highly virulent and causes hemorrhagic fever in humans and nonhuman primates [1] .",
"In humans , Marburg virus disease ( MVD ) typically begins with high fever accompanied by a severe headache , chills , myalgia and malaise .",
"Fo... | [
"Marburg virus ( MARV ) is an Ebola-like virus in the family Filovirdae that causes sporadic outbreaks of severe hemorrhagic fever with a case fatality rate as high as 90% .",
"AVI-7288 , a positively charged antisense phosphorodiamidate morpholino oligomer ( PMOplus ) targeting the viral nucleoprotein gene , was... | [
"Marburg virus ( MARV ) is a filovirus closely related to Ebola virus and similarly causes hemorrhagic fever in humans .",
"MARV is endemic throughout parts of tropical Africa .",
"Severe outbreaks of Marburg virus disease ( MVD ) have occurred involving hundreds of human cases .",
"No effective MARV antivira... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"recreation",
"medicine and health sciences",
"decision theory",
"elderly",
"decision making",
"applied mathematics",
"social sciences",
"neuroscience",
"simulation and modeling",
"age groups",
"developmental biology",
"physiological processes",
"cognitive psychology",
"organism developmen... | Age-dependent Pavlovian biases influence motor decision-making | journal.pcbi.1006304 | null | [
[
"Optimal decision-making requires choices that maximise reward and minimise punishment .",
"Two key mechanisms play an important role in shaping the level of sub-optimality observed; a flexible , instrumental , value-dependent process , and a hard-wired , Pavlovian , value-independent process [1–3] .",
... | [
"Motor decision-making is an essential component of everyday life which requires weighing potential rewards and punishments against the probability of successfully executing an action .",
"To achieve this , humans rely on two key mechanisms; a flexible , instrumental , value-dependent process and a hardwired , Pa... | [
"Decisions in everyday life often require weighing the probability of successfully executing an action ( e . g . , successfully crossing a street ) against potential rewards and punishments .",
"Although older individuals take fewer risks during such motor decision-making scenarios , the underlying mechanism rema... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"computational neuroscience",
"biology",
"computational biology"
] | Power-Law Inter-Spike Interval Distributions Infer a Conditional Maximization of Entropy in Cortical Neurons | journal.pcbi.1002461 | null | [
[
"The sequences of electrical pulses , or spikes , recorded from in vivo cortical neurons are stochastic and highly irregular [1]–[3] .",
"Thus , the brain is a highly noisy information machine .",
"Shannon's information theory and mutual information have often been used to extract the information repr... | [
"The brain is considered to use a relatively small amount of energy for its efficient information processing .",
"Under a severe restriction on the energy consumption , the maximization of mutual information ( MMI ) , which is adequate for designing artificial processing machines , may not suit for the brain .",
... | [
"The brain is a highly noisy information machine , making a striking contrast with man-made electric computers to which noise is merely harmful .",
"However , little is known about the way neurons process information in the noisy states .",
"Here , we explore the principle of noisy neural information processing... | 2012 |
[
"Introduction",
"Results/Discussion",
"Materials and Methods"
] | [
"molecular biology/bioinformatics",
"computational biology/sequence motif analysis"
] | Reconstruction of Protein Backbones from the BriX Collection of Canonical Protein Fragments | journal.pcbi.1000083 | null | [
[
"High-resolution structure determination of proteins and protein complexes via experimental methods occurs at a significantly slower pace than the collection of novel protein sequences .",
"As a result , less than 30% of human proteins have a known structure in the Protein Data Bank and the percentage for... | [
"As modeling of changes in backbone conformation still lacks a computationally efficient solution , we developed a discretisation of the conformational states accessible to the protein backbone similar to the successful rotamer approach in side chains .",
"The BriX fragment database , consisting of fragments from... | [
"Large-scale DNA sequencing efforts produce large amounts of protein sequence data .",
"However , in order to understand the function of a protein , its tertiary three-dimensional structure is required .",
"Despite worldwide efforts in structural biology , experimental protein structures are determined at a sig... | 2008 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious diseases",
"public health and epidemiology",
"mathematics",
"chicken",
"human"
] | Risk Maps for the Spread of Highly Pathogenic Avian Influenza in Poultry | journal.pcbi.0030071 | null | [
[
"Outbreaks of highly contagious animal infections such as foot-and-mouth disease , classical swine fever , and highly pathogenic avian influenza traditionally have been and continue to be important loss factors in production animals throughout the world .",
"In recent years , several large epidemics have ... | [
"Devastating epidemics of highly contagious animal diseases such as avian influenza , classical swine fever , and foot-and-mouth disease underline the need for improved understanding of the factors promoting the spread of these pathogens .",
"Here the authors present a spatial analysis of the between-farm transmi... | [
"Modern approaches in the epidemiology of infectious diseases include the use of mechanistic mathematical models to analyze and predict the dynamics of disease transmission .",
"Modelling work during the massive epidemic of foot-and-mouth-disease in 2001 in Great Britain has provided an important example of how s... | 2007 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"children",
"parasite groups",
"medicine and health sciences",
"pathology and laboratory medicine",
"plasmodium",
"drugs",
"variant genotypes",
"tropical diseases",
"immunology",
"parasitic diseases",
"genetic mapping",
"parasitology",
"age groups",
"apicomplexa",
"signs and symptoms",
... | The Incidence and Differential Seasonal Patterns of Plasmodium vivax Primary Infections and Relapses in a Cohort of Children in Papua New Guinea | journal.pntd.0004582 | null | [
[
"Globally , over a billion inhabitants are exposed to Plasmodium vivax and suffer from an estimated 70 to 80 million cases per year [1] .",
"It has been increasingly recognized that P vivax can cause severe and fatal disease [2 , 3] .",
"Effective control measures are needed .",
"Designing interve... | [
"Plasmodium vivax has the ability to relapse from dormant parasites in the liver weeks or months after inoculation , causing further blood-stage infection and potential onward transmission .",
"Estimates of the force of blood-stage infections arising from primary infections and relapses are important for designin... | [
"Plasmodium vivax is the most widespread of the malaria species affecting humans .",
"It has the ability for parasites to lie dormant in liver cells and then to relapse weeks or months later , causing further blood-stage infections and onward transmission .",
"Relapses present a challenge to control and elimina... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"genome-wide association studies",
"invertebrates",
"alkaloids",
"medicine and health sciences",
"genetic networks",
"rna interference",
"chemical compounds",
"disaccharides",
"social sciences",
"carbohydrates",
"organic compounds",
"animals",
"animal models",
"behavioral pharmacology",
... | Genetics of cocaine and methamphetamine consumption and preference in Drosophila melanogaster | journal.pgen.1007834 | null | [
[
"Illicit use of cocaine and methamphetamine constitutes a significant public health problem that incurs great socioeconomic costs in the United States and worldwide [1–3] .",
"Cocaine and the amphetamine class of drugs are potent central nervous system stimulants that act by raising synaptic concentration... | [
"Illicit use of psychostimulants , such as cocaine and methamphetamine , constitutes a significant public health problem .",
"Whereas neural mechanisms that mediate the effects of these drugs are well-characterized , genetic factors that account for individual variation in susceptibility to substance abuse and ad... | [
"Illicit use of cocaine and methamphetamine is a major public health problem .",
"Whereas the neurological effects of these drugs are well characterized , it remains challenging to determine genetic risk factors for substance abuse in human populations .",
"The fruit fly , Drosophila melanogaster , presents an ... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"plant biology/plant growth and development",
"plant biology/plant genetics and gene expression"
] | Genetic Control of Organ Shape and Tissue Polarity | journal.pbio.1000537 | A combination of experimental analysis and mathematical modelling shows how the genetic control of tissue polarity plays a fundamental role in the development and evolution of form. | [
[
"Changes in tissue shape during development may involve growth , cell rearrangements , or a combination of the two .",
"In the case of plants , where cells are held in place by their walls , shape changes arise purely through differential growth [1]–[3] .",
"Thus , plants provide a simplified system f... | [
"The mechanisms by which genes control organ shape are poorly understood .",
"In principle , genes may control shape by modifying local rates and/or orientations of deformation .",
"Distinguishing between these possibilities has been difficult because of interactions between patterns , orientations , and mechan... | [
"Genes are known to control the shape of biological structures , like flowers , hearts , and limbs , yet how they do this is poorly understood .",
"A working hypothesis is that genes control shape by modulating local rates at which growing tissue deforms .",
"Evaluating this idea has been difficult , however , ... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genomics",
"genome evolution",
"population genetics",
"biology",
"evolutionary biology",
"genomic evolution",
"population biology",
"evolutionary genetics",
"genetics and genomics"
] | Genome Patterns of Selection and Introgression of Haplotypes in Natural Populations of the House Mouse (Mus musculus) | journal.pgen.1002891 | null | [
[
"Genomic approaches allow an increasingly deeper insight into the forces that shape the evolution of genomes in populations .",
"While it is evident that genome evolution depends on a balance of mutation , neutral evolution , negative selection and adaptation , the relative importance of each of these par... | [
"General parameters of selection , such as the frequency and strength of positive selection in natural populations or the role of introgression , are still insufficiently understood .",
"The house mouse ( Mus musculus ) is a particularly well-suited model system to approach such questions , since it has a defined... | [
"Although there is abundant evidence for phenotypic adaptation in natural populations , it is still a challenge to understand the underlying genetic processes .",
"House mice have colonized the world in several successive waves , the most recent ones in the wake of the spread of human agriculture and trans-oceani... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"circuit models",
"visual system",
"neural networks",
"computational neuroscience",
"biology",
"sensory systems",
"neuroscience"
] | Synchronous Chaos and Broad Band Gamma Rhythm in a Minimal Multi-Layer Model of Primary Visual Cortex | journal.pcbi.1002176 | null | [
[
"An increase of activity in the gamma band ( 30–100 Hz ) is observed in Local Field Potential ( LFP ) and Multi-Unit Activity ( MUA ) recordings [1]–[14] , as well as in EEG and Electrocorticogram studies [15] , [16] in primary visual cortex ( V1 ) upon visual stimulation .",
"Gamma activity is modulated ... | [
"Visually induced neuronal activity in V1 displays a marked gamma-band component which is modulated by stimulus properties .",
"It has been argued that synchronized oscillations contribute to these gamma-band activity .",
"However , analysis of Local Field Potentials ( LFPs ) across different experiments reveal... | [
"Visual stimulation elicits neuronal responses in visual cortex .",
"When the contrast of the used stimuli increases , the power of this induced activity is boosted over a broad frequency range ( 30–100 Hz ) , called the “gamma band . ”",
"It would be tempting to hypothesize that this phenomenon is due to the e... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Discovery of a Small Non-AUG-Initiated ORF in Poleroviruses and Luteoviruses That Is Required for Long-Distance Movement | journal.ppat.1004868 | null | [
[
"RNA viruses are models of efficiency in compressing maximum information , such as coding and regulatory signals , into minimum sequence space .",
"To do this , RNA viruses often employ noncanonical translation mechanisms [1 , 2] .",
"For example , many viruses encode genes in overlapping open reading... | [
"Viruses in the family Luteoviridae have positive-sense RNA genomes of around 5 . 2 to 6 . 3 kb , and they are limited to the phloem in infected plants .",
"The Luteovirus and Polerovirus genera include all but one virus in the Luteoviridae .",
"They share a common gene block , which encodes the coat protein ( ... | [
"In order to maximize coding capacity , RNA viruses often encode overlapping genes and use unusual translational control mechanisms .",
"Plant viruses express proteins required for movement of the virus through the plant , often from non-canonically translated open reading frames ( ORFs ) .",
"Viruses in the ec... | 2015 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [] | T-Cell Responses Are Associated with Survival in Acute Melioidosis Patients | journal.pntd.0004152 | null | [
[
"Melioidosis is a severe and often fatal disease common in Southeast Asia and Northern Australia , caused by the soil-dwelling bacterium Burkholderia pseudomallei .",
"The main routes of infection are skin inoculation , inhalation , and ingestion of the organism from the environment [1] .",
"The known... | [
"Melioidosis is an increasingly recognised cause of sepsis and death across South East Asia and Northern Australia , caused by the bacterium Burkholderia pseudomallei .",
"Risk factors include diabetes , alcoholism and renal disease , and a vaccine targeting at-risk populations is urgently required .",
"A bette... | [
"Melioidosis is a key cause of death in South East Asia and Northern Australia .",
"It is caused by the soil-dwelling bacteria Burkholderia pseudomallei , and presents as a range of clinical illnesses including pneumonia and bloodstream infections .",
"About two-thirds of patients with melioidosis in Thailand h... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Kaposi’s Sarcoma-Associated Herpesvirus (KSHV) Induces the Oncogenic miR-17-92 Cluster and Down-Regulates TGF-β Signaling | journal.ppat.1005255 | null | [
[
"Kaposi’s sarcoma-associated herpes virus ( KSHV ) is a member of the gammaherpesvirus family and is associated with Kaposi’s sarcoma ( KS ) , a subset of multicentric Castleman’s disease ( MCD ) , and primary effusion lymphoma ( PEL ) [1 , 2 , 3] .",
"KSHV has two distinct phases of infection , latent an... | [
"KSHV is a DNA tumor virus that causes Kaposi’s sarcoma .",
"Upon KSHV infection , only a limited number of latent genes are expressed .",
"We know that KSHV infection regulates host gene expression , and hypothesized that latent genes also modulate the expression of host miRNAs .",
"Aberrant miRNA expression... | [
"MiRNAs are small non-coding RNAs which decrease gene expression and function as oncogenes or tumor suppressors .",
"Dysregulation of miRNAs is a hallmark of many human cancers .",
"Recently , it was revealed that the miR-17-92 cluster , up-regulated in many cancers , plays a central role in down-regulation of ... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"infectious diseases",
"immunology",
"biology",
"microbiology",
"parasitology"
] | Enhancing Blockade of Plasmodium falciparum Erythrocyte Invasion: Assessing Combinations of Antibodies against PfRH5 and Other Merozoite Antigens | journal.ppat.1002991 | null | [
[
"The pathogenic blood-stages of the Plasmodium falciparum life-cycle , whereby merozoites invade and multiply within erythrocytes , cause the symptoms and severe manifestations of malaria – a disease resulting in 600 , 000 to 1 . 2 million deaths annually 1 , 2] .",
"There is thus a pressing need for a hi... | [
"No vaccine has yet proven effective against the blood-stages of Plasmodium falciparum , which cause the symptoms and severe manifestations of malaria .",
"We recently found that PfRH5 , a P . falciparum-specific protein expressed in merozoites , is efficiently targeted by broadly-neutralizing , vaccine-induced a... | [
"Malaria is the most devastating parasitic disease of humans , resulting in an estimated 0 . 6–1 million deaths per year .",
"The symptoms of malaria are caused when merozoites invade and replicate within red blood cells , and therefore a vaccine which induced antibodies that effectively prevent this invasion pro... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"molecular biology",
"developmental biology"
] | Inhibitory Phosphorylation of Separase Is Essential for Genome Stability and Viability of Murine Embryonic Germ Cells | journal.pbio.0060015 | A single point mutation of separase that blocks its phosphorylation has a profound and dominant effect on germ cell biology. | [
[
"Faithful transmission of duplicated genetic material is of fundamental importance to the viability of all organisms .",
"In eukaryotes , sister chromatids are closely connected by cohesin complexes established during S phase .",
"The core cohesin complex is composed of the protein subunits Smc1 , Smc... | [
"Activity of separase , a cysteine protease that cleaves sister chromatid cohesin at the onset of anaphase , is tightly regulated to ensure faithful chromosome segregation and genome stability .",
"Two mechanisms negatively regulate separase: inhibition by securin and phosphorylation on serine 1121 .",
"To gaug... | [
"Higher eukaryotes rely on a separate cell lineage , the germline , to pass genetic information from generation to generation .",
"To ensure faithful transmission of genetic information , cell cycle checkpoint mechanisms are engaged during mitotic and meiotic divisions of germ cells .",
"The identity and functi... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"cell biology/nuclear structure and function",
"genetics and genomics/gene expression",
"cell biology/cell growth and division",
"cell biology",
"genetics and genomics/nuclear structure and function",
"cell biology/microbial growth and development",
"genetics and genomics/gene function",
"microbiology... | B-Cyclin/CDKs Regulate Mitotic Spindle Assembly by Phosphorylating Kinesins-5 in Budding Yeast | journal.pgen.1000935 | null | [
[
"Cyclin-dependent kinases ( CDKs ) complexed with various cyclins coordinate many duplication and segregation events during the eukaryotic cell division cycle [1] , [2] .",
"The duplication of the cell's microtubule organizing center , the centrosome , and the subsequent separation of the duplicated centr... | [
"Although it has been known for many years that B-cyclin/CDK complexes regulate the assembly of the mitotic spindle and entry into mitosis , the full complement of relevant CDK targets has not been identified .",
"It has previously been shown in a variety of model systems that B-type cyclin/CDK complexes , kinesi... | [
"The assembly of a bipolar mitotic spindle is essential for the accurate segregation of sister chromatids during mitosis and , hence , for successful cell division .",
"Spindle assembly depends on the successful duplication of the spindle poles , followed by their separation to opposing ends of the cell .",
"Al... | 2010 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"neurological disorders/prion diseases",
"biochemistry/protein folding"
] | Trans-Dominant Inhibition of Prion Propagation In Vitro Is Not Mediated by an Accessory Cofactor | journal.ppat.1000535 | null | [
[
"Prion diseases are fatal neurodegenerative diseases with inherited , sporadic , and infectious etiologies [1]–[3] .",
"The fundamental pathogenic event underlying prion diseases is generally believed to be the misfolding of the normal , host-encoded cellular prion protein ( PrPC ) into a pathogenic confo... | [
"Previous studies identified prion protein ( PrP ) mutants which act as dominant negative inhibitors of prion formation through a mechanism hypothesized to require an unidentified species-specific cofactor termed protein X . To study the mechanism of dominant negative inhibition in vitro , we used recombinant PrPC ... | [
"Over the past two decades , various investigators have observed that heterozygous animals possessing two different forms of the gene encoding the prion protein ( PrP ) are more difficult to infect with some strains of infectious prions than homozygous animals possessing only the most commonly occurring form of the... | 2009 |
[
"Introduction",
"Methods",
"Results/Discussion"
] | [
"computational biology"
] | Inferring Pathway Activity toward Precise Disease Classification | journal.pcbi.1000217 | null | [
[
"Analysis of genome-wide expression profiles has become a widespread technique for identifying diagnostic markers of various disease states , outcomes , or responses to treatment [1]–[5] .",
"Markers are selected by scoring each individual gene for how well its expression pattern can discriminate between ... | [
"The advent of microarray technology has made it possible to classify disease states based on gene expression profiles of patients .",
"Typically , marker genes are selected by measuring the power of their expression profiles to discriminate among patients of different disease states .",
"However , expression-b... | [
"The advent of microarray technology has drawn immense interest to identify gene expression levels that can serve as biomarkers for disease .",
"Marker genes are selected by examining each individual gene to see how well its expression level discriminates different disease types .",
"In complex diseases such as... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genetics and genomics/epigenetics",
"plant biology/plant genetics and gene expression",
"genetics and genomics/plant genetics and gene expression"
] | The De Novo Cytosine Methyltransferase DRM2 Requires Intact UBA Domains and a Catalytically Mutated Paralog DRM3 during RNA–Directed DNA Methylation in Arabidopsis thaliana | journal.pgen.1001182 | null | [
[
"Repetitive DNA in eukaryotic genomes is often transcriptionally silent , due to genome defense mechanisms directed against transposons and other mobile DNA [1] , [2] .",
"In plant genomes repetitive sequences are associated with DNA cytosine methylation [3]–[8] , which is required for transcriptional sil... | [
"Eukaryotic DNA cytosine methylation can be used to transcriptionally silence repetitive sequences , including transposons and retroviruses .",
"This silencing is stable between cell generations as cytosine methylation is maintained epigenetically through DNA replication .",
"The Arabidopsis thaliana Dnmt3 cyto... | [
"Nuclear DNA quantity varies widely between species and is poorly correlated with gene number .",
"Variation in genome size can be explained by differing amounts of repetitive DNA .",
"Repetitive DNA may be mobile , meaning it can increase its copy number within genomes .",
"To prevent this , plants and anima... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"cell cycle inhibitors",
"viruses and cancer",
"cell cycle and cell division",
"cell processes",
"microbiology",
"viruses",
"mitosis",
"virus effects on host gene expression",
"herpesviruses",
"human cytomegalovirus",
"chromosome biology",
"medical microbiology",
"microbial pathogens",
"vi... | PUL21a-Cyclin A2 Interaction is Required to Protect Human Cytomegalovirus-Infected Cells from the Deleterious Consequences of Mitotic Entry | journal.ppat.1004514 | null | [
[
"HCMV ( also referred to as human herpesvirus-5 , HHV5 ) is widely distributed in the human population .",
"Acute HCMV infection can cause severe complications in immunocompromised individuals , like neonates , transplant recipients and AIDS patients .",
"Persistent HCMV infection has been implicated ... | [
"Entry into mitosis is accompanied by dramatic changes in cellular architecture , metabolism and gene expression .",
"Many viruses have evolved cell cycle arrest strategies to prevent mitotic entry , presumably to ensure sustained , uninterrupted viral replication .",
"Here we show for human cytomegalovirus ( H... | [
"Cyclin A2 is a key regulator of the cell division cycle .",
"Interactors of Cyclin A2 typically contain short sequence elements ( RXL/Cy motifs ) that bind with high affinity to a hydrophobic patch in the Cyclin A2 protein .",
"Two types of RXL/Cy-containing factors are known:",
"i ) cyclin-dependent kinase ... | 2014 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"clinical research design",
"geographical locations",
"spatial epidemiology",
"social sciences",
"tropical diseases",
"human mobility",
"viruses",
"seasons",
"research design",
"case series",
"neglected tropical diseases",
"waves",
"traveling waves",
"huma... | Spatio-temporal dynamics of dengue in Brazil: Seasonal travelling waves and determinants of regional synchrony | journal.pntd.0007012 | null | [
[
"Dengue fever is a mosquito-borne viral disease that causes serious health and economic burden in tropical and sub-tropical regions [1] .",
"Population growth , urbanisation , international travel and changes in climate patterns have led to significant geographic expansion and continued rise in dengue cas... | [
"Dengue continues to be the most important vector-borne viral disease globally and in Brazil , where more than 1 . 4 million cases and over 500 deaths were reported in 2016 .",
"Mosquito control programmes and other interventions have not stopped the alarming trend of increasingly large epidemics in the past few ... | [
"In this paper we studied the synchronization of dengue epidemics in Brazilian regions .",
"We found that a typical dengue season in Brazil can be described as a wave travelling from the western part of the country towards the east , with the exception of the two most northern equatorial states that experienced i... | 2019 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [] | High Prevalence of Cysticercosis in People with Epilepsy in Southern Rwanda | journal.pntd.0002558 | null | [
[
"Epilepsy is a common chronic neurological disorder with a median prevalence of 15 in 1000 in sub-saharan Africa [1] , [2] , and from 7 to 49 in 1000 in Rwanda [3] , [4] .",
"Studies on the etiology of epilepsy in the tropics have revealed the importance of central nervous system ( CNS ) infections , such... | [
"Neurocysticercosis ( NCC ) , the central nervous system infection by Taenia solium larvae , is a preventable and treatable cause of epilepsy .",
"In Sub-Saharan Africa , the role of NCC in epilepsy differs geographically and , overall , is poorly defined .",
"We aimed at contributing specific , first data for ... | [
"Neurocysticercosis ( NCC ) is the infection of the brain with larvae of the pig tapeworm ( Taenia solium ) , which results from the ingestion of , e . g . , food or water contaminated with the eggs of this helminth .",
"Seizures and epilepsy are the most often reported clinical manifestations .",
"The diagnosi... | 2013 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"public and occupational health",
"research design",
"medicine and health sciences",
"plant science",
"disease ecology",
"survey research",
"survey methods",
"infectious disease epidemiology",
"epidemiology",
"environmental epidemiology",
"global health",
"plant pathology",
"biology and life... | Influence of Household Rat Infestation on Leptospira Transmission in the Urban Slum Environment | journal.pntd.0003338 | null | [
[
"In developing countries , leptospirosis is an emerging health problem affecting urban slum communities [1]–[4] .",
"Annual epidemics of the disease typically occur during periods of seasonal rainfall [1] , [5]–[8] .",
"Lack of sanitation infrastructure such as open sewage systems and poor refuse coll... | [
"The Norway rat ( Rattus norvegicus ) is the principal reservoir for leptospirosis in many urban settings .",
"Few studies have identified markers for rat infestation in slum environments while none have evaluated the association between household rat infestation and Leptospira infection in humans or the use of i... | [
"The Norway rat is an important reservoir for urban leptospirosis , a life-threatening zoonotic disease .",
"In urban settings , leptospirosis transmission occurs primarily in the peri-domiciliary environment of the slums .",
"Rodent control is one of the most frequent strategies to prevent leptospirosis , but ... | 2014 |
[
"Introduction",
"Results/Discussion",
"Materials and Methods"
] | [
"biomacromolecule-ligand interactions",
"molecular complexes",
"molecular dynamics",
"classical mechanics",
"molecular mechanics",
"newton's laws of motion",
"protein folding",
"protein structure",
"thermodynamics",
"physical chemistry",
"computer and information sciences",
"proteins",
"biop... | Computational Modeling of Allosteric Regulation in the Hsp90 Chaperones: A Statistical Ensemble Analysis of Protein Structure Networks and Allosteric Communications | journal.pcbi.1003679 | null | [
[
"Allosteric regulation is an effective mechanism to control activity and dynamic adaptability of proteins in the cell during signal transduction , metabolism , catalysis , and gene regulation [1]–[4] .",
"Protein allostery is determined by the underlying thermodynamics of a system , where long-range inter... | [
"A fundamental role of the Hsp90 chaperone in regulating functional activity of diverse protein clients is essential for the integrity of signaling networks .",
"In this work we have combined biophysical simulations of the Hsp90 crystal structures with the protein structure network analysis to characterize the st... | [
"Functional versatility and structural adaptability of the Hsp90 chaperones are regulated by allosteric interactions that allow for diverse functions including modulation of ATP hydrolysis and binding with cochaperones and client proteins .",
"By integrating molecular simulations and network-based approaches we h... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"systems biology",
"biochemistry",
"biochemical simulations",
"model organisms",
"neurospora crassa",
"biochemistry simulations",
"enzyme metabolism",
"enzymes",
"yeast and fungal models",
"metabolic networks",
"biology",
"computational biology"
] | Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM | journal.pcbi.1003126 | null | [
[
"First discovered as an orange mold infestation of Paris bakeries in 1843 [1] , the filamentous fungus Neurospora crassa has become a model organism for eukaryotic biology and the cornerstone of a vibrant research community [2] .",
"Work on Neurospora has led to essential discoveries in circadian rhythms ... | [
"The filamentous fungus Neurospora crassa played a central role in the development of twentieth-century genetics , biochemistry and molecular biology , and continues to serve as a model organism for eukaryotic biology .",
"Here , we have reconstructed a genome-scale model of its metabolism .",
"This model consi... | [
"Few organisms have been as foundational to the development of modern genetics and cellular metabolism as Neurospora crassa .",
"Given the wealth of knowledge available for this filamentous fungus , the effort required to manually curate a high-quality genome-scale metabolic reconstruction would be daunting .",
... | 2013 |
[
"Introduction",
"Methods",
"Results",
"Discussion",
"Conclusion"
] | [
"geomorphology",
"animal types",
"livestock",
"valleys",
"medicine and health sciences",
"landforms",
"ruminants",
"topography",
"vector-borne diseases",
"geographical locations",
"vertebrates",
"domestic animals",
"animals",
"mammals",
"zambia",
"population biology",
"zoology",
"a... | Exploring the effect of human and animal population growth on vector-borne disease transmission with an agent-based model of Rhodesian human African trypanosomiasis in eastern province, Zambia | journal.pntd.0006905 | null | [
[
"Human African trypanosomiasis ( HAT ) , also known as sleeping sickness , is a neglected tropical disease ( NTD ) [1] , one of a group of the most common conditions which affect the poorest 500 million people living in sub-Saharan Africa [2] .",
"HAT is a vector-borne , parasitic disease which is caused ... | [
"This paper presents the development of an agent-based model ( ABM ) to investigate Trypanosoma brucei rhodesiense human African trypanosomiasis ( rHAT ) disease transmission .",
"The ABM model , fitted at a fine spatial scale , was used to explore the impact of a growing host population on the spread of disease ... | [
"African trypanosomiasis is a parasitic disease which affects humans and other animals in 36 sub-Saharan African countries .",
"The disease is transmitted by the tsetse fly , and the human form of the disease is known as sleeping sickness .",
"With human and animal populations growing across Africa , demand for... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"transfection",
"cell cycle and cell division",
"cell processes",
"neuronal differentiation",
"neuroscience",
"notch signaling",
"cell differentiation",
"developmental biology",
"molecular biology techniques",
"embryos",
"research and analysis methods",
"specimen preparation and treatment",
... | Mib1 prevents Notch Cis-inhibition to defer differentiation and preserve neuroepithelial integrity during neural delamination | journal.pbio.2004162 | null | [
[
"The vertebrate neuroepithelium is initially composed of elongated progenitors polarized along the apical–basal axis that actively proliferate .",
"After a phase of expansion , these progenitors start producing neurons through asymmetric and eventually symmetric neurogenic divisions .",
"Following mit... | [
"The vertebrate neuroepithelium is composed of elongated progenitors whose reciprocal attachments ensure the continuity of the ventricular wall .",
"As progenitors commit to differentiation , they translocate their nucleus basally and eventually withdraw their apical endfoot from the ventricular surface .",
"Ho... | [
"The process of neural delamination , whereby nascent neurons detach from the ventricular surface of the neural tube after differentiation , is still poorly characterized .",
"The vertebrate neural tube is initially exclusively composed of neuroepithelial progenitors whose apical attachments ensure the integrity ... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"bacteriology",
"medicine and health sciences",
"pathology and laboratory medicine",
"intracellular pathogens",
"pathogens",
"population genetics",
"haemophilus influenzae",
"microbiology",
"cloning",
"gene pool",
"molecular biology techniques",
"population biology",
"dna",
"bacteria",
"... | Transformed Recombinant Enrichment Profiling Rapidly Identifies HMW1 as an Intracellular Invasion Locus in Haemophilus influenzae | journal.ppat.1005576 | null | [
[
"Genetic mapping in bacteria historically relied on screening mutant libraries for loss-of-function mutations , followed by laborious isolation and identification of the disrupted loci .",
"Recent innovations in mutagenesis approaches like TnSeq can accelerate the process and aid in characterizing gene fu... | [
"Many bacterial species actively take up and recombine homologous DNA into their genomes , called natural competence , a trait that offers a means to identify the genetic basis of naturally occurring phenotypic variation .",
"Here , we describe “transformed recombinant enrichment profiling” ( TREP ) , in which na... | [
"Many bacteria are naturally competent , actively taking up DNA from their surroundings and incorporating it into their genomes by homologous recombination .",
"This cellular process has had a large impact on the evolution of these species , for example by enabling pathogens to acquire virulence factors and antib... | 2016 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"respiratory medicine/respiratory infections",
"infectious diseases/neglected tropical diseases",
"infectious diseases/helminth infections",
"public health and epidemiology/infectious diseases",
"infectious diseases/respiratory infections",
"infectious diseases/tropical and travel-associated diseases"
] | Ziehl-Neelsen Staining Technique Can Diagnose Paragonimiasis | journal.pntd.0001048 | null | [
[
"Paragonimiasis is a primary pulmonary food-borne trematodiasis and zoonosis present in numerous countries , especially in tropical Asia where 293 million people are estimated at risk of infection [1] .",
"Causing symptoms similar to pulmonary tuberculosis ( TB ) , it is frequently misdiagnosed and treate... | [
"We evaluated the Ziehl-Neelsen staining ( ZNS ) technique for the diagnosis of paragonimiasis in Laos and compared different modifications of the ZNS techniques .",
"We applied the following approach: We ( 1 ) examined a paragonimiasis index case's sputum with wet film direct examination ( WF ) and ZNS; ( 2 ) re... | [
"Lung fluke ( Paragonimus ) infection causes similar symptoms to pulmonary TB and is an important differential diagnosis in endemic areas .",
"Standard diagnosis is wet film ( WF ) microscopic examination of sputum samples .",
"For the last fifty years , Ziehl-Neelsen stain ( ZNS ) has been believed to destroy ... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"ophthalmology/cataracts and other lens disorders",
"genetics and genomics/animal genetics",
"genetics and genomics/gene expression",
"genetics and genomics/complex traits",
"genetics and genomics/disease models",
"genetics and genomics/gene function",
"genetics and genomics",
"genetics and genomics/p... | EPHA2 Is Associated with Age-Related Cortical Cataract in Mice and Humans | journal.pgen.1000584 | null | [
[
"Cataract is the leading cause of visual impairment worldwide , with approximately 37 million people affected , accounting for 48% of global blindness [1] .",
"Cataract is defined as any opacity of the crystalline lens resulting from either alteration in lens cell structure or changes in lens proteins or ... | [
"Age-related cataract is a major cause of blindness worldwide , and cortical cataract is the second most prevalent type of age-related cataract .",
"Although a significant fraction of age-related cataract is heritable , the genetic basis remains to be elucidated .",
"We report that homozygous deletion of Epha2 ... | [
"Cataract is the leading cause of blindness .",
"Cataract may form at any age , but the peak incidence is bimodal—in the perinatal period or later than 50 years of age .",
"The early onset forms follow Mendelian inheritance patterns and are rare .",
"Age-related cataract accounts for 18 million cases of blind... | 2009 |
[
"Introduction",
"Materials and Methods",
"Results and Discussion"
] | [
"medicine",
"infectious diseases",
"public health and epidemiology",
"genetics",
"biology",
"genomics",
"evolutionary biology",
"public health",
"genetics and genomics"
] | Mitochondrial Genome of the Eyeworm, Thelazia callipaeda (Nematoda: Spirurida), as the First Representative from the Family Thelaziidae | journal.pntd.0002029 | null | [
[
"Thelazia callipaeda Railliet and Henry , 1910 , known as the ‘oriental eye-worm’ , because of its geographical distribution in Asian countries ( including China , India , Japan , Korea and Thailand ) , is frequently reported as being responsible for thelaziosis of humans , carnivores ( dogs , foxes and cats ... | [
"Human thelaziosis is an underestimated parasitic disease caused by Thelazia species ( Spirurida: Thelaziidae ) .",
"The oriental eyeworm , Thelazia callipaeda , infects a range of mammalian definitive hosts , including canids , felids and humans .",
"Although this zoonotic parasite is of socio-economic signifi... | [
"Human thelaziosis is an underestimated parasitic disease caused by the eyeworm Thelazia callipaeda ( Spirurida: Thelaziidae ) .",
"Although this parasite is of significance in humans in many Asian countries , its genetics , epidemiology and biology are poorly understood .",
"Mitochondrial ( mt ) DNA can provid... | 2013 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious diseases",
"ecology and environmental sciences",
"medicine and health sciences",
"chagas disease",
"ecology",
"epidemiology",
"neglected tropical diseases",
"biology and life sciences",
"tropical diseases",
"protozoan infections",
"population ecology",
"parasitic diseases",
"dise... | Modeling Disease Vector Occurrence When Detection Is Imperfect II: Drivers of Site-Occupancy by Synanthropic Triatoma brasiliensis in the Brazilian Northeast | journal.pntd.0002861 | null | [
[
"Triatoma brasiliensis is a member of the ‘brasiliensis species complex’ , which includes the main domestic-peridomestic vectors of the Chagas disease parasite , Trypanosoma cruzi , in the Caatinga eco-region of northeastern Brazil [1]–[4] .",
"Wild T . brasiliensis breed in rocky outcrops , usually in as... | [
"Understanding the drivers of habitat selection by insect disease vectors is instrumental to the design and operation of rational control-surveillance systems .",
"One pervasive yet often overlooked drawback of vector studies is that detection failures result in some sites being misclassified as uninfested; naïve... | [
"Chagas disease prevention depends on the control of its insect vectors — large blood-sucking bugs called triatomines .",
"One commonly neglected problem of vector studies is imperfect detection , whereby some sites are mistakenly classified as uninfested .",
"We address this drawback by combining repeated samp... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | BCG Skin Infection Triggers IL-1R-MyD88-Dependent Migration of EpCAMlow CD11bhigh Skin Dendritic cells to Draining Lymph Node During CD4+ T-Cell Priming | journal.ppat.1005206 | null | [
[
"Lymph nodes ( LNs ) make use of lymphatic drainage and a specialized microanatomy to facilitate productive encounters between antigen-laden Dendritic cells ( DCs ) and naïve T cells [1] .",
"As sentinel phagocytes that reconnoiter for infection , DCs employ an array of pattern-recognition receptors ( PRR... | [
"The transport of antigen from the periphery to the draining lymph node ( DLN ) is critical for T-cell priming but remains poorly studied during infection with Mycobacterium bovis Bacille Calmette-Guérin ( BCG ) .",
"To address this we employed a mouse model to track the traffic of Dendritic cells ( DCs ) and myc... | [
"The arrival of bacilli in the lymph node is a bottleneck for initiating T cell responses to mycobacteria but remains poorly studied .",
"To address this we used a mouse model to track the entry of cells and bacteria into the lymph node during skin infection with Mycobacterium bovis BCG , the live tuberculosis va... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"virology/virulence factors and mechanisms",
"virology/viral replication and gene regulation",
"cell biology/nuclear structure and function",
"virology/immunodeficiency viruses",
"computational biology/genomics"
] | HIV Integration Targeting: A Pathway Involving Transportin-3 and the Nuclear Pore Protein RanBP2 | journal.ppat.1001313 | null | [
[
"To complete the early steps of infection , retroviral preintegation complexes ( PICs ) must access the nucleus of the infected cell and integrate the viral cDNA into host chromatin .",
"Gammaretroviruses such as MLV require nuclear envelope breakdown during mitosis to access cellular chromosomes and comp... | [
"Genome-wide siRNA screens have identified host cell factors important for efficient HIV infection , among which are nuclear pore proteins such as RanBP2/Nup358 and the karyopherin Transportin-3/TNPO3 .",
"Analysis of the roles of these proteins in the HIV replication cycle suggested that correct trafficking thro... | [
"HIV continues to be responsible for approximately two million deaths worldwide each year .",
"As part of the viral replication cycle , the viral cDNA is transported through the nuclear pore into the nucleus where it integrates into the host cell genome .",
"HIV integrates non-randomly , likely choosing integra... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | A Systems Approach Identifies Essential FOXO3 Functions at Key Steps of Terminal Erythropoiesis | journal.pgen.1005526 | null | [
[
"Erythropoiesis ensures the daily production of over 200 billion RBCs whose main function is to carry oxygen .",
"Decreased production of RBCs is associated with many human disorders involving impaired erythroblast maturation .",
"The generation of RBCs in vitro from embryonic stem cells or human-indu... | [
"Circulating red blood cells ( RBCs ) are essential for tissue oxygenation and homeostasis .",
"Defective terminal erythropoiesis contributes to decreased generation of RBCs in many disorders .",
"Specifically , ineffective nuclear expulsion ( enucleation ) during terminal maturation is an obstacle to therapeut... | [
"Red blood cells ( RBCs ) are highly specialized cells that transport oxygen throughout the body and are essential for survival .",
"However , RBCs have a limited lifespan and need to be replenished continuously by stem cells in the bone marrow .",
"Mammalian RBCs are unique in that in order to fully mature the... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"oncology/breast cancer",
"genetics and genomics/gene expression",
"genetics and genomics/genetics of disease",
"genetics and genomics/gene function",
"genetics and genomics/cancer genetics",
"genetics and genomics/bioinformatics"
] | ESR1 Is Co-Expressed with Closely Adjacent Uncharacterised Genes Spanning a Breast Cancer Susceptibility Locus at 6q25.1 | journal.pgen.1001382 | null | [
[
"Breast cancer is the most common malignancy in women , accounting for more than 400 , 000 deaths per year worldwide [1] .",
"Approximately 80% of human breast carcinomas present as oestrogen receptor α-positive ( ER+ve ) disease and ER status is arguably the most clinically important biological factor in... | [
"Approximately 80% of human breast carcinomas present as oestrogen receptor α-positive ( ER+ve ) disease , and ER status is a critical factor in treatment decision-making .",
"Recently , single nucleotide polymorphisms ( SNPs ) in the region immediately upstream of the ER gene ( ESR1 ) on 6q25 . 1 have been assoc... | [
"Recent genome-wide analysis has revealed that the way in which genes are arranged on chromosomes and the conformation of these chromosomes are crucial for the regulation of gene expression .",
"Reflecting this arrangement , clusters of genes which are regulated together have been discovered .",
"We have identi... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | The Nutrient-Responsive Hormone CCHamide-2 Controls Growth by Regulating Insulin-like Peptides in the Brain of Drosophila melanogaster | journal.pgen.1005209 | null | [
[
"Organisms need to coordinate growth and metabolism with their nutritional status to ensure proper development and the maintenance of homeostasis .",
"In multicellular animals , nutritional information is mostly perceived by peripheral organs .",
"It is subsequently relayed to other peripheral organs ... | [
"The coordination of growth with nutritional status is essential for proper development and physiology .",
"Nutritional information is mostly perceived by peripheral organs before being relayed to the brain , which modulates physiological responses .",
"Hormonal signaling ensures this organ-to-organ communicati... | [
"Animals need to couple growth with nutritional availability for proper development and physiology , which leads to better survival .",
"Nutritional information is mostly perceived by peripheral organs , particularly metabolic organs such as adipose tissue and gut , before being relayed to the brain , which modul... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"humoral immunity",
"viral immune evasion",
"immunity",
"virology",
"biology and life sciences",
"immunology",
"microbiology"
] | Human Cytomegalovirus Fcγ Binding Proteins gp34 and gp68 Antagonize Fcγ Receptors I, II and III | journal.ppat.1004131 | null | [
[
"Human cytomegalovirus ( HCMV ) constitutes the prototypical human pathogenic β-herpesvirus found worldwide with high immunoglobulin G ( IgG ) seroprevalence rates of 50–98% [1] .",
"Despite the expression of a very large antigenic proteome of approximately 750 translational products [2] , HCMV avoids ste... | [
"Human cytomegalovirus ( HCMV ) establishes lifelong infection with recurrent episodes of virus production and shedding despite the presence of adaptive immunological memory responses including HCMV immune immunoglobulin G ( IgG ) .",
"Very little is known how HCMV evades from humoral and cellular IgG-dependent i... | [
"Herpes viruses persist lifelong continuously alternating between latency and virus production and transmission .",
"The latter events occur despite the presence of immune IgG antibodies .",
"IgG acts by neutralization of virions and activation of immune cells bearing one or more surface receptors , called FcγR... | 2014 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"public health and epidemiology/health policy",
"infectious diseases/neglected tropical diseases",
"science policy",
"infectious diseases/helminth infections",
"public health and epidemiology/infectious diseases",
"surgery"
] | Impact of Increased Economic Burden Due to Human Echinococcosis in an Underdeveloped Rural Community of the People's Republic of China | journal.pntd.0000801 | null | [
[
"Since the inception of market reforms in the early 1980s , the annual health expenditure of People's Republic of China ( P . R . China ) has increased consistently [1] , [2] .",
"But , contrary to this increase , two national healthcare surveys [3] , [4] showed that health insurance decreased from 30 . 2... | [
"Ningxia is located in western People's Republic of China , which is hyperendemic for human cystic echinococcosis ( CE ) throughout the entire area with alveolar echinococcosis ( AE ) hyperendemic in the south .",
"This is in part due to its underdeveloped economy .",
"Despite the recent rapid growth in P . R .... | [
"This paper compares medical expenditure for hospital treatment of echinococcosis in NHAR , western People's Republic of China , for different years , different regions and different socioeconomic groups .",
"The results show that the level of household income strongly influences health care decisions .",
"This... | 2010 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious diseases",
"veterinary diseases",
"zoonoses",
"medicine and health sciences",
"veterinary microbiology",
"neglected tropical diseases",
"biology and life sciences",
"tropical diseases",
"microbiology",
"brucellosis",
"veterinary science"
] | A Protein-Conjugate Approach to Develop a Monoclonal Antibody-Based Antigen Detection Test for the Diagnosis of Human Brucellosis | journal.pntd.0002926 | null | [
[
"Human brucellosis is most commonly caused by two species of the genus Brucella , typically B . abortus from cattle and B . melitensis from goats and sheep .",
"The definitive diagnosis of brucellosis rests upon demonstration of the causative bacterium in a suspected patient's body fluid , typically by cu... | [
"Human brucellosis is most commonly diagnosed by serology based on agglutination of fixed Brucella abortus as antigen .",
"Nucleic acid amplification techniques have not proven capable of reproducibly and sensitively demonstrating the presence of Brucella DNA in clinical specimens .",
"We sought to optimize a m... | [
"Brucellosis is a OneHealth disease reflecting the risk for human infection by interaction with and relation to affected animal populations .",
"The disease is often difficult to diagnose because of lack of precise or accessible diagnostic reagents , and because culture is complex , hazardous and relatively insen... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Phosphatidylthreonine and Lipid-Mediated Control of Parasite Virulence | journal.pbio.1002288 | An exclusive membrane lipid, phosphatidylthreonine, is revealed to be naturally abundant in the widespread protist parasite Toxoplasma gondii, where it has evolved adaptively and is essential for parasite virulence. | [
[
"Intracellular protozoan parasites impose a substantial threat to human and animal health .",
"Toxoplasma gondii is one of the most prevalent protozoan parasites , infecting nearly all warm-blooded vertebrates , including humans [1] .",
"Over the last two decades , T . gondii has also become a popular... | [
"The major membrane phospholipid classes , described thus far , include phosphatidylcholine ( PtdCho ) , phosphatidylethanolamine ( PtdEtn ) , phosphatidylserine ( PtdSer ) , and phosphatidylinositol ( PtdIns ) .",
"Here , we demonstrate the natural occurrence and genetic origin of an exclusive and rather abundan... | [
"Lipids are essential constituents of biological membranes , and most organisms across the tree of life use a relatively limited repertoire of lipids in their membranes .",
"This work reveals the natural and abundant presence of an exclusive lipid phosphatidylthreonine ( PtdThr ) in Toxoplasma gondii , a ubiquito... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biochemistry",
"proteins",
"protein folding",
"prions",
"protein structure",
"biology and life sciences",
"protein misfolding",
"molecular biology",
"macromolecular structure analysis"
] | What Makes a Protein Sequence a Prion? | journal.pcbi.1004013 | null | [
[
"Amyloid structures are associated with an increasing number of human disorders [1] .",
"Prions have been considered a particular subclass of amyloids in which the aggregation process self-perpetuates in vivo , thus becoming infectious .",
"However , increasing evidence suggests that in vivo protein c... | [
"Typical amyloid diseases such as Alzheimer's and Parkinson's were thought to exclusively result from de novo aggregation , but recently it was shown that amyloids formed in one cell can cross-seed aggregation in other cells , following a prion-like mechanism .",
"Despite the large experimental effort devoted to ... | [
"Protein conformational disorders include several neurodegenerative diseases .",
"These pathologies are initiated by conformational changes in specific polypeptides that , in many cases , result in their spontaneous self-assembly to form toxic amyloids .",
"Prions are a subclass of amyloids with the ability to ... | 2015 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion",
"Conclusion"
] | [] | Detailed Contact Data and the Dissemination of Staphylococcus aureus in Hospitals | journal.pcbi.1004170 | null | [
[
"Chains of transmission in communicable diseases are often identified by ad hoc strategies , combining retrospective information on locations attended and pathogen genetics to identify time-consistent transmission paths . [1]",
"In contrast with such undertakings , “digital epidemiology” propose to use ne... | [
"Close proximity interactions ( CPIs ) measured by wireless electronic devices are increasingly used in epidemiological models .",
"However , no evidence supports that electronically collected CPIs inform on the contacts leading to transmission .",
"Here , we analyzed Staphylococcus aureus carriage and CPIs rec... | [
"Recent advances in communication technologies allow monitoring high-resolution contact networks .",
"Close proximity interactions ( CPIs ) measured by wireless sensors are increasingly used to inform contact networks for the dissemination of pathogens in computational models , although empirical justification is... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"molecular biology/dna replication",
"molecular biology/histone modification",
"virology/persistence and latency",
"virology/viral replication and gene regulation",
"molecular biology/transcription initiation and activation",
"virology/viruses and cancer",
"molecular biology/chromatin structure"
] | EBNA1-Mediated Recruitment of a Histone H2B Deubiquitylating Complex to the Epstein-Barr Virus Latent Origin of DNA Replication | journal.ppat.1000624 | null | [
[
"Epstein-Barr virus ( EBV ) is a gamma herpesvirus that infects over ninety percent of people worldwide .",
"As part of its latent life cycle , EBV efficiently immortalizes the host cell and predisposes it to a number of malignancies , including Burkitt's lymphoma , nasopharyngeal carcinoma , gastric carc... | [
"The EBNA1 protein of Epstein-Barr virus ( EBV ) plays essential roles in enabling the replication and persistence of EBV genomes in latently infected cells and activating EBV latent gene expression , in all cases by binding to specific recognition sites in the latent origin of replication , oriP .",
"Here we sho... | [
"Epstein-Barr virus ( EBV ) infections persist for the lifetime of the host largely due to the actions of the EBNA1 viral protein .",
"EBNA1 enables the replication and stable persistence of EBV genomes and activates the expression of other EBV genes by binding to specific DNA sequences in the EBV genome .",
"W... | 2009 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"public health and epidemiology/epidemiology",
"public health and epidemiology/infectious diseases",
"infectious diseases/epidemiology and control of infectious diseases"
] | Risk Factors for Tungiasis in Nigeria: Identification of Targets for Effective Intervention | journal.pntd.0000087 | null | [
[
"The parasitic skin disease tungiasis is caused by the permanent penetration of the female sand flea Tunga penetrans into the epidermis of its host .",
"After penetration , the female undergoes a hypertrophy and reaches the size of a pea .",
"Tungiasis has many features of a neglected tropical disease... | [
"The parasitic skin disease tungiasis ( caused by the flea Tunga penetrans ) affects resource-poor communities in Latin America , the Caribbean and sub-Saharan Africa .",
"Prevalences in endemic areas are high , and severe pathology occurs commonly .",
"However , risk factors for infestation have never been ass... | [
"Tungiasis is a parasitic skin disease caused by the sand flea Tunga penetrans .",
"After penetration into the skin , the flea grows and reaches the size of a pea .",
"The disease is a neglected public health problem in endemic areas in Latin America , the Caribbean and Africa , and causes considerable morbidit... | 2007 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genetic networks",
"applied mathematics",
"dna-binding proteins",
"dna transcription",
"simulation and modeling",
"algorithms",
"mathematics",
"network analysis",
"research and analysis methods",
"chemical properties",
"physical chemistry",
"computer and information sciences",
"dimerization... | Reduction of multiscale stochastic biochemical reaction networks using exact moment derivation | journal.pcbi.1005571 | null | [
[
"Many biochemical reaction networks ( BRNs ) in a cell include species whose copy numbers are small [1–3] ( e . g . one or a few copies of genes or tens of mRNAs ) , which lead to large fluctuations in the system .",
"Such stochastic dynamics of BRNs can be described by the chemical master equation ( CME ... | [
"Biochemical reaction networks ( BRNs ) in a cell frequently consist of reactions with disparate timescales .",
"The stochastic simulations of such multiscale BRNs are prohibitively slow due to high computational cost for the simulations of fast reactions .",
"One way to resolve this problem uses the fact that ... | [
"Molecules inside a cell undergo various transformations via biochemical reactions with disparate rates .",
"For instance , while transcriptional factors bind and unbind gene promoters in a time scale of seconds , mRNA transcription takes at least several minutes .",
"For such systems regulated by both fast and... | 2017 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"microbiology"
] | A Single-Step Sequencing Method for the Identification of Mycobacterium tuberculosis Complex Species | journal.pntd.0000253 | null | [
[
"The Mycobacterium tuberculosis complex ( MTC ) comprises several closely related species responsible for strictly human and zoonotic tuberculosis ( Figure 1 ) .",
"In addition to M . tuberculosis , which represents the leading cause of human tuberculosis worldwide and is now emerging as extensively drug-... | [
"The Mycobacterium tuberculosis complex ( MTC ) comprises closely related species responsible for strictly human and zoonotic tuberculosis .",
"Accurate species determination is useful for the identification of outbreaks and epidemiological links .",
"Mycobacterium africanum and Mycobacterium canettii are typic... | [
"The Mycobacterium tuberculosis complex ( MTC ) comprises several closely related species responsible for strictly human and zoonotic tuberculosis .",
"Some of the species are restricted to Africa and were responsible for the high prevalence of tuberculosis .",
"However , their identification at species level i... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | Quantitative Analysis of the Association Angle between T-cell Receptor Vα/Vβ Domains Reveals Important Features for Epitope Recognition | journal.pcbi.1004244 | null | [
[
"T-cells play a major role in cell-mediated adaptive immune responses necessary for the defense against foreign invaders and transformed malignant cells .",
"Heterodimeric T-cell receptors ( TCR ) recognize antigenic peptides presented on the surface of cells by major histocompatibility complex ( MHC ) mo... | [
"T-cell receptors ( TCR ) play an important role in the adaptive immune system as they recognize pathogen- or cancer-based epitopes and thus initiate the cell-mediated immune response .",
"Therefore there exists a growing interest in the optimization of TCRs for medical purposes like adoptive T-cell therapy .",
... | [
"The recognition of antigenic peptides by cytotoxic T-cells is one of the crucial steps during the adaptive immune response .",
"Thus a detailed understanding of this process is not only important for elucidating the mechanism behind T-cell signaling , but also for various emerging new medical applications like T... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biochemistry",
"biochemistry/chemical biology of the cell",
"biochemistry/bioinformatics",
"computational biology/metabolic networks",
"biochemistry/theory and simulation"
] | An Allosteric Mechanism for Switching between Parallel Tracks in Mammalian Sulfur Metabolism | journal.pcbi.1000076 | null | [
[
"Methionine , an essential amino acid , plays a significant role in intracellular one-carbon and sulfur metabolism consequently linking antioxidant and methylation homeostasis ( Figure 1 ) .",
"Since methionine is involved in many intracellular processes its levels in blood and in different organs need to... | [
"Methionine ( Met ) is an essential amino acid that is needed for the synthesis of S-adenosylmethionine ( AdoMet ) , the major biological methylating agent .",
"Methionine used for AdoMet synthesis can be replenished via remethylation of homocysteine .",
"Alternatively , homocysteine can be converted to cystein... | [
"Methionine is an essential amino acid that is highly toxic at elevated levels , and the liver is primarily responsible for buffering its concentration in circulation .",
"Intracellularly , methionine is needed for the synthesis of S-adenosylmethionine ( AdoMet ) , the major biological methylating agent .",
"Me... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"virology",
"immunology",
"genetics and genomics"
] | Commitment to the Regulatory T Cell Lineage Requires CARMA1 in the Thymus but Not in the Periphery | journal.pbio.1000051 | The organ-specific requirement for CARMA1-dependent signaling in the thymus suggests that regulatory T cells of thymic or peripheral origin may have different roles in vivo. | [
[
"Two major mechanisms enforce self-tolerance: negative selection in the thymus and dominant tolerance in the periphery .",
"The importance of both mechanisms is underscored by the phenotypes of autoimmune regulator ( Aire ) knockout [1] and scurfy mice [2] , which have defects in negative selection or dom... | [
"Regulatory T ( Treg ) cells expressing forkhead box P3 ( Foxp3 ) arise during thymic selection among thymocytes with modestly self-reactive T cell receptors .",
"In vitro studies suggest Foxp3 can also be induced among peripheral CD4+ T cells in a cytokine dependent manner .",
"Treg cells of thymic or peripher... | [
"In mammals , CD4+ T cells are essential for controlling infections , but have the potential to attack host tissues as well , resulting in autoimmune disease .",
"A subset of CD4+ T cells , regulatory T cells ( Treg ) —identified by the expression of the forkhead transcription factor Foxp3—serve to prevent immuno... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"taxonomy",
"z chromosomes",
"population genetics",
"phylogenetics",
"data management",
"phylogenetic analysis",
"population biology",
"computer and information sciences",
"sex chromosomes",
"chromosome biology",
"autosomes",
"evolutionary systematics",
"genetic loci",
"cell biology",
"h... | Recombination rate variation shapes barriers to introgression across butterfly genomes | journal.pbio.2006288 | null | [
[
"The genealogical relationships among closely related species can be complex , varying across the genome and among individuals .",
"This phylogenetic heterogeneity can be caused both by incomplete lineage sorting ( ILS ) in ancestral populations and by introgressive hybridisation , causing some parts of t... | [
"Hybridisation and introgression can dramatically alter the relationships among groups of species , leading to phylogenetic discordance across the genome and between populations .",
"Introgression can also erode species differences over time , but selection against introgression at certain loci acts to maintain p... | [
"Many species occasionally hybridise and share genetic material with related species .",
"Interspecific gene flow may be counteracted by natural selection at particular ‘barrier loci’ .",
"As a result , a pair of species can end up sharing more genetic variation in some parts of their genome than in others , an... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"infectious diseases/prion diseases"
] | Atypical/Nor98 Scrapie Infectivity in Sheep Peripheral Tissues | journal.ppat.1001285 | null | [
[
"Transmissible spongiform encephalopathies ( TSE ) , or prion diseases , are fatal neurodegenerative disorders occurring in sheep ( scrapie ) , cattle ( bovine spongiform encephalopathy - BSE ) , or humans ( Creutzfeldt-Jakob disease - CJD ) .",
"The key event in TSE is the conversion of a normal cellular... | [
"Atypical/Nor98 scrapie was first identified in 1998 in Norway .",
"It is now considered as a worldwide disease of small ruminants and currently represents a significant part of the detected transmissible spongiform encephalopathies ( TSE ) cases in Europe .",
"Atypical/Nor98 scrapie cases were reported in ARR/... | [
"Following the bovine spongiform encephalopathy ( BSE ) crisis and the identification of its zoonotic properties , a sanitary policy has been implemented based on both eradication of transmissible spongiform encephalopathies ( TSE ) in food-producing animals and exclusion of known infectious materials from the food... | 2011 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"evidence-based healthcare/clinical decision-making",
"infectious diseases/neglected tropical diseases",
"evidence-based healthcare/health services research and economics",
"public health and epidemiology/health services research and economics"
] | Cost-Effectiveness Analysis of Combination Therapies for Visceral Leishmaniasis in the Indian Subcontinent | journal.pntd.0000818 | null | [
[
"Despite their toxicity , pentavalent antimonials are still widely used as first line treatment for visceral leishmaniasis ( VL ) except in the Indian subcontinent where emerging drug resistance in Bihar State in India [1] and Nepal [2] required a change in drug policy .",
"Current therapeutic options inc... | [
"Visceral leishmaniasis is a systemic parasitic disease that is fatal unless treated .",
"We assessed the cost and cost-effectiveness of alternative strategies for the treatment of visceral leishmaniasis in the Indian subcontinent .",
"In particular we examined whether combination therapies are a cost-effective... | [
"Visceral leishmaniasis ( VL ) is a serious health problem in the Indian subcontinent affecting the rural poor .",
"It has a significant economic impact on concerned households .",
"The development of drug resistance is a major problem and threatens control efforts under the VL elimination initiative .",
"Wit... | 2010 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"reverse transcriptase-polymerase chain reaction",
"sequencing techniques",
"invertebrates",
"medicine and health sciences",
"immune physiology",
"enzyme-linked immunoassays",
"immunology",
"geographical locations",
"vertebrates",
"animals",
"mammals",
"preventive medicine",
"molecular biolo... | Comparison of the dynamics of Japanese encephalitis virus circulation in sentinel pigs between a rural and a peri-urban setting in Cambodia | journal.pntd.0006644 | null | [
[
"Even though the number of cases has decreased substantially over the past decades with the implementation of childhood vaccination programs in many Asian countries , Japanese Encephalitis virus ( JEV ) remains the most important cause of acute encephalitis in Eastern and Southern Asia [1 , 2] .",
"Accord... | [
"Japanese encephalitis is mainly considered a rural disease , but there is growing evidence of a peri-urban and urban transmission in several countries , including Cambodia .",
"We , therefore , compared the epidemiologic dynamic of Japanese encephalitis between a rural and a peri-urban setting in Cambodia .",
... | [
"The number of Japanese encephalitis cases has decreased substantially over the past decades with the implementation of childhood vaccination programs .",
"Japanese encephalitis virus , however , remains the most important cause of acute viral encephalitis in Eastern and Southern Asia , with an estimated 68 , 000... | 2018 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"larvicides",
"invertebrates",
"medicine and health sciences",
"ecology and environmental sciences",
"onchocerca volvulus",
"rivers",
"helminths",
"tropical diseases",
"social sciences",
"parasitic diseases",
"animals",
"onchocerca",
"political science",
"aquatic environments",
"pharmace... | Update on the current status of onchocerciasis in Côte d’Ivoire following 40 years of intervention: Progress and challenges | journal.pntd.0006897 | null | [
[
"Onchocerciasis ( also known as “river blindness” ) is a serious public health problem that has hindered socioeconomic development in endemic areas in sub-Saharan Africa [1] .",
"The disease is caused by the filarial parasite Onchocerca volvulus that is transmitted by Simulium black flies .",
"This in... | [
"Onchocerciasis control in Côte d’Ivoire started with aerial insecticide spraying in 1974 and continued with community directed treatment with ivermectin ( CDTi ) from 1992 to the present .",
"Onchocerciasis and lymphatic filariasis ( LF ) are co-endemic in 46 of the 81 health districts in the country .",
"Four... | [
"Onchocerciasis has recently been targeted for elimination in Côte d’Ivoire .",
"With support of international donors the country’s integrated Neglected Tropical Diseases ( NTD ) program has recently achieved 100% geographical coverage for mass drug administration in districts endemic for lymphatic filariasis and... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | A Truncated NLR Protein, TIR-NBS2, Is Required for Activated Defense Responses in the exo70B1 Mutant | journal.pgen.1004945 | null | [
[
"Powdery mildew fungi are obligate biotrophic pathogens that cause widespread disease in many plant species , including economically important crops such as barley [1] , wheat [2] and tomato [3] as well as model plants such as Arabidopsis [4] .",
"Powdery mildew fungal spores germinate on the leaf surface... | [
"During exocytosis , the evolutionarily conserved exocyst complex tethers Golgi-derived vesicles to the target plasma membrane , a critical function for secretory pathways .",
"Here we show that exo70B1 loss-of-function mutants express activated defense responses upon infection and express enhanced resistance to ... | [
"Secretory pathways play an important role in the plant immune response by delivering antimicrobial compounds and metabolites to the site of infection .",
"The evolutionarily conserved exocyst complex is involved in exocytosis , the final step in the secretory pathway .",
"We showed that loss of the function of... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"biology"
] | Generation of Functional Blood Vessels from a Single c-kit+ Adult Vascular Endothelial Stem Cell | journal.pbio.1001407 | Adult vascular endothelial stem cells are shown to reside in the blood vessel wall endothelium. When isolated, these cells are capable of clonal expansion and generate functional blood vessels in vivo. | [
[
"The early blood vessels of the embryo and yolk sac in mammals develop by aggregation of de-novo-forming angioblasts into a primitive vascular plexus ( vasculogenesis ) .",
"Blood vessels arise from endothelial precursors , which share an origin with hematopoietic progenitors [1]–[3] .",
"In adults , ... | [
"In adults , the growth of blood vessels , a process known as angiogenesis , is essential for organ growth and repair .",
"In many disorders including cancer , angiogenesis becomes excessive .",
"The cellular origin of new vascular endothelial cells ( ECs ) during blood vessel growth in angiogenic situations ha... | [
"Angiogenesis—the growth of blood vessels—is essential for organ growth and repair , but also occurs during tumorigenesis and in certain inflammatory disorders .",
"All blood vessels are lined by endothelial cells ( ECs ) —thin , flattened cells that form a continuous monolayer throughout the entire circulatory s... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Ty3 Retrotransposon Hijacks Mating Yeast RNA Processing Bodies to Infect New Genomes | journal.pgen.1005528 | null | [
[
"RNA processing bodies ( PB ) are ribonucleoprotein ( RNP ) granules that contain proteins associated with cytoplasmic deadenylation , decapping and 5’ to 3’ degradation of RNAs in eukaryotic cells [reviewed in [1–5]] .",
"In previous work we showed that artificial overexpression of the long-terminal-repe... | [
"Retrotransposition of the budding yeast long terminal repeat retrotransposon Ty3 is activated during mating .",
"In this study , proteins that associate with Ty3 Gag3 capsid protein during virus-like particle ( VLP ) assembly were identified by mass spectrometry and screened for roles in mating-stimulated retrot... | [
"Cells undergoing changes in gene expression programs such as nutritional deprivation and other stresses exhibit formation of ribonucleoprotein ( RNP ) complexes .",
"In Saccharomyces cerevisiae , the majority of investigations to date involve analysis of P-body ( PB ) and stress-granule RNP formation following n... | 2015 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine",
"bacterial diseases",
"infectious diseases",
"oral diseases",
"oral medicine"
] | Porphyromonas gingivalis and Treponema denticola Exhibit Metabolic Symbioses | journal.ppat.1003955 | null | [
[
"Chronic periodontitis is an inflammatory disease of the supporting tissues of the teeth with a polymicrobial aetiology .",
"However , whilst the concepts of the roles of particular oral bacterial species in disease have changed over the past two decades there is wide consensus that anaerobic , proteolyti... | [
"Porphyromonas gingivalis and Treponema denticola are strongly associated with chronic periodontitis .",
"These bacteria have been co-localized in subgingival plaque and demonstrated to exhibit symbiosis in growth in vitro and synergistic virulence upon co-infection in animal models of disease .",
"Here we show... | [
"Unlike the traditional view that most diseases are caused by infection with a single bacterial species , some chronic diseases including periodontitis result from the perturbation of the natural microbiota and the proliferation of a number of opportunistic pathogens .",
"Both Porphyromonas gingivalis and Trepone... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine and health sciences",
"pathology and laboratory medicine",
"entomology",
"host-pathogen interactions",
"viral transmission and infection",
"virology",
"biology and life sciences",
"microbiology",
"pathogenesis",
"zoology",
"viral load",
"quantitative parasitology",
"parasitology"
] | On the Front Line: Quantitative Virus Dynamics in Honeybee (Apis mellifera L.) Colonies along a New Expansion Front of the Parasite Varroa destructor | journal.ppat.1004323 | null | [
[
"The honeybee , Apis mellifera , plays an essential role in modern agriculture .",
"In addition to honey production , honeybees provide critical ecosystem services , primarily pollination , for a large range of high-value agricultural crops [1] .",
"However , during the last half-century honeybees hav... | [
"Over the past fifty years , annual honeybee ( Apis mellifera ) colony losses have been steadily increasing worldwide .",
"These losses have occurred in parallel with the global spread of the honeybee parasite Varroa destructor .",
"Indeed , Varroa mite infestations are considered to be a key explanatory factor... | [
"Honeybees currently face a dramatic decline worldwide .",
"The main honeybee parasite - Varroa destructor - plays a key role in these mortalities , since uncontrolled infestation inevitably results in the death of the colony .",
"The pathological effects of Varroa infestations are partly attributed to the asso... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biochemistry",
"cell biology",
"computational biology",
"biophysics",
"genetics and genomics"
] | Dynamics and Design Principles of a Basic Regulatory Architecture Controlling Metabolic Pathways | journal.pbio.0060146 | A quantitative, high-temporal resolution study of gene induction in a metabolic pathway reveals an intricate connection between the regulatory architecture and the dynamic response of the system, pointing to possible principles underlying the design of these pathways. | [
[
"In the past several years , genomic approaches have dramatically accelerated the discovery of biological regulatory networks .",
"Combined with detailed biochemical and genetic studies , these approaches have yielded the intricate wiring diagrams for many biological systems .",
"Although revealing , ... | [
"The dynamic features of a genetic network's response to environmental fluctuations represent essential functional specifications and thus may constrain the possible choices of network architecture and kinetic parameters .",
"To explore the connection between dynamics and network design , we have analyzed a gener... | [
"Single-cell organisms must constantly adjust their gene expression programs to survive in a changing environment .",
"Interactions between different molecules form a regulatory network to mediate these changes .",
"While the network connections are often known , figuring out how the network responds dynamicall... | 2008 |
[
"Introduction",
"Results/Discussion",
"Materials and Methods"
] | [
"evolutionary biology",
"cell biology",
"cell biology/gene expression",
"evolutionary biology/microbial evolution and genomics"
] | A Simple Screen to Identify Promoters Conferring High Levels of Phenotypic Noise | journal.pgen.1000307 | null | [
[
"Clonal populations of unicellular organisms growing under constant conditions often show substantial variation in phenotypic traits .",
"The rate at which some of these traits vary is so high that it cannot result from mutational change .",
"Rather , this phenotypic noise has been shown to result fro... | [
"Genetically identical populations of unicellular organisms often show marked variation in some phenotypic traits .",
"To investigate the molecular causes and possible biological functions of this phenotypic noise , it would be useful to have a method to identify genes whose expression varies stochastically on a ... | [
"According to the conventional view , the characteristics of an organism are determined by nature and nurture—by its genes and by the environment it lives in .",
"Consequently , one would expect that two organisms that share the same genes and live in the same environment have identical characteristics .",
"Rec... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"animal genetics",
"rna interference",
"gene regulation",
"cell differentiation",
"dna transcription",
"gene function",
"epithelial cells",
"animal models",
"eukaryotic cells",
"developmental biology",
"caenorhabditis elegans",
"model organisms",
"cell division",
"stem cells",
"molecular... | The Caenorhabditis elegans GATA Factor ELT-1 Works through the Cell Proliferation Regulator BRO-1 and the Fusogen EFF-1 to Maintain the Seam Stem-Like Fate | journal.pgen.1002200 | null | [
[
"The regulation of the decision between cell proliferation and differentiation is a key aspect of metazoan development , ensuring that the correct number and type of cells are present .",
"The RUNX family of transcription factors ( RUNX1 , 2 and 3 ) , together with their binding partner CBFβ , are key pla... | [
"Seam cells in Caenorhabditis elegans provide a paradigm for the stem cell mode of division , with the ability to both self-renew and produce daughters that differentiate .",
"The transcription factor RNT-1 and its DNA binding partner BRO-1 ( homologues of the mammalian cancer-associated stem cell regulators RUNX... | [
"Stem cells can both produce differentiated cells and self-renew , producing more stem cells .",
"Choosing between these opposing options is critical for development .",
"Here , we have investigated the molecular genetics underlying this choice in the nematode worm , C . elegans , using the seam cells as a mode... | 2011 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious diseases",
"medicine and health sciences",
"population modeling",
"dengue fever",
"genetics",
"neglected tropical diseases",
"biology and life sciences",
"population genetics",
"infectious disease modeling",
"computational biology",
"evolutionary biology",
"viral diseases",
"infe... | Stability of the wMel Wolbachia Infection following Invasion into Aedes aegypti Populations | journal.pntd.0003115 | null | [
[
"Insect populations can evolve to respond rapidly to infectious agents including endosymbionts .",
"Examples include the evolution of host suppressors that alter sex ratio of endosymbionts that cause male killing in Hypolimnas bolina [1] and changes in the lifespan effects induced by wMelPop Wolbachia inf... | [
"The wMel infection of Drosophila melanogaster was successfully transferred into Aedes aegypti mosquitoes where it has the potential to suppress dengue and other arboviruses .",
"The infection was subsequently spread into two natural populations at Yorkeys Knob and Gordonvale near Cairns , Queensland in 2011 .",
... | [
"The wMel infection is a Wolbachia infection introduced into Aedes aegypti mosquito populations; wMel can provide potential suppression of dengue if the infection persists in populations .",
"We show that the infection has persisted at a high frequency since its initial introduction into two natural populations i... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"behavioral neuroscience",
"cognitive neuroscience",
"social and behavioral sciences",
"psychology",
"cognitive psychology",
"computational neuroscience",
"biology",
"computational biology",
"neuroscience"
] | Saccadic Momentum and Facilitation of Return Saccades Contribute to an Optimal Foraging Strategy | journal.pcbi.1002871 | null | [
[
"The effect of inhibition of return ( IOR ) was first described by Posner & Cohen [1] .",
"When ( covert ) attention is attracted by a peripheral cue , reaction times to a subsequent probe stimulus in the same location depend in an intriguing way on the temporal offset between cue and probe: When the prob... | [
"The interest in saccadic IOR is funneled by the hypothesis that it serves a clear functional purpose in the selection of fixation points: the facilitation of foraging .",
"In this study , we arrive at a different interpretation of saccadic IOR .",
"First , we find that return saccades are performed much more o... | [
"Sometimes humans look at the same location twice .",
"To appreciate the importance of this inconspicuous statement you have to consider that we move our eyes several billion ( 109 ) times during our lives and that looking at something is a necessary condition to enable conscious visual awareness .",
"Thus , un... | 2013 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine",
"anatomy and physiology",
"cadherins",
"biomechanics",
"rickettsia",
"cardiovascular",
"bacterial diseases",
"cell mechanics",
"infectious diseases",
"cell adhesion",
"biology",
"cardiovascular system",
"biophysics",
"cell biology",
"physiology",
"vascular biology",
"mole... | Rickettsiae Induce Microvascular Hyperpermeability via Phosphorylation of VE-Cadherins: Evidence from Atomic Force Microscopy and Biochemical Studies | journal.pntd.0001699 | null | [
[
"Spotted fever group ( SFG ) rickettsioses are composed of over 25 species of rickettsiae that are causative agents of a wide spectrum of diseases , ranging from the virulent Rocky Mountain spotted fever ( Rickettsia rickettsii ) and severe systemic Mediterranean spotted fever ( R . conorii ) to the recently ... | [
"The most prominent pathophysiological effect of spotted fever group ( SFG ) rickettsial infection of microvascular endothelial cells ( ECs ) is an enhanced vascular permeability , promoting vasogenic cerebral edema and non-cardiogenic pulmonary edema , which are responsible for most of the morbidity and mortality ... | [
"Rickettsial diseases are serious human infections .",
"Some spotted fever group ( SFG ) rickettsial pathogens are bioterror agents .",
"A major clinical hallmark of SFG rickettsial disease is the infection of endothelial cells leading to enhanced vascular permeability .",
"Previous studies show that SFG rick... | 2012 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"death rates",
"medicine and health sciences",
"pathology and laboratory medicine",
"infectious disease epidemiology",
"pathogens",
"vector-borne diseases",
"mathematics",
"population biology",
"infectious disease control",
"life expectancy",
"public and occupational health",
"infectious disea... | Robustness of the reproductive number estimates in vector-borne disease systems | journal.pntd.0006999 | null | [
[
"Over the last few decades there has been a global rise in the emergence and re-emergence of vector-borne infectious diseases [1] .",
"The continuing threat of Plasmodium falciparum malaria [2 , 3] and dengue [4] , the rapid , near pandemic spread of Zika virus [5] or the recent epizootic outbreak of Yers... | [
"The required efforts , feasibility and predicted success of an intervention strategy against an infectious disease are partially determined by its basic reproduction number , R0 .",
"In its simplest form R0 can be understood as the product of the infectious period , the number of infectious contacts and the per-... | [
"Many infectious diseases of public health concern , such as dengue , Zika and malaria , are transmitted by insect vectors .",
"Control effort required to curb their continued spread or even prevent their establishment in the first place are partially determined by the disease’s basic reproduction number , R0 .",... | 2018 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"taxonomy",
"invertebrates",
"ecology and environmental sciences",
"helminths",
"population genetics",
"geographical locations",
"animals",
"genetic mapping",
"trematodes",
"phylogenetics",
"data management",
"phylogenetic analysis",
"molecular biology techniques",
"population biology",
... | Molecular discrimination of Opisthorchis-like eggs from residents in a rural community of central Thailand | journal.pntd.0006030 | null | [
[
"Opisthorchis viverrini , a fish-borne trematode ( FBT ) , is one of the main public health problems in Southeast Asia , while Clonorchis sinensis is commonly found in Japan , the Republic of Korea , China , Taiwan and Vietnam [1 , 2] .",
"In Thailand , more than 3 . 3 million people are predominantly inf... | [
"Opisthorchis viverrini infection is a major public health problem in northern and northeastern Thailand .",
"The chronic infection of O . viverrini is related to cholangiocarcinoma which causes high mortality in endemic areas .",
"Therefore , the diagnosis , treatment , control and prevention of O . viverrini ... | [
"O . viverrini infection is highly prevalent in northern and northeastern Thailand .",
"The diagnosis of the infection is usually achieved by finding the eggs in feces .",
"However , these eggs are difficult to differentiate morphologically from other Opisthorchis-like eggs .",
"Our study evaluated the preval... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine and health sciences",
"engineering and technology",
"signal processing",
"social sciences",
"limbs (anatomy)",
"neuroscience",
"noise reduction",
"simulation and modeling",
"systems science",
"mathematics",
"statistics (mathematics)",
"vision",
"research and analysis methods",
"m... | When Optimal Feedback Control Is Not Enough: Feedforward Strategies Are Required for Optimal Control with Active Sensing | journal.pcbi.1005190 | null | [
[
"Despite the abundance in the degrees of freedom of the human body , our movements occupy a very small subset of all possible movements , showing remarkably stereotypical patterns of motion for a given task .",
"There is a long history which posits that such stereotypy arises from each possible movement i... | [
"Movement planning is thought to be primarily determined by motor costs such as inaccuracy and effort .",
"Solving for the optimal plan that minimizes these costs typically leads to specifying a time-varying feedback controller which both generates the movement and can optimally correct for errors that arise with... | [
"The dominant theory of how movements are planned suggests that a task specifies a motor cost in terms of effort and accuracy and the motor system chooses a movement to minimize this cost .",
"The pre-eminent theory is that this results an optimal feedback controller that both generates the movement and can corre... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine and health sciences",
"body fluids",
"enzyme-linked immunoassays",
"oxides",
"chemical compounds",
"pneumococcus",
"pathology and laboratory medicine",
"pathogens",
"ketones",
"microbiology",
"pyruvate",
"animal models",
"model organisms",
"hydrogen peroxide",
"immunologic tech... | Pyruvate Oxidase as a Critical Link between Metabolism and Capsule Biosynthesis in Streptococcus pneumoniae | journal.ppat.1005951 | null | [
[
"Streptococcus pneumoniae is a major human pathogen whose disease manifestations range from sinusitis and otitis media to pneumonia , bacteremia , and meningitis .",
"The pneumococcus produces a number of important virulence factors , including the polysaccharide capsule , one of the most widely distribut... | [
"The pneumococcus is one of the most prodigious producers of hydrogen peroxide amongst bacterial pathogens .",
"Hydrogen peroxide production by the pneumococcus has been implicated in antibiotic synergism , competition between other bacterial colonizers of the nasopharynx , and damage to epithelial cells .",
"H... | [
"The pneumococcus polysaccharide capsule is one of the most critical virulence determinants produced by this major human pathogen .",
"The pneumococcus also produces prodigious amounts of hydrogen peroxide via the enzymatic reaction catalyzed by pyruvate oxidase , SpxB .",
"Deletion of spxB resulted in the loss... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"cell binding",
"antimicrobials",
"cell physiology",
"medicine and health sciences",
"luciferase",
"defensins",
"pathology and laboratory medicine",
"viral transmission and infection",
"enzymes",
"pathogens",
"drugs",
"immunology",
"biological cultures",
"microbiology",
"enzymology",
"... | Alpha-defensin-dependent enhancement of enteric viral infection | journal.ppat.1006446 | null | [
[
"Enteric α-defensins are effector peptides of the innate immune system that are abundantly expressed in both the human and mouse small intestine .",
"Produced exclusively by specialized epithelial cells called Paneth cells , enteric α-defensins are broadly antimicrobial against bacterial and viral infecti... | [
"The small intestinal epithelium produces numerous antimicrobial peptides and proteins , including abundant enteric α-defensins .",
"Although they most commonly function as potent antivirals in cell culture , enteric α-defensins have also been shown to enhance some viral infections in vitro .",
"Efforts to dete... | [
"Enteric α-defensins are an ancient form of host defense against pathogens , but until recently there was no robust in vitro system available to study their functions upon secretion from the cells that produce them naturally in vivo .",
"Here , using small intestinal enteroids as a source of naturally secreted α-... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genetics and genomics/animal genetics",
"molecular biology/histone modification",
"developmental biology",
"physiology/reproductive physiology",
"genetics and genomics/epigenetics"
] | MLL2 Is Required in Oocytes for Bulk Histone 3 Lysine 4 Trimethylation and Transcriptional Silencing | journal.pbio.1000453 | Conditional knockout mouse strategies identify the histone methyltranferase MLL2 as a key player in epigenetic reprogramming of female gametes. | [
[
"Mammalian epigenomes are fundamentally reprogrammed during gametogenesis and pre-implantation development to establish the ground state of pluripotency in the epiblast cells of the blastocyst [1]–[5] .",
"Despite the importance of this epigenetic reprogramming , how such changes are achieved is not well ... | [
"During gametogenesis and pre-implantation development , the mammalian epigenome is reprogrammed to establish pluripotency in the epiblast .",
"Here we show that the histone 3 lysine 4 ( H3K4 ) methyltransferase , MLL2 , controls most of the promoter-specific chromatin modification , H3K4me3 , during oogenesis an... | [
"It is well established that gametes and early mammalian embryos undergo extensive epigenetic changes , which are changes in phenotype or gene expression that do not entail changes in DNA sequence .",
"However , the machinery responsible for epigenetic modification in these situations is poorly understood .",
"... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"invertebrates",
"ecology and environmental sciences",
"chemical compounds",
"atmospheric science",
"green fluorescent protein",
"social sciences",
"neuroscience",
"animals",
"animal models",
"instinct",
"luminescent proteins",
"model organisms",
"drosophila melanogaster",
"experimental or... | Avoidance response to CO2 in the lateral horn | journal.pbio.2006749 | null | [
[
"Animals use the olfactory system to find partners or food and to avoid predators .",
"To a certain extent , the ability to navigate the olfactory environment is hardwired .",
"This ability is expanded with life experiences that result in olfactory associations .",
"The architecture of the olfacto... | [
"In flies , the olfactory information is carried from the first relay in the brain , the antennal lobe , to the mushroom body ( MB ) and the lateral horn ( LH ) .",
"Olfactory associations are formed in the MB .",
"The LH was ascribed a role in innate responses based on the stereotyped connectivity with the ant... | [
"Behavioral responses to a stimulus in the environment may be hardwired or acquired with experience .",
"In the olfactory system of the fruit fly Drosophila melanogaster , associations of odors are formed in a brain structure called the mushroom body .",
"A different brain region , the lateral horn , is thought... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"molecular biology/histone modification",
"molecular biology/chromatin structure",
"molecular biology/transcription initiation and activation"
] | Bidirectional Transcription Directs Both Transcriptional Gene Activation and Suppression in Human Cells | journal.pgen.1000258 | null | [
[
"Over the past few years it has become increasingly apparent that many RNA-mediated modes of gene regulation are operative in biological systems [1] .",
"It is only now becoming appreciated just how pervasive this network is and to what extent it may be possible to apply this phenomenon for therapeutic be... | [
"Small RNAs targeted to gene promoters in human cells have been shown to modulate both transcriptional gene suppression and activation .",
"However , the mechanism involved in transcriptional activation has remained poorly defined , and an endogenous RNA trigger for transcriptional gene silencing has yet to be id... | [
"Non-coding RNAs have been shown to modulate transcriptional expression of genes in human cells .",
"This form of gene regulation has been shown to be the result of RNA directing silent state epigenetic changes to the targeted gene promoter .",
"Shortly after this seminal observation , small RNAs targeted to AT... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"viruses",
"infectious diseases",
"virology",
"immunology",
"microbiology",
"vertebrates",
"mus (mouse)",
"animals"
] | Cell-Specific IRF-3 Responses Protect against West Nile Virus Infection by Interferon-Dependent and -Independent Mechanisms | journal.ppat.0030106 | null | [
[
"West Nile virus ( WNV ) is a mosquito-borne , positive polarity , single-stranded RNA virus in the Flaviviridae family .",
"In humans , WNV causes a spectrum of illness that ranges from a self-limiting WNV fever to flaccid paralysis and fatal encephalitis [1] .",
"WNV is endemic in Africa , Europe , ... | [
"Interferon regulatory factor ( IRF ) -3 is a master transcription factor that activates host antiviral defense programs .",
"Although cell culture studies suggest that IRF-3 promotes antiviral control by inducing interferon ( IFN ) -β , near normal levels of IFN-α and IFN-β were observed in IRF-3−/− mice after i... | [
"West Nile virus ( WNV ) is a mosquito-transmitted RNA virus that infects birds , horses , and humans , and it has become an emerging infectious disease threat in the Western hemisphere , including all of the continental United States .",
"WNV invades the brain and spinal cord and infects and injures neurons , ca... | 2007 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biochemistry",
"proteins",
"gene expression",
"genetics",
"epigenetics",
"biology",
"molecular genetics",
"genetics and genomics"
] | Structural Basis of Transcriptional Gene Silencing Mediated by Arabidopsis MOM1 | journal.pgen.1002484 | null | [
[
"Transcriptional gene silencing ( TGS ) refers to the stable repression of transcription and mainly affects transposons , chromosomal repeats and transgenic inserts; however , it may also suppress the expression of certain protein-coding genes .",
"In multicellular eukaryotes , TGS can persist through mit... | [
"Shifts between epigenetic states of transcriptional activity are typically correlated with changes in epigenetic marks .",
"However , exceptions to this rule suggest the existence of additional , as yet uncharacterized , layers of epigenetic regulation .",
"MOM1 , a protein of 2 , 001 amino acids that acts as ... | [
"Epigenetic shifts in transcriptional activities are usually correlated with changes in chromatin properties and covalent modification of DNA and/or histones .",
"There are , however , exceptional regulators that are able to switch epigenetic states without the apparent involvement of changes in chromatin or DNA ... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Plasmodium falciparum Adhesins Play an Essential Role in Signalling and Activation of Invasion into Human Erythrocytes | journal.ppat.1005343 | null | [
[
"The most lethal form of malaria in humans is caused by Plasmodium falciparum .",
"The merozoite form of this parasite invades red blood cells beginning with initial recognition and attachment to erythrocytes ( reviewed in [1] .",
"This interaction is dynamic and involves considerable deformation of t... | [
"The most severe form of malaria in humans is caused by the protozoan parasite Plasmodium falciparum .",
"The invasive form of malaria parasites is termed a merozoite and it employs an array of parasite proteins that bind to the host cell to mediate invasion .",
"In Plasmodium falciparum , the erythrocyte bindi... | [
"Malaria parasites must invade red blood cells to survive within the human host .",
"Members of the erythrocyte binding-like ( EBL ) and reticulocyte binding-like ( Rh ) protein families , which are present at the apical tip of merozoites as single-pass transmembrane proteins , mediate recognition of red blood ce... | 2015 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"legs",
"pathology and laboratory medicine",
"tropical diseases",
"limbs (anatomy)",
"bacterial diseases",
"signs and symptoms",
"neglected tropical diseases",
"forearms",
"bacteria",
"elbow",
"infectious diseases",
"buruli ulcer",
"musculoskeletal system",
... | The location of Australian Buruli ulcer lesions—Implications for unravelling disease transmission | journal.pntd.0005800 | null | [
[
"Buruli ulcer ( BU ) , listed by the World Health Organisation ( WHO ) as a neglected tropical disease , is a destructive infection of the subcutaneous tissue caused by the acid-fast bacillus Mycobacterium ulcerans [1 , 2] .",
"It is endemic in at least 33 countries and is the third most prevalent mycobac... | [
"Buruli ulcer ( BU ) , caused by Mycobacterium ulcerans , is increasing in incidence in Victoria , Australia .",
"To improve understanding of disease transmission , we aimed to map the location of BU lesions on the human body .",
"Using notification data and clinical records review , we conducted a retrospectiv... | [
"Buruli ulcer is an emerging tropical disease that is also increasingly common in the temperate Australian state of Victoria .",
"The mode of transmission of this geographically restricted infection remains elusive .",
"We have accurately mapped the location of 649 PCR-confirmed Buruli lesions affecting 579 pat... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"infectious diseases",
"influenza",
"viral diseases"
] | Glycomic Analysis of Human Respiratory Tract Tissues and Correlation with Influenza Virus Infection | journal.ppat.1003223 | null | [
[
"Influenza virus infection in humans presents an economic and social health burden to society .",
"Yearly infections are normally due to H1N1 , H3N2 or influenza B strains while pandemics occur at 30–40 year intervals due to antigenic shift or the emergence of new strains , such as the introduction of H1N... | [
"The first step in influenza infection of the human respiratory tract is binding of the virus to sialic ( Sia ) acid terminated receptors .",
"The binding of different strains of virus for the receptor is determined by the α linkage of the sialic acid to galactose and the adjacent glycan structure .",
"In this ... | [
"This study was performed to determine what possible glycan receptors for influenza were present in the human respiratory tract .",
"We compared the glycans present on existing published glycan arrays with the actual glycans identified in the human respiratory tract by mass spectrometric analysis to determine how... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"immunology",
"biology",
"genomics",
"genetics and genomics"
] | A Spontaneous Mutation of the Rat Themis Gene Leads to Impaired Function of Regulatory T Cells Linked to Inflammatory Bowel Disease | journal.pgen.1002461 | null | [
[
"Immune-mediated diseases are multifactorial disorders , resulting from complex interactions between multiple genes and the environment [1] .",
"Deciphering the genetic bases of these diseases is a difficult task .",
"Genetic association studies in human have recently identified numerous risk loci ass... | [
"Spontaneous or chemically induced germline mutations , which lead to Mendelian phenotypes , are powerful tools to discover new genes and their functions .",
"Here , we report an autosomal recessive mutation that occurred spontaneously in a Brown-Norway ( BN ) rat colony and was identified as causing marked T cel... | [
"Deciphering the genetic basis of human diseases and understanding the function of mammalian genes are among the main challenges for today's geneticists .",
"In this regard , rodent models represent invaluable tools to identify new genes and to study the mechanisms of action of genes implicated in human diseases ... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"infographics",
"action potentials",
"medicine and health sciences",
"neurochemistry",
"neural networks",
"membrane potential",
"electrophysiology",
"neuroscience",
"simulation and modeling",
"network analysis",
"neurotransmitters",
"research and analysis methods",
"computer and information ... | Recurrently connected and localized neuronal communities initiate coordinated spontaneous activity in neuronal networks | journal.pcbi.1005672 | null | [
[
"Neuronal systems , including brain circuits’ in vivo and cultured networks , intrinsically generate coordinated and spatiotemporally propagating spontaneous spiking activity during their development [1] .",
"This type of spontaneous activity ( or “waves” ) has been studied in several brain circuits , inc... | [
"Developing neuronal systems intrinsically generate coordinated spontaneous activity that propagates by involving a large number of synchronously firing neurons .",
"In vivo , waves of spikes transiently characterize the activity of developing brain circuits and are fundamental for activity-dependent circuit form... | [
"Coordinated spontaneous spiking activity is fundamental for the normal formation of brain circuits during development .",
"However , how ensembles of neurons generate these events remains unclear .",
"To address this question , in the present study , we investigated the network properties that might be require... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"biotechnology",
"non-coding rna sequences",
"vernalization",
"rna extraction",
"plant physiology",
"long non-coding rnas",
"plant science",
"genetically modified plants",
"epigenetics",
"plants",
"flowering plants",
"extraction techniques",
"chromatin",
"genetic engineering",
"research ... | Modular function of long noncoding RNA, COLDAIR, in the vernalization response | journal.pgen.1006939 | null | [
[
"Epigenetic regulation of gene expression in eukaryotes is coordinated by a series of molecular events , including chromatin modification , long noncoding RNAs ( lncRNAs ) , RNA modification , and DNA modification [1–4] .",
"The vernalization response in plants is one example in which epigenetic regulatio... | [
"The long noncoding RNA COLDAIR is necessary for the repression of a floral repressor FLOWERING LOCUS C ( FLC ) during vernalization in Arabidopsis thaliana .",
"The repression of FLC is mediated by increased enrichment of Polycomb Repressive Complex 2 ( PRC2 ) and subsequent trimethylation of Histone H3 Lysine 2... | [
"Vernalization is an epigenetic response to winter cold necessary for the onset of flowering in spring .",
"The epigenetically stable repression of a floral repressor , FLC , is a hallmark of the vernalization response in the model plant Arabidopsis .",
"Vernalization-mediated repression of FLC is achieved by c... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"parastic protozoans",
"biochemistry",
"rna",
"molecular cell biology",
"nucleic acids",
"gene expression",
"gene regulation",
"molecular genetics",
"protozoology",
"biology",
"computational biology",
"microbiology",
"parasitology"
] | The microRNAs in an Ancient Protist Repress the Variant-Specific Surface Protein Expression by Targeting the Entire Coding Sequence | journal.ppat.1003791 | null | [
[
"The deeply branching protozoan parasite Giardia lamblia , is responsible for the diarrheal disease giardiasis , which affects over 200 million people worldwide [1] , [2] .",
"In developing countries , multiple exposures to the pathogen result in repeated chronic infections .",
"The persistence of inf... | [
"microRNAs ( miRNA ) have been detected in the deeply branched protist , Giardia lamblia , and shown to repress expression of the family of variant-specific surface proteins ( VSPs ) , only one of which is expressed in Giardia trophozoite at a given time .",
"Three next-generation sequencing libraries of Giardia ... | [
"Giardia lamblia is a protozoan parasite causing the diarrheal disease giardiasis .",
"Variant-specific surface proteins ( VSP ) in Giardia are likely involved in its evasion of host immune response .",
"Their expression is regulated by microRNAs ( miRNA ) .",
"To determine the full complement of miRNAs in Gi... | 2014 |
[
"Introduction",
"Discussion"
] | [
"computational biology/macromolecular structure analysis",
"rheumatology/rheumatoid arthritis",
"rheumatology/autoimmunity, autoimmune, and inflammatory diseases",
"pharmacology/drug development",
"computational biology/protein structure prediction",
"biochemistry/biomacromolecule-ligand interactions",
... | A Variant of TNFR2-Fc Fusion Protein Exhibits Improved Efficacy in Treating Experimental Rheumatoid Arthritis | journal.pcbi.1000669 | null | [
[
"Overproduction of TNFα is an underlying mechanism of autoimmune diseases , including RA , ankylosing spondylitis and psoriatic arthritis [1]–[2] .",
"Blocking excess TNFa by its antagonists including TNF receptor 2-IgG1 fusion protein ( Etanercept ) and anti-TNFα monoclonal antibodies ( Infliximab and Ad... | [
"Etanercept , a TNF receptor 2-Fc fusion protein , is currently being used for the treatment of rheumatoid arthritis ( RA ) .",
"However , 25% to 38% of patients show no response which is suspected to be partially due to insufficient affinity of this protein to TNFα .",
"By using computational protein design , ... | [
"Rheumatoid arthritis ( RA ) is a frequently occurring , chronic , debilitating disease .",
"TNFα plays a pivotal role in regulating its inflammatory response .",
"TNFα inhibition with TNF receptor 2-Fc fusion protein ( TNFR2-Fc ) was effective in the treatment of RA .",
"However , quite a few patients may no... | 2010 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion",
"Conclusion"
] | [
"medicine and health sciences",
"tropical diseases",
"parasitic diseases",
"odorant binding proteins",
"genome analysis",
"neglected tropical diseases",
"insect vectors",
"zoology",
"agrochemicals",
"insect pheromones",
"proteins",
"epidemiology",
"gene expression",
"protozoan infections",... | Under-Expression of Chemosensory Genes in Domiciliary Bugs of the Chagas Disease Vector Triatoma brasiliensis | journal.pntd.0005067 | null | [
[
"Chagas disease is a potentially fatal parasitic disease caused by Trypanosoma cruzi , an endemic kinetoplastida that has infected five million people in Latin America [1] and is transmitted by blood-sucking bugs ( Hemiptera , Reduviidae , Triatominae ) .",
"Chemical control campaigns against Chagas disea... | [
"In Latin America , the bloodsucking bugs Triatominae are vectors of Trypanosoma cruzi , the parasite that causes Chagas disease .",
"Chemical elimination programs have been launched to control Chagas disease vectors .",
"However , the disease persists because native vectors from sylvatic habitats are able to (... | [
"In Latin America , bloodsucking bugs are vectors of Trypanosoma cruzi , the parasite that causes Chagas disease , which is one of the most important public health problems for rural human populations .",
"Though chemical control campaigns have been effective against vectors , the disease persists because native ... | 2016 |
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