headings list | keywords list | title stringlengths 20 281 | id stringlengths 20 20 | toc stringlengths 57 522 ⌀ | sections list | abstract list | summary list | year stringclasses 13
values |
|---|---|---|---|---|---|---|---|---|
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"bacteriology",
"microbial metabolism",
"functional genomics",
"microbiology",
"gene function",
"genome analysis tools",
"gene expression",
"biology",
"systems biology",
"genetic screens",
"genetics",
"genomics",
"gene prediction",
"genetics and genomics"
] | Evidence-Based Annotation of Gene Function in Shewanella oneidensis MR-1 Using Genome-Wide Fitness Profiling across 121 Conditions | journal.pgen.1002385 | null | [
[
"Advances in sequencing technology have ushered in a new era of bacterial genomics .",
"At low cost , a single individual can sequence the complete genome of a bacterial isolate in less than a week .",
"While this explosion in genome sequencing and gene discovery is breathtaking , it also serves as a ... | [
"Most genes in bacteria are experimentally uncharacterized and cannot be annotated with a specific function .",
"Given the great diversity of bacteria and the ease of genome sequencing , high-throughput approaches to identify gene function experimentally are needed .",
"Here , we use pools of tagged transposon ... | [
"Many computationally predicted gene annotations in bacteria are incomplete or wrong .",
"Consequently , experimental methods to systematically determine gene function in bacteria are required .",
"Here , we describe a genetic approach to meet this challenge .",
"We constructed a large transposon mutant libra... | 2011 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"blood cells",
"medicine and health sciences",
"immune physiology",
"enzyme-linked immunoassays",
"pathology and laboratory medicine",
"immune cells",
"body fluids",
"pathogens",
"immunology",
"microbiology",
"cloning",
"viruses",
"rna viruses",
"molecular biology techniques",
"antibodie... | A human inferred germline antibody binds to an immunodominant epitope and neutralizes Zika virus | journal.pntd.0005655 | null | [
[
"Zika virus ( ZIKV ) belongs to the genus Flavivirus of the Flaviviridae family and is related to dengue virus ( DENV ) , yellow fever virus ( YFV ) , Japanese encephalitis virus ( JEV ) , and west Nile virus ( WNV ) [1] .",
"The globally distributed mosquito species of the Aedes genus , vectors for many ... | [
"The isolation of neutralizing monoclonal antibodies ( nmAbs ) against the Zika virus ( ZIKV ) might lead to novel preventative strategies for infections in at-risk individuals , primarily pregnant women .",
"Here we describe the characterization of human mAbs from the plasmablasts of an acutely infected patient ... | [
"Antibody affinity maturation through somatic hypermutation ( SHM ) is thought to be critical for the development of antibodies with virus-neutralizing activity .",
"Contrary to this notion , we describe novel human anti-Zika virus ( ZIKV ) antibodies with very low mutation levels , isolated from plasmablasts ear... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genetics",
"biology",
"microbiology",
"genetics and genomics"
] | A Single Nucleotide Polymorphism in Tetherin Promotes Retrovirus Restriction In Vivo | journal.ppat.1002596 | null | [
[
"In order to infect and persist in the host , retroviruses such as HIV-1 encode proteins that counteract innate resistance genes that are also referred to as “restriction factors” .",
"Host restriction factors have the potential to directly interfere with specific steps of the retrovirus life cycle and ha... | [
"Tetherin is a membrane protein of unusual topology expressed from rodents to humans that accumulates enveloped virus particles on the surface of infected cells .",
"However , whether this ‘tethering’ activity promotes or restricts retroviral spread during acute retrovirus infection in vivo is controversial .",
... | [
"Significant portions of the human and mouse genomes are comprised of retroviral sequences , revealing the long history of conflict between mammalian hosts and retroviruses that led to the evolution of host restriction factors .",
"Nucleotide mutations in restriction factor genes provide a glimpse of this ongoing... | 2012 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"infectious diseases/neglected tropical diseases",
"public health and epidemiology/epidemiology",
"infectious diseases/helminth infections",
"public health and epidemiology/global health",
"public health and epidemiology/infectious diseases",
"infectious diseases/epidemiology and control of infectious dis... | Assessing the Impact of Misclassification Error on an Epidemiological Association between Two Helminthic Infections | journal.pntd.0000995 | null | [
[
"Polyparasitism is a common feature in parasite endemic regions , which includes most developing countries [1] , [2] .",
"High prevalence of co-infection with soil-transmitted helminths ( STHs ) , which include roundworm ( Ascaris lumbricoides ) , whipworm ( Trichuris trichiura ) , and hookworm ( Ancylost... | [
"Polyparasitism can lead to severe disability in endemic populations .",
"Yet , the association between soil-transmitted helminth ( STH ) and the cumulative incidence of Schistosoma japonicum infection has not been described .",
"The aim of this work was to quantify the effect of misclassification error , which... | [
"Hookworm , roundworm , and whipworm are collectively known as soil-transmitted helminths .",
"These worms are prevalent in most of the developing countries along with another parasitic infection called schistosomiasis .",
"The tests commonly used to detect infection with these worms are less than 100% accurate... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"text mining",
"public health and epidemiology",
"pain management",
"genetic polymorphism",
"epidemiology",
"anesthesiology",
"population genetics",
"biology",
"computational biology",
"population biology",
"anesthesiology and pain management",
"disease informatics"
] | Integrative Approach to Pain Genetics Identifies Pain Sensitivity Loci across Diseases | journal.pcbi.1002538 | null | [
[
"A significant number of diseases are associated with pain , thereby affecting the quality of life of many individuals .",
"The Institute of Medicine's recent report titled , “Relieving Pain in America” presented pain as a public health challenge , and emphasized the need for an integrative approach to un... | [
"Identifying human genes relevant for the processing of pain requires difficult-to-conduct and expensive large-scale clinical trials .",
"Here , we examine a novel integrative paradigm for data-driven discovery of pain gene candidates , taking advantage of the vast amount of existing disease-related clinical lite... | [
"The mechanisms underlying pain are incompletely understood , and are hard to study due to the subjective and complex nature of pain .",
"From a genetics perspective , the discovery of genes relevant for the processing of pain in humans has been slow and genome-wide association studies have not been successful in... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"developmental biology/morphogenesis and cell biology",
"cell biology/morphogenesis and cell biology",
"developmental biology/pattern formation",
"cell biology/developmental molecular mechanisms",
"computational biology"
] | Computer Simulation of Cellular Patterning Within the Drosophila Pupal Eye | journal.pcbi.1000841 | null | [
[
"Epithelial patterning , in which cells assume required positions within emerging epithelia , is essential to the development of all animals .",
"Such patterning results from local interactions that correctly localize each cell using limited molecular information .",
"Simple patterns can employ a sing... | [
"We present a computer simulation and associated experimental validation of assembly of glial-like support cells into the interweaving hexagonal lattice that spans the Drosophila pupal eye .",
"This process of cell movements organizes the ommatidial array into a functional pattern .",
"Unlike earlier simulation... | [
"During development , organs are assembled through a complex combination of cell proliferation , programmed cell death , cell movements , etc .",
"These aspects of tissue maturation must be achieved with a limited gene set—to achieve complexity , tissues utilize patterning mechanisms .",
"That is , “rules” are ... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"microbiology/innate immunity"
] | Murine Gamma-Herpesvirus 68 Hijacks MAVS and IKKβ to Initiate Lytic Replication | journal.ppat.1001001 | null | [
[
"Host cells activate innate immune signaling pathways to defend against invading pathogens .",
"Pattern recognition receptors , including Toll-like receptors and cytosolic sensors ( such as NOD-like receptors and RIG-I-like receptors ) , recognize pathogen-associated structural components and initiate sig... | [
"Upon viral infection , the mitochondrial antiviral signaling ( MAVS ) -IKKβ pathway is activated to restrict viral replication .",
"Manipulation of immune signaling events by pathogens has been an outstanding theme of host-pathogen interaction .",
"Here we report that the loss of MAVS or IKKβ impaired the lyti... | [
"Innate immunity represents the first line of defense against pathogen infection .",
"Recent studies uncovered an array of sensors that detect pathogen-associated molecular patterns and induce antiviral cytokine production via two closely related kinase complexes , i . e . , the IKKα/β/γ and TBK-1/IKKε .",
"To ... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"ecology/plant-environment interactions",
"ecology/global change ecology",
"infectious diseases",
"ecology",
"ecology/community ecology and biodiversity",
"ecology/population ecology",
"ecology/ecosystem ecology"
] | A Disease-Mediated Trophic Cascade in the Serengeti and its Implications for Ecosystem C | journal.pbio.1000210 | The removal of rinderpest had cascading effects on herbivore populations, fire, tree density, and even ecosystem carbon in the Serengeti ecosystem of East Africa. | [
[
"In addition to being a prominent structural feature of savanna and forest ecosystems , tree cover has far-reaching consequences for ecosystem function [1] , [2] .",
"Trees are a key component of stored carbon ( C ) , and thus important in the potential for ecosystems to act as carbon dioxide ( CO2 ) sink... | [
"Tree cover is a fundamental structural characteristic and driver of ecosystem processes in terrestrial ecosystems , and trees are a major global carbon ( C ) sink .",
"Fire and herbivores have been hypothesized to play dominant roles in regulating trees in African savannas , but the evidence for this is conflict... | [
"Diseases are known to play important roles in regulating and structuring populations , but the consequences of disease outbreaks for entire communities and ecosystems are not as well understood .",
"The Serengeti wildebeest were historically kept at low numbers by the rinderpest virus , but underwent a populatio... | 2009 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | Meteorologically Driven Simulations of Dengue Epidemics in San Juan, PR | journal.pntd.0004002 | null | [
[
"In the last decade dengue infections have increased dramatically in the Americas with cases now occurring in the southern U . S . , Mexico and Central America , across the Caribbean , and as far south as Argentina in South America [1] .",
"The Pan American outbreak in 2010 resulted in 1 . 7 million cases... | [
"Meteorological factors influence dengue virus ecology by modulating vector mosquito population dynamics , viral replication , and transmission .",
"Dynamic modeling techniques can be used to examine how interactions among meteorological variables , vectors and the dengue virus influence transmission .",
"We de... | [
"Numerous studies have investigated meteorological and climatic influences on mosquito transmitted viruses .",
"However , dengue ecology is complex , necessitating an understanding of the interactions among components in the system .",
"We estimate dengue fever cases in San Juan , Puerto Rico using a mathematic... | 2015 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"vaccines",
"medicine",
"vaccination",
"complement system",
"clinical immunology",
"immunity",
"immunology",
"biology",
"microbiology",
"immune system"
] | The Effect of Human Factor H on Immunogenicity of Meningococcal Native Outer Membrane Vesicle Vaccines with Over-Expressed Factor H Binding Protein | journal.ppat.1002688 | null | [
[
"Neisseria meningitidis causes sepsis and meningitis with relatively high rates of fatalities or severe permanent sequelae [1] , [2] .",
"Licensed quadrivalent polysaccharide-protein conjugate vaccines are available against four capsular groups: A , C , W135 and Y . Development of conjugate vaccines again... | [
"The binding of human complement inhibitors to vaccine antigens in vivo could diminish their immunogenicity .",
"A meningococcal ligand for the complement down-regulator , factor H ( fH ) , is fH-binding protein ( fHbp ) , which is specific for human fH .",
"Vaccines containing recombinant fHbp or native outer ... | [
"Vaccines containing factor H-binding protein ( fHbp ) are being developed for protection against bacterial meningitis and sepsis caused by meningococci .",
"The antigen was identified from genomic sequences and only later found to bind a human complement protein , factor H ( fH ) , but not fH from non-human spec... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"sequencing techniques",
"phosphorylation",
"gene regulation",
"cell cycle and cell division",
"cell processes",
"circadian oscillators",
"chronobiology",
"molecular biology techniques",
"rna sequencing",
"research and analysis methods",
"small interfering rnas",
"proteins",
"gene expression... | G1/S cell cycle regulators mediate effects of circadian dysregulation on tumor growth and provide targets for timed anticancer treatment | journal.pbio.3000228 | A study of “jet-lagged” cells reveals a specific molecular mechanism regulating cell proliferation that it impacted by circadian disruption, underscoring the importance of administering anti-cancer treatment at a specific time of day. | [
[
"In response to day–night cycles produced by earth's 24-hour rotation around its axis , almost all living organisms have evolved circadian clocks , endogenous timekeeping systems that adapt physiology to daily changes in the environment .",
"In mammals , the circadian timing system consists of a central l... | [
"Circadian disruption has multiple pathological consequences , but the underlying mechanisms are largely unknown .",
"To address such mechanisms , we subjected transformed cultured cells to chronic circadian desynchrony ( CCD ) , mimicking a chronic jet-lag scheme , and assayed a range of cellular functions .",
... | [
"Circadian misalignment caused by altered sleep–wake cycles , shift work , or frequent jet lag increases susceptibility to several disorders , including cancer .",
"However , the mechanisms by which circadian disruption contributes to disease are not well understood , and so we addressed this issue by investigati... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"ecology",
"paleontology",
"biology",
"evolutionary biology"
] | Speciation and Extinction Drive the Appearance of Directional Range Size Evolution in Phylogenies and the Fossil Record | journal.pbio.1001260 | The appearance of directional trends in the evolution of species range sizes can arise from stochastic models and need not imply the existence of underlying trends. | [
[
"The geographic area occupied by a species is known to vary through time [1] , [2] , but whether these dynamics follow any regular trends or are instead largely idiosyncratic remains controversial [3]–[6] .",
"A number of recent studies , however , have revealed a remarkable pattern whereby the relative r... | [
"While the geographic range of a species is a fundamental unit of macroecology and a leading predictor of extinction risk , the evolutionary dynamics of species' ranges remain poorly understood .",
"Based on statistical associations between range size and species age , many studies have claimed support for genera... | [
"The changing distribution of species over the surface of the Earth , likened by Darwin to “a grand game of chess with the World for a board” , is a central theme in the evolution of life .",
"Studies of the fossil record and molecular estimates of species ages appear to show that species follow a predictable tre... | 2012 |
[
"Introduction",
"Methodology",
"Results",
"Discussion"
] | [
"infectious diseases/epidemiology and control of infectious diseases"
] | Reductions in the Prevalence and Incidence of Geohelminth Infections following a City-wide Sanitation Program in a Brazilian Urban Centre | journal.pntd.0000588 | null | [
[
"Soil-transmitted helminths , or geohelminths , form one of the most important groups of infectious agents and are the cause of serious global health problems; more than a billion people are currently infected by at least one species of this group of pathogens [1] .",
"At a global level , the most importa... | [
"In the city of Salvador , a large urban centre in Northeast Brazil , a city-wide sanitation intervention started in 1997 , aimed at improving the sewerage coverage of households from 26% to 80% .",
"Our aim was to study the impact of the intervention on the prevalence and incidence of geohelminths in the school-... | [
"In the city of Salvador , a large urban centre in Northeast Brazil , a city-wide sanitation intervention started in 1997 , aiming to improve the sewerage coverage of households from 26% to 80% .",
"Our aim was to study the impact of the intervention on the prevalence and incidence of geohelminths in the school-a... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"ecology",
"marine and aquatic sciences",
"biology",
"population biology",
"marine biology"
] | Using Grizzly Bears to Assess Harvest-Ecosystem Tradeoffs in Salmon Fisheries | journal.pbio.1001303 | Using grizzly bears as surrogates for “salmon ecosystem” function, the authors develop a generalizable ecosystem-based management framework that enables decision-makers to quantify ecosystem-harvest tradeoffs between wild and human recipients of natural resources like fish. | [
[
"Due to the impacts of fisheries on non-target species and ecological processes , there is growing pressure to apply ecosystem-based fisheries management ( EBFM ) [1]–[4] .",
"Guiding principles exist , but EBFM cannot be implemented without quantitative methods that can guide policy .",
"Additionally... | [
"Implementation of ecosystem-based fisheries management ( EBFM ) requires a clear conceptual and quantitative framework for assessing how different harvest options can modify benefits to ecosystem and human beneficiaries .",
"We address this social-ecological need for Pacific salmon fisheries , which are economic... | [
"Commercial fisheries that harvest salmon for human consumption can end up diverting nutrients that would normally be directed to terrestrial and aquatic ecosystems .",
"We examined this problem for Pacific salmon fisheries by using grizzly bears as indicators of salmon ecosystem function .",
"Bear densities va... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"soleus muscles",
"medicine and health sciences",
"toxins",
"pathology and laboratory medicine",
"metabolic processes",
"neuroscience",
"toxicology",
"toxic agents",
"paralysis",
"signs and symptoms",
"proteolysis",
"bioassays and physiological analysis",
"muscle electrophysiology",
"resea... | Botulinum neurotoxin C mutants reveal different effects of syntaxin or SNAP-25 proteolysis on neuromuscular transmission | journal.ppat.1006567 | null | [
[
"Few species of the bacterial genus Clostridium produce botulinum neurotoxins ( BoNTs ) , which cause the flaccid paralysis of botulism [1] .",
"BoNTs are divided into at least seven different serotypes ( BoNT/A to G ) that comprise an increasing number of subtypes [1–3] .",
"BoNTs are the most poison... | [
"Botulinum neurotoxin serotype C ( BoNT/C ) is a neuroparalytic toxin associated with outbreaks of animal botulism , particularly in birds , and is the only BoNT known to cleave two different SNARE proteins , SNAP-25 and syntaxin .",
"BoNT/C was shown to be a good substitute for BoNT/A1 in human dystonia therapy ... | [
"The seven established Botulinum Neurotoxins serotypes ( BoNT/A to G ) and the many BoNT subtypes , the causative agents of botulism , are the most poisonous substances known ( lethal doses in the low ng/kg range ) .",
"Due to their toxicological properties , BoNTs are Janus-faced toxins: potent pathogenic factor... | 2017 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"cell binding",
"blood serum",
"cell physiology",
"medicine and health sciences",
"body fluids",
"viral transmission and infection",
"microbiology",
"parasitic diseases",
"parasitic protozoans",
"protozoan life cycles",
"developmental biology",
"trypomastigotes",
"protozoans",
"epimastigot... | The Trypomastigote Small Surface Antigen (TSSA) regulates Trypanosoma cruzi infectivity and differentiation | journal.pntd.0005856 | null | [
[
"Trypanosoma cruzi is the protozoan agent of Chagas disease , of major medical and economic significance throughout Latin America , and an emergent threat to global public health [1] .",
"This parasite alternates between blood-sucking triatomine vectors and a wide spectrum of susceptible , mammalian hosts... | [
"TSSA ( Trypomastigote Small Surface Antigen ) is an antigenic , adhesion molecule displayed on the surface of Trypanosoma cruzi trypomastigotes .",
"TSSA displays substantial sequence identity to members of the TcMUC gene family , which code for the trypomastigote mucins ( tGPI-mucins ) .",
"In addition , TSSA... | [
"Infection with Trypanosoma cruzi produces a chronic and debilitating infectious disease known as Chagas disease , of major significance in Latin America and an emergent threat to global public health .",
"In the absence of vaccines and/or appropriate chemotherapies , the search for parasite effectors that suppor... | 2017 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"kala-azar",
"invertebrates",
"medicine and health sciences",
"tropical diseases",
"geographical locations",
"sand flies",
"parasitic diseases",
"animals",
"neglected tropical diseases",
"infectious disease control",
"insect vectors",
"bangladesh",
"agrochemicals",
"infectious diseases",
... | Effect of insecticide-treated bed nets on visceral leishmaniasis incidence in Bangladesh. A retrospective cohort analysis | journal.pntd.0007724 | null | [
[
"Visceral leishmaniasis ( VL ) —also known as kala-azar ( KA ) in the Indian sub-continent—is a deadly parasitic disease transmitted by the female Phlebotomus argentipes sand fly .",
"In the South-East Asia Region , humans are the only proven reservoir of the parasite , Leishmania donovani .",
"Kala-a... | [
"Visceral leishmaniasis ( VL ) is a parasitic disease , transmitted by the sand fly species Phlebotomus argentipes in the Indian sub-continent .",
"Effective vector control is highly desirable to reduce vector density and human and vector contact in the endemic communities with the aim to curtail disease transmis... | [
"Visceral leishmaniasis ( VL ) is a deadly parasitic disease , transmitted by the sand fly species Phlebotomus argentipes in the Indian sub-continent .",
"Humans are the only proven reservoir of the parasite , Leishmania donovani .",
"Effective vector control is highly desirable to reduce vector density and hum... | 2019 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious diseases",
"clinical immunology",
"immunology",
"parasitic diseases",
"immune response"
] | Stage Progression and Neurological Symptoms in Trypanosoma brucei rhodesiense Sleeping Sickness: Role of the CNS Inflammatory Response | journal.pntd.0001857 | null | [
[
"Human African trypanosomiasis ( HAT ) , also known as Sleeping Sickness , is caused by the protozoan hemoflagellate Trypanosoma brucei ssp .",
"After inoculation of the parasite by the tsetse fly vector , the disease progresses through two stages .",
"In the hemolymphatic , or early stage of disease ... | [
"Human African trypanosomiasis progresses from an early ( hemolymphatic ) stage , through CNS invasion to the late ( meningoencephalitic ) stage .",
"In experimental infections disease progression is associated with neuroinflammatory responses and neurological symptoms , but this concept requires evaluation in Af... | [
"Human African trypanosomiasis , caused by the parasites Trypanosoma brucei rhodesiense and T . b . gambiense , is clinically defined by two diagnostic stages , an early stage where the parasites appear to be localised to the blood and lymphatic systems , and a late stage where the parasites are also localised in t... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Site-Directed Spin Labeling Reveals Pentameric Ligand-Gated Ion Channel Gating Motions | journal.pbio.1001714 | null | [
[
"Chemical signaling in the brain and periphery relies on the rapid opening and closing of pentameric ligand-gated ion channels ( pLGICs ) , which include nicotinic acetylcholine ( nAChRs ) , serotonin-type-3 ( 5-HT3Rs ) , γ-aminobutyric acid-A ( GABAARs ) , and glycine ( GlyRs ) receptors [1] .",
"These r... | [
"Pentameric ligand-gated ion channels ( pLGICs ) are neurotransmitter-activated receptors that mediate fast synaptic transmission .",
"In pLGICs , binding of agonist to the extracellular domain triggers a structural rearrangement that leads to the opening of an ion-conducting pore in the transmembrane domain and ... | [
"Ligand-gated ion channels reside in the membranes of nerve and muscle cells .",
"These proteins form channels that span the membrane , where they transduce chemical signals into changes in electrical excitability .",
"Neurotransmitters bind to the extracellular surface of these proteins to trigger global struc... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"complement system",
"immunology",
"microbiology",
"host-pathogen interaction",
"immune defense",
"bacterial pathogens",
"mycology",
"medical microbiology",
"microbial pathogens",
"biology",
"yeast",
"immune system",
"immunity",
"innate immunity"
] | Microbes Bind Complement Inhibitor Factor H via a Common Site | journal.ppat.1003308 | null | [
[
"Complement system ( C ) is an important part of innate immunity in human plasma , and the alternative pathway of complement ( AP ) is the first line of defense against invading microbes .",
"AP is spontaneously activated on all unprotected surfaces leading to covalent binding of the main complement opson... | [
"To cause infections microbes need to evade host defense systems , one of these being the evolutionarily old and important arm of innate immunity , the alternative pathway of complement .",
"It can attack all kinds of targets and is tightly controlled in plasma and on host cells by plasma complement regulator fac... | [
"Complement is an important arm of innate immunity .",
"Activation of this plasma protein cascade leads to opsonization of targets for phagocytosis , direct lysis of Gram-negative bacteria , and enhancement of the inflammatory and acquired immune responses .",
"No specific signal is needed for activation of the... | 2013 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"education",
"behavioral and social aspects of health",
"engineering and technology",
"sociology",
"tropical diseases",
"social sciences",
"neuroscience",
"parasitic diseases",
"health care",
"academic skills",
"cognitive psychology",
"global health",
"liter... | Rural youths' understanding of gene x environmental contributors to heritable health conditions: The case of podoconiosis in Ethiopia | journal.pntd.0006763 | null | [
[
"Advances in genomics are increasing scientific understanding that most health conditions worldwide are caused by the joint influence of genetic and environmental ( GxE ) factors [1] .",
"However , the mechanisms underlying GxE interactions are complex and not well understood by the public [2] .",
"Ac... | [
"Assess the feasibility of engaging youth to disseminate accurate information about gene by environmental ( GxE ) influences on podoconiosis , a neglected tropical lymphedema endemic in southern Ethiopia .",
"A cross sectional survey was conducted with 377 youth randomly selected from 2 districts of Southern Ethi... | [
"This study considers the feasibility of engaging rural Ethiopian youth as lay health workers ( LHWs ) with the objective to improve community understanding of the joint influences of genetics and environment on health .",
"Identifying LHWs to accurately convey contributors to the heritable but preventable neglec... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"molecular biology/bioinformatics",
"cell biology/cell growth and division",
"computational biology/synthetic biology",
"computer science"
] | Molecular Predictors of 3D Morphogenesis by Breast Cancer Cell Lines in 3D Culture | journal.pcbi.1000684 | null | [
[
"Genome-wide association studies of expression and clinical data have emerged as a powerful methodology for identifying biomarkers of human diseases .",
"While the literature is rich with supervised or unsupervised clustering of genomic information [1] , methods for studying the relationships between geno... | [
"Correlative analysis of molecular markers with phenotypic signatures is the simplest model for hypothesis generation .",
"In this paper , a panel of 24 breast cell lines was grown in 3D culture , their morphology was imaged through phase contrast microscopy , and computational methods were developed to segment a... | [
"Cell culture models are an important vehicle for understanding biological processes and evaluation of therapeutic reagents .",
"More importantly , the literature suggests that tumor cells grown in 3D exhibit pronounced drug and radiation resistances that are remarkably similar to that of tumors in vivo .",
"Th... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"none",
"infectious diseases",
"public health and epidemiology",
"computational biology"
] | Can Influenza Epidemics Be Prevented by Voluntary Vaccination? | journal.pcbi.0030085 | null | [
[
"Previously , both complex [1–3] and simple models [4–7] of influenza transmission dynamics have been analyzed to determine what proportion of the population would need to be vaccinated to prevent influenza epidemics and pandemics .",
"However , none of these modeling studies have shown whether this criti... | [
"Previous modeling studies have identified the vaccination coverage level necessary for preventing influenza epidemics , but have not shown whether this critical coverage can be reached .",
"Here we use computational modeling to determine , for the first time , whether the critical coverage for influenza can be a... | [
"Currently , a major public health concern is the next influenza pandemic; yet it remains unclear how to control such a crisis .",
"By using novel mathematical modeling techniques , here we predict the likely impact of voluntary vaccination programs on controlling influenza epidemics and pandemics .",
"We const... | 2007 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine and health sciences",
"muscle tissue",
"enzymes",
"enzymology",
"simulation and modeling",
"camp signaling cascade",
"lyases",
"cellular structures and organelles",
"research and analysis methods",
"animal cells",
"proteins",
"coated pits",
"biological tissue",
"chemistry",
"ce... | A Computational Modeling and Simulation Approach to Investigate Mechanisms of Subcellular cAMP Compartmentation | journal.pcbi.1005005 | null | [
[
"For nearly 40 years , subcellular compartmentation has been offered as an explanation for how cAMP , the ubiquitous and diffusible second messenger , can both regulate a multitude of cellular functions and elicit specific and selective responses .",
"Despite widespread recognition of the importance of cA... | [
"Subcellular compartmentation of the ubiquitous second messenger cAMP has been widely proposed as a mechanism to explain unique receptor-dependent functional responses .",
"How exactly compartmentation is achieved , however , has remained a mystery for more than 40 years .",
"In this study , we developed comput... | [
"Subcellular compartmentation of the ubiquitous second messenger cAMP has been widely proposed as a mechanism to explain how this one signaling molecule produces unique receptor-dependent functional responses .",
"But , how exactly compartmentation occurs , is unknown .",
"This is because there has been no way ... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"evolutionary biology",
"protein folding",
"evolutionary modeling",
"biology",
"computational biology",
"evolutionary selection",
"biophysics",
"evolutionary processes"
] | Evolutionary Optimization of Protein Folding | journal.pcbi.1002861 | null | [
[
"The catalog of naturally occurring protein structures [1] exhibits a large disparity of folding times ( from microseconds [2] , to hours [3] ) .",
"This disparity is the result of roughly 3 . 8 billion years of evolution during which new protein structures were created and optimized .",
"The evolutio... | [
"Nature has shaped the make up of proteins since their appearance , 3 . 8 billion years ago .",
"However , the fundamental drivers of structural change responsible for the extraordinary diversity of proteins have yet to be elucidated .",
"Here we explore if protein evolution affects folding speed .",
"We esti... | [
"Nature has come up with an enormous variety of protein three-dimensional structures , each of which is thought to be optimized for its specific function .",
"A fundamental biological endeavor is to uncover the driving evolutionary forces for discovering and optimizing new folds .",
"A long-standing hypothesis ... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biochemistry",
"rna",
"rna structure",
"proteins",
"enzymes",
"chaperone proteins",
"biology and life sciences",
"enzymology",
"rna stability",
"long non-coding rnas",
"ribozymes"
] | DEAD-Box Helicase Proteins Disrupt RNA Tertiary Structure Through Helix Capture | journal.pbio.1001981 | Single-molecule fluorescence experiments reveal how DEAD-box proteins unfold structured RNAs to promote conformational transitions and refolding to the native functional state. | [
[
"Structured RNAs are involved in many essential biological processes such as pre-mRNA splicing , regulation of gene expression , protein synthesis , and maintenance of chromosome ends [1]–[5] .",
"These functions require the RNAs to fold into specific structures and , for some , to transition between func... | [
"DEAD-box helicase proteins accelerate folding and rearrangements of highly structured RNAs and RNA–protein complexes ( RNPs ) in many essential cellular processes .",
"Although DEAD-box proteins have been shown to use ATP to unwind short RNA helices , it is not known how they disrupt RNA tertiary structure .",
... | [
"In addition to carrying genetic information from DNA to protein , RNAs function in many essential cellular processes .",
"This often requires the RNA to form a specific three-dimensional structure , and some functions require cycling between multiple structures .",
"However , RNAs have a strong propensity to b... | 2014 |
[
"Introduction",
"Results/Discussion",
"Materials and Methods"
] | [
"cellular stress responses",
"gene regulation",
"regulatory proteins",
"dna-binding proteins",
"microbiology",
"dna transcription",
"gene function",
"prokaryotic models",
"model organisms",
"molecular genetics",
"applied microbiology",
"cofactors",
"proteins",
"gene expression",
"compara... | CorE from Myxococcus xanthus Is a Copper-Dependent RNA Polymerase Sigma Factor | journal.pgen.1002106 | null | [
[
"Myxococcus xanthus is a soil-dwelling δ-proteobacterium of the group of myxobacteria used as a model to study multicellular behavior and differentiation , because it exhibits a complex developmental cycle triggered by starvation [1] .",
"However , M . xanthus cells not only have to adapt their metabolism... | [
"The dual toxicity/essentiality of copper forces cells to maintain a tightly regulated homeostasis for this metal in all living organisms , from bacteria to humans .",
"Consequently , many genes have previously been reported to participate in copper detoxification in bacteria .",
"Myxococcus xanthus , a prokary... | [
"Copper exerts a dual effect on living organisms .",
"It is essential for life , but an excess provokes cell damage , forcing cells to maintain a regulated homeostasis for this metal . These two antagonistic biological effects of copper are clearly illustrated by two human genetic disorders , Menkes syndrome and ... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"syllables",
"linguistics",
"medicine and health sciences",
"diagnostic radiology",
"functional magnetic resonance imaging",
"engineering and technology",
"signal processing",
"social sciences",
"neuroscience",
"magnetic resonance imaging",
"simulation and modeling",
"brain mapping",
"comput... | Prediction Errors but Not Sharpened Signals Simulate Multivoxel fMRI Patterns during Speech Perception | journal.pbio.1002577 | Neuroimaging and computational modelling explain how the human brain uses prior expectations to improve our perception of degraded speech. | [
[
"The observation that our perception of the world not only depends on sensory input but also on our prior knowledge has been of longstanding interest in psychology [1] and neuroscience [2–5] .",
"There is widespread agreement that sensory input and prior knowledge are combined in neural representations; b... | [
"Successful perception depends on combining sensory input with prior knowledge .",
"However , the underlying mechanism by which these two sources of information are combined is unknown .",
"In speech perception , as in other domains , two functionally distinct coding schemes have been proposed for how expectati... | [
"Perception inevitably depends on combining sensory input with prior expectations .",
"This is particularly critical for identifying degraded input .",
"However , the underlying neural mechanism by which expectations influence sensory processing is unclear .",
"Predictive Coding theories suggest that the brai... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"infectious diseases",
"microbiology",
"genetics and genomics"
] | The Parasexual Cycle in Candida albicans Provides an Alternative Pathway to Meiosis for the Formation of Recombinant Strains | journal.pbio.0060110 | The opportunistic pathogen Candida albicans has a cryptic parasexual mating cycle involving epigenetic switching and chromosome loss. This study demonstrates that genetic recombination occurs during the mating cycle and that this requires the activity of Spo11, a protein necessary for meiotic recombination in other euk... | [
[
"In most sexually reproducing eukaryotes , meiosis is used to precisely halve the DNA content in the cell , often for the formation of haploid gametes from diploid precursor cells .",
"This specialized form of cell division involves one round of DNA replication followed by two successive rounds of DNA div... | [
"Candida albicans has an elaborate , yet efficient , mating system that promotes conjugation between diploid a and α strains .",
"The product of mating is a tetraploid a/α cell that must undergo a reductional division to return to the diploid state .",
"Despite the presence of several “meiosis-specific” genes i... | [
"Candida albicans is an important human fungal pathogen that has an unconventional sexual cycle .",
"Efficient mating requires that diploid cells of opposite mating type first switch from the more common “white” phase to the “opaque” phase and then undergo cell fusion .",
"The resulting tetraploid strains can r... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"ecology and environmental sciences",
"population genetics",
"geographical locations",
"human genomics",
"invertebrate genomics",
"simulation and modeling",
"dna",
"population biology",
"research and analysis methods",
"europe",
"ecological metrics",
"genomics",
"species diversity",
"anima... | Human demographic history has amplified the effects of background selection across the genome | journal.pgen.1007387 | null | [
[
"Genetic diversity within a species is shaped by the complex interplay of mutation , demography , genetic drift , and natural selection .",
"These evolutionary forces operate in concert to shape patterns of diversity at both the local scale and genome-wide scale .",
"For example , in recombining speci... | [
"Natural populations often grow , shrink , and migrate over time .",
"Such demographic processes can affect genome-wide levels of genetic diversity .",
"Additionally , genetic variation in functional regions of the genome can be altered by natural selection , which drives adaptive mutations to higher frequencie... | [
"Patterns of genetic diversity within a species are affected at broad and fine scales by population size changes ( “demography” ) and natural selection .",
"From both population genetics theory and observation on genomic sequence data , it is known that demography can alter genome-wide average neutral genetic div... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"immune system proteins",
"biochemistry",
"protein interactions",
"proteins",
"protein structure",
"biology",
"computational biology",
"proteomics",
"protein engineering",
"macromolecular structure analysis"
] | Computational Design of the Affinity and Specificity of a Therapeutic T Cell Receptor | journal.pcbi.1003478 | null | [
[
"T cell receptors ( TCRs ) are key elements of adaptive immunity , as they specifically recognize antigenic peptides bound to MHC proteins ( pMHCs ) on cell surfaces and are responsible for initiating immune responses against targeted cells .",
"The TCR-pMHC interaction is of considerable importance in he... | [
"T cell receptors ( TCRs ) are key to antigen-specific immunity and are increasingly being explored as therapeutics , most visibly in cancer immunotherapy .",
"As TCRs typically possess only low-to-moderate affinity for their peptide/MHC ( pMHC ) ligands , there is a recognized need to develop affinity-enhanced T... | [
"T cell receptors ( TCRs ) play a major role in immunity , recognizing peptide antigens presented by major histocompatibility complex proteins .",
"Due to their capacity to target intracellularly produced proteins and initiate cell killing , there is significant interest developing TCR-based therapeutic strategie... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"oncology",
"medicine and health sciences",
"cancer genetics",
"ewing sarcoma",
"genetics",
"biology and life sciences",
"cancers and neoplasms",
"sarcomas"
] | The Genomic Landscape of the Ewing Sarcoma Family of Tumors Reveals Recurrent STAG2 Mutation | journal.pgen.1004475 | null | [
[
"The Ewing sarcoma family of tumors ( EFT ) is a group of malignant small round blue cell tumors that arise in bone or soft tissue .",
"Ewing sarcoma ( ES ) is the second most common type of primary bone tumor to affect children and adolescents and accounts for 2 . 9% of all childhood cancers [1] .",
... | [
"The Ewing sarcoma family of tumors ( EFT ) is a group of highly malignant small round blue cell tumors occurring in children and young adults .",
"We report here the largest genomic survey to date of 101 EFT ( 65 tumors and 36 cell lines ) .",
"Using a combination of whole genome sequencing and targeted sequen... | [
"The Ewing sarcoma family of tumors is a group of aggressive cancers that primarily affects the pediatric and young adult population .",
"Increasingly , genomics are being used to better define the disease biology and to identify targets for therapy in many cancer types .",
"Here , we report one of the first an... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"computational biology/literature analysis",
"computational biology/genomics"
] | On the Growth of Scientific Knowledge: Yeast Biology as a Case Study | journal.pcbi.1000320 | null | [
[
"Scientific knowledge refers to the body of facts and principles that are known in a given field .",
"Modern civilization is built on the knowledge that humans have acquired about the world they live in , and the future of the human species and society critically depends on further accumulation of scienti... | [
"The tempo and mode of human knowledge expansion is an enduring yet poorly understood topic .",
"Through a temporal network analysis of three decades of discoveries of protein interactions and genetic interactions in baker's yeast , we show that the growth of scientific knowledge is exponential over time and that... | [
"It is of great interest to understand the patterns and mechanisms of scientific knowledge growth , but such studies have been hampered by the lack of ideal cases in which the structure of the knowledge is known , the knowledge is quantifiable , and the process of knowledge discovery is well understood and document... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine and health sciences",
"pathology and laboratory medicine",
"microbial cultures",
"pathogens",
"vibrio",
"biological cultures",
"tropical diseases",
"microbiology",
"geographical locations",
"vaccines",
"diarrhea",
"bacterial diseases",
"vibrio cholerae",
"signs and symptoms",
"... | Use of oral cholera vaccine as a vaccine probe to determine the burden of culture-negative cholera | journal.pntd.0007179 | null | [
[
"An estimated 2 . 9 million cases and 95 000 deaths occur each year due to cholera , caused primarily by Vibrio cholerae ( V . cholerae ) O1 , in endemic countries [1] .",
"Until now , microbiological cultures of stools have provided an accepted gold standard for diagnosing cholera in patients with diarrh... | [
"Analyses of stool from patients with acute watery diarrhea ( AWD ) using sensitive molecular diagnostics have challenged whether fecal microbiological cultures have acceptably high sensitivity for cholera diagnosis .",
"If true , these findings imply that current estimates of the global burden of cholera , which... | [
"Conventional microbiological culture has remained a relatively uncontested ‘gold standard’ for the diagnosis of cholera; however , emerging methods , including sensitive molecular tests , challenge the current paradigm .",
"One pivotal article demonstrated that culture failed to detect cholera in one-third of th... | 2019 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"infectious disease epidemiology",
"epidemiology",
"biology and life sciences",
"population biology"
] | Statistical Modeling Reveals the Effect of Absolute Humidity on Dengue in Singapore | journal.pntd.0002805 | null | [
[
"Dengue fever ( DF ) is the most common vector-borne viral disease in humans and is distributed worldwide , mainly in tropical and subtropical countries .",
"In recent decades , dengue has been expanding globally possibly due to climate change [1] and highly intra and extra-country connectivity through tr... | [
"Weather factors are widely studied for their effects on indicating dengue incidence trends .",
"However , these studies have been limited due to the complex epidemiology of dengue , which involves dynamic interplay of multiple factors such as herd immunity within a population , distinct serotypes of the virus , ... | [
"As dengue virus transmission is through a human-to-mosquito-to-human cycle , the influence of meteorological factors on dengue is likely to be associated with their impact on mosquito populations and behavior .",
"Other than the influence of weather factors , the shift of dominant serotypes and pre-emptive measu... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Prp4 Kinase Grants the License to Splice: Control of Weak Splice Sites during Spliceosome Activation | journal.pgen.1005768 | null | [
[
"Introns are removed from pre-mRNAs by spliceosomes , which are highly dynamic macromolecular complexes consisting of five small nuclear RNAs ( snRNAs; U1 , U2 , U5 , and U4/U6 ) associated with specific proteins in subcomplexes called snRNPs .",
"In vitro , spliceosomal subcomplexes assemble on pre-mRNAs... | [
"The genome of the fission yeast Schizosaccharomyces pombe encodes 17 kinases that are essential for cell growth .",
"These include the cell-cycle regulator Cdc2 , as well as several kinases that coordinate cell growth , polarity , and morphogenesis during the cell cycle .",
"In this study , we further characte... | [
"Prp4 is an essential protein kinase that is involved in the splicing of some introns .",
"Using a conditional mutant of Prp4 , we showed that a subset of genes , including several cell cycle–regulatory genes , are dependent on Prp4 for splicing .",
"Furthermore , we could convert genes between Prp4-dependent a... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"neuroscience/sensory systems",
"computational biology/computational neuroscience",
"computational biology/systems biology"
] | Asymmetric Excitatory Synaptic Dynamics Underlie Interaural Time Difference Processing in the Auditory System | journal.pbio.1000406 | In order to localize sounds in the environment, the auditory system detects and encodes differences in signals between each ear. The exquisite sensitivity of auditory brain stem neurons to the differences in rise time of the excitation signals from the two ears allows for neuronal encoding of microsecond interaural tim... | [
[
"In order to localize acoustic objects along the horizontal plane , the nervous system is able to distinguish microsecond differences in the arrival time of sound at the two ears , referred to as interaural time differences ( ITDs ) .",
"Low sound frequencies are the most useful signals for detecting ITDs... | [
"Low-frequency sound localization depends on the neural computation of interaural time differences ( ITD ) and relies on neurons in the auditory brain stem that integrate synaptic inputs delivered by the ipsi- and contralateral auditory pathways that start at the two ears .",
"The first auditory neurons that resp... | [
"Animals can locate the source of a sound by detecting microsecond differences in the arrival time of sound at the two ears .",
"Neurons encoding these interaural time differences ( ITDs ) receive an excitatory synaptic input from each ear .",
"They can perform a microsecond computation with excitatory synapses... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"caenorhabditis",
"neuroscience"
] | Food Deprivation Attenuates Seizures through CaMKII and EAG K+ Channels | journal.pgen.0030156 | null | [
[
"The excitability of neuromuscular circuits must be regulated to ensure appropriate behavioral responses under different conditions .",
"When cell excitability is irregular due to channelopathy defects , inappropriate motor output can lead to different medical conditions .",
"One member of the ether-a... | [
"Accumulated research has demonstrated the beneficial effects of dietary restriction on extending lifespan and increasing cellular stress resistance .",
"However , reducing nutrient intake has also been shown to direct animal behaviors toward food acquisition .",
"Under food-limiting conditions , behavioral cha... | [
"We investigated the mechanisms used during dietary stress conditions that regulate the behavioral output of excitable cells .",
"In the roundworm Caenorhabditis elegans , males must display the proper behavioral response to potential food sources or mating partners .",
"This regulation is disrupted by loss of ... | 2007 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"circuit models",
"computational neuroscience",
"biology",
"neuroscience",
"coding mechanisms"
] | Efficient “Communication through Coherence” Requires Oscillations Structured to Minimize Interference between Signals | journal.pcbi.1002760 | null | [
[
"Task-dependent changes in the power and inter-region coherence of oscillatory network activity are observed in many brain regions and behavioral tasks [1]–[3] .",
"A possible function of such activity is to modulate functional connectivity among anatomically connected regions [4]–[6] .",
"This may pl... | [
"The ‘communication through coherence’ ( CTC ) hypothesis proposes that selective communication among neural networks is achieved by coherence between firing rate oscillation in a sending region and gain modulation in a receiving region .",
"Although this hypothesis has stimulated extensive work , it remains uncl... | [
"Distributed regions of mammalian brains transiently engage in coherent oscillations , often at specific stages of behavioral or cognitive tasks .",
"This activity may play a role in controlling information flow among connected regions , allowing the brain's connectivity structure to be flexibly reconfigured in r... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"auditory system",
"developmental biology",
"gene identification and analysis",
"genetics",
"molecular genetics",
"biology",
"sensory systems",
"neuroscience",
"genetics and genomics",
"cell differentiation",
"gene function"
] | A Mutation in the Srrm4 Gene Causes Alternative Splicing Defects and Deafness in the Bronx Waltzer Mouse | journal.pgen.1002966 | null | [
[
"Hair cells of the hearing and balance organs are specialized mechanoreceptors that convert mechanical stimuli to electrical signals .",
"These signals are transmitted to the central nervous system via connecting afferent neurons .",
"Hair cells of the hearing organ are specialized further as inner ha... | [
"Sensory hair cells are essential for hearing and balance .",
"Their development from epithelial precursors has been extensively characterized with respect to transcriptional regulation , but not in terms of posttranscriptional influences .",
"Here we report on the identification and functional characterization... | [
"The identification of novel deafness-causing mutations has been instrumental in revealing unexpected mechanisms that are required for development of the sound- and gravity-sensing hair cells of the inner ear .",
"The Bronx waltzer ( bv ) mouse is characterized by defects in hair-cell development , as well as by ... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"infectious diseases/hiv infection and aids",
"immunology/immune response",
"microbiology/immunity to infections"
] | HIV-1 gp41 and TCRα Trans-Membrane Domains Share a Motif Exploited by the HIV Virus to Modulate T-Cell Proliferation | journal.ppat.1001085 | null | [
[
"The transmembrane domains ( TMDs ) of the T-cell receptor ( TCR ) play an important role in the assembly of the receptor complex .",
"The mosaic assembly of the TCR complex , composed of the TCR-α and β subunits and the invariant CD3 co-receptor chains , gives rise to one of the most remarkable and compl... | [
"Viruses have evolved several strategies to modify cellular processes and evade the immune response in order to successfully infect , replicate , and persist in the host .",
"By utilizing in-silico testing of a transmembrane sequence library derived from virus protein sequences , we have pin-pointed a nine amino-... | [
"HIV uses several mechanisms that allow it to evade immune control , in order to successfully infect , replicate , and persist in the host .",
"Here we report a new mechanism .",
"We utilized bioinformatics and identified a region within the transmembrane domain ( TMD ) of the envelop proteins of viruses that h... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genetics and genomics",
"developmental biology/aging"
] | The Anticonvulsant Ethosuximide Disrupts Sensory Function to Extend C. elegans Lifespan | journal.pgen.1000230 | null | [
[
"Pharmacological compounds that extend lifespan could delay the progression of age-related degenerative changes and age-related illnesses such as Alzheimer's disease and cardiovascular disease .",
"In addition , the characterization of drugs that extend lifespan can elucidate endogenous mechanisms involve... | [
"Ethosuximide is a medication used to treat seizure disorders in humans , and we previously demonstrated that ethosuximide can delay age-related changes and extend the lifespan of the nematode Caenorhabditis elegans .",
"The mechanism of action of ethosuximide in lifespan extension is unknown , and elucidating ho... | [
"Aging is a major factor that contributes to disease and disability in humans , but no medicines have been demonstrated to delay human aging .",
"We previously conducted a screen for FDA-approved drugs that can extend the lifespan of the nematode worm C . elegans , resulting in the identification of ethosuximide ... | 2008 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [] | Discrimination between E. granulosus sensu stricto, E. multilocularis and E. shiquicus Using a Multiplex PCR Assay | journal.pntd.0004084 | null | [
[
"In the most recent taxonomic revision , nine species were recognized in the genus Echinococcus [1] .",
"Of these , the most important and widespread are E . granulosus sensu stricto ( genotypes G1-G3 ) and E . multilocularis , which cause cystic echinococcosis ( CE ) and alveolar echinococcosis ( AE ) , ... | [
"Infections of Echinococcus granulosus sensu stricto ( s . s ) , E . multilocularis and E . shiquicus are commonly found co-endemic on the Qinghai-Tibet plateau , China , and an efficient tool is needed to facilitate the detection of infected hosts and for species identification .",
"A single-tube multiplex PCR a... | [
"The canid adapted intestinal tapeworms , Echinococcus granulosus , E . multilocularis and E . shuiqucus are well known to be endemic in Northwestern China .",
"The first two species can cause fatal disease in humans .",
"Although E . shiquicus has not been reported to infect humans , all three species can be t... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"auditory system",
"developmental neuroscience",
"biology and life sciences",
"sensory systems",
"neuroscience",
"neural circuit formation"
] | Mutation of Npr2 Leads to Blurred Tonotopic Organization of Central Auditory Circuits in Mice | journal.pgen.1004823 | null | [
[
"The sense of hearing is mediated by precisely organized neural circuits that encode the frequency content , timing , and intensity of sounds .",
"Frequency information is encoded in the spatial organization of hair cells in the cochlea , with high frequencies detected in the base and low frequencies in t... | [
"Tonotopy is a fundamental organizational feature of the auditory system .",
"Sounds are encoded by the spatial and temporal patterns of electrical activity in spiral ganglion neurons ( SGNs ) and are transmitted via tonotopically ordered processes from the cochlea through the eighth nerve to the cochlear nuclei ... | [
"Millions of people suffer from debilitating hearing defects , ranging from a complete inability to detect sound to more subtle changes in how sounds are encoded by the nervous system .",
"Many forms of deafness are due to mutations in genes that impair the development or function of hair cells , which are respon... | 2014 |
[
"Introduction",
"Results and Discussion",
"Materials and Methods"
] | [
"bacteriology",
"genome-wide association studies",
"medicine and health sciences",
"pathology and laboratory medicine",
"pathogens",
"variant genotypes",
"brassica",
"microbiology",
"plant physiology",
"genetic mapping",
"plant science",
"model organisms",
"genome analysis",
"plant patholo... | Differentiation between MAMP Triggered Defenses in Arabidopsis thaliana | journal.pgen.1006068 | null | [
[
"Pathogens pose a constant threat to their hosts .",
"While lacking the adaptive immune system present in mammals , plants have evolved a two-tiered immune system of considerable specificity .",
"The first tier of defense involves the recognition of microbe associated molecular patterns ( MAMPs ) that... | [
"A first line of defense against pathogen attack for both plants and animals involves the detection of microbe-associated molecular patterns ( MAMPs ) , followed by the induction of a complex immune response .",
"Plants , like animals , encode several receptors that recognize different MAMPs .",
"While these re... | [
"Specialized receptors encoded by plants detect different components of bacterial machinery , and initiate an immune response .",
"These recognition events are thought to induce largely redundant defense signaling , the magnitude of which varies quantitatively among populations , perhaps in response to environmen... | 2016 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"body fluids",
"pathology and laboratory medicine",
"european union",
"cost-effectiveness analysis",
"economic analysis",
"pathogens",
"blood counts",
"geographical locations",
"microbiology",
"social sciences",
"habits",
"retroviruses",
"viruses",
"rna vi... | Low prevalence of HTLV1/2 infection in a population of immigrants living in southern Italy | journal.pntd.0006601 | null | [
[
"Human T cell leukemia virus type 1 ( HTLV-1 ) or 2 ( HTLV-2 ) infection has a worldwide distribution , with an estimate of up to 15–20 million people affected [1] .",
"The prevalence changes substantially according to the geographical area , and is higher in specific risk groups such as intravenous drug ... | [
"To assess the prevalence of HTLV-1 and HTLV-2 infections in a cohort of immigrants living in southern Italy .",
"We screened for antibody to HTLV-1/2 infection 1 , 498 consecutive immigrants born in endemic areas ( sub-Saharan Africa or southern-Asia ) by a commercial chemiluminescent microparticle immunoassay .... | [
"As in Italy the immigrants constitute one tenth of the whole population and its contribution to blood donation is strongly desired we believe that to start screening for HTLV-1 and HTLV-2 infections in all donors from endemic countries at least on their first donation is a practice useful for a correct cost-effect... | 2018 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"public health and epidemiology/epidemiology",
"infectious diseases/viral infections",
"public health and epidemiology/infectious diseases",
"ecology/population ecology",
"infectious diseases/epidemiology and control of infectious diseases"
] | Effects of a Five-Year Citywide Intervention Program To Control Aedes aegypti and Prevent Dengue Outbreaks in Northern Argentina | journal.pntd.0000427 | null | [
[
"The global incidence of dengue has increased exponentially since 1955 to reach 1–50 million infections per year in 2000–2005 [1] .",
"Dengue has become the most important arboviral disease of humans , and an increasing urban health and economic problem in tropical and subtropical regions worldwide .",
... | [
"Dengue has propagated widely through the Americas .",
"Most countries have not been able to maintain permanent larval mosquito control programs , and the long-term effects of control actions have rarely been documented .",
"The study design was based on a before-and-after citywide assessment of Aedes aegypti l... | [
"Dengue has become the most important viral disease of humans transmitted by arthropods in tropical and subtropical urban regions .",
"Most countries have not been able to maintain permanent larval mosquito control programs against Aedes aegypti , the main vector of dengue and yellow fever , partly because of mis... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genetics and genomics/genomics",
"developmental biology/embryology",
"genetics and genomics/gene expression",
"developmental biology/pattern formation",
"genetics and genomics/chromosome biology",
"developmental biology/developmental molecular mechanisms"
] | Noncanonical Compensation of Zygotic X Transcription in Early Drosophila melanogaster Development Revealed through Single-Embryo RNA-Seq | journal.pbio.1000590 | Mmany genes from the X chromosome are expressed at the same level in female and male embryos during early Drosophila development, prior to the establishment of MSL-mediated dosage compensation, suggesting the existence of a novel mechanism. | [
[
"The earliest stages of animal development are under maternal control until mRNAs deposited prior to fertilization degrade and zygotic transcription is initiated during a period known as the maternal to zygotic transition ( MZT ) .",
"In Drosophila melanogster , the MZT occurs amidst the 14 rapid and sync... | [
"When Drosophila melanogaster embryos initiate zygotic transcription around mitotic cycle 10 , the dose-sensitive expression of specialized genes on the X chromosome triggers a sex-determination cascade that , among other things , compensates for differences in sex chromosome dose by hypertranscribing the single X ... | [
"Variation in gene dose can have profound effects on animal development .",
"Yet every generation , animals must cope with differences in sex chromosome numbers .",
"Drosophila compensate for the difference in X chromosome dosage ( two in females , one in males ) with a mechanism that allows for more transcript... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"genome expression analysis",
"neurobiology of disease and regeneration",
"animal genetics",
"genetic mutation",
"gene regulation",
"neuroscience",
"dna transcription",
"gene function",
"animal models",
"retinal disorders",
"model organisms",
"molecular genetics",
"gene express... | Mechanistically Distinct Mouse Models for CRX-Associated Retinopathy | journal.pgen.1004111 | null | [
[
"CRX ( Accession: AAH53672 . 1 ) is an Otd/OTX-like ‘paired’ homeodomain transcription factor that is preferentially expressed in vertebrate rod and cone photoreceptor cells in the retina and pinealocytes in the brain [1] , [2] .",
"CRX plays an essential role in the development and maintenance of functio... | [
"Cone-rod homeobox ( CRX ) protein is a “paired-like” homeodomain transcription factor that is essential for regulating rod and cone photoreceptor transcription .",
"Mutations in human CRX are associated with the dominant retinopathies Retinitis Pigmentosa ( RP ) , Cone-Rod Dystrophy ( CoRD ) and Leber Congenital... | [
"The transcription factor Cone-Rod Homeobox ( CRX ) plays a central role in regulating gene expression of rod and cone photoreceptors , the primary light sensing cells of the retina .",
"Mutations in the human CRX gene have been associated with the retinal degeneration diseases Retinitis Pigmentosa ( RP ) , Cone-... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"vero cells",
"medicine and health sciences",
"coronaviruses",
"luciferase",
"pathology and laboratory medicine",
"enzymes",
"pathogens",
"sars coronavirus",
"biological cultures",
"microbiology",
"enzymology",
"viruses",
"rna viruses",
"research and analysis methods",
"infectious diseas... | The papain-like protease determines a virulence trait that varies among members of the SARS-coronavirus species | journal.ppat.1007296 | null | [
[
"The coronaviruses ( CoV , family Coronaviridae ) are among the most relevant groups of viruses with zoonotic potential .",
"CoVs are large , positive-sense , single-stranded RNA viruses that cause acute and prolonged infections in a variety of mammals and birds .",
"Pathogenic human CoVs include memb... | [
"SARS-coronavirus ( CoV ) is a zoonotic agent derived from rhinolophid bats , in which a plethora of SARS-related , conspecific viral lineages exist .",
"Whereas the variability of virulence among reservoir-borne viruses is unknown , it is generally assumed that the emergence of epidemic viruses from animal reser... | [
"Novel detection and sequencing technologies have greatly improved our knowledge of virus diversity in nature .",
"Metaviromic screening of zoonotic animal reservoirs has become an established approach in pathogen surveillance and pandemic preparedness research .",
"However , knowledge of viral genomes and host... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine and health sciences",
"action potentials",
"fish",
"goldfish",
"nervous system",
"membrane potential",
"vertebrates",
"electrophysiology",
"neuroscience",
"animals",
"simulation and modeling",
"osteichthyes",
"animal models",
"ion channels",
"model organisms",
"experimental o... | A computational model for gonadotropin releasing cells in the teleost fish medaka | journal.pcbi.1006662 | null | [
[
"Several types of excitable cells elicit electrical pulses called action potentials ( APs ) , which , depending on cell type , can trigger neurotransmitter release , cellular contraction , hormone release or other actions .",
"APs are generated by a combination of ion channels in the plasma membrane , whi... | [
"Pituitary endocrine cells fire action potentials ( APs ) to regulate their cytosolic Ca2+ concentration and hormone secretion rate .",
"Depending on animal species , cell type , and biological conditions , pituitary APs are generated either by TTX-sensitive Na+ currents ( INa ) , high-voltage activated Ca2+ curr... | [
"Excitable cells elicit electrical pulses called action potentials ( APs ) , which are generated and shaped by a combination of ion channels in the cell membrane .",
"Since one type of ion channels is permeable to Ca2+ ions , there is typically an influx of Ca2+ during an AP .",
"Pituitary cells therefore use A... | 2019 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious diseases/protozoal infections",
"infectious diseases/neglected tropical diseases",
"infectious diseases/skin infections",
"dermatology/skin infections"
] | Miltefosine in the Treatment of Cutaneous Leishmaniasis Caused by Leishmania braziliensis in Brazil: A Randomized and Controlled Trial | journal.pntd.0000912 | null | [
[
"The principal species causing cutaneous leishmaniasis ( CL ) in Brazil is Leishmania braziliensis which most often leads to a cutaneous form of the disease characterized by one or more ulcers with raised borders , most frequently located on the upper and lower extremities , but also found on the head , face ... | [
"Cutaneous leishmaniasis ( CL ) is treated with parenteral drugs for decades with decreasing rate cures .",
"Miltefosine is an oral medication with anti-leishmania activity and may increase the cure rates and improve compliance .",
"This study is a randomized , open-label , controlled clinical trial aimed to ev... | [
"Cutaneous leishmaniasis ( CL ) is characterized by skin ulcerations and occurs in rural poor areas of developing countries .",
"It is treated with daily injections of antimony for 20 days , which is associated with irregular use and increasingly lower cure rates .",
"Miltefosine is an oral medication with acti... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Material and methods"
] | [
"timber",
"infographics",
"taxonomy",
"ecology and environmental sciences",
"plant products",
"wolves",
"vertebrates",
"animals",
"mammals",
"ethnicities",
"phylogenetics",
"data management",
"aquatic environments",
"phylogenetic analysis",
"bodies of water",
"latin american people",
... | Population genomics of grey wolves and wolf-like canids in North America | journal.pgen.1007745 | null | [
[
"Grey wolves ( Canis lupus ) currently occupy a wide range of habitats across North America , including the tundra , taiga , desert , plain , and boreal forest .",
"Analysing ~40–50 , 000 SNPs from genotype arrays , the hitherto most comprehensive studies have identified seven North American grey wolf pop... | [
"North America is currently home to a number of grey wolf ( Canis lupus ) and wolf-like canid populations , including the coyote ( Canis latrans ) and the taxonomically controversial red , Eastern timber and Great Lakes wolves .",
"We explored their population structure and regional gene flow using a dataset of 4... | [
"Full genome sequencing is becoming an increasingly valuable tool for both the management of animal populations , as well as fundamental to improving our understanding of their evolutionary history .",
"The grey wolf ( Canis lupus ) is a keystone species in North America whose population structure and admixture h... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Recruitment of TREX to the Transcription Machinery by Its Direct Binding to the Phospho-CTD of RNA Polymerase II | journal.pgen.1003914 | null | [
[
"Gene expression is a fundamental process of every living cell .",
"In eukaryotes , RNA polymerase II ( RNAPII ) transcribes protein-coding genes to synthesize messenger RNA ( mRNA ) .",
"In addition to RNAPII , a plethora of transcription factors is needed for efficient and regulated transcription in... | [
"Messenger RNA ( mRNA ) synthesis and export are tightly linked , but the molecular mechanisms of this coupling are largely unknown .",
"In Saccharomyces cerevisiae , the conserved TREX complex couples transcription to mRNA export and mediates mRNP formation .",
"Here , we show that TREX is recruited to the tra... | [
"Gene expression is a fundamental cellular process that translates the information stored in the DNA into proteins , the workhorses of the cell .",
"Eukaryotic cells contain a nucleus , where the genetic information is stored and transcribed by RNA polymerase II into messenger ( m ) RNAs .",
"These copies of th... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine and health sciences",
"action potentials",
"markov models",
"membrane potential",
"ocular anatomy",
"electrophysiology",
"neuroscience",
"probability distribution",
"mathematics",
"ganglion cells",
"thermodynamics",
"entropy",
"animal cells",
"hidden markov models",
"probabilit... | Error-Robust Modes of the Retinal Population Code | journal.pcbi.1005148 | null | [
[
"Understanding the manner in which population of neurons encode information is fundamental to systems neuroscience .",
"Recent years have seen rapid progress in experimental techniques for recording simultaneously from hundreds of neurons of more [1–5] , which provide us with excellent access to the activ... | [
"Across the nervous system , certain population spiking patterns are observed far more frequently than others .",
"A hypothesis about this structure is that these collective activity patterns function as population codewords–collective modes–carrying information distinct from that of any single cell .",
"We inv... | [
"Neurons in most parts of the nervous system represent and process information in a collective fashion , yet the nature of this collective code is poorly understood .",
"An important constraint placed on any such collective processing comes from the fact that individual neurons’ signaling is prone to corruption b... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Protein Composition of Infectious Spores Reveals Novel Sexual Development and Germination Factors in Cryptococcus | journal.pgen.1005490 | null | [
[
"The formation of survival structures in response to adverse conditions is an essential tool used by diverse organisms across biology to propagate life on earth .",
"Spores are a particularly successful cell type used by many microorganisms , including bacteria , fungi , and protozoa to survive unsuitable... | [
"Spores are an essential cell type required for long-term survival across diverse organisms in the tree of life and are a hallmark of fungal reproduction , persistence , and dispersal .",
"Among human fungal pathogens , spores are presumed infectious particles , but relatively little is known about this robust ce... | [
"Spores are a critical cell type that allow long-term survival of diverse organisms from bacteria to fungi to plants .",
"Among fungi , spores are often formed when growth conditions are poor; spores can then disperse to more favorable environments and reinitiate growth .",
"Spores of some environmental fungi c... | 2015 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | Global Transcriptional Dynamics of Diapause Induction in Non-Blood-Fed and Blood-Fed Aedes albopictus | journal.pntd.0003724 | null | [
[
"Dengue virus ( DENV ) and Chikungunya virus ( CHIKV ) are ( re ) emerging arboviruses transmitted primarily by the mosquitoes Aedes aegypti and Aedes albopictus .",
"Estimates of annual DENV infections range from 50–390 million [1 , 2] .",
"Although levels of CHIKV infection are much lower , a 2005–2... | [
"Aedes albopictus is a vector of increasing public health concern due to its rapid global range expansion and ability to transmit Dengue virus , Chikungunya virus and a wide range of additional arboviruses .",
"Traditional vector control strategies have been largely ineffective against Ae .",
"albopictus and no... | [
"The mosquito , Aedes albopictus , is an aggressive human biter capable of transmitting Dengue virus , Chikungunya virus and at least 22 additional viruses that cause human illness .",
"Over the last 30 years , this mosquito has spread from its native Asian range to all continents except Antarctica .",
"Efforts... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"blood cells",
"medicine and health sciences",
"immune cells",
"multiple sclerosis",
"nervous system",
"neurodegenerative diseases",
"immunology",
"neuroscience",
"demyelinating disorders",
"clinical medicine",
"optic nerve",
"eye diseases",
"adoptive transfer",
"spinal cord",
"white blo... | Suppression of IL-12p70 formation by IL-2 or following macrophage depletion causes T-cell autoreactivity leading to CNS demyelination in HSV-1-infected mice | journal.ppat.1006401 | null | [
[
"Multiple sclerosis ( MS ) is due to degradation of the myelin sheath [1] and visual disorders due to demyelination of the optic nerve is the early sign of individuals diagnosed with MS [2 , 3] .",
"Thus , optic neuritis can be used as an early factor for detection of MS . Both genetic and environmental f... | [
"We have established two mouse models of central nervous system ( CNS ) demyelination that differ from most other available models of multiple sclerosis ( MS ) in that they represent a mixture of viral and immune triggers .",
"In the first model , ocular infection of different strains of mice with a recombinant H... | [
"Several mouse models of multiple sclerosis ( MS ) are now available .",
"We have established two new mouse models .",
"In the first model , ocular infection of different strains of mice with HSV-IL-2 recombinant virus causes CNS demyelination .",
"In the second model , CNS demyelination was induced by differ... | 2017 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine and health sciences",
"vesicles",
"electrochemical cells",
"helminths",
"parasite evolution",
"vertebrates",
"parasitic diseases",
"animals",
"echinococcus",
"parasitology",
"xenopus",
"endocrine physiology",
"animal models",
"model organisms",
"amphibians",
... | The role of fibroblast growth factor signalling in Echinococcus multilocularis development and host-parasite interaction | journal.pntd.0006959 | null | [
[
"The flatworm parasite E . multilocularis ( fox-tapeworm ) is the causative agent of alveolar echinococcosis ( AE ) , one of the most dangerous zoonoses of the Northern hemisphere .",
"Infections of intermediate hosts ( rodents , humans ) are initiated by oral uptake of infectious eggs which contain the p... | [
"Alveolar echinococcosis ( AE ) is a lethal zoonosis caused by the metacestode larva of the tapeworm Echinococcus multilocularis .",
"The infection is characterized by tumour-like growth of the metacestode within the host liver , leading to extensive fibrosis and organ-failure .",
"The molecular mechanisms of p... | [
"To ensure proper communication between their different cell populations , animals rely on secreted hormones and cytokines that act on receptors of target cells .",
"Most of the respective cytokines , such as FGFs , evolved over 500 million years ago and are present in similar form in all animals , including para... | 2019 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"blood cells",
"sequencing techniques",
"medicine and health sciences",
"immune cells",
"enzyme-linked immunoassays",
"immune physiology",
"immunology",
"vaccines",
"nucleoproteins",
"protein sequencing",
"cytotoxic t cells",
"molecular biology techniques",
"infectious disease control",
"g... | Long-lived CD8+ T cell responses following Crimean-Congo haemorrhagic fever virus infection | journal.pntd.0006149 | null | [
[
"Crimean-Congo haemorrhagic fever virus ( CCHFV ) is a member of the Nairoviridae family and has a tripartite , single-stranded , negative sense RNA genome [1–3] .",
"The three segments are referred to as the large ( L ) , medium ( M ) and small ( S ) segments [4] .",
"The L segment encodes the viral ... | [
"Crimean-Congo haemorrhagic fever virus ( CCHFV ) is a member of the Orthonairovirus genus of the Nairoviridae family and is associated with haemorrhagic fever in humans .",
"Although T lymphocyte responses are known to play a role in protection from and clearance of viral infections , specific T cell epitopes ha... | [
"Crimean-Congo haemorrhagic fever virus ( CCHFV ) is a tick-borne virus that causes haemorrhagic fever with fatalities in humans .",
"Clinical disease has been described in Africa , Asia , Eastern Europe , the Middle East , Turkey and more recently Greece , India and Spain .",
"In the absence of specific anti-v... | 2017 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"cell physiology",
"cell motility",
"medicine and health sciences",
"leptospira",
"actin filaments",
"pathology and laboratory medicine",
"pathogens",
"endothelial cells",
"microbiology",
"junctional complexes",
"epithelial cells",
"tight junctions",
"bacteria",
"bacterial pathogens",
"a... | Leptospira interrogans causes quantitative and morphological disturbances in adherens junctions and other biological groups of proteins in human endothelial cells | journal.pntd.0005830 | null | [
[
"The causative agents of leptospirosis , Leptospira species , are Gram-negative spirochetes of the class Spirochaetales , along with Borrelia and Treponema [1] .",
"The genus Leptospira has at least 22 species with 300 serovars and are classified as pathogenic , saprophytic , and intermediate types [2–4] ... | [
"Pathogenic Leptospira transmits from animals to humans , causing the zoonotic life-threatening infection called leptospirosis .",
"This infection is reported worldwide with higher risk in tropical regions .",
"Symptoms of leptospirosis range from mild illness to severe illness such as liver damage , kidney fai... | [
"Pathogenic Leptospira causes the life-threatening infection called leptospirosis worldwide .",
"Symptoms of leptospirosis range from mild illness to severe illness such as organ damage , meningitis , and fatal hemorrhagic disease .",
"Invasive species of Leptospira spread to multiple tissues , and damage the l... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"invertebrates",
"chemical compounds",
"hela cells",
"molecular probe techniques",
"biological cultures",
"immunoblotting",
"organic compounds",
"animals",
"animal models",
"drosophila melanogaster",
"model organisms",
"immunoprecipitation",
"materials science",
"experimental organism syst... | CHMP1B is a target of USP8/UBPY regulated by ubiquitin during endocytosis | journal.pgen.1007456 | null | [
[
"Endocytosis of activated plasma membrane receptors is induced by ubiquitin linkage and plays a crucial role in cell signaling modulation through their subsequent sorting to either recycling vesicles or to lysosomes via multivesicular bodies ( MVBs ) .",
"For example , endocytosis of the Epidermal Growth ... | [
"Integration and down-regulation of cell growth and differentiation signals rely on plasma membrane receptor endocytosis and sorting towards either recycling vesicles or degradative lysosomes via multivesicular bodies ( MVB ) .",
"In this process , the endosomal sorting complex-III required for transport ( ESCRT-... | [
"In multicellular organisms , the interpretation and transmission of cell growth and differentiation signals strongly rely on plasma membrane receptors .",
"Once activated by their ligands , these receptors activate downstream signaling cascades and are rapidly internalized into intracellular vesicles that fuse i... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | DNA Repair Cofactors ATMIN and NBS1 Are Required to Suppress T Cell Activation | journal.pgen.1005645 | null | [
[
"Defects in T cell development can result due to inefficient repair of DNA lesions that are generated in a programmed manner during the recombination of variable , diverse and joining ( VDJ ) gene segments , a process that is crucial for the generation of the T cell receptor ( TCR ) [1] .",
"Therefore , p... | [
"Proper development of the immune system is an intricate process dependent on many factors , including an intact DNA damage response .",
"The DNA double-strand break signaling kinase ATM and its cofactor NBS1 are required during T cell development and for the maintenance of genomic stability .",
"The role of a ... | [
"Defects in DNA repair pathways can lead to pathogenesis within the immune system , an example of which is inflammatory bowel disease ( IBD ) .",
"Yet the underlying genetic causes of IBD are often unclear .",
"The DNA repair kinase ATM is crucial for the proper development and function of the immune system .",... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"blood cells",
"heme",
"fish",
"medicine and health sciences",
"immune physiology",
"immune cells",
"spleen",
"immunology",
"rna extraction",
"vertebrates",
"animals",
"animal models",
"osteichthyes",
"developmental biology",
"model organisms",
"experimental organism systems",
"embry... | Hrg1 promotes heme-iron recycling during hemolysis in the zebrafish kidney | journal.pgen.1007665 | null | [
[
"Heme is an iron-containing porphyrin that acts as an essential cofactor in numerous biological processes such as oxygen transport , miRNA processing , electron transfer , and circadian clock control [1] .",
"In humans , total body iron store is a composite of dietary iron absorption , which accounts for ... | [
"Heme-iron recycling from senescent red blood cells ( erythrophagocytosis ) accounts for the majority of total body iron in humans .",
"Studies in cultured cells have ascribed a role for HRG1/SLC48A1 in heme-iron transport but the in vivo function of this heme transporter is unclear .",
"Here we present genetic... | [
"Total body iron stores in mammals is a composite of iron absorption from diet and iron recycled by macrophages from dying red blood cells ( RBCs ) .",
"Upon erythrophagocytosis of RBCs , the hemoglobin is degraded and heme is imported from the phagosomal compartment into the cytoplasm so that the iron can be rel... | 2018 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"public health and epidemiology/infectious diseases",
"public health and epidemiology",
"public health and epidemiology/health policy"
] | Cost-Effectiveness of Chagas Disease Vector Control Strategies in Northwestern Argentina | journal.pntd.0000363 | null | [
[
"Over the past 15 years , the burden of Chagas disease has been significantly reduced ( from ∼30 million human cases in 1990 to ∼9–11 million in 2006 ) as a consequence of the direct actions promoted by several multinational regional initiatives [1] , [2] .",
"The key for such success was the long term im... | [
"Control and prevention of Chagas disease rely mostly on residual spraying of insecticides .",
"In Argentina , vector control shifted from a vertical to a fully horizontal strategy based on community participation between 1992 and 2004 .",
"The effects of such strategy on Triatoma infestans , the main domestic ... | [
"Despite decreasing rates of prevalence and incidence , Chagas disease remains a serious problem in Latin America , especially for the rural poor .",
"Without vaccines , control and prevention rely mostly on residual spraying of insecticides .",
"Under the aegis of the Southern Cone Initiative , and in agreemen... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Methods",
"Supporting Information"
] | [
"biotechnology",
"oncology",
"computational biology",
"biophysics",
"homo (human)"
] | In Silico Elucidation of the Molecular Mechanism Defining the Adverse Effect of Selective Estrogen Receptor Modulators | journal.pcbi.0030217 | null | [
[
"Early identification of the adverse effects of preclinical and commercial drugs is crucial in developing highly efficient therapeutics , since unexpected adverse drug effects contribute to one-third of all drug failures in the late stage of drug development [1] .",
"Conventional practices for identifying... | [
"Early identification of adverse effect of preclinical and commercial drugs is crucial in developing highly efficient therapeutics , since unexpected adverse drug effects account for one-third of all drug failures in drug development .",
"To correlate protein–drug interactions at the molecule level with their cli... | [
"Early identification of the side effects of preclinical and commercial drugs is crucial in developing highly efficient therapeutics , as unexpected side effects account for one-third of all drug failures in drug development and lead to drugs being withdrawn from the market .",
"Compared with the experimental ide... | 2007 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genetics",
"biology",
"molecular cell biology",
"genetics and genomics"
] | The Translation Initiation Factor eIF4E Regulates the Sex-Specific Expression of the Master Switch Gene Sxl in Drosophila melanogaster | journal.pgen.1002185 | null | [
[
"Translation initiation is mediated by the binding of a pre-initiation complex to the 5′ cap of the mRNA ( reviewed in [1] , [2] ) that in turn recruits the small subunit of the 40S ribosome to the mRNA .",
"The pre-initiation complex consists of the cap binding protein , eIF4E , and a scaffolding protein... | [
"In female fruit flies , Sex-lethal ( Sxl ) turns off the X chromosome dosage compensation system by a mechanism involving a combination of alternative splicing and translational repression of the male specific lethal-2 ( msl-2 ) mRNA .",
"A genetic screen identified the translation initiation factor eif4e as a g... | [
"Gene expression in eukaryotes is a complex process that occurs in several discrete steps .",
"Some of those steps are separated into different sub-cellular compartments and thus might be expected to occur independently of one another and involve entirely distinct factors .",
"For example pre-mRNA splicing take... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"biology"
] | The HCMV gH/gL/UL128-131 Complex Triggers the Specific Cellular Activation Required for Efficient Viral Internalization into Target Monocytes | journal.ppat.1003463 | null | [
[
"Human cytomegalovirus ( HCMV ) is a betaherpesvirus characterized by worldwide prevalence in the human population .",
"Although infection of immunocompetent individuals is usually mild or asymptomatic , increasing evidence shows that HCMV infection is a strong risk factor in the development of several ca... | [
"We have established that HCMV acts as a specific ligand engaging and activating cellular integrins on monocytes .",
"As a result , integrin signaling via Src activation leads to the functional activation of paxillin required for efficient viral entry and for the biological changes in monocytes needed for viral d... | [
"We previously demonstrated that HCMV , by engaging cellular receptors , changes the biology of blood monocytes , allowing for efficient viral entry into these cells and their use as virus-carriers in HCMV systemic spread .",
"However , it was unclear how HCMV induces receptor-mediated signaling in infected cells... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"biotechnology",
"genome evolution",
"plant products",
"computational biology",
"departures from diploidy",
"sequence assembly tools",
"plant science",
"tetraploidy",
"fiber crops",
"phylogenetic analysis",
"genome analysis",
"crops",
"plant genomics",
"molecular biology techniques",
"re... | DNA Sequence Evolution and Rare Homoeologous Conversion in Tetraploid Cotton | journal.pgen.1006012 | null | [
[
"Domesticated cotton has a polyploid genome consisting of an AT- and DT-genome ( the “T” subscript indicates tetraploid nucleus ) .",
"Approximately 1 mya , a polyploidization event gave rise to six described AD allotetraploid species with genome sizes ~2400 Mbp , mostly native to Central and South Americ... | [
"Allotetraploid cotton species are a vital source of spinnable fiber for textiles .",
"The polyploid nature of the cotton genome raises many evolutionary questions as to the relationships between duplicated genomes .",
"We describe the evolution of the cotton genome ( SNPs and structural variants ) with the gre... | [
"The polyploid genome of domesticated cotton contains two different copies of most genes because its genome is duplicated .",
"Instead of 13 chromosomes like its wild relatives , domesticated cotton has 26 chromosomes ( 13 AT chromosomes and 13 DT chromosomes ) .",
"Differences in the gene copies may hold keys ... | 2016 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"cardiomyopathies",
"immune cells",
"cytokines",
"immunity to infections",
"immunology",
"parasitic diseases",
"cardiovascular",
"neglected tropical diseases",
"immunoregulation",
"infectious diseases",
"t cells",
"immune response",
"immune system",
"chagas disease",
"clini... | Deficient Regulatory T Cell Activity and Low Frequency of IL-17-Producing T Cells Correlate with the Extent of Cardiomyopathy in Human Chagas' Disease | journal.pntd.0001630 | null | [
[
"At the present time , about 7 . 7 million people are infected and 28 million are at risk of being infected with Trypanosoma cruzi in Central and South America [1]–[3] .",
"This hemoflagellate protozoan is the etiological agent of Chagas' disease .",
"Most of the infected individuals remain asymptomat... | [
"Myocardium damage during Chagas' disease results from the immunological imbalance between pro- and production of anti-inflammatory cytokines and has been explained based on the Th1–Th2 dichotomy and regulatory T cell activity .",
"Recently , we demonstrated that IL-17 produced during experimental T . cruzi infec... | [
"Dilated cardiomyopathy is one of the clinical forms of Chagas' disease ( CD ) after the infection caused by the parasite Trypanosoma cruzi .",
"Even though strategies adopted in most Latin-American countries in the last decades towards vector control have been effective in reducing the incidence of CD , active t... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine and health sciences",
"nuclear staining",
"pathology and laboratory medicine",
"enzymes",
"cell cycle and cell division",
"pathogens",
"cell processes",
"bacillus",
"dna-binding proteins",
"microbiology",
"enzymology",
"membrane staining",
"prokaryotic models",
"dna replication",... | Rv0004 is a new essential member of the mycobacterial DNA replication machinery | journal.pgen.1007115 | null | [
[
"The ability to maintain , replicate , and express genetic information encoded in DNA is critical to all domains of life .",
"DNA replication studies in Escherichia coli and Bacillus subtilis have elucidated the mechanisms of bacterial DNA replication initiation , elongation , and termination , but the ap... | [
"DNA replication is fundamental for life , yet a detailed understanding of bacterial DNA replication is limited outside the organisms Escherichia coli and Bacillus subtilis .",
"Many bacteria , including mycobacteria , encode no identified homologs of helicase loaders or regulators of the initiator protein DnaA ,... | [
"DNA is the molecule that encodes all of the genetic information of an organism .",
"In order to pass genes onto the next generation , DNA has to first be copied through a process called DNA replication .",
"Most of the initial studies on bacterial DNA replication were performed in Escherichia coli and Bacillus... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | Abiotic Stresses Antagonize the Rice Defence Pathway through the Tyrosine-Dephosphorylation of OsMPK6 | journal.ppat.1005231 | null | [
[
"Plants , as sessile organisms , are continuously exposed to various environmental stresses in nature .",
"To cope with such conditions using limited resources , plants have evolved various mechanisms that enable resource allocation to the most life-threatening stress [1] [2] .",
"Such tradeoffs betwe... | [
"Plants , as sessile organisms , survive environmental changes by prioritizing their responses to the most life-threatening stress by allocating limited resources .",
"Previous studies showed that pathogen resistance was suppressed under abiotic stresses .",
"Here , we show the mechanism underlying this phenome... | [
"Chemical defence inducers make plants resistant to diseases such as rice blast .",
"However , plants sometimes become more pathogen susceptible under abiotic stresses even in their presence .",
"Because such regulation prioritizes the responses to the most life-threatening stress , it could be necessary for pl... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"developmental biology",
"organism development",
"genetics",
"biology",
"neuroscience",
"genetics and genomics"
] | Developmental Transcriptional Networks Are Required to Maintain Neuronal Subtype Identity in the Mature Nervous System | journal.pgen.1002501 | null | [
[
"Tremendous progress has been made in delineating the transcriptional mechanisms that diversify neuronal subtype identities during development .",
"Spatiotemporally-patterned transcription factor cascades act within increasingly diversified progenitor populations to specify postmitotic neuron subtype fate... | [
"During neurogenesis , transcription factors combinatorially specify neuronal fates and then differentiate subtype identities by inducing subtype-specific gene expression profiles .",
"But how is neuronal subtype identity maintained in mature neurons ?",
"Modeling this question in two Drosophila neuronal subtyp... | [
"For neurons to function properly , they must establish and then maintain their unique , subtype-specific gene expression profiles .",
"These unique gene expression profiles are established during development by networks of DNA–binding proteins , termed transcription factors ( TFs ) .",
"However , how neurons m... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genetics",
"biology",
"microbiology",
"genetics and genomics"
] | Telomere Length Affects the Frequency and Mechanism of Antigenic Variation in Trypanosoma brucei | journal.ppat.1002900 | null | [
[
"Trypanosoma brucei is an extracellular human pathogen with an unparalleled capacity to evade host humoral immunity .",
"The causative agent of African sleeping sickness in humans and nagana in cattle , T . brucei is transmitted into the bloodstream of its host by a tsetse vector and can grow to densities... | [
"Trypanosoma brucei is a master of antigenic variation and immune response evasion .",
"Utilizing a genomic repertoire of more than 1000 Variant Surface Glycoprotein-encoding genes ( VSGs ) , T . brucei can change its protein coat by “switching” from the expression of one VSG to another .",
"Each active VSG is ... | [
"A broad array of human pathogens ( including bacteria , fungi and parasites ) vary the proteins on their cell surface to escape the immune response of their hosts .",
"This process , called antigenic variation , relies on a repertoire of variant protein encoding genes in the genome and the organism's ability to ... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods",
"Supporting Information"
] | [
"infectious diseases",
"gastroenterology and hepatology",
"microbiology",
"animals",
"eubacteria"
] | Structure–Function Aspects of PstS in Multi-Drug–Resistant Pseudomonas aeruginosa | journal.ppat.0040043 | null | [
[
"Infection due to P . aeruginosa continues to be a major cause of mortality among critically ill and immuno-compromised patients despite the development of newer and more powerful antibiotics .",
"Both the immunoevasive nature of P . aeruginosa as well as its acquisition of multi-drug resistance makes eli... | [
"The increasing prevalence of multi-drug–resistant ( MDR ) strains of Pseudomonas aeruginosa among critically ill humans is of significant concern .",
"In the current study , we show that MDR clinical isolates of P . aeruginosa representing three distinct genotypes that display high virulence against intestinal e... | [
"The resistance of bacteria to multiple antibiotics is a major problem in critically ill patients who often become colonized by highly lethal pathogens such as Pseudomonas aeruginosa .",
"During the course of critical illness , as many as 50% of patients' intestinal tracts become colonized with P . aeruginosa , w... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"meiosis",
"invertebrates",
"medicine and health sciences",
"reproductive system",
"gonads",
"caenorhabditis",
"cell cycle and cell division",
"cell processes",
"meiotic prophase",
"animals",
"animal models",
"dna damage",
"caenorhabditis elegans",
"model organisms",
"experimental organi... | BRCA1-BARD1 associate with the synaptonemal complex and pro-crossover factors and influence RAD-51 dynamics during Caenorhabditis elegans meiosis | journal.pgen.1007653 | null | [
[
"The genetic information encoded by DNA must be accurately copied and transmitted from one generation to the next .",
"In somatic cells , DNA is duplicated and equally partitioned into daughter cells via mitosis , whereas in germ cells , which give rise to gametes , chromosome segregation relies on meiosi... | [
"During meiosis , the maternal and paternal homologous chromosomes must align along their entire length and recombine to achieve faithful segregation in the gametes .",
"Meiotic recombination is accomplished through the formation of DNA double-strand breaks , a subset of which can mature into crossovers to link t... | [
"Sexually reproducing species rely on meiosis to transmit their genetic information across generations .",
"Parental chromosomes ( homologues ) undergo many distinctive processes in their complex journey from attachment to segregation .",
"The physiological induction of DNA double strand breaks is crucial for p... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"biology"
] | Plasmodium falciparum Merozoite Invasion Is Inhibited by Antibodies that Target the PfRh2a and b Binding Domains | journal.ppat.1002075 | null | [
[
"Invasion of apicomplexan parasites into host cells is a complex process involving multiple ligands stored in apical organelles known as micronemes and rhoptries ( for review see [1] ) .",
"The ligands are released from these compartments onto the invasive zoite form of the parasite during egress or invas... | [
"Plasmodium falciparum , the causative agent of the most severe form of malaria in humans invades erythrocytes using multiple ligand-receptor interactions .",
"The P . falciparum reticulocyte binding-like homologue proteins ( PfRh or PfRBL ) are important for entry of the invasive merozoite form of the parasite i... | [
"The causative agent of the most severe form of malaria in humans is the protozoan parasite Plasmodium falciparum .",
"These parasites are carried by a mosquito that infects humans during feeding resulting in injection of sporozoite forms that infect and develop in the liver into the merozoite stage .",
"The me... | 2011 |
[
"Introduction",
"Model",
"Results",
"Discussion"
] | [
"action potentials",
"medicine and health sciences",
"markov models",
"membrane potential",
"vertebrates",
"electrophysiology",
"neuroscience",
"animals",
"mammals",
"primates",
"optimization",
"systems science",
"mathematics",
"old world monkeys",
"computer and information sciences",
... | Neuron’s eye view: Inferring features of complex stimuli from neural responses | journal.pcbi.1005645 | null | [
[
"The question of how the brain encodes information from the natural world forms one of the primary areas of study within neuroscience .",
"For many sensory systems , particularly vision and audition , the discovery that single neurons modulate their firing of action potentials in response to particular st... | [
"Experiments that study neural encoding of stimuli at the level of individual neurons typically choose a small set of features present in the world—contrast and luminance for vision , pitch and intensity for sound—and assemble a stimulus set that systematically varies along these dimensions .",
"Subsequent analys... | [
"Many neuroscience experiments begin with a set of reduced stimuli designed to vary only along a small set of variables .",
"Yet many phenomena of interest—natural movies , objects—are not easily parameterized by a small number of dimensions .",
"Here , we develop a novel Bayesian model for clustering stimuli b... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"infectious diseases",
"public health and epidemiology",
"veterinary diseases",
"zoology",
"epidemiology",
"biology",
"microbiology",
"evolutionary biology",
"population biology",
"public health",
"veterinary science"
] | West Nile Virus Experimental Evolution in vivo and the Trade-off Hypothesis | journal.ppat.1002335 | null | [
[
"West Nile virus ( WNV , family Flaviviridae: Flavivirus ) is an arthropod-borne virus ( arbovirus ) that has demonstrated remarkable success since being introduced to North America in 1999 .",
"Within three years after its introduction the virus had adapted to local mosquito vectors and within 8 years ha... | [
"In nature , arthropod-borne viruses ( arboviruses ) perpetuate through alternating replication in vertebrate and invertebrate hosts .",
"The trade-off hypothesis proposes that these viruses maintain adequate replicative fitness in two disparate hosts in exchange for superior fitness in one host .",
"Releasing ... | [
"Arthropod-borne viruses , including West Nile virus ( WNV ) have long been considered to be subject to a fitness “trade-off” because they must replicate in at least two taxonomically divergent hosts in order to perpetuate .",
"Results of studies testing this trade-off hypothesis have been inconsistent and largel... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"developmental biology",
"model organisms",
"genetics",
"biology and life sciences",
"research and analysis methods"
] | Wnt Signaling Interacts with Bmp and Edn1 to Regulate Dorsal-Ventral Patterning and Growth of the Craniofacial Skeleton | journal.pgen.1004479 | null | [
[
"A fundamental question in skeletal biology is how cartilages and bones with distinct shapes arise from skeletogenic precursor cells .",
"Much of the craniofacial skeleton derives from neural crest ( NC ) cells that migrate in streams into the pharyngeal arches and contain anterior-posterior ( A-P ) patte... | [
"Craniofacial development requires signals from epithelia to pattern skeletogenic neural crest ( NC ) cells , such as the subdivision of each pharyngeal arch into distinct dorsal ( D ) and ventral ( V ) elements .",
"Wnt signaling has been implicated in many aspects of NC and craniofacial development , but its ro... | [
"Craniofacial abnormalities are among the most common birth defects .",
"Understanding the molecular mechanisms underlying craniofacial disorders is crucial for developing treatment strategies .",
"Much of the craniofacial skeleton arises from specialized embryonic structures known as pharyngeal arches .",
"P... | 2014 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine",
"public health and epidemiology",
"mathematics",
"effective population size",
"epidemiology",
"infectious disease epidemiology",
"genetics",
"population genetics",
"biology",
"evolutionary biology",
"nonlinear dynamics",
"genetics and genomics"
] | Simple Epidemiological Dynamics Explain Phylogenetic Clustering of HIV from Patients with Recent Infection | journal.pcbi.1002552 | null | [
[
"Phylogenetic clusters of closely related virus such as HIV arise from the epidemiological dynamics and transmission by infected hosts .",
"If virus is phylogenetically clustered , it is an indication that the hosts are connected by a short chain of transmissions [1] .",
"If super-infection is rare , ... | [
"Phylogenies of highly genetically variable viruses such as HIV-1 are potentially informative of epidemiological dynamics .",
"Several studies have demonstrated the presence of clusters of highly related HIV-1 sequences , particularly among recently HIV-infected individuals , which have been used to argue for a h... | [
"Diversity of viral genetic sequences depends on epidemiological mechanisms and dynamics , however the exact mechanisms responsible for patterns observed in phylogenies of HIV remain poorly understood .",
"We observe that virus taken from patients with early/acute HIV infection are more likely to be closely relat... | 2012 |
[
"Introduction",
"Methods",
"Discussion"
] | [
"biology"
] | Contact Irritant Responses of Aedes aegypti Using Sublethal Concentration and Focal Application of Pyrethroid Chemicals | journal.pntd.0002074 | null | [
[
"Dengue , transmitted primarily by Aedes aegypti mosquitoes , is the most important mosquito-borne viral disease affecting humans worldwide [1] .",
"It is caused by four serotypes that produce a spectrum of clinical illness ranging from unapparent or mild disease , to an influenza-like illness , to a fata... | [
"Previous studies have demonstrated contact irritant and spatial repellent behaviors in Aedes aegypti following exposure to sublethal concentrations of chemicals .",
"These sublethal actions are currently being evaluated in the development of a push-pull strategy for Ae .",
"aegypti control .",
"This study re... | [
"Dengue virus is spread by Aedes aegypti , a mosquito that prefers to feed on humans .",
"Chemicals used at toxic levels is currently the only confirmed effective strategy for dengue vector control , but insecticide resistance issues are threatening this approach .",
"Other chemical actions that break vector-hu... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Ergot Alkaloids (Re)generate New Leads as Antiparasitics | journal.pntd.0004063 | null | [
[
"Schistosomiasis is a neglected tropical disease that infects over 200 million people worldwide , burdening economies with an annual loss of several million disability-adjusted life years [1–3] .",
"The disease is caused by parasitic flatworms of the genus Schistosoma and treatment is largely reliant on a... | [
"Praziquantel ( PZQ ) is a key therapy for treatment of parasitic flatworm infections of humans and livestock , but the mechanism of action of this drug is unresolved .",
"Resolving PZQ-engaged targets and effectors is important for identifying new druggable pathways that may yield novel antiparasitic agents .",
... | [
"The parasitic infection schistosomiasis afflicts millions of people worldwide and is clinically treated using a single drug , praziquantel ( PZQ ) .",
"Despite the fact that PZQ has served as a stalwart anthelmintic for decades , the molecular basis of action of this clinical agent is poorly understood .",
"Th... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biology"
] | A Putative Homologue of CDC20/CDH1 in the Malaria Parasite Is Essential for Male Gamete Development | journal.ppat.1002554 | null | [
[
"Progression of mitosis in the cell-cycle is dependent upon a number of complex , sequential processes that are governed by a series of essential cell cycle regulatory proteins .",
"Anaphase and mitotic exit is regulated by the conserved multi-subunit E3 ubiquitin ligase Anaphase Promoting Complex/Cycloso... | [
"Cell-cycle progression is governed by a series of essential regulatory proteins .",
"Two major regulators are cell-division cycle protein 20 ( CDC20 ) and its homologue , CDC20 homologue 1 ( CDH1 ) , which activate the anaphase-promoting complex/cyclosome ( APC/C ) in mitosis , and facilitate degradation of mito... | [
"Malaria parasites are single cell organisms that multiply via asexual division at different stages in the life-cycle: in the liver and red blood cells of the vertebrate host and gut of the mosquito vector .",
"The precursor sexual stages ( male and female gametocytes ) form in red blood cells , then following in... | 2012 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [] | Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data | journal.pcbi.1004336 | null | [
[
"The process of protein synthesis is central to all living organisms .",
"It has been actively researched for over five decades , and by now the individual steps of this process are known in great detail at the molecular and mechanistic levels [1] .",
"Gene adaptation to the tRNA pool , mRNA secondary... | [
"Translation of RNA to protein is a core process for any living organism .",
"While for some steps of this process the effect on protein production is understood , a holistic understanding of translation still remains elusive .",
"In silico modelling is a promising approach for elucidating the process of protei... | [
"Translation , the process of synthesizing proteins from mRNA templates , is an essential biological process in all living organisms .",
"A better understanding of this process will have ramifications in various fields—from gene regulation , disease understanding and medicine to biotechnology and synthetic biolog... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"cell biology",
"developmental biology"
] | Two-Dimensional Patterning by a Trapping/Depletion Mechanism: The Role of TTG1 and GL3 in Arabidopsis Trichome Formation | journal.pbio.0060141 | Trapping of a protein in a specialized cell is shown to cause a depletion of this protein in surrounding cells, thus regulating the spacing pattern produced in plant hair cells. | [
[
"During the development of animals and plants , specific cell types need to be placed in a regular pattern within a field of cells .",
"In the simplest scenario , this occurs in a two-dimensional sheet of cells .",
"Mathematical modeling of such a spacing pattern has uncovered two general principles .... | [
"Trichome patterning in Arabidopsis serves as a model system to study how single cells are selected within a field of initially equivalent cells .",
"Current models explain this pattern by an activator–inhibitor feedback loop .",
"Here , we report that also a newly discovered mechanism is involved by which patt... | [
"Trichomes , the specialized hair cells found on plant leaves , represent a model system to study how cellular interactions coordinate the development and arrangement of a collection of initially equivalent cells into regularly placed specialized cells .",
"It was assumed that a regulatory feedback loop of positi... | 2008 |
[
"Introduction",
"Results and discussion",
"Conclusions",
"Methods"
] | [
"genome evolution",
"population genetics",
"vertebrates",
"social sciences",
"animals",
"mammals",
"animal behavior",
"evolutionary adaptation",
"population biology",
"zoology",
"genomics",
"genetic polymorphism",
"behavior",
"molecular evolution",
"chipmunks",
"comparative genomics",
... | Temporal genomic contrasts reveal rapid evolutionary responses in an alpine mammal during recent climate change | journal.pgen.1008119 | null | [
[
"Rapid environmental change threatens global biodiversity and has led to population declines in many species [1–5] .",
"Although phenotypic plasticity may enable populations to track rapidly changing climates , evolutionary adaptation will often be essential for long-term persistence [6] .",
"Disentan... | [
"Many species have experienced dramatic changes in their abundance and distribution during recent climate change , but it is often unclear whether such ecological responses are accompanied by evolutionary change .",
"We used targeted exon sequencing of 294 museum specimens ( 160 historic , 134 modern ) to generat... | [
"Museum specimens represent an irreplaceable archive that can be used to understand how species respond to rapid environmental change .",
"We recovered genomic data from archived samples spanning a century of climate change in co-distributed declining versus stable species of montane chipmunks .",
"Applying nov... | 2019 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"schistosoma",
"invertebrates",
"schistosoma mansoni",
"medicine and health sciences",
"pathology and laboratory medicine",
"helminths",
"antiviral therapy",
"enzymes",
"immunology",
"tropical diseases",
"enzymology",
"metalloproteases",
"parasitic diseases",
"animals",
"diarrhea",
"pr... | Aberrant plasma MMP and TIMP dynamics in Schistosoma - Immune reconstitution inflammatory syndrome (IRIS) | journal.pntd.0006710 | null | [
[
"HIV-patients initiating antiretroviral therapy ( ART ) while dealing with a co-infection are at risk of developing immune reconstitution inflammatory syndrome ( IRIS ) .",
"IRIS is described as a clinical deterioration of HIV patients in the first weeks or months after starting ART , often marked by tiss... | [
"Among the different faces of immune reconstitution inflammatory syndrome ( IRIS ) developing in HIV-patients , no clinical definition has been reported for Schistosomiasis-IRIS ( Schisto-IRIS ) .",
"Although Schisto-IRIS remains largely uninvestigated , matrix metalloproteinases ( MMP ) and tissue inhibitors of ... | [
"A subset of HIV-patients starting antiretroviral therapy are at risk of developing immune-driven worsening symptoms of a previously treated opportunistic infection .",
"This paradoxical immune reconstitution inflammatory syndrome ( IRIS ) has been abundantly described in common co-infections such as M . tubercul... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genetics and genomics/epigenetics",
"genetics and genomics/bioinformatics",
"computational biology/genomics",
"computational biology/transcriptional regulation"
] | Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals | journal.pcbi.1000216 | null | [
[
"DNA in eukaryotes is highly packaged into nucleosome arrays , which together compact ∼75–90% of the genome [1] .",
"Because most DNA is wrapped in nucleosomes , and nucleosomes occlude their DNA from access to most other DNA binding proteins , revealing the detailed organization of nucleosomes across gen... | [
"The detailed positions of nucleosomes profoundly impact gene regulation and are partly encoded by the genomic DNA sequence .",
"However , less is known about the functional consequences of this encoding .",
"Here , we address this question using a genome-wide map of ∼380 , 000 yeast nucleosomes that we sequenc... | [
"The detailed positions of nucleosomes along genomes have critical roles in transcriptional regulation .",
"Consequently , it is important to understand the principles that govern the organization of nucleosomes in vivo and the functional consequences of this organization .",
"Here we report on progress in iden... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"animal genetics",
"trait locus",
"heredity",
"gene expression",
"genetics",
"molecular genetics",
"biology",
"genomics",
"structural genomics",
"genetics and genomics"
] | A Complex Genomic Rearrangement Involving the Endothelin 3 Locus Causes Dermal Hyperpigmentation in the Chicken | journal.pgen.1002412 | null | [
[
"Fibromelanosis ( FM ) is characterized by intense pigmentation of the dermal layer of skin across the entire body , which results in a dark blue appearance when viewed through the clear epidermis ( Figure 1 ) .",
"The term Fibromelanosis was coined to denote the association of pigmentation with internal ... | [
"Dermal hyperpigmentation or Fibromelanosis ( FM ) is one of the few examples of skin pigmentation phenotypes in the chicken , where most other pigmentation variants influence feather color and patterning .",
"The Silkie chicken is the most widespread and well-studied breed displaying this phenotype .",
"The pr... | [
"The process of animal domestication has been a long and ongoing effort of the human race to cultivate beneficial traits in agriculturally productive or otherwise beneficial species .",
"We are just now beginning to understand the effect this type of selection pressure has had on genetic variation and overall gen... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"sequencing techniques",
"dermatology",
"medicine and health sciences",
"otology",
"ear infections",
"genome analysis",
"molecular biology techniques",
"mammalian genomics",
"rna sequencing",
"research and analysis methods",
"genome complexity",
"antisense rna",
"gene expression",
"warts",... | The full transcription map of mouse papillomavirus type 1 (MmuPV1) in mouse wart tissues | journal.ppat.1006715 | null | [
[
"Human papillomaviruses are a group of small , non-enveloped , epitheliotropic DNA tumor viruses whose infection can result in benign lesions ( called warts or papillomas ) and in some cases cause malignancies .",
"Certain genotypes of HPVs , such as HPV-16 , HPV-18 , and HPV-31 , that infect mucosal epit... | [
"Mouse papillomavirus type 1 ( MmuPV1 ) provides , for the first time , the opportunity to study infection and pathogenesis of papillomaviruses in the context of laboratory mice .",
"In this report , we define the transcriptome of MmuPV1 genome present in papillomas arising in experimentally infected mice using a... | [
"Papillomavirus ( PV ) infections lead to development of both benign warts and cancers .",
"Because PVs are epitheliotropic and species specific , it has been extremely challenging to study PV infection in the context of a naturally occurring infection in a tractable laboratory animal .",
"The recent discovery ... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | An RxLR Effector from Phytophthora infestans Prevents Re-localisation of Two Plant NAC Transcription Factors from the Endoplasmic Reticulum to the Nucleus | journal.ppat.1003670 | null | [
[
"Lacking an adaptive immune system , plants have evolved a two-tier surveillance system to detect and deflect pathogen incursions .",
"The first layer is triggered by receptor-like kinase pattern recognition receptors ( RLK-PRRs ) , which recognise conserved non-self molecules or pathogen associated molec... | [
"The potato late blight pathogen Phytophthora infestans secretes an array of effector proteins thought to act in its hosts by disarming defences and promoting pathogen colonisation .",
"However , little is known about the host targets of these effectors and how they are manipulated by the pathogen .",
"This wor... | [
"The plant immune system is activated following the perception of exposed , essential and invariant microbial molecules that are recognised as non-self .",
"A major component of plant immunity is the transcriptional induction of genes involved in a wide array of defence responses .",
"In turn , adapted pathogen... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"cell physiology",
"medicine and health sciences",
"cell division analysis",
"cell cycle and cell division",
"cell processes",
"cloning",
"surgical and invasive medical procedures",
"cell polarity",
"stem cells",
"bioassays and physiological analysis",
"molecular biology techniques",
"epigenet... | Aging alters the epigenetic asymmetry of HSC division | journal.pbio.2003389 | null | [
[
"Hematopoietic homeostasis depends on the ability of hematopoietic stem cells ( HSCs ) to balance symmetric and asymmetric divisions over an organism’s lifespan .",
"Asymmetric divisions allow one daughter cell to differentiate while the other retains its stem cell potential .",
"In contrast , symmetr... | [
"Hematopoietic stem cells ( HSCs ) balance self-renewal and differentiation to maintain homeostasis .",
"With aging , the frequency of polar HSCs decreases .",
"Cell polarity in HSCs is controlled by the activity of the small RhoGTPase cell division control protein 42 ( Cdc42 ) .",
"Here we demonstrate—using ... | [
"Stem cells are unique cells that can differentiate to produce more stem cells or other types of cells and can divide both symmetrically ( to produce daughter cells with the same fate ) and asymmetrically ( to produce one daughter cell that retains stem cell potential and one that differentiates ) .",
"The mechan... | 2018 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"public health and epidemiology"
] | Best Practices in Dengue Surveillance: A Report from the Asia-Pacific and Americas Dengue Prevention Boards | journal.pntd.0000890 | null | [
[
"Dengue virus , which is most commonly transmitted by the Aedes aegypti mosquito , is the most important mosquito-borne viral disease affecting humans [1] .",
"Caused by one of four serotypes , dengue fever ( DF ) produces a spectrum of clinical illness that ranges from an influenza-like illness to a fata... | [
"Dengue fever is a virus infection that is spread by the Aedes aegypti mosquito and can cause severe disease especially in children .",
"Dengue fever is a major problem in tropical and sub-tropical regions of the world .",
"We invited dengue experts from around the world to attend meetings to discuss dengue sur... | [
"The Pediatric Dengue Vaccine Initiative organized Dengue Prevention Boards in the Asia-Pacific and the Americas regions consisting of dengue experts from endemic countries .",
"Both Boards convened meetings to review issues in surveillance .",
"Through presentations , facilitated discussions , and surveys , th... | 2010 |
[
"Introduction",
"Results and discussion",
"Concluding remarks",
"Materials and methods"
] | [
"horizontal gene transfer",
"genome evolution",
"invertebrate genomics",
"sequence assembly tools",
"gene transfer",
"genome analysis",
"genomic libraries",
"genomics",
"molecular evolution",
"comparative genomics",
"animal genomics",
"eukaryota",
"rotifers",
"genetics",
"biology and lif... | Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species | journal.pbio.2004830 | null | [
[
"The bdelloid rotifers are a class of microscopic invertebrates found in freshwater habitats worldwide .",
"Two life history characteristics make these soft-bodied filter feeders unusual among animals .",
"First , bdelloids famously lack males [1] or cytological evidence of meiosis [2 , 3] and are onl... | [
"Bdelloid rotifers are a class of microscopic invertebrates that have existed for millions of years apparently without sex or meiosis .",
"They inhabit a variety of temporary and permanent freshwater habitats globally , and many species are remarkably tolerant of desiccation .",
"Bdelloids offer an opportunity ... | [
"Bdelloid rotifers are microscopic animals that live in freshwater habitats throughout the world .",
"Two life history characteristics distinguish these common invertebrates as extraordinary .",
"First , they have existed for millions of years apparently without sex: males have not been reported , and females p... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"microarrays",
"genome expression analysis",
"genomics",
"gene expression",
"genetics",
"molecular genetics",
"biology",
"computational biology",
"genetics and genomics",
"dna transcription"
] | Analysis of a Gene Regulatory Cascade Mediating Circadian Rhythm in Zebrafish | journal.pcbi.1002940 | null | [
[
"The circadian rhythm evolved as an adaptation to the Earth's daily light cycle .",
"In complex animals , each tissue or cell type contains a functional clock that is controlled by the central pacemaker .",
"In mammals , the suprachiasmatic nucleus ( SCN ) in the hypothalamus acts as the central circa... | [
"In the study of circadian rhythms , it has been a puzzle how a limited number of circadian clock genes can control diverse aspects of physiology .",
"Here we investigate circadian gene expression genome-wide using larval zebrafish as a model system .",
"We made use of a spatial gene expression atlas to investi... | [
"For most animals whose lives are dependent on the sun , circadian clocks govern their daily behaviors and physiology .",
"In different animals , novel functions under the circadian clock's control can evolve as adaptations to their specific environment .",
"A zebrafish demonstrates a remarkably high level of i... | 2013 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"biochemistry",
"immunology",
"biology"
] | Premolis semirufa (Walker, 1856) Envenomation, Disease Affecting Rubber Tappers of the Amazon: Searching for Caterpillar-Bristles Toxic Components | journal.pntd.0001531 | null | [
[
"Moths and butterflies are insects of the Lepidoptera order , of which the young stage is called larva .",
"The larval form of some families of moths containing urticating hairs is known as caterpillar .",
"Although caterpillar venoms have not been analyzed as much as the venoms from snakes , spiders ... | [
"The caterpillar of the moth Premolis semirufa ( Lepidoptera: Arctiidae ) , commonly named Pararama , is endemic of the Amazon basin .",
"Accidental contact with these caterpillar bristles causes local symptoms such as intense heat , pain , edema and itching which last for three to seven days; however , after mul... | [
"Pararama , the popular name of the larval form of the moth Premolis semirufa inhabits rubber plantations in the Amazon region and the accidental contact of the skin with the caterpillar's bristles or cocoons results in immediate and intense heat , pain , edema , and itching .",
"In many cases a chronic inflammat... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"biophysics/theory and simulation",
"computational biology"
] | A Novel Three-Phase Model of Brain Tissue Microstructure | journal.pcbi.1000152 | null | [
[
"Brain tissue is naturally divided into two domains , the intracellular space ( ICS ) and the extracellular space ( ECS ) .",
"The ICS is a tightly packed composite of neurons , glia and their cellular extensions , and the ECS is the microenvironment that separates brain cells [1] .",
"The structural ... | [
"We propose a novel biologically constrained three-phase model of the brain microstructure .",
"Designing a realistic model is tantamount to a packing problem , and for this reason , a number of techniques from the theory of random heterogeneous materials can be brought to bear on this problem .",
"Our analysis... | [
"The goal of the present work is to develop a biologically constrained three-dimensional model of the brain microstructure .",
"This is an important task because the brain's three-dimensional microstructure cannot be directly visualized , yet a knowledge of its structure is essential for understanding normal brai... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"bacterial pathogens",
"host-pathogen interaction",
"biology",
"microbiology"
] | Shigella IpaH0722 E3 Ubiquitin Ligase Effector Targets TRAF2 to Inhibit PKC–NF-κB Activity in Invaded Epithelial Cells | journal.ppat.1003409 | null | [
[
"The intestinal epithelium deploys multiple sensors and defense systems against microbial intrusion .",
"Microbial components and infection-associated cellular damage are recognized as pathogen-associated molecular patterns ( PAMPs ) and as danger-associated molecular patterns ( DAMPs ) , respectively .",... | [
"NF-κB plays a central role in modulating innate immune responses to bacterial infections .",
"Therefore , many bacterial pathogens deploy multiple mechanisms to counteract NF-κB activation .",
"The invasion of and subsequent replication of Shigella within epithelial cells is recognized by various pathogen reco... | [
"In response to bacterial infection , host cells induce a plethora of innate immune responses to combat the infection .",
"However , many bacterial pathogens have developed sophisticated mechanisms to evade the host's immune system .",
"Because NF-κB is crucial for innate immune responses against bacterial infe... | 2013 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious diseases",
"biology",
"genomics",
"microbiology",
"genetics and genomics"
] | Footprint of Positive Selection in Treponema pallidum subsp. pallidum Genome Sequences Suggests Adaptive Microevolution of the Syphilis Pathogen | journal.pntd.0001698 | null | [
[
"Syphilis continues to be a common and serious disease , affecting at least 25 million persons worldwide [1] .",
"It is a recognized cofactor in the transmission and acquisition of HIV [2] , [3] , and is a major cause of stillbirth and perinatal morbidity particularly in the developing world [4] , [5] .",... | [
"In the rabbit model of syphilis , infection phenotypes associated with the Nichols and Chicago strains of Treponema pallidum ( T . pallidum ) , though similar , are not identical .",
"Between these strains , significant differences are found in expression of , and antibody responses to some candidate virulence f... | [
"During infection , the agent of syphilis , Treponema pallidum subsp .",
"pallidum ( T . pallidum ) , successfully evades the host immune defenses and establishes a persistent infection that can cause blindness , paralysis , or even death in some individuals that progress to the tertiary stage of the disease .",
... | 2012 |
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