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",
"Materials and Methods",
"Results",
"Discussion"
] | [
"viral transmission and infection",
"vector biology",
"virology",
"emerging viral diseases",
"biology",
"microbiology",
"viral replication",
"viral vectors"
] | Variation in Vector Competence for Dengue Viruses Does Not Depend on Mosquito Midgut Binding Affinity | journal.pntd.0001172 | null | [
[
"Dengue viruses , which cause millions of cases of dengue fever ( DF ) and dengue hemorrhagic fever ( DHF ) each year in over 100 countries , are transmitted by two species of mosquitoes , Aedes aegypti and Aedes albopictus .",
"These vectors directly determine the rates of transmission of dengue viruses ... | [
"Dengue virus genotypes of Southeast Asian origin have been associated with higher virulence and transmission compared to other genotypes of serotype 2 ( DEN-2 ) .",
"We tested the hypothesis that genetic differences in dengue viruses may result in differential binding to the midgut of the primary vector , Aedes ... | [
"Several factors , such as mosquito and virus genetics and environmental variables , determine the ability of mosquitoes to transmit dengue viruses .",
"In this report , we describe new and important information that in some ways contradicts what is in the literature .",
"Midgut infection barriers have been des... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"invertebrates",
"medicine and health sciences",
"gene regulation",
"microbiology",
"animals",
"wolbachia",
"invertebrate genomics",
"animal models",
"drosophila melanogaster",
"model organisms",
"micrornas",
"bacteria",
"drosophila",
"research and analysis methods",
"small interfering r... | Wolbachia Blocks Viral Genome Replication Early in Infection without a Transcriptional Response by the Endosymbiont or Host Small RNA Pathways | journal.ppat.1005536 | null | [
[
"Arthropod-borne viruses ( arboviruses ) pose a considerable threat to human and animal health , yet effective control measures have proven difficult to implement [1 , 2] .",
"In recent years novel means of reducing their replication in arthropod vectors have been suggested as an alternative way to reduce... | [
"The intracellular endosymbiotic bacterium Wolbachia can protect insects against viral infection , and is being introduced into mosquito populations in the wild to block the transmission of arboviruses that infect humans and are a major public health concern .",
"To investigate the mechanisms underlying this anti... | [
"The intracellular endosymbiotic bacterium Wolbachia can protect insects against viral infection .",
"However , the mechanisms underlying this antiviral activity are poorly understood .",
"We have developed a new model system combining Wolbachia-infected Drosophila melanogaster cell culture and the model mosqui... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biotechnology",
"bioengineering",
"systems biology",
"biological systems engineering",
"control theory",
"mathematics",
"molecular biology",
"applied mathematics",
"synthetic biology",
"biology",
"nonlinear dynamics",
"genetics and genomics",
"engineering"
] | Construction and Modelling of an Inducible Positive Feedback Loop Stably Integrated in a Mammalian Cell-Line | journal.pcbi.1002074 | null | [
[
"Synthetic biology can be used to uncover the design principles of natural biological systems through the rational construction of simplified regulatory networks [1] .",
"So far , it has been shown that feedback and feed-forward loops are essential regulatory motifs involved in transcriptional regulation ... | [
"Understanding the relationship between topology and dynamics of transcriptional regulatory networks in mammalian cells is essential to elucidate the biology of complex regulatory and signaling pathways .",
"Here , we characterised , via a synthetic biology approach , a transcriptional positive feedback loop ( PF... | [
"Synthetic Biology aims at designing and building new biological functions in living organisms .",
"At the same time , Synthetic Biology approaches can be used to uncover the design principles of natural biological systems through the rational construction of simplified regulatory networks .",
"Mathematical mod... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"auditory system",
"biology",
"sensory systems",
"sensory perception",
"neuroscience"
] | Competing Sound Sources Reveal Spatial Effects in Cortical Processing | journal.pbio.1001319 | Neurons in the avian auditory forebrain show strong sensitivity to the spatial configuration of two competing sources, even though there is only weak spatial dependence for any single source. | [
[
"Past studies of spatial effects in auditory cortex have focused on how spatial location is encoded .",
"These studies typically find that single-unit spatial tuning in cortex is weak [1]–[4] , not topographically organized [5] , [6] , and not encoded independently of other perceptually important features... | [
"Why is spatial tuning in auditory cortex weak , even though location is important to object recognition in natural settings ?",
"This question continues to vex neuroscientists focused on linking physiological results to auditory perception .",
"Here we show that the spatial locations of simultaneous , competin... | [
"When a listener is presented with many sound sources at once , it is easier to understand a particular source when it comes from a different spatial location than the other competing sources .",
"However , past studies of auditory cortex generally find that in response to a single sound source , there is not a p... | 2012 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"tropical diseases",
"microbiology",
"geographical locations",
"parasitic diseases",
"parasitic protozoans",
"parasitology",
"protozoans",
"africa",
"cameroon",
"parasitic intestinal diseases",
"malarial parasites",
"people and places",
"helminth infections"... | The Effect of Intestinal Parasitic Infection on the Clinical Outcome of Malaria in Coinfected Children in Cameroon | journal.pntd.0004673 | null | [
[
"Malaria and intestinal parasitic infections ( IPIs ) are parasitic diseases that are highly endemic in Sub-Saharan Africa , especially in impoverished and poor sanitary settings .",
"In 2013 , there were 198 million cases and 584000 deaths as a result of malaria worldwide [1] .",
"The majority of dea... | [
"The interaction between intestinal parasites and malaria is still not clear .",
"Data in published literature are conflicting .",
"We studied the effect of intestinal parasitic infection ( IPI ) on the clinical outcome of malaria in coinfected children .",
"In a cross sectional study performed between Octobe... | [
"Coinfection with malaria and intestinal parasites are common in Sub-Saharan Africa , particularly in impoverished and poor sanitary settings .",
"The interaction between intestinal parasites and malaria in coinfected children is still not clear .",
"Some published papers suggest intestinal parasites , especial... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"children",
"acoustics",
"education",
"visual signals",
"sociology",
"social sciences",
"neuroscience",
"age groups",
"probability distribution",
"mathematics",
"vision",
"families",
"schools",
"probability theory",
"people and places",
"physics",
"psychology",
"biology and life sc... | The Development of Audio-Visual Integration for Temporal Judgements | journal.pcbi.1004865 | null | [
[
"Imagine you are at an academic conference .",
"A heated debate turns nasty and one scientist is repeatedly hit before falling to the floor .",
"You are later asked how many punches were thrown .",
"You confidently answer ‘3’; you were able to combine information from audition and vision , having ... | [
"Adults combine information from different sensory modalities to estimate object properties such as size or location .",
"This process is optimal in that",
"( i ) sensory information is weighted according to relative reliability: more reliable estimates have more influence on the combined estimate and",
"( ii... | [
"To complete everyday activities , such as judging where or when something occurred , we combine information from multiple senses such as vision and audition .",
"In adults , this merging of information is optimal: more reliable sensory estimates have more influence ( higher weight ) in the combined , multisensor... | 2016 |
[
"Introduction",
"Results/Discussion",
"Materials and Methods"
] | [
"molecular neuroscience",
"developmental neuroscience",
"behavioral neuroscience",
"biology",
"neuroscience"
] | EGL-13/SoxD Specifies Distinct O2 and CO2 Sensory Neuron Fates in Caenorhabditis elegans | journal.pgen.1003511 | null | [
[
"The capacity of the nervous system to sense and respond to fluctuations in the external and internal environment is essential for homeostasis and survival .",
"Neuronally controlled homeostatic buffering is delivered through cellular and systemic physiological adjustments and by seeking optimal environme... | [
"Animals harbor specialized neuronal systems that are used for sensing and coordinating responses to changes in oxygen ( O2 ) and carbon dioxide ( CO2 ) .",
"In Caenorhabditis elegans , the O2/CO2 sensory system comprises functionally and morphologically distinct sensory neurons that mediate rapid behavioral resp... | [
"During the development of an organism , certain neurons are programmed to perform specific tasks .",
"For example , motor neurons coordinate locomotion and sensory neurons recognize specific environmental cues .",
"The molecular mechanisms that generate specific neuronal classes are not fully understood .",
... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"eye lens",
"medicine and health sciences",
"methods and resources",
"ocular anatomy",
"marmosets",
"vertebrates",
"animals",
"mammals",
"notch signaling",
"animal models",
"primates",
"cell signaling",
"experimental organism systems",
"eyes",
"calcium signaling",
"research and analysi... | Gene expression in response to optical defocus of opposite signs reveals bidirectional mechanism of visually guided eye growth | journal.pbio.2006021 | null | [
[
"Myopia ( nearsightedness ) is an eye disorder characterized by blurred distance vision caused by negative refractive errors when the eye grows too long for its optical power .",
"It is widespread [1] , and the prevalence has been increasing around the world at an alarming rate , reaching 80%–90% in sever... | [
"Myopia ( nearsightedness ) is the most common eye disorder , which is rapidly becoming one of the leading causes of vision loss in several parts of the world because of a recent sharp increase in prevalence .",
"Nearwork , which produces hyperopic optical defocus on the retina , has been implicated as one of the... | [
"The worldwide prevalence of myopia is predicted to increase from the current 23% to about 50% in the next three decades .",
"Although much effort has been directed towards elucidating the mechanisms underlying refractive eye development and myopia , treatment options for myopia are mostly limited to optical corr... | 2018 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | A Novel Clinical Grading Scale to Guide the Management of Crusted Scabies | journal.pntd.0002387 | null | [
[
"Scabies is a parasitic infestation caused by the mite Sacroptes scabiei var hominis .",
"Globally , over 300 million people are estimated to be affected [1] .",
"The mite is endemic in disadvantaged and impoverished communities [2] , [3] .",
"In Australia Indigenous people suffer a significant di... | [
"Crusted scabies , or hyperinfestation with Sarcoptes scabiei , occurs in people with an inadequate immune response to the mite .",
"In recent decades , data have emerged suggesting that treatment of crusted scabies with oral ivermectin combined with topical agents leads to lower mortality , but there are no gene... | [
"Crusted scabies is a severe skin condition caused by a microscopic parasitic mite .",
"It occurs in people whose immune system does not react properly to the mite and it leads to crusting and cracking of the skin and can cause death .",
"The usual treatment for crusted scabies is a tablet called ivermectin com... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genetics and genomics/gene discovery",
"cell biology/cellular death and stress responses",
"genetics and genomics/complex traits",
"genetics and genomics/genetics of disease",
"cell biology/cell adhesion",
"genetics and genomics/medical genetics"
] | Identification and Replication of Three Novel Myopia Common Susceptibility Gene Loci on Chromosome 3q26 using Linkage and Linkage Disequilibrium Mapping | journal.pgen.1000220 | null | [
[
"Myopia is the most common eye disorder , affecting an estimated 36% of adults over 20 years in the United States [1] and up to 61% in East Asia [2] .",
"Myopia is a significant cause of vision loss [3] , and is becoming the most common single cause of blindness in the working age population [4] .",
"... | [
"Refractive error is a highly heritable quantitative trait responsible for considerable morbidity .",
"Following an initial genome-wide linkage study using microsatellite markers , we confirmed evidence for linkage to chromosome 3q26 and then conducted fine-scale association mapping using high-resolution linkage ... | [
"Successful gene mapping strategies for common disease continue to require careful consideration of basic study design with the advent of genome-wide association studies .",
"Here , we take advantage of prior information that the heritability of the quantitative trait myopia in the general population is high and ... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"plant science",
"rna interference",
"plant biology",
"gene expression",
"plant genetics",
"biology",
"molecular cell biology",
"molecular biology"
] | Functional Specialization of the Plant miR396 Regulatory Network through Distinct MicroRNA–Target Interactions | journal.pgen.1002419 | null | [
[
"MicroRNAs ( miRNAs ) are small RNA molecules , ∼21 nt in length , that are widespread regulators of gene expression in animals and plants [reviewed in [1] , [2]] .",
"They recognize target RNAs by base complementarity and guide them to cleavage or translational arrest [1] .",
"MiRNA-encoding genes ar... | [
"MicroRNAs ( miRNAs ) are ∼21 nt small RNAs that regulate gene expression in animals and plants .",
"They can be grouped into families comprising different genes encoding similar or identical mature miRNAs .",
"Several miRNA families are deeply conserved in plant lineages and regulate key aspects of plant devel... | [
"Plants and other multicellular organisms need precise spatio-temporal control of gene expression , and this regulatory capacity depends , in part , on small RNAs .",
"MicroRNAs ( miRNAs ) are one class of ∼21 nt small RNAs that originate from endogenous fold-back precursors found in plants and animals .",
"The... | 2012 |
[
"Introduction",
"Material and methods",
"Results",
"Discussion"
] | [
"invertebrates",
"species colonization",
"medicine and health sciences",
"ecology and environmental sciences",
"body fluids",
"pathology and laboratory medicine",
"togaviruses",
"viral transmission and infection",
"invasive species",
"pathogens",
"microbiology",
"saliva",
"animals",
"alpha... | Anopheles mosquitoes may drive invasion and transmission of Mayaro virus across geographically diverse regions | journal.pntd.0006895 | null | [
[
"Mayaro virus ( MAYV ) is a member of the genus Alphavirus ( family Togaviridae ) which was first isolated from the blood of five febrile workers in Mayaro County , Trinidad , in 1954 [1] .",
"MAYV has a single-stranded positive-sense RNA genome of approximately 11 . 7 kb and is classified into three geno... | [
"The Togavirus ( Alphavirus ) Mayaro virus ( MAYV ) was initially described in 1954 from Mayaro County ( Trinidad ) and has been responsible for outbreaks in South America and the Caribbean .",
"Imported MAYV cases are on the rise , leading to invasion concerns similar to Chikungunya and Zika viruses .",
"Littl... | [
"Mayaro virus ( MAYV ) is a mosquito-borne Alphavirus responsible for outbreaks in South America and the Caribbean .",
"In this study we infected different species of mosquito ( belonging to the genera Aedes , Anopheles and Culex ) with MAYV and tested their capacity to transmit the virus at different time points... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"medicine and health sciences",
"nervous system",
"neuronal differentiation",
"brain",
"vertebrates",
"marmosets",
"neuroscience",
"animals",
"mammals",
"cell differentiation",
"primates",
"animal models",
"developmental biology",
"brain mapping",
"experimental organism systems",
"old ... | A blueprint of mammalian cortical connectomes | journal.pbio.2005346 | null | [
[
"Mapping and understanding the wiring of the cerebral cortex at the micro- , meso- , and macroscale level is a central challenge in neuroscience [1–9] .",
"Extensive studies have mapped the structural connections among cortical areas—that is , the macroscale connectional architecture—in different mammals ... | [
"The cerebral cortex of mammals exhibits intricate interareal wiring .",
"Moreover , mammalian cortices differ vastly in size , cytological composition , and phylogenetic distance .",
"Given such complexity and pronounced species differences , it is a considerable challenge to decipher organizational principles... | [
"The cerebral cortex is wired in a highly intricate manner and exhibits striking differences across mammals—for instance , in overall size and number of neurons .",
"Here , we uncover common , but also species-specific , principles that link the physical , cellular , and connectional architecture of mouse , cat ,... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"invertebrates",
"medicine and health sciences",
"toxins",
"vesicles",
"pathology and laboratory medicine",
"enzymes",
"enzymology",
"animals",
"toxicology",
"toxic agents",
"animal models",
"drosophila melanogaster",
"model organisms",
"signs and symptoms",
"experimental organism system... | Anthrax edema toxin disrupts distinct steps in Rab11-dependent junctional transport | journal.ppat.1006603 | null | [
[
"Bacterial pathogens enhance infectivity by secreting toxins that deregulate immune signaling pathways or disrupt host cellular barriers .",
"One class of toxins produced by diverse bacterial species dramatically increases intracellular concentrations of cAMP .",
"This striking evolutionary convergenc... | [
"Various bacterial toxins circumvent host defenses through overproduction of cAMP .",
"In a previous study , we showed that edema factor ( EF ) , an adenylate cyclase from Bacillus anthracis , disrupts endocytic recycling mediated by the small GTPase Rab11 .",
"As a result , cargo proteins such as cadherins fai... | [
"Recent anthrax outbreaks in Zambia and northern Russia and biodefense preparedness highlight the need for new therapies to counteract fatal late-stage pathologies in patients infected with Bacillus anthracis .",
"Indeed , two toxins secreted by this pathogen—edema toxin ( ET ) and lethal toxin ( LT ) —can cause ... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"animal genetics",
"genome evolution",
"gene regulation",
"neuroscience",
"developmental biology",
"stem cells",
"molecular genetics",
"developmental neuroscience",
"animal cells",
"gene expression",
"molecular evolution",
"neural crest",
"evolutionary genetics",
"molecular biology",
"in... | BMPs Regulate msx Gene Expression in the Dorsal Neuroectoderm of Drosophila and Vertebrates by Distinct Mechanisms | journal.pgen.1004625 | null | [
[
"In both Drosophila melanogaster and vertebrates , Bone Morphogenetic Proteins ( BMPs ) are expressed in the epidermal ectoderm abutting the dorsal border of the neuroectoderm [1] .",
"The genetic network that underlies formation of a centralized nervous system consisting of segregated motor and sensory c... | [
"In a broad variety of bilaterian species the trunk central nervous system ( CNS ) derives from three primary rows of neuroblasts .",
"The fates of these neural progenitor cells are determined in part by three conserved transcription factors: vnd/nkx2 . 2 , ind/gsh and msh/msx in Drosophila melanogaster/vertebrat... | [
"The trunk nervous system of both vertebrates and invertebrates develops from three primary rows of neural stem cells whose fate is determined by neural identity genes expressed in an evolutionarily conserved dorso-ventral pattern .",
"Establishment of this pattern requires a shared signaling pathway in both grou... | 2014 |
[
"Introduction",
"Materials and Methods",
"Results and Discussion"
] | [] | Towards a Molecular Understanding of the Link between Imatinib Resistance and Kinase Conformational Dynamics | journal.pcbi.1004578 | null | [
[
"The revolutionary discovery of the potent anticancer drug imatinib ( Gleevec , 2001 ) [1] had a huge impact on cancer therapy .",
"This drug has a striking efficacy in the early stages of chronic myeloid leukemia ( CML ) , with 90% of patients showing remission [2 , 3] .",
"Imatinib targets the Abl t... | [
"Due to its inhibition of the Abl kinase domain in the BCR-ABL fusion protein , imatinib is strikingly effective in the initial stage of chronic myeloid leukemia with more than 90% of the patients showing complete remission .",
"However , as in the case of most targeted anti-cancer therapies , the emergence of dr... | [
"Imatinib remains the most important and studied anti-cancer drug for cancer therapy in its new paradigm .",
"Due to its inhibition of the Abl kinase domain , imatinib is strikingly effective in the initial stage of chronic myeloid leukemia with more than 90% of the patients showing a complete remission .",
"Ho... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"genome expression analysis",
"functional genomics",
"integrative physiology",
"anatomy and physiology",
"physiological processes",
"genetics and genomics",
"musculoskeletal system",
"geriatrics",
"gene expression",
"biology",
"systems biology",
"physiogenomics",
"physiology",
... | Molecular Networks of Human Muscle Adaptation to Exercise and Age | journal.pgen.1003389 | null | [
[
"Discovery of the biological determinants of muscle mass and functional molecular phenotypes has substantial bearing on the fields of human performance ( e . g . hypertrophy , strength or endurance adaptations [1] , [2] ) and human health ( countering muscle atrophy and deconditioning occurring in older age o... | [
"Physical activity and molecular ageing presumably interact to precipitate musculoskeletal decline in humans with age .",
"Herein , we have delineated molecular networks for these two major components of sarcopenic risk using multiple independent clinical cohorts .",
"We generated genome-wide transcript profile... | [
"A fundamental challenge for modern medicine is to generate new strategies to cope with the rising proportion of older people within society , as unaddressed it will make many health care systems financially unviable .",
"Ageing impacts both quality of life and longevity through reduced musculoskeletal function .... | 2013 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine and health sciences",
"enzyme-linked immunoassays",
"onchocerca volvulus",
"helminths",
"purification techniques",
"immunology",
"tropical diseases",
"parasitic diseases",
"animals",
"onchocerca",
"nematode infections",
"neglected tropical diseases",
"onchocercia... | Identification and characterization of the Onchocerca volvulus Excretory Secretory Product Ov28CRP, a putative GM2 activator protein | journal.pntd.0007591 | null | [
[
"Human onchocerciasis also known as River Blindness is a tropical disease caused by the parasitic nematode Onchocerca volvulus and is the world’s second leading cause of infectious blindness after trachoma .",
"The infective larval stages ( L3 ) are transmitted through the bites of infective blackflies of... | [
"Onchocerca volvulus is the nematode pathogen responsible for human onchocerciasis also known as “River blindness” , a neglected tropical disease that affects up to 18 million people worldwide .",
"Helminths Excretory Secretory Products ( ESPs ) constitute a rich repertoire of molecules that can be exploited for ... | [
"Human onchocerciasis is a neglected tropical disease affecting millions in endemic tropical countries and is the world’s second leading cause of infectious blindness .",
"Onchocerca volvulus , the causative agent of the disease is a tissue dwelling nematode diagnosed by identification of microfilaria larval stag... | 2019 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion",
"Conclusions"
] | [
"blood cells",
"invertebrates",
"medicine and health sciences",
"immune cells",
"pathology and laboratory medicine",
"immunology",
"vertebrates",
"fibrin",
"animals",
"mammals",
"primates",
"lymph nodes",
"signs and symptoms",
"lymphatic system",
"kidneys",
"old world monkeys",
"whit... | Ivermectin treatment of Loa loa hyper-microfilaraemic baboons (Papio anubis): Assessment of microfilarial load reduction, haematological and biochemical parameters and histopathological changes following treatment | journal.pntd.0005576 | null | [
[
"Loa loa is a parasitic filarial nematode of humans , restricted to the rainforest and forest fringes of West and Central Africa [1] , causing the relatively well-tolerated disease-loiasis .",
"Loiasis has two very characteristic clinical features: Calabar swellings , corresponding to an angioedema of all... | [
"Individuals with high intensity of Loa loa are at risk of developing serious adverse events ( SAEs ) post treatment with ivermectin .",
"These SAEs have remained unclear and a programmatic impediment to the advancement of community directed treatment with ivermectin .",
"The pathogenesis of these SAEs followin... | [
"The pathogenesis of the serious adverse reactions that occur in patients carrying high loads ( usually > 30 , 000mf/mL ) of circulating Loa loa parasites and treated with ivermectin has to date not been clearly defined at the tissue level .",
"These reactions , which can result in the death of many of those affe... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"neuroscience/motor systems",
"genetics and genomics/complex traits",
"genetics and genomics/genetics of disease",
"neuroscience/neurobiology of disease and regeneration",
"cardiovascular disorders/myocardial infarction",
"genetics and genomics/medical genetics",
"genetics and genomics/population geneti... | Genetic Determinants of Circulating Sphingolipid Concentrations in European Populations | journal.pgen.1000672 | null | [
[
"Sphingolipids are essential components of plasma membranes and endosomes and are believed to play critical roles in cell surface protection , protein and lipid transport and sorting , and cellular signalling cascades .",
"They are known to have roles in both health and disease [1] , [2] .",
"Several ... | [
"Sphingolipids have essential roles as structural components of cell membranes and in cell signalling , and disruption of their metabolism causes several diseases , with diverse neurological , psychiatric , and metabolic consequences .",
"Increasingly , variants within a few of the genes that encode enzymes invol... | [
"Although several rare monogenic diseases are caused by defects in enzymes involved in sphingolipid biosynthesis and metabolism , little is known about the major variants that control the circulating levels of these important bioactive molecules .",
"As well as being essential components of plasma membranes and e... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"statistics",
"messenger rna",
"plasmid construction",
"organisms",
"protein expression",
"fungi",
"mathematics",
"dna construction",
"molecular biology techniques",
"cellular structures and organelles",
"research and analysis methods",
"translation initiation",
"gene expression",
"molecul... | Conserved mRNA-granule component Scd6 targets Dhh1 to repress translation initiation and activates Dcp2-mediated mRNA decay in vivo | journal.pgen.1007806 | null | [
[
"After being transcribed and processed in the nucleus , and exported to the cytoplasm , mRNAs can either engage with the translational machinery for protein synthesis , undergo storage in a translationally silent state , or be targeted for degradation .",
"Cellular mRNAs can alternate between these proces... | [
"Scd6 protein family members are evolutionarily conserved components of translationally silent mRNA granules .",
"Yeast Scd6 interacts with Dcp2 and Dhh1 , respectively a subunit and a regulator of the mRNA decapping enzyme , and also associates with translation initiation factor eIF4G to inhibit translation in c... | [
"Previous work showed that Scd6 homologs in Drosophila , Xenopus , and humans are associated with translationally repressed mRNAs in RNA granules , and that they interact with other mRNA silencing factors , including homologs of RNA helicase Dhh1 .",
"However , there is little evidence that such Scd6 homologs are... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"infectious diseases",
"medicine and health sciences",
"evolutionary rate",
"simulation and modeling",
"immunity",
"infectious disease epidemiology",
"epidemiology",
"biology and life sciences",
"immunology",
"evolutionary biology",
"evolutionary immunology",
"evolutionary processes",
"epide... | Accounting for non-stationarity in epidemiology by embedding time-varying parameters in stochastic models | journal.pcbi.1006211 | null | [
[
"Our approach is based on three main components: an epidemiological model embedded in a state-space framework , a diffusion process for each time-varying parameter and an up-to-date Bayesian inference technique based on adaptive PMCMC .",
"The main advantage of the state-space framework is the use of two ... | [
"The spread of disease through human populations is complex .",
"The characteristics of disease propagation evolve with time , as a result of a multitude of environmental and anthropic factors , this non-stationarity is a key factor in this huge complexity .",
"In the absence of appropriate external data source... | [
"As our world becomes more and more globalized , infectious disease poses an ever-increasing threat to human health .",
"The multitude of environmental and behavioral factors , which account for the spread of infectious diseases , are ever-evolving and thus infectious diseases propagation is complex .",
"In the... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"computational biology/population genetics",
"genetics and genomics",
"public health and epidemiology",
"computational biology/genomics"
] | Genome-Wide Meta-Analysis for Serum Calcium Identifies Significantly Associated SNPs near the Calcium-Sensing Receptor (CASR) Gene | journal.pgen.1001035 | null | [
[
"Calcium is the most abundant mineral in the human body contributing approximately one kilogram to the average adult human body mass .",
"Whereas 99% of calcium is stored in the skeleton and teeth , the remaining 1% circulates in the bloodstream and is involved in many physiological processes including it... | [
"Calcium has a pivotal role in biological functions , and serum calcium levels have been associated with numerous disorders of bone and mineral metabolism , as well as with cardiovascular mortality .",
"Here we report results from a genome-wide association study of serum calcium , integrating data from four indep... | [
"Calcium levels in blood serum play an important role in many biological processes .",
"The regulation of serum calcium is under strong genetic control .",
"This study describes the first meta-analysis of a genome-wide association study from four cohorts totaling 12 , 865 participants of European and Indian Asi... | 2010 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion",
"Conclusions"
] | [
"bacteriology",
"antimicrobials",
"livestock",
"organismal evolution",
"medicine and health sciences",
"pathology and laboratory medicine",
"pathogens",
"drugs",
"microbiology",
"vertebrates",
"animals",
"antibiotic resistance",
"microbial evolution",
"pharmacology",
"bacterial pathogens... | Markov Networks of Collateral Resistance: National Antimicrobial Resistance Monitoring System Surveillance Results from Escherichia coli Isolates, 2004-2012 | journal.pcbi.1005160 | null | [
[
"The evolution of acquired antimicrobial resistance ( AMR ) in pathogenic microorganisms is one of the foremost challenges in public health today .",
"Antimicrobial drug use in medicine and agriculture generates selective pressure that selects for AMR in bacterial populations and facilitates emergence of ... | [
"Surveillance of antimicrobial resistance ( AMR ) is an important component of public health .",
"Antimicrobial drug use generates selective pressure that may lead to resistance against to the administered drug , and may also select for collateral resistances to other drugs .",
"Analysis of AMR surveillance dat... | [
"Surveillance of antimicrobial resistance patterns is an important responsibility in modern public health .",
"Due to the genetic configuration of bacterial pathogens , the use of a single antimicrobial drug may select for bacteria that are resistant to multiple other antimicrobial drugs via set of mechanisms col... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"infectious diseases/neglected tropical diseases",
"neurological disorders/infectious diseases of the nervous system",
"microbiology/innate immunity",
"immunology/innate immunity",
"immunology/genetics of the immune system",
"infectious diseases/bacterial infections",
"microbiology/medical microbiology"... | The Influence of Host and Bacterial Genotype on the Development of Disseminated Disease with Mycobacterium tuberculosis | journal.ppat.1000034 | null | [
[
"It is estimated that one third of the world's population is infected with Mycobacterium tuberculosis ( M . tuberculosis ) , although the majority will never develop active disease .",
"The factors that govern the development of tuberculosis disease are complex and incompletely understood .",
"Various... | [
"The factors that govern the development of tuberculosis disease are incompletely understood .",
"We hypothesized that some strains of Mycobacterium tuberculosis ( M . tuberculosis ) are more capable of causing disseminated disease than others and may be associated with polymorphisms in host genes responsible for... | [
"Tuberculosis , caused by the bacterium Mycobacterium tuberculosis , kills over 2 million people each year .",
"It is estimated that approximately one-third of the world population is infected with M . tuberculosis , though the majority will never develop active disease .",
"The most severe form of tuberculosis... | 2008 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"schistosoma",
"invertebrates",
"schistosoma mansoni",
"medicine and health sciences",
"helminths",
"tropical diseases",
"parasitic diseases",
"animals",
"mathematics",
"statistics (mathematics)",
"pharmaceutics",
"neglected tropical diseases",
"research and analysis methods",
"schistosoma... | The Schistosomiasis Clinical Trials Landscape: A Systematic Review of Antischistosomal Treatment Efficacy Studies and a Case for Sharing Individual Participant-Level Data (IPD) | journal.pntd.0004784 | null | [
[
"Despite its heavy burden worldwide , schistosomiasis remains a neglected tropical disease ( NTD ) which fails to attract enough attention from research and funding bodies to generate novel drugs and diagnostics [1 , 2] .",
"Currently , only one drug , praziquantel ( PZQ ) , is available to treat schistos... | [
"Schistosomiasis control mainly relies on preventive chemotherapy with praziquantel ( PZQ ) distributed through mass drug administration .",
"With a target of 260 million treatments yearly , reliably assessing and monitoring efficacy is all-important .",
"Recommendations for treatment and control of schistosomi... | [
"Schistosomiasis is a parasitic disease prevalent in tropical climates , especially Africa .",
"To control morbidity and eventually eliminate the disease , the World Health Organisation recommends that populations living in endemic areas be preventively treated with praziquantel .",
"This means hundreds of mill... | 2016 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"pathology and laboratory medicine",
"clinical research design",
"tropical diseases",
"parasitic diseases",
"wolbachia",
"nematode infections",
"research design",
"filariasis",
"signs and symptoms",
"pharmaceutics",
"neglected tropical diseases",
"bacteria",
... | Adverse events following single dose treatment of lymphatic filariasis: Observations from a review of the literature | journal.pntd.0006454 | null | [
[
"Infection with the filarial nematode parasites Wuchereria bancrofti , Brugia malayi , or Brugia timori is known as lymphatic filariasis ( LF ) .",
"These infections cause severe , disabling conditions including lymphedema , elephantiasis , and hydroceles in tens of millions of people in tropical and subt... | [
"WHO’s Global Programme to Eliminate Lymphatic Filariasis ( LF ) uses mass drug administration ( MDA ) of anthelmintic medications to interrupt LF transmission in endemic areas .",
"Recently , a single dose combination of ivermectin ( IVM ) , diethylcarbamazine ( DEC ) , and albendazole ( ALB ) was shown to be ma... | [
"WHO’s Global Programme to Eliminate Lymphatic Filariais ( LF ) supports annual mass drug administration to over 400 million people in LF-endemic areas each year .",
"Two drug combinations ( either DEC or ivermectin , given with albendazole ) have been recommended in most endemic areas .",
"With the exception o... | 2018 |
[
"Introduction",
"Discussion",
"Materials and Methods"
] | [
"developmental biology",
"cell biology",
"genetics",
"biology and life sciences",
"microbiology",
"evolutionary biology",
"molecular biology"
] | A Complex Genetic Switch Involving Overlapping Divergent Promoters and DNA Looping Regulates Expression of Conjugation Genes of a Gram-positive Plasmid | journal.pgen.1004733 | null | [
[
"Bacteria exchange genetic material at high rates by different processes , which are collectively named Horizontal Gene Transfer ( HGT ) .",
"HGT can be beneficial for bacteria because the newly acquired DNA may endow them with novel features enabling them to adapt to changing conditions in the environmen... | [
"Plasmid conjugation plays a significant role in the dissemination of antibiotic resistance and pathogenicity determinants .",
"Understanding how conjugation is regulated is important to gain insights into these features .",
"Little is known about regulation of conjugation systems present on plasmids from Gram-... | [
"Plasmids are extrachromosomal , autonomously replicating units that are harbored by many bacteria .",
"Many plasmids encode transfer function allowing them to be transferred into plasmid-free bacteria by a process named conjugation .",
"Since many of them also carry antibiotic resistance genes , plasmid-mediat... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"medicine and health sciences",
"vesicles",
"microbiology",
"viral structure",
"epithelial cells",
"membrane fusion",
"rice",
"experimental organism systems",
"seedlings",
"plants",
"cellular structures and organelles",
"insect vectors",
"endosomes",
"research and analysis methods",
"inf... | Tenuivirus utilizes its glycoprotein as a helper component to overcome insect midgut barriers for its circulative and propagative transmission | journal.ppat.1007655 | null | [
[
"Arthropod insects play critical roles in epidemics of numerous animal and plant viruses [1–3] .",
"Based on the mode of transmission , plant viruses can be classified into non-persistent , semi-persistent or persistent transmitted viruses [4–6] .",
"For non-persistent or semi-persistent transmissions... | [
"Many persistent transmitted plant viruses , including rice stripe virus ( RSV ) , cause serious damage to crop production worldwide .",
"Although many reports have indicated that a successful insect-mediated virus transmission depends on a proper interaction between the virus and its insect vector , the mechanis... | [
"Over 75% of the known plant viruses are insect transmitted .",
"Understanding how plant viruses interact with their insect vectors during virus transmission is a key step towards the successful management of plant viruses worldwide .",
"Several models for the direct or indirect virus–insect vector interactions... | 2019 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"invertebrates",
"innate immune system",
"medicine and health sciences",
"body fluids",
"immune physiology",
"cytokines",
"helminths",
"immunology",
"hookworms",
"vertebrates",
"parasitic diseases",
"animals",
"mammals",
"vaccines",
"developmental biology",
"molecular development",
"... | A highly expressed intestinal cysteine protease of Ancylostoma ceylanicum protects vaccinated hamsters from hookworm infection | journal.pntd.0007345 | null | [
[
"Human hookworms ( Necator americanus , Ancylostoma duodenale , and Ancylostoma ceylanicum ) are soil-transmitted nematodes ( STNs ) that infect the small intestine and feed on blood [1] .",
"Human STNs encompass three phylogenetically distant parasites: hookworms , large roundworms ( Ascaris lumbricoides... | [
"Human hookworms ( Necator americanus , Ancylostoma duodenale , and Ancylostoma ceylanicum ) are intestinal blood-feeding parasites that infect ~500 million people worldwide and are among the leading causes of iron-deficiency anemia in the developing world .",
"Drugs are useful against hookworm infections , but h... | [
"Hookworms are voracious , blood-feeding , soil-transmitted nematode parasites .",
"Adult hookworms infect the small intestine , causing iron-deficiency anemia and other complications .",
"Hookworms are among the most disabling parasites of the developing world .",
"Drugs are useful for controlling hookworm d... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"invertebrates",
"medicine and health sciences",
"neural networks",
"nervous system",
"caenorhabditis",
"social sciences",
"neuroscience",
"animals",
"biomechanics",
"biological locomotion",
"motor neurons",
"animal models",
"caenorhabditis elegans",
"model organisms",
"brain mapping",
... | Spatiotemporal Feedback and Network Structure Drive and Encode Caenorhabditis elegans Locomotion | journal.pcbi.1005303 | null | [
[
"The exact process through which the nematode Caenorhabditis elegans ( C . elegans ) generates the rhythmic activity necessary for locomotion remains unclear [1] .",
"In many other species , a Central Pattern Generator ( CPG ) is typically the source of rhythmic activity [2–6] .",
"There is insufficie... | [
"Using a computational model of the Caenorhabditis elegans connectome dynamics , we show that proprioceptive feedback is necessary for sustained dynamic responses to external input .",
"This is consistent with the lack of biophysical evidence for a central pattern generator , and recent experimental evidence that... | [
"The nematode C . elegans lives a complex and rich life despite having only 302 neurons .",
"The full connectivity between these neurons ( its “connectome” ) has been measured , making it an ideal model system for understanding how neural processing generates behavior .",
"However , unlike most animals , it doe... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genetic networks",
"caulobacter",
"gene regulation",
"microbiology",
"next-generation sequencing",
"developmental biology",
"genome analysis",
"microbial growth and development",
"bacteria",
"microbial genomics",
"bacterial genomics",
"genome complexity",
"bacterial genomes",
"caulobacter... | The Global Regulatory Architecture of Transcription during the Caulobacter Cell Cycle | journal.pgen.1004831 | null | [
[
"The regulation of timing and ordered progression of cell cycle events is central to the survival of any organism and is one of the fundamental processes of life .",
"The gram-negative α-proteobacterium Caulobacter crescentus ( Caulobacter , hereafter ) is an important model organism for the study of the ... | [
"Each Caulobacter cell cycle involves differentiation and an asymmetric cell division driven by a cyclical regulatory circuit comprised of four transcription factors ( TFs ) and a DNA methyltransferase .",
"Using a modified global 5′ RACE protocol , we globally mapped transcription start sites ( TSSs ) at base-pa... | [
"The generation of diverse cell types occurs through two fundamental processes; asymmetric cell division and cell differentiation .",
"Cells progress through these developmental changes guided by complex and layered genetic programs that lead to differential expression of the genome .",
"To explore how a geneti... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | The Structural Basis for Activation and Inhibition of ZAP-70 Kinase Domain | journal.pcbi.1004560 | null | [
[
"ZAP–70 is part of the Syk family of protein kinases , and a key player in the adaptive immune system .",
"[1] It is expressed in T cells and natural killer cells [2] and is essential for their development and function .",
"Inactivating mutations of ZAP–70 cause selective T cell deficiency in humans ,... | [
"ZAP–70 ( Zeta-chain-associated protein kinase 70 ) is a tyrosine kinase that interacts directly with the activated T-cell receptor to transduce downstream signals , and is hence a major player in the regulation of the adaptive immune response .",
"Dysfunction of ZAP–70 causes selective T cell deficiency that in ... | [
"ZAP–70 is a key protein kinase in the adaptive immune system .",
"It is essential for development and function of T cells and natural killer cells , and associated mutations can lead to conditions such as severe combined immunodeficiency ( SCID ) .",
"Here , simulations of the ZAP–70 kinase domain are used to ... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"computational biology/macromolecular structure analysis"
] | The Overlap of Small Molecule and Protein Binding Sites within Families of Protein Structures | journal.pcbi.1000668 | null | [
[
"Protein–protein interactions are a broad class of therapeutic and chemical biology targets [1] .",
"Traditionally these targets were thought to be refractory to small molecule modulation .",
"However , recent efforts have led to interaction modulators that are valuable tools in mapping signalling net... | [
"Protein–protein interactions are challenging targets for modulation by small molecules .",
"Here , we propose an approach that harnesses the increasing structural coverage of protein complexes to identify small molecules that may target protein interactions .",
"Specifically , we identify ligand and protein bi... | [
"Proteins function through their interactions with other biological molecules , including other proteins .",
"Often times , these interactions underlie cellular processes that go awry in disease .",
"Therefore , modulating these interactions with small molecules is an active area of research for new drugs to tr... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine and health sciences",
"neural networks",
"brain",
"social sciences",
"neuroscience",
"learning and memory",
"perception",
"cognitive psychology",
"mathematics",
"human performance",
"statistics (mathematics)",
"cognition",
"memory",
"vision",
"computer and information sciences"... | Deep Neural Networks as a Computational Model for Human Shape Sensitivity | journal.pcbi.1004896 | null | [
[
"Understanding how the human visual system processes visual information involves building models that would account for human-level performance on a multitude of tasks .",
"For years , despite the best efforts , computational understanding of even the simplest everyday tasks such as object and scene recog... | [
"Theories of object recognition agree that shape is of primordial importance , but there is no consensus about how shape might be represented , and so far attempts to implement a model of shape perception that would work with realistic stimuli have largely failed .",
"Recent studies suggest that state-of-the-art ... | [
"Shape plays an important role in object recognition .",
"Despite years of research , no models of vision could account for shape understanding as found in human vision of natural images .",
"Given recent successes of deep neural networks ( DNNs ) in object recognition , we hypothesized that DNNs might in fact ... | 2016 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"cost-effectiveness analysis",
"economic analysis",
"tropical diseases",
"geographical locations",
"social sciences",
"vaccines",
"bacterial diseases",
"age groups",
"animal behavior",
"neglected tropical diseases",
"infectious disease control",
"zoology",
"... | The impact and cost-effectiveness of controlling cholera through the use of oral cholera vaccines in urban Bangladesh: A disease modeling and economic analysis | journal.pntd.0006652 | null | [
[
"The Ganges River Delta and Bay of Bengal , including Bangladesh , are considered the birthplace of cholera and the origin of six of the seven cholera pandemics recorded in modern times[1] .",
"While national population-based estimates of cholera incidence are lacking in Bangladesh , the perception among ... | [
"Cholera remains an important public health problem in major cities in Bangladesh , especially in slum areas .",
"In response to growing interest among local policymakers to control this disease , this study estimated the impact and cost-effectiveness of preventive cholera vaccination over a ten-year period in a ... | [
"While oral cholera vaccines are increasingly being used in the past few years , mainly to curtail or preempt cholera outbreaks , they have yet to be used on a large scale to control endemic cholera in a high-burden country like Bangladesh .",
"This study examines the potential impact on disease and value of vacc... | 2018 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"blood cells",
"inflammatory diseases",
"cardiomyopathies",
"medicine and health sciences",
"immune cells",
"enzyme-linked immunoassays",
"immunology",
"tropical diseases",
"parasitic diseases",
"parasitic protozoans",
"protozoans",
"neglected tropical diseases",
"immunologic techniques",
... | Distinct monocyte subset phenotypes in patients with different clinical forms of chronic Chagas disease and seronegative dilated cardiomyopathy | journal.pntd.0006887 | null | [
[
"Chagas disease , caused by infection with the intracellular protozoan parasite Trypanosoma cruzi , affects 6–7 million people and represents the most frequent cause of infectious cardiomyopathy in the world [1 , 2] .",
"Three factors are likely associated with the development of the more severe clinical ... | [
"Chronic infection with Trypanosoma cruzi leads to a constant stimulation of the host immune system .",
"Monocytes , which are recruited in response to inflammatory signals , are divided into classical CD14hiCD16— , non-classical CD14loCD16+ and intermediate CD14hiCD16+ subsets .",
"In this study , we evaluated... | [
"Monocytes are key players during infection , and they leave the bloodstream and migrate into tissues in response to inflammatory signals .",
"Although the recruitment of monocytes is essential for the effective control and clearance of microorganisms , they can also be highly damaging to neighboring tissues .",
... | 2018 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | Fecal Occult Blood and Fecal Calprotectin as Point-of-Care Markers of Intestinal Morbidity in Ugandan Children with Schistosoma mansoni Infection | journal.pntd.0002542 | null | [
[
"With over 207 million people worldwide infected with schistosomiasis , mostly in sub-Saharan Africa , there is still a pressing need to optimize field-appropriate tools for morbidity staging and monitoring of clinical disease [1] .",
"In recent years there has been a scale-up of schistosomiasis control p... | [
"Calprotectin is a calcium-binding cytoplasmic protein found in neutrophils and increasingly used as a marker of bowel inflammation .",
"Fecal occult blood ( FOB ) is also a dependable indicator of bowel morbidity .",
"The objective of our study was to determine the applicability of these tests as surrogate mar... | [
"The severity of intestinal schistosomiasis , a disease caused by Schistosoma mansoni infection , is likely under-reported in part due to the scarcity of field-appropriate morbidity markers .",
"Downstream potential complications of this disease include anemia , failure to thrive , and chronic multi-organ damage ... | 2013 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious diseases",
"public health and epidemiology",
"epidemiology",
"neglected tropical diseases",
"parasitic diseases"
] | Mapping of Schistosomiasis and Soil-Transmitted Helminthiasis in the Regions of Centre, East and West Cameroon | journal.pntd.0001553 | null | [
[
"Recent years have witnessed an increased interest in the control of neglected tropical diseases ( NTDs ) , and today there exists a global momentum for the control of these diseases , as well as an unprecedented opportunity for cost-effective action , through an integrated control [1]–[5] .",
"Interest i... | [
"Schistosomiasis and soil-transmitted helminthiasis ( STH ) are widely distributed in Cameroon .",
"Although mass drug administration ( MDA ) of mebendazole is implemented nationwide , treatment with praziquantel was so far limited to the three northern regions and few health districts in the southern part of Cam... | [
"Schistosomiasis and soil-transmitted helminthiasis ( STH ) are a major public health problem in Cameroon .",
"The national control strategy of these diseases was based on historical data collected 25 years ago , which might be outdated in some situations due to several factors including control activities , impr... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"immunology",
"microbiology",
"molecular genetics",
"signaling in cellular processes",
"biology",
"molecular biology",
"immune system",
"systems biology",
"signal transduction",
"immunity",
"virology",
"genetics",
"molecular cell biology",
"genetics and genomics"
] | Stochastic Expression of the Interferon-β Gene | journal.pbio.1001249 | The analysis of stochastic interferon-beta gene expression in virus-infected mammalian cells reveals that the levels of components required for virtually every step in the virus induction pathway are limiting. | [
[
"Eukaryotic cells respond to extracellular signals and environmental stresses by coordinately activating specific sets of genes .",
"Signals from the cell surface or cytoplasm trigger signaling pathways that culminate in the binding of distinct combinations of coordinately activated transcription factors ... | [
"Virus infection of mammalian cells induces the production of high levels of type I interferons ( IFNα and β ) , cytokines that orchestrate antiviral innate and adaptive immunity .",
"Previous studies have shown that only a fraction of the infected cells produce IFN .",
"However , the mechanisms responsible for... | [
"Eukaryotic cells can respond to extracellular signals by triggering the activation of specific genes .",
"Viral infection of mammalian cells , for example , induces a high level of expression of type I interferons ( IFNα and β ) , proteins required for antiviral immunity that protects cells from the infection ."... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"bacteriology",
"biofilms",
"chemical compounds",
"metabolic processes",
"biological cultures",
"microbiology",
"threonine",
"organic compounds",
"fermentation",
"enterobacteriaceae",
"amino acids",
"bacteria",
"research and analysis methods",
"amino acid metabolism",
"proteins",
"chem... | Biofilm microenvironment induces a widespread adaptive amino-acid fermentation pathway conferring strong fitness advantage in Escherichia coli | journal.pgen.1006800 | null | [
[
"Bacteria rapidly adapt to changes in available resources and environmental fluctuations due to their remarkable ability to finely tune their physiology and metabolism [1 , 2] .",
"Although bacterial adaptations have been primarily studied in liquid cultures composed of free-swimming planktonic cells , ex... | [
"Bacterial metabolism has been studied primarily in liquid cultures , and exploration of other natural growth conditions may reveal new aspects of bacterial biology .",
"Here , we investigate metabolic changes occurring when Escherichia coli grows as surface-attached biofilms , a common but still poorly character... | [
"Whereas Escherichia coli does not naturally produce the 1-propanol unless subjected to extensive genetic modifications , we show that this important industrial commodity is produced in hypoxic conditions inside biofilms .",
"1-propanol production corresponds to a native threonine fermentation pathway previously ... | 2017 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"invertebrates",
"classical mechanics",
"fluid mechanics",
"caenorhabditis",
"surface tension",
"animals",
"animal models",
"membrane proteins",
"developmental biology",
"caenorhabditis elegans",
"viscosity",
"model organisms",
"materials science",
"experimental organism systems",
"damag... | The importance of mechanical constraints for proper polarization and psuedo-cleavage furrow generation in the early Caenorhabditis elegans embryo | journal.pcbi.1006294 | null | [
[
"The geometry of a cell can have a profound influence on cell function and survival [1–4] .",
"Cell geometry is generated by internal structures such as the cytoskeleton , and can also be externally imposed by interactions with neighboring cells or mechanical structures like an eggshell .",
"Eggshells... | [
"Intracellular polarization , where a cell specifies a spatial axis by segregation of specific factors , is a fundamental biological process .",
"In the early embryo of the nematode worm Caenorhabditis elegans ( C . elegans ) , polarization is often accompanied by deformations of the cortex , a highly contractile... | [
"Polarization , whereby molecules and proteins are asymmetrically distributed throughout the cell , is a vital process for many cellular functions .",
"In the early C . elegans embryo the asymmetric distribution of cell cytoskeleton during the initiation of polarization leads to asymmetric contractions which are ... | 2018 |
[
"Introduction",
"Materials and methods",
"Results and discussion"
] | [
"blood cells",
"flow cytometry",
"medicine and health sciences",
"immune cells",
"enzyme-linked immunoassays",
"pathology and laboratory medicine",
"pathogens",
"immunology",
"microbiology",
"vertebrates",
"animals",
"mammals",
"cell differentiation",
"retroviruses",
"primates",
"immun... | Tracking KLRC2 (NKG2C)+ memory-like NK cells in SIV+ and rhCMV+ rhesus macaques | journal.ppat.1007104 | null | [
[
"Although NK cells have traditionally been thought to be innate immune cells that lack the antigen-specificity seen in the adaptive immune system , NK cells have very recently been reported to possess memory and memory-like functions [1–8] .",
"Though this area of investigation is currently developing , s... | [
"Natural killer ( NK ) cells classically typify the nonspecific effector arm of the innate immune system , but have recently been shown to possess memory-like properties against multiple viral infections , most notably CMV .",
"Expression of the activating receptor NKG2C is elevated on human NK cells in response ... | [
"Natural killer ( NK ) cells are a crucial component of the early innate immune response , and although NK cell responses have been thought be only non-specific , recent evidence suggests that NK cells are capable of expanding with some specificity , indicative of a memory-like adaptive response .",
"The activati... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"phosphorylation",
"molecular probe techniques",
"293t cells",
"cell cycle and cell division",
"biological cultures",
"cell processes",
"immunoblotting",
"dna-binding proteins",
"mitosis",
"epigenetics",
"molecular biology techniques",
"chromatin",
"research and analysis methods",
"chromos... | Murine leukemia virus p12 tethers the capsid-containing pre-integration complex to chromatin by binding directly to host nucleosomes in mitosis | journal.ppat.1007117 | null | [
[
"The retroviral Gag polyprotein plays essential roles at multiple stages of the viral life cycle .",
"In late infection , Gag mediates the assembly and release of progeny viral particles .",
"It is then proteolyically cleaved during viral maturation into a number of individual proteins .",
"In add... | [
"The murine leukaemia virus ( MLV ) Gag cleavage product , p12 , is essential for both early and late steps in viral replication .",
"The N-terminal domain of p12 binds directly to capsid ( CA ) and stabilises the mature viral core , whereas defects in the C-terminal domain ( CTD ) of p12 can be rescued by additi... | [
"In addition to matrix , capsid and nucleocapsid , the Gag polyproteins of many retroviruses also encode additional cleavage products , such as the p12 protein of murine leukemia virus .",
"p12 is essential for both early and late replication events , but its function during early infection remains poorly charact... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"mathematics",
"diabetes and endocrinology",
"computational biology/systems biology"
] | A Three Species Model to Simulate Application of Hyperbaric Oxygen Therapy to Chronic Wounds | journal.pcbi.1000451 | null | [
[
"Chronic leg ulceration is a significant socioeconomic problem [1] .",
"Those who suffer from leg ulcers experience considerable pain , immobility and decreased quality of life [2] .",
"Approximately 3% of the over 60 age group suffer from lower limb ulceration [3] .",
"A successfully healing woun... | [
"Chronic wounds are a significant socioeconomic problem for governments worldwide .",
"Approximately 15% of people who suffer from diabetes will experience a lower-limb ulcer at some stage of their lives , and 24% of these wounds will ultimately result in amputation of the lower limb .",
"Hyperbaric Oxygen Ther... | [
"In the time it takes you to read this paragraph , one person will have undergone a lower limb amputation due to diabetic foot disease .",
"With the global diabetes population on the rise and set to reach 330 million by 2025 , the need for research into therapies and technologies that have the potential to preven... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"social sciences",
"neuroscience",
"cognitive psychology",
"computational neuroscience",
"vision",
"neuronal tuning",
"animal cells",
"behavior",
"psychology",
"cellular neuroscience",
"cell biology",
"single neuron function",
"neurons",
"psychophysics",
"biology and life sciences",
"c... | An Extended Normalization Model of Attention Accounts for Feature-Based Attentional Enhancement of Both Response and Coherence Gain | journal.pcbi.1005225 | null | [
[
"Attention to visual features like a specific orientation or motion direction has been shown to enhance visual responses to the attended feature across visual cortex in both monkey neurophysiology [1] and human fMRI data [2–4] .",
"Prior studies have reported that feature-based attention enhances response... | [
"Paying attention to a sensory feature improves its perception and impairs that of others .",
"Recent work has shown that a Normalization Model of Attention ( NMoA ) can account for a wide range of physiological findings and the influence of different attentional manipulations on visual performance .",
"A key p... | [
"We report a pattern of feature-based attentional effects on human psychophysical performance , which cannot be accounted for by the Normalization Model of Attention using biologically plausible parameters .",
"Specifically , this prominent model of attentional modulation predicts that attention to a visual featu... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"theoretical biology",
"biology",
"evolutionary biology"
] | Evolutionary Dynamics of Strategic Behavior in a Collective-Risk Dilemma | journal.pcbi.1002652 | null | [
[
"Cooperation , between selfish individuals in public goods games [1]–[8] , becomes particularly challenging when the prospects are uncertain and a critical number of cooperative acts is required .",
"Investing in the prevention of climate change is in vain if too many other do not invest [9]–[13] .",
... | [
"A collective-risk social dilemma arises when a group must cooperate to reach a common target in order to avoid the risk of collective loss while each individual is tempted to free-ride on the contributions of others .",
"In contrast to the prisoners' dilemma or public goods games , the collective-risk dilemma en... | [
"The evolution of cooperation is a fascinating topic with a wide range of applications , from microbial evolution to global cooperation of humans in the context of climate change .",
"Motivated by the prospect of dangerous climate change , behavioral experiments of a ‘collective-risk dilemma’ were conducted , whe... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"gene regulation",
"regulatory proteins",
"dna-binding proteins",
"dna transcription",
"developmental biology",
"speciation",
"transcription factors",
"molecular development",
"population biology",
"thermodynamics",
"entropy",
"proteins",
"gene expression",
"physics",
"morphogens",
"po... | Biophysics and population size constrains speciation in an evolutionary model of developmental system drift | journal.pcbi.1007177 | null | [
[
"The genotype-phenotype map we use is a modification of the one described in [17] .",
"The evolutionary task set for the gene regulation module is to turn an exponentially decaying morphogen gradient ( M ) across a field of cells in an embryo into a sharp step function profile of a downstream transcriptio... | [
"Developmental system drift is a likely mechanism for the origin of hybrid incompatibilities between closely related species .",
"We examine here the detailed mechanistic basis of hybrid incompatibilities between two allopatric lineages , for a genotype-phenotype map of developmental system drift under stabilisin... | [
"The process of speciation is of fundamental importance to the field of evolution as it is intimately connected to understanding the immense bio-diversity of life .",
"There is still relatively little understanding of the underlying genetic mechanisms that give rise to hybrid incompatibilities with results sugges... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"cell physiology",
"fluorescence imaging",
"medicine and health sciences",
"vesicles",
"pathology and laboratory medicine",
"viral transmission and infection",
"pathogens",
"microbiology",
"orthomyxoviruses",
"viruses",
"membrane fusion",
"rna viruses",
"cellular structures and organelles",
... | Interferon-induced transmembrane protein 3 blocks fusion of sensitive but not resistant viruses by partitioning into virus-carrying endosomes | journal.ppat.1007532 | null | [
[
"Fusion of enveloped viruses with the host cell membrane is a key step leading to infection .",
"Viral fusion is initiated upon interactions between virus surface glycoproteins and cellular receptor ( s ) and/or upon the reduction in pH that follows endocytosis ( reviewed in [1–3] ) .",
"The extensive... | [
"Late endosome-resident interferon-induced transmembrane protein 3 ( IFITM3 ) inhibits fusion of diverse viruses , including Influenza A virus ( IAV ) , by a poorly understood mechanism .",
"Despite the broad antiviral activity of IFITM3 , viruses like Lassa virus ( LASV ) , are fully resistant to its inhibitory ... | [
"Expression of interferon-induced transmembrane proteins ( IFITMs ) in target cells potently inhibits fusion of many unrelated enveloped viruses , including the Influenza A virus , whereas arenaviruses , such as the Lassa fever virus , are resistant to these factors .",
"The mechanism by which IFITMs interfere wi... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"invertebrates",
"rna interference",
"gene regulation",
"animals",
"animal models",
"developmental biology",
"drosophila melanogaster",
"model organisms",
"experimental organism systems",
"epigenetics",
"sexual dimorphism",
"morphogenesis",
"drosophila",
"research and analysis methods",
... | Precise staging of beetle horn formation in Trypoxylus dichotomus reveals the pleiotropic roles of doublesex depending on the spatiotemporal developmental contexts | journal.pgen.1008063 | null | [
[
"Beetle horns are used as weapons for intraspecific combats between males .",
"Beetle horns display sexual dimorphism in many Scarab species , and their shapes , numbers , sizes and forming regions are highly diverged even among closely related species [1–3] .",
"Interestingly , the diversified horn f... | [
"Many scarab beetles have sexually dimorphic exaggerated horns that are an evolutionary novelty .",
"Since the shape , number , size , and location of horns are highly diverged within Scarabaeidae , beetle horns are an attractive model for studying the evolution of sexually dimorphic and novel traits .",
"In be... | [
"Beetles in the family Scarabaeidae have various types of horns on their heads and thoraces , and the shape , size , number , and location of these horns are highly diversified within the group .",
"In addition , many scarab beetle horns are sexually dimorphic .",
"The acquisition of these evolutionarily novel ... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"computer science",
"biology"
] | RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State | journal.pcbi.1002968 | null | [
[
"Enhancers are distal regulatory elements with key roles in the regulation of gene expression .",
"In higher eukaryotes , a diverse repertoire of transcription factors bind to enhancers to orchestrate critical cellular events including differentiation [1] , [2] , maintenance of cell-identity [3] , [4] and... | [
"Transcriptional enhancers play critical roles in regulation of gene expression , but their identification in the eukaryotic genome has been challenging .",
"Recently , it was shown that enhancers in the mammalian genome are associated with characteristic histone modification patterns , which have been increasing... | [
"Enhancers are regions in the genome that can activate the expression of a gene irrespective of their location with respect to the gene .",
"Identifying these elements is critical in understanding regulatory differences between different cell-types .",
"Since enhancers lack characteristic sequence features and ... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | Thermodynamics and H2 Transfer in a Methanogenic, Syntrophic Community | journal.pcbi.1004364 | null | [
[
"Microorganisms in nature engage in a variety of interactions with other species in their environment .",
"Syntrophy is one such type of inter-species interaction in which one species lives off the metabolic by-products of another [1–3] .",
"Synthetic methanogenic communities [4] are typically tightly... | [
"Microorganisms in nature do not exist in isolation but rather interact with other species in their environment .",
"Some microbes interact via syntrophic associations , in which the metabolic by-products of one species serve as nutrients for another .",
"These associations sustain a variety of natural communit... | [
"Natural and engineered microbial communities can contain up to hundreds of interacting microbes .",
"These interactions may be positive , negative , or neutral , as well as obligate or facultative .",
"Syntrophy is an obligate , positive interaction , in which one species lives off the metabolic by-products of... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"infectious diseases",
"hiv",
"virology",
"retrovirology and hiv immunopathogenesis",
"biology",
"microbiology",
"viral diseases"
] | Preservation of Tetherin and CD4 Counter-Activities in Circulating Vpu Alleles despite Extensive Sequence Variation within HIV-1 Infected Individuals | journal.ppat.1003895 | null | [
[
"The HIV-1 genes nef , vpu , vif and vpr are known as accessory genes and early in vitro studies showed them dispensable for viral replication in some tissue culture cell lines [1] .",
"In vivo , however , these proteins are essential for the transmission and persistence of immunodeficiency viruses .",
... | [
"The HIV-1 Vpu protein is expressed from a bi-cistronic message late in the viral life cycle .",
"It functions during viral assembly to maximise infectious virus release by targeting CD4 for proteosomal degradation and counteracting the antiviral protein tetherin ( BST2/CD317 ) .",
"Single genome analysis of vp... | [
"The accessory protein Vpu , encoded by HIV-1 , performs at least two major roles in the virus life cycle , namely the degradation of newly synthesized CD4 molecules and the counteraction of a host antiviral protein , tetherin .",
"These activities promote the release of infectious viruses from host cells , and r... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine and health sciences",
"decision making",
"brain",
"social sciences",
"neuroscience",
"number theory",
"optimization",
"cognitive psychology",
"mathematics",
"cognition",
"computational neuroscience",
"real numbers",
"neuronal tuning",
"coding mechanisms",
"computer and informat... | Robust and efficient coding with grid cells | journal.pcbi.1005922 | null | [
[
"Optimising neuronal systems for efficient processing and representation of information is a key principle for both understanding and designing neuronal circuits [1] , but deciding whether a particular neuronal phenomenon reflects an optimisation process is often difficult .",
"Grid cells in the medial en... | [
"The neuronal code arising from the coordinated activity of grid cells in the rodent entorhinal cortex can uniquely represent space across a large range of distances , but the precise conditions for optimal coding capacity are known only for environments with finite size .",
"Here we consider a coding scheme that... | [
"Navigation in natural , open environments poses serious challenges to animals as the distances to be represented may span several orders of magnitudes and are potentially unbounded .",
"The recently discovered grid cells in the rodent brain are though to play a crucial role in generating unique representations f... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"developmental biology/aging",
"diabetes and endocrinology"
] | Molecular Evolution and Functional Characterization of Drosophila Insulin-Like Peptides | journal.pgen.1000857 | null | [
[
"The ability of organisms to respond appropriately to changes in their environment is key to survival and reproductive success .",
"An essential environmental variable for all organisms is their food supply and energetically demanding processes , such as growth , metabolism and reproduction are matched to... | [
"Multicellular animals match costly activities , such as growth and reproduction , to the environment through nutrient-sensing pathways .",
"The insulin/IGF signaling ( IIS ) pathway plays key roles in growth , metabolism , stress resistance , reproduction , and longevity in diverse organisms including mammals ."... | [
"The insulin/IGF signalling ( IIS ) pathway plays key roles in growth , metabolism , reproduction , and longevity in animals as diverse as flies and mammals .",
"Most multicellular animals contain multiple IIS ligands , including 7 in the fruit fly Drosophila melanogaster ( DILP1-7 ) , implying that the diverse f... | 2010 |
[
"Introduction",
"Results and Discussion",
"Materials and Methods"
] | [
"plastids",
"molecular probe techniques",
"enzymes",
"plant cell biology",
"brassica",
"enzymology",
"chloroplasts",
"plant science",
"model organisms",
"chaperone proteins",
"molecular biology techniques",
"plants",
"cellular structures and organelles",
"enzyme chemistry",
"research and... | Specific Hsp100 Chaperones Determine the Fate of the First Enzyme of the Plastidial Isoprenoid Pathway for Either Refolding or Degradation by the Stromal Clp Protease in Arabidopsis | journal.pgen.1005824 | null | [
[
"Organelles like mitochondria and plastids play fundamental roles in all eukaryotic organisms .",
"In particular , plastids were acquired by a symbiosis between photosynthetic cyanobacteria and eukaryotic cells .",
"Today , plastids ( like mitochondria ) are intimately integrated into the metabolism o... | [
"The lifespan and activity of proteins depend on protein quality control systems formed by chaperones and proteases that ensure correct protein folding and prevent the formation of toxic aggregates .",
"We previously found that the Arabidopsis thaliana J-protein J20 delivers inactive ( misfolded ) forms of the pl... | [
"In this paper we report a relatively simple mechanism by which plant chloroplasts deal with inactive forms of DXS , the main rate-determining enzyme for the production of plastidial isoprenoids relevant for photosynthesis and development .",
"We provide evidence supporting that particular members of the Hsp100 c... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"blood cells",
"innate immune system",
"medicine and health sciences",
"parasite groups",
"immune cells",
"immune physiology",
"cytokines",
"plasmodium",
"spleen",
"immunology",
"tropical diseases",
"parasitic diseases",
"cell differentiation",
"parasitology",
"parasitemia",
"developme... | Promotion of Expansion and Differentiation of Hematopoietic Stem Cells by Interleukin-27 into Myeloid Progenitors to Control Infection in Emergency Myelopoiesis | journal.ppat.1005507 | null | [
[
"Emergency myelopoiesis is inflammation-induced hematopoiesis , which is critical for controlling systemic infection with pathogens such as a virus , bacteria , or parasite [1 , 2] .",
"In contrast to adaptive immune cells such as T cells and B cells , which can vigorously proliferate in response to their... | [
"Emergency myelopoiesis is inflammation-induced hematopoiesis to replenish myeloid cells in the periphery , which is critical to control the infection with pathogens .",
"Previously , pro-inflammatory cytokines such as interferon ( IFN ) -α and IFN-γ were demonstrated to play a critical role in the expansion of h... | [
"Emergency myelopoiesis is inflammation-induced hematopoiesis that is critical for controlling infection with pathogens , but the molecular mechanism remains incompletely understood .",
"Here , we clarify that one of the interleukin ( IL ) -6/IL-12 family cytokines , IL-27 , plays an important role in emergency m... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"neural networks",
"engineering and technology",
"signal processing",
"vertebrates",
"social sciences",
"neuroscience",
"animals",
"mammals",
"primates",
"multivariate analysis",
"mathematics",
"statistics (mathematics)",
"white noise",
"computational neuroscience",
"vision",
"old worl... | Stimulus-Driven Population Activity Patterns in Macaque Primary Visual Cortex | journal.pcbi.1005185 | null | [
[
"Dimensionality reduction has been applied to neural population activity to study decision making [1 , 2] , motor control [3–5] , olfaction [6] , working memory [7 , 8] , visual attention [9] , audition [10] , rule learning [11] , speech [12] , and more ( for a review , see [13] ) .",
"In many cases , dim... | [
"Dimensionality reduction has been applied in various brain areas to study the activity of populations of neurons .",
"To interpret the outputs of dimensionality reduction , it is important to first understand its outputs for brain areas for which the relationship between the stimulus and neural response is well ... | [
"A central goal in systems neuroscience is to understand how large populations of neurons work together to enable us to sense , to reason , and to act .",
"To go beyond single-neuron and pairwise analyses , recent studies have applied dimensionality reduction methods to neural population activity to reveal tantal... | 2016 |
[
"Introduction",
"Results/Discussion",
"Methods"
] | [
"genetics and genomics/microbial evolution and genomics",
"evolutionary biology/microbial evolution and genomics",
"genetics and genomics/comparative genomics",
"evolutionary biology/evolutionary and comparative genetics",
"molecular biology/molecular evolution",
"microbiology/microbial evolution and geno... | A Deviation from the Bipolar-Tetrapolar Mating Paradigm in an Early Diverged Basidiomycete | journal.pgen.1001052 | null | [
[
"In fungi , sexual reproduction systems have been well characterized at the molecular level in numerous species belonging to the Ascomycota and the Basidiomycota , revealing striking similarities with sex determining regions in animals and plants [1] along with unique features such as the occurrence of thousa... | [
"In fungi , sexual identity is determined by specialized genomic regions called MAT loci which are the equivalent to sex chromosomes in some animals and plants .",
"Usually , only two sexes or mating types exist , which are determined by two alternate sets of genes ( or alleles ) at the MAT locus ( bipolar system... | [
"Sexual reproduction in fungi is regulated by genomic regions called MAT loci that determine sexual identity in a manner comparable to that of sex chromosomes in animal and plants .",
"In most fungi , sexual reproduction is bipolar , i . e . , two alternate and distinct sets of genes at the MAT locus determine tw... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"animal models",
"sequence analysis",
"medicine",
"oncology",
"model organisms",
"biology",
"genomics",
"mouse",
"computational biology"
] | Insertional Mutagenesis and Deep Profiling Reveals Gene Hierarchies and a Myc/p53-Dependent Bottleneck in Lymphomagenesis | journal.pgen.1004167 | null | [
[
"The oncogenic potential of murine γ-retroviruses ( MLVs ) stems from proviral integration into host DNA , a mutagenic process which can result in activation or disruption of critical host cell genes [1] .",
"Moreover , by sequential integrations in the nascent tumour cell , MLVs can drive multiple steps ... | [
"Retroviral insertional mutagenesis ( RIM ) is a powerful tool for cancer genomics that was combined in this study with deep sequencing ( RIM/DS ) to facilitate a comprehensive analysis of lymphoma progression .",
"Transgenic mice expressing two potent collaborating oncogenes in the germ line ( CD2-MYC , -Runx2 )... | [
"Cancers are known to arise by a series of mutational and non-mutational ( epigenetic ) events but the advent of cancer genome sequencing highlights the growing challenge of separating important ( driver ) from irrelevant ( passenger ) mutations .",
"Retroviruses that induce cancer by inserting into host DNA and ... | 2014 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"pathology and laboratory medicine",
"cross-sectional studies",
"tropical diseases",
"vertebrates",
"database searching",
"parasitic diseases",
"dogs",
"animals",
"mammals",
"research design",
"mathematics",
"statistics (mathematics)",
"neglected tropical di... | Potential risk factors associated with human alveolar echinococcosis: Systematic review and meta-analysis | journal.pntd.0005801 | null | [
[
"Alveolar echinococcosis ( AE ) is considered as one of the most dangerous parasitic zoonoses occurring in the northern hemisphere .",
"The life cycle of the parasite is maintained by definitive hosts shedding eggs with the faeces and the subsequent ingestion of these eggs by suitable intermediate hosts .... | [
"Human alveolar echinococcosis ( AE ) is a severe zoonotic disease caused by the metacestode stage of Echinococcus multilocularis .",
"AE is commonly associated with a long incubation period that may last for more than ten years .",
"The objective of this systematic literature review was to identify and summari... | [
"Human alveolar echinococcosis is a severe zoonotic disease caused by the metacestode stage of the tapeworm Echinococcus multilocularis .",
"The objective of this systematic literature review was to identify and summarize the current knowledge on potential risk factors associated with human alveolar echinococcosi... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"carbohydrate metabolism",
"protein metabolism",
"chemical compounds",
"ketones",
"glucose metabolism",
"pyruvate",
"regulator genes",
"monomers (chemistry)",
"gene types",
"sequence motif analysis",
"bacteria",
"research and analysis methods",
"pseudomonas",
"sequence analysis",
"polyme... | One ligand, two regulators and three binding sites: How KDPG controls primary carbon metabolism in Pseudomonas | journal.pgen.1006839 | null | [
[
"Soil-dwelling Pseudomonas spp .",
"are exposed to a complex and dynamic physical and chemical environment , and must constantly adapt their cell physiology by changing the expression patterns of membrane proteins , secreted small molecules , and enzymes [1] .",
"This ability to gauge the surroundings... | [
"Effective regulation of primary carbon metabolism is critically important for bacteria to successfully adapt to different environments .",
"We have identified an uncharacterised transcriptional regulator; RccR , that controls this process in response to carbon source availability .",
"Disruption of rccR in the... | [
"Here we show how Pseudomonas controls multiple different primary carbon metabolism pathways by sensing levels of KDPG , an Entner Doudoroff ( ED ) pathway intermediate .",
"KDPG binds to two highly similar transcription factors; the ED regulator HexR and the previously uncharacterised protein RccR .",
"RccR in... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Role of Tomato Lipoxygenase D in Wound-Induced Jasmonate Biosynthesis and Plant Immunity to Insect Herbivores | journal.pgen.1003964 | null | [
[
"Higher plants respond to insect attack and wounding by activating the expression of genes involved in herbivore deterrence , wound healing , and other defense-related processes [1]–[7] .",
"The wound response of tomato ( Solanum lycopersicum ) provides an attractive model to understand the signal transdu... | [
"In response to insect attack and mechanical wounding , plants activate the expression of genes involved in various defense-related processes .",
"A fascinating feature of these inducible defenses is their occurrence both locally at the wounding site and systemically in undamaged leaves throughout the plant .",
... | [
"Plants have evolved sophisticated strategies to defend themselves against insect attack .",
"Wound-inducible proteinase inhibitors ( PIs ) in tomato ( Solanum lycopersicum ) provide an attractive model to understand the signal transduction events leading from localized injury to the systemic expression of defens... | 2013 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine and health sciences",
"chemical compounds",
"geographical locations",
"microbiology",
"malathion",
"organic compounds",
"animals",
"organophosphates",
"developmental biology",
"pharmacology",
"insect vectors",
"agrochemicals",
"infectious diseases",
"antimicrob... | Laboratory selection of Aedes aegypti field populations with the organophosphate malathion: Negative impacts on resistance to deltamethrin and to the organophosphate temephos | journal.pntd.0006734 | null | [
[
"Aedes aegypti ( Linnaeus , 1762 ) is the main vector of dengue , Zika and chikungunya viruses , which are currently serious public health problems in Brazil [1] .",
"Specific medications are not available for any of these viruses .",
"One dengue vaccine was recently approved but it confers only parti... | [
"Resistance to pyrethroids and to the organophosphate temephos is widespread in Brazilian populations of the dengue vector , Aedes aegypti .",
"Thereof , since 2009 Insect Growth Regulators are employed as larvicides , and malathion is used against adults .",
"We performed laboratory selection with malathion of... | [
"Dengue , Zika and chikungunya viruses affect millions of people worldwide .",
"Due to the lack of specific antivirals or to the limited supply of vaccines , focus remains on the control of the main vector , Aedes aegypti .",
"Although the importance of social participation in the elimination of A . aegypti bre... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Methods and Models"
] | [
"classical mechanics",
"engineering and technology",
"symmetry",
"microbiology",
"viral structure",
"geometry",
"simulation and modeling",
"mathematics",
"nanoparticles",
"damage mechanics",
"nanotechnology",
"research and analysis methods",
"bending",
"deformation",
"biophysics",
"phy... | Fluctuating Nonlinear Spring Model of Mechanical Deformation of Biological Particles | journal.pcbi.1004729 | null | [
[
"Single-molecule techniques , such as Atomic Force Microscopy ( AFM ) , have become widely available to explore the physical properties of biological assemblies .",
"These techniques have triggered extensive research efforts to explore the protein shells of plant and animal viruses , and bacteriophages ."... | [
"The mechanical properties of virus capsids correlate with local conformational dynamics in the capsid structure .",
"They also reflect the required stability needed to withstand high internal pressures generated upon genome loading and contribute to the success of important events in viral infectivity , such as ... | [
"Dynamic force experiments , which have become available to explore the physical properties of biological assemblies , oftentimes reveal results that are difficult to understand without theoretical framework .",
"We employed a multiscale modeling approach—a combination of Molecular Dynamics simulations of atomic ... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genetics and genomics/animal genetics",
"genetics and genomics/gene discovery",
"virology/mechanisms of resistance and susceptibility, including host\n genetics",
"genetics and genomics/genetics of the immune system",
"genetics and genomics/complex traits",
"immunology/immune respo... | NK Cell Receptor/H2-Dk–Dependent
Host Resistance to Viral Infection Is Quantitatively Modulated by
H2q Inhibitory Signals | journal.pgen.1001368 | null | [
[
"Natural killer ( NK ) cells play an important role in the innate immune response",
"against tumors , MHC-mismatched bone-marrow grafts , and pathogens [1]–[2] .",
"These cells",
"also contribute to defense against parasites and intracellular bacteria , and they",
"are critical for the control... | [
"The cytomegalovirus resistance locus Cmv3 has been linked to an",
"epistatic interaction between two loci: a Natural Killer ( NK ) cell receptor gene",
"and the major histocompatibility complex class I ( MHC-I ) locus .",
"To demonstrate",
"the interaction between Cmv3 and",
"H2k , we generated double co... | [
"Effective natural killer ( NK ) cell responses against virally infected cells are",
"regulated by NK cell receptors that specifically recognize target cells .",
"In the",
"current study , we validated the specific interaction taking place between NK",
"cell receptors and MHC class I molecules on the surfac... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | Cerebellar Nuclear Neurons Use Time and Rate Coding to Transmit Purkinje Neuron Pauses | journal.pcbi.1004641 | null | [
[
"Cerebellar nucleus ( CN ) neurons are crucial to the olivo-cerebellar circuit as they provide the sole output of the entire cerebellum [1 , 2] .",
"CN neuron’s firing patterns are of great importance for motor related tasks and representation of movement parameters [3] .",
"Within the cerebellum , th... | [
"Neurons of the cerebellar nuclei convey the final output of the cerebellum to their targets in various parts of the brain .",
"Within the cerebellum their direct upstream connections originate from inhibitory Purkinje neurons .",
"Purkinje neurons have a complex firing pattern of regular spikes interrupted by ... | [
"Neurons can transmit information by two different coding strategies: Rate coding , where the firing rate of the neuron is vital , and time coding where timing of individual spikes carries relevant information .",
"In this study we analyze the importance of brief cessations in firing of the presynaptic neuron ( p... | 2015 |
[
"Introduction",
"Models",
"Results and Discussion"
] | [
"infographics",
"chemical compounds",
"engineering and technology",
"enzymes",
"synthetic biology",
"enzymology",
"lactones",
"mathematical models",
"esters",
"dna transcription",
"systems science",
"mathematics",
"research and analysis methods",
"computer and information sciences",
"pro... | Quorum-Sensing Synchronization of Synthetic Toggle Switches: A Design Based on Monotone Dynamical Systems Theory | journal.pcbi.1004881 | null | [
[
"We benchmark our design by comparing it to Toggle B2 [4] , see Fig SI-1 . 1 in S1 Text .",
"Despite remarkable properties of design B2 , observed experimentally in controllable experimental settings [4] , and studied theoretically [16 , 17] , the fact that their functional repertoire includes not only a ... | [
"Synthetic constructs in biotechnology , biocomputing , and modern gene therapy interventions are often based on plasmids or transfected circuits which implement some form of “on-off” switch .",
"For example , the expression of a protein used for therapeutic purposes might be triggered by the recognition of a spe... | [
"For the last decade , outstanding progress has been made , and considerable practical experience has accumulated , in the construction of elementary genetic circuits that perform various tasks , such as memory storage and logical operations , in response to both exogenous and endogenous stimuli .",
"Using modern... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"developmental biology",
"plant science",
"plant growth and development",
"plant biology",
"biology"
] | FTIP1 Is an Essential Regulator Required for Florigen Transport | journal.pbio.1001313 | FT-INTERACTING PROTEIN 1 is a novel protein that is involved in transporting florigen, a long-known mobile signal that induces flowering in plants in response to day length, from companion cells to sieve elements in the phloem of Arabidopsis. | [
[
"The transition to flowering , which is crucial for the reproductive success , is the most dramatic phase change in flowering plants .",
"Plants are able to adjust the timing of this transition in response to environmental conditions , such as photoperiod , temperature , and availability of nutrients .",
... | [
"The capacity to respond to day length , photoperiodism , is crucial for flowering plants to adapt to seasonal change .",
"The photoperiodic control of flowering in plants is mediated by a long-distance mobile floral stimulus called florigen that moves from leaves to the shoot apex .",
"Although the proteins en... | [
"The transition to flowering is the most dramatic phase change in flowering plants and is crucial for reproductive success .",
"Such a transition from vegetative to reproductive growth is controlled by seasonal changes in day length .",
"Studies originally performed in the 1930s were the first to suggest that d... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genome complexity",
"genomics",
"genome evolution",
"genetics",
"synthetic biology",
"biology and life sciences",
"comparative genomics",
"molecular genetics",
"computational biology",
"evolutionary biology"
] | Reviving the Dead: History and Reactivation of an Extinct L1 | journal.pgen.1004395 | null | [
[
"L1 ( LINE-1 , Long INterspersed Element-1 ) belongs to the superfamily of autonomously replicating , retrotransposable elements that lack long terminal repeats .",
"Functional L1s are 6 , 000–7 , 000 bp long and made up of a 5′ untranslated region ( 5′UTR ) , two non-overlapping open reading frames ( ORF... | [
"Although L1 sequences are present in the genomes of all placental mammals and marsupials examined to date , their activity was lost in the megabat family , Pteropodidae , ∼24 million years ago .",
"To examine the characteristics of L1s prior to their extinction , we analyzed the evolutionary history of L1s in th... | [
"Most of a typical mammalian genome is occupied by transposable elements , which have played an important role in shaping these genomes , and L1s account for approximately half of this transposable element load .",
"Mammals have evolved several mechanisms to control L1 retrotransposition , and yet L1s remain acti... | 2014 |
[
"Introduction",
"Results/Discussion",
"Materials and Methods",
"Supporting Information"
] | [
"evolutionary biology",
"drosophila",
"physiology"
] | Gene Duplication and Adaptive Evolution of Digestive Proteases in Drosophila arizonae Female Reproductive Tracts | journal.pgen.0030148 | null | [
[
"Extensive research across a broad range of taxa has revealed that the proteins involved in sexual reproduction often evolve rapidly due to positive selection ( reviewed in [1–3] ) .",
"Although the selective forces that underlie this pattern remain unclear , it frequently has been postulated that adaptiv... | [
"It frequently has been postulated that intersexual coevolution between the male ejaculate and the female reproductive tract is a driving force in the rapid evolution of reproductive proteins .",
"The dearth of research on female tracts , however , presents a major obstacle to empirical tests of this hypothesis .... | [
"In a broad range of organisms , including humans , molecular interactions between the male ejaculate and the female reproductive tract play integral roles in sexual reproduction .",
"Although these interactions are essential , the biochemical composition of the male ejaculate can change rapidly over short evolut... | 2007 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"antimicrobials",
"neonatology",
"children",
"medicine and health sciences",
"pathology and laboratory medicine",
"maternal health",
"pathogens",
"drugs",
"immunology",
"sociology",
"microbiology",
"social sciences",
"biomarkers",
"pediatrics",
"diarrhea",
"age groups",
"women's heal... | Epidemiology of enteroaggregative Escherichia coli infections and associated outcomes in the MAL-ED birth cohort | journal.pntd.0005798 | null | [
[
"Enteroaggregative Escherichia coli ( EAEC ) infections have been increasingly recognized as important enteropathogens since their initial discovery by patterns of adherence to HEp-2 cells in E . coli isolates from Chilean children with diarrhea [1] .",
"EAEC have since been associated with foodborne outb... | [
"Enteroaggregative E . coli ( EAEC ) have been associated with mildly inflammatory diarrhea in outbreaks and in travelers and have been increasingly recognized as enteric pathogens in young children with and without overt diarrhea .",
"We examined the risk factors for EAEC infections and their associations with e... | [
"Enteroaggregative E . coli ( EAEC ) are pathogens that infect the intestine and can cause diarrhea .",
"They are also commonly identified among young children in low-resource settings , who can carry the pathogen without symptomatic diarrhea .",
"We examined the risk factors for EAEC infections and their assoc... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Host-Specific Enzyme-Substrate Interactions in SPM-1 Metallo-β-Lactamase Are Modulated by Second Sphere Residues | journal.ppat.1003817 | null | [
[
"β-lactam antibiotics ( penicillins , cephalosporins , monobactams and carbapenems ) are the most dependable and frequently employed chemotherapeutic agents for eradicating bacterial infections [1] .",
"Their safety and efficacy as antimicrobial agents derives from their ability to selectively inhibit cel... | [
"Pseudomonas aeruginosa is one of the most virulent and resistant non-fermenting Gram-negative pathogens in the clinic .",
"Unfortunately , P . aeruginosa has acquired genes encoding metallo-β-lactamases ( MβLs ) , enzymes able to hydrolyze most β-lactam antibiotics .",
"SPM-1 is an MβL produced only by P . aer... | [
"The presence of Zn ( II ) -containing metallo-β-lactamases ( MβLs ) that confer resistance to all penicillins , cephalosporins and carbapenems in Pseudomonas aeruginosa adds significantly to the threat of this pathogen in our health care system .",
"SPM-1 is an MβLs widely distributed in South America and only f... | 2014 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"biochemistry/structural genomics",
"biochemistry/protein folding",
"biochemistry/drug discovery"
] | Substrate Binding Mode and Its Implication on Drug Design for Botulinum Neurotoxin A | journal.ppat.1000165 | null | [
[
"Clostridium botulinum neurotoxins ( CNTs ) are the most potent toxins known to humans since even one billionth of an ounce is fatal .",
"Seven antigenically distinct botulinum neurotoxins are produced by the bacterium Clostridium botulinum and they share considerable sequence homology , and structural an... | [
"The seven antigenically distinct serotypes of Clostridium botulinum neurotoxins , the causative agents of botulism , block the neurotransmitter release by specifically cleaving one of the three SNARE proteins and induce flaccid paralysis .",
"The Centers for Disease Control and Prevention ( CDC ) has declared th... | [
"Botulinum neurotoxins are the most poisonous substance to humans .",
"The ease with which the bacteria can be grown , its potency and persistence have made it a potential bioterrorism agent , and accordingly , botulinum neurotoxin has been declared as Category A agent by the Centers of Disease Control and Preven... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | Understanding Variation in Transcription Factor Binding by Modeling Transcription Factor Genome-Epigenome Interactions | journal.pcbi.1003367 | null | [
[
"Central to transcriptional regulation of gene expression is the regulation of the quantities of transcription factors ( TF ) bound to genomic regulatory sequences .",
"The information used to quantitatively control TF-DNA binding is not only encoded in the genomic sequences , but likely is also embedded ... | [
"Despite explosive growth in genomic datasets , the methods for studying epigenomic mechanisms of gene regulation remain primitive .",
"Here we present a model-based approach to systematically analyze the epigenomic functions in modulating transcription factor-DNA binding .",
"Based on the first principles of s... | [
"We developed a model-based approach to systematically analyze the epigenomic functions in modulating transcription factor-DNA binding .",
"We postulated the existence of TF-specific epigenomic motifs , which could explain why some TFs appeared to have different DNA binding motifs derived from in vivo and in vitr... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"systems biology",
"mathematics",
"biology",
"computational biology",
"signaling networks",
"nonlinear dynamics"
] | Equation-Free Analysis of Two-Component System Signalling Model Reveals the Emergence of Co-Existing Phenotypes in the Absence of Multistationarity | journal.pcbi.1002396 | null | [
[
"Phenotypic heterogeneity in populations of genetically identical ( isogenic ) cells is one of the major discoveries resulting from a systems approach to molecular and cell biology .",
"Application of single cell imaging techniques has demonstrated that individual cells in clonal populations may have very... | [
"Phenotypic differences of genetically identical cells under the same environmental conditions have been attributed to the inherent stochasticity of biochemical processes .",
"Various mechanisms have been suggested , including the existence of alternative steady states in regulatory networks that are reached by m... | [
"It is a surprising fact that genetically identical bacteria , living in identical conditions , can develop in completely different ways: for example , one subpopulation might grow very fast and another very slowly .",
"These different phenotypes are thought to be one reason why bacteria that cause disease can su... | 2012 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"biotechnology",
"invertebrates",
"ecology and environmental sciences",
"medicine and health sciences",
"tropical diseases",
"animals",
"transgenic engineering",
"population modeling",
"neglected tropical diseases",
"population biology",
"genetic engineering",
"infectious diseases",
"genetic... | Feasible Introgression of an Anti-pathogen Transgene into an Urban Mosquito Population without Using Gene-Drive | journal.pntd.0002827 | null | [
[
"The mosquito-borne dengue virus , transmitted primarily by the yellow fever mosquito Aedes aegypti ( Linnaeus ) is estimated to cause approximately 390 million infections each year ( [1] ) .",
"No widespread prophylactic treatments are currently available for dengue , and thus vector population control r... | [
"Introgressing anti-pathogen constructs into wild vector populations could reduce disease transmission .",
"It is generally assumed that such introgression would require linking an anti-pathogen gene with a selfish genetic element or similar technologies .",
"Yet none of the proposed transgenic anti-pathogen ge... | [
"Dengue is transmitted by the Aedes aegypti mosquito .",
"Releases of genetically sterile males have been shown to reduce wild mosquito numbers .",
"An alternative approach is to release mosquitoes carrying genes blocking dengue transmission .",
"It is often assumed that spreading such genes in mosquito popul... | 2014 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | Arsenic Exposure and Outcomes of Antimonial Treatment in Visceral Leishmaniasis Patients in Bihar, India: A Retrospective Cohort Study | journal.pntd.0003518 | null | [
[
"In the late twentieth century , the emergence of high rates of treatment failure with antimonial compounds for visceral leishmaniasis ( VL ) caused a public health crisis in Bihar state , India [1] .",
"VL , also known as kala-azar , is a significant health problem in India causing up to 282 , 000 clinic... | [
"In the late twentieth century , emergence of high rates of treatment failure with antimonial compounds ( SSG ) for visceral leishmaniasis ( VL ) caused a public health crisis in Bihar , India .",
"We hypothesize that exposure to arsenic through drinking contaminated groundwater may be associated with SSG treatme... | [
"The parasitic disease visceral leishmaniasis ( VL ) causes a significant burden of illness and death in India .",
"The main drug used to treat VL , which is based on the chemical element antimony , stopped working well in about half of all patients in the late twentieth century .",
"We hypothesised that arseni... | 2015 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"mycobacterium leprae",
"medicine and health sciences",
"biopsy",
"tropical diseases",
"surgical and invasive medical procedures",
"organisms",
"bacterial diseases",
"neglected tropical diseases",
"molecular biology techniques",
"dna",
"bacteria",
"extraction techniques",
"research and analy... | Development and evaluation of a droplet digital PCR assay for the diagnosis of paucibacillary leprosy in skin biopsy specimens | journal.pntd.0007284 | null | [
[
"Leprosy , a chronic infectious disease caused by M . leprae , has a tropism for macrophages in skin and Schwann cells in peripheral nerves [1] .",
"This disease is quite variable , affecting people in different ways according to their immune response .",
"At one end of the spectrum , patients with a ... | [
"The reduced amounts of Mycobacterium leprae ( M . leprae ) among paucibacillary ( PB ) patients reflect the need to further optimize methods for leprosy diagnosis .",
"An increasing number of reports have shown that droplet digital polymerase chain reaction ( ddPCR ) is a promising tool for diagnosis of infectio... | [
"Leprosy , or Hansen’s disease , is a chronic bacterial disease caused by M . leprae .",
"Although it is curable and early treatment averts most disabilities , it remains an important global health concern .",
"This is mainly due to delayed diagnosis .",
"In leprosy , a reliable and early diagnostic tool , is... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"streptococci",
"microbiology",
"host-pathogen interaction",
"animal models",
"bacterial diseases",
"drosophila melanogaster",
"model organisms",
"bacterial pathogens",
"infectious diseases",
"infectious diseases of the nervous system",
"biology",
"mouse",
"streptococcal infect... | Glycosaminoglycan Binding Facilitates Entry of a Bacterial Pathogen into Central Nervous Systems | journal.ppat.1002082 | null | [
[
"Bacterial meningitis is one of the top ten causes of infection-related mortality worldwide [1] .",
"Meningitis is particularly devastating in the newborn infant , and 20–50% of survivors can suffer permanent neurological sequelae including deafness , seizures , hydrocephalus , cerebral palsy and/or cogni... | [
"Certain microbes invade brain microvascular endothelial cells ( BMECs ) to breach the blood-brain barrier ( BBB ) and establish central nervous system ( CNS ) infection .",
"Here we use the leading meningitis pathogen group B Streptococcus ( GBS ) together with insect and mammalian infection models to probe a po... | [
"Streptococcus agalactiae ( Group B Streptococcus , GBS ) is a leading cause of meningitis in human newborn infants .",
"The bacterial and host factors that allow this pathogen to cross the blood-brain barrier ( BBB ) and cause central nervous system ( CNS ) infection are not well understood .",
"Here we demons... | 2011 |
[
"Regulatory T-cell responses in retroviral infections",
"Mechanisms of Treg expansion and/or accrual during retroviral infection",
"Targets of Treg suppression during retrovirus infection",
"Effect of HIV infection on Treg functionality",
"Mechanisms of suppression",
"Treg immunotherapy in lentiviral infe... | [
"blood cells",
"hiv infections",
"innate immune system",
"medicine and health sciences",
"immune cells",
"immune physiology",
"pathology and laboratory medicine",
"cytokines",
"pathogens",
"immunology",
"microbiology",
"retroviruses",
"viruses",
"immunodeficiency viruses",
"developmental... | Regulatory T cells in retroviral infections | journal.ppat.1006776 | null | [
[
"Seminal experiments in 1995 proved the existence of a subset of T cells termed regulatory T cells ( Tregs ) , with immunosuppressive properties critical for the control of autoimmune diseases [1] .",
"Tregs have been demonstrated to suppress both the proliferation and function of effector T-cell subsets ... | [
"Tight regulation of immune responses is not only critical for preventing autoimmune diseases but also for preventing immunopathological damage during infections in which overactive immune responses may be more harmful for the host than the pathogen itself .",
"Regulatory T cells ( Tregs ) play a critical role in... | [
"Regulatory T cells ( Tregs ) play a very complex role in retroviral infections , and the balance of beneficial versus detrimental effects from Tregs can change between the acute and chronic phase of infection .",
"Therefore , the development of therapeutics to treat chronic retroviral infections via modulation o... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"invertebrates",
"medicine and health sciences",
"nervous system",
"electrophysiology",
"neuroscience",
"homeostatic mechanisms",
"animals",
"animal models",
"physiological processes",
"drosophila melanogaster",
"model organisms",
"synaptic plasticity",
"homeostasis",
"bioassays and physio... | C-terminal Src Kinase Gates Homeostatic Synaptic Plasticity and Regulates Fasciclin II Expression at the Drosophila Neuromuscular Junction | journal.pgen.1005886 | null | [
[
"Throughout a metazoan’s lifespan , its nervous system encounters numerous challenges to function .",
"Responding to stress requires the flexibility afforded by forms of neuroplasticity .",
"Yet even in plastic neurons , functional outputs of synapses must be kept within physiologically appropriate ra... | [
"Forms of homeostatic plasticity stabilize neuronal outputs and promote physiologically favorable synapse function .",
"A well-studied homeostatic system operates at the Drosophila melanogaster larval neuromuscular junction ( NMJ ) .",
"At the NMJ , impairment of postsynaptic glutamate receptor activity is offs... | [
"Homeostasis is a fundamental topic in biology .",
"Individual cells and systems of cells constantly monitor their environments and adjust their outputs in order to maintain physiological properties within ranges that can support life .",
"The nervous system is no exception .",
"Synapses and circuits are endo... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"microbiology/cellular microbiology and pathogenesis",
"immunology/immunity to infections",
"microbiology/innate immunity",
"immunology/leukocyte activation"
] | Type I Interferon Induction Is Detrimental during Infection with the Whipple's Disease Bacterium, Tropheryma whipplei | journal.ppat.1000722 | null | [
[
"Over the past decades , activated macrophages were mainly considered as cells that secrete inflammatory mediators and kill intracellular pathogens .",
"However , studies have now revealed activated macrophages as a continuum of cells with phenotypic and functional heterogeneity [1] , [2] .",
"Schemat... | [
"Macrophages are the first line of defense against pathogens .",
"Upon infection macrophages usually produce high levels of proinflammatory mediators .",
"However , macrophages can undergo an alternate polarization leading to a permissive state .",
"In assessing global macrophage responses to the bacterial ag... | [
"Innate immune cells are sentinels allowing the host to sense invading pathogens .",
"Among them , macrophages are highly microbicidal and are able to kill microorganisms .",
"However , several pathogens have evolved strategies to hijack macrophage responses in order to survive or replicate .",
"Tropheryma wh... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"eukaryotes",
"molecular biology",
"mammals"
] | An Aromatic Sensor with Aversion to Damaged Strands Confers Versatility to DNA Repair | journal.pbio.0050079 | How does XPC (an enzyme responsible for DNA repair) know where the damage is? It seems to recognize undamaged DNA displaced by the defect rather than the damaged base itself. | [
[
"One of the most formidable challenges in DNA metabolism is that faced by the initiator of the nucleotide excision repair reaction as it locates damaged sites in the context of a large excess of mostly undamaged residues .",
"This challenge is further complicated by an astounding diversity of target lesio... | [
"It was not known how xeroderma pigmentosum group C ( XPC ) protein , the primary initiator of global nucleotide excision repair , achieves its outstanding substrate versatility .",
"Here , we analyzed the molecular pathology of a unique Trp690Ser substitution , which is the only reported missense mutation in xer... | [
"DNA is constantly exposed to damaging agents such as ultraviolet light , carcinogens , or reactive metabolic byproducts causing thousands of DNA lesions in a typical human cell every hour .",
"To prevent irreversible mutations , many of these different lesions are eliminated by a DNA repair system known as “nucl... | 2007 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"molecular biology"
] | The Echinococcus granulosus Antigen B Gene Family Comprises at Least 10 Unique Genes in Five Subclasses Which Are Differentially Expressed | journal.pntd.0000784 | null | [
[
"Antigen B ( EgAgB ) is the most abundant protein generated by the pathogenic larval stage ( hydatid cyst or metacestode ) of Echinococcus granulosus , the cause of cystic echinococcosis ( CE ) .",
"Synthesized and secreted by both cyst germinal layer and protoscoleces [1] , the protein is highly immunoge... | [
"Antigen B ( EgAgB ) is a major protein produced by the metacestode cyst of Echinococcus granulosus , the causative agent of cystic hydatid disease .",
"This protein has been shown to play an important role in modulating host immune responses , although its precise biological function still remains unknown .",
... | [
"Antigen B ( EgAgB ) is a major protein produced by the metacestode cyst of Echinococcus granulosus and plays an important role in modulating host immune responses , although its precise biological function still remains unknown .",
"Previous studies suggested the EgAgB gene family is variable between isolates an... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genome-wide association studies",
"rheumatology",
"medicine and health sciences",
"pelvis",
"genome analysis",
"cartilage",
"osteoarthritis",
"musculoskeletal system",
"genomics",
"arthritis",
"hip",
"connective tissue",
"biological tissue",
"gene expression",
"joints (anatomy)",
"gen... | Novel Genetic Variants for Cartilage Thickness and Hip Osteoarthritis | journal.pgen.1006260 | null | [
[
"In spite of advances in the understanding of OA , the absence of effective therapeutic targets demonstrates that a better comprehension of its causes and pathophysiological mechanisms is needed .",
"Since genome-wide genetic studies are hypothesis-free and do not suffer from the bias of previous knowledg... | [
"Osteoarthritis is one of the most frequent and disabling diseases of the elderly .",
"Only few genetic variants have been identified for osteoarthritis , which is partly due to large phenotype heterogeneity .",
"To reduce heterogeneity , we here examined cartilage thickness , one of the structural components o... | [
"Osteoarthritis ( OA ) is the most common form of arthritis and a leading cause of chronic disability in the western society affecting millions of people .",
"OA is a degenerative joint disease characterized by changes in all joint tissues , including cartilage , bone and synovium , causing chronic pain and loss ... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods",
"Supporting Information"
] | [
"viruses",
"in vitro",
"guinea pig",
"virology"
] | Influenza Virus Transmission Is Dependent on Relative Humidity and Temperature | journal.ppat.0030151 | null | [
[
"Influenza A virus , of the family Orthomyxoviridae , carries an RNA genome consisting of eight segments of negative-stranded RNA .",
"This genome encodes one or two non-structural proteins and nine structural proteins , which , together with a host cell–derived lipid envelope , comprise the influenza vir... | [
"Using the guinea pig as a model host , we show that aerosol spread of influenza virus is dependent upon both ambient relative humidity and temperature .",
"Twenty experiments performed at relative humidities from 20% to 80% and 5 °C , 20 °C , or 30 °C indicated that both cold and dry conditions favor transmissio... | [
"In temperate regions influenza epidemics recur with marked seasonality: in the northern hemisphere the influenza season spans November to March , while in the southern hemisphere epidemics last from May until September .",
"Although seasonality is one of the most familiar features of influenza , it is also one o... | 2007 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"infectious diseases",
"mental health",
"biology",
"neuroscience"
] | Prion Replication Occurs in Endogenous Adult Neural Stem Cells and Alters Their Neuronal Fate: Involvement of Endogenous Neural Stem Cells in Prion Diseases | journal.ppat.1003485 | null | [
[
"Prion diseases or transmissible spongiform encephalopathies ( TSEs ) are fatal neurodegenerative disorders , which include Creutzfeldt-Jakob disease in humans , scrapie in sheep and goats , and bovine spongiform encephalopathy in cattle .",
"Their origin can be genetic , sporadic or infectious and there ... | [
"Prion diseases are irreversible progressive neurodegenerative diseases , leading to severe incapacity and death .",
"They are characterized in the brain by prion amyloid deposits , vacuolisation , astrocytosis , neuronal degeneration , and by cognitive , behavioural and physical impairments .",
"There is no tr... | [
"Prion diseases are irreversible progressive neurodegenerative diseases , leading to severe incapacity and death .",
"They are considered to be caused by an abnormally folded infectious protein named PrPSc .",
"They are characterized in the brain by prion amyloid deposits , vacuolisation , astrocyte proliferati... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"developmental biology",
"genome evolution",
"evolutionary biology",
"chromosome biology",
"gene expression",
"genetics",
"biology",
"genomics",
"genomic evolution",
"genetics and genomics",
"cell differentiation",
"gene function"
] | A Genetic Basis for a Postmeiotic X Versus Y Chromosome Intragenomic Conflict in the Mouse | journal.pgen.1002900 | null | [
[
"Transmission distorters ( TDs ) , also known as segregation distorters or meiotic drivers , are genetic elements that are transmitted to the next generation with a higher frequency than the expected 1∶1 Mendelian inheritance ratio .",
"TDs have the tendency to accumulate in low recombination regions wher... | [
"Intragenomic conflicts arise when a genetic element favours its own transmission to the detriment of others .",
"Conflicts over sex chromosome transmission are expected to have influenced genome structure , gene regulation , and speciation .",
"In the mouse , the existence of an intragenomic conflict between X... | [
"Both copies of a gene have normally an equal chance of being inherited; however , some genes can act “selfishly” to be transmitted to >50% of offspring: a phenomenon known as transmission distortion .",
"Distorting genes on the X or Y chromosome leads to an excess of female/male offspring respectively .",
"Thi... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Evolutionary Trade-Offs Underlie the Multi-faceted Virulence of Staphylococcus aureus | journal.pbio.1002229 | This study shows that, contrary to expectation, toxin secretion inversely correlates with disease severity for the major human pathogen Staphylococcus aureus. | [
[
"The development of effective , long-term control strategies against microbial pathogens crucially relies on a thorough understanding of the many factors that contribute to the evolution and maintenance of enhanced virulence .",
"Bacterial toxins are well established as playing a key role in virulence [1–... | [
"Bacterial virulence is a multifaceted trait where the interactions between pathogen and host factors affect the severity and outcome of the infection .",
"Toxin secretion is central to the biology of many bacterial pathogens and is widely accepted as playing a crucial role in disease pathology .",
"To understa... | [
"Global efforts to counter the growing problem of antibiotic resistance and develop alternative treatment strategies rely on a fuller understanding of when and why opportunistic pathogens cause disease .",
"Recent advances in DNA sequencing technologies have opened up new opportunities to study infectious organis... | 2015 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine and health sciences",
"tropical diseases",
"vector-borne diseases",
"parasitic diseases",
"animals",
"parasitic protozoans",
"protozoans",
"neglected tropical diseases",
"infectious disease control",
"insect vectors",
"zoology",
"infectious diseases",
"agrochemic... | Non-randomized controlled trial of the long-term efficacy of an Ecohealth intervention against Chagas disease in Yucatan, Mexico | journal.pntd.0006605 | null | [
[
"Chagas disease is a vector-borne parasitic disease causing major morbidity and mortality in the Americas , with at least 6 million persons currently infected .",
"The burden of Chagas disease is estimated at 29 million disability-adjusted life years ( DALYs ) and it leads to health care costs of $24 . 73... | [
"Non-domiciliated intrusive triatomine vectors are responsible for a low but significant transmission of Trypanosoma cruzi to humans .",
"Their control is a challenge as insecticide spraying is of limited usefulness , and alternative strategies need to be developed for a sustainable control .",
"We performed a ... | [
"Intrusive triatomine bugs such as Triatoma dimidiata in the Yucatan peninsula , Mexico , are responsible for the transmission of Trypanosoma cruzi to humans , which can lead to Chagas disease .",
"The control of these bugs is a challenge as insecticide spraying is poorly effective , and alternative strategies ne... | 2018 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"pathology and laboratory medicine",
"host-pathogen interactions",
"biology and life sciences",
"microbiology",
"pathogenesis",
"parasitology"
] | Leishmania amazonensis Amastigotes Highly Express a Tryparedoxin Peroxidase Isoform That Increases Parasite Resistance to Macrophage Antimicrobial Defenses and Fosters Parasite Virulence | journal.pntd.0003000 | null | [
[
"Leishmania spp .",
"are the causative agent of the neglected tropical disease leishmaniasis , causing significant morbidity and mortality worldwide .",
"Leishmaniasis presents with a broad spectrum of clinical symptoms , ranging from self-healing cutaneous lesions to life-threatening systemic disease... | [
"Professional phagocytes generate a myriad of antimicrobial molecules to kill invading microorganisms , of which nitrogen oxides are integral in controlling the obligate intracellular pathogen Leishmania .",
"Although reactive nitrogen species produced by the inducible nitric oxide synthase ( iNOS ) can promote t... | [
"Pathogens of the genus Leishmania are the causative agents of leishmaniasis , a neglected tropical disease responsible for significant morbidity and mortality worldwide .",
"Although it is well accepted that host-derived leishmanicidal molecules mediate resolution of Leishmania infection , some Leishmania specie... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"developmental biology/organogenesis",
"developmental biology/plant growth and development"
] | Quantitative Control of Organ Shape by Combinatorial Gene Activity | journal.pbio.1000538 | A novel combination of molecular genetics, shape analysis, and computational modelling shows how the complex three-dimensional shape of the Snapdragon flower can arise through local gene activity. | [
[
"Although major progress has been made in the genetic dissection of organ and appendage development , the process whereby gene activities lead to particular tissue shapes is still poorly understood .",
"For example , wing morphogenesis in Drosophila is one of the best defined developmental systems [1] , y... | [
"The development of organs with particular shapes , like wings or flowers , depends on regional activity of transcription factors and signalling molecules .",
"However , the mechanisms that link these molecular activities to the morphogenetic events underlying shape are poorly understood .",
"Here we describe a... | [
"A major challenge in developmental biology is to understand how patterns of gene activity are translated into complex three-dimensional forms , like hearts , wings , or flowers .",
"Addressing this problem has not been easy , partly because of the difficulties in quantifying the effects of genes on shape and als... | 2010 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious diseases"
] | Monitoring Toxicity Associated with Parenteral Sodium Stibogluconate in the Day-Case Management of Returned Travellers with New World Cutaneous Leishmaniasi | journal.pntd.0001688 | null | [
[
"Cutaneous leishmaniasis ( CL ) develops after inoculation of the skin with protozoan parasites of the genus Leishmania , transmitted by the bite of phlebotomine sandflies .",
"Cutaneous nodules form and then ulcerate , typically within weeks of initial infection .",
"The annual worldwide incidence of... | [
"Patients with New World cutaneous leishmaniasis ( NWCL ) caused by Leishmania Viannia are treated with parenteral sodium stibogluconate ( SbV ) to reduce the risk of development of mucocutanous leishmaniasis .",
"Our centre manages patients with NWCL on an outpatient-basis .",
"This study was conducted to asse... | [
"Sodium stibogluconate ( SbV ) , a pentavalent antimonial , administered parenterally , is the recommended treatment for South American cutaneous leishmaniasis , caused by Leishmania Viannia , which is a neglected disease that affects many people resident in Central and South America , as well as travellers to the ... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"infectious diseases/hiv infection and aids",
"infectious diseases"
] | Transmission of HIV-1 CTL Escape Variants Provides HLA-Mismatched Recipients with a Survival Advantage | journal.ppat.1000033 | null | [
[
"Avoidance of host anti-viral responses is a major factor influencing the evolution of HIV genomes .",
"Of particular importance for virus survival , and a major contributor to ongoing HIV-1 diversification worldwide , is continual escape from anti-HIV host cytotoxic T lymphocyte ( CTL ) responses .",
... | [
"One of the most important genetic factors known to affect the rate of disease progression in HIV-infected individuals is the genotype at the Class I Human Leukocyte Antigen ( HLA ) locus , which determines the HIV peptides targeted by cytotoxic T-lymphocytes ( CTLs ) .",
"Individuals with HLA-B*57 or B*5801 alle... | [
"Following infection with HIV , it is well established that a person's genetic makeup is a major determinant of how quickly they will progress to AIDS .",
"Particularly important is the class I Human leukocyte antigen ( HLA ) gene that is responsible for alerting the immune system to HIV's presence .",
"One of ... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"developmental biology",
"otology",
"genetic mutation",
"gene expression",
"genetics",
"molecular genetics",
"hearing disorders",
"biology",
"otorhinolaryngology",
"morphogenesis",
"genetics of disease",
"gene function"
] | SLC26A4 Targeted to the Endolymphatic Sac Rescues Hearing and Balance in Slc26a4 Mutant Mice | journal.pgen.1003641 | null | [
[
"Enlargement of the vestibular aqueduct ( EVA; OMIM #600791 ) is a malformation of the temporal bone that is commonly observed in children with sensorineural hearing loss [1] , [2] , [3] , [4] , [5] .",
"Mutations of SLC26A4 are the most common cause for EVA-associated hearing loss that can either be non-... | [
"Mutations of SLC26A4 are a common cause of human hearing loss associated with enlargement of the vestibular aqueduct .",
"SLC26A4 encodes pendrin , an anion exchanger expressed in a variety of epithelial cells in the cochlea , the vestibular labyrinth and the endolymphatic sac .",
"Slc26a4Δ/Δ mice are devoid o... | [
"Mutations of SLC26A4 are the most common cause for hearing loss associated with a swelling of the inner ear .",
"This human disease is largely recapitulated in a mutant mouse model .",
"Mutant mice lack Slc26a4 expression and their inner ears swell during embryonic development , which leads to failure of the c... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"molecular biology/rna-protein interactions",
"computational biology/molecular genetics",
"computational biology/alternative splicing",
"molecular biology/rna splicing",
"molecular biology/bioinformatics",
"genetics and genomics/genetics of disease",
"computational biology/genomics"
] | Fine-Scale Variation and Genetic Determinants of Alternative Splicing across Individuals | journal.pgen.1000766 | null | [
[
"Alternative splicing ( AS ) allows for multiple mRNA isoforms to be transcribed from a single gene locus , potentially creating much greater protein diversity from our roughly 25 thousand human genes [1] .",
"AS is very common in higher order organisms and , especially through the lens of newer , high th... | [
"Recently , thanks to the increasing throughput of new technologies , we have begun to explore the full extent of alternative pre–mRNA splicing ( AS ) in the human transcriptome .",
"This is unveiling a vast layer of complexity in isoform-level expression differences between individuals .",
"We used previously ... | [
"Alternative splicing ( AS ) , through the alternative use of exons , can produce many different mRNA transcripts from the same genomic locus , thus possibly resulting in the production of many different proteins .",
"We know that splicing differences between individuals exist and that these changes are often ass... | 2009 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [] | Identification and Characterization of Microsatellite Markers Derived from the Whole Genome Analysis of Taenia solium | journal.pntd.0004316 | null | [
[
"Cysticercosis is an infection caused by the larval stage of the cestode Taenia solium .",
"When the larval stages infect the central nervous system , the infection is known as neurocysticercosis ( NCC ) and is the most common cause of adult-onset seizures in endemic regions worldwide .",
"Crude estim... | [
"Infections with Taenia solium are the most common cause of adult acquired seizures worldwide , and are the leading cause of epilepsy in developing countries .",
"A better understanding of the genetic diversity of T . solium will improve parasite diagnostics and transmission pathways in endemic areas thereby faci... | [
"Taenia solium , the pork tapeworm , is an important pathogen as it is a major cause of acquired epilepsy in developing countries .",
"The parasite was eliminated from most developed countries decades ago due to improvement in sanitary conditions but it remains a common infection across Asia , Africa and Latin Am... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biotechnology",
"biochemistry",
"synthetic biology",
"biology and life sciences",
"evolutionary biology"
] | The Robustness of a Signaling Complex to Domain Rearrangements Facilitates Network Evolution | journal.pbio.1002012 | The broad tolerance of domain-rearranging mutations by a yeast signaling network suggests that signaling complexes have loose spatial constraints, making manipulation and perhaps evolution easier. | [
[
"Cell signaling networks possess a remarkably modular organization .",
"This modularity has attracted the attention of synthetic biologists , for it offers a plausible approach to engineer novel and useful cellular behaviors .",
"At the center of this modular organization are protein domains , which a... | [
"The rearrangement of protein domains is known to have key roles in the evolution of signaling networks and , consequently , is a major tool used to synthetically rewire networks .",
"However , natural mutational events leading to the creation of proteins with novel domain combinations , such as in frame fusions ... | [
"Cells use complex protein interaction networks to sense and process external signals .",
"Proteins involved in signaling are often composed of multiple functional units called domains .",
"Because domains are modular , mutations that rearrange domains among proteins have the potential to result in the creation... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"blood cells",
"phosphorylation",
"medicine and health sciences",
"immune cells",
"recombination reactions",
"pathology and laboratory medicine",
"molecular probe techniques",
"enzymes",
"pathogens",
"gene regulation",
"immunology",
"immunoblotting",
"microbiology",
"enzymology",
"retrov... | HTLV-1 Tax Induces Formation of the Active Macromolecular IKK Complex by Generating Lys63- and Met1-Linked Hybrid Polyubiquitin Chains | journal.ppat.1006162 | null | [
[
"Human T-cell leukemia virus type 1 ( HTLV-1 ) is etiologically associated with adult T-cell leukemia ( ATL ) , an aggressive and lethal malignancy of CD4+ T cells , and with HTLV-1-associated myelopathy/tropical spastic paraparesis ( HAM/TSP ) [1 , 2] .",
"The HTLV-1 provirus genome encodes a transactiva... | [
"The Tax protein of human T-cell leukemia virus type 1 ( HTLV-1 ) is crucial for the development of adult T-cell leukemia ( ATL ) , a highly malignant CD4+ T cell neoplasm .",
"Among the multiple aberrant Tax-induced effects on cellular processes , persistent activation of transcription factor NF-κB , which is ac... | [
"NF-κB is a key transcription factor that regulates many physiologically important cellular processes .",
"However , persistent activation of NF-κB leads to chronic inflammation , autoimmunity and malignancy .",
"Infection with the human retrovirus HTLV-1 causes adult T-cell leukemia , and HTLV-1 Tax-mediated p... | 2017 |
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