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headings list	keywords list	title stringlengths 20 281	id stringlengths 20 20	toc stringlengths 57 522 ⌀	sections list	abstract list	summary list	year stringclasses 13 values
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "classical mechanics", "light microscopy", "geometry", "developmental biology", "mathematics", "microscopy", "damage mechanics", "embryos", "plants", "morphogenesis", "research and analysis methods", "bending", "embryology", "deformation", "algae", "physics", "eukaryota", "cell bio...	The noisy basis of morphogenesis: Mechanisms and mechanics of cell sheet folding inferred from developmental variability	journal.pbio.2005536	null	[ [ "‘The phenomena are always the same , and this is what matters to us , but their variations , for the greater or for the lesser , are beyond count .", "’ Thus opined Xavier Bichat in the account of his investigations into life and death [1] and thereby spelt out how , to the present day , questions in dev...	[ "Variability is emerging as an integral part of development .", "It is therefore imperative to ask how to access the information contained in this variability .", "Yet most studies of development average their observations and , discarding the variability , seek to derive models , biological or physical , that ...	[ "Biological noise is unavoidable in—and even necessary for—development .", "Here , we ask whether this variability can teach us something about the process that underlies it .", "We show how to access the information hidden in the variability in an analysis of the variability of cell sheet folding in the green ...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "infectious diseases", "cell biology", "microbiology", "genetics and genomics" ]	Biogenesis of the Trypanosome Endo-Exocytotic Organelle Is Cytoskeleton Mediated	journal.pbio.0060105	RNAi of the parasite protein BILBO1 prevents the biogenesis of the endocytic and exocytotic organelle in Trypanosoma brucei, kills the parasite, and reveals novel insights into how this pathogen organizes and uses one of its distinctive organelles.	[ [ "Endocytosis and exocytosis in trypanosomes is performed by the flagellar pocket ( FP ) , an important organelle that is sequestered within the cytoplasm of the posterior region of the cell .", "On the basis of its protein composition , the FP membrane is biochemically distinct from the flagellar or pelli...	[ "Trypanosoma brucei is a protozoan parasite that is used as a model organism to study such biological phenomena as gene expression , protein trafficking , and cytoskeletal biogenesis .", "In T . brucei , endocytosis and exocytosis occur exclusively through a sequestered organelle called the flagellar pocket ( FP ...	[ "Trypanosomes are ubiquitous unicellular parasites that infect humans , animals , insects , and plants .", "African , Asian , and some South American trypanosomes have evolved the amazing ability to change their surface coat proteins , an essential strategy for their survival .", "The surface coat proteins are ...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology/animal models of infection", "virology/antivirals, including modes of action and resistance", "infectious diseases/viral infections", "infectious diseases/respiratory infections", "infectious diseases/antimicrobials and drug resistance" ]	Oseltamivir–Resistant Pandemic H1N1/2009 Influenza Virus Possesses Lower Transmissibility and Fitness in Ferrets	journal.ppat.1001022	null	[ [ "A novel swine-origin H1N1 influenza virus emerged in Mexico in April 2009 and rapidly spread worldwide , causing the first influenza pandemic of the 21st century [1] , [2] .", "Most confirmed human cases of H1N1/2009 influenza have been uncomplicated and mild [3] , but the increasing number of cases and ...	[ "The neuraminidase ( NA ) inhibitor oseltamivir offers an important immediate option for the control of influenza , and its clinical use has increased substantially during the recent H1N1 pandemic .", "In view of the high prevalence of oseltamivir-resistant seasonal H1N1 influenza viruses in 2007–2008 , there is ...	[ "Most of the currently circulating pandemic H1N1/2009 ( “swine” ) influenza viruses are susceptible to the anti-influenza drug oseltamivir .", "Many countries have stockpiled oseltamivir for pandemic preparedness , and to date only a small proportion of the H1N1/2009 viruses isolated have been oseltamivir-resista...	2010
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "learning", "neural networks", "social sciences", "neuroscience", "learning and memory", "synaptic plasticity", "cognitive psychology", "human performance", "neuronal plasticity", "computer and information sciences", "developmental neuroscience", "animal cells", "human learning", "behavior...	A model of human motor sequence learning explains facilitation and interference effects based on spike-timing dependent plasticity	journal.pcbi.1005632	null	[ [ "Humans can improve their performance in sequential movement tasks through practice , but such motor learning has shown puzzling and seemingly contradictory results .", "On the one hand , a wide variety of proactive and retroactive interference effects have been observed when multiple tasks have to be lea...	[ "The ability to learn sequential behaviors is a fundamental property of our brains .", "Yet a long stream of studies including recent experiments investigating motor sequence learning in adult human subjects have produced a number of puzzling and seemingly contradictory results .", "In particular , when subject...	[ "From dialing a phone number to driving home after work , much of human behavior is inherently sequential .", "But how do we learn such sequential behaviors and what neural plasticity mechanisms support this learning ?", "Recent experiments on sequence learning in human adults have produced a range of confusing...	2017
[ "Introduction", "Description of the Accident", "Clinical Outcomes of Exposed Children", "Key Lessons from the Lübeck Disaster", "Implications for the Understanding of the “TB Susceptibility” Phenotype", "A Historical Event" ]	[]	Tuberculosis in Newborns: The Lessons of the “Lübeck Disaster” (1929–1933)	journal.ppat.1005271	null	[ [ "Tuberculosis ( TB ) is an enduring global public health challenge , with 9 million new cases of disease each year [1] .", "Approximately one-third of the world’s population has been infected with Mycobacterium tuberculosis , yet less than 10% of infected individuals develop clinical disease during their ...	[ "In an accident later known as the Lübeck disaster , 251 neonates were orally given three doses of the new Bacille Calmette–Guérin ( BCG ) antituberculosis ( TB ) vaccine contaminated with Mycobacterium tuberculosis .", "A total of 173 infants developed clinical or radiological signs of TB but survived the infect...	[ "The Lübeck disaster is a unique event in the history of tuberculosis when 251 newborns were accidentally infected with a virulent strain of Mycobacterium tuberculosis .", "The disaster happened while BCG was introduced as an anti-TB vaccine .", "In an exemplary multidisciplinary investigation , the disaster wa...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "microarrays", "systems biology", "genomics", "evolutionary biology", "gene regulation", "genetics", "regulatory networks", "molecular genetics", "biology", "computational biology", "genomic evolution", "comparative genomics", "genetics and genomics" ]	Coupled Evolution of Transcription and mRNA Degradation	journal.pbio.1001106	null	[ [ "Work on the regulation of mRNA levels has traditionally focused on transcription , although mRNA levels reflect the balance between transcription and mRNA degradation .", "Recent studies have shown that regulation of mRNA degradation also has a central role in control of gene expression , and in certain ...	[ "mRNA levels are determined by the balance between transcription and mRNA degradation , and while transcription has been extensively studied , very little is known regarding the regulation of mRNA degradation and its coordination with transcription .", "Here we examine the evolution of mRNA degradation rates betw...	[ "The regulation of mRNA levels in the cell is important to ensure , for instance , timely cellular responses to changes in the environment .", "mRNA transcription and mRNA degradation directly affect mRNA levels and it would make sense to have a system in place that would coordinate these opposing processes .", ...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology/germ cells", "cell biology/cell growth and division", "developmental biology/stem cells" ]	C. elegans Nucleostemin Is Required for Larval Growth and Germline Stem Cell Division	journal.pgen.1000181	null	[ [ "The nucleolus is a dynamic structure to which an increasing diversity of functions is ascribed .", "Previously known primarily as the central site of ribosome subunit biosynthesis , the nucleolus has recently been recognized as a coordination center for many processes related to cell growth and prolifera...	[ "The nucleolus has shown to be integral for many processes related to cell growth and proliferation .", "Stem cells in particular are likely to depend upon nucleolus-based processes to remain in a proliferative state .", "A highly conserved nucleolar factor named nucleostemin is proposed to be a critical link b...	[ "Stem cells are carefully poised between the alternate fates of proliferation and differentiation .", "The regulation of this choice is a complex one that occurs on many different levels .", "One major influence controlling this choice derives signals emanating from the nucleolus , which serves dual roles as th...	2008
[ "Introduction", "Materials and Methods", "Results", "Discussion", "Conclusion" ]	[ "sequencing techniques", "medicine and health sciences", "canada", "pathology and laboratory medicine", "pathogens", "geographical locations", "microbiology", "vertebrates", "rna extraction", "animals", "mammals", "viruses", "north america", "rna viruses", "phylogenetic analysis", "mit...	Spatio-temporal Analysis of the Genetic Diversity of Arctic Rabies Viruses and Their Reservoir Hosts in Greenland	journal.pntd.0004779	null	[ [ "Rabies , an ancient disease known for millennia , is caused by lyssaviruses of the Rhabdoviridae family [1] .", "The prototypical rabies virus ( RABV ) has a global distribution and the domestic dog is the host reservoir responsible for the vast majority of the estimated 60 , 000 human rabies cases annua...	[ "There has been limited knowledge on spatio-temporal epidemiology of zoonotic arctic fox rabies among countries bordering the Arctic , in particular Greenland .", "Previous molecular epidemiological studies have suggested the occurrence of one particular arctic rabies virus ( RABV ) lineage ( arctic-3 ) , but hav...	[ "Next to dog-mediated rabies , wildlife rabies continues to pose a public health problem , particularly in the northern hemisphere .", "Control of this zoonosis at the animal source has been proven the most efficient route to reduction of human rabies burden .", "Successful elimination of red fox-mediated rabie...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "molecular probe techniques", "messenger rna", "developmental biology", "northern blot", "mitochondria", "molecular biology techniques", "bioenergetics", "rna isolation", "cellular structures and organelles", "gel electrophoresis", "research and analysis methods", "electrophoretic techniques",...	Defects of mitochondrial RNA turnover lead to the accumulation of double-stranded RNA in vivo	journal.pgen.1008240	null	[ [ "The turnover of RNA is determined by its rate of synthesis and degradation , and together with the rate of translation , determines the level of gene expression of a given transcript .", "These processes are not constant and individual RNA species have different half-lives and rates of translation .", ...	[ "The RNA helicase SUV3 and the polynucleotide phosphorylase PNPase are involved in the degradation of mitochondrial mRNAs but their roles in vivo are not fully understood .", "Additionally , upstream processes , such as transcript maturation , have been linked to some of these factors , suggesting either dual rol...	[ "Although a number of factors have been implemented in the turnover of mitochondrial ( mt ) DNA-derived transcripts , their exact functions and interplay with one another is not entirely clear .", "Several of these factors have been proposed to co-ordinately regulate both transcript maturation , as well as degrad...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "evolutionary biology", "genetics and genomics/complex traits", "genetics and genomics/gene expression" ]	Quantitative and Molecular Genetic Analyses of Mutations Increasing Drosophila Life Span	journal.pgen.1001037	null	[ [ "Understanding the genetic and environmental factors affecting variation in life span and health span is of major interest for human health and evolutionary biology .", "As the world population ages , the incidence of age-related diseases , such as Alzheimer's disease , cancer , cardiovascular disease and...	[ "Understanding the genetic and environmental factors that affect variation in life span and senescence is of major interest for human health and evolutionary biology .", "Multiple mechanisms affect longevity , many of which are conserved across species , but the genetic networks underlying each mechanism and cros...	[ "Recent advances in medical science as well as vastly improved living conditions have resulted in a steady increase in human life span , with a concomitant increase in health issues associated with aging .", "In addition , understanding life history evolution requires that we know why organisms age and why there ...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Actions, Action Sequences and Habits: Evidence That Goal-Directed and Habitual Action Control Are Hierarchically Organized	journal.pcbi.1003364	null	[ [ "There is now considerable evidence from studies of instrumental conditioning in rats and humans that the performance of reward-related actions reflects the involvement of two learning processes , one controlling the acquisition of goal-directed actions and the other of habits [1]–[4] .", "This evidence s...	[ "Behavioral evidence suggests that instrumental conditioning is governed by two forms of action control: a goal-directed and a habit learning process .", "Model-based reinforcement learning ( RL ) has been argued to underlie the goal-directed process; however , the way in which it interacts with habits and the st...	[ "In order to make choices that lead to desirable outcomes , individuals tend to deliberate over the consequences of various alternatives .", "This goal-directed deliberation is , however , slow and cognitively demanding .", "As a consequence , under appropriate conditions decision-making can become habitual and...	2013
[ "Introduction", "Results", "Discussion", "Material and Methods" ]	[ "sequencing techniques", "chemical characterization", "medicine and health sciences", "gene regulation", "regulatory proteins", "dna-binding proteins", "cell differentiation", "physiological processes", "developmental biology", "micrornas", "transcription factors", "molecular biology technique...	MiR144/451 Expression Is Repressed by RUNX1 During Megakaryopoiesis and Disturbed by RUNX1/ETO	journal.pgen.1005946	null	[ [ "The transcription factor RUNX1 ( or AML1 , acute myeloid leukemia 1 ) is a critical regulator of embryonic and adult hematopoiesis ( reviewed in [1–3] ) .", "Alteration in RUNX1 due to chromosomal translocations and mutations are causally connected to the onset of acute myeloid leukemia in humans [4] .",...	[ "A network of lineage-specific transcription factors and microRNAs tightly regulates differentiation of hematopoietic stem cells along the distinct lineages .", "Deregulation of this regulatory network contributes to impaired lineage fidelity and leukemogenesis .", "We found that the hematopoietic master regula...	[ "The regulatory network between transcription factors , epigenetic cofactors and microRNAs is decisive for normal hematopoiesis .", "The transcription factor RUNX1 is important for the establishment of a megakaryocytic gene expression program and the concomitant repression of erythroid genes during megakaryocytic...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "computer science", "mathematical computing", "gene expression", "biology", "molecular cell biology", "computing methods", "molecular biology" ]	PERT: A Method for Expression Deconvolution of Human Blood Samples from Varied Microenvironmental and Developmental Conditions	journal.pcbi.1002838	null	[ [ "Heterogeneity as a description of a biological sample typically refers to the co-existence of phenotypically and functionally distinct cell populations therein .", "In a dynamic system such as in vitro stem cell growth and differentiation , cells continuously self-renew , differentiate and die in respons...	[ "The cellular composition of heterogeneous samples can be predicted using an expression deconvolution algorithm to decompose their gene expression profiles based on pre-defined , reference gene expression profiles of the constituent populations in these samples .", "However , the expression profiles of the actual...	[ "The cellular composition of heterogeneous samples can be predicted from reference gene expression profiles that represent the homogeneous , constituent populations of the heterogeneous samples .", "However , existing methods fail when the reference profiles are not representative of the constituent populations ....	2012
[ "Introduction", "Results/Discussion", "Methods" ]	[ "developmental biology", "medicine and health sciences", "molecular development", "genetics", "biology and life sciences", "computational biology", "genetics of disease", "pediatrics" ]	Finding Novel Molecular Connections between Developmental Processes and Disease	journal.pcbi.1003578	null	[ [ "The study of the health implications of developmental processes has now entered the genomic era .", "The recent sequencing of an entire fetal genome [1] has demonstrated the possibility of applying molecular methods to design novel prenatal diagnostics .", "The development of therapeutic approaches f...	[ "Identifying molecular connections between developmental processes and disease can lead to new hypotheses about health risks at all stages of life .", "Here we introduce a new approach to identifying significant connections between gene sets and disease genes , and apply it to several gene sets related to human d...	[ "Understanding the roles that genes involved in normal human development can play in disease processes is an important part of predicting disease risk and designing novel treatment approaches .", "In this study , we have identified classes of disease that are associated with a surprisingly large number of genes i...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "evolutionary biology/human evolution", "genetics and genomics/population genetics" ]	Association of the OCA2 Polymorphism His615Arg with Melanin Content in East Asian Populations: Further Evidence of Convergent Evolution of Skin Pigmentation	journal.pgen.1000867	null	[ [ "The remarkable variation observed in skin , hair and iris pigmentation in human populations is the result of differences in the amount , type and distribution of the pigment melanin , which is synthesized by specialized cells known as melanocytes .", "Pigmentation is a complex trait , influenced by numer...	[ "The last decade has witnessed important advances in our understanding of the genetics of pigmentation in European populations , but very little is known about the genes involved in skin pigmentation variation in East Asian populations .", "Here , we present the results of a study evaluating the association of 10...	[ "Our knowledge of the genetic basis of normal pigmentation variation in human populations is quite incomplete .", "Recent studies have identified some of the genes responsible for the reduction in melanin content in European populations , but this is not the case for other population groups , such as East Asians ...	2010
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "action potentials", "medicine and health sciences", "nervous system", "membrane potential", "electrophysiology", "neuroscience", "signal inhibition", "synaptic plasticity", "interneurons", "calcium signaling", "neuronal dendrites", "developmental neuroscience", "animal cells", "signal tra...	Inhibition as a Binary Switch for Excitatory Plasticity in Pyramidal Neurons	journal.pcbi.1004768	null	[ [ "To successfully interact with our environment , we need to adjust to new or changing conditions .", "It is widely accepted that this ability involves alterations of synaptic connections in the brain , so-called synaptic plasticity [1] .", "While synaptic plasticity fulfills key requirements for the i...	[ "Synaptic plasticity is thought to induce memory traces in the brain that are the foundation of learning .", "To ensure the stability of these traces in the presence of further learning , however , a regulation of plasticity appears beneficial .", "Here , we take up the recent suggestion that dendritic inhibiti...	[ "We must constantly learn in order to meet the demands of a dynamically changing environment .", "The basis of learning is believed to be synaptic plasticity , i . e . the potential of neuronal connections to change .", "Depending on context , however , it may be either useful to learn and modify connections or...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cellular stress responses", "genetic mutation", "microbiology", "gene function", "model organisms", "cell division", "cell growth", "molecular genetics", "chromosome biology", "biology", "cell biology", "genetics", "yeast and fungal models", "molecular cell biology", "genetics and genom...	The Role of Autophagy in Genome Stability through Suppression of Abnormal Mitosis under Starvation	journal.pgen.1003245	null	[ [ "Autophagy is a protein degradation pathway that is conserved from yeast to mammals .", "Previous studies have reported the functions and molecular mechanisms of autophagy , including the identification of autophagy-related genes [1] , [2] , the characterization of the molecular mechanisms of each autopha...	[ "The coordination of subcellular processes during adaptation to environmental change is a key feature of biological systems .", "Starvation of essential nutrients slows cell cycling and ultimately causes G1 arrest , and nitrogen starvation delays G2/M progression .", "Here , we show that budding yeast cells can...	[ "A nutrient stress such as nitrogen depletion induces pleiotropic responses in eukaryotic cells .", "For example , nutrient starvation slows cell cycling and ultimately causes G1 arrest .", "In addition , it is known that nitrogen starvation delays G2/M progression .", "However , the mechanism as to how G2/M-...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "biology" ]	Integrin α PAT-2/CDC-42 Signaling Is Required for Muscle-Mediated Clearance of Apoptotic Cells in Caenorhabditis elegans	journal.pgen.1002663	null	[ [ "During the development of multicellular organisms , cells that are unnecessary , damaged , or harmful undergo programmed cell death ( apoptosis ) [1] .", "Apoptotic cells are recognized and subsequently internalized by engulfing cells [2] , [3] .", "Improper engulfment of apoptotic cells has been lin...	[ "Clearance of apoptotic cells by engulfment plays an important role in the homeostasis and development of multicellular organisms .", "Despite the fact that the recognition of apoptotic cells by engulfment receptors is critical in inducing the engulfment process , the molecular mechanisms are still poorly underst...	[ "When cells undergo apoptosis , their corpses are quickly recognized and phagocytosed by engulfing cells .", "Although many cell types , such as muscle cells and epithelial cells , possess the ability to remove apoptotic cells , little is known about the receptors and signaling pathways used for apoptotic cell up...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "viral classification", "emerging viral diseases", "microbiology", "rna viruses", "emerging infectious diseases", "neglected tropical diseases", "infectious disease control", "lassa fever", "viral disease diagnosis", "viral hemorrhagic fevers", "infectious diseases", "biology", ...	Molecular Diagnostics for Lassa Fever at Irrua Specialist Teaching Hospital, Nigeria: Lessons Learnt from Two Years of Laboratory Operation	journal.pntd.0001839	null	[ [ "Lassa fever is a viral hemorrhagic fever that was first described in 1969 in the town of Lassa in the North-East of Nigeria [1] .", "It is endemic in the West African countries of Sierra Leone , Guinea , Liberia , and Nigeria ( [2] , [3] and references therein ) .", "Cases imported to Europe indicate...	[ "Lassa fever is a viral hemorrhagic fever endemic in West Africa .", "However , none of the hospitals in the endemic areas of Nigeria has the capacity to perform Lassa virus diagnostics .", "Case identification and management solely relies on non-specific clinical criteria .", "The Irrua Specialist Teaching H...	[ "In the past , diagnostic testing for Lassa fever patients in Nigeria has been performed nearly exclusively outside of the country .", "Patients thus were managed on-site based on clinical suspicion alone , posing risks to patients and health care workers and exhausting resources .", "To tackle this problem , w...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "cell physiology", "medicine and health sciences", "enzymes", "enzymology", "cell polarity", "physiological processes", "model organisms", "sex pheromones", "cellular structures and organelles", "research and analysis methods", "proteins", "cell membranes", "biochemistry", "biochemical sim...	Modelling of Yeast Mating Reveals Robustness Strategies for Cell-Cell Interactions	journal.pcbi.1004988	null	[ [ "Cell-to-cell signaling via diffusible molecules is an important mode of communication between cells in many mammalian systems such as neuron axon guidance [1] , immune cell recognition [2] , and angiogenesis [3] .", "These interactions involve sensing an attractant from the partner and responding by movi...	[ "Mating of budding yeast cells is a model system for studying cell-cell interactions .", "Haploid yeast cells secrete mating pheromones that are sensed by the partner which responds by growing a mating projection toward the source .", "The two projections meet and fuse to form the diploid .", "Successful mati...	[ "One of the riddles of Nature is how cells interact with one another to create complex cellular networks such as the neural networks in the brain .", "Forming precise connections between irregularly shaped cells is a challenge for biology .", "We developed computational methods for simulating these complex cell...	2016
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "microbial metabolism", "macromolecular assemblies", "microbiology", "dna transcription", "protein structure", "dna", "dna structure", "bacterial pathogens", "proteins", "gene expression", "biology", "biophysics", "molecular biology", "biochemistry", "gram negative", "nucleic acids", ...	The Transcription Factor AmrZ Utilizes Multiple DNA Binding Modes to Recognize Activator and Repressor Sequences of Pseudomonas aeruginosa Virulence Genes	journal.ppat.1002648	null	[ [ "Pseudomonas aeruginosa is an opportunistic , Gram negative bacterium that causes a variety of infections , mainly in immune-challenged patients [1]–[3] .", "More notably , chronic lung infection by P . aeruginosa is the leading cause of death in patients with the autosomal recessive disorder cystic fibro...	[ "AmrZ , a member of the Ribbon-Helix-Helix family of DNA binding proteins , functions as both a transcriptional activator and repressor of multiple genes encoding Pseudomonas aeruginosa virulence factors .", "The expression of these virulence factors leads to chronic and sustained infections associated with worse...	[ "The bacterium Pseudomonas aeruginosa causes a variety of human infections and is the leading cause of death in patients with cystic fibrosis .", "The main reason for the severity of these infections arises from the ability of P . aeruginosa to express virulence factors that protect it from the host immune system...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "neural networks", "computational neuroscience", "single neuron function", "biology", "neuroscience", "coding mechanisms" ]	Noise Suppression and Surplus Synchrony by Coincidence Detection	journal.pcbi.1002904	null	[ [ "Simultaneously recording the activity of multiple neurons provides a unique tool to observe the activity in the brain .", "The immediately arising question of the meaning of the observed correlated activity between different cells [1] , [2] is tightly linked to the problem how information is represented ...	[ "The functional significance of correlations between action potentials of neurons is still a matter of vivid debate .", "In particular , it is presently unclear how much synchrony is caused by afferent synchronized events and how much is intrinsic due to the connectivity structure of cortex .", "The available a...	[ "Whether spike timing conveys information in cortical networks or whether the firing rate alone is sufficient is a matter of controversial debate , touching the fundamental question of how the brain processes , stores , and conveys information .", "If the firing rate alone is the decisive signal used in the brain...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "plant science", "chagas disease", "infectious disease epidemiology", "epidemiology", "plant pathology", "biology and life sciences", "tropical diseases", "neglected tropical diseases", "protozoan infections", "parasitic diseases" ]	Profile of Trypanosoma cruzi Infection in a Tropical Medicine Reference Center, Northern Italy	journal.pntd.0003361	null	[ [ "Chagas disease ( CD ) is a protozoan zoonosis caused by Trypanosoma cruzi ( T . cruzi ) , with a widespread distribution from the South of the United States to Mexico , Central and South America [1] .", "Current data indicate that between 7 and 8 million people are infected in this area [2] .", "Othe...	[ "Chagas disease ( CD ) is endemic in Central and South America , Mexico and even in some areas of the United States .", "However , cases have been increasingly recorded also in non-endemic countries .", "The estimated number of infected people in Europe is in a wide range of 14000 to 181000 subjects , mostly re...	[ "Chagas disease is endemic in Central and South America , Mexico and part of the United States .", "However , migration flows permitted a diffusion outside those borders , so nowadays there are infected people living in Europe , mostly in Spain , Italy and the United Kingdom .", "This manuscript describes the p...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Penton-Dodecahedral Particles Trigger Opening of Intercellular Junctions and Facilitate Viral Spread during Adenovirus Serotype 3 Infection of Epithelial Cells	journal.ppat.1003718	null	[ [ "The main structural proteins of the icosahedral capsids of adenoviruses ( Ads ) are the hexon and penton base .", "The penton base forms pentamers located at the 12 vertices of the Ad particle .", "Each pentamer anchors one copy of a trimeric fiber protein .", "The C-terminal part of the fibers ,...	[ "Human adenovirus serotypes Ad3 , Ad7 , Ad11 , and Ad14 use the epithelial junction protein desmoglein 2 ( DSG2 ) as a receptor for infection .", "During Ad infection , the fiber and penton base capsid proteins are produced in vast excess and form hetero-oligomers , called pentons .", "It has been shown for Ad3...	[ "We have recently reported that a group of human Ads uses DSG2 as a receptor for infection .", "Among the DSG2-interacting Ads is serotype 3 , which is widely distributed in the human population .", "During Ad3 infection , subviral particles ( PtDd ) formed by two capsid proteins are produced in vast excess and...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "neuroscience/neural homeostasis", "computational biology/transcriptional regulation" ]	Emergence of Noise-Induced Oscillations in the Central Circadian Pacemaker	journal.pbio.1000513	Computational modeling and experimentation explain how intercellular coupling and intracellular noise can generate oscillations in a mammalian neuronal network even in the absence of cell-autonomous oscillators.	[ [ "Mammalian circadian clocks are cell autonomous and self-sustained within the central pacemaker , the suprachiasmatic nucleus ( SCN ) , as well as within peripheral tissues and fibroblasts [1]–[4] .", "Circadian rhythms are generated at the molecular level by an autoregulatory transcriptional and translat...	[ "Bmal1 is an essential transcriptional activator within the mammalian circadian clock .", "We report here that the suprachiasmatic nucleus ( SCN ) of Bmal1-null mutant mice , unexpectedly , generates stochastic oscillations with periods that overlap the circadian range .", "Dissociated SCN neurons expressed flu...	[ "The suprachiasmatic nucleus ( SCN ) is the master circadian pacemaker in mammals that controls and coordinates physiological processes in a daily manner .", "The SCN is composed of a network of cells , with each cell acting as an autonomous oscillator .", "In isolated individual cells , timekeeping is not prec...	2010
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell death", "autophagic cell death", "molecular probe techniques", "293t cells", "biological cultures", "cell processes", "immunoblotting", "mitochondria", "molecular biology techniques", "bioenergetics", "peroxisomes", "cellular structures and organelles", "extraction techniques", "rese...	Peroxisomes support human herpesvirus 8 latency by stabilizing the viral oncogenic protein vFLIP via the MAVS-TRAF complex	journal.ppat.1007058	null	[ [ "In response to virus infection , a host innate immune response is activated to restrict virus replication and dissemination .", "Activation of innate immune antiviral responses relies on signaling pathways relaying viral nucleic acid recognition to the transcriptional machinery .", "Upon RNA virus in...	[ "Human herpesvirus 8 ( HHV-8 ) is causally related to human malignancies .", "HHV-8 latent viral FLICE-inhibitory protein ( vFLIP ) is a viral oncoprotein that is linked to pathogenesis , but how its expression is regulated is largely unknown .", "In an attempt to understand the role of the mitochondrial antivi...	[ "HHV-8 , also known as Kaposi’s sarcoma associated herpesvirus ( KSHV ) , is the etiological agent of several malignancies occurring in individuals with severe immunosuppression , as occurs in acquired immunodeficiency syndrome and transplantation .", "The viral latent proteins , required for persistent infection...	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "genomics", "genetics", "microbiology", "biology", "evolutionary biology" ]	Genetic Structure and Evolution of the Leishmania Genus in Africa and Eurasia: What Does MLSA Tell Us	journal.pntd.0002255	null	[ [ "Protozoa of the Leishmania genus are part of the Trypanosomatids family , which also includes American and African Trypanosomes that cause Chagas disease and sleeping sickness .", "Compared to other human vector-borne protozoan parasitic diseases , such as malaria or trypanosomiases , leishmaniasis appea...	[ "Leishmaniasis is a complex parasitic disease from a taxonomic , clinical and epidemiological point of view .", "The role of genetic exchanges has been questioned for over twenty years and their recent experimental demonstration along with the identification of interspecific hybrids in natura has revived this deb...	[ "The mechanisms of genomic and genetic evolution in the Leishmania order , a protozoan group that contains about twenty pathogenic species , are the focus of much debate .", "Although these parasites have been considered for years to reproduce clonally , recent works have demonstrated both experimental and in nat...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology" ]	Stat5 Signaling Specifies Basal versus Stress Erythropoietic Responses through Distinct Binary and Graded Dynamic Modalities	journal.pbio.1001383	Stat5 signaling in erythroblasts can assume either a binary, low-intensity form, essential for basal erythropoiesis, or a graded, high-intensity response, restricted to early erythroblasts and to erythropoietic stress.	[ [ "Healthy individuals at sea level continuously generate red blood cells in a process known as “basal erythropoiesis” that is essential to life .", "Erythropoiesis increases by up to 10-fold its basal rate in response to hypoxic stress , as may occur at high altitude , or in response to anemia or hemorrhag...	[ "Erythropoietin ( Epo ) -induced Stat5 phosphorylation ( p-Stat5 ) is essential for both basal erythropoiesis and for its acceleration during hypoxic stress .", "A key challenge lies in understanding how Stat5 signaling elicits distinct functions during basal and stress erythropoiesis .", "Here we asked whether...	[ "Hormone signaling through the erythropoietin ( Epo ) pathway is required both for the continuous replacement of red blood cells ( RBCs ) that are lost through aging ( a process known as \"basal erythropoiesis\" ) and to boost tissue oxygen when bleeding , in anemia or at high altitude ( \"stress erythropoiesis\" )...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "learning", "cell physiology", "action potentials", "medicine and health sciences", "neural networks", "membrane potential", "brain", "social sciences", "electrophysiology", "neuroscience", "learning and memory", "cognitive psychology", "mathematics", "algebra", "cognition", "memory", ...	Gamma Synchronization Influences Map Formation Time in a Topological Model of Spatial Learning	journal.pcbi.1005114	null	[ [ "For years it has been assumed that the cognitive map is Cartesian , containing detailed information about locations , distances and angles .", "Undoubtedly , such information is provided by various brain regions , but increasing evidence suggests that the hippocampal map is topological in nature .", ...	[ "The mammalian hippocampus plays a crucial role in producing a cognitive map of space—an internalized representation of the animal’s environment .", "We have previously shown that it is possible to model this map formation using a topological framework , in which information about the environment is transmitted t...	[ "One of the goals of theoretical systems neuroscience is to connect parameters of neuronal activity observed in electrophysiological experiments , such as cell firing rates , frequencies and amplitudes of the brain rhythms , with cognitive phenomena that emerge at the scale of large groups of cells .", "In previo...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "mycetoma", "engineering and technology", "tropical diseases", "geographical locations", "sudan", "surgical and invasive medical procedures", "health care", "decision analysis", "signs and symptoms", "management engineering",...	Predictors of Post-operative Mycetoma Recurrence Using Machine-Learning Algorithms: The Mycetoma Research Center Experience	journal.pntd.0005007	null	[ [ "Eumycetoma is a chronic granulomatous destructive and mutilating subcutaneous fungal infection [1 , 2] .", "The disease is endemic in many tropical and subtropical regions in what is known as the Mycetoma Belt [3 , 4] .", "It has many medical , health , socio-economic detrimental bearings on the affe...	[ "Post-operative recurrence in mycetoma after adequate medical and surgical treatment is common and a serious problem .", "It has health , socio-economic and psychological detrimental effects on patients and families .", "It is with this in mind , we set out to determine the predictors of post-operative recurren...	[ "Post-operative recurrence in mycetoma is a thoughtful problem .", "It has numerous undesirable medical , health , socio-economic and psychological impacts on the affected patients and their families , communities and health authorities in endemic regions .", "It is an important motive for patients to drop out ...	2016
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "virology/virion structure, assembly, and egress", "virology/immunodeficiency viruses", "virology/viral replication and gene regulation" ]	Dynamics of HIV-1 Assembly and Release	journal.ppat.1000652	null	[ [ "Assembly and release of progeny virions are fundamental steps in viral replication .", "In the case of retroviruses , such as human immunodeficiency virus type 1 ( HIV-1 ) , the viral structural polyprotein Gag plays a central role in mediating both of these processes which occur concomitantly at the pla...	[ "Assembly and release of human immunodeficiency virus ( HIV ) occur at the plasma membrane of infected cells and are driven by the Gag polyprotein .", "Previous studies analyzed viral morphogenesis using biochemical methods and static images , while dynamic and kinetic information has been lacking until very rece...	[ "Human immunodeficiency virus ( HIV ) particles are formed and released at the plasma membrane of the infected cell .", "Here , we analyzed the dynamics of HIV assembly and release making use of fluorescently labeled HIV structural proteins .", "We determined that assembly of the viral protein shell occurs with...	2009
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "medicine and health sciences", "gene regulation", "diet", "animals", "invertebrate genomics", "dna transcription", "animal models", "drosophila melanogaster", "model organisms", "nutrition", "experimental organism systems", "genome analysis", "drosophila", "research and...	Longevity is determined by ETS transcription factors in multiple tissues and diverse species	journal.pgen.1008212	null	[ [ "Ageing is characterised by a steady systematic decline in biological function , and increased likelihood of disease[1] .", "Understanding the basic biology of ageing therefore promises to help improve the overall health of older people , who constitute an ever-increasing proportion of our populations .",...	[ "Ageing populations pose one of the main public health crises of our time .", "Reprogramming gene expression by altering the activities of sequence-specific transcription factors ( TFs ) can ameliorate deleterious effects of age .", "Here we explore how a circuit of TFs coordinates pro-longevity transcriptional...	[ "Understanding the basic biology of ageing may help us to reduce the burden of ill-health that old age brings .", "Ageing is modulated by changes to gene expression , which are orchestrated by the coordinate activity of proteins called transcription factors ( TFs ) .", "E-twenty six ( ETS ) TFs are a large fami...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "uterus", "medicine and health sciences", "chemical characterization", "reproductive system", "maternal health", "obstetrics and gynecology", "gene regulation", "regulatory proteins", "dna-binding proteins", "hormones", "women's health", "connective tissue cells", "pregnancy", "transcripti...	The Promyelocytic Leukemia Zinc Finger Transcription Factor Is Critical for Human Endometrial Stromal Cell Decidualization	journal.pgen.1005937	null	[ [ "For healthy couples , the chance for conception per menstrual cycle is only thirty-to-forty percent [1] , underscoring the remarkable inefficiency of human reproduction .", "Moreover , approximately a third of pregnancies detected early by human chorionic gonadotropin assay fail to result in live births ...	[ "Progesterone , via the progesterone receptor ( PGR ) , is essential for endometrial stromal cell decidualization , a cellular transformation event in which stromal fibroblasts differentiate into decidual cells .", "Uterine decidualization supports embryo implantation and placentation as well as subsequent events...	[ "Following embryo attachment to the uterine epithelium , the underlying decidualized stroma is critical for further invasion by the conceptus into the maternal compartment .", "Because endometrial decidualization is required early in the continuum of events that lead to a successful pregnancy , abnormal deciduali...	2016
[ "Introduction", "Results", "Discussion" ]	[ "biophysics/biomacromolecule-ligand interactions", "biophysics/cell signaling and trafficking structures", "biophysics/theory and simulation" ]	Dynamic Allostery in the Methionine Repressor Revealed by Force Distribution Analysis	journal.pcbi.1000574	null	[ [ "Protein allostery plays a key role in the regulation of cellular functions such as transcription or enzymatic action [1] .", "It crucially governs the formation of protein or protein-DNA complexes as well as the functional activity of individual proteins .", "Allosteric signals used by nature are div...	[ "Many fundamental cellular processes such as gene expression are tightly regulated by protein allostery .", "Allosteric signal propagation from the regulatory to the active site requires long-range communication , the molecular mechanism of which remains a matter of debate .", "A classical example for long-rang...	[ "Proteins carry out most of the cellular processes , from metabolic reactions to the regulation and expression of genes .", "Tight and effective regulation of the executing protein machinery is commonly achieved by allostery .", "The only general requirement for allosteric communication is the transmission of a...	2009
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "sequencing techniques", "invertebrates", "medicine and health sciences", "in situ hybridization", "molecular probe techniques", "brain", "vertebrates", "mice", "neuroscience", "animals", "mammals", "animal models", "osteichthyes", "developmental biology", "drosophila melanogaster", "m...	Lef1-dependent hypothalamic neurogenesis inhibits anxiety	journal.pbio.2002257	null	[ [ "Recent work has demonstrated that innate behaviors can be highly conserved across diverse animal models [1] .", "Individual neuronal populations that mediate these behaviors are specified during embryogenesis by transcription factors that can also be conserved across species [2] .", "However , molecu...	[ "While innate behaviors are conserved throughout the animal kingdom , it is unknown whether common signaling pathways regulate the development of neuronal populations mediating these behaviors in diverse organisms .", "Here , we demonstrate that the Wnt/ß-catenin effector Lef1 is required for the differentiation ...	[ "Humans , mice , fish , and even flies exhibit anxiety-like behavior despite the fact that their brain anatomy varies widely .", "This study reveals another common thread that runs through these diverse animals: the molecular origins of their shared behavior .", "Gene knockout experiments in mouse and zebrafish...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell motility", "medicine and health sciences", "actin filaments", "myofibrils", "rna interference", "muscle tissue", "muscle proteins", "epigenetics", "contractile proteins", "actins", "animal cells", "proteins", "genetic interference", "gene expression", "structural proteins", "biol...	Filamin actin-binding and titin-binding fulfill distinct functions in Z-disc cohesion	journal.pgen.1006880	null	[ [ "Arguably , the most complex actin-related cellular structure is the sarcomere , the basic contractile unit of muscle cells .", "The sarcomere consists of antiparallel actin thin filaments and myosin thick filaments .", "The thin filaments are anchored to a big protein complex termed the Z-disc at bot...	[ "Many proteins contribute to the contractile properties of muscles , most notably myosin thick filaments , which are anchored at the M-line , and actin thin filaments , which are anchored at the Z-discs that border each sarcomere .", "In humans , mutations in the actin-binding protein Filamin-C result in myopathi...	[ "The Z-disc is a macromolecular complex required to attach and stabilize actin thin filaments in the sarcomere , the smallest contractile unit of striated muscles .", "Mutations in Z-disc-associated proteins typically result in muscle disorders .", "Dimeric filamin organizes actin filaments , localizes at the Z...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "transcription activators", "fungal genetics", "gene regulation", "microbiology", "fungal evolution", "molecular genetics", "molecular biology techniques", "mutagenesis and gene deletion techniques", "fungal pathogens", "mycology", "proteins", "medical microbiology", "gene expression", "mi...	Telomeric ORFs (TLOs) in Candida spp. Encode Mediator Subunits That Regulate Distinct Virulence Traits	journal.pgen.1004658	null	[ [ "Candida albicans is a commensal yeast commonly recovered from mucosal surfaces in humans .", "C . albicans is also a versatile opportunistic pathogen , responsible for a variety of superficial infections as well as more severe , life threatening infections in severely immunocompromised patients .", "...	[ "The TLO genes are a family of telomere-associated ORFs in the fungal pathogens Candida albicans and C . dubliniensis that encode a subunit of the Mediator complex with homology to Med2 .", "The more virulent pathogen C . albicans has 15 copies of the gene whereas the less pathogenic species C . dubliniensis has ...	[ "Candida albicans and C . dubliniensis are fungal pathogens of humans .", "Both species possess TLO genes encoding proteins with homology to the Med2 subunit of Mediator .", "The more virulent pathogen C . albicans has 15 copies of the TLO gene whereas the less pathogenic species C . dubliniensis has only two (...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetic networks", "transcription activators", "functional genomics", "gene regulation", "cell processes", "dna-binding proteins", "cell differentiation", "epithelial cells", "gene function", "developmental biology", "stem cells", "branching morphogenesis", "genome analysis", "transcripti...	The Co-factor of LIM Domains (CLIM/LDB/NLI) Maintains Basal Mammary Epithelial Stem Cells and Promotes Breast Tumorigenesis	journal.pgen.1004520	null	[ [ "Mouse mammary gland morphogenesis begins during mid-gestation with the development of two bilateral epithelial ridges along the ventral epidermis that form invasive , multipotent stem cell-enriched placodes migrating into the underlying mesenchyme , later branching to form a rudimentary ductal tree by birth ...	[ "Mammary gland branching morphogenesis and ductal homeostasis relies on mammary stem cell function for the maintenance of basal and luminal cell compartments .", "The mechanisms of transcriptional regulation of the basal cell compartment are currently unknown .", "We explored these mechanisms in the basal cell ...	[ "Recent advancements in mammary gland biology demonstrate conflicting models in maintenance of basal and luminal cell compartments by either unipotent or bipotent mammary stem cells .", "However , the molecular mechanisms underlying control of the basal cell compartment , including stem cells , remain poorly unde...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "biotechnology", "bioengineering", "medicine", "physics", "infectious diseases", "medical devices", "diagnostic medicine", "drugs and devices", "biology", "microbiology", "biophysics", "parasitology" ]	The Iron Distribution and Magnetic Properties of Schistosome Eggshells: Implications for Improved Diagnostics	journal.pntd.0002219	null	[ [ "Schistosomiasis is a helminth infection representing a major health burden for humans in tropical and developing nations .", "Some 200 million people are infected , and 600 million are currently estimated to be at risk of infection [1] .", "Recently , schistosomiasis control efforts have been increas...	[ "Schistosoma mansoni and Schistosoma japonicum are the most frequent causative agents of human intestinal schistosomiasis .", "Approximately 200 million people in the world are infected with schistosomes .", "Diagnosis of schistosomiasis is often difficult .", "High percentages of low level infections are mis...	[ "In the present study , we investigated the mechanism underlying a novel diagnostic method for Schistosoma – one of the most widespread and frequently occurring parasites infecting humans in tropical countries .", "In recent years , the world has seen significant reduction in the burden of Schistosoma infections ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunology/cellular microbiology and pathogenesis", "immunology/immunity to infections", "microbiology/immunity to infections", "immunology/innate immunity" ]	MARCO, TLR2, and CD14 Are Required for Macrophage Cytokine Responses to Mycobacterial Trehalose Dimycolate and Mycobacterium tuberculosis	journal.ppat.1000474	null	[ [ "Mycobacterium tuberculosis ( Mtb ) , a causative agent of human tuberculosis , is responsible for 8 million new infections and 2 million deaths yearly .", "One third of the world population is currently estimated to be infected with M . tuberculosis , although less than 10% of those infected show clinica...	[ "Virtually all of the elements of Mycobacterium tuberculosis ( Mtb ) pathogenesis , including pro-inflammatory cytokine production , granuloma formation , cachexia , and mortality , can be induced by its predominant cell wall glycolipid , trehalose 6 , 6′-dimycolate ( TDM/cord factor ) .", "TDM mediates these pot...	[ "The causative agent of tuberculosis , Mycobacterium tuberculosis , has a lipid-rich cell wall that contains a high percentage of mycolic acids .", "These mycolic acids contribute to both the impermeable nature of the cell wall and to the immunostimulatory properties of the bacterium .", "Indeed , it has been k...	2009
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "biotechnology", "medicine", "diagnostic medicine", "physiology", "biology", "anatomy and physiology", "cardiovascular" ]	Mesenchymal Bone Marrow Cell Therapy in a Mouse Model of Chagas Disease. Where Do the Cells Go?	journal.pntd.0001971	null	[ [ "Chagas disease is a serious public health problem in all Latin American countries [1] , where it is estimated that 15–16 million people are infected with the its causative agent , the parasite Trypanosoma cruzi ( T . cruzi ) [2] .", "Although T . cruzi is endemic in Latin America , thousands of people ar...	[ "Chagas disease , resulting from infection with the parasite Trypanosoma cruzi ( T . cruzi ) , is a major cause of cardiomyopathy in Latin America .", "Drug therapy for acute and chronic disease is limited .", "Stem cell therapy with bone marrow mesenchymal cells ( MSCs ) has emerged as a novel therapeutic opti...	[ "Chagas disease , resulting from infection with the parasite Trypanosoma cruzi , is a major cause of heart disease in Latin America .", "Treatment options are limited to a small number of drugs that were developed more than four decades ago and which have various drawbacks .", "Stem cell therapy with bone marro...	2012
[ "Introduction", "Results", "Discussion", "Material and Methods" ]	[ "infectious diseases", "immunology/innate immunity", "genetics and genomics/gene expression" ]	The Major Yolk Protein Vitellogenin Interferes with the Anti-Plasmodium Response in the Malaria Mosquito Anopheles gambiae	journal.pbio.1000434	Functional gene analysis in malaria mosquitoes reveals molecules underpinning the trade-off between efficient reproduction and the antiparasitic response.	[ [ "Malaria is a mosquito-borne parasitic disease affecting annually an estimated 250 million people , of which close to 1 million ( mostly children in sub-Saharan Africa ) succumb to the disease ( World Health Organization fact sheet #94 , April 2010; http://www . who . int/mediacentre/factsheets/fs094/en/index...	[ "When taking a blood meal on a person infected with malaria , female Anopheles gambiae mosquitoes , the major vector of human malaria , acquire nutrients that will activate egg development ( oogenesis ) in their ovaries .", "Simultaneously , they infect themselves with the malaria parasite .", "On traversing th...	[ "Malaria annually claims the lives of almost 1 million infants and imposes a major socio-economic burden on Africa and other tropical regions .", "Meanwhile , the detailed biological interactions between the malaria parasite and its Anopheles mosquito vector remain largely enigmatic .", "What we do know is that...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Sequence Features and Transcriptional Stalling within Centromere DNA Promote Establishment of CENP-A Chromatin	journal.pgen.1004986	null	[ [ "Centromeres are the chromosomal sites upon which kinetochores are assembled to ensure accurate segregation of sister chromatids into daughter cells .", "Most kinetochores are built upon a specialized type of chromatin in which canonical histone H3 is replaced by the histone variant CENP-A .", "Althou...	[ "Centromere sequences are not conserved between species , and there is compelling evidence for epigenetic regulation of centromere identity , with location being dictated by the presence of chromatin containing the histone H3 variant CENP-A .", "Paradoxically , in most organisms CENP-A chromatin generally occurs ...	[ "The kinetochore directs the separation of chromosomes and is assembled at a special region of the chromosome—the centromere .", "DNA is wrapped around particles called nucleosomes , which contain histone proteins .", "The nucleosomes at centromeres are specialized , and contain the centromere-specific histone ...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "neglected tropical diseases", "infectious diseases", "infectious disease control" ]	Health Access Livelihood Framework Reveals Potential Barriers in the Control of Schistosomiasis in the Dongting Lake Area of Hunan Province, China	journal.pntd.0002350	null	[ [ "Health disparities exist in all societies and recent data suggest that they might be widening [1]–[4] .", "Yet , many have argued that the existence of disparities in health status is unfair , should reasonable actions exist for their avoidance or mitigation [1] , [4]–[10] .", "The concept of ‘fairne...	[ "Access to health care is a major requirement in improving health and fostering socioeconomic development .", "In the People's Republic of China ( P . R . China ) , considerable changes have occurred in the social , economic , and health systems with a shift from a centrally planned to a socialist market economy ...	[ "China has made great strides toward reducing the burden of schistosomiasis , facilitated by sustained political commitment and a multi-faceted , integrated control strategy .", "The ultimate goal is disease elimination , which might be challenging due to high rates of re-infection , clusters of re-emergence , an...	2013
[ "Introduction", "Results", "Discussion", "Appendix A" ]	[ "neural networks", "social sciences", "neuroscience", "human performance", "artificial intelligence", "vision", "neuronal tuning", "computer and information sciences", "animal cells", "behavior", "psychology", "cellular neuroscience", "cell biology", "neurons", "psychophysics", "biolog...	Modeling second-order boundary perception: A machine learning approach	journal.pcbi.1006829	null	[ [ "Many of the most common functions of sensory systems involve detection , identification or discrimination of particular stimuli .", "For example , a critically important ability of early visual processing is to segment images into distinct regions , which may correspond to cohesive surfaces or objects [1...	[ "Visual pattern detection and discrimination are essential first steps for scene analysis .", "Numerous human psychophysical studies have modeled visual pattern detection and discrimination by estimating linear templates for classifying noisy stimuli defined by spatial variations in pixel intensities .", "Howev...	[ "Many naturally occurring visual boundaries are defined by spatial differences in features other than luminance , for example by differences in texture or contrast .", "Quantitative models of such “second-order” boundary perception cannot be estimated using the standard regression techniques ( known as “classific...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Hnrnph1 Is A Quantitative Trait Gene for Methamphetamine Sensitivity	journal.pgen.1005713	null	[ [ "Substance use disorders ( SUDs ) involving psychostimulants such as cocaine and methamphetamine ( MA ) are heritable; however , their major genetic determinants remain poorly defined [1–4] .", "In particular , genome-wide association studies ( GWAS ) of psychostimulant abuse have yet to discover the unde...	[ "Psychostimulant addiction is a heritable substance use disorder; however its genetic basis is almost entirely unknown .", "Quantitative trait locus ( QTL ) mapping in mice offers a complementary approach to human genome-wide association studies and can facilitate environment control , statistical power , novel g...	[ "Both genetic and environmental factors can powerfully modulate susceptibility to substance use disorders .", "Quantitative trait locus ( QTL ) mapping is an unbiased discovery-based approach that is used to identify novel genetic factors and provide new mechanistic insight into phenotypic variation associated wi...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics", "biology", "microbiology", "genetics and genomics" ]	Portrait of Candida albicans Adherence Regulators	journal.ppat.1002525	null	[ [ "Microorganisms naturally exist primarily in association with surfaces in communities called biofilms .", "Central to the formation of biofilms is the ability of microbial cells to adhere to substrates .", "Adherence mechanisms are diverse , and involve specific cell surface proteins ( adhesins ) , mo...	[ "Cell-substrate adherence is a fundamental property of microorganisms that enables them to exist in biofilms .", "Our study focuses on adherence of the fungal pathogen Candida albicans to one substrate , silicone , that is relevant to device-associated infection .", "We conducted a mutant screen with a quantita...	[ "Most microorganisms adhere to surfaces in nature , leading to formation of complex communities called biofilms .", "Pathogen adherence to medical devices is the basis for device-associated infection .", "We have focused on the control of adherence in the fungal pathogen Candida albicans .", "We find that thi...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "plant growth and development", "plant biology", "gene regulation", "histone modification", "plant science", "epigenetics", "molecular genetics", "plants", "leafs", "gene expression", "plant genetics", "biology", "genetics", "molecular cell biology", "gene networks", "genetics and geno...	Histone Deacetylase HDA6 Is Functionally Associated with AS1 in Repression of KNOX Genes in Arabidopsis	journal.pgen.1003114	null	[ [ "The initiation of leaf primordia is established by recruitment of cells from the flanks of the shoot apical meristem ( SAM ) .", "Meristem activity in the shoot apex is specified in part by the class I KNOTTED-LIKE HOMOBOX ( KNOX ) genes [1]–[3] .", "Lateral organs , such as leaves , are initiated on...	[ "ASYMMETRIC LEAVES 1 ( AS1 ) is a MYB-type transcription repressor that controls leaf development by regulating KNOX gene expression , but the underlying molecular mechanism is still unclear .", "In this study , we demonstrated that AS1 can interact with the histone deacetylase HDA6 in vitro and in vivo .", "Th...	[ "AS1 is a MYB-type transcription repressor that controls leaf patterning by repressing class-1 KNOX gene expression .", "The molecular mechanism by which AS1 represses KNOX gene expression is still unclear .", "In this study , we found that AS1 interacted with the histone deacetylase HDA6 .", "Furthermore , H...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "genetics and genomics", "homo (human)" ]	Linkage Analysis of a Model Quantitative Trait in Humans: Finger Ridge Count Shows Significant Multivariate Linkage to 5q14.1	journal.pgen.0030165	null	[ [ "Finger ridges and ridge patterns are highly heritable , durable , and age-independent", "human traits and have been studied as a model quantitative trait in humans for over", "80 years [1]", ".", "They develop between approximately the 13th and 18th weeks of gestation , and in", "the abse...	[ "The finger ridge count ( a measure of pattern size ) is one of the most heritable", "complex traits studied in humans and has been considered a model human polygenic", "trait in quantitative genetic analysis .", "Here , we report the results of the first", "genome-wide linkage scan for finger ridge count i...	[ "Finger ridge count ( an index of the size of the fingerprint pattern ) has been", "used as a model trait for the study of human quantitative genetics for over", "80 years .", "Here , we present the first genome-wide linkage scan for finger", "ridge count in a large sample of 2 , 114 offspring from 922 nucl...	2007
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "blood cells", "medicine and health sciences", "immune cells", "enzyme-linked immunoassays", "pathology and laboratory medicine", "immunology", "tropical diseases", "parasitic diseases", "parasitic protozoans", "protozoans", "neglected tropical diseases", "immunologic techniques", "antibody ...	Treatment Success in Trypanosoma cruzi Infection Is Predicted by Early Changes in Serially Monitored Parasite-Specific T and B Cell Responses	journal.pntd.0004657	null	[ [ "Chagas disease is the highest impact parasitic disease in Latin America and the most common cause of infectious myocarditis in the world [1] .", "The goal of treatment of humans in the chronic phase of Trypanosoma cruzi infection is to prevent the development of heart disease and infection by via blood t...	[ "Chagas disease is the highest impact parasitic disease in Latin America .", "We have proposed that changes in Trypanosoma cruzi-specific immune responses might serve as surrogate indicators of treatment success .", "Herein , we addressed in a long-term follow-up study whether cure achieved after treatment can ...	[ "This study demonstrates that alterations in immunological parameters early after treatment with benznidazole in Chagas disease patients are predictors of treatment efficacy .", "Cure was associated with an early decline in T . cruzi-specific IFN-γ-producing T cells and in antibody titers and with high basal leve...	2016
[ "Introduction", "Materials and Methods", "Results and Discussion" ]	[]	Lipid-Free Antigen B Subunits from Echinococcus granulosus: Oligomerization, Ligand Binding, and Membrane Interaction Properties	journal.pntd.0003552	null	[ [ "Cystic echinococcosis ( CE ) , one of two major types of hydatid disease , is a worldwide zoonosis caused by the larval stage ( metacestode ) of Echinococcus granulosus sensu lato ( E . granulosus s . l . ) , which includes a series of species traditionally considered to comprise different strains or genotyp...	[ "The hydatid disease parasite Echinococcus granulosus has a restricted lipid metabolism , and needs to harvest essential lipids from the host .", "Antigen B ( EgAgB ) , an abundant lipoprotein of the larval stage ( hydatid cyst ) , is thought to be important in lipid storage and transport .", "It contains a wid...	[ "Echinococcus granulosus is a causative agent of hydatidosis , a parasitic disease that affects humans and livestock with significant economic and public health impact worldwide .", "Antigen B ( EgAgB ) , an abundant product of E . granulosus larvae , is a lipoprotein that carries a wide variety of lipids , inclu...	2015
[ "Introduction", "Results", "Discussion", "Models" ]	[ "action potentials", "medicine and health sciences", "second messenger system", "mechanisms of signal transduction", "nervous system", "membrane potential", "electrophysiology", "neuroscience", "simulation and modeling", "synaptic plasticity", "neuronal plasticity", "research and analysis meth...	Stability and Competition in Multi-spike Models of Spike-Timing Dependent Plasticity	journal.pcbi.1004750	null	[ [ "Spike-timing dependent plasticity ( STDP ) is a form of activity-dependent synaptic plasticity that appears throughout the nervous system [1 , 2 , 3] .", "In STDP , pairs of pre- and postsynaptic action potentials potentiate a synapse when the presynaptic spike precedes the postsynaptic spike , and depre...	[ "Spike-timing dependent plasticity ( STDP ) is a widespread plasticity mechanism in the nervous system .", "The simplest description of STDP only takes into account pairs of pre- and postsynaptic spikes , with potentiation of the synapse when a presynaptic spike precedes a postsynaptic spike and depression otherw...	[ "Synaptic plasticity is believed to underlie learning and memory by competitive strengthening and weakening of synapses in neural networks .", "However , the ability to form new memories while maintaining the old ones involves an intricate balance between synaptic stability and competition .", "In one of the mo...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Comparison of Two Quantitative Real Time PCR Assays for Rickettsia Detection in Patients from Tunisia	journal.pntd.0003487	null	[ [ "Rickettsioses are vector borne diseases caused by Gram negative obligate intracellular rods belonging to the genus Rickettsia [1] .", "This genus contains 28 validated species , which are divided into four groups: typhus group ( TG ) , spotted fever group ( SFG ) , the ancestral group and the transitiona...	[ "Quantitative real time PCR ( qPCR ) offers rapid diagnosis of rickettsial infections .", "Thus , successful treatment could be initiated to avoid unfavorable outcome .", "Our aim was to compare two qPCR assays for Rickettsia detection and to evaluate their contribution in early diagnosis of rickettsial infecti...	[ "Rickettsial diagnosis is challenging in routine laboratory .", "Serology offers only retrospective diagnosis .", "We aimed to introduce molecular methods in routine diagnosis of these infections .", "The lack of standardized methods led us to compare real time PCR assays previously reported in order to imple...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "markov models", "chromosome structure and function", "statistics", "histone modification", "mathematics", "epigenetics", "chromatin", "chromosome biology", "gene expression", "chromatin modification", "genetic loci", "probability theory", "chromosomes", "cell biology", "genetics", "bi...	Exploring chromatin hierarchical organization via Markov State Modelling	journal.pcbi.1006686	null	[ [ "The packing of two meters of DNA in the few-micrometer nucleus results in a structure that performs multiple roles , from forming a structural scaffold of chromatin to facilitating active expression and silencing of genetic material [1 , 2] .", "The beginning of interest in the biophysical characterizati...	[ "We propose a new computational method for exploring chromatin structural organization based on Markov State Modelling of Hi-C data represented as an interaction network between genomic loci .", "A Markov process describes the random walk of a traveling probe in the corresponding energy landscape , mimicking the ...	[ "A new era in chromatin research started with the availability of Hi-C data and new experimental techniques driving improvements in data resolution enable us to achieve a deeper understanding of the chromatin structure and function , while calling , at the same time , for the development of more advanced analytical...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "chitin", "invertebrates", "medicine and health sciences", "luciferase", "locusts", "gene regulation", "enzymes", "enzymology", "animals", "insect pests", "physiological processes", "developmental biology", "micrornas", "nymphs", "materials science", "pests", "macromolecules", "mat...	miR-71 and miR-263 Jointly Regulate Target Genes Chitin synthase and Chitinase to Control Locust Molting	journal.pgen.1006257	null	[ [ "Molting is a crucial process in insect growth and development [1 , 2] .", "Chitin , as a vital component of the cuticle of the epidermis , plays key roles in maintaining morphology and the molting process [3] .", "Because chitin is absent in plants and vertebrates , and insect growth and development ...	[ "Chitin synthase and chitinase play crucial roles in chitin biosynthesis and degradation during insect molting .", "Silencing of Dicer-1 results in reduced levels of mature miRNAs and severely blocks molting in the migratory locust .", "However , the regulatory mechanism of miRNAs in the molting process of locu...	[ "Molting is a crucial process in the growth and development in insects .", "Disturbing the molting process represents an attractive strategy for developing safe and effective insecticides .", "The migratory locust is a hemimetabolous pest that undergoes five molting stages in its life cycle .", "Similar molti...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "keratinocytes", "pathology and laboratory medicine", "gene regulation", "pathogens", "microbiology", "cell differentiation", "epithelial cells", "viruses", "developmental biology", "dna replication", "dna viruses", "hpv-31", "dna", "epigenetics", "chrom...	Sp100 colocalizes with HPV replication foci and restricts the productive stage of the infectious cycle	journal.ppat.1006660	null	[ [ "Human papillomaviruses ( HPVs ) establish a persistent infection in the cutaneous and mucosal epithelia of their hosts [1] .", "The virus infects the basal layer of keratinocytes through a micro-fissure and establishes a persistent reservoir of infection in these dividing cells .", "When the infected...	[ "We have shown previously that Sp100 ( a component of the ND10 nuclear body ) represses transcription , replication and establishment of incoming human papillomavirus ( HPV ) DNA in the early stages of infection .", "In this follow up study , we show that Sp100 does not substantially regulate viral infection in t...	[ "Host restriction factors act to limit viral infection as part of the intrinsic immune system .", "Upon entry into cells , human papillomaviruses ( HPV ) encounter anti-viral nuclear bodies , called ND10 , and components of these bodies , such as Sp100 , restrict early viral infection .", "If HPV escapes these ...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "traumatic injury", "medicine and health sciences", "innate immune system", "immune cells", "immune physiology", "pathology and laboratory medicine", "cytokines", "nervous system", "immunology", "cell processes", "microglial cells", "age groups", "developmental biology", "...	Peripherally derived macrophages modulate microglial function to reduce inflammation after CNS injury	journal.pbio.2005264	null	[ [ "The immune system plays a pivotal role in development and homeostatic functions of the central nervous system ( CNS ) [1] .", "Immune system dysfunction can give rise to CNS disease [2] and its response to injury shapes recovery [3–5] .", "The cellular response to CNS injuries is stereotyped and invo...	[ "Infiltrating monocyte-derived macrophages ( MDMs ) and resident microglia dominate central nervous system ( CNS ) injury sites .", "Differential roles for these cell populations after injury are beginning to be uncovered .", "Here , we show evidence that MDMs and microglia directly communicate with one another...	[ "The immune and the central nervous systems are now thought to be inextricably linked .", "In response to injury , the immune system shapes CNS recovery through a complex of molecular and cellular mediators .", "However , it is unclear how the kinetics , magnitude , and components of this response can be harnes...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing techniques", "invertebrates", "medicine and health sciences", "nucleases", "enzymes", "dna-binding proteins", "enzymology", "animals", "alleles", "genetic mapping", "mutation", "gene sequencing", "molecular biology techniques", "insect vectors", "research and analysis methods...	The creation and selection of mutations resistant to a gene drive over multiple generations in the malaria mosquito	journal.pgen.1007039	null	[ [ "Naturally occurring gene drives—selfish genetic elements that are able to bias their own inheritance and rapidly invade a population , even starting from very low frequencies—have inspired proposals to harness their power to spread into a population of insect disease vectors traits that manipulate their biol...	[ "Gene drives have enormous potential for the control of insect populations of medical and agricultural relevance .", "By preferentially biasing their own inheritance , gene drives can rapidly introduce genetic traits even if these confer a negative fitness effect on the population .", "We have recently develope...	[ "Gene drives are selfish genetic elements that are able to bias their own inheritance among offspring .", "Starting from very low frequencies they can rapidly invade a population in just a few generations , even when imposing a fitness cost .", "Gene drives based on the precise DNA cutting enzyme CRISPR have be...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Flavodoxin-Like Proteins Protect Candida albicans from Oxidative Stress and Promote Virulence	journal.ppat.1005147	null	[ [ "Oxidative stress poses a great threat to cells .", "Unchecked oxidative damage to DNA , proteins , and lipids causes disruption of physiological processes , harmful mutations , and cell death [1] .", "To prevent these destructive effects , cells utilize a variety of mechanisms to protect against oxid...	[ "The fungal pathogen Candida albicans causes lethal systemic infections in humans .", "To better define how pathogens resist oxidative attack by the immune system , we examined a family of four Flavodoxin-Like Proteins ( FLPs ) in C . albicans .", "In agreement with previous studies showing that FLPs in bacteri...	[ "Oxidative damage is a fundamental problem for cells and a particular challenge for microbial pathogens , which require special mechanisms to resist the oxidative attack by the host immune system .", "We identified four proteins in the human fungal pathogen Candida albicans that belong to a large family of enzyme...	2015
[ "Introduction", "Results and discussion", "Materials and methods" ]	[ "invertebrates", "medicine and health sciences", "pathology and laboratory medicine", "caenorhabditis", "gene regulation", "pathogens", "immunology", "microbiology", "animals", "dna transcription", "pseudomonas aeruginosa", "animal models", "caenorhabditis elegans", "regulator genes", "m...	Global transcriptional regulation of innate immunity by ATF-7 in C. elegans	journal.pgen.1007830	null	[ [ "Convergent genetic studies of host defense of Drosophila melanogaster and mammalian innate immune signaling revealed a commonality in signaling pathways of innate immunity that has helped motivate the study of pathogen resistance mechanisms in genetically tractable host organisms such as Caenorhabditis elega...	[ "The nematode Caenorhabditis elegans has emerged as a genetically tractable animal host in which to study evolutionarily conserved mechanisms of innate immune signaling .", "We previously showed that the PMK-1 p38 mitogen-activated protein kinase ( MAPK ) pathway regulates innate immunity of C . elegans through p...	[ "Innate immunity is the first line of defense against invading microbes across metazoans .", "Caenorhabditis elegans lacks adaptive immunity and is therefore particularly dependent on mounting an innate immune response against pathogens .", "A major component of this response is the conserved PMK-1/p38 MAPK sig...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Guanine Holes Are Prominent Targets for Mutation in Cancer and Inherited Disease	journal.pgen.1003816	null	[ [ "At least fifteen cancer genome sequencing projects were reported between 2007 and 2011 [1]–[15] , and this number is now increasing very rapidly .", "These studies have been critical for addressing mechanisms of somatic mutation , such as those associated with single base substitutions ( SBSs ) , which n...	[ "Single base substitutions constitute the most frequent type of human gene mutation and are a leading cause of cancer and inherited disease .", "These alterations occur non-randomly in DNA , being strongly influenced by the local nucleotide sequence context .", "However , the molecular mechanisms underlying suc...	[ "A large number of DNA mutations identified in cells from patients with cancer or human inherited disease were analyzed to address a fundamental issue in human pathology , viz , the mutational mechanisms that cause irreversible changes to DNA .", "By using bioinformatics and computational methods , we found that ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "diabetes and endocrinology/type 2 diabetes", "computational biology/metabolic networks", "computational biology/systems biology", "computational biology/transcriptional regulation" ]	Metabolic Network Topology Reveals Transcriptional Regulatory Signatures of Type 2 Diabetes	journal.pcbi.1000729	null	[ [ "Metabolic phenotypes at a cellular level are essentially characterized by concentrations of metabolites and fluxes through the reactions that make up the metabolic network .", "Fluxes , in turn , are dependent on metabolite levels , enzyme activities , abundance of effectors and possibly other variables ...	[ "Type 2 diabetes mellitus ( T2DM ) is a disorder characterized by both insulin resistance and impaired insulin secretion .", "Recent transcriptomics studies related to T2DM have revealed changes in expression of a large number of metabolic genes in a variety of tissues .", "Identification of the molecular mecha...	[ "Type 2 diabetes mellitus is a complex metabolic disease recognized as one of the main threats to human health in the 21st century .", "Recent studies of gene expression levels in human tissue samples have indicated that multiple metabolic pathways are dysregulated in diabetes and in individuals at risk for diabe...	2010
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "children", "medicine and health sciences", "pathology and laboratory medicine", "cryptosporidium", "parasitic diseases", "parasitic protozoans", "diarrhea", "age groups", "protozoans", "signs and symptoms", "gastroenterology and hepatology", "families", "blastocystis", "protozoan infectio...	Prevalence and Risk Factors for Intestinal Protozoan Infections with Cryptosporidium, Giardia, Blastocystis and Dientamoeba among Schoolchildren in Tripoli, Lebanon	journal.pntd.0004496	null	[ [ "Parasitic infections , and in particular those caused by protozoa , are a major public health problem worldwide .", "They are among the most widespread human infections in developing countries , with children being the most vulnerable population [1] .", "In particular , intestinal protozoans , such a...	[ "Intestinal protozoan infections are confirmed as major causes of diarrhea , particularly in children , and represent a significant , but often neglected , threat to public health .", "No recent data were available in Lebanon concerning the molecular epidemiology of protozoan infections in children , a vulnerable...	[ "Intestinal parasites can infect the gastrointestinal tract of humans .", "Means of exposure include ingestion of contaminated fruits and vegetables , consumption of infected water and personal contact .", "Protozoa are considered one of the major groups of parasites .", "Children are particularly susceptible...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public health and epidemiology", "immune physiology", "clinical research design", "infectious disease epidemiology", "flavivirus", "dengue", "anatomy and physiology", "cohort studies", "neglected tropical diseases", "antibodies", "japanese encephalitis", "infectious diseases", ...	Preexisting Japanese Encephalitis Virus Neutralizing Antibodies and Increased Symptomatic Dengue Illness in a School-Based Cohort in Thailand	journal.pntd.0001311	null	[ [ "The dengue viruses ( DENV ) and Japanese encephalitis virus ( JEV ) are closely-related members of the virus family Flaviviridae .", "DENV and JEV co-circulate in the Indian subcontinent and in Southeast Asia , where they are important causes of human disease and mortality .", "The co-occurrence of J...	[ "Dengue viruses ( DENVs ) and Japanese encephalitis virus ( JEV ) have significant cross-reactivity in serological assays; the clinical implications of this remain undefined .", "An improved understanding of whether and how JEV immunity modulates the clinical outcome of DENV infection is important as large-scale ...	[ "Dengue viruses ( DENVs ) and Japanese encephalitis virus ( JEV ) have significant cross-reactivity in serological assays , but the possible clinical implications of this remain poorly understood .", "Interactions between these flaviviruses are potentially important for public health because wild-type JEV continu...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "hematology/hematopoiesis", "computational biology/transcriptional regulation", "genetics and genomics/gene expression", "cell biology/developmental molecular mechanisms", "genetics and genomics/bioinformatics", "developmental biology/cell differentiation", "molecular biology/bioinformatics", "develop...	A Large Gene Network in Immature Erythroid Cells Is Controlled by the Myeloid and B Cell Transcriptional Regulator PU.1	journal.pgen.1001392	null	[ [ "Cellular identities are established through the actions of master regulatory transcription factors .", "In addition to promoting their lineage-specific gene expression programs , these factors may also inhibit the transcriptional programs of alternative cell lineages [1] .", "These inhibitory functio...	[ "PU . 1 is a hematopoietic transcription factor that is required for the development of myeloid and B cells .", "PU . 1 is also expressed in erythroid progenitors , where it blocks erythroid differentiation by binding to and inhibiting the main erythroid promoting factor , GATA-1 .", "However , other mechanisms...	[ "Cellular identities are established by master regulatory transcription factors that promote cell type–specific gene expression .", "In some instances such factors also inhibit differentiation of alternative , closely related lineages .", "PU . 1 is an Ets family transcription factor that is required for myeloi...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "children", "medicine and health sciences", "pathology and laboratory medicine", "pathogens", "microbiology", "cryptosporidium", "parasitic protozoans", "diarrhea", "age groups", "protozoans", "signs and symptoms", "gastroenterology and hepatology", "infants", "cardiobacterium hominis", ...	The Burden of Cryptosporidium Diarrheal Disease among Children < 24 Months of Age in Moderate/High Mortality Regions of Sub-Saharan Africa and South Asia, Utilizing Data from the Global Enteric Multicenter Study (GEMS)	journal.pntd.0004729	null	[ [ "Cryptosporidium , the highly infectious protozoan that causes diarrhea in immunocompetent and immunocompromised subjects [1–4] , is transmitted via contaminated water or food [1 , 3 , 5] , swimming or bathing in surface waters [1 , 3] and by direct person-to-person contact [6] , particularly in developing co...	[ "The importance of Cryptosporidium as a pediatric enteropathogen in developing countries is recognized .", "Data from the Global Enteric Multicenter Study ( GEMS ) , a 3-year , 7-site , case-control study of moderate-to-severe diarrhea ( MSD ) and GEMS-1A ( 1-year study of MSD and less-severe diarrhea [LSD] ) wer...	[ "Cryptosporidium is a protozoan that causes diarrhea and malnutrition in young children in developing countries , and is associated with diarrhea cases and outbreaks in developed countries .", "To date , limited information exists on the burden of Cryptosporidium diarrheal disease in sub-Saharan Africa and South ...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "sequencing techniques", "medicine and health sciences", "clinical laboratory sciences", "body fluids", "cell cycle and cell division", "cell processes", "social sciences", "saliva", "twins", "germ cells", "next-generation sequencing", "developmental biology", "mutation", "genome analysis"...	Distinguishing genetically between the germlines of male monozygotic twins	journal.pgen.1007756	null	[ [ "Estimates of the incidence of human twinning range from <8 per 1000 live births in Asia to >18 per 1000 live births in Central Africa [1] .", "This considerable geographic variation is mainly attributable to dizygotic ( DZ ) twinning and likely reflects the influence of social , environmental and genetic...	[ "Identification of the potential donor ( s ) of human germline-derived cells is an issue in many criminal investigations and in paternity testing .", "The experimental and statistical methodology necessary to work up such cases is well established but may be more challenging if monozygotic ( MZ ) twins are involv...	[ "In many instances of practical forensic casework , particularly when connected to sexual assault , genetic analysis is carried out to identify the likely donor of a sperm sample left at the crime scene .", "The experimental and statistical methodology for such investigations is well established .", "In cases i...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Proteasome Inhibition Suppresses Dengue Virus Egress in Antibody Dependent Infection	journal.pntd.0004058	null	[ [ "Dengue has emerged to be the most important mosquito-borne viral disease globally .", "An estimated 390 million infections occur annually while another 3 billion people that live in or travel to the tropics are at constant risk of infection with any of the four dengue virus ( DENV ) serotypes [1] .", ...	[ "The mosquito-borne dengue virus ( DENV ) is a cause of significant global health burden , with an estimated 390 million infections occurring annually .", "However , no licensed vaccine or specific antiviral treatment for dengue is available .", "DENV interacts with host cell factors to complete its life cycle ...	[ "The lack of either licensed vaccine or antiviral drug has resulted in approximately 400 million dengue infections annually .", "A possible rapid approach to a specific therapeutic for dengue is to use a licensed inhibitor of a host factor critically required by dengue virus ( DENV ) to complete its life cycle ."...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "connectomics", "neuroanatomy", "anatomy", "nervous system", "biology and life sciences", "comparative anatomy", "neuroscience" ]	Comparative Analysis of the Macroscale Structural Connectivity in the Macaque and Human Brain	journal.pcbi.1003529	null	[ [ "Over a century of research has revealed that the brain is inhomogeneous and can be divided based on functional , macro- and micro- structural criteria [1]–[4] .", "The regions resulting from such a division are linked through fibre bundles that constitute the neural substrate for the exchange of informat...	[ "The macaque brain serves as a model for the human brain , but its suitability is challenged by unique human features , including connectivity reconfigurations , which emerged during primate evolution .", "We perform a quantitative comparative analysis of the whole brain macroscale structural connectivity of the ...	[ "What are the commonalities and differences of human brains when compared to the brains of other primates ?", "The brain can be conceived as a complex network .", "Its topological properties constrain its function .", "Ethical and technical reasons necessitate the use of animal brains , like the macaque monke...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Papillomavirus-Associated Tumor Formation Critically Depends on c-Fos Expression Induced by Viral Protein E2 and Bromodomain Protein Brd4	journal.ppat.1005366	null	[ [ "Papillomaviruses ( PV ) are small double-stranded ( ds ) DNA viruses that are able to cause epithelial tumors , including cancers of the cervix uteri and the oropharynx and are likely to be involved in the development of non-melanoma skin cancer [1] .", "Expression of viral oncogenes E6 and E7 that dysre...	[ "We investigated the mechanism of how the papillomavirus E2 transcription factor can activate promoters through activator protein ( AP ) 1 binding sites .", "Using an unbiased approach with an inducible cell line expressing the viral transcription factor E2 and transcriptome analysis , we found that E2 induces th...	[ "Human Papillomaviruses ( HPV ) are the etiological agents of cervical cancer and of skin cancer in individuals with the inherited disease epidermodysplasia verruciformis ( EV ) .", "While the role of the viral oncogenes E6/E7 as drivers of tumorigenesis in cervical cancer has been firmly established , the contri...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular cell biology", "genetics", "biology" ]	The Cohesion Protein SOLO Associates with SMC1 and Is Required for Synapsis, Recombination, Homolog Bias and Cohesion and Pairing of Centromeres in Drosophila Meiosis	journal.pgen.1003637	null	[ [ "Meiosis is a specialized type of cell division that generates haploid gametes from diploid germ cells .", "It encompasses a single round of DNA replication followed by two rounds of chromosome division in which first homologous chromosomes then sister chromatids segregate .", "During prophase of the ...	[ "Cohesion between sister chromatids is mediated by cohesin and is essential for proper meiotic segregation of both sister chromatids and homologs .", "solo encodes a Drosophila meiosis-specific cohesion protein with no apparent sequence homology to cohesins that is required in male meiosis for centromere cohesion...	[ "Sexual reproduction entails an intricate 2-step division called meiosis in which homologous chromosomes and sister chromatids are sequentially segregated to yield gametes ( eggs and sperm ) with exactly one copy of each chromosome .", "The Drosophila meiosis protein SOLO is essential for cohesion between sister ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Intracellular Uropathogenic E. coli Exploits Host Rab35 for Iron Acquisition and Survival within Urinary Bladder Cells	journal.ppat.1005083	null	[ [ "Urinary tract infections ( UTIs ) are one of the most common bacterial infections in humans , affecting at least 50% of women at some point in their lifetime .", "UTIs constitute significant morbidity and economic burden , accounting for more than 1 million hospitalizations and $2 . 4 billion in medical ...	[ "Recurrent urinary tract infections ( UTIs ) caused by uropathogenic E . coli ( UPEC ) are common and morbid infections with limited therapeutic options .", "Previous studies have demonstrated that persistent intracellular infection of bladder epithelial cells ( BEC ) by UPEC contributes to recurrent UTI in mouse...	[ "Urinary tract infections ( UTIs ) are common and costly infectious diseases , affecting half of all women .", "Many women suffer from recurrent UTIs , for which no effective therapy currently exists .", "Intracellular persistence within bladder epithelial cells ( BEC ) by uropathogenic E . coli ( UPEC ) contri...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "blood cells", "medicine and health sciences", "body fluids", "immune cells", "gene regulation", "immunology", "tropical diseases", "parasitic diseases", "parasitic protozoans", "protozoans", "leishmania", "neglected tropical diseases", "infectious diseases", "white blood cells", "zoonos...	Blood Transcriptional Profiling Reveals Immunological Signatures of Distinct States of Infection of Humans with Leishmania infantum	journal.pntd.0005123	null	[ [ "Infections with the protozoan parasites Leishmania donovani or L . infantum ( chagasi ) result in clinical outcomes that range from asymptomatic infection to active visceral leishmaniasis ( VL ) .", "When disease occurs , symptoms often include fever , hepatosplenomegaly , cachexia , pancytopenia and hyp...	[ "Visceral leishmaniasis ( VL ) can be lethal if untreated; however , the majority of human infections with the etiological agents are asymptomatic .", "Using Illumina Bead Chip microarray technology , we investigated the patterns of gene expression in blood of active VL patients , asymptomatic infected individual...	[ "Infections of humans with the protozoan parasites L . donvani and L . infantum can lead to the development of the disease visceral leishmaniasis , but also to an asymptomatic status .", "However , the mechanisms that result in these clinical outcomes after infection are poorly understood .", "In this study , w...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "viral classification", "microbiology", "hepatitis", "rna viruses", "viral nucleic acid", "hepatitis c", "infectious diseases", "biology", "viral replication", "molecular biology", "viral evolution", "rna", "nucleic acids", "virology", "viral diseases", "molecular cell bi...	Productive Homologous and Non-homologous Recombination of Hepatitis C Virus in Cell Culture	journal.ppat.1003228	null	[ [ "RNA viruses are rapidly adapting to their environment .", "The error-prone viral polymerases and the lack of proofreading mechanisms for most RNA viruses lead to high mutation rates .", "Genetic recombination between viral genomes is an additional mechanism increasing genetic diversity , which has pr...	[ "Genetic recombination is an important mechanism for increasing diversity of RNA viruses , and constitutes a viral escape mechanism to host immune responses and to treatment with antiviral compounds .", "Although rare , epidemiologically important hepatitis C virus ( HCV ) recombinants have been reported .", "I...	[ "Genetic recombination is the alternative joining of nucleic acids leading to novel combinations of genetic information .", "While DNA recombination in cells is of importance for evolution and adaptive immunity , RNA recombination often has only transient effects .", "However , RNA viruses are rapidly evolving ...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases/infectious diseases of the nervous system", "virology/vaccines", "infectious diseases/neglected tropical diseases", "neurological disorders/infectious diseases of the nervous system", "infectious diseases/viral infections", "public health and epidemiology/preventive medicine", "infe...	A Simplified 4-Site Economical Intradermal Post-Exposure Rabies Vaccine Regimen: A Randomised Controlled Comparison with Standard Methods	journal.pntd.0000224	null	[ [ "Rabies is a neglected disease affecting particularly tropical developing countries [1] .", "Estimates of the Global use of rabies post-exposure prophylaxis ( PEP ) are rising .", "In China , it was 8 million in 2005 [2] , yet rabies currently kills more people than any other infectious disease there ...	[ "The need for economical rabies post-exposure prophylaxis ( PEP ) is increasing in developing countries .", "Implementation of the two currently approved economical intradermal ( ID ) vaccine regimens is restricted due to confusion over different vaccines , regimens and dosages , lack of confidence in intradermal...	[ "All human deaths from rabies result from failure to give adequate prophylaxis .", "After a rabid animal bite , immediate wound cleaning , rabies vaccine and immunoglobulin injections effectively prevent fatal infection .", "Immunoglobulin is very rarely available in developing countries , where prevention reli...	2008
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "invertebrates", "dengue virus", "medicine and health sciences", "pathology and laboratory medicine", "pathogens", "rna extraction", "microbiology", "animals", "wolbachia", "viruses", "rna viruses", "infectious disease control", "insect vectors", "bacteria", "extraction techniques", "d...	Wolbachia-Based Dengue Virus Inhibition Is Not Tissue-Specific in Aedes aegypti	journal.pntd.0005145	null	[ [ "Dengue fever , caused by the dengue virus ( DENV ) , is the most prevalent arthropod transmitted virus , endemic in over 100 countries [1 , 2] .", "The virus is comprised of four antigenically distinct serotypes ( 1–4 ) [3 , 4] .", "DENV is transmitted by Aedes aegypti and Ae .", "albopictus with...	[ "Dengue fever , caused by the dengue virus ( DENV ) , is now the most common arbovirus transmitted disease globally .", "One novel approach to control DENV is to use the endosymbiotic bacterium , Wolbachia pipientis , to limit DENV replication inside the primary mosquito vector , Aedes aegypti .", "Wolbachia th...	[ "Dengue fever caused by the dengue virus ( DENV ) is transmitted by the mosquito , Aedes aegypti .", "To control the disease , an intracellular bacterium called Wolbachia has been introduced into Ae .", "aegypti where it blocks/limits success of infection of DENV .", "The mechanistic basis of blocking is not ...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "microbiology/microbial evolution and genomics" ]	A New Perspective on Listeria monocytogenes Evolution	journal.ppat.1000146	null	[ [ "The opportunistic pathogen Listeria monocytogenes causes life-threatening infections in animal and in human populations at risk .", "This facultative intracellular bacterium is widespread in the environment and infections occur through ingestion of contaminated food [1] , [2] .", "Although the specie...	[ "Listeria monocytogenes is a model organism for cellular microbiology and host–pathogen interaction studies and an important food-borne pathogen widespread in the environment , thus representing an attractive model to study the evolution of virulence .", "The phylogenetic structure of L . monocytogenes was determ...	[ "Listeria monocytogenes is a pathogen transmitted through contaminated food and is responsible for severe infections , including meningitis and abortion in animals and humans .", "It is known that many distinct strains of this pathogen exist , and that they differ in their virulence and epidemic potential .", "...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "biology", "model organisms" ]	A forkhead Transcription Factor Is Wound-Induced at the Planarian Midline and Required for Anterior Pole Regeneration	journal.pgen.1003999	null	[ [ "Planarians can regenerate from nearly any injury , but how missing tissues are recognized and replaced is poorly understood .", "The adult population of proliferating cells ( neoblasts ) in Schmidtea mediterranea includes pluripotent stem cells [1] and is responsible for new tissue production in regenera...	[ "Planarian regeneration requires positional information to specify the identity of tissues to be replaced as well as pluripotent neoblasts capable of differentiating into new cell types .", "We found that wounding elicits rapid expression of a gene encoding a Forkhead-family transcription factor , FoxD .", "Wou...	[ "Regeneration is widespread in the animal kingdom .", "Planarians are able to regenerate entire bodies from almost any fragment type .", "This ability requires a cell population called neoblasts , which include pluripotent stem cells , for the production of all missing tissues , as well as the information to fo...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "neuroscience/behavioral neuroscience", "neuroscience/neural homeostasis" ]	Dopamine Signalling in Mushroom Bodies Regulates Temperature-Preference Behaviour in Drosophila	journal.pgen.1001346	null	[ [ "To counteract the harmful effects of environmental temperature fluctuation , animals use homeostatic thermoregulatory mechanisms and/or behavioral responses to maintain optimal body temperature .", "Mammals regulate their body temperatures with various physiological responses such as change of metabolic ...	[ "The ability to respond to environmental temperature variation is essential for survival in animals .", "Flies show robust temperature-preference behaviour ( TPB ) to find optimal temperatures .", "Recently , we have shown that Drosophila mushroom body ( MB ) functions as a center controlling TPB .", "However...	[ "Temperature affects almost all aspects of animal development and physiological processes .", "The dependence of the body temperature of small insects on ambient temperature and other heat sources makes it plausible that neuronal mechanisms for sensing temperature and behavioral responses for maintaining body tem...	2011
[ "Introduction", "Model", "Results", "Discussion" ]	[ "mathematics/statistics", "immunology/leukocyte development" ]	The Dynamics of T-Cell Receptor Repertoire Diversity Following Thymus Transplantation for DiGeorge Anomaly	journal.pcbi.1000396	null	[ [ "The steady state T-cell population size arises in the balance among several", "phenomena , including the rapid and extensive expansion of rare clones through", "activation-induced peripheral division and their subsequent contraction ( which", "constitute , in part , the T-cell immune response ) a...	[ "T cell populations are regulated both by signals specific to the T-cell receptor", "( TCR ) and by signals and resources , such as cytokines and space , that act", "independently of TCR specificity .", "Although it has been demonstrated that", "disruption of either of these pathways has a profound effect o...	[ "Protective adaptive immunity depends crucially on the enormous diversity of the", "T-cell receptor repertoire , the antigen receptors expressed collectively on", "T-cell populations .", "T cells develop from T-cell precursors that originate in the", "bone marrow and migrate to the thymus , where their T ce...	2009
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	NINL and DZANK1 Co-function in Vesicle Transport and Are Essential for Photoreceptor Development in Zebrafish	journal.pgen.1005574	null	[ [ "Dysfunction of cilia is the underlying defect in a growing group of pleiotropic genetic disorders , the ciliopathies .", "Cilia are ubiquitous microtubule-based organelles involved in fluid propulsion ( motile cilia ) or signal transduction ( primary cilia ) and ciliopathy-associated proteins localize to...	[ "Ciliopathies are Mendelian disorders caused by dysfunction of cilia , ubiquitous organelles involved in fluid propulsion ( motile cilia ) or signal transduction ( primary cilia ) .", "Retinal dystrophy is a common phenotypic characteristic of ciliopathies since photoreceptor outer segments are specialized primar...	[ "The cytoplasmic dynein 1 motor complex is known to be essential for photoreceptor outer segment formation and function .", "NINL , an important interaction partner of three ciliopathy-associated proteins ( lebercilin , USH2A and CC2D2A ) , was previously shown to associate with this motor complex .", "In this ...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "immunomodulation", "medicine", "biochemistry", "infectious diseases", "immune cells", "metabolic pathways", "t cells", "parasitology", "immunology", "biology", "microbiology", "metabolism", "immune response" ]	Arginase Activity - A Marker of Disease Status in Patients with Visceral Leishmaniasis in Ethiopia	journal.pntd.0002134	null	[ [ "Visceral leishmaniasis ( VL ) is a neglected tropical disease caused by parasites of the Leishmania ( L . ) donovani complex .", "The incidence of VL is estimated to be 500 000 cases every year , with approximately 50 000 deaths , predominantly in India , Bangladesh , Brazil , Nepal and Sudan .", "It...	[ "The underlying mechanisms resulting in the profound immune suppression characteristic of human visceral leishmaniasis ( VL ) are not fully understood .", "Here , we tested the hypothesis that arginase , an enzyme associated with immunosuppression , is higher in patients with VL and contributes to impaired T cell...	[ "Leishmaniases , a group of diseases caused by a parasite , Leishmania , belong to the most neglected tropical diseases: they are mainly found in low-income countries and affect the poorest populations .", "These parasites infect cells of the immune system called macrophages , which can kill the intracellular par...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "epidemiology" ]	Occurrence of Nontuberculous Mycobacterial Pulmonary Infection in an Endemic Area of Tuberculosis	journal.pntd.0002340	null	[ [ "Nontuberculous mycobacteria ( NTM ) are environmental opportunistic pathogens that are natural inhabitants of soil [1] and drinking water [2] , [3] .", "Humans and their agronomic animals are literally surrounded by nontuberculous mycobacteria [4] .", "Risk factors for NTM pulmonary disease include: ...	[ "The majority of investigations of the epidemiology of nontuberculous mycobacteria ( NTM ) have focused on highly developed nations with a low prevalence of tuberculosis .", "In contrast , the Para state of north Brazil represents an area of high tuberculosis prevalence and increasing NTM incidence .", "Toward ...	[ "Nontuberculous mycobacteria ( NTM ) are environmental organisms that are naturally found in soil , water , dust and other sites .", "Several case reports and studies on the prevalence of pulmonary NTM disease have been published , nevertheless , the impact and the exact magnitude of NTM infections in countries w...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "infectious diseases", "drugs and devices", "biology", "microbiology" ]	A Candida Biofilm-Induced Pathway for Matrix Glucan Delivery: Implications for Drug Resistance	journal.ppat.1002848	null	[ [ "Candida spp .", "are an increasingly common cause of bloodstream infections in hospitalized patients [1] , [2] .", "This rise in incidence is at least in part related to the organism's ability to produce biofilm infections on medical devices [3] .", "A biofilm is a community of microbes attached ...	[ "Extracellular polysaccharides are key constituents of the biofilm matrix of many microorganisms .", "One critical carbohydrate component of Candida albicans biofilms , β-1 , 3 glucan , has been linked to biofilm protection from antifungal agents .", "In this study , we identify three glucan modification enzyme...	[ "Biofilms are a community of microbes that grow attached to each other and adherent to a surface .", "One distinguishing feature of this form of growth is the presence of a surrounding extracellular matrix which is proposed to provide a structural scaffold and protection for biofilm cells .", "This later functi...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "invertebrates", "parasite groups", "medicine and health sciences", "immune physiology", "plasmodium", "immunology", "tropical diseases", "geographical locations", "parasitic diseases", "parasitic protozoans", "animals", "parasitology", "apicomplexa", "protozoans", "antibodies", "stron...	Integration of Multiplex Bead Assays for Parasitic Diseases into a National, Population-Based Serosurvey of Women 15-39 Years of Age in Cambodia	journal.pntd.0004699	null	[ [ "In many tropical and sub-tropical countries , the disease burden represented by neglected tropical diseases ( NTDs ) is substantial , yet information on the prevalence and distribution of these diseases is limited because of the significant costs associated with disease-specific surveys .", "Even with th...	[ "Collection of surveillance data is essential for monitoring and evaluation of public health programs .", "Integrated collection of household-based health data , now routinely carried out in many countries through demographic health surveys and multiple indicator surveys , provides critical measures of progress i...	[ "In 2012 a comprehensive national serosurvey to assess immunity to vaccine preventable diseases such as polio , rubella , measles , and tetanus was conducted among women of child bearing age in Cambodia .", "We were able to test this sample set using a multiplex bead assay in order to measure specific antibody re...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "evolutionary biology/animal genetics", "evolutionary biology/microbial evolution and genomics", "evolutionary biology/evolutionary ecology", "microbiology/microbial evolution and genomics", "microbiology/parasitology", "ecology/population ecology", "molecular biology" ]	Intergenomic Arms Races: Detection of a Nuclear Rescue Gene of Male-Killing in a Ladybird	journal.ppat.1000987	null	[ [ "Cytoplasmic sex ratio distorters have been reported from many invertebrates [1] .", "One group of distorters comprises a diverse array of bacteria which distort the secondary sex ratio of their hosts towards females by killing male hosts early in embryogenesis [2] , [3] .", "Infected females gain an ...	[ "Many species of arthropod are infected by deleterious inherited micro-organisms .", "Typically these micro-organisms are inherited maternally .", "Consequently , some , particularly bacteria of the genus Wolbachia , employ a variety of strategies that favour female over male hosts .", "These strategies inclu...	[ "Normally , in sexually reproducing organisms , the sex ratio ( ratio of males to females ) is 1∶1 .", "However , examples are known where this is not the case and there are more females than males in a population .", "Extreme bias in sex ratio can lead to females failing to find a mate .", "We studied Cheilo...	2010
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "genomics", "evolutionary biology", "origin of life", "biology", "computational biology", "comparative genomics" ]	Comparative Analysis of RNA Families Reveals Distinct Repertoires for Each Domain of Life	journal.pcbi.1002752	null	[ [ "Following demonstration that RNA can act as genetic material [1]–[3] and biological catalyst [4] , [5] , the study of the origin and early evolution of life on Earth has been heavily focused on the potential for an RNA world .", "The RNA world hypothesis is that RNA was both genetic material and main bio...	[ "The RNA world hypothesis , that RNA genomes and catalysts preceded DNA genomes and genetically-encoded protein catalysts , has been central to models for the early evolution of life on Earth .", "A key part of such models is continuity between the earliest stages in the evolution of life and the RNA repertoires ...	[ "In cells , DNA carries recipes for making proteins , and proteins perform chemical reactions , including replication of DNA .", "This interdependency raises questions for early evolution , since one molecule seemingly cannot exist without the other .", "A resolution to this problem is the RNA world , where RNA...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "immune cells", "pathology and laboratory medicine", "intracellular pathogens", "chikungunya infection", "antigen-presenting cells", "pathogens", "immunology", "infectious disease immunology", "antibody response", "infectious diseases", "inflammation", "animal...	Multiple Immune Factors Are Involved in Controlling Acute and Chronic Chikungunya Virus Infection	journal.pntd.0003354	null	[ [ "The arthritogenic alphaviruses comprise a group of globally distributed , mosquito-borne , single-stranded positive-sense RNA viruses that cause sporadic outbreaks of predominantly rheumatic disease .", "They include the predominantly Afro-Asian chikungunya virus ( CHIKV ) , the primarily Australian Ross...	[ "The recent epidemic of the arthritogenic alphavirus , chikungunya virus ( CHIKV ) has prompted a quest to understand the correlates of protection against virus and disease in order to inform development of new interventions .", "Herein we highlight the propensity of CHIKV infections to persist long term , both a...	[ "The largest epidemic ever recorded for chikungunya virus ( CHIKV ) started in 2004 in Africa , then spread across Asia and recently caused tens of thousands of cases in Papua New Guinea and the Caribbean .", "This mosquito-borne alphavirus primarily causes an often debilitating , acute and chronic polyarthritis/...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biophysics/macromolecular assemblies and machines", "biophysics/theory and simulation", "cell biology/cytoskeleton" ]	Monte Carlo Analysis of Neck Linker Extension in Kinesin Molecular Motors	journal.pcbi.1000980	null	[ [ "Motor proteins in the kinesin superfamily are molecular machines that use the energy derived from ATP hydrolysis to transport organelles and other cellular cargo along microtubules .", "The 14 kinesin families are structurally diverse and display differences in motor velocity , directionality , and proce...	[ "Kinesin stepping is thought to involve both concerted conformational changes and diffusive movement , but the relative roles played by these two processes are not clear .", "The neck linker docking model is widely accepted in the field , but the remainder of the step – diffusion of the tethered head to the next ...	[ "Kinesin molecular motors provide a valuable model for uncovering the interplay between nanoscale mechanics and biochemistry at the level of single protein molecules .", "The mechanism by which kinesin motors “walk” along microtubules involves both conformational changes in the motor domains , or “heads” , as wel...	2010
[ "Introduction", "Results and discussion", "Materials and methods" ]	[ "blood serum", "medicine and health sciences", "rna interference", "body fluids", "enzymes", "microbiology", "enzymology", "genomic library screening", "parasitic protozoans", "dna damage", "protozoans", "epigenetics", "dna", "molecular biology techniques", "research and analysis methods...	Genome-wide and protein kinase-focused RNAi screens reveal conserved and novel damage response pathways in Trypanosoma brucei	journal.ppat.1006477	null	[ [ "Faithful genome transmission is necessary for the growth and propagation of all organisms .", "Damage to the genome can arise from a myriad of sources , including exposure to mutagenic chemicals and metabolic or replicative by-products .", "If damage is left unrepaired , the genetic information can b...	[ "All cells are subject to structural damage that must be addressed for continued growth .", "A wide range of damage affects the genome , meaning multiple pathways have evolved to repair or bypass the resulting DNA lesions .", "Though many repair pathways are conserved , their presence or function can reflect th...	[ "Damage to the genome is a universal threat to life .", "Though the repair pathways used to tackle damage can be widely conserved , lineage-specific specialisations are found , reflecting the differing life styles of extant organisms .", "Using RNAi coupled with next generation sequencing we have screened for g...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "blood cells", "medicine and health sciences", "immune physiology", "immune cells", "immunology", "vertebrates", "animals", "mammals", "vaccines", "preventive medicine", "primates", "antibodies", "vaccination and immunization", "antibody response", "old world monkeys", "public and occu...	Early Transcriptional Signatures of the Immune Response to a Live Attenuated Tetravalent Dengue Vaccine Candidate in Non-human Primates	journal.pntd.0004731	null	[ [ "Over the last 50 years , the incidence of dengue has increased 30-fold , and now more than half of the world’s population is at risk of dengue virus ( DENV ) infection [1] .", "Transmitted by Aedes mosquitos , DENV has become the leading cause of mosquito-borne viral infections worldwide , with an estima...	[ "The development of a vaccine against dengue faces unique challenges , including the complexity of the immune responses to the four antigenically distinct serotypes .", "Genome-wide transcriptional profiling provides insight into the pathways and molecular features that underlie responses to immune system stimula...	[ "Dengue has become the leading cause of mosquito-borne virus infections worldwide .", "Despite considerable effort , development of a successful vaccine against dengue virus ( DENV ) has been challenging due to the co-circulation of the four DENV serotypes in endemic areas—to which humans develop distinct immune ...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "rna", "computational chemistry", "molecular dynamics", "nucleic acids", "biophysic al simulations", "chemistry", "biology", "computational biology", "biophysics simulations", "biophysics" ]	Understanding the Origins of Bacterial Resistance to Aminoglycosides through Molecular Dynamics Mutational Study of the Ribosomal A-Site	journal.pcbi.1002099	null	[ [ "A well-known problem related to the use of antibacterial compounds is the emergence of resistant bacterial strains [1] .", "Bacteria constantly improve their resistance techniques by utilizing their abilities to mutate quickly .", "Their proliferation rate can be as short as minutes [2] , and bacteri...	[ "Paromomycin is an aminoglycosidic antibiotic that targets the RNA of the bacterial small ribosomal subunit .", "It binds in the A-site , which is one of the three tRNA binding sites , and affects translational fidelity by stabilizing two adenines ( A1492 and A1493 ) in the flipped-out state .", "Experiments ha...	[ "In hospitals throughout the world , aminoglycosidic antibiotics are used to combat even the most severe bacterial infections .", "However , the continuous emergence of resistant bacteria has created an urgent need to improve these antibiotics .", "Aminoglycosides bind to bacterial ribosomal RNA .", "Experime...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "european union", "pathology and laboratory medicine", "tropical diseases", "geographical locations", "parasitic diseases", "animals", "pulmonology", "chronic obstructive pulmonary disease", "diarrhea", "signs and symptoms", "gastroenterology ...	Strongyloides stercoralis infection: A systematic review of endemic cases in Spain	journal.pntd.0007230	null	[ [ "Strongyloidiasis is a disease caused by soil-transmitted helminths , mainly by the species Strongyloides stercoralis .", "This intestinal nematode infects an estimated 300 million people worldwide , although this is probably underestimated .", "It is one of the most neglected of the neglected tropica...	[ "Strongyloides stercoralis infection , a neglected tropical disease , is widely distributed .", "Autochthonous cases have been described in Spain , probably infected long time ago .", "In recent years the number of diagnosed cases has increased due to the growing number of immigrants , travelers and refugees , ...	[ "S . stercoralis is a soil transmitted helminth that is common in many subtropical and tropical countries , but is also found in other regions of the world .", "In this study we reviewed all published material on endemic infection of S . stercoralis acquired in Spain issued before 31st May 2018 .", "We collecte...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "pharmacokinetics", "pharmacology", "biology and life sciences", "immunology", "toxicology" ]	Pharmacokinetics of Naja sumatrana (Equatorial Spitting Cobra) Venom and Its Major Toxins in Experimentally Envenomed Rabbits	journal.pntd.0002890	null	[ [ "Snake envenomation remains a neglected tropical disease prevalent in the Southeast Asia region , including Malaysia [1] , [2] .", "It affects not only the population in the rural area but also the suburban regions due to rapid urbanization , and the encroaching of human activities into the natural habita...	[ "The optimization of snakebite management and the use of antivenom depend greatly on the knowledge of the venom's composition as well as its pharmacokinetics .", "To date , however , pharmacokinetic reports on cobra venoms and their toxins are still relatively limited .", "In the present study , we investigated...	[ "Naja sumatrana is a medically important cobra species in Southeast Asia .", "The optimization of snakebite management and the use of antivenom depend greatly on the knowledge of the venom's composition , its biological activities , as well as its pharmacokinetics .", "The present study on the pharmacokinetics ...	2014
[ "Introduction", "Model", "Results/Discussion" ]	[ "developmental biology/morphogenesis and cell biology", "biophysics/theory and simulation", "mathematics/statistics" ]	Modeling and Inferring Cleavage Patterns in Proliferating Epithelia	journal.pcbi.1000412	null	[ [ "The spatial and temporal regulation of cell shape and cell proliferation are key", "mechanisms that direct tissue morphogenesis during development .", "Much of our", "knowledge of tissue morphogenesis comes from the study of simple epithelial", "monolayers , 2D planar sheets of strongly adher...	[ "The regulation of cleavage plane orientation is one of the key mechanisms driving", "epithelial morphogenesis .", "Still , many aspects of the relationship between local", "cleavage patterns and tissue-level properties remain poorly understood .", "Here we", "develop a topological model that simulates th...	[ "Cell division is one of the key mechanisms driving organismal growth and", "morphogenesis .", "Yet many aspects of the relationship between local cell division", "( how a cell chooses an orientation to divide ) and global tissue architecture", "( e . g . , regular versus irregular cells ) remain poorly und...	2009
[ "Introduction", "Results/Discussion", "Methods" ]	[]	Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast	journal.pcbi.1004418	null	[ [ "Transcription factors ( TFs ) regulate expression of target genes by interacting with specific TF binding sites ( TFBSs ) .", "Because knowledge of TFBSs is crucial for understanding regulatory relationships between TFs and their target genes , a number of in silico TFBS identification approaches have be...	[ "Transcription factor ( TF ) binding is determined by the presence of specific sequence motifs ( SM ) and chromatin accessibility , where the latter is influenced by both chromatin state ( CS ) and DNA structure ( DS ) properties .", "Although SM , CS , and DS have been used to predict TF binding sites , a predic...	[ "Identification of transcription factor binding sites based on sequence motifs is typically accompanied by a high false positive rate .", "Increasing evidence suggests that there are many other factors besides DNA sequence that may affect the binding and interaction of TFs with DNA .", "Through the integration ...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Role of Cellular Heparan Sulfate Proteoglycans in Infection of Human Adenovirus Serotype 3 and 35	journal.ppat.1000189	null	[ [ "Human adenoviruses ( Ads ) have been classified into six species ( A to F ) currently containing 51 serotypes .", "Most Ad serotypes utilize the coxsackie-adenovirus-receptor , CAR , as a primary attachment receptor [1] .", "However , this is not the case for species B Ad serotypes [1] .", "Speci...	[ "Species B human adenoviruses ( Ads ) are increasingly associated with outbreaks of acute respiratory disease in U . S . military personnel and civil population .", "The initial interaction of Ads with cellular attachment receptors on host cells is via Ad fiber knob protein .", "Our previous studies showed that...	[ "In this study , we attempted to identify binding receptors that are used by the two human adenovirus ( Ad ) serotypes 3 and 35 .", "Ad3 uses yet-unknown receptors and is one of the most common Ads causing epidemic conjunctivitis , and respiratory and gastrointestinal diseases .", "Ad35 uses the complement rece...	2008
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "molecular probe techniques", "gene regulation", "enzymes", "microbiology", "dna-binding proteins", "immunoblotting", "enzymology", "sumoylation", "immunoprecipitation", "epigenetics", "molecular biology techniques", "ligases", "chromatin", "research and analysis methods", "chromosome bi...	SUMO modification of a heterochromatin histone demethylase JMJD2A enables viral gene transactivation and viral replication	journal.ppat.1006216	null	[ [ "Epigenetics connects genotype to phenotype and disease .", "Histone modifications are important epigenetic events in the regulation of chromatin structure and gene transcription .", "Different from acetylation , histone lysine methylation was long considered to be irreversible and therefore garnered ...	[ "Small ubiquitin-like modifier ( SUMO ) modification of chromatin has profound effects on transcription regulation .", "By using Kaposi’s sarcoma associated herpesvirus ( KSHV ) as a model , we recently demonstrated that epigenetic modification of viral chromatin by SUMO-2/3 is involved in regulating gene express...	[ "Epigenetic dysregulation connects genotype to diseases .", "An understanding of epigenetic regulation holds promise for clinical use .", "The profound epigenetic changes that occur during the latent-to-lytic switch of the Kaposi’s sarcoma associated herpesvirus ( KSHV ) life cycle make it an attractive model s...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genome expression analysis", "organismal evolution", "microbiology", "escherichia coli", "prokaryotic models", "model organisms", "microbial evolution", "biology", "evolutionary genetics", "systems biology", "adaptation", "genomics", "evolutionary biology", "evolutionary processes", "ge...	Fitness Landscape Transformation through a Single Amino Acid Change in the Rho Terminator	journal.pgen.1002744	null	[ [ "Rho-dependent termination is a crucial component of transcriptional regulation in bacteria , and is estimated to terminate approximately half of the transcripts present in E . coli [1] , [2] .", "Recent studies have shown that this type of transcription termination is particularly prevalent in prophage a...	[ "Regulatory networks allow organisms to match adaptive behavior to the complex and dynamic contingencies of their native habitats .", "Upon a sudden transition to a novel environment , the mismatch between the native behavior and the new niche provides selective pressure for adaptive evolution through mutations i...	[ "Bacteria rely on complex genetic regulatory networks to respond to hazards or opportunities that they encounter .", "These networks consist of a series of sensory modules , coupled with various response elements that must be appropriately activated to deal with a given set of environmental conditions; all of the...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "immune cells", "nk cells", "virology", "immunology", "biology", "microbiology", "viral diseases" ]	The Viral KSHV Chemokine vMIP-II Inhibits the Migration of Naive and Activated Human NK Cells by Antagonizing Two Distinct Chemokine Receptors	journal.ppat.1003568	null	[ [ "NK cells are innate immune lymphocytes that comprise approximately 10% of peripheral blood lymphocytes and are phenotypically characterized by the presence of CD56 , the expression of NKp46 , and the lack of CD3 expression [1] .", "The majority ( approximately 90% ) of naïve human NK cells in the periphe...	[ "Natural killer ( NK ) cells are innate immune cells able to rapidly kill virus-infected and tumor cells .", "Two NK cell populations are found in the blood; the majority ( 90% ) expresses the CD16 receptor and also express the CD56 protein in intermediate levels ( CD56Dim CD16Pos ) while the remaining 10% are CD...	[ "NK cells belong to the innate immune system , able to rapidly kill tumors and various pathogens .", "They reside in the blood and in various tissues and traffic to different infected organs through the usage of different chemokines and chemokine receptors .", "KSHV is a master of immune evasion , and around a ...	2013

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