Split (3)

train · 24.8k rows

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", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "biopsy", "engineering and technology", "tropical diseases", "geographical locations", "parasitic diseases", "surgical and invasive medical procedures", "neglected tropical diseases", "onchocerciasis", "infectious disease control", "africa", "senegal", "scienc...	Feasibility of utilizing the SD BIOLINE Onchocerciasis IgG4 rapid test in onchocerciasis surveillance in Senegal	journal.pntd.0005884	null	[ [ "Onchocerciasis , commonly known as river blindness , is caused by the filarial parasite O . volvulus ( Ov ) that affects an estimated 37 million people , with an estimated 187 million living in areas at risk of infection , primarily in Africa . [1 , 2]", "An estimated 1 . 1 million disability-adjusted li...	[ "As effective onchocerciasis control efforts in Africa transition to elimination efforts , different diagnostic tools are required to support country programs .", "Senegal , with its long standing , successful control program , is transitioning to using the SD BIOLINE Onchocerciasis IgG4 ( Ov16 ) rapid test over ...	[ "As onchocerciasis control programs succeed and transition to elimination efforts , different diagnostic tools are needed .", "The goal of this study was to determine if integrating the Ov16 rapid test is feasible based on acceptability , usability , and cost .", "A study was conducted in 13 villages in southea...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "virology/diagnosis", "infectious diseases/viral infections", "public health and epidemiology/infectious diseases", "pediatrics and child health" ]	Clinical and Virological Features of Dengue in Vietnamese Infants	journal.pntd.0000657	null	[ [ "Dengue represents a substantial disease burden in many tropical and sub-tropical countries , particularly in children and young adults [1] .", "Infection with any one of the four dengue virus ( DENV ) serotypes can lead to a sub-clinical infection , or to clinical disease ranging in severity from a non-s...	[ "Infants account for a small proportion of the overall dengue case burden in endemic countries but can be clinically more difficult to manage .", "The clinical and laboratory features in infants with dengue have not been extensively characterised .", "This prospective , cross-sectional descriptive study of infa...	[ "Dengue is a major public health problem in tropical and subtropical countries , including Vietnam .", "Dengue cases occur in children and young adults; however , severe dengue also occurs in infants less than 1 year of age .", "Prompt recognition of dengue is important for appropriate case management , particu...	2010
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases", "ecology and environmental sciences", "medicine and health sciences", "epidemiology", "vector biology", "biology and life sciences", "disease vectors" ]	Patterns of Geographic Expansion of Aedes aegypti in the Peruvian Amazon	journal.pntd.0003033	null	[ [ "Aedes aegypti is the vector of several arboviruses of major global health importance , including dengue virus ( DENV ) , yellow fever virus , and chikungunya and Mayaro viruses .", "Of these , dengue virus is the most prevalent and geographically extensive , with approximately 2 . 5 billion people at ris...	[ "In the Peruvian Amazon , the dengue vector Aedes aegypti is abundant in large urban centers such as Iquitos .", "In recent years , it has also been found in a number of neighboring rural communities with similar climatic and socioeconomic conditions .", "To better understand Ae .", "aegypti spread , we compa...	[ "Ae .", "aegypti mosquitoes carry a number of viruses that cause human disease , including dengue and yellow fever .", "Over the past 30 years , the burden of dengue has increased exponentially , due to urbanization , poor waste and water management , human transportation , and expanding mosquito populations ."...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "diagnostic radiology", "functional magnetic resonance imaging", "neural networks", "applied mathematics", "social sciences", "light", "neuroscience", "electromagnetic radiation", "magnetic resonance imaging", "algorithms", "simulation and modeling", "optimiza...	Deep image reconstruction from human brain activity	journal.pcbi.1006633	null	[ [ "While the externalization of states of the mind is a long-standing theme in science fiction , it is only recently that the advent of machine learning-based analysis of functional magnetic resonance imaging ( fMRI ) data has expanded its potential in the real world .", "Although sophisticated decoding and...	[ "The mental contents of perception and imagery are thought to be encoded in hierarchical representations in the brain , but previous attempts to visualize perceptual contents have failed to capitalize on multiple levels of the hierarchy , leaving it challenging to reconstruct internal imagery .", "Recent work sho...	[ "Machine learning-based analysis of human functional magnetic resonance imaging ( fMRI ) patterns has enabled the visualization of perceptual content .", "However , prior work visualizing perceptual contents from brain activity has failed to combine visual information of multiple hierarchical levels .", "Here ,...	2019
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "neuropsychiatric disorders", "medicine and health sciences", "adhd", "decision making", "anxiety disorders", "obsessive-compulsive disorder", "social sciences", "neuroscience", "health care", "age groups", "cognitive psychology", "mathematics", "cognition", "behavioral disorders", "pati...	Increased decision thresholds enhance information gathering performance in juvenile Obsessive-Compulsive Disorder (OCD)	journal.pcbi.1005440	null	[ [ "A core feature of psychiatric illness includes personal suffering and functional impairments in daily life [1 , 2] often coupled with a negative impact on a sufferer’s social environment [3] .", "Whilst this overall negative impact is well recognised , the possibility that some manifestations of psychopa...	[ "Patients with obsessive-compulsive disorder ( OCD ) can be described as cautious and hesitant , manifesting an excessive indecisiveness that hinders efficient decision making .", "However , excess caution in decision making may also lead to better performance in specific situations where the cost of extended del...	[ "Patients with obsessive-compulsive disorder ( OCD ) report to suffer from indecisiveness and overly cautious decision making .", "Although many studies captured such a bias experimentally , little is known about the cognitive mechanisms driving such an indecisiveness .", "In this study , we investigated 16 juv...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "stiffness", "mechanical properties", "medicine and health sciences", "ellipses", "nervous system", "limbs (anatomy)", "geometry", "biomechanics", "mathematics", "materials science", "elbow", "musculoskeletal mechanics", "muscle physiology", "musculoskeletal system", "arms", "anatomy",...	Muscle Synergies Heavily Influence the Neural Control of Arm Endpoint Stiffness and Energy Consumption	journal.pcbi.1004737	null	[ [ "Limb impedance control by the central nervous system ( CNS ) has been a subject of much study and debate over the past three decades .", "Numerous experiments and theoretical analyses have studied the biomechanical and neuromuscular capabilities of the CNS to regulate the impedance of a limb ( e . g . , ...	[ "Much debate has arisen from research on muscle synergies with respect to both limb impedance control and energy consumption .", "Studies of limb impedance control in the context of reaching movements and postural tasks have produced divergent findings , and this study explores whether the use of synergies by the...	[ "The manner in which the nervous system coordinates the multiple muscles in the body is complex .", "It has been studied for decades , but a more full understanding is needed to enable the development of effective evaluation and treatment methods in disorders that cause neuromuscular disability such as cerebral p...	2016
[ "Introduction", "Models", "Results", "Discussion" ]	[]	Model-Based Analysis of Cell Cycle Responses to Dynamically Changing Environments	journal.pcbi.1004604	null	[ [ "The cell cycle is the process by which cells alternate replication of their DNA with cell division .", "As a central process in the life of a cell , it is subject to multiple forms of regulation .", "These range from hormonal and growth factor signals in higher organisms , down to nutrient and stress...	[ "Cell cycle progression is carefully coordinated with a cell’s intra- and extracellular environment .", "While some pathways have been identified that communicate information from the environment to the cell cycle , a systematic understanding of how this information is dynamically processed is lacking .", "We a...	[ "The cell cycle is an exquisitely tuned process , alternating between states of cell growth , DNA replication , mitosis , and cytokinesis .", "While this process is robust , it is also responsive to diverse environmental signals .", "For example , cell cycle events may be delayed or advanced in response to chan...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunology", "biology" ]	Thy1+ Nk Cells from Vaccinia Virus-Primed Mice Confer Protection against Vaccinia Virus Challenge in the Absence of Adaptive Lymphocytes	journal.ppat.1002141	null	[ [ "Immunological memory allows the immune system to provide enhanced host protection upon secondary exposure to an infectious pathogen .", "Memory has long been considered the sole province of adaptive lymphocytes .", "Lymphocytes recognize pathogens via unique somatically-rearranged antigen receptors ,...	[ "While immunological memory has long been considered the province of T- and B- lymphocytes , it has recently been reported that innate cell populations are capable of mediating memory responses .", "We now show that an innate memory immune response is generated in mice following infection with vaccinia virus , a ...	[ "Immunological memory is a hallmark of adaptive immunity and provides the basis for our ability to become ‘immune’ to pathogens to which we have previously been exposed , and provides the basis for vaccination .", "For decades , the paradigm held that only the classical adaptive lymphocytes were capable of formin...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	At the Edge of Chaos: How Cerebellar Granular Layer Network Dynamics Can Provide the Basis for Temporal Filters	journal.pcbi.1004515	null	[ [ "Many models of the cerebellum assume that the granular layer recodes its mossy-fiber inputs into a more diverse set of granule-cell outputs [1–4] .", "It is further assumed that the recoded signals , which travel via granule-cell ascending axons and parallel fibers to Purkinje cells and molecular layer i...	[ "Models of the cerebellar microcircuit often assume that input signals from the mossy-fibers are expanded and recoded to provide a foundation from which the Purkinje cells can synthesize output filters to implement specific input-signal transformations .", "Details of this process are however unclear .", "While...	[ "The cerebellum plays an important role in the learning of precise movements , and in humans holds 80% of all the neurons in the brain , due to numerous small cells called “granule cells” embedded in the granular layer .", "It is widely thought that the granular layer receives , transforms and delays input signal...	2015
[ "Introduction", "Methods", "Results and Discussion" ]	[ "invertebrates", "medicine and health sciences", "body fluids", "chikungunya infection", "tropical diseases", "vector-borne diseases", "saliva", "animals", "wolbachia", "neglected tropical diseases", "infectious disease control", "insect vectors", "bacteria", "infectious diseases", "epid...	The wMel Strain of Wolbachia Reduces Transmission of Chikungunya Virus in Aedes aegypti	journal.pntd.0004677	null	[ [ "Chikungunya virus ( CHIKV; Togaviridae , Alphavirus ) has recently re-emerged out of Africa and caused explosive outbreaks of arthritic disease in Southeast Asia , India , Europe and currently the Americas [1–4] .", "The current outbreak in the Americas is cause for great concern because CHIKV is spreadi...	[ "New approaches to preventing chikungunya virus ( CHIKV ) are needed because current methods are limited to controlling mosquito populations , and they have not prevented the invasion of this virus into new locales , nor have they been sufficient to control the virus upon arrival .", "A promising candidate for ar...	[ "New approaches to preventing chikungunya virus ( CHIKV ) infection are needed because the endemic range of this virus is expanding and because current methods are limited to controlling mosquito populations , and this approach has not effectively controlled this virus .", "A promising candidate for arbovirus con...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genome expression analysis", "cytokines", "statistics", "immune activation", "immunity to infections", "immunology", "microbiology", "host-pathogen interaction", "mathematics", "immune defense", "viral disease diagnosis", "inflammation", "virulence factors and mechanisms", "viral immune e...	Temporal Dynamics of Host Molecular Responses Differentiate Symptomatic and Asymptomatic Influenza A Infection	journal.pgen.1002234	null	[ [ "Influenza viruses are highly infectious and can cause acute respiratory illness in human hosts .", "Infected hosts present a variety of clinical symptoms including fever , runny nose , sore throat , myalgias , and malaise with potentially more serious complications such as viral pneumonia [1] .", "Ma...	[ "Exposure to influenza viruses is necessary , but not sufficient , for healthy human hosts to develop symptomatic illness .", "The host response is an important determinant of disease progression .", "In order to delineate host molecular responses that differentiate symptomatic and asymptomatic Influenza A infe...	[ "The transcriptional responses of human hosts towards influenza viral pathogens are important for understanding virus-mediated immunopathology .", "Despite great advances gained through studies using model organisms , the complete temporal host transcriptional responses in a natural human system are poorly unders...	2011
[ "Introduction", "Models", "Results", "Discussion" ]	[]	A Systematic Bayesian Integration of Epidemiological and Genetic Data	journal.pcbi.1004633	null	[ [ "Epidemiological data for infectious disease , defined here as clinical observation , diagnostic test results and associated covariates such as location , only indirectly reflect underlying contact structures , exposure times , and other aspects of disease dynamics .", "Developments in Bayesian data-augme...	[ "Genetic sequence data on pathogens have great potential to inform inference of their transmission dynamics ultimately leading to better disease control .", "Where genetic change and disease transmission occur on comparable timescales additional information can be inferred via the joint analysis of such genetic s...	[ "In the midst of increasingly available sequence data of pathogens , a key challenge is to better integrate these data with traditional epidemiological data , with the proximate goal of reliable prediction and the ultimate aim of effective management of disease outbreaks .", "Although substantial advances have be...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biophysics", "biology and life sciences", "biophysical simulations" ]	Energy Landscape of All-Atom Protein-Protein Interactions Revealed by Multiscale Enhanced Sampling	journal.pcbi.1003901	null	[ [ "Protein-protein interactions are the fundamental components in the interaction networks describing cellular processes such as metabolic reactions and signal transduction .", "When trying to acquire a more detailed understanding of the association and dissociation processes of protein complexes , however ...	[ "Protein-protein interactions are regulated by a subtle balance of complicated atomic interactions and solvation at the interface .", "To understand such an elusive phenomenon , it is necessary to thoroughly survey the large configurational space from the stable complex structure to the dissociated states using t...	[ "Dynamic nature of the protein-protein interactions is an important element of cellular processes such as metabolic reactions and signal transduction , but its atomistic details are still unclear .", "Computational survey using molecular dynamics simulation is a straightforward method to elucidate these atomistic...	2014
[ "Introduction", "Results", "Discussion", "Methods", "Data and software availability" ]	[ "statistics", "gene regulation", "population genetics", "geographical locations", "multivariate analysis", "mathematics", "molecular genetics", "population biology", "structural genomics", "discrete mathematics", "combinatorics", "research and analysis methods", "europe", "mathematical and...	Expression reflects population structure	journal.pgen.1007841	null	[ [ "Genes mirror geography to the extent that in global populations without admixture , individuals can be localized to within hundreds of kilometers purely on the basis of their genotype [1–3] .", "Population structure in genotypes is revealed via projection of single nucleotide polymorphism ( SNP ) data on...	[ "Population structure in genotype data has been extensively studied , and is revealed by looking at the principal components of the genotype matrix .", "However , no similar analysis of population structure in gene expression data has been conducted , in part because a naïve principal components analysis of the g...	[ "Increasingly complex , high dimensional , multi-modal genomics datasets warrant investigation into analysis techniques that can reveal structure in the data without over-fitting .", "Here , we show that the coupling of principal component analysis to canonical correlation analysis offers an efficient approach to...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "phosphorylation", "medicine and health sciences", "cardiovascular physiology", "vegf signaling", "endothelial cells", "electrophysiology", "neuroscience", "epithelial cells", "angiogenesis", "developmental biology", "ion channels", "calcium signaling", "cellular structures and organelles", ...	Computational investigation of sphingosine kinase 1 (SphK1) and calcium dependent ERK1/2 activation downstream of VEGFR2 in endothelial cells	journal.pcbi.1005332	null	[ [ "Angiogenesis is the growth of new capillaries from the pre-existing vasculature .", "The process of angiogenesis involves increased proliferation , survival , and migration of the endothelial cells that form the foundation of a developing vascular bed [1] .", "This process is critically involved in b...	[ "Vascular endothelial growth factor ( VEGF ) is a powerful regulator of neovascularization .", "VEGF binding to its cognate receptor , VEGFR2 , activates a number of signaling pathways including ERK1/2 .", "Activation of ERK1/2 is experimentally shown to involve sphingosine kinase 1 ( SphK1 ) activation and its...	[ "Vascular endothelial growth factor ( VEGF ) signaling is a potent regulator of angiogenesis , the growth and development of new vessels out of a preexisting vascular network .", "Angiogenesis requires enhanced survival , proliferation , and motility of the vascular endothelial cells .", "Crucial signaling endp...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "bacteriology", "genome expression analysis", "microbial metabolism", "genetic networks", "transcription activators", "genome evolution", "gene regulation", "dna-binding proteins", "microbiology", "dna transcription", "gene function", "next-generation sequencing", "genome analysis", "trans...	Global Analysis of Photosynthesis Transcriptional Regulatory Networks	journal.pgen.1004837	null	[ [ "Photosynthetic organisms are central to life on the planet .", "Their ability to harness solar energy and fix atmospheric carbon dioxide makes them integral parts of most ecosystems .", "Furthermore , many photosynthetic microbes , either naturally or via modifications , are capable of producing a va...	[ "Photosynthesis is a crucial biological process that depends on the interplay of many components .", "This work analyzed the gene targets for 4 transcription factors: FnrL , PrrA , CrpK and MppG ( RSP_2888 ) , which are known or predicted to control photosynthesis in Rhodobacter sphaeroides .", "Chromatin immun...	[ "Photosynthetic organisms are among the most abundant life forms on earth .", "Their unique ability to harvest solar energy and use it to fix atmospheric carbon dioxide is at the foundation of the global food chain .", "This paper reports the first comprehensive analysis of networks that control expression of p...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "mitosis", "cell division", "chromosome biology", "chromosome structure and function", "centromeres", "biology", "molecular cell biology" ]	Functional Dissection of the Drosophila melanogaster Condensin Subunit Cap-G Reveals Its Exclusive Association with Condensin I	journal.pgen.1003463	null	[ [ "Chromosome condensation is a critical process ensuring faithful distribution of the replicated genetic information onto the daughter cells .", "While the exact mechanism underlying the longitudinal compaction of the dispersed interphase chromatin into the rod-like and sturdy metaphase chromosomes is stil...	[ "The heteropentameric condensin complexes have been shown to participate in mitotic chromosome condensation and to be required for unperturbed chromatid segregation in nuclear divisions .", "Vertebrates have two condensin complexes , condensin I and condensin II , which contain the same structural maintenance of ...	[ "The accurate duplication and segregation of chromosomes during cell divisions are prerequisites for ensuring genetic stability within an individual organism and in entire populations .", "Among the many components involved in regulating these processes , a protein complex called condensin plays a crucial role in...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology", "caenorhabditis", "neuroscience" ]	Open Syntaxin Docks Synaptic Vesicles	journal.pbio.0050198	Experiments in C. elegans support a model for synaptic vesicle docking in which the active zone protein UNC-13 converts syntaxin from the closed to the open state, and open syntaxin acts directly in docking vesicles to the plasma membrane.	[ [ "Fusion of synaptic vesicles with the plasma membrane is thought to occur in three ordered steps: docking , priming , and fusion [1] .", "The biological state of a synaptic vesicle can be defined by three distinct parameters: morphology ( its location in the synapse ) ; physiology ( its release competence...	[ "Synaptic vesicles dock to the plasma membrane at synapses to facilitate rapid exocytosis .", "Docking was originally proposed to require the soluble N-ethylmaleimide–sensitive fusion attachment protein receptor ( SNARE ) proteins; however , perturbation studies suggested that docking was independent of the SNARE...	[ "Like Olympic swimmers crouched on their starting blocks , synaptic vesicles prepare for fusion with the neuronal plasma membrane long before the starting gun fires .", "This preparation enables vesicles to fuse rapidly , synchronously , and in the correct place when the signal finally arrives .", "A well-known...	2007
[ "Introduction", "Materials & methods", "Results", "Discussion" ]	[ "information entropy", "medicine and health sciences", "action potentials", "nervous system", "membrane potential", "electrophysiology", "neuroscience", "nerve fibers", "neuronal dendrites", "thermodynamics", "computer and information sciences", "entropy", "animal cells", "axons", "physi...	Energy-efficient information transfer at thalamocortical synapses	journal.pcbi.1007226	null	[ [ "Information transmission in the brain is energetically expensive [1–7] , yet has to satisfy demands of speed and signal-to-noise reliability [8 , 9] .", "In order to balance these competing demands , the brain may tend towards a design which prioritises energy efficiency at the expense of computational p...	[ "We have previously shown that the physiological size of postsynaptic currents maximises energy efficiency rather than information transfer across the retinothalamic relay synapse .", "Here , we investigate information transmission and postsynaptic energy use at the next synapse along the visual pathway: from rel...	[ "Compared to other organs , the brain consumes a vast amount of energy for its size .", "Most of this energy is used to power the electrical and chemical processes that support neural computation .", "As the energy supply to the brain is limited , it follows that this computation should be energetically efficie...	2019
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "phosphorylation", "medicine and health sciences", "chemical compounds", "messenger rna", "microbiology", "protozoan life cycles", "organic compounds", "parasitic protozoans", "purines", "developmental biology", "nutrition", "protozoans", "leishmania", "promastigotes", "malnutrition", ...	Nutritional stress targets LeishIF4E-3 to storage granules that contain RNA and ribosome components in Leishmania	journal.pntd.0007237	null	[ [ "Leishmania are heteroxenous pathogenic parasites that live in the alimentary tract of sandflies as extracellular flagellated promastigotes .", "Upon transmission to the mammalian host , the parasites enter macrophages and become obligatory intracellular and non-motile amastigotes , residing within phagol...	[ "Leishmania parasites lack pathways for de novo purine biosynthesis .", "The depletion of purines induces differentiation into virulent metacyclic forms .", "In vitro , the parasites can survive prolonged periods of purine withdrawal changing their morphology to long and slender cells with an extended flagellum...	[ "Cells respond to cellular stress by decreasing protein translation , to prevent the formation of partially folded or misfolded new polypeptides whose accumulation can be detrimental to living cells .", "Under such conditions , the cells benefit from storing inactive mRNAs and stalled ribosomal particles , to mai...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology/membranes and sorting", "virology/host invasion and cell entry", "cell biology/cytoskeleton" ]	Human Papillomavirus Type 16 Entry: Retrograde Cell Surface Transport along Actin-Rich Protrusions	journal.ppat.1000148	null	[ [ "Virus entry into target cells is a multistep process that starts with the initial binding of incoming particles to cellular receptors and attachment factors .", "After binding , animal viruses typically display a period of lateral movement before viruses are internalized by endocytosis or penetrate the p...	[ "The lateral mobility of individual , incoming human papillomavirus type 16 pseudoviruses ( PsV ) bound to live HeLa cells was studied by single particle tracking using fluorescence video microscopy .", "The trajectories were computationally analyzed in terms of diffusion rate and mode of motion as described by t...	[ "To replicate , viruses have to enter into host cells .", "Since they have no means of locomotion , they rely entirely on cellular transport systems to access the cellular compartments where replication occurs .", "Following individual virus particles by video microscopy , we found that human papillomavirus typ...	2008
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "microbiome", "pathology and laboratory medicine", "enterococcus infections", "immunology", "tropical diseases", "microbiology", "opportunistic infections", "parasitic diseases", "liver diseases", "bacterial diseases", "signs and symptoms", "gastroenterology a...	Exclusive dependence of IL-10Rα signalling on intestinal microbiota homeostasis and control of whipworm infection	journal.ppat.1007265	null	[ [ "A single layer of intestinal epithelial cells ( IECs ) in conjunction with the overlaying mucus acts as a primary barrier to viruses , bacteria and parasites entering the body via the gastrointestinal tract [1] .", "Paradoxically , the intestinal epithelium is also the host tissue for diverse pathogens i...	[ "The whipworm Trichuris trichiura is a soil-transmitted helminth that dwells in the epithelium of the caecum and proximal colon of their hosts causing the human disease , trichuriasis .", "Trichuriasis is characterized by colitis attributed to the inflammatory response elicited by the parasite while tunnelling th...	[ "The human gut is home to millions of bacteria , collectively called the microbiota , and also to parasites that include whipworms .", "The interactions between gut cells , the microbiota and whipworms define conditions for balanced parasitism .", "Cells lining the gut host whipworms but also interact with gut ...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Acceleration of the Glycolytic Flux by Steroid Receptor Coactivator-2 Is Essential for Endometrial Decidualization	journal.pgen.1003900	null	[ [ "Progression of embryo implantation into a receptive endometrium relies on endometrial stromal cells ( ESCs ) undergoing decidualization , a critical cellular transformation process which determines the depth of embryo invasion and placentation [1]–[3] .", "Therefore , inadequate decidualization of ESCs c...	[ "Early embryo miscarriage is linked to inadequate endometrial decidualization , a cellular transformation process that enables deep blastocyst invasion into the maternal compartment .", "Although much of the cellular events that underpin endometrial stromal cell ( ESC ) decidualization are well recognized , the i...	[ "Failure of an embryo to correctly implant into the endometrium is a common cause of pregnancy failure or early embryo miscarriage .", "Although advances in our understanding of oocyte and embryo development have significantly increased pregnancy success rates , these rates remain unacceptably low due in part to ...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "yeast and fungi", "cell biology", "genetics and genomics", "computational biology" ]	Determinants of Protein Abundance and Translation Efficiency in S. cerevisiae	journal.pcbi.0030248	null	[ [ "DNA microarrays are now commonly used to measure the expression levels of large numbers of genes simultaneously [1] .", "Since proteins are the direct mediators of cellular processes , the abundance level of each protein is likely to be a better indicator of the cellular state than its corresponding mRNA...	[ "The translation efficiency of most Saccharomyces cerevisiae genes remains fairly constant across poor and rich growth media .", "This observation has led us to revisit the available data and to examine the potential utility of a protein abundance predictor in reinterpreting existing mRNA expression data .", "O...	[ "DNA microarrays measuring gene expression levels have been a mainstay of systems biology research , but since proteins are more direct mediators of cellular processes , protein abundance levels are likely to be a better indicator of the cellular state .", "However , as proteomic measurements are still lagging be...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "biochemistry", "infectious diseases", "virology" ]	High-Throughput SHAPE Analysis Reveals Structures in HIV-1 Genomic RNA Strongly Conserved across Distinct Biological States	journal.pbio.0060096	Development of novel, quantitative, high-throughput RNA structure analysis tools allows the outline of structure-function relationships for the first 10% of an HIV genome, discovery of structural differences between regulatory and coding regions, and analysis of protein-RNA interactions inside authentic virions.	[ [ "As is the case with many natural RNAs , the function of the HIV RNA genome is strongly linked to its ability to form higher-order structure and to interact with protein effectors in each stage of its replication cycle .", "The 5′ end of the HIV genome alone contains a noncoding , highly structured region...	[ "Replication and pathogenesis of the human immunodeficiency virus ( HIV ) is tightly linked to the structure of its RNA genome , but genome structure in infectious virions is poorly understood .", "We invent high-throughput SHAPE ( selective 2′-hydroxyl acylation analyzed by primer extension ) technology , which ...	[ "The function of the RNA genome of the human immunodeficiency virus ( HIV ) is determined both by its sequence and by its ability to fold back on itself to form specific higher-order structures .", "In order to describe physical structures in a region of the HIV RNA genome known to play multiple , critical roles ...	2008
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Anopheles Midgut Epithelium Evades Human Complement Activity by Capturing Factor H from the Blood Meal	journal.pntd.0003513	null	[ [ "Mosquitoes can transmit important parasitic diseases such as malaria and filariasis and viral diseases such as yellow fever , dengue , Rift Valley fever and the West Nile virus .", "Anopheles , Aedes , Culex , Coquillettidia , Mansonia and Ochlerotatus species are the best known disease transmitting mosq...	[ "Hematophagous vectors strictly require ingesting blood from their hosts to complete their life cycles .", "Exposure of the alimentary canal of these vectors to the host immune effectors necessitates efficient counteractive measures by hematophagous vectors .", "The Anopheles mosquito transmitting the malaria p...	[ "Mosquitoes are important vectors in the transmission of many human diseases .", "Their life cycle requires a blood meal to be completed .", "Ingested blood contains bioactive molecules belonging to the innate immune defense mechanisms against microbes , like the complement system , that can damage foreign cell...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "neuroscience/sensory systems", "genetics and genomics/genetics of disease", "otolaryngology/ear pathologies", "otolaryngology/audiology", "biochemistry/membrane proteins and energy transduction" ]	The Novel Mouse Mutation Oblivion Inactivates the PMCA2 Pump and Causes Progressive Hearing Loss	journal.pgen.1000238	null	[ [ "PMCA2 is one of four isoforms of the plasma membrane Ca2+ pumps of mammalian cells [1] , [2] .", "The expression of PMCA2 and PMCA3 is largely restricted to brain and muscle , whereas PMCA1 and 4 are ubiquitously expressed .", "PMCA2 and PMCA3 are more active in exporting Ca2+ than the ubiquitous iso...	[ "Progressive hearing loss is common in the human population , but we have few clues to the molecular basis .", "Mouse mutants with progressive hearing loss offer valuable insights , and ENU ( N-ethyl-N-nitrosourea ) mutagenesis is a useful way of generating models .", "We have characterised a new ENU-induced mo...	[ "Progressive hearing loss is very common in the human population , but we know little about the causes .", "Environmental and genetic factors each may contribute .", "Knowledge of the genetic variants involved in hearing loss and understanding of the molecular and cellular mechanism of their action will aid the...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "antimicrobials", "virology", "emerging viral diseases", "microbial control", "biology and life sciences", "microbiology", "antivirals" ]	Cyclophilin A Associates with Enterovirus-71 Virus Capsid and Plays an Essential Role in Viral Infection as an Uncoating Regulator	journal.ppat.1004422	null	[ [ "Cyclophilins ( Cyps ) are key cellular factors that function in numerous cellular processes , including transcriptional regulation , immune response , protein secretion , and mitochondrial function [1] .", "Cyps possess peptidyl-prolyl cis-trans isomerase activity and have high affinity for the immunosup...	[ "Viruses utilize host factors for their efficient proliferation .", "By evaluating the inhibitory effects of compounds in our library , we identified inhibitors of cyclophilin A ( CypA ) , a known immunosuppressor with peptidyl-prolyl cis-trans isomerase activity , can significantly attenuate EV71 proliferation ....	[ "Enterovirus 71 ( EV71 ) is the major causative agent of hand-foot-and-mouth disease ( HFMD ) in Asia-Pacific region and caused over one million infection cases and nine hundred deaths in the year of 2010 in China mainland .", "EV71 is known to infect the young children for the sake of their undeveloped immune sy...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Relationship between Antibody Susceptibility and Lipopolysaccharide O-Antigen Characteristics of Invasive and Gastrointestinal Nontyphoidal Salmonellae Isolates from Kenya	journal.pntd.0003573	null	[ [ "NTS are a major but neglected cause of invasive disease ( hence iNTS disease ) in Africa [1–3] .", "Salmonella enterica serovars Typhimurium and Enteritidis account for nearly 80% of all human isolates reported globally [4] .", "While in developed countries , these predominantly cause a mild self-lim...	[ "Nontyphoidal Salmonellae ( NTS ) cause a large burden of invasive and gastrointestinal disease among young children in sub-Saharan Africa .", "No vaccine is currently available .", "Previous reports indicate the importance of the O-antigen of Salmonella lipopolysaccharide for virulence and resistance to antibo...	[ "Nontyphoidal Salmonellae ( NTS ) are an emerging major cause of invasive bacterial disease in African children aged less than 5 years and immunocompromised adults , with an estimated case fatality rate of 20–25% .", "NTS also cause diarrhoea , a killer of about 1 . 5 million young children annually , mainly in l...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "learning", "children", "ecology and environmental sciences", "sociology", "social sciences", "neuroscience", "learning and memory", "age groups", "cultural evolution", "cognitive psychology", "animal behavior", "population biology", "zoology", "families", "foraging", "human learning",...	The life history of learning: Demographic structure changes cultural outcomes	journal.pcbi.1006821	null	[ [ "Cultural transmission can occur via multiple modes of learning; for example , an individual can learn from parents ( termed vertical transmission ) , from non-parental adults ( oblique transmission ) , or from peers ( horizontal transmission ) [1] .", "Studies of enculturation and socialization of childr...	[ "Human populations show rich cultural diversity .", "Underpinning this diversity of tools , rituals , and cultural norms are complex interactions between cultural evolutionary and demographic processes .", "Most models of cultural change assume that individuals use the same learning modes and methods throughout...	[ "Human populations show great cultural variety and complexity , which cultural evolutionary theory seeks to explain by applying ideas about evolution to the ways in which cultural traits change over time .", "We combined cultural evolutionary theory with information about how people learn over their lifetimes—cha...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "genetics and genomics/genetics of the immune system", "genetics and genomics/complex traits", "rheumatology/systemic lupus erythematosos", "rheumatology/autoimmunity, autoimmune, and inflammatory diseases", "public health and epidemiology/epidemiology", "genetics and genomics/genetics of disease", "gen...	Specificity of the STAT4 Genetic Association for Severe Disease Manifestations of Systemic Lupus Erythematosus	journal.pgen.1000084	null	[ [ "Systemic lupus erythematosus ( SLE ) ( OMIM 152700 ) is a disabling and chronic autoimmune disease with remarkable heterogeneity .", "The eleven classification criteria for SLE established by the American College of Rheumatology [1] – any four of which can confirm classification as SLE – include arthriti...	[ "Systemic lupus erythematosus ( SLE ) is a genetically complex disease with heterogeneous clinical manifestations .", "A polymorphism in the STAT4 gene has recently been established as a risk factor for SLE , but the relationship with specific SLE subphenotypes has not been studied .", "We studied 137 SNPs in t...	[ "Systemic lupus erythematosus is a chronic disabling autoimmune disease , most commonly striking women in their thirties or forties .", "It can cause a wide variety of clinical manifestations , including kidney disease , arthritis , and skin disorders .", "Prognosis varies greatly depending on these clinical fe...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "meiosis", "medicine and health sciences", "reproductive system", "spermatocytes", "cell cycle and cell division", "messenger rna", "cell processes", "reproductive physiology", "germ cells", "genome analysis", "sperm", "spermatids", "genomics", "animal cells", "chromosome biology", "ge...	UPF2-Dependent Nonsense-Mediated mRNA Decay Pathway Is Essential for Spermatogenesis by Selectively Eliminating Longer 3'UTR Transcripts	journal.pgen.1005863	null	[ [ "Spermatogenesis is a complex cellular differentiation process through which male germline stem cells develop sequentially into spermatogonia , spermatocytes , spermatids , and eventually spermatozoa [1] .", "Both meiosis ( i . e . spermatocyte development ) and spermiogenesis ( i . e . spermatid differen...	[ "During transcription , most eukaryotic genes generate multiple alternative cleavage and polyadenylation ( APA ) sites , leading to the production of transcript isoforms with variable lengths in the 3’ untranslated region ( 3’UTR ) .", "In contrast to somatic cells , male germ cells , especially pachytene spermat...	[ "3’UTR length control has been identified as a critical mechanism through which the cell establishes and maintains its functional identity .", "Developing male germ cells , especially spermatocytes and spermatids , display a transcriptome enriched in short 3’UTR transcripts , which has been demonstrated to be ess...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Identification of 526 Conserved Metazoan Genetic Innovations Exposes a New Role for Cofactor E-like in Neuronal Microtubule Homeostasis	journal.pgen.1003804	null	[ [ "Metazoans , or multicellular animals , represent the epitome of biological complexity .", "Prerequisite for generating this complexity was the development of a multicellular lifestyle , and the ability to coordinate cell division , migration and differentiation to optimize the overall fitness of the orga...	[ "The evolution of metazoans from their choanoflagellate-like unicellular ancestor coincided with the acquisition of novel biological functions to support a multicellular lifestyle , and eventually , the unique cellular and physiological demands of differentiated cell types such as those forming the nervous , muscle...	[ "The evolution of multicellular animals ( metazoans ) from their single-celled ancestor required new molecular tools to create and coordinate the various biological functions involved in a communal , or multicellular , lifestyle .", "This would eventually include the unique cellular and physiological demands of s...	2013
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "breast tumors", "cancer risk factors", "blastomas", "cancers and neoplasms", "carcinomas", "basic cancer research", "oncology", "neurological tumors", "mathematics", "statistics (mathematics)", "genome analysis", "adenocarcinomas", "gene expression", "bre...	Association between expression of random gene sets and survival is evident in multiple cancer types and may be explained by sub-classification	journal.pcbi.1006026	null	[ [ "The last two decades have seen a proliferation of papers , each proposing a set of genes that are important for cancer progression , metastasis , or patient stratification [1–7] , where most of the findings stem from the computational analysis of gene-expression data from large patient cohorts .", "While...	[ "One of the goals of cancer research is to identify a set of genes that cause or control disease progression .", "However , although multiple such gene sets were published , these are usually in very poor agreement with each other , and very few of the genes proved to be functional therapeutic targets .", "Furt...	[ "Multiple gene sets have been published as predictive of cancer progression and metastasis in several cancer types .", "Although many of these sets proved to be highly predictive of survival , even gene sets for the same cancer ( but from different data-sets or different analyses ) exhibit very little overlap and...	2018
[ "Introduction", "Results and Discussion", "Materials and Methods" ]	[ "biochemistry", "genetics", "biology", "genomics", "microbiology", "genetics and genomics" ]	Recognition and Degradation of Plant Cell Wall Polysaccharides by Two Human Gut Symbionts	journal.pbio.1001221	Competition for nutrients contained in diverse types of plant cell wall-associated polysaccharides may explain the evolution of substrate-specific catabolic gene modules in common bacterial members of the human gut microbiota.	[ [ "The human distal gut is home to a densely populated microbial community ( microbiota ) that plays key roles in health and nutrition .", "The microbial symbionts that occupy this habitat produce an arsenal of enzymes that degrade dietary complex carbohydrates ( glycans ) that cannot be hydrolyzed by host ...	[ "Symbiotic bacteria inhabiting the human gut have evolved under intense pressure to utilize complex carbohydrates , primarily plant cell wall glycans in our diets .", "These polysaccharides are not digested by human enzymes , but are processed to absorbable short chain fatty acids by gut bacteria .", "The Bacte...	[ "Bacteria inhabiting the human gut are critical for digestion of the plant-derived glycans that compose dietary fiber .", "Enzymes produced by the human body cannot degrade these abundant dietary components , and without bacterial assistance they would go unused .", "We investigated the molecular strategies emp...	2011
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "blood cells", "medicine and health sciences", "chemical characterization", "immune physiology", "enzyme-linked immunoassays", "pathology and laboratory medicine", "immune cells", "pathogens", "immunology", "microbiology", "retroviruses", "viruses", "immunodeficiency viruses", "rna viruses...	Identification of HIV gp41-specific antibodies that mediate killing of infected cells	journal.ppat.1007572	null	[ [ "Eliciting an antibody response to the HIV Envelope protein is thought to be the most likely path to an effective vaccine , and there is evidence that both neutralizing and non-neutralizing HIV-specific antibodies can contribute to protection .", "Indeed , the only HIV vaccine trial to demonstrate measura...	[ "Antibodies that mediate killing of HIV-infected cells through antibody-dependent cellular cytotoxicity ( ADCC ) have been implicated in protection from HIV infection and disease progression .", "Despite these observations , these types of HIV antibodies are understudied compared to neutralizing antibodies .", ...	[ "Anti-HIV antibodies can mediate activity by neutralizing cell-free virus , or binding to infected cells and driving antibody-dependent cellular cytotoxicity ( ADCC ) .", "While numerous discovery efforts have identified and characterized neutralizing antibodies , much less is known about antibodies that mediate ...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/gene expression", "genetics and genomics/functional genomics", "microbiology/innate immunity", "immunology/innate immunity", "genetics and genomics/gene function", "microbiology/parasitology", "infectious diseases/protozoal infections", "immunology/immunity to infections" ]	Caspar Controls Resistance to Plasmodium falciparum in Diverse Anopheline Species	journal.ppat.1000335	null	[ [ "The innate immune system of the African malaria vector , Anopheles gambiae , is the mosquito's main line of defense against Plasmodium parasites and is engaged at multiple stages of parasite infection [1] , [2] .", "As part of this defense , two major signaling pathways , Toll and Imd , transduce the pat...	[ "Immune responses mounted by the malaria vector Anopheles gambiae are largely regulated by the Toll and Imd ( immune deficiency ) pathways via the NF-kappaB transcription factors Rel1 and Rel2 , which are controlled by the negative regulators Cactus and Caspar , respectively .", "Rel1- and Rel2-dependent transcri...	[ "The relationship between malaria parasites and the mosquitoes that transmit them to humans comprises complex molecular interactions including mosquito immune responses .", "Anopheles can mount potent anti-Plasmodium immune responses; we show here that the gene caspar , which encodes a negative regulator of the i...	2009
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "protein metabolism", "protein interactions", "veterinary prion diseases", "protein folding", "protein structure", "glycoproteins", "veterinary science", "infectious diseases", "veterinary diseases", "proteins", "zoonotic diseases", "biology", "recombinant proteins", "biophys...	Critical Significance of the Region between Helix 1 and 2 for Efficient Dominant-Negative Inhibition by Conversion-Incompetent Prion Protein	journal.ppat.1003466	null	[ [ "Prion diseases or transmissible spongiform encephalopathies ( TSEs ) are fatal infectious neurodegenerative disorders causing Creutzfeldt-Jakob disease ( CJD ) in humans , bovine spongiform encephalopathy ( BSE ) in cattle , scrapie in sheep and goat , and chronic wasting disease ( CWD ) in cervids [1]–[5] ....	[ "Prion diseases are fatal infectious neurodegenerative disorders in man and animals associated with the accumulation of the pathogenic isoform PrPSc of the host-encoded prion protein ( PrPc ) .", "A profound conformational change of PrPc underlies formation of PrPSc and prion propagation involves conversion of Pr...	[ "Prion diseases are deadly infectious diseases of the brain characterized by accumulation of a pathologic protein ( PrPSc ) which is derived from the normal prion protein ( PrPc ) .", "Prions replicate by direct contact in a template-directed refolding process which involves conversion of PrPC into PrPSc .", "I...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "immunology", "tropical diseases", "fibrosis", "biomarkers", "endocrine physiology", "bacterial diseases", "developmental biology", "signs and symptoms", "eye diseases", "growth factors", "neglected tropical diseases", "i...	Increased Epithelial Expression of CTGF and S100A7 with Elevated Subepithelial Expression of IL-1β in Trachomatous Trichiasis	journal.pntd.0004752	null	[ [ "Trachoma is a blinding disease initiated by infection of the conjunctival epithelium with the intracellular bacterium Chlamydia trachomatis ( Ct ) .", "Individuals living in trachoma-endemic communities are repeatedly infected with Ct , which causes a follicular conjunctivitis .", "Chronic , recurren...	[ "To characterize the histological appearance and expression of pro-inflammatory mediators , growth factors , matrix metalloproteinases and biomarkers of epithelial-mesenchymal transition ( EMT ) in healthy control and trachomatous trichiasis ( TT ) conjunctival tissue .", "Conjunctival biopsies were taken from 20...	[ "Progressive scarring of the conjunctiva in individuals with trachoma causes the eyelids to contract , drawing the eyelashes inwards ( trichiasis ) so that they scratch the cornea , causing pain and eventually blindness .", "Disease is initiated in childhood by repeated conjunctival infection with Chlamydia trach...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "microbiology/environmental microbiology", "genetics and genomics/microbial evolution and genomics", "evolutionary biology/microbial evolution and genomics", "microbiology/microbial evolution and genomics", "microbiology/microbial physiology and metabolism", "genetics and genomics/population genetics" ]	Fast Growth Increases the Selective Advantage of a Mutation Arising Recurrently during Evolution under Metal Limitation	journal.pgen.1000652	null	[ [ "Adaptation is a product of genetic modification and natural selection imposed by environmental challenges .", "A complete understanding of adaptation of biological systems thus requires identification of how selection acts upon organismal traits and mapping adaptive phenotypes to underlying genotypic cha...	[ "Understanding the evolution of biological systems requires untangling the molecular mechanisms that connect genetic and environmental variations to their physiological consequences .", "Metal limitation across many environments , ranging from pathogens in the human body to phytoplankton in the oceans , imposes s...	[ "Effects of mutations can change under different genetic backgrounds or environmental factors , also known as epistasis and genotype-by-environment interactions ( G×E ) , respectively .", "Though epistasis and G×E are traditionally treated as distinct phenomena , our study of a beneficial mutation highlights thei...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "fluorescence imaging", "action potentials", "medicine and health sciences", "data acquisition", "membrane potential", "electrophysiology", "neuroscience", "ion channels", "neuroimaging", "research and analysis methods", "computer and information sciences", "imaging techniques", "animal cell...	Inferring Neuronal Dynamics from Calcium Imaging Data Using Biophysical Models and Bayesian Inference	journal.pcbi.1004736	null	[ [ "Calcium imaging has been used to record neuronal activity indirectly [1] .", "Individual neurons or neuronal populations are labeled by applying fluorescent calcium indicators so that the intracellular calcium transients become measurable by optical means .", "The technique has a temporal resolution ...	[ "Calcium imaging has been used as a promising technique to monitor the dynamic activity of neuronal populations .", "However , the calcium trace is temporally smeared which restricts the extraction of quantities of interest such as spike trains of individual neurons .", "To address this issue , spike reconstruc...	[ "Calcium imaging of single neurons enables the indirect observation of neuronal dynamics , for example action potential firing .", "In contrast to the precise timing of spike trains , the calcium trace is temporally rather smeared and measured as a fluorescence trace .", "Consequently , several methods have bee...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases", "infectious disease immunology", "reproductive immunology", "immune evasion", "medicine and health sciences", "women's health", "clinical immunology", "virology", "biology and life sciences", "immunology", "microbiology", "tumor immunology", "immunomodulation" ]	HPV16-E7 Expression in Squamous Epithelium Creates a Local Immune Suppressive Environment via CCL2- and CCL5- Mediated Recruitment of Mast Cells	journal.ppat.1004466	null	[ [ "Cervical and other anogenital cancers represent around 5% of all cancers , and are mostly due to infection of anogenital epithelium by one of more than 15 recognized “high risk” human papillomaviruses ( HPV ) [1] .", "Worldwide , ∼50% of sexually active women are believed to become infected by HPV16 , th...	[ "Human Papillomavirus ( HPV ) 16 E7 protein promotes the transformation of HPV infected epithelium to malignancy .", "Here , we use a murine model in which the E7 protein of HPV16 is expressed as a transgene in epithelium to show that mast cells are recruited to the basal layer of E7-expressing epithelium , and t...	[ "Worldwide , around 50% of sexually active women are believed to become infected by Human papillomavirus type 16 , the major cause of cervical cancer , and 2% will remain infected and therefore at lifetime risk of developing cancer .", "Why some women remain infected is unknown .", "Here we used a mouse enginee...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "rna interference", "molecular probe techniques", "gene regulation", "enzymes", "rna extraction", "enzymology", "mutation", "fungi", "rna helicases", "epigenetics", "molecular biology techniques", "extraction techniques", "research and analysis methods", "small interfering rnas", "mutant...	A non-canonical RNA degradation pathway suppresses RNAi-dependent epimutations in the human fungal pathogen Mucor circinelloides	journal.pgen.1006686	null	[ [ "RNA interference ( RNAi ) is a complex gene regulatory system that blocks the expression of target genes and is highly conserved in most eukaryotic organisms .", "The discovery of RNAi mechanisms , along with the development of next generation sequencing technologies , has revealed a myriad of regulatory...	[ "Mucorales are a group of basal fungi that includes the casual agents of the human emerging disease mucormycosis .", "Recent studies revealed that these pathogens activate an RNAi-based pathway to rapidly generate drug-resistant epimutant strains when exposed to stressful compounds such as the antifungal drug FK5...	[ "Mucormycosis is a fungal infection that is attracting the attention of both clinical and research communities because of the lack of effective antifungal treatments and its often fatal prognosis .", "Our previous studies revealed an RNAi-mediated epimutation mechanism that operates in the casual human fungal pat...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Autozygome Sequencing Expands the Horizon of Human Knockout Research and Provides Novel Insights into Human Phenotypic Variation	journal.pgen.1004030	null	[ [ "Autozygosity , or the biparental inheritance of the identical founder haplotypes , is a genomic signature of a limited reproductive pool as in the case of populations with a high rate of consanguinity or a significant founder effect; although it is also observed but at a much smaller scale in outbred populat...	[ "The use of autozygosity as a mapping tool in the search for autosomal recessive disease genes is well established .", "We hypothesized that autozygosity not only unmasks the recessiveness of disease causing variants , but can also reveal natural knockouts of genes with less obvious phenotypic consequences .", ...	[ "Identification of disease-causing gene variants by taking advantage of autozygosity mapping in consanguineous pedigrees is well established .", "However , autozygous intervals can also result in making homozygous those loss of function variants in genes that may not result in a discernible phenotype even under a...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "soil-transmitted helminths", "neglected tropical diseases" ]	Podoconiosis and Soil-Transmitted Helminths (STHs): Double Burden of Neglected Tropical Diseases in Wolaita Zone, Rural Southern Ethiopia	journal.pntd.0002128	null	[ [ "People living in rural areas of low-income countries are commonly affected by more than one of the neglected tropical diseases ( NTDs ) .", "These conditions share common risk factors including lack of clean water or poor sanitation , and commonly promote poverty through their impact on child health and ...	[ "Both podoconiosis and soil-transmitted helminth ( STH ) infections occur among barefoot people in areas of extreme poverty; however , their co-morbidity has not previously been investigated .", "We explored the overlap of STH infection and podoconiosis in Southern Ethiopia and quantified their separate and combi...	[ "Podoconiosis and soil-transmitted helminth infections are neglected tropical diseases occurring among barefoot people in areas of extreme poverty , and both promote poverty through effects on education , economic productivity and disability .", "In Ethiopia , little research on podoconiosis has been conducted an...	2013
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "reverse transcriptase-polymerase chain reaction", "dengue virus", "medicine and health sciences", "enzyme-linked immunoassays", "pathology and laboratory medicine", "pathogens", "immunology", "tropical diseases", "vector-borne diseases", "microbiology", "organisms", "viruses", "research des...	Immune status alters the probability of apparent illness due to dengue virus infection: Evidence from a pooled analysis across multiple cohort and cluster studies	journal.pntd.0005926	null	[ [ "Dengue is an important vector-borne disease found across much of the world [1] .", "The four dengue virus serotypes have complex immunological interactions whereby infection with one serotype is thought to lead to a period of short-term protective immunity against all serotypes , followed by a period in ...	[ "Dengue is an important vector-borne pathogen found across much of the world .", "Many factors complicate our understanding of the relationship between infection with one of the four dengue virus serotypes , and the observed incidence of disease .", "One of the factors is a large proportion of infections appear...	[ "Dengue disease severity is known to vary widely from the very severe to asymptomatic .", "There is a wide range of estimates of how many infections result in each of these outcomes .", "It is known that after a first infection the outcome of a second infection with a different serotype varies over time , but t...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "meiosis", "chromosome structure and function", "microbiology", "model organisms", "cell division", "dna", "chromosome biology", "biology", "molecular biology", "biochemistry", "cell biology", "nucleic acids", "yeast and fungal models", "dna repair", "dna recombination", "molecular cel...	The Ecm11-Gmc2 Complex Promotes Synaptonemal Complex Formation through Assembly of Transverse Filaments in Budding Yeast	journal.pgen.1003194	null	[ [ "Meiosis is a special type of cell cycle necessary for sexual reproduction [1] .", "During meiosis , a diploid cell undergoes one round of DNA replication followed by two rounds of successive nuclear segregation , meiosis I and meiosis II respectively .", "At meiosis I , homologous chromosomes are seg...	[ "During meiosis , homologous chromosomes pair at close proximity to form the synaptonemal complex ( SC ) .", "This association is mediated by transverse filament proteins that hold the axes of homologous chromosomes together along their entire length .", "Transverse filament proteins are highly aggregative and ...	[ "Meiosis is central to the life cycle of sexually reproducing organisms .", "The first round of division ( meiosis I ) is unique to meiosis in that homologous chromosomes are segregated to opposite poles .", "The tight association between homologous chromosomes is essential for their faithful segregation .", ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "computational biology/systems biology", "microbiology" ]	Transcriptome and Proteome Exploration to Model Translation Efficiency and Protein Stability in Lactococcus lactis	journal.pcbi.1000606	null	[ [ "In the era of “omics” , systems biology has emerged with the availability of genome-wide data from different levels , i . e . genome , transcriptome , proteome , metabolome [1] , [2] .", "This approach aims at integrating omics data , mainly through computational and mathematical models [3] , [4] so as t...	[ "This genome-scale study analysed the various parameters influencing protein levels in cells .", "To achieve this goal , the model bacterium Lactococcus lactis was grown at steady state in continuous cultures at different growth rates , and proteomic and transcriptomic data were thoroughly compared .", "Ratios ...	[ "This work is in the field of systems biology .", "Via an in-depth comparison of proteomic and transcriptomic data in various culture conditions , our objective was to better understand the regulation of protein levels .", "We have demonstrated that bacteria exert a tight control on intracellular protein levels...	2009
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "immunopathology", "medicine", "infectious diseases", "parasitic diseases", "immunity", "leishmaniasis", "neglected tropical diseases", "immunology", "biology", "microbiology", "immunoregulation", "immunomodulation", "immune response" ]	Involvement of CD4+ Foxp3+ Regulatory T Cells in Persistence of Leishmania donovani in the Liver of Alymphoplastic aly/aly Mice	journal.pntd.0001798	null	[ [ "Visceral leishmaniasis ( VL ) is a chronic and fatal disease caused by the intracellular protozoan parasites Leishmania donovani and L . infantum ( chagasi ) , which infect a range of mammalian hosts , including humans , dogs and rodents [1] .", "Liver , spleen , bone marrow ( BM ) and lymph nodes are th...	[ "Visceral leishmaniasis ( VL ) is a chronic and fatal disease in humans and dogs caused by the intracellular protozoan parasites , Leishmania donovani and L . infantum ( L . chagasi ) .", "Relapse of disease is frequent in immunocompromised patients , in which the number of VL cases has been increasing recently ....	[ "The protozoan parasite Leishmania donovani is the causative agent of visceral leishmaniasis ( VL ) with a variety of outcomes ranging from asymptomatic to fatal infection .", "In the last decade , an increasing number of VL cases in immunocompromised conditions have been reported .", "Loss of the control of pa...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "hepatitis c", "medicine", "infectious diseases", "hepatitis", "virology", "biology", "microbiology", "viral replication", "viral packaging", "viral replication complex", "viral diseases" ]	Analysis of Functional Differences between Hepatitis C Virus NS5A of Genotypes 1–7 in Infectious Cell Culture Systems	journal.ppat.1002696	null	[ [ "Hepatitis C virus ( HCV ) chronically infects 130–170 million people and leads to increased risk of severe liver disease .", "HCV belongs to the Flaviviridae family and has a positive-strand RNA genome containing one long open reading frame ( ORF ) .", "The ORF encodes a polyprotein that is co- and p...	[ "Hepatitis C virus ( HCV ) is an important cause of chronic liver disease .", "Several highly diverse HCV genotypes exist with potential key functional differences .", "The HCV NS5A protein was associated with response to interferon ( IFN ) -α based therapy , and is a primary target of currently developed direc...	[ "Hepatitis C virus ( HCV ) is a major public health burden and leads to chronic liver disease , including liver cirrhosis and liver cancer .", "Understanding the biological functions of the virus is crucial to the development of a vaccine and to improve current therapy through development of directly-acting antiv...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "stiffness", "mechanical properties", "cell motility", "chemical bonding", "actin filaments", "classical mechanics", "cell processes", "molecular strains", "mechanical energy", "materials science", "physical chemistry", "contractile proteins", "actins", "proteins", "chemistry", "cross-...	Structural organization and energy storage in crosslinked actin assemblies	journal.pcbi.1006150	null	[ [ "The cytoskeleton protein actin assembles into three major structures in yeast cells , including endocytic actin patches , actin cables , and the contractile ring [1 , 2] .", "In actin cables and the contractile ring , formin-nucleated actin filaments are crosslinked into long bundles with a length on the...	[ "During clathrin-mediated endocytosis in yeast cells , short actin filaments ( < 200nm ) and crosslinking protein fimbrin assemble to drive the internalization of the plasma membrane .", "However , the organization of the actin meshwork during endocytosis remains largely unknown .", "In addition , only a small ...	[ "In many cellular processes that involve the deformation of membranes or the movement of vesicles and organelles , the energy from biochemical reactions is converted into forces .", "The biological filaments called actin are one of the major force producing machineries of the cell .", "It is commonly believed t...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Human Non-neutralizing HIV-1 Envelope Monoclonal Antibodies Limit the Number of Founder Viruses during SHIV Mucosal Infection in Rhesus Macaques	journal.ppat.1005042	null	[ [ "The induction of HIV-1 broadly reactive neutralizing antibodies ( bnAbs ) by experimental vaccines is a critical goal of HIV-1 vaccine development efforts .", "However , bnAbs cannot be induced by existing HIV-1 vaccine candidates [1] .", "The RV144 ALVAC/AIDSVAX B/E HIV-1 vaccine efficacy trial demo...	[ "HIV-1 mucosal transmission begins with virus or virus-infected cells moving through mucus across mucosal epithelium to infect CD4+ T cells .", "Although broadly neutralizing antibodies ( bnAbs ) are the type of HIV-1 antibodies that are most likely protective , they are not induced with current vaccine candidate...	[ "Antibodies specifically recognize antigenic sites on pathogens and can mediate multiple antiviral functions through engagement of effector cells via their Fc region .", "Current HIV-1 vaccine candidates induce polyclonal antibody responses with multiple antiviral functions , but do not induce broadly neutralizin...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell death", "invertebrates", "neurobiology of disease and regeneration", "medicine and health sciences", "rna interference", "cancer treatment", "cell processes", "animals", "pleurae", "animal models", "oncology", "developmental biology", "drosophila melanogaster", "model organisms", "...	Ionizing radiation induces stem cell-like properties in a caspase-dependent manner in Drosophila	journal.pgen.1007659	null	[ [ "Regeneration is essential to tissue homeostasis and health .", "Conversely , regeneration of tumors after treatment leads to tumor recurrence and treatment failure .", "Understanding mechanisms that underlie regeneration is therefore important not only for understanding basic biology but also for opt...	[ "Cancer treatments including ionizing radiation ( IR ) can induce cancer stem cell-like properties in non-stem cancer cells , an outcome that can interfere with therapeutic success .", "Yet , we understand little about what consequences of IR induces stem cell like properties and why some cancer cells show this r...	[ "Ionizing Radiation ( IR ) , alone or in combination with other therapies , is used to treat an estimated half of all cancer patients .", "Yet , we understand little about why some tumors cells respond to treatment while others grow back ( regenerate ) .", "We identified specific pools of cells within a Drosoph...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases", "medicine and health sciences", "biology and life sciences", "malaria", "parasitic diseases" ]	A Cysteine Protease Inhibitor of Plasmodium berghei Is Essential for Exo-erythrocytic Development	journal.ppat.1004336	null	[ [ "Every year over 200 million people suffer from malaria infection worldwide , with an estimated 655 , 000 deaths annually ( WHO , 2011 ) .", "The causative agent of malaria is the unicellular parasite Plasmodium that belongs to the phylum Apicomplexa .", "Much effort has been made to develop drugs aga...	[ "Plasmodium parasites express a potent inhibitor of cysteine proteases ( ICP ) throughout their life cycle .", "To analyze the role of ICP in different life cycle stages , we generated a stage-specific knockout of the Plasmodium berghei ICP ( PbICP ) .", "Excision of the pbicb gene occurred in infective sporozo...	[ "Coordinated protease activity is essential to parasite survival .", "Throughout its life cycle , the Plasmodium parasite expresses a potent cysteine protease inhibitor that has the potential to inhibit parasite as well as host cell cysteine proteases .", "We have generated a stage-specific knockout of this inh...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "infographics", "sequencing techniques", "vertebrates", "dogs", "animals", "mammals", "alternative splicing", "genome analysis", "molecular biology techniques", "mammalian genomics", "rna sequencing", "animal management", "animal performance", "research and analysis methods", "computer a...	BinPacker: Packing-Based De Novo Transcriptome Assembly from RNA-seq Data	journal.pcbi.1004772	null	[ [ "The advent of RNA-seq techniques are changing how transcription , splicing variations and associated mechanisms can be studied since they provide unprecedented accuracy about the mRNA expression level [1] .", "They allow accurate elucidation of all splicing variants , including the rare and lowly express...	[ "High-throughput RNA-seq technology has provided an unprecedented opportunity to reveal the very complex structures of transcriptomes .", "However , it is an important and highly challenging task to assemble vast amounts of short RNA-seq reads into transcriptomes with alternative splicing isoforms .", "In this ...	[ "The availability of RNA-seq technology drives the development of algorithms for transcriptome assembly from very short RNA sequences .", "However , the problem of how to ( de novo ) assemble transcriptome using RNA-seq datasets has not been modeled well; e . g . sequence coverage information has even not been ac...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "chromosome structure and function", "microbiology", "telomeres", "model organisms", "molecular genetics", "chromatin", "chromosome biology", "biology", "cell biology", "genetic screens", "genetics", "yeast and fungal models", "saccharomyces cerevisiae", "molecular cell biology", "geneti...	Rif2 Promotes a Telomere Fold-Back Structure through Rpd3L Recruitment in Budding Yeast	journal.pgen.1002960	null	[ [ "The physical ends of linear chromosomes resemble double-strand breaks ( DSBs ) in many respects with the exception that DSBs result in the activation of the DNA damage response and are eventually subject to repair; activities to which telomeres are refractory [1] .", "This essential quality of telomeres ...	[ "Using a genome-wide screening approach , we have established the genetic requirements for proper telomere structure in Saccharomyces cerevisiae .", "We uncovered 112 genes , many of which have not previously been implicated in telomere function , that are required to form a fold-back structure at chromosome ends...	[ "Impaired telomere elongation eventually results in telomere dysfunction and can lead to diseases such as dyskeratosis congenita , which is associated with bone-marrow failure and pulmonary fibrosis .", "Cancer cells require continuous telomere maintenance to ensure continued cellular proliferation .", "Therefo...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "flow cytometry", "complement system", "medicine and health sciences", "immune physiology", "enzyme-linked immunoassays", "pathology and laboratory medicine", "pathogens", "immunology", "microbiology", "bacterial diseases", "enterobacteriaceae", "antibodies", "immunologic techniques", "bac...	Bactericidal Immunity to Salmonella in Africans and Mechanisms Causing Its Failure in HIV Infection	journal.pntd.0004604	null	[ [ "African clades of nontyphoidal Salmonella ( NTS ) , particularly S . enterica serovars Typhimurium and Enteritidis , are a major cause of bacteremia in sub-Saharan Africa [1 , 2] .", "Case fatality rates are around 20–25% [1] , and up to 47% in HIV-infected adults [3] prior to the availability of antiret...	[ "Nontyphoidal strains of Salmonella are a leading cause of death among HIV-infected Africans .", "Antibody-induced complement-mediated killing protects healthy Africans against Salmonella , but increased levels of anti-lipopolysaccharide ( LPS ) antibodies in some HIV-infected African adults block this killing ."...	[ "Bacteremia caused by nontyphoidal Salmonellae are a major health burden in Africa .", "While antibody-induced complement-mediated killing protects healthy Africans against Salmonella , increased levels of anti-LPS antibodies in some HIV-infected Africans block this killing .", "Little is known about the mechan...	2016
[ "Introduction", "Results and Discussion", "Materials and Methods" ]	[]	Structural Determinants of Phenotypic Diversity and Replication Rate of Human Prions	journal.ppat.1004832	null	[ [ "Prions are a novel class of infectious agents that are composed solely of self-replicating misfolded protein aggregates [1] .", "In mammals , prions cause a group of invariably fatal and rapidly progressive neurodegenerative diseases , originally described as transmissible spongiform encephalopathies ( T...	[ "The infectious pathogen responsible for prion diseases is the misfolded , aggregated form of the prion protein , PrPSc .", "In contrast to recent progress in studies of laboratory rodent-adapted prions , current understanding of the molecular basis of human prion diseases and , especially , their vast phenotypic...	[ "Sporadic Creutzfeldt-Jakob disease ( sCJD ) represents ~90% of all human prion diseases worldwide .", "This neurodegenerative disease , which is transmissible and invariably fatal , is characterized by variable progression rates and remarkable diversity of clinical and pathological traits .", "The infectious s...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular biology/bioinformatics", "genetics and genomics/epigenetics", "genetics and genomics/comparative genomics", "evolutionary biology/evolutionary and comparative genetics" ]	Evolutionary Breakpoints in the Gibbon Suggest Association between Cytosine Methylation and Karyotype Evolution	journal.pgen.1000538	null	[ [ "Gibbons ( Hylobatidae ) are small arboreal apes that inhabit the tropical and semi-deciduous forests of Southeast Asia and a portion of South- and East-Asia; their closest relatives are the great apes ( human , chimpanzee , gorilla and orangutan ) .", "They are an excellent model in which to study mechan...	[ "Gibbon species have accumulated an unusually high number of chromosomal changes since diverging from the common hominoid ancestor 15–18 million years ago .", "The cause of this increased rate of chromosomal rearrangements is not known , nor is it known if genome architecture has a role .", "To address this que...	[ "Mammalian genomes are remarkably stable ( with few exceptions ) .", "In humans , wrong recombination events occur quite rarely , manifesting themselves in genomic disorders or cancer .", "On exceptional occasions , the rate of genome evolution has been accelerated by genome-wide reshuffling events giving rise ...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Protective mAbs and Cross-Reactive mAbs Raised by Immunization with Engineered Marburg Virus GPs	journal.ppat.1005016	null	[ [ "Filoviruses are filamentous , enveloped viruses that can cause highly lethal hemorrhagic fever in both humans and non-human primates .", "The filovirus family includes the major genera ebolavirus and marburgvirus and the newly discovered cuevavirus .", "In the ebolavirus genus are five known species:...	[ "The filoviruses , which include the marburg- and ebolaviruses , have caused multiple outbreaks among humans this decade .", "Antibodies against the filovirus surface glycoprotein ( GP ) have been shown to provide life-saving therapy in nonhuman primates , but such antibodies are generally virus-specific .", "M...	[ "The filoviruses have caused multiple outbreaks among humans this decade , including a 90% lethal outbreak of Marburg virus in Angola and a significant , sustained outbreak of Ebola virus in West Africa .", "The viral surface glycoprotein ( GP ) , which enables filoviruses to infect host cells , is the primary ta...	2015
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "cell biology/membranes and sorting", "microbiology/cellular microbiology and pathogenesis" ]	SNARE Protein Mimicry by an Intracellular Bacterium	journal.ppat.1000022	null	[ [ "Chlamydia are obligate intracellular bacterial pathogens of eukaryotic cells .", "They infect a variety of animals , including humans , and cause acute and chronic diseases [1]–[3] .", "Chlamydia replicate primarily within epithelial cells , in a membrane-bound compartment called the inclusion .", ...	[ "Many intracellular pathogens rely on host cell membrane compartments for their survival .", "The strategies they have developed to subvert intracellular trafficking are often unknown , and SNARE proteins , which are essential for membrane fusion , are possible targets .", "The obligate intracellular bacteria C...	[ "Chlamydiae are obligate intracellular bacteria that have co-evolved with eukaryotic cells and adapted to a wide range of hosts , causing several diseases in humans and animals .", "For example , one species pathogenic to humans , Chlamydia trachomatis , is the leading cause of preventable blindness and of bacter...	2008
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "body fluids", "tropical diseases", "dna-binding proteins", "parasitic diseases", "animals", "parasitology", "urine", "polymerases", "neglected tropical diseases", "molecular biology techniques", "strongyloides stercoralis", "research and an...	Strong-LAMP: A LAMP Assay for Strongyloides spp. Detection in Stool and Urine Samples. Towards the Diagnosis of Human Strongyloidiasis Starting from a Rodent Model	journal.pntd.0004836	null	[ [ "Strongyloidiasis , a soil-transmitted helminth human infection , is considered by World Health Organization ( WHO ) as a neglected condition affecting an estimated 30–100 million people worldwide [1] .", "The accuracy of these estimates remains actually uncertain due to lack of efficient guidelines for s...	[ "Strongyloides stercoralis , the chief causative agent of human strongyloidiasis , is a nematode globally distributed but mainly endemic in tropical and subtropical regions .", "Chronic infection is often clinically asymptomatic but it can result in severe hyperinfection syndrome or disseminated strongyloidiasis ...	[ "Human strongyloidiasis , a soil-transmitted infection mainly caused by Strongyloides stercoralis , is one of the most neglected among the so-called neglected tropical diseases ( NTDs ) .", "The difficult diagnosis lead to an underreporting of infection rates .", "Strongyloidiasis can easily be misdiagnosed bec...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Rescue of DNA-PK Signaling and T-Cell Differentiation by Targeted Genome Editing in a prkdc Deficient iPSC Disease Model	journal.pgen.1005239	null	[ [ "Studying the molecular pathology of human disease is often difficult due to the limited availability of particular primary cells , their limited lifespan , or because complex developmental differentiation procedures cannot be easily followed in vivo .", "In vitro disease modeling with induced pluripotent...	[ "In vitro disease modeling based on induced pluripotent stem cells ( iPSCs ) provides a powerful system to study cellular pathophysiology , especially in combination with targeted genome editing and protocols to differentiate iPSCs into affected cell types .", "In this study , we established zinc-finger nuclease-...	[ "Due to the limited availability and lifespan of some primary cells , in vitro disease modeling with induced pluripotent stem cells ( iPSCs ) offers a valuable complementation to in vivo studies .", "The goal of our study was to establish an in vitro disease model for severe combined immunodeficiency ( SCID ) , a...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics", "epigenetics", "biology", "chromatin", "genetics and genomics" ]	Drosophila Yemanuclein and HIRA Cooperate for De Novo Assembly of H3.3-Containing Nucleosomes in the Male Pronucleus	journal.pgen.1003285	null	[ [ "Assembly of octameric nucleosomes in eukaryotic chromatin is a stepwise process where deposition of a histone H3-H4 heterotetramer precedes incorporation of two H2A-H2B dimers [1] .", "While the bulk of de novo chromatin assembly occurs during genome replication and mainly involves canonical histone H3 ,...	[ "The differentiation of post-meiotic spermatids in animals is characterized by a unique reorganization of their nuclear architecture and chromatin composition .", "In many species , the formation of sperm nuclei involves the massive replacement of nucleosomes with protamines , followed by a phase of extreme nucle...	[ "Chromosome organization relies on a basic functional unit called the nucleosome , in which DNA is wrapped around a core of histone proteins .", "However , during male gamete formation , the majority of histones are replaced by sperm-specific proteins that are adapted to sexual reproduction but incompatible with ...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "computational neuroscience", "biology", "neuroscience", "coding mechanisms" ]	Coding and Decoding with Adapting Neurons: A Population Approach to the Peri-Stimulus Time Histogram	journal.pcbi.1002711	null	[ [ "Encoding and decoding of information with populations of neurons is a fundamental question of computational neuroscience [1]–[3] .", "A time-varying stimulus can be encoded in the active fraction of a population of neurons , a coding procedure that we will refer to as population coding ( Fig . 1 ) .", ...	[ "The response of a neuron to a time-dependent stimulus , as measured in a Peri-Stimulus-Time-Histogram ( PSTH ) , exhibits an intricate temporal structure that reflects potential temporal coding principles .", "Here we analyze the encoding and decoding of PSTHs for spiking neurons with arbitrary refractoriness an...	[ "How can information be encoded and decoded in populations of adapting neurons ?", "A quantitative answer to this question requires a mathematical expression relating neuronal activity to the external stimulus , and , conversely , stimulus to neuronal activity .", "Although widely used equations and models exis...	2012
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "antimicrobials", "organismal evolution", "medicine and health sciences", "ecology and environmental sciences", "soil ecology", "parasite evolution", "drugs", "microbiology", "parasitology", "simulation and modeling", "systems science", "mathematics", "antibiotics", "microbial evolution", ...	Spatial dynamics of synthetic microbial mutualists and their parasites	journal.pcbi.1005689	null	[ [ "The evolution of complexity is largely grounded in the emergence of new forms of cooperation capable of holding together higher-order entities from simpler ones .", "Cooperative interactions have played a great role in the so-called major transitions in evolution [1] .", "Cooperation pervades the ris...	[ "A major force contributing to the emergence of novelty in nature is the presence of cooperative interactions , where two or more components of a system act in synergy , sometimes leading to higher-order , emergent phenomena .", "Within molecular evolution , the so called hypercycle defines the simplest model of ...	[ "In order to achieve greater levels of complexity , complex systems often display cooperative interactions that enable the formation and stabilisation of mutualisms .", "Theoretical models have shown that closed chains of cooperative species or hypercycles might have been crucial in the evolution towards complexi...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "bacteriology", "public health and epidemiology", "infectious disease epidemiology", "microbiology", "spatial epidemiology", "emerging infectious diseases", "microbial evolution", "population biology", "bacterial pathogens", "genetic epidemiology", "epidemiology", "microbial pathogens", "bio...	Phylogeography and Molecular Epidemiology of Yersinia pestis in Madagascar	journal.pntd.0001319	null	[ [ "Throughout recorded history , Yersinia pestis , etiologic agent of plague , has spread multiple times from foci in Central Asia in greatly widening swaths as human-mediated transport became more efficient [1] .", "Plague attained its current global distribution during the current “third” pandemic , which...	[ "Plague was introduced to Madagascar in 1898 and continues to be a significant human health problem .", "It exists mainly in the central highlands , but in the 1990s was reintroduced to the port city of Mahajanga , where it caused extensive human outbreaks .", "Despite its prevalence , the phylogeography and mo...	[ "Plague , caused by the bacterium Yersinia pestis , has been a problem in Madagascar since it was introduced in 1898 .", "It mainly affects the central highlands , but also has caused several large outbreaks in the port city of Mahajanga , after it was reintroduced there in the 1990s .", "Despite its prevalence...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "model organisms", "genetics", "biology", "microbiology" ]	Anthranilate Fluorescence Marks a Calcium-Propagated Necrotic Wave That Promotes Organismal Death in C. elegans	journal.pbio.1001613	Death of the nematode Caenorhabditis elegans involves a conserved necrotic cell death cascade which generates endogenous blue anthranilate fluorescence, allowing death to be visualized.	[ [ "While mechanisms of cell death such as apoptosis are well characterized [1] , less is known about the mechanisms of organismal death , particularly in invertebrate model organisms .", "Here we investigate organismal death in the nematode C . elegans , using a newly discovered , endogenous fluorescent mar...	[ "For cells the passage from life to death can involve a regulated , programmed transition .", "In contrast to cell death , the mechanisms of systemic collapse underlying organismal death remain poorly understood .", "Here we present evidence of a cascade of cell death involving the calpain-cathepsin necrosis pa...	[ "In the nematode Caenorhabditis elegans , intestinal lysosome-related organelles ( or “gut granules” ) contain a bright blue fluorescent substance of unknown identity .", "This has similar spectral properties to lipofuscin , a product of oxidative damage known to accumulate with age in postmitotic mammalian cells...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	A Novel Actin mRNA Splice Variant Regulates ACTG1 Expression	journal.pgen.1003743	null	[ [ "All mammals express six isoforms of actin: α-cardiac ( Actc1 , NM_009608 ) , α-skeletal ( Acta1 , NM_009606 ) , α-aortic ( Acta2 , NM_007392 ) , γ-enteric ( Actg2 , NM_009610 ) , β-cytoplasmic ( Actb , NM_007393 ) , and γ-cytoplasmic ( Actg1 , NM_009609 ) .", "Each actin is encoded on a separate chromoso...	[ "Cytoplasmic actins are abundant , ubiquitous proteins in nucleated cells .", "However , actin expression is regulated in a tissue- and development-specific manner .", "We identified a novel cytoplasmic-γ-actin ( Actg1 ) transcript that includes a previously unidentified exon ( 3a ) .", "Inclusion of this exo...	[ "Actin is a well-studied protein that plays an essential role in nearly all cell types .", "Cytoplasmic actins are considered to be ubiquitously expressed in most tissues of the body with the exception of developing skeletal muscle , where muscle specific actins are up-regulated and γ-actin is repressed .", "In...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "innate immune system", "medicine and health sciences", "immune cells", "immune physiology", "cytokines", "spleen", "immunology", "microbiology", "cloning", "developmental biology", "molecular development", "molecular biology techniques", "cytotoxic t cells", "digestive sy...	Cytomegalovirus-Specific IL-10-Producing CD4+ T Cells Are Governed by Type-I IFN-Induced IL-27 and Promote Virus Persistence	journal.ppat.1006050	null	[ [ "Human cytomegalovirus ( HCMV ) is a ubiquitous β-herpesvirus that establishes lifelong infection .", "Infectious virus is usually acquired by horizontal transmission via mucosal secretions and urine .", "HCMV infection is typically asymptomatic in healthy individuals .", "However in the immunocom...	[ "CD4+ T cells support host defence against herpesviruses and other viral pathogens .", "We identified that CD4+ T cells from systemic and mucosal tissues of hosts infected with the β-herpesviridae human cytomegalovirus ( HCMV ) or murine cytomegalovirus ( MCMV ) express the regulatory cytokine interleukin ( IL ) ...	[ "Viruses including the pathogenic β-herpesvirus human cytomegalovirus ( HCMV ) can replicate within and disseminate from mucosal tissues .", "Understanding how to improve antiviral immune responses to restrict virus replication in the mucosa could help counter virus transmission .", "Studies in the murine cytom...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "diabetes and endocrinology" ]	Genetic Deficiency of Glycogen Synthase Kinase-3β Corrects Diabetes in Mouse Models of Insulin Resistance	journal.pbio.0060037	The insulin signaling pathway negatively regulates glycogen synthase kinase 3. The current studies demonstrate that this enzyme is rate limiting for pancreatic β-cell replication and survival.	[ [ "Despite treatment with agents that enhance β-cell function and insulin action , reduction in β-cell mass is relentless in type 2 diabetes ( T2DM ) [1–4] .", "Why β-cells fail in some individuals is a central issue in diabetes research today .", "The molecular mechanisms enabling β-cell adaptation to ...	[ "Despite treatment with agents that enhance β-cell function and insulin action , reduction in β-cell mass is relentless in patients with insulin resistance and type 2 diabetes mellitus .", "Insulin resistance is characterized by impaired signaling through the insulin/insulin receptor/insulin receptor substrate/PI...	[ "Diabetes is often characterized by a failure of insulin production by pancreatic β-cells to properly regulate glucose homeostasis .", "Insulin resistance can lead to β-cell failure , and our studies have focused on elucidating the mechanisms involved in this postnatal failure .", "In this study , we evaluated ...	2008
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "microbial pathogens", "host-pathogen interaction", "biology", "microbiology", "pathogenesis" ]	Adhesins of Leptospira interrogans Mediate the Interaction to Fibrinogen and Inhibit Fibrin Clot Formation In Vitro	journal.pntd.0002396	null	[ [ "The spirochete Leptospira interrogans is a highly invasive pathogen and the causal agent of leptospirosis , one of the most widespread zoonosis of human and veterinary concern [1] , [2] .", "The transmission occurs through contact with environmental water contaminated by leptospires shed in the urine of ...	[ "We report in this work that Leptospira strains , virulent L . interrogans serovar Copenhageni , attenuated L . interrogans serovar Copenhageni and saprophytic L . biflexa serovar Patoc are capable of binding fibrinogen ( Fg ) .", "The interaction of leptospires with Fg inhibits thrombin- induced fibrin clot form...	[ "Leptospirosis is probably the most widespread zoonosis in the world .", "Caused by spirochaetes of the genus Leptospira , it has greater incidence in tropical and subtropical regions .", "The disease has become prevalent in cities with sanitation problems and a large population of urban rodent reservoirs , whi...	2013
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "cancer detection and diagnosis", "medicine and health sciences", "lymphatic mapping", "cost-effectiveness analysis", "education", "economic analysis", "sociology", "geographical locations", "tropical diseases", "social sciences", "parasitic diseases", "ethnicities", "oncology", "filariasi...	The rationale and cost-effectiveness of a confirmatory mapping tool for lymphatic filariasis: Examples from Ethiopia and Tanzania	journal.pntd.0005944	null	[ [ "Endemicity mapping is the essential first step for countries striving to eliminate neglected tropical diseases .", "For lymphatic filariasis ( LF ) , a parasitic disease targeted by the World Health Organization ( WHO ) for elimination as a public health problem by 2020 [1] , endemicity mapping ( or ‘map...	[ "Endemicity mapping is required to determining whether a district requires mass drug administration ( MDA ) .", "Current guidelines for mapping LF require that two sites be selected per district and within each site a convenience sample of 100 adults be tested for antigenemia or microfilaremia .", "One or more ...	[ "Mapping is used by lymphatic filariasis ( LF ) elimination programs to determine if mass drug administration ( MDA ) is required .", "The current mapping approach , designed to be simple and practical , has worked well in high-prevalence settings but concerns about its reliability in low-prevalence settings have...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "cell death", "autophagic cell death", "medicine and health sciences", "viral transmission and infection", "cell processes", "vector-borne diseases", "microbiology", "light microscopy", "viral structure", "rice", "microscopy", "experimental organism systems", "insect vectors", "plants", ...	Autophagy pathway induced by a plant virus facilitates viral spread and transmission by its insect vector	journal.ppat.1006727	null	[ [ "Many viral pathogens that cause significant global health and agricultural problems are transmitted via insect vectors .", "To maximize transmission efficiency , viruses generally can modulate the biology and behavior of their vectors [1 , 2] .", "Many arthropod-borne animal viruses ( arboviruses ) a...	[ "Many viral pathogens are persistently transmitted by insect vectors and cause agricultural or health problems .", "Generally , an insect vector can use autophagy as an intrinsic antiviral defense mechanism against viral infection .", "Whether viruses can evolve to exploit autophagy to promote their transmissio...	[ "Of the approximately 700 plant viruses , more than 75% are transmitted by insect vectors .", "However , the detailed mechanisms underlying the cellular responses induced by viral infection in insect vectors are poorly understood .", "We found that a plant reovirus could activate the autophagic process during p...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "action potentials", "medicine and health sciences", "neural networks", "nervous system", "membrane potential", "electrophysiology", "neuroscience", "mathematics", "phase diagrams", "algebra", "network analysis", "computer and information sciences", "animal cells", "cellular neuroscience",...	Firing rate equations require a spike synchrony mechanism to correctly describe fast oscillations in inhibitory networks	journal.pcbi.1005881	null	[ [ "Since the seminal work of Wilson and Cowan [1] , population models of neuronal activity have become a standard tool of analysis in computational neuroscience .", "Rather than focus on the microscopic dynamics of neurons , these models describe the collective properties of large numbers of neurons , typic...	[ "Recurrently coupled networks of inhibitory neurons robustly generate oscillations in the gamma band .", "Nonetheless , the corresponding Wilson-Cowan type firing rate equation for such an inhibitory population does not generate such oscillations without an explicit time delay .", "We show that this discrepancy...	[ "Population models describing the average activity of large neuronal ensembles are a powerful mathematical tool to investigate the principles underlying cooperative function of large neuronal systems .", "However , these models do not properly describe the phenomenon of spike synchrony in networks of neurons .", ...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "action potentials", "medicine and health sciences", "nervous system", "membrane potential", "brain", "electrophysiology", "neuroscience", "synaptic plasticity", "cerebellum", "eyes", "sensory physiology", "developmental neuroscience", "cerebral cortex", "animal cells", "head", "visual...	Spike burst-pause dynamics of Purkinje cells regulate sensorimotor adaptation	journal.pcbi.1006298	null	[ [ "The cerebellum controls fine motor coordination including online adjustments of eye movements [1] .", "Within the cerebellar cortex , the inhibitory projections of Purkinje cells to medial vestibular nuclei ( MVN ) mediate the acquisition of accurate oculomotor control [2 , 3] .", "Here , we consider...	[ "Cerebellar Purkinje cells mediate accurate eye movement coordination .", "However , it remains unclear how oculomotor adaptation depends on the interplay between the characteristic Purkinje cell response patterns , namely tonic , bursting , and spike pauses .", "Here , a spiking cerebellar model assesses the r...	[ "Cerebellar Purkinje cells regulate accurate eye movement coordination .", "However , it remains unclear how cerebellar-dependent oculomotor adaptation depends on the interplay between Purkinje cell characteristic response patterns: tonic , high frequency bursting , and post-complex spike pauses .", "We explore...	2019
[ "Introduction", "Results", "Discussion", "Materials and methods", "Relationship in expression level between protein complex genes and linker histone genes across tissues" ]	[ "dna-binding proteins", "genetic mapping", "epigenetics", "mammalian genomics", "chromatin", "chromosome biology", "proteins", "gene expression", "autosomes", "chromosome pairs", "histones", "genetic loci", "animal genomics", "biochemistry", "protein complexes", "cell biology", "here...	Chromosome-wide co-fluctuation of stochastic gene expression in mammalian cells	journal.pgen.1008389	null	[ [ "Gene expression is subject to considerable stochasticity that is known as expression noise , formally defined as the expression variation of a given gene among isogenic cells in the same environment [1–3] .", "Gene expression noise is a double-edged sword .", "On the one hand , it can be deleterious ...	[ "Gene expression is subject to stochastic noise , but to what extent and by which means such stochastic variations are coordinated among different genes are unclear .", "We hypothesize that neighboring genes on the same chromosome co-fluctuate in expression because of their common chromatin dynamics , and verify ...	[ "Gene expression is subject to substantial stochastic noise or fluctuation .", "We hypothesize that expressions of neighboring genes on the same chromosome co-fluctuate because of their common chromatin dynamics .", "To test this hypothesis , we make use of the fact that each diploid cell contains a maternal an...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	ARID1A Is Essential for Endometrial Function during Early Pregnancy	journal.pgen.1005537	null	[ [ "Endometriosis is one of the most significant diseases affecting females of reproductive-age and affects an estimated 5 million women in the United States .", "Endometriosis is defined as the presence of endometrium-like tissue outside of the uterine cavity .", "The incidence increases up to 50% in pa...	[ "AT-rich interactive domain 1A gene ( ARID1A ) loss is a frequent event in endometriosis-associated ovarian carcinomas .", "Endometriosis is a disease in which tissue that normally grows inside the uterus grows outside the uterus , and 50% of women with endometriosis are infertile .", "ARID1A protein levels wer...	[ "Endometriosis afflicts about 10% of women of reproductive age and is a major cause of pain and infertility .", "We showed attenuation of endometrial ARID1A in women with endometriosis as compared to women without endometriosis , and thus hypothesized that ARID1A plays an important role in ensuring normal fertili...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "invertebrates", "crystal structure", "condensed matter physics", "dna-binding proteins", "vertebrates", "animals", "notch signaling", "mammals", "dna transcription", "animal models", "drosophila melanogaster", "model organisms", "protein structure", "amniotes", "dna", "dna structure",...	Structure and Function of the Su(H)-Hairless Repressor Complex, the Major Antagonist of Notch Signaling in Drosophila melanogaster	journal.pbio.1002509	The transcription factor CSL regulates gene expression in response to Notch pathway signaling. The X-ray structure of the complex between the fruit fly version of CSL, Su(H), and its antagonist, Hairless, reveals a novel binding mode and unanticipated structural plasticity.	[ [ "The Notch pathway is a highly conserved cell-to-cell signaling mechanism that is essential for cell fate decisions during embryogenesis and postnatal tissue homeostasis [1] .", "In humans , aberrant Notch signaling underlies the pathogenesis of many diseases , including certain types of cancer [2] , cong...	[ "Notch is a conserved signaling pathway that specifies cell fates in metazoans .", "Receptor-ligand interactions induce changes in gene expression , which is regulated by the transcription factor CBF1/Su ( H ) /Lag-1 ( CSL ) .", "CSL interacts with coregulators to repress and activate transcription from Notch t...	[ "Notch signaling is a form of cell-to-cell communication , in which extracellular receptor-ligand interactions ultimately result in changes in gene expression .", "The Notch pathway is highly conserved from the model organism Drosophila melanogaster to humans .", "When mutations occur within Notch pathway compo...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Anthelmintic Activity In Vivo of Epiisopiloturine against Juvenile and Adult Worms of Schistosoma mansoni	journal.pntd.0003656	null	[ [ "Schistosomiasis is a disease mainly found in tropical regions , whose infectious agents are Schistosoma spp .", ", including Schistosoma mansoni [1] .", "This disease is currently one of the most widely occurring neglected tropical diseases with high levels of incidence in Asia , Africa and Latin Ame...	[ "Schistosomiasis is a serious disease currently estimated to affect more that 207 million people worldwide .", "Due to the intensive use of praziquantel , there is increasing concern about the development of drug-resistant strains .", "Therefore , it is necessary to search for and investigate new potential schi...	[ "Schistosomiasis , a disease caused by worms from the genus Schistosoma , is one of the most widespread neglected tropical diseases in the world .", "Due to the intensive use of praziquantel , some reports of drug resistance have emerged .", "Thus it is important to search for new chemotherapeutic agents for th...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "sequencing techniques", "taxonomy", "organismal evolution", "medicine and health sciences", "pathology and laboratory medicine", "pathogens", "population genetics", "microbiology", "viruses", "phylogenetics", "data management", "rna viruses", "microbial evolution", "molecular biology tech...	Nonstructural Proteins Are Preferential Positive Selection Targets in Zika Virus and Related Flaviviruses	journal.pntd.0004978	null	[ [ "The Flavivirus genus ( family Flaviviridae ) comprises a large number of viral species , many of which are important human pathogens; these include dengue virus ( DENV ) , yellow fever virus ( YFV ) , Japanese encephalitis virus ( JEV ) , West Nile virus ( WNV ) , and the latest emerged pathogen , Zika virus...	[ "The Flavivirus genus comprises several human pathogens such as dengue virus ( DENV ) , Japanese encephalitis virus ( JEV ) , and Zika virus ( ZIKV ) .", "Although ZIKV usually causes mild symptoms , growing evidence is linking it to congenital birth defects and to increased risk of Guillain-Barré syndrome .", ...	[ "Zika virus is mainly transmitted by mosquitoes and is phylogenetically related to other human pathogens ( e . g . dengue virus ) .", "After the outbreak in South America , the WHO declared that the spread of ZIKV should be regarded as a public health emergency .", "In fact , growing evidence suggests that ZIKV...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "public health and epidemiology", "veterinary diseases", "public health", "veterinary science" ]	Clinical Manifestations of Human Brucellosis: A Systematic Review and Meta-Analysis	journal.pntd.0001929	null	[ [ "Brucellosis is one of the most common zoonotic infections globally [1] .", "This bacterial disease causes not only a severely debilitating and disabling illness , but it also has major economic ramifications due to time lost by patients from normal daily activities [2] and losses in animal production [3]...	[ "The objectives of this systematic review , commissioned by WHO , were to assess the frequency and severity of clinical manifestations of human brucellosis , in view of specifying a disability weight for a DALY calculation .", "Thirty three databases were searched , with 2 , 385 articles published between January...	[ "Brucellosis is a bacterial disease transmitted to humans by consumption of infected , unpasteurised animal milk or through direct contact with infected animals , particularly aborted foetuses .", "The livestock production losses resulting from these abortions have a major economic impact on individuals and commu...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "cell biology", "molecular biology" ]	An Endoribonuclease Functionally Linked to Perinuclear mRNP Quality Control Associates with the Nuclear Pore Complexes	journal.pbio.1000008	When errors in messenger RNA processing or packaging occur along the path from the site of transcription to the nuclear pore complex, the conserved RNA-degrading enzyme Swt1 comes into the game.	[ [ "Nuclear export of messenger RNA ( mRNA ) is a fundamental process of eukaryotic gene expression .", "In yeast , newly synthesized pre-mRNAs are cotranscriptionally assembled into messenger ribonucleoprotein particles ( mRNPs ) with the assistance of transcription-export ( TREX ) complexes .", "The TH...	[ "Nuclear mRNA export is a crucial step in eukaryotic gene expression , which is in yeast coupled to cotranscriptional messenger ribonucleoprotein particle ( mRNP ) assembly and surveillance .", "Several surveillance systems that monitor nuclear mRNP biogenesis and export have been described , but the mechanism by...	[ "Nuclear export of messenger RNA ( mRNA ) is a crucial step during eukaryotic gene expression .", "Newly synthesized precursor mRNAs are processed during synthesis , packaged into messenger ribonucleoprotein particles ( mRNPs ) , and transported through the nuclear pore complex to the cytoplasm .", "To avoid nu...	2009
[ "Introduction", "Methods and Materials", "Results", "Discussion" ]	[]	Efficacy of Rifampin Plus Clofazimine in a Murine Model of Mycobacterium ulcerans Disease	journal.pntd.0003823	null	[ [ "Buruli ulcer ( BU ) , or Mycobacterium ulcerans disease , has become a more readily treatable disease since 2004 with the transition from only surgery and skin grafting to antibiotic therapy with the combination of rifampin ( RIF ) and streptomycin ( STR ) , the WHO preferred regimen or with RIF plus a fluor...	[ "Treatment of Buruli ulcer , or Mycobacterium ulcerans disease , has shifted from surgical excision and skin grafting to antibiotic therapy usually with 8 weeks of daily rifampin ( RIF ) and streptomycin ( STR ) .", "Although the results have been highly favorable , administration of STR requires intramuscular in...	[ "Buruli ulcer ( BU ) is caused by Mycobacterium ulcerans and its toxin , mycolactone .", "Since 2004 , BU has been treated primarily with antibiotics rather than surgery and skin grafting .", "The current first-line regimen is an oral drug , rifampin ( RIF ) , and an injectable drug , streptomycin ( STR ) , dai...	2015
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "blood cells", "t helper cells", "medicine and health sciences", "immune cells", "engineering and technology", "applied mathematics", "platelet aggregation", "immunology", "simulation and modeling", "algorithms", "mathematics", "network analysis", "research and analysis methods", "computer...	Analyzing pharmacological intervention points: A method to calculate external stimuli to switch between steady states in regulatory networks	journal.pcbi.1007075	null	[ [ "Biological networks are often formed by interacting proteins and molecules .", "Their change in time is often biologically regulated to adapt to different conditions .", "Detailed mathematical models describe changes of proteins , for instance their phosphorylation state or activity in general by dif...	[ "Once biological systems are modeled by regulatory networks , the next step is to include external stimuli , which model the experimental possibilities to affect the activity level of certain network’s nodes , in a mathematical framework .", "Then , this framework can be interpreted as a mathematical optimal cont...	[ "Organisms can be seen as molecular networks being able to react on external stimuli .", "Experiments are performed to understand the underlying regulating mechanisms within the molecular network .", "A common purpose for these efforts is to reveal mechanisms with which the molecular networks can be affected to...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "kala-azar", "children", "medicine and health sciences", "immune physiology", "spleen", "tropical diseases", "geographical locations", "south sudan", "parasitic diseases", "age groups", "mathematics", "forecasting", "statistics (mathematics)", "nutrition", "neglected tropical diseases", ...	A clinical severity scoring system for visceral leishmaniasis in immunocompetent patients in South Sudan	journal.pntd.0005921	null	[ [ "Visceral leishmaniasis ( VL , or kala-azar ) is a neglected tropical disease which is caused by the obligate intracellular protozoa of the Leishmania donovani complex ( L . donovani and L . infantum ) ( 1 ) .", "In East Africa VL is caused by L . donovani , and is transmitted anthroponotically by phlebot...	[ "South Sudan is one of the most endemic countries for visceral leishmaniasis ( VL ) , and is frequently affected by large epidemics .", "In resource-limited settings , clinicians require a simple clinical tool to identify VL patients who are at increased risk of dying , and who need specialised treatment with lip...	[ "Visceral leishmaniasis ( VL ) , also known as kala-azar , is a neglected tropical disease caused by a parasite ( Leishmania ) and transmitted to humans through the bite of a sandfly .", "South Sudan is one of the highest endemic countries for VL , frequently affected by epidemics .", "In South Sudan are differ...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "clinical immunology", "immunology", "biology" ]	Human Herpesvirus 8 (HHV8) Sequentially Shapes the NK Cell Repertoire during the Course of Asymptomatic Infection and Kaposi Sarcoma	journal.ppat.1002486	null	[ [ "Human herpesvirus 8 ( HHV8 ) , although known as Kaposi's sarcoma-associated herpesvirus ( KSHV ) , is a γ herpes virus able to establish a predominantly latent , life-long infection in host's monocytes , dendritic cells ( DCs ) , B lymphocytes , and endothelial cells .", "HHV8 is the etiological agent o...	[ "The contribution of innate immunity to immunosurveillance of the oncogenic Human Herpes Virus 8 ( HHV8 ) has not been studied in depth .", "We investigated NK cell phenotype and function in 70 HHV8-infected subjects , either asymptomatic carriers or having developed Kaposi's sarcoma ( KS ) .", "Our results rev...	[ "Natural Killer ( NK ) cells are part of the innate immune response against virus infections and tumors .", "Their activation is the net result of signals emanating from a panel of inhibitory and activating receptors recognizing specific ligands on target cells .", "Human Herpes Virus 8 ( HHV8 ) is an oncogenic...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	PNUTS/PP1 Regulates RNAPII-Mediated Gene Expression and Is Necessary for Developmental Growth	journal.pgen.1003885	null	[ [ "Development must be tightly coupled with cellular metabolism to ensure that necessary nutritional and energetic requirements are met and the available resources are utilised effectively to sustain appropriate levels of tissue growth .", "A particularly dramatic example of how development is coupled to me...	[ "In multicellular organisms , tight regulation of gene expression ensures appropriate tissue and organismal growth throughout development .", "Reversible phosphorylation of the RNA Polymerase II ( RNAPII ) C-terminal domain ( CTD ) is critical for the regulation of gene expression states , but how phosphorylation...	[ "During development , cells rely on appropriate patterns of gene expression to regulate metabolism in order to meet cellular demands and maintain rapid tissue growth .", "Conversely , dysregulation of gene expression is critical in various disease states , such as cancer , and during ageing .", "A key mechanism...	2013
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "urology", "medicine and health sciences", "classical mechanics", "pathology and laboratory medicine", "pathogens", "tropical diseases", "microbiology", "vertebrates", "animals", "mammals", "primates", "treponematoses", "bacterial diseases", "signs and symptoms", "ulcers", "sexually tr...	Gene target selection for loop-mediated isothermal amplification for rapid discrimination of Treponema pallidum subspecies	journal.pntd.0006396	null	[ [ "Human yaws is a tropical skin disease of children caused by the bacterium Treponema pallidum subsp .", "pertenue ( TPE ) [1] .", "Skin ulcers are the most characteristic clinical manifestations associated with infection in all three active disease stages ( primary , secondary , and tertiary yaws ) [2...	[ "We show proof of concept for gene targets ( polA , tprL , and TP_0619 ) that can be used in loop-mediated isothermal amplification ( LAMP ) assays to rapidly differentiate infection with any of the three Treponema pallidum subspecies ( pallidum ( TPA ) , pertenue ( TPE ) , and endemicum ( TEN ) ) and which are kno...	[ "Sustainable eradication of human yaws benefits from applicable and reliable assays to detect possible reemerging yaws cases .", "Our study provides proof of concept for LAMP assays that are capable of rapid diagnoses and discrimination of active Treponema pallidum infection .", "While current clinical diagnosi...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "plant science", "molecular cell biology", "plant biology", "genetics", "biology", "genomics", "microbiology", "genetics and genomics" ]	Trehalose Biosynthesis Promotes Pseudomonas aeruginosa Pathogenicity in Plants	journal.ppat.1003217	null	[ [ "The ubiquitous bacterium Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen that infects a wide diversity of hosts .", "For example , P . aeruginosa strain PA14 is infectious in several model genetic hosts including the plant Arabidopsis thaliana [1] , the insect Drosophila melanogaster [2]...	[ "Pseudomonas aeruginosa strain PA14 is a multi-host pathogen that infects plants , nematodes , insects , and vertebrates .", "Many PA14 factors are required for virulence in more than one of these hosts .", "Noting that plants have a fundamentally different cellular architecture from animals , we sought to iden...	[ "Pseudomonas aeruginosa is an opportunistic human bacterial pathogen that infects a wide range of plants and animals , including the model laboratory plant Arabidopsis thaliana .", "P . aeruginosa utilizes many of the same virulence-related factors to infect both plants and animals .", "However , because plants...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "viral transmission and infection", "microbiology", "animal models of infection", "infectious diseases", "viral entry", "virulence factors and mechanisms", "viral immune evasion", "biology", "infectious disease modeling", "host cells", "viral persistence and latency", "virology" ...	Murid Herpesvirus-4 Exploits Dendritic Cells to Infect B Cells	journal.ppat.1002346	null	[ [ "Dendritic cells ( DCs ) act as sentinels against infection: they encode pathogen-responsive receptors , abound at pathogen entry sites , and orchestrate both innate and adaptiveimmune responses [1] , [2] .", "Virus-infected DCs are generally immunogenic [3]–[5] , and DC infection may be important for opt...	[ "Dendritic cells ( DCs ) play a central role in initiating immune responses .", "Some persistent viruses infect DCs and can disrupt their functions in vitro .", "However , these viruses remain strongly immunogenic in vivo .", "Thus what role DC infection plays in the pathogenesis of persistent infections is u...	[ "We detect invading viruses with dendritic cells and eliminate them with lymphocytes .", "A key interaction is lymphocyte activation by dendritic cells presenting viral antigens .", "Not all viruses can be eliminated , and some that persist deliberately colonize lymphocytes and dendritic cells , such that paras...	2011
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "invertebrates", "dengue virus", "medicine and health sciences", "reproductive system", "body fluids", "pathology and laboratory medicine", "pathogens", "microbiology", "animals", "viruses", "germ cells", "developmental biology", "oocytes", "rna viruses", "insect vectors", "infectious ...	Demonstration of efficient vertical and venereal transmission of dengue virus type-2 in a genetically diverse laboratory strain of Aedes aegypti	journal.pntd.0006754	null	[ [ "Dengue viruses ( DENV ) include four serologically related but genetically distinct viruses , DENV1-4 ( Flavivirus; Flaviviridae ) .", "DENV are arthropod-borne viruses ( arboviruses ) transmitted between susceptible humans by the bite of infected Aedes spp .", "DENV and their mosquito vectors are pr...	[ "Aedes aegypti is the primary mosquito vector of dengue viruses ( DENV; serotypes 1–4 ) .", "Human-mosquito transmission cycles maintain DENV during epidemics but questions remain regarding how these viruses survive when human infections and vector abundance are minimal .", "Aedes mosquitoes can transmit DENV w...	[ "Aedes aegypti mosquitoes are the primary vectors of dengue viruses ( DENV ) and other medically important arthropod-borne viruses ( yellow fever , Zika , chikungunya ) .", "DENVs replicate in Ae .", "aegypti and humans in a transmission cycle that maintains the virus in nature .", "However , adverse conditio...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "systems biology", "model organisms", "molecular cell biology", "genetics", "biology", "microbiology", "evolutionary biology", "genetics and genomics" ]	Adaptive Evolution of the Lactose Utilization Network in Experimentally Evolved Populations of Escherichia coli	journal.pgen.1002444	null	[ [ "Changes in gene regulation are an important and common cause of adaptation .", "Support for this comes from bioinformatic evidence that changes in regulatory elements are associated with presumably adaptive phenotypic changes ( reviewed in [1] , [2] ) , comparative experimental studies [3] and from exper...	[ "Adaptation to novel environments is often associated with changes in gene regulation .", "Nevertheless , few studies have been able both to identify the genetic basis of changes in regulation and to demonstrate why these changes are beneficial .", "To this end , we have focused on understanding both how and wh...	[ "Differences in gene regulation underlie many important biological processes and are thought to be important for the adaption of organisms to novel environments .", "Here we focus on the regulation of a group of well-studied genes , the lac operon , that control the utilization of lactose sugar , and we examine h...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "escherichia coli", "biochemistry", "prokaryotic models", "genomics", "model organisms", "genome evolution", "evolutionary biology", "proteins", "microbial evolution", "chaperone proteins", "evolutionary modeling", "transmembrane transport proteins", "biology", "computational biology", "...	Genome-scale Co-evolutionary Inference Identifies Functions and Clients of Bacterial Hsp90	journal.pgen.1003631	null	[ [ "In eukaryotes , the universally conserved and essential chaperone Hsp90 aids the folding of key proteins in development and responses to environmental stimuli [1]–[3] .", "In yeast , up to 10% of all proteins are estimated to be Hsp90 clients under standard culture conditions [4] .", "Hsp90 function ...	[ "The molecular chaperone Hsp90 is essential in eukaryotes , in which it facilitates the folding of developmental regulators and signal transduction proteins known as Hsp90 clients .", "In contrast , Hsp90 is not essential in bacteria , and a broad characterization of its molecular and organismal function is lacki...	[ "Hsp90 is a chaperone protein that aids the folding of many other proteins ( clients ) , which tend to be signal transduction proteins .", "Hsp90 is particularly important when organisms are under environmental or mutational stress ( e . g . in cancerous cells ) .", "Although Hsp90 is well-studied in eukaryotic...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "protein transport", "organisms", "invertebrates", "signal transduction", "developmental biology", "caenorhabditis elegans", "animal genetics", "invertebrate genetics", "cell biology", "secretory pathway", "caenorhabditis", "genetics", "nematoda", "biology and life sciences", "cell proce...	An AGEF-1/Arf GTPase/AP-1 Ensemble Antagonizes LET-23 EGFR Basolateral Localization and Signaling during C. elegans Vulva Induction	journal.pgen.1004728	null	[ [ "C . elegans vulval cell induction requires a highly conserved Epidermal Growth Factor Receptor ( EGFR ) /Ras GTPase/Mitogen Activated Protein Kinase ( MAPK ) signaling pathway providing an in vivo model in which to study signaling in a polarized epithelia [1] , [2] .", "During larval development , an equ...	[ "LET-23 Epidermal Growth Factor Receptor ( EGFR ) signaling specifies the vulval cell fates during C . elegans larval development .", "LET-23 EGFR localization on the basolateral membrane of the vulval precursor cells ( VPCs ) is required to engage the LIN-3 EGF-like inductive signal .", "The LIN-2 Cask/LIN-7 V...	[ "In the nematode , Caenorhabditis elegans , an evolutionarily conserved Epidermal Growth Factor Receptor ( EGFR ) signaling pathway is required to induce three epithelial cells to initiate a program of vulva development .", "EGFR on the basolateral membrane is essential to engage and transmit this signal .", "H...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "animal types", "medicine and health sciences", "body fluids", "microtubules", "vertebrates", "pets and companion animals", "dogs", "animals", "mammals", "respiratory system", "dyneins", "molecular motors", "mammalian genomics", "cellular structures and organelles", "zoology", "cytoske...	NME5 frameshift variant in Alaskan Malamutes with primary ciliary dyskinesia	journal.pgen.1008378	null	[ [ "Primary ciliary dyskinesia ( PCD ) is a rare genetic disease caused by defects in the structure or function of the motile cilia .", "Motile cilia are present in the respiratory tract including the paranasal sinuses , in the auditory tube and middle ear , in male and female reproductive tracts , sperm cel...	[ "Primary ciliary dyskinesia ( PCD ) is a hereditary defect of motile cilia in humans and several domestic animal species .", "Typical clinical findings are chronic recurrent infections of the respiratory tract and fertility problems .", "We analyzed an Alaskan Malamute family , in which two out of six puppies w...	[ "Motile cilia are required for clearing mucous , infectious agents and inhaled dust from the airways .", "Primary ciliary dyskinesia ( PCD ) is a hereditary defect of motile cilia .", "Clinical findings may include recurrent airway infections , fertility problems , and sometimes hydrocephalus .", "We analyzed...	2019
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "dermatology", "research design", "comparative effectiveness research", "symptom scales", "medicine and health sciences", "video recording", "imaging techniques", "ectoparasitic infections", "clinical research design", "photography", "neglected tropical diseases", "tropical diseases", "field...	Treatment of Tungiasis with Dimeticone: A Proof-of-Principle Study in Rural Kenya	journal.pntd.0003058	null	[ [ "Tungiasis ( sand flea disease ) is a neglected tropical disease frequent in South America , The Caribbean and in sub-Saharan Africa .", "[1] , [2] , [3] .", "It is prevalent in resource-poor rural and urban communities , where animal reservoirs are present and people live in poverty [2] , [4] , [5] ,...	[ "Tungiasis ( sand flea disease ) is a neglected tropical disease , prevalent in resource-poor communities in South America and sub-Saharan Africa .", "It is caused by an inflammatory response against penetrated female sand fleas ( Tunga penetrans ) embedded in the skin of the host .", "Although associated with ...	[ "Tungiasis ( sand flea disease ) , a parasitic skin disease , causes important morbidity , and eventually leads to mutilation of the feet .", "Hitherto , the only effective treatment is the surgical extraction of embedded sand fleas .", "In the endemic areas this is done using inappropriate sharp instruments an...	2014
[ "Introduction", "Materials and Methods", "Results and Discussion" ]	[ "medicine", "infectious diseases", "emerging infectious diseases", "biology", "microbiology", "viral diseases", "ebola hemorrhagic fever" ]	A Replicating Cytomegalovirus-Based Vaccine Encoding a Single Ebola Virus Nucleoprotein CTL Epitope Confers Protection against Ebola Virus	journal.pntd.0001275	null	[ [ "Ebola virus ( EBOV ) , a member of the Filoviridae family , causes rapidly progressing viral hemorrhagic fever culminating in multi-organ failure , shock and death [1] .", "EBOV can be subdivided into four distinct and a fifth putative species [2] , [3] .", "EBOV species differ in level of virulence ...	[ "Human outbreaks of Ebola virus ( EBOV ) are a serious human health concern in Central Africa .", "Great apes ( gorillas/chimpanzees ) are an important source of EBOV transmission to humans due to increased hunting of wildlife including the ‘bush-meat’ trade .", "Cytomegalovirus ( CMV ) is an highly immunogenic...	[ "Human outbreaks of hemorrhagic disease caused by Ebola virus ( EBOV ) are a serious health concern in Central Africa .", "Great apes ( gorillas/chimpanzees ) are an important source of EBOV transmission to humans .", "Candidate EBOV vaccines do not spread from the initial vaccinee .", "In addition to being h...	2011
[ "Introduction", "Methods", "Results/Discussion" ]	[ "computational biology/evolutionary modeling", "evolutionary biology/bioinformatics", "computational biology/genomics" ]	Detecting Network Communities: An Application to Phylogenetic Analysis	journal.pcbi.1001131	null	[ [ "In networks , module or community structure plays a central role when it comes to", "understand network topology and dynamics .", "To advance solutions to many problems", "related to biological networks , we need to identify , thus , the community structure", "in datasets .", "Consequentl...	[ "This paper proposes a new method to identify communities in generally weighted", "complex networks and apply it to phylogenetic analysis .", "In this case , weights", "correspond to the similarity indexes among protein sequences , which can be used", "for network construction so that the network structure ...	[ "Complex weighted networks have been applied to uncover organizing principles of", "complex biological , technological , and social systems .", "We propose herein a new", "method to identify communities in such structures and apply it to phylogenetic", "analysis .", "Recent studies using this theory in ge...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "geomorphology", "children", "medicine and health sciences", "enzyme-linked immunoassays", "body fluids", "landforms", "education", "topography", "tropical diseases", "sociology", "social sciences", "geographical locations", "parasitic diseases", "age groups", "filariasis", "neglected ...	Interruption of onchocerciasis transmission in Bioko Island: Accelerating the movement from control to elimination in Equatorial Guinea	journal.pntd.0006471	null	[ [ "Onchocerciasis is a parasitic disease caused by the filarial worm Onchocerca volvulus .", "It is transmitted through the bites of infected Simulium blackflies , which breed in fast-flowing streams and rivers .", "Symptoms include rashes , severe itching and various skin lesions , and blindness .", ...	[ "Onchocerciasis , also known as river blindness , is a parasitic disease .", "More than 99 percent of all cases occur in Africa .", "Bioko Island ( Equatorial Guinea ) is the only island endemic for onchocerciasis in the world .", "Since 2005 , when vector Simulium yahense was eliminated , there have not been...	[ "Onchocerciasis , commonly called river blindness , is a chronic parasitic disease particularly prevalent in Africa .", "It is transmitted through the bites of infected Simulium blackflies .", "Onchocerciasis is endemic in Equatorial Guinea .", "Huge achievements have been made in human and vector control dur...	2018

Subsets and Splits

No community queries yet

The top public SQL queries from the community will appear here once available.