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", "Results", "Discussion", "Methods" ]	[ "cell physiology", "biochemistry", "ion channels", "proteins", "physiology", "biology", "anatomy and physiology" ]	Local Ca2+ Entry Via Orai1 Regulates Plasma Membrane Recruitment of TRPC1 and Controls Cytosolic Ca2+ Signals Required for Specific Cell Functions	journal.pbio.1001025	null	[ [ "Store-operated Ca2+ entry ( SOCE ) is activated in response to a reduction of [Ca2+] in the ER .", "SOCE generates local and global [Ca2+]i signals that regulate a wide variety of cellular functions [1] , [2] .", "The first store-operated Ca2+ channel to be characterized , the Ca2+ release-activated ...	[ "Store-operated Ca2+ entry ( SOCE ) has been associated with two types of channels: CRAC channels that require Orai1 and STIM1 and SOC channels that involve TRPC1 , Orai1 , and STIM1 .", "While TRPC1 significantly contributes to SOCE and SOC channel activity , abrogation of Orai1 function eliminates SOCE and acti...	[ "Store-operated Ca2+ entry is present in all cell types and determines sustained cytosolic [Ca2+] increases that are critical for regulating a wide variety of physiological functions .", "This Ca2+ entry mechanism is activated in response to depletion of Ca2+ in the endoplasmic reticulum ( ER ) .", "When ER [Ca...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "hypothyroidism", "endocrinology", "graves' disease", "thyroid", "hashimoto disease" ]	Identification of Novel Genetic Loci Associated with Thyroid Peroxidase Antibodies and Clinical Thyroid Disease	journal.pgen.1004123	null	[ [ "Autoimmune thyroid disease ( AITD ) , including Hashimoto's thyroiditis and Graves' disease , is one of the most common autoimmune diseases , affecting 2–5% of the general population [1] , [2] , [3] .", "Thyroid dysfunction has been associated with osteoporosis , depression , atrial fibrillation , heart ...	[ "Autoimmune thyroid diseases ( AITD ) are common , affecting 2-5% of the general population .", "Individuals with positive thyroid peroxidase antibodies ( TPOAbs ) have an increased risk of autoimmune hypothyroidism ( Hashimoto's thyroiditis ) , as well as autoimmune hyperthyroidism ( Graves' disease ) .", "As ...	[ "Individuals with thyroid peroxidase antibodies ( TPOAbs ) have an increased risk of autoimmune thyroid diseases ( AITD ) , which are common in the general population and associated with increased cardiovascular , metabolic and psychiatric morbidity and mortality .", "As the causative genes of TPOAbs and AITD rem...	2014
[ "Introduction", "Results", "Discussion", "Material and Methods" ]	[ "medicine", "infectious diseases", "immunity", "innate immunity", "immunology", "biology", "microbiology", "host-pathogen interaction", "viral diseases" ]	Identification of DNA-Damage DNA-Binding Protein 1 as a Conditional Essential Factor for Cytomegalovirus Replication in Interferon-γ-Stimulated Cells	journal.ppat.1002069	null	[ [ "Cytomegaloviruses ( CMVs ) constitute prototypical β-herpesviruses .", "50–95% of the global adult population are infected lifelong with human CMV ( HCMV ) .", "HCMV is a leading cause of disease burden of newborns in western countries due to transplacental transmission of the virus from the mother t...	[ "The mouse cytomegaloviral ( MCMV ) protein pM27 represents an indispensable factor for viral fitness in vivo selectively , antagonizing signal transducer and activator of transcription 2 ( STAT2 ) -mediated interferon signal transduction .", "We wished to explore by which molecular mechanism pM27 accomplishes th...	[ "Cytomegaloviruses are strictly species-specific .", "Mouse cytomegalovirus ( MCMV ) is a prototypical β-herpesvirus , infecting Mus musculus as natural host and is closely related to the human pathogenic cytomegalovirus ( HCMV , HHV-5 ) which both establish lifelong infection .", "Thus , MCMV infection constit...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "transfer rna", "chemical characterization", "crystal structure", "gel shift assay", "hela cells", "gene regulation", "biological cultures", "condensed matter physics", "cell cultures", "molecular biology techniques", "crystallography", "cellular structures and organelles", "research and ana...	DENR–MCTS1 heterodimerization and tRNA recruitment are required for translation reinitiation	journal.pbio.2005160	null	[ [ "Eukaryotic translation reinitiation is a process that is only recently becoming understood at the mechanistic and functional levels .", "Unlike prokaryotic ribosomes , eukaryotic ribosomes were thought to engage mainly in a single round of initiation , extension , and termination on an individual mRNA ."...	[ "The succession of molecular events leading to eukaryotic translation reinitiation—whereby ribosomes terminate translation of a short open reading frame ( ORF ) , resume scanning , and then translate a second ORF on the same mRNA—is not well understood .", "Density-regulated reinitiation and release factor ( DENR...	[ "Usually , eukaryotic ribosomes translate only a single open reading frame ( ORF ) on an mRNA and then dissociate from the mRNA .", "In some cases , when there is a short upstream open reading frame ( uORF ) that precedes the main ORF , ribosomes can translate the uORF , terminate translation , and then undergo a...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "protein interactions", "pneumococcus", "enzymes", "enzymology", "microbiology", "glycoside hydrolases", "protein structure", "glycosylation", "glycoproteins", "bacterial pathogens", "protein structure determination", "proteins", "medical microbiology", "streptococcus", "microbial pathog...	Unravelling the Multiple Functions of the Architecturally Intricate Streptococcus pneumoniae β-galactosidase, BgaA	journal.ppat.1004364	null	[ [ "The cell surfaces of bacterial pathogens are complex landscapes of molecules that create an elaborate interface between the host and the bacterium .", "Integral to this landscape are cell-surface presented proteins that provide a variety of functions from cellular maintenance to communicating with the ex...	[ "Bacterial cell-surface proteins play integral roles in host-pathogen interactions .", "These proteins are often architecturally and functionally sophisticated and yet few studies of such proteins involved in host-pathogen interactions have defined the domains or modules required for specific functions .", "Str...	[ "The adherence of bacteria to host cells is a critical step in most bacterial infections; yet , mechanisms are poorly understood for many bacteria , including Streptococcus pneumoniae ( pneumococcus ) , a human pathogen of global relevance .", "The surface of this bacterium is decorated with a landscape of large ...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "visual system", "neural networks", "computational neuroscience", "biology", "sensory systems", "neuroscience" ]	A Model of Binocular Rivalry and Cross-orientation Suppression	journal.pcbi.1002991	null	[ [ "Binocular rivalry is a visual phenomenon in which perception alternates between incompatible monocular images presented to the two eyes [1]–[4] .", "For example , when one eye is presented with an oriented grating and the other eye is presented with an orthogonal grating , observers experience alternatin...	[ "Binocular rivalry and cross-orientation suppression are well-studied forms of competition in visual cortex , but models of these two types of competition are in tension with one another .", "Binocular rivalry occurs during the presentation of dichoptic grating stimuli , where two orthogonal gratings presented se...	[ "Binocular rivalry is a visual illusion that occurs when the two eyes are presented with incompatible images .", "Instead of perceiving a mixture of the two images , most people tend to experiences alternations in which they only see one image at a time .", "Binocular rivalry is more than just an interesting il...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "public health", "medicine", "infectious diseases", "schistosomiasis", "public health and epidemiology", "clinical research design", "clinical trials", "drug policy", "neglected tropical diseases", "parasitic diseases", "meta-analyses" ]	A Multicentre Randomized Controlled Trial of the Efficacy and Safety of Single-Dose Praziquantel at 40 mg/kg vs. 60 mg/kg for Treating Intestinal Schistosomiasis in the Philippines, Mauritania, Tanzania and Brazil	journal.pntd.0001165	null	[ [ "Schistosomiasis is a parasitic infection caused by blood flukes ( flatworms ) of the class Trematoda: Schistosoma haematobium ( causing urinary schistosomiasis ) , S . mansoni , S . japonicum , S . intercalatum and S . mekongi ( causing intestinal schistosomiasis ) .", "A recent systematic review of evid...	[ "Praziquantel at 40 mg/kg in a single dose is the WHO recommended treatment for all forms of schistosomiasis , but 60 mg/kg is also deployed nationally .", "Four trial sites in the Philippines , Mauritania , Tanzania and Brazil enrolled 856 patients using a common protocol , who were randomised to receive praziqu...	[ "Control of urinary and intestinal schistosomiasis is based on mass administration of praziquantel at the World Health Organization ( WHO ) recommended dose of 40 mg/kg , though some countries use 60 mg/kg .", "This multi-country randomized clinical trial compared the efficacy ( cure and egg reduction rates three...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/disease models", "genetics and genomics/genetics of disease", "neurological disorders", "cell biology/cellular death and stress responses" ]	Extracellular Dopamine Potentiates Mn-Induced Oxidative Stress, Lifespan Reduction, and Dopaminergic Neurodegeneration in a BLI-3–Dependent Manner in Caenorhabditis elegans	journal.pgen.1001084	null	[ [ "Mn is the twelfth most prevalent natural element in the Earth's crust [1] and is an essential transition metal required for normal growth , development and cellular homeostasis [2] , [3] .", "It acts as a cofactor for multiple enzymes ( Mn superoxide dismutase , pyruvate carboxylase , arginase , and glut...	[ "Parkinson's disease ( PD ) -mimicking drugs and pesticides , and more recently PD-associated gene mutations , have been studied in cell cultures and mammalian models to decipher the molecular basis of PD .", "Thus far , a dozen of genes have been identified that are responsible for inherited PD .", "However th...	[ "In Parkinson's disease ( PD ) , motor neurons that produce dopamine degenerate , leading to a characteristic syndrome including tremor , rigidity , and bradykinesia .", "The mechanisms leading to PD have been under intense investigation , identifying hereditary mutations responsible for about 8% of the cases .",...	2010
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Variability in Tuberculosis Granuloma T Cell Responses Exists, but a Balance of Pro- and Anti-inflammatory Cytokines Is Associated with Sterilization	journal.ppat.1004603	null	[ [ "Mycobacterium tuberculosis ( Mtb ) remains a major threat to global health .", "The latest World Health Organization analysis of the global burden of tuberculosis ( TB ) estimates 8 . 7 million new cases , 9 . 6–13 . 0 million prevalent cases , and 1 . 4 million deaths per year in 2011 [1] .", "Howev...	[ "Lung granulomas are the pathologic hallmark of tuberculosis ( TB ) .", "T cells are a major cellular component of TB lung granulomas and are known to play an important role in containment of Mycobacterium tuberculosis ( Mtb ) infection .", "We used cynomolgus macaques , a non-human primate model that recapitul...	[ "The characteristic feature of Mycobacterium tuberculosis ( Mtb ) infection is the formation of lesions , which are organized structures of immune cells in the lungs called granulomas , which contain the bacteria .", "When the granuloma functions effectively , it can kill the bacteria .", "T cells ( a type of i...	2015
[ "Introduction", "Results and Discussion", "Materials and Methods" ]	[ "bacillus", "microbiology", "escherichia coli", "prokaryotic models", "model organisms", "molecular cell biology", "rna synthesis", "bacterial pathogens", "research and analysis methods", "proteins", "medical microbiology", "gene expression", "microbial pathogens", "biochemistry", "rna",...	Predicting the Minimal Translation Apparatus: Lessons from the Reductive Evolution of Mollicutes	journal.pgen.1004363	null	[ [ "Mollicutes constitute a monophyletic class that share a common ancestor with Gram-positive bacteria of low G+C content or Firmicutes but have adopted a parasitic life style ( Figure S1 ) [1] .", "During their coevolution with their eukaryotic hosts , mollicutes progressively lost the genes coding for cel...	[ "Mollicutes is a class of parasitic bacteria that have evolved from a common Firmicutes ancestor mostly by massive genome reduction .", "With genomes under 1 Mbp in size , most Mollicutes species retain the capacity to replicate and grow autonomously .", "The major goal of this work was to identify the minimal ...	[ "In all cells , proteins are synthesized from the message encoded by mRNA using complex machineries involving many proteins and RNAs .", "In this process , named translation , the ribosome plays a central role .", "The elements involved in both ribosome biogenesis and its function are extremely conserved in all...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Elucidation of the RamA Regulon in Klebsiella pneumoniae Reveals a Role in LPS Regulation	journal.ppat.1004627	null	[ [ "The microbial response to antimicrobial challenge is multifactorial and can be conferred by a combination of extrinsic or intrinsic mechanisms .", "Those intrinsic mechanisms that confer pleiotropic phenotypes can provide a “stepping stone” to surmounting both the host or drug response .", "Intrinsic...	[ "Klebsiella pneumoniae is a significant human pathogen , in part due to high rates of multidrug resistance .", "RamA is an intrinsic regulator in K . pneumoniae established to be important for the bacterial response to antimicrobial challenge; however , little is known about its possible wider regulatory role in ...	[ "Bacteria can rapidly evolve under antibiotic pressure to develop resistance , which occurs when target genes mutate , or when resistance-encoding genes are transferred .", "Alternatively , microbes can simply alter the levels of intrinsic proteins that allow the organism to “buy” time to resist antibiotic pressu...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Temperature Stress Mediates Decanalization and Dominance of Gene Expression in Drosophila melanogaster	journal.pgen.1004883	null	[ [ "Canalization , the buffering of a phenotype against environmental or genetic perturbation , has been independently suggested by Schmalhausen [1] and Waddington [2] .", "Most models of canalization assume that canalization evolves in a response to stabilizing selection ( reviewed in [3 , 4] ) , but using ...	[ "The regulatory architecture of gene expression remains an area of active research .", "Here , we studied how the interplay of genetic and environmental variation affects gene expression by exposing Drosophila melanogaster strains to four different developmental temperatures .", "At 18°C we observed almost comp...	[ "Gene expression is the most direct link between the genetically encoded information and the phenotype .", "We analyzed the patterns of gene expression in two different D . melanogaster genotypes and their offspring at four different temperatures to determine if gene expression regulation is modulated by temperat...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "systems biology", "signal transduction", "signaling in cellular processes", "transcriptional signaling", "cellular stress responses", "regulatory networks", "signaling networks", "biology", "molecular cell biology", "computational biology" ]	Overexpression of Heat Shock Protein 72 Attenuates NF-κB Activation Using a Combination of Regulatory Mechanisms in Microglia	journal.pcbi.1003471	null	[ [ "Hsp72 is the major cytosolic inducible form of the 70 kDa family of heat shock proteins ( HSP70 ) .", "Overexpression of Hsp72 is known to protect cells from injury and is positively associated with outcome in models of stroke [1] , [2] , [3] , [4] , [5] .", "Besides the role it plays as a molecular ...	[ "Overexpression of the inducible heat shock protein 70 , Hsp72 , has broadly cytoprotective effects and improves outcome following stroke .", "A full understanding of how Hsp72 protects cells against injury is elusive , though several distinct mechanisms are implicated .", "One mechanism is its anti-inflammator...	[ "Inducing heat shock or overexpressing certain heat shock proteins ( HSPs ) is known to protect against brain injury , such as that resulting from stroke .", "Understanding the mechanisms underlying protection at the cellular and molecular level is a subject of intense research , as such knowledge may prove benef...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "mosquitoes", "vector biology", "biology", "microbiology", "vectors and hosts" ]	The JNK Pathway Is a Key Mediator of Anopheles gambiae Antiplasmodial Immunity	journal.ppat.1003622	null	[ [ "Malaria is a worldwide disease that is highly endemic in Sub-Saharan Africa and causes over half a million deaths annually .", "The mosquito Anopheles gambiae is a major vector of Plasmodium falciparum , the parasite responsible for most cases of human malaria in Africa .", "An .", "gambiae can m...	[ "The innate immune system of Anopheles gambiae mosquitoes limits Plasmodium infection through multiple molecular mechanisms .", "For example , midgut invasion by the parasite triggers an epithelial nitration response that promotes activation of the complement-like system .", "We found that suppression of the JN...	[ "The mosquito Anopheles gambiae is a major vector of human malaria , a disease caused by Plasmodium falciparum parasites that results in more than half a million deaths each year .", "Several signaling pathways in the mosquito have been shown to mediate the mosquito immune responses to Plasmodium infection .", ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular biology/transcription initiation and activation", "genetics and genomics/gene expression" ]	Genetic Interactions of MAF1 Identify a Role for Med20 in Transcriptional Repression of Ribosomal Protein Genes	journal.pgen.1000112	null	[ [ "Nuclear gene transcription in proliferating cells is dedicated primarily to the synthesis of ribosomes and tRNAs .", "As illustrated by studies in Saccharomyces cerevisiae , the doubling of cell mass with each cell cycle involves the production of ∼200 , 000 ribosomes along with 3–6 million molecules of ...	[ "Transcriptional repression of ribosomal components and tRNAs is coordinately regulated in response to a wide variety of environmental stresses .", "Part of this response involves the convergence of different nutritional and stress signaling pathways on Maf1 , a protein that is essential for repressing transcript...	[ "The Maf1 protein is an essential negative regulator of transcription by RNA polymerase III in S . cerevisiae and functions to integrate responses from diverse nutritional and stress signaling pathways that coordinately regulate ribosome and tRNA synthesis .", "These signaling pathways are not well-defined , and ...	2008
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "293t cells", "enzymes", "gene regulation", "biological cultures", "enzymology", "chromatids", "fungi", "dna replication", "dna", "epigenetics", "ligases", "chromatin", "research and analysis methods", "small interfering rnas", "chromosome biology", "proteins", "gene expression", "...	Cul4-Ddb1 ubiquitin ligases facilitate DNA replication-coupled sister chromatid cohesion through regulation of cohesin acetyltransferase Esco2	journal.pgen.1007685	null	[ [ "Faithful genetic inheritance requires precise chromatin replication and separation of sister chromatids into two daughter cells .", "To ensure accurate chromosome segregation in eukaryotic cells , each pair of sister chromatids must be aligned properly and held together by a cohesin complex from S phase ...	[ "Cohesin acetyltransferases ESCO1 and ESCO2 play a vital role in establishing sister chromatid cohesion .", "How ESCO1 and ESCO2 are controlled in a DNA replication-coupled manner remains unclear in higher eukaryotes .", "Here we show a critical role of CUL4-RING ligases ( CRL4s ) in cohesion establishment via ...	[ "During the cycle of cell division and proliferation , each chromosome is copied into twin sister chromatids .", "To make sure a complete set of chromosomes are correctly passed on from generation to generation , the twins must be tethered together by a multi-protein ring called cohesin .", "ESCO1 and ESCO2 hav...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "computational biology/genomics", "computational biology/transcriptional regulation" ]	Spatio-Temporal Dynamics of Yeast Mitochondrial Biogenesis: Transcriptional and Post-Transcriptional mRNA Oscillatory Modules	journal.pcbi.1000409	null	[ [ "Cell construction requires the tight linking of various molecular processes , from", "nuclear transcription to the site-specific production of proteins .", "The control of", "the orchestration of these processes remains poorly understood .", "In classical", "experimental conditions , coor...	[ "Examples of metabolic rhythms have recently emerged from studies of budding", "yeast .", "High density microarray analyses have produced a remarkably detailed", "picture of cycling gene expression that could be clustered according to", "metabolic functions .", "We developed a model-based approach for the...	[ "In bacterial and eukaryotic cells , gene expression is regulated at both the", "transcriptional and translational levels .", "In eukaryotes these two processes", "cannot be directly coupled because the nuclear membrane separates the", "chromosomes from the ribosomes .", "Although the transcription levels...	2009
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "biology", "computational biology" ]	Dynamic Fluctuations Provide the Basis of a Conformational Switch Mechanism in Apo Cyclic AMP Receptor Protein	journal.pcbi.1003141	null	[ [ "The Escherichia coli cAMP Receptor Protein ( CRP ) ( also known as Catabolite Activator Protein , CAP ) activates the transcription of more than 150 genes .", "Upon binding of cAMP ( cyclic AMP ) , the transcriptional activity of CRP is altered resulting in a change in the affinity for its target CRP-dep...	[ "Escherichia coli cyclic AMP Receptor Protein ( CRP ) undergoes conformational changes with cAMP binding and allosterically promotes CRP to bind specifically to the DNA .", "In that , the structural and dynamic properties of apo CRP prior to cAMP binding are of interest for the comprehension of the activation mec...	[ "Protein dynamics are central in allosteric communication .", "The cooperative character of atomic motions is key in the propagation of the allosteric signal and in the protein functioning .", "Here , we explored the dynamics of cAMP Receptor Protein ( CRP ) as an apo unbound monomer/dimer and a holo dimer by m...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "vero cells", "medicine and health sciences", "immune physiology", "chemical compounds", "viral transmission and infection", "biological cultures", "immunology", "microbiology", "organic compounds", "geoinformatics", "protein synthesis", "chaperone proteins", "amino acids", "antibodies", ...	Spatial and Temporal Resolution of Global Protein Synthesis during HSV Infection Using Bioorthogonal Precursors and Click Chemistry	journal.ppat.1005927	null	[ [ "The manipulation of cellular metabolic processes during virus infection promotes or tempers virus production and determines the outcome of infection not only at the cellular level but also e . g . , acute versus long-term persistence , latency , reactivation and transmission [1] .", "With regard to infec...	[ "We used pulse-labeling with the methionine analogue homopropargylglycine ( HPG ) to investigate spatiotemporal aspects of protein synthesis during herpes simplex virus ( HSV ) infection .", "In vivo incorporation of HPG enables subsequent selective coupling of fluorochrome-capture reagents to newly synthesised p...	[ "All viruses reprogram infected cells for the synthesis , modification and targeted localisation of virus-encoded and host proteins .", "Advances in proteomics and mass spectrometry have provided broad insight into these processes , but these approaches have limited ability to investigate spatial aspects of infec...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "epidemiology", "biology and life sciences", "tropical diseases", "toxicology", "health care" ]	Cost-effectiveness of Antivenoms for Snakebite Envenoming in Nigeria	journal.pntd.0003381	null	[ [ "Snakebite envenoming is a major public health problem among agricultural communities in the savanna region of West Africa [1]–[3] .", "A recent global appraisal estimated an incidence of envenomings in West Africa of 8 . 87–93 . 3/100 , 000 persons per year ( PPY ) and a mortality rate of 0 . 504–5 . 9/1...	[ "Snakebite envenoming is a major public health problem throughout the rural tropics .", "Antivenom is effective in reducing mortality and remains the mainstay of therapy .", "This study aimed to determine the cost-effectiveness of using effective antivenoms for Snakebite envenoming in Nigeria .", "Economic an...	[ "Snake bite is a major public health problem throughout rural communities in West Africa and leads to a significant number of deaths and disabilities per year .", "Even though effective antivenoms exist against the locally prevalent carpet viper and other poisonous snakes , they are generally not available in com...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "invertebrates", "cell death", "medicine and health sciences", "nervous system", "gene regulation", "cell processes", "neuroscience", "animals", "animal models", "regulator genes", "drosophila melanogaster", "model organisms", "neuronal death", "gene types", "drosophila", "research and...	Neuronal Cell Fate Specification by the Convergence of Different Spatiotemporal Cues on a Common Terminal Selector Cascade	journal.pbio.1002450	A study of neuropeptide neurons in the Drosophila nervous system reveals that two different combinations of spatiotemporal cues—active in different progenitors—converge on a common terminal selector gene to trigger a similar neuronal subtype identity.	[ [ "During nervous system development , vast numbers of different neuronal subtypes are generated , and understanding the process of cell fate specification remains a major challenge .", "Studies have shown that establishment of distinct neuronal identities requires complex cascades of regulatory information...	[ "Specification of the myriad of unique neuronal subtypes found in the nervous system depends upon spatiotemporal cues and terminal selector gene cascades , often acting in sequential combinatorial codes to determine final cell fate .", "However , a specific neuronal cell subtype can often be generated in differen...	[ "A fundamental challenge in developmental neurobiology is to understand how the great diversity of neuronal subtypes is generated during nervous system development .", "Neuronal subtype cell fate is established in a stepwise manner , starting with spatial and temporal cues that confer distinct identities to neura...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Mycetoma in the Sudan: An Update from the Mycetoma Research Centre, University of Khartoum, Sudan	journal.pntd.0003679	null	[ [ "Mycetoma is a unique neglected tropical disease .", "It is a morbid chronic progressive inflammatory condition caused by certain fungi ( eumycetoma ) or bacteria ( actinomycetoma ) [1 , 2 , 3] .", "It is characterised by devastating distortions , disabilities , high morbidity and it has various negat...	[ "This communication reports on the Mycetoma Research Centre of the University of Khartoum , Sudan experience on 6 , 792 patients seen during the period 1991–2014 . The patients were predominately young ( 64% under 30 years old ) males ( 76% ) .", "The majority ( 68% ) were from the Sudan mycetoma belt and 28% wer...	[ "Many researchers consider the Sudan as the mycetoma homeland .", "The first report on mycetoma was at the turn of the eighteenth century , and since then many documents on mycetoma have been reported .", "However , there is no recent report on mycetoma in the country .", "In 1977 Mahgoub published data on my...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "bacterial diseases", "infectious diseases", "cholera", "neglected tropical diseases", "infectious disease control" ]	Use of Oral Cholera Vaccines in an Outbreak in Vietnam: A Case Control Study	journal.pntd.0001006	null	[ [ "Cholera is increasingly being reported , and more countries are now experiencing outbreaks [1] , some lasting for several months .", "In 2001 , the World Health Organization ( WHO ) recommended the use of oral cholera vaccines ( OCV ) in populations at risk in endemic areas but not reactively once an out...	[ "Killed oral cholera vaccines ( OCVs ) are available but not used routinely for cholera control except in Vietnam , which produces its own vaccine .", "In 2007–2008 , unprecedented cholera outbreaks occurred in the capital , Hanoi , prompting immunization in two districts .", "In an outbreak investigation , we ...	[ "Simple measures such as adequate sanitation and clean water stops the spread of cholera; however , in areas where these are not available , cholera spreads quickly and may lead to death in a few hours if treatment is not initiated immediately .", "The use of life-saving rehydration therapy is the mainstay in cho...	2011
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "legs", "pathology and laboratory medicine", "togaviruses", "chikungunya infection", "pathogens", "tropical diseases", "microbiology", "limbs (anatomy)", "alphaviruses", "viruses", "animal models", "model organisms", "chikungunya virus", "rna viruses", "...	Lower temperatures reduce type I interferon activity and promote alphaviral arthritis	journal.ppat.1006788	null	[ [ "Studying the role of temperature in regulating viral infections and viral pathologies has an eclectic history .", "The Australian nurse , Elizabeth Kenny ( 1880–1952 ) , pioneered the treatment of polio with application of heat packs to affected limbs [1 , 2] , although the mechanistic basis for this tre...	[ "Chikungunya virus ( CHIKV ) belongs to a group of mosquito-borne alphaviruses associated with acute and chronic arthropathy , with peripheral and limb joints most commonly affected .", "Using a mouse model of CHIKV infection and arthritic disease , we show that CHIKV replication and the ensuing foot arthropathy ...	[ "Chikungunya virus ( CHIKV ) and Ross River virus are mosquito-borne alphaviruses that cause epidemics of human arthritic disease that usually last from weeks to months .", "Arthropathy predominantly manifests in the joints of limbs and the joints at the extremities ( e . g . hand and feet ) .", "Herein we show...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "biology" ]	ISG15 Is Critical in the Control of Chikungunya Virus Infection Independent of UbE1L Mediated Conjugation	journal.ppat.1002322	null	[ [ "Chikungunya virus is a member of the genus Alphavirus , which are enveloped positive-strand RNA viruses transmitted by mosquitoes .", "It was first isolated in Tanzania in 1952 , and reported to cause severe fever as well as myalgia , joint pain and rash within 2–5 days of infection [1] , [2] .", "Re...	[ "Chikungunya virus ( CHIKV ) is a re-emerging alphavirus that has caused significant disease in the Indian Ocean region since 2005 .", "During this outbreak , in addition to fever , rash and arthritis , severe cases of CHIKV infection have been observed in infants .", "Challenging the notion that the innate imm...	[ "Type I interferon plays a critical role in the host defense to viral infection .", "Signaling through the type I IFN receptor allows for the induction of hundreds of interferon stimulated genes ( ISGs ) that generate an antiviral state within host cells .", "The ubiquitin-like molecule ISG15 has been shown to ...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/hiv infection and aids", "virology/viral replication and gene regulation", "virology/host antiviral responses" ]	The SET Complex Acts as a Barrier to Autointegration of HIV-1	journal.ppat.1000327	null	[ [ "Soon after HIV-1 enters a susceptible target cell , the viral genomic RNA is reverse transcribed within the reverse transcription complex ( RTC ) to double-stranded DNA [1] .", "The RTC matures into the preintegration complex ( PIC ) , which delivers the viral DNA to the nucleus for integration into a ch...	[ "Retroviruses and retrotransposons are vulnerable to a suicidal pathway known as autointegration , which occurs when the 3′-ends of the reverse transcript are activated by integrase and then attack sites within the viral DNA .", "Retroelements have diverse strategies for suppressing autointegration , but how HIV-...	[ "When HIV-1 infects a cell , its genomic RNA is copied into DNA .", "The ends of the viral DNA are then activated by the viral integrase enzyme to enable DNA insertion into a host cell chromosome .", "However , the activated ends can alternately insert into the virus itself by a process called autointegration ,...	2009
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Forecasting Influenza Epidemics in Hong Kong	journal.pcbi.1004383	null	[ [ "Influenza causes a significant public health burden worldwide .", "Recent studies have shown that reliable forecasts of influenza epidemics can be generated in real time [1–3] .", "Particularly , operational forecasts of influenza epidemics have been developed for temperate regions such as the contin...	[ "Recent advances in mathematical modeling and inference methodologies have enabled development of systems capable of forecasting seasonal influenza epidemics in temperate regions in real-time .", "However , in subtropical and tropical regions , influenza epidemics can occur throughout the year , making routine fo...	[ "Influenza causes high levels of morbidity , mortality , and economic burden .", "Accurate forecasts of epidemic timing and magnitude would provide public health sectors valuable advance information in support of the planning and deployment of intervention measures .", "Such forecast systems have been developed...	2015
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "plant biology/plant genomes and evolution", "evolutionary biology/plant genomes and evolution", "computational biology/comparative sequence analysis", "computational biology/molecular genetics", "evolutionary biology/genomics", "molecular biology/bioinformatics", "evolutionary biology/bioinformatics", ...	Genome-Wide Double-Stranded RNA Sequencing Reveals the Functional Significance of Base-Paired RNAs in Arabidopsis	journal.pgen.1001141	null	[ [ "Recent discoveries reveal that RNAs perform a variety of tasks—ranging from the regulation of gene expression ( e . g . small RNAs ( smRNAs ) , and riboswitches ) to catalytic activities ( e . g . group I self-splicing introns ) —and indicate that this functionality is intimately linked to their three-dimens...	[ "The functional structure of all biologically active molecules is dependent on intra- and inter-molecular interactions .", "This is especially evident for RNA molecules whose functionality , maturation , and regulation require formation of correct secondary structure through encoded base-pairing interactions .", ...	[ "At the heart of RNA functionality , maturation , and regulation is the formation of intricate secondary structures that are dependent on specific nucleotide base-pairing interactions encoded within their sequences .", "These interactions can either be within ( intra-molecular ) or between ( inter-molecular ( het...	2010
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "developmental biology/embryology", "genetics and genomics/animal genetics", "developmental biology/stem cells", "developmental biology/morphogenesis and cell biology", "cell biology/cell signaling", "cell biology/nuclear structure and function", "cell biology/cell growth and division", "cell biology/...	Essential Role of Chromatin Remodeling Protein Bptf in Early Mouse Embryos and Embryonic Stem Cells	journal.pgen.1000241	null	[ [ "The packaging of eukaryotic DNA into chromatin provides a general mechanism for the modulation of gene activity and DNA metabolism through alterations of chromatin architecture .", "The structure and composition of chromatin can be altered by a number of distinct pathways , including post-translational m...	[ "We have characterized the biological functions of the chromatin remodeling protein Bptf ( Bromodomain PHD-finger Transcription Factor ) , the largest subunit of NURF ( Nucleosome Remodeling Factor ) in a mammal .", "Bptf mutants manifest growth defects at the post-implantation stage and are reabsorbed by E8 . 5 ...	[ "While the chromatin of eukaryotes provides an efficient means to compact large amounts of DNA into a small nucleus , it renders the DNA relatively inaccessible .", "ATP-dependent chromatin remodeling complexes mobilize nucleosomes and provide a means to gain access to DNA in chromatin .", "While the biochemica...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/helminth infections", "immunology/innate immunity" ]	Involvement of the Cytokine MIF in the Snail Host Immune Response to the Parasite Schistosoma mansoni	journal.ppat.1001115	null	[ [ "Schistosomiasis , the second most widespread human parasitic disease after malaria [1] , is caused by helminth parasites of the genus Schistosoma and more than 200 million people in 74 countries suffer from the pathological consequences of this disease [2] .", "Human infection requires contact with fresh...	[ "We have identified and characterized a Macrophage Migration Inhibitory Factor ( MIF ) family member in the Lophotrochozoan invertebrate , Biomphalaria glabrata , the snail intermediate host of the human blood fluke Schistosoma mansoni .", "In mammals , MIF is a widely expressed pleiotropic cytokine with potent p...	[ "Schistosoma mansoni , a parasitic blood fluke that causes intestinal schistosomiasis in humans , requires an intermediate host , a freshwater snail of the genus Biomphalaria for its transmission .", "Infection of the snail triggers marked cellular and humoral immune responses , but the molecular mechanisms of th...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics", "biology", "genomics", "genetics and genomics" ]	The Epistatic Relationship between BRCA2 and the Other RAD51 Mediators in Homologous Recombination	journal.pgen.1002148	null	[ [ "Homologous recombination ( HR ) maintains genome integrity by accurately repairing double-strand breaks ( DSBs ) that arise during the mitotic cell cycle or are induced by radiotherapy [1] , [2] .", "HR also plays an important role in releasing the replication forks that stall at damaged template DNA str...	[ "RAD51 recombinase polymerizes at the site of double-strand breaks ( DSBs ) where it performs DSB repair .", "The loss of RAD51 causes extensive chromosomal breaks , leading to apoptosis .", "The polymerization of RAD51 is regulated by a number of RAD51 mediators , such as BRCA1 , BRCA2 , RAD52 , SFR1 , SWS1 , ...	[ "Mutations in BRCA1 and BRCA2 predispose hereditary breast and ovarian cancer .", "Such mutations sensitize to chemotherapeutic agents , including camptothecin , cisplatin , and poly ( ADP-ribose ) polymerase ( PARP ) inhibitor , since RAD51 mediators including both BRCA proteins promote repair of DNA lesions ind...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Molecular Recognition by a Polymorphic Cell Surface Receptor Governs Cooperative Behaviors in Bacteria	journal.pgen.1003891	null	[ [ "Cell-cell recognition is critical for differentiating friend from foe and for allowing populations of cells to coordinate multicellular functions [1] , [2] .", "Many eukaryotes simplify aspects of cellular self-recognition by clonal expansion from a single fertilized cell , wherein a privileged environme...	[ "Cell-cell recognition is a fundamental process that allows cells to coordinate multicellular behaviors .", "Some microbes , such as myxobacteria , build multicellular fruiting bodies from free-living cells .", "However , how bacterial cells recognize each other by contact is poorly understood .", "Here we sh...	[ "How individual cells recognize each other to cooperate and assemble functional tissues is a fundamental question in biology .", "Although multicellularity is a trait that is typically associated with eukaryotes , certain groups of bacteria also exhibit complex multicellular behaviors , which are perhaps best exe...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "membrane proteins", "biochemistry", "enzyme structure", "lipids", "transmembrane proteins", "cell biology", "enzymes", "transferases", "biology and life sciences", "enzymology", "isoprenoids", "cellular structures and organelles", "cell membranes" ]	Structure of a Membrane-Embedded Prenyltransferase Homologous to UBIAD1	journal.pbio.1001911	A crystal structure of a member of the UbiA family of membrane-embedded prenyltransferases reveals the architecture of the active site and suggests a possible mechanism for catalysis.	[ [ "Vitamin K is an essential cofactor required for the posttranslational modification of proteins involved in blood-clotting and normal bone metabolism .", "One of the major forms of vitamin K in humans , menaquinone-4 , is produced by cleaving the phytyl group from dietary phylloquinone to produce menadion...	[ "Membrane-embedded prenyltransferases from the UbiA family catalyze the Mg2+-dependent transfer of a hydrophobic polyprenyl chain onto a variety of acceptor molecules and are involved in the synthesis of molecules that mediate electron transport , including Vitamin K and Coenzyme Q . In humans , missense mutations ...	[ "The biosynthesis of Vitamin K and Coenzyme Q requires the transfer of a long , hydrophobic moiety known as an isoprenyl onto an aromatic acceptor compound .", "This process is catalyzed by a family of proteins known as the UbiA proteins , which are embedded in the hydrophobic environment of cell membranes .", ...	2014
[ "Introduction", "Model", "Results", "Discussion" ]	[ "cognitive science", "medicine and health sciences", "neural networks", "engineering and technology", "nervous system", "signal processing", "brain", "neuroscience", "cerebral hemispheres", "left hemisphere", "systems science", "mathematics", "brain mapping", "network analysis", "crystal...	Phase-lags in large scale brain synchronization: Methodological considerations and in-silico analysis	journal.pcbi.1006160	null	[ [ "Many processes in nature are oscillatory , from heart beats and birds flapping their wings , to firing of neurons [1] and brain rhythms [2] .", "Oscillators are rarely isolated and they interact when coexisting in the same environment , thus synchronizing by adjusting their rhythms [3] .", "Synchroni...	[ "Architecture of phase relationships among neural oscillations is central for their functional significance but has remained theoretically poorly understood .", "We use phenomenological model of delay-coupled oscillators with increasing degree of topological complexity to identify underlying principles by which t...	[ "Functional connectivity , and in particular , phase coupling between distant brain regions may be fundamental in regulating neuronal processing and communication .", "However , phase relationships between the nodes of the brain and how they are confined by its spatio-temporal structure , have been mostly overloo...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology", "virology", "viruses and cancer", "gene expression", "genetics", "biology and life sciences", "epigenetics", "microbiology", "molecular cell biology" ]	Epstein-Barr Virus Down-Regulates Tumor Suppressor DOK1 Expression	journal.ppat.1004125	null	[ [ "Cellular transformation induced by oncogenic viruses often involves the activation of growth-promoting signaling pathways and the inactivation of tumor suppressor genes .", "The downstream of tyrosine kinase 1gene ( DOK1 ) has emerged as a newly identified tumor suppressor gene that encodes a multi-domai...	[ "The DOK1 tumor suppressor gene encodes an adapter protein that acts as a negative regulator of several signaling pathways .", "We have previously reported that DOK1 expression is up-regulated upon cellular stress , via the transcription factor E2F1 , and down-regulated in a variety of human malignancies due to a...	[ "Many oncogenic viruses exhibit cellular transforming properties , often involving oncogenes activation and tumor suppressor genes inactivation .", "The DOK1 gene is a newly identified tumor suppressor gene with altered expression via hypermethylation of its promoter in a variety of human cancers , including head...	2014
[ "Introduction", "Materials and methods", "Results/Discussion" ]	[ "invertebrates", "medicine and health sciences", "microcephaly", "pathology and laboratory medicine", "atmospheric science", "pathogens", "geographical locations", "microbiology", "social sciences", "animals", "health care", "viruses", "developmental biology", "rna viruses", "el ni単o-sou...	After the epidemic: Zika virus projections for Latin America and the Caribbean	journal.pntd.0006007	null	[ [ "Zika virus ( ZIKV ) is a vector-borne disease that is transmitted among humans through the bite of infectious Aedes mosquitoes .", "ZIKV is a member of the Flaviviridae family , and genus Flavivirus .", "The symptoms of ZIKV infection are usually mild and similar to those of other arboviral infection...	[ "Zika is one of the most challenging emergent vector-borne diseases , yet its future public health impact remains unclear .", "Zika was of little public health concern until recent reports of its association with congenital syndromes .", "By 3 August 2017 ∼217 , 000 Zika cases and ∼3 , 400 cases of associated c...	[ "In February 2016 the World Health Organisation ( WHO ) declared Zika virus infection in the Americas as a Public Health Emergency of International Concern ( PHEIC ) .", "By November 2016 , Zika was declared a long-term public health challenge .", "This change of status implies that Zika is likely to become an ...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biotechnology", "genome-wide association studies", "plant genomes", "quantitative trait association studies", "quantitative trait loci", "population genetics", "quantitative traits", "statistical analysis of genetic association", "genome analysis", "trait locus analysis", "plant genomics", "d...	Natural CMT2 Variation Is Associated With Genome-Wide Methylation Changes and Temperature Seasonality	journal.pgen.1004842	null	[ [ "Arabidopsis thaliana has colonized a wide range of habitats across the world and it is therefore an attractive model for studying the genetic mechanisms underlying environmental adaptation [1] .", "Several large collections of A . thaliana accessions have either been whole-genome re-sequenced or high-den...	[ "As Arabidopsis thaliana has colonized a wide range of habitats across the world it is an attractive model for studying the genetic mechanisms underlying environmental adaptation .", "Here , we used public data from two collections of A . thaliana accessions to associate genetic variability at individual loci wit...	[ "A central problem when studying adaptation to a new environment is the interplay between genetic variation and phenotypic plasticity .", "Arabidopsis thaliana has colonized a wide range of habitats across the world and it is therefore an attractive model for studying the genetic mechanisms underlying environment...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "antimicrobials", "medicine and health sciences", "pathology and laboratory medicine", "pathogens", "drugs", "immunology", "microbiology", "antibiotic resistance", "pharmaceutics", "antibiotics", "pharmacology", "antimicrobial resistance", "pathogenesis", "immune response", "immunity", ...	Integrating Antimicrobial Therapy with Host Immunity to Fight Drug-Resistant Infections: Classical vs. Adaptive Treatment	journal.pcbi.1004857	null	[ [ "Overcoming antimicrobial resistance is currently considered an international medical priority [1 , 2] .", "The evolution of drug resistance affects our ability to treat new infections as well as carry out hospital procedures that rely on the prophylactic use of antibiotics such as surgeries and organ tra...	[ "Antimicrobial resistance of infectious agents is a growing problem worldwide .", "To prevent the continuing selection and spread of drug resistance , rational design of antibiotic treatment is needed , and the question of aggressive vs . moderate therapies is currently heatedly debated .", "Host immunity is an...	[ "The evolution and spread of antimicrobial resistance is a major global problem , and a cause of substantial human mortality .", "As the discovery of new antibiotics does not follow the rate at which new resistances develop , a more judicial use of available drugs is needed .", "Here we develop a mathematical m...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "mosquitoes", "immunity", "vector biology", "innate immunity", "virology", "biology", "microbiology" ]	Phenoloxidase Activity Acts as a Mosquito Innate Immune Response against Infection with Semliki Forest Virus	journal.ppat.1002977	null	[ [ "The transmission of arboviruses by mosquitoes and other arthropod vectors has considerable adverse impacts on human and animal health .", "This group of pathogens consists primarily of viruses in the families Flaviviridae , Togaviridae Bunyaviridae , and Reoviridae [1]–[4] .", "Arboviruses replicate ...	[ "Several components of the mosquito immune system including the RNA interference ( RNAi ) , JAK/STAT , Toll and IMD pathways have previously been implicated in controlling arbovirus infections .", "In contrast , the role of the phenoloxidase ( PO ) cascade in mosquito antiviral immunity is unknown .", "Here we ...	[ "Arboviruses are transmitted to vertebrates by arthropod vectors such as mosquitoes .", "Infection of mosquitoes with arboviruses activates immune defence responses including the RNA interference pathway .", "Another component of the insect immune system is the phenoloxidase ( PO ) cascade , which produces mela...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "liver", "immune physiology", "spleen", "microbiology", "vertebrates", "parasitic diseases", "protozoan life cycles", "mammals", "animals", "electromagnetic radiation", "parasitic protozoans", "developmental biology", "protozoans", "leishmania", "promast...	New insights into experimental visceral leishmaniasis: Real-time in vivo imaging of Leishmania donovani virulence	journal.pntd.0005924	null	[ [ "Protozoan parasites of the genus Leishmania are the causative agents of leishmaniasis , a neglected disease with worldwide distribution .", "With 350 million people at risk and 300 000 estimated cases , the visceral form of leishmaniasis ( VL ) can be fatal if not treated .", "The symptoms could vary...	[ "ClinicalTrials . gov 2013-0047 ." ]	[ "Visceral leishmaniasis is a chronic disease caused by the life-threatening parasite Leishmania donovani .", "This chronicity character is a major concern in experimental models of visceral leishmaniasis , since infected animals do not develop any visible sign or symptom before one/two months after infection .", ...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	ShcA Protects against Epithelial–Mesenchymal Transition through Compartmentalized Inhibition of TGF-β-Induced Smad Activation	journal.pbio.1002325	The adaptor protein ShcA protects epithelial cells from transitioning toward a mesenchymal phenotype by controlling partitioning of the TGF-β receptor and repressing downstream Smad2/3 activation.	[ [ "Shc proteins are intracellular adaptor proteins that relay signals from membrane-associated receptors , including receptor tyrosine ( Tyr ) kinases ( RTKs ) , cytokine receptors and integrins .", "They interact with phospho-Tyr residues through their N-terminal PTB domain and C-terminal SH2 domain and en...	[ "Epithelial–mesenchymal transition ( EMT ) is a normal cell differentiation event during development and contributes pathologically to carcinoma and fibrosis progression .", "EMT often associates with increased transforming growth factor-β ( TGF-β ) signaling , and TGF-β drives EMT , in part through Smad-mediated...	[ "TGF-β family proteins control cell differentiation and various cell functions .", "Increased TGF-β signaling , acting through heteromeric receptor complexes , contributes to carcinoma progression and fibrosis .", "TGF-β drives epithelial–mesenchymal transdifferentiation ( EMT ) , which enables cell migration a...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Exposure to an Indoor Cooking Fire and Risk of Trachoma in Children of Kongwa, Tanzania	journal.pntd.0003774	null	[ [ "Trachoma remains the leading infectious cause of preventable blindness in the world , and a significant public health problem in endemic areas . [1]", "Elimination of trachoma by 2020 can only be achieved if all affected areas have effective control programs in place at a prudential period before the tar...	[ "Elimination of blinding trachoma by 2020 can only be achieved if affected areas have effective control programs in place before the target date .", "Identifying risk factors for active disease that are amenable to intervention is important to successfully design such programs .", "Previous studies have linked ...	[ "Trachoma remains the leading preventable cause of infectious blindness in the world .", "Identifying risk factors for active disease that are amenable to intervention is key to successfully designing effective control programs to eliminate blinding trachoma .", "Association between cooking fire and eye inflamm...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The Structure of the RNA-Dependent RNA Polymerase of a Permutotetravirus Suggests a Link between Primer-Dependent and Primer-Independent Polymerases	journal.ppat.1005265	null	[ [ "RNA viruses strictly depend upon their RNA-dependent polymerases ( RdRPs ) for genome transcription and replication .", "Detailed structural and functional knowledge of RdRPs using different replication-transcription strategies may provide essential clues for the control of virus propagation .", "Alt...	[ "Thosea asigna virus ( TaV ) , an insect virus belonging to the Permutatetraviridae family , has a positive-sense single-stranded RNA ( ssRNA ) genome with two overlapping open reading frames , encoding for the replicase and capsid proteins .", "The particular TaV replicase includes a structurally unique RNA-depe...	[ "RNA dependent RNA polymerases ( RdRPs ) are the catalytic components of the RNA replication and transcription machineries , and thus central players in the life cycle of RNA viruses .", "The in-depth understanding of both the structure and regulation of viral RdRPs displaying different replication-transcription ...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "microbiology", "gene function", "telomeres", "model organisms", "molecular genetics", "dna", "mycology", "chromosome biology", "biology", "molecular biology", "yeast", "cell biology", "nucleic acids", "genetic screens", "gene identification and analysis", "genetics", "yeast and fung...	Telomerase-Null Survivor Screening Identifies Novel Telomere Recombination Regulators	journal.pgen.1003208	null	[ [ "Telomeres are special DNA-protein structures found at the ends of eukaryotic chromosomes .", "Telomeres are crucial for genome integrity because they prevent chromosome ends from degradation or fusing with each other [1] .", "In budding yeast Saccharomyces cerevisiae , telomeric DNA consists of ∼350 ...	[ "Telomeres are protein–DNA structures found at the ends of linear chromosomes and are crucial for genome integrity .", "Telomeric DNA length is primarily maintained by the enzyme telomerase .", "Cells lacking telomerase will undergo senescence when telomeres become critically short .", "In Saccharomyces cerev...	[ "Homologous recombination is a means for an organism or a cell to repair damaged DNA in its genome .", "Eukaryotic chromosomes have a linear configuration with two ends that are special DNA–protein structures called telomeres .", "Telomeres can be recognized by the cell as DNA double-strand breaks and subjected...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "plant biology", "gene function", "plant science", "pest control", "plant pathology", "molecular genetics", "gene expression", "plant genetics", "biology", "agriculture", "gene identification and analysis", "plant pathogens", "genetics", "genetics and genomics" ]	The Cysteine Rich Necrotrophic Effector SnTox1 Produced by Stagonospora nodorum Triggers Susceptibility of Wheat Lines Harboring Snn1	journal.ppat.1002467	null	[ [ "Like other parasites , fungal pathogens secrete a battery of molecules known as effectors during the infection process .", "These effectors can alter plant biological processes resulting in successful colonization [1] , [2] .", "Conversely , recognition of effectors by the plant innate immune system ...	[ "The wheat pathogen Stagonospora nodorum produces multiple necrotrophic effectors ( also called host-selective toxins ) that promote disease by interacting with corresponding host sensitivity gene products .", "SnTox1 was the first necrotrophic effector identified in S . nodorum , and was shown to induce necrosis...	[ "In this manuscript we describe the cloning of SnTox1 from Stagonospora nodorum , the gene encoding the first host selective toxin ( SnTox1 ) identified in this fungus .", "SnTox1 induces necrosis and promotes disease on wheat lines harboring the Snn1 gene .", "We verified the function of the SnTox1 gene by exp...	2012
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "sequencing techniques", "vertebrates", "animals", "blastulas", "developmental biology", "genome analysis", "sequence motif analysis", "epigenetics", "dna", "embryos", "molecular biology techniques", "dna methylation", "chromatin", "research and analysis methods", "sequence analysis", ...	Unlinking the methylome pattern from nucleotide sequence, revealed by large-scale in vivo genome engineering and methylome editing in medaka fish	journal.pgen.1007123	null	[ [ "DNA methylation is central to the epigenetic control of transcription in vertebrates and is essential for cell differentiation and embryonic development [1–3] .", "While the cytosines in cytosine-guanine ( CpG ) dinucleotides are extensively methylated throughout vertebrate genomes , unmethylated CpGs ar...	[ "The heavily methylated vertebrate genomes are punctuated by stretches of poorly methylated DNA sequences that usually mark gene regulatory regions .", "It is known that the methylation state of these regions confers transcriptional control over their associated genes .", "Given its governance on the transcript...	[ "The genomes of vertebrate animals are naturally and extensively modified by methylation .", "The DNA methylation is essential to normal functions of cells , hence the whole animal , since it governs gene expression .", "Defects in the establishment and maintenance of proper methylation pattern are commonly ass...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "chemistry", "biology" ]	Binding Polymorphism in the DNA Bound State of the Pdx1 Homeodomain	journal.pcbi.1003160	null	[ [ "Specific DNA binding plays a key role in the protein-DNA recognition process necessary for the regulation of gene expression .", "Binding determinants are complex , including direct amino acid-base contacts , indirect water-mediated contacts , and local geometry of the DNA sequence [1] .", "Although ...	[ "The subtle effects of DNA-protein recognition are illustrated in the homeodomain fold .", "This is one of several small DNA binding motifs that , in spite of limited DNA binding specificity , adopts crucial , specific roles when incorporated in a transcription factor .", "The homeodomain is composed of a 3-hel...	[ "All organisms require the capability to control gene expression .", "In eukaryotes , transcription factors play an important role in gene regulation by recognizing specific DNA control regions associated with each gene .", "The DNA binding domains of transcription factors belong to evolutionarily conserved fam...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "veterinary diseases", "veterinary virology", "veterinary science" ]	Host Alternation Is Necessary to Maintain the Genome Stability of Rift Valley Fever Virus	journal.pntd.0001156	null	[ [ "Most arthropod-borne viruses ( arboviruses ) are RNA viruses , although they use a variety of strategies to ensure their replication and transmission .", "The feature that best distinguishes RNA genomes from DNA ones is the high mutation rate of the former during replication .", "Misincorporation err...	[ "Most arthropod-borne viruses ( arboviruses ) are RNA viruses , which are maintained in nature by replication cycles that alternate between arthropod and vertebrate hosts .", "Arboviruses appear to experience lower rates of evolution than RNA viruses that replicate in a single host .", "This genetic stability i...	[ "Arthropod-borne viruses are transmitted among vertebrate hosts by insect vectors .", "Unusually , Rift Valley fever virus ( RVFV ) can also be transmitted by direct contacts of animals/humans with infectious tissues .", "What are the molecular mechanisms and evolutionary events leading to adopt one mode of tra...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "death rates", "children", "medicine and health sciences", "pathology and laboratory medicine", "european union", "education", "infectious disease epidemiology", "pathogens", "sociology", "geographical locations", "microbiology", "social sciences", "viruses", "age groups", "dna viruses",...	Modeling the impact of changes in day-care contact patterns on the dynamics of varicella transmission in France between 1991 and 2015	journal.pcbi.1006334	null	[ [ "Varicella is a vaccine-preventable infectious disease caused by exposure to Varicella-Zoster Virus ( VZV ) .", "The pathogen is antigenically stable so that , in principle , no changes in transmission or immunogenicity caused by mutations of the virus are expected over time [1] .", "In France , about...	[ "Annual incidence rates of varicella infection in the general population in France have been rather stable since 1991 when clinical surveillance started .", "Rates however show a statistically significant increase over time in children aged 0–3 years , and a decline in older individuals .", "A significant incre...	[ "During the last decades , an increasing circulation of varicella in the early childhood has been observed in France .", "A plausible explanation of this trend may rely on the progressive increase of day-care attendance in the past years , which could have anticipated the exposure of young children to the infecti...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "small intestine", "medicine and health sciences", "chemical compounds", "pathology and laboratory medicine", "sialic acids", "sphingolipids", "pathogens", "vibrio", "tropical diseases", "microbiology", "carbohydrates", "organic compounds", "diarrhea", "bacterial diseases", "physiologica...	Human evolutionary loss of epithelial Neu5Gc expression and species-specific susceptibility to cholera	journal.ppat.1007133	null	[ [ "Cholera is a life-threatening , human-specific disease caused by the noninvasive enteric bacterium Vibrio cholerae that affects millions of people worldwide [1] .", "Humans are infected after ingestion of food or water contaminated with the pathogen .", "Bacteria that survive passage through the acid...	[ "While infectious agents have typical host preferences , the noninvasive enteric bacterium Vibrio cholerae is remarkable for its ability to survive in many environments , yet cause diarrheal disease ( cholera ) only in humans .", "One key V . cholerae virulence factor is its neuraminidase ( VcN ) , which releases...	[ "Ingestion of food or water contaminated with the bacterium Vibrio cholerae can cause fatal diarrheal disease ( cholera ) in humans , but not in other mammals exposed to the bacterium .", "This unusual pathogen uses a specialized enzyme V . cholerae neuraminidase ( VcN ) to cleave sugars called sialic acids and t...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "functional genomics", "chromosome structure and function", "microbiology", "histone modification", "model organisms", "epigenetics", "chromatin", "chromosome biology", "gene expression", "biology", "molecular biology", "cell biology", "genetics", "yeast and fungal models", "genomics", ...	A Barcode Screen for Epigenetic Regulators Reveals a Role for the NuB4/HAT-B Histone Acetyltransferase Complex in Histone Turnover	journal.pgen.1002284	null	[ [ "The epigenetic landscape in the cell is dynamic and shaped by histone modifying and demodifying enzymes .", "In addition , histones themselves can also be dynamic; they can be moved along the DNA through the action of ATP-dependent nucleosome remodeling enzymes or can be evicted and replaced by new histo...	[ "Dynamic modification of histone proteins plays a key role in regulating gene expression .", "However , histones themselves can also be dynamic , which potentially affects the stability of histone modifications .", "To determine the molecular mechanisms of histone turnover , we developed a parallel screening me...	[ "Packaging of eukaryotic genomes by the histone proteins influences many processes that use the DNA , such as transcription , repair , and replication .", "One well-known mechanism of regulation of histone function is the covalent modification of histone proteins .", "Replacement of modified histones by new his...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "biophysics", "neuroscience" ]	Resolving the Fast Kinetics of Cooperative Binding: Ca2+ Buffering by Calretinin	journal.pbio.0050311	A novel and relatively simple mathematical model for the kinetics of cooperative binding reveals, the tuning of Ca2+-buffering kinetics due to cooperative binding in calretinin.	[ [ "In all eukaryotic cells , Ca2+ signals play a crucial role in the regulation of many cellular processes , including gene expression , cytoskeleton dynamics , cell cycle , cell death , neurotransmission , and signal transduction .", "To achieve its role as messenger , the intracellular Ca2+ concentration ...	[ "Cooperativity is one of the most important properties of molecular interactions in biological systems .", "It is the ability to influence ligand binding at one site of a macromolecule by previous ligand binding at another site of the same molecule .", "As a consequence , the affinity of the macromolecule for t...	[ "The binding of a ligand to a protein is one of the most important steps in determining the function of these two interactive biological partners .", "In many cases , successive binding steps occur at multiple sites such that binding at one site influences ligand binding at other sites .", "This concept is call...	2007
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "molecular biology/bioinformatics", "mathematics/statistics", "computational biology/sequence motif analysis" ]	Measuring Global Credibility with Application to Local Sequence Alignment	journal.pcbi.1000077	null	[ [ "The study of genomics , and much of computational molecular biology , is about the inference or prediction of discrete , high-dimensional ( high-D ) unobserved variables , based on observed data .", "For example , in RNA secondary structure prediction , the challenge is to select a specific set of base p...	[ "Computational biology is replete with high-dimensional ( high-D ) discrete prediction and inference problems , including sequence alignment , RNA structure prediction , phylogenetic inference , motif finding , prediction of pathways , and model selection problems in statistical genetics .", "Even though predicti...	[ "Sequence alignment is the cornerstone capability used by a multitude of computational biology applications , such as phylogeny reconstruction and identification of common regulatory mechanisms .", "Sequence alignment methods typically seek a high-scoring alignment between a pair of sequences , and assign a stati...	2008
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "medicine and health sciences", "vesicles", "viral transmission and infection", "molecular probe techniques", "endothelial cells", "rna extraction", "immunoblotting", "microbiology", "vertebrates", "neuroscience", "animals", "epithelial cells", "molecular biology technique...	Exosomes serve as novel modes of tick-borne flavivirus transmission from arthropod to human cells and facilitates dissemination of viral RNA and proteins to the vertebrate neuronal cells	journal.ppat.1006764	null	[ [ "Exosomes are small membranous extracellular microvesicles ( 30 to 250 nm in diameter ) of endocytic origin formed in late endosomal compartments ( as multivesicular bodies; MVBs ) of several different cell types [1–5] .", "Initially , exosomes were considered as garbage bins to discard the unwanted cellu...	[ "Molecular determinants and mechanisms of arthropod-borne flavivirus transmission to the vertebrate host are poorly understood .", "In this study , we show for the first time that a cell line from medically important arthropods , such as ticks , secretes extracellular vesicles ( EVs ) including exosomes that medi...	[ "In this study we have demonstrated that cells from the medically important vector tick , secretes exosomes that mediate transmission of tick-borne Langat ( LGTV ) viruses from arthropod to human and other vertebrate host cells .", "This study not only provides evidence that suggest tick-borne pathogens use arthr...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing techniques", "engineering and technology", "astronomical sciences", "astronomical instruments", "genome analysis", "genetic elements", "optical equipment", "molecular biology techniques", "rna sequencing", "research and analysis methods", "sequence analysis", "computer and informat...	Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression	journal.pcbi.1006453	null	[ [ "Transposable elements ( TEs ) represent the largest class of biochemically functional DNA elements in mammalian genomes[1 , 2] comprising nearly 50% of the human genome .", "As many of these transcriptionally active elements originated as retroelements , we refer to the set of RNA molecules transcribed f...	[ "Characterization of Human Endogenous Retrovirus ( HERV ) expression within the transcriptomic landscape using RNA-seq is complicated by uncertainty in fragment assignment because of sequence similarity .", "We present Telescope , a computational software tool that provides accurate estimation of transposable ele...	[ "Almost half of the human genome is composed of Transposable elements ( TEs ) , but their contribution to the transcriptome , their cell-type specific expression patterns , and their role in disease remains poorly understood .", "Recent studies have found many elements to be actively expressed and involved in key...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "evolutionary modeling", "genetics", "population genetics", "biology", "computational biology" ]	Coalescent Tree Imbalance and a Simple Test for Selective Sweeps Based on Microsatellite Variation	journal.pcbi.1003060	null	[ [ "Consider the coalescent tree for a sample of size .", "It is a binary tree without left-right orientation , with ordered internal nodes and branch lengths representing a measure of time .", "All leaves are aligned on the bottom line , representing the present .", "We use the term tree topology wh...	[ "Selective sweeps are at the core of adaptive evolution .", "We study how the shape of coalescent trees is affected by recent selective sweeps .", "To do so we define a coarse-grained measure of tree topology .", "This measure has appealing analytical properties , its distribution is derived from a uniform , ...	[ "It is one of the major interests in population genetics to contrast the properties and consequences of neutral and non-neutral modes of evolution .", "As is well-known , positive Darwinian selection and genetic hitchhiking drastically change the profile of genetic diversity compared to neutral expectations .", ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases", "medicine and health sciences", "gastroenterology and hepatology", "biology and life sciences", "immunology" ]	Incomplete Deletion of IL-4Rα by LysMCre Reveals Distinct Subsets of M2 Macrophages Controlling Inflammation and Fibrosis in Chronic Schistosomiasis	journal.ppat.1004372	null	[ [ "Tissue macrophages exhibit substantial plasticity and can quickly change their function in response to different stimuli found in the local milieu [1] , and distinct subsets with characteristic functional activities have been described .", "Alternatively activated macrophages ( AAMs ) , also called M2 or...	[ "Mice expressing a Cre recombinase from the lysozyme M-encoding locus ( Lyz2 ) have been widely used to dissect gene function in macrophages and neutrophils .", "Here , we show that while naïve resident tissue macrophages from IL-4Rαflox/deltaLysMCre mice almost completely lose IL-4Rα function , a large fraction ...	[ "Chronic injury and inflammation lead to irreversible fibrosis in a range of diseases and infections .", "Macrophages alternatively activated by the immune system are capable of regulating inflammation and fibrosis , but our understanding of the source and function of these cells is incomplete .", "Mice genetic...	2014
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "keratinocytes", "pathology and laboratory medicine", "pathogens", "hpv-11", "microbiology", "cell differentiation", "epithelial cells", "viruses", "developmental biology", "dna replication", "dna viruses", "viral genome", "dna", "microbial genomics", "v...	Roles for E1-independent replication and E6-mediated p53 degradation during low-risk and high-risk human papillomavirus genome maintenance	journal.ppat.1007755	null	[ [ "Papillomaviruses ( PV ) are small double-stranded DNA viruses which infect stratified epithelia , with the completion of their life cycle being intimately linked to the terminal differentiation program of keratinocytes .", "One of the most distinctive characteristics of papillomaviruses is their genotype...	[ "Human papillomaviruses ( HPV ) have genotype-specific disease associations , with high-risk alpha types causing at least 5% of all human cancers .", "Despite these conspicuous differences , our data show that high- and low- risk HPV types use similar approaches for genome maintenance and persistence .", "Durin...	[ "Human papillomavirus research has been prioritised towards understanding the progression of high-risk HPV infections to malignant cancer , rather than the regulation of the HPV productive cycle .", "Low-risk HPV types are often considered as a ‘less effective’ version of their high-risk counterparts .", "To da...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "epistasis", "aging", "developmental biology", "genome analysis tools", "genetic networks", "functional genomics", "organism development", "model organisms", "genetic screens", "heredity", "genetics", "yeast and fungal models", "biology", "genomics", "gene networks" ]	High-Resolution Profiling of Stationary-Phase Survival Reveals Yeast Longevity Factors and Their Genetic Interactions	journal.pgen.1004168	null	[ [ "Lifespan is a complex trait with clear genetic underpinnings [1] .", "Mutations in the insulin/IGF-1 receptor gene daf-2 increase the lifespan of Caenorhabditis elegans [2] and Drosophila melanogaster [3] , while mice lacking the insulin receptor in adipose tissue live longer as well [4] .", "Studies...	[ "Lifespan is influenced by a large number of conserved proteins and gene-regulatory pathways .", "Here , we introduce a strategy for systematically finding such longevity factors in Saccharomyces cerevisiae and scoring the genetic interactions ( epistasis ) among these factors .", "Specifically , we developed a...	[ "The budding yeast Saccharomyces cerevisiae has emerged as an important model for the genetic analysis of aging , and insights gained about this process in yeast cells enhance our understanding of aging in other organisms , including humans .", "Even in yeast , our knowledge of the number and identity of the gene...	2014
[ "Introduction", "Methods", "Results and discussion" ]	[ "invertebrates", "medicine and health sciences", "body fluids", "microbiome", "chemical compounds", "disaccharides", "metabolic processes", "microbiology", "carbohydrates", "organic compounds", "animals", "molecular biology techniques", "insect vectors", "bacteria", "microbial genomics",...	Amino acid metabolic signaling influences Aedes aegypti midgut microbiome variability	journal.pntd.0005677	null	[ [ "Aedes aegypti mosquitoes are a primary vector for multiple arboviruses that infect humans including dengue virus , chikungunya virus , yellow fever virus and Zika virus .", "Dengue alone inflicts a staggering disease burden , with approximately 3 . 9 billion people globally at risk of contracting the vir...	[ "The mosquito midgut microbiota has been shown to influence vector competence for multiple human pathogens .", "The microbiota is highly variable in the field , and the sources of this variability are not well understood , which limits our ability to understand or predict its effects on pathogen transmission .", ...	[ "The mosquito midgut microbiota plays an important role in mosquito susceptibility to human pathogens and therefore is an important component of mosquito disease transmission .", "The microbiota can be highly variable , however , and the sources of this variation are not well understood .", "In this work , we a...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/gene discovery", "genetics and genomics/gene expression", "genetics and genomics/functional genomics", "developmental biology/plant growth and development", "plant biology/plant growth and development", "developmental biology/developmental molecular mechanisms" ]	DEP and AFO Regulate Reproductive Habit in Rice	journal.pgen.1000818	null	[ [ "Flowering is an important process essential for sexual reproduction , seed development and fruit production .", "Although flowering is composed of a series of typically irreversible sequential events , reversion from floral to vegetative growth is frequently observed in nature .", "Reversions can be ...	[ "Sexual reproduction is essential for the life cycle of most angiosperms .", "However , pseudovivipary is an important reproductive strategy in some grasses .", "In this mode of reproduction , asexual propagules are produced in place of sexual reproductive structures .", "However , the molecular mechanism of ...	[ "Sexual reproduction is essential for the life cycle of most flowering plants .", "However , pseudovivipary , in which floral organs are replaced by bulbils or plantlets , provides an asexual means for many grasses to reproduce in extreme environments .", "Although the molecular mechanism of pseudovivipary is s...	2010
[ "Introduction", "Results", "Discussion", "Model" ]	[ "computer science", "theoretical biology", "genetics", "population biology", "biology", "computational biology", "evolutionary biology", "computerized simulations" ]	Mate Choice and the Origin of Menopause	journal.pcbi.1003092	null	[ [ "Evolutionary theories of life history predict that selection should operate against living beyond the age of reproduction [1]–[3] .", "Postmenopausal survival is , however , a characteristic that almost is uniquely human [4] , reported otherwise only in whales [5] , [6] or captive chimpanzees [7]; data f...	[ "Human menopause is an unsolved evolutionary puzzle , and relationships among the factors that produced it remain understood poorly .", "Classic theory , involving a one-sex ( female ) model of human demography , suggests that genes imparting deleterious effects on post-reproductive survival will accumulate .", ...	[ "The origin and evolution of menopause is understood poorly and explanations remain contentious .", "Virtually ignored among explanations is the effect that mate choice can exert on an evolving population .", "We designed and used a computational model and computer simulation to show that male mating preference...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma mansoni", "medicine and health sciences", "parasite groups", "plasmodium", "helminths", "plasmodium yoelii", "tropical diseases", "parasitic diseases", "parasitic protozoans", "animals", "parasitology", "animal models", "apicomplexa", "model...	Schistosoma mansoni infection suppresses the growth of Plasmodium yoelii parasites in the liver and reduces gametocyte infectivity to mosquitoes	journal.pntd.0006197	null	[ [ "Malaria and schistosomiasis are two of the most important parasitic diseases in the tropics , and together constitute a severe burden to public health and to the economic development of endemic countries .", "Malaria is estimated to cause 429 , 000 deaths per year , 70% of those occurring in children age...	[ "Malaria and schistosomiasis are major parasitic diseases causing morbidity and mortality in the tropics .", "Epidemiological surveys have revealed coinfection rates of up to 30% among children in Sub-Saharan Africa .", "To investigate the impact of coinfection of these two parasites on disease epidemiology and...	[ "Malaria and schistosomiasis are parasitic infectious diseases that cause severe morbidity and mortality in the tropics .", "Chronic schistosomiasis causes malnutrition and impaired intellectual development to children while malaria can cause fatal acute infections .", "Since coinfection of these two parasites ...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "bacteriology", "microbial mutation", "genomics", "functional genomics", "microbial physiology", "medicine and health sciences", "pathology and laboratory medicine", "host-pathogen interactions", "genetic screens", "genome analysis", "gene identification and analysis", "medical microbiology", ...	New Insights into How Yersinia pestis Adapts to Its Mammalian Host during Bubonic Plague	journal.ppat.1004029	null	[ [ "Plague ( caused by the bacterium Yersinia pestis ) is one of the diseases that has most greatly affected the course of history [1] , [2] and is still an international public health concern .", "The WHO has even categorized this disease as re-emergent in some parts of the world .", "This problem is he...	[ "Bubonic plague ( a fatal , flea-transmitted disease ) remains an international public health concern .", "Although our understanding of the pathogenesis of bubonic plague has improved significantly over the last few decades , researchers have still not been able to define the complete set of Y . pestis genes nee...	[ "In order to understand and combat infectious diseases , it is essential to characterize the full set of genes required by pathogenic bacteria to overcome the many immunological and physiological challenges encountered during infection .", "Here , we used a genome-scale approach to identify genes required by the ...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Phosphorylation at the Homotypic Interface Regulates Nucleoprotein Oligomerization and Assembly of the Influenza Virus Replication Machinery	journal.ppat.1004826	null	[ [ "Influenza viruses are major human respiratory pathogens that cause isolated seasonal outbreaks as well as the sporadic emergence of severe pandemics [1] .", "Influenza A virus ( Orthomyxoviridae ) is a segmented , negative-sense RNA virus .", "Like all other negative-sense RNA viruses , the influenza...	[ "Negative-sense RNA viruses assemble large ribonucleoprotein ( RNP ) complexes that direct replication and transcription of the viral genome .", "Influenza virus RNPs contain the polymerase , genomic RNA and multiple copies of nucleoprotein ( NP ) .", "During RNP assembly , monomeric NP oligomerizes along the l...	[ "Replication and transcription by negative-sense RNA viruses occurs in large macromolecular complexes .", "These complexes contain the viral polymerase , genomic RNA , and multiple copies of nucleoprotein that bind RNA and oligomerize to coat the genome .", "For influenza virus , nucleoprotein ( NP ) non-specif...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology/cell growth and division", "cell biology/developmental molecular mechanisms", "cell biology/cell signaling" ]	The Nuclear Receptor DHR3 Modulates dS6 Kinase–Dependent Growth in Drosophila	journal.pgen.1000937	null	[ [ "During development , cell growth arrests when organs reach their appropriate size [1] such that differentiation acts to impede further growth .", "However , the growth-regulating module can be reactivated in specific cell types to maintain homeostasis in the adult .", "Moreover , pathological setting...	[ "S6 kinases ( S6Ks ) act to integrate nutrient and insulin signaling pathways and , as such , function as positive effectors in cell growth and organismal development .", "However , they also have been shown to play a key role in limiting insulin signaling and in mediating the autophagic response .", "To identi...	[ "In biological systems , the execution of morphogenic programs requires coordinated integration of the essential processes of growth , proliferation , and differentiation .", "Signaling networks embedded within these processes include the insulin and nutrient pathways required for cell growth and the steroid horm...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "protein synthesis", "protein synthesis inhibitors", "proteins", "biology and life sciences", "transmembrane receptors", "cell-free protein synthesis" ]	Signal Peptide-Binding Drug as a Selective Inhibitor of Co-Translational Protein Translocation	journal.pbio.1002011	A small chemical drug CADA specifically binds to the signal peptide of the membrane pre-protein CD4, disturbing its synthesis, impeding the routing to and expression on the cell surface.	[ [ "CD4 is a type I integral membrane glycoprotein that is expressed on the surface of thymocytes , T-helper lymphocytes , and cells of the macrophage/monocyte lineage [1] .", "It plays a central role in immune responses but also represents an obligatory component of the cellular receptor complex for HIV [2]...	[ "In eukaryotic cells , surface expression of most type I transmembrane proteins requires translation and simultaneous insertion of the precursor protein into the endoplasmic reticulum ( ER ) membrane for subsequent routing to the cell surface .", "This co-translational translocation pathway is initiated when a hy...	[ "All cells are highly crowded with proteins that , once synthesized , have to reach their proper subcellular location in order to maintain the cellular homeostasis .", "Approximately 30% of the proteome needs to be sorted from the cytosol and inserted into , or transported through , biological membranes .", "Fo...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunology/antigen processing and recognition", "virology/immune evasion" ]	B Cell Recognition of the Conserved HIV-1 Co-Receptor Binding Site Is Altered by Endogenous Primate CD4	journal.ppat.1000171	null	[ [ "The human immunodeficiency virus ( HIV-1 ) exterior envelope glycoprotein , gp120 , and the transmembrane glycoprotein , gp41 , are non-covalently associated to comprise the trimeric , functional viral spike .", "These glycoproteins mediate entry and represent the sole virally encoded targets for neutral...	[ "The surface HIV-1 exterior envelope glycoprotein , gp120 , binds to CD4 on the target cell surface to induce the co-receptor binding site on gp120 as the initial step in the entry process .", "The binding site is comprised of a highly conserved region on the gp120 core , as well as elements of the third variable...	[ "A major goal of HIV-1 vaccine research is to design novel candidates capable of neutralizing the vast array of viruses circulating in the human population .", "One approach is to base the vaccine upon the HIV-1 outer surface envelope glycoproteins to generate antibodies .", "However , during persistent infecti...	2008
[ "Introduction", "Materials and Methods", "Results and Discussion" ]	[]	Comparison of Phylogeny, Venom Composition and Neutralization by Antivenom in Diverse Species of Bothrops Complex	journal.pntd.0002442	null	[ [ "Envenomation by snakebites , which is incorporated by the World Health Organization ( WHO ) in its list of neglected tropical diseases , constitutes an important worldwide public health concern , particularly in the rural areas of tropical countries as Africa , Asia and Latin America , affecting mostly agric...	[ "In Latin America , Bothrops snakes account for most snake bites in humans , and the recommended treatment is administration of multispecific Bothrops antivenom ( SAB – soro antibotrópico ) .", "However , Bothrops snakes are very diverse with regard to their venom composition , which raises the issue of which ven...	[ "Snakebite envenomation is a serious health issue in Latin America , particularly in the Amazon , where antivenom administration may be delayed due to logistic constraints .", "Bothrops snakes are involved in most of the snakebite-related accidents in Brazil .", "This work reports a comparative study of the tox...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "evidence-based healthcare/clinical decision-making", "infectious diseases/neglected tropical diseases", "infectious diseases/tropical and travel-associated diseases", "critical care and emergency medicine/sepsis and multiple organ failure" ]	Differential Cytokine Gene Expression According to Outcome in a Hamster Model of Leptospirosis	journal.pntd.0000582	null	[ [ "Leptospirosis is the most widespread zoonosis occurring worldwide with possible fatal outcomes [1] .", "Though most often an endemic disease , epidemics have been associated with particular meteorological events [2]–[4] or clusters of cases related to occupations or leisure activities [5]–[8] .", "It...	[ "Parameters predicting the evolution of leptospirosis would be useful for clinicians , as well as to better understand severe leptospirosis , but are scarce and rarely validated .", "Because severe leptospirosis includes septic shock , similarities with predictors evidenced for sepsis and septic shock were studie...	[ "Leptospirosis is a widespread bacterial infection that is transmitted by soil or water contaminated by the urine of infected animals , or directly from these animals .", "It has highly diverse clinical presentations , making its differential diagnosis difficult .", "Though most cases are minor and self-resolvi...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "rna interference", "decision making", "social sciences", "neuroscience", "reproductive physiology", "cognition", "epigenetics", "animal cells", "taste", "genetic interference", "gene expression", "olfactory receptor neurons", "biochemistry", "rna", "sen...	Neuropeptides Modulate Female Chemosensory Processing upon Mating in Drosophila	journal.pbio.1002455	During pregnancy, women frequently report that their food preferences change—sometimes dramatically. This study unravels a mechanism that changes a mated female’s perception of odors and tastes and thereby adapts her food choices to her reproductive state.	[ [ "The behavior of females in most animal species changes significantly as a consequence of mating .", "Those changes are interpreted from an evolutionary standpoint as the female’s preparation to maximize the fitness of her offspring .", "In general , they entail a qualitative and quantitative change i...	[ "A female’s reproductive state influences her perception of odors and tastes along with her changed behavioral state and physiological needs .", "The mechanism that modulates chemosensory processing , however , remains largely elusive .", "Using Drosophila , we have identified a behavioral , neuronal , and gene...	[ "Food choices often correlate with nutritional needs or physiological states of an animal .", "For instance , during pregnancy , women frequently report that their food preferences change—sometimes dramatically .", "In part , this change in preference is brought about by a change in the perception of smells and...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "invertebrates", "animals", "invertebrate genomics", "animal models", "drosophila melanogaster", "model organisms", "epigenetics", "molecular biology techniques", "chromatin", "drosophila", "polytene chromosomes", "heterochromatin", "research and analysis methods", "genome complexity", "...	Comparative Genomic Analyses Provide New Insights into the Evolutionary Dynamics of Heterochromatin in Drosophila	journal.pgen.1006212	null	[ [ "The organization of eukaryotic genomes into euchromatin and heterochromatin represents one of the most important and still unsolved aspects of genome evolution .", "Heterochromatin was originally identified from the early observation that specific regions of interphase nuclei possess distinctive staining...	[ "The term heterochromatin has been long considered synonymous with gene silencing , but it is now clear that the presence of transcribed genes embedded in pericentromeric heterochromatin is a conserved feature in the evolution of eukaryotic genomes .", "Several studies have addressed the epigenetic changes that e...	[ "This study concerns the evolutionary dynamics underlying the emergence of heterochromatic single-copy genes in D . melanogaster heterochromatin .", "By combining genome annotation analysis and high-resolution cytology , we have performed a comparative mapping of the orthologs of 53 single-copy genes of D . melan...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "tropical diseases", "geographical locations", "parasitic diseases", "health care", "bacterial diseases", "health services administration and management", "signs and symptoms", "ulcers", "neglected tropical diseases", "infect...	Implementing active community-based surveillance-response system for Buruli ulcer early case detection and management in Ghana	journal.pntd.0006776	null	[ [ "Buruli ulcer ( BU ) is one of the most neglected debilitating tropical diseases caused by Mycobacterium ulcerans .", "Though , BU-related fatality is very rare , it causes considerable morbidity and disability [1–3] , which lead to stigma and anguish among infected individuals and affected families .", ...	[ "Buruli Ulcer ( BU ) is one of the most neglected debilitating tropical diseases caused by Mycobacterium ulcerans , which causes considerable morbidity and disability .", "Building on earlier findings that community-based interventions could enhance case detection and reduce treatment dropout and defaulter rates ...	[ "The study revealed that it is feasible to train periphery health workers and community-based volunteers to implement a community-based active surveillance–response system for early buruli ulcer ( BU ) case detection , diagnosis and treatment at outpatient clinics .", "At the end of 12 months follow-up , there we...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing techniques", "luciferase", "molecular probe techniques", "prions", "enzymes", "enzymology", "immunoblotting", "nucleotides", "chaperone proteins", "molecular biology techniques", "research and analysis methods", "artificial gene amplification and extension", "proteins", "oxidor...	Distinct Prion Domain Sequences Ensure Efficient Amyloid Propagation by Promoting Chaperone Binding or Processing In Vivo	journal.pgen.1006417	null	[ [ "The ability of some proteins to adopt alternative conformations expands the functional range of the proteome by allowing individual proteins to access multiple conformers .", "For a unique and expanding class of proteins , these conformational transitions are extensive and lead to the assembly of the pro...	[ "Prions are a group of proteins that can adopt a spectrum of metastable conformations in vivo .", "These alternative states change protein function and are self-replicating and transmissible , creating protein-based elements of inheritance and infectivity .", "Prion conformational flexibility is encoded in the ...	[ "Protein misfolding and assembly into ordered aggregates known as amyloid has emerged as a novel mechanism for regulation of protein function .", "In the case of prion proteins , the resulting amyloid is transmissible , creating protein-based elements of infectivity and inheritance .", "These unusual properties...	2016
[ "Introduction", "Result", "Discussion", "Materials and methods" ]	[ "phosphorylation", "medicine and health sciences", "fish", "molecular probe techniques", "cell processes", "immunoblotting", "vertebrates", "animals", "animal models", "organisms", "physiological processes", "developmental biology", "osteichthyes", "model organisms", "experimental organi...	Marcksb plays a key role in the secretory pathway of zebrafish Bmp2b	journal.pgen.1008306	null	[ [ "Early vertebrate development involves the formation and patterning of body plan , such as dorsoventral axis formation and anteroposterior axis formation .", "Bone morphogenetic protein ( BMP ) signaling gradient is critical for the specification of ventral and posterior cell fate [1] .", "Like other ...	[ "During vertebrate early embryogenesis , the ventral development is directed by the ventral-to-dorsal activity gradient of the bone morphogenetic protein ( BMP ) signaling .", "As secreted ligands , the extracellular traffic of BMP has been extensively studied .", "However , it remains poorly understood that ho...	[ "Bone morphogenetic proteins ( BMPs ) are extracellular proteins which belong to the transforming growth factor-β ( TGF-β ) superfamily .", "BMP signaling is essential for embryonic development , organogenesis , and tissue regeneration and homeostasis , and tightly linked to various diseases and tumorigenesis .",...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "protozoans", "leishmania", "pathology and laboratory medicine", "host-pathogen interactions", "parasitology", "protozoology", "biology and life sciences", "microbiology", "pathogenesis", "parasitic protozoans", "organisms" ]	Leishmania aethiopica Field Isolates Bearing an Endosymbiontic dsRNA Virus Induce Pro-inflammatory Cytokine Response	journal.pntd.0002836	null	[ [ "In the highlands of Ethiopia , patients infected with L . aethiopica mostly develop localized cutaneous lesions , which can self heal .", "There is no accurate national figure for the overall burden of cutaneous leishmaniasis ( CL ) in Ethiopia , although some estimates suggest annual incidence to range ...	[ "Infection with Leishmania parasites causes mainly cutaneous lesions at the site of the sand fly bite .", "Inflammatory metastatic forms have been reported with Leishmania species such as L . braziliensis , guyanensis and aethiopica .", "Little is known about the factors underlying such exacerbated clinical pre...	[ "Leishmania RNA virus ( LRV ) has been detected in Leishmania ( Viannia ) braziliensis and guyanensis species , parasites causing not only cutaneous but also mucosal and disseminated leishmaniases .", "In a mouse model , the viral dsRNA genome within L . guyanensis parasites is recognized by host Toll-like recept...	2014
[ "Introduction", "Results/Discussion", "Methods" ]	[ "physics", "biochemistry", "protein chemistry", "biochemistry simulations", "proteins", "biophysic al simulations", "evolutionary modeling", "protein structure", "evolutionary biology", "biology", "hemoproteins", "biophysics", "computational biology" ]	Positively Selected Sites in Cetacean Myoglobins Contribute to Protein Stability	journal.pcbi.1002929	null	[ [ "Upon adapting to the aquatic environment , marine mammals acquired features that improved their diving skills such as increased blood volume and hematocrit , efficient modes of locomotion ( stroke-and-glide swimming ) [1] , [2] and ∼10–20 times higher myoglobin ( Mb ) concentration ( CMb ) in the skeletal mu...	[ "Since divergence ∼50 Ma ago from their terrestrial ancestors , cetaceans underwent a series of adaptations such as a ∼10–20 fold increase in myoglobin ( Mb ) concentration in skeletal muscle , critical for increasing oxygen storage capacity and prolonging dive time .", "Whereas the O2-binding affinity of Mbs is ...	[ "In this work , we identify positive selection in cetacean myoglobins and an early , significant divergence event .", "While O2-binding is nearly unchanged , positive selection acts to introduce and later maintain stability .", "Stability correlates with abundance across the species , supporting that selection ...	2013
[ "Introduction", "Methods", "Results", "Discussion", "Conclusion" ]	[ "invertebrates", "rubber", "medicine and health sciences", "ecology and environmental sciences", "elastomers", "infectious disease epidemiology", "tropical diseases", "parasitic diseases", "animals", "parasitic protozoans", "protozoans", "materials science", "infectious disease control", "...	Risk of exposure to potential vector mosquitoes for rural workers in Northern Lao PDR	journal.pntd.0005802	null	[ [ "Today we have entered the Anthropocene epoch , in recognition of the major impact human beings have on the environment [1] .", "Many of the changes in land use and climate are also likely to increase the risk of vector-borne diseases [2–6] .", "One of the largest environmental changes in South-East A...	[ "One major consequence of economic development in South-East Asia has been a rapid expansion of rubber plantations , in which outbreaks of dengue and malaria have occurred .", "Here we explored the difference in risk of exposure to potential dengue , Japanese encephalitis ( JE ) , and malaria vectors between rubb...	[ "Rapid economic development in South-East Asia has resulted in a high demand for rubber , leading to the felling of natural forest and the expansion of rubber plantations .", "Hundred-thousands of people work in these man-made forests throughout the region , with some studies showing a higher risk of vector-borne...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "ears", "precursor cells", "neuroscience", "cell differentiation", "outer hair cells", "developmental biology", "organ of corti", "inner ear", "embryos", "embryology", "animal cells", "biological tissue", "head", "inner hair cells", "cellular neuroscienc...	Six1 is essential for differentiation and patterning of the mammalian auditory sensory epithelium	journal.pgen.1006967	null	[ [ "In response to a variety of signals , the prosensory progenitors in the floor of the mammalian cochlear duct enter terminal mitosis and then differentiate into a mosaic of mechanosensory hair cells ( one row of inner and three rows of outer hair cells ) interdigitated with several subtypes of nonsensory supp...	[ "The organ of Corti in the cochlea is a two-cell layered epithelium: one cell layer of mechanosensory hair cells that align into one row of inner and three rows of outer hair cells interdigitated with one cell layer of underlying supporting cells along the entire length of the cochlear spiral .", "These two types...	[ "Auditory sensory hair cells and surrounding supporting cells are derived from common prosensory progenitors , which undergo rearrangements through intercalation to achieve extension and establish the mosaic structure between hair and supporting cells .", "Hair cells are susceptible to damage from a variety of in...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "blood cells", "t helper cells", "organismal evolution", "hiv infections", "medicine and health sciences", "immune cells", "immune physiology", "pathology and laboratory medicine", "evolutionary biology", "pathogens", "immunology", "microbiology", "cloning", "retroviruses", "viruses", ...	The low spike density of HIV may have evolved because of the effects of T helper cell depletion on affinity maturation	journal.pcbi.1006408	null	[ [ "Viruses gain entry into their host cells by attaching to specific receptors on the host surface .", "The proteins that mediate entry comprise the viral spike .", "Since the host receptor does not mutate rapidly , spike proteins , while often being highly mutable , have conserved regions that bind to ...	[ "The spikes on virus surfaces bind receptors on host cells to propagate infection .", "High spike densities ( SDs ) can promote infection , but spikes are also targets of antibody-mediated immune responses .", "Thus , diverse evolutionary pressures can influence virus SDs .", "HIV’s SD is about two orders of ...	[ "The spike protein on the virus surface mediates its entry to the host cell and a high spike density promotes infection .", "HIV has a spike density that is almost two orders of magnitude lower than other viruses .", "This unique feature of HIV has defied explanation since it was first observed .", "By bringi...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma mansoni", "medicine and health sciences", "body fluids", "pathology and laboratory medicine", "helminths", "pathogens", "tropical diseases", "microbiology", "parasitic diseases", "animals", "retroviruses", "viruses", "immunodeficiency viruses"...	Prevalence and clinical relevance of helminth co-infections among tuberculosis patients in urban Tanzania	journal.pntd.0005342	null	[ [ "Tuberculosis ( TB ) , caused by Mycobacterium tuberculosis remains a challenging disease to control .", "Indeed , over two billion people are estimated to be infected with M . tuberculosis worldwide [1] .", "Moreover one billion people are infected with soil-transmitted helminths , schistosomes , fil...	[ "Helminth infections can negatively affect the immunologic host control , which may increase the risk of progression from latent Mycobacterium tuberculosis infection to tuberculosis ( TB ) disease and alter the clinical presentation of TB .", "We assessed the prevalence and determined the clinical relevance of he...	[ "Tuberculosis ( TB ) , caused by the bacterium Mycobacterium tuberculosis , and parasitic worm infections are typical diseases of poverty .", "They often overlap geographically , and can occur in the same individual .", "Parasitic worm infections contribute to the down-regulation of the essential immune respons...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "cell biology", "computational biology" ]	A Third Measure-Metastable State in the Dynamics of Spontaneous Shape Change in Healthy Human's White Cells	journal.pcbi.1001117	null	[ [ "We remind ourselves that there are neurobiological limits on the both the resolution afforded by empirically meaningful partitions [16] , and the minimal length of a neurobiologically defensible time series [17] .", "In these studies I must be concerned with how long the cells being observed maintain the...	[ "Human polymorphonuclear leucocytes , PMN , are highly motile cells with average 12-15 µm diameters and prominent , loboid nuclei .", "They are produced in the bone marrow , are essential for host defense , and are the most populous of white blood cell types .", "PMN also participate in acute and chronic inflam...	[ "Human white blood cells , polymorphonuclear leucocytes ( PMN ) , were microscopically imaged and analyzed as single living cells .", "PMN are generally observed in a spheroid Idling state transitioning to an activated , egg-shaped , translocating state when triggered by the body's signals of infection or inflamm...	2011
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "spatially-explicit model", "thin filament regulation", "physiology", "myosin", "biophysics", "muscle contraction" ]	Sarcomere Lattice Geometry Influences Cooperative Myosin Binding in Muscle	journal.pcbi.0030115	null	[ [ "Muscle contraction is initiated by Ca2+ binding to troponin and the subsequent movement of tropomyosin on the thin filament , enabling myosin to cyclically attach and detach to actin ( cross-bridge cycling ) [1–7] .", "Underlying this process are myriad factors that contribute to the magnitude and time c...	[ "In muscle , force emerges from myosin binding with actin ( forming a cross-bridge ) .", "This actomyosin binding depends upon myofilament geometry , kinetics of thin-filament Ca2+ activation , and kinetics of cross-bridge cycling .", "Binding occurs within a compliant network of protein filaments where there i...	[ "Striated muscle is highly structured , and the molecular organization of muscle filaments varies within individuals ( by fiber type ) and taxonomically .", "The consequences of filament arrangement on muscle contraction , however , remain largely unknown .", "We explore how filament arrangement affects force p...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "space exploration", "astronomical sciences", "anatomy and physiology", "muscle", "animal models", "model organisms", "musculoskeletal system", "cell membrane", "cytochemistry", "cell adhesion", "extracellular matrix", "biology", "biochemistry", "cell biology", "physiology", "molecular...	Calpains Mediate Integrin Attachment Complex Maintenance of Adult Muscle in Caenorhabditis elegans	journal.pgen.1002471	null	[ [ "Muscle is a multifunctional tissue [1]–[4] with a well appreciated role in locomotion .", "The contractile properties of muscle that allow for coordinated locomotion require a complex protein based machinery [5] and substantial metabolic input [6] .", "To balance demand with metabolic cost , the quan...	[ "Two components of integrin containing attachment complexes , UNC-97/PINCH and UNC-112/MIG-2/Kindlin-2 , were recently identified as negative regulators of muscle protein degradation and as having decreased mRNA levels in response to spaceflight .", "Integrin complexes transmit force between the inside and outsid...	[ "Muscle is a dynamic tissue that grows in response to use and nutrition and shrinks in response to lack of use , poor nutrition , or disease .", "Loss of muscle mass is an important public health problem , but we understand little of the genes that regulate muscle shrinkage .", "We have found that , in adult wo...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "veterinary science", "biology" ]	Molecular Detection of Ehrlichia canis in Dogs in Malaysia	journal.pntd.0001982	null	[ [ "Ehrlichia canis is a gram-negative obligatory intracellular bacterium with a tropism for monocytes and macrophages in the family Anaplasmataceae and order Rickettsiales [1] , [2] .", "Canine monocytic ehrlichiosis ( CME ) caused by E . canis is a tick-borne disease of dogs .", "E . canis is transmitt...	[ "An epidemiological study of Ehrlichia canis infection in dogs in Peninsular Malaysia was carried out using molecular detection techniques .", "A total of 500 canine blood samples were collected from veterinary clinics and dog shelters .", "Molecular screening by polymerase chain reaction ( PCR ) was performed ...	[ "Canine vector-borne diseases are a worldwide concern particularly in the tropics and sub-tropics that provide favourable climatic conditions for the vectors .", "Malaysia , a tropical paradise , is thus home to a wide range of vectors as well as the pathogens that they harbor .", "Ehrlichia canis , a ubiquitou...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The Human Blood Metabolome-Transcriptome Interface	journal.pgen.1005274	null	[ [ "Blood is a connective tissue , which not only ensures nutrient and oxygen supply of all organs of the human body , but also the communication between them .", "Among the variety of key tasks performed by blood are immunological functions through white blood cells .", "Due to its diverse functionality...	[ "Biological systems consist of multiple organizational levels all densely interacting with each other to ensure function and flexibility of the system .", "Simultaneous analysis of cross-sectional multi-omics data from large population studies is a powerful tool to comprehensively characterize the underlying mole...	[ "Biological systems operate on multiple , intertwined organizational layers that can nowadays be accesses by high-throughput measurement methods , the so-called ‘omics’ technologies .", "A major aim in the field of systems biology is to understand the flow of biological information between the different layers at...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "text mining", "computer science", "natural language processing", "biology", "computational biology" ]	‘HypothesisFinder:’ A Strategy for the Detection of Speculative Statements in Scientific Text	journal.pcbi.1003117	null	[ [ "Biomedical information published in the scientific articles can be grossly divided into “established knowledge” and “emerging knowledge” .", "Established knowledge , supported by facts and repeated , independent validation of experimental findings , is widely accepted in the scientific community; this kn...	[ "Speculative statements communicating experimental findings are frequently found in scientific articles , and their purpose is to provide an impetus for further investigations into the given topic .", "Automated recognition of speculative statements in scientific text has gained interest in recent years as system...	[ "Published speculations about possible molecular mechanisms underlying normal and diseased biological processes provide valuable input for the generation of new scientific hypotheses .", "However , a systematic gathering of all scientific speculation that exists in a given context is a non-trivial task and , if d...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "ecology and environmental sciences", "medicine and health sciences", "tropical diseases", "parasitic diseases", "animal phylogenetics", "phylogenetics", "speciation", "neglected tropical diseases", "zoology", "infectious diseases", "epidemiology", "protozoan infections", "evolutionary syste...	Phylogeny and Niche Conservatism in North and Central American Triatomine Bugs (Hemiptera: Reduviidae: Triatominae), Vectors of Chagas' Disease	journal.pntd.0003266	null	[ [ "Triatomine bugs ( Reduviidae: Triatominae ) are vectors of Trypanosoma cruzi , the etiologic agent of Chagas disease , which is the most common parasitic disease in the Americas [1] .", "Although T . cruzi transmission can occur without vector involvement ( i . e . T . cruzi contamination through infecte...	[ "The niche conservatism hypothesis states that related species diverge in niche characteristics at lower rates than expected , given their lineage divergence .", "Here we analyze whether niche conservatism is a common pattern among vector species ( Hemiptera: Reduviidae: Triatominae ) of Trypanosoma cruzi that in...	[ "Knowledge regarding the evolutionary history of insect vectors of pathogens is essential to design precise and appropriately integrated control strategies , since species' dispersal and invasive capacity are key components to prevent human-vector interaction .", "Given several well-known invasive or dispersal ev...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "population genetics", "biology", "human genetics", "evolutionary biology", "evolutionary genetics" ]	The Genetic Correlation between Height and IQ: Shared Genes or Assortative Mating?	journal.pgen.1003451	null	[ [ "Taller people tend to be smarter .", "Although the relationship is modest , height and IQ are consistently correlated at ∼ . 10– . 20 [24] , [25] , [26] .", "Three studies have examined the etiology of this correlation using a bivariate ACE “classical” twin design which uses the covariation of monozy...	[ "Traits that are attractive to the opposite sex are often positively correlated when scaled such that scores increase with attractiveness , and this correlation typically has a genetic component .", "Such traits can be genetically correlated due to genes that affect both traits ( “pleiotropy” ) and/or because ass...	[ "Traits that are attractive to the opposite sex are often positively correlated when scaled such that scores increase with attractiveness , and this correlation typically has a genetic component .", "Such traits can be genetically correlated due to genes that affect both traits and/or because assortative mating (...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "biofilms", "bacteriology", "medicine and health sciences", "immune physiology", "pathology and laboratory medicine", "acinetobacter infections", "pathogens", "immunology", "microbiology", "membrane proteins", "bacterial diseases", "fungi", "outer membrane proteins", "experimental organism...	The Hyr1 protein from the fungus Candida albicans is a cross kingdom immunotherapeutic target for Acinetobacter bacterial infection	journal.ppat.1007056	null	[ [ "Acinetobacter baumannii has emerged as a frequent cause of healthcare-associated infections , ranging from bacteremia , pneumonia , urinary tract infections , to skin and wound infections , including those seen in the military theatre [1–10] .", "Its emergence in the healthcare environment is ascribed to...	[ "Different pathogens share similar medical settings and rely on similar virulence strategies to cause infections .", "We have previously applied 3-D computational modeling and bioinformatics to discover novel antigens that target more than one human pathogen .", "Active and passive immunization with the recombi...	[ "Different pathogens share similar medical settings and rely on similar virulence strategies to cause infections .", "We have applied computational modeling and bioinformatics to discover novel antigens that target organisms sharing ecological niches in the intensive care units ( ICUs ) : the fungus Candida albic...	2018
[ "Introduction", "Results", "Discussion", "Material and methods" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "chemical compounds", "aliphatic amino acids", "gene regulation", "pathogens", "microbiology", "operons", "organic compounds", "physiological processes", "mutation", "regulator genes", "homeostasis", "gene types", "amin...	Cyclic di-AMP regulation of osmotic homeostasis is essential in Group B Streptococcus	journal.pgen.1007342	null	[ [ "Cyclic nucleotides are signalling molecules , commonly called second messengers , which regulate cellular processes by binding to targeted effectors [1–3] .", "Specific cyclic di-nucleotides are synthesized by prokaryotes and eukaryotes , and this specificity is exploited by host cells to monitor bacteri...	[ "Cyclic nucleotides are universally used as secondary messengers to control cellular physiology .", "Among these signalling molecules , cyclic di-adenosine monophosphate ( c-di-AMP ) is a specific bacterial second messenger recognized by host cells during infections and its synthesis is assumed to be necessary fo...	[ "Nucleotide-based second messengers play central functions in bacterial physiology and host-pathogen interactions .", "Among these signalling nucleotides , cyclic-di-AMP ( c-di-AMP ) synthesis was originally assumed to be essential for bacterial growth .", "In this study , we confirmed that the only di-adenylat...	2018
[ "Introduction", "Results and Discussion", "Materials and Methods" ]	[]	TrpA1 Regulates Defecation of Food-Borne Pathogens under the Control of the Duox Pathway	journal.pgen.1005773	null	[ [ "Encountering other organisms in nature offers opportunities of benefits or dangers depending on the relationship of the organisms facing each other .", "We intimately interact with bacteria in the gut , and the control of such interaction is the key to the health of animals [1–3] .", "Although pathog...	[ "Pathogen expulsion from the gut is an important defense strategy against infection , but little is known about how interaction between the intestinal microbiome and host immunity modulates defecation .", "In Drosophila melanogaster , dual oxidase ( Duox ) kills pathogenic microbes by generating the microbicidal ...	[ "The amount and pattern of defecation are often determined by the bacterial composition in the gut , and can have a significant impact on human health .", "It is however unknown how changes in the bacterial community affect defecation .", "A chemical defense system called the Duox pathway is known to kill ill-c...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology and life sciences", "microbiology", "virology" ]	The Downregulation of GFI1 by the EZH2-NDY1/KDM2B-JARID2 Axis and by Human Cytomegalovirus (HCMV) Associated Factors Allows the Activation of the HCMV Major IE Promoter and the Transition to Productive Infection	journal.ppat.1004136	null	[ [ "Human cytomegalovirus ( HCMV ) is a double stranded DNA virus that belongs to the beta-herpesvirus subfamily of the herpesvirus family .", "Other members of this subfamily are the human herpes viruses 6 and 7 ( HHV-6 and HHV-7 ) .", "HCMV seroprevalence varies widely among populations residing in dif...	[ "Earlier studies had suggested that epigenetic mechanisms play an important role in the control of human cytomegalovirus ( HCMV ) infection .", "Here we show that productive HCMV infection is indeed under the control of histone H3K27 trimethylation .", "The histone H3K27 methyltransferase EZH2 , and its regulat...	[ "Human cytomegalovirus ( HCMV ) is a significant pathogen that belongs to the herpesvirus family .", "Here we show that the histone H3K27 methyltransferase EZH2 and its regulators JARID2 and NDY1/KDM2B are required for the establishment of productive infection .", "Mechanistically , the EZH2-NDY1/KDM2B-JARID2 a...	2014
[ "Introduction", "Methods", "Results", "Discussion", "Conclusions" ]	[ "medicine", "infectious diseases", "public health and epidemiology", "mathematics", "epidemiology", "statistics", "infectious disease epidemiology", "neglected tropical diseases", "leishmaniasis", "biostatistics", "infectious disease control", "infectious disease modeling" ]	Treatment of Visceral Leishmaniasis: Model-Based Analyses on the Spread of Antimony-Resistant L. donovani in Bihar, India	journal.pntd.0001973	null	[ [ "Visceral leishmaniasis ( VL ) , also known as Kala-azar ( KA ) , causes each year about 200 , 000 to 400 , 000 cases with about 20 , 000 to 40 , 000 deaths worldwide .", "About 70% of the VL burden occurs in the Indian subcontinent , mostly in the state of Bihar [1] .", "The disease is caused by the ...	[ "Pentavalent antimonials have been the mainstay of antileishmanial therapy for decades , but increasing failure rates under antimonial treatment have challenged further use of these drugs in the Indian subcontinent .", "Experimental evidence has suggested that parasites which are resistant against antimonials hav...	[ "The protozoan flagellate Leishmania donovani causes the neglected , life-threatening disease visceral leishmaniasis .", "Parasites are transmitted from man to man by the bite of the sand fly Phlebotomus argentipes , the vector of the disease .", "Pentavalent antimonials have been the mainstay of antileishmania...	2012
[ "Background", "Results and discussion", "Maximum expected accuracy", "Conclusion" ]	[ "computer applications", "rna sequences", "education", "molecular probe techniques", "applied mathematics", "rna structure prediction", "rna stem-loop structure", "simulation and modeling", "algorithms", "mathematics", "molecular biology techniques", "thermodynamics", "research and analysis ...	Interactive implementations of thermodynamics-based RNA structure and RNA–RNA interaction prediction approaches for example-driven teaching	journal.pcbi.1006341	null	[ [ "Bioinformatics analyses have become indispensable to biological research .", "While platforms like Galaxy enable the setup of tool pipelines without expert knowledge [1 , 2] , one requires a general understanding of underlying concepts and algorithms to be able to successfully apply and adapt these pipel...	[ "The investigation of RNA-based regulation of cellular processes is becoming an increasingly important part of biological or medical research .", "For the analysis of this type of data , RNA-related prediction tools are integrated into many pipelines and workflows .", "In order to correctly apply and tune these...	[ "RNA molecules are central players in many cellular processes .", "Thus , the analysis of RNA-based regulation has provided valuable insights and is often pivotal to biological and medical research .", "In order to correctly select appropriate algorithms and apply available RNA structure and RNA–RNA interaction...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "squamous cell lung carcinoma", "protein interactions", "applied mathematics", "protein interaction networks", "carcinomas", "cancers and neoplasms", "simulation and modeling", "oncology", "algorithms", "protein expression", "mathematics", "network analysis", ...	A Multi-Method Approach for Proteomic Network Inference in 11 Human Cancers	journal.pcbi.1004765	null	[ [ "The availability of proteomic datasets such as PANCAN11 where protein levels are measured across different conditions provides a unique opportunity to study the functions of proteins .", "However , the analysis of function requires knowledge of interactions .", "For instance , in the protein-folding ...	[ "Protein expression and post-translational modification levels are tightly regulated in neoplastic cells to maintain cellular processes known as ‘cancer hallmarks’ .", "The first Pan-Cancer initiative of The Cancer Genome Atlas ( TCGA ) Research Network has aggregated protein expression profiles for 3 , 467 patie...	[ "Pan-cancer proteomic datasets from The Cancer Genome Atlas provide a unique opportunity to study the functions of proteins in human cancers .", "Such datasets , where proteins are measured in different conditions and where correlations are informative , can enable the discovery of potentially causal protein-prot...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases/neglected tropical diseases", "immunology/innate immunity", "infectious diseases/helminth infections" ]	A Large Repertoire of Parasite Epitopes Matched by a Large Repertoire of Host Immune Receptors in an Invertebrate Host/Parasite Model	journal.pntd.0000813	null	[ [ "Understanding host-parasite interactions represents a major challenge in evolutionary biology .", "Parasites cause substantial deleterious effects on their hosts , and therefore represent a major driving force for their evolution [1] .", "In parallel , parasites have to cope with the evolving host-de...	[ "For many decades , invertebrate immunity was believed to be non-adaptive , poorly specific , relying exclusively on sometimes multiple but germ-line encoded innate receptors and effectors .", "But recent studies performed in different invertebrate species have shaken this paradigm by providing evidence for vario...	[ "Contrary to the traditional view that immunity in invertebrates is limited to innate mechanisms , recent studies have shown that these several species of protostome invertebrates express putative immune receptors that can be somatically diversified in a way resulting in an analogy with Immunoglobulins or T Cell Re...	2010
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Immunodiagnosis of Paracoccidioidomycosis due to Paracoccidioides brasiliensis Using a Latex Test: Detection of Specific Antibody Anti-gp43 and Specific Antigen gp43	journal.pntd.0003516	null	[ [ "Neglected tropical diseases ( NTDs ) , a group of chronic diseases caused by debilitating parasitic , bacterial , viral , and fungal infections are among the most common causes of illness in the poorest people living in developing countries [1] .", "Fungal infections represent an important health problem...	[ "Paracoccidioidomycosis ( PCM ) is a life-threatening systemic disease and is a neglected public health problem in many endemic regions of Latin America .", "Though several diagnostic methods are available , almost all of them present with some limitations .", "A latex immunoassay using sensitized latex particl...	[ "Paracoccidioidomycosis is one of the most prevalent systemic mycoses in Latin America , and still poses a significant threat to the health of human hosts , especially those with an impaired immune system .", "Early and accurate diagnosis is mandatory for the implementation of effective treatment .", "Currently...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "computer science/systems and control theory", "neuroscience/theoretical neuroscience" ]	How Synchronization Protects from Noise	journal.pcbi.1000637	null	[ [ "Synchronization phenomena are pervasive in biology .", "In neuronal networks [1]–[3] , a large number of studies have sought to unveil the mechanisms of synchronization , from both physiological [4] , [5] and computational viewpoints ( see for instance [6] and references therein ) .", "In addition , ...	[ "The functional role of synchronization has attracted much interest and debate: in particular , synchronization may allow distant sites in the brain to communicate and cooperate with each other , and therefore may play a role in temporal binding , in attention or in sensory-motor integration mechanisms .", "In th...	[ "Synchronization phenomena are pervasive in biology , creating collective behavior out of local interactions between neurons , cells , or animals .", "On the other hand , many of these systems function in the presence of large amounts of noise or disturbances , making one wonder how meaningful behavior can arise ...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Probing the Metabolic Network in Bloodstream-Form Trypanosoma brucei Using Untargeted Metabolomics with Stable Isotope Labelled Glucose	journal.ppat.1004689	null	[ [ "Trypanosoma brucei is a protozoan parasite , sub-species of which are responsible for human African trypanosomiasis ( HAT ) and animal African trypanosomiasis ( Nagana ) [1] .", "Current treatments for HAT are inadequate , and new preventative and therapeutic options are urgently required [2] .", "Th...	[ "Metabolomics coupled with heavy-atom isotope-labelled glucose has been used to probe the metabolic pathways active in cultured bloodstream form trypomastigotes of Trypanosoma brucei , a parasite responsible for human African trypanosomiasis .", "Glucose enters many branches of metabolism beyond glycolysis , whic...	[ "In this work we have followed the distribution of carbon derived from glucose in bloodstream form trypanosomes , the causative agent of African trypanosomiasis , revealing it to enter a diverse range of metabolites .", "The work involved using 13C-labelled glucose and following the fate of the labelled carbon wi...	2015

Subsets and Splits

No community queries yet

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