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headings list	keywords list	title stringlengths 20 281	id stringlengths 20 20	toc stringlengths 57 522 ⌀	sections list	abstract list	summary list	year stringclasses 13 values
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "oncology", "medicine", "mathematics", "applied mathematics" ]	A Race between Tumor Immunoescape and Genome Maintenance Selects for Optimum Levels of (epi)genetic Instability	journal.pcbi.1002370	null	[ [ "In 1909 , Paul Ehrlich was the first to propose the idea that the immune system scans for and eliminates nascent transformed cells in the human body [1] .", "This hypothesis received much interest from both immunologists and cancer researchers and led to experiments with tumors transplanted into mice; th...	[ "The human immune system functions to provide continuous body-wide surveillance to detect and eliminate foreign agents such as bacteria and viruses as well as the body's own cells that undergo malignant transformation .", "To counteract this surveillance , tumor cells evolve mechanisms to evade elimination by the...	[ "Immunologic surveillance is a function of the immune system which serves to constantly monitor the body for microorganisms , foreign tissue , and cancer cells .", "To evade this surveillance and subsequent elimination , cancer cells evolve strategies to prevent being recognized and killed by immune system cells;...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "microbial evolution", "biology", "microbiology", "bacterial pathogens" ]	An Allele of an Ancestral Transcription Factor Dependent on a Horizontally Acquired Gene Product	journal.pgen.1003060	null	[ [ "The phenotypic properties that distinguish closely related bacterial species are often ascribed to differences in gene content [1] , [2] .", "These differences typically result from the acquisition of genetic material by horizontal gene transfer , a process that can readily transform a bacterial species ...	[ "Changes in gene regulatory circuits often give rise to phenotypic differences among closely related organisms .", "In bacteria , these changes can result from alterations in the ancestral genome and/or be brought about by genes acquired by horizontal transfer .", "Here , we identify an allele of the ancestral ...	[ "Horizontally acquired genes are typically viewed as independent units that confer new traits when introduced into different bacterial species .", "However , preexisting proteins in a bacterium can impact the ability of horizontally acquired gene products to bring about new functions when they target ancestral pa...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "cell biology/cell growth and division", "cell biology", "developmental biology/pattern formation", "developmental biology/plant growth and development", "plant biology/plant cell biology", "plant biology", "cell biology/plant genetics and gene expression", "developmental bi...	Endoreplication Controls Cell Fate Maintenance	journal.pgen.1000996	null	[ [ "Many different cell cycle programs can be found in developing multicellular organisms [1] .", "Typically , embryonic cell cycles are short with a rapid sequence of the DNA-synthesis phase ( S-phase ) and mitosis ( M-phase ) rapidly generating cells or nuclei in a syncytium .", "At later stages of dev...	[ "Cell-fate specification is typically thought to precede and determine cell-cycle regulation during differentiation .", "Here we show that endoreplication , also known as endoreduplication , a specialized cell-cycle variant often associated with cell differentiation but also frequently occurring in malignant cell...	[ "Differentiating cells often amplify their nuclear DNA content through a special cell-cycle variant , called endoreplication , in which cell division is skipped .", "Although this process is widespread from humans to plants , not much is currently known about the biological importance of endoreplication .", "Mo...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "bacteriology", "medicine", "biochemistry", "infectious diseases", "bacterial diseases", "genetics", "genetics and genomics", "biology", "microbiology", "glycobiology", "bacterial pathogens" ]	Peptidoglycan-Modifying Enzyme Pgp1 Is Required for Helical Cell Shape and Pathogenicity Traits in Campylobacter jejuni	journal.ppat.1002602	null	[ [ "Campylobacter jejuni is a helical , highly motile , Gram-negative ε-Proteobacterium and a prevalent zoonotic organism existing asymptomatically in the intestinal tract of birds and other animal species [1]–[3] .", "However , ingestion of as few as 500 bacteria can result in human disease [4] .", "C ....	[ "The impact of bacterial morphology on virulence and transmission attributes of pathogens is poorly understood .", "The prevalent enteric pathogen Campylobacter jejuni displays a helical shape postulated as important for colonization and host interactions .", "However , this had not previously been demonstrated...	[ "Bacterial cell shape is dictated by the composition of the cell envelope component peptidoglycan .", "Some important pathogens have a characteristic helical corkscrew morphology that may help them burrow into mucus overlaying cells to initiate colonization and pathogenicity .", "One example is Campylobacter je...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	A Flexible, Efficient Binomial Mixed Model for Identifying Differential DNA Methylation in Bisulfite Sequencing Data	journal.pgen.1005650	null	[ [ "DNA methylation—the covalent addition of methyl groups to cytosine bases—is a major epigenetic gene regulatory mechanism observed in a wide variety of species .", "DNA methylation influences genome-wide gene expression patterns , is involved in genomic imprinting and X-inactivation , and functions to sup...	[ "Identifying sources of variation in DNA methylation levels is important for understanding gene regulation .", "Recently , bisulfite sequencing has become a popular tool for investigating DNA methylation levels .", "However , modeling bisulfite sequencing data is complicated by dramatic variation in coverage ac...	[ "DNA methylation is an important epigenetic modification involved in regulating gene expression .", "It can be measured at base-pair resolution , on a genome-wide scale , by coupling sodium bisulfite conversion with high-throughput sequencing ( a technique known as ‘bisulfite sequencing’ ) .", "However , the da...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "invertebrates", "caenorhabditis", "neuroscience", "animals", "invertebrate genomics", "animal models", "mutation", "caenorhabditis elegans", "model organisms", "cellular structures and organelles", "research and analysis methods", "mutant strains", "animal cells", "animal genomics", "se...	Accelerating Gene Discovery by Phenotyping Whole-Genome Sequenced Multi-mutation Strains and Using the Sequence Kernel Association Test (SKAT)	journal.pgen.1006235	null	[ [ "A powerful , tried and true approach to identify which genes function in a particular biological process is to create collections of organisms harbouring multiple mutations via random mutagenesis , followed by screening the mutant library for organisms that exhibit the desired altered phenotypes .", "Alt...	[ "Forward genetic screens represent powerful , unbiased approaches to uncover novel components in any biological process .", "Such screens suffer from a major bottleneck , however , namely the cloning of corresponding genes causing the phenotypic variation .", "Reverse genetic screens have been employed as a way...	[ "Model organisms are useful tools for uncovering new genes involved in a biological process via genetic screens .", "Such an approach is powerful , but suffers from drawbacks that can slow down gene discovery .", "In forward genetics screens , difficult-to-map phenotypes present daunting challenges , and whole-...	2016
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "mus (mouse)", "genetics and genomics" ]	Deletion of the MBII-85 snoRNA Gene Cluster in Mice Results in Postnatal Growth Retardation	journal.pgen.0030235	null	[ [ "The human genetic locus 15q11-q13 is subject to genomic imprinting that is controlled by a bipartite imprinting center ( IC ) [1] .", "Imprinting defects or chromosomal rearrangements/deletions within this locus ( Figure", "1 ) are responsible for the development of two clinical disorders—Angelman ( ...	[ "Prader-Willi syndrome ( PWS [MIM 176270] ) is a neurogenetic disorder characterized by decreased fetal activity , muscular hypotonia , failure to thrive , short stature , obesity , mental retardation , and hypogonadotropic hypogonadism .", "It is caused by the loss of function of one or more imprinted , paternal...	[ "Prader-Willi syndrome , or PWS , is a complex neurogenetic disorder and the most common genetic cause of life-threatening childhood obesity .", "Newborns have poor muscle tone , making suckling difficult , which leads to poor weight gain .", "After infancy , they experience extreme hunger , leading to obesity ...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "reverse transcriptase-polymerase chain reaction", "invertebrates", "medicine and health sciences", "reproductive system", "animals", "germ cells", "organisms", "developmental biology", "silkworms", "forms of dna", "molecular biology techniques", "dna", "sperm", "research and analysis meth...	Transgenic Expression of the piRNA-Resistant Masculinizer Gene Induces Female-Specific Lethality and Partial Female-to-Male Sex Reversal in the Silkworm, Bombyx mori	journal.pgen.1006203	null	[ [ "Most animal species have two sexes and display various sexual dimorphisms .", "Mechanisms of sex determination are highly different among phyla [1–3] .", "In many reptile species , the temperature at which eggs are incubated determines their sex [4] .", "In Daphnia magna , a shortening of the pho...	[ "In Bombyx mori ( B . mori ) , Fem piRNA originates from the W chromosome and is responsible for femaleness .", "The Fem piRNA-PIWI complex targets and cleaves mRNAs transcribed from the Masc gene .", "Masc encodes a novel CCCH type zinc-finger protein and is required for male-specific splicing of B . mori doub...	[ "In the silkworm , Bombyx mori , a W-chromosome-linked gene Feminizer ( Fem ) determines femaleness .", "Fem transcript yields a piRNA ( Fem piRNA ) and Fem- piRNA-PIWI complex targets and cleaves mRNAs transcribed from the Masculinizer ( Masc ) .", "Masc is required for male-specific expression of Bmdsx , whic...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "biotechnology", "medicine", "animal types", "pathology", "immunology", "microbiology", "anatomy and physiology", "model organisms", "veterinary anatomy and physiology", "veterinary science", "veterinary medicine", "infectious diseases", "veterinary diseases", "veterinary microbiology", ...	Tissue Tropism and Target Cells of NSs-Deleted Rift Valley Fever Virus in Live Immunodeficient Mice	journal.pntd.0001421	null	[ [ "Rift Valley fever virus ( RVFV ) is an arthropod-borne member of the Bunyaviridae family , genus Phlebovirus that causes recurrent outbreaks affecting humans and animals .", "The virus can be transmitted by Aedes and Culex mosquitoes [1] , although it can also be transmitted by inhalation or physical con...	[ "Rift Valley fever virus ( RVFV ) causes disease in livestock and humans .", "It can be transmitted by mosquitoes , inhalation or physical contact with the body fluids of infected animals .", "Severe clinical cases are characterized by acute hepatitis with hemorrhage , meningoencephalitis and/or retinitis .", ...	[ "Rift Valley fever , caused by a member of the Bunyaviridae family , has spread during recent years to most sub-Saharan African countries , in Egypt and in the Arabian peninsula .", "The virus can be transmitted by insect vectors or by direct contacts with infectious tissues .", "The analysis of virus replicati...	2011
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "algorithms", "genome sequencing", "computer science", "genomics", "mathematics", "biology", "computational biology", "discrete mathematics", "combinatorics" ]	Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space	journal.pcbi.1003010	null	[ [ "The second generation of DNA sequencing instruments is revolutionizing the way molecular biologists design and carry out investigations in genomics and genetics .", "These new sequencing technologies ( e . g . , Illumina , ABI SOLiD ) can produce a significantly greater number of reads at a fraction of t...	[ "For the vast majority of species – including many economically or ecologically important organisms , progress in biological research is hampered due to the lack of a reference genome sequence .", "Despite recent advances in sequencing technologies , several factors still limit the availability of such a critical...	[ "The problem of obtaining the full genomic sequence of an organism has been solved either via a global brute-force approach ( called whole-genome shotgun ) or by a divide-and-conquer strategy ( called clone-by-clone ) .", "Both approaches have advantages and disadvantages in terms of cost , manual labor , and the...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "plant growth and development", "symbiosis", "genetics", "plant genetics", "molecular genetics", "biology and life sciences", "species interactions", "molecular biology" ]	Local and Systemic Regulation of Plant Root System Architecture and Symbiotic Nodulation by a Receptor-Like Kinase	journal.pgen.1004891	null	[ [ "Plant growth requires the continuous development of the root system and its adaptation to changing environmental soil conditions .", "Mechanisms controlling root system architecture at the whole-plant level , including the systemic coordination of shoot and root development , are key breeding targets for...	[ "In plants , root system architecture is determined by the activity of root apical meristems , which control the root growth rate , and by the formation of lateral roots .", "In legumes , an additional root lateral organ can develop: the symbiotic nitrogen-fixing nodule .", "We identified in Medicago truncatula...	[ "Despite the essential functions of roots in plant access to water and nutrients , root system architecture has not been directly considered for crop breeding improvement , but it is now considered key for a “second green revolution . ”", "In this study , we aimed to decipher integrated molecular mechanisms coord...	2014
[ "Introduction", "Materials & methods", "Results", "Discussion" ]	[ "blood cells", "medicine and health sciences", "immune cells", "immunology", "simulation and modeling", "clinical medicine", "mathematics", "protein structure", "tcr signaling cascade", "discrete mathematics", "combinatorics", "research and analysis methods", "immune system proteins", "whi...	MHC binding affects the dynamics of different T-cell receptors in different ways	journal.pcbi.1007338	null	[ [ "The interaction between T-cell receptors ( TCRs ) on the surface of T-cells and peptides bound by Major Histocompatibility Complexes ( MHCs ) on the surface of antigen presenting cells is one of the most important processes of the adaptive immune system [1] .", "In the case of MHC class I molecules intra...	[ "T cells use their T-cell receptors ( TCRs ) to scan other cells for antigenic peptides presented by MHC molecules ( pMHC ) .", "If a TCR encounters a pMHC , it can trigger a signalling pathway that could lead to the activation of the T cell and the initiation of an immune response .", "It is currently not clea...	[ "The interaction between T-cells and other cells is one of the most important interactions in the human immune system .", "If T-cells are not triggered major parts of the immune system cannot be activated or are not working effectively .", "Despite many years of research the exact mechanism of how a T-cell is i...	2019
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "conservation science", "oil palm", "ecology and environmental sciences", "ecology", "ecosystems", "forests", "agriculture", "forest ecology", "biology and life sciences", "social sciences", "plants", "agricultural economics", "economics", "organisms", "terrestrial environments" ]	Global economic trade-offs between wild nature and tropical agriculture	journal.pbio.2001657	null	[ [ "Growing global demands for food and biofuels generate pressures for deforestation across the tropics [1] .", "Much of this deforestation is carried out without information on the spatial distribution of benefits and costs of deforestation [2] .", "Studies estimating the trade-offs between the economi...	[ "Global demands for agricultural and forestry products provide economic incentives for deforestation across the tropics .", "Much of this deforestation occurs with a lack of information on the spatial distribution of benefits and costs of deforestation .", "To inform global sustainable land-use policies , we co...	[ "Tropical forests are often destroyed to clear land for agriculture or to harvest forestry products , such as timber .", "However , the benefits derived from agriculture and these products are countered by the costs to the environment and the loss of ecosystem systems ( the benefits that nature provides to humans...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "animal models", "medicine", "bacterial diseases", "infectious diseases", "model organisms", "clinical immunology", "immunity", "global health", "immunology", "biology", "microbiology" ]	Development of Functional and Molecular Correlates of Vaccine-Induced Protection for a Model Intracellular Pathogen, F. tularensis LVS	journal.ppat.1002494	null	[ [ "Most vaccines against infectious diseases in clinical use today act by stimulating the production of antibodies , which block virus entry , neutralize toxins , or otherwise limit infection through a variety of mechanisms .", "Measurements of serum antibodies have therefore been applied to predict success...	[ "In contrast with common human infections for which vaccine efficacy can be evaluated directly in field studies , alternative strategies are needed to evaluate efficacy for slowly developing or sporadic diseases like tularemia .", "For diseases such as these caused by intracellular bacteria , serological measures...	[ "Diseases such as tuberculosis ( caused by Mycobacterium tuberculosis ) or tularemia ( caused by Francisella tularensis ) result from infections by microbes that live within cells of a person's body .", "New vaccines are being developed against such intracellular pathogens , but some will be difficult to test , b...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "immunology", "biology", "immunomodulation", "immune response" ]	Glycoprotein N of Human Cytomegalovirus Protects the Virus from Neutralizing Antibodies	journal.ppat.1002999	null	[ [ "Cytomegaloviruses ( CMV ) have co-evolved with their respective hosts .", "During this long and continuing co-evolution these viruses have adapted to the host defense systems and vice versa to allow the life-long persistence of these viruses .", "As a result , infections in immunocompetent hosts are ...	[ "Herpes viruses persist in the infected host and are transmitted between hosts in the presence of a fully functional humoral immune response , suggesting that they can evade neutralization by antiviral antibodies .", "Human cytomegalovirus ( HCMV ) encodes a number of polymorphic highly glycosylated virion glycop...	[ "Herpes viruses are transmitted between individuals in cell free form and successful spread benefits from mechanisms that limit the loss of infectivity by the activity of virus neutralizing antibodies .", "Human cytomegalovirus ( HCMV ) is an important pathogen and understanding how the virus can evade antiviral ...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology" ]	Functional Analysis of NopM, a Novel E3 Ubiquitin Ligase (NEL) Domain Effector of Rhizobium sp. Strain NGR234	journal.ppat.1002707	null	[ [ "Type 3 effector proteins of pathogenic Gram-negative bacteria are transported into eukaryotic host cells through the bacterial type 3 secretion system ( T3SS ) , which forms a needle-like pilus [1]–[3] .", "Various effectors from phytopathogenic bacteria act as virulence factors by suppressing activation...	[ "Type 3 effector proteins secreted via the bacterial type 3 secretion system ( T3SS ) are not only virulence factors of pathogenic bacteria , but also influence symbiotic interactions between nitrogen-fixing nodule bacteria ( rhizobia ) and leguminous host plants .", "In this study , we characterized NopM ( nodul...	[ "Many Gram-negative bacterial pathogens possess type 3 secretion systems , which deliver effector proteins into eukaryotic host cells through needle-like structures .", "Effectors manipulate the host cell and many of them suppress host defense responses .", "Interestingly , certain symbiotic strains of rhizobia...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "organismal evolution", "genome evolution", "viral classification", "microbiology", "molecular cell biology", "dna viruses", "microbial evolution", "gene expression", "biology", "molecular biology", "viral evolution", "protein translation", "virology", "genetics", "genomics", "evolutio...	Translation in Giant Viruses: A Unique Mixture of Bacterial and Eukaryotic Termination Schemes	journal.pgen.1003122	null	[ [ "The first giant virus , Mimivirus , was discovered ten years ago [1] .", "This double stranded DNA virus infecting amoebae of the Acanthamoeba genus exhibits a record-breaking particle more than 700 nm in diameter and a 1 . 2 Mb genome , larger than several cellular genomes [2] .", "Remarkably this v...	[ "Mimivirus and Megavirus are the best characterized representatives of an expanding new family of giant viruses infecting Acanthamoeba .", "Their most distinctive features , megabase-sized genomes carried in particles of size comparable to that of small bacteria , fill the gap between the viral and cellular world...	[ "Giant viruses , such as Mimivirus and Megavirus , have huge near-micron-sized particles and possess more genes than several cellular organisms .", "Furthermore their genomes encode functions not supposed to be in a virus , such as components of the protein translation apparatus .", "Since Lwoff in 1957 , virus...	2012
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "genome-wide association studies", "geographical locations", "cloning", "ethnicities", "mathematics", "statistics (mathematics)", "genome analysis", "latin american people", "molecular biology techniques", "research and analysis methods", "han chinese people", "genomic signal processing", "c...	Genome-wide association studies and CRISPR/Cas9-mediated gene editing identify regulatory variants influencing eyebrow thickness in humans	journal.pgen.1007640	null	[ [ "Hair has a range of important functions in primates and has been speculated to be subject to intense natural and sexual selection [1] .", "Although humans have lost most terminal body hair to allow the development of more efficient sweating as an adaptation to bipedal life , considerable facial hair rema...	[ "Hair plays an important role in primates and is clearly subject to adaptive selection .", "While humans have lost most facial hair , eyebrows are a notable exception .", "Eyebrow thickness is heritable and widely believed to be subject to sexual selection .", "Nevertheless , few genomic studies have explored...	[ "Hair plays an important role in primates and is clearly subject to adaptive selection .", "While humans have lost most facial hair , eyebrows are a notable exception .", "Eyebrow thickness is heritable and widely believed to be subject to sexual selection .", "Nevertheless , few genomic studies have explored...	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "complex systems", "computerized simulations", "physics", "cell motility", "computer science", "mathematics", "applied mathematics", "biophysics simulations", "biology", "microbiology", "microbial growth and development", "biophysics" ]	Interconnected Cavernous Structure of Bacterial Fruiting Bodies	journal.pcbi.1002850	null	[ [ "The organization of Myxococcus xanthus , the most studied species of the myxobacteria , into structures known as fruiting bodies has long been studied not only as an example of collective motion of bacteria , but also as a simplified model for developmental morphogenesis [1] , [2] .", "Individual M . xan...	[ "The formation of spore-filled fruiting bodies by myxobacteria is a fascinating case of multicellular self-organization by bacteria .", "The organization of Myxococcus xanthus into fruiting bodies has long been studied not only as an important example of collective motion of bacteria , but also as a simplified mo...	[ "Understanding bacteria self-organization is an active area of research with broad implications in both microbiology and developmental biology .", "Myxococcus xanthus undergoes multicellular aggregation and differentiation under starvation and is widely used as a model organism for studying bacteria self-organiza...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "neglected tropical diseases" ]	High Seroprevalence of Rift Valley Fever and Evidence for Endemic Circulation in Mbeya Region, Tanzania, in a Cross-Sectional Study	journal.pntd.0001557	null	[ [ "The Rift Valley fever virus ( RVFV ) , a member of the genus Phlebovirus in the family Bunyaviridae , was first isolated in 1930 during an outbreak in Kenya .", "Rift Valley fever ( RVF ) occurs endemically and epidemically in most parts of sub-Saharan Africa and epidemically in Egypt , Madagascar and th...	[ "The Rift Valley fever virus ( RVFV ) is an arthropod-borne phlebovirus .", "RVFV mostly causes outbreaks among domestic ruminants with a major economic impact .", "Human infections are associated with these events , with a fatality rate of 0 . 5–2% .", "Since the virus is able to use many mosquito species of...	[ "We describe a high seropositivity rate for Rift Valley fever virus , in up to 29 . 3% of tested individuals from the shore of Lake Malawi in southwestern Tanzania , and much lower rates from areas distant to the lake .", "Rift Valley fever disease or outbreaks have not been observed there in the past , which sug...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases/neglected tropical diseases", "immunology/immune response", "dermatology/skin infections", "cell biology/membranes and sorting", "cell biology/microbial growth and development", "immunology/innate immunity", "infectious diseases/viral infections", "virology/emerging viral diseases...	Dermal-Type Macrophages Expressing CD209/DC-SIGN Show Inherent Resistance to Dengue Virus Growth	journal.pntd.0000311	null	[ [ "Dengue is probably the most important mosquito-transmitted viral disease of humans worldwide .", "It is caused by dengue virus ( DV ) , which exists as four serotypes ( DV1-4 ) and circulates in an endemic-epidemic mode in most tropical and sub-tropical territories .", "Transmission of DV to humans o...	[ "An important question in dengue pathogenesis is the identity of immune cells involved in the control of dengue virus infection at the site of the mosquito bite .", "There is evidence that infection of immature myeloid dendritic cells plays a crucial role in dengue pathogenesis and that the interaction of the vir...	[ "Mosquito-transmitted pathogens are a major challenge to humans due to ever-increasing distribution of the vector worldwide .", "Dengue virus causes morbidity and mortality , and no anti-viral treatment or vaccine are currently available .", "The virus is injected into the skin when an infected mosquito probes ...	2008
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "nucleic acid synthesis", "pathology and laboratory medicine", "pathogens", "messenger rna", "dna-binding proteins", "microbiology", "viruses", "protein synthesis", "polymerases", "rna viruses", "rna isolation", "molecular biology techniques", "rna synthesis...	Tick-borne encephalitis virus inhibits rRNA synthesis and host protein production in human cells of neural origin	journal.pntd.0007745	null	[ [ "The Flaviviridae family contains arthropod-borne viruses including medically important pathogens with worldwide distribution and impact , such as dengue virus ( DENV ) , yellow fever virus ( YFV ) , West Nile virus ( WNV ) , Japanese encephalitis virus ( JEV ) , Zika virus ( ZIKV ) , and tick-borne encephali...	[ "Tick-borne encephalitis virus ( TBEV ) , a member of the genus Flavivirus ( Flaviviridae ) , is a causative agent of a severe neuroinfection .", "Recently , several flaviviruses have been shown to interact with host protein synthesis .", "In order to determine whether TBEV interacts with this host process in i...	[ "Tick-borne encephalitis virus ( TBEV ) is a causative agent of a severe human neuroinfection that threatens Europe and Asia .", "Little is known about the interaction of this neurotropic virus with neural cells , even though this may be important to better understand why or how TBEV can cause high pathogenicity ...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular biology/post-translational regulation of gene expression", "virology/virulence factors and mechanisms", "infectious diseases/viral infections", "biochemistry/cell signaling and trafficking structures", "virology/viruses and cancer" ]	NRP/Optineurin Cooperates with TAX1BP1 to Potentiate the Activation of NF-κB by Human T-Lymphotropic Virus Type 1 Tax Protein	journal.ppat.1000521	null	[ [ "Human T-Lymphotropic Virus type 1 ( HTLV-1 ) is the etiological agent of Adult T cell Leukemia/Lymphoma ( ATL ) and of HTLV-Associated Myelopathy/Tropical Spastic Paraparesis ( HAM/TSP ) [1]–[3] .", "HTLV-1 contains a unique pX region in the 3′ portion of its genome , which encodes regulatory and accesso...	[ "Nuclear factor ( NF ) -κB is a major survival pathway engaged by the Human T-Lymphotropic Virus type 1 ( HTLV-1 ) Tax protein .", "Tax1 activation of NF-κB occurs predominantly in the cytoplasm , where Tax1 binds NF-κB Essential Modulator ( NEMO/IKKγ ) and triggers the activation of IκB kinases .", "Several in...	[ "Oncogenic viruses ( i . e . , viruses that can induce cancer ) have usually been found to deregulate several cellular signaling pathways controlling cell survival and proliferation .", "Among those , the NF-κB pathway is particularly important .", "In this study , we focus on the Human T-Lymphotropic Virus typ...	2009
[ "Introduction", "Results", "Discussion", "Materials And Methods" ]	[ "cardiovascular disorders/congenital heart disease", "genetics and genomics/animal genetics", "genetics and genomics/disease models" ]	A Mutation in the Mitochondrial Fission Gene Dnm1l Leads to Cardiomyopathy	journal.pgen.1001000	null	[ [ "Idiopathic dilated cardiomyopathy ( DCM ) is characterised by unexplained left ventricular ( LV ) cavity enlargement with LV systolic impairment [1] .", "DCM is an important cause of congestive heart failure ( CHF ) with a prevalence of 36 cases per 100 , 000 in the United States [2] .", "Although th...	[ "Mutations in a number of genes have been linked to inherited dilated cardiomyopathy ( DCM ) .", "However , such mutations account for only a small proportion of the clinical cases emphasising the need for alternative discovery approaches to uncovering novel pathogenic mutations in hitherto unidentified pathways ...	[ "Heart disease is very common .", "Some cases of heart disease are strongly influenced by lifestyle and diet , whereas others have a strong genetic component .", "A certain form of heart failure , known as dilated cardiomyopathy ( DCM ) quite often runs in families suggesting that a defective gene or genes unde...	2010
[ "Introduction", "Results and Discussion", "Materials and Methods" ]	[]	A Genome Scan for Genes Underlying Microgeographic-Scale Local Adaptation in a Wild Arabidopsis Species	journal.pgen.1005361	null	[ [ "Recent advances in next-generation sequencing ( NGS ) technologies have enabled a genome-scale analysis to infer the phylogenetic history , demography , and selection of natural populations .", "One of the intriguing challenges in ecological genomics is to identify the genes underlying local adaptation [...	[ "Adaptive divergence at the microgeographic scale has been generally disregarded because high gene flow is expected to disrupt local adaptation .", "Yet , growing number of studies reporting adaptive divergence at a small spatial scale highlight the importance of this process in evolutionary biology .", "To inv...	[ "Where does a local adaptation take place ?", "In general , an adaptive divergence is predicted to occur between isolated populations because gene flow will erode and prevent the divergence .", "Therefore , previous genome-wide studies that aim to find the adaptive genes have compared populations that are usual...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics and genomics/gene discovery", "genetics and genomics/genetics of the immune system", "genetics and genomics/genetics of disease", "immunology/genetics of the immune system", "genetics and genomics/medical genetics" ]	Identification of a Shared Genetic Susceptibility Locus for Coronary Heart Disease and Periodontitis	journal.pgen.1000378	null	[ [ "Coronary Heart Disease ( CHD ) is the leading cause of death worldwide [1] , [2] .", "It is a systemic disease which is propagated by several environmental and behavioural risk factors [3]–[7] with inflammation as an important additional risk [8] .", "It has a strong genetic basis [9] , but despite d...	[ "Recent studies indicate a mutual epidemiological relationship between coronary heart disease ( CHD ) and periodontitis .", "Both diseases are associated with similar risk factors and are characterized by a chronic inflammatory process .", "In a candidate-gene association study , we identify an association of a...	[ "Coronary heart disease ( CHD ) and periodontitis are the most widespread diseases in the Western industrialized world and pose a substantial health threat to populations worldwide .", "CHD is a leading cause for premature death , and periodontitis is the major cause for tooth loss in adults over 40 years .", "...	2009
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "bioengineering", "medicine", "hepatitis c", "biological systems engineering", "infectious diseases", "biotechnology", "hepatitis", "viral diseases", "engineering" ]	A Viral Dynamic Model for Treatment Regimens with Direct-acting Antivirals for Chronic Hepatitis C Infection	journal.pcbi.1002339	null	[ [ "Chronic hepatitis C ( CHC ) affects approximately 180 million people worldwide and is a frequent cause of increased risk for hepatic fibrosis , cirrhosis , hepatic failure , and hepatocellular carcinoma [1] , [2] , [3] , [4] .", "The treatment objective for CHC is SVR , or viral eradication , which is co...	[ "We propose an integrative , mechanistic model that integrates in vitro virology data , pharmacokinetics , and viral response to a combination regimen of a direct-acting antiviral ( telaprevir , an HCV NS3-4A protease inhibitor ) and peginterferon alfa-2a/ribavirin ( PR ) in patients with genotype 1 chronic hepatit...	[ "Hepatitis C virus chronically infects approximately 180 million people worldwide .", "The treatment aim for patients chronically infected with hepatitis C is viral eradication or sustained viral response ( SVR ) .", "Historical standard of care for HCV treatment was peginterferon-alfa and ribavirin .", "Rece...	2012
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "dengue virus", "medicine and health sciences", "pathology and laboratory medicine", "togaviruses", "chikungunya infection", "pathogens", "tropical diseases", "microbiology", "animals", "alphaviruses", "viruses", "chikungunya virus", "rna viruses", "forecasting", "math...	Detecting the impact of temperature on transmission of Zika, dengue, and chikungunya using mechanistic models	journal.pntd.0005568	null	[ [ "Epidemics of dengue , chikungunya , and Zika are sweeping through the Americas , and are part of a global public health crisis that places an estimated 3 . 9 billion people in 120 countries at risk [1] .", "Dengue virus ( DENV ) distribution and intensity in the Americas has increased over the last three...	[ "Recent epidemics of Zika , dengue , and chikungunya have heightened the need to understand the seasonal and geographic range of transmission by Aedes aegypti and Ae .", "albopictus mosquitoes .", "We use mechanistic transmission models to derive predictions for how the probability and magnitude of transmission...	[ "Understanding the drivers of recent Zika , dengue , and chikungunya epidemics is a major public health priority .", "Temperature may play an important role because it affects virus transmission by mosquitoes , through its effects on mosquito development , survival , reproduction , and biting rates as well as the...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology/cellular death and stress responses", "microbiology/innate immunity", "immunology/innate immunity", "infectious diseases/bacterial infections", "microbiology/cellular microbiology and pathogenesis" ]	Mycobacterium tuberculosis Eis Regulates Autophagy, Inflammation, and Cell Death through Redox-dependent Signaling	journal.ppat.1001230	null	[ [ "Mycobacterium tuberculosis ( Mtb ) is an intracellular pathogen that can survive and even multiply within host macrophages [1] , [2] .", "Mtb can persist within phagosomes by interfering with intracellular membrane trafficking and by arresting phagosome maturation in infected host cells [3] .", "Path...	[ "The “enhanced intracellular survival” ( eis ) gene of Mycobacterium tuberculosis ( Mtb ) is involved in the intracellular survival of M . smegmatis .", "However , its exact effects on host cell function remain elusive .", "We herein report that Mtb Eis plays essential roles in modulating macrophage autophagy ,...	[ "Tuberculosis is a global health problem: at least one-third of the world's population is infected with Mycobacterium tuberculosis ( Mtb ) .", "Mtb is a successful pathogen that enhances its own intracellular survival by arresting phagolysosomal fusion .", "Recently , autophagy has emerged as a host defense str...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/protozoal infections", "infectious diseases/tropical and travel-associated diseases", "microbiology/parasitology", "genetics and genomics/gene expression" ]	Temperature Shift and Host Cell Contact Up-Regulate Sporozoite Expression of Plasmodium falciparum Genes Involved in Hepatocyte Infection	journal.ppat.1000121	null	[ [ "Protozoan parasites of the genus Plasmodium are the causative agents of malaria , the most devastating parasitic disease in humans .", "The infection is initiated when Plasmodium sporozoites are deposited in the skin of their vertebrate hosts through the bite of an infected female Anopheles mosquito .", ...	[ "Plasmodium sporozoites are deposited in the skin by Anopheles mosquitoes .", "They then find their way to the liver , where they specifically invade hepatocytes in which they develop to yield merozoites infective to red blood cells .", "Relatively little is known of the molecular interactions during these init...	[ "Sporozoites , the infective form of the malaria parasites Plasmodium , are deposited in the skin by Anopheles mosquitoes .", "They then find their way to the liver where they specifically invade hepatocytes , in which they develop to yield another form , the merozoite , infective to red blood cells .", "Relati...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	MYB64 and MYB119 Are Required for Cellularization and Differentiation during Female Gametogenesis in Arabidopsis thaliana	journal.pgen.1003783	null	[ [ "The alternation between haploid gametophyte and diploid sporophyte generations is a fundamental aspect of the plant life cycle .", "In all species , gametophytes are essential for gamete formation .", "Angiosperms have two gametophytes: a female gametophyte , which is also referred to as the embryo s...	[ "In angiosperms , the egg cell forms within the multicellular , haploid female gametophyte .", "Female gametophyte and egg cell development occurs through a unique process in which a haploid spore initially undergoes several rounds of synchronous nuclear divisions without cytokinesis , resulting in a single cell ...	[ "Female gamete formation in angiosperms occurs through a unique process in which a haploid spore initially undergoes a series of free nuclear divisions without cytokinesis , resulting in a single cell containing multiple nuclei .", "The nuclei then differentiate and are partitioned with cell walls to generate the...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immune cells", "viral transmission and infection", "immunologic subspecialties", "antigen-presenting cells", "immunity to infections", "immunology", "microbiology", "host-pathogen interaction", "animal models", "adaptive immunity", "model organisms", "immune defense", "immunoregulation", ...	Unique Type I Interferon Responses Determine the Functional Fate of Migratory Lung Dendritic Cells during Influenza Virus Infection	journal.ppat.1002345	null	[ [ "Influenza virus replicates productively in the epithelial cells of the respiratory tract [1] , [2] .", "In close contact to the infected epithelial cells lies a network of specialized antigen presenting cells ( APCs ) known as dendritic cells ( DCs ) [3] , [4] .", "Two major subsets of lung DCs known...	[ "Migratory lung dendritic cells ( DCs ) transport viral antigen from the lungs to the draining mediastinal lymph nodes ( MLNs ) during influenza virus infection to initiate the adaptive immune response .", "Two major migratory DC subsets , CD103+ DCs and CD11bhigh DCs participate in this function and it is not cl...	[ "Migratory lung dendritic cells ( DCs ) control the initiation of the adaptive immune responses to influenza virus by expanding virus-specific T cells in draining lymph nodes ( MLNs ) that will subsequently clear the pathogen from the respiratory tract .", "Here we demonstrate that both subsets of lung DCs , CD10...	2011
[ "Introduction", "Results", "Discussion", "Experimental Procedures" ]	[ "blood cells", "humoral immunity", "medicine and health sciences", "immune cells", "immunology", "tropical diseases", "parasitic diseases", "parasitic protozoans", "protozoans", "white blood cells", "malarial parasites", "animal cells", "t cells", "immune response", "antibody-producing c...	IFNAR1-Signalling Obstructs ICOS-mediated Humoral Immunity during Non-lethal Blood-Stage Plasmodium Infection	journal.ppat.1005999	null	[ [ "Although robust immunity to malaria is difficult to generate in humans through natural infection or vaccination [1 , 2] , it is nonetheless clear that Plasmodium-specific antibodies offer the best known form of immunological protection against blood-stage parasites [3 , 4 , 5 , 6 , 7 , 8] , and may also cont...	[ "Parasite-specific antibodies protect against blood-stage Plasmodium infection .", "However , in malaria-endemic regions , it takes many months for naturally-exposed individuals to develop robust humoral immunity .", "Explanations for this have focused on antigenic variation by Plasmodium , but have considered ...	[ "Plasmodium parasites cause malaria by invading , replicating within , and rupturing out of red blood cells .", "Natural immunity to malaria , which depends on generating Plasmodium-specific antibodies , often takes years to develop .", "Explanations for this focus on antigenic variation by the parasite , but c...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "sequencing techniques", "recombination-based assay", "chromosome structure and function", "cloning", "telomeres", "dna replication", "dna", "molecular biology techniques", "research and analysis methods", "sequence analysis", "artificial gene amplification and extension", "chromosome biology"...	Multiple Rad52-Mediated Homology-Directed Repair Mechanisms Are Required to Prevent Telomere Attrition-Induced Senescence in Saccharomyces cerevisiae	journal.pgen.1006176	null	[ [ "Telomeres , nucleoprotein structures located at the ends of linear chromosomes , prevent natural chromosome ends from being recognized as DNA double-strand breaks ( DSBs ) [1] .", "Due to incomplete DNA replication and nucleolytic degradation , telomeres shorten with each round of replication , which can...	[ "Most human somatic cells express insufficient levels of telomerase , which can result in telomere shortening and eventually senescence , both of which are hallmarks of ageing .", "Homology-directed repair ( HDR ) is important for maintaining proper telomere function in yeast and mammals .", "In Saccharomyces c...	[ "Telomeres are essential structures located at the ends of chromosomes .", "The canonical DNA replication machinery is unable to fully replicate DNA at chromosome ends , causing telomeres to shorten with every round of cell division .", "This shortening can be counteracted by an enzyme called telomerase , but i...	2016
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "agriculture", "biology" ]	Towards Establishment of a Rice Stress Response Interactome	journal.pgen.1002020	null	[ [ "A major limitation of crop production is imposed by a suite of abiotic and biotic stresses resulting in 30%–60% yield losses globally each year [1] .", "The burgeoning field of systems biology provides new methodologies to make sense of plant stress responses , which are often controlled by highly comple...	[ "Rice ( Oryza sativa ) is a staple food for more than half the world and a model for studies of monocotyledonous species , which include cereal crops and candidate bioenergy grasses .", "A major limitation of crop production is imposed by a suite of abiotic and biotic stresses resulting in 30%–60% yield losses gl...	[ "A major limitation of crop production is imposed by a suite of abiotic and biotic stresses resulting in 30%–60% yield losses globally each year .", "In this paper , we used a yeast-based approach to identify rice proteins that govern the rice stress response .", "We validated the role of these new proteins usi...	2011
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "neglected tropical diseases", "infectious diseases", "buruli ulcer" ]	Long Term Streptomycin Toxicity in the Treatment of Buruli Ulcer: Follow-up of Participants in the BURULICO Drug Trial	journal.pntd.0002739	null	[ [ "Buruli ulcer ( BU ) is a Neglected Tropical Disease caused by infection with Mycobacterium ulcerans .", "Necrotic skin lesions characterize the disease , often with typical undermined edges .", "Treatment delay may result in disfigurement and functional limitations [1] .", "Though isolated cases ...	[ "Buruli Ulcer ( BU ) is a tropical infectious skin disease that is currently treated with 8 weeks of intramuscular streptomycin and oral rifampicin .", "As prolonged streptomycin administration can cause both oto- and nephrotoxicity , we evaluated its long term toxicity by following-up former BU patients that had...	[ "Buruli Ulcer is an infectious skin disease , mainly occurring in West Africa .", "Previously , the disease was treated exclusively by surgery , but in the last decade , effective treatment with antibiotics has been established .", "The WHO recommended regimen consists of 8 weeks of oral rifampicin combined wit...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public health and epidemiology", "infectious disease epidemiology", "preventive medicine", "mathematical computing", "mathematics", "neglected tropical diseases", "infectious disease control", "infectious diseases", "disease ecology", "epidemiology", "infectious disease modeling",...	Optimal Timing of Insecticide Fogging to Minimize Dengue Cases: Modeling Dengue Transmission among Various Seasonalities and Transmission Intensities	journal.pntd.0001367	null	[ [ "Dengue virus ( DENV ) infection is a mosquito-borne viral disease of serious health concern in recent decades .", "More than two-fifths of the global population is considered to be at risk of dengue infection , principally in the tropics and sub-tropics [1] .", "Increases in dengue epidemics are like...	[ "Dengue infection is endemic in many regions throughout the world .", "While insecticide fogging targeting the vector mosquito Aedes aegypti is a major control measure against dengue epidemics , the impact of this method remains controversial .", "A previous mathematical simulation study indicated that insectic...	[ "Dengue virus infection is a serious infectious disease transmitted by Aedes mosquitoes in the tropics and sub-tropics .", "Disease control often involves the use of insecticide fogging against mosquito vectors .", "However , the effectiveness of this method for reducing dengue cases , in addition to appropriat...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "animal genetics", "genetic mutation", "sexual differentiation", "genetics", "biology", "morphogenesis", "cytogenetics", "genetics and genomics" ]	Mammalian BTBD12 (SLX4) Protects against Genomic Instability during Mammalian Spermatogenesis	journal.pgen.1002094	null	[ [ "SLX1 and SLX4 were identified , together with MUS81 and MMS4 ( Eme1 in mammals ) , in a S . cerevisiae screen for genes required for the viability of sgs1-deficient cells [1] .", "Slx1 is the founding member of a family of proteins with a predicted URI nuclease domain whose activity is enhanced 500-fold ...	[ "The mammalian ortholog of yeast Slx4 , BTBD12 , is an ATM substrate that functions as a scaffold for various DNA repair activities .", "Mutations of human BTBD12 have been reported in a new sub-type of Fanconi anemia patients .", "Recent studies have implicated the fly and worm orthologs , MUS312 and HIM-18 , ...	[ "Mutations in genes essential for genome maintenance during meiosis can result in severe disruptions to spermatogenesis and subsequent low fertility and/or birth defects in mammals .", "The mammalian homolog of yeast Slx4 , BTBD12 , plays a critical role in somatic cell repair in mice .", "Here , we show that t...	2011
[ "Introduction", "Model", "Results", "Discussion" ]	[]	From Birdsong to Human Speech Recognition: Bayesian Inference on a Hierarchy of Nonlinear Dynamical Systems	journal.pcbi.1003219	null	[ [ "Can we learn something about how humans recognize speech from how birds recognize song ?", "The last common ancestor of humans and birds lived about 300 million years ago , nevertheless human and songbird communication share several striking features at the cognitive , neuronal and molecular level [1] , ...	[ "Our knowledge about the computational mechanisms underlying human learning and recognition of sound sequences , especially speech , is still very limited .", "One difficulty in deciphering the exact means by which humans recognize speech is that there are scarce experimental findings at a neuronal , microscopic ...	[ "Neuroscience still lacks a concrete explanation of how humans recognize speech .", "Even though neuroimaging techniques are helpful in determining the brain areas involved in speech recognition , there are rarely mechanistic explanations at a neuronal level .", "Here , we assume that songbirds and humans solve...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "physics", "developmental biology", "cell motility", "mathematics", "cell migration", "biology", "nonlinear dynamics", "morphogenesis", "biophysics" ]	Modeling and Measuring Signal Relay in Noisy Directed Migration of Cell Groups	journal.pcbi.1003041	null	[ [ "Eukaryotic cells frequently transduce external chemical gradients into directed cell migration [1] , a phenomenon known as chemotaxis .", "Seminal work in the last few decades has identified components of the intracellular biochemical networks mediating cell response to external chemical gradients and fo...	[ "We develop a coarse-grained stochastic model for the influence of signal relay on the collective behavior of migrating Dictyostelium discoideum cells .", "In the experiment , cells display a range of collective migration patterns , including uncorrelated motion , formation of partially localized streams , and cl...	[ "Collective cell migration is observed in various biological processes including angiogenesis , gastrulation , fruiting body formation , and wound healing .", "Dictyostelium discoideum , for example , exhibits highly dynamic patterns such as streams and clumps during its early phases of collective motion and has ...	2013
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "genetics and genomics/animal genetics", "genetics and genomics/gene discovery", "evolutionary biology/evolutionary and comparative genetics", "genetics and genomics/complex traits", "developmental biology/developmental evolution", "evolutionary biology/morphogenesis and cell biology", "evolutionary bio...	Non-Coding Changes Cause Sex-Specific Wing Size Differences between Closely Related Species of Nasonia	journal.pgen.1000821	null	[ [ "Somatic sexual differentiation is an ancient feature of animals , yet sex differences in morphological traits can evolve rapidly .", "Because of this , between-species genetic analysis of recently evolved sexual differences has been proposed as a way of identifying the genes and genetic changes that unde...	[ "The genetic basis of morphological differences among species is still poorly understood .", "We investigated the genetic basis of sex-specific differences in wing size between two closely related species of Nasonia by positional cloning a major male-specific locus , wing-size1 ( ws1 ) .", "Male wing size incre...	[ "The regulation of cell size and cell numbers is an important part of determining the size of organs in development , as well as of controlling cell over-proliferation in diseases such as cancer and diabetes .", "How the regulation of cell size and number can change to produce different organ sizes is not well un...	2010
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "action potentials", "medicine and health sciences", "neural networks", "membrane potential", "brain", "electrophysiology", "random variables", "neuroscience", "covariance", "mathematics", "statistics (mathematics)", "network analysis", "research and analysis methods", "computer and inform...	A theoretical framework for analyzing coupled neuronal networks: Application to the olfactory system	journal.pcbi.1005780	null	[ [ "As experimental tools advance , measuring whole-brain dynamics with single-neuron resolution becomes closer to reality [1–4] .", "However , a task that remains technically elusive is to measure the interactions within and across brain regions that govern such system-wide dynamics .", "Here we develop...	[ "Determining how synaptic coupling within and between regions is modulated during sensory processing is an important topic in neuroscience .", "Electrophysiological recordings provide detailed information about neural spiking but have traditionally been confined to a particular region or layer of cortex .", "He...	[ "Sensory processing is known to span multiple regions of the nervous system .", "However , electrophysiological recordings during sensory processing have traditionally been limited to a single region or brain layer .", "With recent advances in experimental techniques , recorded spiking activity from multiple re...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing techniques", "classical mechanics", "chemical compounds", "phosphates", "enzymes", "split-decomposition method", "enzymology", "multiple alignment calculation", "damage mechanics", "protein structure", "molecular biology techniques", "research and analysis methods", "sequence ana...	Similarity in Shape Dictates Signature Intrinsic Dynamics Despite No Functional Conservation in TIM Barrel Enzymes	journal.pcbi.1004834	null	[ [ "Understanding a proteins’ inherent flexibility , or intrinsic dynamics , is fundamental to understanding the mechanism with which they are able to perform their function .", "Yet we know little about the conservation of dynamic properties in a structural fold , whether the similarity is due to or regardl...	[ "The conservation of the intrinsic dynamics of proteins emerges as we attempt to understand the relationship between sequence , structure and functional conservation .", "We characterise the conservation of such dynamics in a case where the structure is conserved but function differs greatly .", "The triosephos...	[ "Proteins are dynamic entities , and their flexibility is intimately linked with function .", "Some suggest that function drives the conservation of flexibility in proteins , while it has also been observed that proteins with similar structures also exhibit similar flexibility .", "To investigate the role of sh...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Nuclear Fragile X Mental Retardation Protein Is localized to Cajal Bodies	journal.pgen.1003890	null	[ [ "Fragile X syndrome , one of the most frequent human genetic diseases , is caused by the silencing of the FMR1 gene that codes for a heterogeneous set of Fragile X Mental Retardation protein ( FMRP ) isoforms [1]–[3] .", "FMRP , particularly abundant in neurons [4] , contains two KH domains and an RGG box...	[ "Fragile X syndrome is caused by loss of function of a single gene encoding the Fragile X Mental Retardation Protein ( FMRP ) .", "This RNA-binding protein , widely expressed in mammalian tissues , is particularly abundant in neurons and is a component of messenger ribonucleoprotein ( mRNP ) complexes present wit...	[ "Fragile X syndrome is the most common form of inherited mental retardation affecting approximately 1/7000 females and 1/4000 males worldwide .", "The syndrome is due to the silencing of a single gene , the Fragile Mental Retardation 1 ( FMR1 ) , that codes for a protein called the Fragile X mental retardation pr...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "developmental biology", "genomics", "functional genomics", "organism development", "genome analysis", "gene expression", "genetics", "biology and life sciences", "comparative genomics", "molecular genetics", "computational biology" ]	Integrating Diverse Datasets Improves Developmental Enhancer Prediction	journal.pcbi.1003677	null	[ [ "Eukaryotic gene expression is regulated by a highly orchestrated network of events , including the binding of regulatory proteins to DNA , chemical modifications to DNA and nucleosomes , recruitment of the transcriptional machinery , splicing , and post-transcriptional modifications .", "Enhancers are ge...	[ "Gene-regulatory enhancers have been identified using various approaches , including evolutionary conservation , regulatory protein binding , chromatin modifications , and DNA sequence motifs .", "To integrate these different approaches , we developed EnhancerFinder , a two-step method for distinguishing developm...	[ "The human genome contains an immense amount of non-protein-coding DNA with unknown function .", "Some of this DNA regulates when , where , and at what levels genes are active during development .", "Enhancers , one type of regulatory element , are short stretches of DNA that can act as “switches” to turn a gen...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience/behavioral neuroscience", "neuroscience/cognitive neuroscience", "neuroscience/motor systems", "neuroscience/experimental psychology", "computational biology/systems biology" ]	Inferring Visuomotor Priors for Sensorimotor Learning	journal.pcbi.1001112	null	[ [ "Uncertainty poses a fundamental problem for perception , action and decision-making .", "Despite our sensory inputs providing only a partial and noisy view of the world , and our motor outputs being corrupted by significant amounts of noise , we are able to both perceive and act on the world in what appe...	[ "Sensorimotor learning has been shown to depend on both prior expectations and sensory evidence in a way that is consistent with Bayesian integration .", "Thus , prior beliefs play a key role during the learning process , especially when only ambiguous sensory information is available .", "Here we develop a nov...	[ "When learning a new skill , such as riding a bicycle , we can adjust the commands we send to our muscles based on two sources of information .", "First , we can use sensory inputs to inform us how the bike is behaving .", "Second , we can use prior knowledge about the properties of bikes and how they behave in...	2011
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "mathematics", "statistics", "genetics", "statistical methods", "population genetics", "population biology", "biology", "genomics", "biostatistics", "computational biology" ]	Genic Intolerance to Functional Variation and the Interpretation of Personal Genomes	journal.pgen.1003709	null	[ [ "Many approaches are available that attempt to prioritize mutations in terms of their prior probabilities of conferring risk of disease , notably including population allele frequency and measures of conservation at either the phylogenetic level [1] or in terms of amino acid characteristics [2]–[6] .", "H...	[ "A central challenge in interpreting personal genomes is determining which mutations most likely influence disease .", "Although progress has been made in scoring the functional impact of individual mutations , the characteristics of the genes in which those mutations are found remain largely unexplored .", "Fo...	[ "This work uses empirical single nucleotide variant data from the NHLBI Exome Sequencing Project to introduce a genome-wide scoring system that ranks human genes in terms of their intolerance to standing functional genetic variation in the human population .", "It is often inferred that genes carrying relatively ...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "computer science/natural and synthetic vision", "neuroscience/cognitive neuroscience", "neuroscience/sensory systems", "neuroscience/motor systems", "neuroscience/natural and synthetic vision", "neuroscience/theoretical neuroscience" ]	The Natural Statistics of Audiovisual Speech	journal.pcbi.1000436	null	[ [ "Organisms are exposed to a continuous stream of signals which are dynamic , multimodal , extended , time varying in nature and typically characterized by sequences of inputs with particular time constants , durations , repetition rates , etc .", "[1] .", "This complex input space is transduced and sa...	[ "Humans , like other animals , are exposed to a continuous stream of signals , which are dynamic , multimodal , extended , and time varying in nature .", "This complex input space must be transduced and sampled by our sensory systems and transmitted to the brain where it can guide the selection of appropriate act...	[ "When we watch someone speak , how much work is our brain actually doing ?", "How much of this work is facilitated by the structure of speech itself ?", "Our work shows that not only are the visual and auditory components of speech tightly locked ( obviating the need for the brain to actively bind such informat...	2009
[ "Introduction", "Results", "Discussion" ]	[ "medicine", "public health and epidemiology", "emerging infectious diseases", "epidemiology", "infectious disease epidemiology", "biology", "microbiology" ]	Chikungunya Fever: A Clinical and Virological Investigation of Outpatients on Reunion Island, South-West Indian Ocean	journal.pntd.0002004	null	[ [ "Chikungunya virus ( CHIKV ) is an arbovirus ( genus Alphavirus , family Togaviridae ) , transmitted by the bite of infected mosquitoes ( Aedes aegypti = Stegomya aegypti and Aedes albopictus = Stegomya albopicta ) , that causes Chikungunya fever ( CHIK ) , an acute febrile illness characterized by severe and...	[ "Chikungunya virus ( CHIKV ) is responsible for acute febrile polyarthralgia and , in a proportion of cases , severe complications including chronic arthritis .", "CHIKV has spread recently in East Africa , South-West Indian Ocean , South-Asia and autochthonous cases have been reported in Europe .", "Although a...	[ "The mosquito-transmitted chikungunya virus is responsible for acute febrile polyarthralgia and , in a proportion of cases , complications including chronic arthritis .", "Since 2005 , it has massively re-emerged in the Old World .", "Although the large majority of patients are outpatients , the most detailed s...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "computational neuroscience", "single neuron function", "biology", "sensory systems", "neuroscience", "coding mechanisms" ]	Receptive Field Inference with Localized Priors	journal.pcbi.1002219	null	[ [ "A fundamental problem in systems neuroscience is to determine how sensory stimuli are functionally related to a neuron's response .", "A popular mathematical description of this encoding relationship is the “cascade” model , which consists of a linear filter followed by a noisy nonlinear spiking process ...	[ "The linear receptive field describes a mapping from sensory stimuli to a one-dimensional variable governing a neuron's spike response .", "However , traditional receptive field estimators such as the spike-triggered average converge slowly and often require large amounts of data .", "Bayesian methods seek to o...	[ "A central problem in systems neuroscience is to understand how sensory neurons convert environmental stimuli into spike trains .", "The receptive field ( RF ) provides a simple model for the first stage in this encoding process: it is a linear filter that describes how the neuron integrates the stimulus over tim...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunology/innate immunity", "virology", "virology/animal models of infection", "immunology/immunity to infections", "virology/host antiviral responses" ]	Myd88 Is Required for an Antibody Response to Retroviral Infection	journal.ppat.1000298	null	[ [ "The HIV pandemic has spurred intensive research into retroviruses , and yet an effective vaccine for HIV has remained elusive .", "Acute HIV infection stimulates both B and T cell responses , but the antibody response is ineffective , possibly due to shielding of neutralizing epitopes [1] , [2] .", "...	[ "Although retroviruses have been extensively studied for many years , basic questions about how retroviral infections are detected by the immune system and which innate pathways are required for the generation of immune responses remain unanswered .", "Defining these pathways and how they contribute to the anti-r...	[ "Efforts to develop vaccines against the retrovirus HIV by inducing immune responses involving antibodies or T cells have been unsuccessful .", "Although antibodies can be generated against HIV , they fail to neutralize the virus .", "Thus , a more fundamental understanding of how neutralizing antibody response...	2009
[ "Introduction", "Models", "Results", "Discussion" ]	[ "cell death", "medicine and health sciences", "cell cycle and cell division", "cell processes", "simulation and modeling", "physiological processes", "developmental biology", "fungi", "model organisms", "systems science", "nutrition", "mathematics", "organism development", "experimental or...	A modeling study of budding yeast colony formation and its relationship to budding pattern and aging	journal.pcbi.1005843	null	[ [ "Budding yeast Saccharomyces cerevisiae has been an ideal model system to study many biological processes crucial to the development of uni-cellular or multi-cellular organisms , such as cell polarization , cytokinesis and cell aging .", "It became a favorable model system because of its experimental trac...	[ "Budding yeast , which undergoes polarized growth during budding and mating , has been a useful model system to study cell polarization .", "Bud sites are selected differently in haploid and diploid yeast cells: haploid cells bud in an axial manner , while diploid cells bud in a bipolar manner .", "While previo...	[ "Budding yeast is a model organism in understanding fundamental aspects of eukaryotic cells , such as cell polarization and cell aging .", "Previously , extensive research has focused on the molecular mechanisms of biological processes in yeast , but many questions regarding yeast budding remain unsolved .", "F...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Non-linear Membrane Properties in Entorhinal Cortical Stellate Cells Reduce Modulation of Input-Output Responses by Voltage Fluctuations	journal.pcbi.1004188	null	[ [ "Membrane voltage in cortical neurons is dominated by fluctuations mediated by random synaptic activity [1–4] .", "Because probabilistic threshold crossings associated with fluctuations lower spike threshold , enabling spike response to otherwise sub-threshold inputs [5 , 6] , it has been hypothesized tha...	[ "The presence of voltage fluctuations arising from synaptic activity is a critical component in models of gain control , neuronal output gating , and spike rate coding .", "The degree to which individual neuronal input-output functions are modulated by voltage fluctuations , however , is not well established acro...	[ "The membrane voltage of neurons in vivo is dominated by noisy “background” fluctuations generated by network-based synaptic activity from nearby cells .", "It has been speculated that membrane voltage fluctuations in neurons play an important role in scaling the relationship between input amplitude and spike rat...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "methods and resources", "optogenetics", "engineering and technology", "lasers", "social sciences", "vertebrates", "neuroscience", "animals", "mammals", "primates", "brain mapping", "bioassays and physiological analysis", "vision", "optical equipment", "...	Long-term all-optical interrogation of cortical neurons in awake-behaving nonhuman primates	journal.pbio.2005839	null	[ [ "Optogenetic techniques enable the functional characterization of neuronal populations and circuits with high spatial and temporal precision [1–7] .", "Though relatively understudied as compared to rodents , optogenetics techniques have been applied to the study of high-level cognition circuits in NHPs [8...	[ "Whereas optogenetic techniques have proven successful in their ability to manipulate neuronal populations—with high spatial and temporal fidelity—in species ranging from insects to rodents , significant obstacles remain in their application to nonhuman primates ( NHPs ) .", "Robust optogenetics-activated behavio...	[ "This report details the first successful application of long-term all-optical interrogation techniques in monkeys .", "We have overcome obstacles that prevented the combination of single- and two-photon ( 1P and 2P ) optogenetic stimulation with 2P imaging in awake-behaving monkeys , retesting targeted individua...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "cost-effectiveness analysis", "engineering and technology", "economic analysis", "tropical diseases", "social sciences", "parasitic diseases", "animals", "health care", "vaccines", "decision analysis", "developmental biology", "ectoparasiti...	A systematic review of scabies transmission models and data to evaluate the cost-effectiveness of scabies interventions	journal.pntd.0007182	null	[ [ "Scabies is a common dermatological conditions [1] , affecting more than 130 million people at any time [2] .", "It is a neglected disease caused by the mite Sarcoptes Scabiei [3] .", "Scabies often results in severe itching , and in some patients , including those with compromised immunity , it may p...	[ "Scabies is a common dermatological condition , affecting more than 130 million people at any time .", "To evaluate and/or predict the effectiveness and cost-effectiveness of scabies interventions , disease transmission modelling can be used .", "To review published scabies models and data to inform the design ...	[ "Scabies is a neglected tropical disease affecting more than 130 million people , with major costs on health care systems worldwide .", "While effective treatments exist , it is unknown which treatment strategies result in the best outcomes against the lowest costs , and to what extent this differs between commun...	2019
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "body fluids", "parasitic diseases", "animals", "nematode infections", "brugia", "insect vectors", "research and analysis methods", "infectious diseases", "spectrum analysis techniques", "aedes aegypti", "chemistry", "mass spectrometry", "...	Assessment of MALDI-TOF mass spectrometry for filariae detection in Aedes aegypti mosquitoes	journal.pntd.0006093	null	[ [ "Mosquitoes are blood-sucking arthropods with a global distribution .", "They represent a huge threat to humans and animals as vectors of pathogens [1 , 2] .", "In passing from host to host , some mosquito species may transmit parasitic diseases ( i . e . malaria , lymphatic filariosis and dirofilario...	[ "Matrix Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry ( MALDI-TOF MS ) is an emerging tool for routine identification of bacteria , archaea and fungi .", "It has also been recently applied as an accurate approach for arthropod identification .", "Preliminary studies have shown that the M...	[ "Filariosis is a disease group affecting humans and animals , caused by nematode parasites of the family Onchocercidae , superfamily Filarioidea .", "These parasites can be transmitted , essentially , by mosquitoes during blood meals of infected female specimens .", "Screening vectors for these filariae current...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "virology/new therapies, including antivirals and immunotherapy", "virology/antivirals, including modes of action and resistance", "virology" ]	A Novel Small Molecule Inhibitor of Hepatitis C Virus Entry	journal.ppat.1001086	null	[ [ "Hepatitis C virus ( HCV ) , a member of the Flaviviridae family of positive-strand RNA viruses , chronically infects approximately 170 million people worldwide [1] , [2] .", "Over time , ongoing virus replication within the liver often leads to severe clinical manifestations such as fibrosis , cirrhosis ...	[ "Small molecule inhibitors of hepatitis C virus ( HCV ) are being developed to complement or replace treatments with pegylated interferons and ribavirin , which have poor response rates and significant side effects .", "Resistance to these inhibitors emerges rapidly in the clinic , suggesting that successful ther...	[ "Approximately 170 million people worldwide are chronically infected with hepatitis C virus ( HCV ) , which is a leading cause of chronic liver disease .", "Current treatments are not optimal; however , several molecules that inhibit HCV replication are in development .", "However , resistance to individual ant...	2010
[ "Introduction", "Results", "Discussion", "Material and Methods" ]	[ "genetics and genomics", "biochemistry", "developmental biology" ]	Dynamic Switch of Negative Feedback Regulation in Drosophila Akt–TOR Signaling	journal.pgen.1000990	null	[ [ "The development of multi-cellular organisms depends on the precise choreography of a diverse array of signal transduction pathways .", "Besides the requirement of some signaling events to occur in a spatial or temporal on-off manner , other pathways need to stay homeostatically active within physiologica...	[ "Akt represents a nodal point between the Insulin receptor and TOR signaling , and its activation by phosphorylation controls cell proliferation , cell size , and metabolism .", "The activity of Akt must be carefully balanced , as increased Akt signaling is frequently associated with cancer and as insufficient Ak...	[ "The development of multi-cellular organisms depends on the precise choreography of a diverse array of signal transduction pathways .", "This requires balanced regulation by activating as well as repressing signals .", "Negative feedback , defined as a signaling response counteracting the stimulus , is a freque...	2010
[ "Introduction", "Results", "Discussion", "Models" ]	[ "genetics and genomics/population genetics" ]	Sexually Antagonistic “Zygotic Drive” of the Sex Chromosomes	journal.pgen.1000313	null	[ [ "Sex chromosomes are unusual compared to the autosomes for three reasons .", "First , when present in the heterogametic sex , the two types of sex chromosome are transmitted to opposite sex offspring .", "Second , it is common for recombination to be suppressed over a part or all of their length .", ...	[ "Genomic conflict is perplexing because it causes the fitness of a species to decline rather than improve .", "Many diverse forms of genomic conflict have been identified , but this extant tally may be incomplete .", "Here , we show that the unusual characteristics of the sex chromosomes can , in principle , le...	[ "Our study describes a new form of sexual genomic conflict that operates through the process of antagonistic green-beard effects .", "Although past theoretical and empirical work indicated that green-beard effects rarely operate in nature , our new theory shows why this conclusion may have to be reevaluated .", ...	2008
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "carbohydrate metabolism", "medicine and health sciences", "respiratory infections", "chemical compounds", "viral transmission and infection", "microbiology", "carbohydrates", "glucose metabolism", "parasitic protozoans", "pulmonology", "protozoan life cycles", "parasitic diseases", "organic...	Modulation of host central carbon metabolism and in situ glucose uptake by intracellular Trypanosoma cruzi amastigotes	journal.ppat.1006747	null	[ [ "Chagas disease is a vector-borne parasitic disease caused by the kinetoplastid protozoan parasite Trypanosoma cruzi .", "Acute T . cruzi infection is most often asymptomatic or characterized by flu-like symptoms , but can cause severe and fatal myocarditis in the first weeks following infection [1] .", ...	[ "Obligate intracellular pathogens satisfy their nutrient requirements by coupling to host metabolic processes , often modulating these pathways to facilitate access to key metabolites .", "Such metabolic dependencies represent potential targets for pathogen control , but remain largely uncharacterized for the int...	[ "The kinetoplastid protozoan , Trypanosoma cruzi , is a highly successful parasite with a broad mammalian host range and the capacity to colonize a variety of tissues within a given host to establish life-long infection .", "T . cruzi infection causes Chagas disease in humans , characterized by severe cardiomyopa...	2017
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "antimicrobials", "medicine and health sciences", "body fluids", "pathology and laboratory medicine", "pathogens", "drugs", "microbiology", "diabetes mellitus", "diarrhea", "bacterial diseases", "antibiotic resistance", "endocrine disorders", "signs and symptoms", "antibiotics", "enterob...	Non-typhoidal Salmonella blood stream infection in Kuwait: Clinical and microbiological characteristics	journal.pntd.0007293	null	[ [ "Salmonella enterica subspecies enterica serovar Typhi and Salmonella Paratyphi A , B and C cause enteric fever , a systemic febrile illness that occurs only in humans .", "There are more than 2500 serovars of non-typhoidal Salmonella ( NTS ) .", "NTS infects a variety of hosts and are frequently zoon...	[ "Non-typhoidal Salmonella ( NTS ) bacteremia is a significant cause of morbidity and mortality worldwide .", "It is considered to be an emerging and neglected tropical disease in Africa .", "We studied this in two tertiary hospitals–Al Farwaniya and Al Amiri–in Kuwait , a subtropical country , from April 2013-M...	[ "Salmonella organisms are classified into typhoidal Salmonella ( causing enteric fever ) and non-typhoidal Salmonella ( NTS ) ( causing infections other than enteric fever ) .", "Apart from causing other infections , NTS causes blood-stream infection ( bacteremia and septicemia ) .", "NTS blood stream infection...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "developmental biology", "model organisms", "genetics", "genetics and genomics", "biology", "respiratory medicine", "pulmonology" ]	Multiple Roles and Interactions of Tbx4 and Tbx5 in Development of the Respiratory System	journal.pgen.1002866	null	[ [ "The development of the respiratory system represents an evolutionary hallmark that allowed vertebrates to survive on land utilizing air as a source of oxygen .", "Because the respiratory system is dispensable for embryonic survival in mammals , defects in development of the respiratory system manifest at...	[ "Normal development of the respiratory system is essential for survival and is regulated by multiple genes and signaling pathways .", "Both Tbx4 and Tbx5 are expressed throughout the mesenchyme of the developing lung and trachea; and , although multiple genes are known to be required in the epithelium , only Fgfs...	[ "Defective development of the mammalian respiratory system can lead to tracheal , bronchial , or pulmonary malformations causing severe consequences at birth or during postnatal life .", "Studies using mouse genetics have begun to reveal complex regulatory mechanisms that guide the development of the respiratory ...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "biology", "neuroscience" ]	Modeling the Seasonal Adaptation of Circadian Clocks by Changes in the Network Structure of the Suprachiasmatic Nucleus	journal.pcbi.1002697	null	[ [ "The circadian rhythm is a 24 h rhythm which can be found in many organisms ranging from cyanobacteria and fungi to mammals [1] , [2] , [3] .", "There is a huge interest in studying the circadian rhythm because of the well-known effects of jet-lag after traveling and diseases related to shift-work [4] , [...	[ "The dynamics of circadian rhythms needs to be adapted to day length changes between summer and winter .", "It has been observed experimentally , however , that the dynamics of individual neurons of the suprachiasmatic nucleus ( SCN ) does not change as the seasons change .", "Rather , the seasonal adaptation o...	[ "Circadian clocks drive the temporal coordination of internal biological processes , which in turn determine daily rhythms in physiology and behavior in the most diverse organisms .", "In mammals , the 24-hour timing clock resides in the suprachiasmatic nucleus ( SCN ) of the hypothalamus .", "The SCN is a netw...	2012
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "helminths", "hookworms", "parasitic diseases", "animals", "genome analysis", "molecular biology techniques", "ancylostoma", "research and analysis methods", "infectious diseases", "zoonoses", "genomics", "artificial gene amplification and e...	A novel, species-specific, real-time PCR assay for the detection of the emerging zoonotic parasite Ancylostoma ceylanicum in human stool	journal.pntd.0005734	null	[ [ "Ancylostoma ceylanicum is the only predominantly animal-infecting hookworm species known to successfully develop into adults within the human intestine [1] .", "This zoonotic species has been reported to infect animals and humans in Southeast Asia , South America , South Africa , Melanesia and Australia ...	[ "Molecular-based surveys have indicated that Ancylostoma ceylanicum , a zoonotic hookworm , is likely the second most prevalent hookworm species infecting humans in Asia .", "Most current PCR-based diagnostic options for the detection of Ancylostoma species target the Internal Transcribed Spacer ( ITS ) regions o...	[ "Historically , Ancylostoma ceylanicum has been viewed as an uncommon cause of human hookworm infection , with minimal public health importance .", "However , recent reports have indicated that this zoonotic hookworm causes a much greater incidence of infection within certain human populations than was previously...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma mansoni", "species colonization", "ecology and environmental sciences", "ecological niches", "invasive species", "helminths", "china", "malacology", "geographical locations", "animals", "multivariate analysis", "gastropods", "mathematics", "...	Prediction of the potential global distribution for Biomphalaria straminea, an intermediate host for Schistosoma mansoni	journal.pntd.0006548	null	[ [ "Invasive species can often pose threats to the ecosystem functioning and biodiversity at the global scale , especially when they spread diseases[1] .", "There are a growing number of studies conducted for risk assessment , monitoring and management of invasive species and reduction of negative impacts ."...	[ "Schistosomiasis is a snail-borne parasitic disease and is endemic in many tropical and subtropical countries .", "Biomphalaria straminea , an intermediate host for Schistosoma mansoni , is native to the southeastern part of South America and has established in other regions of South America , Central America and...	[ "Biomphalaria straminea is an intermediate host of Schistosoma mansoni .", "This snail has not only established in peripheral countries but also survived in different water habitats in Hong Kong and adjacent cities of mainland China .", "Ecological niche models were used to predict the potential global distribu...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "community ecology", "spatial and landscape ecology", "ecosystem modeling", "mathematics", "ecology", "food web structure", "statistics", "theoretical ecology", "biology", "computational biology", "statistical methods", "terrestrial ecology" ]	Spatial Guilds in the Serengeti Food Web Revealed by a Bayesian Group Model	journal.pcbi.1002321	null	[ [ "Food webs , networks of feeding relationships in ecosystems , connect the biotic interactions among organisms with energy flows , thus linking together population dynamics , ecosystem function , and network topology .", "Ecologists have been using this powerful conceptual tool for more than a century [1]...	[ "Food webs , networks of feeding relationships in an ecosystem , provide fundamental insights into mechanisms that determine ecosystem stability and persistence .", "A standard approach in food-web analysis , and network analysis in general , has been to identify compartments , or modules , defined by many links ...	[ "The relationships among organisms in an ecosystem can be described by a food web , a network representing who eats whom .", "Food web organization has important consequences for how populations change over time , how one species extinction can cause others , and how robustly ecosystems respond to disturbances ."...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "bacterial diseases", "infectious diseases", "streptococcal pharyngitis", "medicine and health sciences", "toxic shock syndrome", "population modeling", "biology and life sciences", "infectious disease modeling", "computational biology", "infectious disease control", "pharyngitis", "streptococ...	Bacterial Superantigens Promote Acute Nasopharyngeal Infection by Streptococcus pyogenes in a Human MHC Class II-Dependent Manner	journal.ppat.1004155	null	[ [ "S . pyogenes ( commonly known as the β-hemolytic Group A Streptococcus ) is a prominent bacterial pathogen that causes a diverse range of clinical manifestations .", "Globally , S . pyogenes is responsible for over 600 million cases of pharyngitis , and more than one half million deaths primarily from co...	[ "Establishing the genetic determinants of niche adaptation by microbial pathogens to specific hosts is important for the management and control of infectious disease .", "Streptococcus pyogenes is a globally prominent human-specific bacterial pathogen that secretes superantigens ( SAgs ) as ‘trademark’ virulence ...	[ "Streptococcus pyogenes is the most common cause of bacterial pharyngitis , also known as ‘strep throat’ .", "However , this organism is also responsible for a range of other important human illnesses including necrotizing fasciitis and rheumatic heart disease ( RHD ) .", "Indeed , complications from RHD and in...	2014
[ "Introduction", "Models and methods", "Results", "Discussion" ]	[ "information entropy", "neural networks", "engineering and technology", "electronics", "applied mathematics", "signaling networks", "random variables", "neuroscience", "covariance", "simulation and modeling", "algorithms", "mathematics", "network analysis", "research and analysis methods",...	Estimating information in time-varying signals	journal.pcbi.1007290	null	[ [ "For their survival , reproduction , and differentiation , cells depend on their ability to respond and adapt to continually changing environmental conditions .", "Environmental information must be sensed and often transduced to the nucleus , where an appropriate response is initiated , usually by selecti...	[ "Across diverse biological systems—ranging from neural networks to intracellular signaling and genetic regulatory networks—the information about changes in the environment is frequently encoded in the full temporal dynamics of the network nodes .", "A pressing data-analysis challenge has thus been to efficiently ...	[ "Cells represent changes in their own state or in the state of their environment by temporally varying the concentrations of intracellular signaling molecules , mimicking in a simple chemical context the way we humans represent our thoughts and observations through temporally varying patterns of sounds that constit...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/prion diseases" ]	Accelerated High Fidelity Prion Amplification Within and Across Prion Species Barriers	journal.ppat.1000139	null	[ [ "Prion diseases are transmissible , fatal , and incurable neurodegenerative disorders of the central nervous system ( CNS ) that include bovine spongiform encephalopathy ( BSE ) , ovine scrapie , chronic wasting disease ( CWD ) of cervids and human Creutzfeldt-Jakob disease ( CJD ) .", "While inoculation ...	[ "Experimental obstacles have impeded our ability to study prion transmission within and , more particularly , between species .", "Here , we used cervid prion protein expressed in brain extracts of transgenic mice , referred to as Tg ( CerPrP ) , as a substrate for in vitro generation of chronic wasting disease (...	[ "Prions are unique pathogens that result from conversion of a normal host-encoded prion protein , PrPC , into a self-propagating , disease-associated conformation , referred to as PrPSc .", "An important aspect of prion diseases is their transmissibility , frequently as epidemics .", "The contagious transmissio...	2008
[ "Introduction", "Materials and methods", "Results and discussion" ]	[ "phosphorylation", "chemical compounds", "enzymes", "ketones", "microbiology", "enzymology", "parasitic protozoans", "protozoan life cycles", "pyruvate", "phosphatases", "developmental biology", "trypomastigotes", "protozoans", "enzyme metabolism", "enzyme chemistry", "proteins", "ac...	Reprogramming of Trypanosoma cruzi metabolism triggered by parasite interaction with the host cell extracellular matrix	journal.pntd.0007103	null	[ [ "The protozoan T . cruzi , the etiological agent of Chagas’ disease , affects a wide range of mammalian hosts , including humans .", "It is estimated that 8 million people are infected and 25 million are at risk , most of them living in areas of poor socioeconomic development [1] .", "The cell cycle o...	[ "Trypanosoma cruzi , the etiological agent of Chagas’ disease , affects 8 million people predominantly living in socioeconomic underdeveloped areas .", "T . cruzi trypomastigotes ( Ty ) , the classical infective stage , interact with the extracellular matrix ( ECM ) , an obligatory step before invasion of almost ...	[ "Adhesion of Trypanosoma cruzi to distinct elements of ECM involving different surface proteins from the infective stage of the parasite has been described .", "Despite the relevance of ECM for T . cruzi infection , the signaling pathways triggered in trypomastigotes upon interactions with ECM are less well under...	2019
[ "Introduction", "Results and discussion", "Methods" ]	[ "learning", "cognitive neurology", "medicine and health sciences", "dendritic structure", "anesthetics", "drugs", "brain", "social sciences", "neuroscience", "learning and memory", "cognitive neuroscience", "cognitive psychology", "pharmacology", "dentate gyrus", "neuronal dendrites", ...	Early postnatal exposure to isoflurane causes cognitive deficits and disrupts development of newborn hippocampal neurons via activation of the mTOR pathway	journal.pbio.2001246	null	[ [ "Several large retrospective analyses link exposure to anesthetics and surgery within the first 3 years of life with subsequent effects on cognitive function , as measured by worsened performance on school assessments , an increase in billing codes relevant to learning disorders , and deficits in neuropsychol...	[ "Clinical and preclinical studies indicate that early postnatal exposure to anesthetics can lead to lasting deficits in learning and other cognitive processes .", "The mechanism underlying this phenomenon has not been clarified and there is no treatment currently available .", "Recent evidence suggests that ane...	[ "The United States Food and Drug Administration has recently warned that exposure to anesthetic and sedative drugs during the third trimester of prenatal development and during the first 3 years of life may cause lasting impairments in cognitive function .", "The mechanisms by which this undesirable side effect o...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "computational biology/genomics" ]	Accurate Quantification of Functional Analogy among Close Homologs	journal.pcbi.1001074	null	[ [ "The idea that protein sequence similarity implies shared function is a central paradigm in modern biology , allowing experimental knowledge obtained from model organisms such as yeast or mouse to be applied to our understanding of human diseases , or to be transferred via functional annotations to newly sequ...	[ "Correctly evaluating functional similarities among homologous proteins is necessary for accurate transfer of experimental knowledge from one organism to another , and is of particular importance for the development of animal models of human disease .", "While the fact that sequence similarity implies functional ...	[ "Common ancestry is a central tenet of modern biology , as genes from different species often show a high degree of sequence similarity , making it possible to study analogous processes across model organisms .", "However , many genes belong to large families with several duplicates and the relationship between g...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Multiple Changes of Gene Expression and Function Reveal Genomic and Phenotypic Complexity in SLE-like Disease	journal.pgen.1005248	null	[ [ "SLE is a chronic autoimmune disorder caused by multiple genetic and environmental risk factors .", "The disease tends to be clinically heterogeneous [1] , with manifestations ranging from relatively mild symptoms such as skin rash to severe impairment of functions of kidney , heart , lung , central nervo...	[ "The complexity of clinical manifestations commonly observed in autoimmune disorders poses a major challenge to genetic studies of such diseases .", "Systemic lupus erythematosus ( SLE ) affects humans as well as other mammals , and is characterized by the presence of antinuclear antibodies ( ANA ) in patients’ s...	[ "Autoimmune disorders display complex phenotypes with clinically diverse manifestations , which together with complex genetic inheritance and environmental factors triggering the disease may complicate the diagnosis and investigation of the disease mechanism .", "The use of dog breeds may facilitate the analysis ...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "death rates", "invertebrates", "children", "medicine and health sciences", "body fluids", "demography", "nervous system", "neuroscience", "animals", "cranial nerves", "age groups", "gastropods", "molecular biology techniques", "population biology", "snails", "neuroimaging", "familie...	Angiostrongylus cantonensis Infection on Mayotte Island, Indian Ocean, 2007-2012	journal.pntd.0004635	null	[ [ "Human angiostrongyliasis ( HA ) , also called nervous angiostrongyliasis , is a parasitic disease due to the lungworm A . cantonensis .", "A . cantonensis has been described for the first time in a rat in China , and the first human case has been reported in Taiwan in 1945 [1 , 2] .", "The disease ha...	[ "Human angiostrongyliasis ( HA ) is a neurological helminthic disease caused by the lung worm Angiostrongylus cantonensis .", "It is suspected in the combination of travel or a residence in an endemic area and eosinophilic meningitis .", "In Mayotte , an island in the Indian Ocean , cases are rare but regular ....	[ "Human angiostrongyliasis is a neurological helminthic disease caused by the lung worm Angiostrongylus cantonensis , and most cases are reported from Asia , particularly Thailand and China .", "In Mayotte , an overseas French Territory in the Indian Ocean , cases are rare but regular , with life-threatening clini...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	CCR2+ Inflammatory Dendritic Cells and Translocation of Antigen by Type III Secretion Are Required for the Exceptionally Large CD8+ T Cell Response to the Protective YopE69-77 Epitope during Yersinia Infection	journal.ppat.1005167	null	[ [ "Dendritic cells ( DCs ) play a major role in protective immunity against pathogens .", "For example , DCs are required to prime naïve antigen specific CD8+ T cells to become effector cells that secrete cytokines and/or are cytolytic [1 , 2] .", "When DCs acquire endogenous antigens , e . g . , viral ...	[ "During Yersinia pseudotuberculosis infection of C57BL/6 mice , an exceptionally large CD8+ T cell response to a protective epitope in the type III secretion system effector YopE is produced .", "At the peak of the response , up to 50% of splenic CD8+ T cells recognize the epitope YopE69-77 .", "The features of...	[ "Dendritic cells ( DCs ) direct host protective adaptive immune responses during infection .", "How different subpopulations of DCs contribute to the formation of antigen-specific CD8+ T cells is incompletely understood .", "Infection of C57BL/6 mice with the bacterial pathogen Yersinia pseudotuberculosis resul...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "children", "medicine and health sciences", "microbiome", "pathology and laboratory medicine", "immunology", "permeability", "microbiology", "biomarkers", "diarrhea", "age groups", "signs and symptoms", "materials science", "gastroenterology and hepatology", "bacteria", "families", "di...	Environmental enteric dysfunction pathways and child stunting: A systematic review	journal.pntd.0006205	null	[ [ "One-quarter of children under the age of 5 years are stunted , defined as a height-for-age > 2 standard deviations below the median as defined by the World Health Organization growth standards .", "Children whose linear growth is impaired during the first 1000 days after conception have an increased risk...	[ "Environmental enteric dysfunction ( EED ) is commonly defined as an acquired subclinical disorder of the small intestine , characterized by villous atrophy and crypt hyperplasia .", "EED has been proposed to underlie stunted growth among children in developing countries .", "A collection of biomarkers , organi...	[ "Globally , one-quarter of children under the age of five are affected by poor linear growth , known as stunting .", "Interventions , including giving children supplemental foods or improving hygiene to prevent diarrhea , have only been partially successful at restoring normal growth .", "Environmental enteric ...	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "chemical ecology", "animal behavior", "zoology", "ecology", "entomology", "olfactory system", "sensory systems", "biology", "neuroethology", "neuroscience", "parasitology" ]	A Multi-species Bait for Chagas Disease Vectors	journal.pntd.0002677	null	[ [ "The flagellate parasite Trypanosoma cruzi ( Chagas ) , the etiological agent of Chagas disease , is transmitted to humans by vectors of the subfamily Triatominae .", "In part as a result of the distribution of vectors , Chagas disease occurs exclusively in Latin America where it is estimated that 90 mill...	[ "Triatomine bugs are the insect vectors of Trypanosoma cruzi , the etiological agent of Chagas disease .", "These insects are known to aggregate inside shelters during daylight hours and it has been demonstrated that within shelters , the aggregation is induced by volatiles emitted from bug feces .", "These sig...	[ "Chagas disease is a parasitic infection affecting approximately 12 million people , and is considered to be one of the most severe burdens for public health in Latin America .", "Control of the disease is based on attempted elimination of domestic populations of triatomine bugs , the insects transmitting the dis...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "immunology/cellular microbiology and pathogenesis", "infectious diseases", "infectious diseases/neglected tropical diseases", "virology", "virology/mechanisms of resistance and susceptibility, including host genetics", "infectious diseases/viral infections", "immunology/immunity to infections" ]	Immunological and Viral Determinants of Dengue Severity in Hospitalized Adults in Ha Noi, Viet Nam	journal.pntd.0000967	null	[ [ "Dengue virus ( DENV ) infections range in severity from asymptomatic to a syndrome characterized by a haemorrhagic tendency and vascular permeability [1] .", "The events that precipitate endothelial cell dysfunction and vascular leak are incompletely understood .", "Numerous studies including several...	[ "The relationships between the infecting dengue serotype , primary and secondary infection , viremia and dengue severity remain unclear .", "This cross-sectional study examined these interactions in adult patients hospitalized with dengue in Ha Noi .", "158 patients were enrolled between September 16 and Novemb...	[ "Dengue is estimated to affect 50 million people each year and can occur as explosive outbreaks that overwhelm health systems .", "Despite significant advances the available knowledge is not sufficient to predict the outcome of individual infections or the occurrence of epidemics .", "Studies from low dengue tr...	2011
[ "Introduction", "Results and Discussion", "Materials and Methods" ]	[ "electrophysiological properties", "cellular neuroscience", "synaptic plasticity", "action potentials", "computational neuroscience", "single neuron function", "neurotransmission", "physiology", "biology and life sciences", "computational biology", "electrophysiology", "neuroscience", "neuro...	High Bandwidth Synaptic Communication and Frequency Tracking in Human Neocortex	journal.pbio.1002007	Because of fast recovery from synaptic depression and fast-initiated action potentials, neuronal information transfer can have a substantially higher bandwidth in human neocortical circuits than in those of rodents.	[ [ "Human cognitive abilities clearly stand out from those of other mammals [1] .", "Evolutionary development of brain size , encephalization , neocortical thickening , and specialization of cortical circuits [2] , [3] most likely underlie the superior human mental capacity , but other factors may contribute...	[ "Neuronal firing , synaptic transmission , and its plasticity form the building blocks for processing and storage of information in the brain .", "It is unknown whether adult human synapses are more efficient in transferring information between neurons than rodent synapses .", "To test this , we recorded from c...	[ "Our ability to think , memorize information , and act appropriately depends on circuits of connected neurons in the brain .", "In these circuits , neurons pass information to each other using electric pulses ( action potentials ) that cause the release of chemical neurotransmitters , which alter the membrane ele...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "emerging infectious diseases", "biology", "microbiology", "host-pathogen interaction", "parasitology" ]	Investigating the Host Binding Signature on the Plasmodium falciparum PfEMP1 Protein Family	journal.ppat.1002032	null	[ [ "Plasmodium falciparum erythrocyte membrane protein 1 ( PfEMP1 ) is a", "clonally variant adhesion protein that mediates binding of infected erythrocytes", "( IE ) to blood microvasculature and other host cells [1] .", "Adherence of IEs to", "microvascular endothelium is a major virulence fact...	[ "The Plasmodium falciparum erythrocyte membrane protein 1", "( PfEMP1 ) family plays a central role in antigenic variation and cytoadhesion of", "P . falciparum infected erythrocytes .", "PfEMP1", "proteins/var genes are classified into three main", "subfamilies ( UpsA , UpsB , and UpsC ) that are hypothe...	[ "The malaria parasite Plasmodium falciparum persists in the human", "host partly by avoiding elimination in the spleen during blood stage infection .", "This strategy depends principally upon members of the large and diverse PfEMP1", "family of proteins that are exported to the surface of infected erythrocyte...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell death", "autophagic cell death", "chemical compounds", "cell cycle and cell division", "tor signaling", "cell processes", "carbohydrates", "organic compounds", "fungal structure", "glucose", "mitosis", "mutation", "glucose signaling", "appressoria", "mycology", "mutant strains", ...	Glucose-ABL1-TOR Signaling Modulates Cell Cycle Tuning to Control Terminal Appressorial Cell Differentiation	journal.pgen.1006557	null	[ [ "The conserved TOR signaling pathway controls cell growth and proliferation across taxa and disease states by regulating metabolic processes in response to available nutrients and energy [1–4] .", "Amino acids signal to TOR directly via a class of small GTPases that , in mammalian cells , recruit TORC1 to...	[ "The conserved target of rapamycin ( TOR ) pathway integrates growth and development with available nutrients , but how cellular glucose controls TOR function and signaling is poorly understood .", "Here , we provide functional evidence from the devastating rice blast fungus Magnaporthe oryzae that glucose can me...	[ "TOR kinase coordinates cell development with nutrient availability .", "Due to its roles in many debilitating diseases , it is important that all aspects of TOR regulation are understood .", "Nonetheless , how cellular glucose controls TOR function and downstream activities is largely unknown .", "Here , we ...	2017
[ "Introduction", "Results/Discussion", "Methods" ]	[ "computational biology/metabolic networks" ]	Sampling the Solution Space in Genome-Scale Metabolic Networks Reveals Transcriptional Regulation in Key Enzymes	journal.pcbi.1000859	null	[ [ "Systems Biology aims to use mathematical models to integrate different kinds of data in order to achieve a global understanding of cellular functions .", "The data to be integrated differ both in their nature and measurability .", "The availability of DNA microarrays allows for the comparative analys...	[ "Genome-scale metabolic models are available for an increasing number of organisms and can be used to define the region of feasible metabolic flux distributions .", "In this work we use as constraints a small set of experimental metabolic fluxes , which reduces the region of feasible metabolic states .", "Once ...	[ "The sequencing of full genomes and the development of high-throughput analysis technologies have made available both genome-scale metabolic networks and simultaneous transcription data for all the genes of an organism .", "Genome-scale metabolic models , with the assumption of steady state for the internal metab...	2010
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases", "infectious disease immunology", "medicine and health sciences", "clinical immunology", "immunity", "medical microbiology", "biology and life sciences", "immunology", "microbiology", "vaccination and immunization", "immunomodulation", "parasitology" ]	Combining Cationic Liposomal Delivery with MPL-TDM for Cysteine Protease Cocktail Vaccination against Leishmania donovani : Evidence for Antigen Synergy and Protection	journal.pntd.0003091	null	[ [ "Visceral leishmaniasis ( VL ) caused by Leishmania donovani is a fatal disease with an estimated 360 , 000 new cases all over the world with almost 10% annual case fatality in the Indian subcontinent alone [1] .", "It is a neglected tropical disease inevitably associated with poverty and immunosuppressio...	[ "With the paucity of new drugs and HIV co-infection , vaccination remains an unmet research priority to combat visceral leishmaniasis ( VL ) requiring strong cellular immunity .", "Protein vaccination often suffers from low immunogenicity and poor generation of memory T cells for long-lasting protection .", "Cy...	[ "Conventional chemotherapy of visceral leishmaniasis ( VL ) typically relies on pentavalent antimonials that suffer from extensive drug resistance in India .", "Development of preventive vaccination is undoubtedly a better alternative to completely eradicate the disease .", "With this in mind , we chose to targ...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "molecular biology" ]	Characterization of the Entamoeba histolytica Ornithine Decarboxylase-Like Enzyme	journal.pntd.0000115	null	[ [ "Entamoeba histolytica is a unicellular protozoan parasite that infects about 50 million people each year and may cause potentially life-threatening diseases such as hemorrhagic colitis and/or extraintestinal abscesses [1] .", "The infections are primarily treated by antiamoebic therapy .", "Drugs of ...	[ "The polyamines putrescine , spermidine , and spermine are organic cations that are required for cell growth and differentiation .", "Ornithine decarboxylase ( ODC ) , the first and rate-limiting enzyme in the polyamine biosynthetic pathway , is a highly regulated enzyme .", "To use this enzyme as a potential d...	[ "Entamoeba histolytica is a unicellular protozoan parasite that infects about 50 million people each year and can cause potentially life-threatening diseases such as hemorrhagic colitis and extraintestinal abscesses .", "The infections are primarily treated by antiamoebic therapy .", "Drugs of choice for invasi...	2008
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases/viral infections", "microbiology/cellular microbiology and pathogenesis", "virology/host invasion and cell entry" ]	The M/GP5 Glycoprotein Complex of Porcine Reproductive and Respiratory Syndrome Virus Binds the Sialoadhesin Receptor in a Sialic Acid-Dependent Manner	journal.ppat.1000730	null	[ [ "At the end of the 1980s , a new syndrome was described affecting pig herds in North America and Canada [1] , [2] .", "This ‘mystery swine disease’ manifested itself in respiratory problems and reproductive disorders and was eventually designated Porcine Reproductive and Respiratory Syndrome ( PRRS ) , re...	[ "The porcine reproductive and respiratory syndrome virus ( PRRSV ) is a major threat to swine health worldwide and is considered the most significant viral disease in the swine industry today .", "In past years , studies on the entry of the virus into its host cell have led to the identification of a number of es...	[ "The porcine reproductive and respiratory syndrome virus ( PRRSV ) is a major threat to swine health worldwide .", "The virus specifically targets subpopulations of macrophages , central players in the immune system , and can persist in animals for extended periods of time due to a hampered immunity .", "At pre...	2010
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "neuroscience/neuronal signaling mechanisms", "neuroscience/theoretical neuroscience" ]	Optimal Information Transfer in the Cortex through Synchronization	journal.pcbi.1000934	null	[ [ "Gamma band synchronization has been found in many cortical areas and in a variety of tasks .", "It has been studied most extensively in the visual cortex of cats and monkeys [1]–[8] .", "Several authors have proposed that these synchronizations influence the interactions among neuronal groups [9] , [...	[ "In recent experimental work it has been shown that neuronal interactions are modulated by neuronal synchronization and that this modulation depends on phase shifts in neuronal oscillations .", "This result suggests that connections in a network can be shaped through synchronization .", "Here , we test and expa...	[ "Different brain areas are involved in any cognitive task .", "This implies that information has to be transmitted between different brain areas .", "Recent experimental results suggest that synchronization plays a crucial role in information exchange between cortical areas .", "They show that synchronization...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology and life sciences", "microbiology", "virology" ]	EBNA3C Augments Pim-1 Mediated Phosphorylation and Degradation of p21 to Promote B-Cell Proliferation	journal.ppat.1004304	null	[ [ "Epstein-Barr virus ( EBV ) , a ubiquitous lymphotropic herpesvirus , latently infects human populations worldwide [1] .", "EBV infection is typically asymptomatic and is an important etiological factor which contributes to different human malignancies [2] .", "EBV is consistently associated with naso...	[ "Epstein–Barr virus ( EBV ) , a ubiquitous human herpesvirus , can latently infect the human population .", "EBV is associated with several types of malignancies originating from lymphoid and epithelial cell types .", "EBV latent antigen 3C ( EBNA3C ) is essential for EBV-induced immortalization of B-cells .", ...	[ "The oncogenic serine/threonine kinase Pim-1 is upregulated in a number of human cancers including lymphomas , gastric , colorectal and prostate carcinomas .", "EBV nuclear antigen 3C ( EBNA3C ) is essential for EBV-induced transformation of human primary B-lymphocytes .", "Our current study revealed that EBNA3...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "microbial metabolism", "host-pathogen interaction", "biology", "microbiology", "pathogenesis", "bacterial pathogens" ]	Glutamate Utilization Couples Oxidative Stress Defense and the Tricarboxylic Acid Cycle in Francisella Phagosomal Escape	journal.ppat.1003893	null	[ [ "Francisella tularensis is a Gram-negative bacterium causing the disease tularemia in a large number of animal species .", "This highly infectious bacterial pathogen can be transmitted to humans in numerous ways [1] , including direct contact with sick animals , inhalation , ingestion of contaminated wate...	[ "Intracellular bacterial pathogens have developed a variety of strategies to avoid degradation by the host innate immune defense mechanisms triggered upon phagocytocis .", "Upon infection of mammalian host cells , the intracellular pathogen Francisella replicates exclusively in the cytosolic compartment .", "He...	[ "Intracellular bacterial pathogens have developed a variety of strategies to avoid degradation by the host innate immune defense mechanisms triggered upon phagocytocis .", "We show here for the first time that glutamate acquisition is essential for phagosomal escape and virulence of an intracellular pathogen .", ...	2014
[ "Introduction", "Materials and Methods", "Results and Discussion" ]	[ "ecology and environmental sciences", "medicine and health sciences" ]	Ocular Pentastomiasis in the Democratic Republic of the Congo	journal.pntd.0003041	null	[ [ "Pentastomiasis is a neglected zoonotic disease caused by the larval stage ( nymphs ) of pentastomids , a unique and enigmatic group of crustacean-related parasites .", "The parasites usually have an indirect lifecycle , involving various intermediate and definitive hosts .", "Linguatula serrata , a s...	[ "Ocular pentastomiasis is a rare infection caused by the larval stage of pentastomids , an unusual group of crustacean-related parasites .", "Zoonotic pentastomids have a distinct geographical distribution and utilize reptiles or canids as final hosts .", "Recently , an increasing number of human abdominal infe...	[ "Ocular pentastomiasis is a severely neglected parasitic disease .", "Most human infections are linked to the consumption and/or handling of snakes .", "Here we present a series of cases from a remote area of the Democratic Republic of the Congo .", "Two patients had an infection with Armillifer grandis .", ...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "sequencing techniques", "medicine and health sciences", "bovine tuberculosis", "tropical diseases", "bacterial diseases", "neglected tropical diseases", "molecular biology techniques", "sequence motif analysis", "bacteria", "research and analysis methods", "sequence analysis", "infectious dis...	RNA Aptamer That Specifically Binds to Mycolactone and Serves as a Diagnostic Tool for Diagnosis of Buruli Ulcer	journal.pntd.0004950	null	[ [ "Buruli ulcer Disease ( BUD ) has been listed among neglected tropical diseases , the causative agent is an ecological pathogen known as M . ulcerans [1 , 2] .", "Among mycobacterial diseases , it is the third utmost after tuberculosis and leprosy .", "It has been recounted in more than 30 tropical co...	[ "Buruli ulcer ( BU ) is a subcutaneous skin disease listed among the neglected tropical diseases by the World Health Organization ( WHO ) .", "Early case detection and management is very important to reduce morbidity and the accompanied characteristic disfiguring nature of BU .", "Since diagnosis based on clini...	[ "Buruli ulcer disease is a subcutaneous necrotizing skin disease caused by ecological Mycobacterium ulcerans .", "The availability of antibiotic treatment makes it imperative for early detection of the disease to avoid the disfiguring and morbid effects associated with the disease .", "Currently available detec...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Leishmania infantum Amastigotes Trigger a Subpopulation of Human B Cells with an Immunoregulatory Phenotype	journal.pntd.0003543	null	[ [ "Leishmaniasis is an infection caused by protozoan parasites of the genus Leishmania and is one of the most significant neglected tropical diseases , with 350 million people in 98 countries worldwide at risk of developing one of the forms of the disease [1] .", "Visceral leishmaniasis ( VL ) is the most s...	[ "Visceral leishmaniasis is caused by the protozoan parasites Leishmania infantum and Leishmania donovani .", "This infection is characterized by an uncontrolled parasitization of internal organs which , when left untreated , leads to death .", "Disease progression is linked with the type of immune response gene...	[ "Leishmaniasis is an infection caused by protozoan parasites of the genus Leishmania and is a significant neglected tropical disease , with 350 million people in 98 countries at risk of developing one of the forms of the disease .", "Visceral leishmaniasis is characterized by an uncontrolled parasitization of int...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "virology/diagnosis", "infectious diseases/viral infections", "public health and epidemiology/infectious diseases", "public health and epidemiology/environmental health" ]	Evaluation of Chikungunya Diagnostic Assays: Differences in Sensitivity of Serology Assays in Two Independent Outbreaks	journal.pntd.0000753	null	[ [ "Chikungunya virus ( CHIKV ) has seen a resurgence in recent years , with outbreaks being described in Republic of Congo in 2000 , La R'eunion in 2005 , India , Sri Lanka , Malaysia and Gabon in 2006 , Italy in 2007 , Singapore and Thailand in 2008 [1] , [2] , [3] , [4] , [5] , [6] , [7] , [8] , [9] .", "...	[ "The sensitivity and specificity of two in-house MAC-ELISA assays were tested and compared with the performance of commercially-available CTK lateral flow rapid test and EUROIMMUN IFA assays for the detection of anti-Chikungunya virus ( CHIKV ) IgM .", "Each MAC-ELISA assay used a whole virus-based antigen derive...	[ "Chikungunya is a mounting public health concern in many parts of the world .", "Definitive diagnosis is critical in differentiating the diseases , especially in dengue endemic areas .", "There are some commercial chikungunya kits and published molecular protocols available , but no comprehensive comparative ev...	2010
[ "Introduction", "Results", "Discussion" ]	[ "medicine and health sciences", "toxins", "body fluids", "pathology and laboratory medicine", "geographical locations", "vertebrates", "animals", "toxicology", "toxic agents", "urine", "reptiles", "research and analysis methods", "venoms", "spectrum analysis techniques", "sri lanka", "...	Clinical and Pharmacological Investigation of Myotoxicity in Sri Lankan Russell’s Viper (Daboia russelii) Envenoming	journal.pntd.0005172	null	[ [ "Snake bite is a significant public health issue in the tropics [1] .", "Coagulopathy , neuromuscular paralysis , acute kidney injury and local effects are the most important clinical syndromes of snake envenoming [2] .", "Russell’s viper bites cause a large number of envenomings across Asia , and are...	[ "Sri Lankan Russell’s viper ( Daboia russelii ) envenoming is reported to cause myotoxicity and neurotoxicity , which are different to the effects of envenoming by most other populations of Russell’s vipers .", "This study aimed to investigate evidence of myotoxicity in Russell’s viper envenoming , response to an...	[ "There are many gaps in our knowledge of muscle damage caused by snake venoms .", "Russell’s vipers are more medically important than any other snake in Asia .", "Sri Lankan Russell’s viper ( Daboia russelii ) bites have been reported to cause muscle damage in humans , which is not reported for other Russell’s ...	2016
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "immunopathology", "molecular cell biology", "microbial physiology", "medical microbiology", "immunology", "biology", "microbiology", "host-pathogen interaction" ]	Mycobacterium tuberculosis Responds to Chloride and pH as Synergistic Cues to the Immune Status of its Host Cell	journal.ppat.1003282	null	[ [ "Mycobacterium tuberculosis ( Mtb ) causes a chronic infection in approximately one third of the human population and remains an important public health problem [1] .", "The macrophage ( MØ ) is the major host cell for much of Mtb's life cycle , and a defining feature of Mtb's pathogenesis is its ability ...	[ "The ability of Mycobacterium tuberculosis ( Mtb ) to thrive in its phagosomal niche is critical for its establishment of a chronic infection .", "This requires that Mtb senses and responds to intraphagosomal signals such as pH . We hypothesized that Mtb would respond to additional intraphagosomal factors that co...	[ "Mycobacterium tuberculosis ( Mtb ) is the causative agent of tuberculosis , a disease that remains a major global health problem .", "To ensure its long-term survival in the host , Mtb must be able to sense and respond to changes in its immediate environment , such as the pH differences that occur in the phagoso...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "learning", "invertebrates", "cell motility", "medicine and health sciences", "caenorhabditis", "social sciences", "neuroscience", "learning and memory", "animals", "endocrine physiology", "animal models", "caenorhabditis elegans", "model organisms", "cognitive psychology", "experimental...	DAF-16/FOXO promotes taste avoidance learning independently of axonal insulin-like signaling	journal.pgen.1008297	null	[ [ "A common strategy for animals to respond to starvation conditions is to change behaviors based on the nutritional state .", "Insulin/IGF signaling plays a key role in physiological and behavioral responses to nutritional stimuli .", "For instance , insulin signaling is involved in nutritional conditi...	[ "The avoidance of starvation is critical for the survival of most organisms , thus animals change behavior based on past nutritional conditions .", "Insulin signaling is important for nutritional state-dependent behavioral plasticity , yet the underlying regulatory mechanism at the cellular level remains unclear ...	[ "Animals change behavior based on remembered experiences of hunger and appetite .", "Signaling by insulin and insulin-like peptides in the nervous system plays key roles in behavioral responses to hunger and satiety .", "In C . elegans , insulin-like signaling in the gustatory sensory neuron ASER regulates lear...	2019
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "meiosis", "enzymes", "isomerases", "microbiology", "model organisms", "dna", "dna structure", "molecular genetics", "dna synthesis", "mycology", "genomics", "enzyme classes", "chromosome biology", "biology", "molecular biology", "yeast", "biochemistry", "cell biology", "nucleic ...	Genome-Wide Analysis of Heteroduplex DNA in Mismatch Repair–Deficient Yeast Cells Reveals Novel Properties of Meiotic Recombination Pathways	journal.pgen.1002305	null	[ [ "Meiotic crossovers ( COs ) are reciprocal exchanges of chromosome arms between homologous chromosomes ( homologs ) .", "They generate genetic diversity and establish physical links between homologs .", "In many organisms COs are crucial for accurate homolog segregation at meiotic division I , and the...	[ "Meiotic DNA double-strand breaks ( DSBs ) initiate crossover ( CO ) recombination , which is necessary for accurate chromosome segregation , but DSBs may also repair as non-crossovers ( NCOs ) .", "Multiple recombination pathways with specific intermediates are expected to lead to COs and NCOs .", "We revisite...	[ "Sexual reproduction consists in fusing two complementary gametes carrying only one set of chromosomes ( haploids ) to form a cell with two sets of homologous chromosomes ( diploid ) .", "Gametes are generated through meiosis , a specialized cell division occurring in diploid organisms .", "For proper meiotic d...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "chromosome biology", "chromosome structure and function", "gene expression", "genetics", "epigenetics", "biology", "genomics", "chromatin", "genetics and genomics", "histone modification" ]	Histone Crosstalk Directed by H2B Ubiquitination Is Required for Chromatin Boundary Integrity	journal.pgen.1002175	null	[ [ "There is growing consensus that the non-random chromosomal arrangement of genes in higher eukaryotes enables the sharing of specific chromatin environments that facilitate co-regulation .", "Recent genomic profiling of histone modifications , chromatin factors and nuclear proximity in Drosophila and mamm...	[ "Genomic maps of chromatin modifications have provided evidence for the partitioning of genomes into domains of distinct chromatin states , which assist coordinated gene regulation .", "The maintenance of chromatin domain integrity can require the setting of boundaries .", "The HS4 insulator element marks the 3...	[ "The transcription of genes in eukaryotes occurs within the context of chromatin , a complex of DNA , histone proteins , and regulatory factors .", "Whole-genome profiling of chromatin proteins and histones that are post-translationally modified has revealed that genomes are organized into domains of distinct chr...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "chemical compounds", "cell processes", "permeability", "ions", "light", "organic compounds", "parasitic protozoans", "electromagnetic radiation", "light scattering", "mutation", "trypanosoma brucei gambiense", "monomers (chemistry)", "protozoans", "materials science", "basic amino acids...	Pentamidine Is Not a Permeant but a Nanomolar Inhibitor of the Trypanosoma brucei Aquaglyceroporin-2	journal.ppat.1005436	null	[ [ "A specific aquaglyceroporin , TbAQP2 , is required for high-affinity uptake of pentamidine into human African trypanosomiasis parasites , Trypanosoma brucei [1–3] .", "Additionally , a trypanosome adenosine transporter mediates pentamidine transport , albeit at lower efficiency [2] .", "Aquaglyceropo...	[ "The chemotherapeutic arsenal against human African trypanosomiasis , sleeping sickness , is limited and can cause severe , often fatal , side effects .", "One of the classic and most widely used drugs is pentamidine , an aromatic diamidine compound introduced in the 1940s .", "Recently , a genome-wide loss-of-...	[ "Pentamidine is usable only in the early , non-cerebral stage of human African trypanosomiasis .", "An aquaglyceroporin , TbAQP2 , is required for high-affinity pentamidine uptake .", "This study established the mechanism .", "Pentamidine does not pass TbAQP2 but blocks the unique selectivity filter via a sin...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell binding", "cell physiology", "uterus", "medicine and health sciences", "reproductive system", "maternal health", "obstetrics and gynecology", "variant genotypes", "alleles", "genetic mapping", "women's health", "pregnancy", "molecular biology techniques", "pregnancy complications", ...	Expression Quantitative Trait Locus Mapping Studies in Mid-secretory Phase Endometrial Cells Identifies HLA-F and TAP2 as Fecundability-Associated Genes	journal.pgen.1005858	null	[ [ "Natural variation in fertility traits is heritable in humans [1] , yet identifying genes contributing to these traits remains challenging .", "Although genome-wide association studies ( GWAS ) have identified variants associated with many other complex phenotypes , its application to fertility traits is ...	[ "Fertility traits in humans are heritable , however , little is known about the genes that influence reproductive outcomes or the genetic variants that contribute to differences in these traits between individuals , particularly women .", "To address this gap in knowledge , we performed an unbiased genome-wide ex...	[ "Little is known about the genetics of female fertility .", "In this study , we addressed this gap in knowledge by first searching for genetic variants that regulate gene expression in uterine endometrial cells , and then testing those functional variants for associations with the length of time to pregnancy in f...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Fmrp Interacts with Adar and Regulates RNA Editing, Synaptic Density and Locomotor Activity in Zebrafish	journal.pgen.1005702	null	[ [ "Fragile X syndrome ( FXS ) is the most common single-gene inherited neurodevelopmental disorder causing mental retardation .", "This disorder is characterized by an array of behavioral and cognitive disabilities , including autism , anxiety , epileptic seizures , hyperactivity , attention deficits , and ...	[ "Fragile X syndrome ( FXS ) is the most frequent inherited form of mental retardation .", "The cause for this X-linked disorder is the silencing of the fragile X mental retardation 1 ( fmr1 ) gene and the absence of the fragile X mental retardation protein ( Fmrp ) .", "The RNA-binding protein Fmrp represses pr...	[ "The most frequent inherited mental retardation disorder is fragile X syndrome , which is characterized by learning disabilities , cognitive impairment , anxiety , and hyperactive behavior .", "The genetic cause of this disorder is the silencing of the fmr1 gene , which encodes the RNA-binding protein Fmrp .", ...	2015

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