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headings list	keywords list	title stringlengths 20 281	id stringlengths 20 20	toc stringlengths 57 522 ⌀	sections list	abstract list	summary list	year stringclasses 13 values
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "gene regulation", "regulatory proteins", "dna-binding proteins", "nucleosome mapping", "transcription factors", "epigenetics", "molecular biology techniques", "chromatin", "research and analysis methods", "small interfering rnas", "gene mapping", "chromosome biology", "proteins", "genetic...	The Chromatin Remodelling Enzymes SNF2H and SNF2L Position Nucleosomes adjacent to CTCF and Other Transcription Factors	journal.pgen.1005940	null	[ [ "The genomes of eukaryotes exist predominantly as chromatin .", "The fundamental subunit of chromatin is the nucleosome which consists of 147 bp of DNA wrapped around an octamer of histone proteins [1] .", "Typically nucleosomes are distributed along DNA with defined spacing at distinct loci in a give...	[ "Within the genomes of metazoans , nucleosomes are highly organised adjacent to the binding sites for a subset of transcription factors .", "Here we have sought to investigate which chromatin remodelling enzymes are responsible for this .", "We find that the ATP-dependent chromatin remodelling enzyme SNF2H play...	[ "CTCF is a transcriptional regulator acting as an insulator element interfering with enhancer function and as a boundary between chromatin domains .", "CTCF has been shown to organise an exquisite array of phased nucleosomes flanking its binding sites .", "Here we identified SNF2H as the enzyme primarily respon...	2016
[ "Introduction", "Results/Discussion", "Methods" ]	[]	Mechanical and Assembly Units of Viral Capsids Identified via Quasi-Rigid Domain Decomposition	journal.pcbi.1003331	null	[ [ "The genomic material of many viruses is encapsidated inside icosahedral protein shells with diameters in the 20–100 nm range .", "The number of structurally inequivalent protein units that tessellate these capsids is usually very small [1] , [2] .", "This , in turn , is reflected in the limited reper...	[ "Key steps in a viral life-cycle , such as self-assembly of a protective protein container or in some cases also subsequent maturation events , are governed by the interplay of physico-chemical mechanisms involving various spatial and temporal scales .", "These salient aspects of a viral life cycle are hence well...	[ "The genetic material of viruses is packaged inside capsids constituted from a few tens to thousands of proteins .", "The latter can organize in multimers that serve as fundamental blocks for the viral shell assembly or that control the capsid conformational transitions and response to mechanical stress .", "In...	2013
[ "Introduction", "Models", "Results", "Discussion" ]	[]	Recombination Enhances HIV-1 Envelope Diversity by Facilitating the Survival of Latent Genomic Fragments in the Plasma Virus Population	journal.pcbi.1004625	null	[ [ "Patients infected with HIV-1 require lifelong highly active antiretroviral therapy ( HAART ) to suppress infection .", "Treatment cessation typically leads to HIV viral rebound to pre-therapy levels; the resurgence is thought to be associated with activation of long-lived , latently HIV-infected cells ."...	[ "HIV-1 is subject to immune pressure exerted by the host , giving variants that escape the immune response an advantage .", "Virus released from activated latent cells competes against variants that have continually evolved and adapted to host immune pressure .", "Nevertheless , there is increasing evidence tha...	[ "Increasing evidence suggests that HIV-1 released from activated latent cells survives in productively infected cells in patient plasma despite competition against better adapted virus variants that have evolved in response to the host immune pressure .", "Long-term survival requires that latent virus forms adapt...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "parasite groups", "ecology and environmental sciences", "rivers", "plasmodium", "population genetics", "tropical diseases", "geographical locations", "parasitic diseases", "parasitic protozoans", "parasitology", "apicomplexa", "protozoans", "aquatic environ...	Population Genetics of Plasmodium vivax in Four Rural Communities in Central Vietnam	journal.pntd.0004434	null	[ [ "Vietnam has been extremely successful in decreasing the country’s malaria burden , thanks to the large scale implementation of control interventions such as insecticide-treated bed nets , indoor residual spraying , and prompt , free-of-charge diagnosis and treatment; the number of cases fell from 130 , 000 i...	[ "The burden of malaria in Vietnam has drastically reduced , prompting the National Malaria Control Program to officially engage in elimination efforts .", "Plasmodium vivax is becoming increasingly prevalent , remaining a major problem in the country's central and southern provinces .", "A better understanding ...	[ "In Vietnam , Plasmodium vivax ( P . vivax ) is the second most frequent human malaria parasite and a major obstacle to countrywide malaria elimination .", "Knowing the local parasite structure is useful for elimination efforts .", "Therefore , we analyzed , with a panel of 14 microsatellite markers , 234 P . v...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "herpes simplex virus", "vero cells", "medicine and health sciences", "pathology and laboratory medicine", "pathogens", "biological cultures", "dna-binding proteins", "microbiology", "dna transcription", "viruses", "dna replication", "dna viruses", "epigenetics", "dna", "chromatin", "h...	An Essential Viral Transcription Activator Modulates Chromatin Dynamics	journal.ppat.1005842	null	[ [ "The genes of the nuclear-replicating double stranded ( ds ) DNA virus herpes simplex virus 1 ( HSV-1 ) are expressed in a coordinate manner .", "VP16 , a virion protein , first activates expression of the five immediate early ( IE ) genes , in part through the recruitment of the histone demethylase LSD1 ...	[ "Although ICP4 is the only essential transcription activator of herpes simplex virus 1 ( HSV-1 ) , its mechanisms of action are still only partially understood .", "We and others propose a model in which HSV-1 genomes are chromatinized as a cellular defense to inhibit HSV-1 transcription .", "To counteract sile...	[ "The nuclear-replicating DNA viruses of the family herpesviridae cause a variety of diseases .", "Eight herpesviruses infect humans .", "Three of them , including herpes simplex virus 1 ( HSV-1 ) , belong to the alpha-herpesvirus sub-family .", "Viruses in this family have the fastest replication cycles of al...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "computational biology/systems biology", "biophysics/theory and simulation", "neuroscience/theoretical neuroscience" ]	Spontaneous Local Gamma Oscillation Selectively Enhances Neural Network Responsiveness	journal.pcbi.1000342	null	[ [ "Understanding the responsiveness of a cortical neural network is a fundamental", "requirement for any study of sensory information processing in the brain .", "Several", "experiments show that various factors can affect the neuronal response property and", "information flow in nervous systems...	[ "Synchronized oscillation is very commonly observed in many neuronal systems and", "might play an important role in the response properties of the system .", "We have", "studied how the spontaneous oscillatory activity affects the responsiveness of a", "neuronal network , using a neural network model of the...	[ "In the nervous system , information is delivered and processed digitally via", "voltage spikes transmitted between cells .", "A neural system is characterized by", "its input/output spike signal patterns .", "Generally , a network of neurons shows a", "very different response pattern than that of a singl...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Integrative Modelling of the Influence of MAPK Network on Cancer Cell Fate Decision	journal.pcbi.1003286	null	[ [ "Mitogen-activated protein kinase ( MAPK ) cascades can be activated by a wide variety of stimuli , such as growth factors and environmental stresses .", "They affect diverse cellular activities , including gene expression , cell cycle machinery , apoptosis and differentiation .", "A recurrent feature...	[ "The Mitogen-Activated Protein Kinase ( MAPK ) network consists of tightly interconnected signalling pathways involved in diverse cellular processes , such as cell cycle , survival , apoptosis and differentiation .", "Although several studies reported the involvement of these signalling cascades in cancer deregul...	[ "Depending on environmental conditions , strongly intertwined cellular signalling pathways are activated , involving activation/inactivation of proteins and genes in response to external and/or internal stimuli .", "Alterations of some components of these pathways can lead to wrong cell behaviours .", "For inst...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "fluorescence imaging", "invertebrates", "meiosis", "medicine and health sciences", "reproductive system", "gonads", "caenorhabditis", "cell cycle and cell division", "cell processes", "light microscopy", "animals", "animal models", "caenorhabditis elegans", "model organisms", "microscop...	Meiotic recombination modulates the structure and dynamics of the synaptonemal complex during C. elegans meiosis	journal.pgen.1006670	null	[ [ "Sexual reproduction depends on the specialized cell division program of meiosis , which allows diploid organisms to form haploid gametes .", "Reduction in chromosome number from the diploid to the haploid state occurs during the first meiotic division , when homologous chromosomes segregate to opposite p...	[ "During meiotic prophase , a structure called the synaptonemal complex ( SC ) assembles at the interface between aligned pairs of homologous chromosomes , and crossover recombination events occur between their DNA molecules .", "Here we investigate the inter-relationships between these two hallmark features of th...	[ "Reliable chromosome inheritance during sexual reproduction depends on the formation of temporary connections between homologous chromosomes that enable them to segregate toward opposite spindle poles at the meiosis I division .", "These connections are established during an extended meiotic prophase characterize...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "hematology/hematopoiesis", "developmental biology/stem cells", "computational biology/transcriptional regulation" ]	Modeling Reveals Bistability and Low-Pass Filtering in the Network Module Determining Blood Stem Cell Fate	journal.pcbi.1000771	null	[ [ "Appropriate spatiotemporal control of gene expression is central to metazoan development .", "[1] .", "Combinatorial interactions of regulatory proteins with regulatory regions of DNA and the basal transcriptional machinery form the building blocks of complex gene regulatory networks ( GRNs ) .", ...	[ "Combinatorial regulation of gene expression is ubiquitous in eukaryotes with multiple inputs converging on regulatory control elements .", "The dynamic properties of these elements determine the functionality of genetic networks regulating differentiation and development .", "Here we propose a method to quanti...	[ "Hematopoiesis—blood cell development—has long served as a model for study of cellular differentiation and its control by underlying gene regulatory networks .", "The Scl-Gata2-Fli1 triad is a network module essential for the development of hematopoietic stem cells but its mechanistic role is not well understood ...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "proteins", "biology", "microbiology", "biophysics", "bacterial pathogens" ]	Structural Insights into a Unique Legionella pneumophila Effector LidA Recognizing Both GDP and GTP Bound Rab1 in Their Active State	journal.ppat.1002528	null	[ [ "Rab GTPases play a crucial role in vesicular trafficking through shuttling between cytosol and membranes , a process that is controlled by several regulatory proteins [1]–[4] .", "GDP dissociation inhibitors ( GDIs ) preferentially interact with and deliver GDP-bound Rabs to their target membranes , wher...	[ "The intracellular pathogen Legionella pneumophila hijacks the endoplasmic reticulum ( ER ) -derived vesicles to create an organelle designated Legionella-containing vacuole ( LCV ) required for bacterial replication .", "Maturation of the LCV involved acquisition of Rab1 , which is mediated by the bacterial effe...	[ "Legionella pneumophila delivers 275 validated substrates into the host cytosol by its Dot/Icm type IV secretion system .", "Several substrates including SidM/DrrA and LidA directly interact with the host Rab GTPases and interfere with the vesicle secretion pathway .", "SidM/DrrA is necessary for Rab1 recruitme...	2012
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "microbiology", "viral structure", "dna replication", "dna", "immunologic techniques", "microbial genomics", "research and analysis methods", "viral genomics", "genomic signal processing", "immunoassays", "comparative genomics", "viral packaging", "viral replication", "virions", "immunof...	Spatiotemporal dynamics of HSV genome nuclear entry and compaction state transitions using bioorthogonal chemistry and super-resolution microscopy	journal.ppat.1006721	null	[ [ "Virtually all DNA virus classes including herpesviruses , adenoviruses , hepatitis B virus , parvoviruses and polyomaviruses must deposit their genomes within the nucleus for transcription , genome replication and subsequent capsid assembly .", "Genome transport and entry to the nucleus is also a prerequ...	[ "We investigated the spatiotemporal dynamics of HSV genome transport during the initiation of infection using viruses containing bioorthogonal traceable precursors incorporated into their genomes ( HSVEdC ) .", "In vitro assays revealed a structural alteration in the capsid induced upon HSVEdC binding to solid su...	[ "Virtually all DNA virus classes as well as many RNA viruses must deposit their genomes within the nucleus for transcription , genome replication and subsequent capsid assembly .", "While infecting capsids have been studied by various methods and biochemical approaches have been used to investigate the bulk genom...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "enzymes", "metabolic networks", "nucleotides", "bioenergetics", "enzyme kinetics", "mitochondrial diseases", "theoretical biology", "biochemistry simulations", "metabolic pathways", "biology", "biochemistry", "biochemical simulations", "nucleic acids", "genetics", "energy-producing orga...	Enzyme Kinetics of the Mitochondrial Deoxyribonucleoside Salvage Pathway Are Not Sufficient to Support Rapid mtDNA Replication	journal.pcbi.1002078	null	[ [ "Mitochondrial DNA ( mtDNA ) replication [1] , and the mitochondrial nucleoside salvage pathway that generates the precursor deoxyribonucleoside triphosphates ( dNTPs ) for mitochondrial DNA replication , have generally been believed to function independently of nuclear DNA ( nDNA ) replication and cytoplasmi...	[ "Using a computational model , we simulated mitochondrial deoxynucleotide metabolism and mitochondrial DNA replication .", "Our results indicate that the output from the mitochondrial salvage enzymes alone is inadequate to support a mitochondrial DNA replication duration of as long as 10 hours .", "We find that...	[ "The powerhouses of human cells , mitochondria , contain DNA that is distinct from the primary genome , the DNA in the nucleus of cells .", "The mitochondrial genome needs to be replicated often to ensure continued generation of ATP ( adenosine triphosphate ) which is the energy currency of the cell .", "Proble...	2011
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "fish", "ecology and environmental sciences", "methods and resources", "relational databases", "vertebrates", "computer hardware", "computers", "animals", "animal models", "osteichthyes", "developmental biology", "model organisms", "experimental organism systems", "molecular biology techni...	FishNET: An automated relational database for zebrafish colony management	journal.pbio.3000343	With the continued growth of zebrafish as a genetic model system, the ability to robustly catalogue and monitor the animals within a zebrafish colony is critical. This paper presents an open-source, non-coding–based, relational database solution that streamlines data entry, saves valuable time, and enables easy real-ti...	[ [ "The fecundity , rapid development , external fertilization , amenability to both forward [1–7] and reverse [8–11] genetic approaches , conservation of core vertebrate protein-coding genes [12] , small size , and inexpensive husbandry costs make zebrafish a powerful vertebrate model for studying human physiol...	[ "The zebrafish Danio rerio is a powerful model system to study the genetics of development and disease .", "However , maintenance of zebrafish husbandry records is both time intensive and laborious , and a standardized way to manage and track the large amount of unique lines in a given laboratory or centralized f...	[ "FishNET facilitates remote tracking of individual zebrafish lines and links associated biological resources to enable robust and efficient colony management and storage of laboratory information related to zebrafish ." ]	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "children", "medicine and health sciences", "immune physiology", "maternal health", "obstetrics and gynecology", "immunology", "tropical diseases", "parasitic diseases", "vaccines", "preventive medicine", "age groups", "women's health", "infants", "infectious disease control", "antibodie...	Parasitic infections during pregnancy need not affect infant antibody responses to early vaccination against Streptococcus pneumoniae, diphtheria, or Haemophilus influenzae type B	journal.pntd.0007172	null	[ [ "The global burden of vaccine-preventable diseases remains high , especially among children under 5 years old , with 1 to 2 million deaths recorded annually [1] .", "The encapsulated bacteria Streptococcus pneumoniae and Haemophilus influenzae type B ( Hib ) cause the majority of child deaths from pneumon...	[ "Globally , vaccine-preventable diseases remain a significant cause of early childhood mortality despite concerted efforts to improve vaccine coverage .", "One reason for impaired protection may be the influence of prenatal exposure to parasitic antigens on the developing immune system .", "Prior research had s...	[ "This mother-baby cohort study continued our investigations into the potential impact of a mother’s parasitic infection ( s ) during pregnancy on a baby’s ability to respond to early life vaccinations .", "In a rural Kenyan setting where malaria and helminth infections are common , we tested infants’ anti-vaccine...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "microbial evolution", "biology", "microbiology" ]	Cellular Variability of RpoS Expression Underlies Subpopulation Activation of an Integrative and Conjugative Element	journal.pgen.1002818	null	[ [ "Integrative and conjugative elements ( ICE ) are a newly recognized class of mobile DNA elements in prokaryotes [1]–[4] .", "ICE come in different families , represented by the host cell range and gene similarities , but all have a similar mechanistic ‘life-style’ [2] .", "Under most circumstances th...	[ "Conjugative transfer of the integrative and conjugative element ICEclc in the bacterium Pseudomonas knackmussii is the consequence of a bistable decision taken in some 3% of cells in a population during stationary phase .", "Here we study the possible control exerted by the stationary phase sigma factor RpoS on ...	[ "Horizontal gene transfer is one of the amazing phenomena in the prokaryotic world , by which DNA can be moved between species with means of a variety of specialized “elements” and/or specific host cell mechanisms .", "In particular the molecular decisions that have to be made in order to transfer DNA from one ce...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "dna damage", "biochemistry", "dermatology", "skin neoplasms", "medicine and health sciences", "skin tumors", "biology and life sciences", "dna repair", "dna", "biochemical activity" ]	A Mouse Model Uncovers LKB1 as an UVB-Induced DNA Damage Sensor Mediating CDKN1A (p21WAF1/CIP1) Degradation	journal.pgen.1004721	null	[ [ "Ultraviolet ( UV ) radiation represents the number one leading cause for skin cancer .", "UV radiation can cause genetic mutations to DNA that if not repaired can lead to skin cancer .", "Elucidation of the mechanisms involved in UV-induced DNA damage response is important to understand the human dis...	[ "Exposure to ultraviolet ( UV ) radiation from sunlight accounts for 90% of the symptoms of premature skin aging and skin cancer .", "The tumor suppressor serine-threonine kinase LKB1 is mutated in Peutz-Jeghers syndrome and in a spectrum of epithelial cancers whose etiology suggests a cooperation with environmen...	[ "Environmental insults are directly involved in cancer development .", "In particular , Ultraviolet ( UV ) radiation has been associated to the acquisition of different types skin cancer and premature skin aging .", "UV radiation causes modifications in the genetic material of cells ( DNA ) that if not repaired...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "cell binding", "phosphorylation", "cell physiology", "cell motility", "ecology and environmental sciences", "chemical compounds", "atmospheric science", "enzymes", "enzymology", "organic compounds", "fluorophotometry", "developmental biology", "serine", "amino acids", "research and anal...	Paxillin phosphorylation at serine 273 and its effects on Rac, Rho and adhesion dynamics	journal.pcbi.1006303	null	[ [ "In multicellular organisms , cell migration is key to proper development and maintenance of physiological processes such as embryogenesis , axonal outgrowth in neurons , and wound healing [1–5] .", "Additionally , aberrant migration can lead to pathological effects such as cancer metastasis [1 , 3–7] .",...	[ "Focal adhesions are protein complexes that anchor cells to the extracellular matrix .", "During migration , the growth and disassembly of these structures are spatiotemporally regulated , with new adhesions forming at the leading edge of the cell and mature adhesions disassembling at the rear .", "Signalling p...	[ "Cellular migration is crucial in both physiological and pathological functions .", "Maintenance of proper migration and development of aberrant migration are effectuated by cellular machinery involving protein complexes , called adhesions , that anchor the cell to its environment .", "Over time , these adhesio...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biomacromolecule-ligand interactions", "biochemistry", "nucleic acids", "proteins", "enzymes", "genetics", "gene expression", "biology", "biophysics", "gene function" ]	Chromatin Targeting Signals, Nucleosome Positioning Mechanism and Non-Coding RNA-Mediated Regulation of the Chromatin Remodeling Complex NoRC	journal.pgen.1004157	null	[ [ "Nucleosomes present a major obstacle for the binding of sequence-specific DNA-binding factors , the interaction of positively charged histone tails with DNA and the masking of DNA binding sites that face in towards the histone octamer surface [1] , [2] .", "As a result , all DNA-dependent processes , suc...	[ "Active and repressed ribosomal RNA ( rRNA ) genes are characterised by specific epigenetic marks and differentially positioned nucleosomes at their promoters .", "Repression of the rRNA genes requires a non-coding RNA ( pRNA ) and the presence of the nucleolar remodeling complex ( NoRC ) .", "ATP-dependent chr...	[ "Tumour cells overexpress ribosomal RNA ( rRNA ) , which is required for ribosome assembly and cell growth .", "rRNA gene repression is mediated by the chromatin remodeling complex ( NoRC ) and a non-coding RNA that binds to this enzyme .", "This study addresses the mechanism of nucleosome positioning by NoRC a...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	The Cost of Annual versus Biannual Community-Directed Treatment of Onchocerciasis with Ivermectin: Ghana as a Case Study	journal.pntd.0002452	null	[ [ "Human onchocerciasis or river blindness is a neglected tropical disease ( NTD ) caused by the parasitic filarial nematode Onchocerca volvulus and transmitted by the bites of Simulium blackflies [1] .", "In addition to ocular pathology ( vision loss , blindness ) , and increased host mortality [2] , [3] ,...	[ "It has been proposed that switching from annual to biannual ( twice yearly ) mass community-directed treatment with ivermectin ( CDTI ) might improve the chances of onchocerciasis elimination in some African foci .", "However , historically , relatively few communities have received biannual treatments in Africa...	[ "The African Programme for Onchocerciasis Control ( APOC ) has recently been extended until 2025 , with renewed commitment towards onchocerciasis elimination .", "This aim is aligned with the goals stated by the World Health Organization and the London Declaration on Neglected Tropical Diseases in January 2012 ."...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biomacromolecule-ligand interactions", "organismal evolution", "microbial mutation", "enzymes", "macromolecular assemblies", "population genetics", "evolutionary selection", "microbiology", "mutation", "mechanisms of resistance and susceptibility", "biocatalysis", "protein folding", "microb...	Selective Pressure Causes an RNA Virus to Trade Reproductive Fitness for Increased Structural and Thermal Stability of a Viral Enzyme	journal.pgen.1003102	null	[ [ "The ability of a single mutational substitution to modulate fitness across environments is the most important consequence of natural selection under environmental change .", "Understanding the antagonistic tradeoffs of pleiotropic mutations that promote survival in changing environments is therefore esse...	[ "The modulation of fitness by single mutational substitutions during environmental change is the most fundamental consequence of natural selection .", "The antagonistic tradeoffs of pleiotropic mutations that can be selected under changing environments therefore lie at the foundation of evolutionary biology .", ...	[ "The most fundamental mechanism of natural selection in a changing environment is the modulation of fitness by mutations .", "It is the tradeoffs offered by these mutations that drive evolution .", "However , fitness tradeoffs are rarely understood at the molecular level , in terms of how the selected mutations...	2012
[ "Introduction", "Results", "Discussion", "Materials & methods" ]	[ "plant anatomy", "ecology and environmental sciences", "brassica", "plant physiology", "plant science", "model organisms", "experimental organism systems", "plant pathology", "evolutionary adaptation", "plant ecology", "plants", "flowering plants", "arabidopsis thaliana", "research and ana...	AtHKT1 drives adaptation of Arabidopsis thaliana to salinity by reducing floral sodium content	journal.pgen.1007086	null	[ [ "Although plants are sessile and are passively exposed to varying environments , they can successfully complete their life cycle and disperse across a range of environmental conditions .", "These capabilities are attributable to their physiological plastic and complex gene regulation networks , as well as...	[ "Arabidopsis thaliana high-affinity potassium transporter 1 ( AtHKT1 ) limits the root-to-shoot sodium transportation and is believed to be essential for salt tolerance in A . thaliana .", "Nevertheless , natural accessions with ‘weak allele’ of AtHKT1 , e . g . Tsu-1 , are mainly distributed in saline areas and ...	[ "Identifying the genetic variation driving plant adaptation to salinity is critical for understanding natural selection and evolutionary mechanisms .", "In this study , we have revealed that the gene AtHKT1 drives natural variation in the adaptation of A . thaliana to salinity .", "Our evidences directly show t...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "learning", "invertebrates", "plant anatomy", "medicine and health sciences", "legs", "sociology", "social sciences", "limbs (anatomy)", "neuroscience", "learning and memory", "animals", "plant science", "cognitive psychology", "animal behavior", "zoology", "bees", "foraging", "mus...	Associative Mechanisms Allow for Social Learning and Cultural Transmission of String Pulling in an Insect	journal.pbio.1002564	Bumblebees can be trained to pull strings to obtain a reward, can learn to string pull through observation, and can culturally spread string pulling throughout a colony.	[ [ "Social learning is widespread in animals [1 , 2] and can enable novel behavior routines , sometimes introduced by a single “innovator , ” to spread among individuals in a group [1–5] .", "Examples are potato washing and termite fishing in primates , pinecone stripping in rodents and milk bottle opening i...	[ "Social insects make elaborate use of simple mechanisms to achieve seemingly complex behavior and may thus provide a unique resource to discover the basic cognitive elements required for culture , i . e . , group-specific behaviors that spread from “innovators” to others in the group via social learning .", "We f...	[ "Social insects make use of simple mechanisms to achieve many seemingly complex behaviors and thus may be able to provide a unique resource for uncovering the basic cognitive elements required for culture .", "Here , we first show that bumblebees can be trained to pull a string to access a reward , but most could...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Deconstructing Interocular Suppression: Attention and Divisive Normalization	journal.pcbi.1004510	null	[ [ "The perception of a brief target stimulus presented to one eye is suppressed by the simultaneous presentation of a dissimilar competitor stimulus to the other eye .", "This phenomenon , called interocular suppression , can be so strong that it renders the ( otherwise easily visible ) target invisible [1–...	[ "In interocular suppression , a suprathreshold monocular target can be rendered invisible by a salient competitor stimulus presented in the other eye .", "Despite decades of research on interocular suppression and related phenomena ( e . g . , binocular rivalry , flash suppression , continuous flash suppression )...	[ "In interocular suppression , a visible target presented in one eye can be rendered invisible by a competing image ( the competitor ) presented in the other eye .", "This phenomenon is a striking demonstration of the discrepancy between physical inputs to the visual system and perception , and it also allows neur...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases/helminth infections" ]	Treatment Response of Cystic Echinococcosis to Benzimidazoles: A Systematic Review	journal.pntd.0000524	null	[ [ "Cystic echinococcosis ( CE , hydatid disease ) is a parasitic disease of worldwide prevalence .", "Hydatid cysts occur mainly in the liver ( 70% ) and the lung ( 20% ) .", "Clinical symptoms and signs depend on their localisation , size , and number .", "Currently four treatment modalities are in...	[ "Over the past 30 years , benzimidazoles have increasingly been used to treat cystic echinococcosis ( CE ) .", "The efficacy of benzimidazoles , however , remains unclear .", "We systematically searched MEDLINE , EMBASE , SIGLE , and CCTR to identify studies on benzimidazole treatment outcome .", "A large het...	[ "Cystic echinococcosis ( CE ) is a parasitic infection of worldwide occurrence transmitted to humans by dogs .", "After infection cysts develop , mainly in the liver and lung .", "Ultrasound-based staging of cysts into active , transitional , and inactive has opened new venues for treatment and follow-up .", ...	2009
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "flow cytometry", "cell motility", "medicine and health sciences", "immune cells", "immune physiology", "pathology and laboratory medicine", "spleen", "pathogens", "immunology", "microbiology", "orthomyxoviruses", "viruses", "rna viruses", "cytotoxic t cells", "antibodie...	Mucosal CD8+ T cell responses induced by an MCMV based vaccine vector confer protection against influenza challenge	journal.ppat.1008036	null	[ [ "Respiratory infections caused by influenza viruses usually are associated with mild-to-moderate disease symptoms but are linked with high morbidity and mortality in susceptible populations like the elderly , young children , patients with co-morbidities and immunocompromised patients .", "Influenza virus...	[ "Cytomegalovirus ( CMV ) is a ubiquitous β-herpesvirus that establishes life-long latent infection in a high percentage of the population worldwide .", "CMV induces the strongest and most durable CD8+ T cell response known in human clinical medicine .", "Due to its unique properties , the virus represents a pro...	[ "Vaccines against influenza typically induce immune responses based on antibodies , small molecules that recognize the virus particles outside of cells and neutralize them before they infect a cell .", "However , influenza rapidly evolves , escaping immune recognition , and the fastest evolution is seen in the pa...	2019
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "parasite groups", "plasmodium", "population genetics", "tropical diseases", "parasitic diseases", "parasitic protozoans", "parasitology", "ethnicities", "apicomplexa", "protozoans", "mathematics", "dna", "population biology", "discrete mathematics", "co...	Quantifying connectivity between local Plasmodium falciparum malaria parasite populations using identity by descent	journal.pgen.1007065	null	[ [ "Molecular tools show great promise for helping us understand and contain the spatial spread of pathogens , and the application of population genetic approaches to monitoring and controlling infectious diseases is becoming routine .", "Routes and volumes of non-sexually recombining pathogens , such as the...	[ "With the rapidly increasing abundance and accessibility of genomic data , there is a growing interest in using population genetic approaches to characterize fine-scale dispersal of organisms , providing insight into biological processes across a broad range of fields including ecology , evolution and epidemiology ...	[ "The spatiotemporal dispersal of organisms can inform efforts to conserve endangered species , to contain the spread of drug resistance , and to eliminate disease .", "As genomic data become increasingly more affordable and accessible via public depositories , the demand for methods capable of extracting fine-sca...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases/protozoal infections", "infectious diseases/neglected tropical diseases", "infectious diseases/epidemiology and control of infectious diseases" ]	Focus–Specific Clinical Profiles in Human African Trypanosomiasis Caused by Trypanosoma brucei rhodesiense	journal.pntd.0000906	null	[ [ "Human African trypanosomiasis is caused by infection with African trypanosomes , which are transmitted by the haematophagous tsetse fly .", "Trypanosoma brucei gambiense ( T . b . gambiense ) HAT is present in West and Central Africa and T . b . rhodesiense HAT is found in East and Southern Africa .", ...	[ "Diverse clinical features have been reported in human African trypanosomiasis ( HAT ) foci caused by Trypanosoma brucei rhodesiense ( T . b . rhodesiense ) giving rise to the hypothesis that HAT manifests as a chronic disease in South-East African countries and increased in virulence towards the North .", "Such ...	[ "T . b .", "gambiense and T . b .", "rhodesiense cause human African trypanosomiasis ( HAT ) .", "These parasite subspecies differ in their rate of progression to central nervous system ( CNS ) infection , and consequently to coma and death .", "Variation in disease progression and severity has also been do...	2010
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "biogeography", "animal types", "ecology and environmental sciences", "milk", "medicine and health sciences", "body fluids", "ruminants", "population genetics", "geographical locations", "vertebrates", "diet", "animals", "mammals", "nutrition", "population biology", "zoology", "bacte...	Genetic diversity and potential routes of transmission of Mycobacterium bovis in Mozambique	journal.pntd.0006147	null	[ [ "Bovine tuberculosis ( BTB ) is an infectious disease caused by Mycobacterium bovis that affects cattle , other domesticated animals and many free ranging or captive wildlife species .", "BTB is of global concern on at least three socio-economic levels: the negative impact on animal production; the potent...	[ "Bovine tuberculosis is a zoonotic disease with largely unknown impact in Africa , with risk factors such as HIV and direct contact with animals or consumption of Mycobacterium bovis infected animal products .", "In order to understand and quantify this risk and design intervention strategies , good epidemiologic...	[ "Bovine tuberculosis is a rather neglected zoonotic disease caused by Mycobacterium bovis that is of global concern owing to the persistence of the bacillus in reservoirs that can spread bovine tuberculosis between animals and humans .", "Africa remains understudied regarding this pathogen , and should be an area...	2018
[ "Introduction", "Rule 1: Use version control", "Rule 2: Document your code and usage", "Rule 3: Make common operations easy to control", "Rule 4: Version your releases", "Rule 5: Reuse software (within reason)", "Rule 6: Rely on build tools and package managers for installation", "Rule 7: Do not requi...	[ "sequence analysis", "operating systems", "computer and information sciences", "sequence alignment", "bioinformatics", "engineering and technology", "research assessment", "computer software", "database and informatics methods", "software engineering", "reproducibility", "software tools", "s...	Ten simple rules for making research software more robust	journal.pcbi.1005412	null	[ [ "Scientific software is typically developed and used by a single person , usually a graduate student or postdoc [1] .", "It may produce the intended results in their hands , but what happens when someone else wants to run it ?", "Everyone with a few years of experience feels a bit nervous when told to...	[ "Software produced for research , published and otherwise , suffers from a number of common problems that make it difficult or impossible to run outside the original institution or even off the primary developer’s computer .", "We present ten simple rules to make such software robust enough to be run by anyone , ...	[ "Many researchers have found out the hard way that there’s a world of difference between “works for me on my machine” and “works for other people on theirs . ”", "Many common challenges can be avoided by following a few simple rules; doing so not only improves reproducibility but can accelerate research ." ]	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "ecology and environmental sciences", "medicine and health sciences", "animals", "population modeling", "veterinary science", "infectious diseases", "veterinary diseases", "zoonoses", "epidemiology", "infectious disease modeling", "population ecology", "insects", "disease ...	Predicting the Mosquito Species and Vertebrate Species Involved in the Theoretical Transmission of Rift Valley Fever Virus in the United States	journal.pntd.0003163	null	[ [ "Rift Valley fever virus ( RVFV ) is an emerging infectious disease in Africa and the Middle East .", "If introduced to North America , RVFV is capable of serious health and socioeconomic consequences potentially incapacitating large numbers of humans , decimating susceptible farm animals , and instigatin...	[ "Rift Valley fever virus ( RVFV ) is a mosquito-borne virus in the family Bunyaviridiae that has spread throughout continental Africa to Madagascar and the Arabian Peninsula .", "The establishment of RVFV in North America would have serious consequences for human and animal health in addition to a significant eco...	[ "In anticipation of continued pathogen emergence in the U . S . due to globalization climate change , and other factors , the development of proactive management plans and interventions to predict and then intervene is going to be more efficient and effective than retrospective plans developed after pathogen emerge...	2014
[ "Introduction", "Discussion", "Methods" ]	[ "genetics and genomics/genomics", "public health and epidemiology/epidemiology", "genetics and genomics/physiogenomics", "genetics and genomics/gene expression" ]	Deciphering Normal Blood Gene Expression Variation—The NOWAC Postgenome Study	journal.pgen.1000873	null	[ [ "There is growing evidence that transcriptome analysis of peripheral blood cells is a valuable tool for determining signatures related to disease [1]–[5] and drug-response [6] .", "Differences in blood gene expression may also reflect the effects of a particular exposure , such as smoking [7] , metal fume...	[ "There is growing evidence that gene expression profiling of peripheral blood cells is a valuable tool for assessing gene signatures related to exposure , drug-response , or disease .", "However , the true promise of this approach can not be estimated until the scientific community has robust baseline data descri...	[ "As a major defence and transport system , blood cells are capable of adjusting gene expression in response to various clinical , biochemical , and pathological conditions .", "Here , we expand our understanding about the nature and extent of variation in gene expression from blood among healthy individuals .", ...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	A Latex Metabolite Benefits Plant Fitness under Root Herbivore Attack	journal.pbio.1002332	Dandelion plants protect their roots from the larva of the common cockchafer beetle by accumulating and releasing a sesquiterpene lactone deterrent in their exuded latex.	[ [ "Plants produce over 200 , 000 different metabolites that are not directly needed for their growth and development [1] .", "Many of these so-called secondary metabolites have a negative impact on insect herbivores [2–6] , leading to the hypothesis that they evolved as defenses against the latter [7] .", ...	[ "Plants produce large amounts of secondary metabolites in their shoots and roots and store them in specialized secretory structures .", "Although secondary metabolites and their secretory structures are commonly assumed to have a defensive function , evidence that they benefit plant fitness under herbivore attack...	[ "Plant roots produce diverse and abundant blends of bioactive metabolites .", "One potential function of these compounds is to protect roots against the devastating effects of below ground herbivore attack .", "However , examples demonstrating such a protective function in native plant-herbivore systems are lac...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "classical mechanics", "engineering and technology", "vibration", "ears", "signal processing", "neuroscience", "surgical and invasive medical procedures", "labyrinth supporting cells", "epithelial cells", "outer hair cells", "organ of corti", "functional elect...	Static length changes of cochlear outer hair cells can tune low-frequency hearing	journal.pcbi.1005936	null	[ [ "Our ability to hear is due to an intricate mechanotransduction process that takes place inside the inner ear .", "Sound-evoked waves on the basilar membrane , an elastic structure stretching along the cochlear canal , cause the deflection of mechanosensitive hair bundles of the sensory cells , thus gatin...	[ "The cochlea not only transduces sound-induced vibration into neural spikes , it also amplifies weak sound to boost its detection .", "Actuators of this active process are sensory outer hair cells in the organ of Corti , whereas the inner hair cells transduce the resulting motion into electric signals that propag...	[ "Outer hair cells are highly specialized force producers inside the inner ear: they can change length when stimulated electrically .", "However , how exactly this electromotile effect contributes to the astonishing sensitivity and frequency selectivity of the inner ear has remained unclear .", "Here we show for...	2018
[ "Introduction", "Models", "Results", "Discussion" ]	[]	Posterior Probability Matching and Human Perceptual Decision Making	journal.pcbi.1004342	null	[ [ "Human decision making is partly random , in the sense that a person can make different decisions on different occasions based on the same information .", "Probability matching is a theory of decision making that aims to account for this randomness .", "Suppose a person believes that response A has a ...	[ "Probability matching is a classic theory of decision making that was first developed in models of cognition .", "Posterior probability matching , a variant in which observers match their response probabilities to the posterior probability of each response being correct , is being used increasingly often in model...	[ "Decision making is partly random: a person can make different decisions at different times based on the same information .", "The theory of probability matching says that one reason for this randomness is that people usually choose the response that they think is most likely to be correct , but they sometimes in...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "biotechnology", "sequencing techniques", "medicine and health sciences", "immune physiology", "pathology and laboratory medicine", "engineering and technology", "pathogens", "synthetic biology", "immunology", "microbiology", "synthetic bioengineering", "retroviruses", "organisms", "immuno...	Integrating linear optimization with structural modeling to increase HIV neutralization breadth	journal.pcbi.1005999	null	[ [ "Computational design has been used successfully by protein engineers for many years to alter the physicochemical properties of proteins [1 , 2] .", "In the simplest case , protein design involves optimizing the amino acid sequence of a protein to accommodate a desired 3-D conformation .", "This appro...	[ "Computational protein design has been successful in modeling fixed backbone proteins in a single conformation .", "However , when modeling large ensembles of flexible proteins , current methods in protein design have been insufficient .", "Large barriers in the energy landscape are difficult to traverse while ...	[ "In this article , we report a new approach for protein design , which combines traditional structural modeling with machine learning and integer programming .", "Using this method , we are able to design antibodies that are predicted to bind large panels of antigenically diverse HIV variants .", "The combinati...	2018
[ "Introduction", "Results", "Discussion", "Material and methods" ]	[ "medicine and health sciences", "pineal gland", "in situ hybridization", "molecular probe techniques", "cell cycle and cell division", "cell processes", "social sciences", "neuroscience", "notch signaling", "developmental biology", "molecular biology techniques", "embryos", "research and ana...	A Notch-mediated, temporal asymmetry in BMP pathway activation promotes photoreceptor subtype diversification	journal.pbio.2006250	null	[ [ "The development of a functional nervous system requires the production of an amazing diversity of cell types .", "The precise identity of each neuron is acquired through a complex process referred to as neuronal subtype specification .", "Although different molecular mechanisms have been reported to ...	[ "Neural progenitors produce neurons whose identities can vary as a function of the time that specification occurs .", "Here , we describe the heterochronic specification of two photoreceptor ( PhR ) subtypes in the zebrafish pineal gland .", "We find that accelerating PhR specification by impairing Notch signal...	[ "A major goal in the field of developmental neurobiology is to identify the mechanisms that underly the diversification of the subtypes of neurons that are needed for the function of the nervous system .", "When investigating these mechanisms , time is an often-overlooked variable .", "Here , we show that in th...	2019
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "meiosis", "homologous chromosomes", "spermatocytes", "cell cycle and cell division", "cell processes", "germ cells", "dna damage", "dna", "sperm", "sex chromosomes", "animal cells", "chromosome biology", "autosomes", "biochemistry", "cell biology", "nucleic acids", "genetics", "bi...	Transition from a meiotic to a somatic-like DNA damage response during the pachytene stage in mouse meiosis	journal.pgen.1007439	null	[ [ "DNA damage response is one of the most critical processes for cell survival and proliferation .", "Of the different forms of DNA damage , double-strand breaks ( DSBs ) are by far the most harmful .", "DSBs can arise spontaneously as a consequence of exposure to physical and chemical agents or followi...	[ "Homologous recombination ( HR ) is the principal mechanism of DNA repair acting during meiosis and is fundamental for the segregation of chromosomes and the increase of genetic diversity .", "Nevertheless , non-homologous end joining ( NHEJ ) mechanisms can also act during meiosis , mainly in response to exogeno...	[ "DNA repair is critical for both somatic and meiotic cells .", "During meiosis , hundreds of DNA double strand breaks ( DSBs ) are introduced endogenously .", "To repair this damage , meiotic cells use a specialized version of the homologous recombination ( HR ) pathway that uses specific meiotic recombinases ,...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases", "veterinary diseases", "zoonoses", "medicine and health sciences", "population modeling", "epidemiology", "infectious disease epidemiology", "biology and life sciences", "population biology", "infectious disease modeling", "computational biology", "infectious disease con...	Transmission and Control of Plasmodium knowlesi: A Mathematical Modelling Study	journal.pntd.0002978	null	[ [ "Despite advances in the control and treatment of malaria more than half the world's population remain at risk of infection and disease .", "Of the estimated 216 million episodes of disease occurring worldwide in 2010 , 13% were estimated to occur in South-East Asia [1] .", "In 2004 , large numbers of...	[ "Plasmodium knowlesi is now recognised as a leading cause of malaria in Malaysia .", "As humans come into increasing contact with the reservoir host ( long-tailed macaques ) as a consequence of deforestation , assessing the potential for a shift from zoonotic to sustained P . knowlesi transmission between humans ...	[ "Plasmodium knowlesi is a malaria of macaques which is now recognised as a leading cause of human malaria in Malaysia .", "Although current human infections are a result of human-macaque contact , there is a potential for P . knowlesi to be transmitted solely among humans .", "The authors developed a multi-host...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "aging", "physiological processes", "developmental biology", "organism development", "physiology", "genetics", "epigenetics", "biology", "anatomy and physiology", "genetics and genomics" ]	MicroRNA Predictors of Longevity in Caenorhabditis elegans	journal.pgen.1002306	null	[ [ "Inter-individual variation in human longevity has not been found to be under substantial genetic control , with heritability generally between 15% and 30% [1] , [2] .", "At the same time , shared environmental factors contribute little in these human studies , and can be completely controlled in large-sc...	[ "Neither genetic nor environmental factors fully account for variability in individual longevity: genetically identical invertebrates in homogenous environments often experience no less variability in lifespan than outbred human populations .", "Such variability is often assumed to result from stochasticity in da...	[ "Why do some individuals live longer than others ?", "Unexpectedly , genetic differences contribute surprisingly little to lifespan variation in humans .", "The situation is thrown into relief in studies of C . elegans , in which genetically identical siblings reared in identical environments usually experience...	2011
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "computational biology/genomics", "microbiology" ]	De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis	journal.pgen.1000891	null	[ [ "Fungi are heterotrophic eukaryotes found in nearly all ecosystems .", "About 100 , 000 fungi have been described to date , but conservative estimates predict at least 1 . 5 million different species [1] , [2] .", "Fungi exhibit a wide range of different lifestyles , particularly as saprobes , pathoge...	[ "Filamentous fungi are of great importance in ecology , agriculture , medicine , and biotechnology .", "Thus , it is not surprising that genomes for more than 100 filamentous fungi have been sequenced , most of them by Sanger sequencing .", "While next-generation sequencing techniques have revolutionized genome...	[ "Fungi have immense impacts on ecosystems and affect many aspects of society .", "They are used as convenient organisms for fundamental research because their typically haploid genetics enable straightforward phenotyping of mutations and because most fungal cells can differentiate the entire organism .", "Fungi...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "microbiology/microbial evolution and genomics", "microbiology/medical microbiology", "infectious diseases/antimicrobials and drug resistance" ]	Inverse Correlation between Promoter Strength and Excision Activity in Class 1 Integrons	journal.pgen.1000793	null	[ [ "Integrons are natural genetic elements that can acquire , exchange and express genes within gene cassettes .", "The integron platform is composed of a gene , intI , that encodes a site-specific recombinase , IntI , a recombination site , attI , and a functional promoter , Pc , divergent to the integrase ...	[ "Class 1 integrons are widespread genetic elements that allow bacteria to capture and express gene cassettes that are usually promoterless .", "These integrons play a major role in the dissemination of antibiotic resistance among Gram-negative bacteria .", "They typically consist of a gene ( intI ) encoding an ...	[ "Integrons are widespread bacterial genetic elements able to capture and express gene cassettes that often encode antibiotic resistance determinants .", "Gene cassettes are usually promoterless and are transcribed from a common promoter , Pc .", "Pc is located within the coding sequence of the integron integras...	2010
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "virology", "dengue fever", "neglected tropical diseases", "dengue", "biology", "microbiology", "viral diseases", "viral disease diagnosis" ]	Evaluation of the Traditional and Revised WHO Classifications of Dengue Disease Severity	journal.pntd.0001397	null	[ [ "Dengue is an arthropod-borne viral disease with increasing prevalence in the last three decades , resulting in serious public health problems worldwide .", "With no vaccine or specific treatment to mitigate the natural history of the disease , a tool that can help clinicians detect and provide timely tre...	[ "Dengue is a major public health problem worldwide and continues to increase in incidence .", "Dengue virus ( DENV ) infection leads to a range of outcomes , including subclinical infection , undifferentiated febrile illness , Dengue Fever ( DF ) , life-threatening syndromes with fluid loss and hypotensive shock ...	[ "Dengue is a mosquito-transmitted viral disease that is a major public health problem worldwide .", "Dengue virus ( DENV ) infection leads to Dengue Fever ( DF ) and a spectrum of life-threatening syndromes with fluid loss and hypotensive shock or other severe manifestations .", "Recently , the traditional Worl...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "pathology and laboratory medicine", "cardiovascular anatomy", "293t cells", "pathogens", "immunology", "biological cultures", "microbiology", "cell differentiation", "dna transcription", "viruses", "developmental biology", "...	Hypoxia-inducible factor-1α plays roles in Epstein-Barr virus’s natural life cycle and tumorigenesis by inducing lytic infection through direct binding to the immediate-early BZLF1 gene promoter	journal.ppat.1006404	null	[ [ "Epstein-Barr virus ( EBV ) is a ubiquitous human gamma herpesvirus that infects over 90% of the world’s population .", "In healthy hosts , primary infection after childhood often results in infectious mononucleosis ( IM ) .", "Following primary infection , EBV establishes a life-long latent infection...	[ "When confronted with poor oxygenation , cells adapt by activating survival signaling pathways , including the oxygen-sensitive transcriptional regulators called hypoxia-inducible factor alphas ( HIF-αs ) .", "We report here that HIF-1α also regulates the life cycle of Epstein-Barr virus ( EBV ) .", "Incubation...	[ "Most adults throughout the world are infected with Epstein-Barr virus ( EBV ) , a human herpesvirus frequently associated in a latent state with some cancers of epithelial and B-cell origin such as nasopharyngeal carcinoma and Burkitt lymphoma , respectively .", "To develop an oncolytic therapy for treating pati...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "allosteric regulation", "medicine and health sciences", "enzymes", "metabolic processes", "metabolic networks", "enzymology", "glycolysis", "physiological processes", "homeostasis", "network analysis", "enzyme metabolism", "enzyme kinetics", "enzyme chemistry", "computer and information s...	Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials	journal.pcbi.1006356	null	[ [ "We are interested in studying the “catalytic potential” of an enzyme—its capacity to catalyze a reaction—from a network-level perspective .", "An enzyme achieves its catalytic potential when all individual enzyme species are in an active form; an enzyme with allosteric regulation modulates its utilizatio...	[ "Allosteric regulation has traditionally been described by mathematically-complex allosteric rate laws in the form of ratios of polynomials derived from the application of simplifying kinetic assumptions .", "Alternatively , an approach that explicitly describes all known ligand-binding events requires no simplif...	[ "Enzymatic rate laws have historically been used to simulate the dynamics of complex metabolic networks with regulated reactions represented by allosteric rate laws .", "Here , we use detailed elementary reaction descriptions of regulatory enzymes that allow for the explicit computation of the fraction of the enz...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell death", "nuclear staining", "gene regulation", "cell processes", "green fluorescent protein", "cloning", "luminescent proteins", "immunoprecipitation", "mitochondria", "molecular biology techniques", "bioenergetics", "cellular structures and organelles", "tropomyosin", "research and ...	Hey1- and p53-dependent TrkC proapoptotic activity controls neuroblastoma growth	journal.pbio.2002912	null	[ [ "The neurotrophins nerve growth factor ( NGF ) , brain-derived neurotrophic factor ( BDNF ) , neurotrophin-3 ( NT-3 ) , NT-4/5 , and their respective receptors neurotrophin receptor p75 ( p75NTR ) and tropomyosin receptor kinases ( TrkA ) , B , and C have been notably studied for their critical role in neurod...	[ "The neurotrophin-3 ( NT-3 ) receptor tropomyosin receptor kinase C ( TrkC/NTRK3 ) has been described as a dependence receptor and , as such , triggers apoptosis in the absence of its ligand NT-3 .", "This proapoptotic activity has been proposed to confer a tumor suppressor activity to this classic tyrosine kinas...	[ "Tropomyosin receptor kinase C ( TrkC ) is a transmembrane receptor at the cell surface and has been described to work paradoxically both as an oncogene and as a tumor suppressor .", "We partly solved this paradox in a previous study , demonstrating that TrkC is a double-facet receptor: Upon interaction with its ...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Speed Controls in Translating Secretory Proteins in Eukaryotes - an Evolutionary Perspective	journal.pcbi.1003294	null	[ [ "In dividing cells , the process of translation elongation consumes most of the cell energy and resources [1]–[3] .", "The rate of translation must be tightly controlled for coping with the cell demands and its limited resources .", "Specifically , translation efficiency is determined by the amount of...	[ "Protein translation is the most expensive operation in dividing cells from bacteria to humans .", "Therefore , managing the speed and allocation of resources is subject to tight control .", "From bacteria to humans , clusters of relatively rare tRNA codons at the N′-terminal of mRNAs have been implicated in at...	[ "Measurements of translation by ribosomal profiling and additional large-scale methods support the notion that the elongation speed and ribosomal occupancy are tightly regulated .", "We revisited the proteomes of a number of organisms , from yeast to human , and focused on the appearance of codons' clusters that ...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	When Can Species Abundance Data Reveal Non-neutrality?	journal.pcbi.1004134	null	[ [ "The extent to which ecological processes can be inferred from macroecological patterns has long been debated [1–4] .", "The appearance of common patterns in species abundance distributions ( SADs ) for different communities suggests that the same ecological mechanisms structure these communities [5 , 6] ...	[ "Species abundance distributions ( SAD ) are probably ecology’s most well-known empirical pattern , and over the last decades many models have been proposed to explain their shape .", "There is no consensus over which model is correct , because the degree to which different processes can be discerned from SAD pat...	[ "In order to predict and mitigate the response of ecological communities to global change , we need to understand the processes that allow multiple species to coexist in close proximity .", "A classic idea in Ecology is that species coexist because they occupy different “niches” .", "However , random processes ...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "bacteriology", "innate immune system", "medical microbiology", "microbial pathogens", "biology and life sciences", "immunology", "microbiology", "bacterial biochemistry", "bacterial pathogens", "immune system" ]	Peptidoglycan Recognition Proteins Kill Bacteria by Inducing Oxidative, Thiol, and Metal Stress	journal.ppat.1004280	null	[ [ "Mammalian Peptidoglycan Recognition Proteins ( PGRPs ) are a family of four evolutionary conserved antibacterial innate immunity proteins [1]–[3] .", "Three PGRPs ( PGLYRP1 , PGLYRP3 , and PGLYRP4 ) are directly bactericidal [4] , [5] and one PGRP ( PGLYRP2 ) is a peptidoglycan-lytic amidase [6] .", ...	[ "Mammalian Peptidoglycan Recognition Proteins ( PGRPs ) are a family of evolutionary conserved bactericidal innate immunity proteins , but the mechanism through which they kill bacteria is unclear .", "We previously proposed that PGRPs are bactericidal due to induction of reactive oxygen species ( ROS ) , a mecha...	[ "Bacterial infections are still a major cause of morbidity and mortality because of increasing antibiotic resistance .", "New targets for developing new approaches to antibacterial therapy are needed , because discovering new or improving current antibiotics have become increasingly difficult .", "One such appr...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biotechnology", "applied microbiology", "medicine", "veterinary diseases", "zoonotic diseases", "immunology", "biology", "veterinary science", "immune response" ]	Reactive Oxygen Species Production and Brugia pahangi Survivorship in Aedes polynesiensis with Artificial Wolbachia Infection Types	journal.ppat.1003075	null	[ [ "Lymphatic filariasis ( LF ) affects 120 million people globally and has been a leading cause of morbidity in South Pacific regions [1] .", "An ongoing global campaign to eliminate LF relies upon mass drug administration ( MDA ) strategies .", "However , because of inherent issues associated with MDA ...	[ "Heterologous transinfection with the endosymbiotic bacterium Wolbachia has been shown previously to induce pathogen interference phenotypes in mosquito hosts .", "Here we examine an artificially infected strain of Aedes polynesiensis , the primary vector of Wuchereria bancrofti , which is the causative agent of ...	[ "Lymphatic filariasis ( LF ) , the leading cause of morbidity in South Pacific regions , is caused by a filarial worm , Wuchereria bancrofti .", "Elimination of LF in the South Pacific requires an approach integrating both mass drug administration and strategies targeting the primary mosquito vector , Aedes polyn...	2012
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell motility", "innate immune system", "medicine and health sciences", "organoids", "immune physiology", "cytokines", "pathology and laboratory medicine", "immunology", "biological cultures", "cell differentiation", "colitis", "developmental biology", "signs and symptoms", "gastroenterol...	The colonic epithelium plays an active role in promoting colitis by shaping the tissue cytokine profile	journal.pbio.2002417	null	[ [ "IBD , comprised of Crohn’s disease ( CD ) and ulcerative colitis ( UC ) , is characterized by chronic inflammation of the gastrointestinal tract .", "The symptoms of IBD , which include diarrhea , abdominal pain , and intestinal blockage , are chronic and debilitating and , in extreme cases , can result ...	[ "Inflammatory bowel disease ( IBD ) is a chronic condition driven by loss of homeostasis between the mucosal immune system , the commensal gut microbiota , and the intestinal epithelium .", "Our goal is to understand how these components of the intestinal ecosystem cooperate to control homeostasis .", "By combi...	[ "Chronic inflammation of the gastrointestinal track is the common defect shared by inflammatory bowel diseases ( IBDs ) , such as Crohn’s disease and ulcerative colitis , which affect many people around the world .", "However , the genetic and physiologic complexities of IBDs have made it difficult to identify th...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Combining Natural Sequence Variation with High Throughput Mutational Data to Reveal Protein Interaction Sites	journal.pgen.1004918	null	[ [ "Protein activity , folding and stability are regulated by the interactions of proteins with other macromolecules .", "Thus , the identification of sites on a protein where these interactions occur is a critical but difficult undertaking .", "In some cases , structural analyses provide these sites at ...	[ "Many protein interactions are conserved among organisms despite changes in the amino acid sequences that comprise their contact sites , a property that has been used to infer the location of these sites from protein homology .", "In an inter-species complementation experiment , a sequence present in a homologue ...	[ "The interactions of proteins with each other are essential for almost all biological processes .", "Many of the sites of protein contact have evolved to maintain these interactions , but use different sets of amino acid residues .", "As a result , the residues at a contact site in a protein from one species mi...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "african trypanosomiasis", "neglected tropical diseases" ]	Towards an Optimal Design of Target for Tsetse Control: Comparisons of Novel Targets for the Control of Palpalis Group Tsetse in West Africa	journal.pntd.0001332	null	[ [ "Tsetse flies ( Diptera: Glossinidae ) infest about10 million km2 of sub-Saharan Africa where they transmit trypanosomes which cause Human African Trypanosomiasis ( HAT; also known as sleeping sickness ) and African Animal Trypanosomiasis ( AAT; also known as Nagana ) .", "This complex of diseases has an ...	[ "Tsetse flies of the Palpalis group are the main vectors of sleeping sickness in Africa .", "Insecticide impregnated targets are one of the most effective tools for control .", "However , the cost of these devices still represents a constraint to their wider use .", "The objective was therefore to improve the...	[ "Tsetse flies transmit trypanosomes causing sleeping sickness and nagana .", "Controlling tsetse prevents transmission of these diseases .", "Insecticide impregnated targets are highly effective but are too costly .", "This study aims to improve the cost effectiveness of targets .", "Experiments were perfor...	2011
[ "Introduction", "Results/Discussion", "Methods" ]	[ "computational biology/molecular dynamics", "biochemistry/biomacromolecule-ligand interactions", "biochemistry/theory and simulation", "biophysics/theory and simulation" ]	Computational Fragment-Based Binding Site Identification by Ligand Competitive Saturation	journal.pcbi.1000435	null	[ [ "Fragment-based drug discovery relies on a simple premise: identify small-molecule fragments that bind to a target region of the protein and then evolve or link them to create a larger high-affinity molecule .", "To a first approximation , the binding free-energies of fragments bound in non-overlapping po...	[ "Fragment-based drug discovery using NMR and x-ray crystallographic methods has proven utility but also non-trivial time , materials , and labor costs .", "Current computational fragment-based approaches circumvent these issues but suffer from limited representations of protein flexibility and solvation effects ,...	[ "Fragment-based drug discovery is based on a simple yet powerful principle: instead of trying to screen through the vast number of possible drug-like compounds during the drug discovery process , screen representative drug-like fragments , which are far fewer in number .", "Once a suitable fragment is discovered ...	2009
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "group-specific staining", "body weight", "medicine and health sciences", "hematoxylin staining", "brown adipose tissue", "animal models", "model organisms", "adipocytes", "physiological parameters", "connective tissue cells", "obesity", "experimental organism systems", "mitochondria", "ph...	Metabolic benefits of inhibition of p38α in white adipose tissue in obesity	journal.pbio.2004225	null	[ [ "White adipose tissue ( WAT ) and brown adipose tissue ( BAT ) are two major types of adipose tissues , which play different physiological roles in whole-body energy homeostasis [1 , 2] .", "The main function of WAT is to store excess energy as triglycerides ( TGs ) for utilization during nutrient shortag...	[ "p38 has long been known as a central mediator of protein kinase A ( PKA ) signaling in brown adipocytes , which positively regulate the transcription of uncoupling protein 1 ( UCP-1 ) .", "However , the physiological role of p38 in adipose tissues , especially the white adipose tissue ( WAT ) , is largely unknow...	[ "The functional brown adipose tissue ( BAT ) identified in human adults consists of not only classic brown adipocytes but also brown-like adipocytes ( beige adipocytes ) , both of which are important for energy homeostasis .", "Due to the same ability to convert fat into heat as brown adipocytes , beige adipocyte...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "viral entry", "viral transmission and infection", "virology", "biology", "microbiology", "viral structure", "viral evolution" ]	The Merkel Cell Polyomavirus Minor Capsid Protein	journal.ppat.1003558	null	[ [ "The icosahedral polyomavirus capsid is constructed from 72 pentameric capsomers of the major capsid protein , VP1 [1] .", "VP1 mediates attachment of the virus to cell surface glycan receptors [2] , [3] , initiating infectious entry and delivery of the encapsidated circular ∼5 kb dsDNA viral genome to ho...	[ "The surface of polyomavirus virions is composed of pentameric knobs of the major capsid protein , VP1 .", "In previously studied polyomavirus species , such as SV40 , two interior capsid proteins , VP2 and VP3 , emerge from the virion to play important roles during the infectious entry process .", "Translation...	[ "Merkel cell polyomavirus ( MCV or MCPyV ) is a recently discovered member of the viral family Polyomaviridae .", "The virus plays a causal role in Merkel cell carcinoma , a highly lethal form of skin cancer .", "MCV encodes a major capsid protein , VP1 , which forms the non-enveloped surface of the virion .", ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "biology" ]	Fatal Prion Disease in a Mouse Model of Genetic E200K Creutzfeldt-Jakob Disease	journal.ppat.1002350	null	[ [ "Inherited prion diseases , such as gCJD and Gerstmann–Sträussler–Scheinker ( GSS ) , are autosomal dominant disorders linked to mutations in the gene encoding the prion protein ( PrP ) , denominated PRNP [1] , [2] .", "The largest focus of gCJD was identified among Libyan Jews carrying a missense mutatio...	[ "Genetic prion diseases are late onset fatal neurodegenerative disorders linked to pathogenic mutations in the prion protein-encoding gene , PRNP .", "The most prevalent of these is the substitution of Glutamate for Lysine at codon 200 ( E200K ) , causing genetic Creutzfeldt-Jakob disease ( gCJD ) in several clus...	[ "Inherited prion diseases , such as genetic CJD , are dominant disorders linked to mutations in the gene encoding the prion protein , PrP .", "Since therapeutic intervention in all types of human prion diseases has failed , we propose that therapeutic efforts should be directed mostly to the development of preven...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell physiology", "protein interactions", "applied mathematics", "simulation and modeling", "algorithms", "receptor physiology", "mathematics", "protein structure prediction", "protein structure", "sequence motif analysis", "protein structure databases", "research and analysis methods", "se...	High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock	journal.pcbi.1005905	null	[ [ "Proteins are the workhorses inside living cells , and interactions among them are critical for various important biological processes [1] .", "A significant fraction of these interactions ( 15–40% ) [2] are peptide mediated , where a short stretch of residues from one partner contributes most to its bind...	[ "Peptide-protein interactions contribute a significant fraction of the protein-protein interactome .", "Accurate modeling of these interactions is challenging due to the vast conformational space associated with interactions of highly flexible peptides with large receptor surfaces .", "To address this challenge...	[ "Peptide-protein interactions are crucial components of various important biological processes in living cells .", "High-resolution structural information of such interactions provides insight about the underlying biophysical principles governing the interactions , and a starting point for their targeted manipula...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "animal models", "medicine", "applied chemistry", "nuclear magnetic resonance", "model organisms", "chemistry", "biology", "computational biology", "metabolic networks", "biophysics", "rat", "cardiovascular", "chemical properties" ]	Sensitivity Analysis of Flux Determination in Heart by H218O -provided Labeling Using a Dynamic Isotopologue Model of Energy Transfer Pathways	journal.pcbi.1002795	null	[ [ "In heart , the mechanisms that ensure energy production meets demand over a wide range of workloads , remains unclear .", "Fundamental to this search is an accurate understanding of the recycling fluxes of ATP , ADP , Pi , and phosphocreatine ( PCr ) between the mitochondrial inner membrane space and the...	[ "To characterize intracellular energy transfer in the heart , two organ-level methods have frequently been employed: inversion and saturation transfer , and dynamic labeling .", "Creatine kinase ( CK ) fluxes obtained by following oxygen labeling have been considerably smaller than the fluxes determined by satura...	[ "In heart , the movement of energy metabolites between force-producing myosin , other ATPases , and mitochondria is vital for its function and closely related to heart pathologies .", "In addition to diffusion , transport of ATP , ADP , Pi , and phosphocreatine occurs along parallel pathways such as the adenylate...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "analytical chemistry", "chemistry", "biology" ]	Modeling of the N-Glycosylated Transferrin Receptor Suggests How Transferrin Binding Can Occur within the Surface Coat of Trypanosoma brucei	journal.ppat.1002618	null	[ [ "The tsetse-transmitted Trypanosoma brucei group of parasites cause human African trypanosomiasis and nagana in cattle and constitute a serious health problem for people and livestock in 36 countries of sub-Saharan Africa .", "T . brucei exists in the mammalian host as the bloodstream form trypomastigote ...	[ "The transferrin receptor of bloodstream form Trypanosoma brucei is a heterodimer encoded by expression site associated genes 6 and 7 .", "This low-abundance glycoprotein with a single glycosylphosphatidylinositol membrane anchor and eight potential N-glycosylation sites is located in the flagellar pocket .", "...	[ "The tsetse fly transmitted parasite that causes human African trypanosomiasis , or sleeping sickness , scavenges iron from the bloodstream of the infected individual so that it can live , multiply and ultimately cause disease .", "To do this , it places a glycoprotein ( a protein with carbohydrate chains attache...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "cell biology", "genetics and genomics", "eukaryotes", "computational biology" ]	Bottleneck Genes and Community Structure in the Cell Cycle Network of S. pombe	journal.pcbi.0030103	null	[ [ "The cell cycle is a highly controlled ordered set of events , culminating in cell division into two daughter cells .", "The cell division requires doubling of the genome ( DNA ) during the synthesis phase ( S phase ) and halving of that genome during mitosis ( M phase ) .", "The period between M and ...	[ "The identification of cell cycle–related genes is still a difficult task , even for organisms with relatively few genes such as the fission yeast .", "Several gene expression studies have been published on S . pombe showing similarities but also discrepancies in their results .", "We introduce a network in whi...	[ "Because of the diversity in technological and analytical approaches , published microarray studies on a given organism show similarities as well as differences .", "While a great amount of data is now available , there is a general need for comprehensive methodologies that would allow us to analyze and compare a...	2007
[ "Introduction", "Methods", "Results and discussion" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "health services research", "sociology", "tropical diseases", "geographical locations", "social sciences", "health care", "bacterial diseases", "research design", "scientists", "signs and symptoms", "ulcers", "neglected t...	Developing a Buruli ulcer community of practice in Bankim, Cameroon: A model for Buruli ulcer outreach in Africa	journal.pntd.0006238	null	[ [ "Buruli ulcer ( BU ) is one of several neglected tropical skin diseases that afflict the rural population of sub-Saharan Africa , especially the poor living in areas with limited access to health infrastructure [1 , 2] .", "BU stands out as one of the most disabling of all neglected tropical diseases .", ...	[ "In the Cameroon , previous efforts to identify Buruli ulcer ( BU ) through the mobilization of community health workers ( CHWs ) yielded poor results .", "In this paper , we describe the successful creation of a BU community of practice ( BUCOP ) in Bankim , Cameroon composed of hospital staff , former patients ...	[ "Buruli ulcer ( BU ) is a neglected tropical disease primarily found in West Africa largely effecting the rural poor .", "BU has a known cause and cure , but an unknown route of transmission and a poorly understood incubation period .", "If not treated early and in a timely manner , BU often progresses to an ad...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology/germ cells" ]	OAZ-t/OAZ3 Is Essential for Rigid Connection of Sperm Tails to Heads in Mouse	journal.pgen.1000712	null	[ [ "As many as 15% of human couples [1] are infertile , and male infertility is associated with about half of these cases .", "A decrease in sperm production has recently been reported [1] .", "Although advances in medical technology have allowed some infertile couples to have children , more than half o...	[ "Polyamines are known to play important roles in the proliferation and differentiation of many types of cells .", "Although considerable amounts of polyamines are synthesized and stored in the testes , their roles remain unknown .", "Ornithine decarboxylase antizymes ( OAZs ) control the intracellular concentra...	[ "Polyamines are essential for cell proliferation and differentiation , but their role in these processes is unknown .", "Ornithine decarboxylase antizymes ( OAZs ) are enzymes that control the concentration of polyamines in cells .", "To elucidate the role of one of these enzymes , OAZ-t , in the regulation of ...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "biology and life sciences", "medicine and health sciences" ]	Heterogeneous Feeding Patterns of the Dengue Vector, Aedes aegypti, on Individual Human Hosts in Rural Thailand	journal.pntd.0003048	null	[ [ "Dengue is the most important arboviral diseases of humans worldwide .", "It occurs throughout most tropical regions .", "An estimated 390 million people are infected each year and approximately 96 million people suffer from clinically apparent disease annually [1] , [2] .", "Aedes aegypti is the ...	[ "Mosquito biting frequency and how bites are distributed among different people can have significant epidemiologic effects .", "An improved understanding of mosquito vector-human interactions would refine knowledge of the entomological processes supporting pathogen transmission and could reveal targets for minimi...	[ "Dengue , a potentially lethal infection impacting hundreds of millions of human lives annually , is caused by viruses transmitted during mosquito blood feeding .", "With no vaccine or treatment commercially available , understanding the underlying factors linked to virus exposure is critical for developing more ...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "b vitamins", "invertebrates", "species colonization", "ecology and environmental sciences", "medicine and health sciences", "chemical compounds", "invasive species", "sociology", "social sciences", "diet", "animals", "wolbachia", "organic compounds", "social systems", "riboflavin", "a...	Symbiotic microbiota may reflect host adaptation by resident to invasive ant species	journal.ppat.1007942	null	[ [ "Rapid development of global trade and travel have created conditions for long-distance migration and concomitantly increased the threat of biological invasion by exotic species [1] .", "Invasive species can affect the distribution , abundance and reproduction of native taxa [2 , 3] and disturb the struct...	[ "Exotic invasive species can influence the behavior and ecology of native and resident species , but these changes are often overlooked .", "Here we hypothesize that the ghost ant , Tapinoma melanocephalum , living in areas that have been invaded by the red imported fire ant , Solenopsis invicta , displays behavi...	[ "Insects display a wide range of dependence on symbiotic bacteria for basic functions .", "Responses by resident species to selective pressures imposed by invasive species , as well as specific underlying mechanisms that give rise to these responses are still poorly understood .", "Here we investigate the role ...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "public health and epidemiology", "pediatrics and child health" ]	The High Burden of Cholera in Children: Comparison of Incidence from Endemic Areas in Asia and Africa	journal.pntd.0000173	null	[ [ "Cholera is an acute , diarrheal illness caused by infection of the intestine with O1 or O139 serogroups of Vibrio cholerae [1] .", "Profuse watery diarrhea and vomiting can lead to dehydration and shock .", "Without treatment , death can occur within hours .", "Oral and intravenous rehydration th...	[ "Cholera remains an important public health problem .", "Yet there are few reliable population-based estimates of laboratory-confirmed cholera incidence in endemic areas around the world .", "We established treatment facility–based cholera surveillance in three sites in Jakarta ( Indonesia ) , Kolkata ( India )...	[ "Cholera is an often forgotten disease affecting the world's forgotten people .", "When a large cholera outbreak occurs , the disease appears briefly on the radar of public attention .", "Some unfortunate populations around the world suffer recurrent episodes of cholera but their plight goes unnoticed .", "We...	2008
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "molecular biology" ]	Loop-Mediated Isothermal Amplification (LAMP) Method for Rapid Detection of Trypanosoma brucei rhodesiense	journal.pntd.0000147	null	[ [ "Human African trypanosomiasis is endemic in tropical Africa .", "In eastern and southern Africa the disease is caused by Trypanosoma brucei rhodesiense , while T . b .", "gambiense infections are common in central and West Africa .", "T . b .", "rhodesiense causes an acute form of disease , w...	[ "Loop-mediated isothermal amplification ( LAMP ) of DNA is a novel technique that rapidly amplifies target DNA under isothermal conditions .", "In the present study , a LAMP test was designed from the serum resistance-associated ( SRA ) gene of Trypanosoma brucei rhodesiense , the cause of the acute form of Afric...	[ "Control of human African trypanosomiasis ( HAT ) or sleeping sickness relies on diagnosis and treatment of infected patients .", "However , the diagnostic tests in routine use have limited sensitivity , due to a characteristically low parasitaemia in infected individuals .", "Differentiation of infections by T...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/animal genetics", "microbiology/innate immunity", "immunology/innate immunity", "genetics and genomics/genetics of disease", "infectious diseases/bacterial infections", "microbiology/cellular microbiology and pathogenesis" ]	Susceptibility to Anthrax Lethal Toxin-Induced Rat Death Is Controlled by a Single Chromosome 10 Locus That Includes rNlrp1	journal.ppat.1000906	null	[ [ "Anthrax lethal toxin ( LT ) , a major virulence factor of Bacillus anthracis , is composed of two proteins , lethal factor ( LF ) and protective antigen ( PA ) .", "PA binds to cellular receptors and facilitates LF entry into the cytosol ( for review see [1] ) .", "LF is a protease which cleaves and ...	[ "Anthrax lethal toxin ( LT ) is a bipartite protease-containing toxin and a key virulence determinant of Bacillus anthracis .", "In mice , LT causes the rapid lysis of macrophages isolated from certain inbred strains , but the correlation between murine macrophage sensitivity and mouse strain susceptibility to to...	[ "Inflammasomes are multiprotein cytoplasmic complexes that respond to a variety of danger signals by activating the host innate immune response .", "The sensor components of these complexes are NLR ( NOD-like receptor ) proteins .", "In this report , a recombinant inbred rat strain collection was used to geneti...	2010
[ "Introduction", "Construction of GRN model", "Results", "Discussion", "Models" ]	[]	Pluripotency, Differentiation, and Reprogramming: A Gene Expression Dynamics Model with Epigenetic Feedback Regulation	journal.pcbi.1004476	null	[ [ "In multicellular organisms , cells that exhibit stemness during development can both self-renew and differentiate into other cell types .", "In contrast , differentiated cells lose the ability to further differentiate into other cell types and terminally differentiated cells can only self-renew .", "...	[ "Embryonic stem cells exhibit pluripotency: they can differentiate into all types of somatic cells .", "Pluripotent genes such as Oct4 and Nanog are activated in the pluripotent state , and their expression decreases during cell differentiation .", "Inversely , expression of differentiation genes such as Gata6 ...	[ "Characterization of pluripotent states , in which cells can both self-renew and differentiate , and the irreversible loss of pluripotency are important research areas in developmental biology .", "In particular , an understanding of these processes is essential to the reprogramming of cells for biomedical applic...	2015
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "genome-wide association studies", "developmental biology", "genetic mutation", "gene expression", "genetics", "epigenetics", "biology", "dna modification", "genetics and genomics", "cell differentiation", "dna transcription", "histone modification" ]	DNA Methylation and Histone Modifications Regulate De Novo Shoot Regeneration in Arabidopsis by Modulating WUSCHEL Expression and Auxin Signaling	journal.pgen.1002243	null	[ [ "Differentiated somatic tissues of plants can be reprogrammed to generate various organs , a process called de novo organogenesis .", "This feature is not only critical for in vitro plant propagation and application of biotechnology , but also provides a good experimental system for understanding regulato...	[ "Plants have a profound capacity to regenerate organs from differentiated somatic tissues , based on which propagating plants in vitro was made possible .", "Beside its use in biotechnology , in vitro shoot regeneration is also an important system to study de novo organogenesis .", "Phytohormones and transcript...	[ "Plants have a strong ability to generate organs from differentiated somatic tissues .", "Due to this feature , shoot regeneration in vitro has been used as an important way for producing whole plants in agriculture and biotechnology .", "Phytohormones and the transcription factor WUSCHEL ( WUS ) are essential ...	2011
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "evolutionary biology/microbial evolution and genomics", "computational biology/systems biology", "computational biology/genomics" ]	Loss of Genetic Redundancy in Reductive Genome Evolution	journal.pcbi.1001082	null	[ [ "Living organisms evolved to be functional in frequently harsh and variable environments , buffering internal molecular noise , genetic variation and unpredictable environmental fluctuations .", "Such ability is termed robustness [1] .", "One common source of robustness is genetic redundancy , in whic...	[ "Biological systems evolved to be functionally robust in uncertain environments , but also highly adaptable .", "Such robustness is partly achieved by genetic redundancy , where the failure of a specific component through mutation or environmental challenge can be compensated by duplicate components capable of pe...	[ "Bacteria have found many niches in which to live , and one of them is inside eukaryotic cells .", "These intracellular bacteria include endosymbionts like Buchnera aphidicola , which provides its host , an aphid , with essential amino acids , as well as many pathogenic bacteria such as Mycobacterium leprae and R...	2011
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling	journal.pcbi.1004343	null	[ [ "Homology modeling is by far the most widely used computational approach to predict the 3D structures of proteins , and almost all protein structure prediction servers rely chiefly on homology modeling , as seen in the community-wide blind benchmark “Critical Assessment of Techniques for Protein Structure Pre...	[ "Homology modeling predicts the 3D structure of a query protein based on the sequence alignment with one or more template proteins of known structure .", "Its great importance for biological research is owed to its speed , simplicity , reliability and wide applicability , covering more than half of the residues i...	[ "Since a protein’s function is largely determined by its structure , predicting a protein’s structure from its amino acid sequence can be very useful to understand its molecular functions and its role in biological pathways .", "By far the most widely used computational approach for protein structure prediction r...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "biochemistry", "infectious diseases", "veterinary diseases", "proteins", "zoonotic diseases", "genetics", "biology", "parasitic diseases", "zoology", "biophysics", "genetics and genomics", "veterinary science" ]	Echinococcus granulosus Antigen B Structure: Subunit Composition and Oligomeric States	journal.pntd.0001551	null	[ [ "Echinococcus granulosus is the causative agent of cystic hydatid disease ( CHD ) , a worldwide zoonotic infection that affects humans and livestock [1] .", "Antigen B ( AgB ) is the major protein secreted by the E . granulosus pathogenic larval stage ( metacestode or hydatid cyst ) .", "Since its fir...	[ "Antigen B ( AgB ) is the major protein secreted by the Echinococcus granulosus metacestode and is involved in key host-parasite interactions during infection .", "The full comprehension of AgB functions depends on the elucidation of several structural aspects that remain unknown , such as its subunit composition...	[ "Antigen B ( AgB ) is the major secretory protein of the Echinococcus granulosus hydatid cyst , the causative agent of cystic hydatid disease .", "Structurally , AgB is a multisubunit protein formed by 8-kDa subunits , but it is not known which subunits are secreted by a single parasite ( cyst ) and how they inte...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Hairless Streaks in Cattle Implicate TSR2 in Early Hair Follicle Formation	journal.pgen.1005427	null	[ [ "In 1901 , the German dermatologist Alfred Blaschko proposed that congenital linear skin lesions could develop independently of the nervous system [1] .", "Blaschko observed a common non-random developmental pattern of the skin and described it extensively depicting the shape of the pattern lines [1 , 2] ...	[ "Four related cows showed hairless streaks on various parts of the body with no correlation to the pigmentation pattern .", "The stripes occurred in a consistent pattern resembling the lines of Blaschko .", "The non-syndromic hairlessness phenotype observed occurred across three generations of a single family a...	[ "The identification of causal mutations of rare monogenic disorders provides an insight into the function of single genes .", "We herein report an example which demonstrates that the bovine species presents an excellent system for identifying these inherited phenotypes .", "The individual health status of moder...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Disproportionate Contributions of Select Genomic Compartments and Cell Types to Genetic Risk for Coronary Artery Disease	journal.pgen.1005622	null	[ [ "Coronary artery disease ( CAD ) and myocardial infarction ( MI ) remain among the leading causes of infirmity and death worldwide despite advances in and widespread adoption of medical therapies treating this disease .", "Studies have shown a large genetic component for CAD , with the heritability estima...	[ "Large genome-wide association studies ( GWAS ) have identified many genetic loci associated with risk for myocardial infarction ( MI ) and coronary artery disease ( CAD ) .", "Concurrently , efforts such as the National Institutes of Health ( NIH ) Roadmap Epigenomics Project and the Encyclopedia of DNA Elements...	[ "Coronary artery disease ( CAD ) and its subcomponent , myocardial infarction ( MI ) , are the leading causes of infirmity and death worldwide .", "Large-scale genetic association studies have identified many genetic markers associated with CAD and MI .", "However , it has been difficult to determine the precis...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	STAT2 Knockout Syrian Hamsters Support Enhanced Replication and Pathogenicity of Human Adenovirus, Revealing an Important Role of Type I Interferon Response in Viral Control	journal.ppat.1005084	null	[ [ "Human adenoviruses ( Ads ) are non-enveloped , double-stranded DNA viruses that are classified into over 60 types ( Ad1 , Ad2 , etc . ) , which in turn are grouped into 7 species ( A to G ) ( for a review on Ad biology , see [1 , 2] ) .", "Infection with the more frequent types is very common; about 40 t...	[ "Human adenoviruses have been studied extensively in cell culture and have been a model for studies in molecular , cellular , and medical biology .", "However , much less is known about adenovirus replication and pathogenesis in vivo in a permissive host because of the lack of an adequate animal model .", "Pres...	[ "The biology of human adenoviruses has been studied extensively; however , much less is known about the replication and pathogenesis of the virus in a permissive host .", "Our laboratory pioneered the use of Syrian hamsters to study the pathogenesis of human adenoviruses .", "Syrian hamsters are permissive for ...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "bacteriology", "cell death", "organismal evolution", "microbial mutation", "genome evolution", "cell processes", "population genetics", "microbiology", "developmental biology", "mutation", "molecular cell biology", "cell growth", "microbial evolution", "molecular genetics", "population ...	Selection of Orphan Rhs Toxin Expression in Evolved Salmonella enterica Serovar Typhimurium	journal.pgen.1004255	null	[ [ "Bacteria often reside in complex communities such as biofilms in which cells from multiple species touch one another in a three-dimensional network [1] .", "These environments provide opportunities for cellular interactions , yet the mechanisms underlying contact-dependent competition and cooperation hav...	[ "Clonally derived bacterial populations exhibit significant genotypic and phenotypic diversity that contribute to fitness in rapidly changing environments .", "Here , we show that serial passage of Salmonella enterica serovar Typhimurium LT2 ( StLT2 ) in broth , or within a mouse host , results in selection of an...	[ "Salmonella Typhimurium is a bacterium that causes intestinal diseases in a number of animals including humans .", "In mice , this pathogen invades tissues , causing symptoms similar to typhoid fever .", "In an effort to understand the evolution of this pathogen , we grew S . Typhimurium in either liquid broth ...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "systems biology", "fungi", "mycology", "microbial physiology", "biology and life sciences", "microbiology", "biophysics", "organisms", "yeast" ]	Yeast Mating and Image-Based Quantification of Spatial Pattern Formation	journal.pcbi.1003690	null	[ [ "Cells communicate with each other by detecting and responding to external cues and stimuli .", "In cellular systems one can find several examples where cells coordinate growth in specific regions by sensing and responding to small differences in the concentrations of substances that provide positional in...	[ "Communication between cells is a ubiquitous feature of cell populations and is frequently realized by secretion and detection of signaling molecules .", "Direct visualization of the resulting complex gradients between secreting and receiving cells is often impossible due to the small size of diffusing molecules ...	[ "Haploid budding yeast cells cannot actively move to find a mating partner , like some flagellated bacteria do .", "Instead they must grow a so-called shmoo – a mating projection – precisely into the direction of a potential partner .", "They communicate with each other by releasing pheromones into their enviro...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology", "biology", "microbiology", "host-pathogen interaction" ]	3D Reconstruction of VZV Infected Cell Nuclei and PML Nuclear Cages by Serial Section Array Scanning Electron Microscopy and Electron Tomography	journal.ppat.1002740	null	[ [ "Varicella-zoster virus ( VZV ) is an alphaherpesvirus that causes varicella ( chickenpox ) and herpes zoster ( shingles ) [1] .", "The host range of VZV is restricted to humans and its life cycle in the human host depends upon tropism for skin , lymphocytes and neurons in sensory ganglia , where it estab...	[ "Varicella-zoster virus ( VZV ) is a human alphaherpesvirus that causes varicella ( chickenpox ) and herpes zoster ( shingles ) .", "Like all herpesviruses , the VZV DNA genome is replicated in the nucleus and packaged into nucleocapsids that must egress across the nuclear membrane for incorporation into virus pa...	[ "Varicella-zoster virus ( VZV ) , the cause of varicella and zoster , is a human herpesvirus that replicates in the host cell nucleus where viral genomes are packaged into virion nucleocapsids .", "We have recently identified antiviral PML ( promyelocytic leukemia ) nuclear cages that sequester VZV nucleocapsids ...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Cell Cycle–Dependent Differentiation Dynamics Balances Growth and Endocrine Differentiation in the Pancreas	journal.pbio.1002111	During the development of the pancreas, the asymmetric or symmetric differentiation of progenitor cells into endocrine cells results from stochastic priming of mitotic progenitors at different stages of the cell cycle.	[ [ "The pancreas is an organ performing vital exocrine and endocrine roles in nutrient metabolism and glucose homeostasis .", "In the mouse , multipotent pancreatic progenitor cells ( MPCs ) emerge from the endoderm around embryonic day 9 . 0 ( E9 . 0 ) [1] .", "This population , characterized by the exp...	[ "Organogenesis relies on the spatiotemporal balancing of differentiation and proliferation driven by an expanding pool of progenitor cells .", "In the mouse pancreas , lineage tracing at the population level has shown that the expanding pancreas progenitors can initially give rise to all endocrine , ductal , and ...	[ "In order to form organs of the right size and cell composition , progenitor cells must balance their proliferation and their differentiation into functional cell types .", "Here we study how individual progenitor cells in the developing pancreas execute their choices to either expand their pool or differentiate ...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/comparative genomics", "genetics and genomics/genetics of the immune system" ]	A Novel System of Polymorphic and Diverse NK Cell Receptors in Primates	journal.pgen.1000688	null	[ [ "Natural killer ( NK ) cells are bone marrow-derived lymphocytes that form an essential part of the immune response against pathogens and are involved in the elimination of tumour cells .", "Equipped with a diverse array of germline-encoded receptors that are able to mediate inhibitory or activating signa...	[ "There are two main classes of natural killer ( NK ) cell receptors in mammals , the killer cell immunoglobulin-like receptors ( KIR ) and the structurally unrelated killer cell lectin-like receptors ( KLR ) .", "While KIR represent the most diverse group of NK receptors in all primates studied to date , includin...	[ "Most receptors of natural killer ( NK ) cells interact with highly polymorphic major histocompatibility complex ( MHC ) class I molecules and thereby regulate the activity of NK cells against infected or malignant target cells .", "Whereas humans , apes , and Old and New World monkeys use the family of killer ce...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "viral latency", "genetic mutation", "cytokines", "viruses and cancer", "immune activation", "viral enzymes", "immunology", "microbiology", "host-pathogen interaction", "membrane receptor signaling", "immunologic techniques", "animal models of infection", "stat signaling family", "signalin...	The Anti-interferon Activity of Conserved Viral dUTPase ORF54 is Essential for an Effective MHV-68 Infection	journal.ppat.1002292	null	[ [ "Virus infection induces numerous immune responses in the host , the earliest of which is the innate immune response [1] , [2] .", "The innate immune response is comprised of many layers of non-specific defense , including anatomical barriers , such as skin and mucosa , the complement system , inflammatio...	[ "Gammaherpesviruses such as KSHV and EBV establish lifelong persistent infections through latency in lymphocytes .", "These viruses have evolved several strategies to counteract the various components of the innate and adaptive immune systems .", "We conducted an unbiased screen using the genetically and biolog...	[ "Human gammaherpesviruses , Kaposi's sarcoma-associated herpesvirus and Epstein-Barr virus , are the cause of several malignancies , especially in patients immunocompromised due to HIV infection .", "The study of these human gammaherpesviruses is difficult due to their inability to replicate in cell culture and t...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "microbial mutation", "genetic mutation", "genome evolution", "chromosome structure and function", "population genetics", "microbiology", "genome sequencing", "model organisms", "mutation types", "microbial evolution", "forms of evolution", "microbial physiology", "chromosome biology", "bi...	Recurrent Rearrangement during Adaptive Evolution in an Interspecific Yeast Hybrid Suggests a Model for Rapid Introgression	journal.pgen.1003366	null	[ [ "Eukaryotic genome content and architecture can vary dramatically as populations of organisms evolve , or as populations of cells evolve during disease processes like cancer [1] , [2] .", "Chromosome number may change , resulting in polyploidy and/or aneuploidy , or chromosomes may be restructured by tran...	[ "Genome rearrangements are associated with eukaryotic evolutionary processes ranging from tumorigenesis to speciation .", "Rearrangements are especially common following interspecific hybridization , and some of these could be expected to have strong selective value .", "To test this expectation we created de n...	[ "Interspecific hybridization occurs when two different species mate and produce viable offspring .", "While hybrid offspring are usually sterile , like the mule , which results from a horse–donkey mating , sometimes they are fertile , creating new species .", "Indeed , many plant and animal species have arisen ...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences" ]	A Cross-sectional Serological Study of Cysticercosis, Schistosomiasis, Toxocariasis and Echinococcosis in HIV-1 Infected People in Beira, Mozambique	journal.pntd.0003121	null	[ [ "The study of HIV and helminth coinfection is a topic of great interest in endemic regions because little is known about the synergism that may exist between HIV and tisular helminths .", "Important questions remain regarding the increased susceptibility to helminths , HIV replication enhancement , worsen...	[ "Helminthic infections are highly endemic in Mozambique , due to limited access to healthcare and resources for disease prevention .", "Data on the subclinical prevalence of these diseases are scarce due to the fact that an immunological and imaging diagnosis is not often available in endemic areas .", "We cond...	[ "In Mozambique many parasitic diseases persist as a result of low living standards and environmental contamination from human and animal fecal waste .", "Parasites undermine the health of Mozambique's poorest inhabitants and will be difficult to eradicate without a considerable improvement in the sanitary conditi...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "genome-wide association studies", "animal types", "medicine and health sciences", "pathology and laboratory medicine", "variant genotypes", "vertebrates", "pets and companion animals", "dogs", "animals", "mammals", "genetic mapping", "signs and symptoms", "genome analysis", "sequence moti...	MKLN1 splicing defect in dogs with lethal acrodermatitis	journal.pgen.1007264	null	[ [ "Acrodermatitis enteropathica in humans ( OMIM #201100 ) is an inherited disorder of zinc metabolism .", "Affected patients display an inflammatory rash , diarrhea and a general failure to thrive [1–3] .", "This disease is caused by variants in the SLC39A4 gene encoding a zinc transporter that mediate...	[ "Lethal acrodermatitis ( LAD ) is a genodermatosis with monogenic autosomal recessive inheritance in Bull Terriers and Miniature Bull Terriers .", "The LAD phenotype is characterized by poor growth , immune deficiency , and skin lesions , especially at the paws .", "Utilizing a combination of genome wide associ...	[ "Lethal acrodermatitis ( LAD ) is an autosomal recessive hereditary disease in dogs .", "It is characterized by poor growth , immune deficiency and characteristic skin lesions of the paws and of the face .", "We mapped the LAD locus to a ~1 . 11 Mb segment on canine chromosome 14 .", "Whole genome sequence da...	2018
[ "Introduction", "Models", "Results", "Discussion" ]	[ "learning", "medicine and health sciences", "neurochemistry", "decision making", "nervous system", "dopaminergics", "social sciences", "electrophysiology", "neuroscience", "learning and memory", "simulation and modeling", "synaptic plasticity", "cognitive psychology", "cognition", "neuro...	Learning Reward Uncertainty in the Basal Ganglia	journal.pcbi.1005062	null	[ [ "In situations where actions are associated with rewards , knowledge of the reliability of rewards for alternative choices is critical for selecting the optimal action .", "Normative models have suggested that optimal foraging requires adaptively switching between risk aversion and risk seeking depending ...	[ "Learning the reliability of different sources of rewards is critical for making optimal choices .", "However , despite the existence of detailed theory describing how the expected reward is learned in the basal ganglia , it is not known how reward uncertainty is estimated in these circuits .", "This paper pres...	[ "To maximize their chances for survival , animals need to base their decisions not only on the average consequences of chosen actions , but also on the variability of the rewards resulting from these actions .", "For example , when an animal’s food reserves are depleted , it should prefer to forage in an area whe...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "plant anatomy", "microtubules", "biological cultures", "microbiology", "light microscopy", "viral structure", "plant science", "microscopy", "cell cultures", "protein structure", "confocal microscopy", "cellular structures and organelles", "flower anatomy", "cytoskeleton", "research and...	In cultured cells the baculovirus P10 protein forms two independent intracellular structures that play separate roles in occlusion body maturation and their release by nuclear disintegration	journal.ppat.1007827	null	[ [ "The Baculoviridae is a diverse family of insect-specific viruses that contain circular , supercoiled dsDNA genomes ranging from 80 to 180 kilobase pairs ( kbp ) [1 , 2] .", "Baculoviruses are characterised by rod shaped virions between 250–400 nm in length and 30–70 nm in diameter [3 , 4] that are embedd...	[ "P10 is a small , abundant baculovirus protein that accumulates to high levels in the very late stages of the infection cycle .", "It is associated with a number of intracellular structures and implicated in diverse processes from occlusion body maturation to nuclear stability and lysis .", "However , studies h...	[ "High-resolution 3D electron microscopy has revealed the complexity of structures formed by P10 , a small 10kDa protein that accumulates to very high levels in baculovirus-infected cells .", "We demonstrate the formation and presence of two distinct , possibly unique , P10 structures that account for the diverse ...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Analysis of Single Locus Trajectories for Extracting In Vivo Chromatin Tethering Interactions	journal.pcbi.1004433	null	[ [ "What can we learn about the local environment , the external and internal forces and the chromatin itself from the motion of a chromatin locus ?", "This motion can be driven by local diffusion and/or forces between monomers of the model polymer [1–3] .", "Monomers motion is highly correlated due the ...	[ "Is it possible to extract tethering forces applied on chromatin from the statistics of a single locus trajectories imaged in vivo ?", "Chromatin fragments interact with many partners such as the nuclear membrane , other chromosomes or nuclear bodies , but the resulting forces cannot be directly measured in vivo ...	[ "Is it possible to recover the local environment , the external and internal forces acting on a polymer from a single locus trajectories ?", "To study this question , we resolve this reverse cell biology problem by developing a method that uses in vivo live single locus trajectories to extract physical forces app...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "geomorphology", "invertebrates", "medicine and health sciences", "landforms", "hyraxes", "topography", "vertebrates", "sand flies", "parasitic diseases", "animals", "mammals", "parasitic protozoans", "diptera", "protozoans", "leishmania", "insect vectors", "cellular structures and o...	Ecology and seasonality of sandflies and potential reservoirs of cutaneous leishmaniasis in Ochollo, a hotspot in southern Ethiopia	journal.pntd.0007667	null	[ [ "Cutaneous leishmaniasis ( CL ) is a vector-borne disease caused by protozoa of the genus Leishmania and is listed as one of the neglected tropical diseases ( NTD ) [1] .", "It is characterized by nodules or ulcerative skin lesions , which can lead to secondary infections and disfiguring scars .", "In...	[ "Ochollo is a village in southern Ethiopia burdened with cutaneous leishmaniasis ( CL ) , where Phlebotomus pedifer is the only vector for Leishmania aethiopica and hyraxes are confirmed reservoir hosts .", "A detailed description of the different players of transmission , and the ecology and seasonality of the v...	[ "Zoonotic cutaneous leishmaniasis poses a considerable health problem in Ethiopia .", "Efficient disease control can only be accomplished when all players of transmission are well understood and taken into account .", "The aim of our study was to investigate in a village in the south , called Ochollo , whether ...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "neurological disorders/alzheimer disease", "mathematics/statistics", "computer science/systems and control theory", "radiology and medical imaging/magnetic resonance imaging" ]	Network Analysis of Intrinsic Functional Brain Connectivity in Alzheimer's Disease	journal.pcbi.1000100	null	[ [ "Alzheimer's disease ( AD ) is a neurodegenerative disorder characterized by progressive impairment of episodic memory and other cognitive domains resulting in dementia and , ultimately , death .", "Imaging studies in AD have begun a shift from studies of brain structure [1] , [2] to more recent studies h...	[ "Functional brain networks detected in task-free ( “resting-state” ) functional magnetic resonance imaging ( fMRI ) have a small-world architecture that reflects a robust functional organization of the brain .", "Here , we examined whether this functional organization is disrupted in Alzheimer's disease ( AD ) ."...	[ "Alzheimer's disease ( AD ) is a brain disorder characterized by progressive impairment of episodic memory and other cognitive domains resulting in dementia and , ultimately , death .", "Functional neuroimaging studies have identified brain regions that show abnormal brain function in AD .", "Although there is ...	2008
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "pediatrics and child health" ]	Clinically Unapparent Infantile Thiamin Deficiency in Vientiane, Laos	journal.pntd.0000969	null	[ [ "Beriberi , or clinically apparent thiamin deficiency , may present with a variety of syndromes including peripheral neuropathy , myocardial dysfunction , encephalopathy , hypoglycemia and lactic acidosis .", "With the advent of mechanical rice milling in the late 19th century , beriberi became a dominant...	[ "Beriberi occurs in Vientiane , Lao PDR , among breastfed infants .", "Clinical disease may be the tip of an iceberg with subclinical thiamin deficiency contributing to other illnesses .", "Thiamin treatment could improve outcome .", "A cohort of 778 sick infants admitted during one year without clinical evid...	[ "Infantile beriberi , or clinical thiamin ( vitamin B1 ) deficiency in infants , is a forgotten disease in Asia , where 100 years ago it was a major public health problem .", "Infants with this deficiency , commonly aged ∼ 2–3 months , present in cardiac failure but usually rapidly improve if given thiamin inject...	2011
[ "Introduction", "Models", "Results", "Discussion" ]	[ "sequencing techniques", "microbiome", "microbiology", "simulation and modeling", "next-generation sequencing", "metagenomics", "probability distribution", "mathematics", "genome analysis", "molecular biology techniques", "skewness", "microbial genomics", "research and analysis methods", "...	A marginalized two-part Beta regression model for microbiome compositional data	journal.pcbi.1006329	null	[ [ "In recent years , metagenomics studies have been growing rapidly due to the advances of next-generation sequencing ( NGS ) technologies [1] .", "Microbiota have been known to be associated with various diseases , e . g . , obesity and diabetes [2 , 3] , Crohn’s disease [4] , bacterial vaginosis [5] , and...	[ "In microbiome studies , an important goal is to detect differential abundance of microbes across clinical conditions and treatment options .", "However , the microbiome compositional data ( quantified by relative abundance ) are highly skewed , bounded in [0 , 1 ) , and often have many zeros .", "A two-part mo...	[ "Semi-continuous compositional data are typically analyzed using two-part models which separately describe the probability of zero values and the distribution of positive values .", "The second part of the model provides a conditional interpretation of covariate effects on the positive response .", "However , i...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "deletion mutation", "mitochondrial dna", "animals", "invertebrate genomics", "animal models", "mutation", "substitution mutation", "drosophila melanogaster", "model organisms", "experimental organism systems", "forms of dna", "mitochondria", "dna", "bioenergetics", "c...	Deleterious mitochondrial DNA point mutations are overrepresented in Drosophila expressing a proofreading-defective DNA polymerase γ	journal.pgen.1007805	null	[ [ "Mitochondria contain the electron transport chain complexes responsible for generation of most of a cell’s energy and also play crucial roles in Ca2+ buffering , metabolite synthesis , and apoptosis [1–3] .", "In addition to the ~1 , 000–2 , 000 nuclear genes that encode mitochondrial proteins , mitochon...	[ "Mitochondrial DNA ( mtDNA ) mutations cause severe maternally inherited syndromes and the accumulation of somatic mtDNA mutations is implicated in aging and common diseases .", "However , the mechanisms that influence the frequency and pathogenicity of mtDNA mutations are poorly understood .", "To address this...	[ "The energy needs of an animal cell are supplied by tiny organelles known as mitochondria .", "Each of the many mitochondria in a cell has a set of blueprints for making more mitochondria , known as mitochondrial DNA ( mtDNA ) .", "As animals age , their mtDNA acquires irreversible defects called mutations , wh...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Micro-Geographical Heterogeneity in Schistosoma mansoni and S. haematobium Infection and Morbidity in a Co-Endemic Community in Northern Senegal	journal.pntd.0002608	null	[ [ "Schistosomiasis is amongst the most common human parasitic diseases with over 230 million people affected worldwide [1] .", "More than 90% of them live in sub-Saharan Africa [2] .", "The two major species are Schistosoma mansoni and S . haematobium , which are co-endemic in many regions [3] .", "...	[ "Schistosoma mansoni and S . haematobium are co-endemic in many areas in Africa .", "Yet , little is known about the micro-geographical distribution of these two infections or associated disease within such foci .", "Such knowledge could give important insights into the drivers of infection and disease and as s...	[ "In the developing world , over 230 million people are infected with parasitic Schistosoma worms .", "Schistosoma mansoni and S . haematobium are the most abundant species in Africa , affecting the liver and urinary tract , respectively .", "Both parasites are spread through infested freshwater .", "Although ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology/persistence and latency", "gastroenterology and hepatology/hepatology", "virology/new therapies, including antivirals and immunotherapy", "virology/immune evasion", "immunology/immunity to infections" ]	Synergistic Reversal of Intrahepatic HCV-Specific CD8 T Cell Exhaustion by Combined PD-1/CTLA-4 Blockade	journal.ppat.1000313	null	[ [ "Virus-specific CD8 T cells become progressively exhausted during chronic viral infection due to increased level or duration of antigenic stimulation without sufficient CD4 help[1] .", "Among the CD28 family of costimulatory molecules , programmed death-1 ( PD-1 ) is an immune inhibitory receptor that is ...	[ "Viral persistence is associated with hierarchical antiviral CD8 T cell exhaustion with increased programmed death-1 ( PD-1 ) expression .", "In HCV persistence , HCV-specific CD8 T cells from the liver ( the site of viral replication ) display increased PD-1 expression and a profound functional impairment that i...	[ "Hepatitis C virus ( HCV ) is an important human pathogen with a high rate of persistence associated with chronic liver disease that can progress to cirrhosis and hepatocellular carcinoma .", "Chronic HCV infection occurs in the setting of impaired antiviral T cells that over-express an inhibitory receptor PD-1 (...	2009
[ "Introduction", "Discussion", "Materials and Methods" ]	[]	Recurrent Domestication by Lepidoptera of Genes from Their Parasites Mediated by Bracoviruses	journal.pgen.1005470	null	[ [ "Unlike bacteria , which have obtained a notable proportion of their genes through the acquisition of sequences from distantly related organisms , eukaryotes are generally thought to evolve mainly through the modification of existing genetic information [1] .", "However evidence of horizontal gene transfe...	[ "Bracoviruses are symbiotic viruses associated with tens of thousands of species of parasitic wasps that develop within the body of lepidopteran hosts and that collectively parasitize caterpillars of virtually every lepidopteran species .", "Viral particles are produced in the wasp ovaries and injected into host ...	[ "Eukaryotes are generally thought to evolve mainly through the modification of existing genetic information .", "However , evidence of horizontal gene transfer ( HGT ) in eukaryotes-the accidental acquisition of a novel gene from another species , allowing acquisition of novel traits—is now recognized as an impor...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "phosphorylation", "medicine and health sciences", "gene regulation", "immunology", "brassica", "dna transcription", "model organisms", "experimental organism systems", "genome analysis", "sequence motif analysis", "plants", "arabidopsis thaliana", "research and analysis methods", "sequenc...	INDETERMINATE-DOMAIN 4 (IDD4) coordinates immune responses with plant-growth in Arabidopsis thaliana	journal.ppat.1007499	null	[ [ "Plants and animals use pattern recognition receptors ( PRRs ) to rapidly activate defense signaling pathways and immune responses upon pathogen attack [1 , 2] .", "PRR receptors and their associated signaling components possess a wide range of similarities in mammals , plants and invertebrates [3 , 4] ."...	[ "INDETERMINATE DOMAIN ( IDD ) / BIRD proteins are a highly conserved plant-specific family of transcription factors which play multiple roles in plant development and physiology .", "Here , we show that mutation in IDD4/IMPERIAL EAGLE increases resistance to the hemi-biotrophic pathogen Pseudomonas syringae , ind...	[ "This work illustrates the involvement of the IDD family member 4 in the regulation of defense responses against hemibiotrophic pathogens and in processes governing plant growth .", "IDD4 is embedded in widely-ramified regulatory pathways and exerts transcriptional control of key factors that shape and balance gr...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "chemical bonding", "medicine and health sciences", "immune physiology", "crystal structure", "chemical compounds", "immunology", "condensed matter physics", "microbiology", "viral structure", "organic compounds", "crystals", "materials science", "amino acids", "crystallography", "antibo...	Alternative conformations of a major antigenic site on RSV F	journal.ppat.1007944	null	[ [ "Respiratory syncytial virus ( RSV ) is a ubiquitous pneumovirus which infects nearly all children in the U . S . by the age of two , with repeated infections occurring throughout life [1] .", "RSV is a common cause of acute lower respiratory tract infections in young children and the elderly , and in 201...	[ "The respiratory syncytial virus ( RSV ) fusion ( F ) glycoprotein is a major target of neutralizing antibodies arising from natural infection , and antibodies that specifically bind to the prefusion conformation of RSV F generally demonstrate the greatest neutralization potency .", "Prefusion-stabilized RSV F va...	[ "Respiratory syncytial virus ( RSV ) is a pervasive pathogen that causes severe lower respiratory tract infections , leading to ~100 , 000 deaths globally each year and hundreds of millions of dollars in healthcare costs .", "However , despite its prevalence , there is no vaccine for RSV and the only available th...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "blood cells", "cell motility", "medicine and health sciences", "immune cells", "body fluids", "pathology and laboratory medicine", "immunology", "tropical diseases", "lymph nodes", "signs and symptoms", "lymphatic system", "paracoccidioidomycosis", "neglected tropical diseases", "fungal d...	Functional and phenotypic evaluation of eosinophils from patients with the acute form of paracoccidioidomycosis	journal.pntd.0005601	null	[ [ "Paracoccidioidomycosis ( PCM ) is a systemic mycosis caused by dimorphic fungi of the Paracoccidioides genus .", "It is the most prevalent systemic mycosis of Latin America and , in Brazil , it is the leading cause of death among immunocompetent patients [1–4] .", "PCM is caused by inhalation of envi...	[ "Eosinophilia is a typical finding of the acute/juvenile form of paracoccidioidomycosis ( PCM ) , a systemic mycosis endemic in Latin America .", "This clinical form is characterized by depressed cellular immune response and production of Th2 cytokines .", "Moreover , it has been shown that the increased number...	[ "Paracoccidioidomycosis ( PCM ) is a fungal disease endemic of some Latin America countries .", "The acute clinical form of the disease , which affects children and young adults , is the most severe form of PCM .", "It is characterized by a depressed T cell immunity and increased number of blood eosinophils tha...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "systems biology", "evolutionary modeling", "genetics", "regulatory networks", "biology", "computational biology", "gene networks", "genetics and genomics" ]	Criticality Is an Emergent Property of Genetic Networks that Exhibit Evolvability	journal.pcbi.1002669	null	[ [ "Several models of network growth and evolution have been devised to generate networks with specific topological properties ( such as hub-like structures , [10] , [11] ) or with a particular type of dynamical behavior [12] , [13] .", "The ‘dynamics’ of a genetic network , that is , the collective change o...	[ "Accumulating experimental evidence suggests that the gene regulatory networks of living organisms operate in the critical phase , namely , at the transition between ordered and chaotic dynamics .", "Such critical dynamics of the network permits the coexistence of robustness and flexibility which are necessary to...	[ "Dynamically critical systems are those which operate at the border of a phase transition between two behavioral regimes often present in complex systems: order and disorder .", "Critical systems exhibit remarkable properties such as fast information processing , collective response to perturbations or the abilit...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Dengue Virus Non-structural Protein 1 Modulates Infectious Particle Production via Interaction with the Structural Proteins	journal.ppat.1005277	null	[ [ "Dengue is the most prevalent arthropod-borne viral disease affecting around 400 million people worldwide and causing around 25 , 000 deaths per year [1] .", "Dengue virus ( DENV ) infections can lead to a wide range of clinical manifestations , ranging from asymptomatic to life-threatening dengue hemorrh...	[ "Non-structural protein 1 ( NS1 ) is one of the most enigmatic proteins of the Dengue virus ( DENV ) , playing distinct functions in immune evasion , pathogenesis and viral replication .", "The recently reported crystal structure of DENV NS1 revealed its peculiar three-dimensional fold; however , detailed informa...	[ "Dengue virus ( DENV ) is a major arthropod-borne human pathogen , infecting more than 400 million individuals annually worldwide; however , neither a therapeutic drug nor a prophylactic vaccine is currently available .", "Amongst the DENV proteins , non-structural protein 1 ( NS1 ) is one of the most enigmatic ,...	2015

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