Split (3)

train · 24.8k rows

headings list	keywords list	title stringlengths 20 281	id stringlengths 20 20	toc stringlengths 57 522 ⌀	sections list	abstract list	summary list	year stringclasses 13 values
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "applied microbiology", "medicine", "small intestine", "infectious diseases", "soil-transmitted helminths", "drug research and development", "gastroenterology and hepatology", "drugs and devices", "global health", "microbial control", "neglected tropical diseases", "biology", "microbiology",...	Bacillus thuringiensis-derived Cry5B Has Potent Anthelmintic Activity against Ascaris suum	journal.pntd.0002263	null	[ [ "Ascaris lumbricoides , the large roundworm , is the most common parasitic nematode infection of humans with estimates of more than one billion people infected worldwide in mostly lesser developed countries [1] .", "Chronic infections in humans are associated with growth and cognitive stunting , impaired ...	[ "Ascaris suum and Ascaris lumbricoides are two closely related geo-helminth parasites that ubiquitously infect pigs and humans , respectively .", "Ascaris suum infection in pigs is considered a good model for A . lumbricoides infection in humans because of a similar biology and tissue migration to the intestines ...	[ "Ascaris suum is an intestinal parasitic nematode of pigs that is very closely related to Ascaris lumbricoides , a major intestinal parasitic nematode of humans that infects more than one billion people worldwide .", "Because of reduced efficacy and the threat of resistance to the current small set of approved dr...	2013
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "biophysics/theory and simulation", "biochemistry/cell signaling and trafficking structures", "biochemistry/bioinformatics", "biochemistry/theory and simulation", "computational biology/molecular dynamics" ]	The Distinct Conformational Dynamics of K-Ras and H-Ras A59G	journal.pcbi.1000922	null	[ [ "Ras proteins couple cell-surface receptors to intracellular signaling cascades involved in cell proliferation , differentiation and development .", "Signal propagation through Ras is mediated by a regulated GTPase cycle that leads to active and inactive conformations with distinct affinity for downstream...	[ "Ras proteins regulate signaling cascades crucial for cell proliferation and differentiation by switching between GTP- and GDP-bound conformations .", "Distinct Ras isoforms have unique physiological functions with individual isoforms associated with different cancers and developmental diseases .", "Given the s...	[ "The proto-oncogene Ras mediates signaling pathways controlling cell proliferation and development by cycling between active and inactive conformational states .", "Mutations that affect the ability to switch between states are associated with over 25% of human tumors .", "However , despite much effort , detail...	2010
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases/hiv infection and aids", "virology/immunodeficiency viruses", "immunology/immunity to infections", "virology/vaccines" ]	Control of Viremia and Prevention of AIDS following Immunotherapy of SIV-Infected Macaques with Peptide-Pulsed Blood	journal.ppat.1000055	null	[ [ "Several attempts at immunotherapy of HIV using more conventional vaccines have thus far been poorly immunogenic and weakly efficacious in human trials [1] , [2] , [3] , [4] .", "The use of professional antigen-presenting cells such as dendritic cells to deliver HIV immunotherapies has shown strong immuno...	[ "Effective immunotherapies for HIV are needed .", "Drug therapies are life-long with significant toxicities .", "Dendritic-cell based immunotherapy approaches are promising but impractical for widespread use .", "A simple immunotherapy , reinfusing fresh autologous blood cells exposed to overlapping SIV pepti...	[ "Effective immunotherapies for HIV are needed .", "We assessed a simple technique , reinfusion of fresh blood cells incubating with overlapping SIV peptides ( Overlapping Peptide-pulsed Autologous ceLls , OPAL ) , in 36 randomly allocated SIV-infected monkeys .", "We analyzed this therapy for the stimulation of...	2008
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "cell cycle and cell division", "cell processes", "animals", "invertebrate genomics", "dna transcription", "animal models", "developmental biology", "drosophila melanogaster", "model organisms", "experimental organism systems", "morphogenesis", "drosophila", "research and ...	Cyclin G and the Polycomb Repressive complexes PRC1 and PR-DUB cooperate for developmental stability	journal.pgen.1007498	null	[ [ "Developmental stability has been described as the set of processes that buffer disruption of developmental trajectories for a given genotype within a particular environment [1] .", "In other words , developmental stability compensates the random stochastic variation of processes at play during developmen...	[ "In Drosophila , ubiquitous expression of a short Cyclin G isoform generates extreme developmental noise estimated by fluctuating asymmetry ( FA ) , providing a model to tackle developmental stability .", "This transcriptional cyclin interacts with chromatin regulators of the Enhancer of Trithorax and Polycomb ( ...	[ "During development , the part of stochasticity inherent to biological processes induces noise .", "In animals with bilateral symmetry , developmental noise can be estimated by the variance in a population of the difference between the left and the right sides of individuals , the so-called fluctuating asymmetry ...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Thermal Adaptation of Conformational Dynamics in Ribonuclease H	journal.pcbi.1003218	null	[ [ "Structural changes are critical to the ability of proteins to execute biological function .", "Regions known to be in contact with substrates and to undergo conformational changes during the catalytic cycles of enzymes often are identifiable as particularly flexible by NMR spectroscopy [1] , [2] and by c...	[ "The relationship between inherent internal conformational processes and enzymatic activity or thermodynamic stability of proteins has proven difficult to characterize .", "The study of homologous proteins with differing thermostabilities offers an especially useful approach for understanding the functional aspec...	[ "The relationship between enzymatic activity and protein stability has long been a difficult problem in the study of protein biochemistry .", "Enzymes may undergo structural changes in order to bind substrates , catalyze chemical reactions , and release products , but flexibility often is inversely correlated wit...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "neural networks", "brain", "vertebrates", "social sciences", "neuroscience", "animals", "mammals", "learning and memory", "cognition", "memory", "vision", "zoology", "animal cognition", "computer and information sciences", "animal cells", "psychology"...	Integration and multiplexing of positional and contextual information by the hippocampal network	journal.pcbi.1006320	null	[ [ "Following the discovery of place cells , which specifically fire at determined positions in space [1] , the hippocampus was recognized as an essential brain area for spatial representations and memories .", "These cognitive representations , or maps , actually code for more than position in physical spac...	[ "The hippocampus is known to store cognitive representations , or maps , that encode both positional and contextual information , critical for episodic memories and functional behavior .", "How path integration and contextual cues are dynamically combined and processed by the hippocampus to maintain these represe...	[ "As an animal moves in space and receives external sensory inputs , it must dynamically maintain the representations of its position and environment at all times .", "How the hippocampus , the brain area crucial for spatial representations , achieves this task , and manages possible conflicts between different in...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunology", "microbiology", "host-pathogen interaction", "animal models", "caenorhabditis elegans", "model organisms", "staphylococci", "bacterial pathogens", "inflammation", "biology", "immune response", "genetics of the immune system", "immunity", "innate immunity" ]	EGL-9 Controls C. elegans Host Defense Specificity through Prolyl Hydroxylation-Dependent and -Independent HIF-1 Pathways	journal.ppat.1002798	null	[ [ "In mammalian host defense against infection , discrimination of distinct microbes is thought to occur primarily by differential ligation of Pattern Recognition Receptors ( PRRs ) , such as Toll-like Receptor ( TLR ) heterodimers , followed by activation of downstream kinase cascades that control NF-κB and AP...	[ "Understanding host defense against microbes is key to developing new and more effective therapies for infection and inflammatory disease .", "However , how animals integrate multiple environmental signals and discriminate between different pathogens to mount specific and tailored responses remains poorly underst...	[ "Understanding how animals detect infection and mount appropriate responses is key to treating infection and inflammatory disease .", "We use the tractable model Caenorhabditis elegans to study mechanisms of host defense against pathogenic bacteria .", "Here we show that hypoxia-inducible factor ( HIF ) is impo...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Allopurinol Resistance in Leishmania infantum from Dogs with Disease Relapse	journal.pntd.0004341	null	[ [ "Visceral leishmaniasis caused by L . infantum is a potentially fatal disease , which is a serious public health concern in Europe , Asia , North Africa and Latin America .", "The dog is the main reservoir for this zoonotic infection and it has been estimated that in Southwestern Europe alone there are ab...	[ "Visceral leishmaniasis caused by the protozoan Leishmania infantum is a zoonotic , life threatening parasitic disease .", "Domestic dogs are the main peridomestic reservoir , and allopurinol is the most frequently used drug for the control of infection , alone or in combination with other drugs .", "Resistance...	[ "Visceral leishmaniasis caused by Leishmania infantum is a widespread , devastating zoonotic disease .", "Domestic dogs are considered the major reservoir for human L . infantum infection in an area stretching from Portugal to China , and across South America .", "Dogs not only carry infection and transfer it t...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "organismal evolution", "microbial evolution", "virology", "viruses and cancer", "biology and life sciences", "microbiology", "evolutionary theory", "evolutionary biology", "evolutionary genetics", "viral evolution" ]	Larger Mammalian Body Size Leads to Lower Retroviral Activity	journal.ppat.1004214	null	[ [ "Mammalian genomes contain large numbers of endogenous retroviruses ( ERVs ) , derived from multiple independent germline invasions over evolutionary time .", "The human genome contains 31–40 such ERV invasions , termed ‘families’ , each derived from a distinct ancestral exogenous retrovirus [1] , [2] .",...	[ "Retroviruses have been infecting mammals for at least 100 million years , leaving descendants in host genomes known as endogenous retroviruses ( ERVs ) .", "The abundance of ERVs is partly determined by their mode of replication , but it has also been suggested that host life history traits could enhance or supp...	[ "Retroviruses have been invading mammalian genomes for over 100 million years , leaving traces known as endogenous retroviruses ( ERVs ) .", "Early genome sequencing studies revealed a marked difference in the activity of retroviruses among species , with humans largely containing inactive lineages of ERVs , whil...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "sv40", "medicine and health sciences", "pathology and laboratory medicine", "chemical compounds", "aliphatic amino acids", "molecular probe techniques", "enzymes", "pathogens", "microbiology", "enzymology", "immunoblotting", "ubiquitin ligases", "organic compounds", "viruses", "oncology...	Merkel cell polyomavirus Tumor antigens expressed in Merkel cell carcinoma function independently of the ubiquitin ligases Fbw7 and β-TrCP	journal.ppat.1007543	null	[ [ "Merkel cell carcinoma ( MCC ) is an extremely rare , but aggressive , neuroendocrine skin cancer with an incidence of 0 . 7 cases/100 , 000 person-years in the United States , and a less than 45% 5-year survival rate , making MCC almost three times as lethal as melanoma [1 , 2] .", "Although MCC was firs...	[ "Merkel cell polyomavirus ( MCPyV ) accounts for 80% of all Merkel cell carcinoma ( MCC ) cases through expression of two viral oncoproteins: the truncated large T antigen ( LT-t ) and small T antigen ( ST ) .", "MCPyV ST is thought to be the main driver of cellular transformation and has also been shown to incre...	[ "Merkel cell carcinoma ( MCC ) is a very aggressive and deadly neuroendocrine skin cancer .", "Merkel cell polyomavirus ( MCPyV ) contributes to the development and maintenance of 80% of MCCs through the expression of its truncated large tumor antigen ( LT-t ) and small tumor antigen ( ST ) .", "MCPyV ST is tho...	2019
[ "Introduction", "Methods", "Results and discussion" ]	[]	Fluctuating environments select for short-term phenotypic variation leading to long-term exploration	journal.pcbi.1006445	null	[ [ "Evolvability refers to a series of distinct but overlapping concepts that are generally concerned with adaptation , variation , and/or novelty generation [30] .", "Depending on your perspective , evolvability can describe the response to selection at the population level [31 , 32] , the ability of popula...	[ "Genetic spaces are often described in terms of fitness landscapes or genotype-to-phenotype maps , where each genetic sequence is associated with phenotypic properties and linked to other genotypes that are a single mutational step away .", "The positions close to a genotype make up its “mutational landscape” and...	[ "Cyclic environmental change can occur in many different timescales; from slow changes such as glacial cycles , to faster seasonal change , to the day-night cycle .", "All populations and organisms are exposed to changing environments , and understanding their effect on evolutionary trajectories is crucial to pre...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "reverse transcriptase-polymerase chain reaction", "sequencing techniques", "biological cultures", "vertebrates", "animals", "mammals", "animal models", "viruses", "organisms", "model organisms", "rna viruses", "sequence motif analysis", "molecular biology techniques", "research and analys...	Identification of Novel Rosavirus Species That Infects Diverse Rodent Species and Causes Multisystemic Dissemination in Mouse Model	journal.ppat.1005911	null	[ [ "Picornaviruses are positive-sense , single-stranded RNA viruses with icosahedral capsids .", "They infect various animals and human , causing various respiratory , cardiac , hepatic , neurological , mucocutaneous and systemic diseases [1 , 2] .", "Based on genotypic and serological characterization ,...	[ "While novel picornaviruses are being discovered in rodents , their host range and pathogenicity are largely unknown .", "We identified two novel picornaviruses , rosavirus B from the street rat , Norway rat , and rosavirus C from five different wild rat species ( chestnut spiny rat , greater bandicoot rat , Indo...	[ "We identified two novel picornaviruses , rosavirus B and C , infecting street and wild rats respectively in China .", "While rosavirus B was detected from Norway rats , rosavirus C was detected from five different wild rat species ( chestnut spiny rat , greater bandicoot rat , Indochinese forest rat , roof rat a...	2016
[ "Introduction", "Algorithm", "Results and Discussion", "Methods" ]	[ "markov models", "applied mathematics", "simulation and modeling", "fluorophotometry", "algorithms", "probability distribution", "mathematics", "systems science", "clustering algorithms", "statistics (mathematics)", "research and analysis methods", "fluorescence resonance energy transfer", "...	Decoding Single Molecule Time Traces with Dynamic Disorder	journal.pcbi.1005286	null	[ [ "Recent technological advances in single molecule experiments on biomolecules have provided an unprecedented chance to investigate dynamics of proteins and nucleic acids at single molecule ( SM ) level , which has previously been elusive in conventional experiments [1–7] .", "Folding/unfolding pathways gl...	[ "Single molecule time trajectories of biomolecules provide glimpses into complex folding landscapes that are difficult to visualize using conventional ensemble measurements .", "Recent experiments and theoretical analyses have highlighted dynamic disorder in certain classes of biomolecules , whose dynamic pattern...	[ "We have developed a new algorithm to better decode single molecule data with dynamic disorder .", "Our new algorithm , which represents a substantial improvement over other methodologies , can detect the presence of dynamic disorder in each trajectory and quantify the kinetic characteristics of underlying energy...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	What Makes Community Engagement Effective?: Lessons from the Eliminate Dengue Program in Queensland Australia	journal.pntd.0003713	null	[ [ "The WHO has described dengue as “the most important mosquito-borne viral disease in the world” [1] .", "Worldwide , more than 2 . 5 billion people in more than 100 countries are at risk and up to 390 million infections are acquired every year [2 , 3] .", "There are no approved dengue-specific treatme...	[ "Worldwide , more than 40% of the population is at risk from dengue and recent estimates suggest that up to 390 million dengue infections are acquired every year .", "The Eliminate Dengue ( ED ) Program is investigating the use of Wolbachia-infected , transmission-compromised , mosquitoes to reduce dengue transmi...	[ "Community Engagement ( CE ) is gaining increasing recognition as an important dimension of biomedical , public health and global health research , including neglected tropical disease research .", "Yet , there has been little agreement about the specific goals of CE and about the best ways to design , conduct , ...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "obstetrics and gynecology", "pregnancy", "obstetrics", "biology", "microbiology", "malaria", "parasitic diseases", "parasitology" ]	Placental Histopathological Changes Associated with Plasmodium vivax Infection during Pregnancy	journal.pntd.0002071	null	[ [ "Approximately 125 million pregnant women worldwide are exposed to the risks of malaria in pregnancy ( MiP ) each year , resulting in 200 , 000 infant deaths [1] , [2] .", "In areas in which malaria is endemic , pregnant women are more susceptible to Plasmodium infections than their non-pregnant peers .",...	[ "Histological evidence of Plasmodium in the placenta is indicative of placental malaria , a condition associated with severe outcomes for mother and child .", "Histological lesions found in placentas from Plasmodium-exposed women include syncytial knotting , syncytial rupture , thickening of the placental barrier...	[ "Malaria during pregnancy remains a risk for approximately 125 million women each year .", "Adverse outcomes of malaria during pregnancy include maternal anemia and low infant birth weight .", "Additionally , the presence of malaria parasites , namely Plasmodium falciparum , has been associated with the occurre...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "animal types", "medicine and health sciences", "engineering and technology", "vertebrates", "pets and companion animals", "dogs", "animals", "mammals", "alleles", "telecommunications", "amniotes", "zoology", "veterinary science", "genetic epidemiology", "veterinary diseases", "epidemi...	Frequency and distribution of 152 genetic disease variants in over 100,000 mixed breed and purebred dogs	journal.pgen.1007361	null	[ [ "Nearly 700 inherited disorders and traits have been described in the domestic dog [1] , one of the most genetically well-studied species after humans .", "Consequently , the wide variety of modern dog breeds represent an excellent biomedical animal model population for identifying disease-related genes t...	[ "Knowledge on the genetic epidemiology of disorders in the dog population has implications for both veterinary medicine and sustainable breeding .", "Limited data on frequencies of genetic disease variants across breeds exists , and the disease heritage of mixed breed dogs remains poorly explored to date .", "A...	[ "Like any human , dogs may suffer from or pass on a variety of inherited disorders .", "Knowledge of how likely a typical dog is to carry an inherited disorder in its genome , and which disorders are the most common and relevant ones across dog breeds , is valuable for both veterinary care and breeding of healthy...	2018
[ "Introduction", "The node-assessment exercise", "Experiences from the nodes", "Lessons learned", "Conclusions" ]	[ "genome-wide association studies", "medicine and health sciences", "education", "health services research", "sociology", "sports and exercise medicine", "social sciences", "physical activity", "health care", "scientists", "genome analysis", "research and analysis methods", "public and occupa...	Assessing computational genomics skills: Our experience in the H3ABioNet African bioinformatics network	journal.pcbi.1005419	null	[ [ "The Human Heredity and Health in Africa ( H3Africa ) initiative [1] ( http://h3africa . org/ ) , which is funded jointly by the National Institutes of Health ( NIH ) in the United States and the Wellcome Trust in the United Kingdom , aims to bring genomic approaches to the study of the genetic and environmen...	[ "The H3ABioNet pan-African bioinformatics network , which is funded to support the Human Heredity and Health in Africa ( H3Africa ) program , has developed node-assessment exercises to gauge the ability of its participating research and service groups to analyze typical genome-wide datasets being generated by H3Afr...	[ "Many programs have been developed to boost the technical and computational skills of scientists working in low to medium income countries ( LMIC ) , who often struggle to remain competitive with their peers in more developed parts of the world .", "Typically , these programs rely on intensive workshops where stu...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "species colonization", "medicine and health sciences", "ecology and environmental sciences", "invasive species", "binomials", "tropical diseases", "geographical locations", "parasitic diseases", "animals", "parasitic protozoans", "animal models", "protozoans", "mathematic...	Drivers of house invasion by sylvatic Chagas disease vectors in the Amazon-Cerrado transition: A multi-year, state-wide assessment of municipality-aggregated surveillance data	journal.pntd.0006035	null	[ [ "Chagas disease is caused by infection with Trypanosoma cruzi , a protozoan parasite transmitted by blood-sucking bugs known as triatomines [1] .", "The disease is endemic across Latin America , where about 5–6 million people are thought to be infected and over 70 million live at risk of contagion [2] .",...	[ "Insecticide spraying efficiently controls house infestation by triatomine bugs , the vectors of Trypanosoma cruzi .", "The strategy , however , is ineffective against sylvatic triatomines , which can transmit Chagas disease by invading ( without colonizing ) man-made structures .", "Despite growing awareness o...	[ "Triatomine bugs are the vectors of Chagas disease , still a key public health concern in the Americas .", "Insecticide spraying efficiently controls house infestation by triatomines , but is useless against sylvatic bugs–which can transmit the disease by simply invading human residences .", "Although this beha...	2017
[ "Introduction", "Materials and Methods", "Results and Discussion" ]	[]	Whole Genome Sequencing of Field Isolates Reveals a Common Duplication of the Duffy Binding Protein Gene in Malagasy Plasmodium vivax Strains	journal.pntd.0002489	null	[ [ "Merozoite contact and tight junction formation with the red blood cell ( RBC ) initiate the cycle of events that result in human malaria [1] .", "Evidence that these events require specific molecular interactions was revealed through in vitro and in vivo studies demonstrating that P . knowlesi and the hi...	[ "Plasmodium vivax is the most prevalent human malaria parasite , causing serious public health problems in malaria-endemic countries .", "Until recently the Duffy-negative blood group phenotype was considered to confer resistance to vivax malaria for most African ethnicities .", "We and others have reported tha...	[ "Malaria results from infection of human red blood cells ( RBC ) by Plasmodium parasite's merozoite .", "For Plasmodium vivax the process of RBC invasion has been hypothesized to depend on interactions between the parasite's Duffy binding protein ( PvDBP ) and human Duffy blood group antigen because Duffy-negativ...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "public health and epidemiology", "diagnostic medicine", "primary care", "epidemiology", "public health" ]	Diagnosis, Clinical Features, and Self-Reported Morbidity of Strongyloides stercoralis and Hookworm Infection in a Co-Endemic Setting	journal.pntd.0001292	null	[ [ "Infections with the nematodes Strongyloides stercoralis and hookworm ( Ancylostoma duodenale and Necator americanus ) are widespread in tropical and subtropical areas , accounting for a remarkable , yet underappreciated burden [1] .", "For example , hookworm infection is a leading cause of anemia [2] , w...	[ "Infections with Strongyloides stercoralis and other helminths represent important , yet often neglected issues in developing countries .", "Indeed , strongyloidiasis can be fatal , but only a few studies provide information regarding its health relevance in Africa .", "Moreover , clinical data on symptomatolog...	[ "Infections with parasitic worms such as hookworm and threadworm ( Strongyloides stercoralis ) are widespread throughout the developing world .", "However , the symptoms caused by parasitic worms are unspecific and little is known about clinical presentations in endemic countries , and hence doctors' awareness of...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "animal models", "model organisms", "genetic mutation", "gene expression", "genetics", "molecular genetics", "biology", "genetics and genomics" ]	C. elegans SIRT6/7 Homolog SIR-2.4 Promotes DAF-16 Relocalization and Function during Stress	journal.pgen.1002948	null	[ [ "Elucidation of mechanisms regulating stress resistance and longevity has been aided tremendously by the use of invertebrate models .", "FoxO transcription factors regulate multiple biological processes in many organisms [1] .", "In C . elegans and Drosophila , increased FoxO activity promotes longevi...	[ "FoxO transcription factors and sirtuin family deacetylases regulate diverse biological processes , including stress responses and longevity .", "Here we show that the Caenorhabditis elegans sirtuin SIR-2 . 4—homolog of mammalian SIRT6 and SIRT7 proteins—promotes DAF-16–dependent transcription and stress-induced ...	[ "Sensing and responding appropriately to environmental insults is a challenge facing all organisms .", "In the roundworm C . elegans , the FoxO protein DAF-16 moves to the nucleus in response to stress , where it regulates gene expression and plays a key role in ensuring organismal survival .", "In this manuscr...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular biology/dna repair", "genetics and genomics/chromosome biology" ]	ATM Limits Incorrect End Utilization during Non-Homologous End Joining of Multiple Chromosome Breaks	journal.pgen.1001194	null	[ [ "Recent sequencing of cancer genomes has revealed a prevalence of chromosome rearrangements , including interchromosomal translocations and intrachromosomal rearrangements [1] .", "These rearrangements could arise from end joining ( EJ ) of incorrect ends of multiple chromosomal double-strand breaks ( DSB...	[ "Chromosome rearrangements can form when incorrect ends are matched during end joining ( EJ ) repair of multiple chromosomal double-strand breaks ( DSBs ) .", "We tested whether the ATM kinase limits chromosome rearrangements via suppressing incorrect end utilization during EJ repair of multiple DSBs .", "For t...	[ "When a chromosome is fragmented by multiple double-strand breaks ( DSBs ) , each set of DSB ends needs to be matched correctly during repair to avoid chromosomal rearrangements .", "Considering the case of two tandem DSBs , if the ends of different breaks ( incorrect ends ) are used for repair , loss of the inte...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology/membranes and sorting" ]	Distinct Dynamics of Endocytic Clathrin-Coated Pits and Coated Plaques	journal.pbio.1000191	Here we classify endocytic structures at the adherent (bottom) surface of many cells in culture into shorter-lived coated pits and longer-lived coated plaques which internalize by different mechanisms.	[ [ "Clathrin-mediated endocytosis is a mechanism for selective retrieval and internalization of membrane lipids and membrane-bound proteins .", "Clathrin-coated pits capture their molecular cargo as they invaginate from the cell surface and bud inward to form coated vesicles , in a process that involves a co...	[ "Clathrin is the scaffold of a conserved molecular machinery that has evolved to capture membrane patches , which then pinch off to become traffic carriers .", "These carriers are the principal vehicles of receptor-mediated endocytosis and are the major route of traffic from plasma membrane to endosomes .", "We...	[ "Here , we identify and characterize two distinct modes of clathrin-mediated uptake at the plasma membrane .", "The “canonical” coated pit is where assembly of a curved clathrin lattice , linked to deformation of the underlying membrane , gives rise to coated vesicles .", "Clathrin coated “plaques” are extended...	2009
[ "Introduction", "Results and discussion", "Methods" ]	[ "population genetics", "vertebrates", "mice", "animals", "mammals", "cell signaling", "genome analysis", "mammalian genomics", "population biology", "genomic libraries", "geography", "genomic signal processing", "gene expression", "cartography", "animal genomics", "signal transduction"...	The genomic basis of environmental adaptation in house mice	journal.pgen.1007672	null	[ [ "Understanding how organisms adapt to their environment is at the heart of evolutionary biology .", "The recent introduction of the western house mouse ( Mus musculus domesticus ) into North America from Europe provides a unique opportunity to study the genetic basis of environmental adaptation over short...	[ "House mice ( Mus musculus ) arrived in the Americas only recently in association with European colonization ( ~400–600 generations ) , but have spread rapidly and show evidence of local adaptation .", "Here , we take advantage of this genetic model system to investigate the genomic basis of environmental adaptat...	[ "The recent introduction of house mice into North America from Europe provides an opportunity to investigate environmental adaptation in an important genetic model system .", "We found that mice from different latitudes differed in body size and aspects of blood chemistry and behavior , and that those differences...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Evaluation in Cameroon of a Novel, Simplified Methodology to Assist Molecular Microbiological Analysis of V. cholerae in Resource-Limited Settings	journal.pntd.0004307	null	[ [ "Cholera remains a major public health problem in developing countries , particularly in Africa and Asia , where endemic and epidemic disease continues to devastate vulnerable populations .", "The etiologic agent of cholera , V . cholerae , has more than 200 serogroups , differentiated by the O-antigen on...	[ "Vibrio cholerae is endemic in South Asia and Africa where outbreaks of cholera occur widely and are particularly associated with poverty and poor sanitation .", "Knowledge of the genetic diversity of toxigenic V . cholerae isolates , particularly in Africa , remains scarce .", "The constraints in improving thi...	[ "Cholera , caused by the bacterium Vibrio cholerae , causes an estimated 3–5 million cases every year and more than 100 , 000 deaths .", "The highest disease burden is reported from Africa , however , the epidemic potential and transmission patterns among circulating strains is scarcely understood .", "The chal...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "nucleic acids", "genetics", "dna", "biology", "genomics", "molecular cell biology", "molecular biology", "genetics and genomics" ]	DNA Resection at Chromosome Breaks Promotes Genome Stability by Constraining Non-Allelic Homologous Recombination	journal.pgen.1002633	null	[ [ "Large-scale genome rearrangements such as deletions , duplications , and translocations contribute to evolution and cancer [1] , [2] .", "Many of these rearrangements result from homologous recombination [3]–[5] .", "Homologous recombination occurs when a recipient sequence surrounding a DNA double-s...	[ "DNA double-strand breaks impact genome stability by triggering many of the large-scale genome rearrangements associated with evolution and cancer .", "One of the first steps in repairing this damage is 5′→3′ resection beginning at the break site .", "Recently , tools have become available to study the conseque...	[ "Chromosomes encode most of the genetic information necessary for cells to function .", "When large changes in chromosome structure occur , these changes can lead to a variety of diseases , including cancer .", "One type of DNA damage that triggers chromosomal changes is a DNA double-strand break .", "These b...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "mycology", "biology", "microbiology" ]	Therapeutic DNA Vaccine Encoding Peptide P10 against Experimental Paracoccidioidomycosis	journal.pntd.0001519	null	[ [ "Paracoccidioides brasiliensis is a thermally dimorphic fungus that causes a systemic granulomatous disease known as paracoccidioidomycosis ( PCM ) .", "PCM is widespread in Latin America , mainly affecting rural workers , and its incidence has increased in recently deforested areas associated with soil c...	[ "Paracoccidioidomycosis ( PCM ) , caused by Paracoccidioides brasiliensis , is the most prevalent invasive fungal disease in South America .", "Systemic mycoses are the 10th most common cause of death among infectious diseases in Brazil and PCM is responsible for more than 50% of deaths due to fungal infections ....	[ "Paracoccidioidomycosis ( PCM ) is the predominant systemic mycosis in Latin America causing half of the total deaths among systemic fungal infectious diseases in Brazil .", "Chemotherapy is the standard treatment , but the long time required , severe cases of immunosuppression and frequent relapses indicate that...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "computational neuroscience", "single neuron function", "biology", "sensory systems", "neuroscience", "coding mechanisms" ]	In vivo Conditions Induce Faithful Encoding of Stimuli by Reducing Nonlinear Synchronization in Vestibular Sensory Neurons	journal.pcbi.1002120	null	[ [ "The vestibular system provides information about head motion relative to space that is necessary for maintaining posture , computing spatial orientation , and perceiving self-motion .", "Peripheral vestibular afferents encode the detailed time course of either horizontal rotations , vertical rotations , ...	[ "Previous studies have shown that neurons within the vestibular nuclei ( VN ) can faithfully encode the time course of sensory input through changes in firing rate in vivo .", "However , studies performed in vitro have shown that these same VN neurons often display nonlinear synchronization ( i . e . phase lockin...	[ "The vestibular system senses the motion of the head in space and is vital for gaze stability , posture control , and the computation of spatial orientation during everyday life .", "The activities of single vestibular neurons recorded in the brains of awake behaving animals show that they can accurately transmit...	2011
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "bacterial diseases", "infectious diseases", "veterinary diseases", "veterinary bacteriology", "veterinary science", "leptospirosis" ]	Leptospira interrogans Binds to Cadherins	journal.pntd.0002672	null	[ [ "Leptospirosis is a globally widespread zoonotic infection caused by spirochetes of the genus Leptospira .", "The genus contains free-living non-pathogenic species as well as several species that are pathogenic for humans and/or animals .", "The disease in humans varies from a mild , non-specific , se...	[ "Leptospirosis , caused by pathogenic species of Leptospira , is the most widespread zoonosis and has emerged as a major public health problem worldwide .", "The adhesion of pathogenic Leptospira to host cells , and to extracellular matrix ( ECM ) components , is likely to be necessary for the ability of leptospi...	[ "Leptospirosis is a globally widespread bacterial infection caused by pathogenic species of the genus Leptospira .", "The disease manifestations of leptospirosis range from mild , non-specific illness to a severe disease that includes multi-organ failure , widespread damage to blood vessels , and hemorrhage .", ...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biogeography", "livestock", "ecology and environmental sciences", "animal genetics", "china", "population genetics", "geographical locations", "vertebrates", "animals", "animal behavior", "bird genetics", "population biology", "zoology", "geography", "birds", "ecosystems", "behavior...	Ecosystem Interactions Underlie the Spread of Avian Influenza A Viruses with Pandemic Potential	journal.ppat.1005620	null	[ [ "Intensive agriculture has allowed AIV circulating in wild bird populations and multi-host poultry systems ( domestic food birds including chicken , duck , goose , pigeon ) to interact , shaping the diversity of subtypes with pandemic potential [1] .", "The recently emerged H7N9 viruses containing H9N2-or...	[ "Despite evidence for avian influenza A virus ( AIV ) transmission between wild and domestic ecosystems , the roles of bird migration and poultry trade in the spread of viruses remain enigmatic .", "In this study , we integrate ecosystem interactions into a phylogeographic model to assess the contribution of wild...	[ "It is assumed that AIV outbreaks in poultry are introduced from wild birds .", "To test this , we incorporated ecosystem and location of isolation into a comparative genetic analysis .", "We show high rates of viral transmission from domestic to wild birds within a region and , that wild birds could transmit A...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "public health and epidemiology", "immunology" ]	Factors Associated with the Prevalence of Circulating Antigens to Porcine Cysticercosis in Three Villages of Burkina Faso	journal.pntd.0000927	null	[ [ "Burkina Faso is one of the poorest countries in the world ranking 177th out of 182 according to the Human Development Index ( HDI ) [1] .", "Its economy relies predominantly on agriculture ( 40% of GDP ) , with cotton production being the most important , followed by livestock production , accounting for...	[ "Little is known about porcine cysticercosis in Burkina Faso .", "We conducted a pilot study to estimate the prevalence of antigens of Taenia solium cysticercosis and to identify associated factors in pigs of three villages in Burkina Faso , selected to represent different pig management practices: one village wh...	[ "Taenia solium cysticercosis is a neglected tropical infection transmitted between humans and pigs .", "This infection is particularly common in areas where sanitation , hygiene and pig management practices are poor , and can sometimes lead to epilepsy in humans .", "There is very little information about the i...	2011
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "rna", "rna interference", "molecular dynamics", "nucleic acids", "chemistry", "biology", "computational chemistry", "biophysics" ]	Convergent Transmission of RNAi Guide-Target Mismatch Information across Argonaute Internal Allosteric Network	journal.pcbi.1002693	null	[ [ "RNA interference ( RNAi ) is a fundamental mechanism for regulating the expression of genes in a variety of contexts .", "It is a process by which a short dsRNA , such as a short interfering RNA ( siRNA ) or microRNA ( miRNA ) , can induce sequence-specific silencing of genes at the mRNA stage , preventi...	[ "In RNA interference , a guide strand derived from a short dsRNA such as a microRNA ( miRNA ) is loaded into Argonaute , the central protein in the RNA Induced Silencing Complex ( RISC ) that silences messenger RNAs on a sequence-specific basis .", "The positions of any mismatched base pairs in an miRNA determine...	[ "Cells use the process of RNA interference ( RNAi ) to help orchestrate the production of the specific set of proteins needed at a given time .", "A given messenger RNA ( mRNA ) is produced using a gene in the cell's genomic DNA as a template .", "Each mRNA molecule is a blueprint for a particular protein and c...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biomacromolecule-ligand interactions", "biochemistry", "protein chemistry", "molecular complexes", "proteins", "protein structure", "biology and life sciences", "chemistry", "physical sciences", "chemical biology", "biophysics", "molecular biology" ]	Structural and Functional Characterization of a Complex between the Acidic Transactivation Domain of EBNA2 and the Tfb1/p62 Subunit of TFIIH	journal.ppat.1004042	null	[ [ "The Epstein-Barr virus ( EBV ) is a double-stranded DNA-based virus that infects more than 90% of the world's adult population [1] .", "The high level of infectivity is due to the fact that the EBV can be easily transmitted through the exchange of saliva from an infected individual [2] .", "Once tran...	[ "Infection with the Epstein-Barr virus ( EBV ) can lead to a number of human diseases including Hodgkin's and Burkitt's lymphomas .", "The development of these EBV-linked diseases is associated with the presence of nine viral latent proteins , including the nuclear antigen 2 ( EBNA2 ) .", "The EBNA2 protein pla...	[ "Infection with the Epstein-Barr virus ( EBV ) is linked to a number of human diseases and the nuclear antigen EBNA2 is one of nine viral latent proteins that plays a key role in EBV-linked diseases .", "EBNA2 activates expression of both viral and host gene in part through interaction between its C-terminal acid...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology" ]	Targeted Restoration of the Intestinal Microbiota with a Simple, Defined Bacteriotherapy Resolves Relapsing Clostridium difficile Disease in Mice	journal.ppat.1002995	null	[ [ "Clostridium difficile is an anaerobic , Gram-positive bacterium that is the major cause of antibiotic-associated diarrhea and a significant healthcare-associated pathogen [1] .", "C . difficile challenges hospital infection control measures by exploiting an infection cycle involving the excretion of high...	[ "Relapsing C . difficile disease in humans is linked to a pathological imbalance within the intestinal microbiota , termed dysbiosis , which remains poorly understood .", "We show that mice infected with epidemic C . difficile ( genotype 027/BI ) develop highly contagious , chronic intestinal disease and persiste...	[ "Pathological imbalances within the intestinal microbiota , termed dysbiosis , are often associated with chronic Clostridium difficile infections in humans .", "We show that infection of mice with the healthcare pathogen C . difficile leads to persistent intestinal dysbiosis that is associated with chronic diseas...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "invertebrates", "medicine and health sciences", "reproductive system", "gonads", "animals", "cell differentiation", "germ cells", "developmental biology", "g protein coupled receptors", "planarians", "animal cells", "proteins", "flatworms", "transmembrane receptors", "biochemistry", "...	GPCRs Direct Germline Development and Somatic Gonad Function in Planarians	journal.pbio.1002457	Genome-wide analysis of the planarian Schmidtea mediterranea reveals a complement of over 550 G protein-coupled receptors, including two with critical roles in germline development.	[ [ "G protein-coupled receptors ( GPCRs ) play critical roles in sexual reproduction , guiding germ cell migration , mediating hormonal regulation of gamete development , and facilitating the function of accessory reproductive tissues .", "For example , a complex network of peptidergic neurons in the mammali...	[ "Planarians display remarkable plasticity in maintenance of their germline , with the ability to develop or dismantle reproductive tissues in response to systemic and environmental cues .", "Here , we investigated the role of G protein-coupled receptors ( GPCRs ) in this dynamic germline regulation .", "By geno...	[ "G protein-coupled receptors ( GPCRs ) are the largest and most versatile family of cell-surface receptors .", "They play critical roles in various cellular and physiological systems and have emerged as a leading group of therapeutic targets .", "Due to their structural and functional conservation across animal...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "animal genetics", "genetic mutation", "genome evolution", "population genetics", "mutational hypotheses", "gene function", "mutation", "genetic polymorphism", "biology", "evolutionary genetics", "genetic drift", "haplotypes", "natural selection", "genetics", "genomics", "evolutionary ...	Genome-Wide Analysis Reveals Selection for Important Traits in Domestic Horse Breeds	journal.pgen.1003211	null	[ [ "Since domestication of the horse approximately 5 , 000 years ago [1]–[3] , selective breeding has been directed mainly toward the use of the horse in agriculture , transportation , and warfare .", "Within the past 400 years , the founding of formal breed registries and continued breed specialization has ...	[ "Intense selective pressures applied over short evolutionary time have resulted in homogeneity within , but substantial variation among , horse breeds .", "Utilizing this population structure , 744 individuals from 33 breeds , and a 54 , 000 SNP genotyping array , breed-specific targets of selection were identifi...	[ "A breed of the horse typically consists of individuals sharing very similar aesthetic and performance traits .", "However , a great deal of variation in traits exists between breeds .", "The range of variation observed among breeds can be illustrated by the size difference between the Miniature horse ( 0 . 74 ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "animal models", "developmental biology", "cell fate determination", "drosophila melanogaster", "model organisms", "stem cells", "molecular development", "genetics", "biology", "genetics and genomics", "cell differentiation", "gene function" ]	Niche-Associated Activation of Rac Promotes the Asymmetric Division of Drosophila Female Germline Stem Cells	journal.pbio.1001357	An intracellular polarity in activation of the Rac GTPase cooperates with an extracellular signal to ensure a robust pattern of stem cell division in Drosophila female germline stem cells.	[ [ "A robust pattern of asymmetric cell division underlies the ability of adult stem cells to balance self-renewal and differentiation to ensure tissue homeostasis .", "In principle , either of two mechanisms could underlie the asymmetric cell division: first , a polarization in the stem cell could result in...	[ "Drosophila female germline stem cells ( GSCs ) reside adjacent to a cellular niche that secretes Bone Morphogenetic Protein ( BMP ) ligands and anchors the GSCs through adherens junctions .", "The GSCs divide asymmetrically such that one daughter remains in the niche as a GSC , while the other is born away from ...	[ "Adult stem cells are undifferentiated cells within an organism that undergo continual asymmetric division to produce two daughter cells that have different cell fates: one daughter remains a stem cell like its parent , while the other daughter differentiates .", "Thus the stock of stem cells is renewed while new...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Analyzing and Quantifying the Gain-of-Function Enhancement of IP3 Receptor Gating by Familial Alzheimer’s Disease-Causing Mutants in Presenilins	journal.pcbi.1004529	null	[ [ "Alzheimer’s disease ( AD ) is a fatal neurodegenerative disease that leads to cognitive , memory , and behavioral impairments followed by progressive cell death .", "The symptoms of AD include the extracellular deposition of amyloid β ( Aβ ) plaques and intracellular neurofibrillary tangles—aggregates of...	[ "Familial Alzheimer’s disease ( FAD ) -causing mutant presenilins ( PS ) interact with inositol 1 , 4 , 5-trisphosphate ( IP3 ) receptor ( IP3R ) Ca2+ release channels resulting in enhanced IP3R channel gating in an amyloid beta ( Aβ ) production-independent manner .", "This gain-of-function enhancement of IP3R a...	[ "Aberrant Ca2+ signaling caused by IP3R gating dysregulation is implicated in many neurodegenerative diseases such as Alzheimer’s , Huntington’s , Spinocerebellar ataxias , and endoplasmic reticulum stress-induced brain damage .", "Thus understanding IP3R dysfunction is important for the etiology of these disease...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "ophthalmology/retinal disorders", "cell biology/cellular death and stress responses", "genetics and genomics/disease models", "genetics and genomics/genetics of disease", "ophthalmology/inherited eye disorders" ]	Accumulation of Rhodopsin in Late Endosomes Triggers Photoreceptor Cell Degeneration	journal.pgen.1000377	null	[ [ "Inherited retinal degenerative disorders in humans exhibit heterogeneity in their underlying causes and clinical outcomes [1] .", "Diverse causes have been attributed , including disruption of genes that are involved in phototransduction , biosynthesis and folding of the rhodopsin molecule , and the stru...	[ "Progressive retinal degeneration is the underlying feature of many human retinal dystrophies .", "Previous work using Drosophila as a model system and analysis of specific mutations in human rhodopsin have uncovered a connection between rhodopsin endocytosis and retinal degeneration .", "In these mutants , rho...	[ "Irreversible loss of photoreceptor cells has been attributed as a cause of blindness in many retinal degenerative disorders .", "One such group of disorders is retinitis pigmentosa , which affects 1 in 3 , 000 individuals .", "Over 100 mutations in the light-sensing molecule rhodopsin have been identified in p...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biotechnology", "biochemistry", "cell biology", "neurological disorders", "molecular biology" ]	Proteomic Profiling of γ-Secretase Substrates and Mapping of Substrate Requirements	journal.pbio.0060257	Using an unbiased quantitative proteomics approach, novel substrate targets for the protease γ-secretase are identified and analyzed to determine which domains enable their cleavage.	[ [ "In the recently discovered process of regulated intramembrane proteolysis , activated transmembrane proteins are liberated from the lipid bilayer in a two-step mechanism .", "The first cleavage by a class of proteases dubbed secretases or sheddases releases the ectodomain , leaving the protein with a sho...	[ "The presenilin/γ-secretase complex , an unusual intramembrane aspartyl protease , plays an essential role in cellular signaling and membrane protein turnover .", "Its ability to liberate numerous intracellular signaling proteins from the membrane and also mediate the secretion of amyloid-β protein ( Aβ ) has mad...	[ "All cells face the challenge of removing transmembrane proteins from the lipid bilayer for the purpose of signaling or degradation .", "One molecular solution to this problem is the multiprotein enzyme complex γ-secretase , which is able to hydrolyze several known transmembrane proteins within the hydrophobic li...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "invertebrates", "cellular stress responses", "medicine and health sciences", "diagnostic radiology", "pathology and laboratory medicine", "caenorhabditis", "gene regulation", "pathogens", "regulatory proteins", "cell processes", "dna-binding proteins", "microbiology", "animals", "pseudomo...	The Caenorhabditis elegans Protein FIC-1 Is an AMPylase That Covalently Modifies Heat-Shock 70 Family Proteins, Translation Elongation Factors and Histones	journal.pgen.1006023	null	[ [ "How post-translational modifications regulate protein activity is a fundamental question in biology .", "Phosphorylation , methylation or acetylation reversibly control cellular signaling pathways , the misregulation of which is often associated with pathologies , including cancer or autoimmune diseases ...	[ "Protein AMPylation by Fic domain-containing proteins ( Fic proteins ) is an ancient and conserved post-translational modification of mostly unexplored significance .", "Here we characterize the Caenorhabditis elegans Fic protein FIC-1 in vitro and in vivo .", "FIC-1 is an AMPylase that localizes to the nuclear...	[ "Eukaryotic Fic domain containing proteins ( Fic proteins ) AMPylate target proteins at the expense of a single ATP molecule .", "Previous studies have established a first link between target protein AMPylation and the unfolded protein response ( UPR ) in the endoplasmic reticulum .", "Yet , the consequences of...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology", "developmental biology" ]	Dynamic Control of Cell Cycle and Growth Coupling by Ecdysone, EGFR, and PI3K Signaling in Drosophila Histoblasts	journal.pbio.1000079	Integration of the ecdysone, EGF receptor, and PI 3-kinase signaling pathways determines the relative rates of growth and cell division duringDrosophila abdominal cell morphogenesis.	[ [ "Morphogenesis involves the coordination of a wide variety of cellular activities , including progression through the cell cycle , cell growth , and cell rearrangement .", "Over the last decades considerable progress , mostly in cultured cells , has been made in the identification of the crucial regulator...	[ "Regulation of cell proliferation has been extensively studied in cultured cell systems that are characterized by coordinated growth and cell-cycle progression and relatively uniform cell size distribution .", "During the development of multicellular organisms , however , growth and division can be temporally unc...	[ "A fundamental issue in biology is the question of how the rate of cell division is coupled to cell growth .", "Coordination of these processes has been studied extensively in cultured cell systems but to a much lesser extent in intact organisms .", "To study this phenomenon in a physiological setting , we deve...	2009
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "innate immune system", "medicine and health sciences", "immune physiology", "cytokines", "toxoplasma gondii", "immunology", "vertebrates", "mice", "parasitic diseases", "parasitic protozoans", "animals", "mammals", "biomechanics", "biological locomotion", "animal models", "development...	Behavioral Abnormalities in a Mouse Model of Chronic Toxoplasmosis Are Associated with MAG1 Antibody Levels and Cyst Burden	journal.pntd.0004674	null	[ [ "The intracellular protozoan Toxoplasma gondii is an exceptionally successful parasite that infects approximately 1 billion people worldwide .", "Latent infection persists during the lifespan of the intermediate hosts such as human through the formation of cysts in muscle and brain .", "Although genot...	[ "There is marked variation in the human response to Toxoplasma gondii infection .", "Epidemiological studies indicate associations between strain virulence and severity of toxoplasmosis .", "Animal studies on the pathogenic effect of chronic infection focused on relatively avirulent strains ( e . g . type II ) ...	[ "Chronic infection with Toxoplasma gondii , a common neurotropic pathogen , affects approximately 1 billion people worldwide .", "There is marked variation in the human response to infection .", "Epidemiological studies indicate that virulent strains of T . gondii are associated with increased frequency and sev...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "microtubules", "cell processes", "endoplasmic reticulum", "neuroscience", "nerve fibers", "mitochondria", "bioenergetics", "cellular structures and organelles", "cytoskeleton", "animal cells", "axons", "short reports", "axonal transport", "cell membranes", "biochemistry", "cellular ne...	Morphology of mitochondria in spatially restricted axons revealed by cryo-electron tomography	journal.pbio.2006169	null	[ [ "Neurons are architecturally complex cells that can extend axonal projections with elaborate arborization for several hundreds of millimeters ( and in some cases , meters ) to form synaptic connections with local and distal targets [1–3] .", "Depending on the target , presynaptic compartments can either b...	[ "Neurons project axons to local and distal sites and can display heterogeneous morphologies with limited physical dimensions that may influence the structure of large organelles such as mitochondria .", "Using cryo-electron tomography ( cryo-ET ) , we characterized native environments within axons and presynaptic...	[ "Neurons are complex cells that communicate with each other via axons that can extend over distances of a meter or longer .", "Axons place enormous demands on neuronal energy production , and to maintain connections with local and distal targets , neurons have efficient systems that transport mitochondria to area...	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "veterinary diseases", "biology", "zoology", "veterinary science" ]	Clear Genetic Distinctiveness between Human- and Pig-Derived Trichuris Based on Analyses of Mitochondrial Datasets	journal.pntd.0001539	null	[ [ "Soil-transmitted helminths ( = geohelminths ) , including whipworm , are responsible for neglected tropical diseases ( NTDs ) of humans in developing countries [1]–[3] .", "Trichuris trichiura infects ∼600 million people worldwide .", "This parasite is transmitted directly via a direct , faecal-oral ...	[ "The whipworm , Trichuris trichiura , causes trichuriasis in ∼600 million people worldwide , mainly in developing countries .", "Whipworms also infect other animal hosts , including pigs ( T . suis ) , dogs ( T . vulpis ) and non-human primates , and cause disease in these hosts , which is similar to trichuriasis...	[ "Trichuriasis is a neglected tropical disease ( NTD ) caused by parasitic nematodes of the genus Trichuris ( Nematoda ) , causing significant human and animal health problems as well as considerable socio-economic consequences world-wide .", "Although Trichuris species are considered to be relatively host specifi...	2012
[ "Introduction", "Material and Methods", "Results", "Discussion" ]	[]	African Adders: Partial Characterization of Snake Venoms from Three Bitis Species of Medical Importance and Their Neutralization by Experimental Equine Antivenoms	journal.pntd.0003419	null	[ [ "In the Sub-Saharan Africa is annually registered approximately 300 , 000 cases of accidents by snakes which results in 32 , 000 deaths and a large number of victims with permanent local tissue damage and chronic disabilities [1] .", "Snakes belonging to the genus Bitis , Viperidae family , are implicated...	[ "An alarming number of fatal accidents involving snakes are annually reported in Africa and most of the victims suffer from permanent local tissue damage and chronic disabilities .", "Envenomation by snakes belonging to the genus Bitis , Viperidae family , are common in Sub-Saharan Africa .", "The accidents are...	[ "In this report we have characterized the venoms from three species of Bitis snakes involved in accidents with humans in the Sub-Saharan Africa , i . e . , Bitis arietans , Bitis gabonica rhinoceros and Bitis nasicornis .", "These venoms possess a combination of proteases that can directly affect the coagulation ...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "children", "medicine and health sciences", "geographical locations", "anemia", "pediatrics", "age groups", "mathematics", "statistics (mathematics)", "global health", "africa", "families", "research and analysis methods", "public and occupational health", "mathematical and statistical tec...	Deworming in pre-school age children: A global empirical analysis of health outcomes	journal.pntd.0006500	null	[ [ "The large-scale empiric treatment of children for soil-transmitted helminthiasis ( STH ) , commonly known as “deworming” , has become controversial [1–4] .", "This strategy of regular deworming ( also known as ‘preventive chemotherapy’ ) with albendazole or mebendazole has been the main STH control strat...	[ "There is debate over the effectiveness of deworming children against soil-transmitted helminthiasis ( STH ) to improve health outcomes , and current evidence may be limited in study design and generalizability .", "However , programmatic deworming continues throughout low and middle-income countries .", "We pe...	[ "Soil-transmitted helminths are parasitic worms that affect 1 . 5 billion people .", "The global public health strategy is regular deworming of children in endemic settings .", "In this study , we bring an independent dataset with over 320 , 000 pre-school age children across 45 STH-endemic countries to investi...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Chronic Filarial Infection Provides Protection against Bacterial Sepsis by Functionally Reprogramming Macrophages	journal.ppat.1004616	null	[ [ "Helminth infections typically induce type 2 immune responses which are characterized by the induction of Th2 cells , eosinophilia and elevated levels of IgE as well as IL-4 , IL-5 and IL-13 [1] .", "To ensure long term host-parasite co-existence , helminths also suppress inflammatory immune responses and...	[ "Helminths immunomodulate their hosts and induce a regulatory , anti-inflammatory milieu that prevents allergies and autoimmune diseases .", "Helminth immunomodulation may benefit sepsis outcome by preventing exacerbated inflammation and severe pathology , but the influence on bacterial clearance remains unclear ...	[ "As the human immune system evolved in the presence of helminth infections , it is postulated that improved hygiene and subsequent loss of helminth infections and their immunomodulatory functions contributed to the sharp increase of autoimmune diseases and allergies over the last decades .", "Accordingly , helmin...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biotechnology", "genome engineering", "invertebrates", "medicine and health sciences", "parasite groups", "body fluids", "plasmodium", "engineering and technology", "synthetic biology", "tropical diseases", "gene knockout", "parasitic diseases", "animals", "parasitic protozoans", "paras...	CRISPR/Cas9 -mediated gene knockout of Anopheles gambiae FREP1 suppresses malaria parasite infection	journal.ppat.1006898	null	[ [ "Malaria remains one of the most devastating infectious diseases , killing nearly half a million people annually [1] .", "For successful transmission , the malaria parasite has to complete a complex journey in the mosquito vector that involves intimate molecular interactions with the vector’s midgut , hem...	[ "Plasmodium relies on numerous agonists during its journey through the mosquito vector , and these agonists represent potent targets for transmission-blocking by either inhibiting or interfering with them pre- or post-transcriptionally .", "The recently developed CRISPR/Cas9-based genome editing tools for Anophel...	[ "The causative agent of malaria , Plasmodium , has to complete a complex infection cycle in the Anopheles gambiae mosquito vector in order to reach the salivary gland from where it can be transmitted to a human host .", "The parasite’s development in the mosquito relies on numerous host factors ( agonists ) , and...	2018
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "tropical diseases", "geographical locations", "uganda", "parasitic diseases", "parasitology", "neglected tropical diseases", "ethiopia", "africa", "research and analysis methods", "cameroon", "elephantiasis", "podoconiosis", "epidemiology", "research asse...	Global epidemiology of podoconiosis: A systematic review	journal.pntd.0006324	null	[ [ "Podoconiosis is a neglected tropical disease caused by exposure to red clay soil [1 , 2] .", "The disease results from a complex interaction between genes and the environment occurring over many years .", "Mineral particles from the soil penetrate the skin and are taken up by macrophages in the lymph...	[ "Podoconiosis is one of the few diseases that could potentially be eliminated within one generation .", "Nonetheless , the global distribution of the disease remains largely unknown .", "The global atlas of podoconiosis was conceived to define the epidemiology and distribution of podoconiosis through dedicated ...	[ "Podoconiosis is one of the Neglected Tropical Diseases , and causes painful and massive swelling of the lower legs .", "Despite the importance of the disease , its global distribution and epidemiology are poorly understood .", "We conducted a systematic review to assess the global epidemiology of podoconiosis ...	2018
[ "Introduction", "Results/Discussion", "Materials and Methods", "Supporting Information" ]	[ "mus (mouse)", "homo (human)", "genetics and genomics", "neurological disorders" ]	Deletion at ITPR1 Underlies Ataxia in Mice and Spinocerebellar Ataxia 15 in Humans	journal.pgen.0030108	null	[ [ "The use of forward genetics to define novel loci of interest in human disease has become increasingly viable with the implementation of large-scale mutagenesis programs .", "Prior to these initiatives this work was carried out in part by the investigation of spontaneous mutations that cause disorders in ...	[ "We observed a severe autosomal recessive movement disorder in mice used within our laboratory .", "We pursued a series of experiments to define the genetic lesion underlying this disorder and to identify a cognate disease in humans with mutation at the same locus .", "Through linkage and sequence analysis we s...	[ "We have identified a spontaneous in-frame deletion mutation in the gene Itpr1 that causes a recessive movement disorder in mice .", "In an attempt to define whether any similar disease occurs in humans we performed a literature search for diseases linked to the human chromosomal region containing ITPR1 .", "We...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "white cells", "infectious disease control", "hematology" ]	Unconventional Repertoire Profile Is Imprinted during Acute Chikungunya Infection for Natural Killer Cells Polarization toward Cytotoxicity	journal.ppat.1002268	null	[ [ "Emerging and re-emerging viral infectious diseases can cause devastating illnesses in humans and are accordingly one of the principal challenges in global health care today .", "Among these viruses , arthropod-borne arboviruses are especially important because many of them cause fatal diseases in humans ...	[ "Chikungunya virus ( CHIKV ) is a worldwide emerging pathogen .", "In humans it causes a syndrome characterized by high fever , polyarthritis , and in some cases lethal encephalitis .", "Growing evidence indicates that the innate immune response plays a role in controlling CHIKV infection .", "We show here th...	[ "Chikungunya virus ( CHIKV ) infection , which is responsible for devastating human illness , is rapidly becoming a global concern .", "The spread of this disease throughout tropical areas , where it now affects nearly 40 countries , underlines the need to improve our understanding of this infection .", "In 200...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "systems biology", "genome expression analysis", "genomics", "biology", "computational biology", "genetics and genomics" ]	Teasing Apart Translational and Transcriptional Components of Stochastic Variations in Eukaryotic Gene Expression	journal.pcbi.1002644	null	[ [ "The stochastic nature of gene expression promotes cell-to-cell differences in protein level , usually referred to as noise [1] , [2] , [3] .", "Recent studies , both experimental and computational , have revealed that such cell-to-cell variability can be both disadvantageous [4] , [5] , [6] , [7] , [8] ,...	[ "The intrinsic stochasticity of gene expression leads to cell-to-cell variations , noise , in protein abundance .", "Several processes , including transcription , translation , and degradation of mRNA and proteins , can contribute to these variations .", "Recent single cell analyses of gene expression in yeast ...	[ "The stochastic nature of gene expression leads to cell-to-cell differences in protein level referred to as noise .", "Expression noise can be disadvantageous , by affecting the precision of biological functions , but it may also be advantageous by enabling heterogeneous stress-response programs to environmental ...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	A Multi-layered Protein Network Stabilizes the Escherichia coli FtsZ-ring and Modulates Constriction Dynamics	journal.pgen.1005128	null	[ [ "Prokaryotic cell division is a conserved process that requires the formation of a multi-protein complex ( divisome ) at midcell [1] .", "Although many molecular constituents of the divisome have been identified [2] , its in-vivo structural organization remains elusive .", "Understanding divisome arch...	[ "The prokaryotic tubulin homolog , FtsZ , forms a ring-like structure ( FtsZ-ring ) at midcell .", "The FtsZ-ring establishes the division plane and enables the assembly of the macromolecular division machinery ( divisome ) .", "Although many molecular components of the divisome have been identified and their i...	[ "Bacterial cell division is a highly regulated process that must be coordinated with other cellular processes ( i . e . DNA replication and chromosome segregation ) to promote faithful reproduction .", "In Escherichia coli , this regulation is most often mediated through the polymerization of the prokaryotic tubu...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "infectious diseases", "none", "in vitro", "microbiology", "computational biology", "biophysics", "eubacteria" ]	Structure of GrlR and the Implication of Its EDED Motif in Mediating the Regulation of Type III Secretion System in EHEC	journal.ppat.0030069	null	[ [ "The enterohemorrhagic Escherichia coli ( EHEC ) and enteropathogenic E . coli ( EPEC ) are closely related human enteric pathogens [1] .", "EPEC causes severe diarrhea in young children in developing countries , while EHEC is a causative agent of hemorrhagic colitis , which is more common in the industri...	[ "Enterohemorrhagic Escherichia coli ( EHEC ) is a common cause of severe hemorrhagic colitis .", "EHEC's virulence is dependent upon a type III secretion system ( TTSS ) encoded by 41 genes .", "These genes are organized in several operons clustered in the locus of enterocyte effacement .", "Most of the locus...	[ "Attaching and effacing pathogens are a group of enteric pathogens that includes the closely related enterohemorrhagic Escherichia coli ( EHEC ) and enteropathogenic E . coli ( EPEC ) .", "EPEC causes severe diarrhea in young children in developing countries , while EHEC is a causative agent of hemorrhagic coliti...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Suppression of Somatic Expansion Delays the Onset of Pathophysiology in a Mouse Model of Huntington’s Disease	journal.pgen.1005267	null	[ [ "HD is an autosomal dominant neurodegenerative disorder in which the underlying mutation is a CAG expansion within exon 1 of the mutant allele [1–3] .", "Inheriting the expanded HD allele is sufficient to develop disease .", "However , somatic expansion is prominent in HD patients and it has been spec...	[ "Huntington’s Disease ( HD ) is caused by inheritance of a single disease-length allele harboring an expanded CAG repeat , which continues to expand in somatic tissues with age .", "The inherited disease allele expresses a toxic protein , and whether further somatic expansion adds to toxicity is unknown .", "We...	[ "Huntington’s Disease ( HD ) is caused by inheritance of a single disease-length allele harboring an expanded CAG repeat , which continues to expand in somatic tissues with age .", "There is no correction for the inherited mutation , but if somatic expansion contributes to disease , then a therapeutic approach is...	2015
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "blood cells", "innate immune system", "medicine and health sciences", "immune cells", "immune physiology", "pathology and laboratory medicine", "cytokines", "immunology", "microbiology", "sand flies", "parasitic diseases", "parasitic protozoans", "protozoan life cycles", "physiological pr...	Leishmania proteophosphoglycans regurgitated from infected sand flies accelerate dermal wound repair and exacerbate leishmaniasis via insulin-like growth factor 1-dependent signalling	journal.ppat.1006794	null	[ [ "Leishmania is a genus of protozoan parasites transmitted by the bites of infected phlebotomine sand flies .", "Infection by sand fly bite is very efficient and difficult to replicate using needles .", "Along with the parasites , the sand fly injects saliva and a parasite-derived , glycan-rich gel ter...	[ "Leishmania parasites are transmitted to vertebrate hosts by female phlebotomine sand flies as they bloodfeed by lacerating the upper capillaries of the dermis with their barbed mouthparts .", "In the sand fly midgut secreted proteophosphoglycans from Leishmania form a biological plug known as the promastigote se...	[ "Female phlebotomine sand flies efficiently transmit Leishmania parasites , yet the underlying mechanisms remain poorly understood .", "During transmission , promastigote secretory gel ( PSG ) regurgitated from the blocked sand fly gut promote Leishmania infection and exacerbates disease .", "Here we investigat...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "infectious diseases/hiv infection and aids" ]	Relationship between Functional Profile of HIV-1 Specific CD8 T Cells and Epitope Variability with the Selection of Escape Mutants in Acute HIV-1 Infection	journal.ppat.1001273	null	[ [ "The development of vaccines capable of controlling infections by intracellular pathogens , including HIV-1 , poses major challenges , since correlates of protection remain elusive [1] , [2] .", "The initial observation that the appearance of HIV-specific CD8+ T cell responses is temporally associated wit...	[ "In the present study , we analyzed the functional profile of CD8+ T-cell responses directed against autologous transmitted/founder HIV-1 isolates during acute and early infection , and examined whether multifunctionality is required for selection of virus escape mutations .", "Seven anti-retroviral therapy-naïve...	[ "An important role for the polyfunctional T-cell fraction of anti-HIV CD8 responses during chronic HIV infection has previously been suggested .", "This study characterized the role of polyfunctional T-cells directed against the transmitted/founder virus in the selection of viral escape mutants during acute HIV-1...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The Causative Gene in Chanarian Dorfman Syndrome Regulates Lipid Droplet Homeostasis in C. elegans	journal.pgen.1005284	null	[ [ "Most organisms possess a remarkable capacity to sense environmental variation and to modify their physiology accordingly to adapt to such changes .", "During periods of nutrient scarcity , animals prioritize the use of limiting macromolecules for survival benefit , even if it results in a temporary suspe...	[ "AMP-activated kinase ( AMPK ) is a key regulator of many cellular mechanisms required for adjustment to various stresses induced by the changing environment .", "In C . elegans dauer larvae AMPK-null mutants expire prematurely due to hyperactive Adipose Triglyceride Lipase ( ATGL-1 ) followed by rapid depletion ...	[ "Chanarin-Dorfman Syndrome ( CDS ) is a rare metabolic disease characterized by an abnormal accumulation of lipids in various tissues and organs due to a failure in lipid breakdown .", "Characteristic clinical features exhibited by affected patients include scaly skin ( ichthyosis ) , enlarged liver , blurred vis...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	A KH-Domain RNA-Binding Protein Interacts with FIERY2/CTD Phosphatase-Like 1 and Splicing Factors and Is Important for Pre-mRNA Splicing in Arabidopsis	journal.pgen.1003875	null	[ [ "Pre-mRNA processing , including 5′ capping , splicing and 3′ end formation , is highly regulated and often coupled with transcription to increase its accuracy and efficiency .", "The carboxyl terminal domain ( CTD ) of Rpb1 , the largest subunit of RNA polymerase II ( RNAP II ) , serves as a platform for...	[ "Eukaryotic genomes encode hundreds of RNA-binding proteins , yet the functions of most of these proteins are unknown .", "In a genetic study of stress signal transduction in Arabidopsis , we identified a K homology ( KH ) -domain RNA-binding protein , HOS5 ( High Osmotic Stress Gene Expression 5 ) , as required ...	[ "Pre-mRNA processing , including 5′ capping , splicing , and 3′ polyadenylation , is critical for gene expression and is closely coupled with transcription .", "Phosphorylated carboxyl terminal domain ( CTD ) of RNA Polymerase II ( RNAP II ) serves as a platform for the recruitment of pre-mRNA processing factors ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/protozoal infections", "biochemistry/cell signaling and trafficking structures", "microbiology/parasitology", "cell biology/cell signaling" ]	Distinct External Signals Trigger Sequential Release of Apical Organelles during Erythrocyte Invasion by Malaria Parasites	journal.ppat.1000746	null	[ [ "Malaria continues to be a major public health problem in tropical regions of the world .", "It is responsible for significant morbidity and mortality with around 300 to 500 million malaria cases reported annually that result in about 2 million malaria-related deaths [1] .", "Of the Plasmodium species...	[ "The invasion of erythrocytes by Plasmodium merozoites requires specific interactions between host receptors and parasite ligands .", "Parasite proteins that bind erythrocyte receptors during invasion are localized in apical organelles called micronemes and rhoptries .", "The regulated secretion of microneme an...	[ "Malaria remains a major public health problem in many parts of the tropical world .", "All the clinical symptoms of malaria are attributed to the blood stage of the parasite life cycle during which Plasmodium merozoites invade and multiply within host erythrocytes .", "Invasion by Plasmodium merozoites is a co...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "computational biology/literature analysis", "pharmacology/drug development", "molecular biology/bioinformatics" ]	Literature Mining for the Discovery of Hidden Connections between Drugs, Genes and Diseases	journal.pcbi.1000943	null	[ [ "A wealth of knowledge concerning the function of genes and their role in biological processes is present in the biomedical literature , embodied in full text articles or the Medline abstract database .", "Various text mining approaches have been developed to extract information on gene function from this...	[ "The scientific literature represents a rich source for retrieval of knowledge on associations between biomedical concepts such as genes , diseases and cellular processes .", "A commonly used method to establish relationships between biomedical concepts from literature is co-occurrence .", "Apart from its use i...	[ "The biomedical literature is an important source of knowledge on the function of genes and on the mechanisms by which these genes regulate cellular processes .", "Several text mining approaches have been developed to leverage this rich source of information by automatically extracting associations between concep...	2010
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "infectious diseases", "physiology/cardiovascular physiology and circulation", "immunology/immune response", "immunology/innate immunity", "pathology/immunology" ]	Molecular and Cellular Basis of Microvascular Perfusion Deficits Induced by Clostridium perfringens and Clostridium septicum	journal.ppat.1000045	null	[ [ "Gas gangrene is a life-threatening syndrome most commonly associated with invasion of tissue by the anaerobic bacterium , Clostridium perfringens type A . The pathology of gas gangrene is highly complex , but is thought to be mediated by disruptions in tissue perfusion , associated with alterations in platel...	[ "Reduced tissue perfusion leading to tissue ischemia is a central component of the pathogenesis of myonecrosis caused by Clostridium perfringens .", "The C . perfringens α-toxin has been shown capable of inducing these changes , but its potential synergy with perfringolysin O ( θ-toxin ) is less well understood ....	[ "Clostridial myonecrosis is a life-threatening process induced by infection with species such as C . perfringens and C . septicum .", "The associated pathology includes muscle death and a characteristic disruption in tissue perfusion .", "Exotoxins produced by these species have been implicated in the reduction...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "cell physiology", "medicine and health sciences", "immune cells", "protein metabolism", "immunology", "population genetics", "cell metabolism", "mammalian genomics", "population biology", "bacteria", "white blood cells", "animal cells", "t cells", "actinobacteria", "evo...	Within Host Evolution Selects for a Dominant Genotype of Mycobacterium tuberculosis while T Cells Increase Pathogen Genetic Diversity	journal.ppat.1006111	null	[ [ "Microbial pathogens adapt to host environments to establish replicative niches and counter immune responses .", "Adaption , which commonly relies on the generation and transmission of genetic variants with increased fitness , is especially critical for obligate pathogens that must infect , replicate , an...	[ "Molecular epidemiological assessments , drug treatment optimization , and development of immunological interventions all depend on understanding pathogen adaptation and genetic variation , which differ for specific pathogens .", "Mycobacterium tuberculosis is an exceptionally successful human pathogen , yet beyo...	[ "Mycobacterium tuberculosis is amongst the most successful and enigmatic pathogens that has burdened humanity for thousands of years .", "The success of this pathogen depends on unique strategies employed to adapt during infection .", "Understanding these strategies is key to decipher the complexity of M . tube...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "virology", "biology", "microbiology", "host-pathogen interaction" ]	Single Molecule Analysis of Replicated DNA Reveals the Usage of Multiple KSHV Genome Regions for Latent Replication	journal.ppat.1002365	null	[ [ "Kaposi's sarcoma associated herpesvirus , also referred to as human herpesvirus 8 ( HHV8 ) , belongs to the gammaherpesvirus family and is associated with multiple lymphoproliferative diseases including Body Cavity Based Lymphomas ( BCBLs ) and Multicentric Castleman's Disease ( MCDs ) [1] , [2] , [3] .", ...	[ "Kaposi's sarcoma associated herpesvirus ( KSHV ) , an etiologic agent of Kaposi's sarcoma , Body Cavity Based Lymphoma and Multicentric Castleman's Disease , establishes lifelong latency in infected cells .", "The KSHV genome tethers to the host chromosome with the help of a latency associated nuclear antigen ( ...	[ "Kaposi's sarcoma associated herpesvirus ( KSHV ) establishes lifelong infection in the infected host and induces lymphoproliferative diseases , body cavity based lymphomas and sarcomas in immune compromised individuals .", "Herpesviruses including KSHV uses host cellular replication machinery for the replication...	2011
[ "Introduction", "Materials and Methods", "Results and Discussion" ]	[ "invertebrates", "dengue virus", "medicine and health sciences", "pathology and laboratory medicine", "togaviruses", "chikungunya infection", "pathogens", "tropical diseases", "microbiology", "animals", "wolbachia", "alphaviruses", "organisms", "viruses", "chikungunya virus", "rna viru...	Rapid and Non-destructive Detection and Identification of Two Strains of Wolbachia in Aedes aegypti by Near-Infrared Spectroscopy	journal.pntd.0004759	null	[ [ "The mosquito Aedes aegypti is the primary vector of the four human dengue , chikungunya and Zika viruses .", "Options for developing effective vaccines or chemotherapeutics are limited [1] and vector control remains fundamental for the prevention of disease transmission .", "One of the most promising...	[ "The release of Wolbachia infected mosquitoes is likely to form a key component of disease control strategies in the near future .", "We investigated the potential of using near-infrared spectroscopy ( NIRS ) to simultaneously detect and identify two strains of Wolbachia pipientis ( wMelPop and wMel ) in male and...	[ "Near infrared spectroscopy ( NIRS ) is a technique that measures specific frequencies of light absorbed by C-H , O-H , S-H and N-H functional groups .", "Mosquito samples are grouped based upon absorption differences between their chemical properties .", "In this study , we used NIRS to differentiate", "1 ) ...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "oncology", "medicine and health sciences", "cancer genetics", "genetics", "biology and life sciences", "cancers and neoplasms", "gynecological tumors" ]	CDKN2D-WDFY2 Is a Cancer-Specific Fusion Gene Recurrent in High-Grade Serous Ovarian Carcinoma	journal.pgen.1004216	null	[ [ "Ovarian cancer is the most lethal gynecologic malignancy in women .", "Approximately 225 , 500 women are diagnosed with ovarian cancer with an estimated 140 , 200 associated deaths annually [1] .", "Almost 70% of the ovarian cancer cases are the high-grade serous carcinoma ( HG-SC ) subtype [1] , whi...	[ "Ovarian cancer is the fifth leading cause of cancer death in women .", "Almost 70% of ovarian cancer deaths are due to the high-grade serous subtype , which is typically detected only after it has metastasized .", "Characterization of high-grade serous cancer is further complicated by the significant heterogen...	[ "High-grade serous carcinoma ( HG-SC ) is the most common subtype of ovarian cancer observed in women .", "This subtype of ovarian cancer is typically detected at advanced stages due to lack of effective early screening tools .", "Recurrent cancer-specific gene fusions resulting from chromosomal translocations ...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "flow cytometry", "medicine and health sciences", "parasite groups", "immune cells", "plasmodium", "immunology", "tropical diseases", "parasitic diseases", "parasitic protozoans", "parasitology", "parasitemia", "apicomplexa", "protozoans", "quantitative parasitology", "r...	Microvesicles from malaria-infected red blood cells activate natural killer cells via MDA5 pathway	journal.ppat.1007298	null	[ [ "Human malaria is caused by parasites of the genus Plasmodium , and of which , P . falciparum causes most cases of severe malaria .", "The host innate immune system is the first line of defense against Plasmodium infection , and the outcome of early host-parasite interaction is a strong determinant for la...	[ "Natural killer ( NK ) cells provide the first line of defense against malaria parasite infection .", "However , the molecular mechanisms through which NK cells are activated by parasites are largely unknown , so is the molecular basis underlying the variation in NK cell responses to malaria infection in the huma...	[ "Malaria is an important parasitic disease with a major public health concern .", "Malaria pathogenesis involves a complex interplay between parasitic and host factors .", "A better understanding of early host response and the determinants of immunity are essential to developing innovative therapeutic approache...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "transfection", "medicine and health sciences", "coronaviruses", "pathology and laboratory medicine", "respiratory infections", "enzymes", "pathogens", "sars coronavirus", "microbiology", "enzymology", "pulmonology", "viruses", "rna viruses", "molecular biology techniques", "bunyaviruses...	Potent and selective inhibition of pathogenic viruses by engineered ubiquitin variants	journal.ppat.1006372	null	[ [ "Ubiquitination is a post-translational modification mediated by an enzyme cascade that results in the conjugation of ubiquitin ( Ub ) to cellular proteins [1 , 2] .", "This process is regulated in part through activity of cellular deubiquitinating enzymes ( DUBs ) , which remove Ub from cellular proteins...	[ "The recent Middle East respiratory syndrome coronavirus ( MERS-CoV ) , Ebola and Zika virus outbreaks exemplify the continued threat of ( re- ) emerging viruses to human health , and our inability to rapidly develop effective therapeutic countermeasures .", "Many viruses , including MERS-CoV and the Crimean-Cong...	[ "Emerging viruses pose a tremendous challenge to human health .", "While vaccine-based approaches are desirable in terms of infection prevention in the longer term , alternative antiviral strategies are needed , especially when providing treatment options for infected patients during acute outbreaks .", "Here w...	2017
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "ecology and environmental sciences", "medicine and health sciences", "astroparticle physics", "neurochemistry", "particle physics", "nervous system", "astronomical sciences", "electrophysiology", "neuroscience", "mathematics", "algebra", "neurotransmitters", "astrophysics", "extracellular...	Receptor recharge time drastically reduces the number of captured particles	journal.pcbi.1006015	null	[ [ "Particles moving and interacting with traps is a broad description of many biological processes .", "In individual applications , “particles” might represent , for example , molecules or prey , while “traps” could represent receptors or predators .", "Nevertheless , the mathematical description can b...	[ "Many diverse biological systems are described by randomly moving particles that can be captured by traps in their environment .", "Examples include neurotransmitters diffusing in the synaptic cleft before binding to receptors and prey roaming an environment before capture by predators .", "In most cases , the ...	[ "Consider particles that are released into an environment ( think diffusing molecules or plankton ) , and suppose that there are traps in the environment .", "How many particles will be captured by the traps before they escape ?", "In a standard model , the number of captured particles is proportional to the in...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "model organisms", "biology", "evolutionary biology" ]	C. elegans Germ Cells Show Temperature and Age-Dependent Expression of Cer1, a Gypsy/Ty3-Related Retrotransposon	journal.ppat.1002591	null	[ [ "DNA transposons , retrotransposons , and retroviruses that are expressed in germ cells have tremendous potential to damage the genome by creating novel insertions that are transmitted vertically to host progeny .", "Because DNA transposons replicate by an excision and reintegration mechanism ( “cut and p...	[ "Virus-like particles ( VLPs ) have not been observed in Caenorhabditis germ cells , although nematode genomes contain low numbers of retrotransposon and retroviral sequences .", "We used electron microscopy to search for VLPs in various wild strains of Caenorhabditis , and observed very rare candidate VLPs in so...	[ "Retrotransposons and retroviruses pose enormous threats to animal and plants because of their ability to insert into host genes .", "Retroelements that replicate in germ cells can , if left unchecked , expand exponentially in the host genome .", "C . elegans has proven to be an exceptional model system for stu...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "control engineering", "computer science", "control systems", "computational neuroscience", "biology", "computational biology" ]	Learning the Optimal Control of Coordinated Eye and Head Movements	journal.pcbi.1002253	null	[ [ "Previous computational studies on saccadic eye and head movements revolve around two questions .", "The first question concerns the optimality principles underlying the kinematic characteristics , and the second one is about the neural architecture that generates appropriate control signals for driving e...	[ "Various optimality principles have been proposed to explain the characteristics of coordinated eye and head movements during visual orienting behavior .", "At the same time , researchers have suggested several neural models to underly the generation of saccades , but these do not include online learning as a mec...	[ "Human beings and many other species redirect their gaze towards targets of interest through rapid gaze shifts known as saccades .", "These are made approximately three to four times every second , and larger saccades result from fast and concurrent movement of the animal's eyes and head .", "Experimental studi...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases/neglected tropical diseases" ]	Genetic Diversity and Microevolution of Burkholderia pseudomallei in the Environment	journal.pntd.0000182	null	[ [ "The soil dwelling Gram-negative bacterium Burkholderia pseudomallei is the cause of melioidosis .", "This organism is present in the environment across much of southeast Asia and Northern Australia and is increasingly recognised elsewhere , including parts of South America [1] , [2] .", "Infection oc...	[ "The soil dwelling Gram-negative pathogen Burkholderia pseudomallei is the cause of melioidosis .", "The diversity and population structure of this organism in the environment is poorly defined .", "We undertook a study of B . pseudomallei in soil sampled from 100 equally spaced points within 237 . 5 m2 of disu...	[ "The soil dwelling Gram-negative bacterium Burkholderia pseudomallei is the cause of melioidosis , a serious human infection that occurs in Southeast Asia and northern Australia .", "The purpose of this study was to evaluate the population genetic structure of B . pseudomallei in the environment .", "To achieve...	2008
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics and genomics/genomics", "computational biology/population genetics", "evolutionary biology/animal genetics", "computational biology/molecular genetics", "genetics and genomics/chromosome biology", "genetics and genomics/plant genomes and evolution", "computational biology/genomics", "genetic...	Broad-Scale Recombination Patterns Underlying Proper Disjunction in Humans	journal.pgen.1000658	null	[ [ "Like most sexually reproducing organisms , humans undergo meiotic recombination .", "This process plays an important role in evolutionary dynamics , generating new combination of alleles on which natural selection can act ( [1] and references therein ) , and in DNA repair .", "In humans , recombinati...	[ "Although recombination is essential to the successful completion of human meiosis , it remains unclear how tightly the process is regulated and over what scale .", "To assess the nature and stringency of constraints on human recombination , we examined crossover patterns in transmissions to viable , non-trisomic...	[ "In humans , as in most sexually reproducing organisms , recombination plays a fundamental role in meiosis , helping to align chromosomes and to ensure their proper segregation .", "Recombination events are tightly regulated both in terms of their minimum number ( the rule of “crossover assurance” ) and placement...	2009
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "viruses", "infectious diseases", "public health and epidemiology", "virology" ]	Detecting Emerging Transmissibility of Avian Influenza Virus in Human Households	journal.pcbi.0030145	null	[ [ "Outbreaks of highly pathogenic H5N1 avian influenza in Southeast Asia , Europe , and Africa have devastating consequences for poultry [1 , 2] , and have resulted in numerous infections in humans [3–5] .", "Although these infections from the animal reservoir continue to accumulate , the virus does not see...	[ "Accumulating infections of highly pathogenic H5N1 avian influenza in humans underlines the need to track the ability of these viruses to spread among humans .", "A human-transmissible avian influenza virus is expected to cause clusters of infections in humans living in close contact .", "Therefore , epidemiolo...	[ "Recent outbreaks of emerging diseases such as SARS and H5N1 avian influenza have underlined the fact that animal pathogens may acquire the ability to spread efficiently in humans .", "Monitoring the transmissibility of pathogens from the animal reservoir in humans is key for early detection of epidemic spread , ...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "computational biology/population genetics", "computational biology/molecular genetics", "computational biology/genomics" ]	Gene Expression Variability within and between Human Populations and Implications toward Disease Susceptibility	journal.pcbi.1000910	null	[ [ "In both prokaryotic and eukaryotic organisms , variations in gene expression exist widely within and between populations , which can be attributed to either genetic or non-genetic factors .", "Genetic factors are changes in DNA sequence that cause expression differences , such as single nucleotide polymo...	[ "Variations in gene expression level might lead to phenotypic diversity across individuals or populations .", "Although many human genes are found to have differential mRNA levels between populations , the extent of gene expression that could vary within and between populations largely remains elusive .", "To i...	[ "Many human genes have population-specific expression levels , which are linked to population-specific polymorphisms and copy-number variations .", "However , it is unclear whether human genes show similar dynamic range of expression between populations .", "In this work we analyzed HapMap gene expression compe...	2010
[ "Introduction", "Results/Discussion", "Methods" ]	[ "medicine", "immunology", "physical laws and principles", "physical chemistry", "vaccination", "infectious diseases", "proteins", "chemistry", "biology", "physics", "biochemistry", "computer science", "computer modeling", "clinical immunology", "immunity", "viral diseases" ]	On the Effect of Thermodynamic Equilibrium on the Assembly Efficiency of Complex Multi-Layered Virus-Like Particles (VLP): the Case of Rotavirus VLP	journal.pcbi.1002367	null	[ [ "The in vivo assembly of virus-like particles ( VLP ) , multi-protein structures , in unnatural host systems results many times in predominantly malformed structures because the host biology provides neither the adequate spatial and temporal protein expression conditions nor the ideal thermodynamic environmen...	[ "Previous studies have reported the production of malformed virus-like-particles ( VLP ) in recombinant host systems .", "Here we computationally investigate the case of a large triple-layered rotavirus VLP ( RLP ) .", "In vitro assembly , disassembly and reassembly data provides strong evidence of microscopic ...	[ "Virus-like particles ( VLP ) are multi-protein structures with potential to be used in biomedicine as therapeutic or prophylactic vaccines against many worldwide diseases .", "However , due to their complex process of assembly , production yields are commonly low hindering a fast transition from lab- to industri...	2012
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "burholderia", "infectious diseases", "mycobacterium", "listeria", "immunology", "salmonella", "drosophila", "genetics and genomics" ]	Drosophila eiger Mutants Are Sensitive to Extracellular Pathogens	journal.ppat.0030041	null	[ [ "The fruit fly has four main immune mechanisms to fight circulating microbes .", "These mechanisms include secreted antimicrobial peptides ( AMPs ) , melanization , clotting , and phagocytic hemocytes [1−4] .", "The most deeply studied of these mechanisms , AMP secretion , is controlled by the Toll an...	[ "We showed previously that eiger , the Drosophila tumor necrosis factor homolog , contributes to the pathology induced by infection with Salmonella typhimurium .", "We were curious whether eiger is always detrimental in the context of infection or if it plays a role in fighting some types of microbes .", "We ch...	[ "We show that the gene eiger , which is the sole tumor necrosis factor homolog in the fruit fly , can play opposing roles in the fly's response to infections .", "Sometimes eiger contributes to the disease induced by an infection , while at other times it is required to fight an infection .", "Commonly , the fl...	2007
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	The Decay of Motor Memories Is Independent of Context Change Detection	journal.pcbi.1004278	null	[ [ "Motor adaptation driven by performance error generally decays back toward baseline when error information is withheld or held near zero using zero-error clamp ( zEC ) trials [1–12] .", "This effect has conventionally been explained by the intrinsic decay hypothesis , which asserts that new learning is in...	[ "When the error signals that guide human motor learning are withheld following training , recently-learned motor memories systematically regress toward untrained performance .", "It has previously been hypothesized that this regression results from an intrinsic volatility in these memories , resulting in an inevi...	[ "Suppose you are asked to shoot free throws with a basketball .", "If you’re an unskilled shooter , you may at first miss in a consistent way for consecutive shots—perhaps a bit to the right—but you will soon learn to correct that error .", "However , an often-repeated finding is that if error information is wi...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "anatomy", "computational neuroscience", "nervous system", "single neuron function", "biology and life sciences", "computational biology", "motor system", "neuroscience", "coding mechanisms" ]	Predicting the Responses of Repetitively Firing Neurons to Current Noise	journal.pcbi.1003612	null	[ [ "Some neurons fire repetitively in the absence of any input , and many others show repetitive firing with sufficient tonic excitation .", "Because the same neuron may be driven to fire by a large transient synaptic input either from the rest state or when firing repetitively , often no strong distinction ...	[ "We used phase resetting methods to predict firing patterns of rat subthalamic nucleus ( STN ) neurons when their rhythmic firing was densely perturbed by noise .", "We applied sequences of contiguous brief ( 0 . 5–2 ms ) current pulses with amplitudes drawn from a Gaussian distribution ( 10–100 pA standard devia...	[ "Most neurons receive thousands of synaptic inputs per second .", "Each of these may be individually weak but collectively they shape the temporal pattern of firing by the postsynaptic neuron .", "If the postsynaptic neuron fires repetitively , its synaptic inputs need not directly trigger action potentials , b...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "mathematics", "neuroscience/cognitive neuroscience", "computational biology/computational neuroscience", "computational biology" ]	Transient Cognitive Dynamics, Metastability, and Decision Making	journal.pcbi.1000072	null	[ [ "The dynamical approach for studying brain activity has a long history and is currently one of strong interest [1]–[7] .", "Cognitive functions are manifested through the generation and transformation of cooperative modes of activity .", "Different brain regions participate in these processes in disti...	[ "The idea that cognitive activity can be understood using nonlinear dynamics has been intensively discussed at length for the last 15 years .", "One of the popular points of view is that metastable states play a key role in the execution of cognitive functions .", "Experimental and modeling studies suggest that...	[ "The modeling of the temporal structure of cognitive processes is a key step for understanding cognition .", "Cognitive functions such as sequential learning , short-term memory , and decision making in a changing environment cannot be understood using only the traditional view based on classical concepts of nonl...	2008
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Elimination of Schistosomiasis Transmission in Zanzibar: Baseline Findings before the Onset of a Randomized Intervention Trial	journal.pntd.0002474	null	[ [ "Schistosomiasis ranks third after soil-transmitted helminthiasis and leishmaniasis regarding disease burden estimates of neglected tropical diseases ( NTDs ) , and causes an estimated 3 . 3 million disability-adjusted life years ( DALYs ) [1] .", "In Africa alone , it is estimated that some 200 million p...	[ "Gaining and sustaining control of schistosomiasis and , whenever feasible , achieving local elimination are the year 2020 targets set by the World Health Organization .", "In Zanzibar , various institutions and stakeholders have joined forces to eliminate urogenital schistosomiasis within 5 years .", "We repor...	[ "Schistosomiasis is a chronic and debilitating disease caused by parasitic worms .", "It negatively impacts on the health and wellbeing of mainly rural dwellers in tropical and sub-tropical countries .", "The World Health Organization recently put forward an ambitious goal for the year 2020: to control schistos...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "systems biology", "medicine", "infectious diseases", "genetics", "immunology", "biology", "microbiology", "critical care and emergency medicine" ]	A Comprehensive Analysis of In Vitro and In Vivo Genetic Fitness of Pseudomonas aeruginosa Using High-Throughput Sequencing of Transposon Libraries	journal.ppat.1003582	null	[ [ "The complex interaction of a pathogenic bacterium with a host leading to disease can be viewed as the coordinated and highly-regulated actions of a multitude of factors that allows the infecting organisms to successfully colonize tissue , occasionally disseminate and avoid the activities of host defense mech...	[ "High-throughput sequencing of transposon ( Tn ) libraries created within entire genomes identifies and quantifies the contribution of individual genes and operons to the fitness of organisms in different environments .", "We used insertion-sequencing ( INSeq ) to analyze the contribution to fitness of all non-es...	[ "To determine the contribution of all non-essential genes of Pseudomonas aeruginosa to overall fitness in laboratory and infectious settings , we used a high throughput sequencing method that quantitatively identifies the bacterial genes interrupted by random insertion of transposons ( Tn ) into the genome of strai...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "evolutionary biology/genomics", "evolutionary biology/evolutionary ecology", "evolutionary biology/evolutionary and comparative genetics" ]	Analysis of Chimpanzee History Based on Genome Sequence Alignments	journal.pgen.1000057	null	[ [ "At least four distinct populations of chimpanzees have been defined based on morphological and geographic criteria , including bonobos ( Pan paniscus ) and three common chimpanzee populations: eastern ( Pan troglodytes schweinfurthii ) , central ( Pan troglodytes troglodytes ) , and western ( Pan troglodytes...	[ "Population geneticists often study small numbers of carefully chosen loci , but it has become possible to obtain orders of magnitude for more data from overlaps of genome sequences .", "Here , we generate tens of millions of base pairs of multiple sequence alignments from combinations of three western chimpanzee...	[ "Studies of population history traditionally examine a small number of genetic regions in many individuals; however , with genome sequencing technologies it is possible to assemble data sets with thousands more aligned sequences albeit in fewer individuals .", "To explore whether such data can provide useful insi...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "parasite groups", "medicine and health sciences", "body fluids", "plasmodium", "parasitic diseases", "parasitic protozoans", "parasitology", "membrane proteins", "apicomplexa", "protozoans", "phylogenetic analysis", "molecular biology techniques", "cellular structures and organelles", "re...	Variant Exported Blood-Stage Proteins Encoded by Plasmodium Multigene Families Are Expressed in Liver Stages Where They Are Exported into the Parasitophorous Vacuole	journal.ppat.1005917	null	[ [ "Malaria parasites ( Plasmodium spp . ) invade both liver cells and red blood cells ( RBC ) in the vertebrate host .", "They actively remodel the infected RBC ( iRBC ) by exporting and trafficking various proteins to the RBC cytoplasm and the plasma membrane [1–7] .", "These Plasmodium proteins are in...	[ "Many variant proteins encoded by Plasmodium-specific multigene families are exported into red blood cells ( RBC ) .", "P . falciparum-specific variant proteins encoded by the var , stevor and rifin multigene families are exported onto the surface of infected red blood cells ( iRBC ) and mediate interactions betw...	[ "Malaria-parasites invade and multiply in hepatocytes and erythrocytes .", "The human parasite P . falciparum transports proteins encoded by multigene families onto the surface of erythrocytes , mediating interactions between infected red blood cells ( iRBCs ) and other host-cells and are thought to play a key ro...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "phosphorylation", "meiosis", "medicine and health sciences", "reproductive system", "immune physiology", "protein interactions", "spleen", "cell cycle and cell division", "cell processes", "reproductive physiology", "immunoprecipitation", "research and analysis methods", "chromosome biology...	Proteomic Landscape of Tissue-Specific Cyclin E Functions in Vivo	journal.pgen.1006429	null	[ [ "E-type cyclins ( cyclins E1 and E2 , collectively referred to as ‘cyclin E’ ) represent components of the core cell cycle machinery .", "The two E-cyclins are encoded by separate genes , but they show substantial amino acid sequence similarity .", "In proliferating cells , E-cyclins become upregulate...	[ "E-type cyclins ( cyclins E1 and E2 ) are components of the cell cycle machinery that has been conserved from yeast to humans .", "The major function of E-type cyclins is to drive cell division .", "It is unknown whether in addition to their ‘core’ cell cycle functions , E-type cyclins also perform unique tissu...	[ "The proliferation of mammalian cells is driven by proteins called cyclins , which bind and activate their catalytic partners , the cyclin-dependent kinases ( Cdks ) .", "Cyclin-Cdk complexes drive cell proliferation by phosphorylating several cellular proteins .", "This study focuses on the E-type cyclins ( cy...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "cloning", "sequence assembly tools", "genetic mapping", "genome analysis", "molecular biology techniques", "molecular genetics", "plants", "flowering plants", "research and analysis methods", "sequence analysis", "grapevine", "genomic libraries", "sequence alignment", "bioinformatics", ...	Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay	journal.pgen.1007807	null	[ [ "Chardonnay is known for the production of some of the world’s most iconic wines and is predicted to be the result of a cross between the Vitis vinifera cultivars Pinot noir and Gouais blanc [1 , 2] .", "Since first appearing in European vineyards , Chardonnay has spread throughout the world and has becom...	[ "Chardonnay is the basis of some of the world’s most iconic wines and its success is underpinned by a historic program of clonal selection .", "There are numerous clones of Chardonnay available that exhibit differences in key viticultural and oenological traits that have arisen from the accumulation of somatic mu...	[ "Phenotypic variation within a grapevine cultivar arises from an accumulation of mutations from serial vegetative propagation .", "Old cultivars such as Chardonnay have been propagated for centuries resulting in hundreds of available ‘clones’ containing unique genetic mutations and a range of various phenotypic p...	2018
[ "Introduction", "Results/Discussion", "Materials and Methods", "Supporting Information" ]	[ "none", "biochemistry" ]	Evolution of Function in the “Two Dinucleotide Binding Domains” Flavoproteins	journal.pcbi.0030121	null	[ [ "The large disparity between the number of unique protein folds and the number of unique proteins that exist in biological organisms [1] indicates that nature has utilized a relatively small number of folds to generate a large number of different functions .", "Nature's strategy for recruiting a protein s...	[ "Structural and biochemical constraints force some segments of proteins to evolve more slowly than others , often allowing identification of conserved structural or sequence motifs that can be associated with substrate binding properties , chemical mechanisms , and molecular functions .", "We have assessed the fu...	[ "The sequencing of genomes from different species has provided a unique opportunity for comparative analysis and opened the door to a higher level of understanding of living organisms .", "However , identifying the biochemical functions of the protein products coded by these genes has proved to be a major challen...	2007
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "bacterial diseases", "infectious diseases", "test evaluation", "diagnostic medicine", "neglected tropical diseases" ]	Diagnostic Accuracy of a Loop-Mediated Isothermal PCR Assay for Detection of Orientia tsutsugamushi during Acute Scrub Typhus Infection	journal.pntd.0001307	null	[ [ "Scrub typhus , caused by Orientia tsutsugamushi , is an important acute febrile illness in the Asia-Pacific region and is endemic in Thailand and Laos [1]–[2] .", "The clinical discrimination of scrub typhus from other undifferentiated fevers , such as dengue , malaria and leptospirosis , is often very d...	[ "There is an urgent need to develop rapid and accurate point-of-care ( POC ) technologies for acute scrub typhus diagnosis in low-resource , primary health care settings to guide clinical therapy .", "In this study we present the clinical evaluation of loop-mediated isothermal PCR assay ( LAMP ) in the context of...	[ "There is an urgent need for alternative diagnostic methods for scrub typhus , but evaluation of these is hampered because the current serological gold standard ( IFA ) is imperfect .", "In a study from Thailand , 3 of 20 ( 15% ) patients with fever had a positive Orientia tsutsugamushi PCR result despite negativ...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell binding", "cell physiology", "medicine and health sciences", "pathology and laboratory medicine", "viral transmission and infection", "hela cells", "gene regulation", "pathogens", "biological cultures", "tropical diseases", "microbiology", "salmonellosis", "shigella", "bacterial dise...	Analysis of host microRNA function uncovers a role for miR-29b-2-5p in Shigella capture by filopodia	journal.ppat.1006327	null	[ [ "Shigella flexneri ( Shigella ) , a facultative Gram-negative bacterium , is a major causative agent of bacillary dysentery in humans [1 , 2] .", "A key feature in the pathogenesis of Shigella concerns its capability to efficiently colonize the colonic mucosa , in particular the epithelial cells therein ,...	[ "MicroRNAs play an important role in the interplay between bacterial pathogens and host cells , participating as host defense mechanisms , as well as exploited by bacteria to subvert host cellular functions .", "Here , we show that microRNAs modulate infection by Shigella flexneri , a major causative agent of bac...	[ "MicroRNAs are genome-encoded small non-coding RNAs that play a pivotal role in post-transcriptional regulation of gene expression .", "In addition to other biological functions , microRNAs are increasingly recognized as important players in the complex interaction between host and bacterial pathogens .", "In t...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genome-wide association studies", "heredity", "genetics", "biology", "evolutionary biology", "evolutionary genetics", "genetics and genomics", "human genetics" ]	Genetic Architecture of Skin and Eye Color in an African-European Admixed Population	journal.pgen.1003372	null	[ [ "Differences in human skin color have been shaped principally and dramatically by selection [1] , [2] , and therefore the underlying genetic architecture may inform disease-related traits such as obesity or hypertension , for which common susceptibility alleles may have been advantageous to early humans that ...	[ "Variation in human skin and eye color is substantial and especially apparent in admixed populations , yet the underlying genetic architecture is poorly understood because most genome-wide studies are based on individuals of European ancestry .", "We study pigmentary variation in 699 individuals from Cape Verde ,...	[ "Differences in skin and eye color are some of the most obvious traits that underlie human diversity , yet most of our knowledge regarding the genetic basis for these traits is based on the limited range of variation represented by individuals of European ancestry .", "We have studied a unique population in Cape ...	2013
[ "Introduction", "Results", "Discussion", "Model" ]	[ "systems biology", "biophysic al simulations", "biology", "computational biology", "biophysics simulations", "biophysics", "biomechanics" ]	Dynamic Modeling of Cell Migration and Spreading Behaviors on Fibronectin Coated Planar Substrates and Micropatterned Geometries	journal.pcbi.1002926	null	[ [ "Understanding cell migration mechanisms is a critical issue in many biophysical phenomena , including angiogenesis , tumor growth , metastasis , and wound healing [1]–[3] .", "Cell migration is a complex multifaceted process , triggered by chemotaxis and haptotatic responses from the extracellular enviro...	[ "An integrative cell migration model incorporating focal adhesion ( FA ) dynamics , cytoskeleton and nucleus remodeling , actin motor activity , and lamellipodia protrusion is developed for predicting cell spreading and migration behaviors .", "This work is motivated by two experimental works: ( 1 ) cell migratio...	[ "Cell migration is a complex , multifaceted process , triggered by chemotaxis and haptotatic responses from the extracellular matrix ( ECM ) .", "It is triggered by a thin lamellipodium protrusion at the leading edge , followed by the assembly of a number of focal adhesions between the lamellipodium base and the ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/animal genetics", "biochemistry", "genetics and genomics/gene expression", "cell biology", "genetics and genomics/gene function", "biochemistry/transcription and translation", "genetics and genomics/epigenetics", "developmental biology/developmental molecular mechanisms", "cel...	Epigenetic Silencing of Spermatocyte-Specific and Neuronal Genes by SUMO Modification of the Transcription Factor Sp3	journal.pgen.1001203	null	[ [ "A plethora of proteins involved in regulating gene expression such as promoter-specific transcription factors , cofactors and chromatin-modifying enzymes are reversibly modified by the Small Ubiquitin-like MOdifier SUMO ( reviewed in [1] , [2] ) .", "With few exceptions , SUMO modification of transcripti...	[ "SUMO modification of transcription factors is linked to repression of transcription .", "The physiological significance of SUMO attachment to a particular transcriptional regulator , however , is largely unknown .", "We have employed the ubiquitously expressed murine transcription factor Sp3 to analyze the rol...	[ "Cell type–specific gene expression patterns are largely regulated by positively or negatively acting transcription factors binding to promoter and enhancer elements .", "The ubiquitous transcription factor Sp3 represents a paradigm for a dual function transcription factor as it can activate and repress transcrip...	2010
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "learning", "tangents", "ellipses", "social sciences", "geometry", "learning and memory", "neuroscience", "probability distribution", "mathematics", "cognitive psychology", "computational neuroscience", "vision", "coding mechanisms", "animal cells", "probability theory", "psychology", ...	Accuracy Maximization Analysis for Sensory-Perceptual Tasks: Computational Improvements, Filter Robustness, and Coding Advantages for Scaled Additive Noise	journal.pcbi.1005281	null	[ [ "Perception science seeks to determine how perceiving organisms estimate behaviorally relevant properties of the environment based on proximal stimuli captured by the senses .", "Understanding the details of the sensory-perceptual processing that support these abilities with natural stimuli is a primary f...	[ "Accuracy Maximization Analysis ( AMA ) is a recently developed Bayesian ideal observer method for task-specific dimensionality reduction .", "Given a training set of proximal stimuli ( e . g . retinal images ) , a response noise model , and a cost function , AMA returns the filters ( i . e . receptive fields ) t...	[ "In psychophysics and neurophysiology , the stimulus features that are manipulated in experiments are often selected based on intuition , trial-and-error , and historical precedence .", "Accuracy Maximization Analysis ( AMA ) is a Bayesian ideal observer method for determining the task-relevant features ( i . e ....	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology", "biology and life sciences", "immunology", "microbiology", "molecular cell biology" ]	Biogenesis of Influenza A Virus Hemagglutinin Cross-Protective Stem Epitopes	journal.ppat.1004204	null	[ [ "IAV is responsible for considerable human morbidity and mortality , with enormous attendant economic costs .", "Current vaccines are at best effective only for a few years due to the evolution of human IAV strains that escape vaccine- or infection-induced immunity .", "The most relevant immune escape...	[ "Antigenic variation in the globular domain of influenza A virus ( IAV ) hemagglutinin ( HA ) precludes effective immunity to this major human pathogen .", "Although the HA stem is highly conserved between influenza virus strains , HA stem-reactive antibodies ( StRAbs ) were long considered biologically inert .",...	[ "Extensive variation in the IAV HA globular domain severely impedes influenza vaccination .", "Recent findings demonstrate that StRAbs , specific Abs to the highly conserved stem region of HA , can protect hosts against a broad variety of influenza virus strains .", "In investigating the binding of StRAbs to HA...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Trans-generational Immune Priming Protects the Eggs Only against Gram-Positive Bacteria in the Mealworm Beetle	journal.ppat.1005178	null	[ [ "Maternal effects are of paramount importance for offspring fitness when mothers adjust the phenotype of their offspring to match the environment that they are likely to experience [1] .", "For instance , in many different groups of animals , the immunogenic experience of the mother is transferred to othe...	[ "In many vertebrates and invertebrates , offspring whose mothers have been exposed to pathogens can exhibit increased levels of immune activity and/or increased survival to infection .", "Such phenomena , called “Trans-generational immune priming” ( TGIP ) are expected to provide immune protection to the offsprin...	[ "In some insects , the immunological experience of mothers is transferred to their otherwise naïve offspring , protecting them against infection .", "Such a maternal effect has likely evolved from selective pressure imposed by the persistence of some microbial pathogens in the environment between insect generatio...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "molecular biology/post-translational regulation of gene expression", "molecular biology/rna-protein interactions", "genetics and genomics/gene expression", "molecular biology/rna splicing", "biochemistry/bioinformatics" ]	The CUGBP2 Splicing Factor Regulates an Ensemble of Branchpoints from Perimeter Binding Sites with Implications for Autoregulation	journal.pgen.1000595	null	[ [ "Alternative pre-mRNA splicing is prevalent throughout vertebrate genomes where an individual gene can be diversified into hundreds or even thousands of related mRNA isoforms [1] , [2] .", "Functional consequences of alternative splicing can involve changes to a subset of the protein's biochemical propert...	[ "Alternative pre-mRNA splicing adjusts the transcriptional output of the genome by generating related mRNAs from a single primary transcript , thereby expanding protein diversity .", "A fundamental unanswered question is how splicing factors achieve specificity in the selection of target substrates despite the re...	[ "Alternative splicing is a precisely controlled process that determines whether an exon will be included or skipped in the mature mRNA transcript .", "Factors that control alternative splicing bind to RNA sequence motifs in the exon or flanking introns and guide tissue and developmental specific splicing events ....	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "oncology", "systems biology", "text mining", "computer and information sciences", "medicine and health sciences", "computer modeling", "theoretical biology", "basic cancer research", "genetics", "biology and life sciences", "information technology", "computational biology", "computerized si...	Ras-Mediated Deregulation of the Circadian Clock in Cancer	journal.pgen.1004338	null	[ [ "All mammalian cells hold an internal circadian clock able to generate daily-endogenous rhythms with a period of approximately 24 hours .", "Circadian clocks are evolutionary conserved and regulate the expression of about 10% of all genes [1]–[3] .", "This time-generating mechanism enables the organis...	[ "Circadian rhythms are essential to the temporal regulation of molecular processes in living systems and as such to life itself .", "Deregulation of these rhythms leads to failures in biological processes and eventually to the manifestation of pathological phenotypes including cancer .", "To address the questio...	[ "Living systems possess an endogenous time-generating system – the circadian clock - accountable for a 24 hours oscillation in the expression of about 10% of all genes .", "In mammals , disruption of oscillations is associated to several diseases including cancer .", "In this manuscript , we address the followi...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "mathematics", "neuroscience/neuronal signaling mechanisms", "biophysics/theory and simulation", "neuroscience/theoretical neuroscience" ]	Biophysical Basis for Three Distinct Dynamical Mechanisms of Action Potential Initiation	journal.pcbi.1000198	null	[ [ "Action potentials , or spikes , are responsible for transmitting information through the nervous system [1] .", "The biophysical basis of spike generation is well established [2] , but the stereotypic spike shape belies variation in spike initiating mechanisms .", "The myriad different ion channels e...	[ "Transduction of graded synaptic input into trains of all-or-none action potentials ( spikes ) is a crucial step in neural coding .", "Hodgkin identified three classes of neurons with qualitatively different analog-to-digital transduction properties .", "Despite widespread use of this classification scheme , a ...	[ "Information is transmitted through the nervous system in the form of action potentials or spikes .", "Contrary to popular belief , a spike is not generated instantaneously when membrane potential crosses some preordained threshold .", "In fact , different neurons employ different rules to determine when and wh...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "animal models", "cell death", "neurobiology of disease and regeneration", "caenorhabditis elegans", "model organisms", "molecular cell biology", "cell biology", "biology", "neuroscience" ]	The Core Apoptotic Executioner Proteins CED-3 and CED-4 Promote Initiation of Neuronal Regeneration in Caenorhabditis elegans	journal.pbio.1001331	Laser severing of individual axons in the nematode Caenorhabditis elegans revealed that the apoptotic executioner caspase CED-3 and its regulator CED-4/Apaf-1 play an unexpected beneficial role in promoting axonal regeneration.	[ [ "In the injured vertebrate central nervous system ( CNS ) , neurons often survive and sprout but encounter extrinsic and intrinsic barriers to functional regeneration [1] , with devastating consequences for victims .", "The successful repair of neurons severed by accident or surgery is an obvious goal of ...	[ "A critical accomplishment in the rapidly developing field of regenerative medicine will be the ability to foster repair of neurons severed by injury , disease , or microsurgery .", "In C . elegans , individual visualized axons can be laser-cut in vivo and neuronal responses to damage can be monitored to decipher...	[ "Clinical success in reconnecting neurons damaged by injury will require detailed molecular understanding of how mature axons respond to being severed .", "To decipher intrinsic molecular pathways that stimulate axon regeneration , we use the small transparent model , Caenorhabditis elegans , in which individual ...	2012

Subsets and Splits

No community queries yet

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