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headings list	keywords list	title stringlengths 20 281	id stringlengths 20 20	toc stringlengths 57 522 ⌀	sections list	abstract list	summary list	year stringclasses 13 values
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "homo (human)", "genetics and genomics" ]	Novel Crohn Disease Locus Identified by Genome-Wide Association Maps to a Gene Desert on 5p13.1 and Modulates Expression of PTGER4	journal.pgen.0030058	null	[ [ "Crohn disease ( CD ) is a chronic relapsing inflammatory disorder of the intestinal tract , described for the first time in the 1920s [1] .", "Lifetime prevalence has increased to current estimates of ∼0 . 15% in Caucasians .", "The precise environmental causes underlying this rise remain essentially...	[ "To identify novel susceptibility loci for Crohn disease ( CD ) , we undertook a genome-wide association study with more than 300 , 000 SNPs characterized in 547 patients and 928 controls .", "We found three chromosome regions that provided evidence of disease association with p-values between 10−6 and 10−9 .", ...	[ "Individual susceptibility to many common diseases is determined by a combination of environmental and genetic factors .", "Identifying these genetic risk factors is one of the most important objectives of modern medical genetics , as it paves the way towards personalized medicine and drug target identification ....	2007
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Dispersal of Engineered Male Aedes aegypti Mosquitoes	journal.pntd.0004156	null	[ [ "Dengue , an arbovirus , has seen recent re-emergence and spread on a global scale [1] and is now responsible for an estimated 390 million infections annually [2] .", "The vector of dengue is the Aedes mosquito , with Ae .", "aegypti and Ae .", "albopictus responsible for the majority of disease t...	[ "Aedes aegypti , the principal vector of dengue fever , have been genetically engineered for use in a sterile insect control programme .", "To improve our understanding of the dispersal ecology of mosquitoes and to inform appropriate release strategies of ‘genetically sterile’ male Aedes aegypti detailed knowledg...	[ "Vector control using releases of sterile insects is a well-known approach .", "‘Genetically sterile’ male Aedes aegypti have been developed and released in a modern realisation of the sterile insect technique .", "Released engineered males seek out and mate with wild females , with the resultant offspring dyin...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Exocyst-Dependent Membrane Addition Is Required for Anaphase Cell Elongation and Cytokinesis in Drosophila	journal.pgen.1005632	null	[ [ "Cytokinesis results in the physical separation of two daughter cells .", "Immediately prior to the initiation of cytokinesis , cells also begin to elongate along the spindle axis , concomitant with the anaphase spindle elongation that helps drive chromosomal separation .", "To achieve such a fundamen...	[ "Mitotic and cytokinetic processes harness cell machinery to drive chromosomal segregation and the physical separation of dividing cells .", "Here , we investigate the functional requirements for exocyst complex function during cell division in vivo , and demonstrate a common mechanism that directs anaphase cell ...	[ "The cell shape changes that underlie cell division are some of the most fundamental changes in cell morphology .", "Here , we show that a common membrane trafficking pathway is required for both the cell lengthening that occurs during anaphase , and the physical separation of a cell into two equal daughter cells...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Independent Pathways Can Transduce the Life-Cycle Differentiation Signal in Trypanosoma brucei	journal.ppat.1003689	null	[ [ "Eukaryotic developmental events are a response to single or multiple external cues .", "Commonly , the existence of multiple cues ensures that cells do not embark prematurely on a developmental process that could damage their viability or fitness [1] .", "Additionally , the presence of multiple cues ...	[ "African trypanosomes cause disease in humans and livestock , generating significant health and welfare problems throughout sub-Saharan Africa .", "When ingested in a tsetse fly bloodmeal , trypanosomes must detect their new environment and initiate the developmental responses that ensure transmission .", "The ...	[ "African trypanosomes are important pathogens transmitted by tsetse flies in sub-Saharan Africa .", "Upon transmission , trypanosomes detect citrate and cis-aconitate in the bloodmeal , this inactivating a negative regulator of differentiation , the tyrosine phosphatase TbPTP1 .", "One TbPTP1 substrate is anoth...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "medicine and health sciences", "viral transmission and infection", "rna extraction", "microbiology", "light microscopy", "animals", "epithelial cells", "viral vectors", "rice", "confocal laser microscopy", "microscopy", "experimental organism systems", "confocal microscop...	Invasion of midgut epithelial cells by a persistently transmitted virus is mediated by sugar transporter 6 in its insect vector	journal.ppat.1007201	null	[ [ "Many viruses persistently transmitted by arthropods cause serious diseases in plants , animals and humans .", "More than 76% of plant viruses and 40% of mammalian viruses are transmitted to the hosts by specific arthropods , mainly planthoppers , aphids , mosquitoes , and ticks [1 , 2] .", "Frequent ...	[ "Insect transmission is obligatory for persistently transmitted viruses because the vector insect is the only means of virus spread in nature .", "The insect midgut is the first major barrier limiting virus acquisition , but the mechanisms by which viruses are able to cross the cell membrane and then infect the m...	[ "Sap/blood-feeding arthropods are major vectors of viruses that infect plants and vertebrates .", "Studies on the insect midgut , the first barrier for virus transmission , and its interactions with viruses and parasites are fundamental to understanding the transmission mechanism in vector insects and the epidemi...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases", "virology/vaccines", "immunology/immune response", "immunology/innate immunity", "infectious diseases/hiv infection and aids", "infectious diseases/viral infections", "immunology", "virology/immune evasion", "virology/effects of virus infection on host gene expression", "imm...	Innate Immune Sensing of Modified Vaccinia Virus Ankara (MVA) Is Mediated by TLR2-TLR6, MDA-5 and the NALP3 Inflammasome	journal.ppat.1000480	null	[ [ "Attenuated poxviruses are currently being developed as vaccines vectors against various infectious diseases including HIV , malaria and tuberculosis [1] .", "Modified vaccinia virus Ankara ( MVA ) and NYVAC are highly attenuated poxvirus strains due to multiple deletions of viral genes and are replicatio...	[ "Modified vaccinia virus Ankara ( MVA ) is an attenuated double-stranded DNA poxvirus currently developed as a vaccine vector against HIV/AIDS .", "Profiling of the innate immune responses induced by MVA is essential for the design of vaccine vectors and for anticipating potential adverse interactions between nat...	[ "Modified vaccinia virus Ankara ( MVA ) is a highly attenuated , replication-deficient , poxvirus currently developed as a vaccine vector against a broad spectrum of infectious diseases including HIV , tuberculosis and malaria .", "It is well known that robust activation of innate immunity is essential to achieve...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "schistosomiasis", "immune cells", "t cells", "allergy and hypersensitivity", "immunology", "biology", "parasitic diseases", "immunomodulation" ]	Schistosoma mansoni-Mediated Suppression of Allergic Airway Inflammation Requires Patency and Foxp3+ Treg Cells	journal.pntd.0002379	null	[ [ "Over the last century and in strong contrast to third world countries , Western populations have shown a consistent rise in autoimmune disorders ( e . g . Crohn's disease ) and allergic conditions such as asthma [1] .", "Indeed , allergic asthma is the most common disease in industrialized countries , wi...	[ "The continual rise of asthma in industrialised countries stands in strong contrast to the situation in developing lands .", "According to the modified Hygiene Hypothesis , helminths play a major role in suppressing bystander immune responses to allergens , and both epidemiological and experimental studies sugges...	[ "Infections with schistosomes , such as S . mansoni , S . japonicum and S . haematobium , are considered a major public health concern .", "Morbidity arises through granulomatous responses to eggs that become trapped in infected tissues .", "Interestingly , schistosomes belong to the group of helminths that hav...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "melioidosis", "geographical locations", "diabetes mellitus", "bacterial diseases", "endocrine disorders", "medical risk factors", "infectious disease control", "infectious diseases", "epidemiology", "endocrinology", "metabolic disorders", "agriculture", "pe...	Socio-epidemiological and land cover risk factors for melioidosis in Kedah, Northern Malaysia	journal.pntd.0007243	null	[ [ "Melioidosis , once thought to be restricted to Southeast Asia and northern Australia [1] , is now increasingly diagnosed in other tropical regions , including across Africa , the Caribbean , and other parts of Asia [2 , 3] .", "Thriving in soil and surface water , the causative Burkholderia pseudomallei ...	[ "Melioidosis , a fatal infectious disease caused by Burkholderia pseudomallei , is increasingly diagnosed in tropical regions .", "However , data on risk factors and the geographic epidemiology of the disease are still limited .", "Previous studies have also largely been based on the analysis of case series dat...	[ "Although the public health significance of melioidosis as a particularly highly fatal emerging infectious disease threat in the tropics is being recognized , data on the risk factors and the geographic distribution of the disease is still limited .", "Previous studies have also largely been based on the investig...	2019
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "skin", "cell death", "invertebrates", "medicine and health sciences", "integumentary system", "morphogenic segmentation", "cell processes", "egfr signaling", "green fluorescent protein", "animals", "endocrine physiology", "animal models", "developmental biology", "luminescent proteins", ...	EGFR signaling coordinates patterning with cell survival during Drosophila epidermal development	journal.pbio.3000027	Cells lacking essential patterning determinants are eliminated from developing tissues by apoptosis; this study shows that cell death in fruit fly segmentation mutants results from disruption of the pattern of EGFR signalling, which in normal embryos coordinates segment size with patterning information.	[ [ "Defective cells are often eliminated by apoptosis during development and tissue homeostasis [1–4] .", "This has been particularly well studied during the process of cell competition , whereby unfit cells are eliminated when confronted with normal cells within a growing tissue [5] .", "Excess apoptosi...	[ "Extensive apoptosis is often seen in patterning mutants , suggesting that tissues can detect and eliminate potentially harmful mis-specified cells .", "Here , we show that the pattern of apoptosis in the embryonic epidermis of Drosophila is not a response to fate mis-specification but can instead be explained by...	[ "In many tissues , defective cells are eliminated by a process called apoptosis .", "This process prevents the emergence of rogue cells , which could be detrimental to normal physiology .", "Apoptosis is particularly apparent in developing embryos that lack appropriate positional information , and it has been s...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "zika fever", "pathology and laboratory medicine", "chikungunya infection", "infectious disease epidemiology", "pathogens", "tropical diseases", "microbiology", "animals", "viruses", "rna viruses", "neglected tropical diseases", "infectious ...	Emerging trends of Zika apprehension in an epidemic setting	journal.pntd.0006167	null	[ [ "French Guiana , an overseas region and department of France located in the Amazonian forest complex , is composed of two main inhabited geographical regions: a central , urbanized area including a coastal strip along the Atlantic Ocean , where a large part of the population lives , and a more remote area alo...	[ "French Guiana is a territory that has a decades-long history of dengue outbreaks and more recently , in 2014 , a chikungunya outbreak .", "Zika virus ( ZIKV ) emerged in late 2015 and subsequently led to an important outbreak .", "A cross-sectional phone survey was conducted among the general population during...	[ "Although dengue fever has been a focus of many awareness campaigns in Latin America , very little information is available about beliefs , attitudes and behaviors regarding vector-borne diseases among the population of French Guiana .", "Following the end of the first chikungunya outbreak and at the initial onse...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious disease immunology", "theoretical biology", "clinical immunology", "population modeling", "biology and life sciences", "immunology", "computational biology", "immune response" ]	Spatial Heterogeneity and Peptide Availability Determine CTL Killing Efficiency In Vivo	journal.pcbi.1003805	null	[ [ "Cytotoxic T lymphocytes ( CTL ) prevent the spread of intracellular pathogens through T cell receptor ( TCR ) recognition of pathogen-derived peptides presented on MHC class I molecules on the surface of infected cells .", "CTL may have several modes of action but their canonically understood role is to ...	[ "The rate at which a cytotoxic T lymphocyte ( CTL ) can survey for infected cells is a key ingredient of models of vertebrate immune responses to intracellular pathogens .", "Estimates have been obtained using in vivo cytotoxicity assays in which peptide-pulsed splenocytes are killed by CTL in the spleens of immu...	[ "Measurements of the rates at which a single cytotoxic T lymphocyte ( CTL ) can survey for infected cells , and kill them upon encounter , are important for constructing predictive models of vertebrate immune responses to intracellular pathogens .", "The surveillance rate has been estimated previously using combi...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "medicine and health sciences", "model organisms", "women's health", "cell biology", "genetics", "biology and life sciences", "molecular cell biology", "research and analysis methods" ]	Rejuvenation of Meiotic Cohesion in Oocytes during Prophase I Is Required for Chiasma Maintenance and Accurate Chromosome Segregation	journal.pgen.1004607	null	[ [ "In both mitotic and meiotic cells , sister chromatid cohesion is required for accurate chromosome segregation , and the cohesive linkages that hold sister chromatids together depend on the cohesin complex which forms a DNA-entrapping ring [1] , [2] .", "In addition to holding sister chromatids together ,...	[ "Chromosome segregation errors in human oocytes are the leading cause of birth defects , and the risk of aneuploid pregnancy increases dramatically as women age .", "Accurate segregation demands that sister chromatid cohesion remain intact for decades in human oocytes , and gradual loss of the original cohesive l...	[ "Meiosis is a specialized type of cell division that gives rise to sperm and eggs .", "In a woman's thirties , errors in meiotic chromosome segregation rise exponentially , significantly increasing the probability that she will conceive a fetus with Down Syndrome ( Trisomy 21 ) .", "Accurate chromosome segregat...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "biotechnology", "luciferase assay", "chemical compounds", "small molecules", "gene regulation", "applied mathematics", "regulatory proteins", "dna-binding proteins", "organic compounds", "biochemical analysis", "simulation and modeling", "algorithms", "regulator genes", "enzyme assays", ...	Systematic, network-based characterization of therapeutic target inhibitors	journal.pcbi.1005599	null	[ [ "While the number of high-value , candidate therapeutic target proteins has increased dramatically over the past five years , most of them lack a corresponding FDA-approved or late-stage investigational ( i . e . , clinically relevant ) small-molecule inhibitor .", "Furthermore , a large number of these a...	[ "A large fraction of the proteins that are being identified as key tumor dependencies represent poor pharmacological targets or lack clinically-relevant small-molecule inhibitors .", "Availability of fully generalizable approaches for the systematic and efficient prioritization of tumor-context specific protein a...	[ "Most transcription factors are considered “undruggable” in conventional drug discovery .", "However , a large number of them are discovered to be key tumor dependencies .", "Thus , targeting these difficult targets has been a challenge for cancer drug discovery .", "Here , we introduce a novel method , OncoL...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "onchocerca volvulus", "tropical diseases", "geographical locations", "parasitic diseases", "animals", "onchocerca", "ethnicities", "pharmaceutics", "neglected tropical diseases", "pharmacology", "onchocerciasis", "africa", "cameroon", "...	Factors Associated with Ivermectin Non-Compliance and Its Potential Role in Sustaining Onchocerca volvulus Transmission in the West Region of Cameroon	journal.pntd.0004905	null	[ [ "Onchocerciasis is caused by the filarial parasite , Onchocerca volvulus , which is transmitted by Simulium blackflies .", "In humans , the adult stage ( macrofilariae ) are found as worm bundles , within sub-cutaneous nodules or more deeply in the body , living for an average of ten years [1] .", "Th...	[ "Community Directed Treatment with ivermectin is the cornerstone of current efforts to eliminate onchocerciasis .", "However recent studies suggest there are foci where long-term annual distribution of the drug alone has failed to ensure elimination thresholds are reached .", "It is important to achieve high le...	[ "Community Directed Treatment with ivermectin is the cornerstone of current efforts to eliminate onchocerciasis .", "Ivermectin distribution alone has been shown to be able to interrupt transmission but there are foci where long-term distribution of the drug alone has failed to ensure elimination thresholds are r...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "engineering and technology", "trees", "neuroscience", "simulation and modeling", "decision analysis", "decision tree learning", "systems science", "mathematics", "statistics (mathematics)", "management engineering", "artificial intelligence", "plants", "res...	Classifying dynamic transitions in high dimensional neural mass models: A random forest approach	journal.pcbi.1006009	null	[ [ "Neural mass models ( NMM ) approximate the average behaviour of large populations of neurons and therefore provide an efficient way to simulate electrographic data in order to understand the mechanisms of brain ( dys- ) function .", "They have been used to understand a wide variety of physiological and p...	[ "Neural mass models ( NMMs ) are increasingly used to uncover the large-scale mechanisms of brain rhythms in health and disease .", "The dynamics of these models is dependent upon the choice of parameters , and therefore it is crucial to be able to understand how dynamics change when parameters are varied .", "...	[ "Understanding the workings of the healthy brain and the disruptions that lead to disease remains a grand challenge for neuroscience .", "Given the complexity of the brain , mathematical models are becoming increasingly important to elucidate these fundamental mechanisms .", "However , as our fundamental unders...	2018
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "bacteriology", "genetic mutation", "genome evolution", "population genetics", "microbiology", "mutation", "mutation types", "microbial evolution", "microbial physiology", "biology", "evolutionary genetics", "genetic drift", "adaptation", "natural selection", "genetics", "genomics", ...	Repeated, Selection-Driven Genome Reduction of Accessory Genes in Experimental Populations	journal.pgen.1002651	null	[ [ "Bacterial genomes have the potential to rapidly change their size and content as a result of various mechanisms such as deletion , duplication and horizontal gene transfer .", "The net expansion or contraction at the genome scale is thus a function of both the rate at which these events occur and the sub...	[ "Genome reduction has been observed in many bacterial lineages that have adapted to specialized environments .", "The extreme genome degradation seen for obligate pathogens and symbionts appears to be dominated by genetic drift .", "In contrast , for free-living organisms with reduced genomes , the dominant for...	[ "Many free-living bacteria are known to commonly lose large portions of their genomes , but it is unclear what evolutionary forces drive these changes .", "Is this due to random loss in small populations , as is thought to be the case for the extreme genome degradation of intracellular symbionts , or due to selec...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/genomics", "genetics and genomics/gene expression", "pediatrics and child health/child development", "genetics and genomics/chromosome biology", "genetics and genomics/genetics of disease", "developmental biology/molecular development", "genetics and genomics/epigenetics", "deve...	Transcriptional Dysregulation in NIPBL and Cohesin Mutant Human Cells	journal.pbio.1000119	Genome-wide studies using cells from patients with Cornelia de Lange Syndrome reveal a role for cohesin in regulating gene expression in human cells.	[ [ "Cohesin is an evolutionally conserved multisubunit protein complex consisting of an SMC1A and SMC3 heterodimer , and at least two non-SMC proteins SCC1 ( also known as RAD21 or MCD1 ) and SCC3 ( also known as SA or STAG ) .", "Cohesin controls sister chromatid cohesion during S phase with Nipped-B-Like (...	[ "Cohesin regulates sister chromatid cohesion during the mitotic cell cycle with Nipped-B-Like ( NIPBL ) facilitating its loading and unloading .", "In addition to this canonical role , cohesin has also been demonstrated to play a critical role in regulation of gene expression in nondividing cells .", "Heterozyg...	[ "Appropriate segregation of chromosomes to daughter cells depends upon proper cohesion of sister chromatids during mitosis .", "The multiprotein cohesin complex and its regulators are key factors in this process .", "Intriguingly , recent work has shown that the cohesin complex also has other cellular roles , i...	2009
[ "Introduction", "Methods", "Results and Discussion" ]	[ "genome expression analysis", "medicine and health sciences", "genomics", "pathology and laboratory medicine", "entomology", "host-pathogen interactions", "genome analysis", "transcriptome analysis", "genetics", "biology and life sciences", "microbiology", "computational biology", "pathogene...	Dual RNA-seq of Parasite and Host Reveals Gene Expression Dynamics during Filarial Worm–Mosquito Interactions	journal.pntd.0002905	null	[ [ "Human lymphatic filariasis ( LF ) is one of the most debilitating of the neglected tropical diseases , causing severe morbidity as a result of stigmatizing and disabling clinical manifestations ( e . g . , elephantiasis and hydrocele ) [1] , [2] .", "LF results from infection with several species of mosq...	[ "Parasite biology , by its very nature , cannot be understood without integrating it with that of the host , nor can the host response be adequately explained without considering the activity of the parasite .", "However , due to experimental limitations , molecular studies of parasite-host systems have been pred...	[ "In a parasitic relationship , both host and parasite genotypes influence the parameters of their relationship .", "Previous studies examining host-parasite systems have examined the effects of the genotype of the host or the parasite on the relationship , but due to limitations of technology , have rarely examin...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biotechnology", "bacteriology", "organismal evolution", "microbial mutation", "genetic mutation", "retrotransposons", "microbiology", "mutation", "molecular cell biology", "microbial evolution", "dna", "dna structure", "applied microbiology", "transposons", "biology", "evolutionary ge...	Target Site Recognition by a Diversity-Generating Retroelement	journal.pgen.1002414	null	[ [ "Diversity-generating retroelements ( DGRs ) have been identified in numerous bacterial phyla [1] , [2] .", "Although most DGRs are bacterial chromosomal elements , they are prevalent in phage and plasmid genomes as well .", "The prototype DGR was identified in a temperate bacteriophage , BPP-1 , on t...	[ "Diversity-generating retroelements ( DGRs ) are in vivo sequence diversification machines that are widely distributed in bacterial , phage , and plasmid genomes .", "They function to introduce vast amounts of targeted diversity into protein-encoding DNA sequences via mutagenic homing .", "Adenine residues are ...	[ "Diversity-generating retroelements function through a unique , reverse transcriptase–mediated “copy and replace” mechanism that enables repeated rounds of protein diversification , selection , and optimization .", "The ability of DGRs to introduce targeted diversity into protein-coding DNA sequences has the pote...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "children", "medicine and health sciences", "maternal health", "obstetrics and gynecology", "helminths", "tropical diseases", "hookworms", "social sciences", "anthropology", "parasitic diseases", "animals", "health care", "age groups", "women's health", "infants", "p...	A Double-Blind Randomized Controlled Trial of Maternal Postpartum Deworming to Improve Infant Weight Gain in the Peruvian Amazon	journal.pntd.0005098	null	[ [ "Worldwide , more than 200 million children under five years of age fail to reach their full developmental potential [1] .", "Suboptimal nutrition and growth during fetal and early childhood development are widely regarded as having adverse long-term consequences , including higher susceptibility to infec...	[ "Nutritional interventions targeting the critical growth and development period before two years of age can have the greatest impact on health trajectories over the life course .", "Compelling evidence has demonstrated that interventions investing in maternal health in the first 1000 days of life are beneficial f...	[ "Worldwide , over one billion people are infected with intestinal worms ( roundworms , whipworms , and hookworms ) .", "In worm-endemic areas , women of reproductive age are a high risk group for infection because of their poor nutritional status and increased physiological needs during pre-pregnancy , pregnancy ...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/neglected tropical diseases", "infectious diseases/skin infections", "infectious diseases/protozoal infections", "immunology/immunity to infections", "public health and epidemiology/immunization" ]	Vector Transmission of Leishmania Abrogates Vaccine-Induced Protective Immunity	journal.ppat.1000484	null	[ [ "Leishmania are obligate-intracellular protozoan parasites that establish infection in mammalian hosts following transmission to the skin by the bite of an infected Phlebotomine sand fly [1] .", "Different Leishmania species are associated with a spectrum of clinical outcomes in humans , including fatal ,...	[ "Numerous experimental vaccines have been developed to protect against the cutaneous and visceral forms of leishmaniasis caused by infection with the obligate intracellular protozoan Leishmania , but a human vaccine still does not exist .", "Remarkably , the efficacy of anti-Leishmania vaccines has never been ful...	[ "The generation of vaccines that protect against intracellular pathogens such as malaria , human immunodeficiency virus and leishmaniasis have met with limited success .", "A perplexing aspect of this failure as it relates to leishmaniasis is the knowledge that individuals typically get the disease only once , an...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "disease mapping", "infectious diseases", "mosquitoes", "climatology", "epidemiological methods", "meteorology", "infectious disease epidemiology", "epidemiology", "earth sciences", "atmospheric science", "dengue fever", "neglected tropical diseases", "travel-associated disease...	Evaluation of Internet-Based Dengue Query Data: Google Dengue Trends	journal.pntd.0002713	null	[ [ "The global incidence of dengue has increased 30-fold between 1960 and 2010 [1] , with a recent study estimating that there are now 70–140 million cases per year [2] .", "Dengue is caused by infection with any of the four dengue virus ( DENV ) serotypes; the symptoms often include high fever , intense joi...	[ "Dengue is a common and growing problem worldwide , with an estimated 70–140 million cases per year .", "Traditional , healthcare-based , government-implemented dengue surveillance is resource intensive and slow .", "As global Internet use has increased , novel , Internet-based disease monitoring tools have eme...	[ "Dengue is a common and growing problem worldwide .", "Delays in traditional surveillance systems limit the ability of public health agencies to identify and respond to dengue outbreaks efficiently .", "Internet search queries provide near real-time indicators of infectious disease activity and have proven effe...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "phosphorylation", "genome-wide association studies", "medicine and health sciences", "cellular stress responses", "maternal health", "obstetrics and gynecology", "engineering and technology", "cell processes", "hormones", "preterm birth", "women's health", "pregnancy", "genome analysis", ...	Whole exome sequencing reveals HSPA1L as a genetic risk factor for spontaneous preterm birth	journal.pgen.1007394	null	[ [ "Preterm birth ( PTB ) , defined as birth before 37 completed weeks of gestation , is a major global public health concern .", "Worldwide , over 15 million infants ( more than one in ten babies ) are born preterm and of those , more than one million die from complications related to preterm birth each yea...	[ "Preterm birth is a leading cause of morbidity and mortality in infants .", "Genetic and environmental factors play a role in the susceptibility to preterm birth , but despite many investigations , the genetic basis for preterm birth remain largely unknown .", "Our objective was to identify rare , possibly dama...	[ "Preterm birth is the leading cause of infant mortality , and prematurity is further associated with serious morbidities in later life .", "Genetic and environmental risk factors play a role in the susceptibility to preterm birth .", "Despite numerous studies , the genetic basis for preterm birth remains poorly...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "primates", "oncology", "homo (human)", "genetics and genomics" ]	Elevated Rates of Sister Chromatid Exchange at Chromosome Ends	journal.pgen.0030032	null	[ [ "Chromosome ends participate in frequent recombination events .", "Human subtelomeric regions have undergone multiple interchromosomal exchanges during meiosis , giving rise to the highly duplicated structures proximal to telomere repeats [1] .", "Meiotic recombination maps of the human genome show an...	[ "Chromosome ends are known hotspots of meiotic recombination and double-strand breaks .", "We monitored mitotic sister chromatid exchange ( SCE ) in telomeres and subtelomeres and found that 17% of all SCE occurs in the terminal 0 . 1% of the chromosome .", "Telomeres and subtelomeres are significantly enriched...	[ "The ends of chromosomes are evolutionarily dynamic and structurally unusual parts of the human genome .", "Arrays of telomeric repeats cap each end and protect chromosomes from degradation and end-to-end fusions .", "Just inside the telomeres are patchworks of larger DNA segments duplicated on different chromo...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/neglected tropical diseases", "biotechnology/applied microbiology", "microbiology/cellular microbiology and pathogenesis", "cell biology/cellular death and stress responses" ]	C-Terminal Mutants of Apolipoprotein L-I Efficiently Kill Both Trypanosoma brucei brucei and Trypanosoma brucei rhodesiense	journal.ppat.1000685	null	[ [ "Normal human serum ( NHS ) is able to kill T . b .", "brucei , but not T . b .", "rhodesiense and T . b .", "gambiense .", "The lytic factor was identified as being apoL1 [1] , [2] .", "This protein is associated with HDL particles that are efficiently taken up by the parasite through spe...	[ "Apolipoprotein L-I ( apoL1 ) is a human-specific serum protein that kills Trypanosoma brucei through ionic pore formation in endosomal membranes of the parasite .", "The T . brucei subspecies rhodesiense and gambiense resist this lytic activity and can infect humans , causing sleeping sickness .", "In the case...	[ "The serum protein apolipoprotein L-I ( apoL1 ) is responsible for human innate immunity against Trypanosoma brucei brucei , because this protein kills the parasite by generating ionic pores in the lysosomal membrane .", "Two T . brucei subspecies ( T . b . rhodesiense and T . b . gambiense ) can resist apoL1 and...	2009
[ "Introduction", "Methods", "Results", "Discussion", "Genes and protein sequences used" ]	[ "parasite groups", "medicine and health sciences", "plasmodium", "population genetics", "tropical diseases", "immunology", "parasitic diseases", "parasitic protozoans", "genetic mapping", "parasitology", "vaccines", "preventive medicine", "apicomplexa", "protozoans", "molecular biology t...	Plasmodium vivax Cell Traversal Protein for Ookinetes and Sporozoites (PvCelTOS) gene sequence and potential epitopes are highly conserved among isolates from different regions of Brazilian Amazon	journal.pntd.0005344	null	[ [ "Malaria is an infectious parasitic disease with high prevalence and morbidity .", "Globally , it is estimated that 3 . 2 billion people in 95 countries and territories are at risk of being infected and develop the disease .", "In 2015 , malaria caused an estimate of 438 , 000 deaths , mostly in Afric...	[ "The Plasmodium vivax Cell-traversal protein for ookinetes and sporozoites ( PvCelTOS ) plays an important role in the traversal of host cells .", "Although essential to PvCelTOS progress as a vaccine candidate , its genetic diversity remains uncharted .", "Therefore , we investigated the PvCelTOS genetic polym...	[ "Cell-traversal protein for ookinetes and sporozoites ( CelTOS ) presents a pivotal role in the cell traversal of host cells in mosquito and vertebrate hosts .", "For this reason , it has been considered a potential novel alternative for a vaccine against malaria caused by P . falciparum .", "However , little i...	2017
[ "Introduction", "Model", "Results", "Discussion" ]	[ "velocity", "cell physiology", "cell motility", "medicine and health sciences", "classical mechanics", "engineering and technology", "nervous system", "signal processing", "junctional complexes", "electrophysiology", "neuroscience", "cell polarity", "gap junctions", "stem cells", "phase ...	Collective Signal Processing in Cluster Chemotaxis: Roles of Adaptation, Amplification, and Co-attraction in Collective Guidance	journal.pcbi.1005008	null	[ [ "Many individual cells , including white blood cells and bacteria , chemotax—sensing and following gradients of signals .", "Some cells , though , are not loners—they migrate collectively—and cells traveling in clusters and sheets during development must chemotax together .", "Many experiments [1–5] h...	[ "Single eukaryotic cells commonly sense and follow chemical gradients , performing chemotaxis .", "Recent experiments and theories , however , show that even when single cells do not chemotax , clusters of cells may , if their interactions are regulated by the chemoattractant .", "We study this general mechanis...	[ "To get from one part of the body to another , single cells often follow chemical signals .", "Sometimes , though , isolated cells ignore these signals , but a group of cells still manages to travel in a directed way .", "How can this happen ?", "We argue that if the signal changes how the cells interact with...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "chemical compounds", "pathology and laboratory medicine", "enzymes", "pathogens", "bacillus", "enzymology", "microbiology", "cell disruption", "organic compounds", "prokaryotic models", "membrane receptor signaling", "experimental organism systems", "basic ...	Bacterial sensing: A putative amphipathic helix in RsiV is the switch for activating σV in response to lysozyme	journal.pgen.1007527	null	[ [ "One key survival feature of all living organisms is the ability to recognize changes in their environments and respond appropriately .", "One signal transduction system bacteria use to sense and respond to environmental stresses are Extracytoplasmic Function ( ECF ) sigma ( σ ) factors [1 , 2] .", "E...	[ "Extra Cytoplasmic Function ( ECF ) σ factors are a diverse group of alternate σ factors bacteria use to respond to changes in the environment .", "The Bacillus subtilis ECF σ factor σV responds to lysozyme .", "In the absence of lysozyme , σV is held inactive by the anti-σ factor , RsiV .", "In the presence ...	[ "Signal transduction involves", "( i ) sensing a signal ,", "( ii ) a molecular switch triggering a response , and", "( iii ) altering gene expression .", "For Bacillus subtilis’ response to lysozyme , we have a detailed understanding of", "( i ) and", "( iii ) .", "Here we provide insights for a mole...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology/stem cells", "cell biology/nuclear structure and function", "cell biology/cellular death and stress responses", "cell biology/developmental molecular mechanisms", "genetics and genomics/chromosome biology", "genetics and genomics/epigenetics", "genetics and genomics" ]	Windei, the Drosophila Homolog of mAM/MCAF1, Is an Essential Cofactor of the H3K9 Methyl Transferase dSETDB1/Eggless in Germ Line Development	journal.pgen.1000644	null	[ [ "The epigenetic regulation of gene expression by the modification of histone proteins is a very important mechanism to control the differentiation of many cell types during development .", "The N-terminal , outward protruding histone tails are targets of posttranslational modifications , such as acetylati...	[ "The epigenetic regulation of gene expression by the covalent modification of histones is a fundamental mechanism required for the proper differentiation of germ line cells during development .", "Trimethylation of histone 3 lysine 9 ( H3K9me3 ) leads to chromatin silencing and the formation of heterochromatin by...	[ "Germ line cells are the only cells in an organism that are able to transmit their genetic material to the next generation by forming eggs or sperm .", "They do not participate in the formation or function of tissues and organs and therefore show a unique pattern of transcription , with many genes being silenced ...	2009
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "immunology/immunomodulation" ]	The Hookworm Tissue Inhibitor of Metalloproteases (Ac-TMP-1) Modifies Dendritic Cell Function and Induces Generation of CD4 and CD8 Suppressor T Cells	journal.pntd.0000439	null	[ [ "The human hookworms Necator americanus and Ancylostoma duodenale are directly transmitted nematode parasites of the small intestine , and the main species that cause human hookworm infection , a leading cause of iron-deficiency anemia and malnutrition with a prevalence of 600 million cases in the tropical de...	[ "Hookworm infection is a major cause of disease burden for humans .", "Recent studies have described hookworm-related immunosuppression in endemic populations and animal models .", "A Tissue Inhibitor of Metalloproteases ( Ac-TMP-1 ) has been identified as one of the most abundant proteins released by the adult...	[ "Chronic infections with helminths have been suggested to induce suppressor cells by a variety of mechanisms .", "The published immunological and epidemiological data on hookworm infection in humans and animal models suggest that these parasites are particularly successful in establishing chronicity and modulatio...	2009
[ "Introduction", "Results and discussion", "Materials and methods" ]	[ "chronic wasting disease", "animal diseases", "medicine and health sciences", "deer", "canada", "chemical compounds", "ruminants", "prions", "molecular probe techniques", "geographical locations", "immunoblotting", "vertebrates", "animals", "mammals", "organic compounds", "north americ...	Soil humic acids degrade CWD prions and reduce infectivity	journal.ppat.1007414	null	[ [ "Chronic wasting disease ( CWD ) , a fatal prion disease affecting free ranging white-tailed deer , mule deer , elk , moose and reindeer as well as farmed cervids , is the only spongiform encephalopathy ( along with scrapie ) that is environmentally transmitted .", "Currently , CWD-infected cervids are pr...	[ "Chronic wasting disease ( CWD ) , an environmentally transmissible , fatal prion disease is endemic in North America , present in South Korea and has recently been confirmed in northern Europe .", "The expanding geographic range of this contagious disease of free-ranging deer , moose , elk and reindeer has resul...	[ "Chronic wasting disease ( CWD ) is a contagious prion disease affecting several species of captive and wild cervids .", "Environmental prion contamination plays a major role in increasing incidence of CWD , with CWD infectivity being released into the environment by decaying carcasses , or shedding of biological...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "meiosis", "spermatocytes", "cell cycle and cell division", "cell processes", "germ cells", "epigenetics", "chromatin", "sperm", "sex chromosomes", "prophase", "synapsis", "animal cells", "chromosome biology", "gene expression", "autosomes", "cell biology", "genetics", "biology and...	BRDT is an essential epigenetic regulator for proper chromatin organization, silencing of sex chromosomes and crossover formation in male meiosis	journal.pgen.1007209	null	[ [ "The bromodomain is a highly conserved motif that recognizes and binds to acetylated lysine residues , a key step in reading epigenetic marks .", "Among the bromodomain-containing proteins , the BET ( bromodomain and extra-terminal ) subfamily is characterized by the presence of two bromodomains ( hereaft...	[ "The double bromodomain and extra-terminal domain ( BET ) proteins are critical epigenetic readers that bind to acetylated histones in chromatin and regulate transcriptional activity and modulate changes in chromatin structure and organization .", "The testis-specific BET member , BRDT , is essential for the norm...	[ "BRDT , a testis-specific member of the bromodomain and extra-terminal ( BET ) subfamily of epigenetic reader proteins , is essential for the generation of male gametes .", "In post-meiotic cells , BRDT is involved in chromatin organization and transcriptional regulation through its first bromodomain motif , as l...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	The Intolerance of Regulatory Sequence to Genetic Variation Predicts Gene Dosage Sensitivity	journal.pgen.1005492	null	[ [ "Despite strong evidence that regulatory regions can be affected by pathogenic mutations , such as in fragile-X syndrome , β-thalassemia , Charcot-Marie-Tooth neuropathy , breast cancer and others [1–5] , little has been done to quantify stretches of regulatory sequence in the context of both phylogenetic con...	[ "Noncoding sequence contains pathogenic mutations .", "Yet , compared with mutations in protein-coding sequence , pathogenic regulatory mutations are notoriously difficult to recognize .", "Most fundamentally , we are not yet adept at recognizing the sequence stretches in the human genome that are most importan...	[ "Mutations in noncoding sequence can cause disease but are very difficult to recognize .", "Here , we present two approaches intended to help identify noncoding regions of the genome that may carry mutations influencing disease .", "The first approach is based on comparing observed and predicted levels of stand...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "parasite groups", "body fluids", "plasmodium", "engineering and technology", "immunology", "tropical diseases", "nucleotides", "parasitic diseases", "parasitology", "urine", "parasitemia", "apicomplexa", "nanoparticles", "nanotechnology", "cross reactiv...	Colorimetric Detection of Plasmodium vivax in Urine Using MSP10 Oligonucleotides and Gold Nanoparticles	journal.pntd.0005029	null	[ [ "Malaria is the most common infectious disease in the tropics and subtropics [1] .", "Currently , P . vivax is endemic across Asia , the South Pacific , North Africa , Middle East , and South and Central America [2] , and has recently reappeared in regions where it had previously been eradicated , includi...	[ "Plasmodium vivax is the most prevalent cause of human malaria in the world and can lead to severe disease with high potential for relapse .", "Its genetic and geographic diversities make it challenging to control .", "P . vivax is understudied and to achieve control of malaria in endemic areas , a rapid , accu...	[ "To control malaria , there is an urgent need for applying innovative diagnostics and new technologies .", "Nanoparticles can augment detection of malaria at lower parasite levels while providing fast and simple methodology .", "Novel use of MSP10 and gold nanoparticles to identify Plasmodium vivax’s DNA in uri...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "microbial metabolism", "microbial pathogens", "host-pathogen interaction", "biology", "salmonella", "microbiology", "bacterial pathogens" ]	Parallel Exploitation of Diverse Host Nutrients Enhances Salmonella Virulence	journal.ppat.1003301	null	[ [ "Infectious diseases are a major worldwide threat to human health [1] .", "The situation is worsening because of rapidly rising antimicrobial resistance and insufficient development of new antibiotics .", "Most infectious diseases start with a few pathogenic organisms that invade host tissues , but di...	[ "Pathogen access to host nutrients in infected tissues is fundamental for pathogen growth and virulence , disease progression , and infection control .", "However , our understanding of this crucial process is still rather limited because of experimental and conceptual challenges .", "Here , we used proteomics ...	[ "Infectious diseases are a major health problem worldwide .", "To cause disease , pathogens need to acquire host nutrients for growth in infected tissues and for the expression of virulence factors .", "In this study , we investigated Salmonella nutrition and growth in a well-characterized mouse model of human ...	2013
[ "Introduction", "Authorship", "Discussion" ]	[ "computer applications", "open science", "peer review", "computer and information sciences", "data management", "web-based applications", "computer networks", "science policy", "internet", "computer software", "citation analysis", "open source software", "metadata", "scientific publishing"...	Open collaborative writing with Manubot	journal.pcbi.1007128	null	[ [ "There are many existing collaborative writing platforms ( Table 1 ) [6] .", "In general , platforms with “what you see is what you get” ( WYSIWYG ) editors , such as Microsoft Word or Google Docs , require the least technical expertise to use .", "On the flip side , WYSIWYG platforms can be difficult...	[ "Open , collaborative research is a powerful paradigm that can immensely strengthen the scientific process by integrating broad and diverse expertise .", "However , traditional research and multi-author writing processes break down at scale .", "We present new software named Manubot , available at https://manub...	[ "Traditionally , scholarly manuscripts have been written in private by a predefined team of collaborators .", "But now the internet enables realtime open science , where project communication occurs online in a public venue and anyone is able to contribute .", "Dispersed teams of online contributors require new...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	A Lentiviral Vector Expressing Japanese Encephalitis Virus-like Particles Elicits Broad Neutralizing Antibody Response in Pigs	journal.pntd.0004081	null	[ [ "Mosquito-borne Japanese encephalitis virus is a member of the Flavivirus genus in the Flaviviridae family [1–4] .", "Flaviviruses contain a positive single-stranded RNA genome encoding a polyprotein that is processed into three structural proteins , the capsid ( C ) , the precursor of membrane ( prM ) an...	[ "Japanese encephalitis virus ( JEV ) is the major cause of viral encephalitis in Southeast Asia .", "Vaccination of domestic pigs has been suggested as a “one health” strategy to reduce viral disease transmission to humans .", "The efficiency of two lentiviral TRIP/JEV vectors expressing the JEV envelope prM an...	[ "Japanese encephalitis virus is the etiologic agent of the most medically important viral encephalitis in South Asia with thousands of deaths per year .", "The virus is maintained in an enzootic cycle between Culex mosquitoes and amplifying vertebrate hosts , such as wild boars and pigs .", "Vaccination of dome...	2015
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "cancers and neoplasms", "simulation and modeling", "oncology", "mutation", "molecular biology techniques", "mutagenesis and gene deletion techniques", "epigenetics", "dna", "information technology", "data processing", "chromatin", "dna methylation", "resear...	Association analysis using somatic mutations	journal.pgen.1007746	null	[ [ "Somatic mutations play a central role in the development and progression of cancer .", "Associations between somatic mutations and molecular/clinical outcomes can provide important insights into cancer etiology or the mechanism of tumor growth , and potentially contribute to precision cancer therapy .", ...	[ "Somatic mutations drive the growth of tumor cells and are pivotal biomarkers for many cancer treatments .", "Genetic association analysis using somatic mutations is an effective approach to study the functional impact of somatic mutations .", "However , standard regression methods are not appropriate for somat...	[ "Cancer is a genetic disease that is driven by the accumulation of somatic mutations .", "Association studies using somatic mutations is a powerful approach to identify the potential impact of somatic mutations on molecular or clinical features .", "One challenge for such tasks is the non-ignorable somatic muta...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "bacterial diseases", "disease mapping", "infectious diseases", "survey methods", "clinical epidemiology", "tropical diseases (non-neglected)", "infectious disease epidemiology", "epidemiology", "dengue fever", "flavivirus", "influenza", "neglected tropical diseases", "viral di...	Dengue and Other Common Causes of Acute Febrile Illness in Asia: An Active Surveillance Study in Children	journal.pntd.0002331	null	[ [ "Undifferentiated febrile illnesses are common in children living in tropical areas of Asia .", "Common causes include dengue , malaria , leptospirosis , influenza A , Salmonella Typhi , rickettsia , Japanese encephalitis and chikungunya , [1]–[8] .", "The symptoms and differential diagnoses of these ...	[ "Common causes of acute febrile illness in tropical countries have similar symptoms , which often mimic those of dengue .", "Accurate clinical diagnosis can be difficult without laboratory confirmation and disease burden is generally under-reported .", "Accurate , population-based , laboratory-confirmed inciden...	[ "Acute febrile episodes are common in children living in tropical countries .", "Diagnosis can be challenging because symptoms of the more common infectious causes are similar and often mimic those of dengue .", "Asia Pacific has over 70% of the worldwide dengue disease burden , although dengue incidence is gen...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "population genetics", "geographical locations", "jews", "genetic mapping", "ethnicities", "simulation and modeling", "population biology", "research and analysis methods", "europe", "geography", "chromosome biology", "historical geography", "people and places", "haplotypes", "cell biolo...	The time and place of European admixture in Ashkenazi Jewish history	journal.pgen.1006644	null	[ [ "Ashkenazi Jews ( AJ ) , numbering approximately 10 million worldwide [1] , are individuals of Jewish ancestry with a recent origin in Eastern Europe [2] .", "The first individuals to identify as Ashkenazi appeared in Northern France and the Rhineland ( Germany ) around the 10th century [3] .", "Three...	[ "The Ashkenazi Jewish ( AJ ) population is important in genetics due to its high rate of Mendelian disorders .", "AJ appeared in Europe in the 10th century , and their ancestry is thought to comprise European ( EU ) and Middle-Eastern ( ME ) components .", "However , both the time and place of admixture are sub...	[ "The Ashkenazi Jewish population has resided in Europe for much of its 1000-year existence .", "However , its ethnic and geographic origins are controversial , due to the scarcity of reliable historical records .", "Previous genetic studies have found links to Middle-Eastern and European ancestries , but the ad...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "meiosis", "invertebrates", "homologous chromosomes", "spermatocytes", "chromosome structure and function", "anaphase", "centromeres", "metaphase", "cell cycle and cell division", "cell processes", "animals", "germ cells", "animal models", "drosophila melanogaster", "model organisms", ...	Separase Is Required for Homolog and Sister Disjunction during Drosophila melanogaster Male Meiosis, but Not for Biorientation of Sister Centromeres	journal.pgen.1005996	null	[ [ "After their production during S phase , sister chromatids remain paired .", "This sister chromatid cohesion is crucial for proper bipolar chromosome orientation within mitotic spindles during early M phase .", "Sister chromatid cohesion is maintained primarily by cohesin , a protein complex composed ...	[ "Spatially controlled release of sister chromatid cohesion during progression through the meiotic divisions is of paramount importance for error-free chromosome segregation during meiosis .", "Cohesion is mediated by the cohesin protein complex and cleavage of one of its subunits by the endoprotease separase remo...	[ "Sexual reproduction depends on meiosis , a special cell division that occurs in two steps , meiosis I and II .", "Meiosis is distinct in males and females that produce two very different forms of compatible gametes , the sperm and egg , respectively .", "In the fly Drosophila melanogaster , sex-specific differ...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "infectious disease modeling" ]	Modelling the Effects of Population Structure on Childhood Disease: The Case of Varicella	journal.pcbi.1002105	null	[ [ "Varicella is endemic in most Western countries where vaccination has not been implemented [1] , [2] .", "More than 90% people are infected with varicella-zoster-virus ( VZV ) before 12 years of age , but the age-specific seroprevalence of VZV shows large variability between countries [3] .", "For exa...	[ "Realistic , individual-based models based on detailed census data are increasingly used to study disease transmission .", "Whether the rich structure of such models improves predictions is debated .", "This is studied here for the spread of varicella , a childhood disease , in a realistic population of childre...	[ "Individual-based models of disease transmission have increasingly included detailed demographic data to more accurately describe places where population mix and infection occur .", "These models may help to understand in more detail heterogeneities in transmission and improve public health decisions .", "Here ...	2011
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "biogeography", "public health and epidemiology", "spatial epidemiology", "microbiology", "rabies", "phylogenetics", "neglected tropical diseases", "population biology", "infectious diseases", "epidemiology", "biology", "evolutionary systematics", "viral evolution", "ecology"...	National Borders Effectively Halt the Spread of Rabies: The Current Rabies Epidemic in China Is Dislocated from Cases in Neighboring Countries	journal.pntd.0002039	null	[ [ "Rabies is a fatal zoonotic disease , posing a severe public health problem with more than 55 , 000 human rabies deaths occurring annually .", "99% of all fatalities occur in developing countries [1] , [2] and Asia accounts for 80% of the worldwide total [3] .", "After India , China reports the second...	[ "China has seen a massive resurgence of rabies cases in the last 15 years with more than 25 , 000 human fatalities .", "Initial cases were reported in the southwest but are now reported in almost every province .", "There have been several phylogenetic investigations into the origin and spread of the virus with...	[ "Rabies as a fatal zoonotic disease continues to be a public threat to global public health .", "After India , China reports the second highest number of human cases , with more than 117 , 500 deaths and three major epidemics since 1950 .", "China remains in the middle of the third epidemic .", "In this work ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell physiology", "invertebrates", "rna interference", "vesicles", "cloning", "animals", "cell polarity", "animal models", "organisms", "developmental biology", "drosophila melanogaster", "model organisms", "immunoprecipitation", "epigenetics", "molecular biology techniques", "cellula...	Scribbled Optimizes BMP Signaling through Its Receptor Internalization to the Rab5 Endosome and Promote Robust Epithelial Morphogenesis	journal.pgen.1006424	null	[ [ "Epithelial cells are characteristically polarized with apical-basal plasma membrane polarity , which is crucial for tissue homeostasis [1 , 2] .", "Many of intrinsic factors underlying apical-basal polarity have been identified to be tumour suppressors [1 , 2] .", "Multiple distinct but interacting g...	[ "Epithelial cells are characterized by apical-basal polarity .", "Intrinsic factors underlying apical-basal polarity are crucial for tissue homeostasis and have often been identified to be tumor suppressors .", "Patterning and differentiation of epithelia are key processes of epithelial morphogenesis and are fr...	[ "Epithelial morphogenesis is one of the key processes in animal development .", "Evolutionarily conserved growth factors frequently instruct patterning and differentiation in morphogenesis .", "However , little is known about how extracellular cues and epithelial morphogenesis are mutually coordinated in vivo ....	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "t helper cells", "medicine and health sciences", "immune cells", "enzyme-linked immunoassays", "respiratory infections", "immune physiology", "spleen", "immunology", "parasitic diseases", "parasitic protozoans", "pulmonology", "protozoans", "cytotoxic t cells", "immunolog...	Th17 Cells Are More Protective Than Th1 Cells Against the Intracellular Parasite Trypanosoma cruzi	journal.ppat.1005902	null	[ [ "Chronic infection with the protozoan parasite Trypanosoma cruzi results in Chagas disease , a Neglected Tropical Disease currently affecting 8–11 million people worldwide and 300 , 000 people in the United States [1] .", "Humans usually acquire T . cruzi infection via reduviid insect vectors , but infect...	[ "Th17 cells are a subset of CD4+ T cells known to play a central role in the pathogenesis of many autoimmune diseases , as well as in the defense against some extracellular bacteria and fungi .", "However , Th17 cells are not believed to have a significant function against intracellular infections .", "In contr...	[ "Chronic infection with the intracellular parasite Trypanosoma cruzi results in Chagas disease , an illness endemic in more than 20 countries that leads to life-threatening cardiac and gastrointestinal dysfunction .", "Although CD4+ Th1 cells are known to be protective against T . cruzi infection , less is known ...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "immunology", "biology", "microbiology" ]	The Ebola Virus Interferon Antagonist VP24 Directly Binds STAT1 and Has a Novel, Pyramidal Fold	journal.ppat.1002550	null	[ [ "The ebolaviruses and marburgviruses are enveloped , non-segmented , negative-strand RNA viruses that belong to the family Filoviridae .", "There are five antigenically distinct ebolaviruses that are ∼40% different in amino acid sequence , and are each named after the location of the outbreak during which...	[ "Ebolaviruses cause hemorrhagic fever with up to 90% lethality and in fatal cases , are characterized by early suppression of the host innate immune system .", "One of the proteins likely responsible for this effect is VP24 .", "VP24 is known to antagonize interferon signaling by binding host karyopherin α prot...	[ "Ebolaviruses cause severe hemorrhagic fever that is exacerbated by immediate suppression of host immune function .", "VP24 , one of only eight proteins encoded by ebolaviruses , functions in virus replication and assembly , and is thought to contribute to immune suppression by binding to a certain class of molec...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "cell physiology", "cell motility", "actin filaments", "cell polarity", "molecular motors", "actin motors", "cellular structures and organelles", "cytoskeleton", "motor proteins", "dynamic actin filaments", "contractile proteins", "polymer chemistry", "actins", "proteins", "chemistry", ...	Remarkable structural transformations of actin bundles are driven by their initial polarity, motor activity, crosslinking, and filament treadmilling	journal.pcbi.1007156	null	[ [ "Understanding emergent behaviors in the actin cytoskeleton is important , since key biological functions such as cellular growth , division , and motility depend on cytoskeletal dynamics .", "Actin networks are transient and malleable within a single cell , constantly forming and remodeling various micro...	[ "Bundled actin structures play a key role in maintaining cellular shape , in aiding force transmission to and from extracellular substrates , and in affecting cellular motility .", "Recent studies have also brought to light new details on stress generation , force transmission and contractility of actin bundles ....	[ "Actin bundles are a salient feature of the cellular cytoskeleton offering structural integrity to the cell in addition to playing a key functional role in processes such as intracellular transport , mechanosensing and locomotion .", "Even though bundles have been studied extensively for years , a comprehensive p...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunologic subspecialties", "immunology", "biology", "pulmonary immunology" ]	Complement Mediated Signaling on Pulmonary CD103+ Dendritic Cells Is Critical for Their Migratory Function in Response to Influenza Infection	journal.ppat.1003115	null	[ [ "Influenza is a global health problem and current vaccination strategies are still inadequate at providing protection against seasonal and epidemic outbreaks [1] .", "Vaccination strategies aiming to induce a protective CD8+ T cell response hold tremendous potential , since CD8+ T cells are able to recogn...	[ "Trafficking of lung dendritic cells ( DCs ) to the draining lymph node ( dLN ) is a crucial step for the initiation of T cell responses upon pathogen challenge .", "However , little is known about the factors that regulate lung DC migration to the dLN .", "In this study , using a model of influenza infection ,...	[ "Influenza is a global health problem frequented by epidemics and pandemics .", "Current vaccines against influenza offer limited protection hence the need for reformulation and repeated vaccination .", "There is a pressing need to develop newer vaccines that are able to generate T cell response .", "In order...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biotechnology", "medicine and health sciences", "data acquisition", "engineering and technology", "catheters", "membrane potential", "fibrosis", "electrophysiology", "developmental biology", "waves", "cardiology", "bioengineering", "computer and information sciences", "arrhythmia", "atr...	Multiple factors influence the morphology of the bipolar electrogram: An in silico modeling study	journal.pcbi.1006765	null	[ [ "Bipolar catheters are commonly used for electrical mapping of cardiac substrates , with an application for the diagnosis and treatment of various cardiac arrhythmias .", "Low-voltage areas identified based on the bipolar electrograms ( Bi-egms ) typically correspond to scarred tissue and its border , and...	[ "Although bipolar electrograms ( Bi-egms ) are commonly used for catheter mapping and ablation of cardiac arrhythmias , the accuracy and reproducibility of Bi-egms have not been evaluated .", "We aimed to clarify the influence of the catheter orientation ( CO ) , catheter contact angle ( CA ) , local conduction v...	[ "Cardiac arrhythmias are rhythm disorders of the heart leading to abnormal heart function .", "For the diagnosis and treatment of the arrhythmias , clinicians insert catheters into the heart and examine the electrical signal propagation in the heart .", "Among different type of catheters , bipolar catheters hav...	2019
[ "Introduction", "Results", "Discussion" ]	[]	Interpreting the Dependence of Mutation Rates on Age and Time	journal.pbio.1002355	Modeling how the source of mutations relates to their rate of accumulation with age, sex, and number of cell divisions helps to explain perplexing observations about germline and somatic mutations.	[ [ "Because mutations are the ultimate source of all genetic variation , deleterious and advantageous , mutagenesis has been of central interest even before the discovery of DNA as the genetic material ( e . g . , [1] ) , and developing a model of mutational heterogeneity along the genome is a major focus of cur...	[ "Mutations can originate from the chance misincorporation of nucleotides during DNA replication or from DNA lesions that arise between replication cycles and are not repaired correctly .", "We introduce a model that relates the source of mutations to their accumulation with cell divisions , providing a framework ...	[ "We relate how mutations arise to how they accumulate in different sexes , with age and with cell division .", "This model provides a single framework within which to interpret emerging results from evolutionary biology , human genetics , and cancer genetics .", "We show that the accrual of mutations should tra...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics", "biology and life sciences", "developmental biology" ]	Hecate/Grip2a Acts to Reorganize the Cytoskeleton in the Symmetry-Breaking Event of Embryonic Axis Induction	journal.pgen.1004422	null	[ [ "Dorsoventral axis formation is a fundamental process in early vertebrate embryogenesis .", "In many vertebrates such as amphibians and teleosts , evidence indicates that maternally-supplied dorsal determinants trigger the formation of the future dorsal organizer .", "Embryological manipulations have ...	[ "Maternal homozygosity for three independent mutant hecate alleles results in embryos with reduced expression of dorsal organizer genes and defects in the formation of dorsoanterior structures .", "A positional cloning approach identified all hecate mutations as stop codons affecting the same gene , revealing tha...	[ "One of the earliest and most crucial events in animal development is the establishment of the embryonic dorsal axis .", "In amphibians and fish , this event depends on the transport of so-called “dorsal determinants” from one region of the egg , at the pole opposite from the site where the oocyte nucleus lies , ...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "plant anatomy", "trichomes", "microtubules", "pavement cells", "plant cell biology", "brassica", "plant science", "model organisms", "experimental organism systems", "seedlings", "plants", "cellular structures and organelles", "flower anatomy", "cytoskeleton", "research and analysis met...	Reactive oxygen species mediate conical cell shaping in Arabidopsis thaliana petals	journal.pgen.1007705	null	[ [ "Plants have evolved diverse epidermal cell types , that differ in size , morphology , and function , to adapt to life on land [1 , 2] .", "The Arabidopsis thaliana ( A . thaliana ) epidermis contain several well-known cell types , including interlocking jigsaw puzzle-shaped leaf pavement cells , tubular ...	[ "Plants have evolved diverse cell types with distinct sizes , shapes , and functions .", "For example , most flowering plants contain specialized petal conical epidermal cells that are thought to attract pollinators and influence light capture and reflectance , but the molecular mechanisms controlling conical cel...	[ "Plants have diverse cell types with distinct sizes , shapes , and functions .", "For example , most flowering plants contain specialized conical petal epidermal cells that are thought to attract bee pollinators , but the molecular mechanisms controlling conical cell shaping remain unclear .", "Here , through a...	2018
[ "Introduction", "Results", "Discussion", "Methods and Materials" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "pathogens", "immunology", "microbiology", "genomic library screening", "mutation", "fungi", "model organisms", "clinical medicine", "pharmacology", "molecular biology techniques", "genetic interactions", "hypersensitivit...	Mapping the Hsp90 Genetic Network Reveals Ergosterol Biosynthesis and Phosphatidylinositol-4-Kinase Signaling as Core Circuitry Governing Cellular Stress	journal.pgen.1006142	null	[ [ "Hsp90 is an ATP-dependent molecular chaperone that stabilizes components of diverse signal transduction cascades , especially those involved in adaptation to stress [1] .", "Hsp90 function is modulated by co-chaperones , which are thought to mediate recognition of client proteins , many of which cycle dy...	[ "Candida albicans is a leading human fungal pathogen that causes life-threatening systemic infections .", "A key regulator of C . albicans stress response , drug resistance , morphogenesis , and virulence is the molecular chaperone Hsp90 .", "Targeting Hsp90 provides a powerful strategy to treat fungal infectio...	[ "Hsp90 is an essential and conserved molecular chaperone that is required for the folding and function of a wide range of client proteins , especially those involved in signaling and stress responses .", "In the human fungal pathogen Candida albicans , Hsp90 governs drug resistance , morphogenesis , and virulence...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology/vaccines", "virology/immunodeficiency viruses", "immunology/immune response", "virology/animal models of infection", "immunology/immunity to infections" ]	Immunization with Single-Cycle SIV Significantly Reduces Viral Loads After an Intravenous Challenge with SIVmac239	journal.ppat.1000272	null	[ [ "The search for a safe and effective AIDS vaccine continues .", "While live , attenuated strains of SIV afford reliable long-term protection in animal models , at least against closely related challenge viruses , they have the potential to regain a pathogenic phenotype through the accumulation of compensa...	[ "Strains of simian immunodeficiency virus ( SIV ) that are limited to a single cycle of infection were evaluated for the ability to elicit protective immunity against wild-type SIVmac239 infection of rhesus macaques by two different vaccine regimens .", "Six animals were inoculated at 8-week intervals with 6 iden...	[ "AIDS vaccine candidates based on recombinant DNA and/or viral vectors stimulate potent cellular immune responses .", "However , the extent of protection achieved by these vaccines has so far been disappointing .", "While live , attenuated strains of SIV afford more reliable protection in animal models , there ...	2009
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "biotechnology", "materials science", "immunology", "biology", "biomaterials" ]	A New Strategy Based on Smrho Protein Loaded Chitosan Nanoparticles as a Candidate Oral Vaccine against Schistosomiasis	journal.pntd.0001894	null	[ [ "Schistosomiasis remains one of the most prevalent diseases in the world and so a significant public health problem , especially in developing countries [1] .", "This parasitic disease affects more than 240 million people worldwide , with a further 700 million individuals living at risk of infection [2] a...	[ "Schistosomiasis is one of the most important neglected tropical diseases and an effective control is unlikely in the absence of improved sanitation and vaccination .", "A new approach of oral vaccination with alginate coated chitosan nanoparticles appears interesting because their great stability and the ease of...	[ "Schistosomiasis is one of the most important neglected tropical diseases and an effective control is unlikely in the absence of improved sanitation and vaccine .", "The selection of a suitable delivery system and an adjuvant to aid in the stimulation of the appropriate immune response is a critical step in the p...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "elderly", "tropical diseases", "geographical locations", "health care", "age groups", "signs and symptoms", "neglected tropical diseases", "infectious diseases", "taiwan", "intensive care units", "dengue fever", "pain", ...	Symptoms associated with adverse dengue fever prognoses at the time of reporting in the 2015 dengue outbreak in Taiwan	journal.pntd.0006091	null	[ [ "Dengue is a mosquito-borne viral disease that has become a major public health problem owing to its wide geographical extension , high incidence , and disease severity [1 , 2] .", "Southeast Asia and the Western Pacific are most seriously affected by dengue , with 75% of the current globally reported out...	[ "Tainan experienced the most severe dengue epidemic in Taiwan in 2015 .", "This study investigates the association between the signs and symptoms at the time of reporting with the adverse dengue prognoses .", "A descriptive study was conducted using secondary data from the Dengue Disease Reporting System in Tai...	[ "Clinical presentations of dengue fever ( DF ) are diverse and non-specific and often have unpredictable progression and outcomes .", "The patients in the 2015 dengue epidemics in Taiwan were predominantly much older than in other countries in Southeast Asia .", "However , limited data are available in Taiwan o...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "developmental neuroscience", "cellular neuroscience", "neurogenesis", "molecular neuroscience", "biology and life sciences", "neuronal differentiation", "neuroscience", "cell differentiation" ]	Unkempt Is Negatively Regulated by mTOR and Uncouples Neuronal Differentiation from Growth Control	journal.pgen.1004624	null	[ [ "Neural progenitors in the developing human brain generate up to 250 , 000 neurons per minute .", "After differentiating from these neural progenitors , neurons migrate and are then integrated into neural circuits .", "Temporal control of neurogenesis is therefore critical to produce a complete and fu...	[ "Neuronal differentiation is exquisitely controlled both spatially and temporally during nervous system development .", "Defects in the spatiotemporal control of neurogenesis cause incorrect formation of neural networks and lead to neurological disorders such as epilepsy and autism .", "The mTOR kinase integrat...	[ "The development of a functional nervous system requires that nerve cells are generated at exactly the right time and place to be correctly integrated .", "Defects in the timing at which nerve cells are generated , or ‘differentiate’ , lead to neurological disorders such as epilepsy and autism .", "However , ve...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "systems biology", "computer science", "plant science", "computer modeling", "theoretical biology", "plant biology", "biology", "genetics and genomics" ]	Integrative Analysis of Transgenic Alfalfa (Medicago sativa L.) Suggests New Metabolic Control Mechanisms for Monolignol Biosynthesis	journal.pcbi.1002047	null	[ [ "The complex , interwoven structure of lignin , cellulose , and hemicellulose polymers in plant cell walls is the main cause for the recalcitrance of lignocellulosic feedstocks to microbial and enzymatic deconstruction towards fermentable sugars .", "This recalcitrance , in turn , accounts for the high co...	[ "The entanglement of lignin polymers with cellulose and hemicellulose in plant cell walls is a major biological barrier to the economically viable production of biofuels from woody biomass .", "Recent efforts of reducing this recalcitrance with transgenic techniques have been showing promise for ameliorating or e...	[ "Cellulose-based biofuels presently offer the most environmentally attractive and technologically promising alternative to fossil fuels .", "To be viable , biofuels must be derived from non-food crops , such as grasses , wood , bark , and plant residues .", "Techniques for releasing the energy stored in these r...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Computational Model of MicroRNA Control of HIF-VEGF Pathway: Insights into the Pathophysiology of Ischemic Vascular Disease and Cancer	journal.pcbi.1004612	null	[ [ "When cells are exposed to low oxygen tension , cellular adaptation occurs by transcriptionally activating a variety of genes that participate in pathways involving angiogenesis , metabolism and proliferation/survival [1] .", "The oxygen-sensitive transcription factor HIF-1 ( hypoxia-inducible factor 1 ) ...	[ "HRMs ( hypoxia-responsive miRNAs ) are a specific group of microRNAs that are regulated by hypoxia .", "Recent studies revealed that several HRMs including let-7 family miRNAs were highly induced in response to HIF ( hypoxia-inducible factor ) stabilization in hypoxia , and they potently participated in angiogen...	[ "Cells living in a hypoxic environment secrete signals to stimulate new blood vessel growth , a process termed angiogenesis , to acquire more oxygen and nutrients .", "Hypoxia-inducible factor 1 ( HIF-1 ) accumulates in hypoxia and expedites the release of pro-angiogenic cytokines such as vascular endothelial gro...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "enzyme-linked immunoassays", "pathology and laboratory medicine", "tropical diseases", "parasitic diseases", "animals", "echinococcus", "surgical and invasive medical procedures", "pharmaceutics", "neglected tropical diseases", "immunologic tec...	Diagnostic Accuracy of Antigen 5-Based ELISAs for Human Cystic Echinococcosis	journal.pntd.0004585	null	[ [ "Cystic echinococcosis ( CE ) is a neglected zoonotic disease caused by the larval form of the tapeworm Echinococcus granulosus complex .", "The definitive hosts are dogs and other canids , while sheep and other livestock are the natural intermediate hosts; humans are occasional intermediate hosts .", ...	[ "Clinical diagnosis and follow up of cystic echinococcosis ( CE ) are based on imaging complemented by serology .", "Several immunodiagnostic tests are commercially available , but the development of new tools is still needed to overcome the lack of standardization of the target antigen , generally consisting of ...	[ "Cystic echinococcosis is a neglected disease caused by the larval stage of the tapeworm Echinococcus granulosus complex affecting both humans and livestock .", "The disease is considered one of the world’s major zoonoses , and represents a public health problem .", "Clinical diagnosis and follow-up is mainly b...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "medicine and health sciences", "reproductive system", "gonads", "quantitative trait loci", "caenorhabditis", "animals", "germ cells", "epistasis", "animal models", "oocytes", "caenorhabditis elegans", "model organisms", "experimental organism systems", "molecular biolog...	Modeling of a negative feedback mechanism explains antagonistic pleiotropy in reproduction in domesticated Caenorhabditis elegans strains	journal.pgen.1006769	null	[ [ "Most biological traits have a strong heritable , or genetic , component .", "There is a general interest to understand the genetic basis of these traits , often by the identification of quantitative trait nucleotides ( QTNs ) underlying heritable variation segregating within a population .", "Two dec...	[ "Most biological traits and common diseases have a strong but complex genetic basis , controlled by large numbers of genetic variants with small contributions to a trait or disease risk .", "The effect-size of most genetic variants is not absolute and is instead dependent upon multiple factors such as the age and...	[ "Complex traits are influenced by the individual effects of genetic variants in addition to the interactions of the variants with the environment , age , and each other .", "While complex genetic architectures are ubiquitous in natural traits , little is known about the causal mechanisms that create their complex...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "biochemistry", "mammals", "computational biology", "cell biology" ]	Stimulus Design for Model Selection and Validation in Cell Signaling	journal.pcbi.0040030	null	[ [ "One goal of systems biology is to develop detailed models of complex biological systems that quantitatively capture known mechanisms and behaviors , and also make useful predictions .", "Such models serve as a basis for understanding , for the design of experiments , and for the development of clinical i...	[ "Mechanism-based chemical kinetic models are increasingly being used to describe biological signaling .", "Such models serve to encapsulate current understanding of pathways and to enable insight into complex biological processes .", "One challenge in model development is that , with limited experimental data ,...	[ "A major focus of systems biology is the development of mechanism-based models of cell signaling pathways .", "These models hold the promise of encapsulating our understanding of complex biological processes while also predicting new behavior .", "However , as these models become more complex , it can be diffic...	2008
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell physiology", "herpes simplex virus", "medicine and health sciences", "crystal structure", "pathology and laboratory medicine", "viral transmission and infection", "pathogens", "condensed matter physics", "microbiology", "vertebrates", "viral structure", "animals", "mammals", "viruses...	Structural basis of nectin-1 recognition by pseudorabies virus glycoprotein D	journal.ppat.1006314	null	[ [ "There are three major subfamilies , Alpha- , Beta- and Gamma-herpesvirinae , in the Herpesviridae family [1] .", "The three subfamilies differ in their host range capacities .", "In contrast to beta and gamma herpesviruses which exhibit restricted or limited cell-type tropism , the alphaherpesviruses...	[ "An early and yet indispensable step in the alphaherpesvirus infection is the engagement of host receptors by the viral envelope glycoprotein D ( gD ) .", "Of the thus-far identified gD receptors , nectin-1 is likely the most effective in terms of its wide usage by multiple alphaherpesviruses for cell entry .", ...	[ "Both herpes simplex virus ( HSV ) and pseudorabies virus ( PRV ) recognize nectin-1 as the cellular receptor .", "They utilize the envelope glycoprotein D ( gD ) on the virion surface to interact with nectin-1 , initiating the virus infection .", "Although the molecular basis of nectin-1 binding by HSV gD has ...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biofilms", "medicine and health sciences", "pathology and laboratory medicine", "enzymes", "pathogens", "cell cycle and cell division", "cell processes", "rna extraction", "microbiology", "enzymology", "mutation", "fungi", "model organisms", "fungal pathogens", "extraction techniques", ...	Bypass of Candida albicans Filamentation/Biofilm Regulators through Diminished Expression of Protein Kinase Cak1	journal.pgen.1006487	null	[ [ "Candida albicans is an invasive fungal pathogen that causes lethal infections in approximately 400 , 000 people per year worldwide [1] .", "Susceptibility to infection can be caused by a weakened immune system or presence of an implanted medical device , which provides a niche for biofilm formation .", ...	[ "Biofilm formation on implanted medical devices is a major source of lethal invasive infection by Candida albicans .", "Filamentous growth of this fungus is tied to biofilm formation because many filamentation-associated genes are required for surface adherence .", "Cell cycle or cell growth defects can induce ...	[ "The ability of the pathogen Candida albicans to grow on surfaces as biofilms is a determinant of infection ability , because biofilms on implanted medical devices seed infections .", "Biofilm formation by this organism requires growth in the form of filamentous cells and the expression of filamentation-associate...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "sequencing techniques", "biogeography", "medicine and health sciences", "ecology and environmental sciences", "linguistics", "pathology and laboratory medicine", "pathogens", "carcinomas", "population genetics", "microbiology", "cancers and neoplasms", "social sciences", "gastrointestinal t...	Deep sequencing of HBV pre-S region reveals high heterogeneity of HBV genotypes and associations of word pattern frequencies with HCC	journal.pgen.1007206	null	[ [ "The hepatitis B virus ( HBV ) is a DNA virus infecting around 257 million people worldwide ( http://www . who . int/mediacentre/factsheets/fs204/en/ ) and can cause liver diseases and hepatocellular carcinoma ( HCC ) , one of the most common types of liver cancer [1 , 2] .", "About 500 , 000 HBV patients...	[ "Hepatitis B virus ( HBV ) infection is a common problem in the world , especially in China .", "More than 60–80% of hepatocellular carcinoma ( HCC ) cases can be attributed to HBV infection in high HBV prevalent regions .", "Although traditional Sanger sequencing has been extensively used to investigate HBV se...	[ "HBV infection can lead to many liver complications including hepatocellular carcinoma ( HCC ) , one of the most common liver cancers in China .", "High-throughput sequencing technologies have recently been used to study the genotype sequence compositions of HBV infected individuals and to distinguish chronic HBV...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "evolutionary biology/human evolution", "computational biology/genomics", "evolutionary biology/genomics" ]	Pervasive Hitchhiking at Coding and Regulatory Sites in Humans	journal.pgen.1000336	null	[ [ "The neutral theory of molecular evolution [1] postulates that adaptive substitutions occur so rarely that they can be safely ignored in most studies in population genetics or molecular evolution .", "This view has dominated the field of molecular evolution for the past 40 years .", "However , the pas...	[ "Much effort and interest have focused on assessing the importance of natural selection , particularly positive natural selection , in shaping the human genome .", "Although scans for positive selection have identified candidate loci that may be associated with positive selection in humans , such scans do not ind...	[ "There is much reported evidence for positive selection at specific loci in the human genome .", "Additional papers based on comparisons between the genomes of humans and chimpanzees have also suggested that adaptive evolution may be quite common .", "At the same time , it has been surprisingly hard to find una...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Financial and Economic Costs of the Elimination and Eradication of Onchocerciasis (River Blindness) in Africa	journal.pntd.0004056	null	[ [ "To reduce disease prevalence to a locally acceptable level ( i . e . , microfilaria prevalence≤40% or community microfilarial load≤5mf/s [3] ) , all endemic African countries implement annual CDTi in hyper- and meso-endemic areas , and after at least 25-years of CDTi , conduct epidemiological surveillance to...	[ "Onchocerciasis ( river blindness ) is a parasitic disease transmitted by blackflies .", "Symptoms include severe itching , skin lesions , and vision impairment including blindness .", "More than 99% of all cases are concentrated in sub-Saharan Africa .", "Fortunately , vector control and community-directed t...	[ "River blindness ( onchocerciasis ) is a parasitic disease transmitted by blackflies .", "Symptoms include severe itching , skin lesions , and vision impairment including blindness .", "More than 99% of all cases are concentrated in sub-Saharan Africa .", "Fortunately , vector control and community-directed t...	2015
[ "Introduction", "Results", "Discussion", "Material and methods" ]	[ "blastocysts", "uterus", "medicine and health sciences", "reproductive system", "maternal health", "obstetrics and gynecology", "cell cycle and cell division", "cell processes", "departures from diploidy", "cell differentiation", "developmental biology", "women's health", "pregnancy", "mam...	Genome amplification and cellular senescence are hallmarks of human placenta development	journal.pgen.1007698	null	[ [ "It is commonly assumed that trophoblasts of the human placenta exit their cell cycle as they develop into differentiated subtypes .", "This hypothesis follows the assumption that quiescence is a consequence of terminal differentiation in tissues .", "In detail , the villous epithelium of the human pl...	[ "Genome amplification and cellular senescence are commonly associated with pathological processes .", "While physiological roles for polyploidization and senescence have been described in mouse development , controversy exists over their significance in humans .", "Here , we describe tetraploidization and senes...	[ "In tissues , cellular differentiation is normally associated with cell cycle arrest .", "However , in some cases differentiating cells continue their cyclic activity in the absence of cell division .", "This event , referred to as endoreduplication , leads to polyploidy , which means an increased number of chr...	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "virology", "emerging viral diseases", "biology", "microbiology", "viral evolution" ]	Origin and Evolution of Dengue Virus Type 3 in Brazil	journal.pntd.0001784	null	[ [ "Dengue virus ( DENV ) is a member of the genus Flavivirus , family Flaviviridae , and one of the most important arboviral pathogens .", "The single-stranded positive-sense genomic RNA encodes one large open reading frame ( ORF ) as a polyprotein , which undergoes proteolytic processing into three structu...	[ "The incidence of dengue fever and dengue hemorrhagic fever in Brazil experienced a significant increase since the emergence of dengue virus type-3 ( DENV-3 ) at the early 2000s .", "Despite the major public health concerns , there have been very few studies of the molecular epidemiology and time-scale of this DE...	[ "Dengue is a major health problem in the tropics and the incidence of dengue fever and dengue hemorrhagic fever in Brazil experienced a significant increase since the emergence of dengue virus type-3 ( DENV-3 ) .", "In this study , the authors reconstruct the spatio-temporal dispersion pattern of the DENV-3 linea...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "tropical diseases", "global health", "neglected tropical diseases", "infectious disease control", "research facilities", "research and analysis methods", "public and occupational health", "infectious diseases", "agrochemicals", "epidemiology", "dengue fever", ...	Dengue Contingency Planning: From Research to Policy and Practice	journal.pntd.0004916	null	[ [ "Responding to the rapidly increasing public health importance of dengue , the 2002 World Health Assembly Resolution WHA55 . 17 urged greater commitment to dengue among Member States and throughout the World Health Organisation ( WHO ) .", "One response of particular significance was the Revision of the I...	[ "Dengue is an increasingly incident disease across many parts of the world .", "In response , an evidence-based handbook to translate research into policy and practice was developed .", "This handbook facilitates contingency planning as well as the development and use of early warning and response systems for d...	[ "An evidence-based handbook was generated to facilitate deployment of dengue surveillance and response systems for timely and effective management of outbreaks , and to identify the factors required for success .", "Evidence was evaluated using literature reviews , policymaker and stakeholder interviews , assessm...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Natural Selection Constrains Neutral Diversity across A Wide Range of Species	journal.pbio.1002112	Analysis of whole genome genetic variation data from 40 species shows that natural selection disproportionately depletes linked neutral variation in species with large population sizes, explaining why levels of neutral diversity do not scale with population size.	[ [ "The level of neutral genetic diversity within populations is a central parameter for understanding the demographic histories of populations [1] , selective constraints [2] , the molecular basis of adaptive evolution [3] , genome-wide associations with disease [4] , and conservation genetics [5] .", "Cons...	[ "The neutral theory of molecular evolution predicts that the amount of neutral polymorphisms within a species will increase proportionally with the census population size ( Nc ) .", "However , this prediction has not been borne out in practice: while the range of Nc spans many orders of magnitude , levels of gene...	[ "A fundamental goal of population genetics is to understand why levels of genetic diversity vary among species and populations .", "Under the assumptions of the neutral model of molecular evolution , the amount of variation present in a population should be directly proportional to the size of the population .", ...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "phosphorylation", "vesicles", "enzymes", "cell processes", "enzymology", "phosphatases", "membrane receptor signaling", "cellular structures and organelles", "endosomes", "animal cells", "proteins", "exocytosis", "cell membranes", "endocytosis", "biochemistry", "signal transduction", ...	A Computational Model for the AMPA Receptor Phosphorylation Master Switch Regulating Cerebellar Long-Term Depression	journal.pcbi.1004664	null	[ [ "The functional plasticity of neuronal synapses , including long-term potentiation ( LTP ) and long-term depression ( LTD ) , is essential for learning and the encoding of memories [1] .", "The focus of this study is LTD at the parallel fibre-Purkinje cell ( PF-PC ) synapse in the cerebellum , which is be...	[ "The expression of long-term depression ( LTD ) in cerebellar Purkinje cells results from the internalisation of α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid receptors ( AMPARs ) from the postsynaptic membrane .", "This process is regulated by a complex signalling pathway involving sustained protein kinas...	[ "Changes in synaptic strength , which can include long-term potentiation and long-term depression , are important for learning and the encoding of memories across the brain .", "Long-term depression ( LTD ) , in particular , is thought to be essential for motor learning in the cerebellum , and disruption of this ...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/bacterial infections", "genetics and genomics/microbial evolution and genomics", "evolutionary biology/microbial evolution and genomics" ]	Origin, Spread and Demography of the Mycobacterium tuberculosis Complex	journal.ppat.1000160	null	[ [ "The Mycobacterium tuberculosis complex ( MTBC ) is composed of closely related bacterial sub-species that have plagued human and animal populations for thousands of years .", "The most famous member of the MTBC is M . tuberculosis , the etiological agent of tuberculosis in humans that killed 1 . 7 millio...	[ "The evolutionary timing and spread of the Mycobacterium tuberculosis complex ( MTBC ) , one of the most successful groups of bacterial pathogens , remains largely unknown .", "Here , using mycobacterial tandem repeat sequences as genetic markers , we show that the MTBC consists of two independent clades , one co...	[ "The causative agents of tuberculosis , grouped in the Mycobacterium tuberculosis complex , have infected one-third of the present human population and a wide range of other mammals .", "However , paradigmatic questions , such as why , where and when the disease began and expanded , have largely remained unanswer...	2008
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[]	Antimicrobial Peptides Design by Evolutionary Multiobjective Optimization	journal.pcbi.1003212	null	[ [ "Antimicrobial peptides ( AMPs ) are small evolutionally conserved molecules found among all classes of life , from multicellular organisms to bacterial cells [1] , [2] .", "In higher organisms , AMPs play a major role in innate immunity as a part of the first defence line against invading pathogens .", ...	[ "Antimicrobial peptides ( AMPs ) are an abundant and wide class of molecules produced by many tissues and cell types in a variety of mammals , plant and animal species .", "Linear alpha-helical antimicrobial peptides are among the most widespread membrane-disruptive AMPs in nature , representing a particularly su...	[ "In recent years , the increasing and rapid spread of pathogenic microorganisms resistant to conventional antibiotics especially in hospital settings spurred research for the identification of novel molecules endowed with antimicrobial activities and new mechanisms of action .", "Antimicrobial peptides ( AMPs ) r...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "phosphorylation", "cellular stress responses", "second messenger system", "mechanisms of signal transduction", "cell processes", "g-protein signaling", "mapk signaling cascades", "protein kinase signaling cascade", "stress signaling cascade", "proteins", "biochemistry", "signal transduction",...	Amino acid metabolites that regulate G protein signaling during osmotic stress	journal.pgen.1006829	null	[ [ "Cells routinely experience changing and often unfavorable conditions in their environment .", "The ability to adapt to environmental stress and re-establish homeostasis is essential not only to the survival of a cell , but also to the well-being of the organism .", "The response to such physical or c...	[ "All cells respond to osmotic stress by implementing molecular signaling events to protect the organism .", "Failure to properly adapt can lead to pathologies such as hypertension and ischemia-reperfusion injury .", "Mitogen-activated protein kinases ( MAPKs ) are activated in response to osmotic stress , as we...	[ "Just as organisms must adapt to a challenging environment , cells must respond to chemical or physical changes that occur within the organism .", "Regardless of the environmental cue , all cells use molecular signaling pathways to respond to those changes .", "Many are transmitted by G protein-coupled receptor...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Modulation of Global Low-Frequency Motions Underlies Allosteric Regulation: Demonstration in CRP/FNR Family Transcription Factors	journal.pbio.1001651	Allostery in bacterial transcription factors arises from changes in global low-frequency protein dynamics. Amino acids that regulate low-frequency dynamics are identified and seen to be evolutionarily conserved.	[ [ "Small regulatory molecules frequently bind proteins at regions remote from the active site .", "These allosteric events can switch proteins between inactive and active states [1] .", "Knowledge of the molecular basis of allostery derives from a wealth of theoretical and experimental studies and tradi...	[ "Allostery is a fundamental process by which ligand binding to a protein alters its activity at a distinct site .", "There is growing evidence that allosteric cooperativity can be communicated by modulation of protein dynamics without conformational change .", "The mechanisms , however , for communicating dynam...	[ "Allostery is a process by which a molecule binding to one site of a protein alters the activity of the protein at another site .", "Allostery is typically thought to occur through a change in protein structure , but there is now clear evidence that the dynamic properties of a protein can also regulate allostery ...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biotechnology", "engineering and technology", "brassica", "dna-binding proteins", "dna transcription", "plant science", "model organisms", "experimental organism systems", "plant genomics", "epigenetics", "plants", "chromatin", "arabidopsis thaliana", "research and analysis methods", "b...	Transcription-driven chromatin repression of Intragenic transcription start sites	journal.pgen.1007969	null	[ [ "Plasticity at the beginning and end of transcription units multiplies the RNA species that can be generated from genomes .", "Many RNA species result from RNA Polymerase II ( RNAPII ) activity at genes and abundant non-coding genomic regions [1 , 2] .", "Pervasive transcription results in overlapping...	[ "Progression of RNA polymerase II ( RNAPII ) transcription relies on the appropriately positioned activities of elongation factors .", "The resulting profile of factors and chromatin signatures along transcription units provides a “positional information system” for transcribing RNAPII .", "Here , we investigat...	[ "Genes represent DNA elements that are transcribed into mRNA .", "However , the position where transcription actually starts can be dynamically regulated to expand the diversity of RNA isoforms produced from a single gene .", "Functionally , alternative Transcription Start Sites ( TSSs ) may generate protein is...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "particle physics", "annealing (genetics)", "rna structure prediction", "atoms", "mathematics", "statistics (mathematics)", "protein structure prediction", "protein structure", "composite particles", "cellular structures and organelles", "rna annealing", "research and analysis methods", "rna...	Structure Prediction of RNA Loops with a Probabilistic Approach	journal.pcbi.1005032	null	[ [ "RNAs are a type of macromolecule of crucial and versatile biological importance .", "In addition to their long-discovered functions of carrying genetic information and acting as a part of translation machinery , recently they were found to be able to participate in the regulation of gene expressions and ...	[ "The knowledge of the tertiary structure of RNA loops is important for understanding their functions .", "In this work we develop an efficient approach named RNApps , specifically designed for predicting the tertiary structure of RNA loops , including hairpin loops , internal loops , and multi-way junction loops ...	[ "RNA is an important and versatile macromolecule participating in a variety of biological processes .", "In addition to experimental approaches , computational prediction of 3D structure of RNAs and loops is an alternative and important source of gaining structure information and insights into their functions .",...	2016
[ "Introduction", "Material and methods", "Results", "Discussion" ]	[ "rna interference", "crystal structure", "chemical compounds", "condensed matter physics", "enzymology", "phosphonic acids", "nucleotides", "organic compounds", "parasitic protozoans", "purines", "trypanosoma brucei", "protozoans", "epigenetics", "crystallography", "enzyme inhibitors", ...	Evaluation of the Trypanosoma brucei 6-oxopurine salvage pathway as a potential target for drug discovery	journal.pntd.0006301	null	[ [ "Trypanosoma brucei is the etiological agent of Human African Trypanosomiasis ( HAT ) also known as “sleeping sickness” .", "HAT is a neglected disease that mainly affects Sub-Saharan countries , with ~70 million people at risk of infection [1–3] .", "The metacyclic trypomastigote form of T . brucei i...	[ "Due to toxicity and compliance issues and the emergence of resistance to current medications new drugs for the treatment of Human African Trypanosomiasis are needed .", "A potential approach to developing novel anti-trypanosomal drugs is by inhibition of the 6-oxopurine salvage pathways which synthesise the nucl...	[ "Human African Trypanosomiasis ( HAT ) is a life-threatening infectious disease caused by the protozoan parasite , Trypanosoma brucei .", "Current treatments suffer from low efficacy , toxicity issues and complex medication regimens .", "Moreover , an alarming number of these parasites are demonstrating resista...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "mosquitoes", "immunity", "vector biology", "innate immunity", "anopheles", "biology", "microbiology", "host-pathogen interaction", "parasitology" ]	Regulation of Anti-Plasmodium Immunity by a LITAF-like Transcription Factor in the Malaria Vector Anopheles gambiae	journal.ppat.1002965	null	[ [ "In virtually all species , the innate immune system is responsible for the primary response against pathogens .", "Unlike adaptive immunity , the innate immune response does not confer long-lasting protection but instead , relies on the recognition of pathogen–associated molecular patterns ( PAMPS ) .", ...	[ "The mosquito is the obligate vector for malaria transmission .", "To complete its development within the mosquito , the malaria parasite Plasmodium must overcome the protective action of the mosquito innate immune system .", "Here we report on the involvement of the Anopheles gambiae orthologue of a conserved ...	[ "The mosquito innate immune system serves as the primary defense response against invading pathogens , including that of the malaria parasite Plasmodium .", "The mosquito immune response is remarkably efficient in eliminating the parasite as indicated by the low prevalence of Plasmodium oocysts in wild caught mos...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Targeting the Cell Stress Response of Plasmodium falciparum to Overcome Artemisinin Resistance	journal.pbio.1002132	Resistance to artemisinin antimalarial drugs is jeopardizing malaria control. This study shows that proteasome-mediated stress responses can be targeted to overcome artemisinin resistance and suggests alternate therapeutic regimens and monitoring strategies.	[ [ "Malaria remains a scourge of humanity , affecting hundreds of millions of people and causing ~600 , 000 deaths each year [1] .", "Infection with Plasmodium falciparum is responsible for the majority of severe malaria cases .", "During the asexual blood phase of its lifecycle , this protozoan parasite...	[ "Successful control of falciparum malaria depends greatly on treatment with artemisinin combination therapies .", "Thus , reports that resistance to artemisinins ( ARTs ) has emerged , and that the prevalence of this resistance is increasing , are alarming .", "ART resistance has recently been linked to mutatio...	[ "Resistance to artemisinin antimalarials , some of the most effective antimalarial drugs , has emerged in Southeast Asia , jeopardizing malaria control .", "We have undertaken a detailed study of artemisinin-sensitive and-resistant strains of Plasmodium falciparum , the parasite responsible for malaria , taken di...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "veterinary diseases", "immune cells", "immunity", "veterinary virology", "innate immunity", "antigen-presenting cells", "immunology", "biology", "viral diseases", "immunomodulation", "veterinary science" ]	Efficient Sensing of Infected Cells in Absence of Virus Particles by Blasmacytoid Dendritic Cells Is Blocked by the Viral Ribonuclease Erns	journal.ppat.1003412	null	[ [ "Although representing a rare cell type of the immune system , plasmacytoid dendritic cells ( pDC ) are the most important source of systemic interferon ( IFN ) type I in the early phase of many virus infections , and as such a critical early alarm system against viruses [1] , [2] .", "This is based on th...	[ "Plasmacytoid dendritic cells ( pDC ) have been shown to efficiently sense HCV- or HIV-infected cells , using a virion-free pathway .", "Here , we demonstrate for classical swine fever virus , a member of the Flaviviridae , that this process is much more efficient in terms of interferon-alpha induction when compa...	[ "Plasmacytoid dendritic cells ( pDC ) represent the most potent producers of interferon type I and are therefore of major importance in antiviral defences .", "A TLR7-dependent induction of interferon-α in pDC by infected cells in the absence of virions has been demonstrated for hepatitis C virus .", "Here , we...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/infectious diseases of the nervous system", "infectious diseases/viral infections", "virology/host invasion and cell entry" ]	Alteration of Blood–Brain Barrier Integrity by Retroviral Infection	journal.ppat.1000205	null	[ [ "The Blood-Brain barrier ( BBB ) constitutes the interface between the blood and the central nervous system ( CNS ) .", "It is composed of astrocytes , pericytes and brain microvascular endothelial cells .", "This latter cell type forms the major structural and functional element of the BBB , with end...	[ "The blood–brain barrier ( BBB ) , which forms the interface between the blood and the cerebral parenchyma , has been shown to be disrupted during retroviral-associated neuromyelopathies .", "Human T Lymphotropic Virus ( HTLV-1 ) Associated Myelopathy/Tropical Spastic Paraparesis ( HAM/TSP ) is a slowly progressi...	[ "The blood–brain barrier ( BBB ) forms the interface between the blood and the central nervous system ( CNS ) .", "BBB disruption is considered to be a key event in the pathogenesis of retroviral-associated neurological diseases .", "The present paper deals with the susceptibility of the endothelial cells ( i ....	2008
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "skin", "medicine and health sciences", "integumentary system", "in situ hybridization", "molecular probe techniques", "nervous system", "vertebrates", "animals", "developmental biology", "epidermis", "molecular biology techniques", "embryos", "sea squirts", "research and analysis methods"...	Antero-posterior ectoderm patterning by canonical Wnt signaling during ascidian development	journal.pgen.1008054	null	[ [ "Ascidians belong to the tunicates , the sister group of the vertebrates .", "Together with the cephalochordate ( amphioxus ) and vertebrate phyla they form the super-phylum of chordates whose specific body plan includes a notochord and a dorsal hollow neural tube during embryonic life .", "Comparativ...	[ "Wnt/β-catenin signaling is an ancient pathway in metazoans and controls various developmental processes , in particular the establishment and patterning of the embryonic primary axis .", "In vertebrates , a graded Wnt activity from posterior to anterior endows cells with positional information in the central ner...	[ "The Wnt/β-catenin pathway is a system of cell-cell communication .", "It has an ancient origin in animals and plays multiple roles during embryogenesis and adult life .", "In particular , it is involved in determining , in the vertebrate embryo , the identity of the different parts of the body and their relati...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "ecology and environmental sciences", "pathology and laboratory medicine", "sociology", "social sciences", "parasitic diseases", "simulation and modeling", "mathematics", "forecasting", "statistics (mathematics)", "network analysis", "social networks", "resear...	Predicting cryptic links in host-parasite networks	journal.pcbi.1005557	null	[ [ "Complex interactions between host and parasite species can be described as a network , with host and parasite species as two distinct node types connected by links that represent associations between a given parasite and host species .", "Understanding the structure [1] and stability [2 , 3] of host-para...	[ "Networks are a way to represent interactions among one ( e . g . , social networks ) or more ( e . g . , plant-pollinator networks ) classes of nodes .", "The ability to predict likely , but unobserved , interactions has generated a great deal of interest , and is sometimes referred to as the link prediction pro...	[ "The majority of host-parasite associations are poorly understood or not known at all because the number of associations is so vast .", "Further , interactions may shift seasonally , or as a function of changing host densities .", "Consequently , host-parasite networks may be poorly characterized since effects ...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Single Versus Double Dose Praziquantel Comparison on Efficacy and Schistosoma mansoni Re-Infection in Preschool-Age Children in Uganda: A Randomized Controlled Trial	journal.pntd.0003796	null	[ [ "Schistosomiasis is a parasitic water borne neglected tropical disease [1 , 2] of considerable public health relevance in the tropics and subtropics [3 , 4] .", "It is estimated that 200 million people are infected with schistosomiasis worldwide with 85% of the disease burden found in Sub-Saharan Africa [...	[ "Schistosoma mansoni infection is proven to be a major health problem of preschool-age children in sub-Saharan Africa , yet this age category is not part of the schistosomiasis control program .", "The objective of this study was to compare the impact of single and double dose praziquantel ( PZQ ) treatment on cu...	[ "Intestinal schistosomiasis is a parasitic water borne neglected tropical disease of considerable public health relevance in the tropics and subtropics .", "In Uganda , approximately 20 million people are at risk of being infected with S . mansoni , which causes intestinal schistosomiasis , and 4 million individu...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "systems biology", "developmental biology", "cell fate determination", "embryology", "organism development", "molecular development", "genetics", "biology", "genomics", "morphogenesis", "pattern formation", "genetics and genomics", "cell differentiation" ]	Temporal Coordination of Gene Networks by Zelda in the Early Drosophila Embryo	journal.pgen.1002339	null	[ [ "Early development consists of a highly choreographed series of events controlled by temporally and spatially regulated batteries of genes .", "Although the sequence and nature of the events may vary between organisms , features such as the maternal-to-zygotic transition ( MZT ) where control of developme...	[ "In past years , much attention has focused on the gene networks that regulate early developmental processes , but less attention has been paid to how multiple networks and processes are temporally coordinated .", "Recently the discovery of the transcriptional activator Zelda ( Zld ) , which binds to CAGGTAG and ...	[ "Development of a fertilized egg into a multicellular organism comprises a series of precisely timed events initially controlled by factors deposited into the egg .", "Some of these factors are localized to specific regions of the embryo and instruct cells to adopt certain fates .", "In this way , these “morpho...	2011
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Corticosteroids for Dengue – Why Don't They Work?	journal.pntd.0002592	null	[ [ "Dengue is an acute , mosquito-borne illness caused by any of the four types of dengue virus ( DENV1-4 ) .", "There are an estimated 390 million symptomatic and asymptomatic infections per year [1] .", "The clinical evolution is variable , ranging from non-specific febrile illness to severe and someti...	[ "Dysregulated immune responses may contribute to the clinical complications that occur in some patients with dengue .", "In Vietnamese pediatric dengue cases randomized to early prednisolone therapy , 81 gene-transcripts ( 0 . 2% of the 47 , 231 evaluated ) were differentially abundant in whole-blood between high...	[ "Dengue is an acute , mosquito-borne febrile illness and around 390 million cases occur annually in more than 100 countries .", "A host pro-inflammatory immune response is widely believed to contribute to the clinical complications that occur in some patients with dengue .", "Synthetic glucocorticoids , which a...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "chemistry", "biology" ]	Schistosomiasis Control Using Piplartine against Biomphalaria glabrata at Different Developmental Stages	journal.pntd.0002251	null	[ [ "Schistosomiasis is a tropical disease caused by parasitic worms of the genus Schistosoma and is found predominantly in areas without sanitization or clean water , including regions of Africa , South Asia and Central and South America .", "Presently , this disease affects an estimated 200 million people w...	[ "Schistosomiasis is one of the most significant diseases in tropical countries and affects almost 200 million people worldwide .", "The application of molluscicides to eliminate the parasite's intermediate host , Biomphalaria glabrata , from infected water supplies is one strategy currently being used to control ...	[ "Schistosomiasis is a disease caused by parasitic worms of several species of genus Schistosoma that affects almost 200 million people mostly common in Asia , Africa and South America .", "The transmission is carried out by the parasitic larvae hosted in fresh water snails of the genus Biomphalaria .", "Conside...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "viruses", "infectious diseases", "virology", "in vitro", "homo (human)" ]	Escape of HIV-1 from a Small Molecule CCR5 Inhibitor Is Not Associated with a Fitness Loss	journal.ppat.0030079	null	[ [ "The relative replication ability ( fitness ) of a human immunodeficiency virus type 1 ( HIV-1 ) quasispecies is governed by how individual clones fluctuate in dominance as they adapt to the host environment [1] .", "The relative fitness of two viruses in vitro is best estimated by head-to-head competitio...	[ "Fitness is a parameter used to quantify how well an organism adapts to its environment; in the present study , fitness is a measure of how well strains of human immunodeficiency virus type 1 ( HIV-1 ) replicate in tissue culture .", "When HIV-1 develops resistance in vitro or in vivo to antiretroviral drugs such...	[ "When human immunodeficiency virus type 1 ( HIV-1 ) develops resistance in vitro or in vivo to antiretroviral drugs such as reverse transcriptase or protease inhibitors , its replicative fitness is often impaired ( i . e . , it grows at a lower rate or to a lesser extent than the parental , inhibitor-sensitive viru...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "developmental biology", "stem cells", "molecular genetics", "gene expression", "biology", "molecular biology", "hematology", "cell biology", "genetics", "cellular types", "genomics", "molecular cell biology", "computational biology", "genetics and genomics" ]	Tcf7 Is an Important Regulator of the Switch of Self-Renewal and Differentiation in a Multipotential Hematopoietic Cell Line	journal.pgen.1002565	null	[ [ "Stem cells are characterized by the ability to both self renew and undergo cell differentiation .", "Understanding the mechanisms that control the switch between renewal and differentiation is a fundamental and important problem in stem cell biology .", "It is likely that many key components includin...	[ "A critical problem in biology is understanding how cells choose between self-renewal and differentiation .", "To generate a comprehensive view of the mechanisms controlling early hematopoietic precursor self-renewal and differentiation , we used systems-based approaches and murine EML multipotential hematopoieti...	[ "The hematopoietic system has provided a leading model for stem cell studies , and there is great interest in elucidating the mechanisms that control the decision of HSC self-renewal and differentiation .", "This switch is important for understanding hematopoietic diseases and manipulating HSCs for therapeutic pu...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cognitive neuroscience", "functional magnetic resonance imaging", "computational neuroscience", "biology and life sciences", "computational biology", "neuroscience", "neuroimaging" ]	Unsupervised Feature Learning Improves Prediction of Human Brain Activity in Response to Natural Images	journal.pcbi.1003724	null	[ [ "An important goal of contemporary cognitive neuroscience is to characterize the relationship between stimulus features and human brain activity .", "This relationship can be studied from two distinct but complementary perspectives of encoding and decoding [1] .", "The encoding perspective is concerne...	[ "Encoding and decoding in functional magnetic resonance imaging has recently emerged as an area of research to noninvasively characterize the relationship between stimulus features and human brain activity .", "To overcome the challenge of formalizing what stimulus features should modulate single voxel responses ...	[ "An important but difficult problem in contemporary cognitive neuroscience is to find what stimulus features best drive responses in the human brain .", "The conventional approach to solve this problem is to use descriptive encoding models that predict responses to stimulus features that are known a priori .", ...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetic mutation", "gene regulation", "neuroscience", "animal models", "caenorhabditis elegans", "model organisms", "mutation types", "molecular genetics", "gene expression", "gene splicing", "biology", "molecular biology", "mutagenesis", "rna processing", "synapses", "genetic screens...	CELF Family RNA–Binding Protein UNC-75 Regulates Two Sets of Mutually Exclusive Exons of the unc-32 Gene in Neuron-Specific Manners in Caenorhabditis elegans	journal.pgen.1003337	null	[ [ "Alternative splicing of pre-mRNAs is a major source of proteomic complexity in metazoans .", "More than 90% of human multi-exon genes undergo alternative pre-mRNA processing and many alternative splicing events are controlled in tissue- and cell-type dependent manners [1] .", "Mis-splicing of pre-mRN...	[ "An enormous number of alternative pre–mRNA splicing patterns in multicellular organisms are coordinately defined by a limited number of regulatory proteins and cis elements .", "Mutually exclusive alternative splicing should be strictly regulated and is a challenging model for elucidating regulation mechanisms ....	[ "Tissue-specific and mutually exclusive alternative pre–mRNA splicing is a challenging model for elucidating regulation mechanisms .", "We previously demonstrated that evolutionarily conserved RBFOX family RNA–binding proteins ASD-1 and FOX-1 and a muscle-specific RNA–binding protein SUP-12 cooperatively direct m...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "invertebrates", "medicine and health sciences", "rna interference", "cell cycle and cell division", "cell processes", "cloning", "animals", "cell differentiation", "animal models", "developmental biology", "drosophila melanogaster", "model organisms", "epigenetics", "molecular biology tec...	The Hippo Pathway Targets Rae1 to Regulate Mitosis and Organ Size and to Feed Back to Regulate Upstream Components Merlin, Hippo, and Warts	journal.pgen.1006198	null	[ [ "The Hippo Pathway ( also called the Salvador-Warts-Hippo Pathway ) plays a well-appreciated and strongly conserved developmental role in establishing and maintaining organ size .", "Aberrations in signaling pathways can increase rates of cellular growth or proliferation , but once appropriate organ size ...	[ "Hippo signaling acts as a master regulatory pathway controlling growth , proliferation , and apoptosis and also ensures that variations in proliferation do not alter organ size .", "How the pathway coordinates restricting proliferation with organ size control remains a major unanswered question .", "Here we id...	[ "Exquisite control of organ size is critical during animal development and its loss results in pathological conditions .", "The Hippo Tumor Suppressor Pathway coordinates regulation of proliferation , growth , apoptosis , and autophagy to determine and maintain precise control of organ size .", "However , the g...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "evidence-based healthcare/clinical decision-making", "ophthalmology/eye infections", "infectious diseases/neglected tropical diseases", "public health and epidemiology/epidemiology", "public health and epidemiology/infectious diseases", "infectious diseases/bacterial infections", "infectious diseases/e...	Trachoma Prevalence and Associated Risk Factors in The Gambia and Tanzania: Baseline Results of a Cluster Randomised Controlled Trial	journal.pntd.0000861	null	[ [ "Trachoma is caused by ocular infection with serovars A , B , Ba or C of the bacterium Chlamydia trachomatis .", "It is the leading infectious cause of blindness worldwide [1] with an estimated 40 . 6 million people suffering from active trachoma ( trachomatous inflammation , follicular ( TF ) and/or inte...	[ "Blinding trachoma , caused by ocular infection with Chlamydia trachomatis , is targeted for global elimination by 2020 .", "Knowledge of risk factors can help target control interventions .", "As part of a cluster randomised controlled trial , we assessed the baseline prevalence of , and risk factors for , act...	[ "Trachoma is caused by Chlamydia trachomatis and is the leading infectious cause of blindness .", "The World Health Organization's ( WHO ) control strategy includes antibiotic treatment of all community members , facial cleanliness , and environmental improvements .", "By determining how prevalent trachoma is ,...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "mathematical computing", "mathematics", "biology", "microbiology", "parasitology" ]	Modeling Within-Host Effects of Drugs on Plasmodium falciparum Transmission and Prospects for Malaria Elimination	journal.pcbi.1003434	null	[ [ "Plasmodium falciparum , the most virulent of the Plasmodium species that cause malaria in humans , is responsible for hundreds of millions of cases per year [1] .", "The number of fatal outcomes is a matter of considerable debate , with estimates for 2010 ranging from 655 , 000 to 1 , 238 , 000 [2] , [3]...	[ "Achieving a theoretical foundation for malaria elimination will require a detailed understanding of the quantitative relationships between patient treatment-seeking behavior , treatment coverage , and the effects of curative therapies that also block Plasmodium parasite transmission to mosquito vectors .", "Here...	[ "We utilize a within-host mathematical model of malaria transmission to predict the effects of antimalarial treatment across the globe .", "We predict that areas containing 91% of the at-risk population of Southeast Asia can achieve elimination if at least 93–98% of symptomatic individuals are promptly treated wi...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "invertebrates", "rna-binding proteins", "centrosomes", "caenorhabditis", "metaphase", "cell cycle and cell division", "cell processes", "condensed matter physics", "animals", "animal models", "developmental biology", "caenorhabditis elegans", "model organisms", "cytokinesis", "embryos",...	ATX-2, the C. elegans Ortholog of Human Ataxin-2, Regulates Centrosome Size and Microtubule Dynamics	journal.pgen.1006370	null	[ [ "As the primary microtubule-organizing centers , centrosomes are vital for the maintenance of genomic integrity in animal cells [1] .", "The centrosome consists of two barrel-shaped centrioles surrounded by a network of proteins termed pericentriolar materials ( PCM ) .", "To maintain the fidelity of ...	[ "Centrosomes are critical sites for orchestrating microtubule dynamics , and exhibit dynamic changes in size during the cell cycle .", "As cells progress to mitosis , centrosomes recruit more microtubules ( MT ) to form mitotic bipolar spindles that ensure proper chromosome segregation .", "We report a new role...	[ "The microtubule ( MT ) cytoskeleton undergoes dynamic rearrangements during the cell cycle .", "As the primary microtubule-organizing center , centrosomes orchestrate MT dynamics and play a key role in establishing bipolar spindles in mitosis .", "Errors in centrosome assembly lead to missegregation of genomic...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "zygomycosis", "fungal diseases" ]	Sporangiospore Size Dimorphism Is Linked to Virulence of Mucor circinelloides	journal.ppat.1002086	null	[ [ "Zygomycetes and chytridiomycetes are basal lineages of the fungal kingdom and both are paraphyletic and encompass several phyla [1] , [2] .", "Within the Zygomycota , the order Mucorales is a monophyletic group that has been relatively well studied compared to other basal fungal groups .", "However ,...	[ "Mucor circinelloides is a zygomycete fungus and an emerging opportunistic pathogen in immunocompromised patients , especially transplant recipients and in some cases otherwise healthy individuals .", "We have discovered a novel example of size dimorphism linked to virulence .", "M . circinelloides is a heterot...	[ "Mucormycosis is recognized as an emerging infectious disease .", "Compared to other fungal infections , mucormycosis results in high mortality: ∼50% of overall infections and >90% in disseminated infections .", "There is therefore an ongoing need to study these fungal pathogens .", "However , surprisingly li...	2011
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Validation of a Microsphere Immunoassay for Serological Leptospirosis Diagnosis in Human Serum by Comparison to the Current Gold Standard	journal.pntd.0003636	null	[ [ "Leptospirosis is considered to be the most widespread zoonotic disease in the world [1] with clinical diagnosis proving challenging due to the non-specific nature of symptoms associated with the disease .", "There are some 300 leptospiral serovars belonging to a number of different serogroups .", "Cu...	[ "A microsphere immunoassay ( MIA ) utilising Luminex xMap technology that is capable of determining leptospirosis IgG and IgM independently was developed .", "The MIA was validated using 200 human samples submitted for routine leptospirosis serology testing .", "The traditional microscopic agglutination ( MAT )...	[ "Leptospirosis is a zoonotic disease caused by spirochaetes of the genus Leptospira and affects millions of people , worldwide , each year .", "Laboratory diagnosis of leptospirosis currently relies on methods that are flawed in many areas .", "Current methods are outdated , time consuming and expensive .", "...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "infectious diseases of the nervous system", "neurological disorders", "cysticercosis", "neurology", "neglected tropical diseases", "parasitic diseases" ]	Added Value of Antigen ELISA in the Diagnosis of Neurocysticercosis in Resource Poor Settings	journal.pntd.0001851	null	[ [ "More than 80% of people with epilepsy ( PWE ) live in low-income countries [1] , where the prevalence of active epilepsy is approximately twice that of high-income countries [2] .", "Moreover , in many of those countries over 75% of PWE have no access to treatment with anti-epileptic medication [3] .", ...	[ "Neurocysticercosis ( NCC ) is the most common cause of acquired epilepsy in Taenia solium endemic areas , primarily situated in low-income countries .", "Diagnosis is largely based upon the “Del Brutto diagnostic criteria” using the definitive/probable/no NCC diagnosis approach .", "Neuroimaging and specific T...	[ "Neurocysticercosis is a parasitic infection of the central nervous system and a common cause of epilepsy in Taenia solium cysticercosis endemic countries .", "According to the current diagnostic criteria proposed by Del Brutto and colleagues , the diagnosis of neurocysticercosis is mainly based on neuroimaging a...	2012

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