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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" ]	[ "invertebrates", "cell motility", "medicine and health sciences", "reproductive system", "caenorhabditis", "neuroscience", "animals", "animal models", "developmental biology", "caenorhabditis elegans", "model organisms", "experimental organism systems", "nerve fibers", "vulva", "embryos"...	Functional Requirements for Heparan Sulfate Biosynthesis in Morphogenesis and Nervous System Development in C. elegans	journal.pgen.1006525	null	[ [ "Cell migration is key to animal development and physiology .", "To reach their targets , migrating cells rely on guidance factors and morphogens , which can be regulated by heparan sulfate proteoglycans ( HSPGs ) [1] .", "HSPGs are cell-surface or extracellular proteins characterized by the attachmen...	[ "The regulation of cell migration is essential to animal development and physiology .", "Heparan sulfate proteoglycans shape the interactions of morphogens and guidance cues with their respective receptors to elicit appropriate cellular responses .", "Heparan sulfate proteoglycans consist of a protein core with...	[ "During animal development , cells and neurons navigate long distances to reach their final target destinations .", "Migrating cells are guided by extracellular molecular cues , and cellular responses to these cues are regulated by heparan sulfate proteoglycans .", "Heparan sulfate proteoglycans are proteins wi...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genome expression analysis", "functional genomics", "barley", "plant biology", "crop genetics", "dna transcription", "gene function", "genetic maps", "genome analysis tools", "plant science", "linkage maps", "cereals", "crops", "trait locus analysis", "plant pathology", "plant genomic...	Quantitative and Qualitative Stem Rust Resistance Factors in Barley Are Associated with Transcriptional Suppression of Defense Regulons	journal.pgen.1002208	null	[ [ "Plants respond to invading pathogens with several forms of defense , ranging from the generation of toxic chemicals to programmed cell death [1] .", "These defense strategies do not occur coincidentally , but rather by successive rounds of chemical , physical , and enzymatic barriers introduced to impede...	[ "Stem rust ( Puccinia graminis f . sp . tritici; Pgt ) is a devastating fungal disease of wheat and barley .", "Pgt race TTKSK ( isolate Ug99 ) is a serious threat to these Triticeae grain crops because resistance is rare .", "In barley , the complex Rpg-TTKSK locus on chromosome 5H is presently the only known ...	[ "An important step in molecular plant pathology is the identification of the biologically relevant events that are directly involved in mediating resistance to pathogens .", "Historically , it is known that de novo and modulated gene expression are important components of the immune response .", "And yet , how ...	2011
[ "Introduction", "Methods", "Results/Discussion" ]	[ "computational biology/population genetics", "genetics and genomics/complex traits", "computational biology/evolutionary modeling", "genetics and genomics/genetics of disease", "public health and epidemiology/epidemiology", "computational biology/genomics", "mathematics/statistics", "genetics and geno...	An Evolutionary Framework for Association Testing in Resequencing Studies	journal.pgen.1001202	null	[ [ "Several authors have reviewed the potential contribution of low frequency alleles to variation in phenotypes [2]–[7] .", "Absent a change in the properties of new mutations during recent history , which we find implausible , systematic differences between SNPs of varying frequencies must be mediated by n...	[ "Sequencing technologies are becoming cheap enough to apply to large numbers of study participants and promise to provide new insights into human phenotypes by bringing to light rare and previously unknown genetic variants .", "We develop a new framework for the analysis of sequence data that incorporates all of ...	[ "Studies correlating genetic variation to disease and other human traits have examined mostly common mutations , partly because of technological restrictions .", "However , recent advances have resulted in dramatically declining costs of obtaining genomic sequence data , which provides the opportunity to detect r...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "bacteriology", "developmental biology", "microbial mutation", "medical microbiology", "microbial pathogens", "biology and life sciences", "microbial growth and development", "microbiology", "bacterial pathogens" ]	Phase Variation of Poly-N-Acetylglucosamine Expression in Staphylococcus aureus	journal.ppat.1004292	null	[ [ "Phase variation functions as a reversible on/off switch for the expression of a particular gene .", "The result is commonly an alteration in the expression of some cell surface-expressed antigen .", "Slipped-strand mispairing is one mechanism that can lead to the production of a phase variant .", ...	[ "Polysaccharide intercellular adhesin ( PIA ) , also known as poly-N-acetyl-β- ( 1–6 ) -glucosamine ( PIA/PNAG ) is an important component of Staphylococcus aureus biofilms and also contributes to resistance to phagocytosis .", "The proteins IcaA , IcaD , IcaB , and IcaC are encoded within the intercellular adhes...	[ "Staphylococcal polysaccharide intercellular adhesin ( PIA ) , also known as β-1-6-linked N-acetylglucosamine ( PNAG ) plays a role in immune evasion and biofilm formation .", "Evidence suggests that under certain circumstances PIA/PNAG production is beneficial , whereas at times , it may be advantageous for the ...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "rabies", "veterinary diseases", "zoonotic diseases", "neglected tropical diseases", "viral diseases", "veterinary science" ]	High Diversity of Rabies Viruses Associated with Insectivorous Bats in Argentina: Presence of Several Independent Enzootics	journal.pntd.0001635	null	[ [ "Rabies is a fatal infection of the central nervous system primarily transmitted by rabid animal bites .", "Rabies virus ( RABV ) circulates through two different epidemiological cycles: terrestrial and aerial , where dogs , foxs or skunks and bats , respectively , act as most relevant reservoirs and/or v...	[ "Rabies is a fatal infection of the central nervous system primarily transmitted by rabid animal bites .", "Rabies virus ( RABV ) circulates through two different epidemiological cycles: terrestrial and aerial , where dogs , foxes or skunks and bats , respectively , act as the most relevant reservoirs and/or vect...	[ "In Argentina , successful vaccination and control of terrestrial rabies in the 1980s revealed the importance of the aerial route in RABV transmission .", "Current distribution of cases shows a predominance of rabies by hematophagous bats in the Northern regions where rabies is a major public health concern; in c...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular cell biology", "systems biology", "cell biology", "biology and life sciences" ]	Identification of New IκBα Complexes by an Iterative Experimental and Mathematical Modeling Approach	journal.pcbi.1003528	null	[ [ "The nuclear transcription factor κB ( NFκB ) family consists of five DNA-binding proteins ( p65 , p50 , p52 , cRel , RelB ) that differentially modulate gene transcription .", "Since NFκB activation is involved in many cellular processes including inflammation , proliferation , angiogenesis and anti-apop...	[ "The transcription factor nuclear factor kappa-B ( NFκB ) is a key regulator of pro-inflammatory and pro-proliferative processes .", "Accordingly , uncontrolled NFκB activity may contribute to the development of severe diseases when the regulatory system is impaired .", "Since NFκB can be triggered by a huge va...	[ "In unstimulated cells , the transcription factor NFκB resides in the cytosol bound to its inhibitor IκBα .", "Canonical activation of NFκB by numerous stimuli leads to proteasomal depletion of IκBα , thereby liberating NFκB to translocate into the nucleus to induce transcription of genes leading to proliferation...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "cell death", "medicine and health sciences", "immune cells", "nuclear staining", "pathology and laboratory medicine", "pathogens", "immunology", "cell processes", "microbiology", "viruses", "oncology", "immunoprecipitation", "dna viruses", "infectious disease control", ...	KSHV-Mediated Regulation of Par3 and SNAIL Contributes to B-Cell Proliferation	journal.ppat.1005801	null	[ [ "In 1994 , Kaposi's sarcoma-associated herpesvirus ( KSHV ) was first identified [1] .", "Studies have shown that KSHV is predominantly involved in two kinds of cancers , originated through B-cells and endothelial cells [2 , 3] .", "In B-cells , it contributes to primary effusion lymphoma ( PEL ) as w...	[ "Studies have suggested that Epithelial–Mesenchymal Transition ( EMT ) and transformation is an important step in progression to cancer .", "Par3 ( partitioning-defective protein ) is a crucial factor in regulating epithelial cell polarity .", "However , the mechanism by which the latency associated nuclear ant...	[ "Par3 ( partitioning-defective protein ) is characterized as a cell polarity protein with a crucial role in regulating EMT progression in KSHV-infected cells .", "Notably , SNAIL , a major EMT regulator is targeted through expression of Par3 and Latency associated nuclear antigen ( LANA ) during KSHV infection ."...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "biochemistry", "immune system proteins", "infectious diseases", "protein interactions", "proteins", "immunology", "biology", "viral diseases", "cytomegalovirus infection", "immunomodulation" ]	The Human Cytomegalovirus UL11 Protein Interacts with the Receptor Tyrosine Phosphatase CD45, Resulting in Functional Paralysis of T Cells	journal.ppat.1002432	null	[ [ "Infection of immunocompetent individuals with human cytomegalovirus ( CMV ) rarely results in symptomatic disease .", "Following primary infection children and even adults often shed the virus in saliva or urine for weeks or months [1] , suggesting that clearance of CMV by the immune system is a complex ...	[ "Human cytomegalovirus ( CMV ) exerts diverse and complex effects on the immune system , not all of which have been attributed to viral genes .", "Acute CMV infection results in transient restrictions in T cell proliferative ability , which can impair the control of the virus and increase the risk of secondary in...	[ "The human cytomegalovirus ( CMV ) belongs to a class of viruses that interferes with the immune response of its host .", "Accordingly , infection with CMV is a severe risk for immunologically immature newborns and immunocompromised patients such as transplant recipients .", "The mechanisms by which CMV affects...	2011
[ "", "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "reactive oxygen species", "redox signaling", "biological cultures", "condensed matter physics", "animals", "animal models", "developmental biology", "drosophila melanogaster", "model organisms", "electromagnetic fields", "pupae", "experimental organism systems", "cell cul...	Low-intensity electromagnetic fields induce human cryptochrome to modulate intracellular reactive oxygen species	journal.pbio.2006229	null	[ [ "Editor’s Note: This Short Report received positive reviews by experts .", "The Academic Editor has written an accompanying Primer that we are publishing alongside this article ( https://doi . org/10 . 1371/journal . pbio . 3000018 ) .", "The linked Primer presents a complementary expert perspective; ...	[ "Exposure to man-made electromagnetic fields ( EMFs ) , which increasingly pollute our environment , have consequences for human health about which there is continuing ignorance and debate .", "Whereas there is considerable ongoing concern about their harmful effects , magnetic fields are at the same time being a...	[ "Repetitive low-intensity magnetic stimulation has been used in the treatment of disease for over 50 years .", "Associated benefits have included alleviation of depression , memory loss , and symptoms of Parkinson disease , as well as accelerated bone and wound healing and the treatment of certain cancers , indep...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Phospho-dependent Regulation of SAMHD1 Oligomerisation Couples Catalysis and Restriction	journal.ppat.1005194	null	[ [ "HIV-1 replicates poorly in cells of the myeloid lineage and resting T cells through blocks that occur early in infection [1–3] .", "However , in HIV-2 and related simian viruses ( SIVs ) the lentiviral accessory protein Vpx overcomes this restriction by targeting the cellular protein SAMHD1 for proteasom...	[ "SAMHD1 restricts HIV-1 infection of myeloid-lineage and resting CD4+ T-cells .", "Most likely this occurs through deoxynucleoside triphosphate triphosphohydrolase activity that reduces cellular dNTP to a level where reverse transcriptase cannot function , although alternative mechanisms have been proposed recent...	[ "SAMHD1 is a restriction factor that blocks infection of certain immune cells by HIV-1 .", "It was discovered to be an enzyme that catalyses the breakdown of dNTPs , suggesting that it inhibits HIV-1 replication by reducing cellular dNTP pools to such low levels that reverse transcriptase cannot function .", "H...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "geographical locations", "social sciences", "sand flies", "vertebrates", "animals", "parasitic protozoans", "diptera", "mammals", "seasons", "land use", "protozoans", "leishmania", "insect vectors", "human geography", "geography", "...	Distribution and Dispersal of Phlebotomus papatasi (Diptera: Psychodidae) in a Zoonotic Cutaneous Leishmaniasis Focus, the Northern Negev, Israel	journal.pntd.0004819	null	[ [ "Zoonotic cutaneous leishmaniasis ( ZCL ) has long been endemic in Israel [1] .", "Two Leishmania species cause ZCL in Israel: Leishmania major , which is transmitted by Phlebotomus ( Phlebotomus ) papatasi ( Scopoli ) , and Leishmania tropica , which is transmitted by Phlebotomus ( Paraphlebotomus ) serg...	[ "Zoonotic cutaneous leishmaniasis has long been endemic in Israel .", "In recent years reported incidence of cutaneous leishmaniasis increased and endemic transmission is being observed in a growing number of communities in regions previously considered free of the disease .", "Here we report the results of an ...	[ "Cutaneous leishmaniasis is a dermal disease of public health concern in Israel .", "The typical skin lesions are caused by single celled Leishmania parasites that are transmitted by the bite of an infected female sand fly .", "In the last years , the disease has been spreading and emerged in Urim , a small coo...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "plant anatomy", "plant growth and development", "enzymes", "plant embryo anatomy", "enzymology", "plant physiology", "developmental biology", "plant science", "sumoylation", "immunoprecipitation", "seedlings", "plants", "extraction techniques", "ligases", "research and analysis methods"...	An Arabidopsis SUMO E3 Ligase, SIZ1, Negatively Regulates Photomorphogenesis by Promoting COP1 Activity	journal.pgen.1006016	null	[ [ "Sumoylation is a post-translational modification in which SUMO ( small ubiquitin-like modifier ) peptides are covalently attached to a SUMO consensus motif ( ψKxE/D; ψ a large hydrophobic amino acid residue; K , the acceptor lysine; x , any amino acid; E/D , glutamate or aspartate ) in target proteins throug...	[ "COP1 ( CONSTITUTIVE PHOTOMORPHOGENIC 1 ) , a ubiquitin E3 ligase , is a central negative regulator of photomorphogenesis .", "However , how COP1 activity is regulated by post-translational modifications remains largely unknown .", "Here we show that SUMO ( small ubiquitin-like modifier ) modification enhances ...	[ "In darkness , the ubiquitin E3 ligase COP1 accumulates in the nucleus and mediates ubiquitination and degradation of positive regulators of photomorphogenesis , such as HY5 .", "In response to light , COP1 activity is reduced to ensure proper photomorphogenic development .", "However , post-translational modif...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology/membranes and sorting", "cell biology/microbial growth and development", "cell biology/extra-cellular matrix", "infectious diseases/protozoal infections", "evolutionary biology/developmental molecular mechanisms", "infectious diseases/tropical and travel-associated diseases", "evolutionary...	Selective Condensation Drives Partitioning and Sequential Secretion of Cyst Wall Proteins in Differentiating Giardia lamblia	journal.ppat.1000835	null	[ [ "Infectious parasite stages transmitted to a new host via the oral route ( cysts , oocysts , eggs ) require a highly resistant extracellular matrix to protect them in the environment and during passage through the stomach .", "The diplomonad Giardia lamblia ( syn . G . intestinalis , G . duodenalis ) is a...	[ "Controlled secretion of a protective extracellular matrix is required for transmission of the infective stage of a large number of protozoan and metazoan parasites .", "Differentiating trophozoites of the highly minimized protozoan parasite Giardia lamblia secrete the proteinaceous portion of the cyst wall mater...	[ "The protozoan Giardia lamblia is the leading cause for parasite-induced diarrhea with significant morbidity in humans and animals world-wide , and is transmitted by water-resistant cysts .", "Giardia has undergone substantial reductive evolution to a simpler organization than the last common eukaryotic ancestor ...	2010
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "taxonomy", "organismal evolution", "medicine and health sciences", "chemical characterization", "pathology and laboratory medicine", "mitochondrial dna", "pathogens", "microbiology", "social sciences", "hepatitis b virus", "viruses", "phylogenetics", "data management", "archaeology", "p...	The paradox of HBV evolution as revealed from a 16th century mummy	journal.ppat.1006750	null	[ [ "The comparative analysis of viral genomes provides a wide and informative view of evolutionary patterns and processes .", "In particular , viruses often evolve with sufficient rapidity to inform on evolutionary processes over the timespan of direct human observation ( weeks and days ) [1–3] .", "Impo...	[ "Hepatitis B virus ( HBV ) is a ubiquitous viral pathogen associated with large-scale morbidity and mortality in humans .", "However , there is considerable uncertainty over the time-scale of its origin and evolution .", "Initial shotgun data from a mid-16th century Italian child mummy , that was previously pal...	[ "Hepatitis B virus ( HBV ) exerts formidable morbidity and mortality in humans .", "We used ancient DNA techniques to recover the complete genome sequence of an HBV from the mummified remains of a child discovered in the 16th century from Naples , Italy .", "Strikingly , our analysis of this specimen resulted i...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology" ]	The FGFR4-G388R Polymorphism Promotes Mitochondrial STAT3 Serine Phosphorylation to Facilitate Pituitary Growth Hormone Cell Tumorigenesis	journal.pgen.1002400	null	[ [ "Pituitary tumors occur in almost 20% of the population [1] and represent nearly 10% of surgically resected intracranial tumors [2]–[3] .", "They can cause significant health problems due to abnormal hormone production and invasion into surrounding brain structures [2]–[3] .", "However , the mechanism...	[ "Pituitary tumors are common intracranial neoplasms , yet few germline abnormalities have been implicated in their pathogenesis .", "Here we show that a single nucleotide germline polymorphism ( SNP ) substituting an arginine ( R ) for glycine ( G ) in the FGFR4 transmembrane domain can alter pituitary cell growt...	[ "Several human cancers have been associated with increased growth hormone levels .", "Here we show that a frequent single nucleotide polymorphism ( SNP ) associated with increased cancer risk and progression also deregulates pituitary function .", "Through recruitment of a distinct STAT3 signaling cascade , thi...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "biochemistry", "infectious diseases", "in vitro", "immunology", "microbiology", "mus (mouse)", "eubacteria" ]	A Mycobacterium ESX-1–Secreted Virulence Factor with Unique Requirements for Export	journal.ppat.0030105	null	[ [ "The cell surface–associated and secreted proteins of pathogenic bacteria promote the uptake of nutrients; facilitate attachment to specific surfaces , cells , or proteins; function in cell wall maintenance and cell division; and offer protection from harsh environmental conditions , including the host immune...	[ "Specialized secretion systems of pathogenic bacteria commonly transport multiple effectors that act in concert to control and exploit the host cell as a replication-permissive niche .", "Both the Mycobacterium marinum and the Mycobacterium tuberculosis genomes contain an extended region of difference 1 ( extRD1 ...	[ "A major mechanism used by pathogenic bacteria for disabling host defenses is secretion of virulence proteins .", "These effectors are often transported by specialized secretion machines .", "One such pathway , present in Mycobacterium and other Gram-positive genera , is ESX-1 ( early secretory antigenic target...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Modeling the Impact of White-Plague Coral Disease in Climate Change Scenarios	journal.pcbi.1004151	null	[ [ "The study site was located at the shallow water reef ( depth of ca . 1 . 5 m ) off the shore of the Interuniversity Institute ( IUI ) in Eilat .", "The reef is relatively uniform with respect to bathymetry and is situated on a gentle slope ( ca . 3° ) on flat beach-rock .", "The reef did not appear t...	[ "Coral reefs are in global decline , with coral diseases increasing both in prevalence and in space , a situation that is expected only to worsen as future thermal stressors increase .", "Through intense surveillance , we have collected a unique and highly resolved dataset from the coral reef of Eilat ( Israel , ...	[ "Coral reefs are deteriorating at alarming rates , with coral disease outbreaks increasing in prevalence and in space .", "Anomalously high ocean temperatures are thought to significantly contribute to this problem .", "We collected a unique and highly resolved dataset of a White Plague Disease ( WPD ) outbreak...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Smc5/6 Coordinates Formation and Resolution of Joint Molecules with Chromosome Morphology to Ensure Meiotic Divisions	journal.pgen.1004071	null	[ [ "Sexually reproducing organisms reduce their genomic content by half in the gametes such that the normal chromosome copy number is restored in the zygote .", "To achieve this , homologous chromosomes ( homologs ) have to pair and then segregate to opposite spindle poles at the first division of meiosis ."...	[ "During meiosis , Structural Maintenance of Chromosome ( SMC ) complexes underpin two fundamental features of meiosis: homologous recombination and chromosome segregation .", "While meiotic functions of the cohesin and condensin complexes have been delineated , the role of the third SMC complex , Smc5/6 , remains...	[ "Meiosis is a specialized cell division that exactly halves the number of chromosomes transmitted from each parent to their offspring via gamete cells ( such as sperm and eggs ) .", "This requires that matching ( ‘homologous’ ) chromosomes associate and then separate into different cells such that each gamete con...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics and genomics/microbial evolution and genomics" ]	Gene Annotation and Drug Target Discovery in Candida albicans with a Tagged Transposon Mutant Collection	journal.ppat.1001140	null	[ [ "Fungal species of the genus Candida generally live communally on and in the human body , yet Candida infections can become systemic and lethal in up to 60% of immunocompromised patients [1] , [2] .", "C . albicans alone accounts for over 50% of all fungal infections [3] .", "Furthermore , drug resist...	[ "Candida albicans is the most common human fungal pathogen , causing infections that can be lethal in immunocompromised patients .", "Although Saccharomyces cerevisiae has been used as a model for C . albicans , it lacks C . albicans' diverse morphogenic forms and is primarily non-pathogenic .", "Comprehensive ...	[ "Candida albicans is a normal inhabitant in our bodies , yet it can become pathogenic and cause infections that range from the superficial in healthy individuals to deadly in the immunocompromised .", "Comprehensive genetic analysis of C . albicans to identify mechanisms of virulence and new treatment strategies ...	2010
[ "Introduction", "Materials and Methods", "Results/Discussion" ]	[ "genetics and genomics/genomics", "genetics and genomics/gene discovery", "genetics and genomics/comparative genomics", "genetics and genomics/gene expression", "computational biology/comparative sequence analysis", "infectious diseases/helminth infections", "genetics and genomics/gene function", "com...	Intestinal Transcriptomes of Nematodes: Comparison of the Parasites Ascaris suum and Haemonchus contortus with the Free-living Caenorhabditis elegans	journal.pntd.0000269	null	[ [ "The intestine is one of the major organs in nematodes , creating a key surface at the intestinal apical membrane that interacts with the environment .", "While specific cellular characteristics of the intestine can be diverse among nematode species , they typically conform to polarized epithelial cells w...	[ "The nematode intestine is a major organ responsible for nutrient digestion and absorption; it is also involved in many other processes , such as reproduction , innate immunity , stress responses , and aging .", "The importance of the intestine as a target for the control of parasitic nematodes has been demonstra...	[ "Biological properties of the nematode intestine warrant in-depth investigation , the results of which can be utilized in the control of parasitic nematodes that infect humans , livestock , and plants .", "Both the importance of intestinal antigens from Haemonchus contortus in immunity and the damage to H . conto...	2008
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "sequencing techniques", "astronomical sciences", "genome sequencing", "genomic databases", "supernovae", "chromosome mapping", "genome analysis", "molecular biology techniques", "research and analysis methods", "genome complexity", "gene mapping", "chromosome biology", "chromosomal aberrati...	Comprehensive structural variation genome map of individuals carrying complex chromosomal rearrangements	journal.pgen.1007858	null	[ [ "Complex chromosomal rearrangements ( CCRs ) are rearrangements involving more than two chromosomes or more than two breakpoints [1 , 2] .", "Balanced , de novo , CCRs are extremely rare and more than half are associated with an affected phenotype [3] .", "Traditionally in a diagnostic laboratory , ka...	[ "Complex chromosomal rearrangements ( CCRs ) are rearrangements involving more than two chromosomes or more than two breakpoints .", "Whole genome sequencing ( WGS ) allows for outstanding high resolution characterization on the nucleotide level in unique sequences of such rearrangements , but problems remain for...	[ "Unexpected complexities are common findings in the breakpoints of karyotypically balanced complex chromosomal rearrangements ( CCRs ) .", "Such findings are of clinical importance , as they may be the cause of mendelian phenotypes in the rearrangement carrier .", "Whole genome sequencing ( WGS ) allows for hig...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "physiological processes", "genome expression analysis", "genomics", "physiology", "chronobiology", "biology", "anatomy and physiology", "genetics and genomics" ]	Systematic Identification of Rhythmic Genes Reveals camk1gb as a New Element in the Circadian Clockwork	journal.pgen.1003116	null	[ [ "All organisms demonstrate a wide variety of physiological , biochemical and behavioral daily rhythms that are driven by intrinsic oscillators , known as circadian clocks .", "These oscillators work in harmony with the 24 hours periodic changes in environmental conditions .", "The maintenance and sync...	[ "A wide variety of biochemical , physiological , and molecular processes are known to have daily rhythms driven by an endogenous circadian clock .", "While extensive research has greatly improved our understanding of the molecular mechanisms that constitute the circadian clock , the links between this clock and d...	[ "The circadian clock is a molecular pacemaker that drives rhythmic expression of genes with a ∼24-hour period .", "As a result , many physiological processes have daily rhythms .", "Many of the conserved elements that constitute the circadian clock are known , but the links between the clock and dependent proce...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Multilevel Analysis of Trachomatous Trichiasis and Corneal Opacity in Nigeria: The Role of Environmental and Climatic Risk Factors on the Distribution of Disease	journal.pntd.0003826	null	[ [ "Trachoma is the leading infectious cause of blindness worldwide , most recently estimated to be responsible for the loss of 333 , 000 disability-adjusted life years ( DALYs ) in 2010 [1] .", "Recurrent episodes of infection with the bacterium Chlamydia trachomatis and associated inflammation cause cumula...	[ "The distribution of trachoma in Nigeria is spatially heterogeneous , with large-scale trends observed across the country and more local variation within areas .", "Relative contributions of individual and cluster-level risk factors to the geographic distribution of disease remain largely unknown .", "The prima...	[ "Trichiasis ( TT ) and corneal opacity ( CO ) are chronic stages of trachoma , which remains an important cause of blindness .", "This study used multilevel spatial models to investigate risk factors for TT/CO in Nigeria , including data for more than 13 , 500 adults aged 40 years and above collected in the 2007 ...	2015
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "african trypanosomiasis", "population dynamics", "tropical diseases", "parasitic diseases", "parasitology", "neglected tropical diseases", "population biology", "infectious disease control", "veterinary science", "public and occupational health", "infectious di...	Monitoring the elimination of human African trypanosomiasis: Update to 2014	journal.pntd.0005585	null	[ [ "In the last decade of the 20th century , the number of cases of human African trypanosomiasis ( HAT ) , also known as sleeping sickness , reached alarming levels [1 , 2 , 3 , 4] .", "In reaction to this epidemiological situation of a lethal disease , a number of stakeholders came together to support the ...	[ "The World Health Organization ( WHO ) has targeted the elimination of Human African trypanosomiasis ( HAT ) ‘as a public health problem’ by 2020 .", "The selected indicators of elimination should be monitored every two years , and we provide here a comprehensive update to 2014 .", "The monitoring system is und...	[ "Human African trypanosomiasis ( HAT ) , also known as sleeping sickness , is a neglected tropical disease transmitted by tsetse flies , which has been responsible for devastating epidemics in the 20th century .", "Since the last alarming spike in disease incidence during the late 1990s , disease surveillance and...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "sequencing techniques", "organismal evolution", "microbiology", "vertebrates", "genomic library screening", "animals", "mammals", "microbial evolution", "molecular biology techniques", "rna sequencing", "fruit bats", "research and analysis methods", "birds", "genetic interference", "pro...	Fundamental properties of the mammalian innate immune system revealed by multispecies comparison of type I interferon responses	journal.pbio.2004086	null	[ [ "Most emerging human viruses have an animal origin [1] .", "The increase in the global human population , international travel , and ecological changes , in addition to changes in agricultural practices , has led to complicated interactions between wildlife , domestic species , and humans that has enhance...	[ "The host innate immune response mediated by type I interferon ( IFN ) and the resulting up-regulation of hundreds of interferon-stimulated genes ( ISGs ) provide an immediate barrier to virus infection .", "Studies of the type I ‘interferome’ have mainly been carried out at a single species level , often lacking...	[ "The type I interferon ( IFN ) response is triggered upon sensing of an incoming pathogen in an infected cell and results in the expression of hundreds of IFN-stimulated genes ( ISGs , collectively referred to as ‘the interferome’ ) .", "Studies on the interferome have been carried out mainly in human cells and t...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "physiology/integrative physiology", "molecular biology", "neuroscience/neuronal and glial cell biology", "physiology/neural homeostasis" ]	Regulation of Na+/K+ ATPase Transport Velocity by RNA Editing	journal.pbio.1000540	Editing of Na+/K+ ATPase mRNAs modulates the Na+/K+ pump's turnover rate by selectively targeting the release of the final sodium to the outside.	[ [ "Within the animal kingdom , the Na+/K+ ATPase is a nearly ubiquitous membrane protein that uses the free energy of ATP hydrolysis to establish and maintain the Na+ and K+ gradients across cell membranes .", "Na+/K+ pump activity is essential .", "Without it cells would lack the driving force required...	[ "Because firing properties and metabolic rates vary widely , neurons require different transport rates from their Na+/K+ pumps in order to maintain ion homeostasis .", "In this study we show that Na+/K+ pump activity is tightly regulated by a novel process , RNA editing .", "Three codons within the squid Na+/K+...	[ "In order for excitable cells like neurons and muscles to generate electrical signals , they require ion gradients across their plasma membranes .", "For example , sodium concentrations are much lower inside a cell than outside , and for potassium it is the opposite case .", "The job of maintaining these ion gr...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "genetics and genomics", "arabidopsis (thale cress)" ]	Arabidopsis TFL2/LHP1 Specifically Associates with Genes Marked by Trimethylation of Histone H3 Lysine 27	journal.pgen.0030086	null	[ [ "Spatial and temporal patterns of gene transcription are central to the developmental programs of plants and animals .", "Transcriptional repression plays a major role in creating and stabilizing these patterns .", "In plants , roles for transcriptional repression in reproductive development have been...	[ "TERMINAL FLOWER 2/LIKE HETEROCHROMATIN PROTEIN 1 ( TFL2/LHP1 ) is the only Arabidopsis protein with overall sequence similarity to the HETEROCHROMATIN PROTEIN 1 ( HP1 ) family of metazoans and S . pombe .", "TFL2/LHP1 represses transcription of numerous genes , including the flowering-time genes FLOWERING LOCUS ...	[ "Stable repression of gene expression is an important aspect of the developmental programs of higher organisms .", "In plants and animals , DNA is organized within chromatin , which contains at its core a set of evolutionarily conserved proteins called histones .", "These proteins can be modified for example by...	2007
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "phosphorylation", "nucleic acid synthesis", "molecular probe techniques", "rna extraction", "northern blot", "fungi", "molecular biology techniques", "rna synthesis", "cellular structures and organelles", "gel electrophoresis", "extraction techniques", "chemical synthesis", "research and an...	Tor1 and CK2 kinases control a switch between alternative ribosome biogenesis pathways in a growth-dependent manner	journal.pbio.2000245	null	[ [ "All cells must adapt to a constantly changing environment in order to maintain their intracellular equilibrium and to balance growth with survival .", "Several signaling pathways monitor concentrations of available nutrients or presence of harmful conditions and switch on or off specific transcriptional ...	[ "Ribosome biogenesis is a major energy-consuming process in the cell that has to be rapidly down-regulated in response to stress or nutrient depletion .", "The target of rapamycin 1 ( Tor1 ) pathway regulates synthesis of ribosomal RNA ( rRNA ) at the level of transcription initiation .", "It remains unclear wh...	[ "The yeast Saccharomyces cerevisiae must , as a single-celled microorganism , rapidly respond to changes in its environment and carefully balance its energy needs with the available resources .", "One of the major energy-consuming processes in the cell is the production of ribosomes .", "Ribosome biogenesis is ...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "united states", "evolutionary biology", "population genetics", "geographical locations", "genetic mapping", "ethnicities", "simulation and modeling", "north america", "effective population size", "african american people", "population biology", "africa", "research and analysis methods", "...	Ancestry-specific recent effective population size in the Americas	journal.pgen.1007385	null	[ [ "Effective population size is a key factor in evolutionary genetic processes , such as drift and selection , which have important implications for medical genetics [1 , 2] .", "With the development of agriculture , human populations have grown super-exponentially during the past few thousand years [3 , 4]...	[ "Populations change in size over time due to factors such as population growth , migration , bottleneck events , natural disasters , and disease .", "The historical effective size of a population affects the power and resolution of genetic association studies .", "For admixed populations , it is not only the ov...	[ "Using genome-wide genetic data on several hundred individuals sampled from a population , we can estimate the current effective size of the population and the changes in effective size that have occurred over the past hundred generations .", "Many populations in the Americas are admixed , having ancestry from Eu...	2018
[ "Introduction", "Results", "Discussion", "Material and Methods" ]	[ "plant biology", "microbiology", "host-pathogen interaction", "dna transcription", "gene function", "plant science", "fungal reproduction", "mycology", "gene expression", "biology", "pathogenesis", "genetics", "spores", "genetics of disease", "genetics and genomics" ]	The Wor1-like Protein Fgp1 Regulates Pathogenicity, Toxin Synthesis and Reproduction in the Phytopathogenic Fungus Fusarium graminearum	journal.ppat.1002724	null	[ [ "Pathogenic fungi have evolved sophisticated ways to infect their hosts , mainly by adapting to the host environment and by producing pathogenicity-related products such as toxic secondary metabolites , effector proteins and/or extracellular enzymes .", "The expression of genes involved in the adaptation ...	[ "WOR1 is a gene for a conserved fungal regulatory protein controlling the dimorphic switch and pathogenicity determents in Candida albicans and its ortholog in the plant pathogen Fusarium oxysporum , called SGE1 , is required for pathogenicity and expression of key plant effector proteins .", "F . graminearum , a...	[ "Plant pathogenic fungi can have devastating effects on crop yield and quality .", "In addition , these fungi may generate mycotoxins that pose health risks when the contaminated crops are consumed .", "The pathogen Fusarium graminearum infects wheat heads and grows through the rachis by synthesizing trichothec...	2012
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[]	Segmentation and Tracking of Adherens Junctions in 3D for the Analysis of Epithelial Tissue Morphogenesis	journal.pcbi.1004124	null	[ [ "Epithelial cells form cohesive sheets of cells that play diverse structural and functional roles in multicellular organisms such as the covering of internal and external surfaces , compartmentalization of the body into discrete organs , and the regulation of surface and trans-epithelial transport .", "Th...	[ "Epithelial morphogenesis generates the shape of tissues , organs and embryos and is fundamental for their proper function .", "It is a dynamic process that occurs at multiple spatial scales from macromolecular dynamics , to cell deformations , mitosis and apoptosis , to coordinated cell rearrangements that lead ...	[ "Epithelia are the most common tissue type in multicellular organisms .", "Understanding processes that make them acquire their final shape has implications to pathologies such as cancer progression and birth defects such as spina bifida .", "During development , epithelial tissues are remodeled by mechanical f...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "carbohydrate metabolism", "metabolic pathways", "biology", "computational biology", "metabolic networks", "metabolism" ]	In Silico Evidence for Gluconeogenesis from Fatty Acids in Humans	journal.pcbi.1002116	null	[ [ "It is well known that excess sugar in the human diet can be converted both into glycerol and fatty acids and , thus , into lipids such as triglycerides .", "A related question biochemistry students are often asked in their exams is whether the reverse route is also feasible , that is , whether the human ...	[ "The question whether fatty acids can be converted into glucose in humans has a long standing tradition in biochemistry , and the expected answer is “No” .", "Using recent advances in Systems Biology in the form of large-scale metabolic reconstructions , we reassessed this question by performing a global investig...	[ "That sugar can be converted into fatty acids in humans is a well-known fact .", "The question whether the reverse direction , i . e . , gluconeogenesis from fatty acids , is also feasible has been a topic of intense debate since the end of the 19th century .", "With the discovery of the glyoxylate shunt that a...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Evidence for Ubiquitin-Regulated Nuclear and Subnuclear Trafficking among Paramyxovirinae Matrix Proteins	journal.ppat.1004739	null	[ [ "Paramyxoviruses include pathogens of global medical and agricultural concern .", "These viruses occupy broad ecological niches infecting a wide range of hosts including mammals , reptiles , birds and fish , and they cause diverse outcomes ranging from asymptomatic infection to lethal disease .", "Mea...	[ "The paramyxovirus matrix ( M ) protein is a molecular scaffold required for viral morphogenesis and budding at the plasma membrane .", "Transient nuclear residence of some M proteins hints at non-structural roles .", "However , little is known regarding the mechanisms that regulate the nuclear sojourn .", "P...	[ "Elucidating virus-cell interactions is fundamental to understanding viral replication and identifying targets for therapeutic control of viral infection .", "Paramyxoviruses include human and animal pathogens of medical and agricultural significance .", "Their matrix ( M ) structural protein organizes virion a...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "bacteriology", "cell death", "cellular structures", "subcellular organelles", "microbiology", "host-pathogen interaction", "bacterial biochemistry", "microbial growth and development", "proteins", "medical microbiology", "microbial pathogens", "biology", "biochemistry", "cell biology", ...	Targeting of a Chlamydial Protease Impedes Intracellular Bacterial Growth	journal.ppat.1002283	null	[ [ "Chlamydiae are a group of obligate intracellular bacteria that infect humans and animals .", "Chlamydia trachomatis is the most common bacterial agent of sexually transmitted disease with a prevalence of up to about 5% in young women as well as a common cause of eye infections .", "Clinically , the m...	[ "Chlamydiae are obligate intracellular bacteria that propagate in a cytosolic vacuole .", "Recent work has shown that growth of Chlamydia induces the fragmentation of the Golgi apparatus ( GA ) into ministacks , which facilitates the acquisition of host lipids into the growing inclusion .", "GA fragmentation re...	[ "Chlamydiae are bacteria that replicate only inside host ( for instance human ) cells and that are frequent agents of human disease , in particular sexually transmitted disease .", "Chlamydia lives in a vacuole inside the cell , surrounded by a lipid membrane , and must acquire nutrients and other factors from th...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "taxonomy", "sociology", "vertebrates", "social sciences", "animals", "animal phylogenetics", "social systems", "multivariate analysis", "seasons", "phylogenetics", "data management", "animal behavior", "mathematics", "statistics (mathematics)", "phylogenetic analysis", "zoology", "r...	Family living sets the stage for cooperative breeding and ecological resilience in birds	journal.pbio.2000483	null	[ [ "Cooperative breeding is an extreme form of cooperation that occurs when individuals help raise conspecific offspring that are not their own [1] , often while temporarily foregoing their own reproduction [2 , 3] .", "This common form of cooperation has intrigued evolutionary biologists since Darwin [4] an...	[ "Cooperative breeding is an extreme form of cooperation that evolved in a range of lineages , including arthropods , fish , birds , and mammals .", "Although cooperative breeding in birds is widespread and well-studied , the conditions that favored its evolution are still unclear .", "Based on phylogenetic comp...	[ "Cooperative breeding is a common form of cooperation in which individuals help raise conspecific offspring that are not their own .", "It has evolved in a range of lineages , including arthropods , fish , birds , and mammals .", "In birds , cooperative breeding is widespread and well-studied; however , the con...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Mediated Plastid RNA Editing in Plant Immunity	journal.ppat.1003713	null	[ [ "Plastid function relies on nuclear gene expression , and the import of nuclear gene products into plastids [1] .", "In fact , the plastid genome of current land plants encodes 75–80 proteins [2] , whereas nuclear-encoded chloroplast proteins are estimated between 3500 and 4000 [3] .", "Current data a...	[ "Plant regulatory circuits coordinating nuclear and plastid gene expression have evolved in response to external stimuli .", "RNA editing is one of such control mechanisms .", "We determined the Arabidopsis nuclear-encoded homeodomain-containing protein OCP3 is incorporated into the chloroplast , and contribute...	[ "Plastids originated from cyanobacteria that were incorporated into the eukaryotic cell through an endosymbiotic relationship .", "During the gradual evolution from endosymbiont to organelle , most genes of the cyanobacterial genome were transferred to the nuclear genome .", "Therefore , plastid biogenesis and ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/disease models", "physiology/cell signaling", "physiology/muscle and connective tissue", "cell biology/cell signaling" ]	An Alpha-Catulin Homologue Controls Neuromuscular Function through Localization of the Dystrophin Complex and BK Channels in Caenorhabditis elegans	journal.pgen.1001077	null	[ [ "Precise control of membrane excitability , largely determined by ion channels , is of utmost importance for neuronal and muscle function .", "The regulation of ion channel localization , density and gating properties thus provides an effective way to control the excitability within these cells [1] .", ...	[ "The large conductance , voltage- and calcium-dependent potassium ( BK ) channel serves as a major negative feedback regulator of calcium-mediated physiological processes and has been implicated in muscle dysfunction and neurological disorders .", "In addition to membrane depolarization , activation of the BK cha...	[ "Calcium ions are essential for many physiological processes , including neurosecretion and neuronal and muscle excitation .", "Paradoxically , abnormal accumulation of calcium ions is associated with cell death and has been documented as an early event in muscle and neural degenerative diseases .", "One mechan...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "phosphorylation", "chemical compounds", "hela cells", "endoplasmic reticulum", "cell processes", "biological cultures", "organic compounds", "simulation and modeling", "immunoprecipitation", "chaperone proteins", "cell cultures", "amino acids", "cellular structures and organelles", "resea...	Model-Driven Understanding of Palmitoylation Dynamics: Regulated Acylation of the Endoplasmic Reticulum Chaperone Calnexin	journal.pcbi.1004774	null	[ [ "Reversible post-translational modifications of proteins allow cells to regulate processes in time and in space [1–5] .", "Amongst these , S-palmitoylation is unique in that in confers hydrophobicity to proteins by covalent attachment of a fatty acid chain to cysteine residues [6 , 7] [8] .", "In the ...	[ "Cellular functions are largely regulated by reversible post-translational modifications of proteins which act as switches .", "Amongst these , S-palmitoylation is unique in that it confers hydrophobicity .", "Due to technical difficulties , the understanding of this modification has lagged behind .", "To inv...	[ "The endoplasmic reticulum ( ER ) is the largest intracellular organelle of mammalian cells .", "It is responsible for many fundamental cellular functions , such as folding , quality control of membrane and secreted protein , lipid biosynthesis , control of apoptosis and calcium storage .", "Recent studies have...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "genome scans", "neutral theory", "population genetics", "mutation", "mathematics", "statistics (mathematics)", "effective population size", "genome analysis", "biostatistics", "ecological metrics", "genomics", "genetic polymorphism", "evolutionary modeling", "genetic drift", "haplotypes...	Genome-Wide Inference of Ancestral Recombination Graphs	journal.pgen.1004342	null	[ [ "At each genomic position , orthologous DNA sequences drawn from one or more populations are related by a branching structure known as a genealogy [1] , [2] .", "Historical recombination events lead to changes in these genealogies from one genomic position to the next , resulting in a correlation structur...	[ "The complex correlation structure of a collection of orthologous DNA sequences is uniquely captured by the “ancestral recombination graph” ( ARG ) , a complete record of coalescence and recombination events in the history of the sample .", "However , existing methods for ARG inference are computationally intensi...	[ "The unusual and complex correlation structure of population samples of genetic sequences presents a fundamental statistical challenge that pervades nearly all areas of population genetics .", "Historical recombination events produce an intricate network of intertwined genealogies , which impedes demography infer...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases", "in vitro", "microbiology", "chemical biology", "animals", "mus (mouse)" ]	Inhibitors of Pathogen Intercellular Signals as Selective Anti-Infective Compounds	journal.ppat.0030126	null	[ [ "Current treatment of human bacterial infections depends on bactericidal and bacteriostatic antibiotics whose long-term effectiveness is limited by the development of drug resistance and can devastate the host commensal microbial community .", "An alternative approach to combat bacterial pathogens is the ...	[ "Long-term antibiotic use generates pan-resistant super pathogens .", "Anti-infective compounds that selectively disrupt virulence pathways without affecting cell viability may be used to efficiently combat infections caused by these pathogens .", "A candidate target pathway is quorum sensing ( QS ) , which man...	[ "Current treatments of human bacterial infections depend on antibiotics , whose long-term effectiveness is limited as they select for multidrug-resistant pathogens .", "An alternative approach that is likely to limit the development of bacterial super pathogens is to selectively disrupt bacterial virulence mechan...	2007
[ "Introduction", "Material and Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "tropical diseases", "vertebrates", "sand flies", "parasitic diseases", "animals", "mammals", "dogs", "parasitic protozoans", "diptera", "protozoans", "leishmania", "neglected tropical diseases", "insect vectors", "cellular structures an...	Transmission of Leishmania infantum in the Canine Leishmaniasis Focus of Mont-Rolland, Senegal: Ecological, Parasitological and Molecular Evidence for a Possible Role of Sergentomyia Sand Flies	journal.pntd.0004940	null	[ [ "Leishmaniases are vector-borne diseases with complex ecology and epidemiology .", "In humans , they are caused by more than 20 species of Leishmania parasites that live in a wide range of ecosystems and may have different clinical manifestations ( mainly cutaneous , mucocutaneous or visceral ) [1] .", ...	[ "Leishmania ( L . ) infantum is the causative agent in an endemic focus of canine leishmaniasis in the Mont-Rolland district ( Thiès , Senegal ) .", "In this area , the transmission cycle is well established and more than 30% of dogs and 20% of humans are seropositive for L . infantum .", "However , the sand fl...	[ "Leishmaniases , neglected tropical vector-borne diseases , remain today a problem of public health .", "Classically , the sand flies involved in Leishmania transmission belong either to the Phlebotomus genus ( Old World ) or to the Lutzomyia genus ( New World ) .", "In the rural community of Mont-Rolland ( Sen...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular biology/transcription elongation", "virology/persistence and latency", "molecular biology/chromatin structure", "genetics and genomics/gene expression" ]	Yeast Genetic Analysis Reveals the Involvement of Chromatin Reassembly Factors in Repressing HIV-1 Basal Transcription	journal.pgen.1000339	null	[ [ "Following integration into the host cell genome , HIV-1 transcription is the most important step regulating viral replication .", "The main factor involved in this regulation is the viral Tat protein , which binds TAR , a structured RNA element present at the 5′ end of the viral mRNAs .", "The struct...	[ "Rebound of HIV viremia after interruption of anti-retroviral therapy is due to the small population of CD4+ T cells that remain latently infected .", "HIV-1 transcription is the main process controlling post-integration latency .", "Regulation of HIV-1 transcription takes place at both initiation and elongatio...	[ "Acquired immunodeficiency syndrome ( AIDS ) is caused by the human immunodeficiency virus ( HIV ) .", "Drugs used for anti-viral therapy are very efficient in controlling the presence of viral particles in infected patients .", "However , if this therapy is interrupted , rebound of viremia occurs due to the sm...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "geographical locations", "tropical diseases", "parasitic diseases", "animals", "filariasis", "pharmaceutics", "global health", "neglected tropical diseases", "onchocerciasis", "infectious disease control", "insect vectors", "lymphatic filar...	First evidence of lymphatic filariasis transmission interruption in Cameroon: Progress towards elimination	journal.pntd.0005633	null	[ [ "Lymphatic filariasis ( LF ) is among the most widespread neglected tropical diseases .", "In the mid-1990s , it was reported that about 1 . 4 billion people were exposed to the disease worldwide , of whom 120 million were infected and more than 40 million disfigured by the disease [1] .", "One of the...	[ "Lymphatic filariasis ( LF ) is among the 10 neglected tropical diseases targeted for control or elimination by 2020 .", "For LF elimination , the World Health Organization ( WHO ) has proposed a comprehensive strategy including", "( i ) interruption of LF transmission through large-scale annual treatment ( or ...	[ "Lymphatic filariasis ( LF ) affects more than 120 million people worldwide , and is considered the second leading cause of permanent and long-term disability .", "In response to the important burden of this disease , the World Health Organization ( WHO ) elaborated a strategic plan to eliminate LF as a public he...	2017
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "kala-azar", "paraguay", "medicine and health sciences", "population genetics", "geographical locations", "tropical diseases", "vertebrates", "argentina", "parasitic diseases", "parasitic protozoans", "animals", "mammals", "dogs", "protozoans", "leishmania", "neglected tropical disease...	Dispersion of Leishmania (Leishmania) infantum in central-southern Brazil: Evidence from an integrative approach	journal.pntd.0007639	null	[ [ "Human Visceral Leishmaniasis ( hVL ) is a widely distributed neglected disease caused by the protozoans Leishmania ( Leishmania ) infantum in Asia , Africa , Europe and Americas , and L . ( L . ) donovani in Asia and Africa [1] .", "These parasites use the domestic dog as a reservoir , in which it causes...	[ "Leishmania ( Leishmania ) infantum is the zoonotic agent of visceral leishmaniasis ( VL ) , a disease with a global distribution .", "The transmission scenario of VL has been undergoing changes worldwide , with the biologic cycle invading urbanized areas and dispersing the parasites into other previously free ar...	[ "The dispersion of visceral leishmaniasis is an enigma .", "The State of Paraná , in southern Brazil , borders the states of São Paulo and Mato Grosso , which have experienced LV epidemics over the past 20 years .", "Therefore , we expected that the disease would enter this state through the contiguity of epide...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/gene expression", "cell biology/nuclear structure and function", "genetics and genomics/nuclear structure and function", "molecular biology/chromosome structure", "genetics and genomics/chromosome biology", "infectious diseases/protozoal infections", "genetics and genomics/epigene...	A Major Role for the Plasmodium falciparum ApiAP2 Protein PfSIP2 in Chromosome End Biology	journal.ppat.1000784	null	[ [ "Throughout the eukaryotic kingdom , the overall structure of chromosome ends is conserved and characterized by the telomeric tract , composed of short G-rich repeats , and an extensive subtelomeric region consisting of various types and lengths of repeats , also known as telomere-associated sequences ( TAS )...	[ "The heterochromatic environment and physical clustering of chromosome ends at the nuclear periphery provide a functional and structural framework for antigenic variation and evolution of subtelomeric virulence gene families in the malaria parasite Plasmodium falciparum .", "While recent studies assigned importan...	[ "Plasmodium falciparum , like many other unicellular pathogens , uses antigenic variation of surface proteins as a prime mechanism for immune evasion .", "Subtelomeric gene families , including the major virulence family var , encode these antigens , and recent studies highlighted the important contribution of th...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunodeficiency viruses", "medicine", "virology", "epidemiology", "biology", "microbiology" ]	HIV-1 Superinfection Occurs Less Frequently Than Initial Infection in a Cohort of High-Risk Kenyan Women	journal.ppat.1003593	null	[ [ "Development of a safe and effective prophylactic HIV vaccine remains enormously challenging , due to the virus's high diversity and our limited understanding of immune correlates of protection .", "While most effective vaccines are designed to mimic natural infection and protective immune responses to it...	[ "HIV superinfection ( reinfection ) has been reported in several settings , but no study has been designed and powered to rigorously compare its incidence to that of initial infection .", "Determining whether HIV infection reduces the risk of superinfection is critical to understanding whether an immune response ...	[ "HIV-infected individuals with continued exposure are at risk of acquiring a second infection , a process known as superinfection .", "Superinfection has been reported in various at-risk populations , but how frequently it occurs remains unclear .", "Determining the frequency of superinfection compared with ini...	2013
[ "Introduction", "Results", "Model", "Discussion" ]	[ "cell biology", "biophysics/macromolecular assemblies and machines", "computational biology/systems biology", "physics/condensed matter" ]	Charge as a Selection Criterion for Translocation through the Nuclear Pore Complex	journal.pcbi.1000747	null	[ [ "The defining feature of eukaryotic cells is the separation of nuclear and cytoplasmic compartments by the nuclear envelope .", "All nuclear proteins , for example polymerases and transcription factors , are made in the cytoplasm and imported into the nucleus .", "Conversely , RNAs that function in tr...	[ "Nuclear pore complexes ( NPCs ) are highly selective filters that control the exchange of material between nucleus and cytoplasm .", "The principles that govern selective filtering by NPCs are not fully understood .", "Previous studies find that cellular proteins capable of fast translocation through NPCs ( tr...	[ "All proteins that move between the cytoplasm and the nucleus must pass through nuclear pore complexes , large aqueous channels around 40nm in diameter .", "In some cases the nuclear envelope is perforated with several thousand nuclear pore complexes , while in other cases they are few and far between .", "Macr...	2010
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "biogeography", "dengue virus", "taxonomy", "ecology and environmental sciences", "medicine and health sciences", "pathology and laboratory medicine", "pathogens", "population genetics", "geographical locations", "microbiology", "indonesia", "viruses", "phylogenetics", "data management", ...	Molecular characterization and phylogenetic analysis of dengue viruses imported into Taiwan during 2011-2016	journal.pntd.0006773	null	[ [ "Dengue is the most prevalent mosquito-borne viral infection of humans in tropical and subtropical regions of the world [1] .", "In recent decades , the incidence of dengue has grown dramatically; approximately half of the world’s population is now at risk [2] .", "An estimated 390 million dengue infe...	[ "A total of 1 , 596 laboratory-confirmed imported dengue cases were identified in Taiwan during 2011–2016 .", "Most of the imported cases arrived from Southeast Asia as well as the Indian subcontinent , the Pacific region , Latin America , Australia and Africa .", "Phylogenetic analyses of the complete envelope...	[ "Dengue is the most prevalent mosquito-borne viral disease in the world .", "The expansion of dengue viruses to different parts of the world has been accelerated by the increase in worldwide travel and trade .", "In this study , we present the results of a laboratory-based dengue surveillance in Taiwan during 2...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "cell binding", "phosphorylation", "cell physiology", "cell cycle inhibitors", "cell cycle and cell division", "cell processes", "population genetics", "ploidy", "fungi", "model organisms", "experimental organism systems", "cell growth", "population biology", "saccharomyces", "research a...	Dilution and titration of cell-cycle regulators may control cell size in budding yeast	journal.pcbi.1006548	null	[ [ "Balanced growth of proliferating cells requires some coordination between the increasing size of a growing cell and its probability of undergoing DNA synthesis and division .", "In particular , the average time between two successive cell divisions must allow for a doubling in cell mass ( or volume , whi...	[ "The size of a cell sets the scale for all biochemical processes within it , thereby affecting cellular fitness and survival .", "Hence , cell size needs to be kept within certain limits and relatively constant over multiple generations .", "However , how cells measure their size and use this information to reg...	[ "Proliferating cells need to coordinate the initiation of genome replication and cell division with cell growth .", "In particular , the average time between two division events must precisely allow for a doubling in cell volume .", "Any systematic deviation from this balance would lead to progressive changes i...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "livestock", "medicine and health sciences", "enzyme-linked immunoassays", "ruminants", "vertebrates", "sand flies", "dogs", "mammals", "animals", "insect vectors", "immunologic techniques", "digestive system", "research and analysis methods", "sheep", "proteins", "epidemiology", "im...	Recombinant Salivary Proteins of Phlebotomus orientalis are Suitable Antigens to Measure Exposure of Domestic Animals to Sand Fly Bites	journal.pntd.0004553	null	[ [ "Phlebotomine sand flies are the vectors of Leishmania parasites causing leishmaniasis , the disease responsible for an estimated 1 . 3 million new human cases and 20 000 to 30 000 deaths annually [1] .", "During blood-feeding , sand fly females inoculate saliva into the host skin .", "Over the last t...	[ "Certain salivary proteins of phlebotomine sand flies injected into the host skin during blood-feeding are highly antigenic and elicit strong antibody-mediated immune responses in repeatedly-exposed hosts .", "These antibodies can be measured by enzyme-linked immuno sorbent assays ( ELISAs ) using salivary gland ...	[ "The sand fly Phlebotomus orientalis is the main vector of Leishmania donovani , the causative agent of visceral leishmaniasis in East Africa .", "During bloodfeeding , sand flies inject saliva into the host skin and repeated bites result in a specific antibody response in the bitten hosts .", "Antibody respons...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular cell biology", "genetics", "immunology", "biology", "genomics", "microbiology", "genetics and genomics" ]	Severe Acute Respiratory Syndrome Coronavirus Envelope Protein Regulates Cell Stress Response and Apoptosis	journal.ppat.1002315	null	[ [ "Severe acute respiratory syndrome coronavirus ( SARS-CoV ) was identified as the etiological agent of a respiratory disease that emerged in Guandong Province , China at the end of 2002 , and spread to 32 countries in a few months [1] , [2] , [3] , [4] , [5] , [6] , [7] .", "SARS-CoV infected 8000 people ...	[ "Severe acute respiratory syndrome virus ( SARS-CoV ) that lacks the envelope ( E ) gene ( rSARS-CoV-ΔE ) is attenuated in vivo .", "To identify factors that contribute to rSARS-CoV-ΔE attenuation , gene expression in cells infected by SARS-CoV with or without E gene was compared .", "Twenty-five stress respons...	[ "To identify potential mechanisms mediating the in vivo attenuation of SARS-CoV lacking the E gene ( rSARS-CoV-ΔE ) , the effect of the presence of the E gene on host gene expression was studied .", "In rSARS-CoV-ΔE-infected cells , the expression of at least 25 stress response genes was preferentially upregulate...	2011
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "diagnostic medicine", "clinical immunology", "clinical research design", "epidemiology", "biology", "public health", "nephrology" ]	Microproteinuria during Opisthorchis viverrini Infection: A Biomarker for Advanced Renal and Hepatobiliary Pathologies from Chronic Opisthorchiasis	journal.pntd.0002228	null	[ [ "Foodborne trematodiases represent an important group of communicable diseases , and some of the most clinically significant neglected tropical diseases ( NTDs ) affecting East Asia .", "Approximately 680 million people are at risk of infection with the human liver flukes Opisthorchis viverrini and Clonor...	[ "Approximately 680 million people are at risk of infection with Opisthorchis viverrini ( OV ) and Clonorchis sinensis , with an estimated 10 million infected with OV in Southeast Asia alone .", "While opisthorchiasis is associated with hepatobiliary pathologies , such as advanced periductal fibrosis ( APF ) and c...	[ "Approximately 680 million people risk infection with food-borne trematodes , including Opisthorchis viverrini ( OV ) .", "Animal models show that significant kidney pathology results from OV infection as detected by antibodies in urine ( microproteinuria ) .", "However , kidney pathology in humans infected wit...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics of disease", "genetics", "biology", "gene function" ]	The Wilms Tumor Gene, Wt1, Is Critical for Mouse Spermatogenesis via Regulation of Sertoli Cell Polarity and Is Associated with Non-Obstructive Azoospermia in Humans	journal.pgen.1003645	null	[ [ "Infertility is a common health problem which affects about 15–20% of couples .", "Among infertile couples , about 50% are related to male infertility [1] , a major cause of which is azoospermia .", "Genetic causes of azoospermia include autosomal chromosome abnormalities , Y chromosome microdeletions...	[ "Azoospermia is one of the major reproductive disorders which cause male infertility in humans; however , the etiology of this disease is largely unknown .", "In the present study , six missense mutations of WT1 gene were detected in 529 human patients with non-obstructive azoospermia ( NOA ) , indicating a stron...	[ "Infertility is one of the most common health problems , affecting about 15% of the couples in the world .", "In about half of these couples , infertility is related to male reproductive defect .", "Azoospermia is one of the major causes of male infertility in humans .", "Previous studies have found that the ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "cytokines", "hiv", "retrovirology and hiv immunopathogenesis", "immunology", "biology", "viral diseases", "immune system" ]	Chronic Exposure to Type-I IFN under Lymphopenic Conditions Alters CD4 T Cell Homeostasis	journal.ppat.1003976	null	[ [ "Homeostatic forces regulate the number and survival of T cell clones throughout life , allowing only a limited degree of non-antigen driven expansion for each individual cell in order to preserve the diversity of the T cell repertoire [1] .", "This is achieved by a balance between signals that mediate su...	[ "HIV infection and the associated chronic immune activation alter T cell homeostasis leading to CD4 T cell depletion and CD8 T cell expansion .", "The mechanisms behind these outcomes are not totally defined and only partially explained by the direct cytopathic effect of the virus .", "In this manuscript , we a...	[ "While the acute CD4 depletion observed in the initial phase of HIV infection is likely due to direct cytopathic effects of the virus , the mechanism/s underlying the steady decline of the CD4 T cell pool during the chronic phase of infection are unclear and are felt to be associated with “immune activation . ”", ...	2014
[ "Introduction", "Discussion" ]	[ "biochemistry/experimental biophysical methods", "cell biology/cellular death and stress responses", "cardiovascular disorders/arrhythmias, electrophysiology, and pacing", "physiology/cardiovascular physiology and circulation", "biophysics/theory and simulation", "pathology/cellular pathology", "physiol...	A Reaction-Diffusion Model of ROS-Induced ROS Release in a Mitochondrial Network	journal.pcbi.1000657	null	[ [ "The spatial and temporal organization of the mitochondrial network is crucial for understanding its function in cells [1] , [2] .", "Complex spatiotemporal factors not only contribute to physiological signaling [3]–[6] , but determine the fate of the cell under stress .", "In heart cells , we have pr...	[ "Loss of mitochondrial function is a fundamental determinant of cell injury and death .", "In heart cells under metabolic stress , we have previously described how the abrupt collapse or oscillation of the mitochondrial energy state is synchronized across the mitochondrial network by local interactions dependent ...	[ "Cardiac cell injury and death is a key component of cardiac diseases such as heart failure or myocardial infarction , thus it is important to understand the earliest steps leading up to irreversible cell damage .", "Mitochondria are the organelles responsible for generating the energy required to keep the cell r...	2010
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "veterinary science", "veterinary diseases", "zoonoses", "protozoans", "medicine and health sciences", "leishmania", "leishmaniasis", "parasitology", "neglected tropical diseases", "protozoology", "biology and life sciences", "microbiology", "tropical diseases", "parasitic protozoans", "...	In Vitro and In Vivo Miltefosine Susceptibility of a Leishmania amazonensis Isolate from a Patient with Diffuse Cutaneous Leishmaniasis	journal.pntd.0002999	null	[ [ "Leishmania spp .", "are the etiological agents of a spectrum of diseases collectively known as leishmaniasis , endemic in tropical and subtropical areas of the world [1] .", "Leishmania braziliensis and Leishmania amazonensis are the main causative agents of cutaneous leishmaniasis ( CL ) in Brazil ,...	[ "Miltefosine was the first oral compound approved for visceral leishmaniasis chemotherapy , and its efficacy against Leishmania donovani has been well documented .", "Leishmania amazonensis is the second most prevalent species causing cutaneous leishmaniasis and the main etiological agent of diffuse cutaneous lei...	[ "Leishmania amazonensis is the etiological agent of diffuse cutaneous leishmaniasis .", "The disease is extremely difficult to treat and frequently relapses once the treatment is interrupted .", "Although not yet approved in Brazil , miltefosine is an attractive alternative for leishmaniasis treatment due to it...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "meiosis", "medicine and health sciences", "reproductive system", "spermatocytes", "cell cycle and cell division", "cell processes", "germ cells", "oocytes", "epigenetics", "dna", "chromatin", "sperm", "homologous recombination", "synapsis", "animal cells", "chromosome biology", "gen...	MORC2B is essential for meiotic progression and fertility	journal.pgen.1007175	null	[ [ "The microrchidia ( MORC ) protein family forms a conserved class of chromatin remodeling factors found in diverse species from Arabidopsis to human [1] .", "MORC proteins contain GHKL-type ( Gyrase , Hsp90 , histidine kinase , MutL ) ATPase domain and PHD zinc finger domain , implying functions related t...	[ "The microrchidia ( MORC ) family proteins are chromatin-remodelling factors and function in diverse biological processes such as DNA damage response and transposon silencing .", "Here , we report that mouse Morc2b encodes a functional germ cell-specific member of the MORC protein family .", "Morc2b arose speci...	[ "In sexually reproducing organisms , meiosis , a process unique to germ cells , produces haploid gametes .", "Abnormalities in meiosis can lead to infertility , loss of pregnancy , or genetic diseases such as Down syndrome .", "The meiotic processes are tightly regulated by a large number of genes including man...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "body weight", "medicine and health sciences", "immune cells", "immune physiology", "quantitative trait loci", "spleen", "immunology", "clinical medicine", "physiological parameters", "mammalian genomics", "white blood cells", "major histocompatibility complex", "animal cell...	Genomic Modifiers of Natural Killer Cells, Immune Responsiveness and Lymphoid Tissue Remodeling Together Increase Host Resistance to Viral Infection	journal.ppat.1005419	null	[ [ "Yellow fever virus ( YFV ) , once a major scourge of humanity , was one of the first viruses studied experimentally in mammalian hosts [1] .", "In pioneering studies , Nobel Laureate Max Theiler developed an inactivated YFV vaccine [2] , and laid the groundwork for investigations into the genetic basis o...	[ "The MHC class I Dk molecule supplies vital host resistance during murine cytomegalovirus ( MCMV ) infection .", "Natural killer ( NK ) cells expressing the Ly49G2 inhibitory receptor , which specifically binds Dk , are required to control viral spread .", "The extent of Dk-dependent host resistance , however ,...	[ "Uncovering the genetic basis of resistance to viral infection and disease is critical to learning about how immune defenses might be adjusted , how to design better vaccines , and how to elicit effectual immune protection in human populations .", "Prior studies have shown that both MHC and non-MHC genes support ...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "model organisms", "cell biology", "evolutionary biology", "genetics", "biology and life sciences", "molecular cell biology", "neuroscience", "research and analysis methods" ]	Common Transcriptional Mechanisms for Visual Photoreceptor Cell Differentiation among Pancrustaceans	journal.pgen.1004484	null	[ [ "Rhabdomeric ( r ) photoreceptors are one of two fundamental types of photoreceptors that have been described [1] .", "Typically , r- photoreceptors populate the visual systems of protostomes including insects , crustaceans , and annelids ( reviewed in [2] ) .", "This wide phylogenetic distribution an...	[ "A hallmark of visual rhabdomeric photoreceptors is the expression of a rhabdomeric opsin and uniquely associated phototransduction molecules , which are incorporated into a specialized expanded apical membrane , the rhabdomere .", "Given the extensive utilization of rhabdomeric photoreceptors in the eyes of prot...	[ "Visual systems are populated by one of two fundamental types of photoreceptors , ciliary and rhabdomeric .", "Each photoreceptor type is defined by the opsin molecule expressed and the final morphological form adapted to house the phototransduction machinery .", "Here we address whether a common transcriptiona...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "fungal genetics", "sequence assembly tools", "fungi", "plant science", "rice", "genome analysis", "genetic elements", "experimental organism systems", "plant pathology", "plants", "research and analysis methods", "sequence analysis", "mycology", "grasses", "sequence alignment", "anima...	Effector gene reshuffling involves dispensable mini-chromosomes in the wheat blast fungus	journal.pgen.1008272	null	[ [ "Wheat blast is an explosive emerging disease capable of 100% yield losses .", "Little resistance is available in cultivated wheat varieties , and fungicides are not effective under disease favorable conditions [1 , 2] .", "The disease emerged in Brazil in 1985 and spread within South America , limiti...	[ "Newly emerged wheat blast disease is a serious threat to global wheat production .", "Wheat blast is caused by a distinct , exceptionally diverse lineage of the fungus causing rice blast disease .", "Through sequencing a recent field isolate , we report a reference genome that includes seven core chromosomes a...	[ "The emerging blast disease on wheat is proving even harder to control than the ancient , still-problematic rice blast disease .", "Potential wheat resistance identified using strains isolated soon after disease emergence are no longer effective in controlling recent aggressive field isolates from wheat in South ...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "host cells", "pathology and laboratory medicine", "viral transmission and infection", "medical microbiology", "virology", "host-pathogen interactions", "microbial pathogens", "biology and life sciences", "microbiology", "viral replication complex", "pathogenesi...	Efficient Parvovirus Replication Requires CRL4Cdt2-Targeted Depletion of p21 to Prevent Its Inhibitory Interaction with PCNA	journal.ppat.1004055	null	[ [ "Minute Virus of Mice ( MVM ) is an autonomously-replicating parvovirus which induces a DNA damage response resulting in substantial p53 activation which persists throughout the course of viral replication [1] .", "p53 is a well-established activator of p21WAF1/Cip1 ( hereafter referred to as p21 ) expres...	[ "Infection by the autonomous parvovirus minute virus of mice ( MVM ) induces a vigorous DNA damage response in host cells which it utilizes for its efficient replication .", "Although p53 remains activated , p21 protein levels remain low throughout the course of infection .", "We show here that efficient MVM re...	[ "Many DNA viruses induce and then exploit host cellular DNA damage responses to generate a suitable environment for their continued replication .", "Parvoviruses , important disease agents in both humans and animals , rely on host DNA polymerases to replicate their genomes in cell-cycle arrested cells .", "We s...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "sequencing techniques", "medicine and health sciences", "crystal structure", "pathology and laboratory medicine", "chemical compounds", "manganese", "nucleases", "enzymes", "pathogens", "condensed matter physics", "microbiology", "dna-binding proteins", "enzymology", "orthomyxoviruses", ...	Comparative Structural and Functional Analysis of Bunyavirus and Arenavirus Cap-Snatching Endonucleases	journal.ppat.1005636	null	[ [ "Segmented negative strand viruses ( sNSVs ) represent one of the most threatening groups of emerging viruses for global health [1] .", "They are classified in three main families: Orthomyxoviridae , Bunyaviridae and Arenaviridae with respectively six to eight , three and two genome segments [2] .", "...	[ "Segmented negative strand RNA viruses of the arena- , bunya- and orthomyxovirus families uniquely carry out viral mRNA transcription by the cap-snatching mechanism .", "This involves cleavage of host mRNAs close to their capped 5′ end by an endonuclease ( EN ) domain located in the N-terminal region of the viral...	[ "Segmented negative strand viruses ( sNSV ) such as Influenza , Lassa or Hantaan viruses are responsible for a large number of severe human infectious diseases .", "Currently , there are vaccines and antiviral treatments available for influenza but none for the infections caused by other sNSV .", "All carry out...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biotechnology", "biomacromolecule-ligand interactions", "small molecules", "enzymes", "viral enzymes", "microbiology", "protein structure", "proteins", "biology", "viral replication complex", "viral replication", "biophysics", "drug discovery", "biochemistry", "virology", "antivirals"...	Structural and Biochemical Basis for Development of Influenza Virus Inhibitors Targeting the PA Endonuclease	journal.ppat.1002830	null	[ [ "Influenza viruses can cause sporadic global pandemics , and they can result in high mortality rates such as the 1918 pandemic that resulted in 30 to 50 million deaths worldwide [1] .", "The recent 2009 pandemic was caused by a novel H1N1 virus that originated in swine [2] , but of more concern is the imp...	[ "Emerging influenza viruses are a serious threat to human health because of their pandemic potential .", "A promising target for the development of novel anti-influenza therapeutics is the PA protein , whose endonuclease activity is essential for viral replication .", "Translation of viral mRNAs by the host rib...	[ "Seasonal and pandemic influenza have enormous impacts on global public health .", "The rapid emergence of influenza virus strains that are resistant to current antiviral therapies highlights the urgent need to develop new therapeutic options .", "A promising target for drug discovery is the influenza virus PA ...	2012
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "oncology", "medicine", "cancer genetics", "basic cancer research", "genomic imprinting", "genetics", "epigenetics", "biology", "cancers and neoplasms", "gastrointestinal tumors", "hepatocellular carcinoma" ]	Identification of Rtl1, a Retrotransposon-Derived Imprinted Gene, as a Novel Driver of Hepatocarcinogenesis	journal.pgen.1003441	null	[ [ "Hepatocellular carcinoma ( HCC ) is the third leading cause of cancer-related deaths worldwide [1] .", "In contrast to the downward trends in incidence observed for most cancer types , that of HCC continues to rise , particularly in the United States [2] .", "This is due in part to increases in obesi...	[ "We previously utilized a Sleeping Beauty ( SB ) transposon mutagenesis screen to discover novel drivers of HCC .", "This approach identified recurrent mutations within the Dlk1-Dio3 imprinted domain , indicating that alteration of one or more elements within the domain provides a selective advantage to cells dur...	[ "HCC is the third deadliest cancer worldwide , largely due to a lack of effective treatment options .", "Therapeutic approaches targeted at the molecular mechanisms underlying tumor formation and progression have shown great efficacy for treating other tumor types .", "Unfortunately , however , much remains to ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology/morphogenesis and cell biology", "biophysics", "developmental biology/morphogenesis and cell biology" ]	Control of Directed Cell Migration In Vivo by Membrane-to-Cortex Attachment	journal.pbio.1000544	Analysis of cell migration in vivo combined with biophysical measurements reveals how membrane-to-cortex attachment fine-tunes the type of protrusions formed by cells and, as a consequence, controls directed migration during zebrafish gastrulation.	[ [ "During development of the vertebrate body , progenitor cells must migrate from the site at which they are specified to the site where they will eventually form the different body parts .", "Cell migration is the direct result of mechanical forces mediating cell shape changes and cell-substrate translocat...	[ "Cell shape and motility are primarily controlled by cellular mechanics .", "The attachment of the plasma membrane to the underlying actomyosin cortex has been proposed to be important for cellular processes involving membrane deformation .", "However , little is known about the actual function of membrane-to-c...	[ "Cell migration , like any event involving shape changes , is a mechanical process controlled by complex biochemical pathways .", "Here , we examine cell migration in developing embryos with a combination of cell biological tools and atomic force microscopy , so as to investigate how cellular mechanical propertie...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/protozoal infections", "genetics and genomics/epigenetics", "genetics and genomics/microbial evolution and genomics", "microbiology/parasitology" ]	Histone Deacetylases Play a Major Role in the Transcriptional Regulation of the Plasmodium falciparum Life Cycle	journal.ppat.1000737	null	[ [ "Gene expression in the asexual intraerythrocytic developmental cycle ( IDC ) of Plasmodium falciparum and vivax occurs in a continuous cascade with the induction of most genes occurring just once in the cycle , presumably at the time when their products are required [1] , [2] , [3] .", "The next obvious ...	[ "The apparent paucity of molecular factors of transcriptional control in the genomes of Plasmodium parasites raises many questions about the mechanisms of life cycle regulation in these malaria parasites .", "Epigenetic regulation has been suggested to play a major role in the stage specific gene expression durin...	[ "Plasmodium falciparum , a parasitic protozoan , causes the most lethal form of human malaria , killing more than 2 million people per year .", "It has a complex life cycle that involves distinct morphological stages accompanied by stage specific gene expression in both the mosquito and human hosts .", "The lac...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "inflammatory diseases", "medicine and health sciences", "immune cells", "pathology and laboratory medicine", "pathogens", "immunology", "microbiology", "orthomyxoviruses", "pulmonology", "hormones", "epithelial cells", "viruses", "physiological processes", "rna viruses", ...	Progesterone-Based Therapy Protects Against Influenza by Promoting Lung Repair and Recovery in Females	journal.ppat.1005840	null	[ [ "Hormonal contraceptives are listed as an essential medication by the World Health Organization ( WHO ) [1] because of the profound benefits these compounds can have on women’s health outcomes , including decreased rates of maternal mortality and improved perinatal outcomes and child survival , by widening th...	[ "Over 100 million women use progesterone therapies worldwide .", "Despite having immunomodulatory and repair properties , their effects on the outcome of viral diseases outside of the reproductive tract have not been evaluated .", "Administration of exogenous progesterone ( at concentrations that mimic the lute...	[ "Worldwide , the use of hormonal contraceptives is on the rise as a primary intervention for improving women’s health outcomes through reduced maternal mortality and increased childhood survival .", "There are many hormone contraceptive formulations , all of which contain some form of progesterone .", "Although...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology/host antiviral responses", "biochemistry", "microbiology", "immunology/innate immunity" ]	Direct Restriction of Virus Release and Incorporation of the Interferon-Induced Protein BST-2 into HIV-1 Particles	journal.ppat.1000701	null	[ [ "The innate defense against viruses includes specific host cell proteins with intrinsic abilities to restrict viral replication .", "In some cases these restriction factors have been linked to classic aspects of the innate immune response , such as the antiviral state induced by type I interferons .", ...	[ "Investigation of the Vpu protein of HIV-1 recently uncovered a novel aspect of the mammalian innate response to enveloped viruses: retention of progeny virions on the surface of infected cells by the interferon-induced , transmembrane and GPI-anchored protein BST-2 ( CD317; tetherin ) .", "BST-2 inhibits diverse...	[ "The cellular protein BST-2 prevents newly formed particles of HIV-1 and other enveloped viruses from escaping the infected cell by an unclear mechanism .", "Here , we show that BST-2 is appropriately positioned to directly retain newly formed HIV-1 virions on the cell surface and is incorporated into infectious ...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "invertebrates", "medicine and health sciences", "pathology and laboratory medicine", "enzymes", "pathogens", "microbiology", "enzymology", "animals", "developmental biology", "fungi", "insect vectors", "fungal pathogens", "metarhizium", "mycology", "proteins", "medical microbiology", ...	Metarhizium brunneum Blastospore Pathogenesis in Aedes aegypti Larvae: Attack on Several Fronts Accelerates Mortality	journal.ppat.1005715	null	[ [ "Aedes aegypti is the vector of a wide range of viral diseases ( e . g . yellow fever , dengue , Chikungunya and Zika ) [1–5] .", "Dengue fever annually affects 284 to 528 million people around the world [6] .", "The range of this pest appears to be expanding due to global warming [7] .", "Of majo...	[ "Aedes aegypti is the vector of a wide range of diseases ( e . g . yellow fever , dengue , Chikungunya and Zika ) which impact on over half the world’s population .", "Entomopathogenic fungi such as Metarhizium anisopliae and Beauveria bassiana have been found to be highly efficacious in killing mosquito larvae b...	[ "Mosquitoes transmit a range of diseases which have a profound impact on human health .", "Aedes aegypti vectors dengue , one of the fastest emerging diseases and , more recently , the Zika virus , which has been linked to thousands of birth defects over the last two years in Brazil .", "Insect pathogenic fungi...	2016
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "learning", "medicine and health sciences", "neural networks", "social sciences", "homeostatic mechanisms", "learning and memory", "neuroscience", "physiological processes", "cognitive psychology", "homeostasis", "vision", "nervous system physiology", "computer and information sciences", "...	From homeostasis to behavior: Balanced activity in an exploration of embodied dynamic environmental-neural interaction	journal.pcbi.1005721	null	[ [ "In recent years , empirical and theoretical work indicates that homeostatic mechanisms play an important role in the regulation of neural activity .", "At the microscopic level , the balance of local excitation and inhibition ( E/I ) has important computational properties [1–2] .", "The balance of E/...	[ "In recent years , there have been many computational simulations of spontaneous neural dynamics .", "Here , we describe a simple model of spontaneous neural dynamics that controls an agent moving in a simple virtual environment .", "These dynamics generate interesting brain-environment feedback interactions th...	[ "In recent years , there has been growing interest in using computational models based on the human structural connectome to better understand the brain .", "These simulations typically investigate spontaneous neural dynamics , in the absence of tasks , sensory input or motor output .", "Here , we take a differ...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "animal diseases", "medicine and health sciences", "enzymology", "vertebrates", "animals", "mammals", "animal models", "animal prion diseases", "model organisms", "experimental organism systems", "protein structure", "zoology", "enzyme chemistry", "research and analysis methods", "infect...	Full restoration of specific infectivity and strain properties from pure mammalian prion protein	journal.ppat.1007662	null	[ [ "Prion diseases are a class of infectious , invariably fatal neurodegenerative diseases that affect humans and other mammals .", "Examples of prion diseases include Creutzfeldt-Jakob disease ( CJD ) in human patients , chronic wasting disease ( CWD ) in cervids including deer and elk , bovine spongiform e...	[ "The protein-only hypothesis predicts that infectious mammalian prions are composed solely of PrPSc , a misfolded conformer of the normal prion protein , PrPC .", "However , protein-only PrPSc preparations lack significant levels of prion infectivity , leading to the alternative hypothesis that cofactor molecules...	[ "Prions are unusual infectious agents that cause invariably fatal brain diseases .", "Unlike conventional infectious agents such as bacteria or viruses , prions do not possess nucleic acids such as DNA or RNA , and therefore it is not clear how they are able to replicate and cause infection .", "A leading model...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/functional genomics", "genetics and genomics/gene discovery", "developmental biology/developmental molecular mechanisms", "cell biology/cellular death and stress responses" ]	Steroid Hormone Control of Cell Death and Cell Survival: Molecular Insights Using RNAi	journal.pgen.1000379	null	[ [ "Steroid hormones are small hydrophobic signaling molecules which bind to their receptors to control gene expression and initiate the regulation of growth , development , homeostasis and programmed cell death ( PCD ) [1] .", "Components of the steroid-regulated PCD transcriptional regulatory cascades in i...	[ "The insect steroid hormone ecdysone triggers programmed cell death of obsolete larval tissues during metamorphosis and provides a model system for understanding steroid hormone control of cell death and cell survival .", "Previous genome-wide expression studies of Drosophila larval salivary glands resulted in th...	[ "Hormones regulate complex signaling pathways required for the differentiation , growth , survival , and death of cells in diverse organisms .", "The insect steroid hormone 20-hydroxy ecdysone ( ecdysone ) triggers cell death of obsolete larval tissues , such as the midgut and salivary glands , during metamorphos...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "computational biology/metabolic networks", "genetics and genomics/gene expression" ]	Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production	journal.pcbi.1000489	null	[ [ "Metabolism is central to cell physiology and metabolic disturbances play a role in numerous disease states .", "Despite its importance , the ability to study metabolism at a global scale using genomic technologies is limited .", "In principle , complete genome sequences describe the range of metaboli...	[ "Metabolism is central to cell physiology , and metabolic disturbances play a role in numerous disease states .", "Despite its importance , the ability to study metabolism at a global scale using genomic technologies is limited .", "In principle , complete genome sequences describe the range of metabolic reacti...	[ "The ability of cells to survive and grow depends on their ability to metabolize nutrients and create products vital for cell function .", "This is done through a complex network of reactions controlled by many genes .", "Changes in cellular metabolism play a role in a wide variety of diseases .", "However , ...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology", "arabidopsis", "viroids", "plant biology" ]	Processing of Nuclear Viroids In Vivo: An Interplay between RNA Conformations	journal.ppat.0030182	null	[ [ "Viroids , plant pathogens with a minimal non-protein-coding circular RNA genome of 246–401 nt [1] , are classified into two families .", "The members of the first , Pospiviroidae , replicate in the nucleus through an asymmetric rolling-circle mechanism , have a central conserved region ( CCR ) , and cann...	[ "Replication of viroids , small non-protein-coding plant pathogenic RNAs , entails reiterative transcription of their incoming single-stranded circular genomes , to which the ( + ) polarity is arbitrarily assigned , cleavage of the oligomeric strands of one or both polarities to unit-length , and ligation to circul...	[ "Interactions of viroids with their host plants are unique because these subviral pathogenic RNAs lack protein-coding capacity .", "Therefore , hosts must provide all enzymes and auxiliary factors that viroids need for their infectious cycle .", "Replication of viroids entails reiterative transcription of their...	2007
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "innate immune system", "medicine and health sciences", "body fluids", "microbiome", "immune physiology", "cytokines", "immunology", "microbiology", "parasitic protozoans", "physiological processes", "developmental biology", "protozoans", "molecular development", "microbial genomics", "d...	Defining cooperative roles for colonic microbiota and Muc2 mucin in mediating innate host defense against Entamoeba histolytica	journal.ppat.1007466	null	[ [ "Entamoeba histolytica ( Eh ) is a human protozoa parasite that causes the disease amebiasis and that , in 2013 , was responsible for approximately 11 , 300 deaths worldwide [1] .", "Interestingly , of those individuals infected with the parasite , only 10% develop symptoms of the disease while the rest r...	[ "Amebiasis is caused by the protozoan parasite Entamoeba histolytica ( Eh ) , a potentially fatal disease occurring mainly in developing countries .", "How Eh interacts with innate host factors in the gut is poorly understood .", "Eh resides and feed in/on the outer colonic mucus layer and thus share an ecologi...	[ "Entamoeba histolytica ( Eh ) is a human protozoan parasite and the causative agent of amebiasis .", "Amebic colitis causes cellular destruction of the colonic mucosal layers allowing parasites to disseminate to the liver through blood causing amoebic liver abscess , or to other soft organs like the brain and lun...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "systems biology", "mathematics", "statistics (mathematics)", "biology and life sciences", "physical sciences", "computational biology", "biostatistics" ]	A Statistical Method of Identifying Interactions in Neuron–Glia Systems Based on Functional Multicell Ca2+ Imaging	journal.pcbi.1003949	null	[ [ "Information processing in the brain is primarily performed by neurons [1] , [2] .", "Some studies , however , have revealed the existence of crosstalk between neurons and astrocytes [3]–[6] , [6]–[14] that neighbor the neurons and envelop the neuronal synapses [15] .", "The observations in these stud...	[ "Crosstalk between neurons and glia may constitute a significant part of information processing in the brain .", "We present a novel method of statistically identifying interactions in a neuron–glia network .", "We attempted to identify neuron–glia interactions from neuronal and glial activities via maximum-a-p...	[ "Many neuroscientists believe that neurons mainly perform information processing in the brain .", "Glial cells have traditionally been regarded as passive cells , whose roles have been limited to mechanical support and energy transfer to neurons .", "However , some studies have recently demonstrated the existen...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell physiology", "small nucleolar rnas", "gene regulation", "messenger rna", "rna extraction", "polyribosomes", "cellular structures and organelles", "extraction techniques", "research and analysis methods", "gene expression", "cell immortalization", "ribosomes", "biochemistry", "rna", ...	SBDS-Deficient Cells Have an Altered Homeostatic Equilibrium due to Translational Inefficiency Which Explains their Reduced Fitness and Provides a Logical Framework for Intervention	journal.pgen.1006552	null	[ [ "Ribosomopathies are inherited diseases due to the haploinsufficiency of ribosomal proteins or ribosome processing factors [1 , 2] .", "Patients affected by ribosomopathies present multiorgan phenotypes [2] .", "Some relatively common features are bone marrow and skeletal deficits , and cancer predisp...	[ "Ribosomopathies are a family of inherited disorders caused by mutations in genes necessary for ribosomal function .", "Shwachman-Diamond Bodian Syndrome ( SDS ) is an autosomal recessive disease caused , in most patients , by mutations of the SBDS gene .", "SBDS is a protein required for the maturation of 60S ...	[ "Shwachman Diamond syndrome ( SDS ) is an inherited disease .", "SDS presents , as hallmarks , exocrine pancreatic insufficiency , increased rate of infections , and higher incidence of leukemia .", "Most cases are due to mutations in the SBDS gene .", "SBDS encodes for a ribosome maturation factor .", "In ...	2017
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "animal types", "medicine and health sciences", "enzyme-linked immunoassays", "immune physiology", "ruminants", "domestic animals", "immunology", "vertebrates", "sand flies", "animals", "mammals", "dogs", "insect vectors", "immunologic techniques", "zoology", "research and analysis met...	Synthetic peptides as a novel approach for detecting antibodies against sand fly saliva	journal.pntd.0007078	null	[ [ "The specific IgG antibody response against salivary proteins is induced in repeatedly exposed hosts after being bitten by the female sand fly ( reviewed by Ribeiro and Francischetti [1] and Lestinova et al . [2] ) .", "In sand flies this antibody response is species-specific [3 , 4] and correlates with t...	[ "Hosts repeatedly bitten by sand flies develop antibodies against sand fly saliva and screening of these immunoglobulins can be employed to estimate the risk of Leishmania transmission , to indicate the feeding preferences of sand flies , or to evaluate the effectiveness of vector control campaigns .", "Previousl...	[ "Previously , two types of antigens were used for detection of antibodies to sand flies:", "1 ) salivary gland homogenate ( SGH ) , which requires maintaining a sand fly colony and laborious work to obtain a sufficient amount of antigen or", "2 ) recombinant proteins with the need to use cell expression and a c...	2019
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cell death", "medicine and health sciences", "molecular probe techniques", "cell processes", "immunology", "immunoblotting", "cell-mediated immunity", "immune receptor signaling", "dna damage", "dna replication", "membrane receptor signaling", "dna", "molecular biology techniques", "autoi...	DNA damage as a consequence of NLR activation	journal.pgen.1007235	null	[ [ "Plants rely on a dual layered innate immune system to defend against pathogens .", "In a first layer , pattern recognition receptors ( PRRs ) detect pathogen associated molecular patterns ( PAMPs ) , leading to PAMP triggered immunity ( PTI ) [1] .", "To avoid PTI and establish infection , pathogens ...	[ "DNA damage observed during plant immune responses is reported to be an intrinsic component of plant immunity .", "However , other immune responses may suppress DNA damage to maintain host genome integrity .", "Here , we show that immunity-related DNA damage can be abrogated by preventing cell death triggered b...	[ "DNA is constantly subjected to damaging agents that can cause mutations , disease and cell death .", "Not surprisingly , cells have evolved mechanisms to repair damaged DNA and preserve its integrity .", "Recent reports suggested that the innate immune system in plants might actively damage host DNA as a mecha...	2018
[ "Introduction", "Results", "Methods", "Discussion" ]	[ "medicine and health sciences", "neural networks", "scalp", "computational biology", "brain electrophysiology", "social sciences", "electrophysiology", "light", "neuroscience", "electromagnetic radiation", "artificial neural networks", "clinical medicine", "luminance", "artificial intellig...	Shared spatiotemporal category representations in biological and artificial deep neural networks	journal.pcbi.1006327	null	[ [ "Categorization , the act of grouping like with like , is a hallmark of human intelligence .", "Scene categorization in particular is incredibly rapid [1 , 2] and may even be automatic [3] .", "Despite the importance of this problem , little is known about the temporal dynamics of neural activity that...	[ "Visual scene category representations emerge very rapidly , yet the computational transformations that enable such invariant categorizations remain elusive .", "Deep convolutional neural networks ( CNNs ) perform visual categorization at near human-level accuracy using a feedforward architecture , providing neur...	[ "We categorize visual scenes rapidly and effortlessly , but still have little insight into the neural processing stages that enable this feat .", "In a parallel development , deep convolutional neural networks ( CNNs ) have been developed that perform visual categorization with human-like accuracy .", "We hypot...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Meta-analysis of Urine Heme Dipstick Diagnosis of Schistosoma haematobium Infection, Including Low-Prevalence and Previously-Treated Populations	journal.pntd.0002431	null	[ [ "Urogenital schistosomiasis caused by Schistosoma haematobium infection is highly endemic in many developing areas of Africa and the Middle East that lack adequate sanitation and safe water supply [1]–[5] .", "The urinary dipstick for detection of hematuria has long been recommended as a relatively inexpe...	[ "Urogenital schistosomiasis remains highly endemic in Africa .", "Current control is based on drug administration , targeted either to school-age children or to high-risk communities at-large .", "Urine dipsticks for detection of microhematuria offer an inexpensive means for estimating infection prevalence .", ...	[ "Schistosomiasis is a chronic human disease caused by infection with multicellular trematode parasites of Schistosoma species .", "In particular , Schistosoma haematobium colonizes the veins in the pelvis , in and around the urinary tract , and causes inflammation that leads to ulceration and bleeding into the ur...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics", "biology", "model organisms" ]	The Caenorhabditis elegans Iodotyrosine Deiodinase Ortholog SUP-18 Functions through a Conserved Channel SC-Box to Regulate the Muscle Two-Pore Domain Potassium Channel SUP-9	journal.pgen.1004175	null	[ [ "Hypothyroidism , one of the most common endocrine disorders , can cause many different symptoms and can lead to defects in brain development and maturation and retarded postnatal development [1] .", "For thyroid hormone biosynthesis , iodide is recycled by iodotyrosine deiodinase through the deiodination...	[ "Loss-of-function mutations in the Caenorhabditis elegans gene sup-18 suppress the defects in muscle contraction conferred by a gain-of-function mutation in SUP-10 , a presumptive regulatory subunit of the SUP-9 two-pore domain K+ channel associated with muscle membranes .", "We cloned sup-18 and found that it en...	[ "Iodotyrosine deiodinase ( IYD ) controls the recycling of iodide in the biogenesis of thyroid hormones that regulate metabolism .", "Defects in IYD result in congenital hypothyroidism , a multisystem disorder that can lead to growth failure and severe mental retardation .", "We identified the gene sup-18 of th...	2014
[ "Introduction", "Results and Discussion", "Materials and Methods" ]	[]	Feeding and Fasting Signals Converge on the LKB1-SIK3 Pathway to Regulate Lipid Metabolism in Drosophila	journal.pgen.1005263	null	[ [ "Perturbation of energy homeostasis either directly or indirectly causes human health problems such as obesity and type II diabetes [1] .", "Lipid stores are the major energy reserves in animals and are dynamically regulated by alternating between the lipogenesis and lipolysis cycles in response to food a...	[ "LKB1 plays important roles in governing energy homeostasis by regulating AMP-activated protein kinase ( AMPK ) and other AMPK-related kinases , including the salt-inducible kinases ( SIKs ) .", "However , the roles and regulation of LKB1 in lipid metabolism are poorly understood .", "Here we show that Drosophi...	[ "Liver kinase B1 ( LKB1 ) , a serine/threonine kinase , controls 14 different AMP-activated protein kinase ( AMPK ) family kinases , including salt-inducible kinase 3 ( SIK3 ) , suggesting that it plays a variety of roles .", "Using the fruit fly as an in vivo model system , we reveal that LKB1 kinase activity is...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "organismal evolution", "medicine and health sciences", "immune cells", "pathology and laboratory medicine", "fungal genetics", "immunology", "microbiology", "fungal evolution", "microbial evolution", "evolutionary adaptation", "fungal diseases", "fungal pathogens", "infecti...	One Small Step for a Yeast - Microevolution within Macrophages Renders Candida glabrata Hypervirulent Due to a Single Point Mutation	journal.ppat.1004478	null	[ [ "Candida glabrata , like C . albicans , is both a fungal commensal and an opportunistic pathogen of humans .", "The fungus normally co-exists with its host without causing damage , but it can also elicit life-threatening diseases under predisposing conditions , such as prolonged hospitalization , use of c...	[ "Candida glabrata is one of the most common causes of candidemia , a life-threatening , systemic fungal infection , and is surpassed in frequency only by Candida albicans .", "Major factors contributing to the success of this opportunistic pathogen include its ability to readily acquire resistance to antifungals ...	[ "Evolution is not limited to making new species emerge and others perish over the millennia .", "It is also a central force in shorter-term interactions between microbes and hosts .", "A good example can be found in fungi , which are an underestimated cause of human diseases .", "Some fungi exist as commensal...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Cytokinesis-Based Constraints on Polarized Cell Growth in Fission Yeast	journal.pgen.1003004	null	[ [ "Many cells polarize in response to intrinsic and extrinsic signals .", "As cell polarization is generally multifaceted , cells must integrate both negative and positive cues for successful cellular morphogenesis .", "In various organisms , the cell cycle provides a platform on which these cues are or...	[ "The rod-shaped fission yeast Schizosaccharomyces pombe , which undergoes cycles of monopolar-to-bipolar tip growth , is an attractive organism for studying cell-cycle regulation of polarity establishment .", "While previous research has described factors mediating this process from interphase cell tips , we foun...	[ "Many processes , including cell growth , are often regulated differently in distinct cellular regions .", "In the rod-shaped fission yeast Schizosaccharomyces pombe , new cell ends created by cell division initiate growth long after old cell ends inherited from mother cells .", "Though distributions of cell ti...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "evolutionary biology/animal genetics", "virology/virulence factors and mechanisms", "virology/virion structure, assembly, and egress", "virology/immunodeficiency viruses", "virology/animal models of infection", "immunology/innate immunity", "infectious diseases/hiv infection and aids", "virology/host...	Conformational Adaptation of Asian Macaque TRIMCyp Directs Lineage Specific Antiviral Activity	journal.ppat.1001062	null	[ [ "Mammals have evolved antiviral proteins called restriction factors , which contribute to their protection from pathogenic viral infections .", "Expression of restriction factors is invariably enhanced by the innate immune cytokines of the type one interferon family suggesting that restriction factors are...	[ "TRIMCyps are anti-retroviral proteins that have arisen independently in New World and Old World primates .", "All TRIMCyps comprise a CypA domain fused to the tripartite domains of TRIM5α but they have distinct lentiviral specificities , conferring HIV-1 restriction in New World owl monkeys and HIV-2 restriction...	[ "Retroviruses have constantly been infecting mammals throughout their evolution , causing them to evolve defensive mechanisms to protect themselves .", "One of these mechanisms utilises intracellular antiviral molecules referred to as restriction factors .", "Restriction factor sequences have changed through pr...	2010
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "genome-wide association studies", "gene regulation", "dna transcription", "genome analysis tools", "genome databases", "molecular genetics", "gene expression", "biology", "molecular biology", "rna", "nucleic acids", "gene identification and analysis", "genomics", "molecular cell biology",...	Genomic Study of RNA Polymerase II and III SNAPc-Bound Promoters Reveals a Gene Transcribed by Both Enzymes and a Broad Use of Common Activators	journal.pgen.1003028	null	[ [ "The human pol II snRNA genes and type 3 pol III genes have the particularity of containing highly similar promoters , composed of a distal sequence element ( DSE ) that enhances transcription and a proximal sequence element ( PSE ) required for basal transcription .", "In pol II snRNA promoters , the PSE...	[ "SNAPc is one of a few basal transcription factors used by both RNA polymerase ( pol ) II and pol III .", "To define the set of active SNAPc-dependent promoters in human cells , we have localized genome-wide four SNAPc subunits , GTF2B ( TFIIB ) , BRF2 , pol II , and pol III .", "Among some seventy loci occupie...	[ "SNAPc-dependent promoters are unique among cellular promoters in being very similar to each other , even though some of them recruit RNA polymerase II and others RNA polymerase III .", "We have examined all SNAPc-bound promoters present in the human genome .", "We find a surprisingly small number of them , som...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "evolutionary biology", "genetics and genomics/comparative genomics", "neuroscience/sensory systems" ]	Ancient Protostome Origin of Chemosensory Ionotropic Glutamate Receptors and the Evolution of Insect Taste and Olfaction	journal.pgen.1001064	null	[ [ "Ionotropic glutamate receptors ( iGluRs ) are a conserved family of ligand-gated ion channels present in both eukaryotes and prokaryotes .", "By regulating cation flow across the plasma membrane in response to binding of extracellular glutamate and related ligands , iGluRs represent an important signalli...	[ "Ionotropic glutamate receptors ( iGluRs ) are a highly conserved family of ligand-gated ion channels present in animals , plants , and bacteria , which are best characterized for their roles in synaptic communication in vertebrate nervous systems .", "A variant subfamily of iGluRs , the Ionotropic Receptors ( IR...	[ "Ionotropic glutamate receptors ( iGluRs ) are a family of cell surface proteins best known for their role in allowing neurons to communicate with each other in the brain .", "We recently discovered a variant class of iGluRs in the fruit fly ( Drosophila melanogaster ) , named Ionotropic Receptors ( IRs ) , which...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "mutation", "genetic mutation", "genome evolution", "heredity", "genetics", "biology", "genomics", "evolutionary biology", "genomic evolution", "evolutionary processes", "evolutionary genetics", "genotypes" ]	Recombination Dynamics of a Human Y-Chromosomal Palindrome: Rapid GC-Biased Gene Conversion, Multi-kilobase Conversion Tracts, and Rare Inversions	journal.pgen.1003666	null	[ [ "The male-specific region of the human Y chromosome ( MSY ) is constitutively haploid , yet contains a high proportion ( ∼35% ) of pseudo-diploid duplicated regions , eight of which are arranged as large inverted repeats ( ‘palindromes’ , known as P1 - P8; Figure 1a ) , with arms in most cases separated by no...	[ "The male-specific region of the human Y chromosome ( MSY ) includes eight large inverted repeats ( palindromes ) in which arm-to-arm similarity exceeds 99 . 9% , due to gene conversion activity .", "Here , we studied one of these palindromes , P6 , in order to illuminate the dynamics of the gene conversion proce...	[ "The sex-determining role of the human Y chromosome makes it male-specific , and always present in only a single copy .", "This solo lifestyle has endowed it with some bizarre features , among which are eight large DNA units constituting about a quarter of the chromosome's length , and containing many genes impor...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "microbial mutation", "immune physiology", "crystal structure", "pathology and laboratory medicine", "enzyme-linked immunoassays", "body fluids", "pathogens", "immunology", "condensed matter physics", "microbiology", "retroviruses", "viruses", "immunodeficie...	Structure and Recognition of a Novel HIV-1 gp120-gp41 Interface Antibody that Caused MPER Exposure through Viral Escape	journal.ppat.1006074	null	[ [ "The HIV-1 envelope glycoprotein trimer ( Env ) is the only known target for neutralizing antibodies and is thus a focus for vaccine design efforts .", "However , the development of an effective HIV-1 vaccine has been thwarted by the complex nature of Env , and the inability to produce soluble Env immunog...	[ "A comprehensive understanding of the regions on HIV-1 envelope trimers targeted by broadly neutralizing antibodies may contribute to rational design of an HIV-1 vaccine .", "We previously identified a participant in the CAPRISA cohort , CAP248 , who developed trimer-specific antibodies capable of neutralizing 60...	[ "Our understanding of which regions of the HIV-1 envelope are targets for broadly neutralizing antibodies ( likely required for an HIV-1 vaccine ) has expanded greatly in recent years , offering insights for vaccine design .", "For instance , much of solvent-exposed gp41 is now known to be targeted by antibodies ...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Phylum-Level Conservation of Regulatory Information in Nematodes despite Extensive Non-coding Sequence Divergence	journal.pgen.1005268	null	[ [ "Similar expression patterns of orthologous genes imply similarity of developmental programs in different species .", "Numerous such examples have been uncovered , including hox [1] , dlx [2] , and dpp/BMP [3] genes , as well as genetic programs regulating photoreceptor [4] and muscle [5] development in d...	[ "Gene regulatory information guides development and shapes the course of evolution .", "To test conservation of gene regulation within the phylum Nematoda , we compared the functions of putative cis-regulatory sequences of four sets of orthologs ( unc-47 , unc-25 , mec-3 and elt-2 ) from distantly-related nematod...	[ "To explore the phylogenetic limits of conservation of cis-regulatory elements , we used transgenesis to test the functions of enhancers of four genes from several species spanning the phylum Nematoda .", "While we found a striking degree of functional conservation among the examined cis elements , their DNA sequ...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "livestock", "medicine and health sciences", "leptospira", "pathology and laboratory medicine", "ruminants", "pathogens", "tropical diseases", "microbiology", "vertebrates", "geographical locations", "animals", "mammals", "bacterial diseases", "tanzania", "neglected tropical diseases", ...	Assessment of animal hosts of pathogenic Leptospira in northern Tanzania	journal.pntd.0006444	null	[ [ "Leptospirosis is a zoonotic disease caused by infection with a pathogenic serovar of Leptospira bacteria .", "Worldwide , leptospirosis is estimated to affect more than one million people and result in the loss of 2 . 9 million Disability Adjusted Life Years ( DALYs ) each year [1] .", "The greatest ...	[ "Leptospirosis is a zoonotic bacterial disease that affects more than one million people worldwide each year .", "Human infection is acquired through direct or indirect contact with the urine of an infected animal .", "A wide range of animals including rodents and livestock may shed Leptospira bacteria and act ...	[ "Leptospirosis is a globally important disease that is transmitted from animals to people and affects more than 1 million people worldwide each year .", "Leptospirosis is an important cause of febrile illness in northern Tanzania but little is known about the animal hosts of Leptospira infection for people in thi...	2018
[ "Introduction", "Material and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "body fluids", "animal models of disease", "bile", "microbiology", "vertebrates", "tropical diseases", "parasitic diseases", "animals", "mammals", "urine", "metabolomics", "foodborne trematodiases", "metabolites", "amniotes", "neglected tropical diseases...	Exploratory metabolomics study of the experimental opisthorchiasis in a laboratory animal model (golden hamster, Mesocricetus auratus)	journal.pntd.0006044	null	[ [ "Opisthorchiasis is a parasitic infection caused by the liver flukes of the Opisthorchiidae family ( Trematoda; Platyhelminthes ) .", "The family includes the three most important species for human health: C . sinensis , O . viverrini , O . felineus; together they are responsible for more than 45 million ...	[ "Opisthorchiasis is a parasitic infection caused by the liver flukes of the Opisthorchiidae family .", "Both experimental and epidemiological data strongly support a role of these parasites in the etiology of the hepatobiliary pathologies and an increased risk of intrahepatic cholangiocarcinoma .", "Understandi...	[ "Opisthorchiasis is a parasitic infection caused by the liver flukes of the Opisthorchiidae family ( Trematoda; Platyhelminthes ) .", "The liver fluke infections trigger development of the hepatobiliary pathologies such as chronic forms of cholecystitis , cholangitis , pancreatitis , and cholelithiasis .", "How...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Structure of the human ClC-1 chloride channel	journal.pbio.3000218	Cryo-EM structures of the human ClC-1 chloride channel in different conditions reveal the overall architecture and the chloride transport pathway; the structures hint at a mechanism underlying the elusive so-called “slow-gating” regulation, and provide a framework for downstream basic and translational applications.	[ [ "CLC proteins comprise a large family of chloride ( Cl− ) -transporting integral membrane proteins with diverse physiological functions [1–3] .", "The first identified human member , ClC-1 , is essential for maintaining the permeability of Cl− across the plasma membrane of skeletal muscle fibers , gCl , a...	[ "ClC-1 protein channels facilitate rapid passage of chloride ions across cellular membranes , thereby orchestrating skeletal muscle excitability .", "Malfunction of ClC-1 is associated with myotonia congenita , a disease impairing muscle relaxation .", "Here , we present the cryo-electron microscopy ( cryo-EM )...	[ "Chloride transporting CLC proteins are expressed in a wide range of organisms , and the family encompasses several members with numerous roles in human health and disease by allowing movement of chloride ions across the membranes that encapsulate cells and cellular organelles .", "Structurally , CLCs form dimers...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biology" ]	Identification of Chromatin-Associated Regulators of MSL Complex Targeting in Drosophila Dosage Compensation	journal.pgen.1002830	null	[ [ "X-chromosome dosage compensation in male Drosophila provides a model for understanding how a large number of diversely regulated genes along the length of a single chromosome can be targeted for coordinate regulation .", "In Drosophila , the transcript levels of genes along the length of the single male ...	[ "Sex chromosome dosage compensation in Drosophila provides a model for understanding how chromatin organization can modulate coordinate gene regulation .", "Male Drosophila increase the transcript levels of genes on the single male X approximately two-fold to equal the gene expression in females , which have two ...	[ "Gene regulation is essential to all living things .", "For example , levels of gene expression in individual cells must be fine-tuned during development and in response to changing environmental conditions .", "Genes are regulated by DNA binding proteins and by factors that influence DNA packaging into chromat...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "chemical bonding", "medicine and health sciences", "enzymes", "enzymology", "collagens", "histochemistry and cytochemistry techniques", "glycosylation", "hydroxylation", "immunologic techniques", "pepsins", "research and analysis methods", "physical chemistry", "proteins", "connective tis...	Cyclophilin B control of lysine post-translational modifications of skin type I collagen	journal.pgen.1008196	null	[ [ "Collagens comprise a large family of structurally related extracellular matrix proteins in vertebrates [1 , 2] .", "Among the family members , fibrillar type I collagen is the most predominant type , providing connective tissues with form and tensile strength .", "Type I collagen is a heterotrimetric...	[ "Covalent intermolecular cross-linking of collagen is essential for tissue stability .", "Recent studies have demonstrated that cyclophilin B ( CypB ) , an endoplasmic reticulum ( ER ) -resident peptidyl-prolyl cis-trans isomerase , modulates lysine ( Lys ) hydroxylation of type I collagen impacting cross-linking...	[ "Deficiency of cyclophilin B ( CypB ) , an endoplasmic reticulum-resident peptidyl-prolyl cis-trans isomerase , causes recessive osteogenesis imperfecta type IX , resulting in defective connective tissues .", "Recent studies using CypB null mice revealed that CypB modulates lysine hydroxylation of type I collagen...	2019
[ "Introduction", "Model", "Results", "Discussion", "Methods" ]	[ "molecular cell biology", "cell biology", "biophysics theory", "membranes and sorting", "biology", "biophysics" ]	Membrane-Elasticity Model of Coatless Vesicle Budding Induced by ESCRT Complexes	journal.pcbi.1002736	null	[ [ "Lipid membranes enclose the cytosol of biological cells and compartmentalize their interior .", "The structure and contents of cellular membranes are actively controlled to sustain the vital functions of the cell .", "Transport vesicles are used to traffic membrane-bound proteins between cellular com...	[ "The formation of vesicles is essential for many biological processes , in particular for the trafficking of membrane proteins within cells .", "The Endosomal Sorting Complex Required for Transport ( ESCRT ) directs membrane budding away from the cytosol .", "Unlike other vesicle formation pathways , the ESCRT-...	[ "Lipid membranes enclose the cytosol of biological cells and compartmentalize their interior .", "Vesicles are used to transport membrane proteins between cellular compartments .", "The ESCRT protein machinery induces the creation of such vesicles away from the cytosol .", "The resulting vesicles are uncoated...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	DAMP Molecule S100A9 Acts as a Molecular Pattern to Enhance Inflammation during Influenza A Virus Infection: Role of DDX21-TRIF-TLR4-MyD88 Pathway	journal.ppat.1003848	null	[ [ "Pathogen-associated molecular patterns ( PAMPs ) are molecular signatures of pathogens which facilitate induction of the host immune response [1] , [2] .", "PAMPs activate cellular pattern-recognition-receptors ( PRRs ) such as toll-like receptors ( TLRs ) to induce immunity [1] , [2] .", "Wide array...	[ "Pathogen-associated molecular patterns ( PAMPs ) trigger host immune response by activating pattern recognition receptors like toll-like receptors ( TLRs ) .", "However , the mechanism whereby several pathogens , including viruses , activate TLRs via a non-PAMP mechanism is unclear .", "Endogenous “inflammator...	[ "The lung disease severity following influenza A virus ( IAV ) infection is dependent on the extent of inflammation in the respiratory tract .", "Severe inflammation in the lung manifests in development of pneumonia .", "Therefore , it is very critical to identify cellular factors and dissect the molecular/cell...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "infectious diseases", "immunology", "microbiology", "eubacteria" ]	Nod1 Signaling Overcomes Resistance of S. pneumoniae to Opsonophagocytic Killing	journal.ppat.0030118	null	[ [ "Successful pathogens have mechanisms both to avoid triggering inflammatory responses and/or to evade the inflammatory response they induce in their host .", "In the case of the Gram-positive Streptococcus pneumoniae ( Sp ) , a major pathogen of the human respiratory tract , infection involving normally s...	[ "Airway infection by the Gram-positive pathogen Streptococcus pneumoniae ( Sp ) leads to recruitment of neutrophils but limited bacterial killing by these cells .", "Co-colonization by Sp and a Gram-negative species , Haemophilus influenzae ( Hi ) , provides sufficient stimulus to induce neutrophil and complement...	[ "Pathogens are generally studied in the laboratory one species at a time .", "Most exist , however , in complex environments where they must adapt not only to their host but also to other members of the microbial flora .", "Using a mouse model of co-colonization , we have shown that one bacterial species ( Haem...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "applied microbiology", "genome sequencing", "genome complexity", "mycology", "industrial microbiology", "genome evolution", "comparative genomics", "biology", "genomics", "evolutionary biology", "genomic evolution", "microbiology", "yeast" ]	Insights into the Dekkera bruxellensis Genomic Landscape: Comparative Genomics Reveals Variations in Ploidy and Nutrient Utilisation Potential amongst Wine Isolates	journal.pgen.1004161	null	[ [ "Dekkera ( Brettanomyces ) bruxellensis has been described in the population ecology of various fermented beverages , such as wine , beer and cider [1]–[3] , and is of increasing relevance to the biofuel industry [4] .", "Recent genomic sequencing of this species is beginning to reveal the mechanisms by w...	[ "The yeast Dekkera bruxellensis is a major contaminant of industrial fermentations , such as those used for the production of biofuel and wine , where it outlasts and , under some conditions , outcompetes the major industrial yeast Saccharomyces cerevisiae .", "In order to investigate the level of inter-strain va...	[ "The yeast D . bruxellensis is of great importance in biofuel and fermented beverage industries , largely as a contaminant and/or spoilage organism .", "Its lifestyle is not unlike that of the wine/brewing/baking yeast S . cerevisiae , with independent evolutionary pathways having led to this convergence; these s...	2014

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